Boltzmann pb equation has emerged as one of the most widely used method for model ing biomolecular electrostatics. Fast methods for simulation of biomolecule electrostatics. Poissonboltzmann versus sizemodified poissonboltzmann. Part i chapters 1 and 2 begins in chapter 1 with the poisson boltzmann equation, which arises in the debyeh uckel theory of macromolecule electrostatics. Recently, we have described a boundary integral equationbased pb solver accelerated by a new version of the fast multipole method fmm. Schnieders, marcelo marucho, jiajing zhang, nathan a. Louis, mo, 63110 introduction to biomolecular electrostatics throughout the 1990s, biomolecular simulation has. Biomolecular electrostatics, poissonboltzmann equation, numerical methods, finite differencemethods, finite element methods, boundary element methods, adaptivemethods, hybrid methods, mesh generation, electrostatic forces 1 introduction poissonboltzmann pb theory has been a wellestablished model in a broad range of. The understanding of electrostatic properties is a basic aspect of the investigation of. Biomolecular electrostatics, poissonboltzmann equation, immersed. The poissonboltzmann theory of continuum electrostatics with. Numerical study of the poissonboltzmann equation for.
Review continuum molecular electrostatics, salt effects. In doing so, it is important to recognize that the electrostatic force on an atom in a system governed by the pbe is not simply the electrostatic field, e, at the atom multiplied by the atomic charge, q. Chapter 5 covers biomolecular applications of the poisson. Due to the ubiquitous nature of electrostatics in biomolecular systems, a variety of computational methods have been developed for calculating these interactions see refs 16 and references therein. Discontinuousbubbleimmersedfiniteelementmethod for.
It also uses nongraded, adaptive octree grids which, in comparison to uniform grids. Implicit solvent electrostatics in biomolecular simulation. Electrostatics plays a fundamental role in virtually all processes involving biomolecules in solution. Here, the pbe and the smpbe are reevaluated for realistic molecular systems, namely, lipid bilayers, under eight different. Biomolecular electrostatics, poissonboltzmann equation, numerical methods. Poissonboltzmann equation an overview sciencedirect topics. An adaptive fast multipole boundary element method for. Popular computational electrostatics methods for biomolecular systems can be loosely grouped into two categories. In this study, we have explored a secondorder finitedifference numerical method to solve the widely used poissonboltzmann equation for electrostatic.
The poisson boltzmann equation introduced by gouy 12 and chapman 7 describes the electrochemical potential of ions in the di use layer caused by a charged solid that comes into contact with an ionic solution, creating a layer of surface charges and counter. Due to the ubiquitous nature of electrostatics in biomolecular systems, a variety of computational methods have been developed for calculating these interactions see refs 1 6 and references therein. Baker department of biochemistry and molecular biophysics, center for computational biology, washington university in st. The poissonboltzmann equation plays a role in the development of the debyehckel theory of dilute electrolyte solutions. The emphasis is on numerical algorithms and approximations. Liu, march 2011 semianalytical treatment of solvation for molecular mechanics and dynamics, w.
The unknown function ux in the equation represents the electrostatic potential generated by a macromolecule lying in an ionic solvent. One example is the binding of electrolytes to biomolecules in a solution. Biomolecular applications of poissonboltzmann methods. Despite its nonlinearity the pb equation for the mean electrostatic potential can be solved. Apbs solves the equations of continuum electrostatics for large biomolecular assemblages. The ions distribute themselves in the solvent according to the electrostatic potential debyehuckel theory. This distribution is important to determine how the electrostatic. A regularized poissonboltzmann equation is introduced as an auxiliary problem, making it possible to study the original nonlinear equation with delta. A hybrid solver of size modified poissonboltzmann equation by. The poissonboltzmann equation is a useful equation in many settings, whether it be to understand physiological interfaces, polymer science, electron interactions in a semiconductor, or more. This distribution is important to determine how the electrostatic interactions. Biomolecules, boltzmann equation, computational physics, cuda, electrostatics, intel phi, nvidia, package, physics, poisson boltzmann, python, tesla c2075 september 17, 20 by hgpu validation of the pygbe code for poissonboltzmann equation with boundary element methods.
In an ideal situation, this is a sharp boundary located at z 0 which limits the ionic solution to the half space z0. Here, the pbe and the smpbe are reevaluated for realistic molecular systems, namely, lipid bilayers. Reliable computer simulation methods for electrostatic biomolecular models based on the poisson boltzmann equation authors. Adaptive poissonboltzmann solver apbs software for. The poissonboltzmann equation for biomolecular electrostatics. The poissonboltzmann equation can be applied to biomolecular systems. Continuum solvation models, such as poisson boltzmann and generalized born methods, have become increasingly popular tools for investigating the influence of electrostatics on biomolecular structure, energetics and dynamics. Continuum electrostatics modeling of solvation based on the poissonboltzmann pb equation has gained wide acceptance in biomolecular applications. Biomolecular electrostatics, poisson boltzmann equation, numerical methods, finite differencemethods, finite element methods, boundary element methods, adaptivemethods, hybrid methods, mesh generation, electrostatic forces 1 introduction poisson boltzmann pb theory has been a wellestablished model in a broad range of. Some examples i existence, uniqueness, and uniform bound i freeenergy functional. The numerical solution of the poisson boltzmann pb equation is a useful but a computationally demanding tool for studying electrostatic solvation effects in chemical and biomolecular systems. Poissonboltzmann methods for biomolecular electrostatics. The poissonboltzmann theory of continuum electrostatics.
