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Poisson Boltzmann Methods
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Book Synopsis Poisson-Boltzmann Methods by : Qin Cai
Download or read book Poisson-Boltzmann Methods written by Qin Cai and published by . This book was released on 2013 with total page 227 pages. Available in PDF, EPUB and Kindle. Book excerpt: Implicit solvent models based on the Poisson-Boltzmann theory have enjoyed numerous successes in a variety of biological applications where electrostatic interactions are crucial, especially in efficient modeling of solvation and protein-ligand binding free energies. The protein-ligand binding free energy can be used to assess the binding affinity of organic small molecules with a protein during the virtual screening stage of the computer-aided drug design. The reliability of the prediction depends heavily on the accuracy in the modeling of protein-ligand interactions. To improve the accuracy of the Poisson-Boltzmann implicit solvent model, I have developed a number of numerical strategies, including singularity removal, nonlinear solvers of the Poisson-Boltzmann equation, molecular surface refinement, grid dependence reduction, molecular surface integration, and charge-view energy and force computation. In addition, these numerical methods can lead to stable molecular dynamics simulations in the Poisson-Boltzmann implicit solvent framework, which is also beneficial for the virtual screening because implicit solvent molecular dynamics have the potential to sample the configurations of proteins more efficiently, thus expediting the binding free energy calculation. Furthermore, I explore to extend the classical Poisson-Boltzmann model by explicitly tracking the molecule-water interface based on the solution of the Navier-Stokes equation.
Book Synopsis Exploring Higher Accuracy Poisson-Boltzmann Methods for Biomolecular Simulations by : Changhao Wang
Download or read book Exploring Higher Accuracy Poisson-Boltzmann Methods for Biomolecular Simulations written by Changhao Wang and published by . This book was released on 2016 with total page 50 pages. Available in PDF, EPUB and Kindle. Book excerpt: Accurate and efficient treatment of electrostatics is a crucial step in computational analyses of biomolecular structures and dynamics. In this study, we have explored a second-order finite-difference numerical method to solve the widely used Poisson-Boltzmann equation for electrostatic analyses of realistic biomolecules. The so-called immersed interface method was first validated and found to be consistent with the classical weighted harmonic averaging method for a diversified set of test biomolecules. The numerical accuracy and convergence behaviors of the new method were next analyzed in its computation of numerical reaction field grid potentials, energies, and atomic solvation forces. Overall similar convergence behaviors were observed as those by the classical method. Interestingly, the new method was found to deliver more accurate and better-converged grid potentials than the classical method on or nearby the molecular surface, though the numerical advantage of the new method is reduced when grid potentials are extrapolated to the molecular surface. Our exploratory study indicates the need for further improving interpolation/extrapolation schemes in addition to the developments of higher-order numerical methods that have attracted most attention in the field.
Book Synopsis Multilevel Methods for the Poisson-Boltzmann Equation by : Michael Jay Holst
Download or read book Multilevel Methods for the Poisson-Boltzmann Equation written by Michael Jay Holst and published by . This book was released on 1993 with total page 564 pages. Available in PDF, EPUB and Kindle. Book excerpt: Multilevel convergence theory is discussed, and we adapt and apply some recent results to the Galerkin-based methods. Numerical results arepresented for several test problems, including a nonlinear PBE calculation of the electrostatic potential of Superoxide Dismutase, an enzymewhich has recently been linked to Lou Gehrig's disease. We present a collection of performance statistics and benchmarks for the linear andnonlinear methods on a number of sequential and parallel computers, and discuss the software developed in the course of the research."
