Computing the electrostatic free-energy of complex molecules: The variational Coulomb field approximation

2003 ◽  
Vol 119 (6) ◽  
pp. 3516-3528 ◽  
Author(s):  
Daniel Borgis ◽  
Nicolas Lévy ◽  
Massimo Marchi
Keyword(s):  
Free Energy ◽  
Coulomb Field ◽  
Field Approximation ◽  
Complex Molecules ◽  
Electrostatic Free Energy

scholarly journals Evaluation of Hydration Free Energy by Level-Set Variational Implicit-Solvent Model with Coulomb-Field Approximation

2013 ◽  
Vol 9 (3) ◽  
pp. 1778-1787 ◽  
Author(s):  
Zuojun Guo ◽  
Bo Li ◽  
Joachim Dzubiella ◽  
Li-Tien Cheng ◽  
J. Andrew McCammon ◽  
...  
Keyword(s):  
Free Energy ◽  
Level Set ◽  
Coulomb Field ◽  
Field Approximation ◽  
Implicit Solvent ◽  
Hydration Free Energy ◽  
Implicit Solvent Model ◽  
Solvent Model

scholarly journals Yukawa-field approximation of electrostatic free energy and dielectric boundary force

Nonlinearity ◽  
2011 ◽  
Vol 24 (11) ◽  
pp. 3215-3236 ◽  
Author(s):  
Hsiao-Bing Cheng ◽  
Li-Tien Cheng ◽  
Bo Li
Keyword(s):  
Free Energy ◽  
Field Approximation ◽  
Boundary Force ◽  
Electrostatic Free Energy

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.

scholarly journals The Possibility of Many Compensation Points in a Mixed-Spin Ising Ferrimagnetic System

2013 ◽  
Vol 2013 ◽  
pp. 1-6
Author(s):  
Hadey K. Mohamad
Keyword(s):  
Free Energy ◽  
Mean Field ◽  
Field Approximation ◽  
Spin Model ◽  
Mean Field Approximation ◽  
Zero Field ◽  
Mixed Spin ◽  
Simple Cubic ◽  
Simple Cubic Lattice ◽  
The Mean

The magnetic properties of a ferrimagnetic mixed spin-3/2 and spin-5/2 Ising model with different anisotropies are investigated by using the mean-field approximation (MFA). In particular, the effect of magnetic anisotropies on the compensation phenomenon, acting on A-atoms and B-ones for the mixed-spin model, has been considered in a zero field. The free energy of a mixed-spin Ising ferrimagnetic system from MFA of the Hamiltonian is calculated. By minimizing the free energy, we obtain the equilibrium magnetizations and the compensation points. The phase diagram of the system in the anisotropy dependence of transition temperature has been discussed as well. Our results of this model predict the existence of many (two or three) compensation points in the ordered system on a simple cubic lattice.

An evaluation of poisson-boltzmann electrostatic free energy calculations through comparison with experimental mutagenesis data

Biopolymers ◽  
2011 ◽  
pp. n/a-n/a ◽  
Author(s):  
Ronald D. Gorham ◽  
Chris A. Kieslich ◽  
Aaron Nichols ◽  
Noriko U. Sausman ◽  
Marisse Foronda ◽  
...  
Keyword(s):  
Free Energy ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Poisson Boltzmann ◽  
Electrostatic Free Energy

Cylindrical Cell Model for the Electrostatic Free Energy of Polyelectrolyte Complexes

Langmuir ◽  
2004 ◽  
Vol 20 (11) ◽  
pp. 4764-4770 ◽  
Author(s):  
P. Maarten Biesheuvel ◽  
Martien A. Cohen Stuart
Keyword(s):  
Free Energy ◽  
Cell Model ◽  
Polyelectrolyte Complexes ◽  
Cylindrical Cell ◽  
Electrostatic Free Energy
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