2011 Publications Resulting from the Use of NERSC Resources

On their Allocation Year 2012 ERCAP Request Forms Principal Investigators reported 1,770 refereed publications (published or in press) - as well as 93 publications submitted to refereed journals - for the preceding 12 months, based on using, at least in part, NERSC resources.

A

Adams, Paul

Liu H, Sale KL, Simmons BA and Singh S, "Molecular dynamics study of polysaccharides in binary solvent mixtures of an ionic liquid and water." J Phys. Chem. B. 2011 115(34):10251-8.

Aldering, Greg

"Type Ia Supernova Carbon Footprints", Thomas, R. C., Aldering, G., Antilogus, P., Aragon, C., Bailey, S., Baltay, C., Bongard, S., Buton, C., Canto, A., Childress, M., Chotard, N., Copin, Y., Fakhouri, H. K., Gangler, E., Hsiao, E. Y., Kerschhaggl, M., Kowalski, M., Loken, S., Nugent, P., Paech, K., Pain, R., Pecontal, E., Pereira, R., Perlmutter, S., Rabinowitz, D., Rigault, M., Rubin, D., Runge, K., Scalzo, R., Smadja, G., Tao, C., Weaver, B. A., Wu, C., Brown, P. J., Milne, P. A. (2011) Astrophys. J., in press

"SYNAPPS: Data-Driven Analysis for Supernova Spectroscopy", Thomas, R. C., Nugent, P. E., Meza, J. C., (2011) Pub. Astron. Soc. Pacific, 123, 237

"Keck Observations of the Young Metal-poor Host Galaxy of the Super-Chandrasekhar-mass Type Ia Supernova SN 2007if, " Childress, M., Aldering, G., Aragon, C., Antilogus, P., Bailey, S., Baltay, C., Bongard, S., Buton, C., Canto, A., Chotard, N., Copin, Y., Fakhouri, H. K., Gangler, E., Kerschhaggl, M., Kowalski, M., Hsiao, E. Y., Loken, S., Nugent, P., Paech, K., Pain, R., Pecontal, E., Pereira, R., Perlmutter, S., Rabinowitz, D., Runge, K., Scalzo, R., Thomas, R. C., Smadja, G., Tao, C., Weaver, B. A. & Wu, C., (2011), Astrophys. J., 733, 3

"The reddening law of type Ia supernovae: separating intrinsic variability from dust using equivalent widths, " Chotard, N., Gangler, E., Aldering, G., Antilogus, P., Aragon, C., Bailey, S., Baltay, C., Bongard, S., Buton, C., Canto, A., Childress, M., Copin, Y., Fakhouri, H. K., Hsiao, E. Y., Kerschhaggl, M., Kowalski, M., Loken, S., Nugent, P., Paech, K., Pain, R., Pecontal, E., Pereira, R., Perlmutter, S., Rabinowitz, D., Runge, K., Scalzo, R., Smadja, G., Tao, C., Thomas, R. C., Weaver, B. A., Wu, C. & Nearby Supernova Factory, (2011), Astronomy \& Astrophysics, 529,

"Supernova Legacy Survey: using spectral signatures to improve Type Ia supernovae as distance indicators, " Walker, E. S., Hook, I. M., Sullivan, M., Howell, D. A., Astier, P., Balland, C., Basa, S., Bronder, T. J., Carlberg, R., Conley, A., Fouchez, D., Guy, J., Hardin, D., Pain, R., Perrett, K., Pritchet, C., Regnault, N., Rich, J., Aldering, G., Fakhouri, H. K., Kronborg, T., Palanque-Delabrouille, N., Perlmutter, S., Ruhlmann-Kleider, V. & Zhang, T., (2011), Mon. Not. Royal Astron. Soc., 410, 1262

"Spectra, Hubble Space Telescope Light Curves of Six Type Ia Supernovae at $0.511 z 1.12$, the Union2 Compilation", Amanullah, R., Lidman, C., Rubin, D., Aldering, G., Astier, P., Barbary, K., Burns, M. S., Conley, A., Dawson, K. S., Deustua, S. E., Doi, M., Fabbro, S., Faccioli, L., Fakhouri, H. K., Folatelli, G., Fruchter, A. S., Furusawa, H., Garavini, G., Goldhaber, G., Goobar, A., Groom, D. E., Hook, I., Howell, D. A., Kashikawa, N., Kim, A. G., Knop, R. A., Kowalski, M., Linder, E., Meyers, J., Morokuma, T., Nobili, S., Nordin, J., Nugent, P. E., \"Ostman, L., Pain, R., Panagia, N., Perlmutter, S., Raux, J., Ruiz-Lapuente, P., Spadafora, A. L., Strovink, M., Suzuki, N., Wang, L. Wood-Vasey, W. M., Yasuda, N. (2010), Astrophys. J., 716, 712.

Alexandrov, Vitali

V. Alexandrov, N. Gronbech-Jensen, A. Navrotsky, and M. Asta, "First-principles computational study of defect clustering in solid solutions of ThO2 with trivalent oxides," Physical Review B 82, 174115 (2010).

T. Shvareva, V. Alexandrov, M. Asta, and A. Navrotsky, "Energetics of mixing in ThO2 CeO2 fluorite solid solutions," Journal of Nuclear Materials 419, 72 (2011).

Alhassid, Yoram

Y. Alhassid, L. Fang and H. Nakada, Shell Monte Carlo approach: the heavy nuclei, Proceedings of the Tenth International Spring seminar on nuclear physics, Vietri sul Mare, Italy, Journal of Physics: Conference Proceedings 267, 012033 (2011).

C. Gilbreth and Y. Alhassid, A new effective interaction for the two-component trapped Fermi gas: the BEC to BCS crossover, arXiv:1108.2687, to be published in Phys. Rev. A (2011).

Alvarez-Thon, Luis

Rodrigo Ramirez-Tagle, Leonor Alvarado-Soto, Ramiro Arratia-Perez, Radovan Bast,3 and Luis Alvarez-Thon, "Probing the aromaticity of the [(Ht Ac)3 ( 2 -H)6 ], [(Ht Th)3 ( 2 -H)6 ],+, and [(Ht Pa)3 ( 2 -H)6] clusters," J. Chem. Phys. 135, 104506 (2011). [doi:10.1063/1.3632056]

Andricioaei, Ioan

T. D. Lillian, M. Taranova, J. Wereszczynski, I. Andricioaei, and N. C. Perkins. A multiscale dynamic model of DNA supercoil relaxation by topoisomerase IB, Biophys. J., 100, 2016?2023 (2011).

A.C. Stelzer, A.T. Frank, J.D. Kratz, M. Swanson, M.J. Gonzales-Hernandez, I. Andricioaei, D.M. Markovitz and H.M. Al-Hashimi. Discovery of HIV-1 Inhibitors by Targeting an RNA Dynamic Ensemble. Nature Chem. Biol. 7, 553-559 (2011).

E. Nikolova, E. Kim, A. Wise, P. O'Brien, I. Andricioaei and H.M. Al-Hashim, Transient Hoogsteen Base-pairs in Canonical Duplex DNA, Nature, 470, 498-502 (2011).

A.T. Frank and I. Andricioaei,?A Comparative Study on the Ability of Two Implicit-Solvent Lipid Models to Predict Transmembrane Helix Tilt Angles, J. Membrane Biol. 239, 57-62 (2011)

Annamalai, Hanna

Annamalai, H.: Modeling the monsoons in a changing climate. In Elias Carayannis (Ed.) Global Warming / Book 1, InTech Open Access Publisher, ISBN 978-953-308-97-6, in press.

Pillai, P.A., and H. Annamalai: Moist Dynamics of Severe Monsoons over South Asia: Role of the Tropical SST. J. Atmos. Sci., in press.

Prasanna, V and H. Annamalai: Most dynamics of extended monsoon breaks over south Asia. J. Climate (submitted)

Annamalai, H, J. Hafner, K.P. Sooraj and P.A. Pillai, 2011: Global warming shifts monsoon circulation, drying south Asia (Nature, Geosciences, revised)

A. Turner and H. Annamalai 2011: South Asian monsoon and climate change (Nature, Climate Change, revised)

Arons, Jonathan

Sironi L. & Spitkovsky, A. 2011, "Acceleration of Particles at the Termination Shock of a Relativistic Striped Wind," ApJ, in press, arXiv:1107.0977

Sironi L. & Spitkovsky, A. 2011, "Particle Acceleration in Relativistic Magnetized Collisionless Electron-Ion Shocks," ApJ, 726, 75

Gargate, L. & Spitkovsky, A. 2011, "Ion acceleration in non-relativistic astrophysical shocks," ApJ, in press, arXiv:1107.0762

Riquelme, A. & Spitkovsky, A. 2011, "Electron Injection by Whistler Waves in Non-relativistic Shocks," ApJ, 733, 63

Riquelme, A. & Spitkovsky, A. 2010, "Magnetic Amplification by Magnetized Cosmic Rays in Supernova Remnant Shocks," ApJ, 717, 1054

Aspuru-Guzik, Alan

A. N. Sokolov, S. Atahan-Evrenk, R. Mondal, H. B. Akkerman, R. S. Sanchez-Carrera, S. Granados-Focil, J. Schrier, S. C.B. Mannsfeld, A. P. Zoombelt, Z. Bao, A. Aspuru-Guzik, "From computational discovery to experimental characterization of a high hole mobility organic crystal" Nature Commun. 2, 437 (2011).

A. V. Subhas, J. Whealdon, J. Schrier, "Predicting organic thin-film transistor carrier type from single molecule calculations" Comput. Theoret. Chem. 966, 70 (2011)

J. Hachmann, R. Olivares-Amaya, S. Atahan-Evrenk, C. Amador-Bedolla, R. S. Sanchez-Carrera, A. Gold-Parker, L. Vogt, A. M. Brockway, and A. Aspuru-Guzik, "The Harvard Clean Energy Project: Large- Scale Computational Screening and Design of Organic Photovoltaics on the World Community Grid" J. Phys. Chem. Lett., 2011, 2 (17), pp 2241 2251

Asthagiri, Dilip

Weber, V., Merchant, S., and Asthagiri, D. Regularizing binding energy distributions and thermodynamics of hydration. Application to water modeled with classical and ab initio simulations arXiv: 1107.3871 (J. Chem. Phys. Under review)

Dixit, P. D., Asthagiri, D. Separating the role of protein restraints and local metal-site interaction chemistry in the thermodynamics of a zinc finger protein (2011) Biophysical Journal, 101, pp. 1459- 1466.

Dixit, P.D., Asthagiri, D. An elastic-network-based local molecular field analysis of zinc finger proteins (2011) Journal of Physical Chemistry B, 115 (22), pp. 7374-7382.

Dixit, P.D., Asthagiri, D. Thermodynamics of ion selectivity in the KcsA K+ channel (2011) Journal of General Physiology, 137 (5), pp. 427-433. [Invited Perspective. Also featured on ScienceDaily and PHYSORG.com.]

Weber, V., Asthagiri, D. Communication: Thermodynamics of water modeled using ab initio simulations (2010) Journal of Chemical Physics, 133 (14), art. no. 141101. [Top downloaded paper month of October 2010.]

Weber, V., Merchant, S., Dixit, P.D., Asthagiri, D. Molecular packing and chemical association in liquid water simulated using ab initio hybrid Monte Carlo and different exchange-correlation functionals (2010) Journal of Chemical Physics, 132 (20), art. no. 204509.

B

Babikov, Dmitri

M. Ayouz and D. Babikov, "Improved potential energy surface of ozone constructed using the fitting by permutationally invariant monomial functions", invited article to a Special Issue in Advances in Physical Chemistry on "Accurate potential energy surfaces and beyond: chemical reactivity, covalent bonding, long range interactions and spectroscopy", accepted.

L. Wang and D. Babikov, "Adiabatic coherent control in the anharmonic ion trap: Proposal for the vibrational two-qubit system", Phys. Rev. A 83, 052319, 2011.

M. Ivanov and D. Babikov, "Collisional stabilization of van der Waals states in ozone", J. Chem. Phys. 134, 174308, 2011.

M. Ivanov and D. Babikov, "Mixed quantum-classical theory for the collisional energy transfer and the ro-vibrational energy flow: Application to ozone stabilization", J. Chem. Phys. 134, 144107 (16 pages), 2011.

D. Babikov, "Perturbation theory treatment of pseudo-rotation in cyclic- N3", J. Chem. Phys. 134, 114305, 2011.

L. Wang and D. Babikov, "Adiabatic coherent control in the anharmonic ion trap: Numerical analysis of anharmonicities", Phys. Rev. A. 83, 22305, 2011.

M. Ayouz, M. Raoult, S.Galtier, D. Babikov, I. Mikhaylov and V. Kokoouline, "Potential energy surface for CO + H- interaction", J. Chem. Phys., submitted.

Baden, Scott

E. J. Bylaska, K. Tsemekhman, S. B. Baden, J. H. Weare and H. J nsson, "Parallel Implementation of gamma-point Pseudopotential Plane-Wave DFT with Exact Exchange," J. Comp. Chem., 32(1):54-69, January 2011.

Bailey, David

David H. Bailey and Jonathan M. Borwein, "Hand-to-hand combat with thousand-digit integrals," Journal of Computational Science, to appear, updated 17 Jan 2011, available at http://crd.lbl.gov/~dhbailey/dhbpapers/combat.pdf

David H. Bailey, Jonathan M. Borwein, Andrew Mattingly and Glenn Wightwick, "The Computation of Previously Inaccessible Digits of Pi^2 and Catalan's Constant," Notices of the American Mathematical Society, to appear 11 Apr 2011, available at http://crd.lbl.gov/~dhbailey/dhbpapers/bbp-bluegene.pdf

David H. Bailey and Jonathan M. Borwein, "Ancient Indian Square Roots: An Exercise in Forensic Paleo-Mathematics", manuscript, May 2011. PDF

O. DeMasi, J. Meza, and D.H. Bailey. "Dimension reduction using rule ensemble machine learning methods: A numerical study of three ensemble methods". 2011. http://crd.lbl.gov/~dhbailey/dhbpapers/Ensemble_TechReport.pdf.

Sean Whalen, Sean Peisert, and Matt Bishop, "Network-Theoretic Classification of Parallel Computation Patterns," to appear in Proceedings of the First International Workshop on Characterizing Applications for Heterogeneous Exascale Systems (CACHES), Tucson, AZ, June 4, 2011.

Sean Whalen, Sean Peisert, and Matt Bishop, "Anomaly Detection in High Performance Computing," 14th International Symposium on Recent Advances in Intrusion Detection (RAID), Menlo Park, CA, Sept. 20-21, 2011 (submitted).

Sean Whalen, Sophie Engle, Sean Peisert, and Matt Bishop, "Network-Theoretic Classification of Parallel Computation Patterns," submitted to Journal of High Performance Computing Applications, 2011.

[Buluc2011] A. Buluc, S. Williams, L. Oliker, J. Demmel, "Reduced-Bandwidth Multithreaded Algorithms for Sparse Matrix-Vector Multiplication," International Parallel and Distributed Processing Symposium (IPDPS), to appear, 2011.

[Chame2011] Jacqueline Chame, Chun Chen, Mary Hall, Jeffrey K. Hollingsworth, Kumar Mahinthakumar, Gabriel Marin, Shreyas Ramalingam, Sarat Sreepathi, Vamsi Sripathi, Ananta Tiwari, "PERI Autotuning of PFLOTRAN," Journal of Physics, (to appear) Proceedings of SciDAC 2011, July 2011.

[Madduri2011] K. Madduri, K. Ibrahim, S. Williams, E.J. Im, S. Ethier, J. Shalf, L. Oliker, "Gyrokinetic Toroidal Simulations on Leading Multi- and Manycore HPC Systems," Proceedings of SC11, to appear, 2011.

[Rutar2011a] Nick Rutar, Jeffrey K. Hollingsworth, "Data Centric Techniques for Mapping Performance Measurements," 16th International Workshop on High-Level Parallel Programming Models and 16th International Workshop on High-Level Parallel Programming Models and Supportive Environments, May 2011.

[Rutar2011b] Nick Rutar, Jeffrey K. Hollingsworth, "Software Analysis Techniques to Approximate Data Centric Direct Measurements," First International Workshop on High-performance Infrastructure for Scalable Tools, Tuscon, AZ, 2011.

[Williams2011] S. Williams, L. Oliker, J. Carter, J. Shalf, "Extracting Ultra-Scale Lattice Boltzmann Performance via Hierarchical and Distributed Auto-Tuning," Proceedings SC11, to appear, 2011.

[Tiwari2011a] Ananta Tiwari, Jeffrey K. Hollingsworth, Chun Chen, Mary Hall, C Liao, Dan Quinlin, Jacqueline Chame, "Auto-tuning Full Applications: A Case Study," International Journal of High Performance Computing, 2011.

[Tiwari2011b] Ananta Tiwari, Jeffrey K. Hollingsworth, "Adaptive Code Generation and Tuning," IPDPS, May 2011.

Balasubramanian, Krishnan

B. Ramanujam, N. Venkataraman, K. Balasubramanian, Tashi Parsons, Kerstel Schwaiger, H. Nitsche, "Computational Modeling of Ligands Involved in Plutonyl Complexation as a Model for Functionalized Mesoporous Silica Materials", accepted

Y. Sun, K. Balasubramanian, U. B. Rao, T. Pradeep, "First Principles Studies of Two Luminescent Molecular Quantum Clusters of Silver, Ag7(H2MSA)7 and Ag8(H2MSA)8, Based on Experimental Fluorescence Spectra", J Phys. Chem. C. (2011) in press

U. B. Rao, T. Pradeep, Y. Sun, K. Balasubramanian, ""Ag7Au6: A 13 atom alloy quantum cluster", Angew Chem., Accepted

B. Ramanujam, N. Venkataraman, K. Balasubramanian, Tashi Parsons, Kerstel Schwaiger, H. Nitsche,"RELATIVISTIC DFT MODELING OF Pu(VI) COMPLEXES OF VARIOUS MULTI-DENTATE SYSTEMS DERIVATISED OVER SBA-15", Accepted

Balatsky, Alexander

Tanmoy Das, A. V. Balatsky; Stripes, spin resonance and $d_{x^2-y^2}-$pairing symmetry in FeSe-based layered superconductors; Phys. Rev. B 84, 014521 (2011).

Tanmoy Das, A. V. Balatsky; Modulated superconductivity due to vacancy and magnetic order in $A_x$Fe$_{2-x/2}$Se$_2$ [$A=$Cs, K, (Tl,Rb), (Tl,K)] iron-selenide superconductors; accepted in Phys. Rev. B (arXiv:1106.3289).

Tanmoy Das, Jian-Xin Zhu, Matthias J. Graf;

Local suppression of the superfluid density of PuCoGa$_5$ in the Swiss Cheese model; accepted in Phys. Rev. B (arXiv:1105.5109).

Balbuena, Perla

G. E. Ram rez-Caballero and P. B. Balbuena, Confinement-induced changes in magnetic behavior of a Ti monolayer on Pt, Chem. Phys. Lett.. 507 (2011) 117-121.

R. Callejas-Tovar, W. Liao, J. Martinez de la Hoz, and P. B. Balbuena, Molecular dynamics simulations of surface oxidation on Pt(1 1 1) and Pt/PtCo/Pt3Co(1 1 1) J. Phys. Chem C. 115 (2011) 4104-4113.

G. E. Ramirez-Caballero, A. Mathkari, and P. B. Balbuena, Confinement-induced polymerization of ethylene, J. Phys. Chem C. 115 ( 2011) 2134-2139.

J. M. Martinez de la Hoz, D. F. Leon-Quintero, P. Hirunsit, and P. B. Balbuena, Evolution of a Pt(111) surface at high oxygen coverage in acid medium, Chem. Phys. Lett. 498 (2010) 328-333.

G. E. Ramirez-Caballero, P. Hirunsit, and P. B. Balbuena, Shell-anchor-core structures for enhanced stability and catalytic oxygen reduction activity, J. Chem. Phys. 133 (2010) 134705.

P. Hirunsit and P. B. Balbuena, Stability of Pt monolayers on Ir-Co cores with and without a Pd interlayer, J. Phys. Chem. C 114 (2010) 13055-13060.

G. E. Ramirez-Caballero and P. B. Balbuena, Confinement effects on alloy reactivity, Phys. Chem. Chem. Phys. 12 (2010) 12466-12471.

G. E. Ramirez-Caballero and P. B. Balbuena, Dissolution-resistant core-shell materials for acid medium oxygen reduction electrocatalysts, J. Phys. Chem. Lett. 1 (2010) 724-728..

K. Gong, W-F Chen, K. Sasaki, D. Su, M. B. Vukmirovic, W. Zhu, E. L. Izzo, C. Perez-Acosta, P. Hirunsit, P. B. Balbuena, and R. R. Adzic, Platinum monolayer electrocatalysts: Improving the activity for the oxygen reduction reaction with palladium interlayer on IrCo alloy core, J. Electronal. Chem. 649 (2010) 232-237.

Balbuena, Perla

D. A. G mez-Gualdr n, J. Zhao, and P. B. Balbuena, Nanocatalyst structure as a template to define chirality of nascent single-wall carbon nanotubes, J. Chem. Phys. 134 (2011) 014705. Selected for the January 10, 2011 issue of Virtual Journal of Nanoscale Science & Technology, published by the American Institute of Physics and the American Physical Society, http://www.vjnano.org

J. C. Burgos, E. Jones, and P. B. Balbuena, Effect of the metal-substrate interaction strength on the growth of single-walled carbon nanotubes, J. Phys. Chem. C. 115 (2011) 7668-7675.

J. C. Burgos, H. Reyna, B. I. Yakobson and P. B. Balbuena, Interplay of Catalyst Size and Metal-Carbon Interactions on the Growth of Single-Wall Carbon Nanotubes, J. Phys. Chem. C 114 (2010) 6952-6958.

Balch, Alan

Franco, J. U., Hammons, J. C., Rios, D. Olmstead, M. M. Inorg. Chem., 49, 11, 5120-2125.

Bansil, Arun

M.Z. Hasan, Xu S.Y., Xia Y., Wray L.A., Jia S., Meier F., Dil J.H., Osterwalder J., Slomski B., Bansil A., Lin H., and Cava R.J., Topological Phase Transition and Texture Inversion in a Tunable Topological Insulator. Science. 332, 560 (2011).

Y. Sakurai, Itou M., Barbiellini B., Mijnarends P.E., Markiewicz R.S., Kaprzyk S., Gillet J.M., Wakimoto S., Fujita M., Basak S., Wang Y.J., Al-Sawai W., Lin H., Bansil A., and Yamada K., Imaging Doped Holes in a Cuprate Superconductor with High-Resolution Compton Scattering. Science. 332, 698 (2011).

M.Z. Hasan, Wray L.A., Xu S.Y., Xia Y.Q., Hsieh D., Fedorov A.V., Hor Y.S., Cava R.J., Bansil A., and Lin H., A topological insulator surface under strong Coulomb, magnetic and disorder perturbations. Nature Physics. 7, 32 (2011).

M.Z. Hasan, Wray L.A., Xu S.Y., Xia Y.Q., Hor Y.S., Qian D., Fedorov A.V., Lin H., Bansil A., and Cava R.J., Observation of topological order in a superconducting doped topological insulator. Nature Physics. 6, 855 (2010).

M.Z. Hasan, Lin H., Wray L.A., Xia Y.Q., Xu S.Y., Jia S.A., Cava R.J., and Bansil A., Half-Heusler ternary compounds as new multifunctional experimental platforms for topological quantum phenomena. Nature Materials. 9, 546 (2010).

Y. Okada, Dhital C., Zhou W.W., Huemiller E.D., Lin H., Basak S., Bansil A., Huang Y.B., Ding H., Wang Z., Wilson S.D., and Madhavan V., Direct Observation of Broken Time-Reversal Symmetry on the Surface of a Magnetically Doped Topological Insulator. Physical Review Letters. 106, 206805 (2011).

M. Lindroos, Arpiainen V., and Bansil A., Comment on "Circular Dichroism in the Angle-Resolved Photoemission Spectrum of the High-Temperature Bi(2)Sr(2)CaCu(2)O(8-delta) Superconductor: Can These Measurements Be Interpreted as Evidence for Time-Reversal Symmetry Breaking?" Reply. Physical Review Letters. 105, 189702 (2010).

L.A. Wray, Xu S.Y., Xia Y.Q., Qian D., Fedorov A.V., Lin H., Bansil A., Fu L., Hor Y.S., Cava R.J., and Hasan M.Z., Spin-orbital ground states of superconducting doped topological insulators: A Majorana platform. Physical Review B. 83, 224516 (2011).

I. Suominen, Nieminen J., Markiewicz R.S., and Bansil A., Induced superconductivity in noncuprate layers of the Bi(2)Sr(2)CaCu(2)O(8+delta) high-temperature superconductor: Modeling of scanning tunneling spectra. Physical Review B. 83, 024501 (2011).

I. Suominen, Nieminen J., Markiewicz R.S., and Bansil A., Effect of orbital symmetry of the tip on scanning tunneling spectra of Bi(2)Sr(2)CaCu(2)O(8+delta). Physical Review B. 84, 014528 (2011).

G. Seibold, Markiewicz R.S., and Lorenzana J., Spin canting as a result of the competition between stripes and spirals in cuprates. Physical Review B. 83, 205108 (2011).

T. Jarlborg, Barbiellini B., Lin H., Markiewicz R.S., and Bansil A., Renormalization of f levels away from the Fermi energy in electron excitation spectroscopies: Density-functional results for Nd(2-x)Ce(x)CuO(4). Physical Review B. 84, 045109 (2011).

C. Bellin, Barbiellini B., Klotz S., Buslaps T., Rousse G., Strassle T., and Shukla A., Oxygen disorder in ice probed by x-ray Compton scattering. Physical Review B. 83, 094117 (2011).

Baron, Edward

D. Jack, P. H. Hauschildt, & E. Baron, Theoretical light curves of type Ia supernovae, A&A, (2011), 528, A141, 11pp.

Brandon Doull & E. Baron, Comparative Analysis of Peculiar Type Ia 1991bg-like Supernovae Spectra, PASP, (2011), 123, 765-776.

P. H. Hauschildt, & E. Baron, A 3D radiative transfer framework: IX. OpenCL implementation, A&A, (2011), 533, A127, 6pp.

Bartels, Ludwig

M. Luo, W. Lu, D. Kim, E. Chu, J. Wyrick, C. Holzke, D. Salib, K. Cohen, Z. Cheng, D. Sun, Y. Zhu, T. Einstein, and L. Bartels. Coalescence of 3-Phenyl-Propynenitrile on Cu(111) into Interlocking Pinwheel Chains. Journal of Chemical Physics (In press)

Batchelor, Don

P. T. Bonoli, A. Bader, N. Tsujii, R. W. Harvey, E. F. Jaeger, D. B. Batchelor, L. A. Berry, Y. Lin, R. Parker, M. Porkolab, J. C. Wright, S. J. Wukitch and the Alcator C-Mod Team, "Validation of Simulation Capability for RF Wave Propagation and Absorption in the Ion Cyclotron Range of Frequencies on Alcator C-Mod", in Proceedings of the 23rd IAEA Fusion Energy Conf., Daejeon, Korea, Paper THW/p7-01, (2010).

A. Bader, P.T. Bonoli1, R. Granetz, R.W. Harvey, E.F. Jaeger, R. Parker, and S.J. Wukitch, "Fast-Ions on Alcator C-Mod: Comparisons between Simulation and Experiment", in Proceedings of the 19th Topical Conference on Radio-frequency Power in Plasmas, AIP Conference Proceedings, (AIP, NY, 2011).

Foley, S.S.; Elwasif, W.R.; Bernholdt, D.E.; Shet, A.G.; Bramley, R.;, "Many-task applications in the Integrated Plasma Simulator," Many-Task Computing on Grids and Supercomputers (MTAGS), 2010 IEEE Workshop on , vol., no., pp.1-10, 15-15 Nov. 2010 doi: 10.1109/MTAGS.2010.5699425

Batista, Victor

J. Phys. Chem. B 114: 14214-14222, 2010 Reversible Visible-Light Photooxidation of an Oxomanganese Water-Oxidation Catalyst Covalently Anchored to TiO2 Nanoparticles, Gonghu Li, Eduardo M. Sproviero, William R. McNamara, Robert C. Snoeberger III, Robert H. Crabtree, Gary W. Brudvig, and Victor S. Batista.

J. Chem. Theory Comput. 6:755-760, 2010 Characterization of proton coupled electron transfer in a biomimetic oxomanganese complex: Evaluation of the DFT B3LYP level of theory, Ting Wang, Gary Brudvig, and Victor S. Batista.

J. Chem. Theory Comput. 6, 2395-2401, 2010 Study of proton coupled electron transfer in a biomimetic dimanganese water oxidation catalyst with terminal water ligands, Ting Wang, Gary Brudvig, and Victor S. Batista.

Biochemistry, 49, 6302-6304, 2010 Discrimination of saturated aldehydes by the rat I7 olfactory receptor, Michael D. Kurland, Michael B. Newcomer, Zita Peterlin, Kevin Ryan, Stuart Firestein and Victor S. Batista.

Inorganic Chemical Aspects pp. 191-198 (2010) Some Computational Challenges in Energy Research, by Victor S. Batista. Crabtree RH (ed), Wiley, Chichester.

New J. Chem., 35:998-999 (2011) DDQ as an electrocatalyst for amine dehydrogenation, a model system for virtual hydrogen storage, Oana R. Luca, Ting Wang, Steven J. Konezny, Victor S. Batista and Robert H. Crabtree.

Biochemistry 50:6312-6315 (2011). Structural/Functional Role of Chloride in Photosystem II, Ivan Rivalta, Muhamed Amin, Sandra Luber, Serguei Vassiliev, Ravi Pokhrel, Y. Umena, K. Kawakami, Jian-Ren Shen, Doug Bruce, Gary Brudvig, Marilyn Gunner, Victor S. Batista.

Biochemistry 50: 6308-6311 (2011). Supporting Information. S1 state model of the O2-evolving complex of Photosystem II, Sandra Luber, Ivan Rivalta, Y. Umena, K. Kawakami, Jian-Ren Shen, N. Kamiya, Doug Bruce, Gary Brudvig, Victor S. Batista.

J. Phys. Chem. Lett. submitted (2011) Noncollinear Spins Provide a Self-Consistent Treatment of the Low-Spin State of a Biomimetic Oxomanganese Synthetic Trimer Inspired by the Oxygen Evolving Complex of Photosystem II, Sijie Luo, Ivan Rivalta, Victor S. Batista and Donald G. Truhlar.

Batista, Victor

J. Phys. Chem. B 114: 14309-14319, 2010 Single molecule electron transfer dynamics in interfacial donor-bridge-nanoparticle acceptor complexes, Shengye Jin, Robert C. Snoeberger III, Abey Issac, Victor S. Batista and Tianquan Lian.

J. Phys Chem. C 114:1317-1325, 2010 Visible light sensitization of TiO2 surfaces with Alq3 complexes, Luis G. C. Rego, Robson da Silva, Jos A. Freire, Robert C. Snoeberger and Victor S. Batista.

J. Phys. Chem. B 114: 14214-14222, 2010 supporting information Reversible Visible-Light Photooxidation of an Oxomanganese Water-Oxidation Catalyst Covalently Anchored to TiO2 Nanoparticles, Gonghu Li, Eduardo M. Sproviero, William R. McNamara, Robert C. Snoeberger III, Robert H. Crabtree, Gary W. Brudvig, and Victor S. Batista.

J. Chem. Theory Comput. 6:755-760, 2010 supporting information Characterization of proton coupled electron transfer in a biomimetic oxomanganese complex: Evaluation of the DFT B3LYP level of theory, Ting Wang, Gary Brudvig, and Victor S. Batista.

Energy & Environ. Sci. 3, 917-923, 2010 Water-Stable Hydroxamate Anchors for Functionalization of TiO2 Surfaces with Ultrafast Interfacial Electron Transfer, William R. McNamara, Rebecca L. Milot, Hee-eun Song, Robert C. Snoeberger III, Victor S. Batista, Robert H. Crabtree and Gary W. Brudvig.

J. Chem. Theory Comput. 6, 2395-2401, 2010 supporting information Study of proton coupled electron transfer in a biomimetic dimanganese water oxidation catalyst with terminal water ligands, Ting Wang, Gary Brudvig, and Victor S. Batista.

Biochemistry, 49, 6302-6304, 2010 supporting information Discrimination of saturated aldehydes by the rat I7 olfactory receptor, Michael D. Kurland, Michael B. Newcomer, Zita Peterlin, Kevin Ryan, Stuart Firestein and Victor S. Batista.

J. Phys. Chem. C, 114, 19433-19442 (2010) Study of Redox Species and Oxygen Vacancy Defects at TiO2-Electrolyte Interfaces, Robson da Silva, Luis G.C. Rego, Jose A. Freire, Javier Rodriguez, Daniel Laria, and Victor S. Batista.

Inorganic Chemical Aspects pp. 191-198 (2010) Some Computational Challenges in Energy Research, by Victor S. Batista. Crabtree RH (ed), Wiley, Chichester.

J. Phys. Chem. B, 115: 5234-5242 (2011) Tunneling Under Control by Sequences of Unitary Pulses, Rajdeep Saha and Victor S. Batista.

J. Am. Chem. Soc., 133: 6922-6925 (2011) supporting information Covalent Attachment of a Rhenium CO2-Reduction Catalyst to Rutile TiO2 Chantelle L. Anfuso, Robert Snoeberger III, Allen M. Ricks, Weimin Liu, Dequan Xiao, Victor S. Batista and Tianquan Lian

J. Am. Chem. Soc., 133:9014-9022 (2011) supporting information Inverse Design and Synthesis of Acac-Coumarin Anchors for Robust TiO2 Sensitization, Dequan Xiao, Lauren A. Marini, Robert C. Snoeberger, Robert H. Crabtree, and Victor S. Batista.

Bell, John

A. Nonaka, A. S. Almgren, J. B. Bell, H. Ma, S. E. Woosley, and M. Zingale, "From Convection to Explosion: End-to-End Simulation of Type Ia Supernovae," Proceedings of SciDAC 2011, Denver, Colorado, July 2011.

Rantsiou, E.; Burrows, A.; Nordhaus, J.; Almgren, A., ``Induced Rotation in Three-dimensional Simulations of Core-collapse Supernovae: Implications for Pulsar Spins'', Astrophysical Journal, 732, 57 (2011).

W. Zhang, L. Howell, A. Almgren, A. Burrows, and J. Bell "CASTRO: A New Compressible Astrophysical Solver. II. Gray Radiation Hydrodynamics", accepted for publication in the Astrophysical Journal Supplement Series.

A. Donev, A. de la Fuente, J. B. Bell, and A. L. Garcia, "Enhancement of Diffusive Transport by Nonequilibrium Thermal Fluctuations", JSTAT, Vol. 2011, P06014, (2011).

A. Donev, A. de la Fuente, J. B. Bell, and A. L. Garcia, "Diffusive Transport by Thermal Velocity Fluctuations", Phys. Rev. Lett., Vol. 106, No. 20, page 204501, 2011.

M. Day, S. Tachibana, J. Bell, M. Lijewski, V. Beckner and R. Cheng, "A combined computational and experimental characterization of lean premixed turbulent low swirl laboratory flames. I. Methane flames.", accepted for publication in Combustion and Flame. A. J. Aspden, J. B. Bell, S. Dong, and S. E. Woosley, "Burning Thermals in Type Ia Supernovae", Astrophysical Journal, 738, 94-107, (2011).

M. Zingale, A. Nonaka, A. S. Almgren, J. B. Bell, C. M. Malone, and S. E. Woosley, "The Convective Phase Preceding Type Ia Supernovae", Astrophysical Journal, 740, 8 (2011).

A. Nonaka, S. May, A. S. Almgren, and J. B. Bell, "A Three-Dimensional, Unsplit Godunov Method for Scalar Conservation Laws", SIAM J. Sci. Comput., vol. 33, no. 4, 2011.

S. May, A. Nonaka, A. S. Almgren, and J. B. Bell, "An Unsplit, Higher Order Godunov Method Using Quadratic Reconstruction for Advection in Two Dimensions", Comm. App. Math. and Comp. Sci., vol. 6, no. 1, 2011.

A. J. Aspden, M. S. Day, and J. B. Bell, "Turbulence-flame interactions in lean premixed hydrogen: transition to the distributed burning regime", Journal of Fluid Mechanics, 680, 287-320, (2011). doi:10.1017/jfm.2011.164.

A. J. Aspden, J. B. Bell, and S. E. Woosley, "Turbulent Oxygen Flames in Type Ia Supernovae", Astrophysical Journal, 730, 144-151, (2011).

S. E. Woosley, A. R. Kerstein, and A. J. Aspden, "Flames in Type Ia Supernova: Deflagration-Detonation Transition in the Oxygen Burning Flame", Astrophysical Journal, 734, 37-41, (2011).

C. M. Malone, A. Nonaka, A. S. Almgren, J. B. Bell, and M. Zingale "Multidimensional Modeling of Type I X-ray Bursts. I. Two-Dimensional Convection Prior to the Outburst of a pure 4He Accretor", Astrophysical Journal, 728, 118, Feb. 2011.

Ke-Jung Chen, Alexander Heger, and Ann Almgren, "Multi-Dimensional Simulations of Pair-Instability Supernovae", Computer Physics Communications, 182:1, 254-256, 2011.

Benedek, Roy

Simulation of the surface structure of lithium manganese oxide spinel Author(s): Benedek R.; Thackeray M. M. Source: PHYSICAL REVIEW B Volume: 83 Issue: 19 Article Number: 195439 DOI: 10.1103/PhysRevB.83.195439 Published: MAY 31 2011

Pourbaix-like phase diagram for lithium manganese spinels in acid Author(s): Benedek R.; Thackeray M. M.; van de Walle A. Source: JOURNAL OF MATERIALS CHEMISTRY Volume: 20 Issue: 2 Pages: 369-374 DOI: 10.1039/b913226k Published: 2010

The Journal of Physical Chemistry C (submitted 12 September 2011) jp-2011-08793k Title: "Simulation of Aqueous Dissolution of Lithium Manganate Spinel from First Principles" Author(s): Benedek, Roy; Thackeray, Michael; Low, John; Bucko, Tomas

Berg, Bernd

B.A. Berg and Hao Wu, Finite Volume Corrections to the SU(3) Deconfining Temperature due to a Confined Exterior, arXiv:1109.0599, accepted for publication in PoS.

Bethel, Edward (Wes)

Beketayev, K., Weber, G.H., Haranczyk, M., Bremer, P.-T., Hlawitschka, M., Hamann, B., Topology-based Visualization of Transformation Pathways in Complex Chemical Systems, in: Computer Graphics Forum (Special Issue, Proc. Eurographics / IEEE Symposium on Visualization), 30(3), pp. 663-672, European Assiciation for Computer Graphics, June 2011.

Bremer, P.-T., Weber, G.H., Tierny, J., Pascucci, V., Day, M.S., and Bell, J.B., Interactive exploration and analysis of large scale turbulent combustion using topology-based data segmentation, in: IEEE Transactions on Visualization and Computer Graphics, doi: 10.1109/TVCG.2010.253, 17(9), pp. 1307--1324, 2011.

Weber, G.H., Bremer, P.-T. and Pascucci, V., Topological cacti: visualizing contour-based Statistics, in: Topology-based Methods in Visualization IV, Springer-Verlag, Heidelberg, Germany, to appear, 2011.

Jerry Chou, Kesheng Wu, Oliver R bel, Mark Howison, Ji Qiang, Prabhat, Brian Austin, E. Wes Bethel, Rob D. Ryne, and Arie Shoshani. Parallel Index and Query for Large Scale Data Analysis. In Proceedings of Supercomputing 2011, Seattle, WA, USA, 2011. To appear, LBNL publication number pending.

Luke J. Gosink, Christoph Garth, John C. Anderson, E. Wes Bethel, and Kenneth I. Joy. An Application of Multivariate Statistical Analysis for Query-Driven Visualization. IEEE Transactions on Visualization and Computer Graphics, 17(3):264:275, 2011. LBNL-3536E. http://doi.ieeecomputersociety.org/10.1109/TVCG.2010.80 (PDF) (bibtex)

Mark Howison, E. Wes Bethel, Hank Childs. Hybrid Parallelism for Volume Rendering on Large, Multi- and Many-core Systems. IEEE Transactions on Visualization and Computer Graphics (to appear), 2011. LBNL-4370E.

G.H. Weber, P.-T. Bremer, M.S. Day, J.B. Bell, and V. Pascucci. "Feature tracking using reeb graphs." In: V. Pascucci, X. Tricoche, H. Hagen, and J. Tierny, eds., Topological Methods in Data Analysis and Visualization: Theory, Algorithms, and Applications, pp. 241-253. Springer Verlag, 2011. LBNL-4226E.

O. Ruebel, S.V.E. Keranen, M.D. Biggin, D.W. Knowles, G.H. Weber, H. Hagen, B. Hamann, and E.W. Bethel, "Linking Advanced Visualization and MATLAB for the Analysis of 3D Gene Expression Data," Mathematical Methods for Visualization in Medicine and Life Sciences, Proceedings of the 2nd International Workshop on Visualization in Medicine and Life Sciences 2009, Springer Verlag, Heidelberg, Germany, 2011. LBNL-4891E

Min-Yu Huang, Gunther H. Weber, Xiao-Yong Li, Mark D. Biggin, and Bernd Hamann. "Quantitative Visualization of ChIP-chip Data by Using Linked Views." In: Proceedings IEEE International Conference on Bioinformatics and Biomedicine 2010 (IEEE BIBM 2010) Workshops, Workshop on Integrative Data Analysis in Systems Biology (IDASB), pp. 195-200. LBNL-4491E.

Bhattacharjee, Amitava

Yi-Min Huang, A. Bhattacharjee, and Brian P. Sullivan, "Onset of Fast Reconnection in Hall Magnetohydrodynamics Mediated by the Plasmoid Instability", Phys. Plasmas. 18, 072109 (2011)

B. Sullivan, A. Bhattacharjee, and Yi-Min Huang, "On the question of hysteresis in Hall MHD", Physics of Plasmas 17, 114507 (2010)

J. Raeder, P. Zhu, Y. Ge, and G. Siscoe, Tail Force Imbalance and Ballooning Instability Preceding Substorm Onset, J. Geophys. Res. 115, A00I16 (2010)

S. D. Baalrud, A. Bhattacharjee, Y.-M. Huang, and K. Germaschewski, Hall magnetohydrodynamic reconnection in the plasmoid unstable regime, Phys. Plasmas 18, 092108 (2011)

W. Fox, A. Bhattacharjee, and K. Germaschewski, Fast magnetic reconnection in laser-produced plasma bubbles, Phys. Rev. Lett. 106, 215003 (2011)

K. Germaschewski and J. Raeder Using automated code generation to support high performance extended MHD integration in OpenGGCM, in: Numerical Modeling of Space Plasma Flows: ASTRONUM-2010, ASP Conference Series, accepted

N. Bessho and A. Bhattacharjee, Fast reconnection in low-density electron-positron plasmas, Phys. Plasmas, 17, 102104 (2010).

N. Bessho and A. Bhattacharjee, Fast reconnection in low-density hydrogen and pair plasmas, Plasma and Fusion Research, 5, S2017 (2010).

Bonoli, Paul

David L. Green, Erwin F. Jaeger, Guangye Chen, Lee A. Berry, David Pugmire, John M. Canik, Phillip M. Ryan and the RF-SciDAC Team, "Simulation of High Harmonic Fast Wave Heating on the National Spherical Tokamak Experiment", IEEE Transactions on Plasma Science, (August, 2011).

D. L. Green, E. F. Jaeger, L. A. Berry, G. Chen, P. M. Ryan, and J. M. Canik, "Predicting high harmonic ion cyclotron heating efficiency in high confinement mode tokamak plasmas", The Physical Review Letters, accepted for publication, (2011).

M. Murakami, J. M. Park, G. Giruzzi, J. Garcia, P. Bonoli, R. V. Budny, E. J. Doyle, A. Fukuyama, N. Hayashi, M. Honda, A. Hubbard, S. Ide, F. Imbeaux, E.F. Jaeger, T.C. Luce, Y-S. Na, T. Oikawa, T. H. Osborne, V. Parail, A. Polevoi1, R. Prater, A. C. C. Sips, J. Snipes, H. E. St. John, P. B. Snyder, I. Voitsekhovitch, and ITPA/Integrated Operation Scenario Group, "Integrated modeling of steady-state scenarios and heating and current drive mixes for ITER", Nuclear Fusion Vol. 51, 103006 (2011).

John C. Wright, Jungpyo Lee, Ernest Valeo, Paul Bonoli, Cynthia K. Phillips, E. F. Jaeger, and Robert W. Harvey, "Challenges in Self-Consistent Full-Wave Simulations of Lower Hybrid Waves", IEEE Transactions on Plasma Science Vol. 38, No. 9, 2136 (2010).

John Wright and the CSWPI SciDAC Center, "Time Dependent evolution of RF-generated non-thermal particle distributions in fusion plasmas", Invited Paper at the SciDAC 2011 Conference (Denver, CO); also to be published in the Journal of Physics Conference Series (2011).

Borodin, Oleg

1.Vatamanu, J.; Cao, L.; Borodin, O.; Bedrov, D.; Smith, G. D."On the Influence of Surface Topography on the Electric Double Layer Structure and Differential Capacitance of Graphite/ionic Liquid Interfaces" J. Phys. Chem. Lett. 2011, 2, 2267-2272.

2.Vatamanu, J.; Borodin, O.; Smith, G. D. Molecular Simulations of the Electric Double Layer Structure, Differential Capacitance, and Charging Kinetics for N-Methyl-N-propylpyrrolidinium Bis(fluorosulfonyl)imide at Graphite Electrodes J. Phys. Chem., 2011, 115, 3073-3084.

Borrill, Julian

"A Measurement of the Damping Tail of the Cosmic Microwave Background Power Spectrum with the South Pole Telescope", Keisler et al

"Improved constraints on cosmic microwave background secondary anisotropies from the complete 2008 South Pole Telescope data", Shirokoff et al

"Constraints on neutrino interactions using cosmological observations", Smith, Das & Zahn

"A Framework for performance forecasting and optimization of CMB B-mode observations in presence of astrophysical foregrounds", Errard, Stivoli & Stompor

"Spherical harmonic transform on heterogeneous architectures using hybrid programming", Szydlarski, Esterie, Falcou, Grigori & Stompor

Planck Early Results: The Planck mission

Planck Early Results: The thermal performance of Planck

Planck Early Results: First assessment of the High Frequency Instrument in-flight performance

Planck Early Results: First assessment of the Low Frequency Instrument in-flight performance

Planck Early Results: The High Frequency Instrument data processing

Planck Early Results: The Low Frequency Instrument data processing

Planck Early Results: Spectral energy distributions and radio continuum spectra of northern extragalactic radio sources

Planck Early Results: Origin of the submm excess dust emission in the Magellanic Clouds

Planck Early Results: The Planck View of Nearby Galaxies

Planck Early Results: Statistical properties of extragalactic radio sources in the Planck Early Release Compact Source Catalogue

Planck Early Results: Statistical analysis of Sunyaev-Zeldovich scaling relations for X-ray galaxy clusters

Planck Early Results: The Early Release Compact Source Catalog

Planck Early Results: Thermal dust in Nearby Molecular Clouds

Planck Early Results: Dust in the diffuse interstellar medium and the Galactic halo

Planck Early Results: The Galactic Cold Core Population revealed by the first all-sky survey

Planck Early Results: The submillimetre properties of a sample of Galactic cold clumps

Planck Early Results: Properties of the interstellar medium in the Galactic plane

Planck Early Results: New Light on Anomalous Microwave Emission from Spinning Dust Grains

Planck Early Results: All sky temperature and dust optical depth from Planck and IRAS: Constraints on the "dark gas" in our galaxy

Planck Early Results: The Power Spectrum Of Cosmic Infrared Background Anisotropies

Planck Early Results: Cluster Sunyaev-Zeldovich optical scaling relations

Planck Early Results: Calibration of the local galaxy cluster Sunyaev-Zeldovich scaling relations

Planck Early Results: XMM-Newton follow-up for validation of Planck cluster candidates

Planck Early Results: Detection with Planck and confirmation by XMM-Newton of PLCK G266.6-27.3, an exceptionally X-ray luminous and massive galaxy cluster at z~1

Planck Early Results: The all-sky Early Sunyaev-Zeldovich cluster sample

Planck Early Results: ERCSC Validation and Extreme Radio Sources

Planck pre-launch status: the Planck-LFI programme

Planck pre-launch status: expected LFI polarisation capability

All by The Planck Collaboration, to be published in a special edition of Astronomy & Astrophysics

Bourg, Ian

Kwon, K.D., Refson, K., Bone, S., Qiao, R., Yang, W., Liu, Z., Sposito, G., Magnetic ordering in mackinawite (tetragonal FeS): evidence for strong itinerant spin fluctuations, Physical Review B, 83, 064402 (2011).

Kwon, K.D., Refson, K., Sposito, G., Surface complexation of Pb(II) by hexagonal birnessite nanoparticles, Geochimica et Cosmochimica Acta, 74, 6731-6740 (2010).

Bourg, I.C., Sposito, G., Molecular dynamics simulations of the electrical double layer on smectite surfaces contacting concentrated mixed electrolyte (NaCl-CaCl2) solutions, Journal of Colloid and Interface Science 360, 701-715 (2011).

Bowen, Benjamin

Reindl W, Bowen BP, Balamotis MA, Green JE, Northen TR: Multivariate analysis of a 3D mass spectral image for examining tissue heterogeneity. Integr Biol (Camb) 2011.

Lopes LB, Brophy CM, Flynn CR, Yi Z, Bowen BP, Smoke C, Seal B, Panitch A, Komalavilas P: A novel cell permeant peptide inhibitor of MAPKAP kinase II inhibits intimal hyperplasia in a human saphenous vein organ culture model. J Vasc Surg 2010, 52(6):1596-1607.

Lefort N, Glancy B, Bowen B, Willis WT, Bailowitz Z, De Filippis EA, Brophy C, Meyer C, Hojlund K, Yi Z et al: Increased reactive oxygen species production and lower abundance of complex I subunits and carnitine palmitoyltransferase 1B protein despite normal mitochondrial respiration in insulin-resistant human skeletal muscle. Diabetes 2010, 59(10):2444-2452.

Wilmes, Paul ; Bowen, Benjamin P ; Thomas Brian C; Mueller Ryan S; Denef Vincent J; VerBerkmoes Nathan C; Hettich Robert L; Northen Trent R; and Banï¬eld Jillian F. Metabolome-proteome differentiation coupled to microbial divergence. mBio (in Press).

Facciotti M.T., Pang W.L., Lo F-Y., Whitehead K., Koide T., Masumura K., Pan M., Kaur A., Larsen D.J., Reiss D.J., Hoang L., Kalisiak E., Northen T., Trauger S.A., Siuzdak G., Baliga N.S. Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive system analysis. BMC Systems Biology 4:64 (2010)

Baran R, Bowen BP, Bouskill NJ, Brodie EL, Yannone SM, Northen TR (2010) Metabolite Identification in Synechococcus sp. PCC 7002 Using Untargeted Stable Isotope Assisted Metabolite Profiling. Analytical Chemistry 82(21): 9034?9042

Lee, Do Yup, Bowen, Benjamin P, Northen, Trent R. Mass spectrometry based metabolomics, analysis of metabolite-protein interactions, and imaging. Biotechniques, (2010), 49(2): 557-65 (COVER).

Hwang H, Bowen BP, Lefort N, Flynn CR, De Filippis EA, Roberts C, Smoke CC, Meyer C, Hojlund K, Yi Z et al: Proteomics Analysis of Human Skeletal Muscle Reveals Novel Abnormalities in Obesity and Type 2 Diabetes. Diabetes 2010, 59(1):33-42.

Lefort N, Glancy B, Bowen B, Willis WT, Bailowitz Z, De Filippis EA, Brophy C, Meyer C, Hojlund K, Yi ZP et al: Increased Reactive Oxygen Species Production and Lower Abundance of Complex I Subunits and Carnitine Palmitoyltransferase 1B Protein Despite Normal Mitochondrial Respiration in Insulin-Resistant Human Skeletal Muscle. Diabetes 2010, 59(10):2444-2452.

Hojlund K, Yi Z, Lefort N, Langlais P, Bowen B, Levin K, Beck-Nielsen H, Mandarino LJ: Human ATP synthase beta is phosphorylated at multiple sites and shows abnormal phosphorylation at specific sites in insulin-resistant muscle. Diabetologia 2010, 53(3):541-551.

Xie XT, Yi ZP, Bowen B, Wolf C, Flynn CR, Sinha S, Mandarino LJ, Meyer C: Characterization of the Human Adipocyte Proteome and Reproducibility of Protein Abundance by One-Dimensional Gel Electrophoresis and HPLC-ESI-MS/MS. Journal of Proteome Research 2010, 9(9):4521-4534.

Bowen, Benjamin P., Northen, Trent. Dealing with the unknown: Metabolomics and Metabolite Atlases, JASMS (2010). 21(9):1471-1476.

Jansson, Christer, Northen, Trent. Calcifying cyanobacteria-the potential of biomineralization for carbon capture and storage. curr opin biotechnol (2010) 2010 Jun;21(3):365-71

Reindl, Wolfgang; Northen, Trent. Rapid Screening of Fatty Acids Using Nanostructure-Initiator Mass Spectrometry. Analytical Chemistry (2010), 9, 3751-3755.

Bower, Geoffrey

A. P. V. Siemion, G. C. Bower, G. Foster, P. L. McMahon, M. I. Wagner, D. Werthimer, D. Backer, J. Cordes, and J. van Leeuwen, "The Allen Telescope Array Fly's Eye Survey for Fast Radio Transients," ApJ , in press, Sept. 2011.

M. M. Anderson, A. P. V. Siemion, W. C. Barott, G. C. Bower, G. T. Delory, I. de Pater, and D. Werthimer, "The Allen Telescope Array Search for Electrostatic Discharges on Mars," ApJ , in press, Nov. 2011, ADS.

