Related papers: pyJac: analytical Jacobian generator for chemical …
CompHEP, as a partonic event generator, and PYTHIA, as a generator of final states of detectable objects, are interfaced. Thus, integrated tool is proposed for simulation of (almost) arbitrary collision processes at the level of detectable…
Hydrodynamical simulations are increasingly able to accurately model physical systems on stellar, galactic, and cosmological scales, however, the utility of these simulations is often limited by our ability to directly compare them with the…
This article introduces a software package release for geometrically reasoning about the \textit{safety} desiderata of (complex) dynamical systems via level set methods. In emphasis, safety is analyzed with Hamilton-Jacobi equations. In…
Logical models offer a simple but powerful means to understand the complex dynamics of biochemical regulation, without the need to estimate kinetic parameters. However, even simple automata components can lead to collective dynamics that…
Call graphs play an important role in different contexts, such as profiling and vulnerability propagation analysis. Generating call graphs in an efficient manner can be a challenging task when it comes to high-level languages that are…
The development of computational models for the numerical simulation of chemically reacting flows operating in the turbulent regime requires the solution of partial differential equations that represent the balance of mass, linear momentum,…
Reversibility, weak reversibility and deficiency, detailed and complex balancing are generally not "encoded" in the kinetic differential equations but they are realization properties that may imply local or even global asymptotic stability…
We present QDK/Chemistry, a software toolkit for quantum chemistry workflows targeting quantum computers. The toolkit addresses a key challenge in the field: while quantum algorithms for chemistry have matured considerably, the…
We introduce a class of Kac-like kinetic equations on the real line, with general random collisional rules, which include as particular cases models for wealth redistribution in an agent-based market or models for granular gases with a…
We propose the use of automatic differentiation through the programming framework jax for accelerating a variety of analysis tasks throughout gravitational wave (GW) science. Firstly, we demonstrate that complete waveforms which cover the…
Atmospheric models demand a lot of computational power and solving the chemical processes is one of its most computationally intensive components. This work shows how to improve the computational performance of the Multiscale Online…
Conceptual hydrologic models remain the cornerstone of rainfall-runoff modeling, yet their calibration is often slow and numerically fragile. Most gradient-based parameter estimation methods rely on finite-difference approximations or…
Background: Autocatalytic sets are often considered a necessary (but not sufficient) condition for the origin and early evolution of life. Although the idea of autocatalytic sets was already conceived of many years ago, only recently have…
A kinetic approach for the evolution of ultracold neutral plasmas including interionic correlations and the treatment of ionization/excitation and recombination/deexcitation by rate equations is described in detail. To assess the…
Solving for detailed chemical kinetics remains one of the major bottlenecks for computational fluid dynamics simulations of reacting flows using a finite-rate-chemistry approach. This has motivated the use of fully connected artificial…
pyGDM is a python toolkit for electro-dynamical simulations in nano-optics based on the Green Dyadic Method (GDM). In contrast to most other coupled-dipole codes, pyGDM uses a generalized propagator, which allows to cost-efficiently solve…
A goal of systems biology is to understand the dynamics of intracellular systems. Stochastic chemical kinetic models are often utilized to accurately capture the stochastic nature of these systems due to low numbers of molecules. Collecting…
We implement Ananke: an object-oriented Python package for causal inference with graphical models. At the top of our inheritance structure is an easily extensible Graph class that provides an interface to several broadly useful graph-based…
We present a novel and simple method to numerically calculate Fisher Information Matrices for stochastic chemical kinetics models. The linear noise approximation is used to derive model equations and a likelihood function which leads to an…
Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…