Related papers: String Method for the Study of Rare Events
We use effective string theory (EST) to describe a toroidal 2d domain wall embedded in a 3d torus. In particular, we compute the free energy of the domain wall in an expansion in inverse powers of the area, up to the second non-universal…
The kinetics of collective rearrangements in solution, such as protein folding and nanocrystal phase transitions, often involve free energy barriers that are both long and rough. Applying methods of transition path sampling to harvest…
The low-temperature driven or thermally activated motion of several condensed matter systems is often modeled by the dynamics of interfaces (co-dimension-1 elastic manifolds) subject to a random potential. Two characteristic quantitative…
Applying a numerical transfer-matrix formalism, we obtain complex-valued constrained free energies for the two-dimensional square-lattice nearest-neighbor Ising ferromagnet below its critical temperature and in an external magnetic field.…
A system's internal dynamics and its interaction with the environment can be determined by tracking how external perturbations affect its transition rates between states. Quantitative measurements of these rates are crucial for optimizing…
We propose a new method to obtain kinetic properties of infrequent events from molecular dynamics simulation. The procedure employs a recently introduced variational approach [Valsson and Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] to…
We investigate numerically the configurational statistics of strings. The algorithm models an ensemble of global $U(1)$ cosmic strings, or equivalently vortices in superfluid $^4$He. We use a new method which avoids the specification of…
A method combining denoising diffusion probabilistic models (DDPMs) with the string method is presented to generate minimum free energy paths between metastable states in molecular systems. It has been demonstrated in recent work that DDPMs…
By quenching into the metastable region of the three-dimensional Ising model, we investigate the paths that the magnetization (energy) takes as a function of time. We accumulate the magnetization (energy) paths into time-dependent…
In this paper we provide a novel approach to the analysis of kinetic models for label switching, which are used for particle systems that can randomly switch between gradient flows in different energy landscapes. Besides problems in biology…
The accuracy of rate constants calculated using transition state theory depends crucially on the correct identification of a recrossing--free dividing surface. We show here that it is possible to define such optimal dividing surface in…
We present a new method, Non-Stationary Forward Flux Sampling, that allows efficient simulation of rare events in both stationary and non-stationary stochastic systems. The method uses stochastic branching and pruning to achieve uniform…
We introduce a path sampling method for the computation of rate constants for systems with a highly diffusive character. Based on the recently developed algorithm of transition interface sampling (TIS) this procedure increases the…
We analyze a new Monte Carlo method which uses transition matrix in the space of energy. This method gives an efficient reweighting technique. The associated artificial dynamics is a constrained random walk in energy, producing the result…
We consider stochastic networks with pairwise transition rates of the exponential form where the temperature T is a small parameter. Such networks arise in physics and chemistry and serve as mathematically tractable models of complex…
Target search by active agents in rugged energy landscapes has remained a challenge because standard enhanced sampling methods do not apply to irreversible dynamics. We overcome this non-equilibrium rare-event problem by developing an…
The ability to predict accurate thermodynamic and kinetic properties in biomolecular systems is of both scientific and practical utility. While both remain very difficult, predictions of kinetics are particularly difficult because rates, in…
We introduce a rigorous method to microscopically compute the observables which characterize the thermodynamics and kinetics of rare macromolecular transitions for which it is possible to identify a priori a slow reaction coordinate. In…
The computer simulation of many molecular processes is complicated by long time scales caused by rare transitions between long-lived states. Here, we propose a new approach to simulate such rare events, which combines transition path…
The quantization of the transverse motion energy in the continuous potentials of atomic strings and planes can take place under passage of fast charged particles through crystals. The energy levels for electron moving in axial channeling…