Transition path sampling molecular dynamics

The basis of the transition path sampling method is the statistical description of dynamical pathways in terms of a probability distribution. To define such a distribution consider a molecular system evolving in time and imagine that we take snapshots of this system at regularly spaced times fj separated by the time step At. Each of these snapshots, or states, consists of a complete description z of the system in terms of the positions q = <71, <72, , [Pg.252]

Lo et al. used plane wave calculations to examine methanol coupling near a protonated site in chabazite.286,287 Constrained Car-Parrinello molecular dynamics were used to probe potential reaction coordinates for the reaction. These calculations suggest a reaction path that proceeds via formation of stable intermediates of methane and formaldehyde. A novel feature of this work was the use of transition path sampling, a technique to efficiently search for transition states that requires little a priori information regarding the configuration of the final products of a reaction. Methanol coupling in ferrierite (FER) has been examined with periodic DFT calculations by Govind et al.2SS... 

In Section 4 we will use two theoretical techniques (transition path sampling (TPS) and essential dynamics (ED)) to analyze molecular dynamics trajectories. We will explain how we were able to identify in atomic detail collective motions that affect catalysis. 

H. Transition Path Sampling with an Existing Molecular Dynamics Program... 

The transition path sampling techniques we have described assume that an initial reactive pathway is available. Generating such a pathway is therefore an important step in applying the method. In the simplest cases, a trajectory connecting A and B can be obtained by running a long molecular dynamics (or stochastic dynamics) simulation. For most applications, however, the... 

B. Peters, Molecular Simulation, 36, 1265 (2010). Recent Advances in Transition Path Sampling Accurate Reaction Coordinates, Likelihood Maxiniisation and Diffusive Barrier-Crossing Dynamics. 

In chapter 6, we study the diffusion of isobutane in Silicalite. At low pressures, isobutane is preferentially adsorbed at the intersections of Silicalite. As there is a large free energy barrier between two intersections, the jump of an isobutane molecule to a nearby intersection will be a rare event. Therefore, we cannot use conventional Molecular Dynamics (MD) to compute the jump rate (and therefore also the diffusion coefficient). To compute the diffusion coefficient, we have used transition path sampling. In these simulations, we generate an ensemble of MD tra-... 

Figure 11. The solid line depicts the quantum adiabatic free energy curve for the Fe /Fe electron transfer at the water/Pt(lll) interface (obtained by using the Anderson-Newns model, path integral quantum transition state theory, and the umbrella sampling of molecular dynamics. The dashed line shows the curve from the classical calculation as given in Fig. 5. (Reprinted from Ref 14.)...

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