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Sequential sampling models (SSMs) are a widely used framework describing decision-making as a stochastic, dynamic process of evidence accumulation. SSMs popularity across cognitive science has driven the development of various software…
A multiscale theory of interacting continuum mechanics and thermodynamics of mixtures of fluids, electrodynamics, polarization and magnetization is proposed. The mechanical (reversible) part of the theory is constructed in a purely…
We present DataDeps.jl: a julia package for the reproducible handling of static datasets to enhance the repeatability of scripts used in the data and computational sciences. It is used to automate the data setup part of running software…
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…
Detailed chemistry-based computational fluid dynamics (CFD) simulations are computationally expensive due to the solution of the underlying chemical kinetics system of ordinary differential equations (ODEs). Here, we introduce a novel…
We present the preliminary high-level design and features of DynamicPPL.jl, a modular library providing a lightning-fast infrastructure for probabilistic programming. Besides a computational performance that is often close to or better than…
Many uncertainty propagation software exist, written in different programming languages, but not all of them are able to handle functional correlation between quantities. In this paper we review one strategy to deal with uncertainty…
Dynamical systems and physical models defined on idealized continuous phase spaces are known to exhibit non-computable phenomena, examples include the wave equation, recurrent neural networks, or Julia sets in holomorphic dynamics. Inspired…
We present FractionalDiffEq.jl, a comprehensive solver suite for solving fractional differential equations, featuring high-performance numerical algorithms in the Julia programming language. FractionalDiffEq.jl is designed to be…
This paper presents a rewriting-logic-based modeling and analysis technique for physical systems, with focus on thermal systems. The contributions of this paper can be summarized as follows: (i) providing a framework for modeling and…
Fluid dynamics plays a crucial role in various multiphysics applications, including energy systems, electronics cooling, and biomedical engineering. Developing models for complex coupled systems can be challenging and time-consuming. In…
We present a finite-element software library, IRENE, which allows to solve numerically the dynamics of a viscous fluid layer embedded in three-dimensional space. Unlike finite-element libraries present in the literature, IRENE can handle…
Soft matter materials and polymers are widely used in the controlled delivery of drugs. Simulation and modeling provide insight at the atomic scale enabling a level of control unavailable to experiments. We present a workflow protocol for…
Dynamical systems are ubiquitous in science and engineering as models of phenomena that evolve over time. Although complex dynamical systems tend to have important modular structure, conventional modeling approaches suppress this structure.…
Biofilms are communities of microorganisms that grow on virtually all surfaces with sufficient nutrients including aquatic and industrial water systems and medical devices. Biofilms are complex, structured communities where the interplay of…
Time-series learning is the bread and butter of data-driven *clinical decision support*, and the recent explosion in ML research has demonstrated great potential in various healthcare settings. At the same time, medical time-series problems…
We develop a global setting for modeling thermo-visco-elastic materials that satisfy the principles of thermodynamics and are properly invariant. This setting encompasses many known solid and fluid models, as well as new models with…
SpiDy.jl solves the non-Markovian stochastic dynamics of interacting classical spin vectors and harmonic oscillator networks in contact with a dissipative environment. The methods implemented allow the user to include arbitrary memory…
We introduce DiffOpt.jl, a Julia library to differentiate through the solution of optimization problems with respect to arbitrary parameters present in the objective and/or constraints. The library builds upon MathOptInterface, thus…
The (py)LIon package is a set of tools to simulate the classical trajectories of ensembles of ions in electrodynamic traps. Molecular dynamics simulations are performed using LAMMPS, an efficient and feature-rich program. (py)LIon has been…