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HPCF Publications

This page lists publications from use of HPCF as well as technical reports of papers on all aspects of scientific computing and their applications, with links to preprints/reprints whenever possible. Please send your submissions in PDF form to the chair of the user committee, Matthias K. Gobbert. In particular, all publications involving use of machines in HPCF are required to be submitted for inclusion here and will be flagged accordingly.

2017

[1] Lai Wang, Meilin Yu, and Matthias K. Gobbert. A Parallel Performance Study of the High-order Compact Direct Flux Reconstruction Method for Conservation Laws on Maya Cluster. Technical Report HPCF-2017-1, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2017. (HPCF machines used: maya.). [ .pdf ]
[2] Sesmero, E., Brown, J. A. and Thorpe, I. F. Molecular Simulations to Delineate Functional Conformational Transitions in the HCV Polymerase. Journal of Computational Chemistry, Accepted, 2017. (HPCF machines used: maya.)
[3] Sai K. Popuri and Matthias K. Gobbert. A Comparative Evaluation of Matlab, Octave, R, and Julia on Maya. Technical Report HPCF-2017-03, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2017. (HPCF machines used: maya.). [ .pdf ]

Files for download with this report: PopuriHPCF2017/

[4] Jonathan S. Graf and Matthias K. Gobbert. Effective Usage Strategies for the Configuration Modes of the Intel Xeon Phi Knights Landing. Submitted, 2017. (HPCF machines used: maya.)
[5] Jonathan S. Graf. Parallel Performance of Numerical Simulations for Applied Partial Differential Equation Models on the Intel Xeon Phi Knights Landing Processor. Ph.D. Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2017. (HPCF machines used: maya.).
[6] Jonathan S. Graf, Matthias K. Gobbert, and Samuel Khuvis. Long-Time Simulations with Complex Code Using Multiple Nodes of Intel Xeon Phi Knights Landing. Submitted, 2017. (HPCF machines used: maya.)
[7] Muthukumar Thevar. The Effect of K-nearest Neighbors Classifier for Intrusion Detection of Streaming Net-flows in Apache Spark Environment. Ph.D. Thesis, Department of Information Systems, University of Maryland, Baltimore County, 2017. (HPCF machines used: maya.).
[8] Sai C. Pallaprolu, Rishi Sankineni, Muthukumar Thevar, George Karabatis, and Jianwu Wang. Zero-day Attack Identification in Streaming data using Semantics and Spark, accepted by The 6th IEEE International Congress on Big Data (BigDataCongress 2017). (HPCF machines used: maya.).

2016

[1] Daniel Miller, Zhibo Zhang, et al. The Impact of cloud vertical structure on cloud liquid water path retrieval based on the bi-spectral solar reflection method: A theoretical study based on large-eddy simulations. J. Geophys. Res. Atmos., 121, 2016. (HPCF machines used: maya.)
[2]  Chenxi Wang, S. Platnick, Zhibo Zhang, K. Meyer, and P. Yang. Retrieval of ice cloud properties using an optimal estimation algorithm and MODIS infrared observations. Part I: Forward model, error analysis, and information content. J. Geophys. Res. Atmos., 121, 2016. (HPCF machines used: maya.)
[3]  Chenxi Wang, S. Platnick, Zhibo Zhang, K. Meyer, G. Wind, and P. Yang. Retrieval of ice cloud properties using an optimal estimation algorithm and MODIS Infrared observations. Part II: Retrieval evaluation. J. Geophys. Res. Atmos., 121, 2016. (HPCF machines used: maya.)
[4]  Zhibo Zhang, et al. A framework for quantifying the impacts of sub-pixel reflectance variance and covariance on cloud optical thickness and effective radius retrievals based on the bi-spectral method. Submitted. (HPCF machines used: maya.)
[5] Samuel Khuvis. Porting and Tuning Numerical Kernels in Real-World Applications to Many-Core Intel Xeon Phi Accelerators. Ph.D. Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2016. (HPCF machines used: maya.).
[6] Ryan D. Day. Parallel Performance Studies for a Linear Parabolic Test Problem Using the Intel Xeon Phi. M.S. Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2016. (HPCF machines used: maya.).
[7] Marilena Flouri. Tolerance Limits and Confidence Limits for Cost-Effectiveness Analysis. Ph.D. Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2016. (HPCF machines used: maya.).
[8] M. Flouri,S. Zhai, T. Mathew, and I. Bebu. Tolerance limits for ratios of normal random variables. To appear in Biometrical Journal, 2017. (HPCF machines used: maya.)
[9] Jack Slettebak. Pushing the Limits of the Maya Supercomputer with the HPCG Benchmark. UMBC Review: Journal of Undergraduate Research, 17:162-175, 2016. (HPCF machines used: maya.).
[10] George Eskandar, Jennifer Houser, Ellen Prochaska, Jessica Wojtkiewicz, Teresa Lebair, Bradford E. Peercy, Margaret Watts, and Arthur Sherman. Investigating how calcium diffusion affects metabolic oscillations and synchronization of pancreatic beta cells. Spora: A Journal of Biomathematics, 2(1), 2016. (HPCF machines used: maya.).
[11] Ephraim Alfa, Huiyi Chen, Kristen Hansen, Mathew Prindle, Sai K. Popuri, Nadeesri Wijkekoon, Kofi P. Adragni, and Amita Mehta. Using Historical Data for Retrospective Prediction of Rainfall in the Midwest. Technical Report HPCF-2016-11, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2016. (HPCF machines used: maya.). [ .pdf ]
[12] Ethan Crasto, Sydney Kahmann, Paula Rodriguez, Benjamin Smith, Sai K. Popuri, Nadeesri Wijkekoon, Nagaraj K. Neerchal, and Amita Mehta. Enhanced Data Exploration and Visualization Tool for Large Spatio-Temporal Climate Data. Technical Report HPCF-2016-12, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2016. (HPCF machines used: maya.). [ .pdf ]
[13] Ross Flieger-Allison, Lois Miller, Danielle Sykes, Pablo Valle, Sai K. Popuri, Nadeesri Wijkekoon, Nagaraj K. Neerchal, and Amita Mehta. Dimensionality Reduction Using Sliced Inverse Regression in Modeling Large Climate Data. Technical Report HPCF-2016-13, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2016. (HPCF machines used: maya.). [ .pdf ]
[14] Mary Aronne, Samantha Clapp, Soohwan Jung, Abigail Kramer, William Wang, Janita Patwardhan, Bradford E. Peercy, and Arthur Sherman. The Interaction of Calcium and Metabolic Oscillations in Pancreatic Beta Cells. Technical Report HPCF-2016-14, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2016. (HPCF machines used: maya.). [ .pdf ]
[15] Kallista Angeloff, Carlos Barajas, Alexander D. Middleton, Uchenna Osia, Jonathan S. Graf, Matthias K. Gobbert, and Zana Coulibaly. Modeling the Links Between the Chemical, Electrical and Contractile Calcium Dynamics in a Heart Cell. Technical Report HPCF-2016-15, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2016. (HPCF machines used: maya.). [ .pdf ]
[16] Ishmail A. Jabbie, George Owen, Benjamin Whiteley, Jonathan S. Graf, Matthias K. Gobbert, and Samuel Khuvis. Performance Comparison of a Two-Dimensional Elliptic Test Problem on Intel Xeon Phis. Technical Report HPCF-2016-16, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2016. (HPCF machines used: maya.). [ .pdf ]
[17] Sergio Garcia Tapia, Rebecca Hsu, Alyssa Hu, Darren Stevens II, Jonathan S. Graf, Matthias K. Gobbert, and Tyler Simon. Applications of Tensor Decompositions. Technical Report HPCF-2016-17, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2016. (HPCF machines used: maya.). [.pdf ]
[18] J. A. Brown, M. V. Espiritu, J. Abraham, and I. F. Thorpe. Computational Predictions suggest that Structural Similarity in Viral Polymerases may lead to Comparable Allosteric Binding Sites. Virus Research, 222; 80-93 (2016). (HPCF machines used: maya.).
[19] J.C. Polf, M. Chuong, B. Zhang, M. Mehta. Anterior-oriented beam arrangements with daily in vivo range verification for proton therapy of prostate cancer: Rectal toxicity rates, Int. J. Particle Ther., 2(4):510-517, 2016. (HPCF machines used: maya.).
[20] H. Chung, J.C. Polf , B. Badiyan, M. Biagioli, D. Fernandez, K. Latifi , R. Wilder , M. Mehta, M. Chuong. Rectal dose to prostate cancer patients treated with proton therapy with or without rectal spacer, JACMP, 16 (In Press), 2016. (HPCF machines used: maya.).
[21] M. Bakhtiarinejad, S. Lee, and J. Joo. Topology Optimization based on Morphing Mesh for Simultaneous Component Relocation and Frame Structure Design, Struct. Multidiscip. O., 2016. (HPCF machines used: maya.).
[22] S. K. Popuri, R. Flieger-Allison, L. Miller, D. Sykes, P. Valle, N. K. Neerchal, K. P. Adragni, A. Mehta, and M. K. Gobbert. Spatio-temporal analysis of precipitation data via a sufficient dimension reduction in parallel, JSM Proceedings, Section on Statistics and the Environment. 2016. Alexandria, VA: American Statistical Association. 3805-3815. (HPCF machines used: maya.).
[23] Mary Aronne, Samantha Clapp, Soohwan Jung, Abigail Kramer, William Wang, Janita Patwardhan, Arthur Sherman, and Bradford Peercy. The Interaction of Calcium and Metabolic Oscillations in Pancreatic Beta-Cells, Spora: A Journal of Biomathematics, submitted 2016. (HPCF machines used: maya.).
[24] Kallista Angeloff, Carlos Barajas, Alexander D. Middleton, Uchenna Osia, Jonathan S. Graf, Matthias K. Gobbert, and Zana Coulibaly. Examining the Effect of Introducing a Link from Electrical Excitation to Calcium Dynamics in a Cardiomyocyte, Spora: A Journal of Biomathematics, vol. 2, article 6, 2016. (HPCF machines used: maya.).
[25] Ishmail A. Jabbie, George Owen, Benjamin Whiteley, Jonathan S. Graf, Matthias K. Gobbert, and Samuel Khuvis. Performance Comparison of Intel Xeon Phi Knights Landing, submitted 2017. (HPCF machines used: maya.).
[26] Bhaskar, A.S, C. Jantz, C. Welty, S. Drzyzga, and A.J. Miller. Coupling of the Water Cycle with Patterns of Urban Growth in the Baltimore Metropolitan Region, USA., J. of the American Water Resources Association, 2016. (HPCF machines used: maya.).
[27] Cui, Z., C. Welty, A.J. Gold. P. Groffman, S. Kaushal, A.J. Miller. Use of a three-dimensional reactive solute transport model for evaluation of bioreactor placement in channel restoration, J. Env. Quality,45 (3), 2016. (HPCF machines used: maya.).
[28] George Karabatis, and Jianwu Wang, and Ahmed AlEroud. Towards Adaptive Big Data Cyber-attack Detection via Semantic Link Networks. The first Workshop of Mission-Critical Big Data Analytics (MCBDA), 2016. (HPCF machines used: maya).
[29] Ye Yang. The Simultaneous Assessment of Normality and Homoscedasticity in Some Linear Models. Ph.D. Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2016. (HPCF machines used: maya.).
[30] Ye Yang and Thomas Mathew. The simultaneous assessment of normality and homoscedasticity in linear fixed effects models, Submitted, 2016. (HPCF machines used: maya.).
[31] Amanda Plunkett and Junyong Park. Two-Sample Tests for Sparse High Dimensional Binary Data, Communications in Statistics – Theory and Methods, 2016. (HPCF machines used: maya.).

