Research at UMD using HPC Resources: Pubications, etc.

This page is an incomplete collection of some of the publications, etc. that were made possible in part due to the High Performance Computing resources at the University of Maryland. If you are a researcher and wish to add your research using one of the Deepthought clusters to the list, please contact us.

Publications

Click on the title to see more information about a particular publication (if available). Click on an author to see more publications by that author. A page with publications arranged by author is also available.

2018

  1. Volpiani, Pedro S., Matteo Bernardini, and Johan Larsson. Investigating the effects of non-adiabatic walls on shock/boundary-layer interaction at low Reynolds number using direct numerical simulations. 2018 AIAA Aerospace Sciences Meeting. 2018. doi:10.2514/6.2018-1806

2017

  1. Carlos Castillo, Soham De, Xintong Han, Bharat Singh, Abhay Kumar Yadav, and Tom Goldstein. Son of Zorn's Lemma: Targetted Style Transfer Using Instance-Aware Semantic Segmentation. ICASSP 2017 - 2017 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP). doi:10.1109/ICASSP.2017.7952376
  2. Fenggong Wang, Roman V. Tsyshevsky, Anton Zverev, Anatoly Mitrofanov, and Maija M. Kuklja. Can a photosensitive oxide catalyze decomposition of energetic materials?. J. Phys. Chem. C, 2017, 121 (2), pp 1153-1161. doi:10.1021/acs.jpcc.6b10127
  3. Forman, B. A., S. Kumar, J. Le Moigne, and S. Nag. Towards the development of a global, satellite-based, terrestrial snow mission planning tool. 74th Eastern Snow Conference, Ottawa, Ontario, Canada, 2017.
  4. Gao, Xin. Whole genome shotgun sequencing revealed highly polymorphic genes in Escherichia coli O157:H7 collected from cattle fecal samples. 2nd ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines, October 2017, Washington D.C..
  5. Gao, Xin. Whole genome shotgun sequencing revealed highly polymorphic genes in Escherichia coli O157:H7 collected from cattle fecal samples. 7th Annual FDA foods and Veterinary Medicine Science and Research Conference, October 2017, College Park, Maryland.
  6. Kun Fu, Yunhui Gong, Boyang Liu, Yizhou Zhu, Shaomao Xu, Yonggang Yao, Wei Luo, Chengwei Wang, Steven D. Lacey, Jiaqi Dai, Yanan Chen, Yifei Mo, Eric D. Wachsman, Liangbing Hu. Toward garnet electrolyte-based Li metal batteries: An ultrathin, highly effective, artificial solid-state electrolyte/metallic Li interface. Science Advances Vol 3 Num 4 07 Apr 2017 : e1601659. doi:10.1126/sciadv.1601659
  7. Lena Trotochaud, Roman Tsyshevsky, Scott Holdren, Kenan Fears, Ashley R. Head, Yi Yu, Osman Karslolu, Sven Pletincx, Bryan Eichhorn, Jeffrey Owrutsky, Jeffrey Long, Michael Zachariah, Maija M. Kuklja, and Hendrik Bluhm. Spectroscopic and Computational Investigation of Room-Temperature Decomposition of a Chemical Warfare Agent Simulant on Polycrystalline Cupric Oxide. Chemistry of Materials 2017 29 (17), 7483-7496. doi:10.1021/acs.chemmater.7b02489
  8. Liu, L. , M. Hejazi, H. Li, B. A. Forman, and X. Zhang. Vulnerability of US thermoelectric power generation to climate change when incorporating state-level environmental regulations. Nature Energy volume 2, Article number: 17109 (2017). doi:10.1038/nenergy.2017.109
  9. Maija M. Kuklja, Onise Sharia, Roman Tsyshevsky. Manifestations of two-dimensional electron gas in molecular crystals. Surf. Sci. 657 (2017) pp20-27.
