The term molecular mechanics (MM) refers to the use of simple potential-energy functions
(eg, harmonic oscillator or Coulombic potentials) to model molecular systems. Molecular …

The phosphoenolpyruvate (PEP): carbohydrate phosphotransferase system (PTS) is found
only in bacteria, where it catalyzes the transport and phosphorylation of numerous …

NAMD is a parallel molecular dynamics code designed for high‐performance simulation of
large biomolecular systems. NAMD scales to hundreds of processors on high‐end parallel …

The goal of systems biology is to understand the behavior of the whole in terms of
knowledge of the parts. This is hard to achieve in many cases due to the difficulty of …

It has been more than 50 years since the elucidation of the structure of double-helical DNA.
Despite active research and progress in DNA biology and biochemistry, much remains to be …

The paper contributes a general dynamical formulation and numerical solution procedure for
studying nonlinear and three-dimensional dynamics of Kirchhoff rods. Target applications …

A multiscale simulation of a complex between the lac repressor protein (LacI) and a 107-bp-
long DNA segment is reported. The complex between the repressor and two operator DNA …

An elastic rod model of a protein-bound DNA loop is adapted for application in multi-scale
simulations of protein-DNA complexes. The classical Kirchhoff system of equations which …

Hyper-redundant (or snakelike) manipulators have many more degrees of freedom than
required to position and orient an object in space. They have been employed in a variety of …

At many promoters, transcription is regulated by simultaneous binding of a protein to
multiple sites on DNA, but the structures and dynamics of such transcription factor-mediated …