A shadow molecular dynamics scheme for flexible charge models is presented where the shadow Born-Oppenheimer potential is derived from a coarse-grained approximation of range-separated density functional theory. The interatomic potential, including the atomic electronegativities and the charge-independent short-range part of the potential and force terms, is modeled by the linear atomic cluster expansion (ACE), which provides a computationally efficient alternative to many machine learning methods. The shadow molecular dynamics scheme is based on extended Lagrangian (XL) Born-Oppenheimer molecular dynamics (BOMD) [ , , 164]. XL-BOMD provides stable dynamics while avoiding the costly computational overhead associated with solving an all-to-all system of equations, which normally is required to determine the relaxed electronic ground state prior to each force evaluation. To demonstrate the proposed shadow molecular dynamics scheme for flexible charge models using atomic cluster expansion, we emulate the dynamics generated from self-consistent charge density functional tight-binding (SCC-DFTB) theory using a second-order charge equilibration (QEq) model. The charge-independent potentials and electronegativities of the QEq model are trained for a supercell of uranium oxide (UO) and a molecular system of liquid water. The combined ACE+XL-QEq molecular dynamics simulations are stable over a wide range of temperatures both for the oxide and for the molecular systems and provide a precise sampling of the Born-Oppenheimer potential energy surfaces. Accurate ground Coulomb energies are produced by the ACE-based electronegativity model during an NVE simulation of UO, predicted to be within 1 meV of those from SCC-DFTB on average during comparable simulations.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1021/acs.jctc.3c00349 | DOI Listing |
ACS Appl Mater Interfaces
December 2024
TCS Research, Sahyadri Park 2, Rajiv Gandhi Infotech Park, Hinjewadi Phase 3, Pune 411057, India.
Realization of a sustainable hydrogen economy in the future requires the development of efficient and cost-effective catalysts for its production at scale. MXenes (MX) are a class of 2D materials with 'n' layers of carbon or nitrogen (X) interleaved by 'n+1' layers of transition metal (M) and have emerged as promising materials for various applications including catalysts for hydrogen evolution reaction (HER). Their properties are intimately related to both their composition and their atomic structure.
View Article and Find Full Text PDFCancer Sci
December 2024
Department of Molecular Oncology, Graduate School of Medicine, Osaka University, Osaka, Japan.
Patient-derived organoids represent a novel platform to recapitulate the cancer cells in the patient tissue. While cancer heterogeneity has been extensively studied by a number of omics approaches, little is known about the spatiotemporal kinase activity dynamics. Here we applied a live imaging approach to organoids derived from 10 pancreatic ductal adenocarcinoma (PDAC) patients to comprehensively understand their heterogeneous growth potential and drug responses.
View Article and Find Full Text PDFJ Exp Clin Cancer Res
December 2024
Scientific Direction, IRCCS Regina Elena National Cancer Institute, Rome, Italy.
On September 23-24 (2024) the 6th Workshop IRE on Translational Oncology, titled "Cancer Organoids as Reliable Disease Models to Drive Clinical Development of Novel Therapies," took place at the IRCCS Regina Elena Cancer Institute in Rome. This prominent international conference focused on tumor organoids, bringing together leading experts from around the world.A central challenge in precision oncology is modeling the dynamic tumor ecosystem, which encompasses numerous elements that evolve spatially and temporally.
View Article and Find Full Text PDFParasit Vectors
December 2024
Institut de Recherche Biomédicale des Armées (IRBA), Unité de Parasitologie et Entomologie, Marseille, France.
Background: The risk of mosquito-borne disease transmission is increasing in temperate climates with the colonization and proliferation of the Asian tiger mosquito vector Aedes albopictus and the rapid mass transport of passengers returning from tropical regions where viruses are endemic. The prevention of major Aedes-borne viruses heavily relies on the use of insecticides for vector control, mainly pyrethroids. In Europe, only deltamethrin is authorized.
View Article and Find Full Text PDFNat Struct Mol Biol
December 2024
Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina.
Infectious diseases drive wild plant evolution and impact crop yield. Plants, like animals, sense biotic threats through pattern recognition receptors (PRRs). Overly robust immune responses can harm plants; thus, understanding the tuning of defense response mechanisms is crucial for developing pathogen-resistant crops.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!