Keywords:
Membranes (Biology)-Mathematical models.
;
Electronic books.
Description / Table of Contents:
Since molecular processes in membranes occur on a multitude of spatial and time scales, molecular simulations of membranes can also serve as a testing ground for use of multi-scale simulation techniques. This book addresses some of the important issues related to understanding properties and behavior of model biological membranes.
Type of Medium:
Online Resource
Pages:
1 online resource (241 pages)
Edition:
1st ed.
ISBN:
9781351060301
Series Statement:
Series in Computational Biophysics Series
URL:
https://ebookcentral.proquest.com/lib/geomar/detail.action?docID=5788818
DDC:
571.640285
Language:
English
Note:
Cover -- Half Title -- Series Page -- Title Page -- Copyright Page -- Dedication -- Table of Contents -- Series Preface -- About the Editor -- Contributors -- 1. Force Fields for Biomembranes Simulations -- 1 Introduction -- 2 Force Fields -- 3 Validation and Comparisons of Force Fields -- 4 Conclusions -- 2. Mesoscopic Particle-Based Modeling of Self-Assembled Lipid Membranes -- I Introduction -- II The Particle-Based Mesoscopic Approach -- III Explicit Solvent Modeling -- IV Implicit Solvent Modeling -- V Conclusion -- 3. Continuum Elastic Description of Processes in Membranes -- 1 Continuum Modeling Paradigms -- 2 Variables of a Continuum Model -- 3 Pushing the Limits of a Continuum Model -- 4 Molecular Modifications to Continuum Modeling -- 4. Water between Membranes: Structure and Dynamics -- I Introduction -- II Dynamics of Water Between Stacked Membranes at Different Hydration Levels -- III Dependence of Water Dynamics on Distance to Membrane -- IV Effect of Temperature on the Hydration Water Dynamics -- V Extension of the Structural Effect of the Membrane on Interfacial Water -- VI Conclusions -- 5. Simulation Approaches to Short-Range Interactions between Lipid Membranes -- 1 Introduction -- 2 Thermodynamics of Membrane Interactions -- 3 Simulations of Interacting Membranes -- 4 Insights into Short-Range Interactions between Lipid Membranes -- 5 Summary and Outlook -- 6. Free-Energy Calculations of Pore Formation in Lipid Membranes -- 1 Introduction -- 2 Membrane Pores from Experiments -- 3 Modeling Pores in Molecular Dynamics Simulations -- 4 Reaction Coordinates for Free-Energy Calculations of Pore Formation: A Comparison -- 5 Longer Lipid Tails Increase the Free Energy of Pore Formation -- 6 Relative Volume of Lipid Head to Lipid Tails Determines the Metastability of the Pore.
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7 Practical Consideration for PMF Calculations with the Chain Coordinate -- 8 Summary and Outlook -- 7. Free Energy Calculation of Membrane Translocation: What Works When, and Why? -- 1 Introduction -- 2 Methods for Free Energy Calculations -- 3 Translocation of Specific Solutes -- 4 Implications and Recommendations -- 8. Theories and Algorithms for Molecular Permeation through Membranes -- I Introduction -- II Passive Permeation: Definition, Measurements, and Modeling -- III Solubility Diffusion Model -- IV Milestoning -- V Permeation of Blocked Tryptophan with Milestoning -- VI Fluctuations of Membrane Density with Milestoning -- VII Difference of Permeation of Positive and Negative Charged Molecules -- VIII Conclusions -- 9. Nanoparticle-Membrane Interactions: Surface Effects -- 1 Introduction -- 2 Experimental Data in Search for a Molecular-Scale Interpretation -- 3 What We Understood So Far Using Computational Tools -- 4 Perspectives -- 10. Simulations of Membranes Containing General Anesthetics -- 1 Introduction -- 2 Studies Involving Chemically Similar Molecules -- 3 Position of the Anesthetics in the Membrane -- 4 Change of Various Membrane Properties -- 5 Pressure Reversal -- 6 Concluding Remarks -- 11. Cation-Mediated Nanodomain Formation in Mixed Lipid Bilayers -- 1 Introduction -- 2 Methods -- 3 Model Validation -- 4 Results and Discussions -- 5 Conclusion -- 12. Molecular Dynamics Simulations of Gram-Negative Bacterial Membranes -- Slow Diffusion and Importance of Divalent Cations -- Different Dynamics, Not Just Slower -- Specific Binding -- Asymmetric Energetic Barriers for Permeation of Small Molecules -- Larger Simulation Systems: Correlated Lipid Motion -- Summary and Outlook -- Index.
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