Polyelectrolyte theory. 4. Algebraic approximation for the Poisson-Boltzmann free energy of a cylinder

1992 ◽  
Vol 96 (19) ◽  
pp. 7816-7820 ◽  
Author(s):  
M. Gueron ◽  
J. P. Demaret
Keyword(s):  
Free Energy ◽  
Algebraic Approximation ◽  
Poisson Boltzmann ◽  
Polyelectrolyte Theory

scholarly journals Debye-Hückel Free Energy of an Electric Double Layer with Discrete Charges Located at a Dielectric Interface

Membranes ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 129
Author(s):  
Guilherme Volpe Bossa ◽  
Sylvio May
Keyword(s):  
Free Energy ◽  
Double Layer ◽  
Electric Double Layer ◽  
Low Dielectric Constant ◽  
Surface Charges ◽  
Dielectric Interface ◽  
Charge Densities ◽  
Low Dielectric ◽  
Poisson Boltzmann ◽  
The Continuum

Poisson–Boltzmann theory provides an established framework to calculate properties and free energies of an electric double layer, especially for simple geometries and interfaces that carry continuous charge densities. At sufficiently small length scales, however, the discreteness of the surface charges cannot be neglected. We consider a planar dielectric interface that separates a salt-containing aqueous phase from a medium of low dielectric constant and carries discrete surface charges of fixed density. Within the linear Debye-Hückel limit of Poisson–Boltzmann theory, we calculate the surface potential inside a Wigner–Seitz cell that is produced by all surface charges outside the cell using a Fourier-Bessel series and a Hankel transformation. From the surface potential, we obtain the Debye-Hückel free energy of the electric double layer, which we compare with the corresponding expression in the continuum limit. Differences arise for sufficiently small charge densities, where we show that the dominating interaction is dipolar, arising from the dipoles formed by the surface charges and associated counterions. This interaction propagates through the medium of a low dielectric constant and alters the continuum power of two dependence of the free energy on the surface charge density to a power of 2.5 law.

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 Binding Affinities of Sanggenon Derivatives as PTP1B Inhibitors; Using Molecular Dynamics and Free Energy Calculations

2021 ◽  
Author(s):  
Safak OZHAN KOCAKAYA
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Tyrosine Phosphatase ◽  
Decomposition Analysis ◽  
Md Simulations ◽  
Free Energy Calculations ◽  
Energy Decomposition Analysis ◽  
Free Energy Decomposition ◽  
Poisson Boltzmann ◽  
Ptp1b Inhibitors

Abstract Recently, protein tyrosine phosphatase 1B (PTP1B) inhibitors have become the frontier as possible targeting for anti-cancer and antidiabetic drugs. The contemporary observe represents a pc assisted version to investigate the importance of precise residues within the binding web site of PTP1B with numerous Sanggenon derivatives remoted from nature. Molecular dynamics (MD) simulations were performed to estimate the dynamics of the complexes, and absolute binding unfastened energies have been calculated with exclusive additives, and carried out through the usage of the Molecular Mechanics-Poisson-Boltzmann floor region (MM-PB/SA) and Generalized Born surface vicinity (MM-GB/SA) strategies. The effects show that the expected free energies of the complexes are normally constant with the available experimental statistics. MM/GBSA free energy decomposition analysis shows that the residues Asp29, Arg24, Met258, and , Arg254 in the second active site in PTP1B are crucial for the excessive selectivity of the inhibitors.

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
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