Introduction... xvii Complexes and the Origin of Liquid Liquid Immiscibility... xvii Outlook... xxi

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1 CONTENTS Perspectives: Complexes in Liquids, Harden McConnell Introduction... xvii Complexes and the Origin of Liquid Liquid Immiscibility... xvii Outlook... xxi 1 Molecular Theory Applied to Lipid Bilayers and Lipid Protein Interactions Amalie L. Frischknecht and Laura J. D. Frink 1.1. Introduction Essential Elements for Molecular Membrane Theories Fluids Density Functional Theories A Simple Lipid Model Performing Fluids-DFT Calculations for Model Lipid Bilayers Lipid Bilayer Structure Mechanical Properties of Bilayers Conclusions Membrane Elasticity and Mediated Interactions in Continuum Theory: A Differential Geometric Approach Markus Deserno 2.1. Introduction: Biophysics and Scale Separation Continuum Theory for Membranes: A First Look Curvature Elasticity Membrane Stresses and Shape Equilibria Membrane-Mediated Interactions Summary vii

2 viii CONTENTS 3 Structure and Dynamics of Lipid Monolayers: Theory and Applications Svetlana Baoukina, Siewert J. Marrink, and D. Peter Tieleman 3.1. Introduction Lipid Monolayers: Basic Properties and Applications Experimental Studies Theoretical Models Computer Simulations Conclusions and Outlook Multiscale Modeling of Supported Lipid Bilayers Matthew I. Hoopes, Chenyue Xing, and Roland Faller 4.1. Introduction Multiscale Modeling of Membranes Atomistic Modeling Mesoscale Modeling Water-Free Large-Scale Modeling Visualizations Density Profiles Pressure and Lateral Tension Summary and Outlook Collective Dynamics in Lipid Membranes: From Pore Formation to Flip-Flops Andrey A. Gurtovenko and Ilpo Vattulainen 5.1. Introduction Dynamics of Lipids in Membranes Flip-Flops Associated with Asymmetric Distribution of Lipids in Membranes Formation of Transient Water Pores in Lipid Membranes Flip-Flops of Lipid Molecules across Protein-Free Lipid Membranes Summary

3 HANDBOOK OF MODERN BIOPHYSICS, VOLUME 2 ix 6 Spatiotemporal Organization of Spin-Coated Supported Model Membranes Adam Cohen Simonsen 6.1. Introduction Methods for Preparing Supported Membranes Membrane Support Materials Spin Coating Lamellar Lipid Films by Spin Coating Supported Membranes by Hydration of Spin-Coated Precursor Films Membrane Support and Membrane Membrane Interactions Imaging the Membrane Microstructure AFM for Imaging Supported Membranes Fluorescence Microscopy for Imaging Supported Membranes Phase Transitions and Domains in Model Membranes Binary Model Membranes Ternary Model Membranes Appendix Nanopore Analysis of Nucleic Acids: Single-Molecule Studies of Molecular Dynamics, Structure, and Base Sequence Felix Olasagasti and David W. Deamer 7.1. Introduction The Nanopore Apparatus Detection of Single Macromolecules Detection of Macromolecular Complexes Conclusions and Future Prospects Complex Applications of Simple FRAP on Membranes Minchul Kang and Anne K. Kenworthy 8.1. Introduction Principles of Fluorescence Basic Theory of FRAP Further Applications of FRAP Challenges and Artifacts in Confocal FRAP Summary

4 x CONTENTS 9 Punching Holes in Membranes: How Oligomeric Pore-Forming Proteins and Lipids Cooperate to Form Aqueous Channels in Membranes Cécile Fradin, Dmitri Satsoura, and David W. Andrews 9.1. Introduction Pore-Forming Proteins Pore Structures Influence of the Lipids on Pore Formation and Stability Pore Formation Mechanism Summary Morphogens, Membranes and Mechanotransduction in Articular Cartilage Shirley Motaung, Stephanie Chan, and A. Hari Reddi Introduction Morphogens Cartilage Morphogenesis Bone Morphogenetic Proteins Structure and Function of Articular Cartilage Role of Transforming Growth Factor (TGF- ) in Chondrocytes Membranes and Matrix in Mechanotransduction Mechanical Properties of Cartilage Mechanical Signal Transduction Applications of BMPs Summary Lifecycle of a Lipoprotein from a Biophysical Perspective John C. Rutledge, Thomas Huser, John Voss, James Chan, and Atul Parikh Introduction Laser Trapping Raman Spectroscopy for Analysis of Single Lipoproteins Apolipoprotein E Conformational Changes in the Postprandial State TGRL Lipolysis Products and Vascular Inflammation Cell-Free Membrane-Mimetic Model Bilayers to Study Interaction of TGRL with Raft-Like Microenvironments TGRL Lipolysis Products and Increased Endothelial Layer Permeability Monocytes and TGRL Lipolysis Products Summary Conclusions

5 HANDBOOK OF MODERN BIOPHYSICS, VOLUME 2 xi 12 Targeting Apolipoproteins in Magnetic Resonance Imaging Renuka Sriram, Jens O. Lagerstedt, Haris Samardzic, Ulrike Kreutzer, Jitka Petrolova, Hongtao Xie, George A. Kaysen, John C. Voss, Jean F. Desreux, and Thomas Jue Introduction Chylomicrons and Triacylglycerol LDL and Cholesterol Transport HDL and Cholesterol Scavenging Lipoproteins as Indices of CVD Risk Apolipoproteins and CVD Risk ApoA-I and HDL ApoA-I Therapy Imaging Lipoprotein In Vivo Specific apoa-i Contrast Agent Relaxivity Imaging apoa-i in Vivo Summary Problem Solutions Index

Series Editor Thomas Jue University of California Davis Davis, California

Series Editor Thomas Jue University of California Davis Davis, California HANDBOOK OF M ODERN BIOPHYSICS Series Editor Thomas Jue Davis, California For other titles published in this series, go to www.springer.com/series/7845 Roland Faller Thomas Jue Marjorie L. Longo Subhash