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 think
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
W. C. K. Poon, D. Andelman