Related papers: RePlaChem: A dimensionality reduction library for …
Reconstructing numerical simulations from control systems research papers is often hindered by underspecified parameters and ambiguous implementation details. We define the task of Paper to Simulation Recoverability, the ability of an…
In silico tools are important for generating novel hypotheses and exploring alternatives in de novo metabolic pathway design. However, while many computational frameworks have been proposed for retrobiosynthesis, few successful examples of…
The development of materials science is undergoing a shift from empirical approaches to data-driven and algorithm-oriented research paradigm. The state-of-the-art platforms are confined to inorganic crystals, with limited chemical space,…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
MiMiC is a framework for modeling large-scale chemical processes that require treatment at multiple resolutions. It does not aim to implement single-handedly all methods required to treat individual subsystems, but instead, it relegates…
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
Information on the structure of molecules, retrieved via biochemical databases, plays a pivotal role in various disciplines, such as metabolomics, systems biology, and drug discovery. However, no such database can be complete, and the…
We introduce ppsim, a software package for efficiently simulating population protocols, a widely-studied subclass of chemical reaction networks (CRNs) in which all reactions have two reactants and two products. Each step in the dynamics…
Recent results on supercomputers show that beyond 65K cores, the efficiency of molecular dynamics simulations of interfacial systems decreases significantly. In this paper, we introduce a dynamic cutoff method (DCM) for interfacial systems…
Motivation: An essential step in developing computational tools for the inference, optimization, and simulation of biochemical reaction networks is gauging tool performance against earlier efforts using an appropriate set of benchmarks.…
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…
This work presents a reaction mechanism for oxygen plasmas, i.e. a set of reactions and corresponding rate coefficients that are validated against benchmark experiments. The kinetic scheme is validated in a DC glow discharge for gas…
We present mechanoChemML, a machine learning software library for computational materials physics. mechanoChemML is designed to function as an interface between platforms that are widely used for machine learning on one hand, and others for…
With the increasing interest in robotic synthesis in the context of organic chemistry, the automated extraction of chemical procedures from literature is critical. However, this task remains challenging due to the inherent ambiguity of…
Code reproduction is a cornerstone of scientific validity, yet it remains a formidable challenge in computer networking research due to the scarcity of open-source implementations and the complexity of heterogeneous system architectures.…
This study addresses the challenge of simulating realistic particle systems by proposing a novel particle decomposition scheme that improves the parallel performance of surface resolved particle simulations. Realistic particle systems often…
Chemical reactivity models are developed to predict chemical reaction outcomes in the form of classification (success/failure) or regression (product yield) tasks. The vast majority of the reported models are trained solely on chemical…
Numerical simulation of the complex plasma dynamics associated with high power, high frequency microwave breakdown at high pressures, leading to the formation of filamentary plasma structures such as self-organized plasma arrays, is a…
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…
Chemical reaction networks can be automatically generated from graph grammar descriptions, where rewrite rules model reaction patterns. Because a molecule graph is connected and reactions in general involve multiple molecules, the rewriting…