PypKa: A Flexible Python Module for Poisson–Boltzmann-Based pKa Calculations

2020 ◽  
Vol 60 (10) ◽  
pp. 4442-4448
Author(s):  
Pedro B. P. S. Reis ◽  
Diogo Vila-Viçosa ◽  
Walter Rocchia ◽  
Miguel Machuqueiro
Keyword(s):  
Pka Calculations ◽  
Poisson Boltzmann

scholarly journals PypKa: a python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism

2018 ◽  
Author(s):  
Miguel Machuqueiro ◽  
Pedro Reis ◽  
Diogo Vila-Viçosa ◽  
Walter Rocchia
Keyword(s):  
Pka Calculations ◽  
Poisson Boltzmann

scholarly journals pKa Calculations with the Polarizable Drude Force Field and Poisson–Boltzmann Solvation Model

2020 ◽  
Vol 16 (7) ◽  
pp. 4655-4668 ◽  
Author(s):  
Alexey Aleksandrov ◽  
Benoît Roux ◽  
Alexander D. MacKerell
Keyword(s):  
Force Field ◽  
Solvation Model ◽  
Pka Calculations ◽  
Poisson Boltzmann

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 The crystallization enthalpy and entropy of protein solutions: microcalorimetry, van't Hoff determination and linearized Poisson–Boltzmann model of tetragonal lysozyme crystals

2021 ◽  
Vol 23 (4) ◽  
pp. 2686-2696
Author(s):  
Lorena Hentschel ◽  
Jan Hansen ◽  
Stefan U. Egelhaaf ◽  
Florian Platten
Keyword(s):  
Theoretical Description ◽  
Protein Solutions ◽  
Consistent Picture ◽  
Poisson Boltzmann ◽  
Enthalpy And Entropy ◽  
Boltzmann Model ◽  
Lysozyme Crystals ◽  
Solution Parameters

Microcalorimetric and van't Hoff determinations as well as a theoretical description provide a consistent picture of the crystallization enthalpy and entropy of protein solutions and their dependence on physicochemical solution parameters.

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