Computational electrostatics for biological applications : geometric and numerical approaches to the description of electrostatic interaction between macromolecules /: geometric and numerical approaches to the description of electrostatic interaction between macromolecules. ([2015])

• Record Type: Book
• Further Information: Note: Walter Rocchia, Michela Spagnuolo, editors.
• Editors: Rocchia, Walter; Spagnuolo, Michela
• Contents: Foreword; Preface; Contents; 1 Electrostatics Models for Biology; 1.1 Introduction; 1.2 Protein -- Nucleic Acid Interactions; 1.3 Protein -- Protein Interactions; 1.4 pH-Dependence and pKa Calculations; 1.5 Protein Solubility and Aggregation; 1.6 pH Variation and Subcellular Compartments; 1.7 Conclusion; References; 2 Classical Density Functional Theory of Ionic Solutions; 2.1 Introduction; 2.2 Classical DFT of Simple Fluids; 2.2.1 The Generalized van der Waals' Theory; 2.2.2 Grand Potential and Symmetry; 2.3 DFT of Simple Ionic Systems; 2.3.1 Poisson -- Boltzmann DFT. 2.3.2 Approximating Ion Correlations2.4 Examples; 2.4.1 Interaction Between Two Charged Colloidal Particles; 2.4.2 Adsorption of Polyions to Oppositely Charged Surfaces; 2.5 Conclusions; References; 3 A Comprehensive Exploration of Physical and Numerical Parameters in the Poisson -- Boltzmann Equation for Applications to Receptor -- Ligand Binding; 3.1 Introduction; 3.2 Methods and Materials; 3.3 Results and Discussion; 3.3.1 Physical Parameters and Features; 3.3.2 Numerical Parameters; 3.3.3 Experimental Validation; 3.4 Conclusion; References. 4 The Adaptive Cartesian Grid-Based Poisson -- Boltzmann Solver: Energy and Surface Electrostatic Properties4.1 Introduction; 4.1.1 Meshing Options; 4.1.2 The Adaptive Cartesian Grid-Based Poisson -- Boltzmann Solver (CPB); 4.2 Methods; 4.2.1 Least Squares-based Reconstruction (LSR); 4.2.2 Comment on Surface Discontinuities; 4.3 Results; 4.3.1 Mesh Convergence Tests; 4.3.2 Energy-Based Poisson -- Boltzmann Properties; 4.3.3 Electrostatic Solvation Free Energies of Biomolecules; 4.3.4 Electrostatic Binding Free Energies; 4.3.5 Surface-Based Electrostatic Properties; 4.3.6 Sphere Model Problem. 4.3.7 Electrostatic Potential Mapped on Realistic Biomolecular Surfaces4.3.8 Net Induced Surface Charge and Forces for Realistic Biomolecular Geometries; 4.3.9 Poisson -- Boltzmann Forces; 4.4 Conclusions; References; 5 Efficient and Stable Method to Solve Poisson -- Boltzmann Equation with Steep Gradients; 5.1 Introduction; 5.2 Poisson -- Boltzmann Equation; 5.3 Invertible Mappings for PBE; 5.4 Numerical Test; 5.5 Conclusion; References; 6 Boundary-Integral and Boundary-Element Methods for Biomolecular Electrostatics: Progress, Challenges, and Important Lessons from CEBA 2013; 6.1 Overview. 6.2 Background6.3 Computational Workflow; 6.3.1 New Applications for Computational Geometry; 6.3.2 Emerging Workflow Challenges for Meshing; 6.4 New Applications for Boundary-Integral Formulations; 6.4.1 Enclosing Surfaces; 6.4.2 Multiple Biomolecules; 6.5 New Approaches to Discretization; 6.6 Collaborative Efforts to Validate Numerical Methods; 6.7 Discussion; References; 7 The Accuracy of Generalized Born Forces; 7.1 Introduction; 7.2 Electrostatic Forces in Inhomogeneous Continuous Media; 7.3 Generalized Born Models; 7.4 The Accuracy of Generalized Born Versus Poisson -- Boltzmann Forces.
• Publisher Details: Cham : Springer
• Publication Date: 2015
• Copyright Date: 2015
• Extent: 1 online resource
• Subjects: 537.2; Life sciences; Electrostatics; Macromolecules; SCIENCE -- Physics -- Electricity; SCIENCE -- Physics -- Electromagnetism; Electrostatics; Macromolecules; Science -- Life Sciences -- Biophysics; Mathematics -- Applied; Science -- Mathematical Physics; Computers -- Computer Graphics; Mathematics -- Geometry -- General; Biophysics; Maths for scientists; Mathematical physics; Graphics programming; Geometry; Biology -- Data processing; Computer graphics; Geometry; Science -- Life Sciences -- General; Biology, life sciences; Electronic books; Electronic books
• Languages: English
• ISBNs: 9783319122113; 3319122118
• Related ISBNs: 9783319122106; 331912210X
• Notes: Note: Includes bibliographical references.; Note: Vendor-supplied metadata.
• Access Rights: Legal Deposit; Only available on premises controlled by the deposit library and to one user at any one time; The Legal Deposit Libraries (Non-Print Works) Regulations (UK).
• Access Usage: Restricted: Printing from this resource is governed by The Legal Deposit Libraries (Non-Print Works) Regulations (UK) and UK copyright law currently in force.