Biomolecular Thermodynamics
From Theory to Application
 Edition:
 1st
 Author(s):
 Douglas Barrick
 ISBN:
 9781439800195
 Format:
 Paperback
 Publication Date:
 September 14, 2017
 Content Details:
 524 pages
 Language:
 English
Other Available Formats:
 Hardback
 $179.95
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About the Book
Book Summary
"an impressive text that addresses a glaring gap in the teaching of physical chemistry, being specifically focused on biologicallyrelevant systems along with a practical focus…. the ample problems and tutorials throughout are much appreciated."
–Tobin R. Sosnick, Professor and Chair of Biochemistry and Molecular Biology, University of Chicago"Presents both the concepts and equations associated with statistical thermodynamics in a unique way that is at visual, intuitive, and rigorous. This approach will greatly benefit students at all levels."
–Vijay S. Pande, Henry Dreyfus Professor of Chemistry, Stanford University"a masterful tour de force…. Barrick's rigor and scholarship come through in every chapter."
–Rohit V. Pappu, Edwin H. Murty Professor of Engineering, Washington University in St. LouisThis book provides a comprehensive, contemporary introduction to developing a quantitative understanding of how biological macromolecules behave using classical and statistical thermodynamics. The author focuses on practical skills needed to apply the underlying equations in real life examples. The text develops mechanistic models, showing how they connect to thermodynamic observables, presenting simulations of thermodynamic behavior, and analyzing experimental data. The reader is presented with plenty of exercises and problems to facilitate handson learning through mathematical simulation.
Douglas E. Barrick is a professor in the Department of Biophysics at Johns Hopkins University. He earned his Ph.D. in biochemistry from Stanford University, and a Ph.D. in biophysics and structural biology from the University of Oregon.
Features
 Emphasizes problem solving using both real and simulated data
 Develops multiple skill sets, including data analysis and mathematical simulation
 Covers various biochemical problems, including conformational equilibria, ligand binding, chemical denaturation, proton titration, helixcoil transition theory, allostery, and catalysis
 Offers a concise yet thorough and novel approach to understanding the essential aspects of physical chemistry without dry theoretical discussion
 Shows how to apply classical and statistical thermodynamics to complicated biochemical processes, such as ligand binding, cooperativity, and assembly
Reviews
"Presents both the concepts and equations associated with statistical thermodynamics in a unique way that is at visual, intuitive, and rigorous. This approach will greatly benefit students at all levels."
–Vijay S. Pande, Henry Dreyfus Professor of Chemistry, Stanford University"a masterful tour de force…. Barrick's rigor and scholarship come through in every chapter. The focus on biomolecules combined with the detailed demonstrations of how concepts apply to practical aspects of biophysics make this a truly unique contribution. Everyone, from the purported expert to the true novice will gain immensely from this carefully crafted, well motivated, and deeply thought out contribution. This book should live on all of our bookshelves and be consulted routinely as a quick reference or as material for in depth study and training."
—Rohit V. Pappu, Edwin H. Murty Professor of Engineering, Washington University in St. Louis"The author has created an impressive text that addresses a glaring gap in the teaching of physical chemistry, being specifically focused on biologicallyrelevant systems along with a practical focus. It starts by bringing students up to speed on probability theory, multivariate calculus and data fitting, the necessary tools for tackling the advanced topics covered in the remaining dozen chapters and for conducting rigorous interdisciplinary research…. the ample problems and tutorials throughout are much appreciated."
—Tobin R. Sosnick, Professor and Chair, Dept of Biochemistry and Molecular Biology, University of Chicago 
Contents
Probabilities and Statistics in Chemical and Biothermodynamics
Elementary Events.
How Probabilities Combine.
Permutation versus composition.
Discrete Probability Distributions
Continuous Distributions
Mathematical Tools in Thermodynamics
Calculus in Thermodynamics.
Fitting continuous curves to discrete data.
Determining the covariance matrix in leastsquares fitting.
Model testing with the ^{2} and fratio probability distributions.
The Framework of Thermodynamics and the First Law
What is Thermodynamics and What Does it Treat?
Dividing up the Universe: System and Surroundings
Equilibrium, Changes of State, and Reversibility
Thermodynamic Variables and Equations of State
The First law of Thermodynamics
Work
The reversible work associated with four fundamental changes of state.
The heat flow associated with the four fundamental changes in an ideal gas.
The work associated with the irreversible expansion of an ideal gas.
The connection between heat capacities and state functions.
A nonideal model: the van der Walls equation of state
The Second Law and Entropy
Some familiar examples of spontaneous change.
Spontaneous change and statistics
The directionality of heat flow at the macroscopic (classical) level
Free Energy as a Potential for the Laboratory and Biology
Internal energy as a potentialcombining the first and second laws.
Contributions of different chemical species to thermodynamic state functions—molar quantities.
Partial pressures of mixtures of gases.
Legendre transforms of a single variable.
Using Chemical Potentials to Describe Phase Transitions
Phases and their transformations.
The condition for equilibrium between two phases.
How chemical potentials of different phases depend on temperature and pressure: deriving a Tp phase diagram for water.
Additional restrictions from the phase diagram: the ClausiusClapeyron equation and Gibbs' phase rule.
The Concentration Dependence of Chemical Potential, Mixing, and Reactions
The dependence of chemical potential on concentration.
A simple lattice model for nonideal solution behavior.
Chemical reactions
Similarities (and differences) between free energies of reaction and mixing.
How chemical equilibrium depends on temperature
How chemical equilibrium depends on pressure
Conformational Equilibrium
Macromolecular structure.
A simple twostate model for conformational transitions.
Simultaneous visualization of N and D.
The thermal unfolding transition as a way to determine K_{fold} and G°.
A simple geometric way to connect Y_{obs} to K_{fold}.
Fitting conformational transitions to analyze the thermodynamics of unfolding.
A more realistic model thermal unfolding of proteins: the constant heat capacity model.
Measurement of thermal denaturation by differential scanning calorimetry.
Chemical denaturation of proteins.
APPENDIX 1: Differential Scanning Calorimetry
Ensembles that Interact with their Surroundings
Heat exchange and the canonical ensemble.
The canonical partition function.
A canonical ensemble representing a three particle isothermal system.
The isothermal isobaric ensemble and Gibbs free energy.
Partition Functions for Single Molecules and Chemical Reactions
A canonical partition function for a system with one molecule.
The relationship between the molecular and canonical partition functions.
An isothermalisobaric molecular partition function.
A statistical thermodynamic approach to chemical reaction.
The HelixCoil Transition
The noncooperative homopolymer model.
The noncooperative heteropolymer model.
Coupling between the sites and the basis for cooperativity
Coupling between residues through "nearestneighbor" models
Ligand Binding Equilibria from a Macroscopic Perspective
Ligand Binding to a single site
Practical issues in measuring and analyzing binding curves
Binding of multiple ligands
A macroscopic representation of multiple ligand binding.
The binding polynomial P: a partition function for ligand binding.
An example—the macroscopic binding of two ligands.
Binding to multiple different ligands: "heterotropic" binding
A general framework to represent thermodynamic linkage between multiple independent ligands.
Ligand Binding Equilibria from a Microscopic Perspective.
An example of general microscopic binding: three ligand binding sites.
Simplifications to microscopic binding models.
Binding to s identical, independent sites.
Binding to two classes of independent sites.
Binding to identical coupled sites
Explicit structural models for coupling among between binding sites
Allostery in ligand binding