Statistical thermodynamics provides a powerful theoretical framework for analyzing, understanding and predicting the conformational properties of biomolecules. The central quantity is the potential of mean force or effective energy as a function of conformation, which consists of the intramolecular energy and the solvation free energy. The intramolecular energy can be reasonably described by mo...

Systematic numerical investigations of conformational motions in single actin molecules were performed by employing a simple elastic-network (EN) model of this protein. Similar to previous investigations for myosin, we found that G-actin essentially behaves as a strain sensor, responding by well-defined domain motions to mechanical perturbations. Several sensitive residues within the nucleotide...

Molecular landers are molecules comprising of a central rigid molecular wire maintained above a metallic surface by organic spacers, which allows specific ultrahigh vacuum-scanning tunneling microscopy experiments to be performed at the single-molecule level. The understanding of the molecule-surface interactions, intramolecular mechanics, and the possibility to perform extremely precise tip-in...

The DNA is treated using the discretized wormlike bead-chain model, where each “bead” represents a 3 nm segment of relaxed DNA (1, 2). Each bead is assigned a salt-dependent charge qdna according to Stigter (3). The DNA bead-chain is also assigned an intramolecular force field comprising of stretching, bending, twisting terms that capture all aspects of DNA mechanics. The stretching energy Ustr...

In traditional molecular mechanics force fields, intramolecular non-bonded interactions are modelled as intermolecular interactions, and the form of the torsion potential is based on the conformational profiles of small organic molecules. We investigate how a separate model for the intramolecular forces in pharmaceuticals could be more realistic by analysing the low barrier to rotation of the p...

Molecular rotors are a group of fluorescent molecules that form twisted intramolecular charge transfer (TICT) states upon photoexcitation. When intramolecular twisting occurs, the molecular rotor returns to the ground state either by emission of a red-shifted emission band or by nonradiative relaxation. The emission properties are strongly solvent-dependent, and the solvent viscosity is the pri...