2015

[1] Nil Mistry, Jordan Ramsey, Benjamin Wiley, Jackie Yanchuck, Xuan Huang, and Matthias K. Gobbert. Throughput studies on an InfiniBand interconnect via All-to-All communications, 2015. 23rd High Performance Computing Symposium (HPC 2015). (HPCF machines used: tara.).
[2] Xuan Huang and Matthias K. Gobbert. Long-time simulation of calcium induced calcium release in a heart cell using finite element method on a hybrid CPU/GPU node, 2015. 23rd High Performance Computing Symposium (HPC 2015). (HPCF machines used: tara.).
[3] Andrew M. Raim, Nagaraj K. Neerchal, and Jorge G. Morel. Modeling overdispersion in R. Technical Report HPCF-2015-1, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2015. [ .pdf ]

Files for download with this report: OverdispersionModelsInR_0.1.tar.gz, OverdispersionModelsInR_examples.tar.gz

[4] A.S. Bhaskar, C. Welty, R.M. Maxwell, and A.J. Miller. Untangling the effects of urban development on subsurface storage in Baltimore. Water Resources Research, 50, 2015. (HPCF machines used: tara.).
[5] Samuel Khuvis, Matthias K. Gobbert, and Bradford E. Peercy. Time-stepping techniques to enable the simulation of bursting behavior in a physiologically realistic computational islet. Math. Biosci., 263:1-17, 2015. (HPCF machines used: tara.). [ http | .pdf ]
[6] Samuel Khuvis and Matthias K. Gobbert. Parallel performance studies for an elliptic test problem on the cluster maya. Technical Report HPCF-2015-6, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2015. (HPCF machines used: maya.). [ .pdf ]
[7] Jonathan S. Graf and Matthias K. Gobbert. Parallel performance studies for a parabolic test problem on the cluster maya. Technical Report HPCF-2015-7, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2015. (HPCF machines used: maya.). [ .pdf ]
[8] Xuan Huang and Matthias K. Gobbert. Parallel performance studies for a three-species application problem on the cluster maya. Technical Report HPCF-2015-8, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2015. (HPCF machines used: maya.). [ .pdf ]
[9] S. De Souza-Machado, L. L. Strow, E. Maddy, G. Thomas, D. Grainger, and A. Robinson. Using a synergy of AIRS infrared radiances and MODIS L2 optical depths to retrieve daytime atmospheric dust and volcanic ash heights. Atmos. Meas. Tech. Disc, 8:428-448, 2015. (HPCF machines used: tara.).
[10] Brittny C. Davis, Jodian A. Brown, and Ian F. Thorpe. Allosteric Inhibitors Have Distinct Effects, but Also Common Modes of Action, in the HCV Polymerase. Biophys. J., 108(7):1785-1795, 2015. (HPCF machines used: tara.). [ http | .pdf ]
[11] Hyoun-Myoung Cho, Zhibo Zhang, K. Meyer, M. Lebsock, S. Platnik, Andrew S. Ackerman, L. Di Girolamo, L. C.-Labonnote, C. Cornet, J. Riedi, and R. Holz. Frequency and causes of failed MODIS cloud property retrievals for liquid phase clouds over global oceans. J. Geophys. Res. Atmos., 120:4132-4154, 2015. (HPCF machines used: tara.). [ http ]
[12] Xuan Huang. An MPI-CUDA Implementation of a Model for Calcium Induced Calcium Release in a Three-Dimensional Heart Cell on a Hybrid CPU/GPU Cluster. Ph.D. Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2015. (HPCF machines used: tara, maya.).
[13] David P. Stonko, Lathiena Manning, Michelle Starz-Gaiano, and Bradford E. Peercy. A mathematical model of collective cell migration in a three-dimensional, heterogeneous environment. PLoS ONE, 10(4), 2015. (HPCF machines used: tara.). [ http ]
[14] Josephine Mazzi Namayanja. Change Detection in Temporally Evolving Computer Networks. Ph.D. Thesis, Department of Information Systems, University of Maryland, Baltimore County, 2015. (HPCF machines used: maya.).
[15] Brittny Davis. Determining the Molecular Origins of Allostery for the Polymerase from the Hepatitis C Virus. Ph.D. Thesis, Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 2015. (HPCF machines used: tara, maya.).
[16] Alimatou Seck. A fully distributed integrated hydrologic model for quantifying groundwater dynamics in the Chesapeake Bay Watershed. Ph.D. Thesis, Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, 2015. (HPCF machines used: tara.).
[17] A. Seck, C. Welty, and R.M. Maxwell. Spin-up behavior and effects of initial conditions for an integrated hydrologic model. Water Resour. Res., 51:2188-2210, 2015. (HPCF machines used: tara.).
[18]  Jack Slettebak. The HPCG Benchmark for Cluster Computing. Senior Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2015. (HPCF machines used: maya.).
[19]  Kourosh M. Kalayeh, Jonathan S. Graf, and Matthias K. Gobbert. FEM convergence studies for 2-D and 3-D elliptic PDEs with smooth and non-smooth source terms in COMSOL 5.1. Technical Report HPCF-2015-19, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2015. (HPCF machines used: maya.). [ .pdf ]
[20]  Oluwapelumi Adenikinju, Julian Gilyard, Joshua Massey, and Thomas Stitt. Concurrent solutions to linear systems using hybrid CPU/GPU nodes. SIAM Undergraduate Research Online (SIURO), 8, 2015. (HPCF machines used: maya.). [ www | .pdf ]
[21]  Ely Biggs, Tessa Helble, George Jeffreys, Amit Nayak, Elias Al-Najjar, Kofi P. Adragni, and Andrew Raim. Numerical evaluation of minimum average deviance estimation in ultra high dimensional Poisson regression. Technical Report HPCF-2015-21, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2015. (HPCF machines used: maya.). [ .pdf ]
[22]  Joseph U. Emelike, David Harper, Charlotte Z. Mann, Kwame Owusu-Boaitey, Sai Kumar Popuri, Nagaraj K. Neerchal, and Amita Mehta. Assessing decadal climate impacts on water resources within Missouri river sub-basins. Technical Report HPCF-2015-22, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2015. (HPCF machines used: maya.). [ .pdf ]
[23]  Trevor V. Adriaanse, Meshach Hopkins, Rebecca Rachan, Subodh R. Selukar, Elias Al-Najjar, Kofi P. Adragni, and Nusrat Jahan. Statistical analysis of a case-control Alzheimer’s disease: a retrospective approach with sufficient dimension reduction. Technical Report HPCF-2015-23, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2015. (HPCF machines used: maya.). [ .pdf ]
[24]  George Eskander, Jennifer Houser, Ellen Prochaska, Jessica Wojtkiewicz, Teresa Lebair, Bradford E. Peercy, Margaret Watts, and Arthur Sherman. Investigating how calcium diffusion affects metabolic oscillations and synchronization of pancreatic beta cells. Technical Report HPCF-2015-24, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2015. (HPCF machines used: maya.). [ .pdf ]
[25]  Amanda M. Alexander, Erin K. DeNardo, Eric Frazier III, Michael McCauley, Nicholas Rojina, Zana Coulibaly, Bradford E. Peercy, and Leighton T. Izu. Impact of calcium store overload on electrical dynamics of cardiac myocytes. Technical Report HPCF-2015-25, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2015. (HPCF machines used: maya.). [ .pdf ]
[26]  Changling Huang, Christopher C. Lowman, Brandon E. Osborne, Gabrielle M. Salib, Ari Rapkin Blenkhorn, Jonathan S. Graf, Samuel Khuvis, Matthias K. Gobbert, Tylor Simon, and David J. Mountain. Performance studies of the Blossom V algorithm. Technical Report HPCF-2015-26, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2015. (HPCF machines used: maya.). [ .pdf ]
[27]  Fernando X. Avila-Soto, Alec N. Beri, Eric Valenzuela, Abenezer Wudenhe, Ari Rapkin Blenkhorn, Jonathan S. Graf, Samuel Khuvis, Matthias K. Gobbert, and Jerimy Polf. Parallelization for fast image reconstruction using the stochastic origin ensemble method for proton beam therapy. Technical Report HPCF-2015-27, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2015. (HPCF machines used: maya.). [ .pdf ]
