2016 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 Handy computing system at the Institute for Advanced Computational Science at Stony Brook University. 


An Q., Reddy K.M., Dong H.F., Chen M.-W., Oganov A.R., Goddard, W.A. III. (2016). Twinning in boron suboxide (B6O) leading to new crystal structures. Nano Letters 16, 4236-4242 (pdf-file)

Blase, X.; Paul Boulanger; Fabien Bruneval; Marivi Fernández-Serra; and Ivan Duchemin. GW and Bethe-Salpeter study of small water clusters, J. Chem. Phys. Accepted (2016)

Bender, Michael; Chowdhury, Rezaul; Pramod Ganapathi, Samuel McCauley, and Yuan Tang, "The Range 1 Query (R1Q) Problem", Theoretical Computer Science (Special Issue for COCOON'14, Invited Paper), 2016.

Bender, Michael; Rezaul Chowdhury, Alexander Conway, Martín Farach-Colton, Pramod Ganapathi, Rob Johnson, Samuel McCauley, Bertrand Simon, and Shikha Singh, "The I/O Complexity of Computing Prime Tables", Proceedings of the 12th Latin American Theoretical Informatics Symposium (LATIN 2016), Ensenada, Mexico, LNCS 9644, pp. 192-206, 2016.

Calder, A. C., B. K. Krueger, A. P. Jackson, D. E. Willcox, B. J. Miles, and D. M. Cosmic Chandlery with Thermonuclear Supernovae. Townsley Proceedings of Astronum2016 – 11th International Conference on Numerical Modeling of Space Plasma Flows, Monterey, CA, June 6-10, 2016. J. Phys. Conf. Ser. In press. 2016

Conley, R.; T.J. Delaney, and X. JiaoOvercoming Element Quality Dependence of Finite Elements with Adaptive Extended Stencil FEM (AES-FEM)International Journal for Numerical Methods in Engineering, 2016. DOI:10.1002/nme.5246.

Chowdhury, Rezaul; Pramod Ganapathi, Vivek Pradhan, Jesmin Jahan Tithi, and Yunpeng Xiao, "An Efficient Cache-oblivious Parallel Viterbi Algorithm", Proceedings of the 22nd International European Conference on Parallel and Distributed Computing (EuroPar 2016), Grenoble, France, LNCS 9833, pp. 574-587, 2016.

Chowdhury, Rezaul; Pramod Ganapathi, Jesmin Jahan Tithi, Charles Bachmeier, Bradley C. Kuszmaul, Charles E. Leiserson, Armando Solar-Lezama, and Yuan Tang, "AUTOGEN: Automatic Discovery of Cache- Oblivious Parallel Recursive Algorithms for Solving Dynamic Programs", Proceedings of the 21st ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP 2016), Barcelona, Spain, article 10, 2016. (Invited to ACM Transactions on Parallel Computing Special Issue on Best Papers from PPoPP'16).

Davari Esfahani M.M., Wang Z.H., Oganov A.R., Dong H.F., Zhu Q., Wang S.N., Rakitin M.S., Zhou X.F. (2016). Superconductivity of novel tin hydrides (SnnHm) under pressure. Sci. Rep. 6, 22873 (pdf-file)

Dolgirev P. E., Kruglov I. A., Oganov A. R. (2016). Machine learning scheme for fast extraction of chemically interpretable interatomic potentials. AIP Advances 6, 085318. (pdf-file)

Domínguez-Gutiérrez, FJ and  PS KrstićCharge transfer in collisions of H+ with Li (1s22s, 2pz): TD-MADNESS approachJOURNAL OF PHYSICS B: ATOMIC, MOLECULAR AND OPTICAL PHYSICS 49, 195206 (2016).

Domínguez-Gutiérrez, F.J.; F. Bedoya, P.S. Krstić, J.P. Allain, A.L. Neff, K. Luitjohan, "Studies of lithiumization and boronization of ATJ graphite PFCs in NSTX-U", Nuclear Materials and Energy (Elsevier, 2016), 10.1016/j.nme.2016.12.028

Dong H.F., Oganov A.R., Wang Q.G., Wang S.N., Wang Z.H., Zhang J., Davari Esfahani M.M., Zhou X.F., Wu F.G., Zhu Q. (2016). Prediction of a new ground state of superhard compound B6O at ambient conditions. Sci. Rep. 6, 31288 (pdf-file)

Elton, D. and  M. V. Fernández-SerraThe hydrogen-bond network of water supports propagating optical phonon-like modes. Nature Communications 7, Article number: 10193, (2016)

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)

Frey, Vincenz and Arnout van de Rijt. 2016. “Arbitrary Inequality in Reputation Systems.” Nature Scientific Reports 6:38304.

