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2015 Publications

For those who want to assign credit in their publications for the institute, please use the following sentence:

Results in this paper were obtained using the high-performance computing system at the Institute for Advanced Computational Science at Stony Brook University. 


Alfaro, D. A.; and  M. Khairoutdinov. 2015: Thermodynamic constraints on the morphology of simulated midlatitude squall lines. J. Atmos. Sci., 72, 3116-3137

Boffi, N. M.; J. C. Hil;   M. G. Reuter. “Characterizing the Inverses of Block Tridiagonal, Block Toeplitz Matrices”.  Comput. Sci. Discov.  8, 015001 (2015) .

Bretherton, C.S.; and  M. Khairoutdinov. 2015: Convective self-aggregation feedbacks in near-global cloud-resolving simulations of an aquaplanet. J. Adv. Model. Earth Syst., DOI: 10.1002/2015MS000499

Centola, Damon; and   Arnout van de Rijt. 2015.  “Choosing Your Network: Social Preferences in an Online Health Community.”  Social Science & Medicine 125: 19—31.

Cha, Deukhyun; Qin Zhang; Jesmin Jahan Tithi; Alexander Rand;   Rezaul Chowdhury; and Chandrajit Bajaj. "Accelerated Molecular Mechanical and Solvation Energetics on Multicore CPUs and Manycore GPUs," Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM BCB), pp. 222{231, 2015.

Chen P.C., Wang N.,   Oganov A.R., Duan W.H. (2015).  Effects of ferroelectric polarization on surface phase diagram: evolutionary algorithm study of BaTiO3(001) surface.  Phys. Rev. B 92, 085432. ( pdf-file )

Conley, R.; T.J. Delaney; and   X. Jiao. Overcoming Element Quality Dependence of Finite Elements with Adaptive Extended Stencil FEM (AES-FEM), International Journal for Numerical Methods in Engineering, to appear, 2015. Preprint available at

Domínguez-Gutiérrez, FJ;   PS Krstić; R Cabrera-Trujillo. Chapter Fifteen-Multiresolution Approach for Laser-Modified Collisions of Atoms and Ions. Advances in Quantum Chemistry 71, 353-371 (2015)

Dong, H.;   Oganov, A. R.;  Zhu, Q.; and Qian, G. R. (2015). The phase diagram and hardness of carbon nitrides.  Sci. Rep.  5, 9870.( pdf-file).

Dyedov, V.; N. Ray; D. Einstein;   X. Jiao; and T.J. Tautges. AHF: Array-Based Half-Facet Data Structure for Mixed-Dimensional and Non-manifold Meshes, Engineering with Computers, Vol. 31(3), pp. 389-404, 2015. DOI: 10.1007/s00366-014-0378-6.

Essig, R.; J. Mardon,   M. V. Fernández-Serra, A. Soto, T. Volansky and T-T. Yu.  Direct Detection of sub-GeV Dark Matter with Semiconductor Targets arXiV:1509.01598 (submitted to Journal of High Energy Physics)

Elton, D.; and    M. V. Fernández-SerraLong range optical phonons in liquid water arXiv:1507.06363 (under review)

Goncharov A.F., Holtgrewe N., Qian G.R., Hu C.H.,   Oganov A.R., Somayazulu M., Stavrou E., Pickard C.J., Berlie A., Yen F., Mahmood M., Lobanov S.S., Konopkova Z., Prakapenka V.B. (2015).  The backbone NxH compounds at high pressures.  J. Chem. Phys. 142, 214308. ( pdf-file )

Gonzalez, Gabriela; Juhi Tyagi; Idil Akin; Fernanda Page; Michael Schwartz; and   Arnout van de Rijt. 2015. “A Field-Experimental Study of Emergent Mobilization in Online Collective Action.”  Mobilization  20(3):281—303.

Goswami, B.B.; R. P. M. Krishna; P. Mukhopadhyay;   M. F. Khairoutdinov; B. N. Goswami. 2015: Simulation of the Indian Summer Monsoon in the Superparameterized Climate Forecast System version 2: Preliminary Results. J. Climate, in press.

