Why and how do systems react in thermally fluctuating environments?

• DOI: 10.1039/c1cp22504a
• Publication Date: 2011-11-02T12:00:51Z
• Authors: Shinnosuke Kawai; Tamiki Komatsuzaki
• Keywords: Reaction coordinate; Thermal fluctuations; Rank (graph theory); Langevin equation

Many chemical reactions, including those of biological importance, take place in thermally fluctuating environments. Compared to isolated systems, there arise markedly different features due the effects energy dissipation through friction and stochastic driving by random forces reflecting fluctuation environment. Investigation how robustly system reacts under influence thermal fluctuation, elucidating role reaction are significant subjects study reactions. In this article, we start with overviewing generalized Langevin equation (GLE), which has long been used continues be a powerful tool describe surrounded It also further treat nonstationary environment, conventional fluctuation–dissipation theorem no longer holds. Then, within framework present method recently developed extract new coordinate that is decoupled from all other coordinates region rank-one saddle linking reactant product. The buried nonlinear couplings among original force. was ensured sign (=a functional coordinates, velocities, friction, force) at any instant sufficient determine region, or product, finally arrives. We discuss one can extend such GLE stationary environments, where memory exist dynamics reaction.