Boyle, James

Boyle, J. and S. A. Klein, 2010, Impact of horizontal resolution on climate model forecasts of tropical precipitation and diabatic heating for the TWP-ICE period. J. Geophys. Res., 115, D23113, doi:10.1029/2010JD014262

Gettleman, A., Liu, S., S. J. Ghan, Morrison, H., Park, S., Conley, A. J., Klein, S. A, Boyle, J., Mitchell, D. L., Li, J.-L. F., 2010, Global simulations of ice nucleation and ice supersaturation with an improved cloud scheme in the Community Atmosphere Model. J. Geophys. Res., 115, D18216, doi:10.1029/2009JD013797.

Broadbelt, Linda

Konstantinov, I.A. and Broadbelt, L.J., "The Role of Oxazolidinones in L-Proline- Assisted Aldol-Type Reactions," Topics in Catalysis, 2010, 53, 1031-1038.

Konstantinov, I.A. and Broadbelt, L.J., "Reaction Free Energies in Organic Solvents: Comparing Different Quantum Mechanical Methods," Molecular Simulation, 2010, 36(15), 1197.

Brown, Virginia

Safkan et al. Phys. Rev. C75,031001 (2007).

Akdogan, Phys. Rev. C75,031001 (2007)

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Calhoon, William

Calhoon W. H. Jr., Zambon, A. C., Sekar, B., Kiel, B. "Combustor and Augmentor Combustion Modeling for LES Based on Stochastic MOdel Parametrization", ASME Paper GT2011-45126, ASME Turbo Expo 2011, Vancouver, CA

Cameron-Smith, Philip

"Changes in Dimethyl Sulfide Oceanic Distribution due to Climate Change", P. Cameron-Smith, S. Elliott, M. Maltrud, D. Erickson, O. Wingenter, Geophys. Res. Let., 38, L07704, 5 pp., doi:10.1029/2011GL047069, 2011. http://www.agu.org/journals/gl/gl1107/2011GL047069/.

Cannon, William

Cannon, W.R., Rawlins, M. M., Baxter, D., J., Lipton, M., Callister, S., and Bryant, D. A., Large Improvements in MS/MS Based Peptide Identification Rates using a Hybrid Analysis. J. Proteome Res., 2011, 10 (5), pp 2306 2317

Kalyanaraman, A., Latt, B., Baxter, D. J. and Cannon, W.R. and, MapReduce Implementation of a Hybrid Spectral Library- Database Search Method for Peptide Identification. Bioinformatics (2011) 27 (21): 3072-3073. doi: 10.1093/bioinformatics/btr523.

Hugo, A., Baxter, D. J., Kulkarni, G., Kalyanaraman, A., Callister, S. J., and Cannon, W. R.; Proteotyping of Microbial Communities by Optimization of Matches from Tandem Mass Spectrometry. Pacific Symposium in BioComputing, 2012 (in press).

Cannon, W.R., and Baxter, D. J., Analyzing Data for Systems Biology: Working at the Intersection of Thermodynamics and Data Analytics, SciDAC 2011 Proceedings, Denver CO.

Carlson, Joseph

"Ab initio nuclear theory: progress and prospects from quarks to the cosmos," J.P. Vary, Acta Physica Polonica B 42, 397 (2011).

"BEC-BCS crossover and universal relations in unitary Fermi gases," S. Gandolfi, K. E. Schmidt, and J. Carlson, Phys. Rev. A 83, 041601 (2011).

"Can one identify the intrinsic structure of the yrast states in 48Cr after the backbending?," Z. Gao, M. Horoi, Y.S. Chen, and Y.J. Chen, Phys. Rev. C 83, 057303 (2011).

"Cold neutrons trapped in external fields," S. Gandolfi, J. Carlson, and S.C. Pieper, Phys. Rev. Lett. 106, 012501 (2011).

"Configuration Interactions Constrained by Energy Density Functionals," B.A. Brown, A. Signoracci and M. Hjorth-Jensen, Phys. Lett. B 695, 507 (2011).

"Decoupling of Spurious Deep Bound States with the Similarity Renormalization Group," K.A. Wendt, R.J. Furnstahl, and R.J. Perry, Phys. Rev. C 83, 034005 (2011).

"Evolving Nuclear Many-Body Forces with the Similarity Renormalization Group," E.D. Jurgenson, P. Navratil, and R.J. Furnstahl, Phys. Rev. C 83, 034301 (2011).

"Exact-exchange density functional theory for neutron drops," J.E. Drut and L. Platter, Phys. Rev. C 84, 014318 (2011).

"Extracting Scattering Phase-Shifts in Higher Partial-Waves from Lattice QCD Calculations," T. Luu and M.J. Savage, Phys. Rev. D 83, 114508 (2011).

"High-Performance Algorithm for Calculating Non-Spurious Spin- and Parity-Dependent Nuclear Level Densities," R. Senkov, M. Horoi, and V. Zelevinsky, Phys. Lett. B 702, 413 (2011).

"Improved nuclear matter calculations from chiral low-momentum interactions," K. Hebeler, S.K. Bogner, R.J. Furnstahl, A. Nogga, and A. Schwenk, Phys. Rev. C 83, 031301 (2011).

"In-Medium Similarity Renormalization Group for Nuclei," K. Tsukiyama, S.K. Bogner and A. Schwenk, Phys. Rev. Lett. 106, 222502 (2011).

"Isospin mixing in nuclei around N=Z and the superallowed beta decay," W. Satula, J. Dobaczewski, W. Nazarewicz, and M. Rafalski, Acta Physica Polonica B 42, 415 (2011).

"Isospin mixing in the vicinity of the N=Z line," W. Satula, J. Dobaczewski, W. Nazarewicz, M. Borucki, and M. Rafalski, Int. J. Mod. Phys (2011).

Momentum Distribution and Contact of the Unitary Fermi gas J.E. Drut, T.A. L hde, T. Ten Phys. Rev. Lett. 106, 205302 (2011). [arXiv:1012.5474]

Preconditioning the non-relativistic many-fermion problem. T. Ten, J.E. Drut, T.A. L hde [arXiv:1008.3647] (to appear in Comput. Phys. Commun.)

Toward large-scale Hybrid Monte Carlo simulations of the Hubbard model on graphics processing units. K.A. Wendt, J.E. Drut, T.A. L hde Comput. Phys. Commun. 182:1651-1656,2011. [arXiv:1007.3432]

"Solution of the Skyrme Hartree Fock Bogolyubov equations in the Cartesian deformed harmonic-oscillator basis: (VII) hfodd (v2.49t): A new version of the program", N. Schunck, J. Dobaczewski, J. McDonnell, W. Satula, J.A. Sheikh, A. Staszczak, M. Stoitsov, P. Toivanen, Comp. Phys. Comm., (in press) (2011).

"Computing Heavy Elements", N. Schunck, A. Baran, M. Kortelainen, J. McDonnell, J. Mor , W. Nazarewicz, J. Pei, J. Sarich, J. Sheikh, A. Staszczak, M. Stoitsov, S.M. Wild, arXiv:1107.5005 (2011).

"Microscopic calculations of isospin-breaking corrections to superallowed beta-decay", W. Satula, J. Dobaczewski, W. Nazarewicz, and M. Rafalski, Phys. Rev. Lett. 106, 132502 (2011).

Carter, Emily

M. Caspary Toroker, D. D. Kanan, N. Alidoust, L. Y. Isseroff, P. Liao, and E. A. Carter, "First principles scheme to evaluate band edge positions in potential transition metal oxide photocatalysts and photoelectrodes", Phys. Chem. Chem. Phys., 2011, 13 (37), 16644 - 16654.

Cassak, Paul

K. Malakit, M. A. Shay, P. A. Cassak, and C. Bard, "Scaling of asymmetric magnetic reconnection: Kinetic particle-in-cell simulations," J. Geophys. Res., 115, A10223 (2010).

R. Schreier, M. Swisdak, J. F. Drake, and P. A. Cassak, "Three-dimensional simulations of the orientation and structure of reconnection X-lines," Phys. Plasmas, 17, 110704 (2010).

R. N. Baylor, P. A. Cassak, S. Christe, I. G. Hannah, Sam Krucker, D. J. Mullan, M. A. Shay, H. S. Hudson, and R. P. Lin, "Estimates of Densities and Filling Factors from a Cooling Time Analysis of Solar Microflares Observed with RHESSI," Ap. J., 736, 75 (2011).

P. A. Cassak and A. Otto, "Scaling of the Magnetic Reconnection Rate with Symmetric Shear Flow," Phys. Plasmas, 18, 074501 (2011).

P. A. Cassak, "Theory and Simulations of the Scaling of Magnetic Reconnection with Symmetric Shear Flow," Phys. Plasmas, 18, 072106 (2011).

M. T. Beidler and P. A. Cassak, "A Model for Incomplete Reconnection in Sawtooth Crashes," submitted to Phys. Rev. Lett., 2011.

Ceder, Gerbrand

S.P.Ong, V.L.Chevrier, G.Hautier, A.Jain, C.Moore, S.Kim, X.Ma, G.Ceder; Voltage, stability and diffusion barrier differences between sodium-ion and lithium-ion intercalation materials; Energy & Environmental Sciences 4, 3680-3688 (2011)

Cessi, Paola

Cessi, P., C.L. Wolfe, and B.C. Ludka, 2010: Eastern-boundary contribution to the meridional overturning circulation. Journal of Physical Oceanography, 40, 2075-2090.

Cessi, Paola

Wolfe, C.L., and P. Cessi, 2010: What sets the strength of the mid-depth stratification and overturning circulation in eddying ocean models? Journal of Physical Oceanography, 40, 1520-1538.

Wolfe, C.L., and P. Cessi, 2010: The adiabatic pole-to-pole overturning circulation. Submitted to the Journal of Physical Oceanography. In press.

Chan, Yuen-Dat

Low Multiplicity Burst Search at the Sudbury Neutrino Observatory, The SNO Collaboration, Astrophys.J. 728 (2011) 83

Measurement of the e and Total 8B Solar Neutrino Fluxes with the Sudbury Neutrino Observatory Phase-III Data Set, The SNO Collabortion, e-Print: arXiv:1107.2901 [nucl-ex]

C. E. Aalseth et al., Nucl. Phys. B Proc. Suppl. 217, 44 (2011).

M. Boswell et al., IEEE Trans. Nucl. Sci. 58, 1212 (2011).

Chang, Choong-Seock

G.Y. Park, C.S. Chang, I. Joseph, and R. Moyer, Plasma transport in stochastic magnetic field caused by vacuum resonant magnetic perturbations at diverted tokamak edge, Physics of Plasmas 17, 102503 (2010)

G. Dif-Pradalier, P. H. Diamond, V. Grandgirard, Y. Sarazin, J. Abiteboul, X. Garbet, Ph. Ghendrih, and A. Strugarek, S. Ku and C. S. Chang, On the validity of the local diffusive paradigm in turbulent plasma transport, Phys. Rev. E 82, 025401(R) (2010)

R. F. Schmitt, L. Guazzotto, H. Strauss, G. Y. Park, and C.-S. Chang,, Free-boundary magnetohydrodynamic equilibria with flow, Phys. Plasmas 18, 022502 (2011)

G. Dif-Pradalier, P. H. Diamond,b) V. Grandgirard, Y. Sarazin, J. Abiteboul, X. Garbet, Ph. Ghendrih, G. Latu, A. Strugarek, S. Ku, and C. S. Chang, Neoclassical physics in full distribution function gyrokinetics, Physics of Plasmas 18, 062309 (2011)

Weigang Wan, Scott E. Parker, G.Y. Park, C.S. Chang D. Stotler, et, al, The pinch of cold ions from recycling in the tokamak edge pedestal, Phys. Plasmas, 18, 056116 (2011)

Y. Sarazin1, V. Grandgirard1, J. Abiteboul1, S. Allfrey1, X. Garbet1, Ph. Ghendrih1, G. Latu1, A. Strugarek1, G. Dif-Pradalier2, P.H. Diamond2,3, S. Ku4, C.S. Chang4, et al, Predictions on heat transport and plasma rotation from global gyrokinetic simulations, Nuclear Fusion 51, 103023 (2011)

Ye Jin, Sriram Lakshminarasimhan, Neil Shah, Zhenhuan Gong, C.S. Chang,Jackie Chen, Stephane Ethier, Hemanth Kolla, Seung-Hoe Ku, et al, S-preconditioner for Multi-fold Data Reduction with Guaranteed User-controlled Accuracy, ICDM 2011

Sriram Lakshminarasimhan, John Jenkins, Isha Arkatkar, Zhenhuan Gong, Hemanth Kolla, Seung-Hoe Ku, Stephane Ethier, Jackie Chen, C.S. Chang, Scott Klasky, Robert Latham, Robert Ross, and Nagiza F. Samatova, ISABELA-QA: Query-driven Analytics with ISABELA-compressed Extreme-Scale Scientific Data, Super Computing 2011

S. Kaye, R. Maingi, D. Battaglia, R.E. Bell, C.S. Chang, et al, L-H Threshold Studies in NSTX, in press, Nucl. Fusion

Chelikowsky, James

Oxides- N. Sai, K. Leung and J.R. Chelikowsky: Hybrid density functional study of oligothiophene/ZnO interface for photovoltaics, Phys. Rev. B, 83: 121309 (2011).

J. Han, T.-L. Chan and J. R. Chelikowsky: Quantum confinement, core level shifts, and dopant segregation in P-doped Si nanowires, Phys. Rev. B, 82: 153413 (2010).

K. H. Khoo, J. T. Arantes, J. R. Chelikowsky, and G. M. Dalpian: First-Principles Calculations of Lattice-Strained Core-Shell Nanocrystals, Phys. Rev. B 84, 075311 (2011).

T.-L. Chan, S. Zhang and J.R. Chelikowsky: Charged dopants in semiconductor nanowires with partially periodic boundary conditions, Phys. Rev. B, 83: 245440 (2011).

J.R. Chelikowsky, T.-L. Chan, M.M.G Alemany and G. Dalpian: Computational studies of doped nanostructures, Rep. Prog. Phys, 74:046501 (2011)

Chen, Guangshan

Chen, G., M. Notaro, Z. Liu, and Y. Liu, 2011: Simulated local and remote biophysical effects of afforestation over Southeast United States in boreal summer. Journal of Climate, in review Notaro, M., and G. Chen, 2011: Vegetation feedbacks to climate in the global monsoon regions Journal of Climate, in press.

Chen, Jacqueline

E. R. Hawkes, O. Chatakonda, H. Kolla, and J. H. Chen, "A Petascale Direct Numerical Simulation Study of the Modelling of Flame Wrinkling for Large-Eddy Simulations in Intense Turbulence," accepted Combustion and Flame, 2012.

Chen, Liu

Effects of electron dynamics in toroidal momentum transport driven by ion temperature gradient turbulence, I. Holod and Z. Lin, Plasma Phys. Contr. Fusion 52, 035002 (2010).

Fluctuation characteristics and transport properties of collisionless trapped electron mode turbulence, Yong Xiao, Ihor Holod, Wenlu Zhang, Scott Klasky, and Zhihong Lin, Phys. Plasmas 17, 022302 (2010).

Scalings of energetic particle transport by ion temperature gradient Microturbulence, Wenlu Zhang, Viktor Decyk, Ihor Holod, Yong Xiao, Zhihong Lin, and Liu Chen, Phys. Plasmas 17, 055902 (2010).

Trapped Electron Damping of Geodesic Acoustic Mode, Huasen Zhang and Zhihong Lin, Phys. Plasmas 17, 072502 (2010).

Gyrokinetic Simulation of Turbulence Driven Geodesic Acoustic Modes in Edge Plasmas of HL-2A Tokamak, Feng Liu, Z. Lin, J. Q. Dong, K. J. Zhao, Phys. Plasmas 17, 112318 (2010).

Gyrokinetic particle simulations of reversed shear Alfven eigenmode excited by antenna and fast ions, Wenjun Deng, Zhihong Lin, Ihor Holod, Xin Wang, Yong Xiao, and Wenlu Zhang, Phys. Plasmas 17, 112504 (2010).

Gyrokinetic particle simulation of beta-induced Alfven eigenmode, H. S. Zhang, Z. Lin, I. Holod, X. Wang, Y. Xiao, W. L. Zhang, Phys. Plasmas 17, 112505 (2010).

Gyrokinetic simulation of magnetic compressional modes in general geometry, Peter Porazik and Zhihong Lin, Commun. Comput. Phys. 10, 899 (2011).

Gyrokinetic particle simulation of drift-compressional modes in dipole geometry, Peter Porazik and Zhihong Lin, Phys. Plasmas 18, 072107 (2011).

Chen, Shentan

Chen, Shentan; Rousseau, Roger; Raugei, Simone; Dupuis, Michel; DuBois, Daniel L.; Bullock, R. Morris Comprehensive Thermodynamics of Nickel Hydride Bis(Diphosphine) Complexes: A Predictive Model through Computations. Organometallics, 2011, accepted.

Mock, Michael T.; Chen, Shentan; Rousseau, Roger; Dougherty, William G.; Kassel, W. Scott; DuBois, Dianel L.; Bullock, R. Morris A Rare Terminal Dinitrogen Complex of Chromium Chem. Commun., 2011 accepted.

O'Hagan, Molly; Shaw, Wendy; Raugei, Simone; Chen, Shentan; Yang, Jenny Y.; Kilgore, Uriah J.; DuBois, Daniel L.; Bullock, R. Morris Moving Protons with Pendant Amines: Proton Mobility in a Nickel Catalyst for Hydrogen Oxidation. J. Am. Chem. Soc., 2011, 133, 14301. (Highlighted on journal cover)

Dupuis, Michel; Chen, Shentan; Raugei, Simone; DuBois, Daniel L.; Bullock, R. Morris Comment on "New Insights in the Electrocatalytic Proton Reduction and Hydrogen Oxidation by Bioinspired Catalysts: A DFT Investigation" (J. Phys, Chem. A 2010, 114, 11861-11867). J. Phys. Chem. A 2011, 115, 4861.

Chen, Shentan; Raugei, Simone; Rousseau, Roger; Dupuis, Michel; Bullock, R. Morris Homogeneous Ni Catalysts for H2 Oxidation and Production: An Assessment of Theoretical Methods, from Density Functional Theory to Post Hartree-Fock Correlated Wave-Function Theory J. Phys. Chem. A 2010, 114, 12716.

Yang, Jenny Y.; Chen, Shentan; Dougherty, William G.; Kassel, W. Scott; Bullock, R. Morris; DuBois, Daniel L.; Raugei, Simone; Rousseau, Roger; Dupuis, Michel; DuBois, M. Rakowski Hydrogen oxidation catalysis by a nickel diphosphine complex with pendant tert-butyl amines Chem. Commun., 2010, 46, 8618.

Chen, Yang

Yang Chen, Scott E. Parker, J. Lang, and G.-Y. Fu, "Linear gyrokinetic simulation of high-n toroidal Alfven eigenmodes in a burning plasma," Phys. Plasmas 17, 102504 (2010)

Yang Chen and Scott E. Parker, "Fluid electrons with kinetic closure for long wavelength energetic particles driven modes," Phys. Plasmas 18, 055703 (2011)

Weigang Wan, Scott E. Parker, Yang Chen, Gun-Young Park, Choong-Seock Chang, and Daren Stotler, "The pinch of cold ions from recycling in the tokamak edge pedestal," Phys. Plasmas 18, 056116 (2011)

Cheng, Hai-Ping

Title: Anisotropic quasiparticle lifetimes in Fe-based superconductors Author(s): Kemper A. F.; Korshunov M. M.; Devereaux T. P.; et al. Source: PHYSICAL REVIEW B Volume: 83 Issue: 18 Article Number: 184516

Title: First-principles studies of Ta(2)O(5) polymorphs Author(s): Wu Yu-Ning; Li Lan; Cheng Hai-Ping Source: PHYSICAL REVIEW B Volume: 83 Issue: 14 Article Number: 144105

Title: Interaction between water and defective silica surfaces Author(s): Chen Yun-Wen; Cheng Hai-Ping Source: JOURNAL OF CHEMICAL PHYSICS Volume: 134 Issue: 11 Article Number: 114703

Title: Interedge magnetic coupling in transition-metal terminated graphene nanoribbons Author(s): Wang Yan; Cheng Hai-Ping Source: PHYSICAL REVIEW B Volume: 83 Issue: 11 Article Number: 113402

Title: Accurate projected augmented wave datasets for BaFe(2)As(2) Author(s): Cao Chao; Wu Yu-ning; Hamdan Rashid; et al. Source: NEW JOURNAL OF PHYSICS Volume: 12 Article Number: 123029

Title: Metal-terminated graphene nanoribbons Author(s): Wang Yan; Cao Chao; Cheng Hai-Ping Source: PHYSICAL REVIEW B Volume: 82 Issue: 20 Article Number: 205429

Title: Structure and stability of thin water films on quartz surfaces Author(s): Chen Yun-Wen; Cheng Hai-Ping Source: APPLIED PHYSICS LETTERS Volume: 97 Issue: 16 Article Number: 161909

Childs, Hank

- D. Camp, C. Garth, H. Childs, D. Pugmire, and K. Joy, "Streamline Integration using MPI-Hybrid Parallelism on a Large Multi-Core Architecture", IEEE Transactions on Visualization and Computer Graphics, December 2010.

Ching, Wai-Yim

Lei Liang, Paul Rulis and W.Y. Ching, Mechanical properties, electronic structure and bonding of - and - tri-calcium phosphates with surface characterization , Acta Biomaterialia, 6, 3763-3771 (2010). doi:10.1016.

R. H. French, V. A. Parsegian, Rudolf Podgornik, Rick Rajter, Anand Jagota, Jian Luo, Dilip Asthagiri, Manoj Chaudhury, Yet-Ming Chiang, Steve Granick, Mehran Kardar, Roland Kjellander, David Langreth, Jennifer Lewis, Steve Lustig, David Wesolowski, John Wettlaufer, Wai-Yim Ching, Mike Finnis, Frank Houlihan, O. Anatole von Lilienfeld, Carel Jan van Oss, Thomas Zemb, Long Range Interactions In Nanoscale Science , Review of Modern Physics, 82:2, 1887-1944, (2010).

A. Siber, R. F. Rajter, R.H. French, W.Y. Ching, A. Parsegian and R. Podgornik, Optically anisotropic infinite cylinder above an optically anisotropic half-space: Dispersion interaction of a single-walled carbon nanotube with a substrate , J. Vac Sci. Tech. B 28(3), C4A17-C4A24 (2010).

W.Y. Ching, Paul Rulis, Lizhi Ouyang, S. Aryal, and A. Misra, Theoretical study of the elasticity, of the mechanical, behavior, electronic structure, interatomic bonding, and dielectric function of an intergranular glassy film model in prismatic -Si3N4 , Phys. Rev. B 81, 214120-1-14. (2010).

A. Altay, C.B. Carter, P. Rulis, W.Y. Ching, I. Arslan and M.A. G lgun, "Characterizing CA2 and CA6 using ELNES", J. Solid State Chemistry J. Solid State Chem, 183(8) ,1776-1784 (2010).

Lei Liang, Paul Rulis, L. Ouyang, and W.Y. Ching, Ab initio investigation of hydrogen bonding and network structure in a supercooled model of water , Phys. Rev. B 83, 024201-1-7 (2011) . ISSN:1098-0121. AN 2011:152703

Yang Yang, W.Y. Ching, and A. Misra, Higher-Order continuum theory applied to fracture simulation of nano-scale intergranular glassy film , J. of Nanomechanics and Micromechanics. Vol.1, No 2, 2153-5434 (2011). DOI: 10.1061/(ASCE)NM.2153-5477.0000030.

Paul Rulis and W.Y. Ching, Theoretical XANES spectra of Si-K, Si-L, N-K and O-K edges of a prismatic model of intergranular glassy films in -Si3N4 , J. of Materials Science,46(12), 4191-4198 (2011).

W.Y. Ching, S. Aryal, Paul Rulis, Wolfgan Schnick, Prediction of the electronic structure and physical properties of the spinel phase of BeP2N4 . Phys. Rev. B83, 155109-1-8, (2011). DOI: 10.1103.

Altaf Hussain, S. Aryal, P. Rulis, M.S. Choudhry, Jun Chen and W.Y. Ching, Ab initio electronic structure Calculations and optical properties of ordered and disordered Ni3Al , J. Alloy and Compounds, 5230-5037 (2011).

Paul Rulis, Liaoyuan Wang, Ben Walker, and Wai-Yim Ching, Spectral Analysis of the Electronic Structure of -B28. , J. of Superhard Materials (in press)

S. Aryal, Paul Rulis and W.Y. Ching, Mechanism for amorphization in boron carbide (B4C) under uniaxial compression , Phys. Rev. B. (accepted).

Choi, YongMan

K. Kuttiyiel, K. Sasaki, Y. Choi, D. Su, P. Liu, and R. R. Adzic "Bimetallic IrNi core platinum monolayer shell electrocatalysts for the oxygen reduction reaction," Energy & Environmental Science, in press.

F. Yang, Y. Choi, P. Liu, D. Stacchiola, J. Hrbek, and J. Rodriguez "Identification of 5-7 defects in a copper oxide surface," Journal of the American Chemical Society, 133 (30), 1474 (2011).

Y. Choi and P. Liu "Understanding of ethanol decomposition on Rh(111) from density functional theory and kinetic Monte Carlo simulations," Catalysis Today (invited), 165, 64 (2011).

J. X. Wang, C. Ma, Y. Choi, D. Su, Y. Zhu, P. Liu, R. Shi, and R. R. Adzic "Kirkendall Effect and Lattice Contraction in Nanocatalysts: A New Strategy to Achieve Sustainable Activity Enhancement," Journal of the American Chemical Society, 133, 13551 (2011).

L. Yang, Y. Choi, W. Qin, H. Chen, K. Blinn, M. Liu, P. Liu, J. Bai, T. A. Tyson, and M. Liu "Promotion of water-mediated carbon removal by nanostructured barium oxide/nickel interfaces in solid oxide fuel cells," Nature Communications, 2, Article number:357, (2011).

Chou, Mei-Yin

"Theoretical Investigation of Intermediate Phases between Li2NH and LiNH2," Feng Zhang, Yan Wang, and M. Y. Chou, Phys. Rev. B 82, 094112/1-6 (2010).

"Stability of the Hydrogen-Storage Compound Li6Mg(NH)4 from First Principles," Feng Zhang, Yan Wang, and M. Y. Chou, Phys. Rev. B 83, 012101/1-4 (2011).

"Catalytic Effect of near-Surface Alloying on Hydrogen Interaction on the Aluminum Surface," Y. Wang, F. Zhang, P. Lin, R. Stumpf, and M. Y. Chou, Phys. Rev. B 83, 195419/1-5 (2011).

"Theoretical Study of the Vibrational Properties of NaAlH4 with AlH3 Vacancies," Feng Zhang, Yan Wang, and M. Y. Chou, Faraday Discussion 151, 243-251 (2011).

"Oxidation Functional Groups on Graphene: Structural and Electronic Properties," J.-A. Yan and M. Y. Chou, Phys. Rev. B 82, 125403/1-10 (2010).

"Lattice Vibrational Modes and their Frequency Shifts in Semiconductor Nanowires," L. Yang and M. Y. Chou, Nano Lett. 11, 2618-2621 (2011).

"Enhanced Optical Conductivity Induced by Surface States in ABC-stacked Few-Layer Graphene," J. Yan, W. Ruan, and M. Y. Chou, Phys. Rev. B 83, 245418/1-6 (2011).

"Effect of Electrostatic Fields and Charge Doping on the Linear Bands in Twisted Graphene Bilayers," L. Xian, S. Barraza-Lopez, and M. Y. Chou, Phys. Rev. B 84, 075425/1-6 (2011).

Choudhary, Alok

Arifa Nisar, Wei-keng Liao, and Alok Choudhary. Delegation-based I/O Mechanism for High Performance Computing Systems, In the IEEE Transactions on Parallel and Distributed Sytems, preprint, June 2011.

Chen Jin, Saba Sehrish, Wei-Keng Liao, Alok Choudhary, and Karen Schuchardt. Improving the Average Response Time in Collective I/O. In the EuroMPI conference, Santorini, Greece, September 2011.

Bruce Palmer, Karen Schuchardt, Annette Koontz, Robert Jacob, Robert Latham, and Wei-keng Liao. IO for High Resolution Climate Models. In the Workshop on High-Resolution Climate Modeling, June 2010.

Chrzan, Daryl

D. C. Chrzan, M. P. Sherburne, Y. Hanlumyuang, T. Li and J. W. Morris, Jr., "Spreading of dislocation cores in elastically anisotropic body-centered-cubic materials: The case of gum metal," Physical Review B 82, 184202/1-5 (2010).

Chu, Jhih-Wei

Gross, A.S. and Chu, J.-W., On the Molecular Origins of Biomass Recalcitrance: The Interaction Network and Solvation Structures of Cellulose Microfibrils. J. Phys. Chem. B, 2010. 114(42): p. 13333-13341.

Brokaw, J.B. and Chu, J.-W., On the Roles of Substrate Binding and Hinge Unfolding in Conformational Changes of Adenylate Kinase. Biophys. J., 2010. 99(10): p. 3420-3429.

Silvestre-Ryan, J., Lin, Y., and Chu, J.-W., Fluctuograms Reveal the Intermittent Intra-Protein Communication in Subtilisin Carlsberg and Correlate Mechanical Coupling with Co-Evolution. Plos Comput. Biol., 2011. 7(3): p. e1002023.

Cho, H.M., Gross, A.S., and Chu, J.-W., Dissecting Force Interactions in Cellulose Deconstruction Reveals the Required Solvent Versatility for Overcoming Biomass Recalcitrance. J. Am. Chem. Soc., 2011. in press, DOI: 10.1021/ja2046155.

Gross, S.A., Bell, A.T., and Chu, J.-W., The Thermodynamics of Cellulose Solvation in Water and the Ionic Liquid 1-Butyl-3-Methylimidazolim Chloride. J. Phys. Chem. B, 2011. in press.

Lin, Y., Silvestre-Ryan, J., Himmel, M.E., Crowley, M.F., Beckham, G.T., and Chu, J.-W., Protein Allostery at the Solid-Liquid Interface: Endoglucanase Attachment to Cellulose Affects Glucan Clenching in the Binding Cleft. J. Am. Chem. Soc., 2011. in press, DOI: 10.1021/ja206692g.

Chuang, Catherine

Chuang, C. C., J. S. Boyle, S. Xie, and J. T. Kelly, 2011, Sensitivity of Aerosol Indirect Effects to Cloud Nucleation and Autoconversion Parameterizations in Short-Range Weather Forecasts over the Southern Great Plains During May 2003 Intensive Operations Period, J. Geophys. Res., in revision.

Wild, O., A. M. Fiore, D. T. Shindell, R. M. Doherty, W. J. Collins, F. J. Dentener, M. G. Schultz, S. Gong, I. A. Mackenzie, G. Zeng, P. Hess, B. N. Duncan, D. J. Bergmann, S. Szopa, J. E. Jonson, T. J. Keating, A. Zuber, 2011: Future Changes in Surface Ozone: A Parameterized Approach, submitted to Atmospheric Chemistry and Physics.

Fry, M. M., V. Naik, J. J. West, M. D. Schwarzkopf, A. M. Fiore, W. J. Collins, F. J. Dentener, D. T. Shindell, C. Atherton, D. Bergmann, B. N. Duncan, P. Hess, I. A. MacKenzie, E. Marmer, M. Schultz, S. Szopa, O. Wild, G. Zeng, 2011: The influence of ozone precursor emissions from four world regions on tropospheric composition and radiative climate forcing, submitted to Journal of Geophysical Research.

Cohen, Bruce

R.E. Waltz, G.M. Staebler, and W.M. Solomon, "Gyrokinetic simulation of momentum transport with residual stress from diamagnetic level velocity shears", Phys. Plasmas 18 (2011) 042504

(2)G.M. Staebler, R. E. Waltz, and J. E. Kinsey"Discoveries from the exploration of gyro-kinetic momentum transport", Phys. Plasmas 18, 056106 (2011). (APS2010 invited talk)

(3)J.E. Kinsey, G.M. Staebler, J. Candy, R.E. Waltz, and R.V. Budny, "ITER predictions using the GYRO verified and experimentally validated trapped gyro-Landau fluid transport model",Nucl. Fusion 51 (2011) 083001.

Electron heat transport from stochastic fields in gyrokinetic simulations E. Wang, W. M. Nevins, J. Candy, D. Hatch, P. Terry, and W. Guttenfelder Phys. Plasmas 18, 056111 (2011)

Electromagnetic Transport from Microtearing Mode Turbulence W. Guttenfelder, J. Candy, S. M. Kaye, W. M. Nevins, E. Wang, R. E. Bell, G. W. Hammett, B. P. LeBlanc, D. R. Mikkelsen, and H. Yuh Phys. Rev. Lett. 106, 155004 (2011)

AstroGK: Astrophysical gyrokinetics code; Numata, Howes, et al; JOURNAL OF COMPUTATIONAL PHYSICS Volume: 229 Issue: 24 Pages: 9347-9372 DOI: 10.1016/j.jcp.2010.09.006 Published: DEC 10 2010

Particle Pinch in Gyrokinetic Simulations of Closed Field-Line Systems; Kobayashi, Rogers and Dorland; PHYSICS OF PLASMAS Volume: 18 Issue: 4 Article Number: 049902 DOI: 10.1063/1.3570822 Published: APR 2011

Gyrokinetic Simulations of Solar Wind Turbulence from Ion to Electron Scales; Howes, TenBarge, et al; PHYSICAL REVIEW LETTERS Volume: 107 Issue: 3 Article Number: 035004 DOI: 10.1103/PhysRevLett.107.035004 Published: JUL 14 2011

M. A. Dorf, R. H. Cohen, J. C. Compton, M. Dorr, T. D. Rognlien, J. Angus, S.Krasheninnikov, P. Colella, D. Martin, and P. McCorquodale, "Progress with the COGENT Edge Kinetic Code: Collision Operator Options" submitted as a PET-13 conference paper, and will later appear (after the referee process) in the contribution to plasma physics.

Rognlien, T.D., Bodi, K., Cohen, R.H., Dimits, A.M., Dorf M.A, Dorr, M. Krasheninnikov, S.I., Nam, S.K., Ryutov, D.D., Umansky, M.V., and Xu, X.Q. Advances in Understanding Tokamaks Edge/Scrape-off Layer Transport, Proceedings of 23 IAEA Fusion Energy Conference, Daejeon, Republic of Korea, 2010.

M. R. Dorr, R. H. Cohen, P. Colella, M. A. Dorf, J. A. F. Hittinger, and D. F. Martin, Numerical simulation of phase space advection in gyrokinetic models of fusion plasma, Proceedings of SciDAC 2010, 2010 X.Q.Xu, B.D.Dudson, P.B.Snyder, M.V.Umansky, H.R.Wilson and T.Casper Nonlinear ELM simulations based on a nonideal peeling-ballooning model using the BOUT++ code,Nucl. Fusion 51 (2011) (10pp), in production

B. D. Dudson, X. Q. Xu, M. V. Umansky, H. R. Wilson and P. B. Snyder, "Simulation of edge localized modes using BOUT++", Plasma Phys. Control. Fusion, VOL. 53, 054005 (2011).

X.Q.Xu, B.Dudson, P.B.Snyder, M.V.Umansky, and H.Wilson, Nonlinear Simulations of Peeling-Ballooning Modes with Anomalous Electron Viscosity and their Role in Edge Localized Mode Crashes, PHYSICAL REVIEW LETTERS , VOL. 105, 175005 (2010).

X.Q.Xu, B.Dudson, M. V. Umansky, P.B.Snyder, H.Wilson, Nonlinear ELM simulations based on peeling-ballooning modes using the BOUT++ code, 23rd IAEA Fusion Energy Conference, 11-16 October 2010 Daejon, Republic of Korea, http://www-pub.iaea.org/MTCD/Meetings/cn180_papers.asp , THS/P3-05.

T. Y. Xia, X. Q. Xu, B. D. Dudson and J. G. Li, Nonlinear Simulations of Peeling-Ballooning Modes with Parallel Flow and RF Sources, submitted to Contribution to Plasma Physics

X.Q. Xu, K. Bodi, R.H. Cohen, S. Krasheninnikov and T.D. Rognlien, TEMPEST simulations of the plasma transport in a single-null tokamak geometry , Nucl. Fusion 50, 064003 (2010).

Cohen, Marvin

B.C. Shih, Y. Xue, P. Zhang, M.L. Cohen, and S.G. Louie, "Quasiparticle band gap of ZnO: High accuracy from the conventional G0W0 approach," Phys. Rev. Lett. 105, 146401 (2010).

M.L. Cohen, "Predicting and explaining Tc and other properties of BCS superconductors," Modern Phys. Lett. B 25, 2755 (2010). Also in Bardeen, Cooper, and Schrieffer: 50 Years, eds. L.N. Cooper and D. Feldman (World Scientific, Singapore, 2010).

M.L. Cohen and A. Zettl, "The physics of boron nitride nanotubes," Physics Today 63, 34 (2010).

T. Bazhirov, J. Noffsinger, and M.L. Cohen, "Superconductivity and electron-phonon coupling in lithium at high pressures," Phys. Rev. B 82, 184509 (2010).

J. Noffsinger, F. Giustino, B.D. Malone, C.-H. Park, S.G. Louie, and M.L. Cohen, "EPW: A program for calculating the electron-phonon coupling using maximally localized Wannier functions," Comput. Phys. Comm. 181, 2140 (2010).

H.K. Lee, M.L. Cohen, and S.G. Louie, "Selective functionalization of halogens on zigzag graphene nanoribbons: A route to the separation of zigzag graphene nanoribbons," Appl. Phys. Letters 97, 233101 (2010).

F. Giustino, S.G. Louie, and M.L. Cohen, "Electron-phonon renormalization of the direct band gap of diamond," Phys. Rev. Lett. 105, 265501 (2010).

M.L. Cohen, "Electron-phonon induced pairing and its limits for superconducting systems," Physica E 43, 657 (2011).

V.W. Brar, R. Decker, H.-M. Solowan, Y. Wang, L. Maserati, K.T. Chan, H. Lee, C.O. Girit, A Zettl, S.G. Louie, M.L. Cohen, and M.F. Crommie," Gate-controlled ionization and screening of cobalt adatoms on a graphene surface," Nature Physics 7, 43 (2011).

K.T. Chan, H.K. Lee, and M.L. Cohen, "Gated adatoms on graphene studied from first principles," Phys. Rev. B 83, 035405 (2011).

J. Noffsinger and M.L. Cohen, "Superconductivity in monolayer Pb on Si (111) from first principles," Solid State Comm. 151, 421 (2011).

J.J. Crochet, J.D. Sau, J.G. Duque, S.K. Doorn, and M.L. Cohen, "Electrodynamic and excitonic intertube interactions in semiconducting carbon nanotube aggregates," ACS Nano 5, 2611 (2011).

J. Noffsinger and M.L. Cohen, "Electron-phonon coupling and superconductivity in double-walled carbon nanotubes," Phys. Rev B 83, 165420 (2011).

T. Koretsune, S. Saito, and M.L. Cohen, "One-dimensional alkali-doped C60 chains encapsulated in BN nanotubes," Phys. Rev. B 83, 193406 (2011).

M.L. Cohen and B.D. Malone, "Wave-function engineering: Other phases of Si for photovoltaic applications," J. Appl. Phys. 109, 102402 (2011).

K. Kim, Z. Lee, B.D. Malone, K.T. Chan, B. Aleman, W. Regan, W. Gannett, M.F. Crommie, M.L. Cohen, and A. Zettl, "Multiply folded graphene," Physical Review B 83, 245433 (2011).

H. Oh, H.J. Choi, S.G. Louie, and M.L. Cohen, "Fermi surfaces and quantum oscillations in the underdoped high-Tc superconductors YBa2Cu3O6.5 and YBa2Cu4O8," Phys. Rev. B 84, 014518(2011).

Colella, Phillip

G. H. Miller and D. Trebotich "An embedded boundary method for the Navier-Stokes equations on a time-dependent domain", in press Communications in Applied Mathematics and Computational Science (2011)

D. M. Ushizima, G. H. Weber, J. Ajo-Franklin, Y. Kim, A. Macdowell, D. Morozov, P. Nico, D. Parkinson, D. Trebotich, J. Wan, W. Bethel "Analysis and Visualization for Multiscale Control of Geologic CO2" , SciDAC 2011

Q. Zhang, "High-order, multidimensional, and conservative coarse-fine interpolation for adaptive mesh refinement" , Comput. Methods Appl. Mech. Engrg., 200(45-46):3159-3168 (2011)

F. Miniati and D.F. Martin "Constrained-transport Magnetohydrodynamics with Adaptive Mesh Refinement in CHARM", The Astrophysical Journal Supplement Series, 195(1):5 (2011).

B. Van Straalen, P. Colella, D. T. Graves, N. Keen "Petascale Block-Structured AMR Applications Without Distributed Meta-data", presented at EuroPar 2011, Bordeaux, France

B. Kallemov, G. H. Miller, S. Mitran and D. Trebotich "Multiscale Rheology: New Results for the Kinetic Scale", NSTI-Nanotech 2011, Vol. 2, pp. 575-578 (2011)

B. Kallemov, G. H. Miller and D. Trebotich "A Higher-Order Accurate Fluid-Particle Algorithm for Polymer Flows", Molecular Simulation, 37(8):738-745 (2011).

P. McCorquodale and P. Colella, "A high-order finite-volume method for conservation laws on locally refined grids", Communications in Applied Mathematics and Computational Science, Vol. 6 (2011), No. 1, 1-25.

P. Colella, M.R. Dorr, J.A.F. Hittinger, and D.F. Martin "High-Order Finite-Volume Methods in Mapped Coordinates", Journal of Computational Physics, 230(8):2952-2976 (2011)

B. Wang, G. Miller, and P. Colella, "A particle-in-cell method with adaptive phase-space remapping for kinetic plasmas", to appear in SIAM J. on Sci. Comput., (2011).

R.K. Crockett, P. Colella, and D.T. Graves, "A Cartesian grid embedded boundary method for solving the Poisson and heat equations with discontinuous coefficients in three dimensions" Submitted to Journal of Computational Physics .

R.H. Cohen, J. Compton, M. Dorr, J. Hittinger, W.M Nevins, T.D. Rognlien, Z.Q. Xu, P. Colella, and D. Martin, "Testing and Plans for the COGENT edge kinetic code" , (abstract) submitted to Sherwood 2010.

B. Kallemov, G. H. Miller and D. Trebotich "Numerical Simulation of Polymer Flow in Microfluidic Devices" 2009 Proceedings of the Fourth SIAM Conference on Mathematics for Industry (MI09) pp. 93-98 (2010).

E. Ateljevich, P. Colella, D.T. Graves, T.J. Ligocki, J. Percelay, P.O. Schwartz, Q. Shu "CFD Modeling in the San Francisco Bay and Delta" 2009 Proceedings of the Fourth SIAM Conference on Mathematics for Industry (MI09), pp. 99-107 (2010).

Collins, William

Bougamont, M., S. Price, P. Christoffersen, and A.J. Payne (2011). Dynamic patterns of ice stream flow in a 3d higher-order ice sheet model with plastic bed and simplified hydrology. J. Geophys. Res. (in press).

Carter, S.P., H. A. Fricker, D.D. Blankenship, J.V. Johnson, W.H. Lipscomb, S.F. Price, and D.A. Young (2011). Monitoring and modeling five years of subglacial lake activity in the MacAyeal Ice Stream catchment. J. Glaciol. (in press).

Dukowicz, J. K., S.F. Price, and W.H. Lipscomb (2011) Incorporating arbitrary basal topography in the variational formulation of ice sheet models. J. Glaciol., 57, 461-467.

Hagos, S., and L.R. Leung, 2011: On the relationship between uncertainties in tropical divergence and the hydrological cycle in global models. J. Clim., in press.

Lemieux, J.F., S.F. Price, K.J. Evans, D. Knoll, A.G. Salinger, D. Holland, and A.J. Payne (2011). Implementation of the Jacobian-Free Newton-Krylov method for solving the first-order ice sheet momentum balance. J. Comput. Phys. (in press)

Meng, L., P. G. Hess, N. M. Mahowald, J. B. Yavitt, W. J. Riley, Z. M. Subin, D. M. Lawrence, J. Jauhiainen, and D. Fuka, 2011: Improving estimates of methane emissions from the tropics, submitted to Biogeosciences.

Price, S.F., G. Flowers, and C. Schoof (2011). Improving hydrology in land ice models. Eos, 92(19), 164.

Price, S.F., A.J. Payne, I.M. Howat, and B.E. Smith. 2011. Committed sea-level rise for the next century from Greenland ice sheet dynamics during the past decade. PNAS, doi:10.1073/pnas.1017313108.

Reagan, M., G. Moridis, S. Elliott, and M. Maltrud, 2011a: Contribution of oceanic gas hydrate dissociation to the formation of Arctic Ocean methane plumes. Journal of Geophysical Research Oceans, submission 2011JC007189, in press.

Riley, W. J., Z. M. Subin, M. S. Torn, L. Meng, N. Mahowald, P. G. Hess, and D. M. Lawrence (2011), Barriers to predicting changes in global terrestrial methane fluxes: Analyses using CLM4ME, a methane biogeochemistry model integrated in CESM, submitted Biogeosciences.

Stepanenko, V., A. Martynov, K. Joehnk, Z. Subin, M. Perroud, X. Fang, D. Mironov, F. Beyrich, and S. Goyette (2011), A model intercomparison study on the role of turbulent mixing parameterizations and interaction with bottom sediments in a shallow turbid midlatitude lake, submitted Tellus-A

Subin, Z., L. Murphy, F. Li, C. Bonfils, and W. Riley (2011), Boreal Lakes Moderate Seasonal and Diurnal Temperature Variation and Perturb Atmospheric Circulation, Tellus-A.

Subin, Z. M., W. J. Riley, and D. Mironov (2011), An Improved Lake Model for Regional and Global Climate Simulations: Model Structure, Evaluation, and Sensitivity Analyses in CESM1, submitted J. Adv. Model. Earth Sys.

Zhang H., L. Ju, M. Gunzburger, T. Ringler, and S.F. Price (2011). Coupled models and parallel simulations for three-dimensional full Stokes ice sheet modeling. Numer. Math. Theor. Meth. Appl. (in press).

Zhao, C., X. Liu, L.R. Leung, B. Johnson, S. McFarlane, W.I. Gustafson, J.D. Fast, and R. Easter, 2010: The spatial distribution of dust and its shortwave radiative forcing over North Africa: Modeling sensitivities to dust emissions and aerosol size treatments. Atmos. Chem. and Phys., 10, 8821 8838.

Zhao, C., X. Liu, L.R. Leung, and S. Hagos, 2011: Radiative impact of mineral dust on monsoon precipitation variability over West Africa. Atmos. Chem. And Phys., 11, 1879-1893.

D.M. Romps, Z. Kuang, "A transilient matrix for moist convection," Journal of the Atmospheric Sciences, vol. 68, no. 9, 2009-2025, 2011

Chang, C.-Y., J. C. H. Chiang, M. F. Wehner, A. Friedman, and R. Ruedy (2010) Sulfate aerosol control of Tropical Atlantic climate over the 20th century, to appear in Journal of Climate (currently online access doi: 10.1175/2010JCLI4065.1)

Li, F., W.D. Collins, M.F. Wehner, David Williamson, Jerry Olson, C.A. Algieri (2011) Impact of horizontal resolution on simulation of precipitation extremes in an aqua-planet version of Community Atmospheric Model (CAM3). Submitted to Tellus In Press

Li, F., W.D. Collins, M.F. Wehner, David Williamson, Jerry Olson (2011) Response of precipitation extremes to idealized global warming in an aqua-planet climate model: towards a robust projection across different horizontal resolutions. Submitted to Tellus In Press

Sednev, I. and S. Menon 2011: Analyzing numerics of bulk microphysics schemes in community models: warm rain processes. Submitted, Geosci. Mod. Develop. Disc.

Wehner, Michael, David R. Easterling, Jay H. Lawrimore, Richard R. Heim Jr., Russell S. Vose, Benjamin Santer (2011) Projections of Future Drought in the Continental United States and Mexico. Submitted to Journal of Hydrometerology Pending

Wehner, M. F., G. Bala, P. Duffy, A. A. Mirin, and R. Romano, 2010: Towards Direct Simulation of Future Tropical Cyclone Statistics in a High-Resolution Global Atmospheric Model, Advances in Meteorology, Article ID 915303. doi:10.1155/2010/915303.

Compo, Gil

Allan, R., P. Brohan, G.P. Compo, R. Stone, J. Luterbacher, and S. Bronnimman, 2011: The International Atmospheric Circulation Reconstructions over the Earth (ACRE) initiative. Bull. Amer. Met. Soc., in press. doi: 10.1175/2011BAMS3218.1.

Allan R., Compo G., Carton J., 2011: Recovery of Global Surface Weather Observations for Historical Reanalyses and International Users, EOS Transactions, 92, 154.

Blunden, J., D. S. Arndt, and M. O. Baringer, Eds., 2011: State of the Climate in 2010. Bull. Amer. Meteor. Soc., 92, S1-S236. doi:10.1175/1520-0477-92.6.S1.

Br nnimann, S., G.P. Compo, R. Spadin, R. Allan, and W. Adam, 2011: Early ship-based upper-air data and comparison with the Twentieth Century Reanalysis. Clim. Past, 7, 265-276, doi:10.5194/cp-7-265-2011.

Br nnimann, S., and G.P. Compo, 2011: Ozone highs and associated flow features in the first half of the twentieth century in different data sets. Meteorol. Zeit., in press.

Compo, G.P., J.S. Whitaker, P.D. Sardeshmukh, N. Matsui, R.J. Allan, X. Yin, B.E. Gleason, R.S. Vose, G. Rutledge, P. Bessemoulin, S. Br nnimann, M. Brunet, R.I. Crouthamel, A.N. Grant, P.Y. Groisman, P.D. Jones, M. Kruk, A.C. Kruger, G.J. Marshall, M. Maugeri, H.Y. Mok, . Nordli, T.F. Ross, R.M. Trigo, X.L. Wang, S.D. Woodruff, and S.J. Worley, 2011: The Twentieth Century Reanalysis Project. Quarterly J. Roy. Met. Soc., 137, 1-28, doi: 10.1002/qj.776.

Giese B.S., and S. Ray, 2011: El Ni o variability in simple ocean data assimilation (SODA) 1871-2008. J. Geophys. Res.-Oceans., 116, C02024, doi:10.1029/2010JC006695.

Pegion, K., and P.D. Sardeshmukh, 2011: Prospects for improving subseasonal predictions. Mon. Wea. Rev., in press, doi:10.1175/MWR-D-11-00004.1.

Stickler, A. and S. Br nnimann, 2011: Significant bias of the NCEP/NCAR and twentieth-century reanalyses relative to pilot balloon observations over the West African Monsoon region (1940-1957). Quarterly J. Roy. Met. Soc., in press, doi: 10.1002/qj.854.

Wood, K. R., and J.E. Overland, 2010: Early 20th century Arctic warming in retrospect, Int. J. of Climatol., 30, 1269-1279, doi: 10.1002/joc.1973.

Condron, Alan

Condron, A., and P. Winsor (2011), A subtropical fate awaited freshwater discharged from glacial Lake Agassiz, Geophys. Res. Lett., 38, L03705, doi:10.1029/2010GL046011.

Cooper, Valentino

V. R. Cooper, A. S. Henry, S. Takagi and D. J. Singh "First principles prediction of a morphotropic phase boundary in the Bi(Zn1/2Ti1/2)O3-(Bi1/2Sr1/2)(Zn1/2Nb1/2)O3 alloy" Appl. Phys. Lett. 98, 122903 (2011)

B. Xu, D. J. Singh, V. R. Cooper, Y. P. Feng "Design of a low band gap oxide ferroelectric: Bi6Ti4O17" Euro. Phys. Lett. 94, 37006 (2011)

G. Li, V. R. Cooper, J. Cho, S. Du, H. Gao and Z. Zhang "Molecular self-assembly driven by London dispersion forces" (submitted: Phys. Rev. Lett. 2011).

V. R. Cooper "Enhanced two dimensional electron gas charge densities at III-III/I-V oxide heterostructure interfaces" (submitted: Nat. Mater. 2011)

Crivelli, Silvia

The manuscript "Creating Supersecondary Structures with BuildBeta" by Silvia Crivelli and Nelson Max was accepted for publication in the volume "Protein Supersecondary Structure" which is part of the series "Methods in Molecular Biology" (in press). NERSC was acknowledged in the manuscript.

Cummings, Peter

Ganesh, P.; Jiang, D. E. Kent, P. R. C., "Accurate Static and Dynamic Properties of Liquid Electrolytes for Li-Ion Batteries from ab initio Molecular Dynamics," Journal of Physical Chemistry B, 115, 3085-3090 (2011).

Ganesh, P.; Kent, P. R. C. Mochalin, V., "Formation, characterization and dynamics of onion like carbon structures from nanodiamonds using reactive force-fields for electrical energy storage," Journal of Applied Physics, accepted for publication (2011).

Jiang, D. E.; Meng, D.; Wu, J. Z. "Density functional theory for differential capacitance of planar electric double layers in ionic liquids ." Chem. Phys. Lett., 504, 153 (2011).

Wu, J. Z.; Jiang, T.; Jiang, D. E.; Jin, Z. H.; Henderson, D.* "A classical density functional theory for interfacial layering of ionic liquids." Soft Matter, in press.

K. R. Hadley and C. McCabe, A Structurally Relevant Coarse-Grained Model for Cholesterol, Biophysical Journal, 99, 2896-2905 (2010).

G. T. Beckham, Y. J. Bomble, J. F. Matthews, C. B. Taylor, M. G. Resch, J. S. Yarbrough, S. R. Decker, L. Bu, X. C. Zhao, C. McCabe, J. Wohlert, M. Bergenstr hle, J. W. Brady, W. S. Adney, M. E. Himmel, M. F. Crowley, The O-Glycosylated Linker from the Trichoderma reesei Family 7 Cellulase Is a Flexible, Disordered Protein, Biophysical Journal, 99, 3773-3781 (2010).