Book Synopsis The Poisson-Boltzmann Equation by : Ralf Blossey
Download or read book The Poisson-Boltzmann Equation written by Ralf Blossey and published by Springer Nature. This book was released on 2023-02-23 with total page 113 pages. Available in PDF, EPUB and Kindle. Book excerpt: This brief book introduces the Poisson-Boltzmann equation in three chapters that build upon one another, offering a systematic entry to advanced students and researchers. Chapter one formulates the equation and develops the linearized version of Debye-Hückel theory as well as exact solutions to the nonlinear equation in simple geometries and generalizations to higher-order equations. Chapter two introduces the statistical physics approach to the Poisson-Boltzmann equation. It allows the treatment of fluctuation effects, treated in the loop expansion, and in a variational approach. First applications are treated in detail: the problem of the surface tension under the addition of salt, a classic problem discussed by Onsager and Samaras in the 1930s, which is developed in modern terms within the loop expansion, and the adsorption of a charged polymer on a like-charged surface within the variational approach. Chapter three finally discusses the extension of Poisson-Boltzmann theory to explicit solvent. This is done in two ways: on the phenomenological level of nonlocal electrostatics and with a statistical physics model that treats the solvent molecules as molecular dipoles. This model is then treated in the mean-field approximation and with the variational method introduced in Chapter two, rounding up the development of the mathematical approaches of Poisson-Boltzmann theory. After studying this book, a graduate student will be able to access the research literature on the Poisson-Boltzmann equation with a solid background.
Book Synopsis Solving the Poisson-Boltzmann Equation Using Nonlinear Multigrid Methods by : Ilia Antsiferov
Download or read book Solving the Poisson-Boltzmann Equation Using Nonlinear Multigrid Methods written by Ilia Antsiferov and published by . This book was released on 2006 with total page 63 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Solving the Nonlinear Poisson-Boltzmann Equation Using Multigrid Methods by : Ilia Antsiferov
Download or read book Solving the Nonlinear Poisson-Boltzmann Equation Using Multigrid Methods written by Ilia Antsiferov and published by . This book was released on 2006 with total page 126 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Adaptive Pseudo-time Methods for the Poisson-Boltzmann Equation with Eulerian Solvent Excluded Surface by : Benjamin Daniel Jones
Download or read book Adaptive Pseudo-time Methods for the Poisson-Boltzmann Equation with Eulerian Solvent Excluded Surface written by Benjamin Daniel Jones and published by . This book was released on 2021 with total page 58 pages. Available in PDF, EPUB and Kindle. Book excerpt: This work further improves the pseudo-transient approach for the Poisson Boltzmann equation (PBE) in the electrostatic analysis of solvated biomolecules. The numerical solution of the nonlinear PBE is known to involve many difficulties, such as exponential nonlinear term, strong singularity by the source terms, and complex dielectric interface. Recently, a pseudo-time ghost-fluid method (GFM) has been developed in [S. Ahmed Ullah and S. Zhao, Applied Mathematics and Computation, 380, 125267, (2020)], by analytically handling both nonlinearity and singular sources. The GFM interface treatment not only captures the discontinuity in the regularized potential and its flux across the molecular surface, but also guarantees the stability and efficiency of the time integration. However, the molecular surface definition based on the MSMS package is known to induce instability in some cases, and a nontrivial Lagrangian-to-Eulerian conversion is indispensable for the GFM finite difference discretization. In this paper, an Eulerian Solvent Excluded Surface (ESES) is implemented to replace the MSMS for defining the dielectric interface. The electrostatic analysis shows that the ESES free energy is more accurate than that of the MSMS, while being free of instability issues. Moreover, this work explores, for the first time in the PBE literature, adaptive time integration techniques for the pseudo-transient simulations. A major finding is that the time increment Delta t should become smaller as the time increases, in order to maintain the temporal accuracy. This is opposite to the common practice for the steady state convergence, and is believed to be due to the PBE nonlinearity and its time splitting treatment. Effective adaptive schemes have been constructed so that the pseudo-time GFM methods become more efficient than the constant Delta t ones.
