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},
  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.)}
}