2011 Publications

Arnout van de Rijt. 2011. “The Micro-Macro Link for the Theory of Structural Balance.” Journal of Mathematical Sociology 35(1): 94-113.

Chandrajit Bajaj, Rezaul Alam Chowdhury, and Muhibur Rasheed, "A Dynamic Data Structure for Flexible Molecular Maintenance and Informatics",Bioinformatics, vol. 27 (1), pp. 55-62, 2011.

Chandrajit Bajaj, Rezaul Alam Chowdhury, and Vinay Siddavanahalli, "F2Dock: Fast Fourier Protein-Protein Docking", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8 (1), pp. 45-58, 2011.

D. E. Keyes, L. C. McInnes, C. Woodward, W. D. Gropp, E. Myra, M. Pernice, J. Bell, J. Brown, A. Clo, J. Connors, E. Constantinescu, D. Estep, K. Evans, C. Farhat, A. Hakim, G. Hammond, G. Hansen, J. Hill, T. Isaac, X. Jiao, K. Jordan, D. Kaushik, E. Kaxiras, A. Koniges, K. Lee, A. Lott, Q. Lu, J. Magerlein, R. Maxwell, M. McCourt, M. Mehl, R. Pawlowski, A. Peters, D. Reynolds, B. Riviere, U. Rüde, T. Scheibe, J. Shadid, B. Sheehan, M. Shephard, A. Siegel, B. Smith, X. Tang, C. Wilson, and B. Wohlmuth, Multiphysics Simulations: Challenges and Opportunities, Tech. Rep. ANL/MCS-TM-321, Argonne National Laboratory (Dec. 2011).

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, 24, 5134-5156

Density, structure and dynamics of water: the effect of Van der Waals interactionsJue Wang, G. Roman-Perez, Jose M. Soler, Emilio Artacho, and M.V.Fernandez-Serra, J. Chem. Phys. 134, 024516 (2011).

Electronic Transport in Natively Oxidized Silicon Nanowires Mohammad Koleini, Lucio Colombi Ciacchi, and M.V.Fernandez-SerraACS Nano, 5 (4), pp 2839-2846, (2011).

Evaluating Systematic Dependencies of Type Ia Supernovae: The Influence of Deflagration to Detonation Transition Density. A. C. Calder, A. Jackson, B. Krueger, D. Townsley, D. Chamulak, E. Brown, and F. Timmes. Proceedings of The Eleventh International Symposium on Nuclei in the Cosmos, POS (NIC XI) 251, 2011

Goswami, B. B., N. J. Mani, P. Mukhopadhyay, D. E. Waliser, J. J. Benedict, E. D. Maloney, M. Khairoutdinov, and B. N. Goswami (2011), Monsoon intraseasonal oscillations as simulated by the superparameterized Community Atmosphere Model, J. Geophys. Res., 116, D22104, doi:10.1029/2011JD015948.

Kelvin-Helmholtz instabilities as the sources of inhomogeneous mixing in nova explosions. J. Casanova, J. Jos´e, E. Garc´ıa-Berro, S. N. Shore, A. C. CalderNature, 478, 490 2011

Lyakhov A.O., Oganov A.R. (2011). Evolutionary search for superhard materials applied to forms of carbon and TiO2. Phys. Rev. B84, 092103.

Mixing in Classical Nova Outbursts. J. Casanova, J. Jos´e, E. Garc´ıa-Berro, A. C. Calder, S. N. Shore. Proceedings of The Eleventh International Symposium on Nuclei in the Cosmos, POS (NIC XI) 204, 2011

Mixing in classical novae: a 2-D sensitivity study. J. Casanova, J. Jos´e, E. Garc´ıa-Berro, A. C. Calder, S. N. Shore. A&A, 527, A5, 2011

Oganov A.R. (2011). Boron under pressure: phase diagram and novel high-pressure phase. In: Boron rich solids (eds. N. Orlovskaya and M. Lugovy), pp. 207-225. Springer, Berlin.

Oganov A.R., Lyakhov A.O., Valle M. (2011). How evolutionary crystal structure prediction works - and why. Acc. Chem. Res. 44, 227-237 .

Oganov A.R., Solozhenko V.L., Gatti C., Kurakevych O.O., Le Godec Y. (2011). The high-pressure phase of boron, gamma-B28: disputes and conclusions of 5 years after discovery. J. Superhard Materials 33, 363-379.

