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Computational Electrostatics for Biological Applications : Geometric and Numerical Approaches to the Description of Electrostatic Interaction Between Macromolecules / / edited by Walter Rocchia, Michela Spagnuolo
| Computational Electrostatics for Biological Applications : Geometric and Numerical Approaches to the Description of Electrostatic Interaction Between Macromolecules / / edited by Walter Rocchia, Michela Spagnuolo |
| Edizione | [1st ed. 2015.] |
| Pubbl/distr/stampa | Cham : , : Springer International Publishing : , : Imprint : Springer, , 2015 |
| Descrizione fisica | 1 online resource (311 p.) |
| Disciplina |
006.6
516 530.1 570 570.285 570285 571.4 |
| Soggetto topico |
Bioinformatics
Computational biology Biophysics Biological physics Biomathematics Mathematical physics Computer graphics Geometry Computer Appl. in Life Sciences Biological and Medical Physics, Biophysics Mathematical and Computational Biology Theoretical, Mathematical and Computational Physics Computer Graphics |
| ISBN | 3-319-12211-8 |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
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 7.4.1 GBR6 Surface Integral Approximation Model |
| Record Nr. | UNINA-9910298287503321 |
| Cham : , : Springer International Publishing : , : Imprint : Springer, , 2015 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
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Mathematical Modeling in Cultural Heritage [[electronic resource] ] : MACH2021 / / edited by Gabriella Bretti, Cecilia Cavaterra, Margherita Solci, Michela Spagnuolo
| Mathematical Modeling in Cultural Heritage [[electronic resource] ] : MACH2021 / / edited by Gabriella Bretti, Cecilia Cavaterra, Margherita Solci, Michela Spagnuolo |
| Autore | Bretti Gabriella |
| Edizione | [1st ed. 2023.] |
| Pubbl/distr/stampa | Singapore : , : Springer Nature Singapore : , : Imprint : Springer, , 2023 |
| Descrizione fisica | 1 online resource (230 pages) |
| Disciplina | 363.69015118 |
| Altri autori (Persone) |
CavaterraCecilia
SolciMargherita SpagnuoloMichela |
| Collana | Springer INdAM Series |
| Soggetto topico |
Differential equations
Mathematics Differential Equations Applications of Mathematics |
| ISBN | 981-9936-79-9 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Chapter 1: Round Table The impact of Covid-19 pandemic on cultural heritage: from fruition to conservation practises -- Chapter 2: Numerical simulation of the Athens 1999 earthquake including simplified models of the Acropolis and the Parthenon: initial results and outlook -- Chapter 3: Randomness in a nonlinear model of sulphation phenomena -- Chapter 4: Automatic description of rubble masonry geometries by machine learning based approach -- Chapter 5: Themes and reflections upon structural analysis in the field of archaeology -- Chapter 6: A model for craquelure: brittle layers on elastic substrates -- Chapter 7: From point clouds to 3D simulations of marble sulfation -- Chapter 8: A semi-analytical approach to approximate chattering time of rocking structures -- Chapter 9: Numerical modelling of historical masonry structures with the finite element code NOSA-ITACA -- Chapter 10: Mathematical Methods for the Shape Analysis and Indexing of Tangible CH artefacts -- Chapter 11: Multiscale carbonation models – a review -- Chapter 12: Forecasting damage and consolidation: mathematical models of reacting flows in porous media -- Chapter 13: Models and mathematical issues in color film restorations. |
| Record Nr. | UNINA-9910736996603321 |
Bretti Gabriella
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| Singapore : , : Springer Nature Singapore : , : Imprint : Springer, , 2023 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
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