hpcf2013.bib
@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},
volume = 31,
number = 1,
pages = {143--167},
year = 2015,
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
}
@article{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.},
volume = 92,
number = 3,
pages = {591--607},
year = 2015,
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.)}
}
@misc{BhaskarThesis2013,
author = {Bhaskar, A.S.},
title = {\emph{Effects of Urban Development on Groundwater
Flow Systems and Streamflow Generation}},
howpublished = {Ph.D. Thesis, Department of Chemical, Biochemical,
and Environmental Engineering,
University of Maryland, Baltimore County},
year = 2013,
note = {(HPCF machines used: tara.)}
}
@misc{PintoThesis2013,
author = {Pinto, Nuno D.S.},
title = {\emph{Novel Hybrid Chromatofocusing Methods for Protein
Purification}},
howpublished = {Ph.D. Thesis, Department of Chemical, Biochemical,
and Environmental Engineering,
University of Maryland, Baltimore County},
year = 2013,
note = {(HPCF machines used: tara.)}
}