We propose a new global optimization method (Simulated Tempering) for simulating
effectively a system with a rough free-energy landscape (ie, many coexisting states) at finite …

We consider six different secondary structures of proteins and construct two types of Go-type
off-lattice models: with the steric constraints and without. The basic amino acid–amino acid …

The protein molecule is a very complex system, and understanding the folding of natural
proteins remains one of the most challenging problems in biophysics. In recent years there …

I discuss optimized data analysis and Monte Carlo methods. Reweighting methods are
discussed through examples, such as Lee-Yang zeroes in the Ising model and the absence …

We study the kinetics of folding of a heteropolymer containing a specific sequence of
hydrophobic, hydrophilic, and neutral residues. The heteropolymer, representing the alpha …

Folding properties of a two-dimensional toy protein model containing only two amino acid
types, hydrophobic and hydrophilic, respectively, are analyzed. An efficient Monte Carlo …

Proteins are biological macromolecules that perform a large variety of functions in living
organisms. Their function is encoded in the well de ned three dimensional structure which …

We present the results of a self-consistent, unified molecular dynamics study of simple
model heteropolymers in the continuum with emphasis on folding, sequence design, and the …

Much attention has been recently devoted to the development of Monte Carlo schemes for
the simulation of polymer systems. 1–8 From the computational point of view, the main issue …

Protein folding is a relatively fast process considering the astronomical number of
conformations in which a protein could find itself. Within the framework of a lattice model, we …