Biomembrane Simulations

Contents

Series Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix

About the Editor. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi

Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiii

1. Force Fields for Biomembranes Simulations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Alexander P. Lyubartsev and Alexander L. Rabinovich

2. Mesoscopic Particle-Based Modeling of Self-Assembled Lipid Membranes . . . . . . . . . . . . . . 27

Mohamed Laradji and Maria Maddalena Sperotto

3. Continuum Elastic Description of Processes in Membranes . . . . . . . . . . . . . . . . . . . . . . . . . . 51

Alexander J. Sodt

4. Water between Membranes: Structure and Dynamics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

Sotiris Samatas, Carles Calero, Fausto Martelli, and Giancarlo Franzese

5. Simulation Approaches to Short-Range Interactions between Lipid Membranes . . . . . . . . . . 89

Matej Kanduc, Alexander Schlaich, Bartosz Kowalik, Amanuel Wolde-Kidan,

Roland R. Netz, and Emanuel Schneck

6. Free-Energy Calculations of Pore Formation in Lipid Membranes . . . . . . . . . . . . . . . . . . . . 109

N. Awasthi and J. S. Hub

7. Free Energy Calculation of Membrane Translocation: What Works When, and Why?. . . . . 125

Nihit Pokhrel and Lutz Maibaum

8. Theories and Algorithms for Molecular Permeation through Membranes. . . . . . . . . . . . . . . 145

Alfredo E. Cardenas and Ron Elber

9. Nanoparticle-Membrane Interactions: Surface Effects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163

G. Rossi, S. Salassi, F. Simonelli, A. Bartocci, and L. Monticelli

10. Simulations of Membranes Containing General Anesthetics . . . . . . . . . . . . . . . . . . . . . . . . . 177

Pal Jedlovszky

11. Cation-Mediated Nanodomain Formation in Mixed Lipid Bilayers . . . . . . . . . . . . . . . . . . . 199

Sai J. Ganesan, Hongcheng Xu, and Silvina Matysiak

12. Molecular Dynamics Simulations of Gram-Negative Bacterial Membranes . . . . . . . . . . . . 213

Syma Khalid, Graham Saunders, and Taylor Haynes

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223