  10. Matthew A. Conte, William J. Gammerdinger, Kerry L. Bartie, David J. Penman, and Thomas D. Kocher. A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions. BMC Genomics 2017 18:341. doi:10.1186/s12864-017-3723-5
  11. Peng Zhou, Xintong Han, Vlad I. Morariu and Larry S. Davis. Two-Stream Neural Networks for Tampered Face Detection. IEEE CVPR Workshop on Media Forensics, 2017. doi:10.1109/CVPRW.2017.229
  12. Ryan, E. , L. Brucker, and B. A. Forman. Sensitivity of Advanced Microwave Scanning Radiometer (AMSR-E) based snow water equivalent (SWE) retrievals to rain-on- Snow (ROS) events in polar regions. 74th Eastern Snow Conference, Ottawa, Ontario, Canada, 2017.
  13. S. Toosi and J. Larsson. Anisotropic grid-adaptation in large eddy simulations. Comp. & Fluids 156, 146-161, 2017. doi:10.1016/j.compfluid.2017.07.006
  14. Venkataraman Santhanam, Vlad I. Morariu, and Larry S. Davis. Generalized Deep Image to Image Regression. The IEEE Conference on Computer Vision and Pattern Recognition (CVPR) [Spotlight], July 2017.
  15. W. S. Cole, K. W. Mahmud, J. D. Sau and I. B. Spielman. Phase transitions and emergent gauge potentials in strongly interacting spin-orbit coupled bosons. APS March Meeting 2017, abstract id. E13.010.
  16. Wei Luo, Yunhui Gong, Yizhou Zhu, Yiju Li, Yonggang Yao, Ying Zhang, Kun Fu, Glenn Pastel, Chuan-Fu Lin, Gary W. Rubloff, Yifei Mo, Eric D. Wachsman, Liangbing Hu. Reducing Interfacial Resistance between Garnet-Structured Solid-State Electrolyte and Li Metal Anode by a Germanium Layer. Adv. Mater. 2017, 29, 1606042. doi:10.1002/adma.201606042
  17. Xiaogang Han, Yunhui Gong, Kun Fu, Xingfeng He, Gregory T. Hitz, Jiaqi Dai, Alex Pearse, Boyang Liu, Howard Wang, Gary Rubloff, Yifei Mo, Venkataraman Thangadurai, Eric D. Wachsman, Liangbing Hu. Negating Interfacial Impedance in Garnet-Based Solid-State Li-Metal Batteries. Nature Materials 16, 572-579 (2017). doi:10.1038/nmat4821
  18. Xingfeng He, Yizhou Zhu, Yifei Mo. Origin of Fast Ion Diffusion in Super-Ionic Conductors. Nature communications, 8, 15893 (2017). doi:10.1038/ncomms15893
  19. Xintong Han, Bharat Singh, Vlad I. Morariu and Larry S. Davis. VRFP: On-the-fly Video Retrieval using Web Images and Fast Fisher Vector Products. IEEE Transactions on Multimedia Volume: 19, Issue: 7, July 2017. doi:10.1109/TMM.2017.2671414
  20. Xintong Han, Zuxuan Wu, Yu-Gang Jiang and Larry S. Davis. Learning Fashion Compatibility with Bidirectional LSTMs. Proceedings of the 2017 ACM on Multimedia Conference Pages 1078-1086. doi:10.1145/3123266.3123394
  21. Xue, Y. and B. A. Forman. Integration of satellite-based passive microwave brightness temperatures using support vector machines and an ensemble-based land data assimilation framework in order to improve snow estimation in forested regions. IEEE Proceedings of the International Geoscience and Remote Sensing Symposium, Fort Worth, Texas, United States.
  22. Xue, Y. and B. A. Forman. Using a support vector machine and satellite-based passive microwave brightness temperature observations within a land data assimilation system to improve regional snow characterization. 74th Eastern Snow Conference, Ottawa, Ontario, Canada, 2017.
  23. Yizhou Zhu, Xingfeng He, Yifei Mo. Strategies Based on Nitride Materials Chemistry to Stabilize Li Metal Anode. Advanced Science, 1600517 (2017). doi:10.1002/advs.201600517

