Biomembrane Simulations
Computational Studies of Biological Membranes
Series in Computational Biophysics Series

Due to recent advancements in the development of numerical algorithms and computational hardware, computer simulations of biological membranes, often requiring use of substantial computational resources, are now reaching a mature stage. 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 and it

• Shows how simulations improve our understanding of biological membranes and makes connections with experimental results.

• Presents a careful discussion of the force fields used in the membrane simulations including detailed all-atom fields and coarse-grained fields.

• Presents a continuum description of membranes.

• Discusses a variety of issues such as influence of membrane surfaces on properties of water, interaction between membranes across water, nanoparticle permeation across the membrane, action of anesthetics and creation of inhomogeneous regions in membranes.

• Discusses important methodological issues when using simulations to examine phenomena such as pore creation and permeation across membranes.

• Discusses progress recently achieved in modeling bacterial membranes.

It will be a valuable resource for graduate students, researchers and instructors in biochemistry, biophysics, pharmacology, physiology, and computational biology.

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

Max L. Berkowitz, PhD, is a Professor in the Department of Chemistry at the University of North Carolina, Chapel Hill. He earned his PhD from the Weizmann Institute of Science. His research interests include studies of the structural and dynamical properties of aqueous ionic solutions, structure and dynamics of biomembranes, and influence of cavitation effect on biomembranes. He has given numerous invited talks and presentations and is an author or a co-author of more than150 peer-reviewed journal publications. He is a Fellow of the American Physical Society.