Brandon D. Booth, Steven G. Vilt, J. Ben Lewis, Jose L. Rivera, Edward A. Buehler, Clare McCabe, and G. Kane Jennings, Tribological Durability of Silane Monolayers on Silicon, Langmuir 2011, 27, 5909-5917.

Pedro Morgado, Carlos M. C. Laginhas, J. Ben Lewis, Clare McCabe, Luis F. G. Martins, and Eduardo J. M. Filipe, Viscosity of Liquid Perfluoroalkanes and Perfluoroalkylalkane Surfactants, Journal of Physical Chemistry B, 115, 9130 9139, 2011.

A. A. Skelton, J. D. Kubicki, P. Fenter, D. J. Wesolowski, and P. T. Cummings, Simulations of the Quartz/Water Interface: A Comparison of Classical Force Fields, Ab initio Molecular Dynamics and X-ray Reflectivity Experiments, Langmuir, 27, 8700 8709, 2011.

Pedro Morgado, Carlos M.C. Laginhas, Luis F. G. Martins, J. Ben Lewis, Clare McCabe, Felipe J. Blas and Eduardo J. M. Filipe, Systems involving hydrogenated and fluorinated chains: Volumetric properties of Perfluoroalkanes and Perfluoroalkylalkane Surfactants, Journal of Physical Chemistry B, in press 2011.

C.B. Taylor, M.F. Talib, C. McCabe, L. Bu, W.S. Adney, M.E. Himmel, M.F. Crowley, and G.T. Beckham, Computational investigation of glycosylation effects on a Family 1 carbohydrate-binding module, Journal of Biological Chemistry, submitted, 2011.

French WR, Iacovella CR, Cummings PT, The Influence of Molecular Adsorption on Elongating Gold Nanowires, Journal of Physical Chemistry C, In Press DOI:10.1021/jp203837r, 2011

Chunya Wu, Adam A. Skelton, Mingjun Chen, Lukas Vl ek, Peter T. Cummings, Modeling the interaction between integrin-binding peptide (RGD) and rutile surface: The effect of Na+ on peptide adsorption, Journal of Physical Chemistry C, submitted, 2011.

J. L. Rivera, G. K. Jennings and C. McCabe, Frictional Forces in Mixed Hydrophobic Hydrophilic Alkoxysilane Monolayers on Silica, Journal of Chemical Physics, submitted (2011).

D

Daggett, Valerie

Jonsson A.L., Schaeffer R.D., van der Kamp M.W., and Daggett V. Dynameomics: protein dynamics and unfolding across fold space. Biomolecular Concepts 1:335-344, 2010

Schaeffer R.D. and Daggett V. Protein folds and protein folding. Protein Engineering Design & Selection 24:11-19, 2011.

Scouras A.D. and Daggett V. The dynameomics rotamer library: Amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water. Protein Science 20:341-352, 2011.

Toofanny R.D., Simms A.M., Beck D.A.C., and Daggett V. Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection. BMC Bioinformatics 12:334, 2011

Jonsson A.L. and Daggett V. The Effect of Context on the Folding of beta-Hairpins. Journal of Structural Biology, In Press, 2011

Dahmen, Ulrich

Advancements in the Characterization of "Hyper-Thin" Oxynitride Gate Dielectrics Through Exit Wave Reconstruction HRTEM and XPS E.L. Principe, D.G. Watson, C. Kisielowski Microelectronic Failure Analysis, Supp. AMS Intl., 2002

Contrast Transfer Function Design by an Electrostatic Phase Plate for Contrast Enhancement in Transmission Electron Microscopy D. Alloyeau, W.K. Hsieh, E.H. Anderson, G. Benner, M.J. Park, E.D. Gomez, N.P. Balsara and C. Kisielowski in preparation for ultramicroscopy, 2008

Enhancement of Dislocation Velocities by Stress Assisted Kink Nucleation at the Native Oxide/ SiGe Interface E.A. Stach and R. Hull Appl. Phys. Lett., 2001

Davidson, Ronald

Effects of Errors in Velocity Tilt on Maximum Longitudinal Compression during Neutralized Drift Compression of Intense Beam Pulses, I. D. Kaganovich, S. Massidda, E. A. Startsev and R. C. Davidson, submitted for publication (2011).

Novel Hamiltonian Method for Collective Dynamics Analysis of an Intense Charged

Particle Beam Propagating Through a Periodic Focusing Quadrupole Lattice, E. A. Startsev, R. C. Davidson and M. Dorf, Physics of Plasmas 18, 056712 (2011).

Theoretical Study of Transverse-Longitudinal Emittance Coupling , H. Qin, R. C. Davidson, M. Chung, J. J. Barnard and T. F. Wang, Proceedings of the 2011 Particle Accelerator Conference, in press (2011).

Masking the Paul Trap Simulator Experiment (PTSX) Ion Source to Modify the Transverse Distribution Function and Study Beam Stability and Collective Oscillations , E. P. Gilson, R. C. Davidson, P. C. Efthimion, R. Majeski, E.A. Startsev and H. Wang, Proceedings of the 2011 Particle Accelerator Conference, in press (2011).

Development of an Advanced Barium ion Source for a Laser-Induced-Fluorescence Diagnostic on the Paul Trap Simulator Experiment(PTSX) H. Wang, R. C. Davidson, E. P. Gilson, P. C. Efthimion and R. Majeski, Proceedings of the 2011 Particle Accelerator Conference, in press (2011).

Planned Experiments on the Princeton Advanced Test Stand , A. Stepanov, E.P. Gilson, R.C. Davidson, L. Grisham, and I. Kaganovich, Proceedings of the 2011 Particle Accelerator Conference, in press (2011).

Numerical and Analytical Studies of Matched Kinetic Quasi-equilibrium Solutions for an Intense Charged Particle Beam Propagating Through a Periodic Focusing Quadrupole Lattice , E. A. Startsev, R. C. Davidson and M. Dorf, Proceedings of the 2011 Particle Accelerator Conference, in press (2011).

Effects Of Errors in Velocity Tilt on the Maximum Longitudinal Compression During Neutralized Drift Compression of Intense Beam Pulses , I, Kaganovich, R. C. Davidson, E. A. Startsev, S. Massidda, and A. Friedman, Proceedings of the 2011 Particle Accelerator Conference, in press (2011).

Stability Properties of the Electron Return-Current for Intense Ion Beam Propagation Through Background Plasma , E. A. Startsev, R. C. Davidson and V. N. Khudik, Laser and Particle Beams 29, 269 (2011).

A Spectral Method for Halo Particle Definition in Intense Mismatched beams M. A. Dorf, R. C. Davidson and E. A. Startsev, Physics of Plasmas 18, 043109 (2011).

Generalized Courant-Snyder Theory and Kapchinskij-Vladimirskij Distribution for High-Intensity Beams in a Coupled Transverse Focusing Lattice , H. Qin and R. C. Davidson, Physics of Plasmas 18, 056708 (2011).

Numerical and Analytical Studies of Matched Kinetic Quasi-Equilibrium Solutions for Intense Beam Propagation Through a Periodic Focusing Quadrupole Lattice , E. A. Startsev, R. C. Davidson and M. Dorf, submitted for publication (2010).

"Collective Focusing of Intense Ion Beam Pulses for High Energy Density Physics Applications", M. A. Dorf, I. D. Kaganovich, E. A. Startsev and R. C. Davidson, Physics of Plasmas 18, 033106 (2011).

E. V. Belova, R. C. Davidson, C. Myers, Two-Fluid Mechanism of Plasma Rotation in Field-Reversed Configuration, Proceedings of the 23th Int. Conf. Daejeong, Korea, 2010, paper IAEA-IC/P4-3 (International Atomic Energy Agency, Vienna, 2010).

C. Myers, E. V. Belova, M. R. Brown, T. Grey, C. D. Cothran, M. Schaffer, Three-dimensional MHD simulations of counter-helicity spheromak merging in the Swarthmore Spheromak Experiment, submitted to Physics of Plasmas (2011).

De Jong, Wibe

G.S. Groenewold, M.J. van Stipdonk, J. Oomens, W.A. de Jong, M.E. McIlwain, "The gas-phase bis-uranyl nitrate complex [(UO2)2(NO3)5]-: infrared spectrum and structure", Int. J. Mass Spec., ASAP (2011) DOI: 10.1016/j.ijms.2011.06.002

G. Schoendorff, W.A. de Jong, M.J. Van Stipdonk, J.K. Gibson, M.S. Gordon, T.L. Windus, "On the Formation of Hypercoordinated Uranyl Complexes", Inorg. Chem. 50, 8490 (2011)

Massively parallel implementation of the multireference Brillouin Wigner CCSD method, Jiri Brabec, Sriram Krishnamoorthy, Hubertus J.J. van Dam, Karol Kowalski, Jiri Pittner, CPL, (2011) in press

NWChem, N. Govind, EJ Bylaska, WA De Jong, K Kowalski, TP Straatsma, M Valiev, and HJJ van Dam. 2011. "NWChem." In Encyclopedia of Parallel Computing, Springer (in press)

Coupled Cluster Calculations for Large Molecular and Extended Systems Kowalski K, JR Hammond, WA De Jong, PD Fan, M Valiev, D Wang, and N Govind. 2009. "Coupled Cluster Calculations for Large Molecular and Extended Systems." In Computational Methods for Large Systems: Electronic Structure Approaches for Biotechnology and Nanotechnology, Wiley (2011)

Large Scale Plane Wave Based Density Functional Theory: Formalism, Parallelization, and Applications Bylaska EJ, KL Tsemekhman, N Govind, and M Valiev. 2009. "Large Scale Plane Wave Based Density Functional Theory: Formalism, Parallelization, and Applications." In Computational Methods for Large Systems: Electronic Structure Approaches for Biotechnology and Nanotechnology, Wiley (2011)

Advances in Scalable Computational Chemistry: NWChem Straatsma TP, EJ Bylaska, HJJ van Dam, N Govind, WA De Jong, K Kowalski, and M Valiev. 2011. "Advances in Scalable Computational Chemistry: NWChem." Annual Reviews in Computational Chemistry, Elsevier (2011) submitted

NWChem: scalable parallel computational chemistry H.J.J. van Dam, W.A. de Jong, E. Bylaska, N. Govind, K. Kowalski, T.P. Straatsma, M. Valiev, Wiley Interdisciplinary Reviews: Computational Molecular Science, DOI: 10.1002/wcms.62, May 2011

Decyk, Viktor

R. Sanchez, D. E. Newman, J.-N. Leboeuf, and V. K. Decyk, "On the nature of turbulent transport across sheared zonal flows: insights from gyro-kinetic simulations", Plasma Physics and Controlled Fusion 53 (2011) 074018.

Deelman, Ewa

Gideon Juve and Ewa Deelman, Wrangler: Virtual Cluster Provisioning for the Cloud,, short paper, Proceedings of the 20th International Symposium on High Performance Distributed Computing (HPDC 2011), 2011.

Detmold, William

Prediction of the Omega_{bbb} mass from lattice QCD. Stefan Meinel Phys.Rev. D82 (2010) 114514

Devanathan, Ram

Devanathan R, and WJ Weber, "Simulation of collision cascades and thermal spikes in ceramics," Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 268(19) (2010) 2857-2862.

Devereaux, Thomas

C.-C. Chen, C. J. Jia, A. F. Kemper, R. R. P. Singh, and T. P. Devereaux, "Theory of Two-Magnon Raman Scattering in Iron Pnictides and Chalcogenides", Phys. Rev. Lett. 106, 067002 (2011).

C.-C. Chen, R. Applegate, B. Moritz, T. P. Devereaux, and R. R. P. Singh, "Revealing the degree of magnetic frustration by non-magnetic impurities", New J. Phys. 13, 043025 (2011) [Chosen in IOP Select].

C.-C. Chen, B. Moritz, C. J. Jia, S. Johnston, A. P. Sorini, L.-Q. Lee, K. Ko, and T. P. Devereaux, "Numerical studies of photon-based spectroscopies on high-T superconductors", Comp. Phys. Comm. 182 , 106 (2011).

C. J. Jia, B. Moritz, C.-C. Chen, B. Sriram Shastry, and T. P. Devereaux, "A Fidelity Study of the Superconducting Phase Diagram in the 2D Single-band Hubbard Model", Phys. Rev. B 84, 125113 (2011).

Luuk J. P. Ament, Michel van Veenendaal, Thomas P. Devereaux, John P. Hill, and Jeroen van den Brink, "Resonant Inelastic X-ray Scattering Studies of Elementary Excitations", Rev. Mod. Phys. 83, 705 (2011).

Y. J. Kim, A. P. Sorini, C. S. Stock, T. G. Perring, J. van den Brink, and T. P. Devereaux, "Probing high- energy electronic excitations using inelastic neutron scatter- ing", Phys. Rev. B 84, 085132 (2011).

M. Yi, D.H. Lu, J.-H. Chu, J. G. Analytis, A. P. Sorini, A. F. Kemper, B. Moritz, S.-K. Mo, R. G. Moore, M. Hashimoto, W.-S. Lee, Z. Hussain, T. P. Devereaux, I. R. Fisher, and Z.-X. Shen, "Symmetry-breaking orbital anisotropy observed for detwinned Ba(Fe1-xCox)2As2 above the spin density wave transition", PNAS 108, 6878-6883 (2011).

F. Schmitt, B. Moritz, S. Johnston, S.-K. Mo, M. Hashimoto, R. G. Moore, D.-H. Lu, E. Motoyama, M. Greven, T. P. Devereaux, and Z.-X. Shen, "High-energy anomaly in NCCO investigated by ARPES and quantum Monte Carlo simulations", Phys. Rev. B 83, 195123 (2011).

C.-C. Chen, B. Moritz, F. Vernay, J. N. Hancock, S. Johnston, C. J. Jia, G. Chabot-Couture, M. Greven, I. Elfimov, G. A. Sawatzky, and T. P. Devereaux, "Unraveling the Nature of Charge Excitations in La2CuO4 with Momentum-Resolved Cu K-Edge Resonant Inelastic X-Ray Scattering", Phys. Rev. Lett. 105, 177401 (2010).

Shibing Wang, Wendy L. Mao, Adam P. Sorini, Cheng-Chien Chen, Thomas P. Devereaux, Yang Ding, Yuming Xiao, Paul Chow, Nozomu Hiraoka, Hirofumi Ishii, Yong Q. Cai, and Chi-Chang Kao, "High pressure evolution of Fe2O3 electronic structure revealed by X-ray absorption", Phys. Rev. B, 82, 144428 (2010).

Dorland, William

S. Kobayashi, B. Rogers and W. Dorland; Particle Pinch in Gyrokinetic Simulations of Closed Field-Line Systems PHYSICS OF PLASMAS Volume: 18 Issue: 4 Article Number: 049902 DOI: 10.1063/1.3570822 Published: APR 2011

R. Numata, G. Howes, et al; AstroGK: Astrophysical gyrokinetics code; JOURNAL OF COMPUTATIONAL PHYSICS Volume: 229 Issue: 24 Pages: 9347-9372 DOI: 10.1016/j.jcp.2010.09.006 Published: DEC 10 2010

G. Howes, J. TenBarge, et al; Gyrokinetic Simulations of Solar Wind Turbulence from Ion to Electron Scales;PHYSICAL REVIEW LETTERS Volume: 107 Issue: 3 Article Number: 035004 DOI: 10.1103/PhysRevLett.107.035004 Published: JUL 14 2011

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Dupuis, Michel

R. D. Lins, R. Devanathan, and M. Dupuis, Modeling the nanophase structural dynamics of phenylated sulfonated poly ether ether ketone ketone (Ph-SPEEKK) membranes as a function of hydration, Journal of Physical Chemistry B 115 (2011) 1817-1824.

N. Idupulapati, R. Devanathan, and M. Dupuis, Molecular structure and transport dynamics in perfluoro sulfonyl imide membranes, Journal of Physics: Condensed Matter 23 (2011) 234106.

R. Devanathan, A. Venkatnathan, R. J. Rousseau, M. Dupuis, T. Frigato, W. Gu, and V. H. Helms, Atomistic simulation of water percolation and proton hopping in Nafion fuel cell membrane, Journal of Physical Chemistry B 114 (2010) 13681-13690. (Cover article)

T. M. Chang, L. X. Dang, R. Devanathan, and M. Dupuis, Structure and dynamics of N,N-diethyl-N-methylammonium triflate ionic liquid, neat and with water, from molecular dynamics simulations, Journal of Physical Chemistry A 114 (2010) 12764-12774.

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"Evidence for a Bound H-dibaryon from Lattice QCD", S.R. Beane, et.al, Phys.Rev.Lett. 106 (2011) 162001, arXiv:1012.3812.

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P. Erhart and J. Marian "Calculation of the substitutional fraction of ion-implanted He in an -Fe target" J. Nucl. Mater. 414, 426 (2011)

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Beste Bayramoglu, Roland Faller: Structural Properties of Polystyrene in Different Environments: A Molecular Dynamics Study. Phys Chem Chem Phys online before print(DOI: 10.1039/C1CP21724K)

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Qian, Y., W. I. Gustafson Jr., and Fast, J. D., 2010, An investigation of the sub-grid variability of trace gases and aerosols for global climate modeling, Atmos. Chem. Phys., 10, 6917 6946, doi:10.5194/acp-10- 6917-2010. This paper is supported by NERSC computer resources under PI Jerome Fast in 2008-2009. See Acknowledgement in this paper. The paper is open access and available to public

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Climate Impacts of Intermittent Upper Ocean Mixing Induced by Tropical Cyclones (2011) by G. Manucharyan, C. Brierley & A. Fedorov. In Press at the Journal of Geophysical Research (Oceans). doi: 10.1029/2011JC007295

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Eric J. Bylaska et al. (2011) Large Scale Plane Wave Density Functional Theory: Formalism, Parallelization, and Applications in Computational Methods for Large Systems: Electronic Structure Approaches for Biotechnology and Nanotechnology, (John Wiley & Sons, Inc.) Ed. J.R. Reimers. - Shared Cover

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Eric J. Bylaska, Alexandra J. Salter-Blanc, Paul G. Tratnyek (2011) One-Electron Reduction Potentials from Chemical Structure Theory Calculations, In: Aquatic Redox Chemistry; Tratnyek, P., Grundl, T., Haderlein, S. (Eds.); ACS Symp. Ser. No. 1071 Publication Date (Web): September 2, 2011 | doi: 10.1021/bk2011-1071.ch003

Atta-Fynn R, EJ Bylaska, GK Schenter, and WA De Jong. 2011. "Hydration Shell Structure and Dynamics of Curium(III) in Aqueous Solution: First Principles and Empirical Studies." Journal of Physical Chemistry A 115(18):4665-4677.

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Bylaska EJ, KR Glaesemann, AR Felmy, M Vasiliu, DA Dixon, and PG Tratnyek. 2010. "Free Energies for Degradation Reactions of 1,2,3-Trichloropropane from ab initio Electronic Structure Theory." Journal of Physical Chemistry A 114(46):12269-12282.

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A. Ishizaki, G. R. Fleming, "On the interpretation of quantum coherent beats observed in two-dimensional electronic spectra of photosynthetic light harvesting complexes", J. Phys. Chem. B 115, 6227-6233 (2011).

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J. M. Dawlaty, A. Ishizaki, A. D. Kumar, and G. R. Fleming, "Microscopic quantum coherence in photosynthetic light harvesting antenna", Phil. Trans. R. Soc. A (2011). In press.

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Z. Lin, A. Franceschetti, and M.T. Lusk, ACS Nano 5, 2503 (2011).

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A. Gando et al. [ KamLAND Collaboration], "Partial radiogenic heat model for Earth revealed by geoneutrino measurements'', Nature Geoscience 4, 647 651 (2011).

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Freeman, Arthur

Candidates for topological insulators: Pb-based chalcogenide series H. Jin, J.-H. Song, A. J. Freeman, and M. G. Kanatzidis, Candidates for topological insulators: Pb-based chalcogenide series. Phys. Rev. B 83, 041202 (2011).

Dirac cone engineering in Bi2Se3 thin films H. Jin, J.-H. Song, and A. J. Freeman, Dirac cone engineering in Bi2Se3 thin films. Phys. Rev. B 83, 125319 (2011).

Freericks, James

B. Moritz, T. P. Devereaux, and J. K. Freericks, Time-resolved photoemission of correlated electrons driven out of equilibrium, Physical Review B 81, 165112 (2010)

Fridlind, Ann

Avramov, A., A.S. Ackerman, A.M. Fridlind, B. van Diedenhoven, G. Botta, K. Aydin, J. Verlinde, A.V. Korolev, W. Strapp, G.M. McFarquhar, R. Jackson, S.D. Brooks, A. Glen, and M. Wolde, 2011: Towards ice formation closure in Arctic mixed-phase boundary layer clouds during ISDAC. J. Geophys. Res., in press.

Fridlind, A.M., B. van Diedenhoven, A.S. Ackerman, A. Avramov, A. Mrowiec, H. Morrison, P. Zuidema, and M.D. Shupe, 2011: A FIRE-ACE/SHEBA case study of mixed-phase Arctic boundary-layer clouds: Entrainment rate limitations on rapid primary ice nucleation processes. J. Atmos. Sci., in press, doi:10.1175/JAS-D-11-052.1.

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Botta, G., K. Aydin, J. Verlinde, A.E. Avramov, A.S. Ackerman, A.M. Fridlind, G.M. McFarquhar, and M. Wolde, 2011: Millimeter wave scattering from ice crystal aggregates: Comparing cloud model simulations with X- and Ka-band radar measurements. J. Geophys. Res., 116, D00T04, doi:10.1029/2011JD015909.

Morrison, H., P. Zuidema, A.S. Ackerman, A. Avramov, G. de Boer, J. Fan, A.M. Fridlind, T. Hashino, J.Y. Harrington, Y. Luo, M. Ovchinnikov, and B. Shipway, 2011: Intercomparison of cloud model simulations of Arctic mixed-phase boundary layer clouds observed during SHEBA/FIRE-ACE. J. Adv. Model. Earth Syst., 3, M06003, doi:10.1029/2011MS000066.

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Friedman, Alex

S. M. Lund, G. Bazouin, A. Friedman, ?Sheet beam model for intense space-charge and application to Debye screening and self-consistent particle oscillation frequencies in thermal equilibrium beams, ?(submitted to Physical Review STAB, 2011).

S. M. Lund, G. Bazouin, A. Friedman, "Sheet beam model for intense space-charge and application to Debye screening and self-consistent particle oscillation frequencies in thermal equilibrium beams," (submitted to Physical Review STAB, 2011).

J.-L. Vay, C. G. R. Geddes, E. Cormier-Michel, and D. P. Grote, "Modeling Laser Wakefield Accelerators in a Lorentz Boosted Frame," (submitted to Journal of Computational Physics, September 2010).

J.-L. Vay, C. G. R. Geddes, E. Cormier-Michel, and D. P. Grote, "Numerical Methods for Instability Mitigation in the Modeling of Laser Wakefield Accelerators in a Lorentz Boosted Frame," Journal of Computational Physics 230, 5908-5929 (2011).

J.-L. Vay, C. G. R. Geddes, E. Cormier-Michel, and D. P. Grote, "Effects of Hyperbolic Rotation in Minkowski Space on the Modeling of Plasma Accelerators in a Lorentz Boosted Frame," Physics of Plasmas Letters 18, 030701 (2011).

B. I. Cohen, A. M. Dimits, A. Friedman, R. E. Caflisch, "Time-Step Considerations in Particle Simulation Algorithms for Coulomb Collisions in Plasmas," IEEE T. Plasma Sci., 38, 2394, (2010).

A. Friedman, J. J. Barnard, R. H. Cohen, D. P. Grote, S. M. Lund, W. M. Sharp, A. Faltens, E. Henestroza, J.-Y. Jung, J. W. Kwan, E. P. Lee, M. A. Leitner, B. G. Logan, J.-L. Vay, W. L. Waldron, R. C. Davidson, M. Dorf, E. P. Gilson, and I. D. Kaganovich, "Beam dynamics of the Neutralized Drift Compression Experiment-II, a novel pulse-compressing ion accelerator," Phys. Plasmas 17, 056704 (2010).

A. Friedman, J. J. Barnard, R. H. Cohen, D. P. Grote, S. M. Lund, W. M. Sharp, A. Faltens, E. Henestroza, J.-Y. Jung, J. W. Kwan, E. P. Lee, M. A. Leitner, B. G. Logan, J.-L. Vay, W. L. Waldron, R. C. Davidson, M. Dorf, E. P. Gilson, and I. D. Kaganovich, "Developing the Physics Design for NDCX-II, a Unique Pulse- Compressing Ion Accelerator," Proceedings of the 2009 International Computational Accelerator Physics Meeting, 31 August - 4 September 2009, San Francisco (2010).

J.-L. Vay, J. M. Byrd, M. A. Furman, R. Secondo, M. Venturini, J. D. Fox, C. H. Rivetta, W. H fle, CERN, Switzerland, "Simulation of E-Cloud Driven Instability and its Attenuation using a Feedback System in the CERN SPS," Proceedings for the 10th International Particle Accelerator Conference, Kyoto, Japan, 23- 28 May 2010, p. 2438.

W. M. Fawley and J.-L. Vay, "Full Electromagnetic Simulation of Coherent Synchrotron Radiation via the Lorentz-Boosted Frame Approach," Proceedings for the 10th International Particle Accelerator Conference, Kyoto, Japan, 23-28 May 2010, p. 1874.

R. H. Cohen, A. Friedman, D. P. Grote, and J.-L. Vay, "An Implicit, Drift-Lorentz Mover for Plasma and Beam Simulations," Nucl. Instru. Meth. Physics Research A 606, 53 (2009).

Fu, Guoyong

Y. Chen, S.E. Parker, J. Lang and G.Y. Fu, Linear gyrokinetic simulation of high-n toroidal Alfven eigenmodes in a burning plasma , Phys. Plasmas 17, 102504 (2010)

J. Lang and G.Y. Fu, Nonlinear simulation of toroidal Alfven eigenmode with microturbulence-induced radial diffusion , Phys. Plasmas 18, 055902 (2011)

Y. Chen, S.E. Parker, Fluid electrons with kinetic closure for long wavelength energetic particles driven modes , Phys. Plasmas 18, 055703 (2011)

Fung, Inez

Lee, J.-E., B. Lintner, C. K. Boyce, and P. J. Lawrence (2011), Land use change exacerbates tropical South American drought by sea surface temperature variability, Geophys. Res. Lett., doi:10.1029/2011GL049066, in press.

Lee, J.-E., and K. Boyce (2010), Impact of the hydraulic capacity of plants on water and carbon fluxes in tropical South America, J. Geophys. Res., 115, D23123, doi:10.1029/2010JD014568.

Liu, J., I. Fung, E. Kalnay, and J.-S. Kang (2011), CO2 transport uncertainties from the uncertainties in meteorological fields, Geophys. Res. Lett., 38, L12808, doi:10.1029/2011GL047213.

Tseng, Y.-H. and Chien, M.-H. (2011),Parallel Domain-decomposed Taiwan Multi-scale Community Ocean Model (PD-TIMCOM), Computers & Fluids, 45, 77-83.

Furman, Miguel

EXPERIMENTAL OBSERVATIONS OF IN-SITU SECONDARY ELECTRON YIELD REDUCTION IN THE PEP-II PARTICLE ACCELERATOR BEAM LINE, M. T. F. Pivi, G. Collet, F. King, R. Kirby, T. Markiewicz, T. Raubenheimer, J. Seeman, F. Le Pimpec Nuclear Instruments and Methods in Physics Research A 621 (1-3), 47 56, (2010).

SIMULATIONS OF BEAM INSTABILITIES FOR THE RECOMMENDATION OF AN ILC DAMPING RING M. T. F. Pivi, T. Raubenheimer, L. Wang, K. Ohmi, A. Wolski et al. accepted for publication to Physical Review ST Accel. Beams (2011)

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Galli, Giulia

"Ab initio calculations of optical absorption spectra: Solution of the Bethe-Salpeter equation within density matrix perturbation theory", D. Rocca, D. Lu, and G. Galli, J. Chem. Phys. 133, 164109 (2010).

Tailoring nano-heterojunctions for light emission , Tiansu Li, Francois Gygi and Giulia Galli (under review).

Thermal Transport in Nanoporous Silicon: Interplay between Disorder at Mesoscopic and Atomic Scales, Yuping He, Davide Donadio, Joo-Hyoung Lee, Jeffrey C. Grossman, and Giulia Galli, ACS Nano 5, 1839 (2011)

Structure, stability and electronic properties of nanodiamonds, GiuliaGalli in Computer based modeling of novel carbon systems and their peroperties , L. Colombo and A.Fasolino Eds., Springer 2010, p.37.

Gandolfi, Stefano

S. Gandolfi, J. Carlson, Steven C. Pieper, "Cold neutrons trapped in external fields", Phys. Rev. Lett. 106, 012501 (2011).

S. Gandolfi, K. E. Schmidt, J. Carlson, "BEC-BCS crossover and universal relations in unitary Fermi gases", Phys. Rev. A 83, 041601(R) (2011).

Michael McNeil Forbes, Stefano Gandolfi, Alexandros Gezerlis, "Resonantly Interacting Fermions In a Box", Phys. Rev. Lett. 106, 235303 (2011).

Garrett, Bruce

V.-A. Glezakou, S. T. Elbert, S. S. Xantheas and K. Ruedenberg, Analysis of bonding patterns in the valence isoelectronic series O3, S3, SO2 and OS2 in terms of oriented quasi-atomic molecular orbitals Klaus Ruedenberg special issue (invited), Journal of Physical Chemistry A 114, 8923 (2010)

S. Pandelov, J. C. Werhahn, B. M. Pilles, S. S. Xantheas, and H. Iglev, An empirical correlation between the enthalpy of solution of aqueous salts and their ability to form hydrates , Journal of Physical Chemistry A 114, 10454 (2010). Journal cover

S. Yoo, E. Apr , X.-C. Zeng and S. S. Xantheas, Lowest-Energy Structures of Water Clusters (H2O)16 and (H2O)17 from high-level ab initio calculations , Journal of Physical Chemistry Letters 1, 3122 (2010)

J. C. Werhahn, S. Pandelov, S. Yoo, S. S. Xantheas, H. Iglev, Dynamics of Con ned Water Molecules in Aqueous Salt Hydrates , in Ultrafast Phenomena XVII, M. Cherqui, D. M. Jonas, E. Riedle, R. W. Schoenlein, A. J. Taylor (Eds.), Oxford University Press, pp. 463-465 (2011)

S. Yoo and S. S. Xantheas, The Effect of Dispersion Corrections on the Melting Temperature of Liquid Water , Communiction to the Editor, Journal of Chemical Physics 134, 121105 (2011). Featured in the Virtual Journal of Biological Physics Research. 5th most downloaded paper in April 2011

X.-B. Wang and S. S. Xantheas, Photodetachment of Isolated Bicarbonate Anion: Electron Binding Energy of HCO3- , Journal of Physical Chemistry Letters 2, 1204 (2011)

S. Yoo and S. S. Xantheas, The Role of Hydrophobic Surfaces in Altering Water-Mediated Peptide-Peptide Interactions in an Aqueous Environment Victoria Buch Memorial Issue (invited), Journal of Physical Chemistry A 115, 6088 (2011)

J. C. Werhahn, S. Pandelov, S. S. Xantheas, H. Iglev, Dynamics of Weak, Bifurcated and Strong Hydrogen Bonds in Lithium Nitrate Trihydrate , Journal of Physical Chemistry Letters 2, 1633 (2011)

A. Whiteside, S. S. Xantheas, M. Gutowski, Is Electronegativity a Useful Descriptor for the Pseudo- Alkali-Metal NH4 , Chemistry A European Journal, in press DOI: 10.1002/chem.201101949 (2011). Highlighted in Royal Society of Chemistry s Chemistry World

S. Kaneko, Y. Inokuchi, T. Ebata, E. Apr and S. S. Xantheas, Laser Spectroscopic and Theoretical Studies of Encapsulation Complexes of Calix[4]arene , Journal of Physical Chemistry A, in press DOI: 10.1021/jp204577j (2011)

S. Yoo and S. S. Xantheas, Structures, Energetics and Spectroscopic Fingerprints of Water Clusters n=2-21 Vademecum of Computational Chemistry, Ed. J. Leszczynski. Vol III: "Applications: Solids and nanostructures", Eds. M. Papadopoulos and H. Reis, Springer Verlag, in press (2011)

G. Murdachaew, M. Valiev, S.M. Kathmann, and X. Wang, Study of Ion Specific Interactions of Alkali Cations with Dicarboxylate Dianions JACS Comm. submitted, Sept. 2011.

Geddes, Cameron

J.-L. Vay, C.G.R. Geddes, E. Cormier-Michel, D.P. Grote (2011) Effects of Hyperbolic Rotation in Minkowski Space on the Modeling of Plasma Accelerators in a Lorentz Boosted Frame , Physics of Plasmas (letter) 18, 303701. LBNL press release (http://newscenter.lbl.gov/news-releases/2011/03/17/simulating-at-lightspeed),

NERSC Science News (http://www.nersc.gov/news-publications/science-news/2011/boosting-the-next-wave-of-accelerators), DOE Office of Science Science Highlight Series : (http://science.energy.gov/news/science- highlights-series/2011/04-21-11-s).

J.-L. Vay, C.G.R. Geddes, E. Cormier-Michel, D.P. Grote (2011) Numerical methods for instability mitigation in the modeling of laser wakefield accelerators in a Lorentz-boosted frame , Journal of Computational Physics 230, 5908. Featured in TABL http://today.lbl.gov/2011/05/25/boosted-frame-methods-published-in-detail

E. Cormier-Michel, E. Esarey, C.G.R. Geddes, C.B. Schroeder, K. Paul, P.J. Mullowney, J.R. Cary and W.P. Leemans, Control of focusing fields in laser-plasma accelerators using higher-order modes, Phys. Rev. ST Accel. Beams, 14, 031303 (2011). http://prst-ab.aps.org/abstract/PRSTAB/v14/i3/e031303

B.M. Cowan, D.L. Bruhwiler, E. Cormier-Michel, E. Esarey, C.G.R. Geddes, P. Messmer, K.M. Paul, "Characteristics of an envelope model for laser plasma accelerator simulation", Journal of Computational Physics 230, 61 (2011).

W.B. Mori, W. An, V.K. Decyk, W. Lu, F.S. Tsung, R.A. Fonseca, S.F. Martins, J. Vieira, L.O Silva, M. Chen, E. Esarey, C.G.R. Geddes, W.P. Leemans, C.B. Schroeder, J-L. Vay, K. Amyx, D.L. Bruhwiler, J. R.Cary, E. Cormier-Michel, B. Cowan, P. Messmer, C. Huang and T. Antonsen, "Dream beams: Extreme-scale computing enabling new accelerator technologies for the energy and intensity frontiers," Journal of Physics: Conference Series (2010)

Min Chen, Naveen Kumar, Alexander Pukhov, and Tong-Pu Yu, Stabilized radiation pressure dominated ion acceleration from surface modulated thin-foil targets , Phys. Plasmas, 18, 073106 (2011).

Gerber, Robert

Vibrational spectra of beta-Glucose, beta-Glucose and Sucrose: Anharmonic Calculations and Experiment, Brina Brauer, Madeleine Pincu, Victoria Buch, Ilana Bar, John P Simons and R. Benny Gerber, J. Phys. Chem. A 2011, 115, 9498 9509

Isotopic hydration of cellobiose: vibrational spectroscopy and dynamical simulations, Madeleine Pincu, Emilio J Cocinero, Nitzan Mayorkas, Brina Brauer, Benjamin G Davis, R Benny Gerber and John P Simonsdx.doi.org/10.1021/jp112109p | J. Phys. Chem. A 2011, 115, 9498 9509

Raman and infra red spectra of cellobiose in the solid state: what can be learned from single-molecule calculations? Hong-bin Xie, Madeleine Pincu, Brina Brauer, R. Benny Gerber , Ilana Bar , Chemical Physics Letters - in press.

Gerhardt, Lisa

"First search for atmospheric and extraterrestrial neutrino-induced cascades with the IceCube detector," R. Abbasi et al., Accepted Phys. Rev. D (2011).

"Constraints on the Extremely-high Energy Cosmic Neutrino Flux with the IceCube 2008-2009 Data," R. Abbasi et al., Phys. Rev. D83, 092003 (2011).

"Constraints on high-energy neutrino emission from SN 2008D," R. Abbasi et al., Astron. Astrophys. 527, A28 (2011).

"Search for neutrino-induced cascades with five years of AMANDA data," R. Abbasi et al.,Astropart. Phys. 34, 420 (2011).

"Limits on Neutrino Emission from Gamma-Ray Bursts with the 40 String IceCube Detector," R. Abbasi et al.,Phys. Rev. Lett. 106, 141101 (2011).

"Time-Integrated Searches for Point-like Sources of Neutrinos with the 40-String IceCube Detector," R. Abbasi et al., Astrophys. J. 732, 18 (2011).

"Search for a Lorentz-violating sidereal signal with atmospheric neutrinos in IceCube.," R. Abbasi et al.,Phys. Rev. D82, 112003 (2010).

"Measurement of the atmospheric neutrino energy spectrum from 100 GeV to 400 TeV with IceCube.," R. Abbasi et al.,Phys. Rev. D83, 012001 (2011).

"The first search for extremely-high energy cosmogenic neutrinos with the IceCube Neutrino Observatory," R. Abbasi et al., Phys. Rev. D82, 072003 (2010).

"Search for relativistic magnetic monopoles with the AMANDA-II neutrino telescope," R. Abbasi et al., Eur. Phys. J. C69, 361 (2010).

Gezerlis, Alexandros

Effective 3-body interaction for mean-field and density-functional theory Alexandros Gezerlis and G. F. Bertsch Phys. Rev. Lett. {\bf 105}, 212501 (2010) - Selected by the Editors as being of interest to Phys. Rev. C readers.

Resonantly Interacting Fermions In A Box Michael McNeil Forbes, Stefano Gandolfi, and Alexandros Gezerlis Phys. Rev. Lett. 106, 235303 (2011) - Selected for publication in the Virtual Journal of Atomic Quantum Fluids 3, Issue 7 (2011).

Spin-polarized low-density neutron matter Alexandros Gezerlis Phys. Rev. C 83, 065801 (2011)

Mixed-spin pairing condensates in heavy nuclei Alexandros Gezerlis, G. F. Bertsch, and Y. L. Luo Phys. Rev. Lett. 106, 252502 (2011) - Marked as an Editors' Suggestion.

Ghan, Steven

Wang, M; S. J. Ghan, R. C. Easter, M. Ovchinnikov, X. Liu, E. Kassianov, Y. Qian, W. Gustafson, V. E. Larson, D. Schanen, M. Khairoutdinov, and H. Morrison, 2011: The multi-scale aerosol-climate model PNNL-MMF: model description and evaluation. Geoscientific Model Development, 4, 137 168.

Wang, M., S. Ghan, M. Ovchinnikov, X. Liu, R. Easter, E. Kassianov, Y. Qian, R. Marchand, and H. Morrison, 2011: Aerosol indirect effects in a multi-scale aerosol-climate model PNNL-MMF, Atmos. Chem. & Phys., 11, 5431-5455, doi:10.5194/acp-11-5431-2011.

Glimm, James

W. Bo and X. Liu and J. Glimm and X. Li, "A robust front tracking method: Verification and application to simulation of the primary breakup of a liquid jet", SIAM J. Sci. Comput., 2011. Accepted for publication.

J. Glimm and D. H. Sharp and T. Kaman and H. Lim, New Directions for Rayleigh-Taylor Mixing", Philosophical Transactions of The Royal Society A: Turbulent mixing and beyond, 2011. Accepted for publication.

T. Kaman and J. Glimm and D. H. Sharp, Uncertainty Quantification for Turbulent Mixing Simulation, ASTRONUM, Astronomical Society of the Pacific Conference Series, 2011. Accepted for publication.

T. Kaman and H. Lim and Y. Yu and D. Wang and Y. Hu and J.-D. Kim,

L. Wu and J. Glimm and X. Jiao and X.-L. Li and R. Samulyak, "A Numerical Method for the Simulation of Turbulent Mixing and its Basis in Mathematical Theory", Lecture Notes on Numerical Methods for Hyperbolic Equations: Theory and Applications: Short Course Book, 105-129,CRC/Balkema, London, 2011.

Golji, Javad

Moussavi-Baygi R, Jamali Y, Karimi R, Mofrad MR. Biophysical coarse-grained modeling provides insights into transport through the nuclear pore complex. Biophysical Journal. 2011;100(6):1410-9. PMCID: 3059569.

Moussavi-Baygi R, Jamali Y, Karimi R, Mofrad MRK. Brownian Dynamics Simulation of Nucleocytoplasmic Transport: a Coarse-Grained Model for the Functional State of the Nuclear Pore Complex. PLoS Comput Biol. 2011;7(6):e1002049.

Golji J, Lam J, Mofrad MRK. Vinculin Activation Is Necessary for Complete Talin Binding. Biophysical Journal Volume 100((2):332-40 2011

Golji J, Wendorf T, Mofrad MRK. Phosphorylation Primes Vinculin for Activation. Biophysical Journal ACCEPTED 2011

Gratta, Giorgio

N. Ackerman, et al. "Observation of Two-Neutrino Double-Beta Decay in Xe-136 with EXO-200" Phys. Rev. Lett. 107, 212501 (2011)

M. Auger, et al. "The EXO-200 detector, part I: Detector design and construction" arXiv:1202.2192, Submitted to the Journal of Instrumentation (2012)

Greene, Chris

Viatcheslav Kokoouline, Nicolas Douguet, and Chris H. Greene. Breaking bonds with electrons: Dissociative recombination of molecular ions. Chem. Phys. Lett., 507:1, 2011.

N. Douguet, A. Orel, I. Mikhailov, I. F. Schneider, C. H. Greene, and V. Kokoouline. The role of the Jahn-Teller coupling in dissociative recombination of H3O+ and H3+ ions. J. Phys.: Conf. Series, 300:012015, 2011

Annemieke Petrignani, Simon Altevogt, Max H. Berg, Dennis Bing, Manfred Grieser, Jens Hoffmann, Brandon Jordon-Thaden, Claude Krantz, Mario B. Mendes, Oldrich Novotny, Steffen Novotny, Dmitry A. Orlov, Roland Repnow, Tobias Sorg, Julia St@@utzel, Andreas Wolf, Henrik Buhr, Holger Kreckel, Viatcheslav Kokoouline, and Chris H. Greene. Resonant structure of low-energy H3+ dissociative recombination. Phys. Rev. A, 83:032711, 2011.

M. Ayouz, R. Lopes, M. Raoult, O. Dulieu, and V. Kokoouline. Formation of H3- by radiative 2association of H2 and H- in the interstellar medium. Phys. Rev. A, 83:052712, May 2011.

O. Atabek, R. Lefebvre, M. Lepers, A. Jaouadi, O. Dulieu, and V. Kokoouline. Proposal for a laser control of vibrational cooling in Na2 using resonance coalescence. Phys. Rev. Lett., 106:173002, 2011.

M. Lepers, O. Dulieu, and V. Kokoouline. Photoassociation of a cold-atom-molecule pair: Long- range quadrupole-quadrupole interactions. Phys. Rev. A, 82:042711, 2010.

M. Lepers, R. Vexiau, N. Bouloufa, O. Dulieu, and V. Kokoouline. Photoassociation of a cold- atom-molecule pair. ii. second-order perturbation approach. Phys. Rev. A, 83:042707, 2011.

Grossman, Jeffrey

J.-H. Lee and J. C. Grossman, Appl. Phys. Lett. 97, 133102 (2010)

J.-H. Lee and J. C. Grossman, Phys. Rev. B, in press (2011)

Guo, Hua

J. Ma, S. Y. Lin, H. Guo, Z. Sun, D. H. Zhang, D. Xie, J. Chem. Phys., 133, 054302 (2010), State-to-state quantum dynamics of the O(3P) + OH(2 ) H(2S) + O2(3 -g) reaction. (Cover article and one of 20 most downloaded articles from J. Chem. Phys., August 2010)

S. Y. Lin, H. Guo, B. Jiang, S. Zhou, and D. Xie, J. Phys. Chem. A (invited article in the Schinke Festschrift), 114, 9655 (2010), Non-Born-Oppenheimer state-to-state dynamics of the N(2D) + H2 NH( ) + H reaction: Influence of the Renner-Teller coupling.

A. Li, D. Xie, R. Dawes, A. W. Jasper, J. Ma, and H. Guo, J. Chem. Phys., 133, 144306 (2010), Global potential energy surface, vibrational spectrum, and reaction dynamics of the first excited (A2A ) state of HO2.

G. K. Smith, S. Lin, W. Lai, A. Datye, D. Xie, and H. Guo, Surf. Sci., 605, 750 (2011), Density functional theory studies of the initial steps in methanol steam reforming on PdZn and ZnO surfaces.

Z. Li, C. Xie, B. Jiang, D. Xie, L. Lan, Z. Sun, D. H. Zhang, and H. Guo, J. Chem. Phys., 134, 134303 (2011), Quantum and quasi-classical state-to-state dynamics of the NH + H reaction: Competition between abstraction and exchange channels.

J. Ma, H. Guo, C. Xie, A. Li, D. Xie, Phys. Chem. Chem. Phys., 13, 8407 (2011), State-to-state quantum dynamics of the H(2S) + O2(a1 g) O(3P) + OH(X2 ) reaction on the first excited state of HO2(A2A ).

S. Lin, R. Johnson, G. K. Smith, D. Xie, and H. Guo, Phys. Chem. Chem. Phys., 13, 9622 (2011), Pathways for methanol steam reforming involving adsorbed formaldehyde and hydroxyl intermediates on Cu(111): density functional theory studies.

A. Li, C. Xie, D. Xie, and H. Guo, J. Chem. Phys., 134, 194309 (2011), A global ab initio potential energy surface for HNO ( ) and quantum mechanical studies of vibrational states and reaction dynamics.

L. Wang, D. Xie, H. Guo, H. Li, and R. J. LeRoy, P.-N. Roy, J. Mole. Spectrosc. (Bunker and McKellar special issue), 267, 136 (2011), Superfluid response of 4HeN-N2O clusters probed by path integral Monte Carlo simulations.

B. Jiang, D. Xie, and H. Guo, J. Chem. Phys., 134, 231103 (2011), Communication: State-to-state differential cross sections for H2O(B) photodissociation.

Ma and H. Guo, Chem. Phys. Lett. (Editor s Choice), 511, 193 (2011), Full-dimensional quantum state resolved predissociation dynamics HCO2 prepared by photodetaching HCO2-.

R. Dawes, P. Lolur, J. Ma, and H. Guo, J. Chem. Phys. 135, 081102 (2011) Communication: Highly accurate ozone formation potential and implications for kinetics.

B. Jiang, D. Xie, and H. Guo, J. Chem. Phys., 135, 084112 (2011), Calculating of multiple initial state selected reaction probabilities from Chebyshev flux-flux correlation functions: Influence of reactant internal excitations on H + H2O OH + H2.

S. Lin, D. Xie, and H. Guo, ACS Catal., 1, 1263 (2011), The methyl formate pathway in methanol steam reforming on copper: Density functional calculations.

Gutowski, William

Joseph M. PRUSA and William J. GUTOWSKI, 2011. "Multi-Scale Waves in Sound-Proof Global Simulations with EULAG", Acta Geophysica, 59, DOI: 10.2478/s11600-011-0050-0

Zbigniew P. Piotrowski, Andrzej A. WyszogrodzkiI, and Piotr K. Smolarkiewicz, 2011. "Towards petascale simulation of atmospheric circulations with soundproof equations", Acta Geophysica, in press.

H

Haas, Stephan

Visualization of nano-plasmons in graphene, H.P. Dahal, R.A. Muniz, S. Haas, M.J. Graf, A.V. Balatsky, Phil. Mag. Lett. 1 (2011).

Quantum liquids move to a higher dimension, T. Albash and S. Haas, Physics 4, 62 (2011).

Propagation of disturbances in degenerate quantum systems, N. Chancellor and S. Haas, Phys. Rev. B 84, 035130 (2011).

Defect Induced Resonances and Magnetic Patterns in Graphene, Y.C. Chang and S. Haas, Phys. Rev. B {\bf 83}, 085406 (2011).

Statistical properties of random matrix product states, S. Garnerone, T.R. de Oliveira, S. Haas, and P. Zanardi, Phys. Rev. A {\bf 82}, 052312 (2010).

Magnetic Bose-glass phases of coupled antiferromagnetic dimers with site dilution, R. Yu, O. Nohadani, S. Haas, and T. Roscilde, Phys. Rev. B {\bf 82}, 134437 (2010).

Local quenches in frustrated quantum spin chains: Global versus subsystem equilibration, M. Diez, N. Chancellor, S. Haas, L. Campos Venuti, P. Zanardi, Phys. Rev. A {\bf 82}, 032113 (2010).

Impurity-assisted nanoscale localization of plasmonic excitations in graphene, R. A. Muniz, H. P. Dahal, A. V. Balatsky, and S. Haas, Phys. Rev. B {\bf 82}, 081411 (2010).

Phase diagram of magnetization reversal processes in nanorings, W. Zhang and S. Haas, Phys. Rev. B {\bf 81}, 064433 (2010).

How to turn a topological insulator into a superconductor, N. Bray-Ali and S. Haas, Physics {\bf 3}, 11 (2010).

Universal phase diagram of disordered bosons from a doped quantum magnet, R. Yu, S. Haas and T. Roscilde, Euro. Phys. Lett. {\bf 89}, 10009 (2010).

Hall, Alex

Boe J, Hall A, Colas F, McWilliams JC, Qu X, Kurian J, Kapnick SB, Frenzel H (2010) What shapes mesoscale wind anomalies in coastal upwelling zones?, Clim. Dyn. 36, 2037-2049, doi: 10.1007/s00382-011-1058-

Haranczyk, Maciej

S. Ling, M. Gutowski, 'SSC: A tool for constructing libraries for systematic screening of conformers', J. Comp. Chem., 2011, 32, 2047. (FEATURES ON A COVER)

S. Ling, D. Mei, M. Gutowski,'Reactivity of hydrogen and methanol on (001) surfaces of WO3, ReO3, WO3/ReO3 and ReO3/WO3', Catal.Today, 2011, 165, 41.

Harmon, Bruce

"Stochastic Coarsening Model for Pb Islands on a Si(111) Surface", G.P. Zhang, M. Hupalo, M. Li, C.Z. Wang, J.W. Evans, M.C. Tringides, and K.M. Ho, Physical Review B, 82, 165414 (2010).

"Islands and holes as measures of mass balance in growth of the (root 3x root 3)R30 degrees phase of Ag on Si(111)", A. Belianinov B. nal, N. Liu, M.Jin, K.M.Ho , C. Z. Wang M. C. Tringides and P. A. Thiel 2010. Physical Review B. 82:245413.

"Bonding and charge transfer by metal adatom adsorption on graphene", Xiaojie Liu, C. Z. Wang, Y. X. Yao, W. C. Lu, M. Hupalo, M. C. Tringides, and K. M. Ho Phys. Rev. B 83 235411 (2011).

"Nucleation and Growth of Ag Islands on the (R3xR3)R30o Phase of Ag on Si(111)" Alex Belianinov, Baris Unal, K.-M. Ho, C.-Z. Wang, J. W. Evans, M. C. Tringides, and P. A. Thiel Jou. Cond. Matt. 23 265002 (2011)

"Electronic structure and transport of a carbon chain between graphene nanoribbon leads", G. P. Zhang, X. W. Fang, Y. X. Yao, C. Z. Wang, Z. J. Ding, and K. M. Ho, J. Phys. Conden. Matt. 23, 025302 (2011)

"Metal nanostructure formation on graphene: weak vs strong bonding", M. Hupalo, Xiaojie Liu, C. Z. Wang, Wen-Cai Lu, Y. X. Yao, K. M. Ho, and M. C. Tringides, Advanced Mater. 23, 2082 (2011).

"Adsorption and growth morphology of rare-earth metals on graphene studied by ab initio calculations and scanning tunneling microscopy", X. J. Liu, C. Z. Wang, M. Hupalo, Y. X. Yao, M. C. Tringedes, W. C. Lu, K. M. Ho, Phys. Rev. B 82 245408 (2010).

"Strain Effects in Ge/Si and Si/Ge Core/Shell Nanowires", N. Liu, N. Lu, Y. X. Yao, Y. R. Li, C. Z. Wang, K. M. Ho, J. Chem Phys. 115, 15739 (2011)

"Vibrational modes and lattice distortion of a nitrogen-vacancy center in diamond from first-principles calculations", Jianhua Zhang, C. Z. Wang, Z. Z. Zhu, and V. V. Dobrovitski, Phys. Rev. B 83, 035211 (2011).

"Atomic Process of Dislocation Formation in Graphene", Gun-Do Lee, Euijoon Yoon, Nong-moon Hwang, Cai-Zhuang Wang, and Kai-Ming Ho, Phys. Rev. Lett., submitted

"Fe-Fe adatom interaction and growth morphology on graphene", Xiaojie Liu, C. Z. Wang, M. Hupalo, Wen-Cai Lu, P. A. Thiel, K. M. Ho, and M. C. Tringides, Phys. Rev. Lett., submitted.

"Coverage-dependent Collective Diffusion of Dense Pb Wetting Layer on Si(111)", L. Huang, C. Z. Wang, M. Z. Li, and K. M. Ho, Phys. Rev. Lett., submitted.

R. Biswas, C. Xu, 'Nano-crystalline silicon solar cell architecture with absorption at the classical 4n2 limit', Optics Express, 19, A664-A672 (2011). 2. R. Liu, C. Xu, R. Biswas, R. Shinar, J. Shinar, 'Monolithic fabrication of multi-color organic light emitting diodes by controlled MoO3 layers', Appl. Phys. Lett. 99, 093305 (2011).

R. Biswas, C. Xu, W. Zhao, R. Liu, R. Shinar, J. Shinar, 'Simulations of emission from micro-cavity tandem organic light emitting diodes', Journal of Photonics for Energy (JPE) 1, 011016 (2011).

R. Biswas, C. Xu, 'Photonic and Plasmonic Crystal based Enhancement of Solar Cells- Theory of Overcoming the Lambertian Limit', submitted to Journal of Non-Crystalline solids (Aug 2011).