2016

  1. A. Trettel and J. Larsson. Mean velocity scaling for compressible wall turbulence with heat transfer. Phys. Fluids 28, 026102, 2016. doi:10.1063/1.4942022
  2. Ashley R. Head, Roman Tsyshevsky, Lena Trotochaud, Yi Yu, Line Kyhl, Osman Karslolu, Maija M. Kuklja, and Hendrik Bluhm. Adsorption of Dimethyl Methylphosphonate on MoO3: The Role of Oxygen Vacancies. J. Phys. Chem. C 120 (2016) pp29077-29088. doi:10.1021/acs.jpcc.6b07340
  3. B. Cao, K. W. Mahmud, M. Hafezi. Two coupled nonlinear cavities in a driven-dissipative environment. Phys. Rev. A 94, 063805 (2016). doi:10.1103/PhysRevA.94.063805
  4. Bharat Singh, Michael Jones, Tim Marks, Oncel Tuzel and Ming Shao. A Multi-Stream Bi-Directional Recurrent Neural Network for Fine-Grained Action Detection. 2016 IEEE Conference on Computer Vision and Pattern Recognition (CVPR). doi:10.1109/CVPR.2016.216
  5. Forman, B. A., Y. Xue , and J. Wang. Multi-sensor assimilation for global snow: Towards a combined, radiometric and gravimetric data assimilation approach. American Geophysical Union, Fall General Assembly 2016, abstract id. H33H-1642.
  6. J. H. Pixley, Pallab Goswami, and S. Das Sarma. Disorder-driven itinerant quantum criticality of three-dimensional massless Dirac fermions. Phys. Rev. B 93, 085103 (2016). doi:10.1103/PhysRevB.93.085103
  7. K. W. Mahmud, R. Wilson, M. Foss-Feig, M. Hafezi. Driven-dissipative bosons in open boundary and inhomogeneous cavity arrays. APS March Meeting 2016, abstract id. B50.011.
  8. Keck ZY, Wang Y, Lau P, Lund G, Rangarajan S, Fauvelle C, Liao GC, Holtsberg FW, Warfield KL, Aman MJ, Pierce BG, Fuerst TR, Bailey JR, Baumert TF, Mariuzza RA, Kneteman NM, Foung SK. Affinity maturation of a broadly neutralizing human monoclonal antibody that prevents acute hepatitis C virus infection in mice. Hepatology. 2016 Dec;64(6):1922-1933. doi:10.1002/hep.28850
  9. Mo, YF. Accelerating Materials Design and Discovery using Computational Approaches. TechConnect World Innovation Conference, DC (05/2016) (Invited).
  10. Mo, YF. Critical Roles of Interface Engineering in All-Solid-State Li-Ion Batteries: Insights from First Principles Calculations. ECS meeting, San Diego, CA (05/2016) (Invited).
  11. Mo, YF. Design Solid Electrolyte with High Ionic Conductivity and Enhanced Stability using First Principles Computation. ACS Meeting, San Diego, CA (03/2016) (Invited).
  12. Mo, YF. Overcoming Materials Challenges in All-Solid-State Li-ion Batteries: Insights from Computational Modeling. TechConnect World Innovation Conference, DC (05/2016).
  13. Mo, YF. Towards Computational Design of Solid Interfaces using First Principles Computation - A Case Study in All-Solid-State Li-ion Battery. MRS Spring Meeting, Phoenix, AZ (03/2016).
  14. Mo, YF. Understanding Solid Interfaces in All-Solid-State Li-ion Batteries: Insights from First Principles Computation. ACS Meeting, San Diego, CA (03/2016) (Invited).
  15. Mo, YF. Understanding Solid Interfaces in All-Solid-State Li-ion Batteries: Insights from First Principles Computation. MRS Spring Meeting, Phoenix, AZ (03/2016).
  16. R. M. Wilson, K. W. Mahmud, A. Hu, A. V. Gorshkov, M. Hafezi, M. Foss-Feig. Collective phases of strongly interacting cavity photons. Phys. Rev. A 94, 033801 (2016). doi:10.1103/PhysRevA.94.033801
  17. Roman Tsyshevsky, Anton S. Zverev, Anatoly Y. Mitrofanov, Natalya N. Ilyakova, Mikhail V. Kostyanko, Sergey V. Luzgarev, Guzel G. Garifzianova, and Maija M. Kuklja. Role of Hydrogen Abstraction Reaction in Photocatalytic Decomposition of High Energy Density Materials. J. Phys. Chem. C 120 (2016) pp 24835-24846.
  18. Tao, J., R. H. Reichle, R. Koster, Y. Xue , and B. A. Forman. Improving thermodynamic representation in permafrost modeling within the NASA Catchment Land Surface Model. American Geophysical Union, Fall General Assembly 2016, abstract id. C22B-02.
  19. Wang, J. , B. A. Forman, and A. P. Davis. Probabilistic stormwater runoff and water quality modeling in urban Maryland. Journal of Hydrologic Engineering Vol. 23, Issue 2 (February 2018). doi:10.1061/(ASCE)HE.1943-5584.0001600
  20. Xiuquan Zhou, Brandon Wilfong, Hector Vivanco, Johnpierre Paglione, Craig M. Brown, and Efrain E. Rodriguez. Metastable Layered Cobalt Chalcogenides from Topochemical Deintercalation. ournal of the American Chemical Society 2016 138 (50), 16432-16442. doi:10.1021/jacs.6b10229
  21. Xue, Y. and B. A. Forman. Atmospheric and forest decoupling from passive microwave brightness temperature observations over snow-covered terrain in North America. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing PP(99):01-18 October 2016.. doi:10.1109/JSTARS.2016.2614158
  22. Xue, Y. and B. A. Forman. Towards improved snow mass estimation in Alaska: Integration of satellite-based passive microwave brightness temperatures with support vector machines into an ensemble-based land data assimilation system. American Geophysical Union, Fall General Assembly 2016, abstract id. H33H-1665.

