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Research Computing

Research Computing

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    Publications

Accurate Homogeneous Electron Gas Exchange-Correlation Free Energy for Local Spin-Density Calculations

Valentin V. Karasiev*, Travis Sjostrom, James Dufty, and S. B. Trickey. Accurate Homogeneous Electron Gas Exchange-Correlation Free Energy for Local Spin-Density Calculations PHYSICAL REVIEW LETTERS 112, 076403 (2014), 2014-02-20 Abstract: An accurate analytical parametrization for the exchange-correlation free energy of… Read More

Geographic and Taxonomic Disparities in Species Diversity: Dispersal and Diversification Rates Across Wallace’s Line

Christine D. Bacon, François Michonneau, Andrew J. Henderson, Miles J. McKenna, Arwen M. Milroy, and Mark P. Simmons. Geographic and Taxonomic Disparities in Species Diversity: Dispersal and Diversification Rates Across Wallace’s Line  EVOLUTION, 2013-12-05 Abstract: Broad-scale patterns of species diversity… Read More

A Method for Detecting Positive Growth Autocorrelation without Marking Individuals

Mollie E. Brooks, Michael W. McCoy, Benjamin M. Bolker. A Method for Detecting Positive Growth Autocorrelation without Marking Individuals PLOS ONE, 2013-10-28 Abstract: In most ecological studies, within-group variation is a nuisance that obscures patterns of interest and reduces statistical… Read More

Nonempirical generalized gradient approximation free-energy functional for orbital-free simulations

Valentin V. Karasiev, Debajit Chakraborty, Olga A. Shukruto, and S.B. Trickey. Non-empirical generalized gradient approximation free-energy functional for orbital-free simulations PHYSICAL REVIEW B 88, 161108(R) (2013), 2013-10-28 Abstract: We report a purely non-empirical generalized gradient approximation for the non-interacting free… Read More

Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent

Pengfei Li, Benjamin Paul Roberts, Dhruva Kumar Chakravorty, and Kenneth Malcolm Merz. Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal… Read More

Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods

Dhruva K. Chakravorty, Bing Wang, Chul Won Lee, Alfredo J. Guerra, David P. Giedroc, Kenneth M. Merz Jr.. Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods Journal of Biomolecular NMR, 2013-05-14… Read More

Quantum phase transitions in a pseudogap Anderson-Holstein model

Mengxing Cheng and Kevin Ingersent . Quantum phase transitions in a pseudogap Anderson-Holstein model Phys. Rev. B 87, 075145 (2013), 2013-02-26 Abstract: We study a pseudogap Anderson-Holstein model of a magnetic impurity level that hybridizes with a conduction band whose… Read More

A Targeted Enrichment Strategy for Massively Parallel Sequencing of Angiosperm Plastid Genomes

Gregory W. Stull, Michael J. Moore, Venkata S. Mandala, Norman A. Douglas, Heather-Rose Kates, Xinshuai Qi, Samuel F. Brockington, Pamela S. Soltis, Douglas E. Soltis and Matthew A. Gitzendanner. A Targeted Enrichment Strategy for Massively Parallel Sequencing of Angiosperm Plastid… Read More

Power-performance Co-optimization of Throughput Core Architecture using Resistive Memory

Nilanjan Goswami, Bingyi Cao, Tao Li. Power-performance Co-optimization of Throughput Core Architecture using Resistive Memory IEEE International Symposium on High Performance Computer Architecture, 2013-01-25 Abstract: Massively parallel computing on throughput computers such as GPUs requires myriad memory accesses to register… Read More

Finding a needle in the haystack: computational modeling of Mg2+ binding in the active site of protein farnesyltransferase.

Yang Y, Chakravorty DK, Merz KM Jr.. Finding a needle in the haystack: computational modeling of Mg2+ binding in the active site of protein farnesyltransferase. Biochemistry. 2010 Nov 9;49(44):9658-66, 2010-10-05 Abstract: Studies aimed at elucidating the unknown Mg2+ binding site… Read More

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