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2017 Publications

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The authors would like to thank Stony Brook Research Computing and Cyberinfrastructure, and the Institute for Advanced Computational Science at Stony Brook University for access to the high-performance LIred and SeaWulf computing systems, the latter of which was made possible by a $1.4M National Science Foundation grant (#1531492).


Asaadi, Hamidreza and   Barbara Chapman , “Comparative Study of Deep Learning Framework in HPC Environments”, In   2017 New York Scientific Data Summit (NYSDS2017) , August 2017, New York, NY  

Avcu, Enes; Chihiro Shibata, and   Jeffrey Heinz. Subregular Complexity and Deep Learning. In Simon Dobnik, Stergios Chatzikyriakidis, and Shalom Lappin, editors, Proceedings of the Conference on Logic and Machine Learning in Natural Language, 2017. Preprint on arXiv:1705.05940.

Bari, Md Abdullah Shahneous, Abid Malik, Ahmad Qawasmeh and   Barbara Chapman , “A Detailed Analysis of OpenMP Runtime Configurations for Power Constrained Systems”, In   The Eighth International Green and Sustainable Computing Conference (IGSC2017) , October 2017, Orlando, FL

Bazhanova Z.G., Roizen V.V.,   Oganov A.R.  (2017).  High-pressure behavior of the Fe-S system and composition of the Earth's inner core.  Phys. Usp. 60, 1025–1032   

Brini, Emiliano; Miha Lukvsivc, Christopher J. Fennell, Barbara Hribar-Lee,  Marivi Fernandez-Serra and Ken Dill,  How water's properties are encoded in its molecular structure \& energies, submitted (2017)

Calder, A. C.; B. K. Krueger, A. P. Jackson, D. E. Willcox, B. J. Miles, and D. M. Townsley Cosmic Chandlery with Thermonuclear Supernovae.  Proceedings of Astronum2016 -- 11th International Conference on Numerical Modeling of Space Plasma Flows, Monterey, CA, June 6-10, 2016.  J. Phys. Conf. Ser. 837 012005, 2017

Chandlee, Jane; and  Jeffrey Heinz . Computational Phonology. In Mark Aronoff, editor, Oxford Research Encylcopedia of Linguistics. Oxford University Press, 2017.

Chang C.S., Greenwald M., Riley K., ..., Krstic,  P.,   et al., "Fusion Energy Sciences Exascale Requirements Review", Technical Report, An Office of Science review sponsored by ASCR and FES (2017) doi:10.2172/1375639  

Che-Castaldo, C., S. Jenouvrier, C. Youngflesh, K. Shoemaker, G. Humphries, P. McDowall, L. Landrum, M. Holland, Y. Li, R. Ji,   H.J. Lynch. 2017. Pan-Antarctic analysis aggregating spatial estimates of Adélie penguin abundance reveals robust dynamics despite stochastic noise. Nature Communications 8: 832.

Chowdhury, Rezaul; Pramod Ganapathi, Yuan Tang, Jesmin Jahan Tithi. "Provably Efficient Scheduling of Cache-oblivious Wavefront Algorithms", Proceedings of the 29th ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2017), pp. 339-350, 2017.

Chowdhury, Rezaul; Pramod Ganapathi, Steven Tschudi, Jesmin Jahan Tithi, Charles Bachmeier, Bradley C. Kuszmaul, Charles E. Leiserson, Armando Solar-Lezama, and Yuan Tang, "AutoGen: Automatic Discovery of Efficient Recursive Divide-&-Conquer Algorithms for Solving Dynamic Programming Problems," To Appear in the ACM Transactions on Parallel Computing (Special Issue for PPoPP'16, Invited Paper), 2017. 

Chowdhury, Rezaul; and Vijaya Ramachandran. "Cache-oblivious Buffer Heap and Cache-efficient Computation of Shortest Paths in Graphs", To Appear the ACM Transactions on Algorithms (TALG), 2017.