2015

  1. B. A. Forman and Y. Xue. Machine learning predictions of passive microwave brightness temperature over snow-covered land using the Special Sensor Microwave Imager (SSM/I). Physical Geography Vol. 38, Iss. 2, 2017. doi:10.1080/02723646.2016.1236606
  2. Dong-Ling Deng, J. H. Pixley, Xiaopeng Li, and S. Das Sarma. Exponential orthogonality catastrophe in single-particle and many-body localized systems. Phys. Rev. B 92, 220201(R) (2015). doi:10.1103/PhysRevB.92.220201
  3. Forman, B. A.. Feasibility of passive microwave brightness temperature assimilation over snow covered land using machine learning. 72nd Eastern Snow Conference, Sherbrooke, Quebec, Canada, 2015.
  4. Forman, B. A.. Synthetic tests of passive microwave brightness temperature assimilation over snow covered land using machine learning algorithms. American Geophysical Union Annual Meeting, San Francisco, California, United States, 2015.
  5. K. W. Mahmud, R. Wilson, M. Foss-Feig, M. Hafezi. Driven-dissipative bosons in open boundary and inhomogeneous cavity arrays. KITP, Oct 2015, UC Santa Barbara, CA.
  6. Sriram Ganeshan, J.H. Pixley, and S. Das Sarma. Nearest Neighbor Tight Binding Models with an Exact Mobility Edge in One Dimension. Phys. Rev. Lett. 114, 146601 (2015). doi:10.1103/PhysRevLett.114.146601
  7. Xiaopeng Li, Sriram Ganeshan, J.H. Pixley, and S. Das Sarma. Many-Body Localization and Quantum Nonergodicity in a Model with a Single-Particle Mobility Edge. Phys. Rev. Lett. 115, 186601 (2015). doi:10.1103/PhysRevLett.115.186601
  8. Xue, Y. , B. A. Forman, and X. Tao. Can the predictability of the snow water equivalent be enhanced through forest decoupling using leaf area index across snow-covered regions?. 72nd Eastern Snow Conference, Sherbrooke, Quebec, Canada, 2015.
  9. Xue, Y. and B. A. Forman. Investigating the role of total precipitable water and leaf area index in the decoupling of passive microwave brightness temperatures over snowcovered regions of forested terrain in North America. American Geophysical Union Annual Meeting, San Francisco, California, United States, 2015.
  10. Y. Xue and B. A. Forman. Comparison of passive microwave brightness temperature prediction sensitivities over snow-covered land in North America using machine learning algorithms and the Advanced Microwave Scanning Radiometer. Remote Sensing of the Environment, 170:153-165, December 2015. doi:10.1016/j.rse.2015.09.009
  11. Yang X, Gao M, Chen G, Pierce BG, Lu J, Weng NP, Mariuzza RA. Structural Basis for Clonal Diversity of the Public T Cell Response to a Dominant Human Cytomegalovirus Epitope. J Biol Chem. 2015 Nov 27;290(48):29106-19. doi:10.1074/jbc.M115.691311

