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A computationally efficient molecular dynamics method for estimating the rates of rare events that occur by activated processes is described. The system is constrained at " bottleneck " regions on a general many-body reaction coordinate in order to generate a biased configurational distribution. Suitable reweighting of this biased distribution, along with(More)
We detail and considerably extend the analysis recently presented in Science 2006, 311, 832- 835 of the molecular mechanism of water reorientation based on molecular dynamics simulations and the analytic framework of the extended jump model (EJM). The water reorientation is shown to occur through large-amplitude angular jumps due to the exchange of hydrogen(More)
The results of a molecular dynamics (MD) computer simulation are presented for the solvation dynamics of an ion pair instanteously produced from a neutral pair, in a model polar aprotic solvent. These time-dependent fluorescence dynamics are analyzed theoretically to examine the validity of several linear response theory approaches, as well as of various(More)
We report a study of DNA deformations using a coarse-grained mechanical model and quantitatively interpret the allosteric effects in protein-DNA binding affinity. A recent single-molecule study (Kim et al. Science 2013, 339, 816) showed that when a DNA molecule is deformed by specific binding of a protein, the binding affinity of a second protein separated(More)
We offer some thoughts on the much debated issue of dynamical effects in enzyme catalysis, and more specifically on their potential role in the acceleration of the chemical step. Since the term 'dynamics' has been used with different meanings, we find it useful to first return to the Transition State Theory rate constant, its assumptions and the choices it(More)
We extend, via a reformulation in terms of Poisson brackets, the method developed previously (Rey et al., J. Phys. Chem. A, 2009, 113, 8949) allowing analysis of the pathways of an excited molecule's ultrafast vibrational relaxation in terms of intramolecular and intermolecular contributions. In particular we show how to ascertain, through the computation(More)
The influence of a polar and polarizable environment on charge transfer processes at a conical intersection (CI) can be described by a diabatic free energy model yielding coupled surfaces as a function of both molecular coordinates and a solvent coordinate. We extend and apply this model for the S1-S0 CI in protonated Schiff bases, representing a model for(More)