Related papers: Exact rate calculations by trajectory parallelizat…
We apply Thermostatted Ring Polymer Molecular Dynamics (TRPMD), a recently-proposed approximate quantum dynamics method, to the computation of thermal reaction rates. Its short-time Transition-State Theory (TST) limit is identical to…
In physics, it is frequently needed to precisely measure the count rate of some process. Quite often one needs to account for electronics dead time, pile-up and other features of data acquisition system to avoid systematic shifts of the…
We review two recently developed efficient methods for calculating rate constants of processes dominated by rare events in high-dimensional complex systems. The first is transition interface sampling (TIS), based on the measurement of…
We study the dynamics of parallel tempering simulations, also known as the replica exchange technique, which has become the method of choice for simulation of proteins and other complex systems. Recent results for the optimal choice of the…
In this paper, we develop a method for obtaining the approximate solution for the evolution of single-step transformations under non-isothermal conditions. We have applied it to many reaction models and obtained very simple analytical…
Real data are constrained to finite sampling rates, which calls for a suitable mathematical description of the corrections to the finite-time estimations of the dynamic equations. Often in the literature, lower order discrete time…
An algorithm for sampling exactly from the normal distribution is given. The algorithm reads some number of uniformly distributed random digits in a given base and generates an initial portion of the representation of a normal deviate in…
Activated processes from chemical reactions up to conformational transitions of large biomolecules are hampered by barriers which are overcome only by the input of some free energy of activation. Hence, the characteristic and…
A simple expression for the non-equilibrium distribution function in ultra-fast transient processes is proposed. Postulating its dependence on temporal derivatives of the equilibrium integrals of motion, non-equilibrium analogues of the…
We consider Gibbs' definition of chemical equilibrium and connect it with dynamic equilibrium, in terms of no substance formed. We determine the activity coefficient as a function of temperature and pressure, in reactions with or without…
Near equilibrium, thermodynamic intuition suggests that fast, irreversible processes will dissipate more energy and entropy than slow, quasistatic processes connecting the same initial and final states. Here, we test the hypothesis that…
We briefly review simulation schemes for the investigation of rare transitions and we resume the recently introduced Transition Interface Sampling, a method in which the computation of rate constants is recast into the computation of fluxes…
The run-and-tumble particle (RTP) is one of the simplest examples of an active particle in which the direction of constant motion randomly switches. In the one-dimensional (1D) case this means switching between rightward and leftward…
Energy dissipation rate is an important parameter for nearly every experiment on turbulent flow. Mathematically precise relationships between energy dissipation rate and other measurable statistics for the case of anisotropic turbulence are…
We present new algorithms and fast implementations to find efficient approximations for modelling stochastic processes. For many numerical computations it is essential to develop finite approximations for stochastic processes. While the…
Next generation architectures necessitate a shift away from traditional workflows in which the simulation state is saved at prescribed frequencies for post-processing analysis. While the need to shift to in~situ workflows has been…
We developed an efficient active-space particle-particle random phase approximation (ppRPA) approach to calculate accurate charge-neutral excitation energies of molecular systems. The active-space ppRPA approach constrains both indexes in…
The recrossing correction to the transition state theory estimate of a thermal rate can be difficult to calculate when the energy barrier is flat. This problem arises, for example, in polymer escape if the polymer is long enough to stretch…
We demonstrate and characterize a first-principles approach to modeling the mass action dynamics of metabolism. Starting from a basic definition of entropy expressed as a multinomial probability density using Boltzmann probabilities with…
An exact solution for a high speed deterministic traffic model with open boundaries and synchronous update rule is presented. Because of the strong correlations in the model, the qualitative structure of the stationary state can be…