2014

  1. Kang, H & J.B. Klauda. Molecular Dynamics Simulations of Palmitoyloleoyl-phosphatidylglycerol Bilayers. Molecular Simulation. Accepted (2014). doi:10.1080/08927022.2014.926548
  2. Lee, S., A. Tran, M. Allsopp, J.B. Lim, J. Hnin, & J.B. Klauda. CHARMM36 United-Atom Chain Model for Lipids and Surfactants. J. Phys. Chem. B. 118: 547-556 (2014). doi:10.1021/jp410344g
  3. Subramanian, D. J.B. Klauda, and M.A. Anisimov. Mesoscale Phenomena in Ternary Solutions of Tertiary Butyl Alcohol, Water, and Propylene Oxide. J. Phys. Chem. B. 118: 5994-6006 (2014). doi:10.1021/jp4125183
  4. Venable, R.M., A.J. Sodt, B. Rogaski, H. Rui, E. Hatcher, A.D. MacKerell, Jr., R.W. Pastor, and J.B. Klauda. CHARMM All-Atom Additive Force Field for Sphingomyelin: Elucidation of Hydrogen Bonding and of Positive Curvature. Biophys. J. 107: 134-145 (2014). doi:10.1016/j.bpj.2014.05.034
  5. Zhuang, X., J.R. Makover, W. Im, & J.B. Klauda. A Systematic Molecular Dynamics Simulation Study of Temperature Dependent Bilayer Structural Properties. BBA-Biomemb. 1838: 2520-2529 (2014). doi:10.1016/j.bbamem.2014.06.010

2013

  1. F Zhang, XZ Liang, Y Gu, S Su. Cloud-Aerosol-Radiation (CAR) ensemble modeling system: Overall accuracy and efficiency. Adv. Atmos. Sci. (2013) 30: 955. doi:10.1007/s00376-012-2171-z
  2. Subramanian, D., C.T. Boughter, J.B. Klauda, B. Hammouda, and M.A. Anisimov. Mesoscale inhomogeneities in aqueous solutions of small amphiphilic molecules. Faraday Discuss. 167: 217-238 (2013).
  3. Subramanian, D., J.B. Klauda, J. Leys, and M.A. Anisimov. Thermodynamic Anomalies and Structural Fluctuations in Aqueous Solutions of Tertiary Butyl Alcohol. Herald of St. Petersburg University (Vestnik) 2013, 4, 139 - 153.
  4. Villanueva, D.Y., J.B. Lim, & J.B. Klauda. Influence of Ester-modified Lipids on Bilayer Structure. Langmuir. 29, 14196-14203 (2013). doi:10.1021/la403919h
  5. XZ Liang, F Zhang. Cloud-Aerosol-Radiation (CAR) ensemble modeling system. Atmos. Chem. Phys., 13, 8335-8364, 2013. doi:10.5194/acp-13-8335-2013

