An Overview of Electrostatic Free Energy Computations for Solutions and Proteins

2014 ◽  
Vol 10 (7) ◽  
pp. 2690-2709 ◽  
Author(s):  
Yen-Lin Lin ◽  
Alexey Aleksandrov ◽  
Thomas Simonson ◽  
Benoît Roux
Keyword(s):  
Free Energy ◽  
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.

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

scholarly journals The redox potentials of the two-iron plant algal ferredoxins. An electrostatic model

1973 ◽  
Vol 133 (2) ◽  
pp. 283-287 ◽  
Author(s):  
R. J. Kassner ◽  
W. Yang
Keyword(s):  
Electron Transfer ◽  
Free Energy ◽  
Redox Potential ◽  
Negative Charge ◽  
Electrostatic Model ◽  
Redox Potentials ◽  
Electron Transfer Proteins ◽  
Electrostatic Free Energy ◽  
The One ◽  
Charged Ions

The two-iron–sulphur co-ordination centre in plant and algal ferredoxins is considered as a collection of charged ions whose net negative charge is twice that of the one-iron–sulphur protein rubredoxin. Calculation of the electrostatic free-energy changes for reduction of the two types of proteins indicates that the redox potential of the two-iron–sulphur proteins should be more negative than that of the one-iron–sulphur protein and that in biological systems the ferredoxins should function as one-electron transfer proteins.

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