On Variations of the Brightness of Type Ia Supernovae With Age of Host Stellar Population. B. Krueger, A. Jackson, D. Townsley, A. Calder, E. Brown, and F. Timmes. Proceedings of The Eleventh International Symposium on Nuclei in the Cosmos, POS (NIC XI) 253, 2011

R. Jaiman, P. Geubelle, E. Loth, X. Jiao, Transient fluid–structure interaction with non-matching spatial and temporal discretizations, Computers & Fluids, Vol 50, pp. 120–135, 2011.

T. Kaman, H. Lim, Y. Yu, D. Wang, Y. Hu, J.-D. Kim, Y. Li, L. Wu, J. Glimm, X. Jiao, X.-L. Li, and R. Samulyak, A numerical method for the simulation of turbulent mixing and its basis in mathematical theory, in Lecture Notes on Numerical Methods for Hyperbolic Equations: Theory and Applications: Short Course Book, London, 2011, pp. 105–129.

T. Zhang, R. A. DeSimone, H. Chen, C. M. Hamm, J. Yuan, Q. Q. Gong, S. R. Hunt, T. Dassopoulos, R. D. Newberry, D. N. Frank, C. E. Robertson, N. R. Pace, E. Sodergren, G. Weinstock, X. Jiao, W. Zhu, and E. Li. Cluster analysis of genome-wide expression differences in disease-unaffected ileal mucosa in inflammatory bowel diseases. In Proceedings of the IEEE ICCABS’11, pp. 220-225, DOI: 10.1109/ICCABS.2011.5729884, 2011.

The role of hydrogen bonding in water-metal interactions Adrien Poissier, Sriram Ganeshan, and M. V. Fernandez-Serra, Phys. Chem. Chem. Phys.,13, 3375-3384 (2011).

Turbulence-Flame Interaction on the Early Evolution of Flames in Type Ia Supernovae A. Jackson, A. C. Calder, D. Townsley, D. Chamulak, E. Brown, and F. Timmes. Proceedings of The Eleventh International Symposium on Nuclei in the Cosmos, POS (NIC XI) 249, 2011

vanZanten, M.C., B. B. Stevens, L. Nuijens, A. P. Siebesma, A. Ackerman, F. Burnet, A. Cheng, F. Couvreux, H. Jiang, M. Khairoutdinov, Y. Kogan, D. C. Lewellen, D. Mechem, K. Nakamura, A. Noda, B. J. Shipway, J. Slawinska, S. Wang, A. Wyszogrodzki, 2011: Controls on precipitation and cloudiness in simulations of trade-wind cumulus as observed during RICO. J. Adv. in Model. Earth Systems, 3, M06001

Wang, M., S. Ghan, R. Easter, M. Ovchinnikov, X. Liu, E. Kassianov, Y. Qian, W. I. Gustafson Jr., V. E. Larson, D. P. Schanen, M. Khairoutdinov and H. Morrison, 2011: The multi-scale aerosol-climate model PNNL-MMF: model description and evaluation. Geoscientific Model Development 4(1): 137-168.

Wen X.D., Hand L., Labet V., Yang T., Hoffmann R., Ashcroft N.W., Oganov A.R., Lyakhov A.O. (2011). Graphane sheets and crystals under pressure. Proc. Natl. Acad. Sci. 108, 6833-6837.

Yamaguchi, T., D. A. Randall, and M. F. Khairoutdinov, 2011: Cloud Modeling Tests of the ULTIMATE-MACHO Scalar Advection Scheme. Monthly Weather Review, 139, pp.3248-3264

Yuan Tang, Rezaul Alam Chowdhury, Bradley Kuszmaul, Chi-Keung Luk, and Charles Leiserson, "The Pochoir Parallel Stencil Compiler", To appear in the Proceedings of the 23rd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2011), San Jose, California, June 4-6, 2011.

Yuan Tang, Rezaul Alam Chowdhury, Chi-Keung Luk, and Charles Leiserson, "Coding Stencil Computations Using the Pochoir Stencil-Specification Language", Proceedings of the 3rd USENIX Workshop on Hot Topics in Parallelism (HotPar 2011), Berkeley, California, May 26-27, 2011.

Zhou X.-F., Oganov A.R., Dong X., Zhang L., Tian Y., Wang H.-T. (2011). Superconducting high pressure phase of platinum hydride. Phys. Rev. B84, 054543.

Zhu Q., Oganov A.R., Salvado M., Pertierra P., Lyakhov A.O. (2011). Denser than diamond:ab initio search for superdense carbon allotropes. Phys. Rev. B83, 193410.