Book Synopsis Interface Method and Green's Function Based Poisson Boltzmann Equation Solver and Interface Technique Based Molecular Dynamics by : Weihua Geng
Download or read book Interface Method and Green's Function Based Poisson Boltzmann Equation Solver and Interface Technique Based Molecular Dynamics written by Weihua Geng and published by . This book was released on 2008 with total page 292 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Regularization Methods on Solving Poisson's Equation and Poisson Boltzmann Equation with Singular Charge Sources and Diffuse Interfaces by : Siwen Wang
Download or read book Regularization Methods on Solving Poisson's Equation and Poisson Boltzmann Equation with Singular Charge Sources and Diffuse Interfaces written by Siwen Wang and published by . This book was released on 2021 with total page 100 pages. Available in PDF, EPUB and Kindle. Book excerpt: Numerical treatment of singular charges is a grand challenge in solving Poisson-Boltzmann (PB) equation for analyzing electrostatic interactions between the solute biomolecules and the surrounding solvent with ions. For diffuse interface models in which solute and solvent are separated by a smooth boundary, no effective algorithm for singular charges has been developed, because the fundamental solution with a space dependent dielectric function is intractable. In this research work, regularization formulations are introduced to capture the singularity analytically, which are the first of their kind for diffuse interface Poisson's equation and PB models. The success lies in a dual decomposition -- besides decomposing the potential into Coulomb and reaction field components, the dielectric function is also split into a constant base plus space changing part. Using the constant dielectric base, the Coulomb potential is represented analytically via Green's functions. After removing the singularity, the reaction field potential satisfies a regularized PB equation with a smooth source. Some diffuse interface models including a Gaussian convolution surface (GCS) are also introduced. The GCS efficiently generates a diffuse interface for three-dimensional realistic biomolecules. The performance of the proposed regularization is examined by considering both analytical and GCS diffuse interfaces, and compared with the trilinear method. Moreover, the proposed GCS-regularization algorithm is validated by calculating electrostatic free energies for a set of proteins and by estimating salt affinities for seven protein complexes. The results are consistent with experimental data and estimates of sharp interface PB models.
Book Synopsis The Lattice Boltzmann Equation: For Complex States of Flowing Matter by : Sauro Succi
Download or read book The Lattice Boltzmann Equation: For Complex States of Flowing Matter written by Sauro Succi and published by Oxford University Press. This book was released on 2018-04-13 with total page 784 pages. Available in PDF, EPUB and Kindle. Book excerpt: Flowing matter is all around us, from daily-life vital processes (breathing, blood circulation), to industrial, environmental, biological, and medical sciences. Complex states of flowing matter are equally present in fundamental physical processes, far remote from our direct senses, such as quantum-relativistic matter under ultra-high temperature conditions (quark-gluon plasmas). Capturing the complexities of such states of matter stands as one of the most prominent challenges of modern science, with multiple ramifications to physics, biology, mathematics, and computer science. As a result, mathematical and computational techniques capable of providing a quantitative account of the way that such complex states of flowing matter behave in space and time are becoming increasingly important. This book provides a unique description of a major technique, the Lattice Boltzmann method to accomplish this task. The Lattice Boltzmann method has gained a prominent role as an efficient computational tool for the numerical simulation of a wide variety of complex states of flowing matter across a broad range of scales; from fully-developed turbulence, to multiphase micro-flows, all the way down to nano-biofluidics and lately, even quantum-relativistic sub-nuclear fluids. After providing a self-contained introduction to the kinetic theory of fluids and a thorough account of its transcription to the lattice framework, this text provides a survey of the major developments which have led to the impressive growth of the Lattice Boltzmann across most walks of fluid dynamics and its interfaces with allied disciplines. Included are recent developments of Lattice Boltzmann methods for non-ideal fluids, micro- and nanofluidic flows with suspended bodies of assorted nature and extensions to strong non-equilibrium flows beyond the realm of continuum fluid mechanics. In the final part, it presents the extension of the Lattice Boltzmann method to quantum and relativistic matter, in an attempt to match the major surge of interest spurred by recent developments in the area of strongly interacting holographic fluids, such as electron flows in graphene.
