@techreport{PopuriEtAl_Binomial, author = {Sai~K. Popuri and Andrew~M. Raim and Nagaraj~K. Neerchal and Matthias~K. Gobbert}, title = {An Implementation of Binomial Method of Option Pricing using Parallel Computing}, number = {HPCF--2013--1}, institution = {UMBC High Performance Computing Facility, University of Maryland, Baltimore County}, year = 2013, pdf = {http://userpages.umbc.edu/~gobbert/papers/PopuriEtAl_Binomial.pdf}, note = {(HPCF machines used: tara.)} }

@techreport{pbdRtara2013, author = {Andrew~M. Raim}, title = {Introduction to Distributed Computing with {pbdR} at the {UMBC} {H}igh {P}erformance {C}omputing {F}acility}, number = {HPCF--2013--2}, institution = {UMBC High Performance Computing Facility, University of Maryland, Baltimore County}, year = 2013, pdf = {http://userpages.umbc.edu/~gobbert/papers/pbdRtara2013.pdf}, webnotes = {Files for download with this report: \href{http://userpages.umbc.edu/~gobbert/papers/pbdRtara2013.tar.gz}{pbdRtara2013.tar.gz} }, note = {(HPCF machines used: tara.)} }

@article{DavisThorpePSFB2013, author = {Davis, B.~C. and Thorpe, I.~F.}, title = {Thumb inhibitor binding eliminates functionally important dynamics in the hepatitis {C} virus {RNA} polymerase}, journal = {Proteins: Structure, Function and Bioinformatics}, volume = 81, pages = {40--52}, year = 2013, url = {http://dx.doi.org/10.1002/prot.24154}, note = {(HPCF machines used: tara.)} }

@article{WeidlichEtAl2013, author = {Weidlich, I.~E. and Filippov, I.~V. and Brown, J. and Kaushik-Basu, N. and Krishnan, R. and Nicklaus, M.~C. and Thorpe, I.~F.}, title = {Inhibitors for the Hepatitis {C} Virus {RNA} Polymerase Explored by {SAR} with Advanced Machine Learning Methods}, journal = {Bioorganic and Medicinal Chemistry}, volume = 21, pages = {3127--3137}, year = 2013, url = {http://www.sciencedirect.com/science/article/pii/S0968089613002460}, note = {(HPCF machines used: tara.)} }

@article{FioravanteEtAl2013, author = {Fioravante, M. and Shook, A. and Thorpe, I.~F. and Rheingans, P.}, title = {Visualizing Motional Correlations in Molecular Dynamics using Geometric Deformations}, journal = {Computer Graphics Forum}, year = {2013}, volume = 32, number = {3pt3}, pages = {311--320}, url = {http://dx.doi.org/10.1111/cgf.12118}, note = {(HPCF machines used: tara.)} }

@article{DavisThorpeBC2013, author = {Davis, B.~C. and Thorpe, I.~F.}, title = {Molecular simulations illuminate the role of regulatory components of the {RNA} polymerase from Hepatitis {C} Virus in influencing protein structure and dynamics}, journal = {Biochemistry}, year = 2013, volume = 52, number = 26, pages = {4541--4552}, note = {(HPCF machines used: tara.)}, url = {http://pubs.acs.org/doi/abs/10.1021/bi400251g} }

@article{CalciumFV_NMPDE2012, author = {Jonas Sch\"afer and Xuan Huang and Stefan Kopecz and Philipp Birken and Matthias~K. Gobbert and Andreas Meister}, title = {A Memory-Efficient Finite Volume Method for Advection-Diffusion-Reaction Systems with Non-Smooth Sources}, journal = {Numer.\ Methods Partial Differential Equations}, year = {published online (2014)}, note = {(HPCF machines used: tara.)}, url = {http://onlinelibrary.wiley.com/doi/10.1002/num.21897/abstract}, pdf = {http://userpages.umbc.edu/~gobbert/papers/CalciumFV_NMPDE2012.pdf} }

@misc{KhuvisThesis2013, author = {Samuel Khuvis}, title = {Efficiency Improvements in Numerical Methods for Studying Connectivity in a Model of a Pancreatic Islet of Heterogeneous Beta Cells}, howpublished = {M.S.~Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County}, year = {2013}, note = {(HPCF machines used: tara.)} }

@misc{SchaeferThesis2013, author = {Jonas Sch\"{a}fer}, title = {Investigation of Performance of {K}rylov Subspace Methods for Stationary and Time-Dependent Reaction-Advection-Diffusion Equations Discretized by the Finite Volume Method}, howpublished = {Diploma thesis, University of Kassel, Germany}, year = 2013, note = {(HPCF machines used: tara.)} }

@techreport{REU2013Team3bio, author = {Nil Mistry and Jordan Ramsey and Benjamin Wiley and Jackie Yanchuck and Xuan Huang and Andrew Raim and Matthias~K. Gobbert and Nagaraj~K. Neerchal and Philip~J. Farabaugh}, title = {Clustering of Multidimensional Data Sets with Applications to Spatial Distributions of Ribosomal Proteins}, number = {HPCF--2013--10}, institution = {UMBC High Performance Computing Facility, University of Maryland, Baltimore County}, year = 2013, pdf = {http://userpages.umbc.edu/~gobbert/papers/REU2013Team3Bio.pdf}, note = {(HPCF machines used: tara.)} }

@techreport{REU2013Team1, author = {Matthew~G. Bachmann and Ashley~D. Dyas and Shelby~C. Kilmer and Julian Sass and Andrew Raim and Nagaraj~K. Neerchal and Kofi~P. Adragani and George Ostrouchov and Ian~F. Thorpe}, title = {Block Cyclic Distribution of Data in pbd{R} and its Effects on Computational Efficiency}, number = {HPCF--2013--11}, institution = {UMBC High Performance Computing Facility, University of Maryland, Baltimore County}, year = 2013, pdf = {http://userpages.umbc.edu/~gobbert/papers/REU2013Team1.pdf}, note = {(HPCF machines used: tara.)} }

