Related papers: Reaction rate calculation with time-dependent inva…

In dissipative ordinary differential equation systems different time scales cause anisotropic phase volume contraction along solution trajectories. Model reduction methods exploit this for simplifying chemical kinetics via a time scale…

In this paper, we provide a graphic formulation of non-isothermal reaction systems and show that a non-isothermal detailed balanced network system converges (locally) asymptotically to the unique equilibrium within the invariant manifold…

A non-conventional approach to calculating reactions in quantum mechanics is presented. Reaction observables are obtained with bound state calculation techniques. The accuracy of the method to calculate few-nucleon response functions is…

Dynamics between reactants and products are often mediated by a rate-determining barrier and an associated dividing surface leading to the transition state theory rate. This framework is challenged when the barrier is time-dependent because…

Surfaces serve as highly efficient catalysts for a vast variety of chemical reactions. Typically, such surface reactions involve billions of molecules which diffuse and react over macroscopic areas. Therefore, stochastic fluctuations are…

In this paper, a new fractional step method is proposed for simulating stiff and nonstiff chemically reacting flows. In stiff cases, a well-known spurious numerical phenomenon, i.e. the incorrect propagation speed of discontinuities, may be…

Reaction coordinates are widely used throughout chemical physics to model and understand complex chemical transformations. We introduce a definition of the natural reaction coordinate, suitable for condensed phase and biomolecular systems,…

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…

Quantum scattering calculations for strongly interacting molecular systems are computationally demanding due to the large number of molecular states coupled by the anisotropy of atom - molecule interactions. We demonstrate that thermal rate…

Dynamical system models of complex biochemical reaction networks are usually high-dimensional, nonlinear, and contain many unknown parameters. In some cases the reaction network structure dictates that positive equilibria must be unique for…

The adoption of detailed mechanisms for chemical kinetics often poses two types of severe challenges: First, the number of degrees of freedom is large; and second, the dynamics is characterized by widely disparate time scales. As a result,…

Based on our experience in kinetic modeling of coupled multiple metabolic pathways we propose a generic rate equation for the dynamical modeling of metabolic kinetics. Its symmetric form makes the kinetic parameters (or functions) easy to…

An exact invariant is derived for $n$-degree-of-freedom Hamiltonian systems with general time-dependent potentials. The invariant is worked out in two equivalent ways. In the first approach, we define a special {\it Ansatz\/} for the…

It is a well known fact that subdiffusion equations in terms of fractional derivatives can be obtained from Continuous Time Random Walk (CTRW) models with long-tailed waiting time distributions. Over the last years various authors have…

The methodology for modeling grain-surface chemistry has been greatly improved by taking into account the grain size and fluctuation effects. However, the reaction rate coefficients currently used in all practical models of gas-grain…

Particles moving inside a fluid near, and interacting with, invariant manifolds is a common phenomenon in a wide variety of applications. One elementary question is whether we can determine once a particle has entered a neighbourhood of an…

Reactive force fields for molecular dynamics have enabled a wide range of studies in numerous material classes. These force fields are computationally inexpensive as compared to electronic structure calculations and allow for simulations of…

A non-perturbative approach to the time-averaging of nonlinear, autonomous ODE systems is developed based on invariant manifold methodology. The method is implemented computationally and applied to model problems arising in the mechanics of…

Polymer models are a widely used tool to study the prebiotic formation of metabolism at the origins of life. Counts of the number of reactions in these models are often crucial in probabilistic arguments concerning the emergence of…

An impulsive feedback-adaptive control is developed in order to drive trajectories of a dynamical system towards an invariant manifold with fixed and spaced impulsive controls. The approach requires the explicit knowledge of the set of…