Generalized-Ensemble Algorithms

Ideas and Applications
Erscheinungsjahr 2027
ISBN: 978-981-9273-00-3
Verlag: Springer

Buch, Englisch, 349 Seiten, Format (B × H): 155 mm x 235 mm

Reihe: Challenges and Advances in Computational Chemistry and Physics

This book presents the generalized-ensemble algorithms, which are powerful algorithms to simulate complex systems and greatly speed up the convergence to thermal equilibrium. By using the algorithms, one can perform random walks of certain physical quantities or their conjugate parameters, which alleviates the difficulty of conventional methods in which simulations tend to get trapped in states of local-minimum free energy states.

In this book, one of the most commonly used generalized-ensemble algorithms, namely, replica-exchange method (REM) is explained first. The original version performs a random walk in temperature space. The authors then present various extensions of REM by introducing multidimensional replica-exchange method in which multivariable random walks are realized by further enhancing the configurational sampling. Other generalized-ensemble algorithms are also presented for wide applications to many complex systems.

The book explains the basic ideas in detail, and it is not only useful for researchers in academia and industry in the field of computational physics, chemistry, biology, pharmacology, medicine, materials science but also can be used as a textbook for undergraduate and graduate students. 

Zielgruppe

Research

Autoren/Hrsg.

Sugita, Yuji

Okamoto, Yuko

Fachgebiete

• Naturwissenschaften Physik Angewandte Physik Biophysik
• Naturwissenschaften Chemie Chemie Allgemein Chemometrik, Chemoinformatik
• Naturwissenschaften Chemie Chemie Allgemein Pharmazeutische Chemie, Medizinische Chemie
• Naturwissenschaften Physik Physik Allgemein Theoretische Physik, Mathematische Physik, Computerphysik

Inhaltsverzeichnis

Introduction.- Generalized-Ensemble Algorithms and Other Enhanced Sampling Methods.- Replica-Exchange Method in isobaric-isothermal ensemble.- Replica-Exchange Umbrella Sampling (REUS).- Replica-Exchange Free Energy Perturbation (REFEP).- Replica-Exchange Solute Tempering (REST), REST2, and gREST.- Constant pH Replica-Exchange Method.- Replica-Exchange Method in Grandcanonical Ensemble.- Replica-Exchange Permutation.- Multicanonical Algorithm and its Extensions.- Wang-Landau Algorithm and its Extensions.- Simulated Tempering and its Extensions.- Metadynamics and its Extensions.- ?-dynamics.- Tsallis statistics.- Integrated Tempering.- Gaussian Accelerated MD.- Adaptive Biased MD.- Adaptive Biased Force.- Ligand Binding by REUS and REUS/gREST.- Aggregation of amyloid beta.- Conformational changes in SARS-CoV-2 spike protein.- Functional dynamics of multi-drug transporter.- Transmembrane helix assembly in biological membrane.- Summary and Outlook.

Über Autor(innen)

Yuji Sugita received his B.S.(1993), M.S.(1995), and Ph.D. (1998) in chemistry from Kyoto University. After his postdoctoral work at RIKEN, he worked as a research associate at the Institute for Molecular Science from 1998 to 2002. He moved to the Institute for Molecular and Cellular Biology, the University of Tokyo as a lecturer in 2002. He then became an associate chief scientist in RIKEN in 2007 and has been promoted to be a chief scientist in RIKEN since 2012. He has also worked as a team leader of the RIKEN Center for Computational Science (currently as a team principal) and the RIKEN Center for Biosystems Dynamics Research (until March 2025). Since October 2025, he has also worked as a professor at the Department of Physics, the University of Tokyo. His research has focused on the development of enhanced sampling methods and multi-scale molecular dynamics software, and their application to biomolecular structure, dynamics, and function relationships in cellular environments.

Yuko Okamoto received his B.S. and M.S. in physics from Brown University in 1979 and Ph.D. in physics from Cornell University in 1984. After his postdoctoral work at Virginia Polytechnic Institute and State University in 1984–1986, he worked as an assistant professor (later, an associate professor) at Nara Women’s University from 1986 to 1995. He moved to the Institute for Molecular Science and the Graduate University for Advanced Studies in 1995 as an associate professor. He then became a professor of biophysics at Nagoya University in 2005. He has been a professor emeritus of Nagoya University since he retired from it in 2022. His research has focused on the development of enhanced sampling methods in molecular simulations, for example, replica-exchange molecular dynamics and other generalized-ensemble algorithms, and their applications to computational physics/chemistry/biology problems such as protein folding, ligand binding, and prediction of three-dimensional structures of molecules.