@techreport{REU2013Team2, author = {William~J. Bailey and Claire~A. Chambless and Brandynne~M. Cho and Jesse~D. Smith and Andrew~M. Raim and Kofi~P. Adragani and Ian~F. Thorpe}, title = {Identifying Nonlinear Correlations in High Dimensional Data with Application to Protein Molecular Dynamics Simulations}, number = {HPCF--2013--12}, institution = {UMBC High Performance Computing Facility, University of Maryland, Baltimore County}, year = 2013, pdf = {http://userpages.umbc.edu/~gobbert/papers/REU2013Team2.pdf}, note = {(HPCF machines used: tara.)} }

@techreport{REU2013Team3IB, author = {Nil Mistry and Jordan Ramsey and Benjamin Wiley and Jackie Yanchuck and Xuan Huang and Matthias~K. Gobbert and Christopher Mineo and David Mountain}, title = {Contention of Communications in Switched Networks with Applications to Parallel Sorting}, number = {HPCF--2013--13}, institution = {UMBC High Performance Computing Facility, University of Maryland, Baltimore County}, year = 2013, pdf = {http://userpages.umbc.edu/~gobbert/papers/REU2013Team3IB.pdf}, note = {(HPCF machines used: tara.)} }

@techreport{REU2013Team4, author = {Gemma Gearhart and Shuai Jiang and Thomas~J. May and Jane Pan and Samuel Khuvis and Matthias~K. Gobbert and Bradford~E. Peercy and Arthur Sherman}, title = {Investigating Oscillation Loss in Computational Islets}, number = {HPCF--2013--14}, institution = {UMBC High Performance Computing Facility, University of Maryland, Baltimore County}, year = 2013, pdf = {http://userpages.umbc.edu/~gobbert/papers/REU2013Team4.pdf}, note = {(HPCF machines used: tara.)} }

@misc{CornishEtAl2013, author = {Cornish, J. P. and Sanchez-Alberola, N. and O'Neill, P. K. and O'Keefe, R. and Gheba, J. and Erill, I.}, title = {The {SOS} response of the human gut microbiome}, year = {submitted to Biology Direct, 2013}, note = {(HPCF machines used: tara.)} }

@misc{ONeillForderErill2013, author = {O'Neill, P. K. and Forder, R. and Erill, I.}, title = {Informational requirements for transcriptional regulation}, year = {submitted to Journal of Computational Biology, 2013}, note = {(HPCF machines used: tara.)} }

@inproceedings{CoupledPDEsCOMSOL2013, author = {X. Huang and S. Khuvis and S. Askarian and M.~K. Gobbert and B.~E. Peercy}, title = {Coupled {PDE}s with Initial Solution from Data in {COMSOL}~4}, editor = {Jinlan Huang}, booktitle = {Proceedings of the {COMSOL} Conference 2013, Boston, MA}, note = {(HPCF machines used: tara.)}, pdf = {http://userpages.umbc.edu/~gobbert/papers/CoupledPDEs_COMSOL2013.pdf}, year = 2013 }

@misc{Coulibaly1dcalciumRegion2011, author = {Zana~A. Coulibaly and Bradford~E. Peercy and Matthias~K. Gobbert}, title = {Insight into Spontaneous Recurrent Calcium Waves in a 3-{D} Cardiac Cell Based on Analysis of a 1-{D} Deterministic Model}, journal = {Int.\ J. Comp.\ Math.}, note = {published online (2014). (HPCF machines used: tara.)} }

@inproceedings{RaimNeerchalJSM2013, author = {Andrew~M. Raim and Nagaraj~K. Neerchal}, title = {Modeling Overdispersion in Binomial Data with Regression Linked to a Finite Mixture Probability of Success}, booktitle = {JSM Proceedings, Statistical Computing Section. Alexandria, VA: American Statistical Association}, pages = {2760--2774}, year = 2013, url = { http://www.amstat.org/meetings/jsm/2013/onlineprogram/AbstractDetails.cfm?abstractid=309025 }, preprint = {http://www.umbc.edu/~araim1/pub/RaimNeerchalJSM2013.pdf} }

@article{RaimEtAlStamet2013, author = {Andrew~M. Raim and Minglei Liu and Nagaraj~K. Neerchal and Jorge~G. Morel}, title = {On the Method of Approximate {F}isher Scoring for Finite Mixtures of Multinomials}, journal = {Statistical Methodology}, volume = 18, pages = {115--130}, year = 2014, note = {(HPCF machines used: tara.)}, preprint = {http://www.math.umbc.edu/~araim1/papers/RaimEtAlStamet2013.pdf}, url = {http://www.sciencedirect.com/science/article/pii/S1572312713000841} }

@article{GuoLiFrey2013, title = {Development of chromatofocusing techniques employing mixed-mode column packings for protein separations}, author = {Hui Guo and Xiang Li and Douglas D. Frey}, journal = {Journal of Chromatography A}, volume = 1323, pages = {57--65}, year = 2014, note = {(HPCF machines used: tara.)}, issn = {0021-9673}, url = {http://www.sciencedirect.com/science/article/pii/S0021967313017287} }

@misc{Seck_EtAl_2013, author = {Seck, A. and Welty, C. and Maxwell, R.M.}, title = {Evaluation of groundwater resources of the Chesapeake Bay Watershed using an integrated hydrologic model}, note = {Presented at the 2013 Fall Meeting of the American Geophysical Union, December 2013, San Francisco, CA. (HPCF machines used: tara.)} }