Fritz, Michelle; Marivi Fernández-Serra and Jose M. Soler. Optimization of an exchange-correlation density functional for water, J. Chem. Phys. 144, 224101 (2016)

Goncharov A.F., Lobanov S.S., Kruglov I.A., Zhao X.M., Chen X.J., Oganov A.R., Konopkova Z., Prakapenka V.B. (2016). Hydrogen sulfide at high pressure: change in stoichiometry. Phys. Rev. B93, 174105 (pdf-file)

Han, LMyung-Geun; Joseph A. Garlow, Matthieu Bugnet, Simon Divilov, Matthew S. J. Marshall, Lijun Wu, Matthew Dawber, Marivi Fernández-Serra, Gianluigi A. Botton, Sang-Wook Cheong, Frederick J. Walker, Charles H. Ahn, and Yimei Zhu. Coupling of bias-induced crystallographic shear planes with charged domain walls in ferroelectric oxide thin films, Phy. Rev. B (Rapid Comm.), 2016

Harrison, R.J.; G. Beylkin, F. A. Bischoff, J. A. Calvin, G. I. Fann, J. Fosso-Tande, D. Galindo, J. R. Hammond, R. Hartman-Baker, J. C. Hill, J. Jia, J. S. Kottmann, M-J. Y. Ou, J. Pei, L. E. Ratcliff, M. G. Reuter, A. C. Richie-Halford, N. A. Romero, H. Sekino, W. A. Shelton, B. E. Sundahl, W. S. Thornton, E. F. Valeev, Á. Vázquez-Mayagoitia, N. Vence, T. Yanai, Y. Yukoi. “MADNESS: A Multiresolution, Adaptive Numerical Environment for Scientific Simulation”. SIAM J. Sci. Comput., Vol. 38, No. 5, pp. S123-S142 (2016).

Itzhaky, Shachar; Rohit Singh, Armando Solar-Lezama, Kuat Yessenov, Yongquan Lu, Charles Leiserson, and Rezaul Chowdhury, "Deriving Divide-and-Conquer Dynamic Programming Algorithms Using Solver-Aided Transformations", To appear in the Proceedings of the ACM SIGPLAN International Conference on Object-Oriented Programming, Systems, Languages & Applications (OOPSLA 2016), Amsterdam, Netherlands, 2016.

Karpov, P., M. B. Sazo, M. Zingale, W. Zhang, A. C. Calder, Toward simulating Black Widow binaries with CASTRO. JOCSE, submitted, 2016

Katz, Max P.; Zingale, Michael; Calder, Alan C.; Swesty, F. Douglas; Almgren, Ann S.; Zhang, Weiqun. White Dwarf Mergers on Adaptive Meshes. I. Methodology and Code Verification. The Astrophysical Journal, Volume 819, Issue 2, article id. 94, 28 pp. (2016).

Krstić, PredragChapter Two-Response of a DNA Hydrogen Bond to a Force in Liquid, ADVANCES IN QUANTUM CHEMISTRY 72, 13-28 (2016).

Lepeshkin S., Baturin V., Tikhonov E., Matsko N., Uspenskii Y., Naumova A., Feya O., Schoonen M.A., Oganov A.R. (2016). Super-oxidation of silicon nanoclusters: magnetism and reactive oxygen species at the surface. Nanoscale 8, 1816-1820 (pdf-file)

Lindsay, Stuart; Brett Gyarfas, Predrag Krstic, Padmini Krishnakumar, Systems, Devices And Methods For Translocation Control, US Patent  20,160,025,702, 2016; Pub. No.:US 2016/0025702 A1.

Liu, H.; and X. JiaoWLS-ENO: Weighted-Least-Squares Based Essentially Non-Oscillatory Schemes for Finite Volume Methods on Unstructured Meshes, Journal of Computational Physics, Vol. 314, pp. 749-773, 2016. DOI: 10.1016/j.jcp.2016.03.039. 

