We discuss the use of Tsallis generalized mechanics in simulated annealing algorithms. For a small peptide, it is shown that older implementations are not more effective than regular simulated annealing in finding ground-state configurations. We propose a new implementation which leads to an...

We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self-interactions and protein–water interactions. The model contains both hot and cold folding transitions. In addition it predicts a critical point...

The structure of a polypeptide model by means of the Monte Carlo method has been studied. The model chains consisting of two kinds of residues (hydrophobic and hydrophilic) were confined on the (310) hybrid lattice. The residues interacted with the long-range contact potential. The short-range...

We present two recent integer programming models in molecular biology and study practical reformulations to compute solutions to some of these problems. In extension of previously tested linearization techniques, we formulate corresponding semidefinite relaxations and discuss practical rounding...

We calculate the Yang–Lee zeros for characteristic temperatures of the helix–coil transition in a continuum model of polyalanine. The distribution of these zeros differs from predictions of the Zimm–Bragg theory and supports recent claims that polyalanine exhibits a true phase transition....

This is study of a class of lattice polymer models which have a singular lowest-energy conformation and undergo a phase transition from the statistically random state to the unique ground state. Such foldable lattice polymers can be considered as a crude model for protein molecules. The...

We seek to provide a general strategy to permit the study of non-equilibrium aspects of conformational transitions in various types of heteropolymers. The theoretical methods we have developed rely mainly on the Gaussian self-consistent approach that replaces the exact non-linear Langevin...

The properties of correlation functions between spins in a specific spin model with no frustration, and with high frustration are compared. It was already confirmed that the ground state formation of our no frustration model showed two-state Arrhenius-like kinetics, such as observed in protein...

Investigations into the nature of sequence and structural conservation underlying protein folds have recently yielded profound insights into the mechanism of protein folding and stability. Combining this avenue of research with principles being pioneered in the field of network science holds the...