2013 Publications

Are the anomalies in water due to an unapproachable critical point? Commentary by M.V. Fernandez-Serra for the Journal Club for Condensed Matter Physics., April 2013.

Arnout van de Rijt, Eran Shor, Charles Ward and Steven Skiena. "Only Fifteen Minutes? The Social Stratification of Fame in English-Language Media." American Sociological Review 78(2):266-89. 

Calder, Alan C.; Krueger, Brendan K.; Jackson, Aaron P.; Townsley, Dean M. The influence of chemical composition on models of Type Ia supernovae. Frontiers of Physics, Volume 8, Issue 2, pp.168-188.

CN Taylor, J Dadras, KE Luitjohan, JP Allain, PS Krstic, CH Skinner, The role of oxygen in the uptake of deuterium in lithiated graphite. Journal of Applied Physics 114 (22), 223301 (2013)

Evolution of FLASH, a Multiphysics Scientific Simulation Code for High Performance Computing A. Dubey, A. Calder, R. Fisher, C. Graziani, G. C. Jordan, D. Q. Lamb, L. B. Reid, D. Townsley,
K. Weide. Others. Int. J. High Perform. C. (IJHPCA), published online Oct. 3, 2013

Hu C.H., Oganov A.R., Zhu Q., Qian G.R., Frapper G., Lyakhov A.O., Zhou H.Y. (2013). Pressure-Induced Stabilization and Insulator-Superconductor Transition of BH. Phys. Rev. Lett. 110, 165504.

Hu M., Zhao Z.S., Tian F., Oganov A.R., Wang Q.Q., Xiong M., Fan Q.Z., Wen B., He J.L., Yu D.L., Wang H.-T., Xu B., Tian Y.J. (2013). Compressed carbon nanotubes: a family of new multifunctional carbon allotropes. Scientific Reports 3, 1331.

J. Fosso-Tande and R.J. Harrison, “Implicit Solvation Models in a Multiresolution Multiwavelet Basis,” Chem. Phys. Lett. P179-184, 561-2, 2013.

J. Fosso Tande and R.J. Harrison, “Confinement effects of solvation on a molecule physisorbed on a polarizable continuum particle,” Computational and Theoretical Chemistry, P22–30, 1017, 2013.

J Vranjes, PS Krstic, Collisions, magnetization, and transport coefficients in the lower solar atmosphere, ASTRONOMY&ASTROPHYSICS 554, A22 (2013),  http://dx.doi.org/10.1051/0004-6361/201220738  (arXiv preprint arxiv.org/abs/1304.4010v1.pdf)

Jesmin Jahan Tithi, Dhruv Matani, Gaurav Menghani, and Rezaul Chowdhury. “Avoiding locks and atomic instructions in shared-memory parallel BFS using optimistic parallelization”. In Proceedings of the IPDPS Workshop on Multithreaded Architectures and Applications (MTAAP), 2013.
 
Jesmin Jahan Tithi and Rezaul Chowdhury. “Polarization energy on a cluster of multicores”. In Proceedings of the IPDPS Workshop on High Performance Computational Biology (HiComb), 2013.

Khairoutdinov, M. F., and K. A. Emanuel (2013), Rotating radiative-convective equilibrium simulated by a cloud-resolving model, J. Adv. Model. Earth Syst., 5, doi:10.1002/2013MS000253.

Khairoutdinov, M. F., and C.-E. Yang, 2013: Cloud-Resolving Modeling of Aerosol Indirect Effects in Idealized Radiative-Convective Equilibrium with Interactive and Fixed Sea Surface Temperature. Atmos. Chem. Phys., 13, 4133-4144, doi:10.5194/acp-13-4133-2013

Lyakhov A.O., Oganov A.R., Stokes H.T., Zhu Q. (2013). New developments in evolutionary structure prediction algorithm USPEX. Comp. Phys. Comm. 184, 1172-1182.

Mark A Reed, Predrag S Krstic, Weihua Guan, Xiongce Zhao, System and Method for Trapping and Measuring a Charged Particle In a Liquid, US PATENT 8,294,092 (2013).

Matthew G. Reuter and Robert J. Harrison, Rethinking first-principles electron transport theories with projection operators: The problems caused by partitioning the basis set J. Chem. Phys. 139, 114104 (2013); http://dx.doi.org/10.1063/1.4821176.

Ö. Günaydın-Şen, P. Chen, J. Fosso-Tande, T. L. Allen, J. Cherian, T. Tokumoto, P. M. Lahti,S. McGill, R. J. Harrison and J. L. Musfeldt Magnetoelectric, coupling in 4,4′-stilbenedinitrene J. Chem. Phys. 138, 204716 (2013); http://dx.doi.org/10.1063/1.4807053

Oganov A.R., Hemley R.J., Hazen R.M., Jones A.P. (2013). Structure, Bonding, and Mineralogy of Carbon at Extreme Conditions.  Reviews in Mineralogy and Geochemistry 75, 47-77.

