相关论文: Implementing the Independent Reaction Time method …
Sensitivity analysis of biochemical reactions aims at quantifying the dependence of the reaction dynamics on the reaction rates. The computation of the parameter sensitivities, however, poses many computational challenges when taking…
This study connects two methods for modeling reaction times (RTs) in choice tasks: (1) the first-hitting time of a simple diffusion model with a single barrier, representing the cognitive process leading to a response, and (2) Generalized…
We describe a new algorithm for simulating complex Markoff-processes. We have used a reaction-cell method in order to simulate arbitrary reactions. It can be used for any kind of RDS on arbitrary topologies, including fractal dimensions or…
Experiments measuring fission observables encounter false coincidences arising from timing overlap of separate fission product decays. Simulations of both fission observables and particles in detector systems exist, but have not yet been…
In this work we study global well-posedness and large time behaviour for a typical reaction--diffusion system, which include degenerate diffusion, and whose non-linearities arise from chemical reactions. We show that there is an {\it…
Cells must continuously sense and respond to time-varying environmental stimuli. These signals are transmitted and processed by biochemical signalling networks. However, the biochemical reactions making up these networks are intrinsically…
We present a general method to produce well-conditioned continuum reaction-drift-diffusion equations directly from master equations on a discrete, periodic state space. We assume the underlying data to be kinetic Monte Carlo models (i.e.,…
We present a general model allowing one to calculate the distribution function of energetic particles in the interstellar medium, and hence any relevant nuclear reaction rate, for any given time-dependent injection function, as well as in…
A simple and self-consistent approach has been proposed for simulation of the proton-induced soft error rate based on the heavy ion induced single event upset cross-section data and vice versa. The approach relies on the GEANT4 assisted…
Over the past years, radiofrequency ion traps have become an attractive platform for studying chemical reactions as they enable a high degree of control over ion-molecule dynamics. In this review, we summarize techniques for the trapping…
We present a novel scattering emulator utilizing the complex scaling method to enhance nuclear reaction analysis. This approach leverages a single set of reduced bases, allowing for efficient and simultaneous emulation across multiple…
A Grand-canonical Monte-Carlo simulation method extended to simulate a mixture of salts is presented. Due to charge neutrality requirement of electrolyte solutions, ions must be added to or removed from the system in groups. This leads to…
A reaction-diffusion problem with a Caputo time derivative is considered. An integral discretization scheme on a graded mesh along with a decomposition of the exact solution is proposed. The truncation error estimate of the discretization…
Geant4, the leading detector simulation toolkit used in high energy physics, employs a set of physics models to simulate interactions of particles with matter across a wide range of energies. These models, especially the hadronic ones, rely…
Studying chemical reactions, particularly in the gas phase, relies heavily on computing scattering matrix elements. These elements are essential for characterizing molecular reactions and accurately determining reaction probabilities.…
The replication and differentiation of spots in reaction diffusion equations are studied by extending the Gray-Scott model with self-replicating spots to include many degrees of freedom needed to model systems with many chemicals. By…
On the base of the diffusion Monte-Carlo method we develop the method allowing to simulate the quantum systems with complex wave function. The method is exact and there are no approximations on the simulations of the module and the phase of…
We discuss velocity-jump models for chemotaxis of bacteria with an internal state that allows the velocity jump rate to depend on the memory of the chemoattractant concentration along their path of motion. Using probabilistic techniques, we…
Finding representative reaction pathways is necessary for understanding mechanisms of molecular processes, but is considered to be extremely challenging. We propose a new method to construct reaction paths based on mean first-passage times.…
Thermodynamic integration (TI) offers a rigorous method for estimating free-energy differences by integrating over a sequence of interpolating conformational ensembles. However, TI calculations are computationally expensive and typically…