[28]  Wesley Collins, Daniel T. Martinez, Michael Monaghan, Alexey A. Munishkin, Ari Rapkin Blenkhorn, Jonathan S. Graf, Samuel Khuvis, Matthias K. Gobbert, and John C. Linford. Comparison of performance analysis tools for parallel programs applied to CombBLAS. Technical Report HPCF-2015-28, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2015. (HPCF machines used: maya.). [ .pdf ]
[29] Kourosh M. Kalayeh, Jonathan S. Graf, and Matthias K. Gobbert. FEM Convergence for PDEs with Point Sources in 2-D and 3-D. In Proceedings of the COMSOL Conference 2015, Boston, MA, 2015. (HPCF machines used: maya.). [ .pdf ]
[30] Kourosh M. Kalayeh. Finite Element Convergence Studies of a Time-Dependent Test Problem Using COMSOL 5.1. Technical Report HPCF-2015-30, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2015. (HPCF machines used: maya.). [ .pdf ]
[31] Zana Coulibaly. Calcium Dynamics From Randomly Releasing Sparks in Cardiac Myocytes: Analyzing and Simulating a Probabilistic Three-Dimensional Mathematical Model with Point Release Sources. Ph.D. Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2015. (HPCF machines used: tara, maya.).
[32] Zhengtao Cui. Development and Application of a Particle-Tracking Model for Nitrogen Transport and Transformation in Aquifers. Ph.D. Thesis, Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, 2015. (HPCF machines used: tara, maya.).
[33] Yue Hu, Thomas F. Carruthers, Curtis R. Menyuk, Meredith N. Hutchinson, Vincent J. Urick and Keith J. Williams. Simulation of a partially depleted absorber (PDA) photodetector. Opt. Express, 23(16):20402-20417, 2015. (HPCF machines used: tara, maya). [ http | .pdf ]
[34] Matthew W. Brewster, Jonathan S. Graf, Xuan Huang, Zana Coulibaly, Matthias K. Gobbert and Bradford E. Peercy. Calcium Induced Calcium Release with Stochastic Uniform Flux Density in a Heart Cell. In Proceedings of the 47th Summer Computer Simulation Conference (SCSC), Chicago, IL, 2015. (HPCF machines used: tara, maya.). [ .pdf ]
[35] Sarah C. Keane, Xiao Heng, Kun Lu, Siarhei Kharytonchyk, Venkateswaran Ramakrishnan, Gregory Carter, Shawn Barton, Azra Hosic, Alyssa Florwick, Justin Santos, Nicholas C. Bolden, Sayo McCowin, David A. Case, Bruce A. Johnson, Marco Salemi, Alice Telesnitsky and Michael F. Summers. Structure of the HIV-1 RNA packaging signal. Science, 348:917-921, 2015. [ .pdf ]
[36] Joshua D. Brown, Michael F. Summers and Bruce A. Johnson. Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression. J Biomol NMR, 2015. [ .pdf ]
[37] Brown, J. A. and Thorpe, I. F. Dual Allosteric Inhibitors Jointly Modulate Protein Structure and Dynamics in the Hepatitis C Virus Polymerase. Opt. Biochemistry, 54:4131-4141, 2015. (HPCF machines used: tara, maya). [ .pdf ]
[38] Shuyan Zhai. Tolerance Limits and Hypotheses Tests for the Comparison of Dissolution Profiles. Ph.D. Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2015. (HPCF machines used: tara, maya.).
[39] Shuyan Zhai, Thomas Mathew and Yi Huang. Comparison of Drug Dissolution Profiles: A Proposal Based on Tolerance Limits. Statistics in Medicine, 35:5464-5476, 2016. (HPCF machines used: tara, maya).
[40] Jerimy C. Polf and Katia Parodi. Imaging particle beams for cancer treatment. Physics Today, 68(10):28-33, 2015. (HPCF machines used: maya). [ .pdf ]
[41] Andrew M. Raim, Nagaraj K. Neerchal and Jorge G. Morel. An Approximation to the Information Matrix of Exponential Family Finite Mixtures. Annals of the Institute of Statistical Mathematics, 2015. In press. (HPCF machines used: maya). [ http ]
[42] Amanda Plunkett. Analysis and Testing of Sparse High Dimensional Discrete Data. Ph.D. Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, August, 2015. (HPCF machines used: tara, maya.).
[43] Kendall Queen, Annie Dai, David Palensky, Alex Piatski, and Gina Vockeroth. Modeling the Building Blocks of the Pancreatic Islet: Connecting alpha-, beta-, and delta-Cells. UMBC Review: Journal of Undergraduate Research, 16:10-35, 2015.
[44] M.S. Miranda, J.C.G. Esteves da Silva and J.F. Liebman. Gas-phase Thermochemical Properties of Some Tri-substituted Phenols: A Density Functional Theory Study. Journal of Chemical Thermodynamics, 80:65-72, 2015.
[45] M.S. Miranda, P.J.O. Ferreira, J.C.G. Esteves da Silva and J.F. Liebman. Three-Membered Ring Amides: A Calculational and Conceptual Study of the Structure and Energetics of 1,2-Oxaziridine-3-one and Aziridine-2,3-dione. Canad. J. Chem., 93:406-413, 2015.
[46] A. Fattahi, J.F. Liebman, M.S. Miranda, V.M.F. Morais, M.A.R. Matos, L. Lis and S.R. Kass. Indenone and Cyclopentadienone Energetics via Mass Spectrometry: Are These Species Antiaromatic or ‘Merely’ Nonaromatic? International Journal of Mass Spectrometry, 378:175-179, 2015.
[47] M.S. Miranda, D.J.R. Duarte, J.C.G. Esteves da Silva and J.F. Liebman. Protonated Heterocyclic Derivatives of Cyclopropane and Cyclopropanone: Classical Species, Alternate Sites and Ring Fragmentation. Canadian Journal of Chemistry, 93:708-714, 2015.
[48] D.J.R. Duarte, M.S. Miranda, J.C.G. Esteves da Silva and J.F. Liebman. Theoretical Characterization of the Chemical Bonds of Some Three-Membered Ring Compounds Through QTAIM Theory. Structural Chemistry, in press, 2015.
[49] K.D. McDonald, E.O. Ojo and J.F. Liebman. What are the Structures of the Octet Rule Obeying All-Carbon Species Cx (2 ≤ x ≤ 7 and Larger x): A Pedagogical, Mathematical and Pictorial Study. Sustainable Nanosystems: Development, Properties, and Applications” (ed. M.V. Putz and M.C. Mirica), book chapter, in press, 2015.
[50] Yu Wang. The Modeling Equation: Solving The Physically Based Modeling And Animation Problem With A Unified Solution. Ph.D. Thesis, Department of Computer Science and Electrical Engineering, University of Maryland, Baltimore County, 2015. (HPCF machines used: tara, maya.).
[51] Zhibo Zhang, K. Meyer, H. Yu, S. Platnick, P. Colarco, Z. Liu, and L. Oreopoulos. Shortwave direct radiative effects of above cloud aerosols over global oceans derived from eight years of CALIOP and MODIS observations. Atmos. Chem. Phys. Discuss., 15:26357-26421, 2015. (HPCF machines used: maya.)
[52] Robert J. Weiblen. Light Propagation Into, Out of, and Through Mid-Infrared Optical Fibers. Ph.D. Thesis, Department of Computer Science and Electrical Engineering, University of Maryland, Baltimore County, 2015. (HPCF machines used: tara, maya.).
[53] Amanda M. Alexander, Erin K. DeNardo, Eric Frazier III, Michael McCauley, Nicholas Rojina, Zana Coulibaly, Bradford E. Peercy, and Leighton T. Izu. Spontaneous calcium release in cardiac myocytes: Store overload and electrical dynamics. Spora: A Journal of Biomathematics, 1(1), 2015. (HPCF machines used: maya.).
[54] J.C. Polf, S. Avery, D. Mackin, and S. Beddar. Imaging of prompt gamma rays emitted during delivery of clinical proton beams with a Compton camera: feasibility studies for range verification. Phys. Med. Biol., 60:7085-7099, 2015. (HPCF machines used: maya).
[55] Bhaskar, A.S., and C. Welty. Analysis of subsurface storage and streamflow generation in urban watersheds. Water Resources Research, 51, 2015. (HPCF machines used: maya).
[56] Elande Baro. Bayesian Latent Propensity Score Approach for Average Causal Effect Estimation Allowing Covariate Measurement Error. Ph.D. Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2015. (HPCF machines used: maya.).

