Displaying similar documents to “SDPBS Web Server for Calculation of Electrostatics of Ionic Solvated Biomolecules”

Poisson-Fermi Formulation of Nonlocal Electrostatics in Electrolyte Solutions

Jinn-Liang Liu, Dexuan Xie, Bob Eisenberg (2017)

Molecular Based Mathematical Biology

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We present a nonlocal electrostatic formulation of nonuniform ions and water molecules with interstitial voids that uses a Fermi-like distribution to account for steric and correlation efects in electrolyte solutions. The formulation is based on the volume exclusion of hard spheres leading to a steric potential and Maxwell’s displacement field with Yukawa-type interactions resulting in a nonlocal electric potential. The classical Poisson-Boltzmann model fails to describe steric and correlation...

A boundary integral Poisson-Boltzmann solvers package for solvated bimolecular simulations

Weihua Geng (2015)

Molecular Based Mathematical Biology

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Numerically solving the Poisson-Boltzmann equation is a challenging task due to the existence of the dielectric interface, singular partial charges representing the biomolecule, discontinuity of the electrostatic field, infinite simulation domains, etc. Boundary integral formulation of the Poisson-Boltzmann equation can circumvent these numerical challenges and meanwhile conveniently use the fast numerical algorithms and the latest high performance computers to achieve combined improvement...

Stationary solutions of the generalized Smoluchowski-Poisson equation

Robert Stańczy (2008)

Banach Center Publications

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The existence of steady states in the microcanonical case for a system describing the interaction of gravitationally attracting particles with a self-similar pressure term is proved. The system generalizes the Smoluchowski-Poisson equation. The presented theory covers the case of the model with diffusion that obeys the Fermi-Dirac statistic.

Quantization of pencils with a gl-type Poisson center and braided geometry

Dimitri Gurevich, Pavel Saponov (2011)

Banach Center Publications

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We consider Poisson pencils, each generated by a linear Poisson-Lie bracket and a quadratic Poisson bracket corresponding to a so-called Reflection Equation Algebra. We show that any bracket from such a Poisson pencil (and consequently, the whole pencil) can be restricted to any generic leaf of the Poisson-Lie bracket. We realize a quantization of these Poisson pencils (restricted or not) in the framework of braided affine geometry. Also, we introduce super-analogs of all these Poisson...

Computation of Biharmonic Poisson Kernel for the Upper Half Plane

Ali Abkar (2007)

Bollettino dell'Unione Matematica Italiana

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We first consider the biharmonic Poisson kernel for the unit disk, and study the boundary behavior of potentials associated to this kernel function. We shall then use some properties of the biharmonic Poisson kernel for the unit disk to compute the analogous biharmonic Poisson kernel for the upper half plane.

A continuous-time model for claims reserving

T. Rolski, A. Tomanek (2014)

Applicationes Mathematicae

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Prediction of outstanding liabilities is an important problem in non-life insurance. In the framework of the Solvency II Project, the best estimate must be derived by well defined probabilistic models properly calibrated on the relevant claims experience. A general model along these lines was proposed earlier by Norberg (1993, 1999), who suggested modelling claim arrivals and payment streams as a marked point process. In this paper we specify that claims occur in [0,1] according to a...

Modification of Bikerman model with specific ion sizes

Tzyy-Leng Horng, Ping-Hsuan Tsai, Tai-Chia Lin (2017)

Molecular Based Mathematical Biology

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Classical Poisson-Boltzman and Poisson-Nernst-Planck models can only work when ion concentrations are very dilute, which often mismatches experiments. Researchers have been working on the modification to include finite-size effect of ions, which is non-negelible when ion concentrations are not dilute. One of modified models with steric effect is Bikerman model, which is rather popular nowadays. It is based on the consideration of ion size by putting additional entropy term for solvent...

Probabilistic Interpretation for the Nonlinear Poisson-Boltzmann Equation in Molecular Dynamics

Nicolas Perrin (2012)

ESAIM: Proceedings

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The Poisson-Boltzmann (PB) equation describes the electrostatic potential of a biomolecular system composed by a molecule in a solvent. The electrostatic potential is involved in biomolecular models which are used in molecular simulation. In consequence, finding an efficient method to simulate the numerical solution of PB equation is very useful. As a first step, we establish in this paper a probabilistic interpretation of the nonlinear PB equation with Backward Stochastic Differential...