Molecular dynamics simulation of the activation of soft molecules solved in condensed media

Introduction to the reaction theory and cluster dynamics of enzymes

“…We found that in thermal equilibrium there exists a characteristic region of temperatures and densities where energy is mainly concentrated on soft sites. We observed also rather long tails in the energy distribution making high-energy events much more probable than expected from a simple Boltzmann distribution [Ebeling et al, 1995]. Further we have shown that the spectra of the excitations is similar to coloured noise spectra [Ebeling and Podlipchuk, 1996].…”

“…An example are the hard pulses, which we can excite by knocking a piece of matter with a hammer. These excitations have several properties in common with solitons, in particular they are localiced in space.It was shown that the effects of the fusion of such nonlinear soliton-like excitations persist and show analogies to the fusion of solitons [Ebeling et al, 1995]. Especially we studied the influence of this dynamical effect on the energy distribution of soft sites imbedded into the system.…”

“…We will analyze analytically and numerically the basic nonlinear dynamical effects, and in particular the soliton fusion, which was shown to be responsible for an energy localization at definite sites. In earlier work we investigated already 1-d, 2-d and 3-d systems with nonlinear finite-size interactions by simulations [Ebeling et al, 1995]. As well known in such more realistic systems, soliton excitations strictly speaking do not exist.…”

Microscopic Models and Simulations of Local Activation Processes

“…We analyzed analytically and numerically the basic nonlinear dynamical effects, and in particular the soliton fusion, which was shown to be responsible for an energy localization at definite sites. Further we investigated 1D-, 2D-and 3D-systems with nonlinear finite-size interactions by simulations [Ebeling et al, 1995]. As well known in such more realistic systems, soliton excitations strictly speaking do not exist.…”

“…In other words instead of a phenomenological white noise we would like to take into account real molecular noise created by collisions. For this purpose we are using the standard methods of molecular dynamics simulations [Allen & Tildesley, 1990;Norman et al, 1992Norman et al, , 1993Hafskjold & Ikehoshi, 1995;Ebeling et al, 1995. Our simulations are based on a variant of the Verlet velocity algorithm which is explained in [Norman et al, 1993;Ebeling et al, 1995.…”