2014

[1] Joseph P. Cornish, Neus Sanchez-Alberola, Patrick K. ONeill, Ronald O’Keefe, Jameel Gheba, and Ivan Erill. Characterization of the SOS meta-regulon in the human gut microbiome. Bioinformatics, 2014. (HPCF machines used: tara.). [ http ]
[2] David Stonko, Michelle Starz-Gaiano, and Bradford E. Peercy. Implementing a numerical package to model collective cell migration. Technical Report HPCF-2014-2, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2014. (HPCF machines used: tara.). [ .pdf ]
[3] Andrew M. Raim. Computational Methods in Finite Mixtures using Approximate Information and Regression Linked to the Mixture Mean. Ph.D. Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2014. (HPCF machines used: tara.).
[4] Jane Pan, Gemma Gearhart, Shuai Jiang, and Thomas J. May. Loss of metabolic oscillations in a multicellular computational islet of the pancreas. UMBC Review: Journal of Undergraduate Research, 15:31-53, 2014. (HPCF machines used: tara.).
[5] Gemma Gearhart, Shuai Jiang, Thomas J. May, Jane Pan, Samuel Khuvis, Matthias K. Gobbert, Bradford E. Peercy, and Arthur Sherman. Dynamics of computational islet simulations: Islets with majority mutated open KATP channels retain bursting. Letters in Biomathematics, 2014. [Invited paper for the inaugural issue of this journal, published originally in the Proceedings of the Sixth Symposium on BEER 2013] (HPCF machines used: tara.). [ .pdf ]
[6] Samuel Khuvis and Matthias K. Gobbert. Parallel performance studies for an elliptic test problem on maya 2013. Technical Report HPCF-2014-6, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2014. (HPCF machines used: maya.). [ .pdf ]
[7] Jonathan S. Graf and Matthias K. Gobbert. Parallel performance studies for a parabolic test problem on maya 2013. Technical Report HPCF-2014-7, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2014. (HPCF machines used: maya.). [ .pdf ]
[8] Xuan Huang and Matthias K. Gobbert. Parallel performance studies for a three-species application problem on maya 2013. Technical Report HPCF-2014-8, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2014. (HPCF machines used: maya.). [ .pdf ]
[9] David Stonko, Samuel Khuvis, and Matthias K. Gobbert. Numerical methods to solve 2-d and 3-d elliptic partial differential equations using Matlab on the cluster maya. Technical Report HPCF-2014-9, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2014. (HPCF machines used: maya.). [ .pdf ]
[10] Sarah Swatski, Samuel Khuvis, and Matthias K. Gobbert. A comparison of solving the poisson equation using several numerical methods in Matlab and Octave on the cluster maya. Technical Report HPCF-2014-10, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2014. (HPCF machines used: maya.). [ .pdf ]
[11] Nancy Hong, Emily Jasien, Christopher Pagan, Daniel Xie, Zana Coulibaly, Kofi P. Adragni, and Ian F. Thorpe. Nonlinear measurers of correlation and dimensionality reduction with application to protein motion. Technical Report HPCF-2014-11, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2014. (HPCF machines used: maya.). [ .pdf ]
[12] Christopher Evans, Abigail Gartrell, Lauren Gomez, Moise Mouyebe, Darius Oxley, Sai Kumar Popuri, Nagaraj K. Neerchal, and Amita Mehta. Improving the computational efficiency of downscaling GCM data for use in SWAT. Technical Report HPCF-2014-12, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2014. (HPCF machines used: maya.). [ .pdf ]
[13] Annie Dai, David Palensky, Alex Piatski, Kendall Queen, Gina Vockeroth, Teresa Lebair, Bradford E. Peercy, Margaret Watts, and Arthur Sherman. Modeling the building blocks of the pancreatic islet: Connecting alpha, beta, and delta cells. Technical Report HPCF-2014-13, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2014. (HPCF machines used: maya.). [ .pdf ]
[14] Adam Cunningham, Gerald Payton, Jack Slettebak, Jordi Wolfson-Pou, Jonathan S. Graf, Xuan Huang, Samuel Khuvis, Matthias K. Gobbert, Thomas Salter, and David J. Mountain. Pushing the limits of the maya cluster. Technical Report HPCF-2014-14, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2014. (HPCF machines used: maya.). [ .pdf ]
[15] Oluwapelumi Adenikinju, Julian Gilyard, Joshua Massey, Thomas Stitt, Jonathan S. Graf, Xuan Huang, Samuel Khuvis, Matthias K. Gobbert, Yu Wang, and Marc Olano. Real time global illumination solutions to the radiosity algorithm using hybrid CPU/GPU nodes. Technical Report HPCF-2014-15, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2014. (HPCF machines used: maya.). [ .pdf ]
[16] David P. Stonko. A discrete, three-dimensional, force-based mathematical model of collective cell migration. M.S. Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2014. (HPCF machines used: tara.). [ .pdf ]
[17] R. J. Weiblen, A. Docherty, C. R. Menyuk, L. B. Shaw, J. S. Sanghera, and I. D. Aggarwal. Calculation of the expected output spectrum for a mid-infrared supercontinuum source based on As2S3 chalcogenide photonic crystal fibers. Opt. Express, 22(18):22220-22231, 2014. (HPCF machines used: tara.). [ http | .pdf ]
[18] Y. Hu, B.S. Marks, C.R. Menyuk, V.J. Urick, and K.J. Williams. Modeling sources of nonlinearity in a simple p-i-n photodetector. Journal of Lightwave Technology, 32(20):3710-3720, 2014. (HPCF machines used: tara.). [ .pdf ]
[19] Matthew W. Brewster. The influence of stochastic parameters on calcium waves in a heart cell. Senior Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2014. (HPCF machines used: tara.). [ .pdf ]
[20] P.K. O’Neill, R. Forder, and I. Erill. Informational requirements for transcriptional regulation. Journal of Computational Biology, 21(5):373-384, 2014. (HPCF machines used: tara.).
[21] Matthias K. Gobbert, Andreas Meister, and Sven Wallbaum. On unconditionally positivity preserving and conservative methods for systems of advection-diffusion-reaction equations. Proc. Appl. Math. Mech. (PAMM), submitted.
[22] Z. Cui, C. Welty, and R.M. Maxwell. Modeling nitrogen transport and transformation in aquifers using a particle-tracking approach. Computers and Geosciences, 70:1-14, 2014. (HPCF machines used: tara.).
[23] Andrew M. Raim, Nagaraj K. Neerchal, and Jorge G. Morel. Large cluster approximation to the finite mixture information matrix with an application to meta-analysis. In JSM Proceedings, Statistical Computing Section. Alexandria, VA: American Statistical Association, pages 4025-4037, 2014. [ preprint | www: ]
[24] Sarah Swatski. Investigating the use of pMatlab to solve the Poisson equation on the cluster maya. Technical Report HPCF-2014-24, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2014. (HPCF machines used: maya.). [ .pdf ]
[25] Kourosh M. Kalayeh. Parallel performance studies for an elliptic test problem on the cluster maya 2013: Using 1-D and 2-D domain subdivisions. Technical Report HPCF-2014-25, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2014. (HPCF machines used: maya.). [ .pdf ]
[26] Andrei Draganescu. Multigrid preconditioning of linear systems for semi-smooth Newton methods applied to optimization problems constrained by smoothing operators. Optimization Methods and Software, 29(4):786-818, 2014.
[27] Jonathan S. McHenry. Parallel Regularized Maximum Likelihood Estimation for Proportional Odds Models. Ph.D. Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2014. (HPCF machines used: maya.).
[28] Mahsan Bakhtiari Nejad. Topology optimization based on morphing mesh for simultaneous component relocation and frame structure. M.S. Thesis, Department of Mechanical Engineering, University of Maryland, Baltimore County, 2014. (HPCF machines used: tara.).

