Atomic force microscopy of single molecules, steered molecular dynamics and the theory of
stochastic processes have established a new field that investigates mechanical functions of …

1. Introduction 2582. Set-up of MD simulations 2602.1 Constant-pressure dynamics 2602.2
Grand-canonical dynamics 2612.3 Boundary conditions 2613. Force fields 2623.1 Proteins …

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 rapid development of parallel computing systems made it possible to recreate and
predict physical processes on computers. Nowadays, computer simulations complement …

With recent advances in single-molecule manipulation techniques, it is now possible to
measure the mechanical resistance of proteins to external pulling forces applied at specific …

Das Buch behandelt Methoden des wissenschaftlichen Rechnens in der Moleküldynamik,
einem Bereich, der in vielen Anwendungen der Chemie, der Biowissenschaften, der …

Interactive molecular dynamics, a new modeling tool for rapid investigation of the physical
mechanisms of biological processes at the atomic level, is applied to study selectivity and …

The giant protein titin, which is responsible for passive elasticity in muscle fibers, is built
from∼ 300 regular immunoglobulin-like (Ig) domains and FN-III repeats. While the soft …

It is well known that electrostatic interactions play important roles in determining the
thermodynamic stability of proteins. However, the investigation into the role of electrostatic …

We present an experimental and computational analysis of the folding pathway of the 17th
domain of chicken brain α-spectrin, R17. Wild-type R17 folds in a two-state manner and the …