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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…
In complex systems with many degrees of freedom such as peptides and proteins there exist a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped…
In this paper, we present a novel research software, called PEGASE, suitable for the design, validation and deployment of advanced control strategies for complex multi-domain energy systems. PEGASE especially features a highly efficient…
The field of plasma physics heavily relies on simulations to model various phenomena, such as instabilities, turbulence, and nonlinear behaviors that would otherwise be difficult to study from a purely theoretical approach. Simulations are…
Background: Simulated nucleotide or amino acid sequences are frequently used to assess the performance of phylogenetic reconstruction methods. BEAST, a Bayesian statistical framework that focuses on reconstructing time-calibrated molecular…
libEnsemble is a Python-based toolkit for running dynamic ensembles, developed as part of the DOE Exascale Computing Project. The toolkit utilizes a unique generator--simulator--allocator paradigm, where generators produce input for…
We present the Python-based Molecule Builder for ESPResSo (pyMBE), an open source software to design custom Coarse-Grained (CG) models, as well as pre-defined models of polyelectrolytes, peptides and globular proteins in the Extensible…
The Agent Based Model community has a rich and diverse ecosystem of libraries, platforms, and applications to help modelers develop rigorous simulations. Despite this robust and diverse ecosystem, the complexity of life from microbial…
The advancement of machine learning and the availability of large-scale reaction datasets have accelerated the development of data-driven models for computer-aided synthesis planning (CASP) in the past decade. Here, we detail the newest…
Python for Power System Analysis (PyPSA) is a free software toolbox for simulating and optimising modern electrical power systems over multiple periods. PyPSA includes models for conventional generators with unit commitment, variable…
The principles of automation and innovation serve as foundational elements for advancement in contemporary science and technology. Here, we introduce Pygen, an automation platform designed to empower researchers, technologists, and…
In biomolecular systems (especially all-atom models) with many degrees of freedom such as proteins and nucleic acids, there exist an astronomically large number of local-minimum-energy states. Conventional simulations in the canonical…
Single-cell sequencing technologies reveal cellular heterogeneity at high resolution, advancing our understanding of biological complexity. As datasets start to scale to tens of millions of cells, computational workflows face substantial…
Integrating population genetics into community ecology theory is a major goal in ecology and evolution, but analyzing the resulting models is computationally daunting. Here we describe sPEGG ($\underline{\textrm{s}}\textrm{imulating}$…
An open source software package for performing dynamic RMS simulation of small to medium-sized power systems is presented, written entirely in the Python programming language. The main objective is to facilitate fast prototyping of new wide…
The freud Python package is a powerful library for analyzing simulation data. Written with modern simulation and data analysis workflows in mind, freud provides a Python interface to fast, parallelized C++ routines that run efficiently on…
We develop general purpose algorithms for computing and utilizing both the Dyson series and Magnus expansion, with the goal of facilitating numerical perturbative studies of quantum dynamics. To enable broad applications to models with…
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…
Calculating free energies is an important and notoriously difficult task for molecular simulations. The rapid increase in computational power has made it possible to probe increasingly complex systems, yet extracting accurate free energies…
We equip dynamic geometry software (DGS) with a user-friendly method that enables massively parallel calculations on the graphics processing unit (GPU). This interplay of DGS and GPU opens up various applications in education and…