Book Synopsis An Introduction to Aqueous Electrolyte Solutions by : Margaret Robson Wright
Download or read book An Introduction to Aqueous Electrolyte Solutions written by Margaret Robson Wright and published by John Wiley & Sons. This book was released on 2007-06-05 with total page 603 pages. Available in PDF, EPUB and Kindle. Book excerpt: An Introduction to Aqueous Electrolyte Solutions is a comprehensive coverage of the subject including the development of key concepts and theory that focus on the physical rather than the mathematical aspects. Important links are made between the study of electrolyte solutions and other branches of chemistry, biology, and biochemistry, making it a useful cross-reference tool for students studying this important area of electrochemistry. Carefully developed throughout, each chapter includes intended learning outcomes and worked problems and examples to encourage student understanding of this multidisciplinary subject. * a comprehensive introduction to aqueous electrolyte solutions including the development of key concepts and theories * emphasises the connection between observable macroscopic experimental properties and interpretations made at the molecular level * key developments in concepts and theory explained in a descriptive manner to encourage student understanding * includes worked problems and examples throughout An invaluable text for students taking courses in chemistry and chemical engineering, this book will also be useful for biology, biochemistry and biophysics students required to study electrochemistry.
Book Synopsis Fast Solution of the Poisson-Boltzmann Equation by the Reduced Basis Method and Range-separated Canonical Tensor Format by : Cleophas Muganda Kweyu
Download or read book Fast Solution of the Poisson-Boltzmann Equation by the Reduced Basis Method and Range-separated Canonical Tensor Format written by Cleophas Muganda Kweyu and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Multigrid Solution of the Poisson-Boltzmann Equation by : Michael Holst
Download or read book Multigrid Solution of the Poisson-Boltzmann Equation written by Michael Holst and published by . This book was released on 1992 with total page 26 pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: "A multigrid method is presented for the numerical solution of the linearized Poisson-Boltzmann equation arising in molecular biophysics. The equation is discretized with the finite volume method, and the numerical solution of the discrete equations is accomplished with multiple grid techniques originally developed for two-dimensional interface problems occurring in reactor physics. A detailed analysis of the resulting method is presented for several computer architectures, including comparisons to diagonally scaled CG, ICCG, vectorized ICCG and MICCG, and to SOR provided with an optimal relaxation parameter. Our results indicate that the multigrid method is superior to the preconditioned CG methods and SOR, and that the advantage of multigrid grows with the problem size."
Book Synopsis Pseudo-transient Ghost Fluid Methods for the Poisson-Boltzmann Equation with a Two-component Regularization by : Sheik Ahmed Ullah
Download or read book Pseudo-transient Ghost Fluid Methods for the Poisson-Boltzmann Equation with a Two-component Regularization written by Sheik Ahmed Ullah and published by . This book was released on 2019 with total page 142 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Poisson Boltzmann equation (PBE) is a well-established implicit solvent continuum model for the electrostatic analysis of solvated biomolecules. The numerical solution of the nonlinear PBE is still a challenge due to its strong singularity by the source terms, dielectrically distinct regions, and exponential nonlinear terms. In this dissertation, a new alternating direction implicit method (ADI) is proposed for solving the nonlinear PBE using a two-component regularization. This scheme inherits all the advantages of the two-component regularization and the pseudo-time solution of the PBE while possesses a novel approach to combine them. A modified Ghost Fluid Method (GFM) has been introduced to incorporate the nonzero jump condition into the ADI framework to construct a new GFM-ADI method. It produced better results in terms of spatial accuracy and stability compared to the existing ADI methods for PBE and it is simpler to implement by circumventing the work necessary to apply the rigorous 3D interface treatments with the regularization. Moreover, the stability of the GFM-ADI method has been significantly improved in comparing with the non-regularized ADI method, so that stable and efficient protein simulations can be carried out with a pretty large time step size. Two locally one-dimensional (LOD) methods have also been developed for the time-dependent regularized PBE, which are unconditionally stable. Finally, for numerical validation, we have evaluated the solvation free energy for a collection of 24 proteins with various sizes and the salt effect on the protein-protein binding energy of protein complexes.
