Statistical theory of any physical process needs a formulation of possibly simple but adequate models of the phenomena underlying microscopic dynamics. Remarkable progress in studies of internal dynamics of biomolecules acomplished in the recent years has made it possible to formulate such...

Molecular dynamics simulations of plastocyanin, an electron transfer copper containing protein involved in the photosynthetic process, have been performed in both the hydrated and dry state. An analysis of the potential energy fluctuations during a 500 ps dynamical evolution of the macromolecule...

A realistic physical model for the so-called rate-promoting vibration (RPV) at enzyme action is constructed. The origin of the RPV is assumed to be an oscillating electric field produced by long-lived localized vibrational modes in protein dynamics, namely, by the so-called discrete breather...

Protein activities may exhibit oscillations which often occur due to the existence of a negative feedback loop with an effective time delay. Many biological systems are, however, not limited to one feedback loop but consist of multiple loops on different regulatory levels. Here, we analyze the...

Identification of proton-conducting pathways in a protein is a key to understanding the mechanisms of biomolecular proton transfer. Starting from a known protein structure, proton pathways are modeled here as hydrogen bonded networks of proton conducting groups, including proton-exchanging...