Molecular dynamics (MD) is an invaluable tool with which to study protein folding in silico.
Although just a few years ago the dynamic behavior of a protein molecule could be …

The growing interest in the DNA‐based mesoscale systems of biological and nonbiological
nature has encouraged the computational molecular science community to develop coarse …

Over the past two decades, significant experimental advances have increased our ability to
control and manipulate individual DNA molecules. This capability has permitted …

A mesoscale model of DNA is presented (3SPN. 1), extending the scheme previously
developed by our group. Each nucleotide is mapped onto three interaction sites. Solvent is …

The implementation of molecular dynamics (MD) with our physics-based protein united-
residue (UNRES) force field, described in the accompanying paper (Khalili et al. J. Phys …

The mechanical stretching of single proteins has been studied experimentally for about 50
proteins, yielding a variety of force patterns and peak forces. Here we perform a theoretical …

Knotted proteins have their native structures arranged in the form of an open knot. In the last
ten years researchers have been making significant efforts to reveal their folding mechanism …

The Gō-like models of proteins are constructed based on the knowledge of the native
conformation. However, there are many possible choices of a Hamiltonian for which the …

What is the mechanism of two-state protein folding? The rate-limiting step is typically
explored through a Φ-value, which is the mutation-induced change in the transition state …

The Lagrange formalism was implemented to derive the equations of motion for the physics-
based united-residue (UNRES) force field developed in our laboratory. The Cα⊙⊙⊙ Cα …