Computational Modeling and Simulations of Biomolecular Systems

by Benoît Roux (Author)
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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).Contents:

  • Preface
  • Acknowledgments
  • Representation of Molecular Systems
  • Equilibrium Statistical Mechanics
  • Solvation Free Energy
  • Implicit Solvent and Continuum Models
  • Binding Equilibrium
  • Dynamics and Time Correlation Functions
  • Effective Dynamics of Reduced Models
  • Diffusion and Time Evolution of Probability Distribution
  • Transition Rates
  • Dynamics of Discrete State Models
  • Stochastic Simulations
  • Molecular Machines
  • Bibliography
  • Further Reading
  • Index
Readership: Students and researchers in Biophysics, Biochemistry and Biological sciences.Molecular Dynamics; Brownian Dynamics; Transition Rate; Markov Model0Key Features:
  • Simple non-technical textbook
  • Covers all the fundamental concepts in a unifying perspective
  • Covers from atomistic to phenomenological models

Protection
DRM Protected
Format
EPUB
Publication date
August 23, 2021
Publisher
Page count
208
ISBN
9789811232770
File size
4 MB