Head-Gordon, Martin

Zimmerman Paul M.; Head-Gordon Martin; Bell Alexis T., "Selection and Validation of Charge and Lennard-Jones Parameters for QM/MM Simulations of Hydrocarbon Interactions with Zeolites," J. Chem. Theory and Comp., 7(6), 1695-1703 (2011)

Azar J., Kurlancheek W. and Head-Gordon M., "Characterization of electronically excited states in anionic acetonitrile clusters," Phys. Chem Chem Phys. 13(20) 9147-9154 (2011)

Limmer, D.T., and D. Chandler."The putative liquid-liquid transition is a liquid-solid transition in atomistic models of water" J. Chem. Phys., (in press)

Patel, A. J., P. Varilly, D. Chandler and S. Garde. "Quantifying density fluctuations in volumes of all shapes and sizes using indirect umbrella sampling", J Stat. Phys. (in press)

Head-Gordon, Teresa

R. M. Lynden-Bell, N. Giovambattista, P. G. Debenedetti, T. Head-Gordon, P. J. Rossky (2011). Hydrogen bond strength and network effects on hydration of nonpolar molecules. Phys. Chem. Chem. Phys. 13 (7), 2748-2757.

P. S. Nerenberg & T. Head-Gordon (2011). Optimizing protein-solvent force fields to reproduce intrinsic conformational preferences of model peptides. J. Chem. Theory Comput 7 (4), 1220-1230

M. Lin and T. Head-Gordon (2011). Reliable protein structure refinement using a physically derived energy function. J. Comp. Chem. 32, 709-717.

D. Lambrecht, G. N. I. Clark, T. Head-Gordon, M. Head-Gordon (2011). Simulated photoelectron spectra of CN(H2O)- via quasiclassical molecular dynamics. J. Phys. Chem. A 115 (23), 5928 5935.

C. Peng & T. Head-Gordon (2011). Auto-inhibition dynamical mechanism in AMP-activated protein kinase. PLoS Comput Biol 7(7): e1002082. doi:10.1371/journal.pcbi.1002082

A. Ball, A. Phillips, N. L. Fawzi, D. E. Wemmer & T. Head-Gordon (2011). Heterogeneous tertiary structure for intrinsically disordered amyloid-beta42. Biochemistry, 50 (35), 7612-7628.

D. Lambrecht, G. N. I. Clark, T. Head-Gordon, M. Head-Gordon (2011). Exploring the rich energy landscape of sulfate-water clusters via a joint molecular mechanics and ab initio approach. J. Phys. Chem. B (Pavel Hobza Festschrift) Article ASAP DOI: 10.1021/jp206064n.

G. N. I. Clark, G. L. Hura, J. Teixeira, A. K. Soper, T. Head-Gordon (2010). Small angle scattering and the structure of ambient liquid water. Proc. Natl. Acad. Sci. 107, 14003-14007.

Held, Eric

A. Spencer, J.-Y. Ji and E. D. Held, A Finite Element/Fourier Treatment of the Fokker-Planck Equation, under review at the Journal of Computational Physics.

Henkelman, Graeme

G. K. P. Dathar, D. Sheppard, K. J. Stevenson and G. Henkelman, "Calculations of Li ion diffusion in olivine phosphates" Chem. Mater. 23 4032-4307 (2011).

Y. Lu, J. B. Goodenough, G. K. P. Dathar, G. Henkelman, J. Wu, and K. J. Stevenson, "Behavior of Li guest in KNb5O13 host with one-dimensional tunnels and multiple interstitial sites" Chem. Mater. 23 3210-3216 (2011).

Heyden, Andreas

Ammal, S. C., Heyden, A., Nature of Ptn/TiO2 (110) Interface under Water-Gas Shift Reaction Conditions: A Constrained ab Initio Thermodynamics Study, J. Phys. Chem. C (2011) http://dx.doi.org/10.1021/jp2058723.

Suthirakun, S., Ammal, S. C., Xiao, G., Chen, F., zur Loye, H., Heyden, A., Density functional theory study on the electronic structure of n- and p-type doped SrTiO3 at anodic solid oxide fuel cell conditions, accepted for publication in Phys. Rev. B.

Hicks, Elizabeth

Elizabeth Hicks and Robert Rosner. "The effects of burning on the development of 2D turbulence". Vol. 2010, T142. Physica Scripta 2010 014046

Hingerty, Brian

Liu Y, Reeves D, Kropachev K, Cai Y, Ding S, Kolbanovskiy M, Kolbanovskiy A, Bolton JL, Broyde S, Van Houten B, Geacintov NE. Probing for DNA damage with -hairpins: similarities in incision efficiencies of bulky DNA adducts by prokaryotic and human nucleotide excision repair systems in vitro. DNA Repair (Amst). 2011 Jul 15;10(7):684-96.

Cai Y, Ding S, Geacintov NE, Broyde S. Intercalative conformations of the 14R (+)- and 14S (-)-trans-anti-DB[a,l]P-N -dA adducts: molecular modeling and MD simulations. Chem Res Toxicol. 2011 Apr 18;24(4):522-31.

Basu A, Broyde S, Iwai S, Kisker C. DNA damage, mutagenesis, and DNA repair. J Nucleic Acids. 2010 Dec 27;2010:182894.

Cai Y, Wang L, Ding S, Schwaid A, Geacintov NE, Broyde S. A bulky DNA lesion derived from a highly potent polycyclic aromatic tumorigen stabilizes nucleosome core particle structure. Biochemistry. 2010 Nov 23;49(46):9943-5.

Cai Y, Patel DJ, Broyde S, Geacintov NE. Base sequence context effects on nucleotide excision repair. J Nucleic Acids. 2010 Aug 23;2010. pii: 174252.

Broyde S, Patel DJ. DNA repair: How to accurately bypass damage. Nature. 2010 Jun 24;465(7301):1023-4.

Cai Y, Kropachev K, Xu R, Tang Y, Kolbanovskii M, Kolbanovskii A, Amin S, Patel DJ, Broyde S, Geacintov Distant neighbor base sequence context effects in human nucleotide excision repair of a benzo[a]pyrene-derived DNA lesion. J Mol Biol. 2010 Jun 11;399(3):397-409.

Rechkoblit O, Kolbanovskiy A, Malinina L, Geacintov NE, Broyde S, Patel DJ. Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4. Nat Struct Mol Biol. 2010 Mar;17(3):379-88.

Basu A, Broyde S, Iwai S, Kisker C. DNA damage, mutagenesis, and DNA repair. J Nucleic Acids. 2010 Dec 27; 2010:182894.

Ho, Kai-Ming

"CO Oxidation Facilitated by Robust Surface States on Au-Covered Topological Insulators". H. Chen, W.G. Zhu, D. Xiao, and Z.Y. Zhang. Phys. Rev. Lett. 107, 056804 (2011).

"Formation of graphene p-n supperlattices on Pb quantum wedged islands". W.G. Zhu, H. Chen, K.H. Bevan, and Z.Y. Zhang. ACS Nano 5, 3707 (2011).

"Communication: Stable carbon nanoarches in the initial stages of epitaxial growth of graphene on Cu(111)". R.G. Van Wesep, H. Chen, W.G. Zhu, and Z.Y. Zhang. J. Chem. Phys. 134, 171105 (2011).

"Terminating surface electromigration at the source". K.H. Bevan, W.G. Zhu, H. Guo, and Z.Y. Zhang. Phys. Rev. Lett. 106, 156404 (2011).

"Atomic Structure, Energetics, and Dynamics of Topological Solitons in Indium Chains on Si(111) Surfaces". H. Zhang, J.-H. Choi, Y. Xu, X.X. Wang, X.F. Zhai, B. Wang, C.G. Zeng, J.-H. Cho, Z.Y. Zhang, and J. G. Hou. Phys. Rev. Lett. 106, 026801 (2011).

"Tuning Gold Nanorod-Nanoparticle Hybrids into Plasmonic Fano Resonance for Dramatically Enhanced Light Emission and Transmission". Z. K. Zhou, X. N. Peng, Z. J. Yang, Z. S. Zhang, M. Li, X. R. Su, Q. Zhang, X. Shan, Q. Q. Wang, Z. Y. Zhang. Nano Lett. 11, 49 (2011).

"First-principles studies of hydrogen interaction with ultrathin Mg and Mg-based alloy films". M. Yoon, H. H. Weitering, Z. Y. Zhang. Phys. Rev. B. 83, 045413(2011).

"Atomistic Mechanisms and Diameter Selection during Nanorod Growth". D. J. Shu, X. Xiang, Z. W. Wang, Z. Y. Zhang, M. Wang, N.-B. Ming. J. Phys. Chem. C. 115, 31 (2011).

"Stochastic Coarsening Model for Pb Islands on a Si(111) Surface", G.P. Zhang, M. Hupalo, M. Li, C.Z. Wang, J.W. Evans, M.C. Tringides, and K.M. Ho, Physical Review B, 82, 165414 (2010).

"Bonding and charge transfer by metal adatom adsorption on graphene", Xiaojie Liu, C. Z. Wang, Y. X. Yao, W. C. Lu, M. Hupalo, M. C. Tringides, and K. M. Ho Phys. Rev. B 83 235411 (2011).

"Metal nanostructure formation on graphene: weak vs strong bonding", M. Hupalo, Xiaojie Liu, C. Z. Wang, Wen-Cai Lu, Y. X. Yao, K. M. Ho, and M. C. Tringides, Advanced Mater. 23, 2082 (2011).

"Strain Effects in Ge/Si and Si/Ge Core/Shell Nanowires", N. Liu, N. Lu, Y. X. Yao, Y. R. Li, C. Z. Wang, K. M. Ho, J. Chem Phys. 115, 15739 (2011)

Coverage-dependent Collective Diffusion of Dense Pb Wetting Layer on Si(111) , L. Huang, C. Z. Wang, M. Z. Li, and K. M. Ho, Phys. Rev. Lett., submitted.

Hsiao, Eric

Freedman, Wendy L., et al., "The Carnegie Supernova Project: First Near-Infrared Hubble Diagram to z ~ 0.7", The Astrophysical Journal, Volume 704, Issue 2, pp. 1036-1058 (2009).

Folatelli, Gast?n, et al., "The Carnegie Supernova Project: Analysis of the First Sample of Low-Redshift Type-Ia Supernovae", The Astronomical Journal, Volume 139, Issue 1, pp. 120-144 (2010).

Contreras, Carlos, et al., "The Carnegie Supernova Project: First Photometry Data Release of Low-Redshift Type Ia Supernovae", The Astronomical Journal, Volume 139, Issue 2, pp. 519-539 (2010).

Stritzinger, Maximilian D., et al., "The Carnegie Supernova Project: Second Photometry Data Release of Low-redshift Type Ia Supernovae", The Astronomical Journal, Volume 142, Issue 5, article id. 156 (2011).

Im, Hong

Arias, P.G., Im, H.G., Narayanan, P. and Trouve, A. (2011) A computational study of non-premixed flame extinction by water spray, Proc. Combust. Inst. 33:2591-2597.

Yoo, C.S., Lu, T., Chen, J.H. and Law, C.K. (2011) Direct numerical simulations of ignition of a lean n-heptane/air mixture with temperature inhomogeneities at constant volume: Parametric study, Combust. Flame 158:1727-1741.

Narayanan, P., Baum, H.R. and Trouve, A. (2011) Effect of soot addition on extinction limits of luminous laminar counterflow diffusion flames, Proc. Combust. Inst. 33:2539-2446.

Luo, Z., Yoo, C.S., Richardson, E., Chen, J.H., Law, C.K. and Lu, T.F. (2011) Chemical explosive mode analysis for a turbulent lifted ethylene jet flame in highly-heated coflow, Combust. Flame, doi:10.1016/j.combustflame.2011.05.023, in press.

Sarathy, S.M., Westbrook, C.K., Mehl, M., Pitz, W.J., Togbe, C., Dagaut, P., Wang, H., Oehlschlaeger, M.A., Niemann, U., Seshadri, K., Veloo, P.S., Ji, C., Egolfopoulos, F. and Lu, T.F. (2011) Comprehensive chemical kinetic modeling of the oxidation of C8 and larger nalkanes and 2-methylalkanes, Combust. Flame, doi:10.1016/j.combustflame.2011.05.007, in press.

Luo, Z., Lu, T.F. and Liu, J. (2011) A reduced mechanism for ethylene/methane mixtures with excessive NO enrichment, Combust. Flame, 158: 1245-1254.

Sarathy, S.M., Pitz, W.J., Thomson, M.J. and Lu, T.F. (2011) An experimental and kinetic modeling study of methyl decanoate combustion, Proc. Combust. Inst., 33: 399-405.

I

Izzo, Valerie

V.A. Izzo, et al, "Runaway electron confinement modelling for rapid shutdown scenarios in DIII-D, Alcator C-Mod, and ITER." Nuclear Fusion 51 (2011) 063032.

J

Jardin, Stephen

J.A. Breslau, M.S. Chance, J. Chen, G.Y. Fu, S.P. Gerhardt, N. Gorelenkov, S.C. Jardin, and J. Manickam, "Onset and saturation of a non-resonant internal mode in NSTX and implications for AT modes in ITER," Nucl. Fus. 51, 063027 (2011).

Jasper, Ahren

Tao C, Richmond C, Mukarakate C, Dawes R, Kable S, Reid S, Optical-optical double resonance spectroscopy of the S2 state of CHF and CDF: 1. Spectroscopy Analysis. J. Chem Phys. 135 104315 (2011).

Richmond C, Tao C, Mukarakate C, Brown E, Dawes R, Kable S, Reid S, Optical-optical double resonance spectroscopy of the S2 state of CHF and CDF: 2. Predissociation and mode-specific dynamics J. Chem Phys. 135 104316 (2011).

Jellinek, Julius

Li Ma, K. A. Jackson, and J. Jellinek SITE-SPECIFIC POLARIZABILITIES AS PREDICTORS OF FAVORABLE ADSORPTION SITES ON Na_n CLUSTERS Chem. Phys. Lett. 503, 80 (2011)

A. A. Paz, E. P. M. Leiva, J. Jellinek, and M. M. Mariscal PROPERTIES OF ROTATING NANOALLOYS FORMED BY CLUSTER COLLISION: A COMPUTER SIMULATION STUDY J. Chem. Phys. 143, 094701 (2011)

K. Baishya, J. C. Idrobo, S. Ogut, M. Yang, K. A. Jackson, and J. Jellinek FIRST-PRICIPLES ABSORPTION SPECTRA OF Cu_n (n=2-20) CLUSTERS Phys. Rev. B 83, 245402 (2011)

X. Yuan, L. Liu, X. Wang, M. Yang, K. A. Jackson and J. Jellinek THEORETICAL INVESTIGATION OF ADSORPTION OF MOLECULAR OXYGEN ON SMALL COPPER CLUSTERS J. Phys. Chem. A 115, 8705 (2011)

C. Wang, R. S. Berry, and J. Jellinek RANGE EFFECTS OF INTER-PARTICLE FORCES ON STRUCTURES, THERMODYNAMIC PROPERTIES AND POTENTIAL ENERGY LANDSCAPES: (KCl)_32 AND RELATED SYSTEMS Chem Phys. (accepted)

R. Perez de Tudela, D. Lopez-Duran, M. P. de Lara-Castells, R. Prosmiti, O. Roncero, G. Delgado- Barrio, F. A. Gianturco, J. Jellinek, and P. Villareal A QUANTUM CHEMISTRY APPROACH TO ENERGIES, STRUCTURES, AND SPECTROSCOPY OF DOPED HELIUM CLUSTERS In Computational Methods in Science and Engineering, Vol. 1, G. Maroulis and T. E. Simos, Eds., AIP Conference Proceedings (in press)

Jena, Puru

Pradhan, K., Gutsev, G., Weatherford, C., and Jena, P.: Interactions of a Mn atom with halogen atoms and stability of its half filled 3d-shell , J. Chem. Phys. 134, 234311 (2011)

Li, S. and Jena, P.: Reaction Intermediates during Dehydrogenation of Metal Borohydrides: A Cluster Perspective , J. Chem. Phys. 114, 16849 (2010).

Kalpataru Pradhan, Puru Jena, Double exchange mediated ferromagnetic coupling between Co atoms in dicobalt complex, Appl. Phys. Lett. (in press)

Kalpataru Pradhan, Puru Jena, Potential Candidates for Hyperhalogens: A Comparative Study of BO2, AlO2 and VO3 Species, J. Chem. Phys. (in press)

Paduani, C., Wu, M., Willis, M., and Jena, P.: Theoretical Study of the Stability and Electronic Structure of Al(BH4)n and Al(BF4)n (n=1-4) and their Hyperhalogen Behavior , J. Phys. Chem. A J Phys Chem A. 2011 Sep 15; 115(36):10237-43

Samanta, D., Wu, M. M., and Jena, P.: Au(CN)n Complexes: Superhalogens with pesudohalogens as building blocks , Inorg. Chem., 2011, 50 (18), pp 8918 8925

Ji, Chueng Ryong

B.~L.~G.~Bakker and C.~R.~Ji, %``Spin filter in deeply virtual Compton scattering amplitudes,'' Phys.\ Rev.\ D {\bf 83}, 091502 (2011).

H.~M.~Choi and C.~R.~Ji, %``Light-front zero-mode contribution to the tensor form factors for the %exclusive rare $P\to V\ell^+\ell^-$ decays,'' Phys.\ Lett.\ B {\bf 696}, 518 (2011)

H.~M.~Choi and C.~R.~Ji, %``Light-front dynamic analysis of transition form factors in the process of %$P\to V\ell\nu_{\ell}$,'' Nucl.\ Phys.\ A {\bf 856}, 95 (2011) [arXiv:1007.2502 [hep-ph]].

Jiang, De-en

Babarao, R.; Dai, S. Jiang, D. E.* "Understanding the High Solubility of CO2 in an Ionic Liquid with the Tetracyanoborate Anion." J. Phys. Chem. B, 115, 9789 (2011).

Babarao, R.; Dai, S. Jiang, D. E.* "Functionalizing Porous-Aromatic Frameworks with Polar Organic Groups for High-Capacity and Selective CO2 Separation: A Molecular Simulation Study." Langmuir, 27, 3451 (2011).

Babarao, R.; Dai, S. Jiang, D. E.* "Effect of Pore Topology and Accessibility on Gas Adsorption Capacity in Zeolitic-Imidazolate Frameworks: Bringing Molecular Simulation Close to Experiment." J. Phys. Chem. C, 115, 8126 (2011).

Jiang, D. E.*; Overbury, S. H.; Dai, S. "Interaction of Gold Clusters with a Hydroxylated Surface." J. Phys. Chem. Lett., 2, 1211 (2011).

Pei, Y.*; Shao, N.; Li, H.; Jiang, D. E.*; Zeng, X. C.* "Hollow Polyhedral Structures in Small Gold Sulfide Clusters." ACS Nano, 5, 1441 (2011). (Highlighted in the Feb. 14, 2011 issue of C&EN Science & Technology Concentrates).

Jiang, D. E.*; Dai, S. "The Role of Low-Coordinate Oxygen on Co3O4(110) in Catalytic CO Oxidation." Phys. Chem. Chem. Phys., 13, 978 (2011).

Shao, N.; Sun, X. G.; Dai, S. Jiang, D. E.* "Electrochemical Windows of Sulfone-Based Electrolytes for High-Voltage Li-Ion Batteries." J. Phys. Chem. B, in press.

Jiang, D. E.* "Staple Fitness: A Concept to Understand and Predict the Structures of Thiolated Gold Nanoclusters." Chem. Euro. J., in press.

K

Kalinichev, Andrey

Kalinichev, A. G.; Iskrenova-Tchoukova, E.; Ahn, W.-Y.; Clark, M. M.; Kirkpatrick, R. J. Effects of Ca2+ on supramolecular aggregation of natural organic matter in aqueous solutions: A comparison of molecular modeling approaches. Geoderma, 2011, DOI: 10.1016/j.geoderma.2010.09.002.

Iskrenova-Tchoukova, E.; Kalinichev, A. G.; Kirkpatrick, R. J., Metal Cation Complexation with Natural Organic Matter in Aqueous Solutions: Molecular Dynamics Simulations and Potentials of Mean Force. Langmuir 2010, 26, (20), 15909.

Karplus, Martin

V. Ovchinnikov, M. Karplus, and E. Vanden-Eijnden. Free Energy of Conformational Transition Paths in Biomolecules: The String Method and its Application to Myosin VI, J. Chem. Phys. 134, 085103 (2011)

S. Fischer, K. W. Olsen, K. Nam, and M. Karplus. The Unsuspected Pathway of the Allosteric Transition in Hemoglobin, Proc. Natl. Acad. Sci. USA 108, 5608, (2011)

G. Luo and M. Karplus. Determining the Conformational Change that Accompanies Donor-Acceptor Distance Fluctuations: An Umbrella Sampling Analysis, J. Phys. Chem. B 115, 7991, (2011).

M. Karplus. Behind the Folding Funnel Diagram, Nature Chem. Bio. 7, 401, (2011)

G. Zheng, A. Niklasson, and M. Karplus. Lagrangian Formulation with Dissipation of Born-Oppenheimer Molecular Dynamics using the Density-Functional Tight-Binding method (DFTB). J. Chem. Phys., 135, 044122, (2011)

M. Y. Wolfson, K. Nam, and Arup K. Chakraborty. The Effect of Mutations on the Alloreactive T Cell Receptor/Peptide MHC Interface Structure: A Molecular Dynamics Study, J. Phys. Chem. B, 115, 8317, (2011)

R. J. Petrella A Versatile Method for Systematic Conformational Searches: Application to CheY, J. Comput. Chem. 32, 2369, (2011).

Kasen, Daniel

L. Roberts, D. Kasen, W.H. Lee, E. Ramirez-Ruiz, Electromagnetic Transients Powered by Nuclear Decay in the Tidal Tails of Coalescing Compact Binaries, ApJ, 736, 21, (2011).

S. Blondin, D. Kasen, Roepke, R. Kirshner, K. Mandel, Confronting 2D delayed-detonation models with light curves and spectra of Type Ia supernovae, MNRAS in press, arXiv:1107.0009 (2011).

D. Kasen, S.E. Woosley, A. Heger, Pair Instability Supernovae: Light Curves, Spectra, and Shock Breakout, ApJ, 734, 102 (2011).

I. Kleiser, D. Poznanski, D. Kasen, et al., Peculiar Type II supernovae from blue supergiants, MNRAS, 415, 372, (2011).

S.E. Woosley, D. Kasen, Sub-Chandrasekhar Mass Models for Supernovae, ApJ, 734, 38 (2011).

R. Foley and D. Kasen, Measuring Ejecta Velocity Improves Type Ia Supernova Distances, ApJ, 729, 55 (2011).

Kent, Paul

"Phonon softening and metallization of a narrow-gap semiconductor by thermal disorder". O. Delaire, K. Marty, M. B. Stone, P. R. C. Kent, M. S. Lucas, D. L. Abernathy, D. Mandrus, B. C. Sales. Proceedings of the National Academy of Sciences 108 4725 (2011).

"Anomalous Lattice Dynamics near Ferroelectric Instability in PbTe". Y. Zhang, X. Ke, P. R. C. Kent, C. Chen, and J. Yang. Accepted in Phys. Rev. Lett. (2011)

"Simple impurity embedded in a spherical jellium: Approximations of density functional theory compared to quantum Monte Carlo benchmarks". M. Bajdich, P. R. C. Kent, J. Kim, F. A. Reboredo. Phys. Rev. B 84 075131 (2011)

"Anisotropic quasiparticle lifetimes in Fe-based superconductors", Kemper A. F.; Korshunov M. M.; Devereaux T. P.; et al. Phys. Rev. B 83 184516 (2011)

"First-principles studies of Ta(2)O(5) polymorphs", Wu Yu-Ning; Li Lan; Cheng Hai-Ping Phys. Rev. B 83 144105 (2011)

"Interaction between water and defective silica surfaces", Chen Yun-Wen; Cheng Hai-Ping J. Chem. Phys. 134 114703 (2011)

"Interedge magnetic coupling in transition-metal terminated graphene nanoribbons", Wang Yan; Cheng Hai-Ping Phys. Rev. B 83 113402 (2011)

"Accurate projected augmented wave datasets for BaFe(2)As(2)", Cao Chao; Wu Yu-ning; Hamdan Rashid; et al. NEW JOURNAL OF PHYSICS 12 123029 (2011)

"Metal-terminated graphene nanoribbons", Wang Yan; Cao Chao; Cheng Hai-Ping. Phys. Rev. B 82 205429 (2011)

"Structure and stability of thin water films on quartz surfaces", Chen Yun-Wen; Cheng Hai-Ping. APPLIED PHYSICS LETTERS 97 161909 (2011)

"Reactivity of cations in the M1 phase of Mo-V-Te-Nb mixed metal oxide for propane oxidative dehydrogenation," K. Muthukumar, J. Yu, Y. Xu, and V.V. Guliants, Topics in Catalysis, 54 (2011) 605-613

"Aqueous-phase hydrogenation of acetic acid over transition metal catalysts," H. Olcay, L. Xu, Y. Xu, and G.W. Huber, ChemCatChem, 2 (2010) 1420-1424.

Faster Proton Transfer Dynamics of Water on SnO2 Compared to TiO2. N.Kumar, P. R. C. Kent, A. V. Bandura, J. D. Kubicki, D. J. Wesolowski, D. R. Cole and J. O. Sofo. J. Chem. Phys. 134 044706 (2011).

"The Influence of Molecular Adsorption on Elongating Gold Nanowires", William R. French, Christopher R. Iacovella, and Peter T. Cummings. J. Phys. Chem. C, accepted (2011)

"Self-Assembly of DNA Segments on Graphene and Carbon Nanotube Arrays in Aqueous Solution: A Molecular Simulation Study", Xiongce Zhao, J. Phys. Chem. C, 2011, 115 (14), 6181-6189

"Epitaxial Strain-Induced Chemical Ordering in La0.5Sr0.5CoO3 Films on SrTiO3", W. Donner, C. Chen, M. Liu, A. J. Jacobson, Y.-L. Lee, M. Gadre, and D. Morgan, Chem. Mater., 23 (4), 984-988 (2011)

"Strain Effects on Defect Chemistry in Epitaxial Perovskite Thin Films for Solid Oxide Fuel Cells", M. Gadre, Y.-L. Lee, N. Swaminathan, and D. Morgan, ECS Transactions, 35, (2011)

"The Influence of Molecular Adsorption on Elongating Gold Nanowires", French WR, Iacovella CR, Cummings PT. JOURNAL OF PHYSICAL CHEMISTRY C, 115 (38), 18422-18433, (2011)

"Flexible order parameters for quantifying the rate-dependent energy release mechanism of Au nanowires " Iacovella CR, French WR, Cummings PT. Proceedings of SciDAC (2011)

Kherlopian, Armen

Kherlopian AR, Ortega FA, Christini DJ. Cardiac myocyte model parameter sensitivity analysis and model transformation using a genetic algorithm. Genetic and Evolutionary Computation 2011: 755- 758.

Kilin, Dmitri

J. Phys. Chem. C. jp-2011-06594e.R1 (Accepted on Sep. 22/2011) Title: "Theoretical Study of Electron-Phonon Relaxation in Pbse and Cdse Quantum Dots: Evidence for Phonon Memory" Author(s): Kilina, Svetlana; Kilin, Dmitri; Prezhdo, Victor; Prezhdo, Oleg

The Journal of Physical Chemistry jp-2011-055798.R2 (Accepted on Aug. 28/2011) Title: "Optical Properties of Doped Silicon Quantum Dots with Crystalline and Amorphous Structures" Author(s): Mavros, Michael; Micha, David; Kilin, Dmitri

International Journal of Quantum Chemistry QUA-2011-0258 (Accepted on Jun. 28/2011) Title: "Electronic Structure and Optical Absorbance of Doped Amorphous Silicon Slabs" Authors: Ramirez, Jessica; Micha, David; Kilin, Dmitri

Kilin, D., Micha, D. A., (2011), Modeling the Photovoltage of Doped Si Surfaces, Journal of Physical Chemistry C, vol. 115, pp. 770-775.

LaJoie, T., Ramirez, J., Kilin, D., Micha, D., (2010), Optical Properties of Amorphous and Crystalline Silicon Surfaces Functionalized with Ag-n Adsorbates, Int. J. Quantum Chemistry, vol. 110, pp. 3005-3014 .

Kim, Charlson

D.P. Brennan, C.C. Kim, and R.J. LaHay, Nuclear Fusion52, 033004,(2012)

Kim, Kwiseon

Chang CH (2011) Computational Chemical Analysis of [FeFe] Hydrogenase H-Cluster Analogues To Discern Catalytically Relevant Features of the Natural Diatomic Ligand Configuration. J. Phys. Chem. A 115: 8691-704.

Kioupakis, Emmanouil

Indirect Auger recombination as a cause of efficiency droop in nitride light-emitting diodes, Emmanouil Kioupakis, Patrick Rinke, Kris T. Delaney, and Chris G. Van de Walle, Appl. Phys. Lett. 98, 161107 (2011); doi:10.1063/1.3570656

Phonon-assisted optical absorption in silicon from first principles, J. Noffsinger, E. Kioupakis, C. G. Van de Walle, S. G. Louie, and M. L. Cohen

Klein, Richard

Kratter, Kaitlin M.; Matzner, Christopher D.; Krumholz, Mark R.; Klein, Richard I., On the Role of Disks in the Formation of Stellar Systems: A Numerical Parameter Study of Rapid Accretion, The Astrophysical Journal, Volume 708, Issue 2, pp. 1585-1597 (2010).

Krumholz, Mark R.; Cunningham, Andrew J.; Klein, Richard I.; McKee, Christopher F., Radiation Feedback, Fragmentation, and the Environmental Dependence of the Initial Mass Function, The Astrophysical Journal, Volume 713, Issue 2, pp. 1120-1133 (2010).

Hansen, Charles E,. McKee, Christopher F., Klein, Richard I., Anisotropy Lengthens the Decay Time of Turbulence in Molecular Clouds, The Astrophysical Journal, Volume 738, Issue 1, pp. 88-97 (2011).

Hansen, Charles E., Klein, Richard I., McKee, Christopher F., Fisher, Robert, Feedback Effects on Low-Mass Star Formation, The Astrophysical Journal, submitted.

Ko, Kwok

Cho Ng, R.J. England, L.-Q. Lee, R. Noble, V. Rawat, J. Spencer, Transmission and Radiation of an Accelerating Mode in a Photonic Bandgap Fiber, Phys.Rev.ST Accel.Beams 13 (2010) 121301. (Paper was on the cover of the December issue.)

Kong, Lingzhu

Lingzhu Kong, Xifan Wu, and Roberto Car, "Quantum nuclei and local field effects in the x-ray absorption spectra of water", to be submitted to PRL

Koziol, Quincey

Prabhat, Quincey Koziol, Karen Schuchardt, E. Wes Bethel, Jerry Chuo, Mark Howison, Mike McGreevy, Bruce Palmer, Oliver Ruebel and John Wu, "ExaHDF5: An I/O Platform for Exascale Data Models, Analysis and Performance", Scientific Discovery Through Advanced Computing 2011, Invited Paper.

Mark Howison, Andreas Adelmann, E. Wes Bethel, Achim Gsell, Benedikt Oswald, Prabhat. H5hut: A High-Performance I/O Library for Particle-based Simulations. In IASDS10 - Workshop on Interfaces and Abstractions for Scientific Data Storage, Heraklion, Crete, Greece. September 2010. LBNL-4021E.

Mark Howison, Quincey Koziol, David Knaak, John Mainzer and John Shalf

Tuning HDF5 for Lustre File Systems. In IASDS10 - Workshop on Interfaces and Abstractions for Scientific Data Storage, Heraklion, Crete, Greece. September 2010.

Jerry Chou, Kesheng Wu, Oliver Ruebel, Mark Howison, Ji Qiang, Prabhat, Brian Austin, E. Wes Bethel, Rob D. Ryne, and Arie Shoshani. Parallel Index and Query for Large Scale Data Analysis. In Proceedings of Supercomputing 2011, Seattle, WA, USA, 2011.

Kral, Petr

J. W. Bae, R. M. Pearson, N. Patra, S. Sunoqrot, L. Vukovic, P. Kral, and S. Hong, Dendron-mediated self-assembly of highly PEGylated block copolymers: a modulated nanocarrier platform, Chem. Comm. 47, 10302 (2011).

L. Vukovic, S. D. Drake, F. A. Khatib, A. Madriaga, K. S. Brandenburg, P. Kral, and H. Onyuksel, Structure and Dynamics of Highly PEG-ylated Sterically Stabilized Micelles in Aqueous Media, JACS 133, 13481 (2011).

A. Baskin and P. Kral, Electronic Structures of Porous Nanocarbons, Scientific Reports 1, 36 (2011).

J. He, X. -M. Lin, H. Chan, L. Vukovic, P. Kral, and H. M. Jaeger, Diffusion and Filtration Properties of Self-Assembled Gold Nanocrystal Membranes, Nano Letters 11, 2430 (2011).

P. Kral, L. Vukovic, N. Patra, B. Wang, K. Sint and A. Titov, Control of Rotary Motion at the Nanoscale: Motility, actuation, self-assembly, J. Nanosci. Lett. 1, 128 (2011).

N. Patra and P. Kral, Controlled Self-assembly of filled Micelles on Nanotubes, JACS (Communication) 133, 6146 (2011).

H. Chan and P. Kral, Self-standing Nanoparticle Membranes and Capsules, Nanoscale 3, 1881 (2011).

N. Patra, Y. Song, and P. Kral, Self-assembly of Graphene Nanostructures on Nanotubes, ACS Nano 5, 1798 (2011).

Kritz, Arnold

A.Y. Pankin, G. Park, J. Cummings, C.S. Chang, G. Bateman, D. Bunner, R.J. Groebner, J.W. Hughes, B. LaBombard, J.L. Terry, A.H. Kritz, S. Ku, T. Rafiq, and P.B. Snyder, Kinetic Modeling of H-mode Pedestal with Effects from Anomalous Transport and MHD Stability, Problems of Atomic Science and Technology: Plasma Physics, 17, 8 (2011).

A.Y. Pankin, A. Pletzer, S. Vadlamani, J.R. Cary, A. Hakim, S. E. Kruger, M. Miah, T.D. Rognlien, S. Shasharina, G. Bateman, A.H. Kritz, T. Rafiq and FACETS team, Simulation of anomalous transport in tokamaks using the FACETS code, Comp. Phys. Comm, 182, 180, (2011).

Kruger, Scott

A. Pankin, A. Pletzer, S. Vadlamani, A. Hakim, S. Kruger, M. Miah, T. Rognlien, S. Shasharina, G. Bateman, A. Kritz, T. Rafiq, imulation of anomalous transport in tokamaks using the FACETS code - Computer Physics Communications 182, 180 (2011).

2. A.Y Pankin, J. Callen, J.R. Cary, R. Groebner, A. Hakim, S. Kruger, A. Pletzer, S. Shasharina, S. Vadlamani, R. Cohen, A. Kritz, T.D. Rognlien, T. Rafiq, and FACETS team, Stress Tests of Transport Models Using Code, AIP Conference Proceeding 1392 IFP-CNR - CHALMERS Workshop on Nonlinear Phenomena on Fusion Plasmas (2011).

L

Lacis, Andrew

Q. Ma, R. H. Tipping, and N. N. Lavrentieva, Theoretical Studies of N2-Broadened Half-widths of H2O Lines Involving High J Sates. To be submitted.

Q. Ma, R. H. Tipping, and N. N. Lavrentieva, Pair Identity and Smooth Variation Rules Applicable for the Spectroscopic Parameters of H2O Transitions Involving High J States. Mol. Phys. 109, 1925 (2011).

Q. Ma, R. H. Tipping, and R. R. Gamache, Uncertainties Associated with Theoretically Calculated N2- broadened Half-widths of H2O lines, Mol. Phys. Vol. 108, 2225 (2010).

C. Leforestier, R. H. Tipping, and Q. Ma, Temperature Dependence of Mechanisms Responsible for the Water-Vapor Continuum Absorption: II Dimers and collision-induced absorption. J. Chem. Phys. 132, 164302 (2010).

Landman, Uzi

"Dielectron Attachment and Hydrogen Evolution Reaction in Water Clusters", R.N. Barnett, R. Giniger, O. Cheshnovsky, U. Landman, J. Phys. Chem. A 115, 7378 (2011).

"Dielectric Nanodroplets: Structure, Stability, Thermodynamics, Shape Transitions and Electrocrystallization in Applied Electric Fields", W.D. Luedtke, J. Gao, Uzi Landman, J. Phys. Chem. C vol. 115 (42), Oct 27, 2011 (doi.org/10.1021/jp206673j) Feature and Cover Article.

"Unique Nature of the Lowest Landau Level in Finite Graphene Samples with Zigzag Edges: Dirac Electrons with Mixed Bulk-Edge Character", I. Romanovsky, C. Yannouleas, U. Landman, Phys. Rev. B 83, 045421 (2011).

"Temperature-Tunable Selective Methane Catalysis on Au2+: From Cryogenic Partial Oxidation Yielding Formaldehyde to Cold Ethylene Production", S. M. Lang,T. M. Bernhardt, R. N. Barnett, and U. Landman, J. Phys. Chem. 115, 6788 (2011). Cover Article.

Langston, Michael

Abu-Khzam, F. N., H. Fernau, et al. (2010). A Fixed-Parameter Algorithm for String-to-String Correction. Proceedings, Computing: the Australasian Theory Symposium, Brisbane, Australia.

Abu-Khzam, F. N., H. Fernau, et al. (2011). "Charge and Reduce: A Fixed-Parameter Algorithm for String-to-String Correction." Discrete Optimization 8: 41-49.

Abu-Khzam, F. N., M. A. Langston, et al. (2010). A Hybrid Graph Representation for Recursive Backtracking Algorithms. Proceedings, International Frontiers of Algorithmics Workshop, Wuhan, China.

Bodlaender, H. L., M. R. Fellows, et al. (2011). "Quadratic Kernelization for Convex Recoloring of Trees." Algorithmica 61: 362-388.

Bruhn, S., F. Barren s, et al. (accepted for publication). "Increased Expression of IRF4 in Allergen-Challenged CD4+ Cells from Patients with Intermittent Allergic Rhinitis." Allergy, the European Journal of Allergy and Clinical Immunology.

Debroni, J., J. D. Eblen, et al. (2011). A Complete Resolution of the Keller Maximum Clique Problem. Proceedings, ACM-SIAM Symposium on Discrete Algorithms.

Desormeaux, W. J., A. J. Hall, et al. (accepted for publication). "Effects of Edge Lifting on Domination in Graphs." Bulletin of the Institute of Combinatorics and its Applications.

Eblen, J. D., C. A. Phillips, et al. (2011). "The Maximum Clique Enumeration Problem: Algorithms, Applications and Implementations." Lecture Notes in Bioinformatics 6674: 306-319.

Jay, J. J., J. D. Eblen, et al. (2011). "A Systematic Comparison of Genome Scale Clustering Algorithms." Lecture Notes in Bioinformatics 6674: 416-427.

Lynch, R. M., S. Naswa, et al. (2010). "Identifying Genetic Loci and Spleen Gene Coexpression Networks Underlying Immunophenotypes in BXD Recombinant Inbred Mice." Physiological Genomics 41: 244-253.

Mulligan, M. K., L. Lu, et al. (2010). Genetic Analysis of BDNF Expression Cliques and Adult Neurogenesis in the Hippocampus. Proceedings, ORNL Biomedical Science and Engineering Conference: Biomedical Sciences Research and Analysis in Neurosciences, Oak Ridge, Tennessee.

Weerapurage, D. P., J. D. Eblen, et al. (2011). Parallel Vertex Cover: A Case Study in Dynamic Load Balancing. Proceedings, Australasian Symposium on Parallel and Distributed Computing, Perth, Australia.

Lany, Stephan

"Universal Electrostatic Origin of Cation Ordering in A2BO4 Spinel Oxides", V. Stevanovic, M. d'Avezac, and A. Zunger, J. Am. Chem. Soc. 133, 11649 (2011).

"Using design principles to systematically plan the synthesis of candidate hole-conducting transparent oxides: Cu3VO4 and Ag3VO4" , in preparation by G. Trimarchi, H. Peng, J. Im, A.J. Freeman, V. Cloet, A. Raw, K.R. Poeppelmeier, K. Biswas, S. Lany, and A. Zunger. accepted in Physical Review B

J. Vidal, X. Zhang, L. Yu, J.-W. Luo, and A. Zunger, Phys. Rev. B Rapid Communications 84, 041109 (2011).

M. d'Avezac, R. Botts, M. J. Mohlenkamp, and A. Zunger, submitted to SIAM Journal of Scientific Computing.

Lee, Frank

"Efficient implementation of the overlap operator on multi-GPUs", A. Alexandru, M. Lujan, C. Pelissier, B. Gamari, F.X. Lee, submitted to Journal of Computational Physics. http://arxiv.org/abs/1106.4964

"Multi-mass solvers for lattice QCD on GPUs", A. Alexandru, C. Pelissier, B. Gamari, F.X. Lee, submitted to Journal of Computational Physics. http://arxiv.org/abs/1103.5103

"A problem in particle physics and its Bayesian analysis", Joshua Landon, F.X. Lee, and Nozer Singpurwalla, Statistical Science (in press).

"Chiral extrapolation beyond the power-counting regime", J.M.M. Hall, F.X. Lee, D.B. Leinweber, K.F. Liu, N. Mathur, R.D. Young, J.B. Zhang, submitted to Physical Review D. http://arxiv.org/abs/1101.4411

"QCD at non-zero density and canonical partition functions with Wilson fermions", Andrei Alexandru (George Washington U.), Urs Wenger (Bern U.). Sep 2010. 22 pp. Published in Phys.Rev. D83 (2011) 034502

"The Analysis of Space-Time Structure in QCD Vacuum II: Dynamics of Polarization and Absolute X- Distribution", Andrei Alexandru (George Washington U.), Terrence Draper, Ivan Horvath (Kentucky U.), Thomas Streuer (Regensburg U.). Sep 2010. 36 pp. Published in Annals Phys. 326 (2011) 1941-1971

Lee, T. S. Harry

N. Suzuki, T. Sato, T.-S. H. Lee Extraction of electromagnetic transition form factors for nucleon resonances within a dynamical coupled-channels model Phys. Rev. C 82, 045206 (2010) A.M. Sandorfi, S. Holbit, H. Kamano, T.-S. H. Lee

Determining pseudoscalar meson photo-production amplitudes from complete experiments M. Sandorfi, S. Hoblit, H. Kamano, T.-S. H. Lee J. Phys. G {\bf 38}, 053001 (2011)

I. Aznauyan, V.D. Burkert, T.-S. H. Lee, V.I. Mokeev Results from the N* program at JLab. J.Phys.Conf.Ser.299:012008,2011

Lee, Wei-li

Nonlinear flow generation by electrostatic turbulence in tokamaks, W. X. Wang, P. H. Diamond, T. S. Hahm, S. Ethier, G. Rewoldt, W. M. Tang, Phys. Plasmas 17, 072511 (2010).

Characteristics of Turbulence Driven Multiple-Channel Transport in Tokamaks, and Comparison with Experiments, W. X. Wang, T. S. Hahm, S. Ethier, G. Rewoldt, S. M. Kaye, W. M. Tang, W. W. Lee and P. H. Diamond, Proceedings of the 23rd IAEA Fusion Energy Conference, Daejon, Korea (IAEA Vienna, 2010), IAEA-CN- 165/TH-P4-30.

A synthetic diagnostic for validation of electron gyroradius scale turbulence simulations against coherent scattering measurements , F.M. Poli, S. Ethier, W. Wang, T.S. Hahm, E. Mazzucato and D. R. Smith, Phys. Plasmas 17, 112514 (2010).

Trapped Electron Mode Turbulence Driven Intrinsic Rotation in Tokamak Plasmas , W. X. Wang, T. S. Hahm, S. Ethier, L. E. Zakharov and P. H. Diamond, Physical Review Letters 106, 085001 (2011).

Characteristics of turbulence-driven plasma flow and origin of experimental empirical scalings of intrinsic rotation , W. X. Wang, T. S. Hahm, S. Ethier, P. H. Diamond, G. Rewoldt, W. M. Tang and W. W. Lee, Phys. Plasmas 18, 042502 (2011).

Lee, Xuhui

Huang, Jian-Ping, Xuhui Lee and Edward G. Patton.. Entrainment and Budget of Heat, Water Vapor and Carbon Dioxide in a Convective Boundary Layer Driven by Time-Varying Solar Radiation.. Journal of Geophysical Research - Atmospheres. 116 (2011): D06308. DOI: 10.1029/2010JD014938.

Leng, Yongsheng

Lei, Y. J. and Leng, Y. S., "Slick-slip Friction and Energy Dissipation in Boundary Lubrication", Physical Review Letters (in press).

Lei, Y. J. and Leng, Y. S., "Molecular dynamics simulations on the phase transition of simple nonpolar fluids under nanometer confinement", Proceedings of the Institution of Mechanical Engineers, Part N, Journal of Nanoengineering and Nanosystems, 224, 69 (2011).

Lei, Y. J. and Leng, Y. S., "Force oscillation and phase transition of simple fluids under confinement", Physical Review E 82, 040501 (Rapid Communications) (2010).

Lester, William

Zubarev, D. Yu.; You, X.; McClean, J.; Lester, W. A. Jr.; Frenklach, M., "Patterns of local aromaticity in graphene oxyradicals", Journal of Material Chemistry, 2011, 21, 3404.

Wang, J.; Domin, D.; Austin, B.; Zubarev, D. Yu.; McClean, J.; Frenklach, M.; Cui, T.; Lester, W. A. Jr., "A Diffusion Monte Carlo Study of the O-H Bond Dissociation of Phenol", Journal of Physical Chemistry A, 2010, 114, 9832.

Cho, H. M.; Lester, W. A. Jr., "An Explicit Solvent Model for Quantum Monte Carlo: Combined Quantum Monte Carlo and Molecular Mechanics Approach", Journal of Physical Chemistry Letters 2010, 1, 3376.

Zubarev, D. Yu.; Lester, W. A. Jr., "Beyond a Single Solvated Electron: Hybrid Quantum Monte Carlo and Molecular Mechanics Approach" (accepted to ACS Symposium Series "Advances in Quantum Monte Carlo")

Zubarev, D. Yu.; Austin, B. M.; Lester, W. A. Jr., "Practical Aspects of Quantum Monte Carlo for the Electronic Structure of Molecules" (invited contribution, accepted to "Practical Aspects of Computational Chemistry: Methods, Concepts and Applications", Leszczynski, J. and Shukla, M. K. Eds, Springer)

Zubarev, D. Yu.; You, X.; Frenklach, M.; Lester, W. A. Jr.,"Delocalization Effects in Pristine and Oxidized Graphene Substrates" Proceedings of QSCP-XV Cambridge, England Sept. 2010; Springer (in press).

Li, Xiaoyi

Li & Soteriou, "HPC as a key enabler for high fidelity simulation of liquid atomization in aerospace applications", Invited Paper, 2011 SciDAC Conference.

Li, Yan

Liang, Xin-Zhong

Liang, X.-Z., M. Xu, X. Yuan, T. Ling, H.I. Choi, F. Zhang, L. Chen, S. Liu, S. Su, F. Qiao, J.X.L. Wang, K.E. Kunkel, W. Gao, E. Joseph, V. Morris, T.-W. Yu, J. Dudhia, and J. Michalakes, 2010: Development of CWRF for regional weather and climate prediction: General model description and basic skill evaluation. J. Climate (submitted)

Lin, Guang

D. Mei, G. Lin. Effects of heat and mass transfer on the reaction kinetics of CO oxidation on the RuO2(110) catalyst, Catalysis Today, 165 (2011) 56-63.

Z. Xu, Y. Liu, H. du, G. Lin, and CW. Shu, Point-wise Hierarchical Reconstruction for Discontinuous Galerkin and Finite Volume Methods for Solving Conservation Laws, Journal of Computational Physics, in press.

X. Yang, M. Choi, G. Lin, G.E. Karniadakis, Adaptive ANOVA Decomposition of Incompressible and Compressible Flows, Journal of Computational Physics, in press.

X. Shi, G. Lin, J. Zhou, D. Fedosov, A Lattice Boltzmann Fictitious Domain Method for Modeling Red Blood Cell Deformation in Flow, Journal of Computational Physics, in review.

Lin, Guang

D. Mei, G. Lin. Effects of heat and mass transfer on the reaction kinetics of CO oxidation on the RuO2(110) catalyst, Catalysis Today, 165 (2011) 56-63.

X. Yang, M. Choi, G. Lin, G.E. Karniadakis, Adaptive ANOVA Decomposition of Incompressible and Compressible Flows, Journal of Computational Physics, in press.

X. Shi, G. Lin, J. Zhou, D. Fedosov, A Lattice Boltzmann Fictitious Domain Method for Modeling Red Blood Cell Deformation in Flow, Journal of Computational Physics, in review.

Lin, Guang, D. Mei, G. Lin. Effects of heat and mass transfer on the reaction kinetics of CO oxidation on the RuO2(110) catalyst, Catalysis Today, 165 (2011) 56-63.

X. Yang, M. Choi, G. Lin, G.E. Karniadakis, Adaptive ANOVA Decomposition of Incompressible and Compressible Flows, Journal of Computational Physics, in press.

X. Shi, G. Lin, J. Zhou, D. Fedosov, A Lattice Boltzmann Fictitious Domain Method for Modeling Red Blood Cell Deformation in Flow, Journal of Computational Physics, in review.

Lin, Yu

Y. Lin, X. Y. Wang, L. Chen, X. Lu and W. Kong, An improved gyrokinetic electron and fully kinetic ion particle simulation scheme: benchmark with a linear tearing mode, PPCF, 53, 054013, 2011.

X. Y. Wang, Y. Lin, L. Chen, X. Lv, and W. Kong, Investigation of Tearing Instability Using GeFi Particle Simulation Model, Phys. Plasmas, submitted, 2011.

Lin, Zhihong

Gyrokinetic particle simulation of beta-induced Alfven eigenmode, H. S. Zhang, Z. Lin, I. Holod, X. Wang, Y. Xiao, W. L. Zhang, Phys. Plasmas 17, 112505 (2010).

Gyrokinetic Simulation of Turbulence Driven Geodesic Acoustic Modes in Edge Plasmas of HL-2A Tokamak, Feng Liu, Z. Lin, J. Q. Dong, K. J. Zhao, Phys. Plasmas 17, 112318 (2010).

Trapped Electron Damping of Geodesic Acoustic Mode, Huasen Zhang and Zhihong Lin, Phys. Plasmas 17, 072502 (2010).

Scalings of energetic particle transport by ion temperature gradient Microturbulence, Wenlu Zhang, Viktor Decyk, Ihor Holod, Yong Xiao, Zhihong Lin, and Liu Chen, Phys. Plasmas 17, 055902 (2010).

Effects of electron dynamics in toroidal momentum transport driven by ion temperature gradient turbulence, I. Holod and Z. Lin, Plasma Phys. Contr. Fusion 52, 035002 (2010).

E. M. Bass and R. E. Waltz. "Gyrokinetic simulations of mesoscale energetic particle driven Alfvenic turbulent transport embedded in microturbulence." Phys. Plasmas 17, 112319 (2010).

R. E. Waltz. Nonlinear Subcritical MHD Beta Limit, Phys. Plasmas 17, 072501 (2010).

D. A. Spong, B. N. Breizman, D. L. Brower, Ed D'Azevedo, C. B. Deng, A. Konies, Y. Todo, and K. Toi, "Energetic-Particle-Driven Instabilities in General Toroidal Configurations," Contributions to Plasma Physics, Vol. 50 (2010) 708-712.

D. A. Spong, E. D'Azevedo, and Y. Todo, "Clustered frequency analysis of shear Alfv n modes in stellarators," Phys. of Plasmas Vol. 17 (2010) 022106.

B. Tobias, I.G.J. Classen, C.W. Domier, W.W. Heidbrink, N.C. Luhmann, Jr., R. Nazikian, H.K. Park, D. Spong, and M.A. Van Zeeland, "Electron Cyclotron Emission Imaging of Fast Ion Induced Shearing of 2D Alfv n Eigenmodes," Physical Reveiw Letters 106, 075003 (2010).

D. A. Spong, Three-dimensional effects on energetic particle confinement and stability, Phys. of Plasmas, v. 18, 056109 (2011).

B. J. Tobias, R. L. Boivin, J. E. Boom, I. G. J. Classen, C. W. Domier, A. J. H. Donne , W. W. Heidbrink, N. C. Luhmann, Jr., T. Munsat, C. M. Muscatello, R. Nazikian, H. K. Park, D. A. Spong,9 A. D. Turnbull, M. A. Van Zeeland, G. S. Yun, and DIII-D Team, On the application of electron cyclotron emission imaging to the validation of theoretical models of magnetohydrodynamic activity, Phys. of Plasmas, v. 18, 056107 (2011).

Gyrokinetic simulation of magnetic compressional modes in general geometry, Peter Porazik and Zhihong Lin, Commun. Comput. Phys. 10, 899 (2011).

Gyrokinetic particle simulation of drift-compressional modes in dipole geometry, Peter Porazik and Zhihong Lin, Phys. Plasmas 18, 072107 (2011).

Transport of energetic ions due to sawteeth, Alfven eigenmodes and microturbulence, D. C. Pace et al, Nuclear Fusion 51, 043012 (2011).

Liu, Da-Jiang

Dapeng Jing, Yong Han, BariÅŸ ?nal, J. W. Evans, and P. A. Thiel, Formation of irregular Al islands by room- temperature deposition on NiAl(110), MRS Proc. 1318, 73 (2011).

Yong Han, Dapeng Jing, BarÉªÅŸ ?nal, P. A. Thiel, and J. W. Evans, Far-from-equilibrium film growth on alloy surfaces: Ni and Al on NiAl(110), Phys. Rev. B 84, 113414 (2011).

Yong Han, BarÉªÅŸ ?nal, Dapeng Jing, P. A. Thiel, and J. W. Evans, Temperature-dependent growth shapes of Ni nanoclusters on NiAl(110), J. Chem. Phys. 135, 084706 (2011).

