Related papers: pyJac: analytical Jacobian generator for chemical …
Retrosynthesis is one of the fundamental problems in organic chemistry. The task is to identify reactants that can be used to synthesize a specified product molecule. Recently, computer-aided retrosynthesis is finding renewed interest from…
Recurrence plot is a quite easy tool to be used in time series analysis,in particular for measuring unstable periodic orbits embedded in a chaotic dynamical system. Recurrence quantified analysis (RQA) is an advance tool that allows the…
Predicting and enhancing inherent properties based on molecular structures is paramount to design tasks in medicine, materials science, and environmental management. Most of the current machine learning and deep learning approaches have…
Common time-explicit numerical methods for kinetic simulations of plasmas in the low-collisions limit fall into two classes of algorithms: momentum conserving and energy conserving. Each has certain drawbacks. The PIC algorithm does not…
Disentangling the mechanistic details of a chemical reaction pathway is a hard problem that often requires a considerable amount of chemical intuition and a component of luck. Experiments struggle in observing short-life metastable…
Since Lorenz's seminal work on a simplified weather model, the numerical analysis of nonlinear dynamical systems has become one of the main subjects of research in physics. Despite of that, there remains a need for accessible, efficient,…
We introduce the SmoQyDEAC.jl package, a Julia implementation of the Differential Evolution Analytic Continuation (DEAC) algorithm [N. S. Nichols et al., Phys. Rev. E 106, 025312 (2022)] for analytically continuing noisy imaginary time…
We develop a criterion to certify whether causal effects are identifiable in linear structural equation models with latent variables. Linear structural equation models correspond to directed graphs whose nodes represent the random variables…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…
The high cost of chemistry integration is a significant computational bottleneck for realistic reactive-flow simulations using operator splitting. Here we present a methodology to accelerate the solution of the chemical kinetic ordinary…
The PYTHIA program can be used to generate high-energy-physics `events', i.e. sets of outgoing particles produced in the interactions between two incoming particles. The objective is to provide as accurate as possible a representation of…
Carbon dioxide hydrates are ice-like nonstoichiometric inclusion solid compounds with importance to global climate change, and gas transportation and storage. The thermodynamic and kinetic mechanisms that control carbon dioxide nucleation…
The accurate and robust simulation of transcritical real-fluid effects is crucial for many engineering applications, such as fuel injection in internal combustion engines, rocket engines and gas turbines. For example, in diesel engines, the…
Stokesian Dynamics (SD) is a powerful computational framework for simulating the motion of particles in a viscous Newtonian fluid under Stokes-flow conditions. Traditional SD implementations can be computationally expensive as they rely on…
Chemical modelling serves two purposes in dynamical models: accounting for the effect of microphysics on the dynamics and providing observable signatures. Ideally, the former must be done as part of the hydrodynamic simulation but this…
Estimating the heat loads on re-entry vehicles is a crucial part of preparing for atmospheric re-entry manoeuvres. Re-entry flows at high altitudes are in the rarefied regime and are governed by high enthalpies and thermodynamic…
High fidelity scientific simulations modeling physical phenomena typically require solving large linear systems of equations which result from discretization of a partial differential equation (PDE) by some numerical method. This step often…
A Python package for post-processing of plane two-dimensional data from computational fluid dynamics simulations is presented. The package, called turbulucid, provides means for scripted, reproducible analysis of large simulation campaigns…
In chemical analysis made by laboratories one has the problem of determining the concentration of a chemical element in a sample. In order to tackle this problem the guide EURACHEM/CITAC recommends the application of the linear calibration…
Chemical reaction networks taken with mass-action kinetics are dynamical systems that arise in chemical engineering and systems biology. In general, determining whether a chemical reaction network admits multiple steady states is difficult,…