Biomembrane Simulations: Computational Studies of Biological Membranes

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 Kanduč, 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
Pál 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