T. Duguet, Yong Han, Chad Yuen, Dapeng Jing, BarÉªÅŸ ?nal, J. W. Evans, and P. A. Thiel, Self-assembly of metal nanostructures on binary alloy surfaces, Proc. Nat. Acad. Sci. 108, 989 (2011).

T. Duguet, B. ?nal, Y. Han, J. W. Evans, J. Ledieu, C. J. Jenks, J. M. Dubois, V. Fourn?e, and P. A. Thiel, Variation of growth morphology with chemical composition of terraces: Ag on a twofold surface of a decagonal Al-Cu-Co quasicrystal, Phys. Rev. B 82, 224204 (2010).

Yong Han, and Da-Jiang Liu, Shell structure and phase relations in electronic properties of metal nanowires from an electron-gas model, Phys. Rev. B 82, 125420 (2010).

J. W. Evans, Yong Han, BarÉªÅŸ ?nal, Maozhi Li, K. J. Caspersen, Dapeng Jing, A. R. Layson, C. R. Stoldt, Thomas Duguet, and P. A. Thiel, From initial to late stages of epitaxial thin film growth: STM analysis and atomistic or coarse-grained modeling, AIP Conf. Proc. 1270, 26 (2010).

Nanoscale "quantum" islands on metal substrates: microscopy studies and electronic structure analyses, Yong Han, BarÄ±ÅŸ ?nal, Dapeng Jing, Patricia A. Thiel, James W. Evans, and Da-Jiang Liu, Materials 3, 3965 (2010).

Maozhi Li, Yong Han, and J. W. Evans, Comment on "Capture-zone scaling in island nucleation: Universal fluctuation behavior", Phys. Rev. Lett. 104, 149601 (2010).

Yong Han, BarÉªÅŸ ?nal, Dapeng Jing, Feili Qin, C. J. Jenks, Da-Jiang Liu, P. A. Thiel, and J. W. Evans,Formation and coarsening of Ag(110) bilayer islands on NiAl(110): STM analysis and atomistic lattice-gas modeling, Phys. Rev. B 81, 115462 (2010).

Liu, Feng

Hepeng Ding, Anil V. Virkar1 and Feng Liu, Defect configuration and phase stability of cubic versus tetragonal yttria- stabilized zirconia Solid State Ionics (to be submitted)

Hepeng Ding Meilin Liu, Anil V. Virkar, Feng Liu. First principles study on Sr surface segregation in La0.5Sr0.5Co0.25Fe0.75O3

X. B. Niu, G. B. Stringfellow, and Feng Liu "Nonequilibrium Composition Profiles of Alloy Quantum Dots and their Correlation with the Growth Mode", Phys. Rev. Lett. 107, 076101 (2011)

Z. F. Wang, Y. Zhang, and Feng Liu Formation of hydrogenated graphene nanoripples by strain engineering and directed surface self-assembly , Phys. Rev. B 83, 041403(R) (2011).

J. Zhu, Feng Liu, G. B. Stringfellow, and S.-H. Wei Strain-Enhanced Doping in Semiconductors: Effects of Dopant Size and Charge State , Phys. Rev. Lett. 105, 195503 (2010).

Zheng Liu, Chao- Xing Liu, Yong- Shi Wu, Wen- Hui Duan, Feng Liu, and Jian Wu "Stable nontrivial Z_2 topology in ultrathin Bi (111) films: A first-principles study" Phys. Rev. Lett. (2011, in press)

M. Huang, F. Cavallo, Feng Liu and M. G. Lagally Nanomechanical Architecture of Semiconductor Nanomembranes , Nanoscale, 3, 96 (2011)

Liu, Jian

Jian Liu and William H. Miller, ?On short-time and long-time behaviors of various approximate quantum approaches: A study on large molecular systems? (in preparation)

Jian Liu, William H. Miller, Georgios S. Fanourgakis, Sotiris S. Xantheas, Imoto Sho, and Shinji Saito ?Insights in quantum dynamical effects in the Infrared spectroscopy of liquid water from a semiclassical study with an ab initio-based flexible and polarizable force field? Journal of Chemical Physics,135, 244503 (2011)

Jian Liu, Berni J. Alder, and William H. Miller, ?A semiclassical study of the thermal conductivity of low temperature liquids? Journal of Chemical Physics, 135, 114105 (2011) [This paper was selected in Research Highlights of J. Chem. Phys. on Sept. 23, 2011. http://jcp.aip.org/feed/research_highlights This paper was also listed in the top 20 most downloaded articles in September 2011.]

Jian Liu, ?Two more approaches for generating trajectory-based dynamics which conserves the canonical distribution in the phase space formulation of quantum mechanics" Journal of Chemical Physics, 134, 194110 (2011)

Jian Liu and William H. Miller, ?Three approaches for generating trajectory-based dynamics which conserves the canonical distribution in the phase space formulation of quantum mechanics: II. Thermal Correlation Functions? Journal of Chemical Physics, 134, 104102 (2011) [This paper was listed in the top 20 most downloaded articles in March 2011. http://jcp.aip.org/features/most_downloaded?month=3&year=2011]

Jian Liu and William H. Miller, ?An approach for generating trajectory-based dynamics which conserves the canonical distribution in the phase space formulation of quantum mechanics: I. Theories? Journal of Chemical Physics, 134, 104101 (2011) [This paper was also listed in the top 20 most downloaded articles in March 2011. http://jcp.aip.org/features/most_downloaded? month=3&year=2011]

Jian Liu, William H. Miller, Francesco Paesani, Wei Zhang, and David Case, ?Quantum dynamical effects in liquid water: A semiclassical study on the diffusion and the infrared absorption spectrum? Journal of Chemical Physics, 131, 164509 (2009) [This paper has been selected for the November 1, 2009 issue of Virtual Journal of Biological Physics Research.]

Jian Liu and William H. Miller, ?A simple model for the treatment of imaginary frequencies in chemical reaction rates and molecular liquids?, Journal of Chemical Physics, 131, 074113 (2009) [This paper has been selected by the Editors of the Journal of Chemical Physics in a list of ?a few of the many notable JCP articles published in 2009 that present ground-breaking research?. See Editors? Choice ? 2009, http://jcp.aip.org/jcp/editors_choices_2009]

Liu, Keh-Fei

Anyi Li, Andrei Alexandru, Keh-Fei Liu, and Xiangfei Meng, `Finite density phase transition of QCD with $N_f=4$ and $N_f=2$ using canonical ensemble method', Phys. Rev. D82, 054502 (2010).

S. Prelovsek, T. Draper, C.B. Lang, M. Limmer, K.-F. Liu, N. Mathur, and D. Mohler, `Lattice study of light scalar tetraquarks with I=0,2,1/2,3/2: are sigma and kappa tetraquarks?', Phys. Rev. D82, 094507 (2010).

A. Li, A. Alexandru, Y. Chen, T. Doi, S.J. Dong, T. Draper, M. Gong, A. Hasenfratz, I. Horvath, F.X. Lee, K.F. Liu, N. Mathur, T. Streuer, and J.B. Zhang, `Overlap Valence on 2+1 Flavor Domain Wall Fermion Configurations with Deflation and Low-mode Substitution', Phys. Rev. D82, 114501 (2010).

Anyi Li, Andrei Alexandru, and Keh-Fei Liu, `Critical point of $N_f = 3$ QCD from lattice simulations in the canonical ensemble', Accepted for publication in Phys. Rev. D.

Liu, Ping

J. X. Wang, C. Ma, Y. Choi, D. Su, Y. Zhu, P. Liu, R. Si, R. R. Adzic, "Kirkendall effect and lattice contraction in nanocatalysts: a new stratege to enhance sustainable activity", Journal of the American Chemical Society, 133 (2011) 13551-13557.

L. Yang, Y. Choi, W. Qin, H. Chen, K. Blinn, M. Liu, P. Liu, J. Bai, T. A. Tyson, M. Liu, "Promotion of water-mediated carbon removal by nanostructured barium oxide/nickel interfaces in solid oxide fuel cells", Nature Communications, doi:10.1038/ncomms1359.

K. Kuttiyiel, K. Sasaki, Y. Choi, D. Su, P. Liu, R. R. Adzic, "Bimetallic IrNi core platinum monolayer shell electrocatalysts for the oxygen reduction reaction", Energy & Environmental Science, in press.

Y. Choi, P. Liu, "Understanding of ethanol decomposition on Rh(111) from density functional theory and kinetic Monte Carlo simulations", Catalysis Today (2011) 165, 64-70 (invited paper).

F. Yang, Y. Choi, P. Liu, D. Stacchiola, J. Hrbek, J. A. Rodriguez, Identification of 5-7 defects in a copper oxide surface, Journal of the American Chemical Society 133 (2011) 11474-11477.

Louie, Steven

B.-C. Shih, Y. Xue, P. Zhang, M.L. Cohen, and S.G. Louie, 'Quasiparticle band gap of ZnO: High accuracy from the conventional G0W0 approach,' Phys. Rev. Lett. 105, 146401 (2010).

J. Noffsinger, F. Giustino, B.D. Malone, C.-H. Park, S.G. Louie, and M.L. Cohen, 'EPW: A program for calculating the electron-phonon coupling using maximally localized Wannier functions,' Comput. Phys. Comm. 181, 2140 (2010).

H.K. Lee, M.L. Cohen, and S.G. Louie, 'Selective functionalization of halogens on zigzag graphene nanoribbons: A route to the separation of zigzag graphene nanoribbons,' Appl. Phys. Letters 97, 233101 (2010).

F. Giustino, S.G. Louie, and M.L. Cohen, 'Electron-phonon renormalization of the direct band gap of diamond,' Phys. Rev. Lett. 105, 265501 (2010).

B.S. Geng, J. Horng, Y.B. Zhang, T.T. Tang, C.-H. Park, C. Girit, Z. Lao, M. Martin, A. Zettl, M.F. Crommie, S.G. Louie, and F. Wang, 'Optical Spectroscopy of Bilayer Graphene,' Physica Stat. Solidi B 247, 2931 (2010).

E. Kioupakis, M.L. Tiago, and S.G. Louie, 'Quasiparticle Electronic Structure of Bismuth Telluride in the GW Approximation,' Phys. Rev. B 82, 245203 (2010).

O.V. Yazyev, J.E. Moore, and S.G. Louie, 'Spin Polarization and Transport of Surface States in the Topological Insulators Bi2Se3 and Bi2Te3 from First Principles,' Phys. Rev. Lett. 105, 266806 (2010).

V.W. Brar, R. Decker, H.-M. Solowan, Y. Wang, L. Maserati, K.T. Chan, H. Lee, C.O. Girit, A Zettl, S.G. Louie, M.L. Cohen, and M.F. Crommie, 'Gate-controlled Ionization and Screening of Cobalt Adatoms on a Graphene Surface,' Nature Physics 7, 43 (2011).

C.-H. Park, L.Z. Tan, and S.G. Louie, 'Theory of the Electronic and Transport Properties of Graphene Under a Periodic Electric or Magnetic Field,' Physica E 43, 651 (2011).

S.Y. Quek, H.J. Choi, S.G. Louie, and J.B. Neaton, 'Thermopower of Amine Gold-linked Aromatic Molecular Junctions from First Principles,' ACS Nano 5, 551 (2011).

N. Alem et.al., 'Probing the Out-of-Plane Distortion of Single Point Defects in Atomically Thin Hexagonal Boron Nitride at the Picometer Scale,' Phys. Rev. Lett. 106, 126102 (2011).

C.-F. Chen, C.-H. Park, B.W. Boudouris, J. Horng, B. Geng, C. Girit, A. Zettl, M.F. Crommie, R.A. Segalman, S.G. Louie, and F. Wang, 'Controlling Inelastic Light Scattering Quantum Pathways in Graphene,' Nature 471, 617 (2011).

H. Oh, H.J. Choi, S.G. Louie, and M.L. Cohen, 'Fermi Surfaces and Quantum Oscillations in the Underdoped High-Tc Superconductors YBa2Cu3O6.5 and YBa2Cu4O8,' Phys. Rev. B 84, 014518(2011).

D.A. Siegel, C.-H. Park, C. Hwang, J. Deslippe, A.V. Federov, S.G. Louie, and A. Lanzara, 'Many-body Interactions in Quasi-freestanding Graphene,' Proc. Natl. Acad. Sci. U.S.A. 108 11365 (2011).

L.Z. Tan, C.-H. Park, and S.G. Louie, 'New Dirac Fermions in Periodically Modulated Bilayer Graphene,' Nano Lett. 11 2596 (2011).

C. Tao, L. Jiao, O.V. Yazyev, Y.-C. Chen, J. Feng, X. Zhang, R.B. Capaz, J.M. Tour, A. Zettl, S.G. Louie, H. Dai, and M.F. Crommie, 'Spatially Resolving Edge States of Chiral Graphene Nanoribbons,' Nature Physics 7, 616 (2011).

H.C. Hsueh, G.Y. Guo, and S.G. Louie, 'Excitonic Effects in the Optical Properties of an SiC Sheet and Nanotubes,' Phys. Rev. B 84, 85404 (2011).

G.P. Zhang, D.A. Strubbe, S.G. Louie, and T.F. George, 'First-principles Prediction of Optical Second-order Harmonic Generation in the Endohedral N@C60 Compound,' Phys. Rev. A, 023837 (2011).

Lukin, Vyacheslav

T. Gray, V. S. Lukin, M. R. Brown, and C. D. Cothran, "Three-dimensional reconnection and relaxation of merging spheromak plasmas", Physics of Plasmas (2010).

Luzar, Alenka

C. D. Daub, D. Bratko, A. Luzar, Nanoscale Wetting Under Electric Field from Molecular Simulations, Top. Curr. Chem. (2011) DOI: 10.1007/128_2011_188

J. Wang, D. Bratko, A. Luzar, Length-scale dependence of hydration free energy: effect of solute charge, J. Stat. Phys. (2011) DOI 10.1007/s10955-011-0337-1

M

Ma, Chung-Pei

J. DeBuhr, E. Quataert, and C.-P. Ma (2011), Monthly Notices of the Royal Astronomical Society, submitted.

Galaxy-Scale Outflows Driven by Active Galactic Nuclei J. DeBuhr, E. Quataert, and C.-P. Ma (2011), MNRAS, 412, 1341

The Growth of Massive Black Holes in Galaxy Merger Simulations with Feedback by Radiation Pressure J. DeBuhr, E. Quataert, C.-P. Ma, and P. Hopkins (2010), MNRAS, 406, L55

Self-Regulated Black Hole Growth via Momentum Deposition in Galaxy Merger Simulations

Maginn, Edward

"Force field development for uranyl systems", N. Rai and E. J. Maginn, 241st National Meeting and Exposition of the American-Chemical-Society (ACS), Anaheim, CA Date: MAR 27-31, 2011

Abstracts of the American Chemical Society, Volume: 241, Meeting Abstract: 75-NUCL (MAR 27 2011)

Mahanti, S. D.

Mal-Soon Lee, Ferdinand P. Poudeu, and S. D. Mahanti, Electronic structure and thermoelectric properties of Sb-based semiconducting half-Heusler compounds, Phys. Rev. B 83, 085204 (2011).

Dat Do, Mal-Soon Lee, and S. D. Mahanti, Effect of onsite Coulomb repulsion on thermoelectric properties of full-Heusler compounds with pseudogaps, Phys. Rev. B 84, 215104 (2011).

Manson, Steven

Overlapping Resonances in Atomic Ions, W.-C. Chu, H.-L. Zhou, A. Hibbert and S. T. Manson, Phys. Rev. A 82, 013417-1-4 (2010).

Inner Shell Photodetachment of Na- Using the Multi-Configuration Tamm-Dancoff Approximation, J. Jose, G. B. Pradhan, V. Radojevic, S. T. Manson, and P. C. Deshmukh, Publ. Astron. Obs. Belgrade 89, 29-32 (2010).

Photoionization of potassium-like transition metal ions: Ti3+ to Fe7+, A. M. Sossah, H.-L. Zhou, S. T. Manson, Phys. Rev. A 82, 043416-1-13 (2010).

Electron-Impact Ionization of Atoms: Secondary Electron Angular Distributions and Drag Currents, A. S. Baltenkov, S. T. Manson and A. Z. Msezane, Cent. Eur. J. Phys. 9, 1209-1220 (2011).

Valence photodetachment of Li- and Na- using relativistic many-body techniques, J. Jose, G. B. Pradhan, V. Radojevi, S. T. Manson, and P.C. Deshmukh, Phys. Rev. A 85, 053419-1-7 (2011).

Cooper Minima: A Window on Nondipole Photoionization at Low Energy, G. B. Pradhan, J. Jose, P. C. Deshmukh, L. A. LaJohn, R. H. Pratt, and S. T. Manson, J. Phys. B (in press).

Electron correlation effects near the photoionization threshold: The Ar isoelectronic sequence, J. Jose, G. B. Pradhan, V. Radojevi , S. T. Manson, and P.C. Deshmukh, J. Phys. B 44, 195008-1-8 (2011).

Magnetic dichroism in K-shell photoemission from laser excited Li atoms, M. Meyer, A. N. Grum-Grzhimailo, D. Cubaynes, Z. Felfli, E. Heinecke, S. T. Manson, and P. Zimmermann, Phys. Rev. Letters (in press).

Marques, Osni

L. A. Drummond and O. A. Marques. The ACTS Information Center, http://acts.nersc.gov.

Calvin, L. Decobert, J. Dubois and S. Petiton. Hybrid eigenvalue solver using a linear algebra framework for multi-core accelerated petascale supercomputer. 15th SIAM Conference on Parallel Processing for Scientific Computing

L. Anthony Drummond, Vicente Galiano, Violeta Migall n, Jos Penad s: Interfaces for parallel numerical linear algebra libraries in high level languages. Advances in Engineering Software 40(8): 652- 658 (2009)

L. Anthony Drummond, Vicente Galiano, Violeta Migall n, Jos Penad s: PyACTS: A Python Based Interface to ACTS Tools and Parallel Scientific Applications. International Journal of Parallel Programming 37(1): 58-77 (2009)

D. De Cecchis, L.A. Drummond, J.E. Castillo. Design of a Distributed Coupling Toolkit for High Performance Computing environment. Mathematical and Computer Modelling, Available online 18 July 2011

Masunov, Artem

Workalemahu M. Berhanu Artem E. Masunov (2011) Unique example of amyloid aggregates stabilized by main chain H-bond instead of the steric zipper: Molecular dynamics study of the amyloidogenic segment of amylin wild-type and mutants (NNFGAIL) segment of amylin aggregate. Journal of Molecular Modeling, published online: 28 May 2011; DOI 10.1007/s00894-011-1030-7

Workalemahu M. Berhanu Artem E. Masunov (2011) Molecular dynamic simulation of wildtype and mutants of the polymorphic amyloid NNQNTF segments of elk prion: structural stability and thermodynamic of association. Biopolymers. 95,573-590

Workalemahu M. Berhanu Artem E. Masunov (2011). Insights into the full length amylin oligomer aggregation and its implication for design of aggregation inhibitors; a molecular dynamics simulation study. Journal of Molecular Modeling and Graphics. Submitted and under review

Workalemahu M. Berhanu Artem E. Masunov (2011) Alternative packing modes as basis for amyloid polymorphismin five fragments Peptide Science. Accepted

Workalemahu M. Berhanu Artem E. Masunov.(2011)The atomic level interaction of polyphenols (Curcumin, Exifone and Myricetin) with the oligomer aggregate of VQIVYK segment from tau peptide: A molecular dynamic study. Journal of Molecular Modeling. Submitted and under review

Workalemahu M. Berhanu Artem E. Masunov. Comparative molecular dynamic study of human amylin, pramlintide and rat amylin aggregates. Biopolymers. To be submitted

Workalemahu M. Berhanu Artem E. Masunov (2011) Control over aggregation stability and fast release for improving the insulin formulation: Molecular Dynamics study of the amyloid oligomer models. Journal of Molecular Modeling, published online: 15 June 2011; DOI 10.1007/s00894-011-1123-3

Workalemahu M. Berhanu Artem E. Masunov (2011) Can Molecular Dynamics Simulations assist in design of specific inhibitors and imaging agents of amyloid aggregation? Structure, stability and free energy predictions for amyloid oligomers of VQIVYK, MVGGVV and LYQLEN. Journal of Molecular Modeling, Published online: 21 Dec. 2010; DOI 10.1007/s00894-010-0912-4

Author(s): Gangopadhyay Shruba; Masunov Artem E.; Poalelungi Eliza; et al. Title: Weak antiferromagnetic coupling in molecular ring is predicted correctly by density functional theory plus Hubbard U Source: JOURNAL OF CHEMICAL PHYSICS Volume: 132 Issue: 24 Article Number: 244104 DOI: 10.1063/1.3421645 Published: JUN 28 2010

Inerbaev, T. M.; Seal, S.; Masunov, A. E., Density functional study of oxygen vacancy formation and spin density distribution in octahedral ceria nanoparticles. Journal of Molecular Modeling 2010, 16, (10), 1617-1623.

Babu, S.; Thanneeru, R.; Inerbaev, T.; Day, R.; Masunov, A. E.; Schulte, A.; Seal, S., Dopant-mediated oxygen vacancy tuning in ceria nanoparticles. Nanotechnology 2009, 20, (8), 5.

Vincent, A.; Babu, S.; Heckert, E.; Dowding, J.; Hirst, S. M.; Inerbaev, T. M.; Self, W. T.; Reilly, C. M.; Masunov, A. E.; Rahman, T. S.; Seal, S., Protonated nanoplarticle surface governing ligand tethering and cellular targeting. ACS Nano 2009, 3, (5), 1203-1211.

Vincent, A.; Inerbaev, T. M.; Babu, S.; Karakoti, A. S.; Self, W. T.; Masunov, A. E.; Seal, S., Tuning hydrated nanoceria surfaces: Experimental/theoretical investigations of ion exchange and implications in organic and inorganic interactions. Langmuir 2010, 26, (10), 7188-7198.

Kuchma, M. H.; Komanski, C. B.; Colon, J.; Teblum, A.; Masunov, A. E.; Alvarado, B.; Babu, S.; Seal, S.; Summy, J.; Baker, C. H., Phosphate ester hydrolysis of biologically relevant molecules by cerium oxide nanoparticles. Nanomedicine-Nanotechnology Biology and Medicine 2010, 6, (6), 738-744.

J Patel, Pansy D.; Masunov, Artem E. Theoretical Study of Photochromic Compounds: Part 3. Prediction of Thermal Stability JOURNAL OF PHYSICAL CHEMISTRY C 115 20 10292 10297 10.1021/jp200980v MAY 26 2011 2011 0 0 1932-7447 WOS:000290652200059

J Masunov, Artem E. Theoretical Spectroscopy of Carbocyanine Dyes Made Accurate by Frozen Density Correction to Excitation Energies Obtained by TD-DFT INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 110 15 SI 3095 3100 10.1002/qua.22923 DEC 2010 2010 1 1 0020-7608 WOS:000283761900038

J Belfield, Kevin D.; Bondar, Mykhailo V.; Frazer, Andrew; Morales, Alma R.; Kachkovsky, Oleksiy D.; Mikhailov, Ivan A.; Masunov, Artem E.; Przhonska, Olga V. Fluorene-Based Metal-Ion Sensing Probe with High Sensitivity to Zn(2+) and Efficient Two-Photon Absorption JOURNAL OF PHYSICAL CHEMISTRY B 114 28 9313 9321 10.1021/jp104450m JUL 22 2010 2010 4 4 1520-6106 WOS:000279787400026

Mavrikakis, Manos

J. Knudsen, L. R. Merte, L. C. Grabow, F. M. Eichhorn, S. Porsgaard, H. Zeuthen, R. T. Vang, E. Laegsgaard, M. Mavrikakis and F. Besenbacher, "Reduction of FeO/Pt(111) thin films by exposure to atomic hydrogen", Surface Science 604, 11 (2010).

S. Kandoi, P. Ferrin, and M. Mavrikakis, "Hydrogen on and in selected overlayer near-surface alloys and the effect of subsurface hydrogen on the reactivity of alloy surfaces", Topics in Catalysis 53, 384 (2010).

M. Ojeda, R. Nabar, A. U. Nilekar, A. Ishikawa, M. Mavrikakis, and E. Iglesia, "CO activation pathways and the mechanism of the Fischer-Tropsch synthesis", Journal of Catalysis 272, 287 (2010).

A. U. Nilekar, S. Alayoglu, B. Eichhorn, and M. Mavrikakis, "Preferential CO oxidation in hydrogen: Reactivity of core-shell nanoparticles", Journal of the American Chemical Society 132, 7418 (2010).

D. C. Ford, A. U. Nilekar, Y. Xu, and M. Mavrikakis, "Partial and complete reduction of O2 by hydrogen on transition metal surfaces", Surface Science 604, 1565 (2010).

J. Knudsen, L. R. Merte, G. W. Peng, R. T. Vang, A. Resta, E. Laegsgaard, J. N. Andersen, M. Mavrikakis, F. Besenbacher, "Low-Temperature CO Oxidation on Ni(111) and on a Au/Ni(111) Surface Alloy", ACS Nano 4, 4380 (2010). HIGHLIGHTED IN THE JOURNAL COVER.

G. Peng, L. R. Merte, J. Knudsen, R. T. Vang, E. Laegsgaard, F. Besenbacher, M. Mavrikakis, "On the Mechanism of Low-Temperature CO Oxidation on Ni(111) and NiO(111) Surfaces", Journal of Physical Chemistry C 114, 21579 (2010).

S. L. Knupp, M. B. Vukmirovic, P. Haldar, J. A. Herron, M. Mavrikakis, R. R. Adzic, "Platinum Monolayer Electrocatalysts for O2 Reduction: Pt Monolayer on Carbon-Supported PdIr Nanoparticles", Electrocatalysis 1, 213 (2010).

Y. P. Zhai, D. Pierre, R. Si, W. L. Deng, P. Ferrin, A. U. Nilekar, G. W. Peng, J. A. Herron, D. C. Bell, H. Saltsburg, M. Mavrikakis, M. Flytzani-Stephanopoulos, "Alkali-Stabilized Pt-OHx Species Catalyze Low-Temperature Water-Gas Shift Reactions", Science 329, 1633 (2010).

S. Kandoi, J. Greeley, D. Simonetti, J. Shabaker, J. A. Dumesic, M. Mavrikakis, "Reaction Kinetics of Ethylene Glycol Reforming over Platinum in the Vapor versus Aqueous Phases", Journal of Physical Chemistry C 115, 961 (2011).

L. R. Merte, L. C. Grabow, G. Peng, J. Knudsen, H. Zeuthen, W. Kudernatsch, S. Porsgaard, E. Laegsgaard, M. Mavrikakis, F. Besenbacher,"Tip-Dependent Scanning Tunneling Microscopy Imaging of Ultrathin FeO Films on Pt(111)", Journal of Physical Chemistry C 115, 2089 (2011).

L. C. Grabow, M. Mavrikakis, "Mechanism of Methanol Synthesis on Cu through CO2 and CO Hydrogenation", ACS Catalysis 1, 365 (2011).

L. R. Merte, J. Knudsen, F. M. Eichhorn, S. Porsgaard, H. Zeuthen, L. C. Grabow, E. Laegsgaard, H. Bluhm, M. Salmeron, M. Mavrikakis, F. Besenbacher, "CO-Induced Embedding of Pt Adatoms in a Partially Reduced FeOx Film on Pt(111)", Journal of the American Chemical Society 133, 10692 (2011).

McAdams, Harley

AlQuraishi M and McAdams HH (2011) Direct inference of protein-DNA interactions using compressed sensing methods. Proc Natl Acad Sci USA 08:14819-14824. The above article was one of the papers highlighted on the cover of the 9/6/11 issue of PNAS and ran with an associated commentary by Vijay Pande.

McCurdy, C. William

Multiconfiguration time-dependent Hartree-Fock treatment of electronic and nuclear dynamics in diatomic molecules D. J. Haxton, K. V. Lawler, and C. W. McCurdy Phys. Rev. A 83, 063416 (2011)

Mei, Donghai

Mei, D., Du, J. and Neurock, M. First-principles-based kinetic Monte Carlo simulation of nitric oxide reduction over platinum nanoparticles under lean-burn conditions , Ind. Eng. Chem. Res., 49, 10364-10373. (2010)

Mudiyanselage, K., Mei, D., Yi, C. W., Weaver, J. F. and Szanyi, J. Formation, characterization, and reactivity of adsorbed oxygen on BaO/Pt(111) , J. Phys. Chem. C, 114, 20195-20206. (2010)

Kou, R., Shao, Y., Mei, D., Nie, Z., Wang, D., Wang, C. M., Viswanathan, V. V., Park, S., Aksay, I. A., Lin, Y., Wang, Y. and Liu, J. Stabilization of electrocatalytic metal nanoparticles at metal-metal oxide-graphene triple junction points , J. Am. Chem. Soc., 133, 2541-2547. (2011)

Mei, D., Karim, A. M. Wang, Y. Density functional theory study of acetaldehyde hydrodeoxygenation on MoO3 , J. Phys. Chem. C, 115, 8155-8164. (2011)

Mei, D. and Guang, L. Effects of heat and mass transfer on the kinetics of CO oxidation over RuO2(110) catalyst , Catal. Today, 165, 56-63. (2011)

Ling, S. L., Mei, D. and Gutowski, M. Reactivity of hydrogen and methanol on (001) surfaces of WO3, ReO3, WO3/ReO3 and ReO3/WO3 , Catal. Today, 165, 41-48. (2011)

Kwak, J. H., Mei, D., Peden, C. H. F., Rousseau, R. and Szanyi, J. (100) facets of -Al2O3: The active surfaces for alcohol dehydration reactions , Catal. Lett., 141, 649-655 (2011)

Andersen, A., Kathmann, A. M., Lilga, M. A., Albrecht, K. O., Hallen, R. T. and Mei, D. Adsorption of potassium on the MoS2(100) surface: A first-principles investigation , J. Phys. Chem. C., 115, 9025-9040. (2011)

Zhao, Y. F.; Yang, Y.; Mims, C.; Peden, C. H. F.; Li, J. and Mei, D.* Insight into methanol synthesis from CO2 hydrogenation on Cu(111): Complex reaction network and the effects of H2O , J. Catal., 281, 199-211. (2011)

Pan, Y. X.; Mei, D.; Liu, C. J. and Ge, Q. F. Hydrogen adsorption on Ga2O3 surface: A combined experimental and computational study , J. Phys. Chem. C, 115, 10140-10146 (2011)

Kwak, J. H.; Rousseau, R. J.; Mei, D.; Peden, C. H. F. and Szanyi, J. The origin of regioselectivity in 2-butanol dehydration on solid acid catalysts , ChemCatChem, DOI: 10.1002/cctc.201100173, (2011)

Lebarbier, V.; Mei, D.; Kim, D. H.; Andersen, A.; Male, J.; Holladay, J. E.; Rousseau, R. and Wang, Y. Effects of La2O3 on the Mixed Higher Alcohols Synthesis from Syngas over Co Catalysts: A Combined Theoretical and Experimental Study , J. Phys. Chem. C., 115, 17440-17451. (2011)

Mellor-Crummey, John

[Jin et al. IPDPS 2011] G. Jin, L. Adhianto, J. Mellor-Crummey, W. N. Scherer III, and C. Yang. Implementation and Performance Evaluation of the HPC Challenge Benchmarks in Coarray Fortran 2.0. In 25th IEEE International Parallel and Distributed Processing Symposium (IPDPS 2011), May 2011.

[Scherer et al. PGAS 2010] W. N. Scherer III, L. Adhianto, G. Jin, J. Mellor-Crummey, and C. Yang. Hiding Latency in Coarray Fortran 2.0. In 4th Conference on Partitioned Global Address Space (PGAS) Programming Models (PGAS 2010), October 2010.

Mikkelsen, David

W. Guttenfelder, J. Candy, S.M. Kaye, W.M. Nevins, E. Wang, R.E. Bell, G.W. Hammett, B.P. LeBlanc, D.R. Mikkelsen, H. Yuh, Electromagnetic transport from microtearing mode turbulence, Phys. Rev. Lett. 106, 155004 (2011).

E. Wang, W.M. Nevins, J. Candy, D. Hatch, P.W. Terry, W. Guttenfelder, Electron heat transport from stochastic fields in gyrokinetic simulations, Phys. Plasmas 18, 056111 (2011).

W. Guttenfelder, J. Candy, Resolving electron scale turbulence in spherical tokamaks with flow shear, Phys. Plasmas 18, 022506 (2011).

A. E. White, N T Howard, D R Mikkelsen, M J Greenwald, J Candy and R E Waltz, "Feasibility study for a correlation electron cyclotron emission turbulence diagnostic based on nonlinear gyrokinetic simulations " has been accepted for publication in Plasma Physics and Controlled Fusion.

Miller, Thomas

Goodpaster JD, Ananth N, Manby FR, and Miller TF. Exact non-additive kinetic energies for orbital-free density functional theory. J. Chem. Phys., 133 (2010) 084103.

Ananth N and Miller TF. Exact quantum statistics for electronically nonadiabatic systems using continuous path variables. J. Chem. Phys., 133 (2010) 234103.

Goodpaster JD, Barnes TA, and Miller TF. Embedded density functional theory for covalently bonded and strongly interacting subsystems. J. Chem. Phys., 134 (2011) 164108.

Menzeleev AR, Ananth N, and Miller TF. Direct simulation of electron transfer using ring polymer molecular dynamics: Comparison with semiclassical instanton theory and exact quantum methods. J. Chem. Phys., 135 (2011) 074106.

Boekelheide N, Salomon-Ferrer R, and Miller TF. Dynamics and dissipation in enzyme catalysis. Proc. Natl. Acad. Sci. USA, in press.

Miller, William

D. W. H. Swenson, T. Levy, G. Cohen, E. Rabani and W. H. Miller, Application of a Semiclassical Model for the Second-Quantized Many-Electron Hamiltonian to Nonequilibrium Quantum Transport: The Resonant Level Model, J. Chem. Phys. 134, 164103, (2011)

G. Tao and W. H. Miller, Time-Dependent Importance Sampling in Semiclassical Initial Value Representation Calculations for Time Correlation Functions, J. Chem. Phys. 135, 024104, (2011)

Jian Liu, Berni J. Alder, and William H. Miller, A semiclassical study of the thermal conductivity of low temperature liquids Journal of Chemical Physics, 135, 114105, (2011)

Jian Liu, Two more approaches for generating trajectory-based dynamics which conserves the canonical distribution in the phase space formulation of quantum mechanics Journal of Chemical Physics, 134, 194110 (2011)

Jian Liu and William H. Miller, An approach for generating trajectory-based dynamics which conserves the canonical distribution in the phase space formulation of quantum mechanics: II. Thermal correlation functions Journal of Chemical Physics, 134, 104102 (2011)

Jian Liu and William H. Miller, An approach for generating trajectory-based dynamics which conserves the canonical distribution in the phase space formulation of quantum mechanics: I. Theories Journal of Chemical Physics, 134, 104101 (2011)

Montgomery, Jason

Alfred J. Baca, Jason M. Montgomery, Lee R. Cambrea, Mark Moran, Linda Johnson, Jeanine Yacoub, and Tu T. Truong, Optimization of Nanopost Plasmonic Crystals for Surface Enhanced Raman Scattering. 115, 7171 (2011).

Mori, Warren

Theobald W.; Ovchinnikov V.; Ivancic S.; Eichman B.; Nilson P. M.; Delettrez J. A.; Yan R.; Li G.; Marshall F. J.; Meyerhofer D. D.; Myatt J. F.; Ren C.; Sangster T. C.; Stoeckl C.; Zuegel J. D.; Van Woerkom L.; Freeman R. R.; Akli K. U.; Giraldez E.; Stephens R. B., High-intensity laser-plasma interaction with wedge-shaped-cavity targets, Phys. Plasmas 17, 103101 (2010)

X. Kong, M. C. Huang, C. Ren, and V. K. Decyk, Particle-in-cell simulations with charge- conserving current deposition on graphic processing units, Journal of Computational Physics 230, 1676 (2011)

G. Li, R. Yan, C. Ren, J. Tonge, and W. B. Mori, Three-dimensional particle-in-cell simulations of laser channeling in fast ignition, Phys. Plasmas 18, 042730 (2011)

Jared C. Workman1, Eric G. Blackman, and Chuang Ren, "Simulations reveal fast mode shocks in magnetic reconnection outflows," Phys. Plasmas 18, 092902 (2011)

B. B. Pollock et al, Demonstration of a narrow energy spread, 0.5GeV electron beam from a two-stage Laser Wakefield Accelerator , Phys. Rev. Lett., 107, 045001 (2011).

J.Vieira, C.-K. Huang, W.B. Mori, L.O. Silva, Polarized beam conditioning in plasma based acceleration, Phys. Rev. ST-AB 14 071303 (2011)

A. W. Davidson, W. Lu, C. Joshi, L.O. Silva, J. Martins, R. A. Fonseca, W.B. Mori, Numerical Study of Self and Controlled Injection in 3-Dimensional Laser-Driven Wakefields, Proceedings of the PAC-2011 Conference (2011)

Morris, James

Xing-Qiu Chen, Shibing Wang, Wendy Mao, and C. L. Fu, "Pressure-induced behavior of the hydrogen-dominant compound SiH4(H2)2 from first-principles calculation," Phys. Rev. B 82, 104115 (2010).

V. A. Levashov, J. R. Morris, T. Egami, "Viscosity and Atomic Level Stress Correlations in a Model Metallic Liquid," Phys. Rev. Letters 106, 115703 (2011).

V. Wessels, A.K. Gangopadhyay, K.K. Sahu, R.W. Hyers, S.M. Canepari, J.R. Rogers, M.J. Kramer, A.I. Goldman, D. Robinson, J. W. Lee, J.R. Morris, K.F. Kelton, "Rapid Chemical Ordering in Supercooled Liquid Cu46Zr54," Editor's choice article, Phys. Rev. B 83, 094116 (2011).

Msezane, Alfred

Elastic scattering of slow electrons from Y, Ru, Pd, Ag and Pt atoms: search for nanocatalysts Felfli, A. Z. Msezane and d. sokolovski J. Phys. A: At. Mol. Opt. Phys. 44, 135204 (2011)

Low-energy electron elastic scattering from Mn, Cu, Zn, Ni, Ag and Cd atoms Z. Felfli, A. Z. Msezane and D. Sokolovski Phys. Rev. A 83, 052705 (2011)

Low-energy electron elastic collision cross sections for ground and excited Tm, Lu and Hf atoms Z. Felfli, A.Z. Msezane and D. Sokolovski Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, Volume 269, Issue 10, 15 May 2011, Pages 1046-1052

Novel mechanism for nanoscale catalysis Alfred Z. Msezane, Zineb Felfli and Dmitri Sokolovski J. Phys B: At. Mol. Opt. Phys. 43, 201001 (2010)(Fast Track)

Low-energy electron elastic scattering cross sections for excited Au and Pt atoms Z. Felfli, A. R. Eure A. Z. Msezane and D. Sokolovski Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, Volume 268, Issue 9, 1 May 2010, Pages 1370-1375

Complex angular momentum analysis of low-energy elastic scattering from lanthanide atoms Z. Felfli, A. z. Msezane and d. Sokolovski Phys. Rev. A 81, 042707 (2010)

Mundy, Christopher

"Re-examining the properties of the aqueous vapor liquid interface using dispersion corrected density functional theory," Marcel D. Baer, Christopher J. Mundy,Matthew J. McGrath , I. -F. Will Kuo, J. Ilja Siepmann, Douglas J. Tobias, JOURNAL CHEMICAL PHYSICS (IN PRESS)

"Does Nitric Acid Dissociate at the Aqueous Solution Surface," Tanza Lewis, Bernd Winter,Abraham C. Stern, Marcel D. Baer, Christopher J. Mundy,Douglas J. Tobias, and John C. Hemminger, THE JOURNAL OF PHYSICAL CHEMISTRY B, (IN PRESS)

"Dissociation of Strong Acid Revisited: X-ray Photoelectron Spectroscopy and Molecular Dynamics Simulations of HNO(3) in Water," Author(s): Lewis Tanza; Winter Bernd; Stern Abraham C.; et al. JOURNAL OF PHYSICAL CHEMISTRY B Volume 115, 9445-9451 (2011)

"Semiempirical Self-Consistent Polarization Description of Bulk Water, the Liquid-Vapor Interface, and Cubic Ice," Murdachaew Garold; Mundy Christopher J.; Schenter Gregory K.; et al. JOURNAL OF PHYSICAL CHEMISTRY A 115, 6046-6053 (2011)

"Toward an Understanding of the Specific Ion Effect Using Density Functional Theory," Baer Marcel D.; Mundy Christopher J., JOURNAL OF PHYSICAL CHEMISTRY LETTERS 2, 1088-1093 (2011

"Understanding the Surface Potential of Water," Kathmann Shawn M.; Kuo I-Feng William; Mundy Christopher J.; et al, JOURNAL OF PHYSICAL CHEMISTRY B 115, 4369-4377 (2011) [COVER ARTICLE]

L

Najm, Habib

Prager, J., Najm, H.N., Valorani, M., and Goussis, D.A.,"Structure of n-Heptane/Air Triple Flames in Partially-Premixed Mixing Layers", Combustion and Flame, in press.

Neaton, Jeffrey

S. Y. Quek, H. J. Choi, S. G. Louie, and J. B. Neaton, "Thermopower of Amine-Gold Linked Aromatic Molecular Junctions from First Principles", ACS Nano 5, 551 (2011)

E. B. Isaacs, S. Sharifzadeh, B. Ma, and J. B. Neaton, "Relating Trends in First-Principles Electronic Structure and Open-Circuit Voltage in Organic Photovoltaics", J. Phys. Chem. Lett. 2, 2531 (2011).

S. Yang, D. Prendergast, and J. B. Neaton, "Nonlinear variations in the electronic structure of II-VI and III-V wurtzite semiconductors with biaxial strain", Appl. Phys. Lett. 98, 152108 (2011)

J. Bhattacharjee and J. B. Neaton, "Interfacing Carbon Nanotubes of Arbitrary Chiralities into Linear Heterojunctions", Phys. Rev. B 83, 165432 (2011)

N. Adelstein, B. S. Mun, H. L. Ray, P. N. Ross, J. B. Neaton, and L. C. De Jonghe, "Structure and Electronic Properties of Cerium Orthophosphate: Theory and Experiment", Phys. Rev. B 83, 205104 (2011)

A. T. Zayak, Y. Hu, H. Choo, J. Bokor, S. Cabrini, P. J. Schuck, and J. B. Neaton, "Chemical Raman Enhancement for Organic Adsorbates at Metal Surfaces", Phys. Rev. Lett. 106, 083003 (2011)

Negele, John

C. Alexandrou, T. Korzec, G. Koutsou, C. Lorce, J. W. Negele, V. Pascalutsa, A. Tsapalis, M. Vanderhaeghen, "Quark transverse charge densities in the Delta(1232) from lattice QCD'', Nucl. Phys. A825 (2009) 115, arXiv:0901.3457 [hep-ph].

C. Alexandrou, T. Korzec, G. Koutsou, Th. Leontiou, C. Lorce, J. W. Negele, V. Pascalutsa, A. Tsapalis, M. Vanderhaeghen, "Delta-baryon electromagnetic form factors in lattice QCD'', Phys. Rev. D79 (2009) 014507 arXiv:0810.3976 [hep-lat].

C. Alexandrou, T. Korzec, G. Koutsou, J. W. Negele, Y. Proestos, "Electromagnetic form factors of the Omega- in lattice QCD'', Phys. Rev. D82 (2010) 034504 arXiv:1006.0558 [hep-lat].

C. Alexandrou, G. Koutsou, J. W. Negele, Y. Proestos, A. Tsapalis, "Nucleon to Delta transition form factors with Nf = 2+1 dynamical Domain-Wall fermions'', Phys. Rev. D83 (2011) 014501 arXiv:1011.3233 [hep-lat]

C. Alexandrou, E. B. Gregory, T. Korzec, G. Koutsou, J. W. Negele, T. Sato, A. Tsapalis, "The Delta(1232) axial charge and form factors from lattice QCD'', Phys. Rev. Lett. (in press) arXiv:1106.6000 [hep-lat].

B. U. Musch, Ph. Haegler, J. W. Negele, A Schaefer, "Exploring quark transverse momentum distributions with lattice QCD", Phys.Rev.D83:094507 (2011)

J. D. Bratt, R. G. Edwards, M. Engelhardt, Ph. Haegler, H.-W. Lin, M.-F. Lin, H. B. Meyer, B. Musch, J. W. Negele, K. Orginos, A. V. Pochinsky, M. Procura, D. G. Richards, W. Schroers, S. Syritsyn, "Nucleon structure from mixed action calculations using 2+1 flavors of asqtad sea and domain wall valence fermions", Phys.Rev.D82:094502 (2010)

Nerenberg, Paul

Nerenberg PS, Jo B#, So C#, Tripathy A#, and Head-Gordon T. Optimizing solute-water van der Waals interactions to reproduce solvation free energies. Journal of Physical Chemistry B 2012; 116;4524-4534.

Ball KA, Phillips AH, Nerenberg PS, Fawzi NL, Wemmer DE, and Head-Gordon T. Homogeneous and Heterogeneous Tertiary Structure Ensembles of Amyloid-beta; Peptides. Biochemistry 2011; 50:7612-7628.

Nerenberg PS and Head-Gordon T. Optimizing Protein-Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides. Journal of Chemical Theory and Computation 2011; 7:1220-1230.

Newman, David

Newman, Gregory

Commer M., Newman G.A., Williams K.H., and Hubbard S.S., 2011, Three-dimensional induced polarization data inversion for complex resistivity, Geophysics, 76, F157 F171.

Commer M., Maia F.R.N.C., and Newman G.A, 2011, Iterative Krylov solution methods for geophysical electromagnetic simulations on throughput-oriented processing units, International Journal of High Performance Computing Applications, in press.

Um E., Commer M., Newman G.A., Iterative Finite-Difference Solution Analysis of Acoustic Wave Equation in the Laplace-Fourier Domain, Geophysics, accepted for publication.

Ng, Esmond

Hasan Metin Aktulga, Chao Yang, Umit Catalyurek, Pieter Maris, James Vary, and E.G. Ng, On Reducing I/O Overheads in Large-Scale Invariant Subspace Projections . To appear in Proc. 2011 Work on Algorithms and Programming Tools for Next-Generation High-Performance Scientific Software (2011).

Hasan Metin Aktulga, Chao Yang, Esmond Ng, Pieter Maris, and James Vary. "Large-scale Parallel Null Space Calculation for Nuclear Configuration Interaction". To appear in Proc. 2011 High Performance Computational Science Conference (2011).

Ming Gu, Xiaoye S. Li, and Panayot S. Vassilevski, Direction-preserving and Schur-monotonic semi- separable approximations of symmetric positive definite matrices . Submitted to SIAM J. Matrix Anal. Appl. (2010).

X.S. Li, M. Shao, I. Yamazaki, and E.G. Ng, Factorization-based sparse solvers and preconditioners , J. Phy.: Conf. Ser. 180, 012015 (2009) doi:10.1088/1742-6596/180/1/012015

L. Lin, C. Yang, J. Lu, L. Ying and W. E., "A Fast Parallel Algorithm for Selected Inversion of Structured Sparse Matrix with Application to 2D Electronic Structure Calculations". To appear in SIAM J. Sci. Comp. , 2011

L. Lin, C. Yang, J. C. Meza, J. Lu, L. Ying and W. E., "SelInv - An Algorithm for Selected Inversion of a Sparse Symmetric Matrix". ACM Trans. on Math Software , vol, 37, no. 4, pages 1 -- 19, 2011.

E.G. Ng et al., "Advancing Nuclear Physics Through TOPS Solvers and Tools". To appear in Proc. SciDAC 2011 Conference (2011).

J. Xia, S. Chandrasekaran, M. Gu, and X. S. Li, Superfast Multifrontal Method for Structured Linear Systems of Equations , SIAM J. Matrix Analysis and Applications, Vol.31, No.3., 1382-1411, 4 December 2009.

I. Yamazaki, X.S. Li, and E.G. Ng, A Parallel Hybrid Linear Solver for Accelerator Cavity Design . Proc. 10th International Computational Accelerator Physics Conference, 2009.

I. Yamazaki, X.S. Li, and E. Ng, Preconditioning Schur complement systems of highly-indefinite linear systems for a parallel hybrid solver , Numer. Math. Theor. Meth. Appl., 3 (2010), pp. 352-366.

I. Yamazaki and X.S. Li, On techniques to improve robustness and scalability of the Schur complement method , Proc. of VECPAR 2010, 421-434, LNCS 6449, Springer.

Notaro, Michael

Notaro, M., 2011: Simulated impact of vegetation on climate across the North American monsoon region in CCSM3.5. Climate Dynamics, doi:10.1007/s00382-010-0990-0.

Notaro, M., K.-H. Wyrwoll, and G. Chen, 2011: Did aboriginal vegetation burning impact on the Australian summer monsoon? Geophysical Research Letters, doi:10.1029/2011GL047774.

Nugent, Peter

http://arxiv.org/abs/1106.1706

Levitan, D., B. J. Fulton, P. J. Groot, S. R. Kulkarni, E. O. Ofek, T. A. Prince, A. Shporer, J. S. Bloom, S. B. Cenko, M. M. Kasliwal, N. M. Law, P. E. Nugent, D. Poznanski, R. M. Quimby, A. Horesh, B. Sesar, & A. Sternberg, "PTF1 J071912.13+485834.0: An Outbursting AM CVn System Discovered by a Synoptic Survey, " {\em \apj}, {\bf 739}, 2011

Gal-Yam, A., M. M. Kasliwal, I. Arcavi, Y. Green, O. Yaron, S. Ben-Ami, D. Xu, A. Sternberg, R. M. Quimby, S. R. Kulkarni, E. O. Ofek, R. Walters, P. E. Nugent, D. Poznanski, J. S. Bloom, S. B. Cenko, A. V. Filippenko, W. Li, J. M. Silverman, E. S. Walker, M. Sullivan, K. Maguire, D. A. Howell, P. A. Mazzali, D. A. Frail, D. Bersier, P. A. James, C. W. Akerlof, F. Yuan, N. Law, D. B. Fox, & N. Gehrels, "Real-time Detection and Rapid Multiwavelength Follow-up Observations of a Highly Subluminous Type II-P Supernova from the Palomar Transient Factory Survey, " {\em \apj}, {\bf 736}, 2011

van Eyken, J. C., D. R. Ciardi, L. M. Rebull, J. R. Stauffer, R. L. Akeson, C. A. Beichman, A. F. Boden, K. von Braun, D. M. Gelino, D. W. Hoard, S. B. Howell, S. R. Kane, P. Plavchan, S. V. RamÃrez, J. S. Bloom, S. B. Cenko, M. M. Kasliwal, S. R. Kulkarni, N. M. Law, P. E. Nugent, E. O. Ofek, D. Poznanski, R. M. Quimby, C. J. Grillmair, R. Laher, D. Levitan, S. Mattingly, & J. A. Surace, "The Palomar Transient Factory Orion Project: Eclipsing Binaries and Young Stellar Objects, " {\em \aj}, {\bf 142}, 2011

Quimby, R. M., S. R. Kulkarni, M. M. Kasliwal, A. Gal-Yam, I. Arcavi, M. Sullivan, P. Nugent, R. Thomas, D. A. Howell, E. Nakar, L. Bildsten, C. Theissen, N. M. Law, R. Dekany, G. Rahmer, D. Hale, R. Smith, E. O. Ofek, J. Zolkower, V. Velur, R. Walters, J. Henning, K. Bui, D. McKenna, D. Poznanski, S. B. Cenko, & D. Levitan, "Hydrogen-poor superluminous stellar explosions, " {\em \nat}, {\bf 474}, 2011

Sullivan, M., M. M. Kasliwal, P. E. Nugent, D. A. Howell, R. C. Thomas, E. O. Ofek, I. Arcavi, S. Blake, J. Cooke, A. Gal-Yam, I. M. Hook, P. Mazzali, P. Podsiadlowski, R. Quimby, L. Bildsten, J. S. Bloom, S. B. Cenko, S. R. Kulkarni, N. Law, & D. Poznanski, "The Subluminous and Peculiar Type Ia Supernova PTF 09dav, " {\em \apj}, {\bf 732}, 2011

Smith, A. M., S. Lynn, M. Sullivan, C. J. Lintott, P. E. Nugent, J. Botyanszki, M. Kasliwal, R. Quimby, S. P. Bamford, L. F. Fortson, K. Schawinski, I. Hook, S. Blake, P. Podsiadlowski, J. JÃ¶nsson, A. Gal-Yam, I. Arcavi, D. A. Howell, J. S. Bloom, J. Jacobsen, S. R. Kulkarni, N. M. Law, E. O. Ofek, & R. Walters, "Galaxy Zoo Supernovae, " {\em \mnras}, {\bf 412}, 2011

Kasliwal, M. M., S. R. Kulkarni, A. Gal-Yam, O. Yaron, R. M. Quimby, E. O. Ofek, P. Nugent, D. Poznanski, J. Jacobsen, A. Sternberg, I. Arcavi, D. A. Howell, M. Sullivan, D. J. Rich, P. F. Burke, J. Brimacombe, D. Milisavljevic, R. Fesen, L. Bildsten, K. Shen, S. B. Cenko, J. S. Bloom, E. Hsiao, N. M. Law, N. Gehrels, S. Immler, R. Dekany, G. Rahmer, D. Hale, R. Smith, J. Zolkower, V. Velur, R. Walters, J. Henning, K. Bui, & D. McKenna, "Rapidly Decaying Supernova 2010X: A Candidate ".Ia" Explosion, " {\em \apjl}, {\bf 723}, 2010

Arcavi, I., "Core-collapse Supernovae from the Palomar Transient Factory: Indications for a Different Population in Dwarf Galaxies, " {\em \apj}, {\bf 721}, 2010

Ross, N. et al "Ameliorating systematic uncertainties in the angular clustering of galaxies: a study using the SDSS-III, " {\em \mnras}, {\bf , 2011

Slosar, A., et al., "The Lyman-Î± forest in three dimensions: measurements of large scale flux correlations from BOSS 1st-year data, " {\em \jcap}, {\bf 9}, 2011

Eisenstein, D. J., et al., "The Eighth Data Release of the Sloan Digital Sky Survey: First Data from SDSS-III, " {\em \apjs}, {\bf 193}, 2011

White, M. et al., "The Clustering of Massive Galaxies at z ~ 0.5 from the First Semester of BOSS Data, " {\em \apj}, {\bf 728}, 2011

Rabinowitz, D., C. Baltay, N. Ellman, E. Hadjiyska, S. Tourtellote, P. Nugent, J. Bloom, J. Parrent, & D. A. Howell, "Dwarf Nova in Ophiuchus (Lsq J16531857-1617542), " {\em Central Bureau Electronic Telegrams}, {\bf 2757}, 2011

Hadjiyska, E. I., D. Rabinowitz, C. Baltay, R. Zinn, P. Coppi, N. Ellman, & L. R. Miller, "La Silla-QUEST Variability Survey, " {\em Bulletin of the American Astronomical Society}, {\bf 43}, 2011

O

Odyniec, Grazyna

H. Agakishiev, et al. (STAR Collaboration), Observation of the antimatter helium-4 nucleus, Nature 473 (2011) 353

H. Agakishiev, et al. (STAR Collaboration), Measurement of the parity-violating longitudinal single-spin asymmetry for W^{\pm} boson production in polarized proton-proton collisions atsqrt{s} = 500 GeV, Phys. Rev. Lett. 106 (2011) 062002

M. M. Aggarwal, et al. (STAR Collaboration), Measurement of the bottom quark contribution to nonphotonic electron production in p+p collisions at sqrt{s}=200 GeV, Phys. Rev. Lett. 105 (2010) 202301

M. M. Aggarwal, et al. (STAR Collaboration), Higher moments of net proton multiplicity distributions at RHIC, Phys. Rev. Lett. 105 (2010) 022302

B.I. Abelev, et al. (STAR Collaboration), Three-particle coincidence of the long range pseudorapidity correlation in high energy nucleus-nucleus collisions, Phys. Rev. Lett. 105 (2010) 022301

H. Agakishiev, et al. (STAR Collaboration), High pT nonphotonic electron production in p+p collisions at sqrt{s} = 200 GeV, Phys. Rev. D 83 (2011) 052006

B.I. Abelev, et al. (STAR Collaboration), Upsilon cross section in p+p collisions at sqrt{s} = 200 GeV, Phys. Rev. D 82 (2010) 012004

M.M. Aggarwal, et al. (STAR Collaboration), Scaling properties at freeze-out in relativistic heavy-ion collisions, Phys. Rev. C 83 (2011) 034910

H. Agakishiev, et al. (STAR Collaboration), Strange and multistrange particle production in Au+Au collisions at sqrt{s_{NN}} = 62.4 GeV, Phys. Rev. C 83 (2011) 024901

B.I. Abelev, et al. (STAR Collaboration), Parton energy loss in heavy-ion collisions via direct-photon and charged-particle azimuthal correlations, Phys. Rev. C 82 (2010) 034909

M. M. Aggarwal, et al. (STAR Collaboration), Azimuthal di-hadron correlations in d+Au and Au+Au collisions at sqrt{s_{NN}} = 200 GeV measured at the STAR detector, Phys. Rev. C 82 (2010) 024912

M. M. Aggarwal, et al. (STAR Collaboration), Balance functions from Au+Au, d+Au, and p+p collisions at sqrt{s_{NN}} = 200 GeV, Phys. Rev. C 82 (2010) 024905

Oefelein, Joseph

J. C. Oefelein and G. Lacaze. Low temperature injection dynamics and turbulent flame structure in high-pressure supercritical flows. Proceedings of the 23rd International Colloquium on the Dynamics of Explosions and Reactive Systems, July 24-29 2011. Irvine, California.

