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In the context of Service-Oriented Computing, applications can be developed following the REST (Representation State Transfer) architectural style. This style corresponds to a resource-oriented model, where resources are manipulated via…
We substantially update the capabilities of the open-source software instrument Modules for Experiments in Stellar Astrophysics (MESA). MESA can now simultaneously evolve an interacting pair of differentially rotating stars undergoing…
The "IMP Science Gateway Portal" (http://scigate.imp.kiev.ua) for complex workflow management and integration of distributed computing resources (like clusters, service grids, desktop grids, clouds) is presented. It is created on the basis…
Molecular computation based on chemical reaction networks (CRNs) has emerged as a promising paradigm for designing programmable biochemical systems. However, the implementation of complex computations still requires excessively large and…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
This work presents a decoupled framework for multi-step computational chemistry automation built on OpenClaw. OpenClaw serves as the general-purpose agent for task coordination and supervision. Planning skills externalize task descriptions…
We present MUSE, a software framework for combining existing computational tools for different astrophysical domains into a single multiphysics, multiscale application. MUSE facilitates the coupling of existing codes written in different…
MADNESS (multiresolution adaptive numerical environment for scientific simulation) is a high-level software environment for solving integral and differential equations in many dimensions that uses adaptive and fast harmonic analysis methods…
Computational X-ray absorption near-edge structure (XANES) is widely used to probe local coordination environments, oxidation states, and electronic structure in chemically complex systems. However, the use of computational XANES at scale…
Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…
Python Library for simulating unManNed vehiclEs(PLANE) is an open source software module, written in Python, that focuses on Unmanned Aerial Vehicles (UAVs), on their movements and on the mechanics of flight, thus devoting particular…
Large-scale simulation studies can provide invaluable insights across computational engineering efforts, but they are often computationally demanding, requiring the use of distributed computing, which is itself not a simple task.…
Synthetic biology is a rapidly emerging research area, with expected wide-ranging impact in biology, nanofabrication, and medicine. A key technical challenge lies in embedding computation in molecular contexts where electronic…
Energy functions for pure and heterogenous systems are one of the backbones for molecular simulation of condensed phase systems. With the advent of machine learned potential energy surfaces (ML-PESs) a new era has started. Statistical…
Motivation: A Chemical Reaction Network (CRN) is a set of chemical reactions, which can be very complex and difficult to analyze. Indeed, dynamical properties of CRNs can be described by a set of non-linear differential equations that…
A new experimental technique for investigating characteristics of plasma generated with plasmotrons in electrophysical installations was proposed. The technique involves a simultaneous registration of both radiation spectra and images of…
The extraction of molecular structures and reaction data from scientific documents is challenging due to their varied, unstructured chemical formats and complex document layouts. To address this, we introduce MolMole, a vision-based deep…
Process Execution Engines are a vital part of Business Process Management (BPM) and Manufacturing Orchestration Management (MOM), as they allow the business or manufacturing logic (expressed in a graphical notation such as BPMN) to be…
External matching networks are crucial and necessary for operating capacitively coupled plasmas in order to maximize the absorbed power. Experiments show that external circuits in general heavily interact with the plasma in a nonlinear way.…