Chown, S.L.; M.A. McGeoch, A. Terauds, C. Le Bohec, C. van Klaveren-Impagliazzo, J. Whittington, C. Brooks, S. Butchart, B.W.T Coetzee, B. Collen, P. Convey, K.J. Gaston, N. Gilbert, M. Gill, R. Höft, S. Johnston, M.C. Kennicutt II, H. Kriesell, Y. Le Maho,   H.J. Lynch, M. Palomares, R. Puig-Marcó, P. Stoett. 2017. Antarctica and the Strategic Plan for Biodiversity 2011–2020. PLoS Biology 15(3): e2001656.

Davari Esfahani M.M.,   Oganov A.R., Niu H.Y., Zhang J., (2017).  Superconductivity and unexpected chemistry of germanium hydrides under pressure. Phys. Rev. B95, 134506. ( pdf-file)

Davari Esfahani M. M., Zhu Q., Dong H.,   Oganov A.R., Wang S.N., Rakitin M.S., Zhou X.F. (2016). Novel magnesium borides and their superconductivity. Phys.Chem.Chem.Phys.,19, 14486 ( pdf-file)

de Supinski, Bronis R., Stephen L. Olivier, Christian Terboven,   Barbara M. Chapman,  Matthias S. Müller (Eds.), “Scaling OpenMP for Exascale Performance and Portability”,  Proc. 13th International Workshop on OpenMP (IWOMP2017) , Stony Brook, NY, September, 2017  

Donaldson, O.K.; W. Wang, K. Hattar, and   J.R. Trelewicz, Impurity Stabilization of Nanocrystalline Grains in Pulsed Laser Deposited Tantalum,  Journal of Materials Research 32 (7):  1351-1360,   (2017)  link

Dong X.,   Oganov A.R.  (2017). Electrides and their high-pressure chemistry.  In: Correlations in Condensed Matter Under Extreme Conditions, ed. G.N.N. Angilella & A. La Magna, Springer Verlag. Pp. 69-84. ( pdf-file)

Dong X.,   Oganov A. R., Goncharov A. F., Stavrou E., Lobanov S., Saleh G., Qian G.R., Zhu Q., Gatti C., Deringer V. L., Dronskowski R., Zhou X.-F., Prakapenka V. B., Konôpková Z., Popov I. A., Boldyrev A. I., Wang H.-T. (2017). A stable compound of helium and sodium at high pressure. Nature Chemistry, 9, 440–445 (2017) ( pdf-file)

Domínguez-Gutiérrez, F. J.; and  P. S. Krst ic , Chemical sputtering of boronized and oxidized carbon surfaces irradiated by low-energy deuterium atoms”, Journal of Applied Physics 121, 215302 (2017)

Domínguez-Gutiérrez, F. J.; Felipe Bedoya,   P. S. Krstic,  Jean Paul Allain, Stephen Irle, Charles Skinner, Robert Kaita and Bruce E. Koel, "Unraveling the plasma-material interface with real time diagnosis of dynamic boron conditioning in extreme tokamak plasmas", Nuclear Fusion IOP 57, 086050 (2017) 

Foley, C.; M. Lynch, L. H. Thorne, and   H.J. Lynch. 2017. Listing foreign species under the Endangered Species Act: A Primer for Conservation Biologists? BioScience 67(7): 627-637.

Gou H., Zhu L., Huang H.-T., Biswas A., Keefer D.W., Chaloux B.L., Prescher C., Yang L., Kim D.Y., Ward M.D., Lerach J., Wang S.,   Oganov A.R., Epshteyn A., Badding J.V., Strobel T.A. (2017).  From Linear Molecular Chains to Extended Polycyclic Networks: Polymerization of Dicyanoacetylene.  Chem. Mater., 29 (16), 6706–6718  

Han, Longtao;  P.S. Krstic, Igor Kaganovich and Roberto Car, "Migration of a carbon adatom on a charged single-walledcarbon nanotube", Carbon 116, 174-180 (2017).

