A dynamic Monte Carlo algorithm for exploration of dense conformational spaces in heteropolymers

1997 ◽  
Vol 106 (6) ◽  
pp. 2418-2425 ◽  
Author(s):  
R. Ramakrishnan ◽  
Bala Ramachandran ◽  
J. F. Pekny
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Algorithm ◽  
Dynamic Monte Carlo ◽  
Conformational Spaces

scholarly journals Dynamic Monte Carlo algorithm for out-of-equilibrium processes in colloidal dispersions

2018 ◽  
Vol 20 (22) ◽  
pp. 15118-15127 ◽  
Author(s):  
Daniel Corbett ◽  
Alejandro Cuetos ◽  
Matthew Dennison ◽  
Alessandro Patti
Keyword(s):  
Phase Transition ◽  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
Nematic Phase ◽  
Colloidal Dispersions ◽  
Monte Carlo Algorithm ◽  
Equilibrium Processes ◽  
Dynamic Monte Carlo ◽  
Colloidal Rods

Field-induced isotropic-to-nematic phase transition of colloidal rods studied with Dynamic Monte Carlo simulations.

Dynamic Monte Carlo Simulation of thel,l-Lactide Ring-Opening Polymerization

2016 ◽  
Vol 11 (1) ◽  
pp. 1600039 ◽  
Author(s):  
Dimitrios Meimaroglou ◽  
Prokopios Pladis ◽  
Costas Kiparissides
Keyword(s):  
Monte Carlo Simulation ◽  
Monte Carlo ◽  
Ring Opening ◽  
Ring Opening Polymerization ◽  
Dynamic Monte Carlo

Examining sharp restart in a Monte Carlo method for the linearized Poisson–Boltzmann equation

2020 ◽  
Vol 26 (3) ◽  
pp. 223-244
Author(s):  
W. John Thrasher ◽  
Michael Mascagni
Keyword(s):  
Monte Carlo ◽  
Free Energy ◽  
Monte Carlo Algorithm ◽  
Significant Bias ◽  
Poisson Boltzmann ◽  
Electrostatic Free Energy ◽  
Poisson Boltzmann Equation ◽  
The Stability ◽  
Potential Methods ◽  
The Individual

AbstractIt has been shown that when using a Monte Carlo algorithm to estimate the electrostatic free energy of a biomolecule in a solution, individual random walks can become entrapped in the geometry. We examine a proposed solution, using a sharp restart during the Walk-on-Subdomains step, in more detail. We show that the point at which this solution introduces significant bias is related to properties intrinsic to the molecule being examined. We also examine two potential methods of generating a sharp restart point and show that they both cause no significant bias in the examined molecules and increase the stability of the run times of the individual walks.

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