Katz, M. P.; M. Zingale;   A. C. Calder;  F. D. Swesty; A. S. Almgren; and W. Zhang. Double White Dwarf Mergers On Adaptive Meshes I. Methodology and Code Verification. ApJ, submitted, 2015

Lee, J. K.; and  M. Khairoutdinov. 2015: Simplified Land Model (SLM) for use in cloud resolving models: Formulation and evaluation. J. Adv. Model. Earth Syst., 07, doi: 10.1002/2014MS000419

Li, Y. L.; Wang, S. N.;   Oganov, A. R.; Gou, H.; Smith, J. S.; and Strobel, T. A. (2015). Investigation of exotic stable calcium carbides using theory and experiment.  Nat. Commun.  6, 6974.( pdf-file).

Li D.;   Oganov A.R.; Dong X.; Zhou X.F.; Zhu Q.; Qian G.R.; Dong H.F. (2015).  Nitrogen oxides under pressure: stability, ionization, polymerization, and superconductivity.  Sci. Rep.  5 , 16311. ( pdf-file ).

Liu, Y.;   Oganov, A. R.; Wang, S.; Zhu, Q.; Dong, X.; and Kresse, G. (2015). Prediction of new thermodynamically stable aluminum oxides.  Sci. Rep. 5, 9518.( pdf-file).

Lobanov S.S., Zhu Q., Holtgrewe N., Prescher C., Prakapenka V.B.,   Oganov A.R., Goncharov A.F. (2015).  Stable magnesium peroxide at high pressure.  Sci. Rep. 5, 13582. ( pdf-file )

Krstić, Predrag; Brian Ashcroft; and Stuart Lindsay. Physical model for recognition tunneling  Nanotechnology 26, 084001 (2015)

Mannix A. J.; Zhou X.-F.; Kiraly B.; Wood J. D.; Alducin D.; Myers B. D.; Liu X.; Fisher B. L.; Santiago U.; Guest J. R.; Yacaman M. J.; Ponce A.;   Oganov A. R.; Hersam M. C.; and Guisinger N. P. (2015). 
Synthesis of borophenes: Anisotropic, two-dimensional boron polymorphs.  Science  350 , 1513-1516. ( pdf-file ).

Medin, Z.; M. von Steinkirch;   A. C. Calder; C. J. Fontes; C. L. Fryer; and A. L. Hungerford. Sub-Eddington model atmospheres, spectra, and color corrections for X-ray bursting neutron stars. ApJ, in prep., 2015

Miles, B. J.; D. R. van Rossum; D. M. Townsley; F. X. Timmes; A. P. Jackson;   A. C. Calder; and E. F. Brown. On Measuring the Metallicity of Supernova Type Ia Progenitors. ApJ, submitted, 2015

Niu H.Y.,   Oganov A.R., Chen X.Q., Li D.Z. (2015).  Novel stable compounds in the Mg-Si-O system under exoplanet pressures and their implications in planetary science.  Sci. Rep. 5, 18347. ( pdf-file )

Pamuk, B.; P. B. Allen; and  M. V. Fernández-SerraElectronic and nuclear quantum effects on the ice XI/ice Ih phase transition. Phys. Rev. B 92, 124105 (2015)

Pedroza, Luana; A. Poisier; and  M. V. Fernández-SerraLocal order of liquid water at metallic electrode surfaces J. Chem. Phys, 142, 034706 (2015)

Quan, R.; C. S. Pitler; M. A. Ratner;   M. G. Reuter. “Quantitative Interpretations of Break Junction Conductance Histograms in Molecular Electron Transport”  ACS Nano  9, 7704-7713 (2015) .

