Computational Modeling and Simulations of Biomolecular Systems / Benoit Roux.

Format:

Book

Author/Creator:

Roux, Benoît.

Contributor:

World Scientific (Firm)

Language:

English

Subjects (All):

Molecular biology--Mathematical models.

Molecular biology.

Computational Biology.

Medical Subjects:

Computational Biology.

Physical Description:

1 online resource

polychrome

Place of Publication:

Singapore ; Hackensack, NJ : World Scientific Publishing, [2022]

System Details:

text file

Summary:

This textbook originated from the course "Simulation, Modeling, and Computations in Biophysics" that I have taught at the University of Chicago since 2011. The students typically came from a wide range of backgrounds, including biology, physics, chemistry, biochemistry, and mathematics, and the course was intentionally adapted for senior undergraduate students and graduate students. This is not a highly technical book dedicated to specialists. The objective is to provide a broad survey from the physical description of a complex molecular system at the most fundamental level, to the type of phenomenological models commonly used to represent the function of large biological macromolecular machines. The key conceptual elements serving as building blocks in the formulation of different levels of approximations are introduced along the way, aiming to clarify as much as possible how they are interrelated. The only assumption is a basic familiarity with simple mathematics (calculus and integrals, ordinary differential equations, matrix linear algebra, and Fourier-Laplace transforms). Book jacket.

Contents:

Chapter 1 Representation of molecular systems p. 1

Chapter 2 Equilibrium statistical mechanics p. 15

Chapter 3 Solvation free energy p. 27

Chapter 4 Implicit solvent and continuum models p. 39

Chapter 5 Binding equilibrium p. 55

Chapter 6 Dynamics and time correlation functions p. 67

Chapter 7 Effective dynamics of reduced models p. 87

Chapter 8 Diffusion and time evolution of probability distribution p. 107

Chapter 9 Transition rates p. 117

Chapter 10 Dynamics of discrete state models p. 133

Chapter 11 Stochastic simulations p. 147

Chapter 12 Molecular machines p. 167.

Notes:

Electronic reproduction. Singapore Available via World Wide Web.

Description based on online resource; title from digital title page (viewed on November 10, 2021).

ISBN:

9789811232763

9811232768

Publisher Number:

99988833126

Access Restriction:

Restricted for use by site license.