Han, Longtao;  and  Predrag Krstić, "A Path for Synthesis of Boron-Nitride Nanostructures in Volume of Arc Plasma", Nanotechnology 28 (7), 07LT01 (2017).

Heinz, Jeffrey  and William Idsardi, editors. Phonology, Special Issue on Computational Phonology, 34(2), August 2017. Colin Ewen and Ellen Kaisse, editors-in-chiefs.

Heinz, Jeffrey and William Idsardi. Computational Phonology Today. Phonology, 34(2):211--219, August 2017.

Humphries, G.R.W.; C. Che-Castaldo, R. Naveen, M. Schwaller, P. McDowall, M Schrimpf,   H.J. Lynch. 2017. Mapping Application for Penguin Populations and Projected Dynamics (MAPPPD): Data and tools for dynamic management and decision support. Polar Record 53(2): 160-166.

Jensen, A.; M. Strange, G. C. Solomon, S. Smidstrup, K. Stokbro,   M. G. Reuter,  “Complex Band Structure and Transmission,” J. Chem. Phys. 147, 224104 (2017)

Jiang, L., S. Chen,   X. Jiao , Parametric Shape & Topology Optimization: A New Level Set Approach Based on Cardinal Basis Functions, International Journal for Numerical Methods in Engineering, 2017, accepted. DOI: 10.1002/nme.5733.  

Kaltak, Merzuk;  Marivi Fernandez-Serra,  and Mark S. Hybertsen,   Charge localization and ordering in A2Mn8O16 hollandite group oxides: Impact of density functional theory approaches ,   by  Phys. Rev. Materials 1, 075401 (2017)

Karpov, P.; M. B. Sazo, M. Zingale, W. Zhang,   A. C. Calder, Toward simulating Black Widow binaries with CASTRO.  JOCSE, in press, 2017

Khrapov N., Roizen V., Posypkin M., Samtsevich A.,  Oganov A.R.  (2017).  Volunteer computing for computational materials design.  Lob. J. Math. 38 (5), 926-930  

Kokkoni, Elena; Ashkan Zehfroosh, Prasanna Kannappan, Effrosyni Mavroudi, James C. Galloway,   Jeffrey Heinz, Rene Vidal, and Herbert G. Tanner. Principles of Building “Smart” Learning Environments in Pediatric Early Rehabilitation. In Robotics: Science and Systems; Workshop on Perception and Interaction Dynamics in Child-Robot Interaction, 2017.

Kruglov I., Sergeev O., Yanilkin A.,  Oganov A.R. (2017). Energy-free machine learning force field for aluminum. Sci. Rep. 7, 8512 

Kruglov I., Akashi R., Yoshikawa S.,  Oganov A.R., Davari M. (2017).  Refined phase diagram of the H-S system with high-Tc superconductivity.  Phys. Rev. B96, 220101 (Rapid Comm.)  

Kvashnin A.G.,   Oganov A.R., Allahyari Z. (2017).  Computational search for novel hard chromium-based materials.  J. Phys. Chem. Lett. 8, 755-764. ( pdf-file)

Li B.X., Qian G.R.,   Oganov A.R., Boulfelfel S.E., and Faller R. (2017) Mechanism of the fcc-to-hcp phase transformation in solid Ar. J. Chem. Phys.,146, 214502 ( pdf-file)

Lobanov S.S., Dong X., Martirosyan N.S., Samtsevich A.I., Stevanovic V., Gavryushkin P.N., Litasov K.D., Greenberg E., Prakapenka V.B.,  Oganov A.R.,  Goncharov A.F. (2017).  Raman spectroscopy and x-ray diffraction of sp3 CaCO3 at lower mantle pressures.  Phys. Rev. B 96 (10), 104101  

Meyer, F. W., Han, L., Hijazi, H., Bannister, M.E., Unocic, K.A., Parish, C.M.,  Krstić, P.S.,   "Energy dependence of He-ion-induced tungsten nanofuzz formation at non-normal incidence angles".  Nuclear Materials and Energy  12, 366 (2017).