Pdf biological applications of classical electrostatics methods. The poissonboltzmann equation constitutes one of the most. In this study, we have explored a secondorder finitedifference numerical method to solve the widely used poissonboltzmann equation for electrostatic analyses of realistic biomolecules. Keywords boundary element method, biomolecular electrostatics, poissonboltzmann equation. Continuum solvation models, such as poissonboltzmann and generalized born methods, have become increasingly popular tools for investigating the influence of electrostatics on biomolecular structure, energetics and dynamics. Computational and theoretical chemistry 1024, 3444. Exploring higher accuracy poissonboltzmann methods for. Louis, mo, 63110 introduction to biomolecular electrostatics throughout the 1990s, biomolecular simulation has become. Apbs is a software package for modeling biomolecular solvation through solution of the poissonboltzmann equation pbe, one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Fast methods for simulation of biomolecule electrostatics michael d. The discrepancies between the solutions of the pbe and those of the lpbe are well known for systems with a simple geometry, but much less. The solver uses a level set framework to represent sharp, complex interfaces in a simple and robust manner. Pb9,61,67,70,71,88,89,91,101,110112 by including ionion correlations, finite ionic size and molecular structure of. Exploring accurate poissonboltzmann methods for biomolecular.
Models for biomolecular solvation and electrostatics a. Discontinuousbubbleimmersedfiniteelementmethod for poisson. This chapter presents poissonboltzmann pb methods for biomolecular electrostatics. Electrostatics in biomolecular structure and dynamics, chem. Reliable computer simulation methods for electrostatic. Johannes kraus, svetoslav nakov, sergey repin submitted on 29 may 2018. Computation of electrostatic forces on solvated molecules. The poissonboltzmann equation constitutes one of the most fundamental approaches to treat electrostatic effects in solution. The poisson boltzmann equation constitutes one of the most fundamental approaches to treat electrostatic effects in solution. The poissonboltzmann equation is widely used to treat this electrostatic effect in an ionic solution. Accurate estimation of electrostatic binding energy with. Fast boundary element method for the linear poisson. Biomolecular electrostatics with the linearized poisson.
Jul 01, 2004 continuum solvation models, such as poissonboltzmann and generalized born methods, have become increasingly popular tools for investigating the influence of electrostatics on biomolecular structure, energetics and dynamics. Ion models quantum explicit polarizable fixed charge integral equation rism 3d methods dft fieldtheoretic extended models poissonboltzmann phenomenological generalized born, et. Recentprogress in numericalmethods forthepoisson boltzmann. Jan 27, 2005 chapter 5 covers biomolecular applications of the poisson. Recentprogressinnumericalmethodsforthepoisson boltzmann. Meanfield methods provide a way to coarse grain the electrostatic interactions between the solvent and the biomolecules of interest.
Development of fast computational methods to solve the poissonboltzmann equation pbe for. Here we present the application of numerical methods to enable the trivially parallel solution of the poissonboltzmann equation for. In the past two decades, an enhancement of the pbe, the sizemodified poissonboltzmann equation smpbe, has been reported. Computational methods for biomolecular electrostatics. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including. Abstract electrostatics plays a fundamental role in virtually all processes involving biomolecules in solution. Pdf efficient solution of poissonboltzmann equation for. The poisson boltzmann theory of continuum electrostatics with application to variational solvation of molecules bo li department of mathematics and center for theoretical biological physics uc san diego february 3, 2009. Siam journal on numerical analysis society for industrial. The numerical solution of the poissonboltzmann pb equation is a useful but a computationally demanding tool for studying electrostatic solvation effects in chemical and biomolecular systems. We present a solver for the poisson boltzmann equation and demonstrate its applicability for biomolecular electrostatics computation.
Siam journal on numerical analysis siam society for. Summary chapter 5 covers biomolecular applications of the poisson. Continuum electrostatics modeling of solvation based on the poissonboltzmann pb equation has gained wide acceptance in biomolecular applications such as energetic analysis and structural. The poissonboltzmann theory of continuum electrostatics with application to variational solvation of molecules bo li department of mathematics and center for theoretical biological physics uc san diego february 3, 2009. Poissonboltzmann equation, finite element method, finite difference. The development of reliable and fast methods for computing electrostatic free energies has attracted great attention in the past several decades.
