14 papers · ranked by Valyu relevance
Yann Garniron, Thomas Applencourt, Kevin Gasperich, Anouar Benali + 15 more
Quantum Package is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multi-reference second-order perturbation theory (PT2). The determinant-driven…
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With the ever-increasing demand for atomistic structures representative of real-life systems as well as the ad-vent of exascale computers, it has now become necessary and possible to use advanced global optimization (GO) techniques to intelligently sample the potential energy surface (PES). Given the previous studies…
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Recent advances in machine learning force fields (MLFF) have significantly extended the reach of atomistic simulations. Continuous progress in this field requires reliable reference datasets, accurate MLFF architectures, and efficient active learning strategies to enable robust modeling of complex molecular and…
Yann Garniron, Thomas Applencourt, Kevin Gasperich, Anouar Benali + 15 more
Quantum Package is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multi-reference second-order perturbation theory (PT2). The determinant-driven…
Authors not listed
This paper presents GLAS (Git-based Lab Automated Scheduler or Get Lab Automation Simplified), an open-source, robust, and highly expandable Git-based architecture designed for laboratory automation. GLAS can be deployed in both partially and fully automated experimental science laboratories, enabling the development…
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Protein conformational landscapes contain the functionally relevant information useful for understanding biological processes. Mapping out conformational landscapes provides valuable insights into protein behaviors and biological phenomena, and has relevance to therapeutic design. While experimental structural biology…
Viacheslav Bolnykh, Jógvan Magnus Haugaard Olsen, Simone Meloni, Martin P. Bircher + 3 more
We present a highly scalable DFT-based QM/MM implementation developed within MiMiC, a recently introduced multiscale modeling framework that uses a loose-coupling strategy in conjunction with a multiple-program multiple-data (MPMD) approach. The computation of electrostatic QM/MM interactions is parallelized exploiting…
Andrew Simmonett, Bernard Brooks, Thomas Darden
Evaluation of noncovalent electrostatic interactions is the dominant bottleneck in classical molecular dynamics simulations, and evaluation of Coulombic matrix elements similarly limits quantum mechanical self consistent field calculations. These difficulties are a result of the Coulomb operator’s slow decay, which…
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Bayesian optimization (BO) has become increasingly important for experimental optimization across scientific domains, yet implementing BO pipelines requires significant programming expertise and familiarity with specialized frameworks. This creates a barrier for domain experts who could benefit from BO but lack the…
Caroline Arnoux, Luis-Adrian Perez-Covarrubias, Alexandre Khaldi, Quentin Carlier + 4 more
Although additive manufacturing using multi-photon direct laser writing is nowadays considered as a major tool in the fabrication of future nano/micro-objects and optical components, it is currently limited by the low throughput of the writing process. To circumvent this issue, massive parallelization of the write…
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Investigating the molecular structure of soil organic matter (SOM), along with its intramolecular interactions and interactions with other soil components and xenobiotics, is essential due to its ecological importance. However, the complexity and heterogeneity of SOM present significant challenges for systematic…
Yudong Qiu, Daniel Smith, Chaya Stern, Mudong Feng + 1 more
The parameterization of torsional / dihedral angle potential energy terms is a crucial part of developing molecular mechanics force fields. Quantum mechanical (QM) methods are often used to provide samples of the potential energy surface (PES) for fitting the empirical parameters in these force field terms. To ensure…
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Molecular Dynamics (MD) simulations are essential for studying the time evolution of molecular systems. Still, their efficiency is often bottlenecked by file-based Inter-Process Communication (IPC) between MD and Electronic Structure (ES) programs. We present a socket-based IPC implementation that dramatically…
Pavel Pokhilko, Evgeny Epifanovsky, Anna I. Krylov
Using single precision floating point representation reduces the size of data and computation time by a factor of two relative to double precision conventionally used in electronic structure programs. For large-scale calculations, such as those encountered in many-body theories, reduced memory footprint alleviates…