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OpenCAEPoro is a parallel numerical simulation software developed in C++ for simulating multiphase and multicomponent flows in porous media. The software utilizes a set of general-purpose compositional model equations, enabling it to handle…

In this work, the development and implementation of the effective stochastic potential (ESP) method is presented to perform efficient conformational sampling of molecules. The overarching goal of this work is to alleviate the computational…

Microcapsules are a key class of microscale materials with applications in areas ranging from personal care to biomedicine, and with increasing potential to act as extracellular matrix (ECM) models of hollow organs or tissues. Such capsules…

Liquid chromatography-mass spectrometry (LC-MS/MS) data analysis requires adaptable software solutions to meet diverse analytical needs. We present eMZed 3, a modern Python framework for flexible and interactive analysis of LC-MS/MS data.…

Inversions of airborne EM data are often an iterative process, not only requiring that the researcher be able to explore the impact of changing components such as the choice of regularization functional or model parameterization, but also…

ESPSim is an open source JAVA program that enables the comparisons of protein electrostatic potential maps via the computation of an electrostatic similarity measure. This program has been utilized to demonstrate a high degree of…

This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in…

Development of scientific and engineering software is usually different and could be more challenging than the development of conventional enterprise software. The authors were involved in a technology-transfer project between academia and…

The current landscape of scientific research is widely based on modeling and simulation, typically with complexity in the simulation's flow of execution and parameterization properties. Execution flows are not necessarily straightforward…

We update the capabilities of the open-knowledge software instrument Modules for Experiments in Stellar Astrophysics (MESA). RSP is a new functionality in MESAstar that models the non-linear radial stellar pulsations that characterize RR…

Soft, slender structures are ubiquitous in natural and engineered systems, with broad application potential from biomimetic materials to soft robotics. However, there is a notable lack of computational tools that simultaneously preserve…

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…

Self-supervised learning through masked autoencoders has attracted great attention for remote sensing (RS) foundation model (FM) development, enabling improved representation learning across diverse sensors and downstream tasks. However,…

Calculating solvent accessible surface areas (SASA) is a run-of-the-mill calculation in structural biology. Although there are many programs available for this calculation, there are no free-standing, open-source tools designed for easy…

Stellar physics and evolution calculations enable a broad range of research in astrophysics. Modules for Experiments in Stellar Astrophysics (MESA) is a suite of open source libraries for a wide range of applications in computational…

In this paper the full and exhaustive algorithm of formation of a smooth molecular Solvent Excluded Surface- SES, and also Solvent Accessible Surface- SAS is presented. These surfaces are a boundary between molecule and solvent. The basis…

-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…

ESPRESSO is an extremely stable high-resolution spectrograph which is currently being developed for the ESO VLT. With its groundbreaking characteristics it is aimed to be a "science machine", i.e. a fully-integrated instrument to directly…

We review the physics assumptions and input used in ISAJET~7.0 / ISA\-SUSY~1.0 that are relevant for simulating fundamental processes within the framework of the Minimal Supersymmetric Standard Model (MSSM) at $p\bar p$ and $pp$ colliders.…

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…