Computational Electrostatics for Biological Applications

Geometric and Numerical Approaches to the Description of Electrostatic Interaction Between Macromolecules
Softcover Nachdruck of the original 1. Auflage 2015
ISBN: 978-3-319-37934-0
Verlag: Springer International Publishing

Buch, Englisch, 306 Seiten, Paperback, Format (B × H): 155 mm x 235 mm, Gewicht: 4861 g

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.

Zielgruppe

Research

Autoren/Hrsg.

Spagnuolo, Michela

Rocchia, Walter

Fachgebiete

• Naturwissenschaften Biowissenschaften Angewandte Biologie Biophysik
• Naturwissenschaften Physik Angewandte Physik Biophysik
• Naturwissenschaften Biowissenschaften Angewandte Biologie Biomathematik
• Naturwissenschaften Biowissenschaften Molekularbiologie

Inhaltsverzeichnis

ELECTROSTATICS and CONTINUUM SOLVENT MODELS
               
                Electrostatics models for Biology
Classical density functional theories of ionic solutions

Introducing charge hydration asymmetry into continuum electrostatics framework
 
 
NUMERICAL APPROACHES AND SOLVERS
)
Continuum electrostatics for Biological Applications: the DelPhi case
Discontinuous Galerkin schemes for elliptic problems.
 
Surface Electrostatics Using An Adaptive Cartesian Grid-Based Poisson-Boltzmann Solver
 
Design, Development and Applications of the MEAD Suite for Macromolecular Electrostatics
 
Progress and Challenges in Boundary-Integral Methods for Biological Electrostatics
 
Efficient Boundary Element Method with curved elements for implicit solvation in biological systems
 
Generalized Born forces: surface integral formulation.
 
MOLECULAR SURFACE MODELS
 
Molecular surface design with balls
 
State-of-the-art and perspectives of implicit modeling for molecular surfaces
 
A Generic Framework for Delaunay Mesh Generation and Optimization
 
BROADENING THE VIEW
Multiscale multiphysics and multidomain models for biomolecular systems
 
Beyond computation, the representation of electrostatics in biological settings
 
DEALING WITH COMPUTATIONAL COMPLEXITY
NanoShaper: a general and robust ray-casting based tool for processing surfaces at the nanoscale
 
Triangulating Molecular Surfaces with Millions of Atoms
 
Mixed MPI/CUDAimplementation for PB equation 
 
APPLICATIONS TO BIOLOGY AND BIOPHYSICS
 
Control of DNA Minor Groove Width and Electrostatic Potential in Fis Binding Sequences
 
Computing protein binding properties from molecular electrostatic potentials
 
Comparative Poisson-Boltzmann equation calculations for binding free energies focusing on physical and algorithmic parameters
 
Biophysical Applications of the Adaptive Cartesian Grid Poisson-Boltzmann Equation Software Package
 
Structural and electrostaticdeterminants of interaction specificity in G-protein mediated signaling
 
Using structural and physical-chemical parameters to identify functional districts in proteins - the role of electrostatic potential
 
A Molecular Dynamics (MD) insight to the electrostatics of biological (lipid) bilayers. A tool for understanding electroporation mechanisms
 
Modeling protein-ligand interaction with finite absorbing Markov chain
 
Molecular Mechanics - Poisson Boltzmann Surface Area calculations using AMBER program package - application to the human dipeptidyl petidase III
 
Long range Debye-Huckel correction for computation of grid-based electrostatic forces between biomacromolecules
 
APPLICATIONS TO NANOTECHNOLOGY
Modeling opto-electronic properties of a dye molecule in proximity of a semiconductor nanoparticle
 
Modelling of spherical interpolyelectrolyte complexes
 
Mono-functionalized beta-cyclodextrins as simple and sensitive testbeds for implicit solvation methods and model systems of host-guest interactions
 
Specific Aspects of Counterion Condensation onto the Poly(styrene-sulfonate) Anion and Poly(allylammonium) Cation studied by Molecular Dynamics Simulations
 
IPEC Solver: inter-polyelectrolyte complex formation within Poisson-Boltzmann theory