R. N. Dahms, L. M. Pickett, and J. C. Oefelein. A dense fluid approximation for the simulation of Diesel engine fuel injection processes. Proceedings of the 23rd Annual Conference on Liquid Atomization and Spray Systems, May 15-18 2011. Ventura, California.

R. Sankaran and J. C. Oefelein. Efficient data management and analysis for high-fidelity combustion simulations on petascale supercomputers. Proceedings of the 13th International Conference on Numerical Combustion, April 27-29 2011. Corfu, Greece.

G. Lacaze and J. C. Oefelein. A tabulated chemistry model for turbulent nonpremixed flames at high-pressure supercritical conditions. Combustion and Flame, 2011. Accepted.

A. M. Kempf, B. J. Geurts, and J. C. Oefelein. Error analysis of large eddy simulation of the turbulent non-premixed Sydney bluff-body flame. Combustion and Flame, 2011. Accepted.

J. H. Frank, S. A. Kaiser, and J. C. Oefelein. Analysis of scalar mixing dynamics in LES using high-resolution imaging of laser Rayleigh scattering in turbulent non-reacting jets and non-premixed jet flames. Proceedings of the Combustion Institute, 33:1373 1381, 2011.

Ogut, Serdar

K. Baishya, J. C. Idrobo, S. Ogut, M. Yang, K. A. Jackson, and J. Jellinek, "First Principles absorption spectra of Cu_n (n=2-20) Clusters", Physical Review B 83, 245402 (2011).

R. F. Klie, Q. Qiao, T. Paulauskas, A. Gulec, A. Rebola, S. Ogut, M. P. Prange, J.C. Idrobo, S. T. Pantelides, S. Kolesnik, B. Dabrowski, M. Ozdemir, C. Boyraz, D. Mazumdar, and A. Gupta, " The effcts of increased Co-ion spin states on the Seebeck coeffcient in thermoelectric Ca3Co4O9", submitted to Physical Review Letters (August 2011)

Q. Qiao, J. C. Idrobo, S. J. Pennycook, S. Ogut, and R. F. Klie, "80 keV Analysis of the GaAs-SrTiO3 Hetero-interfacial structures", submitted to Physical Review B Rapid Communications (September 2011).

Oliker, Leonid

K. Madduri, K. Ibrahim, S. Williams, E. Im, S. Ethier, J. Shalf, L. Oliker, "Gyrokinetic Toroidal Simulations on Leading Multi- and Manycore HPC Systems", SC11 in press.

S. Williams, L. Oliker, J. Carter, J. Shalf, "Extracting Ultra-Scale Lattice Boltzmann Performance via Hierarchical and Distributed Auto-Tuning", SC11 in press.

L. Oliker, R.Nishtala, R. Biswas, Guest editors, Parallel Computing special issue "Emerging Programming Paradigms for Large-Scale Scientific Computing", in press.

K. Madduri, E. Im, K. Ibrahim, S. Williams, S. Ethier, L. Oliker, "Gyrokinetic Particle-in-Cell Optimization on Emerging Multi- and Manycore Platforms", Parallel Computing Journal, in press.

Rajesh Sudarsan, Julian Borrill, Christopher Cantalupo, Theodore Kisner, Kamesh Madduri, Leonid Oliker, Horst Simon, Yili Zheng, "Cosmic Microwave Background Map-Making at the Petascale and Beyond", International Conference of Supercomputing (ICS) 2011

P. Narayanan, A. Koniges, L. Oliker, R. Preissl, S. Williams, N. Wright, M. Umansky, X. Xu, S. Ethier, W. Wang, J. Candy, J. Cary, "Performance Characterization for Fusion Co-design Applications , Cray Users Group (CUG) 2011.

M. Wehner, L. Oliker, J. Shalf, et al, "Hardware/Software Co-design of Global Cloud System Resolving Models", ournal of Advances in Modeling Ear th Systems, to appear

Orginos, Kostas

"High Statistics Analysis using Anisotropic Clover Lattices: (IV) Volume Dependence of Light Hadron Masses" S.R. Beane, E. Chang, W. Detmold, H.W. Lin, T.C. Luu, K. Orginos, A. Parreno, M.J. Savage, A. Torok, A. Walker-Loud Phys.Rev.D84:014507,2011

"Evidence for a Bound H-dibaryon from Lattice QCD" S.R. Beane, E. Chang, W. Detmold, B. Joo, H.W. Lin, T.C. Luu, K. Orginos, A. Parreno, M.J. Savage, A. Torok, A. Walker-Loud Phys.Rev.Lett.106:162001,2011

Ott, Christian

B. Dasgupta, E. O'Connor, and C. D. Ott, The Role of Collective Neutrino Oscillations in Core-Collapse Supernova Shock Revival, submitted to Phys. Rev. D, 2011.

A. Piro and C. D. Ott, Supernova Fallback onto Magnetars and Propeller-powered Supernovae, Astrophys. J. 736, 108, 2011.

C. D. Ott, C. Reisswig, E. Schnetter, E. O'Connor, U. Sperhake, F. Loffler, P. Diener, E. Abdikamalov, I. Hawke, and A. Burrows. Dynamics and Gravitational Wave Signature of Collapsar Formation, Phys. Rev. Lett. 106, 161103, 2011.

C. Reisswig, C. D. Ott, E. Schnetter, and U. Sperhake, Gravitational Wave Extraction in Simulations of Rotating Stellar Core Collapse, Phys. Rev. D 83, 064008, 2011.

E. O'Connor and C. D. Ott, Black Hole Formation in Failing Core-Collapse Supernovae, Astrophys. J. 730, 70, 2011

O. Korobkin, E. Abdikamalov, E. Schnetter, N. Stergioulas, B. Zink, Stability of general-relativistic accretion disks, Phys. Rev. D 83, 043007, 2011.

T. Brandt, A. Burrows, E. Livne, and C. D. Ott, Results From Core-Collapse Simulations with Multi-Dimensional, Multi-Angle Neutrino Transport. Astrophys. J. 728, 8, 2011

J. Nordhaus, T. D. Brandt, A. Burrows, E. Livne, C. D. Ott, Theoretical support for the hydrodynamic mechanism of pulsar kicks., Phys. Rev. D 82, 103016, 2010.

D. Pollney, C. Reisswig Gravitational memory in binary black hole mergers, Astrophys. J. 732, L13, 2011.

C. Reisswig, D. Pollney Notes on the integration of numerical relativity waveforms, Class. Quantum Grav. 28, 195015, 2011.

N. T. Bishop, D. Pollney, C. Reisswig, Initial data transients in binary black hole evolutions, Class. Quantum Grav. 28, 155019, 2011.

Ozolins, Vidvuds

F. Zhou and V. Ozolins, Crystal field and magnetic structure of UO2 , Physical Review B 83, 085106 (2011)

Feng-Chuan Chuang, Wen-Huan Lin, Zhi-Quan Huang, Chia-Hsiu Hsu, Chien-Cheng Kuo, Vidvuds Ozolins and V Yeh, Electronic structures of an epitaxial graphene monolayer on SiC(0001) after gold intercalation: a first-principles study , Nanotechnology 22, 275704 (2011)

Y. Liu; V. Ozolins, Diffusion-Assisted Formation Mechanism of Molecular Break Junctions: A First-Principles Study of Benzenethiolate on Au(111) , Journal of Physical Chemistry C 115, 3460 (2011)

J. M. An, S. V. Barabash, V. Ozolins, M. van Schilfgaarde, and K. D. Belashchenko, First-principles study of phase stability of Gd-doped EuO and EuS , Phys. Rev. B 83, 064105 (2011)

S. V. Barabash and V. Ozolins, Order, miscibility, and electronic structure of Ag(Bi,Sb)Te2 alloys and (Ag,Bi,Sb)Te precipitates in rocksalt matrix: A first-principles study , Phys. Rev. B 81, 075212 (2010)

S. Huang, D. L. Worthington, M. Asta, V. Ozolins, G. Ghosh and P. K. Liaw, Calculation of impurity diffusivities in -Fe using first-principles methods , Acta Materialia, 2010, 58 (6), 1982-93.

W. Sun, C. Wolverton, A. R. Akbarzadeh, and V. Ozolins, "First-principles prediction of high-capacity, thermodynamically reversible hydrogen storage reactions based on (NH4)2B12H12," Physical Review B 83, 064112 (2011)

Majzoub E. H.; Zhou Fei; Ozolins V., "First-Principles Calculated Phase Diagram for Nanoclusters in the Na-Al-H System: A Single-Step Decomposition Pathway for NaAlH4", Journal of Physical Chemistry C 115, 2636 (2011)

K. Michel, Y. Liu, and V. Ozolins, "The Atomic Structure and Silane-H2 Interactions of SiH4(H2)2 from First-Principles Calculations," Physical Review B 82, 174103 (2010).

Y. Zhang, E. H. Majzoub, V. Ozolins, and C. Wolverton, Theoretical prediction of different decomposition paths for Ca(BH4)2 and Mg(BH4)2, Physical Review B 82, 174107 (2010).

K. Michel and V. Ozolins, Native defect concentrations in NaAlH4 and Na3AlH6 Journal of Physical Chemistry C, in press (2011).

K. Michel and V. Ozolins, Vacancy diffusion in NaAlH4 and Na3AlH6 Journal of Physical Chemistry C, in press (2011).

K. Michel and V. Ozolins, First-principles modeling of diffusion reactions, Ti defects, and the hydrogenation of NaAlH4 Journal of Physical Chemistry C, in press (2011).

P

Pankin, Alexei

A.Y. Pankin, G. Park, J. Cummings, C.S. Chang, G. Bateman, D. Bunner, R.J. Groebner, J.W. Hughes, B. LaBombard, J.L. Terry, A.H. Kritz, S. Ku, T. Rafiq, and P.B. Snyder, Kinetic Modeling of H-mode pedestal with effects from anomalous transport and MHD stability Problems of Atomic Science and Technology: Plasma Physics 17, 2011, 8-12.

A.Y Pankin, J. Callen, J.R. Cary, R. Groebner, A. Hakim, S. Kruger, A. Pletzer, S. Shasharina, S. Vadlamani, R. Cohen, A.H. Kritz, T.D. Rognlien, T. Rafiq, and FACETS team, Stress Tests of Transport Models Using FACETS Code Submitted for publication to AIP Proceedings for CNR-Chalmers workshop.

Patton, Edward

Sullivan, P. P. and E. G. Patton, 2011: The effect of mesh resolution on convective boundary layer statistics and structures generated by large-eddy simulation, Journal of the Atmospheric Sciences, In press.

Paul, Kevin

V.H. Ranjbar and C.Y. Tan, Effect of impedance and higher order chromaticity on the measurement of linear chromaticity, Phys. Rev. ST Accel. Beams 14, 082802 (2011); http://prst-ab.aps.org/abstract/PRSTAB/v14/i8/e082802

Penner, Joyce

Lee, S. S. and J. E. Penner, 2010: Aerosol effects on ice clouds: Can the traditional concept of aerosol indirect effects be applied to aerosol-cloud interactions in cirrus clouds?, Atmos. Chem. Phys., 10, 10345-10358.

Roesler, E. and J. E. Penner, 2010: Can global models ignore the chemical composition of aerosols?, Geophys. Res. Lett., 37, L24809, doi:10.1029/2010GL044282.

Lin, G., J. E. Penner, S. Sillman, D. Taraborrelli, J. Lelieveld, 2011: Global Mechanistic Model of SOA Formation: Effects of Different Chemical Mechanisms, Atmospheric Chemistry and Physics Discussions, in press.

Pennycook, Stephen

J. He, A. Y. Borisevich, S. V. Kalinin, S. J. Pennycook, and S. T. Pantelides, "Control of octahedral tilts and magnetic properties of perovskite oxide heterostructures by substrate symmetry", Phys. Rev. Lett. 105, 227203 (2010).

J. Lee, W. Zhou. J.-C. Idrobo, S.J. Pennycook, and S.T. Pantelides, "Vacancy-driven anisotropic defect distribution in the novel battery-cathode material LiFePO4" Phys. Rev. Lett. 107, 085507 (2011).

Matthew F. Chisholm, Weidong Luo, Mark P. Oxley, Sokrates T. Pantelides, and Ho Nyung Lee, "Atomic-Scale Compensation Phenomena at Polar Interfaces", Phys. Rev. Lett. 105, 197602 (2010).

Jaume Gazquez, Weidong Luo, Mark P. Oxley, Micah Prange, Maria A. Torija, Manish Sharma, Christopher Leighton, Sokrates T. Pantelides, Stephen J. Pennycook, and Maria Varela, "Atomic- resolution imaging of spin-state superlattices in nanopockets within cobaltite thin films", Nano Lett. 11, 973 (2011).

S. J. Pennycook, K. van Benthem, A. G. Marinopoulos, S-H. Oh, S. I. Molina, A. Y. Borisevich, W. Luo, and S. T. Pantelides, "Seeing inside materials by aberration-corrected electron microscopy", accepted for publication in Int. J. Nanotechnol. (2011).

Perlmutter, Saul

The Hubble Space Telescope Cluster Supernova Survey V. Improving The Dark Energy Constraints above z 1 and Building an Early-Type-Hosted Supernova Sample, N. Suzuki et al. 2011 (Supernova Cosmology Project), accepted by ApJ

The Hubble Space Telescope Cluster Supernova Survey II: The Type Ia Supernova Rate in High-Redshift Galaxy Clusters, K. Barbary et al. 2011 (Supernova Cosmology Project), accepted by ApJ

Supernova Constraints and Systematic Uncertainties from the First Three Years of the Supernova Legacy Survey, A. Conley et al. 2011 ApJS, 192, 1

Scaling Relations and Overabundance of Massive Clusters at z ~ 1 from Weak-lensing Studies with the Hubble Space Telescope, M. J. Jee et al. 2011, accepted by ApJ

The Supernova Legacy Survey 3-year sample: Type Ia supernovae photometric distances and cosmological constraints, J. Guy et al. 2010 A&A, 523, 7

Spectra and HST Light Curves of Six Type Ia Supernovae at 0.511 z 1.12 and the UNION2 Compilation, R. Amanullah et al. (Supernova Comoslogy Project) 2010, ApJ, 716, 712

Subaru FOCAS Spectroscopic Observations for High-Redshift Supernovae, T. Morokuma et al. (Supernova Cosmology Project) 2010, PASJ, 62, 19

Persson, Per-Olof

P.-O. Persson, D. Willis, J. Peraire, Numerical Simulation of Flapping Wings using a Panel Method and a High-Order Navier-Stokes Solver, Int. J. Num. Meth. Engrg., accepted.

A. Uranga, P.-O. Persson, M. Drela, J. Peraire, Preliminary Investigation Into the Ects of Cross-Flow on Low Reynolds Number Transition, Proc. 20th AIAA CFD Conference, 2011.

J. Peraire, P.-O. Persson, High-Order Discontinuous Galerkin Methods for CFD. In Adaptive High-Order Methods in Computational Fluid Dynamics, World Scienti

A. Uranga, P.-O. Persson, M. Drela, and J. Peraire, Implicit Large Eddy Simulation of transition to turbulence at low Reynolds numbers using a Discontinuous Galerkin method, Int. J. Num. Meth. Engrg., Vol. 87, No. 1-5, pp. 232-261, 2011.

P.-O. Persson, High-Order LES Simulations using Implicit-Explicit Runge-Kutta Schemes, Proc. 49th AIAA Aerospace Sciences Meeting, 2011.

P.-O. Persson, D. Willis, High Fidelity Simulations of Flapping Wings Designed for Energetically Optimal Flight, Proc. 49th AIAA Aerospace Sciences Meeting, 2011.

Pieper, Steven

Jastrow functions in double-beta decay, J. Engel, J. Carlson, R.B. Wiringa, Phys.Rev.C83:034317,2011

BEC-BCS crossover and universal relations in unitary Fermi gases, S. Gandolfi, K. E. Schmidt, J. Carlson, Phys. Rev. A 83, 041601(R) (2011)

Cold neutrons trapped in external fields, S. Gandolfi, J. Carlson, Steven C. Pieper, Phys.Rev.Lett.106:012501,2011

Density Fluctuation Effects on Collective Neutrino Oscillations in O-Ne-Mg Core-Collapse Supernovae, Phys. Rev. D (in press).

Resonantly Interacting Fermions in a Box , Forbes Michael McNeil; Gandolfi Stefano; Gezerlis Alexandros, Phys. Rev. Lett. 106: 235303, 2011.

Pinar, Ali

Fast pairwise and column-wise matrix computations for Katz scores and commute times, J. Internet Mathematics, to appear.

Pindzola, Michael

M. E. Bautista, C. P. Ballance, and P. Quinet, Atomic data and spectral model for Fe+2, Astrophysical Journal Letters 718, L189 (August 2010)

X. Ren, A. Senftleben, T. Pfluger, A. Dorn, J. P. Colgan, M. S. Pindzola, O. Al-Hagan, D. H. Madison, I. Bray, D. V. Fursa, and J. Ullrich, Tracing multiple scattering patterns in absolute (e,2e) cross sections for H_2 and He over complete solid angle, Physical Review A 82, 032712 (September 2010)

T. G. Lee, S. D. Loch, C. P. Ballance, J. A. Ludlow, and M. S. Pindzola, Electron-impact ionization cross sections for excited states of B, B+, and B+2 and in investigation into n-scaling of ionization cross sections, Physical Review A 82, 042721 (October 2010)

C. P. Ballance, S. D. Loch, M. S. Pindzola, and D. C. Griffin, Dielectronic recombination of W+35, Journal of Physics B 43, 205201 (October 2010)

I. Orban, S. D. Loch, S. Bohm, and R. Schuch, Recombination rate coefficients of Si+10, Astrophysical Journal 721, 1603 (October 2010)

F. J. Robicheaux, S. D. Loch, M. S. Pindzola, and C. P. Ballance, Contribution of near threshold states to recombination in plasmas, Physical Review Letters 105, 233201 (December 2010)

C. Malespin, C. P. Ballance, M. S. Pindzola, M. C. Witthoeft, T. Kallman, and S. D. Loch, Electron-impact excitation of H-like Cr, Mn, Fe, Co, and Ni for applications in modeling X-ray astrophysical sources, Astronomy and Astrophysics Journal 526, A115 (February 2011)

M. S. Pindzola, S. D. Loch, and F. J. Robicheaux, Dielectronic recombination in C+3 above and below the ionization threshold, Physical Review A 83, 042705 (April 2011)

X. Ren, I. Bray, D. V. Fursa, J. P. Colgan, M. S. Pindzola, T. Pfluger, A. Senftleben, S. Xu, A. Dorn, and J. Ullrich, Electron-impact ionization of He: a comprehensive experiment benchmarks theory, Physical Review A 83, 052711 (May 2011)

M. S. Pindzola, J. A. Ludlow, C. P. Ballance, F. J. Robicheaux, and J. P. Colgan, Electron-impact double ionization of B+, Journal of Physics B 44, 105202 (May 2011)

M. S. Pindzola, C. P. Ballance, and S. D. Loch, Electron-impact ionization of C+3 in excited states, Physical Review A 83, 062705 (June 2011)

I. Orban, S. D. Loch, P. Glans, S. Bohm, and R. Schuch, Effects of spin-forbidden resonances on the recombination of Ne+6 and Si+10, Physica Scripta 144, 014035 (June 2011)

J. A. Ludlow, T. G. Lee, C. P. Ballance, S. D. Loch, and M. S. Pindzola, Level resolved R-matrix calculations for the electron-impact excitation of Ne+3 and Ne+6, Physical Review A 84, 022701 (August 2011)

B. M. McLaughlin, T. G. Lee, J. A. Ludlow, E. Landi, S. D. Loch, M. S. Pindzola, and C. P. Ballance, A large-scale R-matrix calculation for electron-impact excitation of Ne+2, Journal of Physics B 44, 175206 (September 2011)

Plewa, Tomasz

Budde, A., Drake, R. P., Kuranz, C. C., Grosskopf, M. J., Plewa, T., & Hearn, N. C., Simulation of fabrication variations in supernova hydrodynamics experiment, High Energy Density Physics, 6, 135

Fryxell, B., Kuranz, C. C., Drake, R. P., Grosskopf, M. J., Budde, A., Plewa, T., Hearn, N., Hansen, J. F., Miles, A. R., & Knauer, J., 2010, The possible effects of magnetic fields on laser experiments of Rayleigh-Taylor instabilities, High Energy Density Physics, 6, 162

Gawryszczak, A., Guzman, J., Plewa, T., & Kifonidis, K., Non-spherical core collapse supernovae III. Evolution towards homology and dependence on the numerical resolution, 2010, Astronomy & Astrophysics, 521, A38

Odrzywolek, A., & Plewa, T., Probing thermonuclear supernova explosions with neutrinos, 2011, Astronomy & Astrophysics, 529, A156

Porter, R. (Jeff)

K. Aamodt et al. (ALICE Collaboration), Production of pions, kaons and protons in pp collisions at sqrt(s)= 900 GeV with ALICE at the LHC, Eur.Phys.J.C 71(6): 1655, 2011

K. Aamodt et al. (ALICE Collaboration), Strange particle production in proton-proton collisions at s = 0.9 TeV with ALICE at the LHC, Eur. Phys. J. C 71 (3), 1594 (2011)

K. Aamodt et al. (ALICE Collaboration), Two-pion Bose-Einstein correlations in central PbPb collisions at sqrt(s_NN) = 2.76 TeV, Phys.Lett.B 696 (4): 328-337, 2011

K. Aamodt et al. (ALICE Collaboration), Centrality Dependence of the Charged-Particle Multiplicity Density at Midrapidity in Pb-Pb Collisions at sqrt(sNN)=2.76 TeV, Phys. Rev. Lett. 106, 032301 (2011)

K. Aamodt et al. (ALICE Collaboration), Suppression of Charged Particle Production at Large Transverse Momentum in Central Pb-Pb Collisions at sqrt(sNN)= 2.76 TeV., Phys. Lett. B696 (2011) 30-39

K. Aamodt et al. (ALICE Collaboration), Elliptic flow of charged particles in Pb-Pb collisions at 2.76 TeV, Phys. Rev. Lett. 105, 252302 (2010)

K. Aamodt et al. (ALICE Collaboration), Charged-particle multiplicity density at mid-rapidity in central Pb-Pb collisions at sqrt(sNN) = 2.76 TeV, Phys. Rev. Lett. 105, 252301 (2010)

K. Aamodt et al. (ALICE Collaboration), Transverse momentum spectra of charged particles in proton proton collisions at s=900 GeV with ALICE at the LHC, Phys. Lett. B693, 53 (2010)

K. Aamodt et al. (ALICE Collaboration), Two-pion Bose-Einstein correlations in pp collisions at sqrt(s)=900 GeV, Phys. Rev. D82, 052001 (2010)

K. Aamodt et al. (ALICE Collaboration), Midrapidity Antiproton-to-Proton Ratio in pp Collisons at sqrt(s)=0.9 and 7 TeV Measured by the ALICE Experiment, Phys. Rev. Lett. 102, 072002 (2010)

K. Aamodt et al. (ALICE Collaboration), Charged-particle multiplicity measurement in proton proton collisions at s=7 TeV with ALICE at LHC, Eur. Phys. J. C68, 345 (2010)

K. Aamodt et al. (ALICE Collaboration), Charged-particle multiplicity measurement in proton proton collisions at s=0.9 and 2.36 TeV with ALICE at LHC, Eur. Phys. J. C 68, 89 (2010)

Pratt, Larry

Lawrence M. Pratt, Stewart Voit, Fabian N. Okeke, Nobuaki Kambe Nickel Catalyzed Alkyl Coupling Reactions: Evaluation of Computational Methods J. Phys. Chem. A, 2011, 115, 2281

Leonardo Degennaro, Rosmara Mansueto, Elisa Carenza, Rosanna Rizzi, Saverio Florio, Lawrence M. Pratt, Renzo Luisi Nitrogen Dynamics and Reactivity of Chiral Aziridines: Generation of Configurationally Stable Aziridinyllithiums Chem. Eur. J. 2011, 17, 4992

Do Hoang Mai, Doan Ngoc Nhuan, Lawrence M. Pratt, Le Ngoc Thach Study on Reaction of Gilman Reagent Lithium dibutylcuprate with Alkyl Halides Journal of Chemistry (Vietnam), 2010, 48 (4B), 139

B. Ramachandran, Purnima Kharidehal,, Lawrence M. Pratt, Stewart Voit, Fabian N. Okeke, Monique Ewan Computational Strategies for Reactions of Aggregated and Solvated Organolithium Carbenoids J. Phys. Chem. A, 2010, 114, 8423

Primack, Joel

Ceverino, Daniel; Dekel, Avishai; Bournaud, Frederic - High-redshift clumpy discs and bulges in cosmological simulations, MNRAS 404, 2151 (2010).

Goerdt, Tobias; Dekel, A.; Sternberg, A.; Ceverino, D.; Teyssier, R.; Primack, J. R. - Gravity-driven Ly-alpha blobs from cold streams into galaxies, MNRAS 407, 613 (2010).

Fumagalli, Michele; Prochaska, J. Xavier; Kasen, Daniel; Dekel, Avishai; Ceverino, Daniel; Primack, Joel R. - Absorption line systems in simulated galaxies fed by cold streams, ApJ in press (arXiv: 1103.2130, 2011)

Genzel, Reinhard, et al. - The Sins Survey of z ~ 2 Galaxy Kinematics: Properties of the Giant Star-forming Clumps, ApJ 733, 101 (2011).

Puliti, Gianluca

Puliti, G., Paolucci, S., Sen, M. (2011). Thermodynamics properties of gold-water nanolayer mixtures using molecular dynamics. Journal of Nanoparticle Research, 13(9), 4277-4293. doi: 10.1007/s11051-011-0373-4.

Pullin, Dale

J. L. Ziegler, R. Deiterding, J. E. Shepherd, and D. I. Pullin. An adaptive high-order hybrid scheme for compressive, viscous flows with detailed chemistry. J. Comput. Physics, 230:75980-7630, 2011.

Punjabi, Alkesh

A. unjabi and H. Ali, Phys. Plasmas 18, 022509 (2011) - 17 pages

H. Ali, A. Punjabi, and E. Nyaku, J. Plasma Phys., accepted for publication on May 6, 2011 - 18 pages

Puzyrev, Yevgeniy

Y. S. Puzyrev, T. Roy, M. Beck, B. R. Tuttle, R. D. Schrimpf, D. M. Fleetwood and S. T. Pantelides, "Dehydrogenation of defects and hot-electron degradation in GaN high-electron-mobility transistors", Journal of Applied Physics, 108, 123705 (2010).

X. Shen, M. P. Oxley, Y. Puzyrev, B. R. Tuttle, G. Duscher, and S. T. Pantelides, "Excess Carbon in Silicon Carbide", Journal of Applied Physics, 109, 034501 (2011).

M. P. Prange, M. P. Oxley, M. Varela, S. J. Pennycook, and S. T. Pantelides, "Simulation of electron-energy-loss spectra including both diffraction and solid-state effects", submitted to Physical Review Letters R.F. Klie, Q. Qiao, T. Paulauskas, and A. Gulec,A. Rebola, M.P. Prange, J.C. Idrobo, and S.T. Pantelides, S. Kolesnik and B. Dabrowski, M. Ozdemir, C. Boyraz, D. Mazumdar, and A. Gupta, "The effects of increased Co-ion spin states on the Seebeck coefficient in thermoelectric Ca3Co4O9", submitted to Physical Review Letters

T. Roy, E. X. Zhang, Y. S. Puzyrev, X. Shen, D. M. Fleetwood, R. D. Schrimpf, U. K. Mishra, J. S. Speck, and S. T. Pantelides, "Temperature-dependence and microscopic origin of low frequency 1/f noise in GaN/AlGaN high electron mobility transistors", submitted to Applied Physics Letters

R

Ram, Abhay

Bo Li and D. R. Ernst, "Gyrokinetic Fokker-Planck Collision Operator," Phys. Rev. Lett. 106 (18), May (2011).

John C. Wright, Jungpyo Lee, Ernest Valeo, Paul Bonoli, Cynthia K. Phillips, E. F. Jaeger, and Robert W. Harvey, "Challenges in Self-Consistent Full-Wave Simulations of Lower Hybrid Waves," IEEE Transactions on Plasma Science Vol. 38, No. 9, 2136 (2010).

John Wright and the CSWPI SciDAC Center, "Time Dependent evolution of RF- generated non-thermal particle distributions in fusion plasmas," Invited Paper at the SciDAC 2011 Conference (Denver, CO); also to be published in the Journal of Physics Conference Series (2011).

Ramachandran, Bala

B. Ramachandran, Purnima Kharidehal, Lawrence M. Pratt, Stewart Voit, Fabian N. Okeke, and Monique Ewan, Computational Strategies for Reactions of Aggregated and Solvated Organolithium Carbenoids, J. Phys. Chem. A 114, 8423-8433 (2010). DOI: 10.1021/jp104246k.

Randall, David

Jones, T. R., and D. A. Randall, 2011: Quantifying the limits of convective parameterizations. J. Geophys. Res., 116, D08210, doi:10.1029/2010JD014913.

Benedict, J. J., and D. A. Randall, 2011: Impacts of idealized air-sea coupling on Madden-Julian Oscillation structure in the super-parameterized CAM. J. Atmos. Sci. (in press)

DeMott, C. A., C. Stan, D. A. Randall, J. L. Kinter III, and M. Khairoutdinov, 2011: The Asian Monsoon in the Super-Parameterized CCSM and its relation to tropical wave activity. J. Climate (in press).

Rasch, Philip

Wang,â€© M.,â€© S.â€© Ghan,â€© M.â€© Ovchinnikov,â€© X.â€© Liu,â€© R.â€© Easter,â€© E.â€© Kassianov,â€© Y.â€© Qian,â€© andâ€© H.â€© Morrison,â€© 2011:â€© Aerosolâ€© Indirectâ€© Effectsâ€© inâ€© aâ€© Multiâ€scaleâ€© Aerosolâ€climateâ€© Modelâ€© PNNLâ€MMF,â€© Atmosphericâ€©Chemistryâ€©andâ€©Physics,â€©11,â€©5431â€5455.â€©DOI:â€©10.5194/acpâ€11â€5431â€2011.â€©

Rashkeev, Sergey

B. Beeler, B. Good, S. Rashkeev, C. Deo, M. Baskes, and M. Okuniewski. First-Principles Calculations of the stability and incorporation of Helium, Xenon and Krypton in Uranium. Journal of Nuclear Materials (in press).

Lucia M. Petkovic, Vivek Utgikar, and Sergey N. Rashkeev. Structural stability and catalytic activity of lanthanum-based perovskites. The Journal of Physical Chemistry C 115, N 17, 8709-8715 (2011).

B. Beeler, B. Good, S. Rashkeev, C. Deo, M. Baskes, and M. Okuniewski. First principles calculations for defects in U. Journal of Physics: Condensed Matter 22, N 50, 505703 (2010).

D. Gryaznov, S. Rashkeev, E.A. Kotomin, E. Heifets, Y. Zhukovskii. Helium behavior in oxide nuclear fuels: First principles modeling. Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms 268, Issue 19, 3090-3094 (2010).

Michael V. Glazoff and Sergey N. Rashkeev. Beryllium Adsorption at Transition Aluminas: Implications for Environmental Science and Oxidation of Aluminum Alloys. The Journal of Physical Chemistry C 114, N 33, 14208 14212 (2010).

E.D. Aluker, A.G. Krechetov, A.Ju. Mitrofanov, D.R. Nurmukhametov, and M. M. Kuklja. Laser initiation of energetic materials: selective photoinitiation regime in PETN. Journal of Physical Chemistry C 115 (14), 6893-6901 (2011).

M.M. Kuklja, Yu. Mastrikov, S.N. Rashkeev, and E.A. Kotomin. The Structural Disorder and Lattice Stability of (Ba,Sr)(Co,Fe)O3 Complex Perovskites. ECS Transactions 35 (1), 2077-2084 (2011).

E. A. Kotomin, R. Merkle, Yu. A. Mastrikov, M.M. Kuklja, J. Maier. First Principles Modeling of Oxygen Incorporation into SOFC Cathode and Oxygen Permeation Membranes. ECS Transactions 35 (1), 823-830 (2011).

O. Sharia, M.M.Kuklja. Ab initio modeling of decomposition chemistry of gaseous and crystalline beta-HMX. The Journal of Physical Chemistry B (in press).

R.V. Tsyshevskiy, O. Sharia, M.M. Kuklja. Effect of impurities on optical properties of Pentaerythritol Teranitrate. APS SCCM proceedings (in press).

Onise Sharia and Maija M. Kuklja, Comparative analysis of decomposition reactions in gaseous and crystalline beta-HMX. APS SCCM proceedings (in press).

Rauchwerger, Lawrence

R.P. Drake, F.W. Doss, R.G. McClarren, M.L. Adams, N. Amato, D. Bingham, C.C. Chou, C. DiStefano, K. Fidkowski, B. Fryxell, T.I. Gombosi, M.J. Grosskopf, J.P. Holloway, B. van der Holst, C.M. Huntington, S. Karni, C.M. Krauland, C.C. Kuranz, E. Larsen, B. van Leer, B. Mallick, D. Marion,W. Martin, J.E. Morel, E.S. Myra, V. Nair, K.G. Powell, L. Rauchwerger, P. Roe, E. Rutter, I.V. Sokolov, Q. Stout, B.R. Torralva, G. Toth, K. Thornton, A.J. Visco, "Radiative Effects in Radiative Shocks in Shock Tubes", High En Rauchwerger, "The STAPL Parallel Container Framework", in Proc. of ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP), San Antonio, TX February 2011.

A. Buss, Harshvardhan, I. Papadopoulos, O. Tkachyshyn, T. Smith, G. Tanase, N. Thomas, X. Xu, M. Bianco, N. Amato, L. Rauchwerger, "STAPL: Standard Template Adaptive Parallel Library", in Proc. of Haifa Experimental Systems Conference (SYSTOR 2010), Haifa, Israel, May 2010 (ACM Digital Library).

Cosmin E. Oancea and Lawrence Rauchwerger, "Extracting Supernovacient Parallelism Conditions from Fortran Codes with Non-Linear Accesses", in Proc. 23nd International Workshop on Languages and Compilers for Parallel Computing (LCPC), Fort Collins, CO, Sept. 2011.

S. D. Pautz, T. Pandya*, and M. L. Adams, Scalable Parallel Prefix Solvers for Discrete Ordinates Transport, Nucl. Sci. Eng., in press (2011).

T. S. Bailey*, J. H. Chang, J. Warsa, M. L. Adams, A piecewise bi-linear discontinuous finite element spatial discretization of the Sn transport equation, Proc. International Conference on Mathematics and Computational Methods applied to Nuclear Science and Engineering, Rio de Janeiro, Brazil, to appear (2011).

J. J. Jarrell* and M. L. Adams, Discrete-ordinates quadrature sets based on linear discontinuous finite elements, Proc. International Conference on Mathematics and Computational Methods applied to Nuclear Science and Engineering, Rio de Janeiro, Brazil, to appear (2011).

Rauchwerger, "The STAPL Parallel Container Framework", in Proc. of ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP), San Antonio, TX February 2011.

S. D. Pautz, T. Pandya*, and M. L. Adams, Scalable Parallel Prefix Solvers for Discrete Ordinates Transport, Nucl. Sci. Eng., in press (2011).

T. Pandya*, M. L. Adams, and W. D. Hawkins, Long characteristics with piecewise linear sources designed for unstructured grids, Proc. International Conference on Mathematics and Computational Methods applied to Nuclear Science and Engineering, Rio de Janeiro, Brazil, to appear (2011).

Z. Wu* and M. L. Adams, Advances in Inverse Transport Methods, Proc. International Conf. on Nuclear Engineering, Xi an, China, May 17-21 (2010).

Antal Buss, Adam Fidel, Harshvardhan, Timmie G. Smith, Gabriel Tanase, NathT. Pandya*, M. L. Adams, and W. D. Hawkins, Long characteristics with piecewise linear sources mato, "Multithreaded Asynchronous Graph Traversal for In- Memory and Semi-External Memory," In Proc. Supercomputing (SC), New Orleans, LA, Nov 2010.

Rehr, John

"Bethe-Salpeter Equation Calculation of Core Excitation Spectra", J. Vinson, E. L. Shirley, J. J. Rehr, and J. J. Kas, Phys. Rev. B 83, 115106 (2011).

"X-ray absorption near-edge spectra of overdoped La2-xSrxCuO4 high-Tc superconductors" Towfiq Ahmed, Tanmoy Das, J. J. Kas, Hsin Lin, B. Barbiellini, Fernando D. Vila, R.S. Markiewicz, A. Bansil, and J. J. Rehr, Phys. Rev. B, 83, 115117 (2011).

"Experimental (XAS, STEM, TPR and XPS) and Theoretical (DFT) Characterization of Supported Rhenium Catalysts" Simon R. Bare, Shelly D. Kelly, Fernando D. Vila, Edwin Boldingh, E. Karapetrova, Josh Kas, George E. Mickelson, Frank S. Modica, Ning Yang, and John J. Rehr, J. Phys. Chem. C 115, 5740 (2011). (This work was featured in the cover of JPC C.)

Reichler, Thomas

Pennell, C. and T. Reichler (2011): On the effective number of climate models, J. Climate, 24 (9), 2358-2367

Rempe, Susan

Jiao, D.; Rempe, S. CO2 solvation free energy using quasi-chemical theory . J. Chem. Phys., 2011.

Jiao, D.; Leung, K.; et al. First Principles Calculations of Atomic Nickel Redox Potentials and Dimerization Free Energies: A Study of Metal Nanoparticle Growth . J. Chem. Theory Comput. 2011.

Ren, Chuang

L.; Freeman R. R.; Akli K. U.; Giraldez E.; Stephens R. B., High-intensity laser-plasma interaction with wedge-shaped-cavity targets, Phys. Plasmas 17, 103101 (2010)

X. Kong, M. C. Huang, C. Ren, and V. K. Decyk, Particle-in-cell simulations with charge- conserving current deposition on graphic processing units, Journal of Computational Physics 230, 1676 (2011)

G. Li, R. Yan, C. Ren, J. Tonge, and W. B. Mori, Three-dimensional particle-in-cell simulations of laser channeling in fast ignition, Phys. Plasmas 18, 042730 (2011)

Jared C. Workman1, Eric G. Blackman, and Chuang Ren, "Simulations reveal fast mode shocks in magnetic reconnection outflows," Phys. Plasmas 18, 092902 (2011)

Risbud, Sumedh

Mingxiang Luo, Francis Sweeney, Sumedh R. Risbud, German Drazer, and Joelle Frechette, Irreversibility and pinching in deterministic particle separation, Appl. Phys. Lett. 99, 064102 (2011) ; doi:10.1063/1.3617425

Rogers, Barrett

``Turbulence and bias-induced flows in simple magnetized toroidal plasmas'', B. Li, B. N. Rogers, K. Gentle, A. Bahhatchargee, Physical Review E Vol. 83, DOI: 10.1103/PhysRevE.83.056406

`` On the supression of turbulence by zonal flows in a simple magnetized plasma'', S. Kobayshi and B. N. Rogers, submitted to Phys. Plasmas (2010)

``Gyrokinetic simulations of the tearing instability'', R. Numata, W. Dorland, N. Loureiro, B. Rogers, A. Schekochihin, T. Tatsuno, submitted to Phys. Plasmas (2010)

``Low-frequency turbulence in a linear magnetized plasma'', B. Rogers and P. Ricci, Phys. Rev. Lett. {\bf 104} (2010)

``Gyrokinetic simulations of a particle pinch regime in closed-fieldline systems'', S. Kobayashi and B. Rogers, Phys. Rev. Lett., vol. 105, Issue 23, id. 235004 (2010)

``Turbulence Phase Space in Simple Magnetized Toroidal Plasmas'', P. Ricci and B. Rogers, Phys. Rev. Lett. 104, 145001, DOI: 10.1103/PhysRevLett.104.145001 (2010)

``Collisional damping of zonal flows due to finite Larmor radius effects'', P. Ricci, B. Rogers, W. Dorland, Phys. Plasmas 17, DOI: 10.1063/1.3447875 (2010)

Rollett, Tony

L. J. Peng and J. R. Morris, "Efficient calculations of hydrogen physisorption in expanded graphite and in amorphous carbon," J. Phys. Chem. C 114, 15522 (2010).

G.I. Toth, J.R. Morris, and L. Granasy, "Ginzburg-Landau type multi-phase-field model for competing fcc and bcc nucleation," Phys. Rev. Letters 106, 045701 (2011).

F. W. Averill and J. R. Morris, "Structural and electronic properties of graphene-graphane interfaces," Phys. Rev. B 84, 035411 (2011).

Romanowicz, Barbara

Lekic, V. & B. Romanowicz, Inferring upper-mantle structure by full waveform tomography with the spectral element method, Geophysical Journal International, 185 (2), 799-831, (2011). DOI: 10.1111/j.1365-246X.2011.04969.x

Lekic, V. & B. Romanowicz, Tectonic regionalization without a priori information: A cluster analysis of upper mantle tomography, Earth and Planetary Science Letters, 308 (1-2), 151-160, (2011). DOI: 10.1016/j.epsl.2011.05.050

Rubin, Edward

Abt B et al. Complete genome sequence of Cellulomonas flavigena type strain (134). Stand Genomic Sci. 2010;3(1):15-25.

Abt B et al. Complete genome sequence of Cellulophaga algicola type strain (IC166). Stand Genomic Sci. 2011 Feb;4(1):72-80.

Abt B et al. Complete genome of Leadbetterella byssophila type strain (4M15). Stand Genomic Sci. 2011 Mar 4;4(1):2-12.

Alterovitz G et al. Ontology engineering. Nat Biotech. 2010;28(2), 128-130. doi: 10.1038/nbt0210-128.

Alverson AJ et al. Origins and Recombination of the Bacterial-Sized Multichromosomal Mitochondrial Genome of Cucumber. Plant Cell. 2011 Jul 8.

Andersen MR et al. Comparative genomics of citric-acid producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88. Genome Res. 2011 Jun;21(6):885-97. Epub 2011 May 4.

Anderson I et al. Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes. PLoS One. 2011 May 25, 6(5):e:20237.

Anderson I et al. Complete genome sequence of Methanothermus fervidus type strain (V24S). Stand Genomic Sci. 2010 Nov20;3(3):315-24.

Antezana E et al. ONTO-ToolKit: enabling bio-ontology engineering via Galaxy. BMC Bioinformatics. 2010;11(Suppl 12), S8. doi: 10.1186/1471-2105-11-S12-S8.

Aswani, A et al. Nonparametric identification of regulatory interactions from spatial and temporal gene expression data. BMC Bioinformatics. 2010;11:413.

Banks JA et al. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science. 2011 May 20;332(6032):960-3. Epub 2011 May 5.

Blumer-Schuette SE et al. Complete genome sequences for the anaerobic, extremely thermophilic plant biomass-degrading bacteria Caldicellulosiruptor hydrothermalis, Caldicellulosiruptor kristjanssonii, Caldicellulosiruptor kronotskyensis, Caldicellulosiruptor owensensis, and Caldicellulosiruptor lactoaceticus. J Bacteriol. 2011 Mar;193(6):1483-4.

Brambilla E et al. Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847). Stand Genomic Sci. 2010 Oct 27;3(2):203-11.

Bresson A et al. Qualitative and quantitative resistances to leaf rust finely mapped within two nucleotide-binding site leucine-rich repeat (NBS-LRR)-rich genomic regions of chromosome 19 in poplar. New Phytol. 2011 Jun 10. doi: 10.1111/j.1469-8137.2011.03786.x.

Brown SD et al. Genome sequence of the mercury-methylating strain Desulfovibrio desulfuricans ND132. J Bacteriol. 2011 Apr;193(8):2078-9.

Brown SD et al. Genome Sequence of Mercury-Methylating and Pleomorphic Desulfovibrio J Bacteriol. 2011;193:4037-4038.

Bruno VM et al. Comprehensive annotation of the transcriptome of the human fungal pathogen Genome Res. 2010 Oct;20(10):1451-8.

Brumm P et al. Functional annotation of Fibrobacter succinogenes S85 carbohydrate active Appl Biochem Biotechnol. 2011 Mar;163(5):649-57.

Cai F et al. â€œBioinformatic Identification and Structural Characterization of a New Carboxysome Shell Protein.â€ Functional Genomics and Evolution of Photosynthetic Systems, ed. Burnap. R.L. and W. Vermaas. In press.

Campbell MA et al. Nitrosococcus watsonii sp. nov., a new species of marine obligate ammonia- oxidizing bacteria that is not omnipresent in the world's oceans, calls to validate the names 'Nitrosococcus halophilus' and 'Nitrosomonas mobilis.' FEMS Microbiol Ecol. 2011 Apr;76(1):39-48.

Cannon GR et al. Carboxysomal carbonic anhydrases: Structure and role in microbial CO2 fixation. Biochimica Biophysica Acta. 2010;1804: 382-392.

ChaÌbera P et al. Excited-state properties of the 16 kDa red carotenoid protein from Arthrospira maxima. Biochim. Biophys. Acta. 2011 1807(1):30-5.

Chain PS et al. Genomics for key players in the N cycle from Guinea pigs to the next frontier. Methods Enzymol. 2011;496:289-318.

Chandler JA et al. Bacterial Communities of Diverse Drosophila Species: Ecological context of a host-microbe model system. PLoS Genetics. In press.

Chertkov O et al. Complete genome sequence of Thermomonospora curvata type strain (B9). Stand Genomic Sci. 2011 Feb;4(1):13-22.

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Wu D et al. Stalking the fourth domain in metagenomic data: searching for and possible discovery of novel deep branches in phylogenetic trees. PLoS One. 2011. 6(3): e18011.

Xie G et al. Community and gene composition of a human dental plaque microbiota obtained by metagenomic sequencing. Mol Oral Microbiol. 2010 Dec;25(6):391-405. doi: 10.1111/j.2041-1014.2010.00587.x.

Yang X et al. Discovery and annotation of small proteins using genomics, proteomics, and computational approaches. Genome Res. 2011 Apr;21(4):634-41. Epub 2011 Mar 2.

Yasawong M et al. Complete genome sequence of Arcanobacterium haemolyticum type strain (11018). Stand Genomic Sci. 2011;3:126-135.

Yilmaz P et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotech. 2011;29:415- 420.

Yilmaz S, Allgaier M, Hugenholtz P. Multiple displacement amplification compromises quantitative analysis of metagenomes. Nat Methods. 2010 Dec;7(12):943-4.

Zeytun A et al. Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6T). Stand Genomic Sci. 2011 Apr;4(2):131-43.

Zhang T et al. Identification of haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance. Green Chem. 2011 July; doi:10.1039/C1GC15193B.

Zhao B et al. Complete Genome Sequence of the Anaerobic Halophilic Alkalithermophile Natranaerobius thermophilus JW/NM-WN-LFT. J Bacteriol. 2011 Aug;193(15):4023-4.

Rubin, Yoram

de Barros FPJ, S. Ezzedine, Y. Rubin. Impact of hydrogeological data on measures of uncertainty, site characterization and environmental performance metrics. Adv Water Resour (2011), doi:10.1016

de Barros FPJ, Y. Rubin, Modelling of block-scale macrodispersion as a random function, J. Fluid Mechanics (2011), doi:10.1017

Nowak, W., F. P. J. de Barros, and Y. Rubin, Bayesian geostatistical design: Task-driven optimal site investigation when the geostatistical model is uncertain, Water Resour. Res., 46, W03535, doi:10.1029/2009WR008312, 2010.

Nowak, W., Y. Rubin and F. P.J. de Barros, A Hypothesis-Driven Approach to Optimal Site Investigation, Submitted for Review, Water Resour. Res., (2011)

Ruebel, Oliver

Keynote Address: Lucy T. Nowell, Office of Advanced Scientific Computing Research, Office of Sciences, U.S. DOE

Visualizing Multiscale Simulation Data: Brain Blood Flow, Leopold Grinberg (Brown University), Joseph Insley (Argonne National Laboratory), Michael Papka (Argonne National Laboratory)

Towards simulation-time data analysis and I/O acceleration on leadership-class systems Venkatram Vishwanath, (Argonne National Laboratory) Mark Hereld, (Argonne National Laboratory) Michael Papka, (Argonne National Laboratory)

Atypical Behavior Identification in Large Scale Network Traffic, Daniel Best (Pacific Northwest National Laboratory), Ryan Hafen (Pacific Northwest National Laboratory), Bryan Olsen (Pacific Northwest National Laboratory), William Pike (Pacific Northwest National Laboratory)

Analysis of Large-Scale Scalar Data Using Hixels, David Thompson (Sandia National Laboratories) Joshua Levine (SCI Institute, Univ. of Utah) Janine Bennett (Sandia National Laboratories) Peer-Timo Bremer (Lawrence Berkeley National Laboratory) Attila Gyulassy (University of Utah) Philippe Pebay (Sandia National Laboratories) Valerio Pascucci (University of Utah)

Revisiting Wavelet Copression with JPEG 2000 to Ensure Data Precision for Large-Scale Data, Jonathan Woodring (Los Alamos National Laboratory), James Ahrens (Los Alamos National Laboratory), Susan Mniszewski (Los Alamos National Laboratory), Christopher Brislawn (Los Alamos National Laboratory), David DeMarle (Kitware Inc.)

Histogram Spectra for Multivariate Time-Varying Volume LOD Selection, Steven Martin Ohio State University Han-Wei Shen Ohio State University

Parallel Clustering for Visualizing Large Scientific Line Data, Jishang Wei (University of California at Davis), Hongfeng Yu (Sandia National Laboratories), Kwan-Liu Ma (University of California at Davis), Jackie Chen (Sandia National Laboratories)

Evaluating the Benefits of An Extended Memory Hierarchy for Parallel Streamline Algorithms, David Camp (University of California at Davis), Hank Childs (Lawrence Berkeley National Laboratory), Amit Chourasia (San Diego Supercomputer Center), Christoph Garth (University of California at Davis), Kenneth Joy (University of California at Davis)

Parallel In Situ Indexing for Data-intensive Computing, Jinoh Kim (Lawrence Berkeley National Laboratory), Hasan Abbasi (University of Tennessee, Knoxville), Luis Chacon (Oak Ridge National Laboratory), Ciprian Docan (Rutgers University), Scott Klasky (Oak Ridge National Laboratory), Qing Liu (Oak Ridge National Laboratory), Norbert Podhorszki (Oak Ridge National Laboratory), Arie Shoshani (Lawrence Berkeley National Laboratory), Kesheng Wu (Lawrence Berkeley National Laboratory)

Incremental, Approximate Database Queries and Uncertainty for Exploratory Visualization, Danyel Fisher (Microsoft Research)

Parallel Visualization on Large Clusters Using MapReduce, Huy Vo Utah/NYU Poly Jonathan Bronson SCI Institute, University of Utah), Brian Summa SCI Institute, University of Utah), Joao Comba Universidade Federal do Rio Grande do Sul), Juliana Freire SCI Institute, University of Utah), Bill Howe Unversity of Washington), Valerio Pascucci University of Utah), Claudio Silva University of Utah)

The ParaView Coprocessing Library: A scalable, general purpose in situ visualization library, Nathan Fabian (Sandia National Laboratories), Kenneth Moreland (Sandia National Laboratories), David Thompson (Sandia National Laboratories), Andy Bauer (Kitware, Inc.), Pat Marion (Kitware Inc.), Berk Geveci (Kitware Inc.), Michel Rasquin (University of Colo

Ryne, Robert

J. Chou, K. Wu, O. Rubel, M. Howison, J. Qiang, Prabhat, B. Austin, E.W. Bethel, R. Ryne, A. Shoshani, "Parallel Index and Query for Large Scale Data Analysis ,. to appear in SuperComputing 2011.

