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2018 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).


Bedoya, F, JP Allain, F Scotti, B LaBombard, R Kaita, and  PS Krstic, Effect of boronization on plasma-facing graphite surfaces and its correlation with the plasma behavior in NSTX-U Nuclear Materials and Energy 17, 211 (2018).

Bender, Michael, Rezaul Chowdhury, Pramod Ganapathi, Samuel McCauley, and Yuan Tang, "The Range 1 Query (R1Q) Problem," Theoretical Computer Science, 743:130-147, 2018.

Bird, S. and Jeffrey Heinz. Phonology. In Ruslan Mitkov, editor, The Oxford Handbook of Computational Linguistics, chapter 1. Oxford University Press, 2nd edition, 2018.

Borowicz, A., P. McDowall, C. Youngflesh, T. Sayre-McCord, H. Clucas, R. Herman, S. Forrest, M. Rider, M. Schwaller, T. Hart, S. Jenouvrier, M.J. Polito, H. Singh, and   H.J. Lynch. 2018. Multi-modal survey of Adélie penguin mega-colonies reveals the Danger Islands as a seabird hotspot. Scientific Reports 3926. doi: 10.1038/s41598-018-22313-w 

Buzi, L., Y. Yang, F.J. Dominguez-Gutierrez, A.O. Nelson, M. Hofman,   P.S.Krstic, R. Kaita, B.E. Koel, Hydrogen retention in lithium and lithium oxide films,  Journal of Nuclear Materials 502, 162 (2018) 

Calder, A. C ., Hoffman, M. M.,Wilcox, D. E., Katz, M. P., Swesty, D., and Ferson, S. Quantification of Incertitude in Black Box Simulation Codes. Proceedings of Astronum2017-- 12th International Conference on Numerical Modeling of Space Plasma Flows, Saint Malo, Franc, 26-30 June, 2017. J. Phys. Conf. Ser. 1031 012016, 2018.

Chandlee, J. and Jeffrey Heinz. Strictly Locality and Phonological Maps. Linguistic Inquiry, 49(1):23--60, Jan 2018.

Chandlee, J., Jeffrey Heinz, and Adam Jardine. Input Strictly Local Opaque Maps. Phonology, 35(2):171--205, Jun 2018.

Cheng, B. and   Trelewicz, J.R.,  Design of Crystalline-Amorphous Nanolaminates Using Deformation Mechanism Maps  Acta Materialia, 153, 314 (2018)  

Chowdhury, RA, V Ramachandran , Cache-Oblivious Buffer Heap and Cache-Efficient Computation of Shortest Paths in Graphs ACM Transactions on Algorithms (TALG) 14 (1), 1
Conley, R., T. J. Delaney, and X. Jiao, High-Order Adaptive Extended Stencil FEM (AES-FEM)Part II: Curved Boundaries,  SIAM Journal on Scientific Computing,  in preparation 2018.
Cunningham, W.S., Gentile, J.M, El-Atwani, O, Taylor, C.N., Efe, M., Maloy, S.A., and Trelewicz, J.R., “Softening due to Grain Boundary Cavity Formation and its Competition with Hardening in Helium Implanted Nanocrystalline Tungsten”, Scientific Reports, 8, 2897, 2018

Devaraj, A., Wang, W., Kovarik, L., Vemuri, R., Jiang, X., Bowden, M.,   Trelewicz, J.R.,  Mathaudhu, S., and Rohatgi, A. Grain Boundary Segregation and Intermetallic Precipitation in Coarsening Resistant Nanocrystalline Aluminum Alloys Under review, Acta Materialia (2018)  

Dolatian, H. and Jeffrey Heinz. Learning reduplication with 2-way finite-state transducers. Proceedings of Machine Learning Research: The 14th International Conference on Grammatical Inference. Wroclaw, Poland. September, 2018, to appear. 

Dolatian, H. and Jeffrey Heinz. Modeling reduplication with 2-way finite-state transducers. Proceedings of the 15th SIGMORPHON Workshop on Computational Research in Phonetics, Phonology, and Morphology. Brussells, Belgium. October 2018, to appear.