2012

  1. Ezzeldin, H.M., J.B. Klauda, & S.D. Solares. Modeling of the Major Gas Vesicle Protein, GvpA: from Protein Sequence to Vesicle Wall Structure. J. Struct. Biol. 179, 18-28 (2012). doi:10.1016/j.jsb.2012.04.015
  2. F Zhang, S Su, X Liang. Dominant role of geometric association on cloud radiative forcing. Abstract A51C-0061 presented at 2012 Fall Meeting, AGU, San Francisco, Calif., 3-7 Dec.
  3. Feng Zhang, X. Liang, S. Su, and X. Kang. Cloud-Aerosol-Radiation Ensemble Modeling System (CAR): One Application on Aerosol Climate Effects. 2012 DOE ASR meeting.
  4. Klauda, J.B., V. Monje, T. Kim, and W. Im. Improving the CHARMM Force Field for Polyunsaturated Fatty Acid Chains. J. Phys. Chem. B. 116, 9424-9431 (2012). doi:10.1021/jp304056p
  5. Lim, J.B., B. Rogaski & J.B. Klauda. Update of the Cholesterol Force Field Parameters in CHARMM. J. Phys. Chem. B. 116, 203-210 (2012). doi:10.1021/jp207925m
  6. Pandit, K.R. & J.B. Klauda. Membrane models of E. coli containing cyclic moieties in the aliphatic lipid chain. BBA-Membranes. 1818, 1205-1210. (2012). doi:10.1016/j.bbamem.2012.01.009
  7. Rogaski, B & J.B. Klauda. Membrane-binding Mechanism of a Peripheral Membrane Protein through Microsecond Molecular Dynamics Simulations. J. Mol. Bio. 423, 847-861 (2012). doi:10.1016/j.jmb.2012.08.015

2011

  1. F Zhang, X Liang, S Su. Cloud-Aerosol-Radiation Ensemble Modeling System. Abstract A21H-05 presented at 2011 Fall Meeting, AGU, San Francisco, Calif., 5-9 Dec.
  2. Lim, J.B. & J.B. Klauda. Lipid chain branching at the Iso- and Anteiso-Positions in Complex Chlamydia Membranes: A Molecular Dynamics Study. BBA-Membranes. 1808, 323-331 (2011). doi:10.1016/j.bbamem.2010.07.036
  3. O'Connor, J.W & J.B. Klauda. Lipid Membranes with a Majority of Cholesterol: Applications to the Ocular Lens and Aquaporin 0. J. Phys. Chem. B. 115, 6455-5464 (2011). doi:10.1021/jp108650u

2010

  1. Jo, S.H., H. Rui, J.B. Lim, J.B. Klauda, & W. Im. Cholesterol Flip-Flop: Insights from Free Energy Simulation Studies. J. Phys. Chem. B. 114, 13342-13348 (2010). doi:10.1021/jp108166k
  2. Klauda, J.B., R.M. Venable, J.A. Freites, J.W. O'Connor, D.J. Tobias, C. Mondragon-Ramirez, I. Vorobyov, A.D. MacKerell, Jr., & R.W. Pastor. Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types. J. Phys. Chem. B. 114, 7830-7843 (2010). doi:10.1021/jp101759q
  3. Pendse, P.Y., B.R. Brooks & J.B. Klauda. Probing the Periplasmic-open State of Lactose Permease in Response to Sugar Binding and Proton Translocation. J. Mol. Biol. 404, 506-521 (2010). doi:10.1016/j.jmb.2010.09.045
  4. Rogaski, B., J.B. Lim, & J.B. Klauda. Sterol Binding and Membrane Lipid Attachment to the Osh4 Protein of Yeast. J. Phys. Chem. B. 114, 13562-13573 (2010). doi:10.1021/jp106890e

2009

  1. Jo, S.H., J.B. Lim, J.B. Klauda, & W. Im. CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes. Biophys. J. 97, 50-58 (2009). doi:10.1016/j.bpj.2009.04.013