James Dama
James Dama
Graduate Student, The University of Chicago
Verified email at uchicago.edu
Title
Cited by
Cited by
Year
Well-tempered metadynamics converges asymptotically
JF Dama, M Parrinello, GA Voth
Physical review letters 112 (24), 240602, 2014
1762014
The theory of ultra-coarse-graining. 1. General principles
JF Dama, AV Sinitskiy, M McCullagh, J Weare, B Roux, AR Dinner, ...
Journal of chemical theory and computation 9 (5), 2466-2480, 2013
1152013
Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly
JMA Grime, JF Dama, BK Ganser-Pornillos, CL Woodward, GJ Jensen, ...
Nature communications 7 (1), 1-11, 2016
732016
Dynamic force matching: A method for constructing dynamical coarse-grained models with realistic time dependence
A Davtyan, JF Dama, GA Voth, HC Andersen
The Journal of Chemical Physics 142 (15), 154104, 2015
632015
Fitting coarse-grained distribution functions through an iterative force-matching method
L Lu, JF Dama, GA Voth
The Journal of chemical physics 139 (12), 09B606_1, 2013
632013
On the representability problem and the physical meaning of coarse-grained models
JW Wagner, JF Dama, AEP Durumeric, GA Voth
The Journal of chemical physics 145 (4), 044108, 2016
582016
Transition-tempered metadynamics: robust, convergent metadynamics via on-the-fly transition barrier estimation
JF Dama, G Rotskoff, M Parrinello, GA Voth
Journal of chemical theory and computation 10 (9), 3626-3633, 2014
482014
The theory of ultra-coarse-graining. 2. Numerical implementation
A Davtyan, JF Dama, AV Sinitskiy, GA Voth
Journal of chemical theory and computation 10 (12), 5265-5275, 2014
372014
Designing free energy surfaces that match experimental data with metadynamics
AD White, JF Dama, GA Voth
Journal of Chemical Theory and Computation 11 (6), 2451-2460, 2015
352015
The theory of ultra-coarse-graining. 3. Coarse-grained sites with rapid local equilibrium of internal states
JF Dama, J Jin, GA Voth
Journal of chemical theory and computation 13 (3), 1010-1022, 2017
322017
Exploring valleys without climbing every peak: more efficient and forgiving metabasin metadynamics via robust On-the-Fly Bias domain restriction
JF Dama, GM Hocky, R Sun, GA Voth
Journal of chemical theory and computation 11 (12), 5638-5650, 2015
312015
Transition-tempered metadynamics is a promising tool for studying the permeation of drug-like molecules through membranes
R Sun, JF Dama, JS Tan, JP Rose, GA Voth
Journal of chemical theory and computation 12 (10), 5157-5169, 2016
272016
Solvent free ionic solution models from multiscale coarse-graining
Z Cao, JF Dama, L Lu, GA Voth
Journal of chemical theory and computation 9 (1), 172-178, 2013
252013
Simulating protein mediated hydrolysis of ATP and other nucleoside triphosphates by combining QM/MM molecular dynamics with advances in metadynamics
R Sun, O Sode, JF Dama, GA Voth
Journal of chemical theory and computation 13 (5), 2332-2341, 2017
212017
Minimizing memory as an objective for coarse-graining
N Guttenberg, JF Dama, MG Saunders, GA Voth, J Weare, AR Dinner
The Journal of chemical physics 138 (9), 094111, 2013
152013
A perturbative solution to metadynamics ordinary differential equation
P Tiwary, JF Dama, M Parrinello
The Journal of chemical physics 143 (23), 234112, 2015
142015
An asymptotic analysis of differential electrical mobility classifiers
AJ Downard, JF Dama, RC Flagan
Aerosol Science and Technology 45 (6), 727-739, 2011
142011
Predicting the sensitivity of multiscale coarse-grained models to their underlying fine-grained model parameters
JW Wagner, JF Dama, GA Voth
Journal of chemical theory and computation 11 (8), 3547-3560, 2015
122015
Mesoscopic coarse-grained representations of fluids rigorously derived from atomistic models
Y Han, JF Dama, GA Voth
The Journal of Chemical Physics 149 (4), 044104, 2018
112018
Designing Alkaline Exchange Membranes from Scratch
H Sarode, MA Vandiver, AM Maes, B Caire, JL Horan, Y Yan, Y Li, ...
ECS Transactions 41 (1), 1761, 2011
42011
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Articles 1–20