Dominguez-Gutierrez,  F. Javier,  Predrag S. Krstic,  Stephan Irle, and Remiglo Cabrera-Trujillo, Low-energy hydrogen uptake by small-cage C n and C n-1B fullerenes,  Carbon 134 , 189 (2018)

Domínguez-Gutiérrez  F. J.,  P. S. Krstić J. P. Allain F. Bedoya M. M. Islam R. Lotfi , and  A. C. T. van Duin,   "Deuterium uptake and sputtering of simultaneous lithiated, boronized, and oxidized carbon surfaces irradiated by low-energy deuterium", Journal of Applied Physics  123, 195901 (2018); 

Donaldson, O.K., Hattar, K., Kaub, T., Thompson, G.B., and Trelewicz, J.R., “Solute Stabilization of Nanocrystalline Tungsten Against Abnormal Grain Growth”, Early Career Scholars in Materials Science: Invited Feature Article, Journal of Materials Research, 33, 1, 2018

Foley, C.M., T. Hart, and   H.J. Lynch . 2018. King Penguin populations increase on South Georgia but explanations remain elusive. In Press at Polar Biology. doi: 10.1007/s00300-018-2271-z

Ghai, A. and   X. Jiao,  Multilevel Incomplete LU-Factorization Preconditioner for Predominantly Symmetric Systems, 15th Copper Mountain Conference on Iterative Methods, March 26-30, 2018, University of Colorado, USA.  

Ghai, A., C. Lu and X. Jiao, A Comparison of Preconditioned Krylov Subspace Methods for Large-Scale Nonsymmetric Linear Systems,  Numerical Linear Algebra with Applications , to appear 2018.

Heinz, J. The computational nature of phonological generalizations. In Larry Hyman and Frans Plank, editors, Phonological Typology, Phonetics and Phonology, chapter 5, pages 126--195. De Gruyter Mouton, 2018.

Humphries, G.R.W.,   C. Che-Castaldo, P. J. Bull, G. Lipstein, A. Ravia, B. Carrión, T. Bolton, A. Ganguly,   H. J. Lynch . 2018. Predicting the future is hard and other lessons from a population time series data science competition.   Ecological Informatics  48: 1-11 .

Jiao, X., R. Conley, and T. J. Delaney, High-Order Adaptive Extended Stencil FEM (AES-FEM)Part I: Convergence and Superconvergence, SIAM Journal on Scientific Computing, submitted 2018.

Khairoutdinov M.F. and K.A. Emanuel, 2018: Intraseasonal Variability in a Cloud-Permitting Near-Global Equatorial Aqua-Planet Model. J. Atmos. Sci., in minor revision.

Khairoutdinov, M., and K. Emanuel, 2018: Intraseasonal Variability in a Cloud-Permitting Near-Global Equatorial Aqua-Planet Model. Journal of Atmospheric Sciences, 75, 4337-4355, doi:10.1175/jas-d-18-0152.1

Krstic ,  P.S., J.P. Allain, F. J. Javier Dominguez-Gutierrez, F. Bedoya, "Unraveling the surface chemistry processes in lithiated and boronized plasma material interfaces   under extreme conditions",    Review article - Open Access   , Matter and Radiation at Extremes (Elsevier) 3, 165-187 (2018)      

Krstic, Predrag, and Longtao Han, Can Hydrogen Catalyze Transitions Between h-BN and c-BN in Volume Plasma?, J. Phys. Chem. C. 122, 936-944 (2018), 10.1021/acs.jpcc.7b10955

Krstic, Predrag, Longtao Han, Stephen Irle and Hiromi Nakai, Simulations of synthesis of the boron-nitride nanostructures in a hot, high pressure gas volume,  Chemical Science 9 , 3803 (2018)

Krylov, Anna, Theresa L. Windus, Taylor Barnes, Eliseo Marin-Rimoldi, Jessica A. Nash, Benjamin Pritchard, Daniel G. A. Smith, Doaa Altarawy, Paul Saxe, Cecilia Clementi, T. Daniel Crawford, Robert J. Harrison, Shantenu Jha, Vijay S. Pande, ad Teresa Head-Gordon. Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science. J. Chem. Phys. 149, 180901 (2018);

Li, Y. , X. Zhao, N. Ray, and X. Jiao, Compact Feature-Aware Hermite-style High-Order Surface Reconstruction,  International Journal for Numerical Methods in Engineering,  in preparation 2018.