Rakitin M. S.,   A.R. Oganov, H. Niu, M. M. D. Esfahani, X.-F. Zhou, G.-R. Qian and V. L. Solozhenko (2015).  A novel phase of beryllium fluoride at high pressure  Phys. Chem. Chem. Phys., 2015,17, 26283-26288 ( pdf-file )

Reiter, D; Y Marandet; K Lawson;   PS Krstic;  R Guirlet; U Fantz; BJ Braams; H-K Chung. Atomic, Molecular and Plasma-Material Interaction Data for Fusion Science and Technology. indc-nds-0679, IAEA (2015)

Shen Y.Q.,   Oganov A.R., Qian G.R., Zhang J., Dong H.F., Zhu Q., Zhou Z.X. (2015).  Novel lithium-nitrogen compounds at ambient and high pressures.  Sci. Rep. 5, 14204. ( pdf-file )

Shor, Eran;   Arnout van de Rijt; Alex Miltsov; Vivek Kulkarni; and Steven Skiena.  2015. “A Paper Ceiling: Explaining the Persistent Underrepresentation of Female Names in Printed News Coverage.”  American Sociological Review 80(5): 960—84.

Sichen, Zhong; Lu Zhao; Yan Liang; Mohammadzaman Zamani; Rob Patro;   Rezaul Chowdhury; Esther Arkin; Joseph Mitchell; and Steven Skiena. "Optimizing Read Reversals for Sequence Compression," Proceedings of the Workshop on Algorithms in Bioinformatics (WABI), pp. 189{202, 2015 (Invited to Algorithms for Molecular Biology Special Issue for WABI'15).

Stavrou, E.; Chen, X.-J.;   Oganov, A. R.; Wang, A. F.; Yan, Y. J.; Luo, X. G.; Goncharov, A. F. (2015). Formation of As-As Interlayer Bonding in the collapsed tetragonal phase of NaFe2As2 under pressure.  Sci. Rep.  5, 9868.( pd f-file).

Song, Hyang-Gi; Michael Restivo;  Arnout van de Rijt; Lori Scarlatos; David Tonjes; and Alex Orlov. 2015. “The Hidden Gender Effect in Online Collaboration: An Experimental Study of Team Performance under Anonymity.”  Computers in Human Behavior  50: 274—82.

Tang, Yuan; Ronghui You; Haibin Kan; Jesmin Jahan Tithi; Pramod Ganapathi; and   Rezaul Chowdhury. "Cache-Oblivious Wavefront: Improving Parallelism of Recursive Dynamic Programming Algorithms without Losing Cache-e ciency," Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP), 2015.

Tian, Xiaonan, Rengan Xu, Yonghong Yan, Sunita Chandrasekaran, Deepak Eachempati, and   Barbara Chapman, “Compiler Transformation of Nested Loops for GPGPUs”, in Concurrency and Computation: Practice and Experience, Special Issue on Programming Models and Applications for Multicores and Manycore, 2015.  PDF  Bibtex

Tithi, Jesmin Jahan; Pramod Ganapathi; Aakrati Talati; Sonal Aggarwal; and   Rezaul Chowdhury. "High-Performance Energy-E cient Recursive Dynamic Programming with Matrix-Multiplication-Like Flexible Kernels," Proceedings of the 29th IEEE International Parallel & Distributed Processing Symposium (IPDPS), 2015.

Tithi, Jesmin Jahan and   Rezaul Chowdhury. "Efficient computation of distance incorporated codon autocorrelation (DICA) score using fast Fourier transform," Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM BCB), pp. 515-516, 2015.

Townsley, D. M.; B. J. Miles; F. X. Timmes;   A. C. Calder; and E. F. Brown. Nucleosynthetic Yields from Multidimensional Simulations of Type Ia Supernovae: Reconstruction of Thickened Flames and Verification for Planar Detonations. ApJ, submitted, 2015

Willcox, D. E.; D. M Townsley;   A. C. Calder; P. A. Denissenkov; and F. Herwig. Type Ia Supernova Explosions from Hybrid Carbon-Oxygen-Neon White Dwarf Progenitors. ApJ, In prep., 2015

Xie C.W.;   Oganov A.R.; Dong D.; Liu N.; Li D.; Debela T.T. (2015).  Rational design of inorganic dielectric materials with expected permittivity.  Sci. Rep.  5 , 16769. ( pdf-file ).