2013

[1] Sai K. Popuri, Andrew M. Raim, Nagaraj K. Neerchal, and Matthias K. Gobbert. An implementation of binomial method of option pricing using parallel computing. Technical Report HPCF-2013-1, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2013. (HPCF machines used: tara.). [ .pdf ]
[2] Andrew M. Raim. Introduction to distributed computing with pbdR at the UMBC High Performance Computing Facility. Technical Report HPCF-2013-2, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2013. (HPCF machines used: tara.). [.pdf ]

Files for download with this report: pbdRtara2013.tar.gz

[3] B. C. Davis and I. F. Thorpe. Thumb inhibitor binding eliminates functionally important dynamics in the hepatitis C virus RNA polymerase. Proteins: Structure, Function and Bioinformatics, 81:40-52, 2013. (HPCF machines used: tara.). [ http ]
[4] I. E. Weidlich, I. V. Filippov, J. Brown, N. Kaushik-Basu, R. Krishnan, M. C. Nicklaus, and I. F. Thorpe. Inhibitors for the hepatitis C virus RNA polymerase explored by SAR with advanced machine learning methods. Bioorganic and Medicinal Chemistry, 21:3127-3137, 2013. (HPCF machines used: tara.). [ http ]
[5] M. Fioravante, A. Shook, I. F. Thorpe, and P. Rheingans. Visualizing motional correlations in molecular dynamics using geometric deformations. Computer Graphics Forum, 32(3pt3):311-320, 2013. (HPCF machines used: tara.). [ http ]
[6] B. C. Davis and I. F. Thorpe. Molecular simulations illuminate the role of regulatory components of the RNA polymerase from hepatitis C virus in influencing protein structure and dynamics. Biochemistry, 52(26):4541-4552, 2013. (HPCF machines used: tara.). [ http ]
[7] Jonas Schäfer, Xuan Huang, Stefan Kopecz, Philipp Birken, Matthias K. Gobbert, and Andreas Meister. A memory-efficient finite volume method for advection-diffusion-reaction systems with non-smooth sources. Numer. Methods Partial Differential Equations, 31(1):143-167, 2015. (HPCF machines used: tara.). [ http | .pdf ]
[8] Samuel Khuvis. Efficiency improvements in numerical methods for studying connectivity in a model of a pancreatic islet of heterogeneous beta cells. M.S. Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2013. (HPCF machines used: tara.).
[9] Jonas Schäfer. Investigation of performance of Krylov subspace methods for stationary and time-dependent reaction-advection-diffusion equations discretized by the finite volume method. Diploma Thesis, University of Kassel, Germany, 2013. (HPCF machines used: tara.).
[10] Nil Mistry, Jordan Ramsey, Benjamin Wiley, Jackie Yanchuck, Xuan Huang, Andrew Raim, Matthias K. Gobbert, Nagaraj K. Neerchal, and Philip J. Farabaugh. Clustering of multidimensional data sets with applications to spatial distributions of ribosomal proteins. Technical Report HPCF-2013-10, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2013. (HPCF machines used: tara.). [ .pdf ]
[11] Matthew G. Bachmann, Ashley D. Dyas, Shelby C. Kilmer, Julian Sass, Andrew Raim, Nagaraj K. Neerchal, Kofi P. Adragani, George Ostrouchov, and Ian F. Thorpe. Block cyclic distribution of data in pbdR and its effects on computational efficiency. Technical Report HPCF-2013-11, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2013. (HPCF machines used: tara.). [ .pdf ]
[12] William J. Bailey, Claire A. Chambless, Brandynne M. Cho, Jesse D. Smith, Andrew M. Raim, Kofi P. Adragani, and Ian F. Thorpe. Identifying nonlinear correlations in high dimensional data with application to protein molecular dynamics simulations. Technical Report HPCF-2013-12, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2013. (HPCF machines used: tara.). [ .pdf ]
[13] Nil Mistry, Jordan Ramsey, Benjamin Wiley, Jackie Yanchuck, Xuan Huang, Matthias K. Gobbert, Christopher Mineo, and David Mountain. Contention of communications in switched networks with applications to parallel sorting. Technical Report HPCF-2013-13, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2013. (HPCF machines used: tara.). [ .pdf ]
[14] Gemma Gearhart, Shuai Jiang, Thomas J. May, Jane Pan, Samuel Khuvis, Matthias K. Gobbert, Bradford E. Peercy, and Arthur Sherman. Investigating oscillation loss in computational islets. Technical Report HPCF-2013-14, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2013. (HPCF machines used: tara.). [.pdf ]
[15] J. P. Cornish, N. Sanchez-Alberola, P. K. O’Neill, R. O’Keefe, J. Gheba, and I. Erill. The SOS response of the human gut microbiome, submitted to Biology Direct, 2013. (HPCF machines used: tara.).
[16] P. K. O’Neill, R. Forder, and I. Erill. Informational requirements for transcriptional regulation, Journal of Computational Biology, 21(5):373-384, 2014. (HPCF machines used: tara.).
[17] X. Huang, S. Khuvis, S. Askarian, M. K. Gobbert, and B. E. Peercy. Coupled PDEs with initial solution from data in COMSOL 4. In Jinlan Huang, editor, Proceedings of the COMSOL Conference 2013, Boston, MA, 2013. (HPCF machines used: tara.). [ .pdf ]
[18] Zana A. Coulibaly, Bradford E. Peercy, and Matthias K. Gobbert. Insight into spontaneous recurrent calcium waves in a 3-D cardiac cell based on analysis of a 1-D deterministic model. Int. J. Comp. Math., 92(3):591-607, 2015. published online (2014). (HPCF machines used: tara.).
[19] Andrew M. Raim and Nagaraj K. Neerchal. Modeling overdispersion in binomial data with regression linked to a finite mixture probability of success. In JSM Proceedings, Statistical Computing Section. Alexandria, VA: American Statistical Association, pages 2760-2774, 2013. [ preprint | www: ]
[20] Andrew M. Raim, Minglei Liu, Nagaraj K. Neerchal, and Jorge G. Morel. On the method of approximate Fisher scoring for finite mixtures of multinomials. Statistical Methodology, 18:115-130, 2014. (HPCF machines used: tara.). [ preprint | http ]
[21] Hui Guo, Xiang Li, and Douglas D. Frey. Development of chromatofocusing techniques employing mixed-mode column packings for protein separations. Journal of Chromatography A, 1323:57-65, 2014. (HPCF machines used: tara.). [ http ]
[22] A. Seck, C. Welty, and R.M. Maxwell. Evaluation of groundwater resources of the chesapeake bay watershed using an integrated hydrologic model. Presented at the 2013 Fall Meeting of the American Geophysical Union, December 2013, San Francisco, CA. (HPCF machines used: tara.).
[23] A.S. Bhaskar. Effects of Urban Development on Groundwater Flow Systems and Streamflow Generation. Ph.D. Thesis, Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, 2013. (HPCF machines used: tara.).
[24] Nuno D.S. Pinto. Novel Hybrid Chromatofocusing Methods for Protein Purification. Ph.D. Thesis, Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, 2013. (HPCF machines used: tara.).

2012

[1] Yu Wang, Marc Olano, Matthias K. Gobbert, and Wesley Griffin. A GPU memory system comparison for an elliptic test problem. Technical Report HPCF-2012-1, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2012. (HPCF machines used: tara.). [ .pdf ]
[2] D. Wicks Kollonige, L. C. Sparling, P. Sawamura, B. Baker, and S. G. Trahan. A case study of complex stratospheric influence on U.S. surface air quality in February 2010, 2012. Submitted. (HPCF machines used: tara.).
[3] V. K. Gupta K. B. Neeves and C. D. Eggleton. Effect of Viscoelasticity on the Analysis of Single-Molecule Force Spectroscopy on Live Cells. Biophysical Journal, 103(1):137-145, 2012. (HPCF machines used: tara.).
[4] V. K. Gupta and C. D. Eggleton. A Theoretical Method to determine unstressed off-rate from multiple bond force spectroscopy. Colloids and Surfaces B Biointerfaces, 95:50-56, 2012. (HPCF machines used: tara.).
[5] Matthew W. Brewster. Study of free alternative numerical computation packages. SIAM Undergraduate Research Online (SIURO), 5, 2012. (HPCF machines used: tara.). [ preprint | .pdf ]
[6] Jonas Schäfer. Performance studies for the two-dimensional Poisson problem discretized by finite differences. Technical Report HPCF-2012-6, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2012. (HPCF machines used: tara.). [ .pdf ]
[7] Sai K. Popuri, Andrew M. Raim, Matthew W. Brewster, and Matthias K. Gobbert. A comparative evaluation of Matlab, Octave, FreeMat, Scilab, and R on tara. Technical Report HPCF-2012-7, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2012. (HPCF machines used: tara.). [ .pdf ]
[8] Randal McKissack. Cluster computing using Intel Concurrent Collections. Senior Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2012. (HPCF machines used: tara.). [ .pdf ]
[9] Robert Forder. Simulating the evolution of transcriptional regulatory motifs. Senior Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2012. (HPCF machines used: tara.). [ .pdf ]
[10] Ecaterina Coman. IDL: A possible alternative to Matlab? Senior Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2012. (HPCF machines used: tara.). [ .pdf ]
[11] Jordan B. Angel, Amy Flores, Justine Heritage, Nathan Wardrip, Andrew M. Raim, Matthias K. Gobbert, Richard C. Murphy, and David J. Mountain. Graph 500 performance on a distributed-memory cluster. Technical Report HPCF-2012-11, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2012. (HPCF machines used: tara.). [ .html | .pdf ]
[12] Rosemary K. Le, Christopher V. Rackauckas, Anne S. Ross, Nehemias Ulloa, Sai K. Popuri, Nagaraj K. Neerchal, and Brian R. Smith. Water quality monitoring of Maryland’s tidal waterways. Technical Report HPCF-2012-12, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2012. In Progress. (HPCF machines used: tara.). [ .html | .pdf ]
[13] Annie Castner, Jenny Louthan, Edwardo Rivera, Christian Weigandt, Jonathan S. McHenry, Nagaraj K. Neerchal, Matthias K. Gobbert, and Michael Dillon. Simulation of a university as a dynamical system. Technical Report HPCF-2012-13, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2012. In Progress. (HPCF machines used: tara.). [ .html | .pdf ]
[14] Andrew M. Raim, Minglei Liu, Nagaraj K. Neerchal, and Jorge G. Morel. An Approximate Fisher Scoring Algorithm for finite mixtures of multinomials. Technical Report HPCF-2012-14, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2012. (HPCF machines used: tara.). [ .pdf ]
[15] Ecaterina Coman, Matthew W. Brewster, Sai K. Popuri, Andrew M. Raim, and Matthias K. Gobbert. A comparative evaluation of Matlab, Octave, FreeMat, Scilab, R, and IDL on tara. Technical Report HPCF-2012-15, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2012. (HPCF machines used: tara.). [ .pdf ]

