相关论文: Implementing the Independent Reaction Time method …
An algorithm has been developed for the Geant4 Monte-Carlo package for the efficient computation of screened Coulomb interatomic scattering. It explicitly integrates the classical equations of motion for scattering events, resulting in…
Stochastic models of biochemical reaction networks are widely used to capture intrinsic noise in cellular systems. The typical formulation of these models are based on Markov processes for which there is extensive research on efficient…
In this article, we propose an efficient method for sampling the relevant state space in condensed phase reactions. In the present method, the reaction is described by solving the electronic Schr\"{o}dinger equation for the solute atoms in…
Reaction prediction, a critical task in synthetic chemistry, is to predict the outcome of a reaction based on given reactants. Generative models like Transformer have typically been employed to predict the reaction product. However, these…
Radical-ion-pair reactions, central in photosynthesis and the avian magnetic compass mechanism, have recently shown to be a paradigm system for applying quantum information science in a biochemical setting. The fundamental quantum master…
Reaction-diffusion models have been used over decades to study biological systems. In this context, evolution equations for probability distribution functions and the associated stochastic differential equations have nowadays become…
The Geant4 photonuclear process is benchmarked by comparing it with experimental data to verify the ability of the Geant4 toolkit to simulate the photo-induced reaction on deformed nuclei in the Giant Dipole Resonance (GDR) region. The…
The reaction-diffusion model can generate a wide variety of spatial patterns, which has been widely applied in chemistry, biology, and physics, even used to explain self-regulated pattern formation in the developing animal embryo. In this…
Geant4 is a toolkit for the simulation of the passage of particles through matter. It provides a comprehensive set of tools for geometry, tracking, detector response, run, event and track management, visualization and user interfaces.…
We briefly review the principles, mathematical bases, numerical shortcuts and applications of fast random walk (FRW) algorithms. This Monte Carlo technique allows one to simulate individual trajectories of diffusing particles in order to…
Can a micron sized sack of interacting molecules autonomously learn an internal model of a complex and fluctuating environment? We draw insights from control theory, machine learning theory, chemical reaction network theory, and statistical…
We consider the problem of efficiently performing simulation and inference for stochastic kinetic models. Whilst it is possible to work directly with the resulting Markov jump process, computational cost can be prohibitive for networks of…
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,…
Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum…
Geant4 is an object-oriented toolkit for the simulation of the passage of particles through matter. Its development was initially motivated by the requirements of physics experiments at high energy hadron colliders under construction in the…
We present a time-dependent quantum algorithm for nuclear inelastic scattering in the time-dependent basis function on qubits approach. This algorithm aims to quantum simulate a subset of the nuclear inelastic scattering problems that are…
The method for simulation of medium-induced rescattering and energy loss of hard partons in ultrarelativistic heavy ion collisions is developed. The model is realized as fast Monte-Carlo tool implemented to modify standard PYTHIA jet event.
By explicitly representing the reaction times of discrete chemical systems as the firing times of independent, unit rate Poisson processes, we develop a new adaptive tau-leaping procedure. The procedure developed is novel in that accuracy…
We develop a framework to evaluate the time-dependent resonant inelastic X-ray scattering (RIXS) signal with the use of non-equilibrium dynamical mean field theory simulations. The approach is based on the solution of a time-dependent…
Estimating the impact of systematic uncertainties in particle physics experiments is challenging, especially since the detector response is unknown analytically in most situations and needs to be estimated through Monte Carlo (MC)…