James F. Dama

Chicago Institute for Psychoanalysis — United States

Biochemistry, Genetics and Molecular Biology · Life Sciences

17h-index1.6kcitations27works0.02yr avg
OpenAlex↗ORCID↗Google Scholar↗Lab page↗

Accepting Students?

No reports yet. Know if this professor is taking students?

Research Topics

Protein Structure and Dynamics(10), Theoretical and Computational Physics(8), Spectroscopy and Quantum Chemical Studies(5), Fuel Cells and Related Materials(4), Material Dynamics and Properties(4)

Publications27 total

Mesoscopic coarse-grained representations of fluids rigorously derived from atomistic models
The Journal of Chemical Physics·2018· 29 cited
Correction to The Theory of Ultra-Coarse-Graining. 3. Coarse-Grained Sites with Rapid Local Equilibrium of Internal States
Journal of Chemical Theory and Computation·2018· 8 cited
Simulating Protein Mediated Hydrolysis of ATP and Other Nucleoside Triphosphates by Combining QM/MM Molecular Dynamics with Advances in Metadynamics
Journal of Chemical Theory and Computation·2017· 51 citedOpen Access
The Theory of Ultra-Coarse-Graining. 3. Coarse-Grained Sites with Rapid Local Equilibrium of Internal States
Journal of Chemical Theory and Computation·2017· 64 cited
CONTRIBUTIONS TOWARDS THE THEORY OF THE BOTTOM-UP COARSE-GRAINING OF COMPLEX MOLECULES
Knowledge@UChicago (University of Chicago)·2017· 2 citedOpen Access
Transition-Tempered Metadynamics Is a Promising Tool for Studying the Permeation of Drug-like Molecules through Membranes
Journal of Chemical Theory and Computation·2016· 70 cited
On the representability problem and the physical meaning of coarse-grained models
The Journal of Chemical Physics·2016· 130 cited
Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly
Nature Communications·2016· 157 citedOpen Access
“Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly”
2016· 10 citedOpen Access
A perturbative solution to metadynamics ordinary differential equation
The Journal of Chemical Physics·2015· 17 citedOpen Access
Fast-Randomized-Iteration-FRI-: improved code
Zenodo (CERN European Organization for Nuclear Research)·2015Open Access
Exploring Valleys without Climbing Every Peak: More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction
Journal of Chemical Theory and Computation·2015· 40 citedOpen Access
Predicting the Sensitivity of Multiscale Coarse-Grained Models to their Underlying Fine-Grained Model Parameters
Journal of Chemical Theory and Computation·2015· 12 cited
Designing Free Energy Surfaces That Match Experimental Data with Metadynamics
Journal of Chemical Theory and Computation·2015· 64 citedOpen Access
Ticketed-DMC: Public Educational Implementation of TDMC
Zenodo (CERN European Organization for Nuclear Research)·2015Open Access
Dynamic force matching: A method for constructing dynamical coarse-grained models with realistic time dependence
The Journal of Chemical Physics·2015· 106 cited
The Theory of Ultra-Coarse-Graining. 2. Numerical Implementation
Journal of Chemical Theory and Computation·2014· 73 cited
Transition-Tempered Metadynamics: Robust, Convergent Metadynamics via On-the-Fly Transition Barrier Estimation
Journal of Chemical Theory and Computation·2014· 90 cited
Well-Tempered Metadynamics Converges Asymptotically
Physical Review Letters·2014· 352 cited
Fitting coarse-grained distribution functions through an iterative force-matching method
The Journal of Chemical Physics·2013· 95 cited
page 1 of 2Next →

Frequent Co-authors

Gregory A. Voth(22), Michele Parrinello(3), Jonathan Weare(3), Rui Sun(3), Ryan Jorn(3), Anton V. Sinitskiy(2), Aaron R. Dinner(2), John M. A. Grime(2), Barbie K. Ganser‐Pornillos(2), Cora L. Woodward(2), Grant J. Jensen(2), Mark Yeager(2), Jacob W. Wagner(2), Aram Davtyan(2), Lanyuan Lu(2), Jaehyeok Jin(2), Gerrick E. Lindberg(2), Chris Knight(2), Martin McCullagh(1), Benoı̂t Roux(1)