Related papers: Efficiency analysis of reaction rate calculation m…
Recently the European Union Agency for Railways (ERA) has received a mandate for 'the development of common safety methods for assessing the safety level and the safety performance of railway operators at national and Union level'.…
Various kinetic Monte Carlo algorithms become inefficient when some of the population sizes in a system are large, which gives rise to a large number of reaction events per unit time. Here, we present a new acceleration algorithm based on…
In this paper we propose and discuss variance reduction techniques for the estimation of quantiles of the output of a complex model with random input parameters. These techniques are based on the use of a reduced model, such as a metamodel…
We study the problem of finding efficient sampling policies in an edge-based feedback system, where sensor samples are offloaded to a back-end server that processes them and generates feedback to a user. Sampling the system at maximum…
Transition state theory formally provides a simplifying approach for determining chemical reaction rates and pathways. Given an underlying potential energy surface for a reactive system, one can determine the dividing surface in phase space…
This paper presents a hybrid optimization methodology for parameter estimation of reactive transport systems. Using reduced-order advection-diffusion-reaction (ADR) models, the computational requirements of global optimization with dynamic…
The use of mathematical methods for the analysis of chemical reaction systems has a very long history, and involves many types of models: deterministic versus stochastic, continuous versus discrete, and homogeneous versus spatially…
Intermolecular hydrogen transfer free radical reactions are common in the combustion process and in a number of organic chemistry reactions. Therefore, evaluating the pressure and temperature-dependent rate constants of them is of great…
The computation of free energy differences through an exponential weighting of out of equilibrium paths (known as the Jarzynski equality) is often used for transitions between states described by an external parameter $\lambda$ in the…
The problem of counting collisions or interactions is common in areas as computer graphics and scientific simulations. Since it is a major bottleneck in applications of these areas, a lot of research has been carried out on such subject,…
Stochastic models for chemical reaction networks have become very popular in recent years. For such models, the estimation of parameter sensitivities is an important and challenging problem. Sensitivity values help in analyzing the network,…
Under certain conditions, the dynamics of coarse-grained models of solvated proteins can be described using a Markov state model, which tracks the evolution of populations of configurations. The transition rates among states that appear in…
The system-level dynamics of multivalent biomolecular interactions can be simulated using a rule-based kinetic Monte Carlo method in which a rejection sampling strategy is used to generate reaction events. This method becomes inefficient…
The shift in chemical equilibria due to isotope substitution is often exploited to gain insight into a wide variety of chemical and physical processes. It is a purely quantum mechanical effect, which can be computed exactly using…
Traffic is essential for many dynamic processes on real networks, such as internet and urban traffic systems. The transport efficiency of the traffic system can be improved by taking full advantage of the resources in the system. In this…
The behavior of some stochastic chemical reaction networks is largely unaffected by slight inaccuracies in reaction rates. We formalize the robustness of state probabilities to reaction rate deviations, and describe a formal connection…
We have developed efficient techniques to solve the first-time problems of Brownian motion. Based on a time-scale separation of recrossings, we show that Eyring's transmission coefficient ($\kappa$) equals to the one ($\kappa_\mathrm{V}$)…
Exploring the free-energy landscape along reaction coordinates or system parameters $\lambda$ is central to many studies of high-dimensional model systems in physics, e.g. large molecules or spin glasses. In simulations this usually…
Solving chemistry is an integral part of reacting flow simulations, usually dominating the computational cost. Among the different strategies to accelerate the solution of chemistry and to achieve realizable simulations, the use of Dynamic…
We calculate the efficiency of a rejection-free dynamic Monte Carlo method for $d$-dimensional off-lattice homogeneous particles interacting through a repulsive power-law potential $r^{-p}$. Theoretically we find the algorithmic efficiency…