Entropy and Free Energy in Structural Biology: From Thermodynamics to Statistical Mechanics to Computer Simulation

Computer simulation is crucial in structural biology for protein structure determination and binding free energy calculation, and Entropy and Free Energy in Structural Biology provides a comprehensive course on simulation technology. The book covers probability theory, classical thermodynamics, non-equilibrium thermodynamics, and advanced methods for polymers and protein systems, with solved problems and examples. It is a valuable resource for advanced undergraduate and graduate students in chemistry, chemical engineering, biochemistry, biophysics, pharmacology, and computational biology.

Format: Paperback / softback
Length: 374 pages
Publication date: 01 April 2022
Publisher: Taylor & Francis Ltd

Computer simulation has emerged as a pivotal force driving development in statistical mechanics. In the realm of structural biology, computer simulation assumes a central role as the primary theoretical tool for determining protein structures and calculating the free energy of binding, both of immense significance in drug design. Entropy and Free Energy in Structural Biology serves as a comprehensive guide, presenting the simulation technology in a systematic manner. This book, structured as a course, comprises four parts:

Part I delves into probability theory, emphasizing the distinction between experimental probability, probability space, and the experimental probability on a computer. It further elaborates on the mathematical structure of product spaces, which are fundamental for solving probability problems and developing simulation methods, particularly for calculating entropy.

Part II provides a brief review of classical thermodynamics, from which a non-traditional derivation of statistical mechanics is formulated. Extensive theoretical aspects of statistical mechanics are examined.

Part III explores various topics in non-equilibrium thermodynamics and statistical mechanics closely related to equilibrium, including Onsager relations, the two Fick's laws, and the Langevin and master equations. The Monte Carlo and molecular dynamics procedures are discussed in detail.

Part IV presents advanced simulation methods for polymers and protein systems, encompassing techniques for conformational search and calculating the potential of mean force and the chemical potential. Thermodynamic integration, methods for calculating absolute entropy, and methodologies for calculating absolute free energy of binding are evaluated.

Enhanced by a multitude of solved problems and examples, this book serves as a valuable resource for researchers and practitioners in structural biology and statistical mechanics. It empowers readers to harness the power of computer simulation to unravel the complex dynamics and properties of biological systems, facilitating advancements in drug discovery and other fields.

Weight: 454g
Dimension: 254 x 178 (mm)
ISBN-13: 9780367427450