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See detailOn the dynamics of reaction coordinates in classical, time-dependent, many-body processes
Meyer, Hugues UL; Voigtmann, Thomas; Schilling, Tanja

in The Journal of chemical physics (2019), 150(17), 174118

Complex microscopic many-body processes are often interpreted in terms of so-called “reaction coordinates,” i.e., in terms of the evolution of a small set of coarse-grained observables. A rigorous method ... [more ▼]

Complex microscopic many-body processes are often interpreted in terms of so-called “reaction coordinates,” i.e., in terms of the evolution of a small set of coarse-grained observables. A rigorous method to produce the equation of motion of such observables is to use projection operator techniques, which split the dynamics of the observables into a main contribution and a marginal one. The basis of any derivation in this framework is the classical Heisenberg equation for an observable. If the Hamiltonian of the underlying microscopic dynamics and the observable under study do not explicitly depend on time, this equation is obtained by a straightforward derivation. However, the problem is more complicated if one considers Hamiltonians which depend on time explicitly as, e.g., in systems under external driving, or if the observable of interest has an explicit dependence on time. We use an analogy to fluid dynamics to derive the classical Heisenberg picture and then apply a projection operator formalism to derive the nonstationary generalized Langevin equation for a coarse-grained variable. We show, in particular, that the results presented for time-independent Hamiltonians and observables in the study by Meyer, Voigtmann, and Schilling, J. Chem. Phys. 147, 214110 (2017) can be generalized to the time-dependent case. [less ▲]

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See detailOn the non-stationary generalized Langevin Equation
Meyer, Hugues UL; Voigtmann, Thomas; Schilling, Tanja

in The Journal of chemical physics (2017), 147(21), 214110

In molecular dynamics simulations and single molecule experiments, observables are usually measured along dynamic trajectories and then averaged over an ensemble (“bundle”) of trajectories. Under ... [more ▼]

In molecular dynamics simulations and single molecule experiments, observables are usually measured along dynamic trajectories and then averaged over an ensemble (“bundle”) of trajectories. Under stationary conditions, the time-evolution of such averages is described by the generalized Langevin equation. By contrast, if the dynamics is not stationary, it is not a priori clear which form the equation of motion for an averaged observable has. We employ the formalism of time-dependent projection operator techniques to derive the equation of motion for a non-equilibrium trajectory-averaged observable as well as for its non-stationary auto-correlation function. The equation is similar in structure to the generalized Langevin equation but exhibits a time-dependent memory kernel as well as a fluctuating force that implicitly depends on the initial conditions of the process. We also derive a relation between this memory kernel and the autocorrelation function of the fluctuating force that has a structure similar to a fluctuation-dissipation relation. In addition, we show how the choice of the projection operator allows us to relate the Taylor expansion of the memory kernel to data that are accessible in MD simulations and experiments, thus allowing us to construct the equation of motion. As a numerical example, the procedure is applied to Brownian motion initialized in non-equilibrium conditions and is shown to be consistent with direct measurements from simulations. [less ▲]

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See detailCommunication: Many-body stabilization of non-covalent interactions: Structure, stability, and mechanics of Ag3Co(CN)6 framework
Liu, Xiaofei; Hermann, Jan; Tkatchenko, Alexandre UL

in The Journal of Chemical Physics (2016), 145(24), 241101

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See detailRelaxations in the metastable rotator phase of n-eicosane
Di Giambattista, Carlo UL; Sanctuary, Roland UL; Perigo, Elio Alberto UL et al

in The Journal of Chemical Physics (2015), 143

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