Mishra, Alok, Lingda Li, Martin Kong, Han Finkel, and   Barbara Chapman,  “Benchmarking and Evaluating Unified Memory for OpenMP GPU Offloading”, In  LLVM-HPC’17: Proceedings of the Fourth Workshop on the LLVM Compiler Infrastructure in HPC , November 2017, Denver, CO.  

Narenpitak, P., C. S. Bretherton, and   M. Khairoutdinov,  2017: Cloud and circulation feedbacks in a near-global aquaplanet cloud-resolving model.   J. Adv. Model. Earth Syst , 9, 1069-1090, doi:10.1002/2016MS000872.

detection by borophene", J. of Materials Chemistry C 5, 5426 (2017).

OKUMOTO, A.; T. SUMI, H. SEKINO and H. GOTO  Numerical calculation on a two-step subdiffusion behavior of lateral protein movement in plasma membranes    Physical Review E,   96  042410 (2017)

Parishani, H.; M. S. Pritchard, C. S. Bretherton, M. C. Wyant, and   M. Khairoutdinov, 2017: Toward low-cloud-permitting cloud superparameterization with explicit boundary layer turbulence, J. Adv. Model. Earth Syst, 9, 1542-1571, doi:10.1002/2017MS000968.

Pedroza, Luana S.; Pedro Brandimarte, Alexandre Reily Rocha,  Marivi Fernandez-SerraFirst principles simulations of a bias-dependent electrochemical cell,  submitted (2017)

Pun,S.C.; Wang W., Khalajhedayati, A.,Schuler,   J.D.,Trelewicz,J.R. and Rupert, T.J. Nanocrystalline Al-Mg with Extreme Strength Due to Grain Boundary Doping,  Materials Science and Engineering A, 696: 400-406 (2017)  link 

Qawasmeh, Ahmad; Maxime R. Hugues, Henri Calandra and   Barbara M. Chapman, “Performance portability in reverse time migration and seismic modelling via OpenACC”, in International Journal of High Performance Computing Applications, Volume 31, 2017.  LINK  Bibtex

Ray, N., I. Grindeanu, X. Zhao, V. Mahadevan, and   X. Jiao , Array-Based Hierarchical Mesh Generation in Parallel, Computer Aided Design, Vol 85, pp. 68–82, 2017, DOI: 10.1016/j.cad.2016.07.011.  

Reuter, M.G. “A Unified Perspective of Complex Band Structure: Interpretations, Formulations, and Applications”. J. Phys.: Condens. Matter, 29, 053001 (2017). 

Sam-ang, P.;  M. G. Reuter. "Characterizing Destructive Interference Effects in Electron Transport,” New J. Phys. 19, 053002 (2017).

Shen,Chen, Xionan Tian, Dounia Khaldi and   Barbara Chapman , “Assessing One-to-One Parallelism Levels Mapping for OpenMP Offloading to GPUs”, In   Proceedings of the 8th International Workshop on Programming Models and Applications for Multicores and Manycores (PMAM17) , pp. 68-73, February 2017, Austin, TX  

Shtukenberg A.G., Zhu Q., Carter D.J., Vogt L., Hoja, J., Schneider, E., Song H.X., Pokroy B., Iryna Polishchuk, Tkatchenko A.,   Oganov A.R., Rohl A.L., Tuckerman M.E., Kahr D. (2017). Powder diffraction and crystal structure prediction identify four new coumarin polymorphs. Chem. Sci., Advance Article ( pdf-file)

Soto, Adrian; Deyu Lu, Shinjae Yoo, and   Marivi Fernandez-Serra,   Unveiling local order via machine learning: an application to liquid water, submitted (2017)

Wang D.H., Zhou H.Y., Hu C.H., Zhong Y.,   Oganov A.R., Rao G.H. (2017).  Prediction of thermodynamically stable Li-B compounds at ambient pressure.  Phys. Chem. Chem. Phys. 19, 8471-8477. ( pdf-file)

Wolfe, Michael, Seyong Lee, Jungwon Kim, Xiaonan Tian, Rengan Xu, Sunita Chandrasekaran and   Barbara M. Chapman , “Implementing the OpenACC Data Model”, In   2017 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) , pp. 662-672, May 2017, Orlando, FL  

Youngflesh, C., S. Jenouvrier, J.T. Hinke, L. DuBois, J. St. Leger, W.Z. Trivelpiece, S.G. Trivelpiece, and   H.J. Lynch. Rethinking ‘normal’: The role of stochasticity in the phenology of a synchronously breeding seabird. In press at Journal of Animal Ecology.

