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We present a detailed comparison of computational efficiency and precision for several free energy difference ($\Delta F$) methods. The analysis includes both equilibrium and non-equilibrium approaches, and distinguishes between…
In this paper, a two-step strategy for parametric sensitivity analysis for such systems is proposed, exploiting advantages and synergies between two recently proposed sensitivity analysis methodologies for stochastic dynamics. The first…
Spatio-temporal biochemical signaling in a large class of protein-protein interaction networks is well modeled by a reaction-diffusion system. The global existence of the solution to the reaction-diffusion system is determined by the…
Finding and sampling multiple reaction channels for molecular transitions remains an important challenge in physical chemistry. Here we show that the weighted ensemble (WE) path sampling method can readily sample multiple channels. In a…
The temperature dependence of the rate of the reaction CH_4+H \to CH_3+H_2 is studied using classical collision theory with a temperature-dependent effective potential derived from a path integral analysis. Analytical expressions are…
Multistep catalytic reactions use two different catalysts for the $A\to B$ and the subsequent $B\to C$ reaction, respectively. Often the employed catalysts are chemically incompatible, such as acid-base systems, which prohibits simple…
It remains a challenging problem to tightly estimate the worst case response time of an application in a distributed embedded system, especially when there are dependencies between tasks. We discovered that the state-of-the art techniques…
We introduce a simple enhanced sampling approach for the calculation of free energy differences and barriers along a one-dimensional reaction coordinate. First, a small number of short nonequilibrium simulations are carried out along the…
For a nonlinear stochastic path planning problem, sampling-based algorithms generate thousands of random sample trajectories to find the optimal path while guaranteeing safety by Lagrangian penalty methods. However, the sampling-based…
Reward comparisons are vital for evaluating differences in agent behaviors induced by a set of reward functions. Most conventional techniques utilize the input reward functions to learn optimized policies, which are then used to compare…
Analysing stationary point databases to extract phenomenological rate constants can become time-consuming for systems with large potential energy barriers. In the present contribution we analyse several different approaches to this problem.…
We present an accelerated algorithm that samples correctly the thermodynamic ensemble in complex systems where the dynamics is controlled by activation barriers. The efficiency of the thermodynamically-weighted activation-relaxation…
Nowadays, the numerical models of real-world structures are more precise, more complex and, of course, more time-consuming. Despite the growth of a computational effort, the exploration of model behaviour remains a complex task. The…
We perform a numerical study of the reaction efficiency in a closed vessel. Starting with a little spot of product, we compute the time needed to complete the reaction in the container following an advection-reaction-diffusion process.…
For many tasks of data analysis, we may only have the information of the explanatory variable and the evaluation of the response values are quite expensive. While it is impractical or too costly to obtain the responses of all units, a…
Because of their multimodality, mixture posterior distributions are difficult to sample with standard Markov chain Monte Carlo (MCMC) methods. We propose a strategy to enhance the sampling of MCMC in this context, using a biasing procedure…
Transition states and minimum energy paths are essential to understand and predict chemical reactivity. Double-ended methods represent a standard approach for their determination. We introduce a new double-ended method that optimizes…
We present three algorithms for calculating rate constants and sampling transition paths for rare events in simulations with stochastic dynamics. The methods do not require a priori knowledge of the phase space density and are suitable for…
It has previously been shown that response transformations can be very effective in improving dimension reduction outcomes for a continuous response. The choice of transformation used can make a big difference in the visualization of the…
A newly developed method for systematically improving the convergence of path integrals for transition amplitudes, introduced in Phys. Rev. Lett. 94 (2005) 180403, Phys. Rev. B 72 (2005) 064302, Phys. Lett. A 344 (2005) 84, and expectation…