Soft Condensed Matter Physics in Molecular and Cell Biology: 1st Edition (Hardback) book cover

Soft Condensed Matter Physics in Molecular and Cell Biology

1st Edition

Edited by W.C.K. Poon, David Andelman

CRC Press

344 pages

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pub: 2006-01-13
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Description

Soft condensed matter physics, which emerged as a distinct branch of physics in the 1990s, studies complex fluids: liquids in which structures with length scale between the molecular and the macroscopic exist. Polymers, liquid crystals, surfactant solutions, and colloids fall into this category. Physicists deal with properties of soft matter systems that are generic and largely independent of chemical details. They are especially fascinated by the way soft matter systems can harness Brownian motion to self-assemble into higher-order structures.

Exploring the generic properties of soft matter offers insights into many fundamental questions that cut across a number of disciplines. Although many of these apply to materials and industrial applications, the focus of this volume is on their applications in molecular and cell biology based on the realization that biology is soft matter come alive.

The chapters in Soft Condensed Matter Physics in Molecular and Cell Biology originated as lectures in the NATO Advanced Science Institute (ASI) and Scottish Universities Summer Schools in Physics with the same name; they represent the thinking of seventeen experts operating at the cutting edge of their respective fields. The book provides a thorough grounding in the fundamental physics of soft matter and then explores its application with regard to the three important classes of biomacromolecules: proteins, DNA, and lipids, as well as to aspects of the biology of cells. The final section of the book considers experimental techniques, covering single molecule force spectroscopy of proteins, the use of optical tweezers, along with X-ray, neutron, and light scattering from solutions.

While this work presents fundamentals that make it a suitable text for graduate students in physics, it also offers valuable insights for established soft condensed matter physicists seeking to contribute to biology, and for biologists wanting to understand what the latest thinking in soft matter physics may be able to contribute to their discipline.

Table of Contents

INTRODUCTION: Coarse graining in biological soft matter

The atomistic description of globular proteins: the tertiary structure

Coarse-graining : level 1 Secondary structure;

Coarse-graining : level 2 Domains

Coarse-graining : level 3 Proteins as colloids

Further coarse-graining

I. SOFT MATTER BACKGROUND

Introduction to colloidal systems

Colloidal phase behaviour; Colloid dynamics

The physics of floppy polymers

Statistical physics of single chains

Statistical physics of many chains

Polymer dynamics

Self-assembly and properties of lipid membranes

The constituents of lipid bilayer membranes

Self assembly

Bilayer membrane phases

Membrane energies

Fluctuations

Domains, shapes and other current issues

Some aspects of membrane elasticity

Gibbs' description

Description in terms of microscopic properties

Equations of equilibrium and shape of interfaces

Introduction to electrostatics in soft and biological matter

The Poisson-Boltzmann theory

Poisson-Boltzmann equation: planar geometry;

Poisson-Boltzmann equation: cylindrical coordinates;

Poisson-Boltzmann equation: spherical coordinates -- Charged colloids

Beyond the Poisson-Boltzmann treatment

Thermal Barrier Hopping in Biological Physics

A preliminary: Diffusion on a flat landscape

First passage times: an exact result

Landscapes and intermediate states

Higher-dimensional barrier crossing

II. BIOLOGICAL APPLICATIONS

Elasticity and dynamics of cytoskeletal filaments and their networks

Single-filament properties

Solutions of semi-flexible polymer

Network elasticity

Nonlinear response

Twisting and stretching DNA: Single-molecule studies

Micromanipulation techniques

Stretching DNA

DNA under torsion

DNA-protein interactions

Interactions and conformational fluctuations in DNA arrays

Electrostatic interactions

Equation of state: No thermal fluctuations; Effect of thermal fluctuations (1) Effect of thermal fluctuations (2)

Sequence-structure relationships in proteins

Energy functions for fold recognition

The evolutionary capacity of proteins

Physical and functional aspects of protein dynamics

Hydration effects and the dynamical transition

Neutron scattering from proteins

Protonation reactions in proteins

Coupling between conformational and protonation state changes in membrane proteins

Analysis of conformational changes in proteins

Models of cell motility

III. EXPERIMENTAL TECHNIQUES

Single-molecule force spectroscopy of proteins

Pattern recognition in force-extension traces

A practical guide to optical tweezers

Basic principles

Heating in optical tweezers

Resonant trapping

Photobleaching in optical tweezers

Displacement detection and detection bandwidth

Signal-to-noise ratio and resolution

Solution Scattering

Static scattering

Dynamic scattering

Examples

Participants' addresses

Lecturers

David Andelman, Tel Aviv University

David Bensimon, Ecole Normale Supèrieure, Paris

Stefan Egelhaaf ,The University of Edinburgh

Ron Elber, Cornell University, Ithaca

Daan Frenkel, Institute of Atomic & Molecular Physics, Amsterdam

Jean-François Joanny, Curie Institute, Paris

Michael Kozlov, Tel Aviv University

Fred MacKintosh, Free University, Amsterdam

Tom McLeish, Leeds University

Peter Olmsted, Leeds University

Rudi Podgornik, University of Ljubljana

Wilson Poon, The University of Edinburgh

Matthias Rief, The Technical University, Munich

Christoph Schmidt, Free University, Amsterdam

Claus Seidel, Max Planck Institute for Biophysical Chemistry, Göttingen

Jeremy Smith, Ruprecht Karls University, Heidelberg

Patrick Warren, Unilever Research, Wirral

About the Editors

W. C. K. Poon, D. Andelman

About the Series

Scottish Graduate Series

Learn more…

Subject Categories

BISAC Subject Codes/Headings:
SCI017000
SCIENCE / Life Sciences / Cytology
SCI055000
SCIENCE / Physics
SCI077000
SCIENCE / Solid State Physics