CECAM - Progress in simulating activated processes

Activated processes are characterised by time-scales longer than the simulation times accessible at present and in the foreseeable future. In an opportune set of variables, they correspond to transitions between metastable states separated by a (free) energy barrier too high to be overcome by thermal fluctuations. Although very difficult to tackle numerically, such processes are relevant in many scientific fields: chemical reactions, phase transitions that require rearrangement of atomistic configurations, formation of nano-materials in complex matrices,biological processe, etc. Examples of activated processes in biological meterials are protein folding, ion and, in particular, proton transfer in intra-membrane channels, electron transfer, conformational changes in poly-peptides and proteins, enzyme catalysis, protein and DNA binding, etc. Methods for studying activated processes have a long and rich history that ranges from thermodynamic integration [1, 2] to metadynamics [3]. Most of these techniques however are hindered by severe limitations when many degrees of freedom are involved in the process, or if an a priori knowledge of the reaction coordinate is impossible. Recently, two strategies have been proposed that start from different but firm theoretical ground and share similar potential to tackle condensed phase problems. The methods are Transition Path Sampling (TPS) of C. Dellago et al. [4] and the combination of the temperature accelerated sampling (TAS) and string method (SM) of E. Vanden Eijnden [5,6]. The aim of this school is to disseminate these modern techniques to the broader community of scientists interested in the simulation of processes and reactions that cannot simulated by standard molecular dynamics at the relevant temperature.

Progress in simulating activated processes

Valle Capore, loc. Valle snc, 02030 Casaprota (RI), Italy

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