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)
Intercalation into DNA (insertion between a pair of base pairs) is a critical step in the function of many anticancer drugs. Despite its importance, a detailed mechanistic understanding of this process at the molecular level is lacking. We have constructed, using extensive atomistic computer simulations and umbrella sampling techniques, a free energy(More)
Excited-state processes at conical intersections (CIs) involving charge transfer phenomena can depend sensitively on the influence of a polar and polarizable environment. We propose here a formulation to describe the chromophore-environment interaction for such situations. In a model study, we focus on an extension of the two-electron two-orbital model by(More)
The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics(More)
We analyzed the frequency of occurrence of traumatic aortic rupture (TAR) in patients with and without thoracic spinal fractures. Among 4,676 blunt chest trauma victims admitted to the hospital between 1972 and 1988, 148 (3.2%) suffered one or more thoracic vertebral fractures. There were 73 patients with one or more fractures of the first eight thoracic(More)
The dynamics of water molecules next to hydrophobic solutes is investigated, specifically addressing the recent controversy raised by the first time-resolved observations, which concluded that some water molecules are immobilized by hydrophobic groups, in strong contrast to previous NMR conclusions. Through molecular dynamics simulations and an analytic(More)
Water hydrogen-bond (HB) dynamics around amino acids in dilute aqueous solution is investigated through molecular dynamics simulations and analytic modeling. We especially highlight the critical role played by hydrophilic HB acceptors: the strength of the HB formed with water has a pronounced effect on the HB dynamics, in accord with several experimental(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 dynamics of water molecules within the hydration shell surrounding a biomolecule can have a crucial influence on its biochemical function. Characterizing their properties and the extent to which they differ from those of bulk water have thus been long-standing questions. Following a tutorial approach, we review the recent advances in this field and the(More)