Soft Condensed Matter Physics in Molecular and Cell Biology

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9780750310239: Soft Condensed Matter Physics in Molecular and Cell Biology

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.

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Contenuti:

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

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Editore: CRC Press (2006)
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