Computational Electrostatics for Biological Applications
Geometric and Numerical Approaches to the Description of Electrostatic Interaction Between Macromolecules Herausgegeben:Rocchia, Walter; Spagnuolo, Michela
Computational Electrostatics for Biological Applications
Geometric and Numerical Approaches to the Description of Electrostatic Interaction Between Macromolecules Herausgegeben:Rocchia, Walter; Spagnuolo, Michela
This book presents established and new approaches to perform calculations of electrostatic interactions at the nanoscale, with particular focus on molecular biology applications. It is based on the proceedings of the Computational Electrostatics for Biological Applications international meeting, which brought together researchers in computational disciplines to discuss and explore diverse methods to improve electrostatic calculations. Fostering an interdisciplinary approach to the description of complex physical and biological problems, this book encompasses contributions originating in the…mehr
This book presents established and new approaches to perform calculations of electrostatic interactions at the nanoscale, with particular focus on molecular biology applications. It is based on the proceedings of the Computational Electrostatics for Biological Applications international meeting, which brought together researchers in computational disciplines to discuss and explore diverse methods to improve electrostatic calculations. Fostering an interdisciplinary approach to the description of complex physical and biological problems, this book encompasses contributions originating in the fields of geometry processing, shape modeling, applied mathematics, and computational biology and chemistry. The main topics covered are theoretical and numerical aspects of the solution of the Poisson-Boltzmann equation, surveys and comparison among geometric approaches to the modelling of molecular surfaces and related discretization and computational issues. It also includes a number of contributions addressing applications in biology, biophysics and nanotechnology. The book is primarily intended as a reference for researchers in the computational molecular biology and chemistry fields. As such, it also aims at becoming a key source of information for a wide range of scientists who need to know how modeling and computing at the molecular level may influence the design and interpretation of their experiments.
ELECTROSTATICS and CONTINUUM SOLVENT MODELSElectrostatics models for BiologyClassical density functional theories of ionic solutionsIntroducing charge hydration asymmetry into continuum electrostatics frameworkNUMERICAL APPROACHES AND SOLVERS)Continuum electrostatics for Biological Applications: the DelPhi caseDiscontinuous Galerkin schemes for elliptic problems.Surface Electrostatics Using An Adaptive Cartesian Grid-Based Poisson-Boltzmann SolverDesign, Development and Applications of the MEAD Suite for Macromolecular ElectrostaticsProgress and Challenges in Boundary-Integral Methods for Biological ElectrostaticsEfficient Boundary Element Method with curved elements for implicit solvation in biological systemsGeneralized Born forces: surface integral formulation.MOLECULAR SURFACE MODELSMolecular surface design with ballsState-of-the-art and perspectives of implicit modeling for molecular surfacesA Generic Framework for Delaunay Mesh Generation and OptimizationBROADENING THE VIEWMultiscale multiphysics and multidomain models for biomolecular systemsBeyond computation, the representation of electrostatics in biological settingsDEALING WITH COMPUTATIONAL COMPLEXITYNanoShaper: a general and robust ray-casting based tool for processing surfaces at the nanoscaleTriangulating Molecular Surfaces with Millions of AtomsMixed MPI/CUDAimplementation for PB equationAPPLICATIONS TO BIOLOGY AND BIOPHYSICSControl of DNA Minor Groove Width and Electrostatic Potential in Fis Binding SequencesComputing protein binding properties from molecular electrostatic potentialsComparative Poisson-Boltzmann equation calculations for binding free energies focusing on physical and algorithmic parametersBiophysical Applications of the Adaptive Cartesian Grid Poisson-Boltzmann Equation Software PackageStructural and electrostatic determinants of interaction specificity