The discrepancies between the solutions of the pbe and those of the lpbe are well known for systems with a simple geometry, but much less for. However, the use of such methods requires accurate and complete structural data as well as force field parameters such as atomic. Biological applications of classical electrostatics methods. In particular, the linear poissonboltzmann approach considered here has been successfully used to account for the salt dependence of a variety of thermodynamic quantities such as binding free energies,4 pk shifts,57 and biomolecular association rate constants. Nov 01, 2002 electrostatics plays a fundamental role in virtually all processes involving biomolecules in solution. This chapter presents poisson boltzmann pb methods for biomolecular electrostatics. Part i chapters 1 and 2 begins in chapter 1 with the poissonboltzmann equation, which arises in the debyeh uckel theory of macromolecule electrostatics. Structures of proteins and other biopolymers are being determined at an increasing rate through structural genomics and other effort. We give an overview of how implicit solvent models are currently used in protein simulations. However, the use of such methods requires accurate and complete structural data as well as force field parameters such as atomic charges and radii. Poissonboltzmann methods for biomolecular electrostatics as mentioned above, the poissonboltzmann equation is derived from a continuum model of the solvent and counterion environment surrounding a biomolecule. Recent progress in numerical methods for the poissonboltzmann equation in biophysical applications.
Jul 01, 2004 due to the ubiquitous nature of electrostatics in biomolecular systems, a variety of computational methods have been developed for calculating these interactions see refs 1 6 and references therein. Abstract electrostatics plays a key role in many biological processes. We present a solver for the poissonboltzmann equation and demonstrate its applicability for biomolecular electrostatics computation. Hendrickson, journal of the american chemical society, 112, 61276129 1990 computational methods for biomolecular electrostatics, f. The poissonboltzmann equation pbe and its linearized form lpbe allow prediction of electrostatic effects for biomolecular systems. It aims to describe the distribution of the electric potential in solution in the direction normal to a charged surface.
We shall derive a poissonboltzmann equation in the application of biomolecular modeling. If the charge density follows a boltzmann distribution, then the poissonboltzmann equation results. Request permission export citation add to favorites. For a biological system, it includes the charges of the solute biomolecules, and the charges of free ions in the solvent. Electrostatics plays important roles in biomolecular interactions, such as between proteins, ligands, and nucleic acids. The understanding of electrostatic properties is a basic aspect of the investigation of biomolecular processes. A widely used electrostatics model in the biomolecular modeling community, the nonlinear poissonboltzmann equation, along with its finite element approximation, are analyzed in this paper. Reliable computer simulation methods for electrostatic biomolecular models based on the poissonboltzmann. The algorithm can be summarized in four steps where. Accurate and efficient treatment of electrostatics is a crucial step in computational analyses of biomolecular structures and dynamics. This software was designed from the ground up using modern design principles to ensure its ability to interface with other computational packages and evolve as methods and applications change over time. Biomolecular applications of poissonboltzmann methods baker. Review continuum molecular electrostatics, salt effects, and. A treecodeaccelerated boundary integral poissonboltzmann solver for electrostatics of solvated biomolecules weihua genga, robert krasnyb, adepartment of mathematics, university of alabama, tuscaloosa, al 35487 usa bdepartment of mathematics, university of michigan, ann arbor, mi 48109 usa abstract we present a treecodeaccelerated boundary integral tabi.
Poissonboltzmann equation an overview sciencedirect. An introduction to biomolecular electrostatics is first given, where the factors influencing long. Understanding biomolecular solvation and electrostatics developing better methods for simulation and modeling. Numerical methods for the poisson boltzmann equation numerical methods for the problem described above fall into two classes, 1 gridbased methods that discretize the entire domain, e. Itisknownas gouychapman theoryinelectrochemistry3,12, as debyehuckeltheory. In this study, we have explored a secondorder finitedifference numerical method to solve the widely used poisson boltzmann equation for electrostatic analyses of realistic biomolecules. Models for biomolecular solvation and electrostatics. A tool for structural biology, j mol recognit 15 6. In this work, a simple mixed discretecontinuum model is considered and boundary element method is used to solve for the solution.
In an ideal situation, this is a sharp boundary located. Li c, li l, petukh m, alexov e, progress in developing poissonboltzmann equation solvers, mol based math biol 1. Siam journal on scientific computing society for industrial. The poissonboltzmann equation i background i the pb equation. The methods that have been used to simulate electrostatics in biological systems may be broadly classified into those which simulate explicitly all molecules of the.
Meanfield methods, such as the poissonboltzmann equation pbe, are often used to calculate the electrostatic properties of molecular systems. The poisson boltzmann equation pbe and its linearized form lpbe allow prediction of electrostatic effects for biomolecular systems. The discrepancies between the solutions of the pbe and those of the lpbe are well known for systems with a simple geometry, but much less for biomolecular systems. This process is dependent upon the electrostatic field generated by the molecule, the electrostatic potential on the surface of the molecule, as well as the electrostatic free energy. Biomolecular electrostatics with the linearized poissonboltzmann.
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