LEADER 07791nam 22009375 450 001 9910298287503321 005 20200701080415.0 010 $a3-319-12211-8 024 7 $a10.1007/978-3-319-12211-3 035 $a(CKB)3710000000305962 035 $a(EBL)1965436 035 $a(SSID)ssj0001385816 035 $a(PQKBManifestationID)11767062 035 $a(PQKBTitleCode)TC0001385816 035 $a(PQKBWorkID)11348852 035 $a(PQKB)11751928 035 $a(DE-He213)978-3-319-12211-3 035 $a(MiAaPQ)EBC1965436 035 $a(PPN)183089782 035 $a(EXLCZ)993710000000305962 100 $a20141129d2015 u| 0 101 0 $aeng 135 $aur|n|---||||| 181 $ctxt 182 $cc 183 $acr 200 10$aComputational Electrostatics for Biological Applications $eGeometric and Numerical Approaches to the Description of Electrostatic Interaction Between Macromolecules /$fedited by Walter Rocchia, Michela Spagnuolo 205 $a1st ed. 2015. 210 1$aCham :$cSpringer International Publishing :$cImprint: Springer,$d2015. 215 $a1 online resource (311 p.) 300 $aDescription based upon print version of record. 311 $a3-319-12210-X 320 $aIncludes bibliographical references. 327 $aForeword; 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 327 $a2.3.2 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 327 $a4 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 327 $a4.3.7 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 327 $a6.2 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 327 $a7.4.1 GBR6 Surface Integral Approximation Model 330 $aThis 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. 606 $aBioinformatics  606 $aComputational biology  606 $aBiophysics 606 $aBiological physics 606 $aBiomathematics 606 $aMathematical physics 606 $aComputer graphics 606 $aGeometry 606 $aComputer Appl. in Life Sciences$3https://scigraph.springernature.com/ontologies/product-market-codes/L17004 606 $aBiological and Medical Physics, Biophysics$3https://scigraph.springernature.com/ontologies/product-market-codes/P27008 606 $aMathematical and Computational Biology$3https://scigraph.springernature.com/ontologies/product-market-codes/M31000 606 $aTheoretical, Mathematical and Computational Physics$3https://scigraph.springernature.com/ontologies/product-market-codes/P19005 606 $aComputer Graphics$3https://scigraph.springernature.com/ontologies/product-market-codes/I22013 606 $aGeometry$3https://scigraph.springernature.com/ontologies/product-market-codes/M21006 615 0$aBioinformatics . 615 0$aComputational biology . 615 0$aBiophysics. 615 0$aBiological physics. 615 0$aBiomathematics. 615 0$aMathematical physics. 615 0$aComputer graphics. 615 0$aGeometry. 615 14$aComputer Appl. in Life Sciences. 615 24$aBiological and Medical Physics, Biophysics. 615 24$aMathematical and Computational Biology. 615 24$aTheoretical, Mathematical and Computational Physics. 615 24$aComputer Graphics. 615 24$aGeometry. 676 $a006.6 676 $a516 676 $a530.1 676 $a570 676 $a570.285 676 $a570285 676 $a571.4 702 $aRocchia$b Walter$4edt$4http://id.loc.gov/vocabulary/relators/edt 702 $aSpagnuolo$b Michela$4edt$4http://id.loc.gov/vocabulary/relators/edt 906 $aBOOK 912 $a9910298287503321 996 $aComputational Electrostatics for Biological Applications$92541205 997 $aUNINA