Xu, C. S.; Xu, B., Yang, Y. R.; Dong ,H. F.;  Oganov, A. R.; Wang, S. Y.; Bellaiche, L. (2015). Prediction of a stable post-post-perovskite structure from first principles.  Phys Rev B, 91, 020101.( pdf-file).

Rengan Xu, Sunita Chandrasekaran,   Barbara Chapman,  “Multi-GPU Support on Shared Memory System using Directive-based Programming Model”, in the Special Issue of Programming Models, Languages and Compilers for Manycore and Heterogeneous Architectures, Journal of Scientific Programming, Article ID 621730, pp. 3:3-3:3, 2015.  LINK  Bibtex

Yanai, Takeshi, George I. Fann, Gregory Beylkin,  Robert J. Harrison, “Multiresolution Quantum Chemistry in Multiwavelet Bases: Excited States from Time-dependent Hartree-Fock and Density Functional Theory via Linear Response,” Phys. Chem. 2015, 17, 31405-31416.

Yu, X.;   Oganov, A. R.; Popov, I. A.; & Boldyrev, A. I. (2015) d-AO spherical aromaticity in Ce6O8.  J. Comput. Chem. 24049. ( pdf-file).

Yu, S.; Zeng, Q.;   Oganov, A. R.; Frapper, G.; & Zhang, L. (2015). Phase stability, chemical bonding and mechanical properties of titanium nitrides: a first-principles study.  Phys. Chem. Chem. Phys.,  17, 11763–11769.( pdf-file).

Yu S.Y.; Jia X., Frapper G.; Li D.;   Oganov A.R.; Zeng Q.F.; Zhang L.T. (2015).  Pressure-driven formation and stabilization of superconductive chromium hydrides.  Sci. Rep.  5 , 17764. ( pdf-file ).

Wang, Z.; Zhou, X.-F.; Zhang, X.; Zhu, Q.; Dong, H.; Zhao, M.; &   Oganov, A. R.  (2015). Phagraphene: A Low-Energy Graphene Allotrope Composed of 5–6–7 Carbon Rings with Distorted Dirac Cones.  Nano Letters.( pdf-file).

Wu, Y;   P Krstic; FY Zhou; F Meyer. Damage at a tungsten surface induced by impacts of self-atoms. Journal of Nuclear Materials 467, 480-487 (2015)

Zeng, Z.; Zeng, Q.; Liu, N.;   Oganov, A. R.; Zeng, Q.; Cui, Y.; and Mao, W. L. (2015). A Novel Phase of Li15Si4 Synthesized under Pressure.  Adv. Energy Mater., 1500214. ( pdf-file).

Zhang, G.; M. A. Ratner;  M. G. Reuter. “Is Molecular Rectification Caused by Asymmetric Electrode Couplings or by a Molecular Bias Drop?” J. Phys. Chem. C 119, 6254-6260 (2015)

Zhang, J.;   Oganov, A. R.; Li, X.; Dong, H.; & Zeng, Q. (2015). Novel compounds in the Zr-O system, their crystal structures and mechanical properties.  Phys. Chem. Chem. Phys.  17, 17301–17310.( pdf-file).

Zhang J.;   Oganov A.R.; Li X.; Xue K.H.; Wang Z.H.; Dong H.F. (2015).  Pressure-induced novel compounds in the Hf-O system from first-principles calculations.  Phys. Rev. B  92 , 184104. ( pdf-file ).

Zhu, Q.;   Oganov, A. R.; & Zeng, Q. F. (2015). Formation of Stoichiometric CsFn Compounds.  Sci. Rep.  5, 7875.( pdf-file).

Zhu, Q.;   Oganov, A. R.; Lyakhov, A. O.; and Yu, X. (2015). Generalized evolutionary metadynamics for sampling the energy landscapes and its applications.  Phys. Rev. B, 92, 024106.( pdf-file).

Zubeltzu, Jon; Fabirano Corsetti;  M.V. Fernandez-Serra; Emilio Artacho.  Confined bilayer water melts like two highly correlated layers of Lennard-Jones particles Submitted (2015)

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