Optimal finite-range atomic basis sets for liquid water and ice Fabiano Corsetti, M.-V. Fernández-Serra, José M. Soler, and Emilio ArtachoJ. Phys.: Condens. Matter 25 (2013) 435504.

P Krishnakumar, B Gyarfas, W Song, S Sen, P Zhang, P Krstic, S Lindsay, Slowing DNA Translocation through a Nanopore Using a Functionalized Electrode , ACS NANO, 2013, 7 (11), pp 10319–10326

P. S. Krstic, J. P. Allain, C. N. Taylor, J. Dadras, S. Maeda, K. Morokuma, J. Jakowski, A. Allouche, and C. H. Skinner, Deuterium uptake in magnetic-fusion devices with lithium-conditioned carbon walls, PHYSICAL REVIEW LETTERS 110, 105001 (2013).

Pragmatic Optimizations for Best Scientic Utilization of Large Supercomputers. A. Dubey, A. Calder, R. Fisher, C. Graziani, G. C. Jordan, D. Q. Lamb, L. B. Reid, D. Townsley, K. Weide. Int. J. High Perform. C. (IJHPCA), 27, 358, 2013

Qian G.R., Dong X., Zhou X.-F., Tian Y., Oganov A.R., Wang H.-T. (2013). Variable cell nudged elastic band method for studying solid-solid structural phase transitions.  Comput. Phys. Comm. 184, 2111-2118.

Reza Basseda and Rezaul Chowdhury. “A parallel bottom-up resolution algorithm using Cilk”. In Proceedings of the IEEE 25th International Conference on Tools with Artificial Intelligence (ICTAI), pp. 95-100, 2013.
 
Rezaul Chowdhury, Francesco Silvestri, Brandon Blakeley, and Vijaya Ramachandran. “Oblivious algorithms for multicores and network of processors”, Journal of Parallel and Distributed Computing, 73 (7), pp. 911–925, 2013.
 
Rezaul Chowdhury, Muhibur Rasheed, Donald Keidel, Maysam Moussalem, Arthur Olson, Michel Sanner, and Chandrajit Bajaj. “Protein-protein docking with F2Dock 2.0 and GB-Rerank”, PLOS ONE, 8 (3), 2013.

Room temperature compressibility and the diffusivity anomaly of liquid water from first principles. Fabiano Corsetti, Emilio Artacho, José M. Soler, S. S. Alexandre, M.-V. Fernández-Serra, J. Chem. Phys. 139, 194502 (2013).

Simulation of quantum zero-point effects in water using a frequency dependent thermostat. Sriram Ganeshan, R. Ramirez, and  M. V. Fernández-SerraPhys. Rev. B 87, 134207 (2013)

The Software Development Process of FLASH, a Multiphysics Simulation Code A. Dubey, K. Antypas, A.C. Calder, B. Fryxell, D.Q. Lamb, P.M. Ricker, L.B. Reid, K. Riley, R. Rosner, A. Siegel, F.X. Timmes N. Vladimirova , Klaus Weide. in press, 2013 in proc. International Workshop on SoftwareEngineering for Computational Science and Engineering (SE-CSE2013), May 18, 2013, In Conjunction with ICSE 2013.

Zeng Q., Peng J., Oganov A.R., Zhu Q., Xie C., Zhang X., Dong D., Zhang L., Cheng L. (2013). Prediction of stable hafnium carbides: Stoichiometries, mechanical properties, and electronic structure Phys. Rev. B88, 214107

Zhang W.W., Oganov A.R., Goncharov A.F., Zhu Q., Boulfelfel S.E., Lyakhov A.O., Stavrou E., Somayazulu M., Prakapenka V.B., Konopkova Z. (2013). Unexpected stoichiometries of stable sodium chlorides. Science 342, 1502-1505.

Zhu Q., Jung D.Y., Oganov A.R., Gatti C., Glass C.W., Lyakhov A.O. (2013). Stability of xenon oxides at high pressures. Nature Chemistry 5 , 61-65.

Zhu Q., Li L., Oganov A.R., Allen P.B. (2013). Evolutionary method for prediction of surface reconstructions with variable stoichiometry.  Phys. Rev. B87, 195317.

Zhu Q., Oganov A.R., Lyakhov A.O. (2013). Novel stable compounds in the Mg-O system under high pressure. Phys. Chem. Chem. Phys. 15, 7796-7700.