Youngflesh, C., S. Jenouvrier, Y. Li, R. Ji, D. G. Ainley, G. Ballard, C. Barbraud, K. Delord, K. M. Dugger, L. M. Emmerson, W. R. Fraser, J. T. Hinke, P. O’B. Lyver, S. Olmastroni, C. J. Southwell, S. G. Trivelpiece, W. Z. Trivelpiece,   H. J. Lynch. 2017. Circumpolar analysis of the Adélie Penguin reveals the importance of environmental variability in phenological mismatch. Ecology 98(4): 940-951.

Yu S.Y., Zeng Q.F.,   Oganov A.R., Frapper G., Huang B., Niu H.Y., Zhang L.T. (2017).  First-principles study of Zr-N crystalline phases: phase stability, electronic and mechanical properties.  RSC Advances 7, 4697-4703. ( pdf-file)

Yu S., Huang B., Zeng Q.F.,   Oganov A.R.,  Zhang L., Frapper G. (2017). Emergence of novel polynitrogen molecule-like species, covalent chains, and layers in magnesium−nitrogen MgxNy phases under high pressure. J. Phys. Chem. C, 121, 11037−11046 ( pdf-file)

Xu, Feng, Lijun Wu, Qingping Meng, M erzuk Kaltak, Jianping Huang, Jessica L. Durham,   Marivi Fernandez-Serra, Litao Sun, Amy C. Marschilok, Esther S. Takeuchi, Kenneth J. Takeuchi, Mark S. Hybertsen and Yimei Zhu,  Visualization of lithium-ion transport and phase evolution within and between manganese oxide nanorods , Nature Communications 8, Article number: 15400 (2017)doi:10.1038/ncomms15400

Zakaryan H.A., Kvashnin A.G.,   Oganov A.R.  (2017).  Stable reconstruction of the (110) surface and its role in pseudocapacitance of rutile-like RuO2.    Sci. Rep. 7, 10357  

Zehfroosh, Ashkan; Elena Kokkoni, Herbert G. Tanner, and   Jeffrey Heinz. Learning models of human-robot interaction from small data. In Proceedings of the 25th IEEE Mediterranean Conference on Control and Automation, pages 223--228, 2017.

Zeng Q.F., Yu S.Y., Li D.,   Oganov A.R.  and Frapper G., (2017). Emergence of novel hydrogen chlorides under high pressure. Phys. Chem. Chem. Phys. 19, 8236-8242. ( pdf-file)

Zhang J.,   Oganov A. R.,  Li X., Niu H. (2017). Pressure-stabilized hafnium nitrides and their properties. Phys. Rev. B 95, 020103(R) ( pdf-file)

Zhang J.,   Oganov A.R., Li X.F., Davari Esfahani M.M., Dong H.F. (2017).  First-principles investigation of Zr-O compounds, their crystal structures and mechanical properties.  J. Appl. Phys. 121, 155104. ( pdf-file)

Zhang, Y.; G.J. Tucker, and   J.R. Trelewicz, Stress-assisted Grain Growth in Nanocrystalline Metals: Grain Boundary Mediated Mechanisms and Stabilization through Alloying,  Acta Materialia, 131: 39 (2017)  link

Zhou, X. and  M.F. Khairoutdinov, 2017: Changes in Temperature and Precipitation Extremes in Superparameterized CAM in Response to Warmer SSTs. J. Climate, 30, 9827–9845,






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