1,721,101 research outputs found
Molecular dynamics simulation of rare events: Calculation of rate constants
No full textWe present a computationally efficient molecular dynamics method based on holonomic constraints devised to estimate the rate constants of rare activated events of short duration.We assume that the process is described by a reaction coordinate , a well-defined function in configuration space, and we constrain the system at the ``bottleneck" region by prescribing the value of . MD trajectories sample now phase space according to a biased configurational distribution and averages can be taken from such a new, {\it Blue Moon }, ensemble with suitable reweighting to study rare events. Applications are not restricted to classical processes and ways to extend the method to quantum activated processes in condensed phases are also outlined
Blue moon approach to rare events
No full textThe Blue Moon ensemble is a computationally efficient molecular dynamics method to estimate the rate constants of rare activated events when the process can be described by a reaction coordinate xi(r), a well-defined function in configuration space. By means of holonomic constraints a number of values of (r) can be prescribed along the relevant path to identify the bottleneck region first and to sample an ensemble of starting conditions to generate activated trajectories. These MD trajectories sample phase space according to a biased configurational distribution. With a suitable re-weighting of averages from such ensemble of trajectories one can characterize completely rare events
Long-time tails in two-dimensional fluids by molecular dynamics
No full textWe report on molecular dynamics simulation of long-time tails in the velocity and stress autocorrelation functions of a dense two-dimensional fluid. Large systems of the order of hundred thousand particles have been investigated, performing canonical averages over an ensemble of trajectories generated on a parallel computer. We find the well-known t(-1) decay for the velocity autocorrelation function at two different densities of the;fluid, together with a faster than linear time dependence for the mean-square displacement at long times. Although there are indications of an asymptotically faster decay, the data are not precise enough to discriminate whether the decay is in agreement with the (t root 1n t)(-1) prediction of consistent mode-coupling theory or it is due to finite size effects. No evidence, within the statistical errors, is found for a long-time tail in the stress autocorrelation function. This finding is in agreement with recent NEMD results [Hoover et al., Phys. Rev. E 51 (1995) 273; Gravina et al., Phys. Rev. E 52 (1995) 6123], who find an analytical dependence of the shear viscosity upon the shear rate with no evidence for divergence in the Green-Kubo value
The role of filament flexibility in the response of a bundle of actin filaments to load in supercritical conditions.
No full textNon Equilibrium Molecular Dynamics calculation of bulk viscosity in simple Lennard-Jones fluid
No full textMOLECULAR DYNAMICS SIMULATIONS COMPLEMENT EXPERIMENTAL DATA ON PROTEIN EMBEDDED IN SUGAR-WATER SYSTEMS
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Protein-solvent coupling in carboxy-myoglobin-sugar-water systems Molecular Dynamics Simulations and Experiments
No full textMolecular Dynamics simulation of carboxy-myoglobin in trehalose and sucrose-water systems
No full textProtein-solvent coupling in carboxy-myoglobin/sugar/water systems by molecular dynamics simulations
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