Liu, Jian; Maria V. Fernández-Serra, and Philip B. Allen. First-principles study of pyroelectricity in GaN and ZnO. Phys. Rev. B 93, 081205(R) (2016)

Liu, Jian; Maria V. Fernández-Serra, and Philip B. Allen, Special quasiordered structures: Role of short-range order in the semiconductor alloy (GaN)1−x(ZnO)x. Phys. Rev. B 93, 054207 (2016)

Matsko N. L., Tikhonov E. V., Baturin V. S., Lepeshkin S. V., Oganov A. R. (2016). The impact of electron correlations on the energetics and stability of silicon nanoclusters. J. Chem. Phys. 145, 074313. (pdf-file)

Medin, Z., M. von Steinkirch, A. C. Calder, C. J. Fontes, C. L. Fryer, and A. L. Hungerford. Model Atmospheres for X-Ray Bursting Neutron Stars. ApJ, 832, 102, 2016

Miles, Broxton J.; van Rossum, Daniel R.; Townsley, Dean M.; Timmes, F. X.; Jackson, Aaron P.; Calder, Alan C.; Brown, Edward F. On Measuring the Metallicity of a Type Ia Supernova’s Progenitor. The Astrophysical Journal, Volume 824, Issue 1, article id. 59, 19 pp. (2016). 

Pedroza, Luana S.; Pedro Brandimarte, Alexandre Reily Rocha, Marivi Fernández-SerraFirst principles simulations of a bias-dependent electrochemical cell, submitted (2016)

Qian G.R., Niu H.Y., Hu C.H., Oganov A.R., Zeng Q.F., Zhou H.Y. (2016). Diverse chemistry of stable hydronitrogens, and implication for planetary and materials sciences. Sci. Rep. 6, 25947 (pdf-file)

Randall, D. R.; C. DeMott; C. Stan; M. Khairoutdinov; J. Benedict; R. McCrary; K. Thayer-Calder; and M. Branson. 2016: Simulations of the Tropical General Circulation with a Multiscale Global Model.Prepared for the Yanai memorial Volume.

Ray, N.; I. Grindeanu; X. Zhao; V. Mahadevan; and X. Jiao. Array-Based Hierarchical Mesh Generation in Parallel, Computer Aided Design, to appear, 2016

Reilly A.M., Cooper R.I., Oganov A.R., Groom C.R. et al. (2016). Report on the Sixth Blind Test of Organic Crystal-Structure Prediction Methods. Acta Cryst B, 72, 4, 439-459 (pdf-file)

Saleh G., Oganov A.R. (2016). High pressure stability and interplay between metallic and ionic bonds. Phys. Chem. Chem. Phys. 18, 2840-2849. (pdf-file).

Saleh G., Oganov A.R. (2016). Pressure-induced stabilization of carbonic acid and other compounds in the C-H-O phase diagram. Sci. Rep. 6, 32486 (pdf-file)

Saleh G., Oganov A.R. (2016). Alkali subhalides: high pressure stability and interplay between metallic and ionic bonds. Phys. Chem. Chem. Phys. 18, 2840-2849. (pdf-file)

Sovan Biswas, Suman Sen, JongOne Im, Sudipta Biswas, Predrag Krstić, Brian Ashcroft, Chad Borges, Yanan Zhao, Stuart Lindsay, Peiming Zhang, Universal Readers Based on Hydrogen Bonding or π-π Stacking for Identification of DNA Nucleotides in Electron Tunnel Junctions, ACS-NANO, 10.1021/acsnano.6b06466, November 17 (2016).

Stavrou E., Lobanov S.V., Dong H.F., Oganov A.R., Prakapenka V.B., Konopkova Z., Goncharov A.F. (2016). Synthesis of ultra-incompressible sp3-hybridized carbon nitride with 1:1 stoichiometry. Chem. Mater. 28, 6925-6033 (pdf-file

Stuart Lindsay; Brett Gvarfas; Predrag Krstić; Padmini Krishnakumar. Systems, devices and methods for translocation control. U.S. Patent US20160025702 A1, january 28, 2016.

Townsley, Dean M.; Miles, Broxton J.; Timmes, F. X.; Calder, Alan C.; Brown, Edward F. A Tracer Method for Computing Type Ia Supernova Yields: Burning Model Calibration, Reconstruction of Thickened Flames, and Verification for Planar Detonations. The Astrophysical Journal Supplement Series, Volume 225, Issue 1, article id. 3, 28 pp. (2016).