in G-protein mediated signalingUsing structural and physical-chemical parameters to identify functional districts in proteins - the role of electrostatic potentialA Molecular Dynamics (MD) insight to the electrostatics of biological (lipid) bilayers. A tool for understanding electroporation mechanismsModeling protein-ligand interaction with finite absorbing Markov chainMolecular Mechanics - Poisson Boltzmann Surface Area calculations using AMBER program package - application to the human dipeptidyl petidase IIILong range Debye-Huckel correction for computation of grid-based electrostatic forces between biomacromoleculesAPPLICATIONS TO NANOTECHNOLOGYModeling opto-electronic properties of a dye molecule in proximity of a semiconductor nanoparticleModelling of spherical interpolyelectrolyte complexesMono-functionalized beta-cyclodextrins as simple and sensitive testbeds for implicit solvation methods and model systems of host-guest interactionsSpecific Aspects of Counterion Condensation onto the Poly(styrene-sulfonate) Anion and Poly(allylammonium) Cation studied by Molecular Dynamics SimulationsIPEC Solver: inter-polyelectrolyte complex formation within Poisson-Boltzmann theory
ELECTROSTATICS and CONTINUUM SOLVENT MODELSElectrostatics models for BiologyClassical density functional theories of ionic solutionsIntroducing charge hydration asymmetry into continuum electrostatics frameworkNUMERICAL APPROACHES AND SOLVERS)Continuum electrostatics for Biological Applications: the DelPhi caseDiscontinuous Galerkin schemes for elliptic problems.Surface Electrostatics Using An Adaptive Cartesian Grid-Based Poisson-Boltzmann SolverDesign, Development and Applications of the MEAD Suite for Macromolecular ElectrostaticsProgress and Challenges in Boundary-Integral Methods for Biological ElectrostaticsEfficient Boundary Element Method with curved elements for implicit solvation in biological systemsGeneralized Born forces: surface integral formulation.MOLECULAR SURFACE MODELSMolecular surface design with ballsState-of-the-art and perspectives of implicit modeling for molecular surfacesA Generic Framework for Delaunay Mesh Generation and OptimizationBROADENING THE VIEWMultiscale multiphysics and multidomain models for biomolecular systemsBeyond computation, the representation of electrostatics in biological settingsDEALING WITH COMPUTATIONAL COMPLEXITYNanoShaper: a general and robust ray-casting based tool for processing surfaces at the nanoscaleTriangulating Molecular Surfaces with Millions of AtomsMixed MPI/CUDAimplementation for PB equationAPPLICATIONS TO BIOLOGY AND BIOPHYSICSControl of DNA Minor Groove Width and Electrostatic Potential in Fis Binding SequencesComputing protein binding properties from molecular electrostatic potentialsComparative Poisson-Boltzmann equation calculations for binding free energies focusing on physical and algorithmic parametersBiophysical Applications of the Adaptive Cartesian Grid Poisson-Boltzmann Equation Software PackageStructural and electrostatic determinants of interaction specificity in G-protein mediated signalingUsing structural and physical-chemical parameters to identify functional districts in proteins - the role of electrostatic potentialA Molecular Dynamics (MD) insight to the electrostatics of biological (lipid) bilayers. A tool for understanding electroporation mechanismsModeling protein-ligand interaction with finite absorbing Markov chainMolecular Mechanics - Poisson Boltzmann Surface Area calculations using AMBER program package - application to the human dipeptidyl petidase IIILong range Debye-Huckel correction for computation of grid-based electrostatic forces between biomacromoleculesAPPLICATIONS TO NANOTECHNOLOGYModeling opto-electronic properties of a dye molecule in proximity of a semiconductor nanoparticleModelling of spherical interpolyelectrolyte complexesMono-functionalized beta-cyclodextrins as simple and sensitive testbeds for implicit solvation methods and model systems of host-guest interactionsSpecific Aspects of Counterion Condensation onto the Poly(styrene-sulfonate) Anion and Poly(allylammonium) Cation studied by Molecular Dynamics SimulationsIPEC Solver: inter-polyelectrolyte complex formation within Poisson-Boltzmann theory
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