James T. Hynes

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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)
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 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)
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)
Conical intersections play a major role in the current understanding of electronic de-excitation in polyatomic molecules, and thus in the description of photochemistry and photophysics of molecular systems. This article reviews aspects of the basic theory underlying the description of non-adiabatic transitions at conical intersections, with particular(More)
Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Abstract We report a study of DNA deformations using a coarse-grained(More)
The reorientation dynamics of interfacial water molecules was recently shown to change non-monotonically next to surfaces of increasing hydrophilicity, with slower dynamics next to strongly hydrophobic (apolar) and very hydrophilic surfaces, and faster dynamics next to surfaces of intermediate hydrophilicities. Through a combination of molecular dynamics(More)