J. Qiang, J. Wu, "Generation of attosecond coherent X-ray radiation through modulation compression," J. Mod. Optics, 1 (2011).

J. Qiang, J. Wu, "Generation of coherent X-ray radiation through modulation compression," Nuclear Instruments & Methods in Physics Research A 640, p. 228 (2011).

S

Saad, Yousef

S. MacLachlan, D. Osei-Kuffuor, and Yousef Saad, Modification and compensation strategies for threshold-based incomplete factorizations. Report umsi-2011-yy, Minnesota Supercomputer Institute, University of Minnesota, Minneapolis, MN, 2011.

H. R. Fang and Y. Saad, A filtered Lanczos procedure for extreme and interior eigenvalue problems. Report umsi-2011-xx, Minnesota Supercomputer Institute, University of Minnesota, Minneapolis, MN, 2011.

Sai, Na

Hybrid density functional study of oligothiophene/ZnO Interface for photovoltaics. N. Sai, K. Leung, J. Chelikowsky, Phys. Rev. B 83, 121309(R) (2011)

Salahuddin, Sayeef

Y. Yoon, D. E. Nikonov, and S. Salahuddin, Role of Phonon Scattering in Graphene Nanoribbon Transistors: Nonequilibrium Green s Function Method with Real Space Approach , Applied Physics Letters, vol. 98, p. 203503 (2011).

Kartik Ganapathi and Sayeef Salahuddin, "Heterojunction Vertical Band-to-Band Tunneling Transistors for Steep Subthreshold Swing and High ON Current", IEEE Electron Dev Lett., Vol. 32, No. 5, pp. 689-691, 2011.

Yoon, Y. and Salahuddin, S., Barrier-free tunneling in a carbon heterojunction transistor. Appl. Phys. Lett., 2010. [issue cove story]

Yoon, Y. and S. Salahuddin, Analysis of InAs vertical and lateral band-to-band tunneling transistors: Leveraging vertical tunneling for improved performance. Appl. Phys. Lett., 2010.

Salahuddin, S., Inverse temperature dependence of subthreshold slope in graphene nanoribbon tunneling transistors. Appl. Phys. Lett., 2010.

Kim, S. and S. Salahuddin, Performance analysis of carbon-based tunnel field-effect transistors for high frequency and ultralow power applications. Appl. Phys. Lett., 2010.

Ford, A., et al., Ultrathin compound semiconductor on insulator layers for high-performance nanoscale transistors. Nature, 2010.

Savage, Martin

Nuclear Physics from Lattice QCD. By S.R. Beane, W. Detmold, K. Orginos, M.J. Savage. [arXiv:1004.2935 [hep-lat]]. Prog.Part.Nucl.Phys. 66 (2011) 1-40.

Evidence for a Bound H-dibaryon from Lattice QCD. By NPLQCD Collaboration (S.R. Beane et al.). [arXiv:1012.3812 [hep-lat]]. Phys.Rev.Lett. 106 (2011) 162001.

High Statistics Analysis using Anisotropic Clover Lattices: (IV) Volume Dependence of Light Hadron Masses. By S.R. Beane, E. Chang, W. Detmold, H.W. Lin, T.C. Luu, K. Orginos, A. Parreno, M.J. Savage et al.. [arXiv:1104.4101 [hep-lat]]. Phys.Rev. D84 (2011) 014507.

Extracting Scattering Phase-Shifts in Higher Partial-Waves from Lattice QCD Calculations. By Thomas Luu, Martin J. Savage. [arXiv:1101.3347 [hep-lat]]. Phys.Rev. D83 (2011) 114508.

Lattice QCD study of mixed systems of pions and kaons. By William Detmold, Brian Smigielski. [arXiv:1103.4362 [hep-lat]]. Phys.Rev. D84 (2011) 014508.

Nucleon-Nucleon Scattering in a Harmonic Potential. By Thomas Luu, Martin J. Savage, Achim Schwenk, James P. Vary. [arXiv:1006.0427 [nucl-th]]. Phys.Rev. C82 (2010) 034003.

Saykally, Richard

A. M. Duffin, C. P. Schwartz, A. H. England, J. S. Uejio, D. Prendergast, and R. J. Saykally "pH-Dependent X-ray Absorption Spectra of Aqueous Boron Oxides," J. Chem. Phys. 134, 154503 (2011).

A. M. Duffin, A. H. England, C. P. Schwartz, J. S. Uejio, G. C. Dallinger, O. Shih, D. Prendergast, and R. J. Saykally "Electronic Structure of Aqueous Borohydride: A Potential Hydrogen Storage Medium" Phys. Chem. Chem. Phys. 13, 17077 (2011). Cover article.

A. H. England, A. M. Duffin, C. P. Schwartz, J. S. Uejio, D. Prendergast, and R. J. Saykally "On the Hydration and Hydrolysis of Carbon Dioxide," Chem. Phys. Letters (2011) - In Press.

Schaefer, Henry

P. R. Schreiner, H. P.Reisenauer, D. Ley, D. Gerbig, C.-H. Wu and W. D. Allen, "Methylhydroxycarbene: Tunneling Control of a Chemical Reaction", Science, 332, 1300 (2011).

T. Lu, J. J. Wilke, Y. Yamaguchi and H. F. Schaefer, "Anharmonic Rovibrational Analysis for Disilacyclopropenylidene (Si2CH2), "J. Chem. Phys., 134, 164101 (2011).

P. N. Ascik, J. J. Wilke, A. C. Simmonett, Y. Yamaguchi and H. F. Schaefer, "The Beryllium Tetramer: Profiling an Elusive Molecule", J. Chem. Phys., 134, 074110 (2011).

B. S. Narendrapurapu, A. C. Simmonett, H. F. Schaefer, J. A. Miller and S. J. Klippenstein, "Combustion Chemistry: Important Features of the C3H5 Potential Energy Surface, Including Allyl Radical, Propargyl + H2, Allene + H, and Eight Transition States", J. Phys. Chem. A, (submitted).

Scheibe, Timothy

Bandara, U. C., A. M. Tartakovsky, and B. J. Palmer, Pore-scale study of capillary trapping mechanisms during CO2 injection in geological formations, accepted August 2011 for publication in International Journal of Greenhouse Gas Control, in press, 2011.

Schiavilla, Rocco

E. Adelberger et al. "Solar fusion cross sections II: the pp chain and CNO cycles", Rev. Mod. Phys. 83, 195 (2011)

L.E. Marcucci et al, "Muon capture on deuteron and 3He", Phys. Rev. C 83, 014002 (2011)

S. Pastore et al, "The two-nucleon charge operator in chiral effective field theory", Phys. Rev. C 84, 024001 (2011)

W. Tornow et al, "Two-body photodisintegration of He-3 between 7-MeV and 16-MeV", Phys. Lett. B 702, 121-126 (2011)

L. Girlanda et al, "Thermal neutron captures on d and 3He", Phys. Rev. Lett. 105, 232502 (2010)

M. Viviani et al, "The parity-violating asymmetry in the 3He(n,p)3H reaction" Phys. Rev. C 82, 044001 (2010)

Schrier, Joshua

M. D. Smith*, S. M. Blau*, K. B. Chang*, Matthias Zeller, J. Schrier, A. J. Norquist, "Beyond Charge Density Matching: The Role of C-H...O Interactions in the Formation of Templated Vanadium Tellurites" Cryst. Growth Des. 11, 4213-4219 (2011).

J. H. Olshansky*, S. M. Blau*, M. Zeller, J. Schrier, A. J. Norquist, "Understanding an order-disorder phase transition in ionothermally synthesized gallium phosphates" Cryst. Growth Des. 11, 3065-3071 (2011)

E. C. Glor*, S. M. Blau*, J. Yeon, M. Zeller, P. S. Halasyamani, J. Schrier, A. J. Norquist, "[R- C7H16N2][V2Te2O10] and [S-C7H16N2][V2Te2O10]; new polar templated vanadium tellurite enantiomers" J. Solid State Chem. 184, 1445-1450 (2011)

Schuchardt, Karen

Jin C, S Sehrish, W Liao, A Choudhary, and KL Schuchardt. 2011. "Improving the Average Response Time in Collective I/O." In EuroMPI.

Bruce Palmer , Annette Koontz, Karen Schuchardt, Ross Heikes , David Randall. 2011. "An IO API for a Global Cloud Resolving Model". In Environmental Modeling and Software

Schultz, David

M. S. Pindzola, F. J. Robicheaux, and J. P. Colgan, Singe and double ionization in C+6 + He collisions, Physical Review A 82, 042719 (October 2010)

J. Simic, D. R. Schultz, R. J. Mawhorter, J. B. Greenwood, C. Winstead, B. V. McCoy, S. J. Smith, and A. Chutjian, Measurement and calculation of absolute single and multiple charge exchange cross sections for Fe+q ions impacting H_2 O, Astrophysical Journal 722, 435 (October 2010)

S. Y. Ovchinnikov, J. B. Sternberg, J. H. Macek, T. G. Lee, and D. R. Schultz, Creating and manipulating vortices in atomic wavefunctions with short electric field pulses, Physical Review Letters 105, 203005 (November 2010)

M. S. Pindzola, T. G. Lee, and J. P. Colgan, Antiproton-impact single and double ionization of H_2, Journal of Physics B 43, 235201 (December 2010)

S. Y. Ovchinnikov, J. H. Macek, L. P. H. Schmidt, and D. R. Schultz, Theoretical demonstration of the feasibility of observing vortices in the ejected electron spectrum in bare-ion - two-electron-atom collisions, Physical Review A 83, 060701 (June 2011)

M. E. Bannister and D. R. Schultz, Electron-impact dissociation of hydrocarbon molecular ions, Atomic and Plasma Material Interaction Data for Fusion 16, 1 (August 2011)

J. P. Colgan, M. S. Pindzola, F. J. Robicheaux, and M. F. Ciapina, Fully differential cross sections for the single ionization of He, Journal of Physics B 44, 175205 (September 2011)

Sednev, Igor

Sednev, I. and S. Menon, 2011: Analyzing numerics of bulk microphysics schemes in community models: warm rain processes. Geosci. Model Dev. Discuss., 4, 1403-1434.

Selloni, Annabella

Aschauer U., Selloni A., "The structure of the rutile TiO2(011) surface in aqueous environment", Physical Review Letters, 106(16), 166102 (2011)

Aschauer, U., Chen, J. & Selloni, A. Peroxide and superoxide states of adsorbed O2 on anatase TiO2 (101) with subsurface defects. Physical Chemistry Chemical Physics 12, 12956-12960 (2010).

Chen, J., Wu, X. & Selloni, A. Electronic structure and bonding properties of cobalt oxide in the spinel structure. Physical Review B 83, 245204 (2011).

Selloni, Annabella

"Theoretical design by first principles molecular dynamics of a bio-inspired electrode-catalyst system for electrocatalytic hydrogen production from acidified water", Zipoli F., Car R., Cohen M. H., and Selloni A. J. Chem. Theo. Comput. 2010, 6, 3490.

"Electrocatalyst design from first principles: a hydrogen-production catalyst inspired by Nature", Zipoli F., Car R., Cohen M. H., and Selloni A. Catalysis Today 2011, 165, 160.

"Oxidation state changes and electron flow in enzymatic- and electro-catalysis via Wannier-function analysis", Sit P. H.-L., Zipoli F., Chen J., Car R., Cohen M. H., Selloni A., Chem. Eur. J. (ASAP).

"Simple, unambiguous theoretical approach to oxidation state determination via first-principles calculations", Sit P. H.-L., Car R., Cohen M. H., Selloni A., Inorg. Chem. (ASAP).

Sengupta, Pinaki

T. Suzuki, Y. Tomita, N. Kawashima and P. Sengupta, Phys. Rev. B, 82, 214404 (2010).

Y. Kohama, et. al. Phys. Rev. Lett. 106, 037203 (20011).

V. S. Zapf, P. Sengupta, C. D. Batista, F. Nasreen, F. Wolff-Fabris, and A. Paduan-Filho, Phys. Rev. B 83, 140405 (2011)

Y. Kato, C. D. Batista, and I. Vekhter, Phys. Rev. Lett. 107, 096401 (2011)

Y. Kato, I. Martin, and C. D. Batista, Phys. Rev. Lett. 105, 266405 (2010)

Shalf, John

Robert Preissl, Nathan Wichmann, Bill Long, John Shalf, Stephane Ethier, Alice Koniges, Multithreaded Global Address Space Communication Techniques for Gyrokinetic Fusion Applications on Ultra-Scale Platforms, SC11, 2011. (nominated for best paper award)

Jens Krueger, David Donofrio, John Shalf, Marghoob Mohiyuddin, Samuel Williams, Leonid Oliker, Franz-Josef Pfreundt, Hardware/Software Co-Design for Energy-Efficient Seismic Modeling, SC11, 2011.

Performance of Density Functional Theory codes on Cray XE6 Zhengji Zhao, and Nicholas Wright Proceedings of the 2011 Cray User Group; May 23-26, 2010; Fairbanks, Alaska.

Acceleration of porous media simulations on the Cray XE6 platform K. Fagnan, M. Lijewski, G. Pau and N. Wright, Proceedings of the 2011 Cray User Group; May 23-26, 2010; Fairbanks, Alaska.

Performance characterization and implications for fusion co-design applications Praveen Narayanan, Alice Koniges, Leonid Oliker, Robert Preissl, Samuel Williams, Nicholas Wright, Stephane Ethier, Weixing Wang, Maxim Umansky, Xueqiao Xu, and Jeff Candy. Proceedings of the 2011 Cray User Group; May 23-26, 2010; Fairbanks, Alaska.

The NERSC- Cray Center of Excellence: Performance Optimization for the Multicore Era. Nicholas J. Wright, Hongzhang Shan, Filip Blagojevic , Harvey Wasserman, John Shalf, Katherine Yelick, Stephane Ethier, Karl

Fuerlinger Marcus Wagner, Nathan Wichmann, Sarah Anderson, and Mike Aamodt. Proceedings of the 2011 Cray User Group; May 23-26, 2010; Fairbanks, Alaska.

Shang, Shunli

S. L. Shang, Y. Wang, D. E. Kim, C. L. Zacherl, Y. Du, and Z. K. Liu, Structural, vibrational, and thermodynamic properties of ordered and disordered Ni1-xPtx alloys from first-principles calculations, Phys. Rev. B 83 (2011) 144204.

S. L. Shang, J. Wang, Y. Wang, Y. Du, and Z. K. Liu, Phonon and thermodynamic properties of Al-Mn compounds: A first-principles study, Comput. Mater. Sci. 50 (2011) 2096-2103.

S. L. Shang, J. E. Saal, Z. G. Mei, Y. Wang, and Z. K. Liu, Magnetic thermodynamics of fcc Ni from first-principles partition function approach, J. Appl. Phys. 180 (2010) 123514.

Y. Wang, S. L. Shang, H. Zhang, L. Q. Chen, and Z. K. Liu, Thermodynamic fluctuations in magnetic states: Fe3Pt as a prototype, Phil. Mag. Lett. 90 (2010) 851-859.

Y. Wang, J. E. Saal, P. P. Wu, J. J. Wang, S. L. Shang, Z. K. Liu, and L. Q. Chen, First-principles lattice dynamics and heat capacity of BiFeO3, Acta Mater. 59 (2011) 4229-4234.

Y. Wang, J. E. Saal, S. L. Shang, X. D. Hui, L. Q. Chen, and Z. K. Liu, Effects of spin structures on Fermi surface topologies in BaFe2As2, Solid State Commun. 151 (2011) 272-275.

Y. Wang, J. J. Wang, J. E. Saal, S. L. Shang, L. Q. Chen, and Z. K. Liu, Phonon dispersion in Sr2RuO4 studied by a first-principles cumulative force- constant approach, Phys. Rev. B 82 (2010) 172503.

Y. Wang, J. E. Saal, Z. G. Mei, P. P. Wu, J. J. Wang, S. L. Shang, Z. K. Liu, and L. Q. Chen, A first-principles scheme to phonons of high temperature phase: No imaginary modes for cubic SrTiO3, Appl. Phys. Lett. 97 (2010) 162907.

Shay, Michael

Wu, P., M. A. Shay, T. D. Phan, M. Oieroset, and M. Oka, Effect of inflow density on ion diffusion region of magnetic reconnection: Particle-in-cell simulations, Physics of Plasmas, In Press, 2011

Parashar, T. N., S. Servidio, M. A. Shay, B. Breech, and W. H. Matthaeus, Effect of driving frequency on excitation of turbulence in a kinetic plasma, Physics of Plasmas, Vol. 18, 092302, 2011.

Shay, M. A., J. F. Drake, J. P. Eastwood, and T. D. Phan, Super-Alfvenic propagation of reconnection signatures and Poynting flux during substorms,, Physics Review Letters, Vol. 107, 065001, 2011.

Parashar, T. N., S. Servidio, B. Breech, M. A. Shay, and W. H. Matthaeus, Kinetic Driven Turbulence: Structure in Space and Time, Physics of Plasmas, Vol. 17, 102304, 2010.

Malakit, K., M. A. Shay, P. A. Cassak, C. Bard, Scaling of asymmetric magnetic reconnection: Kinetic particle-in-cell simulations, Journal of Geophysical Research , Vol. 115, A10223, 2010.

Shields, George

Berhane Temelso, Kaye Archer* and George C. Shields. "Benchmark Structures and Binding Energies of Small Water Clusters with Anharmonicity Corrections" J. Phys. Chem. A. (2011) Accepted.

Berhane Temelso and George C. Shields. "The Effect of Anharmonicity on Hydrogen-Bonded Systems: The Case of Water Clusters"J. Chem. Theory and Comp. 7 (2011) 2804-2817

Robert M. Shields*, Berhane Temelso, Kaye A. Archer,* Thomas E. Morrell* and George C. Shields. "Accurate Predictions of Water Cluster Formation, (H2O)n=2-10" J. Phys. Chem. A 114 (2010) 11725-11737

Shigemitsu, Junko

Eric B. Gregory et al, HPQCD collaboration, Precise B, B_s and B_c meson spectroscopy from full lattice QCD. Phys. Rev. D83:014506 (2011) arXiv:1010.3848.

J. Koponen et al, HPQCD collaboration, Heavy-light current-current correlators, Proceedings Lattice 2010, arXiv:1011.1208.

E. Follana et al, HPQCD collaboration, Masses and decay constants from relativistic highly improved staggered quarks in full lattice QCD, Proceedings Lattice 2010, Pos LATTICE2010:305 (2010).

Sim, Alex

Adaptive Transfer Adjustment in Efficient Bulk Data Transfer Management for Climate Dataset, A. Sim, M. Balman, D. Williams, A. Shoshani, V. Natarajan, Proceedings of the 22nd IASTED International Conference on Parallel and Distributed Computing and Systems (PDPS2010), 2010.

Finding Tropical Cyclones on a Cloud Computing Cluster: Using Parallel Virtualization for Large-Scale Climate Simulation Analysis, D. Hasenkamp, A. Sim, M. Wehner, K. Wu, Proceedings of the 2nd IEEE International Conference on Cloud Computing Technology and Science, 2010.

Finding Tropical Cyclones on Clouds, D. Hasenkamp under the supervision of A. Sim, M. Wehner, K. Wu, ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis (SC10), 2010. Won the Third place in ACM Student Research Poster Competition.

Simeon, Tomekia

Theoretical Prediction of Multiple Binding Sites for Uranyl Sorption on Carbon Nanotubes: A Quantum Chemical Approach.

Sinclair, Donald

Magnetic monopole plasma phase in (2+1)d compact quantum electrodynamics with fermionic matter By Wesley Armour, Simon Hands, John B. Kogut, Biagio Lucini, Costas Strouthos, Pavlos Vranas. Phys.Rev.D84:014502,2011,. [arXiv:1105.3120]

Thermodynamics of lattice QCD with 2 sextet quarks on $N_t$=8 lattices By J.B. Kogut & D.K. Sinclair. [arXiv:1105.3749] ANL-HEP-PR-10-45 (May 2011) 21p (Phys. Rev. D, in press).

Bottomonium above deconfinement in lattice nonrelativistic QCD By G. Aarts, S. Kim, M.P. Lombardo, M.B. Oktay, S.M. Ryan, D.K. Sinclair, J.-I. Skullerud. Phys.Rev.Lett.106:061602,2011,. [arXiv:1010.3725]

Chiral symmetry breaking and monopole dynamics in non-compact QED3 coupled to a four-fermi interaction By W. Armour, John B. Kogut, Costas Strouthos. Phys.Rev.D82:014503,2010,. [arXiv:1004.3053]

Thermodynamics of lattice QCD with 2 flavours of colour-sextet quarks: A model of walking/conformal Technicolor By J.B. Kogut & D.K. Sinclair. Phys.Rev.D81:114507,2010,. [arXiv:1002.2988]

Smit, Berend

M. Haranczyk, J.A. Sethian - Automatic structure analysis in high-throughput characterization of porous materials Journal of Chemical Theory and Computation 6 (2010) 3472-3480

T.F. Willems, C.H. Rycroft, M. Kazi, J.C. Meza, M. Haranczyk Algorithms and tools for high-throughput geometry-based analysis of crystalline porous materials Microporous and Mesoporous Materials doi:10.1016/j.micromeso.2011.08.020

Smith, Jeremy

Barbara Collignon, Roland Schulz, Jeremy Smith, and Jerome Baudry Task-parallel MPI implementation of Autodock4 for docking of very large databases of compounds using High Performance Super-Computers. Journal of Computational Chemistry, 2011,32(6):1202-9

Smoot, George

J.L. Christiansen, E. Albin, T. Fletcher, J. Goldman, I.P.W. Teng, M. Foley, G.F. Smoot, Search for Cosmic Strings in the COSMOS Survey, Phys. Rev. D, (2011).

Snurr, Randall

R. B. Getman, J. H. Miller, K. Wang, R. Q. Snurr, Metal Alkoxide Functionalization in Metal-Organic Frameworks for Enhanced Ambient-Temperature Hydrogen Storage J. Phys. Chem. C. 2011, 115, 2066-2075.

P. Ryan, O.K. Farha, L.J. Broadbelt, R. Q. Snurr, Computational Screening of Metal-Organic Frameworks for Xenon/Krypton Separation. AIChE Journal, 2011, 57, 7, 1759.

Sosonkina, Masha

F. Liu, R. Mundhe, M. Sosonkina, C. Cockrell, M. Aronnax, P. Maris, and J.P. Vary, A data management sys- tem for ab-initio nuclear physics applications, accepted in 2011 Spring Simulation Multiconf., High Performance Computing Symp. (HPC 2011).

A. Srinivasa, M. Sosonkina, P. Maris, and J.P. Vary, Dynamic adaptations in ab-initio nuclear physics calculations on multicore computer architectures, accepted in 12th Int l Workshop on Parallel and Distributed Scientific and Engineering Computing (PDSEC 2011)

J.P. Vary, H. Honkanen, J. Li, P. Maris, A.M. Shirokov, S.J. Brodsky, A. Harindranath, G.F. De Teramond, E.G. Ng, C. Yang and M. Sosonkina, Ab-initio Hamiltonian approach to light nuclei and to quantum field theory, Journal of Physics, 75 (2010), pp. 39 49

F. Liu and M. Sosonkina, A multilevel parallelism support for multi-physics coupling, accepted in Int l Conference on Computational Science (ICCS 2011).

N. Radcliffe, L.T. Watson, M. Sosonkina, A comparison of alternatives for communicating with spawned processes, accepted in 48th Annual ACM Southeast Conference (ACMSE 2011).

Sovinec, Carl

J. R. King, C. R. Sovinec, and V. V. Mirnov, "First-Order Finite-Larmor-Radius Effects on Magnetic Tearing in Pinch Configurations," Physics of Plasmas 18, 042303 (2011).

R. A. Bayliss, C. R. Sovinec, and A. J. Redd, "Zero-beta Modeling of Coaxial Helicity Injection in the HIT-II Spherical Torus," Physics of Plasmas 18, 94502 (2011).

Spentzouris, Panagiotis

Cho Ng, R.J. England, L.-Q. Lee, R. Noble, V. Rawat, J. Spencer, Transmission and Radiation of an Accelerating Mode in a Photonic Bandgap Fiber, Phys.Rev.ST Accel.Beams 13 (2010) 12130

Magnetic control of particle-injection in plasma based accelerators. J. Vieira, S.F. Martins, V.B. Pathak, (Lisbon, IST) R.A. Fonseca, (Lisbon, IST & Lisbon, CFP) , W.B. Mori (UCLA) , L.O. Silva, (Lisbon, IST) . Jul 2011. Published in Phys.Rev.Lett.106:225001,2011.

Simulation of the electron cloud in the Fermilab Main Injector. Paul L.G. Lebrun, (Fermilab) , Seth A. Veitzer, Peter Stoltz, (Tech-X, Boulder) , Panagiotis G. Spentzouris, (Fermilab) , John R. Cary, (Tech-X, Boulder) . FERMILAB-PUB-11-228-APC-CD, May 2011. Submitted to Phys.Rev.ST Accel.Beams Control of focusing fields in laser-plasma accelerators using higher-order modes.

E. Cormier-Michel, E. Esarey, C.G.R. Geddes, C.B. Schroeder, (LBL, Berkeley) , K. Paul, P.J. Mullowney, J.R. Cary, (Tech-X, Boulder) , W.P. Leemans, (LBL, Berkeley) . Mar 1, 2011. (Published Mar 1, 2011).

Published in Phys.Rev.ST Accel.Beams 14:031303,2011 Coupling impedance and wake functions for laminated structures with an application to the Fermilab Booster. Alexandru Macridin, Panagiotis Spentzouris, James Amundson, (Fermilab) , Linda Spentzouris, Daniel McCarron, (IIT, Chicago) . FERMILAB-PUB-11-172-CD, Apr 2011. (Published Jun 1, 2011).

Published in Phys.Rev.ST Accel.Beams 14:061003,2011 T.M. Austin et al., Validation of frequency extraction calculations from time-domain simulations of accelerator cavities, Comput. Sci. Disc. 4 (2011) 015004.

J.-L. Vay, C. G. R. Geddes, E. Cormier-Michel, D. P. Grote, "Numerical methods for instability mitigation in the modeling of laser wakefield accelerators in a Lorentz-boosted frame," Journal of Computational Physics V 230 No. 5908-5929 (2011).

Spera, Frank

F. Spera, M. Ghiorso and D. Nevins (2011), Structure, thermodynamic and transport properties of liquid MgSiO3: Comparison of molecular models and laboratory results, GCA vol 75, p.1272-1296

F. Spera, B. Martin, M. Ghiorso (2011), Transportand thermodynamic properties of eutectic composition liquid in system CaAl2Si2O8-CaMgSi2O6:Application to Terrestrial Magma oceans, American Mineralogist, in Press

Ghiorso, M.S., Cutler, I., Creamer, J.B., Nevins, D., Martin, G.B., Spera, F.J. (2010) A Thermodynamic Theory for Dense Silicate Liquids That Includes Explicit Provision for Variation in Composition and Fluid Structure, Derived From the Rosenfeld-Tarazona Potential Energy- Temperature Scaling Law. EOS Transactions AGU, 89(53), Fall Meeting Supplement, Abstract MR43B-1802.

Spong, Don

D. A. Spong, "3D effects on energetic particle confinement and stability," Fall, 2010 APS/DPP Invited talk; also, Physics of Plasmas 18, 056109 .

D. A. Spong, J. H. Harris, "New QP/QI Symmetric Stellarator Configurations," Plasma and Fusion Research 5, S2039 Special Issue No. 2 (Dec. 10, 2010).

M.J. Schaffer, J.A. Snipes, P. Gohil, P. de Vries, T.E. Evans,M.E. Fenstermacher, X. Gao, A.M. Garofalo, D.A. Gates, C.M. Greenfield, W.W. Heidbrink, G.J. Kramer, R.J. La Haye, S. Liu, A. Loarte, M.F.F. Nave, T.H. Osborne, N. Oyama, J-K. Park, N. Ramasubramanian, H. Reimerdes, G. Saibene, A. Salmi, K. Shinohara, D.A. Spong, W.M. Solomon, T. Tala, J.A. Boedo, V. Chuyanov, E.J. Doyle, M. Jakubowski, H. Jhang, R.M. Nazikian, V.D. Pustovitov, O. Schmitz, R. Srinivasan, T.S. Taylor, M.R. Wade, K-I. You, L. Zeng, and the DIII-D Team, "ITER Test Blanket Module Error Field Simulation Experiments at DIII-D," Nuclear Fusion 51, 103028 (2011).

D.Testa, D.Spong, T.Panis, P.Blanchard, A.Fasoli, and JET-EFDA contributors, "Recent JET Experiments on Alfven Eigenmodes with Intermediate Toroidal Mode Numbers: Measurements and Modeling of n=3 Toroidal Alfven Eigenmodes with the TAEFL code," Nuclear Fusion 51, 043009 (2011).

B. Tobias, I.G.J. Classen, C.W. Domier, W.W. Heidbrink, N.C. Luhmann, Jr., R. Nazikian, H.K. Park, D. Spong, and M.A. Van Zeeland, " Fast Ion Induced Shearing of 2D Alfven Eigenmodes Measured by Electron Cyclotron Emission Imaging," Phys. Rev. Lett. 106, 075003 (2011).

K. Toi, K. Ogawa, M. Isobe, M. Osakabe, D.A. Spong and Y. Todo, "Energetic- ion-driven Global Instabilities in Stellarator/Helical Plasmas and Comparison with Tokamak Plasmas, " Plasma Phys. Control. Fusion special issue on Physics at the Stellarator/Tokamak Interface, 53, 024008 (2011).

K. Shinohara, T. Kurki-Suonio, D. Spong, O. Asunta, K. Tani, E. Strumberger, S. Briguglio, T. Koskela, G. Vlad, S. Gunter, G. Kramer, S. Putvinski, K. Hamamatsu, ITPA Topical Group on Energetic Particles, "Effect of Complex Symmetry-breakings on Alpha Particle Power Loads on First Wall Structures and Equilibrium on ITER," Nuclear Fusion 51, 103028 (2011).

B. J. Tobias, R. L. Boivin, J. E. Boom, I. G. J. Classen, C. W. Domier, A. J. H. Donne, W. W. Heidbrink, N. C. Luhmann, Jr., T. Munsat, C. M. Muscatello, R. Nazikian, H. K. Park, D. A. Spong, A. D. Turnbull, M. A. Van Zeeland, G. S. Yun, and DIII-D Team, "On the application of electron cyclotron emission imaging to the validation of theoretical models of magnetohydrodynamic activity," Phys. of Plasmas 18 (2011) 056107.

C.D. Beidler, K. Allmaier, M.Yu. Isaev, S.V. Kasilov, W. Kernbichler, G.O. Leitold, H. Maassberg, D.R. Mikkelsen, S. Murakami, M. Schmidt, D.A. Spong, V. Tribaldos and A. Wakasa, "Benchmarking of the mono-energetic transport coefficients - results from the International Collaboration on Neoclassical Transport in Stellarators (ICNTS)," Nuclear Fusion 51, 076001 (2011).

Sprangle, Phillip

D. Kaganovich, M.H. Helle, D.F. Gordon, and A. Ting, Measurements and simulations of shock wave generated plasma-vacuum interface, submitted to Phys. Plasmas

Stetcu, Ionel

I. Stetcu, A. Bulgac, P. Magierski, and K.J. Roche, Isovector Giant Dipole Resonance from the 3D Time- Dependent Density Functional Theory for Superfluid Nuclei, submitted to Phys. Rev. C, arXiv:1108.3064v1 (2011).

Stocks, G. Malcolm

Graphene/graphane Interface Energy and Implications for Defects, Frank W. Averill and James R. Morris, Phys. Rev. B 84, 035411 (2011).

Striolo, Alberto

R.K. Kalluri, D. Konatham, A. Striolo, Aqueous NaCl Solutions within Charged Carbon-Slit Pores: Partition Coefficients and Density Distributions from Molecular Dynamics Simulations, Journal of Physical Chemistry C 115 (2011) 13786-13795.

K. Bui, H.M. Duong, A. Striolo, D.V. Papavassiliou, Heat Transfer Properties of Graphene Sheet Nanocomposites and Comparison to Carbon Nanotube Nanocomposites, Journal of Physical Chemistry C 115 (2011) 3872-3880.

21. D. Konatham, K. Bui, D.V. Papavassiliou, A. Striolo, Thermally Conductive Graphene-Based Nanocomposites, Molecular Physics 109 (2011) 97-111.

B.H. Morrow, D.E. Resasco, A. Striolo, M. Buongiorno Nardelli, CO Adsorption on Noble Metal Clusters: Local-Environment Effects, Journal of Physical Chemistry C 115 (2011) 5637-5647.

Striolo, Alberto

T.A. Ho, D.V. Papavassiliou, L.L. Lee, A. Striolo, Water Can Slip on a Hydrophilic Surface, Proceedings of the National Academy of Sciences of the United States of America (2011) in press.

M. Suttipong, N.R. Tummala, B. Kitiyanan, A. Striolo, Role of Surfactant Molecular Structure on Self Assembly: Aqueous SDBS On Carbon Nanotubes, Journal of Physical Chemistry C 115 (2011) 17286- 17296. Also featured in the cover art of J. Phys. Chem. C, issue # 35, September 8th, 2011.

A. Striolo, From Interfacial Water to Macroscopic Observables: A Review, Adsorption Science and Technology 29 (2011) 211-258. Invited article. Featured on the cover of issue #3.

D. Argyris, T. Ho, D. Papavassiliou, A. Striolo, Equilibrium and Transport Properties of Aqueous Electrolytes within Narrow Slit-Shaped Pores: From Molecular Dynamics Results to Nanofluidic Devices, Chemical Engineering Transactions 24 (2011) 1363-1368.

N.R. Tummala, L. Shi, A. Striolo, Molecular Dynamics Simulations of Surfactants at the Silica-Water Interface: Anionic vs. Nonionic Headgroups, Journal of Colloid and Interface Science 362 (2011) 135- 143.

H. Fan, D.E. Resasco, A. Striolo, Amphiphilic Silica Nanoparticles at the Water-Decane Interface: Insights from Atomistic Simulations, Langmuir 27 (2011) 5264-5274.

D. Argyris, P.D. Ashby, A. Striolo, Assessing the Structure of Interfacial Water via AFM: Insights from Simulations, ACS Nano 5 (2011) 2215-2223.

T.A. Ho, D. Argyris, D.V. Papavassiliou, A. Striolo, L.L. Lee, D.R. Cole, Interfacial Water on Crystalline Silica: A Comparative Molecular Dynamics Simulation Study, Molecular Simulation 37 (2011) 172-195.

D. Argyris, T.A. Ho, D.R. Cole, A. Striolo, Molecular Dynamics Studies of Interfacial Water at the Alumina Surface, Journal of Physical Chemistry C 115 (2011) 2038-2046.

N.R. Tummala, B.H. Morrow, D.E. Resasco, A. Striolo, Stabilization of Aqueous Carbon Nanotube Dispersions using Surfactants: Insights from Molecular Dynamics Simulations, ACS Nano 4 (2010) 7193- 7204.

N.R. Tummala, B.P. Grady, and A. Striolo, Lateral Confinement Effects on the Structural Properties of Surfactant Aggregates: SDS on Graphene, Physical Chemistry Chemical Physics 12 (2010) 13137-13143.

D. Argyris, D.R. Cole, and A. Striolo, Ion-Specific Effects Under Confinement: The Role of Interfacial Water, ACS Nano 4 (2010) 2035-2042.

L. Shi, N.R. Tummala, and A. Striolo, A Molecular Dynamics Study for C12E6 and SDS Surfactants at the Water-Vacuum Interface, Langmuir 26 (2010) 5462-5474.

Surendran Assary, Rajeev

Mechanistic insights into the decomposition of fructose to hydroxy-methyl-furfural in neutral and acid environments using high-level quantum chemical methods, Rajeev S. Assary , Paul C. Redfern, Jeff Greeley, Larry A. Curtiss, Journal of Physical Chemistry B, 2011, 115, 4341-49.

Computational Studies of Polysiloxanes as Electrolyte Solvents: Oxidation potentials and Decomposition reactions, Rajeev S. Assary, Larry A. Curtiss, Paul C. Redfern, Zhengcheng Zhang, Khalil Amine, Journal of Physical Chemistry C, 2011, 115,12216-23

Br nsted-Evans-Polanyi relationships for C-C bond formation and cleavage in Thiamine-catalyzed enzyme catalysis for 2-keto acids, Rajeev S. Assary , Linda J. Broadbelt, Larry A. Curtiss, Journal of Molecular Modeling, 2011, available online, (DOI: 10.1007/s00894-011-1062-z).

Theoretical study of 1,2-hydride shift associated with the Isomerization of Glyceraldehyde to Dihydroxy acetone by Lewis acid active site models, Rajeev S. Assary , Larry A. Curtiss, Journal of Physical Chemistry A, 2011, ASAP (DOI: 10.1021/jp204371g)

Thermochemistry and reaction barriers for the formation of Levoglucosenone from Cellobiose, Rajeev S. Assary , Larry A. Curtiss, 2011, ChemCatChem, under review*.

Vibrational Properties of Levulinic acid and furan derivatives: Raman spectroscopy and theoretical calculations, Taijen Kim, Rajeev S. Assary, Larry A. Curtiss, Christopher Marshal, Peter Stair, Journal of Raman Spectroscopy, 2011, available online, (DOI: 10.1002/jrs.2951).

Acid-catalyzed Furfuryl Alcohol Polymerization : Characterizations of Molecular Structures and Thermodynamic Properties, Taijen Kim, Rajeev S. Assary, Larry A. Curtiss, Christopher Marshal, Peter Stair, ChemCatChem, 2011, 3, 1-9 (Cover story, DOI:10.1002/cctc.201100098).

Tang, Ming

"Anisotropic Phase Boundary Morphology in LiFePO4 Olivine Nanoparticles", M. Tang, J. F. Belak, M. R. Dorr, J. Phys. Chem. C 115, 4922 (2011).

Thakur, Bhupender

Stuart Pittel and Bhupender Thakur. "The Density Matrix Renormalization Group and the Nuclear Shell Model,," Acta Physica Polonica B, v.42, 2011, p. 427. Submitted to PRC CG10313

Systematic study of proton-neutron pairing correlations in the nuclear shell model Y. Lei, S. Pittel, N. Sandulescu, A. Poves, B. Thakur, Y.M. Zhao

Tilson, Jeffrey

J L Tilson, W C Ermler, R J Fowler, Chemical Physics Letters. ( in press, Oct 2011)

Toussaint, Doug

Tuning Fermilab Heavy Quarks in 2+1 Flavor Lattice QCD with Application to Hyperfine Splittings, The Fermilab Lattice and MILC Collaborations: C. Bernard, C. DeTar, M. Di Pierro, A.X. El-Khadra, R.T. Evans, E.D. Freeland, E. G miz, Steven Gottlieb, U.M. Heller, J.E. Hetrick, A.S. Kronfeld, J. Laiho, L. Levkova, P.B. Mackenzie, J.N. Simone, R. Sugar, D. Toussaint, R.S. Van de Water, Phys. Rev. D{\bf 83}, 034503 (2011) [arXiv:1003.1937].

Scaling studies of QCD with the dynamical HISQ action, MILC collaboration: A. Bazavov, C. Bernard, C. DeTar, W. Freeman, Steven Gottlieb, U. M. Heller, J. E. Hetrick, J. Laiho, L. Levkova, M. Oktay, J. Osborn, R.L. Sugar, D. Toussaint, R.S. Van de Water, Phys. Rev. D{\bf 82}, 074501 (2010) [arXiv:1004.0342].

Charm annihilation effects on the hyperfine splitting in charmonium, L. Levkova and C. DeTar, Phys. Rev. D{\bf 83}, 074504 (2011) [arXiv:1012.1837 [hep-lat]].

Tsung, Frank

B. J. Winjum, J. E. Fahlen, F. S. Tsung, and W. B. Mori, Phys. Rev. E 81, 045401(R) (2010).

J. E. Fahlen, B. J. Winjum, T. Grismayer, and W. B. Mori, Phys. Rev. E 83, 045401(R) (2011).

M. Tzoufras, A. R. Bell, P. A. Norreys, and F. S. Tsung, J. Comp. Phys. 230, 17, 6475 - 6494 (2011).

B. J. Winjum, J. E. Fahlen, F. S. Tsung, and W. B. Mori, Anomalously Hot Electrons due to Stimulated Raman Rescattering for Parameters Relevant to the National Ignition Facility , in preparation.

M. Tzoufras and A. R. Bell, in preparation Implicit calculation of the electric field for Vlasov-Fokker-Planck codes that employ the KALOS formalism.

M. Tzoufras, A. R. Bell, F. S. Tsung, B. J. Winjum and W. B. Mori in preparation Non-local transport effects on shock ignition targets.

R. Yan, C. Ren, A. Maximov, W. B. Mori, Z. M. Sheng, and F. S. Tsung, Energetic electron generation through staged-acceleration in the two-plasmon-decay instability in inertial confinement fusion , submitted to Phys. Rev. Lett. (2011).

F. S. Tsung et al, Investigation of High Frequency Hybrid Instability Near the Quarter Critical Layer under IFE Relevant Conditions , submitted to Phys. Rev. Lett (2011).

Tyson, Trevor

P. Gao, Z. Chen, T. A. Tyson, T. Wu, K. H. Ahn, Z. Liu, R. Tappero, S. B. Kim, and S.-W. Cheong , High-pressure structural stability of multiferroic hexagonal RMnO3 (R=Y, Ho, Lu) (2011) , Phys. Rev. B 83, 224113 (2011).

Gao, Peng; Chen, Haiyan; Tyson, Trevor A.; Liu, Zhenxian; Bai, Jianming; Wang, Liping; Choi, Youngjai; Cheong, Sang-Wook Anomalous Phonon Behavior in Orthorhombic LuMnO3 at Low Temperature American Physical Society, APS March Meeting 2011, March 21-25, 2011, abstract D33.007

Yu, Tian; Gao, Peng; Tyson, Trevor, Structure and Magnetic Properties of Electron Doped YMnO3 American Physical Society, APS March Meeting 2011, March 21-25, 2011, abstract B33.013

Chen, H.; Wu, T.; Tyson, T.; Tappero, R.; Huang, L.; Kim, S.; Cheong, S.-W. Local and Long-Range High Pressure Structure of Orthorhombic REMnO3 American Physical Society, APS March Meeting 2011, March 21-25, 2011, abstract D33.005

Vahala, George

J. Yepez, G. Vahala, L. Vahala, and M. Soe, Phys. Rev. Lett. 105, 129402 (2010)

G. Vahala, M. Soe, B. Zhang, J. Yepez, L. Vahala, J. Carter and S. Ziegeler, "Unitary qubit lattice simulations of multiscale phenomena in quantum turbulence", accepted as tehcnical paper, SC11 - Seattle 2011.

G. Vahala, B. Zhang, J. Yepez, L. Vahala, and M. Soe, "Unitary qubit lattice gas representation of 2D and quantum turbulence", chapter in Fluid Dynamics (ISBN:979-953-307-111-3), to appear Oct. 2011

B. Zhang, G. Vahala, L. Vahala, and M. Soe, "A unitary quantum lattice gas algorithm for 2D quantum turbulence", accepted for publication, Phys. Rev. E

G. Vahala, J. Yepez, L. Vahala, M. Soe, B. Zhang and S. Ziegeler, "Poincare reucrrence and intermittent loss of quantum kelvin wave cascades in quantum turbulence", accepted for publication, Phys. Rev. E

G. Vahala, J. Yepez, L. Vahala, M. Soe and S. Ziegeler, IEEE Computer Society (accepted for publication)

G. Vahala, J. Yepez, L. Vahala, M. Soe and S. Ziegeler,SPIE 2011

Van de Walle, Chris

"The particle-size dependence of the activation energy for decomposition of lithium amide", Hoang, K., Janotti, A., and Van de Walle, C. G., Angew. Chem. Int. Ed. 50 (2011).

"Point-defect-mediated dehydrogenation of AlH3", L. Ismer, A. Janotti, and C. G. Van de Walle, APL 97, 201902 (2010).

"Stability and mobility of native point defects in AlH3", L. Ismer, A. Janotti, and J. Neugebauer, Journal of Alloys and Compounds 509, S658 (2011).

P.G. Moses, M. Miao, Q. Yan, and C.G. Van de Walle, "Hybrid functional investigations of band gaps and band alignments for AlN, GaN, InN, and InGaN," J. Chem. Phys. 134, 084703 (2011)

J. B. Varley, H. Peelaers, A. Janotti, C. G. Van de Walle, "Hydrogenated cation vacancies in semiconducting oxides," J. Phys.: Condens. Matter 23, 334212 (2011)

E. Kioupakis, P. Rinke, K. T. Delaney, and C. G. Van de Walle, "Indirect Auger recombination as a cause of efficiency droop in nitride light-emitting diodes," Appl. Phys. Lett. 98, 161107 (2011)

Varga, Kalman

V. A. Goncharov and K. Varga Multidomain decomposition approach to time-dependent density functional calculations Phys. Rev. B 83, 035118 (2011)

S. Bubin, K. Varga First-principles time-dependent simulation of laser-assisted desorption of hydrogen atoms from H-Si(111) surface Appl. Phys. Lett. 98, 154101 (2011)

Brandon G. Cook, Peter Dignard, and Kalman Varga Calculation of electron transport in multi-terminal systems using complex absorbing potentials Phys Rev. B 2011,Phys. Rev. B 83, 205105 (2011)

K. Varga Time-dependent density functional study of transport in molecular junctions Phys. Rev. B 83, 195130 (2011)

Joseph A. Driscoll, Sergiy Bubin, and Kalman Varga Laser-enhanced eld emission from nanostructures: a rst-principles study Phys. Rev. B 83, 233405 (2011)

S. Bubin and K. Varga Ground state energy and relativistic corrections for positronium hydride Phys. Rev. A 84, 012509 (2011)

Joseph A. Driscoll , Sergiy Bubin , William R. French and Kalman Varga Time-dependent density functional study of eld emission from nanotubes composed of C, BN, SiC, Si, and GaN Journal of Nanotechnology 22 285702, 2011

Joseph A. Driscoll, Brandon Cook, Sergiy Bubin, and Kalman Varga First-principles study of field emission from carbon nanotubes and graphene nanoribbons J. Appl. Phys. 110, 024304 (2011)

Vary, James

T. Luu, M. J. Savage, A. Schwenk and J. P. Vary, "Nucleon-nucleon scattering in a harmonic potential," Phys. Rev. C 82, 034003 (2010); arXiv:1006.0427

F. Liu, R. Mundhe, M. Sosonkina, C. Cockrell, M. Aronnax, P. Maris and J. P. Vary, "A Data Management System for Ab-Initio Nuclear Physics Applications," accepted for publication in the proceedings of High Performance Computing 2011 (HPC-2011)

J. P. Vary, "Ab initio nuclear theory - progress and prospects from quarks to the cosmos," Acta Physica Polonica B 42, 397(2011).

H. Honkanen, P. Maris, J. P. Vary and S. J. Brodsky, "Electron in a transverse harmonic cavity," Phys. Rev. Lett. 106, 061603 (2011) DOI:10.1103/PhysRevLett.106.061603; arXiv: 1008.0068

T. Abe, P. Maris, T. Otsuka, N. Shimizu, Y. Utsuno and J.P. Vary, "Benchmark calculation of no-core Monte Carlo shell model of light nuclei," accepted for publication in New Faces of Atomic Nuclei, AIP Conf Proc 1355, 173 (2011) .

A. Srinivasa, M. Sosonkina, P. Maris, J. P. Vary, "Dynamic adaptations in ab-initio nuclear physics calculations on multicore computer architectures," Proceedings of 12th IEEE International Workshop on Parallel and Distributed Scientific and Engineering Computing (PDSEC-11) (to appear).

H. J. Pirner and J. P. Vary, "Boundary between hadron and quark/gluon structure of nuclei," Phys. Rev. C 84, 015201(2011); arXiv/1008.4962

H. M. Aktulga, C. Yang, E. G. Ng, P. Maris and J. P. Vary, "Large-scale Parallel Null Space Calculation for Nuclear Configuration Interaction," accepted for publication in HPCS-2011.

A.M. Shirokov, J.P. Vary, V.A. Kulikov, P. Maris, A.I. Mazur, E.A. Mazur, "Light nuclei in ab initio approach with realistic inverse scattering NN-interaction," Izvestia Rossiskoj Academii Nauk, Ser. Fiz. 75 (2011) 499-503 [English translation was published in Bul. Rus. Acad. Sci.: Phys. 75 (2011) 463 467].

Hasan Metin Aktulga, Chao Yang, Umit V. Catalyurek, Pieter Maris, James P. Vary, and Esmond G Ng, "On Reducing I/O Overheads in Large-Scale Invariant Subspace Projections," accepted for publication in the proceedings of HPSS-2011 (to appear).

B.R. Barrett, P. Navratil and J.P. Vary, "Ab initio No Core Shell Model," Nuclear Physics News International, 21, 5 (2011).

S. Bogner, R.J. Furnstahl, H. Hergert, M. Kortelainen, P. Maris, M. Stoitsov and J.P. Vary, "Testing the density matrix expansion against ab initio calculations of trapped neutron drops," accepted for publication in Phys. Rev. C., arXiv 1106.3557

Walkosz, Weronika

W. Walkosz, P. Zapol, and G. B. Stephenson, "Energetics of NH3 adsorption at InN and GaN (0001) surfaces: Density Functional Theory Calculations." (in preparation).

W. Walkosz, P. Zapol, and G. B. Stephenson, "Reaction pathways on InN and GaN surfaces under MOCVD conditions," (in preparation)

R. Tao, R. Todorovic, J. Liu, R. J. Meyer, A. Arnold, W. Walkosz, P. Zapol, A. Romanenko, L. Cooley, and R. F. Klie, "Electron energy loss spectroscopy study of metallic Nb and Nb oxides." (submitted to Journal of Applied Physics).

W

Waltz, Ronald

R.E. Waltz, G.M. Staebler, and W.M. Solomon, "Gyrokinetic simulation of momentum transport with residual stress from diamagnetic level velocity shears", Phys. Plasmas 18 (2011) 042504

G.M. Staebler, R. E. Waltz, and J. E. Kinsey"Discoveries from the exploration of gyro-kinetic momentum transport", Phys. Plasmas 18, 056106 (2011). (APS2010 invited talk)

J.E. Kinsey, G.M. Staebler, J. Candy, R.E. Waltz, and R.V. Budny,

"ITER predictions using the GYRO verified and experimentally validated trapped gyro-Landau fluid transport model",Nucl. Fusion 51 (2011) 083001. (IAEA-FEC2010 invited talk)

Wang, Cai-Zhuang

"Dynamic arrest and glass formation induced by self-aggregation of icosahedral clusters in Zr_{1-x}Cu_{x} alloys", S. G. Hao, C. Z. Wang, M. Z. Li, R. E. Napolitano, and K. M. Ho, Phys. Rev. B, 84, 064204 (2011).

"Competition between fcc and icosahedral short-range orders in pure and samarium-doped liquid aluminum from first principles", X. W. Fang, C. Z. Wang, Y. X. Yao, Z. J. Ding, and K. M. Ho, Phys. Rev. B, 83, 224203 (2011).

"Medium-range icosahedral order in quasicrystal-forming Zr2Pd binary metallic glass", Li Huang, X.W. Fang, C.Z. Wang, M.J. Kramer, Z.J. Ding, and K.M. Ho, Appl. Phys. Lett., 98, 231906 (2011).

"Structure and dynamics of liquid Ni 36Zr 64 by ab initio molecular dynamics", Li Huang, C. Z. Wang, and K. M. Ho, Phys. Rev. B, 83, 184103 (2011).

"Signature of Al11Sm3 fragments in undercooled Al90Sm10 liquid from ab initio molecular dynamics simulations", X W Fang, C Z Wang, Y X Yao, Z J Ding and K M Ho, J. Phys.: Condens. Matter 23, 235104 (2011).

"Atomistic cluster alignment method for local order mining in liquids and glasses", X. W. Fang, C. Z. Wang, Y. X. Yao, Z. J. Ding, and K. M. Ho, Phys. Rev. B, 82, 184204 (2010).

"Fluctuation between icosahedral and BCC short range orders in undercooled Zr liquid", S. Wu, X. W. Fang, S. Y. Wang, C. Z. Wang, Y. X. Yao, K. M. Ho, Z. J. Ding and L. Y. Chen, J. Appl. Phys. Submitted.

"Development of Medium-Range Order in Metallic Cu64. 5Zr35.5 Liquid and Gla", X. W. Fang, C. Z. Wang, S. G. Hao, M. J. Kramer, Y. X. Yao, M. I. Mendelev, Z. J. Ding, R. Napolitano, and K. M. Ho, Scientific Reports, submitted.

"Structural and Dynamical Properties of Liquid Cu80Si20 Alloy by Experimental and ab initio Molecular Dynamics Simulation Studies", S. Wu, M. J. Kramer, X. W. Fang, S. Y. Wang, C. Z. Wang, K. M. Ho, Z. J. Ding, and L. Y. Chen, Phys. Rev. B, submitted.

