Rita V. Rodriguez CNS Division Of Computer and Network Systems
CSE Direct For Computer & Info Scie & Enginr
September 1, 2012
August 31, 2015 (Estimated)
Awarded Amount to Date:
Carlos Camacho email@example.com (Principal Investigator)
Lillian Chong (Co-Principal Investigator)
University of Pittsburgh
MAJOR RESEARCH INSTRUMENTATION
Program Reference Code(s):
Program Element Code(s):
Proposal #: 12-29064
PI(s): Camacho, Carlos J; Chong, Lillian T
Institution: University of Pittsburgh
Title: MRI/Acq.: Computational Resources for Research in Computational and Systems Biology
This project, acquiring a computational instrument, fosters interdisciplinary collaborations and training that promote breakthroughs in the biological sciences. The project is lead by the Department of Computational and Systems Biology (DCSB) in conjunction with the joint Ph.D. program between two institutions in the area: Pittsburgh and Carnegie Mellon Universities. The acquisition, a state-of-the-art 57-node 3392 core computing cluster, is dedicated to research and development of applications and the dissemination of new computational methods. The cluster supports the following research projects:
- Novel molecular methods to access biological timescales of interest;
- Deep-sequencing technologies for high throughput ?omic? data collection; and,
- Methods to leverage high-resolution multi-modal biomedical images/videos in basic research.
Broader impacts should be felt both regionally and nationally. At the involved institutions, the research initiatives the incorporation of developed applications in teaching modules for use at local city high schools, as well as in undergraduate and graduate courses. Access to dedicated computational resources will provide valuable hands on experiences for students. More broadly, the software developed exploits the new computational resources that will be made available to other researchers nationwide.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
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F. F. Wang, M. J. Deible, and K. D. Jordan. "Benchmark Study of the Interaction Energy of a (H2O)16 Cluster," J. Phys Chem. A, v.117, 2013, p. 7606.
Z. D. Pozun, X. Su, and K. D. Jordan. "Establishing the Ground State of the Disjoint Diradical Tetramethyleneethane with Quantum Monte Carlo," J. Am. Chem. Soc, v.135, 2013, p. 13862.
Sarah M. Bartsch, Susan S. Huang, Kim F. Wong, Taliser R. Avery, and Bruce Y. Lee. "The Spread and Control of Norovirus Outbreaks among Hospitals in a Region: A Simulation Model," Open Forum Infect Dis, 2014, p. ofu030v1.
J. Xu, M. Deible, K. Peterson, and K. D. Jordan. "Correlation Consistent Gaussian Basis Sets for H, B-Ne with Dirac-Fock AREP Pseudopotentials: Applications in Quantum Monte Carlo Calculations," J. Chem. Theory Comput., v.9, 2013, p. 2170.
Christopher S. Ewing, Saurabh Bhavsar, Götz Veser, Joseph J. McCarthy, and J. Karl Johnson. "Accurate Amorphous Silica Surface Models from First Principles Thermodynamics of Surface Dehydroxylation," Langmuir, v.30, 2014, p. 5133-5141.
Uchida, H.K., Chan, J., Shrivastava I., Reinhart, B., Grandi, P., Glorisos, G., and Cohen, J. "Novel mutations in gB and gH circumvent the requirement for known gD receptors in HSV-1 entry and cell-to-cell spread," J. Virology, v.87, 2012, p. 1430.
M. J. Deible, M. Kessler, K. Gasperich, and K. D. Jordan. "Quantum Monte Carlo Calculation of the Binding Energy of the Beryllium Dimer," J. Chem. Phys., v.143, 2015, p. 1.
Cheng, M.H. and I. Bahar. "Complete mapping of substrate translocation highlights the significance of LeuT N-terminal segment in regulating transport cycle," PLoS Comput Biol., 2014.
Priedigkeit NM, Wolfe NW, Clark NL.. "Evolutionary signatures amongst disease genes permit novel methods for gene prioritization and construction of informative gene networks.," PLOS Genetics., v.11, 2015, p. e1004967..
Prerna Grover, Haibin Shi, Matthew Baumgartner, Carlos J. Camacho, Thomas E. Smithgall. "Fluorescence Polarization Screening Assays for Small Molecule Allosteric Modulators of ABL Kinase Function," Plos One, v.10, 2015, p. e0133590.
Meslin C, Plakke MS, Deutsch AB, Small BS, Morehouse NI, Clark NL.. "Digestive Organ in the Female Reproductive Tract Borrows Genes from Multiple Organ Systems to Adopt Critical Functions.," Molecular Biology and Evolution., v.32, 2015, p. 1567.
David Ryan Koes, Nicolas A. Pabon, Xiaoyi Deng, Margaret A. Phillips, and Carlos J. Camacho. "A Teach-Discover-Treat Application of ZincPharmer: An Online Interactive Pharmacophore Modeling and Virtual Screening Tool.," Plos One, v.10, 2015, p. e0134697..
Matthew C. Zwier,? Joshua L. Adelman,? Joseph W. Kaus, Adam J. Pratt, Kim F. Wong, Nicholas B. Rego, Ernesto Suárez, Steven Lettieri, David W. Wang, Michael Grabe, Daniel M. Zuckerman, and Lillian T. Chong,. "WESTPA: An Interoperable, Highly Scalable Software Package for Weighted Ensemble Simulation and Analysis," JCTC, v.11, 2015, p. 800.