Files for download with this report: ComanHPCF2012/

[16] Yu Wang, Marc Olano, Matthias K. Gobbert, and Wesley Griffin. Parallel computing for long-time simulations of calcium waves in a heart cell. Proc. Appl. Math. Mech. (PAMM), 12(1):637-638, 2012. (HPCF machines used: tara.). [ reprint | http ]
[17] Aaron Churchill, Guan Wang, Matthias K. Gobbert, and Thomas I. Seidman. Efficient simulation of a reaction-diffusion system with a fast reaction in the asymptotic limit. (HPCF machines used: tara.), submitted, 2012. [ .pdf ]
[18] Rosemary K. Le, Christopher V. Rackauckas, Anne S. Ross, and Nehemias Ulloa. Assessment of statistical methods for water quality monitoring in Maryland’s tidal waterways. SIAM Undergraduate Research Online (SIURO), 6, 2013. (HPCF machines used: tara.). [ preprint | .pdf ]
[19] Matthew Brewster. Alternatives to the mathematical software package MATLAB in research and education. UMBC Review: Journal of Undergraduate Research, 14:50-62, 2013. (HPCF machines used: tara.).
[20] Jordan B. Angel, Amy M. Flores, Justine S. Heritage, Nathan C. Wardrip, Andrew M. Raim, Matthias K. Gobbert, Richard C. Murphy, and David J. Mountain. The Graph 500 benchmark on a medium-size distributed-memory cluster with high-performance interconnect, 2012. Submitted. (HPCF machines used: tara.). [ .pdf ]
[21] Alex C. Szatmary. Deformation and motion of cells and biological capsules in fluid flow, investigated with numerical methods. Ph.D. Thesis, Department of Mechanical Engineering, University of Maryland, Baltimore County, 2012. (HPCF machines used: tara.).

2011

[1] Robert Forder. A parallel simulation of the evolution of transcription factor binding sites. Technical Report HPCF-2011-1, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.). [ .pdf ]
[2] Amanda Peterson. Parameter estimation for the Dirichlet-multinomial distribution. Technical Report HPCF-2011-2, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.). [ .pdf ]
[3] Alex C. Szatmary and Charles D. Eggleton. Elastic capsule deformation in general irrotational linear flows. Fluid Dynamics Research, 44(5), 2012. (HPCF machines used: tara.). [ http ]
[4] F. Jacobsen and K.E. Omland. Species tree inference in a recent radiation of orioles (genus icterus): multiple markers and methods reveal cytonuclear discordance in the northern oriole group. Molecular Phylogenetics and Evolution, 61:460-469, 2011. [ http ]
[5] T. Tesfa, D. G. Tarboton, D. W. Watson, K. A.Schreuders, M. E. Baker, and R. M. Wallace. Extraction of hydrological proximity measures from dems using parallel processing. Environmental Modeling and Software, 26(12):1696-1709, 2011. [ http ]
[6] D. E. Weller, M. E. Baker, and T. E. Jordan. Empirical tests for effects of riparian buffers on watershed nitrate discharges. Ecological Applications, 21(5):1679-1695, 2011.
[7] Hafez Tari, H.-J. Su, and J.D. Hauenstein. Classification and complete solution of the kinetostatics of a compliant Stewart-Gough platform. Mechanism and Machine Theory, 49:177-186, 2012. (HPCF machines used: tara.). [ http ]
[8] R. S. King, M. E. Baker, P. F. Kazyak, and D. E. Weller. How novel is too novel? stream community thresholds at exceptionally low levels of catchment urbanization. Ecological Applications, 21(5):1659-1678, 2011. [ DOI ]
[9] Joseph Cornish, Robert Forder, Ivan Erill, and Matthias K. Gobbert. Simulation of the evolution of information content in transcription factor binding sites using a parallelized genetic algorithm. Technical Report HPCF-2011-9, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.). [ .pdf ]
[10] Matthew Brewster and Matthias K. Gobbert. A comparative evaluation of Matlab, Octave, FreeMat, and Scilab on tara. Technical Report HPCF-2011-10, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.). [ .pdf ]

Files for download with this report: BrewsterGobbertTR2011/

[11] Samantha Allen, Dorothy Kirlew, Neil Obetz, Derek Wade, April Albertine, Nagaraj K. Neerchal, and Martin Klein. Assessment of simple and alternative bayesian ranking methods utilizing parallel computing. Technical Report HPCF-2011-11, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.). [ .html | .pdf ]
[12] Jeremy Bejarano, Koushiki Bose, Tyler Brannan, Anita Thomas, Kofi Adragni, Nagaraj K. Neerchal, and George Ostrouchov. Sampling within k-means algorithm to cluster large datasets. Technical Report HPCF-2011-12, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.). [ .html | .pdf ]
[13] Andrew Coates, Alexey Ilchenko, Matthias K. Gobbert, Nagaraj K. Neerchal, Patrick O’Neill, and Ivan Erill. Optimization of computations used in information theory applied to base pair analysis. Technical Report HPCF-2011-13, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.). [ .html | .pdf ]

Files for download with this report: EHn.py, EHn.m, EHn.c, EHn.h, Makefile,

[14] Richard Adjogah, Randal Mckissack, Ekene Sibeudu, Andrew M. Raim, Matthias K. Gobbert, and Loring Craymer. Intel Concurrent Collections as a method for parallel programming. Technical Report HPCF-2011-14, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.). [ .html | .pdf ]

Files for download with this report: REU2011Team4_code.tgz

[15] Samuel Trahan. Multi-Scale Analysis of Observations of Tropical Cyclones with Applications to High-Resolution Hurricane Modeling. Ph.D. Thesis, Department of Physics, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.).
[16] Samuel Trahan and Lynn Sparling. An analysis of NCEP tropical cyclone vitals and potential effects on forecasting models. Weather and Forecasting, 27:744-756, 2012. (HPCF machines used: tara.). [ http ]
[17] Mattie K. B. Whitmore. Modeling and simulation of groundwater flow and contaminant transport in a cross-section of the delmarva peninsula. M.S. Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.).
[18] David W. Trott and Matthias K. Gobbert. Finite element convergence for time-dependent PDEs with a point source in COMSOL 4.2. In Yeswanth Rao, editor, Proceedings of the COMSOL Conference 2011, Boston, MA, 2011. (HPCF machines used: tara.). [ http |.pdf ]
[19] Mattie K. B. Whitmore, David W. Trott, Bradford E. Peercy, Matthew E. Baker, and Matthias K. Gobbert. COMSOL modeling of groundwater flow and contaminant transport in two-dimensional geometries with heterogeneities. In Yeswanth Rao, editor, Proceedings of the COMSOL Conference 2011, Boston, MA, 2011. (HPCF machines used: tara.). [ .pdf ]
[20] N. Petra, J. Zweck, S. E. Minkoff, A. A. Kosterev, and J. H. Doty III. Modeling and design optimization of a resonant optothermoacoustic trace gas sensor. SIAM J. Applied Mathematics, 71:309-332, 2011. (HPCF machines used: tara.). [ http ]
[21] N. Petra, J. Zweck, S. E. Minkoff, A. A. Kosterev, and J. H. Doty III. Validation of a model of a resonant optothermoacoustic trace gas sensor. In Conference on Lasers and Electro-Optics, Baltimore, MD, 2011. (HPCF machines used: tara.).
[22] J. Zweck and C. R. Menyuk. A chromatic dispersion estimation method for arbitrary modulation formats. In Conference on Lasers and Electro-Optics, Baltimore, MD, 2011. (HPCF machines used: tara.).
[23] Andrei Draganescu. Multigrid preconditioning of linear systems for semismooth Newton methods applied to optimization problems constrained by smoothing operators. Optimization Methods and Software, 2011. Submitted. (HPCF machines used: tara).
[24] V. K. Gupta and C. D. Eggleton. A theoretical method to determine unstressed off-rate from multiple bond rupture force spectroscopy. J. Chemical Physics, 2011. Submitted. (HPCF machines used: tara).
[25] M. A. Talukder and C. R. Menyuk. Temperature-dependent coherent carrier transport in quantum cascade lasers. New J. Phys., 13:083027, 2011. (HPCF machines used: tara.). [ http | .pdf ]
[26] Michael Curtis. A collaborative filtering model: Statistical properties of alternating least squares. UMBC Review: Journal of Undergraduate Research and Creative Works, 13:10-21, 2012. (HPCF machines used: tara.). [ preprint ]
[27] Thomas I. Seidman, Matthias K. Gobbert, David W. Trott, and Martin Kružík. Finite element approximation for time-dependent diffusion with measure-valued source. Numer. Math., 122(4):709-723, 2012. (HPCF machines used: tara.). [ preprint | http ]
[28] R. Chris Wilson. Multivariate Retrieval of Carbon Monoxide. Ph.D. Thesis, Department of Physics, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.). [ .pdf ]
[29] J. H.Lowry, M. E. Baker, and R. D. Ramsey. Determinants of urban tree canopy in residential neighborhoods: household characteristics, urban form, and the geophysical landscape. Urban Ecosystems, pages 1-20, 2011. [ DOI ]
[30] R. S. King and M. E. Baker. An alternative view of ecological community thresholds and appropriate analyses for their detection: comment. Ecological Applications, pages 2833-2839, 2011. [ DOI ]
[31] P. Budy, M. Baker, and S. K. Dahle. Predicting fish growth potential and identifying water quality constraints: a spatially-explicit bioenergetics approach. Environmental Management, 48(4):691-709, 2011. [ DOI ]
[32] F. Hilton, R. Armante, T. August, C. Barnet, A. Bouchard, C. Camy-Peyret, V. Capelle, L. Clarisse, C Clerbaux, P. Coheue, A. Collard, C. Crevoisier, G. Dufour, D. Edwards, F. Faijan, N. Fourrie, A. Gambacorta, M. Goldberg, V. Guidard, D. Hurtmans, S. Illingworth, N. Jacquinet-Husson, T. Kerzenmacher, D. Klaes, L. Lavanant, G. Masiello, M. Matricardi, A. McNally, S. Newman, E. Pavelin, S. Payan, E. Pequignot, S. Peyridieu, T. Phulpin, J. Remedios, P. Schlussel, C. Serio, L. Strow, C. Stubenrauch, J. Taylor, D. Tobin, W. Wolf, and D. Zhou. Hyperspectral earth observation from IASI: five years of accomplishments. Bull. Amer. Met. Soc., 93:347-370, 2012. (HPCF machines used: tara.). [ http ]
[33] L. N. Yurganov, V. Rakitin, A. Dzhola, T. August, E. Fokeeva, M. George, G. Gorchakov, E. Grechko, S. Hannon, A. Karpov, L. Ott, E. Semutnikova, R. Shumsky, and L. Strow. Satellite- and ground-based CO total column observations over 2010 russian fires: accuracy of top-down estimates based on thermal IR satellite data. Atmospheric Chemistry & Physics, 11:7925-7942, 2011. (HPCF machines used: tara.). [ http ]
[34] D. K. Zhou, A. M. Larar, X. Liu, W. L. Smith, L. L. Strow, P. Yang, P. Schlussel, and X. Calbet. Global land surface emissivity retrieved from satellite ultraspectral IR measurements. IEEE Transactions on Geoscience and Remote Sensing, 49:1277-1290, 2011. (HPCF machines used: tara.).
[35] Zhibo Zhang, Steven Platnick, Andrew Ackerman, Graham Feingold, Toshi Matsui, Laurent C-Labonnote, Cornet, and Jerome Riedi. Simulating the radiative and polarization characteristics of drizzling warm clouds using LES and 3-D radiative transfer models. In AGU Annual Fall Meeting, San Francisco, 2011. (HPCF machines used: tara.).
[36] D. Wicks Kollonige. The Impact of Upper Tropospheric Dynamics on Surface Air Quality of the United States. Ph.D. Thesis, Department of Physics, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.).
[37] V. K. Gupta and C. D. Eggleton. Effect of cell and microvillus mechanics on the transmission of applied loads to single bonds in dynamic force spectroscopy. Phys. Rev. E., 84(1), 2011.

