The “protein folding problem” consists of three closely related puzzles:(a) What is the folding
code?(b) What is the folding mechanism?(c) Can we predict the native structure of a protein …

In complex systems with many degrees of freedom such as peptides and proteins, there
exists a huge number of local‐minimum‐energy states. Conventional simulations in the …

We have developed a formulation for molecular dynamics algorithm for the replica-
exchange method. The effectiveness of the method for the protein-folding problem is tested …

The effectiveness of a new algorithm, parallel tempering, is studied for numerical simulations
of biological molecules. These molecules suffer from a rough energy landscape. The …

We have developed a new simulation algorithm for free-energy calculations. The method is
a multidimensional extension of the replica-exchange method. While pairs of replicas with …

In modern-day simulations of many-body systems, much of the computational complexity is
shifted to the identification of slowly changing molecular order parameters called collective …

This book teaches modern Markov chain Monte Carlo (MC) simulation techniques step by
step. The material should be accessible to advanced undergraduate students and is suitable …

The growing adoption of generalized-ensemble algorithms for biomolecular simulation has
resulted in a resurgence in the use of the weighted histogram analysis method (WHAM) to …

Recently, a novel concept for the computation ofessentialfeatures of the dynamics of
Hamiltonian systems (such as molecular dynamics) has been proposed. The realization of …

Introduction to Proteins provides a comprehensive and state-of-the-art introduction to the
structure, function, and motion of proteins for students, faculty, and researchers at all levels …