scholarly journals A fast Monte Carlo algorithm for studying bottle-brush polymers

2011 ◽  
Vol 182 (10) ◽  
pp. 2115-2121 ◽  
Author(s):  
Hsiao-Ping Hsu ◽  
Wolfgang Paul
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Algorithm ◽  
Bottle Brush ◽  
Brush Polymers

Pulling Single Adsorbed Bottle-Brush Polymers off a Flat Surface: A Monte Carlo Simulation

2013 ◽  
Vol 47 (1) ◽  
pp. 427-437 ◽  
Author(s):  
Hsiao-Ping Hsu ◽  
Wolfgang Paul ◽  
Kurt Binder
Keyword(s):  
Monte Carlo Simulation ◽  
Monte Carlo ◽  
Flat Surface ◽  
Bottle Brush ◽  
Brush Polymers

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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