2010

[1] Hafez Tari, Hai-Jun Su, and Tien-Yien Li. A constrained homotopy technique for excluding unwanted solutions from polynomial equations arising in kinematics problems. Mechanism and Machine Theory, 45(6):898-910, 2010. UMBC High Performance Computing Facility HPCF-2010-1 (HPCF machines used: hpc.).
[2] Andrew M. Raim and Matthias K. Gobbert. Parallel performance studies for an elliptic test problem on the cluster tara. Technical Report HPCF-2010-2, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2010. (HPCF machines used: tara.). [ .pdf ]
[3] Hafez Tari and Hai-Jun Su. Complete solution to the eight-point path generation of slider-crank four-bar linkages. Journal of Mechanical Design, 132(8):081003, 2010. UMBC High Performance Computing Facility HPCF-2010-3 (HPCF machines used: hpc.). [ http ]
[4] Michael Muscedere, Andrew M. Raim, and Matthias K. Gobbert. Parallel performance studies for a parabolic test problem on the cluster tara. Technical Report HPCF-2010-4, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2010. (HPCF machines used: tara.). [ .pdf ]
[5] Neeraj Sharma. A comparative study of several numerical computational packages. M.S. Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2010. (HPCF machines used: tara.).
[6] Hafez Tari and Matthias K. Gobbert. A comparative study of the parallel performance of the blocking and non-blocking MPI communication commands on an elliptic test problem on the cluster tara. Technical Report HPCF-2010-6, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2010. (HPCF machines used: tara.). [ .pdf ]
[7] Neeraj Sharma and Matthias K. Gobbert. A comparative evaluation of Matlab, Octave, FreeMat, and Scilab for research and teaching. Technical Report HPCF-2010-7, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2010. (HPCF machines used: tara.). [ .pdf ]
[8] David W. Trott and Matthias K. Gobbert. Finite element convergence studies using COMSOL 4.0a and LiveLink for MATLAB. Technical Report HPCF-2010-8, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2010. (HPCF machines used: tara.). [ .pdf ]

Files for download with this report: 2dpoisson.mph, driver_getmodel.m, getmodel.m, getmodel_unaltered.m

[9] Andrew M. Raim, Matthias K. Gobbert, Nagaraj K. Neerchal, and Jorge G. Morel. Maximum-likelihood estimation of the random-clumped multinomial model as a prototype problem for large-scale statistical computing. Journal of Statistical Computation and Simulation, 83(12):2178-2194, 2013. (HPCF machines used: tara.). [ preprint | http ]
[10] David W. Trott and Matthias K. Gobbert. Conducting finite element convergence studies using COMSOL 4.0. In Yeswanth Rao, editor,Proceedings of the COMSOL Conference 2010, Boston, MA, 2010. (HPCF machines used: tara.). [ .pdf ]
[11] David W. Trott and Matthias K. Gobbert. Parallel performance studies for a three-species application problem on the cluster tara. Technical Report HPCF-2010-11, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2010. (HPCF machines used: tara.). [ .pdf ]
[12] H. H. Aumann and L. L. Strow. Analysis of AIRS and IASI system performance under clear and cloudy conditions. In Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series, volume 7807, 2010. (HPCF machines used: tara.).
[13] A. A. Bradley and S. S. Schwartz. Summary verification measures and their interpretation for ensemble forecasts. Monthly Weather Review, 2010.
[14] V. K. Gupta, I. A. Sraj, K. Konstantopoulos, and C. D. Eggleton. Multi-scale simulation of L-selectin VPSGL-1-dependent homotypic leukocyte binding and rupture. Biomechanics and Modeling in Mechanobiology, 9(5):613-627, 2010. (HPCF machines used: tara.).
[15] M. Habib, A. A. Bradley, S. S. Schwartz, and A. Kruger. Verification of NWS ensemble river forecasts for the Des Moines river. Journal of Hydrometeorology, 2010. In preparation.
[16] A. Seck, C. Welty, and R. M. Maxwell. Considerations in regional integrated hydrologic modeling: Grid resolution, topography, and overland flow processes. In American Geophysical Union, Fall Meeting 2010, 2010. (HPCF machines used: tara.).
[17] I. Sraj, J. Chichester, E. Hoover, R. Jimenez, J. Squier, C. D. Eggleton, and D. W. M. Marr. Cell deformation cytometry using diode-bar optical stretchers. Journal of Biomedical Optics, 15(4):047010, 2010. (HPCF machines used: tara.).
[18] I. Sraj, D. W. M. Marr, and C. D. Eggleton. Linear diode laser bar optical stretchers for cell deformation. Biomedical Optics Express, 1(2):482-488, 2010. (HPCF machines used: tara.).
[19] I. Sraj, A. C. Szatmary, D. W. M. Marr, and C. D. Eggleton. Dynamic ray tracing for modeling optical cell manipulation. Optics Express, 18(16):16702-16714, 2010. (HPCF machines used: tara.).
[20] Hafez Tari and Hai-Jun Su. Complex solution framework for the kinetostatic synthesis of a compliant four-bar mechanism. Mechanism and Machine Theory, 46(8):1137-1152, 2011. (HPCF machines used: tara.).
[21] Sidafa Conde, Teresa Lebair, Christopher Raastad, Virginia Smith, Kyle Stern, David Trott, Matthias K. Gobbert, Bradford E. Peercy, and Arthur Sherman. Enabling physiologically representative simulations of pancreatic beta cells. Technical Report HPCF-2010-21, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2010. (HPCF machines used: tara.). [ .pdf ]
[22] Julia Baum, Cynthia Cook, Michael Curtis, Joshua Edgerton, Scott Rabidoux, Andrew Raim, Nagaraj Neerchal, and Robert Bell. Parallelization of matrix factorization for recommender systems. Technical Report HPCF-2010-22, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2010. (HPCF machines used: tara.). [ .pdf ]
[23] N. Petra, A. A. Kosterev, J. Zweck, S. E. Minkoff, and J. H. Doty III. Numerical and experimental investigation of a resonant optothermoacoustic sensor. In Proceedings of the Lasers and Electro-Optics (CLEO) Conference 2010, San Jose, California, 2010. (HPCF machines used: tara.).
[24] F. Jacobsen, N.R. Friedman, and K.E. Omland. Congruence between nuclear and mitochondrial DNA: combination of multiple nuclear introns resolves a well-supported phylogeny of new world orioles (icterus). Molecular Phylogenetics and Evolution, 56:419-427, 2010.
[25] J. X. Warner, Z. Wei, L. L. Strow, C. D. Barnet, L. C. Sparling, G. Diskin, and G. Sachse. Improved agreement of AIRS tropospheric carbon monoxide products with other EOS sensors using optimal estimation retrievals. Atmospheric Chemistry & Physics, 10:9521-9533, 2010. (HPCF machines used: tara.).