Pamuk , Betül , P. B. Allen, and   M.-V. Fernández-Serra , Insights into the Structure of Liquid Warer from Nuclear Quantum Effects on the Density and Compressibility of Ice Polymorphs.  J. Phys. Chem. B , 2018, 122 (21), pp 5694–5706.

Parishani, H., M. S. Pritchard, C. S. Bretherton, C. R. Terai, M. C. Wyant, M. Khairoutdinov, and B. Singh, 2018: Insensitivity of the cloud response to surface warming under radical changes to boundary layer turbulence and cloud microphysics: Results from the UltraParameterized CAM. Journal of Advances in Modeling Earth Systems, in press.

Pedroza,Luana S., Pedro Brandimarte, Alexandre Reily Rocha,  Marivi Fernandez-Serra , Bias- dependent local structure of water molecules at a metallic inerface  Chem. Sci. , 2018,9, 62-69.

Penchoff, Deborah A.* , Charles Peterson, Jon P. Camden, James Bradshaw, John. D. Auxier, George K. Schweitzer, David M. Jenkins, Robert J. Harrison, Howard L. Hall*. “Structural Analysis of the Complexation of Uranyl, Neptunyl, Plutonyl, and Americyl with Cyclic Imide Dioximes”, ACS Omega, 2018, 3, 10, 13984-13993.

Penchoff, Deborah A.*, Charles C. Peterson, Mark S. Quint, John D. Auxier II, George K. Schweitzer, David M. Jenkins, Robert J. Harrison*, Howard L. Hall*. “Structural Characteristics, Population Analysis, and Binding Energies of [An(NO3)]2+, [with An = Ac - Lr]”, ACS Omega, 2018, 3, 10, 14127-14143.

Schrimpf, M., R. Naveen,   H.J. Lynch.  2018. Population status of the Antarctic shag   Phalacrocorax (atriceps) bransfieldensis . In Press at Antarctic Science

Schwaller, M.R.,   H.J. Lynch , A. Tarroux, and B. Prehn. 2018. A continent-wide search for Antarctic petrel breeding sites with satellite remote sensing.   Remote Sensing of Environment  210: 444-451.

Singh, H., Donetski, D., Attenkofer, K., Cheng, B.,   Trelewicz, J.R., Lubomirsky, I., Stavitski, E., and Frenkel, A.I.,  Investigation of Periodically Driven Systems by X-ray Absorption Spectroscopy Using Synchronous Data Collection Mode    Review of Scientific Instruments, 89, 4, 04511,(2018)   

Vu, M. Ha, Ashkan Zehfroosh, Kristina Strother-Garcia, Michael Sebok, Herbert G. Tanner, and Jeffrey Heinz. Statistical Relational Learning with Unconventional String Models. Frontiers in Robotics and AI, July 2018.

Wang,  X.,  X. Jiao   and Q. Chen, Adaptive Solution Transfer for Nonsmooth Functions Between Nonmatching Meshes, 15th Copper Mountain Conference on Iterative Methods, March 26-30, 2018, University of Colorado, USA.  

Wang, X., X. Jiao, Q. Chen, Y. Li, Adaptive Solution Transfer Between Non-matching Meshes for Coupling Climate Models, 13th World Congress on Computational Mechanics, July 22-27, 2018, New York, NY, USA. 

Youngflesh, C., S. Jenouvrier, J.T. Hinke, L. DuBois, J. St. Leger, W.Z. Trivelpiece, S.G. Trivelpiece, and   H.J. Lynch . 2018. Rethinking “normal”: The role of stochasticity in the phenology of a synchronously breeding seabird. Journal of Animal Ecology doi: 10.1111/1365-2656.12790. 

Zehfroosh, A. , Jeffrey Heinz, and Herbert G. Tanner. Learning option MDPs from small data. In Proceedings of the 2018 American Control Conference, Milwaukee, Wisconsin, USA, June 2018. IEEE Control Systems Society. To appear.