Related papers: Analysis of Transition State Theory Rates upon Spa…
Coarse-graining or model reduction is a term describing a range of approaches used to extend the time-scale of molecular simulations by reducing the number of degrees of freedom. In the context of molecular simulation, standard…
In molecular dynamics (MD) simulations, accessing transition probabilities between states is crucial for understanding kinetic information, such as reaction paths and rates. However, standard MD simulations are hindered by the capacity to…
We study the equation of state of a strongly interacting theory of relativistic bosons and chiral fermions in the vicinity and above the chiral phase transition temperature. Our model resembles presently used low-energy models of QCD in…
The rate of escape of an ideal bead-spring polymer in a symmetric double-well potential is calculated using transition state theory (TST) and the results compared with direct dynamical simulations. The minimum energy path of the transitions…
To study materials phenomena simultaneously at various length scales, descriptions in which matter can be coarse grained to arbitrary levels, are necessary. Attempts to do this in the static regime (i.e. zero temperature) have already been…
Mixed atomistic and continuum methods offer the possibility of carrying out simulations of material properties at both larger length scales and longer times than direct atomistic calculations. The quasi-continuum method links atomistic and…
Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…
We present a shear-transformation-zone (STZ) theoretical analysis of molecular-dynamics simulations of a rapidly sheared metallic glass. These simulations are especially revealing because, although they are limited to high strain rates,…
Coarse-grained (CG) models provide an effective route to reducing the complexity of molecular simulations (MD), but conventional approaches depend heavily on long all-atom MD trajectories to adequately sample configurational space. This…
This Feature Article presents an overview of the current status of Ring Polymer Molecular Dynamics (RPMD) rate theory. We first analyze the RPMD approach and its connection to quantum transition-state theory. We then focus on its practical…
The framework of transition state theory (TST) provides a powerful way for analyzing the dynamics of physical and chemical reactions. While TST has already been successfully used to obtain reaction rates for systems with a single…
We review the formalism of the effective average action in quantum field theory which corresponds to a coarse grained free energy in statistical mechanics. The associated exact renormalization group equation and possible nonperturbative…
We introduce a method "DMT" for approximating density operators of 1D systems that, when combined with a standard framework for time evolution (TEBD), makes possible simulation of the dynamics of strongly thermalizing systems to arbitrary…
An open quantum system with multiple levels coupled to a bosonic environment at zero temperature is investigated systematically using the non-Markovian quantum-state-diffusion (QSD) method [W. T. Strunz, L. Di\'osi, and N. Gisin, Phys. Rev.…
Surprisingly, there exists a quantum flux-side time-correlation function which has a non-zero short-time (t->0+) limit, and thus yields a rigorous quantum generalization of classical transition-state theory (TST). In this Part I of two…
We review some recent coarse-graining and multi-scale methods, but also put forward some new ideas for addressing such issues. We find that, if one is guided by nonequilibrium statistical mechanics and thermodynamics, it is possible to…
A common paradigm used in the construction of equations of state is to decompose the thermodynamics into a superposition of three terms: a static-lattice cold curve, a contribution from the thermal motion of the nuclei, and a contribution…
We present a coarse molecular-dynamics (CMD) approach for the study of stress-induced structural transformations in crystals at finite temperatures. The method relies on proper choice of a coarse variable (order parameter, observable),…
It is a challenge to obtain an accurate model of the state-to-state dynamics of a complex biological system from molecular dynamics (MD) simulations. In recent years, Markov State Models have gained immense popularity for computing…
A combination of first principle molecular dynamics (MD) simulations with a rate equation model (MD-RE approach) is presented to study the trapping and the scattering of rare gas atoms from metal surfaces. The temporal evolution of the atom…