Physics of molecular and cellular processes / / Krastan B. Blagoev and Herbert Levine, editors

• Pubblicazione: Cham, Switzerland : , : Springer Nature Switzerland AG, , [2022]; ©2022
• Descrizione fisica: 1 online resource (265 pages)
• Disciplina: 574.191
• Soggetto topico: Cytology; Molecular biology; Biophysics
• Persona (resp. second.): LevineHerbert <1955->; BlagoevKrastan
• Nota di bibliografia: Includes bibliographical references.
• Nota di contenuto: Intro -- Preface -- Introduction -- Contents -- Contributors -- 1 Nonequilibrium Physics of Molecules and Cells -- 1.1 Thermodynamics -- 1.1.1 Phase Transitions -- 1.2 Foundations of Statistical Physics -- 1.2.1 Liouville Theorem for Hamiltonian Systems -- 1.2.2 Stability of Nonlinear Dynamical Systems -- 1.2.3 Phase Space Dynamics of Dynamical Systems -- 1.2.4 Canonical Ensemble -- 1.2.5 Correlation and Response Functions -- 1.2.6 Linear Response Theory for Hamiltonian Systems -- 1.2.7 Fluctuation-Dissipation Theorem -- 1.2.8 Diffusion -- 1.3 Phase Separation in Living Cells -- 1.3.1 The Szilard Model -- 1.3.2 Nucleation, Growth, Coarsening, and Coalescence in Oversaturated Solutions -- 1.4 A Biophysical Example: Telomere Homeostasis -- 1.4.1 Telomerase Control of Telomere Length -- 1.4.2 Telomere Sister Chromatid Exchange and Biased Diffusion -- References -- 2 Probing the Energy Landscapes of Biomolecular Folding and Function -- 2.1 Energy Landscape Theory: The Interface of Physics and Molecular Biology -- 2.2 The Landscapes of Protein Folding -- 2.2.1 Principle of Minimal Frustration -- 2.2.2 Landscape-Inspired Models for the Study of Folding -- 2.2.3 All-Atom Explicit-Solvent Models -- 2.3 Models for Studying Biomolecular Functional Dynamics -- 2.3.1 Normal Mode Analysis -- 2.3.2 Multi-basin Effective Potential Energy Models -- 2.3.3 Simulations with Semi-empirical All-Atom Models -- 2.4 How Disorder Guides Biomolecular Function -- 2.4.1 Partial Unfolding During Function: Cracking -- 2.4.2 Biomolecular Association: Fly-Casting -- 2.4.3 Molecular Machines: Entropically Guided Rearrangements -- 2.5 Concluding Remarks -- References -- 3 Energetic and Structural Properties of Macromolecular Assemblies -- 3.1 Chemical Composition of Macromolecular Assemblies -- 3.2 The Ribosome -- 3.2.1 Biological Role and Mechanistic Characteristics. ; 3.2.2 Physical Considerations -- 3.2.3 Methods for Probing Ribosome Energetics -- 3.3 Viruses -- 3.3.1 Physical Considerations and Questions -- 3.3.2 Methods for Probing Packaging in Viruses -- 3.4 Concluding Remarks -- References -- 4 Organization of Intracellular Transport -- 4.1 Introduction -- 4.2 Why Intracellular Transport Requires Active Processes? -- 4.3 Components of Intracellular Transport -- 4.4 Current Understanding of Mechanisms of Intracellular Transport -- 4.5 Open Questions and Future Directions -- References -- 5 Introduction to Stochastic Kinetic Models for Molecular Motors -- 5.1 Introduction -- 5.2 Stochastic Kinetic Models -- 5.3 One-State Model -- 5.4 Two-State Model -- 5.5 Solution for an Arbitrary Network -- 5.5.1 Master Equation and Average Run Time -- 5.5.2 Distributions -- 5.5.3 Average Properties -- 5.5.4 Simple Examples -- 5.6 Experiments Performed Under Constant External Load -- 5.7 Advantages and Limitations of Stochastic Kinetic Models -- 5.8 Appendix A: Mathematical Functions -- 5.9 Appendix B: The Distribution of Run Length -- 5.10 Appendix C: Derivation of the Run Time Distribution -- 5.11 Appendix D: Velocity Distribution -- 5.11.1 One-State Model -- 5.11.2 Two-State Model -- 5.12 Appendix E: Averages in the N-state Model -- References -- 6 Physics of the Cell Membrane -- 6.1 The Phospholipid Bilayer -- 6.2 Membrane Proteins -- 6.2.1 Integral Proteins -- 6.2.2 Peripheral Proteins -- 6.2.3 Receptors -- 6.3 Membrane Fusion -- 6.3.1 Intermediate Structures -- 6.3.2 Membrane Tension as a Driving Force -- 6.3.3 Fusion Proteins -- 6.3.4 Electrostatic Forces -- 6.4 Energy Required to Bend a Membrane -- 6.4.1 Fluid Properties of the Plasma Membrane -- 6.4.2 Bending Energies and the Helfrich Hamiltonian -- 6.4.3 Free Energy and Shape of a Bent Membrane -- References -- 7 Introduction to Models of Cell Motility. ; 7.1 Introduction -- 7.2 Random-Walk Models -- 7.3 Looking Under the Hood -- 7.3.1 Dicty -- 7.3.2 E. Coli -- 7.4 Shapes -- 7.4.1 Cellular Potts Model -- 7.4.2 Phase Field Model -- 7.5 Models of Collective Motility -- 7.5.1 Agent-Based Approaches -- 7.5.2 Subcellular Elements -- 7.5.3 Vertex/Voronoi Models -- 7.5.4 Shapes, Revisited -- 7.6 Continuum Models -- References -- 8 Modeling Biological Information Processing Networks -- 8.1 Introduction -- 8.2 Representing Biological Networks and Analyzing their Topology -- 8.3 Dynamic Modeling -- 8.3.1 Modeling T Cell Survival -- 8.3.2 Modeling Epithelial to Mesenchymal Transition (EMT) -- 8.4 Integration of the Interaction Network and Regulatory Rules -- 8.5 Conclusions -- References -- 9 Introduction to Evolutionary Dynamics -- 9.1 Birth-Death Processes -- 9.2 The Kimura Problem -- 9.3 Selection-Mutation Equilibrium -- 9.4 Clonal Interference -- 9.5 The Luria-Delbrück Process -- References.
• Titolo autorizzato: Physics of molecular and cellular processes
• ISBN: 3-030-98606-3
• Formato: Materiale a stampa
• Livello bibliografico: Monografia
• Lingua di pubblicazione: Inglese
• Record Nr.: 996490352203316
• Lo trovi qui: Univ. di Salerno
• Serie: Graduate texts in physics.