Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly - 1st Edition - ISBN: 9780128211359

Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly, Volume 170

1st Edition

Serial Volume Editors: Birgit Strodel Bogdan Barz
Hardcover ISBN: 9780128211359
Imprint: Academic Press
Published Date: 1st March 2020
Page Count: 300
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Table of Contents

1. Pairwise-Additive and Polarizable Atomistic Force Fields for Molecular Dynamics Simulations of Proteins
Justin Lemkul
2. Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers
Adam Liwo
3. Monte Carlo methods in protein folding and assembly
Sandipan Mohanty
4. Enhanced sampling and free energy methods
Qinghua Liao
5. Markov models of molecular simulations of protein folding, protein-protein interactions, and aggregation
Nicolae-viorel Buchete
6. Molecular dynamics simulations with experimental restraints
Kresten Lindorff-Larsen
7. Protein folding simulations
Ivan Coluzza
8. Thermal stability of proteins
Fabio Sterpone
9. Aggregation of short disease-related peptides
Philippe Derreumaux
10. Dichotomy between universality and specificity of amyloid β-protein oligomer formation: Molecular dynamics perspective
Brigita Urbanc
11. Computational studies of protein aggregation mediated by amyloid: Fibril elongation and secondary nucleation
Wei Han


Description

Computational approaches for understanding dynamical systems: protein folding and assembly brings together monographs from the fields of computational biophysics and biochemistry to provide a comprehensive overview of recent progress on in silico methods for studying proteins. The Volume starts with a an overview of the latest developments for protein force fields, including atomistic, polarizable and coarse-grained force fields, which is followed by reviews of enhanced sampling methods based on molecular dynamics (MD) simulations, Monte Carlo methods for protein simulations, and techniques for the inclusion of experimental constraints during MD simulations. As Markov state models have become very popular as a technique for identifying stationary and kinetic information of protein dynamics from MD simulation data, a Volume chapter is devoted to this topic. The focus of the second half of the Volume is on applications of biomolecular simulations by reviewing how such simulations contributed to a better understanding of biological phenomena such as protein folding, the thermal stability of proteins, the interplay between lipid membranes and proteins, and protein aggregation as occurring during viral capsid assembly or in amyloid diseases.

Key Features

    • Presents a comprehensive description of indispensable tools for computational biophysicists
    • The latest advances in protein simulations are presented in a coherent and graphically appealing manner
    • Contains contributions from renowned experts in the field

Readership

Scientists working actively in the field of molecular simulations of proteins. The Volume is also appropriate for new investigators to the field or experimentalists who wish to familiarize themselves with computational methods in biophysics and biochemistry.


Details

No. of pages:
300
Language:
English
Copyright:
© Academic Press 2020
Published:
1st March 2020
Imprint:
Academic Press
Hardcover ISBN:
9780128211359

Ratings and Reviews


About the Serial Volume Editors

Birgit Strodel Serial Volume Editor

Birgit Strodel studied chemistry at Heinrich Heine University Düsseldorf (Germany) and the University of North Carolina at Chapel Hill (USA) and received her PhD in Theoretical Chemistry from the University of Frankfurt/Main (Germany) in 2005. She then joined the group of Prof. David J. Wales at Cambridge University (UK) as a postdoctoral research associate. Since 2009 she heads the Computational Biochemistry Group at the Jülich Research Centre (Germany) and was appointed Professor at Heinrich Heine University Düsseldorf in 2011. Her research interests primarily involve the thermodynamics and kinetics of protein aggregation.

Affiliations and Expertise

Jülich Research Centre, Germany

Bogdan Barz Serial Volume Editor

Bogdan Barz has graduated in 2002 from Babeș-Bolyai University of Cluj-Napoca, Romania. During his Masters in Applied Mathematics and Astronomy at Babeș-Bolyai University between 2002-2004 he also worked as a researcher at the National Institute for Research and Development of Isotopic and Molecular Technologies of Cluj-Napoca. In 2009 he received his PhD from the Physics and Astronomy Department at the University of Missouri in Columbia, MO, USA, followed by a postdoctoral period at the Physics Department at Drexel University, Philadelphia, USA. In 2012 he joined the Institute of Complex Systems at Forschungszentrum Jülich (Research Centre Jülich), Germany as a postdoctoral fellow. In 2018 he became an independent group leader at the Institute of Physical Biology, Heinrich Heine University Düsseldorf, Germany.Bogdan Barz has graduated in 2002 from Babeș-Bolyai University of Cluj-Napoca, Romania. During his Masters in Applied Mathematics and Astronomy at Babeș-Bolyai University between 2002-2004 he also worked as a researcher at the National Institute for Research and Development of Isotopic and Molecular Technologies of Cluj-Napoca. In 2009 he received his PhD from the Physics and Astronomy Department at the University of Missouri in Columbia, MO, USA, followed by a postdoctoral period at the Physics Department at Drexel University, Philadelphia, USA. In 2012 he joined the Institute of Complex Systems at Forschungszentrum Jülich (Research Centre Jülich), Germany as a postdoctoral fellow. In 2018 he became an independent group leader at the Institute of Physical Biology, Heinrich Heine University Düsseldorf, Germany.

Affiliations and Expertise

Heinrich Heine University, Germany