Book Synopsis Computational Chemistry Methods in Structural Biology by : Christo Christov
Download or read book Computational Chemistry Methods in Structural Biology written by Christo Christov and published by Academic Press. This book was released on 2011-09-23 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Published continuously since 1944, the Advances in Protein Chemistry and Structural Biology serial has been a continuous, essential resource for protein chemists. Covering reviews of methodology and research in all aspects of protein chemistry, including purification/expression, proteomics, modeling and structural determination and design, each volume brings forth new information about protocols and analysis of proteins while presenting the most recent findings from leading experts in a broad range of protein-related topics. This volume features articles on Computational Chemistry methods in Structural Biology. Essential resource for protein chemists This volume features articles on Computational Chemistry methods in Structural Biology
Book Synopsis Lattice Boltzmann Method by : A. A. Mohamad
Download or read book Lattice Boltzmann Method written by A. A. Mohamad and published by Springer Science & Business Media. This book was released on 2011-06-27 with total page 186 pages. Available in PDF, EPUB and Kindle. Book excerpt: Lattice Boltzmann Method introduces the lattice Boltzmann method (LBM) for solving transport phenomena – flow, heat and mass transfer – in a systematic way. Providing explanatory computer codes throughout the book, the author guides readers through many practical examples, such as: flow in isothermal and non-isothermal lid driven cavities; flow over obstacles; forced flow through a heated channel; conjugate forced convection; and natural convection. Diffusion and advection-diffusion equations are discussed with applications and examples, and complete computer codes accompany the coverage of single and multi-relaxation-time methods. Although the codes are written in FORTRAN, they can be easily translated to other languages, such as C++. The codes can also be extended with little effort to multi-phase and multi-physics, if the reader knows the physics of the problem. Readers with some experience of advanced mathematics and physics will find Lattice Boltzmann Method a useful and easy-to-follow text. It has been written for those who are interested in learning and applying the LBM to engineering and industrial problems and it can also serve as a textbook for advanced undergraduate or graduate students who are studying computational transport phenomena.
Book Synopsis Introduction To The Lattice Boltzmann Method, An: A Numerical Method For Complex Boundary And Moving Boundary Flows by : Takaji Inamuro
Download or read book Introduction To The Lattice Boltzmann Method, An: A Numerical Method For Complex Boundary And Moving Boundary Flows written by Takaji Inamuro and published by World Scientific. This book was released on 2021-11-19 with total page 166 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book introduces the fundamentals and applications of the lattice Boltzmann method (LBM) for incompressible viscous flows. It is written clearly and easy to understand for graduate students and researchers.The book is organized as follows. In Chapter 1, the SRT- and MRT-LBM schemes are derived from the discrete Boltzmann equation for lattice gases and the relation between the LBM and the Navier-Stokes equation is explained by using the asymptotic expansion (not the Chapman-Enskog expansion). Chapter 2 presents the lattice kinetic scheme (LKS) which is an extension method of the LBM and can save memory because of needlessness for storing the velocity distribution functions. In addition, an improved LKS which can stably simulate high Reynolds number flows is presented. In Chapter 3, the LBM combined with the immersed boundary method (IB-LBM) is presented. The IB-LBM is well suitable for moving boundary flows. In Chapter 4, the two-phase LBM is explained from the point of view of the difficulty in computing two-phase flows with large density ratio. Then, a two-phase LBM for large density ratios is presented. In Appendix, sample codes (available for download) are given for users.
