Chakravorty DK, Parker TM, Guerra AJ, Sherrill CD, Giedroc DP, Merz KM Jr.. Energetics of zinc-mediated interactions in the allosteric pathways of metal sensor proteins J Am Chem Soc. 2013 Jan 9;135(1):30-3, 2012-12-26 Abstract: A metal-mediated interprotomer hydrogen bond has… Read More
pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4
Natali V. Di Russo, Dario A. Estrin, Marcelo A. Martí mail and Adrian E. Roitberg. pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4 PLoS Comput Biol. 2012 November; 8(11): e1002761, 2012-11-01 Abstract:… Read More
pH-Replica Exchange Molecular Dynamics in Proteins Using a Discrete Protonation Method
Danial Sabri Dashti, Yilin Meng and Adrian E. Roitberg . pH-Replica Exchange Molecular Dynamics in Proteins Using a Discrete Protonation Method J. Phys. Chem. B, 2012, 116 (30), pp 8805–8811, 2012-06-13 Abstract: Protonation equilibria in biological molecules modulates structure, dynamics,… Read More
Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations
Yilin Meng Danial Sabri Dashti and Adrian E. Roitberg. Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations J. Chem. Theory Comput., 2011, 7 (9), pp 2721–2727, 2011-07-28 Abstract: Alchemical free energy calculations play a very important… Read More
Integrating Nanophotonics in GPU Microarchitecture
As high-performance computing device, the GPU has exposed bandwidth and latency bottlenecks in on-chip interconnect and off-chip memory access.
Land Use Change in Central Florida and Sensitivity Analysis Based on Agricultural to Urban Extreme Conversion Climate and Society
This paper explored recent land use and land cover change in western central Florida, examining both socioeconomic and biophysical influences on land transformation and the impacts of that change.
The Effect of Spanwise Width on Rectangular Jets With Sidewalls
A CFD study on the effect of spanwise width on a rectangular jet with sidewalls is conducted using a standard k- model with wall functions.
Solution Structure of Mycobacterium tuberculosis NmtR in the Apo State: Insights into Ni(II)-Mediated Allostery
Chul Won Lee†‡, Dhruva K. Chakravorty§, Feng-Ming James Chang†, Hermes Reyes-Caballero†, Yuzhen Ye, Kenneth M. Merz, Jr.§, and David P. Giedroc, Solution Structure of Mycobacterium tuberculosis NmtR in the Apo State: Insights into Ni(II)-Mediated Allostery Biochemistry, 2012, 51 (12), pp 2619–2629,… Read More
A flood pulse driven fish population model for the Okavango Delta, Botswana.
Linhoss, A.C., R. Muñoz-Carpena, M. Allen, G. Kiker, K. Mosepele , A flood pulse driven fish population model for the Okavango Delta, Botswana. Ecological Modelling 228:27–38, 2012-01-30 Abstract [-]: The Okavango Delta is a large, remote, and ecologically significant wetland located in Botswana… Read More
A Computational Study of SrTiO3 Thin Film Deposition: Morphology and Growth Modes
J.L. Wohlwend, C.N. Bosewell, S.R. Phillpot, and S.B. Sinnott, A Computational Study of SrTiO3 Thin Film Deposition: Morphology and Growth Modes Journal of Materials Research 24, 2009-01-01