Related papers: VacHopPy: A Python package for vacancy hopping ana…
An open-source, Python-based Temporal Analysis of Products (TAP) reactor simulation and processing program is introduced. TAPsolver utilizes algorithmic differentiation for the calculation of highly accurate derivatives, which are used to…
Compound AI applications, which compose calls to ML models using a general-purpose programming language like Python, are widely used for a variety of user-facing tasks, from software engineering to enterprise automation, making their…
Molecular dynamics (MD) simulations are powerful tools for elucidating the macroscopic physical properties of materials from microscopic atomic behaviors. However, the massive, high-dimensional datasets generated by MD simulations pose a…
We present PyOECP, a Python-based flexible open-source software for estimating and modeling the complex permittivity obtained from the open-ended coaxial probe (OECP) technique. The transformation of the measured reflection coefficient to…
PySPH is an open-source, Python-based, framework for particle methods in general and Smoothed Particle Hydrodynamics (SPH) in particular. PySPH allows a user to define a complete SPH simulation using pure Python. High-performance code is…
We previously introduced a conformational sampling method, a multi-dimensional virtual-system coupled molecular dynamics (mD-VcMD), to enhance conformational sampling of a biomolecular system by computer simulations. Here, we present a new…
Two models involving particles moving by ``hopping'' in disordered media are investigated: I) A model glass-forming liquid is investigated by molecular dynamics under (pseudo-) equilibrium conditions. ``Standard'' results such as mean…
Viscophoresis refers to the transport of suspended nanoparticles driven by a steep viscosity gradient. This work investigates this new transport effect using a random walk simulation. By modelling position-dependent Brownian motion,…
PySDM is an open-source Python package for simulating the dynamics of particles undergoing condensational and collisional growth, interacting with a fluid flow and subject to chemical composition changes. It is intended to serve as a…
In molecular simulations, efficient methods for investigating equilibration and slow relaxation in dense systems are crucial yet challenging. This study focuses on the diffusional characteristics of monodisperse hard disk systems at…
A diffusion probabilistic model (DPM), which constructs a forward diffusion process by gradually adding noise to data points and learns the reverse denoising process to generate new samples, has been shown to handle complex data…
In recent years, numerical simulations have become indispensable for addressing complex astrophysical problems. The MagnetoHydroDynamics (MHD) framework represents a key tool for investigating the dynamical evolution of astrophysical…
SfePy (Simple finite elements in Python) is a software for solving various kinds of problems described by partial differential equations in one, two or three spatial dimensions by the finite element method. Its source code is mostly (85\%)…
One-dimensional hopping model is useful to describe the motion of microscopic particle in thermal noise environment, such as motor proteins. Recent experiments about the new generation of light-driven rotary molecular motors found that, the…
Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…
Particles confined to a single file, in a narrow quasi-one dimensional channel, exhibit a dynamic crossover from single file diffusion to Fickian diffusion as the channel radius increases and the particles can begin to pass each other. The…
Mechanistic models are important tools to describe and understand biological processes. However, they typically rely on unknown parameters, the estimation of which can be challenging for large and complex systems. We present pyPESTO, a…
Determining molecular abundances in astrophysical environments is crucial for interpreting observational data and constraining physical conditions in these regions. Chemical modelling tools are essential for simulating the complex processes…
Diffusion Policy (DP) has attracted significant attention as an effective method for policy representation due to its capacity to model multi-distribution dynamics. However, current DPs are often based on a single visual modality (e.g., RGB…
This paper introduces a framework for simulating finite dimensional representations of (jump) diffusion sample paths over finite intervals, without discretisation error (exactly), in such a way that the sample path can be restored at any…