Tschudi, S. E.; M. G. Reuter. “Estimating the Landauer-Büttiker Transmission Function from Experimental Data on Single-Molecule Electron Transport”. Nanotechnology 27, 425203 (2016).

van de Rijt, Arnout; Idil Akin, Robb Willer and Matthew Feinberg. 2016. “Success-Breeds-Success in Collective Political Behavior: Evidence from a Field Experiment.” Sociological Science 3: 940-50. 

Wang Q., Oganov A.R., Feya O.D., Zhu Q., Ma D.W. (2016). The unexpectedly rich reconstructions of rutile TiO2(011)-(2x1) surface and the driving forces behind their formation: an ab initio evolutionary study. Phys. Chem. Chem. Phys. 18, 19549 (pdf-file)

Wang Q.G., German K.E., Oganov A.R., Dong H.F., Feya O.D., Zubavichus Y.V., Murzin V. (2016). Explaining stability of transition metal carbides – and why TcC does not exist. RSC Advances 6, 16197-16202 (pdf-file)

Wang, X.; R. Samulyak, X. Jiao, K. Yu, AP-Cloud: Adaptive Particle-in-Cloud method for optimal solutions to Vlasov-Poisson equationJournal of Computational Physics, Vol. 316, 2016. DOI: 10.1016/j.jcp.2016.04.037. 

Wang S.N., Oganov A.R., Qian G.R., Zhu Q., Dong H.F., Davari Esfahani M.M. (2016). Novel superhard B-C-O phases predicted from first principles. Phys. Chem. Chem. Phys. 18, 1859-1863. (pdf-file).

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, 832, 13, 2016

Woerner B.R., Qian G.R., Oganov A.R., Stephens P.W., Dharmagunawardhane H.A.N., Sinclair A., Parise J.B. (2016). Combined theoretical and in situ scattering strategies for optimized discovery and recovery of high-pressure phases: A case study of the GaN-Nb2O5 system. Inorg. Chem. 55, 3384-3392 (pdf-file)

Xie C.W., Oganov A.R., Dong D., Zeng Q.F. (2016). Effects of carbon vacancies on the structures, mechanical properties, and chemical bonding of zirconium carbides: a first-principles study. 
Phys. Chem. Chem. Phys. 18, 12299-12306 (pdf-file)

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.H., Oganov A.R., Popov I.A., Qian G.R., Boldyrev I.A. (2016). Antiferromagnetic stabilization in Ti8O12 cluster. Angew. Chem. Int. Ed. 55, 1699-1703. (pdf-file).

Yu S.Y., Huang B., Jia X.J., Oganov A.R., Zeng Q.F., Zhang L.T., Frapper G. (2016). Exploring the real ground-state structures of molybdenum-nitrogen MoN2 phases. J. Phys. Chem. C120, 11060-11067 (pdf-file)

Zhang W.W., Oganov A.R., Zhu Q., Lobanov S., Stavrou E., Goncharov A.F. (2016). Stability of numerous novel potassium chlorides at high pressure. Sci. Rep. 6, 26265 (pdf-file)

Zhou X.F., Oganov A.R., Wang Z.H., Popov I.A., Boldyrev A.I., Wang H.T. (2016). Two-dimensional magnetic boron. Phys. Rev. B93, 085406 (pdf-file)

Zhu J., Oganov A.R., Feng W.X., Yao Y.G., Zhang S.J., Yu X.H., Zhu J.L., Yu R.C., Jin C.Q., Dai X., Fang Z., Zhao Y.S. (2016). Pressure-induced Ag2Te polymorphs in conjunction with topological non-trivial to metal transition. AIP Advances 6, 085003 (pdf-file)

Zhu Q., Oganov A.R., Zeng Q.F., Zhou X.F. (2016). Structure prediction and its applications in computational materials design. Chem. Model. 12, 219-248.

Zhu Q., Shtukenberg A., Carter D., Yu T.Q., Yang J.X., Chen M., Raiteri P., Oganov A.R., Pokroy B., Polishchuk I., Bygrave P., Day G., Rohl A., Tuckerman M., Kahr B. (2016). Resorcinol Crystallization from the Melt: A New Ambient Phase and New “Riddles”. J. Am. Chem. Soc. 138, 4881-4889 (pdf-file)

Zubeltzu, Jon; Fabirano Corsetti, M.V. Fernández-Serra, Emilio Artacho. Continuous melting through a hexatic phase in confined bilayer water,  Phys. Rev. E (2016)