Wang, Haobin

J. Li, I. Kondov, H. Wang, and M. Thoss, ``Theoretical Study of Photoinduced Electron Transfer Processes in the Dye-Semiconductor System Alizarin-TiO2'', J. Phys. Chem. C, 114, 18481 (2010).

I.R. Craig, M. Thoss, and H. Wang, "Accurate quantum-mechanical rate constants for a linear response Azzouz-Borgis proton transfer model employing the multilayer multiconfiguration time-dependent Hartree approach", J. Chem. Phys., 135, 064504 (2011).

J. Han, X. Chen, L. Shen, Y. Chen, W. Fang, H. Wang, "Energy Transfer Tunes Phosphorescent Color of Single-Dopant White OLED", Chem-Eur. J, accepted.

Wang, Jianwei

F.N. Skomurski, J.W. Wang, R.C. Ewing, and U. Becker (2011) Charge distribution and oxygen diffusion in hyperstoichiometric uranium dioxide UO2+x (x 0.25). Journal of Nuclear Materials. (Accepted).

J. Wang, F. Zhang, J. Lian, R.C. Ewing, and U. Becker (2011) Energetics of defect formation in Gd2Ti2O7 and Gd2Zr2O7 pyrochlore at high pressure. Acta Materialia 59,1607-1618.

Wang, Jun

Peng Gu, Jun Wang, Yifeng Zhu, Hong Jiang, Pengju Shang. Nexus: A Novel Weighted-Graph-Based Prefetching Algorithm for Metadata Servers in Large Scale Storage Systems, IEEE transactions on computers, Vol. 59, No. 1, pp1-15, January 2010.

Saba Sehrish, and Jun Wang. Reduced Function Set Architecture for MPI-IO. The Journal of Supercomputing 59(1): 131-146 (2012).

Wang, Lin-Wang

M. G. Vergniory, J. M. Granadino, A. Garcia-Lekue, L.W. Wang, "Molecular conductivity switching of two benzene rings under electric field", App. Phys. Lett. 97, 262114 (2010).

D.H. Bailey, L.W. Wang, Z. Zhao, J. Meza, E. Strohmaier, B. Lee, "Tuning an electronic structure code", a chapter in "Performance Tuning of Scientific Applications", Editors: D.H. Bailey, R. Lucas, S. William (Chapman & Hall, CRC Computational Science Series, 2010).

N. Vukmirovic, L.W. Wang, "Carrier hopping in disordered semiconducting polymers: How accurate is the Miller-Abrahams model?", App. Phys. Lett. 97, 043305 (2010).

N. Vukmirovic, L.W. Wang, "The density of states and wave function localization in disordered conjugated polymers: a large scale computational study", J. Phys. Chem. B 115, 1792 (2011).

N. Vukmirovic, L.W. Wang, "Overlapping fragments method for electronic structure calculations of large systems", J. Chem. Phys. 134, 094119 (2011).

S. Dag, S.Z. Wang, L.W. Wang, "Large surface dipole moments in ZnO nanorods", Nano Lett. 11, 2348 (2011).

B. L.M. Hendriksen, F. Martin, Y. Qi, C. Mauldin, N. Vukmirovic, A. J. Katan, V. Altoe, S. Aloni, J.M.J. Frechet, L.W. Wang, M. Salmeron, "Electrical transport properties of oligothiophene based molecular films studied by current sensing atomic force microscopy", Nano Lett. (in press).

S.Z. Wang, L.W. Wang, "Charge flow model for atomic structures of nonisovalent alloys", Phys. Rev. B 83, 115208 (2011).

S.Z. Wang, L.W. Wang, "Exciton dissociation in CdSe/CdTe heterostructure nanorods", J. Phys. Chem. Lett. 2, 1 (2011).

Y. Zhang, L.W. Wang, "Global electronic structure of semiconductor alloys through direct large scale computations for III-V alloys GaxIn1-xP", Phys. Rev. B 83, 165208 (2011).

J.M. Granadino-Roldan, N. Vukmirovic, M. Fernandez-Gomez, L.W. Wang, "The role of disorder on the electronic structure of conjugated polymers. The case of poly-2,5-bis(phenylethynyl)-1,3,4-thiadiazole", Phys. Chem. Chem. Phys. 13, 14500 (2011).

I.H. Chu, M. Radulaski, N. Vukmirovic, H.P. Cheng, L.W. Wang, "Charge transport in a quantum dot supercrystal", J. Phys. Chem. B (in press).

G. Liu, S. Xun, N. Vukmirovic, X. Song, P. Olalde-Velasco, H. Zheng, V.S. Battaglia, L.W. Wang, W. Yang, "Polymers with Tailored Electronic Structure for High Capacity Lithium Battery Electrodes", Adv. Mat. (in press).

Washington, Warren

Branstator, G. and H. Teng, 2010: Two limits of initial-value decadal predictability in a CGCM. J. Climate, 23, 6292-6311.

Teng, H. and G. Branstator, 2011: Initial value predictability in prominent modes of north Pacific subsurface temperature in a coupled GCM. Climate Dynamics, 36, 1813-1834.

Fischer, E.M., D.M. Lawrence, and B.M. Sanderson, 2010: Quantifying uncertainties in projections of extremes - a perturbed land surface parameter experiment, Clim. Dynam., online first, doi:10.1007/s00382-010-0915-y.

Greenhouse gas mitigation can reduce sea-ice loss and increase polar bear persistence (SC Amstrup, ET DeWeaver, DC Douglas, BG Marcot, GM Durner, CM Bitz, & DA Bailey, Nature 468, Pages: 955 958)

Hu, A., G. A. Meehl. W. Han, and J. Yin, Effect of the potential melting of the Greenland Ice Sheet on the Meridional Overturning Circulation and global climate in the future. Deep-Sea Research II (2011), doi:10.1016/j.dsr2.2010.10.069

Cai,W., T. Cowan, J. M. Arblaster, and S. Wijffels (2010), On potential causes for an under estimated global ocean heat content trend in CMIP3 models, Geophys. Res. Lett., 37, L17709, doi:10.1029/2010GL044399.

Deser, C., A. S. Phillips, V. Bourdette, and H. Teng, 2011: Uncertainty in climate change projections: The role of internal variability. Climate Dyn., DOI 10.1007/s00382-010-0977-x.

Meehl, G.A., A. Hu, and C. Tebaldi, 2010: Decadal prediction in the Pacific region. J. Climate, 23, 29592973.

Overpeck, J.T., G.A. Meehl, S. Bony, and D.R. Easterling, 2011: Climate data challenges in the 21st century. Science, 331, 700-702. DOI:10.1126/science.1197869.

Han, W., G.A. Meehl, B. Rajagopalan, J.T. Fasullo, A. Hu, J. Lin, W. Large, J.-W. Wang, X. Quan, L.L. Trenary, A. Wallcraft, T. Shinoda, and S. Yeager, 2010: Indian Ocean sea level change in a warming climate, Nature Geoscience, DOI:10.1038/NGEO901.

Benjamin M Sanderson, Brian C O'Neill, Jeffrey T Kiehl, Gerald A Meehl, Reto Knutti and Warren M Washington "The response of the climate system to very high greenhouse gas emission scenarios", Environ. Res. Lett. 6 034005 doi: 10.1088/1748-9326/6/3/034005

Medeiros, B., L. Nuijens, C. Antoniazzi, and B. Stevens (2010), Low latitude boundary layer clouds as seen by CALIPSO, J. Geophys. Res., 115, D23207, doi:10.1029/2010JD014437.

Medeiros, B., C. Deser, R. A. Tomas, and J. E. Kay, 2011: Arctic inversion strength in climate models, J. Climate 24(17), pp. 4733-4740. DOI: 10.1175/2011JCLI3968.1

Arblaster J.M., G.A. Meehl and D.J. Karoly, 2011: Future climate change in the Southern Hemisphere: Competing effects of ozone and greenhouse gases, Geophys. Res. Lett., 38, L02701, doi:10.1029/2010GL045384.

Papers Accepted or In Press

Lawrence, D.M., K.W. Oleson, M.G. Flanner, P.E. Thornton, S.C. Swenson, P.J. Lawrence, X. Zeng, Z.-L. Yang, S. Levis, K. Sakaguchi, G.B. Bonan, and A.G. Slater, 2011: Parameterization improvements and functional and structural advances in version 4 of the Community Land Model. In press J. Adv. Model. Earth Sys.

JB White III and JJ Dongarra. Overlapping Computation and Communication for Advection on Hybrid Parallel Computers. 25th IEEE International Parallel & Distributed Processing Symposium, May 16 20, 2011, in press.

Weber, William

H. Xiao and W. J. Weber, Oxygen Vacancy Formation and Migration in CexTh1-xO2 (0 x 1) Solid Solution, J. Physical Chemistry B 115 [20]: 6524-6533 (2011).

H. Y. Xiao, Y. Zhang, and W. J. Weber, Trapping and diffusion of fission products in ThO2 and CeO2, J. Nuclear Materials 414 [3]: 464-470 (2011).

H. Y. Xiao, G. Duan, X. T. Zu, and W. J. Weber, Ab initio molecular dynamics simulation of pressure-induced phase transformation in BeO, J. Materials Science 46 [19]: 6408-6415 (2011).

X. J. Wang, H.Y. Xiao, X. T. Zu, and W. J. Weber, Study of cerium solubility in Gd2Zr2O7 by DFT + U calculations, J. Nuclear Materials (2011) in press, doi:10.1016/j.jnucmat.2011.08.008.

Wei, Suhuai

J. Zhu, F. Liu, G. B. Stringfellow, and S.-H. Wei, "Strain-enhanced doping in semiconductors: Effects of dopant size and charge state", Phys. Rev. Lett. 195, 195503 (2010).

Y.-H. Kim, J. Kang, and S.-H. Wei, "Origin of enhanced dihydrogen-metal interaction in carboxylate bridged Cu2-paddle-wheel frameworks", Phys. Rev. Lett. 105, 236105 (2010).

W.-J. Yin, S.-H. Wei, M. Al-Jassim, and Y. Yan, "Double-hole-mediated coupling of dopants and its impact on band gap engineering in TiO2", Phys. Rev. Lett. 106, 066801 (2011).

J. Ma, S.-H. Wei, N. R. Neale, and A. J. Nozik, "Effect of surface passivation on dopant distribution in Si quantum dots: The case of B and P doping", Appl. Phys. Lett. 98, 173103 (2011).

W.-J. Yin, S.-H. Wei, M. Al-Jassim, J. Turner, and Y. Yan. "Doping properties of monoclinic BiVO4 studied by first-principle density-functional study", Phys. Rev. B 83, 155102 (2011).

J. Zhu and S.-H. Wei, "Tuning doping site and type by strain: Enhanced p-type doping in Li doped ZnO", Solid State Comm. 151, 1437 (2011).

J. Kang, S.-H. Wei, K. Zhu, and Y.-H. Kim, "First-principles theory of electrochemical capacitance of nanostructured materials: Dipole-assisted subsurface intercalation of lithium in pseudocapacitive TiO2 anatase nanosheets", J. Phys. Chem. C 115, 4909 (2011).

Y. Zhao, C. Ban, Q. Xu, S.-H. Wei, and A. C. Dillon, "Charge-driven structural transformation and valence versatility of boron sheets in magnesium borides", Phys. Rev. B 83, 035406 (2011).

Q. Xu, C. Ban, A. C. Dillon, S.-H. Wei, and Y. Zhao, "First-principles study of lithium borocarbide as a cathode material for rechargeable Li ion batteries", J. Phys. Chem. Lett. 2, 1129 (2011).

Y.-J. Yin, S.-H. Wei, M. Al-Jassim, and Y. Yan, "The trends of oxygen vacancy levels in metals oxides", Appl. Phys. Lett. (in press).

B. Huang, H. J. Xiang and S.-H. Wei, "Controlling doping in graphene through a SiC substrate: A first-principles study", Phys. Rev. B 83, 161405R (2011).

B. Huang, J. Yu, and S.-H. Wei, "Strain control of magnetism in graphene decorated by transition-metal atoms", Phys. Rev. B 84, 075415 (2011).

Wellein, Gerhard

Christian Feichtinger, Johannes Habich, Harald K stler, Georg Hager, Ulrich R de, Gerhard Wellein, A flexible Patch-based lattice Boltzmann parallelization approach for heterogeneous GPU-CPU clusters, Parallel Computing, Volume 37, Issue 9, September 2011, Pages 536-549, ISSN 0167-8191, 10.1016/j.parco.2011.03.005.

Werthimer, Dan

Andrew P.V. Siemion, Geoffrey C. Bower, Griffin Foster, Peter L. McMahon, Mark I. Wagner, Dan Werthimer, Don Backer, Jim Cordes, Joeri van Leeuwen, "The Allen Telescope Array Fly's Eye Survey for Fast Radio Transients," ApJ, in press. 2011

Siemion, A., Von Korff, J., McMahon, P., Korpela, E., Werthimer, D., Anderson, D., Bower, G., Cobb, J., Foster, G., Lebofsky, M., van Leeuwen, J., and Wagner, M., "New SETI sky surveys for radio pulses," Acta Astronautica 67, 1342-1349 (Dec. 2010).

Whangbo, Myung

F. Wu, E. J. Kan, C. Tian and M.-H. Whangbo, "Theoretical analysis of the spin exchange and magnetic dipole-dipole interactions leading to the magnetic structure of Ni3TeO6", Inorg. Chem. 49, 7545 (2010).

C. Lee, E. J. Kan, H. J. Xiang and M.-H. Whangbo, "Theoretical investigation of the magnetic structure and ferroelectric polarization of the multiferroic langasite Ba3NbFe3Si2O14", Chem. Mater. 22, 5290 (2010).

H.-J. Koo and M.-H. Whangbo, "Finite magnetization plateau from a two- dimensional antiferromagnet: Density functional analysis of the magnetic structure of Cu3(P2O6OH)2", Inorg. Chem., 49, 9253 (2010).

C. Tassel, J. Kang, C. Lee, O. Hernandez, Y. Qiu, W. Paulus, B. Lake, T. Guidi, M.-H. Whangbo, H. Kageyama and S.-H. Lee, "Ferromagnetically coupled Shastry-Sutherland quantum spin singlets in (CuCl)LaNb2O7", Phys. Rev. Lett., 105, 167205 (2010).

C. Tian, C. Lee, E. J. Kan, F. Wu and M.-H. Whangbo, "Analysis of the magnetic structure and ferroelectric polarization of monoclinic MnSb2S4 by density functional calculations", Inorg. Chem. 49, 10956 (2010).

Y. Zhang, E. J. Kan, H. J. Xiang, A. Villesuzanne and M.-H. Whangbo, "Density functional theory analysis of the interplay between Jahn-Teller instability, uniaxial magnetism, spin arrangement, metal-metal interaction and spin-orbit coupling in Ca3CoMO6 (M = Co, Rh, Ir)", Inorg. Chem. 50, 1578 (2011).

H.-J. Koo, C. Lee, M.-H. Whangbo, G. J. McIntyre and R. K. Kremer, "On the nature of the spin frustration in the CuO2 ribbon chains of LiCuVO4: Crystal structure determination at 1.6 K, magnetic susceptibility analysis and density functional evaluation of the spin exchange constants", Inorg. Chem., 50, 3582 (2011).

C. Tian, A. C. Wibowo, H.-C. zur Loye and M.-H. Whangbo, "On the magnetic insulating states, spin frustration and dominant spin exchange of the ordered double-perovskites Sr2CuOsO6 and Sr2NiOsO6: Density functional analysis", Inorg. Chem., 50, 4142 (2011).

E. J. Kan, F. Wu, C. Lee, J. Kang and M.-H. Whangbo, "On the high magnetic- ordering temperature of the 5d magnetic oxide Ca3LiOsO6 crystallizing in a trigonal crystal structure: Density functional analysis", Inorg. Chem., 50, 4182 (2011).

J. M. Law, C. Hoch, R. Glaum, I. Heinmaa, R. Stern, J. Kang, C. Lee, M.-H. Whangbo, and R. K. Kremer, "Spin-Peierls transition in the S=1/2 compound TiPO4 featuring large intrachain coupling", Phys. Rev. B, 83, 180414 (2011).

J. M. Law, P. Reuvekamp, R. Glaum, C. Lee, J. Kang, M.-H. Whangbo and R. K. Kremer, "Quasi-one-dimensional antiferromagnetism and multiferroicity in CuCrO4", Phys. Rev. B, 84, 014426 (2011).

E. J. Kan, F. Wu, H. J. Xiang, J. L. Yang and M.-H. Whangbo, "Half-metallic Dirac Point in B-Edge Hydrogenated BN nanoribbons", J. Phys. Chem. C. 115, 17252 (2011).

M.-H. Whangbo, C. Lee and J. K hler, "Metal anions in metal-rich compounds and polar intermetallics", Eur. J. Inorg. Chem. 3841 (2011).

C. Lee, E. J. Kan, M.-H. Whangbo, A. Bussmann-Holder and A. Simon, "Spin/charge redistributions and oxygen atom displacements induced by spin flip and hole doping in the CuO2 layer of high temperature superconductors", J. Supercond. Novel Mag.(DOI: 10.1007/s10948-011-1208-3).

White, Martin

Bhattacharya, Suman, Heitmann, Katrin, White, Martin, LukiÄ‡, Zarija, Wagner, Christian, and Habib, Salman, Mass Function Predictions Beyond Î›CDM, The Astrophysical Journal, 732, 2011

White, Martin, Blanton, M., Bolton, A., Schlegel, D., Tinker, J., Berlind, A., da Costa, L., Kazin, E., Lin, Y.-T., Maia, M., McBride, C. K., Padmanabhan, N., Parejko, J., Percival, W., Prada, F., Ramos, B., Sheldon, E., de Simoni, F., Skibba, R., Thomas, D., Wake, D., Zehavi, I., Zheng, Z., Nichol, R., Schneider, Donald P., Strauss, Michael A., Weaver, B. A., and Weinberg, David H., The Clustering of Massive Galaxies at z ~ 0.5 from the First Semester of BOSS Data, The Astrophysical Journal, 728, 2011

White, Martin, Cohn, J. D., and Smit, Renske, Cluster galaxy dynamics and the effects of large-scale environment, Monthly Notices of the Royal Astronomical Society, 408, 1834, 2010

Carlson, Jordan and White, Martin, Embedding Realistic Surveys in Simulations Through Volume Remapping, The Astrophysical Journal Supplement Series, 190, 314, 2010

Xu, X., White, M., Padmanabhan, N., Eisenstein, D. J., Eckel, J., Mehta, K., Metchnik, M., Pinto, P., and Seo, H.-J., A New Statistic for Analyzing Baryon Acoustic Oscillations, The Astrophysical Journal, 718, 1234, 2010

Heitmann, Katrin, White, Martin, Wagner, Christian, Habib, Salman, and Higdon, David, The Coyote Universe. I. Precision Determination of the Nonlinear Matter Power Spectrum, The Astrophysical Journal, 715, 121, 2010

Wetzel, Andrew R. and White, Martin, What determines satellite galaxy disruption?, Monthly Notices of the Royal Astronomical Society, 403, 1088, 2010

Lawrence, Earl, Heitmann, Katrin, White, Martin, Higdon, David, Wagner, Christian, Habib, Salman, and Williams, Brian, The Coyote Universe. III. Simulation Suite and Precision Emulator for the Nonlinear Matter Power Spectrum, The Astrophysical Journal, 713, 1331, 2010

White, Martin, Pope, Adrian, Carlson, Jordan, Heitmann, Katrin, Habib, Salman, Fasel, Patricia, Daniel, David, and Lukic, Zarija, Particle Mesh Simulations of the LyÎ± Forest and the Signature of Baryon Acoustic Oscillations in the Intergalactic Medium, The Astrophysical Journal, 713, 393, 2010

Whitehouse, Glen

Quon, E.W., Smith, M.J., Whitehouse, G.R. and Wachspress, D.A. "Hierarchical Variable Fidelity Methods for Rotorcraft Aerodynamic Design and Analysis", American Helicopter Society 67th Annual Forum, Virginia Beach, VA, May 3-5, 2011

Whitelam, Stephen

Size-scaling behavior of hydriding phase transformations in nanocrystals Rizia Bardhan, Lester O. Hedges, Cary L. Pint, Ali Javey, Stephen Whitelam*, Jeffrey J. Urban (2011)

Design rules for the self-assembly of a protein crystal, Thomas K. Haxton, Stephen Whitelam (2011)

Limit of validity of Ostwald's rule of stages in a statistical mechanical model of crystallization Lester O. Hedges, Stephen Whitelam (2011)

Wilkins, John

Hyoungki Park and John W. Wilkins, A topological point defect regulates the evolution of extended defects in irradiated silicon, Applied Physics Letters 98, 171915 (2011).

Jeremy W Nicklas and John W Wilkins, Accurate electronic properties of HgCdTe systems using hybrid density functional theory , Accepted in Phys. Rev. B (Rapid Communications)

Jeremy W Nicklas and John W Wilkins, Accurate ab-initio prediction of III-IV direct-indirect gap crossovers, Applied Physics Letters 97, 091902 (2010).

Amita Wadehra, Jeremy W Nicklas, and John W Wilkins, Band offsets of semiconductor heterostructures: A hybrid density functional study, Applied Physics Letters 97, 092119 (2010).

Wirth, Brian

C. Hin and B.D. Wirth, Formation of oxide nanoclusters in nanostructured ferritic alloys during anisothermal heat treatment: A kinetic Monte Carlo study , Materials Science & Engineering A 528 (2011) 2056-2061.

M.J. Demkowicz, P. Bellon and B.D. Wirth, Atomic-scale design of radiation-tolerant nanocomposites , Materials Research Society Bulletin 35 (2010) 992-998.

B.D. Wirth, K. Nordlund, D.G. Whyte, and D. Xu, Fusion materials modeling: Challenges and opportunities , Materials Research Society Bulletin 36 (2011) 216-222.

Wong, Pak

Pak Chung Wong, Han-Wei Shen, and Chaomei Chen, "Top Ten Interaction Challenges in Extreme-Scale Visual Analytics," Expanding the Frontier of Visual Analytics and Visualization, Springer, 2011. To appear.

Boonthanome Nouanesengsey, Teng-Yok Lee, and Han-Wei Shen, Load-balanced Parallel Streamline Generation on Large Scale Vector Fields, IEEE Transactions on Visualization and Computer Graphics, 17(12), 2011.

Lijie Xu, Teng-Yok Lee, and Han-Wei Shen, An information-theoretic framework for flow visualization. IEEE Transactions on Visualization and Computer Graphics, 16(6): 1216-1224, Nov./Dec. 2010.

Peterka, T., Ross, R., Nouanesengsey, B., Lee, T.-Y., Shen, H.-W., Kendall, W., Huang, J.: A Study of Parallel Particle Tracing for Steady-State and Time-Varying Flow Fields. To appear in Proceedings IPDPS'11, Anchorage AK, May 2011.

Teng-Yok Lee, Oleg Mishchenko, Han-Wei Shen, and Roger Crawfis, View point evaluation and streamline filtering for flow visualization, IEEE Pacific Visualization 2011, pp 83-90, March 2011

Boonthanome Nouanesengsy, Jim Ahrens, Jonathan Woodring, and Han-Wei Shen, Revisiting parallel rendering for shared memory machines, Eurographics Symposium

Wood, Andrew

Gangopadhyay, S. and T.P. Pruitt, 2011, "West-Wide Climate Risk Assessments: Bias-Corrected and Spatially Downscaled Surface Water Projections", U.S. Dept. of Interior, Bureau of Reclamation (http://www.usbr.gov/WaterSMART/docs/west-wide-climate-risk-assessments.pdf) and associated reports.

Woosley, Stan

Aspden, A.; Bell, J. B.; Woosley, S. E., ``Distributed Flames and Damk\"ohler Small-Scale Turbulence' in Type Ia Supernovae'' 2010, ApJ, 720, 694.

Aspden, A. J.; Bell, J. B.; Dong, S.; Woosley, S. E., ``Burning Thermals in Type Ia Supernovae'', 2011, ApJ, 738, 94

Aspden, A. J.; Bell, J. B.; Woosley, S. E., ``Turbulent Oxygen Flames in Type Ia Supernovae'', 2011, 730, 144

Joggerst, C. C.; Almgren, A.; Woosley, S. E., ``Three-dimensional Simulations of Rayleigh-Taylor Mixing in Core-collapse Supernovae with Castro'', 2010, ApJ, 723, 353

Malone, C. M.; Nonaka, A.; Almgren, A. S.; Bell, J. B.; Zingale, M., ``Multidimensional Modeling of Type I X-ray Bursts. I. Two-dimensional Convection Prior to the Outburst of a Pure 4He Accretor'' 2011, ApJ, 728, 118.

Nonaka, A.; Almgren, A. S.; Bell, J. B.; Ma, H.; Woosley, S. E., and Zingale, M. 2011, ``From Convection to Explosion: End-to-End Simulation of Type Ia Supernovae'', refereed and accepted, Proceedings of the 2011 SciDAC PI Meeting.

Nordhaus, J.; Burrows, A.; Almgren, A.; Bell, J., `` Dimension as a Key to the Neutrino Mechanism of Core-collapse Supernova Explosion'', 2010, ApJ, 720, 694

Rantsiou, Emmanouela; Burrows, Adam; Nordhaus, Jason; Almgren, Ann, ``nduced Rotation in Three-dimensional Simulations of Core-collapse Supernovae: Implications for Pulsar Spins'', 2011, ApJ, 732, 57

Zhang, W.; Howell, L.; Almgren, A.; Burrows, A.; Bell, J. `` CASTRO: A New Compressible Astrophysical Solver. II. Gray Radiation Hydrodynamic'', 2011, accepted for publication in ApJS, high-resolution version available at https://ccse.lbl.gov/Publications/wqzhang/castro2.pdf

Zingale, M.; Nonaka, A.; Almgren, A. S.; Bell, J. B.; Malone, C. M.; Woosley, S. E. ``The Convective Phase Preceding Type Ia Supernovae'', 2011, ApJ, accepted.

"Dimension as a Key to the Neutrino Mechanism of Core-Collapse Supernova Explosions," (J. Nordhaus, A. Burrows, A. Almgren, & J. Bell), Ap.J., 720, 694-703, 2010 (arXiv:1006.3792).

"The Potential Role of Spatial Dimension in the Neutrino-Driving Mechanism of Core-Collapse Supernova Explosions," (A. Burrows, J. Nordhaus, A. Almgren, & J. Bell), published in a special issue of Computer Physics Communications (Elsevier, B.V.; Holland), doi:10.1016/j.cpc.2010.10.014, 2010 (refereed).

"Results from Core-Collapse Simulations with Multi-Dimensional, Multi-Angle Neutrino Transport," (T.D. Brandt, A. Burrows, & C.D. Ott), Ap.J., 728, 8, 2011 (arXiv:1009.4654).

"Theoretical Support for the Hydrodynamic Mechanism of Pulsar Kicks," (J. Nordhaus, T. Brandt, A. Burrows, E. Livne, & C.D. Ott), Phys. Rev. D, 82, 103016, 2010 (arXiv:1010.0674).

"Induced Rotation in 3D Simulations of Core-Collapse Supernovae: Implications for Pulsar Spins," (E. Rantsiou, A. Burrows, J. Nordhaus, & A. Almgren), Ap.J., 732, 57, 2011 (arXiv:1010.5238).

"Dynamics and Gravitational Wave Signature of Collapsar Formation," (C. D. Ott, C. Reisswig, E. Schnetter, E. O Connor, U. Sperhake, F. Loffler, P. Diener, E. Abdikamalov, I. Hawke, and A. Burrows), accepted to Phys. Rev. D 2011.

"CASTRO: A New Compressible Astrophysical Solver. II. Gray Radiation Hydrodynamics," (W. Zhang, L. Howell, A. Almgren, A. Burrows, & J. Bell), accepted to Ap.J. Suppl., 2011 (arXiv:1105.2466) high- resolution version available at https://ccse.lbl.gov/Publications/wqzhang/castro2.pdf (FYI: the multi- group variant of this code is finished and the associated paper is in preparation).

Zingale, M.; Nonaka, A.; Almgren, A. S.; Bell, J. B.; Malone, C. M.; Woosley, S. E. ``The Convective Phase Preceding Type Ia Supernovae'', 2011, ApJ, accepted.

Wu, Jianzhong

D. Henderson, S. Lamperski, Z. Jin, and J. Wu, "Density functional study of the double layer formed by a high density electrolyte", Journal of Physical Chemistry B, accepted, 2011.

J. Wu, S.L. Zhao, J. Wu and D. Gao, "Separation of ssDNA with a 10- nucleotide resolution under a stretching force in microfluidic channels", Lab on Chip, accepted, 2011

J. Wu, T. Jiang, D. Jiang, Z. Jin, D. Henderson, "A classical density functional theory for interfacial layering of ionic liquids", Soft Matter, accepted, 2011.

S. Zhao and J. Wu, "Site-site direct correlation functions of bulk water", Molecular Physics, accepted, 2011.

S. Zhao, Z. Jin and J. Wu, "New theoretical method for rapid prediction of solvation free energy in water", Journal of Physical Chemistry B, 115, 6971- 6975 (2011).

Z. Jin, Y. P. Tang and J. Wu, "A perturbative density functional theory for square-well fluids", Journal of Chemical Physics, 134 (17), 174702, 2011.

E. R. A. Lima, T. Jiang and J. Wu, "A theoretical study of colloidal forces near amphiphilic polymer brushes", Colloids and Surfaces A, 384, 115-120 (2011).

D. Jiang, D. Meng and J. Wu "Density functional theory for differential capacitance of planar electric double layers in ionic liquids", Chemical Physics Letters, 504, 153 158, 2011.

S. Zhao, J. Wu, D. Gao and J. Wu, "Gaussian fluctuation in end-tethered DNA chains", Journal of Chemical Physics, 134, 065103, 2011.

S. Zhao and J. Wu, "Self-consistent equations governing the dynamics of non-equilibrium colloidal systems", Journal of Chemical Physics, 134, 054514, 2011.

Z. Jin and J. Wu, "A Hybrid MC-DFT Method for Studying Multi-Dimensional Entropic Forces", Journal of Physical Chemistry B, 115 (6), 1450-1460, 2011.

Wu, John

Kesheng Wu, Rishi R Sinha, Chad Jones, Stephane Ethier, Scott Klasky, Kwan-Liu Ma, Arie Shoshani and Marianne Winslett. Finding regions of interest on toroidal meshes. Computational Science & Discovery, Volume 4, Number 1 page 015003. 2011. http://iopscience.iop.org/1749-4699/4/1/015003/

Kamesh Madduri, Kesheng Wu: Massive-Scale RDF Processing Using Compressed Bitmap Indexes. SSDBM 2011: 470-479 39. http://dx.doi.org/10.1007/978-3-642-22351-8_30

Jerry Chou, Kesheng Wu, Prabhat: FastQuery: A General Indexing and Querying System for Scientific Data. SSDBM 2011: 573-574. http://dx.doi.org/10.1007/978-3-642-22351-8_42

Wu, Ruqian

L Zeng, J.X. Cao, E. Helgren, J. Karel, E. Arenholz, L. Ouyang, D.J. Smith, R.Q. Wu, F. Hellman, "Distinct Local Electronic Structure and Magnetism for Mn in Amorphous Si and Ge", Phys. Rev. B, 82, 165202 (2010).

Dongdong Li, Jun Hu, Ruqian Wu and Jia G Lu, "Conductometric chemical sensor based on individual CuO nanowires", Nanotechnology, 21, 485502 (2010).

J.S. Lee, J. T. Sadowski, H. Jang, J.H. Park, J. Hu, R.Q. Wu, J.Y. Kim and C.C. Kao, "Magnetic Nanoparticles Trigger Spin Reorientation Transition in Ni/Fe/Ni/W(110)", Phys. Rev. B 83, 144420 (2011).

Z. Y. Li, S. Qiao, Z. Q. Yang, and R. Q. Wu, "Density-functional studies of spin-orbit splitting in graphene on metals", J. Phys. Cond. 23, 225502 (2011).

Y. N. Zhang, M. Persson, V. Bortolani, R. Q. Wu, "Why viscosities of Ne and Kr monolayers are so different on the Pb(111) surface", 106, 236103 (2011).

Y. Jiang, Y. N. Zhang, J.X. Cao, R. Q. Wu and W. Ho, "Real-space imaging of Kondo screening in a two-dimensional Kondo lattice", Science 333, 324 (2011).

C. Antoniak, H. C. Herper, Y. N. Zhang, A. Warland, T. Kachel, F. Stromberg, B. Krumme, C. Weis, K. Fauth, W. Keune, P. Entel, R.Q. Wu, J. Lindner, and H. Wende, "Induced magnetism on silicon in Fe3Si quasi-Heusler compound", Phys. Rev. B, in press.

Wu, Ruqian

X.F. Yang, J. Hu, R.Q. Wu, and B.E. Koel, "Formation of Pd Monomers and Dimers on a Single-Crystal Pd3Fe(111) Surface", J. Phys. Chem. Lett., 1, 2493 (2010).

J. Hu, D.D. Li, J.G. Lu and R.Q. Wu, "?Effects on electronic properties of molecule adsorption on CuO surface and nanowire", J. Phys. Chem. C, 114, 17120 (2010).

Z.X. Yang, Z.M. Fu, Y.N. Zhang and Ruqian Wu, "The direct CO oxidation by lattice oxygen on Zr- doped ceria surfaces", Cata. Lett. 141,78 (2011).

W.J. Ouyang, A. Shinde, Y.N. Zhang, J.X. Cao, R. Ragan and R.Q. Wu, "Structural and Chemical Properties of Gold Rare Earth Disilicide Core/Shell Nanowires", ACS Nano, 5, 477 (2011).

X.F. Yang, J. Hu, R.Q. Wu, and B.E. Koel, "Mechanism of the enhanced oxidation activity of Pd3Fe3 bimetallic surface", Angew. Chem. Int. ed. in press.

Wuebbles, Donald

J. S. Daniel et al. (D. Wuebbles, coauthor), A Focus on Information and Options for Policymakers. In WMO/UNEP, Scientific Assessment of Ozone Depletion: 2010. World Meteorological Organization Global Ozone Research and Monitoring Project Report No. 52 (2011)

M. Markus, D. J. Wuebbles, X.-Z. Liang, K. Hayhoe, and d. A. R. Kristovich, Diagnostic analysis of future climate scenarios applied to urban flooding in the Chicago metropolitan area. Climatic Change, in press (2011)

K. O. Patten and D. J. Wuebbles, Atmospheric lifetimes and Ozone Depletion Potentials of trans-1-chloro-3,3,3-trifluoropropylene and trans-1,2-dichloroethylene in a three-dimensional model, Atmos. Chem. Phys., 10, 10867-10874 (2010)

D. J. Wuebbles, K. O. Patten, D. Wang, D. Youn, M. Mart nez-Avil s, and J. S. Francisco, Three-dimensional model evaluation of the Ozone Depletion Potentials for n-propyl bromide, trichloroethylene and perchloroethylene, Atmos. Chem. Phys., 11, 2371-2380 (2011)

D. Youn, K. O. Patten, D. J. Wuebbles, H. Lee, and C.-W. So, Potential impact of iodinated replacement compounds CF3I and CH3I on atmospheric ozone: A three-dimensional modeling study, Atmos. Chem. Phys., 10, 10129-10144 (2010)

X. Zhang, X. Shao, K. Hayhoe, and D. J. Wuebbles, Testing the structural stability of temporally dependent functional observations and application to climate projections. Electronic Journal of Statistics, in press (2011)

Y

Yang, Chao

C. Yang, J, Qian, A. Schirotzek, F. Maia, S. Marchesini, Iterative Algorithms for Ptychographic Phase Retrieval, LBNL Report 4598E, Submitted to New Journal of Physics , 2011

F. Maia, C. Yang and S. Marchesini, Compressive auto-indexing in femtosecond nanocrystallography. Ultramicroscopy, vol 111, 2011.

C. Yang and J. Meza, Minimizing the Kohn-Sham Total Energy for Periodic Systems, to appear in Linear Algebra and Its Applications, 2011.

L. Lin, J. Lu, L. Ying and W. E, Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework I: Total energy calculation. arXiv:1102.2520v1, Feb 12, 2011, submitted to Journal of Computational Physic.

L. Lin, J. Lu, L. Ying, and W. E. Optimized local basis function for Kohn-Sham density functional theory. arXiv:1108.0966v1, Aug 4, 2011, submitted to Journal of Computational Physics.

C. Yang, Z. Wang and S. Marchesini, Orientation Determination for 3D Single Molecule Diffraction Imaging, Proc. SPIE, vol, 7800 , 2010.

Yang, Li

"Lattice Vibrational Modes and their Frequency Shifts in Semiconductor Nanowires", Li Yang and M.Y. Chou, Nano Lett., vol 11, 2618 (2011).

"Many-Electron Effects on Optical Absorption Spectra of Strained Graphene", Yufeng Liang, Shouting Huang and Li Yang, submitted to the Journal of Material Research as an invited feature article.

Yao, Weiming

T. Aaltoen et al. The CDF Collaboration, "Measurement of the Top-Quark mass in the Lepton+Jets Channel Using a Matrix Element Technique with the CDF Detector", submitted to PRD, arXiv: 1108.1601

T. Aaltonen et al., The CDF Collaboration, "Combined Tevatron Upper Limit on gg-H-W+W- and Constraints on the Higgs Boson Mass in Fourth-Generation Models", Phys. Rev. D82, 011102.

T. Aaltonen et al., The CDF Collaboration, "Search for Technicolor Particles Produced in Association with a W Boson at CDF", Phys. Rev. Lett. 104, 111802.

Yelick, Katherine

Hiding Latency in Coarray Fortran 2.0. William N. Scherer III, Laksono Adhianto, Guohua Jin, John Mellor-Crummey, and Chaoran Yang. The 4th Conference on Partitioned Global Address Space Programming Models, New York, NY. October 12-15, 2010.

Hybrid PGAS Runtime Support for Multicore Nodes, Filip Blagojevic, Paul Hargrove, Costin Iancu, Katherine Yelick. Conference on Partitioned Global Address Space languages. October 12-14, 2010, New York, NY.

Tuning collective communication for Partitioned Global Address Space programming models, Rajesh Nishtala, Yili Zheng, Paul Hargrove, Katherine A. Yelick. Parallel Computing 37(9): 576-591 (2011).

Oversubscription on multicore processors, C. Iancu, S. Hofmeyr, F. Blagojevic, and Yili Zheng. 24rd International Parallel & Distributed Processing Symposium (IPDPS), 2010.

UPC Collectives Library 2.0, George Almasi, Paul Hargrove, Gabriel Tanase and Yili Zheng. Fifth Conference on Partitioned Global Address Space Programming Models (PGAS11), Oct 2011.

Advanced Communication Techniques for Gyrokinetic Fusion Applications on Ultra-Scale Platforms; Robert Preissl, John Shalf, Alice Koniges, Nathan Wichmann, Bill Long, and Stephane Ethier; Fifth Conference on Partitioned Global Address Space Programming Models (PGAS11), Oct 2011.

Hierarchical Work Stealing on Manycore Clusters â€¨Seung-Jai Min, Costin Iancu and Katherine Yelick;Fifth Conference on Partitioned Global Address Space Programming Models (PGAS11), Oct 2011.

Multithreaded Global Address Space Communication Techniques for Gyrokinetic Fusion Applications on Ultra-Scale Platforms,? Robert Preissl, LBNL; Nathan Wichmann, Bill Long, Cray Inc.; John Shalf, LBNL; Stephane Ethier, PPPL; Alice Koniges, LBNL. SC?11 (?Supercomputing?), Seattle, WA, Novemer 2011. BEST PAPER AWARD NOMINEE

Efficient Data Race Detection for Distributed Memory Parallel Programs,? Chang-Seo Park, University of California, Berkeley; Paul Hargrove, Costin Iancu, LBNL; Koushik Sen, UC Berkeley. SC?11 (?Supercomputing?), Seattle, WA, Novemer 2011.

Yoon, Mina

M. Yoon, Y. Miyamoto, M. Scheffler, New J. Phys. 13, 073039 (2011). "Enhanced dipole moments in photo-excited TTF-TCNQ dimers".

H. Chen, W. G. Zhu, D. Xiao, Z. Y. Zhang, Phys. Rev. Lett. 107 056804 (2011). CO Oxidation Facilitated by Robust Surface States on Au-Covered Topological Insulators.

H. Zhang, J. H. Choi, Y. Xu, X. X. Wang, X. F. Zhai, B. Wang, C. G. Zeng, J.-H. Cho, Z. Y. Zhang, J. G. Hou, Phys. Rev. Lett. 107 019702 (2011). Comment on "Atomic Structure, Energetics, and Dynamics of Topological Solitons in Indium Chains on Si(111) Surfaces" Reply.

R. G. Van Wesep, H. Chen, W. G. Zhu, Z. Y. Zhang, J. Chem. Phys. 134, 171105 (2011). Communication: Stable carbon nanoarches in the initial stages of epitaxial growth of graphene on Cu(111).

K. H. Bevan, W. G. Zhu, H. Guo, Z. Y. Zhang, Phys. Rev. Lett. 106 156404 (2011). Terminating Surface Electromigration at the Source.

X. Y. Xu, K. Seal, X. S. Xu, I. Ivanov, C.-H. Hsueh, N. Hatab, L. F. Yin, X. Q. Zhang, Z.-H. Cheng, B. H. Gu, Z. Y. Zhang, J. Shen, Nano Lett. 2011, in press. High tunability of the SERS response with a metal-multiferroic composite.

M. Yoon, H. H. Weitering, Z. Y. Zhang, Phys. Rev. B. 83, 045413(2011). First-principles studies of hydrogen interaction with ultrathin Mg and Mg-based alloy films.

Z. K. Zhou, X. N. Peng, Z. J. Yang, Z. S. Zhang, M. Li, X. R. Su, Q. Zhang, X. Shan, Q. Q. Wang, Z. Y. Zhang, Nano Lett. 11, 49 (2011). Tuning Gold Nanorod-Nanoparticle Hybrids into Plasmonic Fano Resonance for Dramatically Enhanced Light Emission and Transmission.

H. Zhang, J. H. Choi, Y. Xu, X. X. Wang, X. F. Zhai, B. Wang, C. G. Zeng, J.-H. Cho, Z. Y. Zhang, J. G. Hou, Phys. Rev. Lett. 106 026801 (2011). Atomic Structure, Energetics, and Dynamics of Topological Solitons in Indium Chains on Si(111) Surfaces.

Y. Jia, M. M. Ozer, H. H. Weitering, Z. Y. Zhang, Springer Series in Surface Sciences, Vol. 47, Nanophenomena at Surfaces: Fundamentals of Exotic Condensed Matter Properties, ed. M. Michailov, pp. 67-112, (Springer, New York, 2011). Quantum Size Effects in the Growth and Properties of Ultrathin Metal Films, Alloys, and Related Low-Dimensional Structures.

D. J. Shu, X. Xiang, Z. W. Wang, Z. Y. Zhang, M. Wang, N.-B. Ming, J. Phys. Chem. C. 115, 31 (2011). "Atomistic Mechanisms and Diameter Selection during Nanorod Growth."

W. G. Zhu, H. Chen, K. H. Bevan, Z. Y. Zhang, ACS Nano 5 3707 (2011). Formation of Graphene p-n Supperlattices on Pb Quantum Wedged Islands.

M. Yoon and D. Tom nek, J. Phys.: Condens. Matter 22, 455105 (2010). "Equilibrium structure of ferrofluid aggregates".

Yu, Hua-Gen

J. S. Francisco, J.T. Muckerman, and H.-G. Yu, "HOCO radical chemistry," Acc. Chem. Res. 43, 1519 (2010).

W.-Q. Han, Z. Liu and H.-G. Yu, "Synthesis and optical properties of GaN/ZnO solid soulution nanocrystals," App. Phys. Lett. 96, 183112 (2010).

W.-Q. Han, H.-G. Yu, Z. Liu, "Convert graphene sheets to boron nitride and boron nitride-carbon sheets via a carbon-substitution reaction," App. Phys. Lett. 98, 203112 (2011).

H.-G. Yu, "An optimal density functional theory method for GaN and ZnO," Chem.Phys. Lett. 512, 231 (2011).

H.-G. Yu, "An ab initio molecular dynamics study of the roaming mechanism of the H2 + HOC+ reaction," Phys. Scripta 84, 028104 (2011).

S.-Y. Du, T. Germann, J. Francisco, K. Peterson, H.-G. Yu, and J. Lyons, "The kinetics study of the S + S2 - S3 reaction by the Chaperon mechanism," J. Chem. Phys. 134, 154508 (2011).

T.V. Tscherbul, H.-G. Yu, and A. Dalgarno, "Sympathetic cooling of polyatomic molecules with S-state atoms in a magnetic trap," Phys. Rev. Lett. 106, 073201 (2011).

H.-G. Yu and G. Nyman, "The infrared and UV-visible spectra of polycyclic aromatic hydrocarbons containing (5, 7)-member ring defects: A theoretical study," Astrophys. J. (submitted, 2011).

Zabaras, Nicholas

B. Wen, Z. Li and N. Zabaras, "Thermal response variability of random polycrystalline microstructures", Communications in Computational Physics, Vol. 10, No. 3, pp. 607-634, 2011.

J. Wan and N. Zabaras, "A Bayesian Approach to Multiscale Inverse Problems Using a Sequential Monte Carlo Method", Inverse Problems, Vol. 27 No. 10, 2011.

B. Wen and N. Zabaras, "Investigating Variability of Fatigue Indicator Parameters of Two-phase Nickel-based Superalloy Microstructures", Computational Materials Science, Vol. 51, Issue 1, pp. 455-481, 2012.

I. Bilionis and N. Zabaras, "Multi-output Local Gaussian Process Regression: Applications to Uncertainty Quantification", Journal of Computational Physics, submitted.

Z

Zhang, Bin

Guo-Liang Ma and Bin Zhang Effects of final state interactions on charge separation in relativistic heavy ion collisions Phys. Lett. B 700, 39 (2011)

Bin Zhang and Warner A Wortman Chemical and kinetic equilibrations via radiative parton transport The Proceedings of the International Nuclear Physics Conference 2010, accepted

Zhang, Guoping

Ultrafast demagnetization in ferromagnets and magnetic switching in nanoclusters when the number of photons is kept fixed \\ G. P. Zhang, G. Lefkidis, W. H\"ubner and Y. Bai, J. Applied Physics, {\bf 109}, 07D303 (2011). This paper has been selected for the April 2011 issue of Virtual Journal of Ultrafast Science.

Laser-induced spin protection and switching in a specially designed magnetic dot: A theoretical investigation\\ G. P. Zhang, M. S. Si, and T. F. George, Europhysics Letters {\bf 94}, 17005 (2011).

Microscopic theory of ultrafast spin linear reversal \\ G. P. Zhang, J. Phys.: Condensed Matter {\bf 23}, 206005 (2011).

First-principles prediction of optical second-harmonic generation in the endohedral N@C$_{60}$ compound \\G. P. Zhang, David A. Strubbe, Steven G. Louie and Thomas F. George, Physical Review A {\bf 84}, 023837 (2011).

M S Si and G P Zhang, Resolving photon-shortage mystery in femtosecond magnetism, J. Phys.: Condens. Matter 22, 076005 (2010).

Zhang, Yong

Y. Zhang and L. W. Wang, Global electronic structure of semiconductor alloys through direct large-scale computations for III-V alloys GaxIn1 x P, Phys. Rev. B 83, 165208 (2011).

Zhang, Zhenyu

H. Chen, W.G. Zhu, D. Xiao, and Z.Y. Zhang. "CO Oxidation Facilitated by Robust Surface States on Au-Covered Topological Insulators". Phys. Rev. Lett. 107, 056804 (2011).

W.G. Zhu, H. Chen, K.H. Bevan, and Z.Y. Zhang. "Formation of graphene p-n supperlattices on Pb quantum wedged islands". ACS Nano 5, 3707 (2011).

K.H. Bevan, W.G. Zhu, H. Guo, and Z.Y. Zhang. "Terminating surface electromigration at the source". Phys. Rev. Lett. 106, 156404 (2011).

R.G. Van Wesep, H. Chen, W.G. Zhu, and Z.Y. Zhang. "Communication: Stable carbon nanoarches in the initial stages of epitaxial growth of graphene on Cu(111)". J. Chem. Phys. 134, 171105 (2011).

F.C. Wu, H.P. Lan, Z.Y. Zhang, and P. Cui. "Quantum Efficiency of Intermediate-Band Solar Cells Based on Non-Compensated n-p Codoped TiO2", submitted to Appl. Phys. Lett.

Zheng, Linjin

M. Kotschenreuther, S. Mahajan, P. Valanju, B. Covelle, et al., "Near Term Fission Fusion Hybrids", 23nd IAEA Fusion Energy Conference (in press).

M. Kotschenreuther, P. Valanju and S. Mahajan, "Reprocessing Free Nuclear Fuel Production via Fusion Fission Hybrids", submitted to Fusion Engineering and Design.

R. E. Waltz and F. L. Waelbroeck, "Gyrokinetic simulations with external resonant magnetic perturbations: island torque and nonambipolar transport with plasma rotation", under review (2011).

Eugene Y. Chen, H. L. Berk, B. Breizman, and L. J. Zheng, "Free-boundary toroidal Alfven eigenmodes", Phys. Plasmas 18, 052503 (2011).

S. Futatani, W. Horton, S. Benkadda, I. O. Bespamyantov, and W. L. Rowan, "Fluid Models of Impurity Transport via Drift Wave Turbulence", Physics of Plasmas 17, 072512 (2010).

M. Nakata, T.-H. Watanabe, H. Sugama, and W. Horton, "Effects of parallel dynamics on vortex structures in electron temperature gradient driven turbulence", Physics of Plasmas 18, 012303 (2011).

D. Chagelishvili, et al. "Angular redistribution of nonlinear perturbations: A universal feature of nonuniform flows", Physical Review E 81, 066304 part 2, (2010).

R. Fitzpatrick, and F. L. Waelbroeck, "Locked magnetic island chains in toroidally flow damped tokamak plasmas", Plasma Phys. Control. Fusion 52, 055006 (2010).

R. Fitzpatrick and F. L. Waelbroeck, "A drift-magnetohydrodynamical fluid model of helical magnetic island equilibria in the pedestals of H-mode tokamak plasmas", Phys. Plasmas 17, 062503 (2010).

M. Furukawa, S. Tokuda, and L. J. Zheng, "A numerical matching technique for linear resistive magnetohydrodynamics modes", Phys. Plasmas 17, 052502 (2010).

W. Horton, T. Ditmire, and Yu. P. Zakharov, "Laser experiments to simulate coronal mass ejection driven magnetospheres and astrophysical plasma winds on compact magnetized stars", High Energy Density Physics 6, 190-193 (2010).

W. Horton, J.-H. Kim, G. D. Chagelishvili, et al, "Angular redistribution of nonlinear perturbations: A universal feature of nonuniform flows", Phys Rev. E, accepted May 24, (2010).

O. Yamagishi, H. Sugama and W. Horton, "Interaction of Zonal Flow and Drift Wave Turbulence from Classic DW Models", Transport Task Force Meeting and submitted for publication in Phys of Plasmas (2010).

W. Horton, X. Fu, A. Ivanov, and A. Beklemishev, "Parameter Optimization Studies for a Tandem Mirror Neutron Source", Journal of Fusion Engineering 29, 521 (2010).

M. Kotschenreuther, P. Valanju, S. Mahajan, L. J. Zheng, L. D. Pearlstein, R. H. Bulmer, J. Canik, andR. Maingi, "The super X divertor (SXD) and a compact fusion neutron source (CFNS)", Nucl. Fusion 50 (3), 035003 (2010).

M. Nakata, T.-H. Watanabe, H. Sugama, and W. Horton, "Formation of coherent vortex streets and transport reduction in electron temperature gradient driven turbulence", Phys. Plasmas 17, 042306 (2010).

P. M. Valanju, M. Kotschenreuther, and S. M. Mahajan, "Super X divertors for solving heat and neutron flux problems of fusion devices", Fusion Engineering and Design 85, 46 (2010).

L. J. Zheng and M. Furukawa, "Current-interchange tearing modes: Conversion of interchange-type modes to tearing modes", Phys. Plasmas 17, 052508 (2010).

L. J. Zheng, M. T. Kotschenreuther, and J. W. Van Dam, "Rotational stabilization of resistive wall modes in ITER advanced tokamak scenarios", Phys. Plasmas 17, 056104 (2010).

Zhong, Xiaolin

Prakash, A., Parsons, N., Wang, X., and Zhong, X., High-order shock-fitting methods for direct numerical simulation of hypersonic flow with chemical and thermal nonequilibrium. Journal of Computational Physics, 2011. In Press(Available online 22 August 2011).

Wang, X., and Zhong, X., Development and validation of a high-order shock-fitting non-equilibrium flow solver. AIAA Paper 2011-0365, 2011.

Rawat, P. S., and Zhong, X., Direct Numerical Simulations of Turbulent Flow Interactions with Strong Shocks Using Shock-Fitting Method, AIAA paper 2011-649, January 2011.

Wang, X., and Zhong, X., Development and validation of a high-order shock-fitting non-equilibrium flow solver, AIAA paper 2011-365, January 2011.

Rawat, P.S., and Zhong, X., On High-Order Shock-Fitting and Front-Tracking Schemes for Numerical Simulation of Shock-Disturbance Interactions. Journal of Computational Physics, 229 (19) 2010, p. 6744-6780.

Prakash, A., Parsons, N., Wang, X., and Zhong, X., High-order shock-fitting methods for hypersonic flow with chemical and thermal nonequilibrium, AIAA paper 2010-4997, June 2010.

Rawat, P.S., and Zhong, X. Numerical Simulation of Shock-Turbulence Interactions using High-Order Shock-Fitting Algorithms. AIAA paper 2010-114. 2010.

Zhu, Ping

J. Raeder, P. Zhu, Y. Ge, and G. Siscoe, Tail Force Imbalance and Ballooning Instability Preceding Substorm Onset, J. Geophys. Res. 115, A00I16 (2010).

Zyla, Piotr

O.Kamaev, et al, Physics Letters B693, 236 (2010) "Study of the Rare Hyperon Decay Omega+- - Xi+- pi+ pi-"