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Molecular generation, an essential method for identifying new drug structures, has been supported by advancements in machine learning and computational technology. However, challenges remain in multi-objective generation, model…
An early-stage version of simulation package is developed for electronic structure calculation and dynamics of atom process in large-scale systems, particularly, nm-scale or 10nm-scale systems. We adopted the Extensible Markup Language…
Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be…
relentless is an open-source Python package that enables the optimization of objective functions computed using molecular dynamics simulations. It has a high-level, extensible interface for model parametrization; setting up, running, and…
A new molecular simulation toolkit composed of some lately developed force fields and specified models is presented to study the self-assembly, phase transition, and other properties of polymeric systems at mesoscopic scale by utilizing the…
Probabilistic programming languages (PPLs) are receiving widespread attention for performing Bayesian inference in complex generative models. However, applications to science remain limited because of the impracticability of rewriting…
Language models (LMs) perform well on standardized coding benchmarks but struggle with real-world software engineering tasks such as resolving GitHub issues in SWE-Bench, especially when model parameters are less than 100B. While smaller…
Biochars have been attracting renewed attention as economical and environmentally friendly carbon sequestration materials with a diverse range of applications. However, experimental developments may be limited by the lack of molecular-level…
Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between…
The computer revolution has been driven by a sustained increase of computational speed of approximately one order of magnitude (a factor of ten) every five years since about 1950. In natural sciences this has led to a continuous increase of…
Realistic simulations of detailed, biophysics-based, multi-scale models require very high resolution and, thus, large-scale compute facilities. Existing simulation environments, especially for biomedical applications, are designed to allow…
The genome-scale metabolic model with protein constraint (PC-model) has been increasingly popular for microbial metabolic simulations. We present PROSO Toolbox, a unified and simple-to-use PC-model toolbox that takes any high-quality…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
Large computer models are ubiquitous in the earth sciences. These models often have tens or hundreds of tuneable parameters and can take thousands of core-hours to run to completion while generating terabytes of output. It is becoming…
The context of this work is the design of a software, called MEMSALab, dedicated to the automatic derivation of multiscale models of arrays of micro- and nanosystems. In this domain a model is a partial differential equation. Multiscale…
Herein, epoxy resin is cured by coupling quantum chemical (QC) calculations with molecular dynamics (MD) simulations that enable parameter-free prediction of material characteristics. A polymer network is formed by the reaction between base…
The recent decades have seen various attempts at accelerating the process of developing materials targeted towards specific applications. The performance required for a particular application leads to the choice of a particular material…
Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but…
Anatomy evaluation is crucial for understanding the physiological state, diagnosing abnormalities, and guiding medical interventions. Statistical shape modeling (SSM) is vital in this process. By enabling the extraction of quantitative…
Particle-in-cell methods couple mesh-based methods for the solution of continuum mechanics problems, with the ability to advect and evolve particles. They have a long history and many applications in scientific computing. However, they have…