2009

[1] Neeraj Sharma and Matthias K. Gobbert. Performance studies for multithreading in Matlab with usage instructions on hpc. Technical Report HPCF-2009-1, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2009. (HPCF machines used: hpc.). [ .pdf ]
[2] Amanda K. Gassman and Matthias K. Gobbert. Solving a two-dimensional elliptic model problem with the conjugate gradient method using matrix-free SSOR preconditioning in Matlab. Technical Report HPCF-2009-2, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2009. (HPCF machines used: hpc.). [ .pdf ]
[3] Guan Wang, Aaron Churchill, Matthias K. Gobbert, and Thomas I. Seidman. Efficient computation for a reaction-diffusion system with a fast reaction with continuous and discontinuous initial data using COMSOL Multiphysics. Technical Report HPCF-2009-3, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2009. (HPCF machines used: hpc.). [ .pdf ]
[4] Noemi Petra and Matthias K. Gobbert. Performance studies with COMSOL Multiphysics via scripting and batch processing. Technical Report HPCF-2009-4, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2009. (HPCF machines used: hpc.). [ .pdf ]

Files for download with this report: poisson2d.m, poisson2d_graphics.m, poisson2d_matlab.m, poisson2d_infile.mph, qsub-COMSOL_with_MATLAB, qsub-COMSOL

[5] Guan Wang and Matthias K. Gobbert. Performance comparison between blocking and non-blocking communications for a three-dimensional Poisson problem. Technical Report HPCF-2009-5, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2009. (HPCF machines used: hpc.). [ .pdf ]
[6] Zana Coulibaly, Michael Muscedere, Matthias K. Gobbert, and Bradford E. Peercy. Long-time simulation of calcium waves in a heart cell to study the effects of calcium release flux density and of coefficients in the pump and leak mechanisms on self-organizing wave behavior. Technical Report HPCF-2009-6, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2009. (HPCF machines used: hpc.). [ .pdf ]
[7] Aaron Churchill, Matthias K. Gobbert, and Thomas I. Seidman. Efficient computation for a reaction-diffusion system with a fast reaction in two spatial dimensions using COMSOL Multiphysics. Technical Report HPCF-2009-7, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2009. (HPCF machines used: hpc.). [ .pdf ]
[8] Andrew M. Raim and Matthias K. Gobbert. Parallel performance studies for a maximum likelihood estimation problem using TAO. Technical Report HPCF-2009-8, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2009. (HPCF machines used: hpc.). [ .pdf ]
[9] A. Szatmary and C. D. Eggleton. Modeling fluid-structure interactions in non-periodic viscous flow with the immersed boundary method and Chorin’s projection method in Fourier space. Technical Report HPCF-2009-9, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2009. (HPCF machines used: hpc.).
[10] S. G. DeSouza-Machado, L. L. Strow, B. Imbiriba, K. McCann, R. M. Hoff, S. E. Hannon, J. V. Martins, D. Tanré, J. L. Deuzé, F. Ducos, and O. Torres. Infrared retrievals of dust using AIRS: Comparisons of optical depths and heights derived for a North African dust storm to other collocated EOS A-Train and surface observations. Journal of Geophysical Research (Atmospheres), 115, 2010. (HPCF machines used: hpc.).
[11] Michael J. Reid. Parallel performance studies for a numerical simulator of atomic layer deposition. UMBC Review: Journal of Undergraduate Research, 11:30-41, 2010. (HPCF machines used: hpc.) Pre-print PDF is given here. [ .pdf ]
[12] Yushu Yang. Parallel studies for chemically reacting systems. Technical Report HPCF-2009-12, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2009. (HPCF machines used: hpc.). [ .pdf ]
[13] Noemi Petra and Matthias K. Gobbert. Parallel performance studies for COMSOL Multiphysics using scripting and batch processing. In Yeswanth Rao, editor, Proceedings of the COMSOL Conference 2009, Boston, MA, 2009. (HPCF machines used: hpc.). [ .pdf ]
[14] Matthias K. Gobbert, Aaron Churchill, Guan Wang, and Thomas I. Seidman. COMSOL Multiphysics for efficient solution of a transient reaction-diffusion system with fast reaction. In Yeswanth Rao, editor, Proceedings of the COMSOL Conference 2009, Boston, MA, 2009. (HPCF machines used: hpc.). [ .pdf ]
[15] A. Bhaskar, C. Welty, and R. Maxwell. Urban watershed modeling across landscape scales. In American Geophysical Union, Fall Meeting, 2009. (HPCF machines used: hpc.).
[16] D. A. Elliott, H. H. Aumann, L. L. Strow, and S. E. Hannon. Two-year comparison of radiances from the atmospheric infrared sounder (AIRS) and the infrared atmospheric sounding interferometer (IASI). In Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series, volume 7456, 2009. (HPCF machines used: hpc.).
[17] E. M. Manning, H. H. Aumann, R. G. Deen, Y. Jiang, L. L. Strow, and S. E. Hannon. Spectral calibration in hyperspectral sounders. In Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series, volume 7456, 2009. (HPCF machines used: hpc.).
[18] H. Shen and D. D. Frey. Serial displacement chromatofocusing and its applications in 2D-PAGE and 2D-HPLC. part 1: Theory and general considerations. J. Chromatogr. A, 1216:977-986, 2009.
[19] Shiming Yang and Matthias K. Gobbert. The optimal relaxation parameter for the SOR method applied to the Poisson equation in any space dimensions. Appl. Math. Lett., 22:325-331, 2009. [  http | .pdf ]

2008

[1] Matthias K. Gobbert. Parallel performance studies for an elliptic test problem. Technical Report HPCF-2008-1, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2008. (HPCF machines used: hpc.). [ .pdf ]
[2] Michael Muscedere and Matthias K. Gobbert. Parallel performance studies for a parabolic test problem. Technical Report HPCF-2008-2, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2008. (HPCF machines used: hpc.). [ .pdf ]
[3] Michael J. Reid and Matthias K. Gobbert. Parallel performance studies for a hyperbolic test problem. Technical Report HPCF-2008-3, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2008. (HPCF machines used: hpc.). [ .pdf ]
[4] Shiming Yang and Matthias K. Gobbert. Convergence order studies for elliptic test problems with COMSOL Multiphysics. Technical Report HPCF-2008-4, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2008. (HPCF machines used: kali.). [ .pdf ]
[5] Robin Blasberg and Matthias K. Gobbert. Parallel performance studies for a clustering algorithm. Technical Report HPCF-2008-5, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2008. (HPCF machines used: hpc.). [ .pdf ]
[6] Samuel Trahan. MPI performance on the hpc.rs.umbc.edu cluster. Technical Report HPCF-2008-6, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2008. (HPCF machines used: hpc.). [ www: ]
[7] Robin Blasberg and Matthias K. Gobbert. MVAPICH2 vs. OpenMPI for a clustering algorithm. Technical Report HPCF-2008-7, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2008. (HPCF machines used: hpc.). [ .pdf ]
[8] Robin Blasberg and Matthias K. Gobbert. Clustering large data sets with parallel affinity propagation. Technical Report HPCF-2008-8, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2008. (HPCF machines used: hpc.).
[9] Michael J. Reid. Comparison of parallel performance between MVAPICH2 and OpenMPI applied to a hyperbolic test problem, Senior Thesis, Department of Mathematics and Statistics. UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2008. (HPCF machines used: hpc.). [ .pdf ]
[10] Matthias K. Gobbert and Shiming Yang. Numerical demonstration of finite element convergence for Lagrange elements in COMSOL Multiphysics. In Vineet Dravid, editor, Proceedings of the COMSOL Conference 2008, Boston, MA, 2008. (HPCF machines used: kali.). [.pdf ]
[11] A. Gambacorta, C. Barnet, B. Soden, and L. Strow. An assessment of the tropical humidity-temperature covariance using AIRS.Geophys. Res. Lett., 35, 2008. (HPCF machines used: hpc.).
[12] Matthias K. Gobbert. Long-time simulations on high resolution meshes to model calcium waves in a heart cell. SIAM Journal on Scientific Computing, 30(6):2922-2947, 2008. (HPCF machines used: kali.).
[13] P. Graff, M. Georganopoulos, E. Perlman, and D. Kazanas. A multizone model for simulating the high-energy variability of TeV. The Astrophysical Journal, 689(1):68, 2008.
[14] L. L. Strow and S. E. Hannon. A 4-year zonal climatology of lower tropospheric CO2 derived from ocean-only atmospheric infrared sounder observations. Journal of Geophysical Research (Atmospheres), 113, 2008. (HPCF machines used: hpc.).
[15] D. G. Tarboton and M. E. Baker. Toward an algebra for terrain-based flow analysis. In N. Mount, G. Harvey, G. Priesthall, and P. Apin, editors, Representing, Modelling, and Visualizing the Natural Environment. CRC Press-Taylor & Francis, London, 2008.