159 citations · 445 across the 7 of their papers we have counts for
7 papers
Self-learning Multiscale Simulation for Achieving High Accuracy and High Efficiency Simultaneously
Wenfei Li, Shoji Takada
We propose a new multi-scale molecular dynamics simulation method which can achieve high accuracy and high sampling efficiency simultaneously without aforehand knowledge of the coa…
Microscopic Theory of Protein Folding Rates.II: Local Reaction Coordinates and Chain Dynamics
John J. Portman, Shoji Takada, Peter G. Wolynes
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of prote…
Microscopic Theory of Protein Folding Rates.I: Fine Structure of the Free Energy Profile and Folding Routes from a Variational Approach
John J. Portman, Shoji Takada, Peter G. Wolynes
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approac…
Variational theory for site resolved protein folding free energy surfaces
John J. Portman, Shoji Takada, Peter G. Wolynes
We present a microscopic variational theory for the free energy surface of a fast folding protein that allows folding kinetics to be resolved to the residue level using Debye-Walle…
Entropic droplets and activated events near the glass transition of a random heteropolymer
Shoji Takada, Peter G. Wolynes
The barriers between metastable states near the glass transition of a random heteropolymer are studied using replicas by describing inhomogeneous states. The instanton solution for…
Statics, metastable states and barriers in protein folding: A replica variational approach
Shoji Takada, Peter G. Wolynes
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction mode…