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Accurate and scalable graph neural network force field and molecular dynamics with direct force architecture

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npj Computational Materials 2021年第1期7卷 650-658页

作者： Cheol Woo Park Mordechai Kornbluth jonathan vandermause Chris Wolverton Boris Kozinsky jonathan P.Mailoa Robert Bosch Research and Technology Center CambridgeMA 02139USA Northwestern University EvanstonIL 60208USA Harvard School of Engineering and Applied Sciences CambridgeMA 02138USA

Recently,machine learning(ML)has been used to address the computational cost that has been limiting ab initio molecular dynamics(AIMD).Here,we present GNNFF,a graph neural network framework to directly predict atomic forces from automatically extracted features of the local atomic environment that are translationally-invariant,but rotationally-covariant to the coordinate of the *** demonstrate that GNNFF not only achieves high performance in terms of force prediction accuracy and computational speed on various materials systems,but also accurately predicts the forces of a large MD system after being trained on forces obtained from a smaller ***,we use our framework to perform an MD simulation of Li7P3S11,a superionic conductor,and show that resulting Li diffusion coefficient is within 14%of that obtained directly from *** high performance exhibited by GNNFF can be easily generalized to study atomistic level dynamics of other material systems.

关键词： neural AIMD dynamics

Uncertainty-aware molecular dynamics from Bayesian active learning for phase transformations and thermal transport in SiC

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npj Computational Materials 2023年第1期9卷 2000-2007页

作者： Yu Xie jonathan vandermause Senja Ramakers Nakib H.Protik Anders Johansson Boris Kozinsky John A.Paulson School of Engineering and Applied Sciences Harvard UniversityCambridgeMAUSA Department of Physics Harvard UniversityCambridgeMAUSA Corporate Sector Research and Advance Engineering Robert Bosch GmbHRenningenUSA Interdisciplinary Centre for Advanced Materials Simulation Ruhr-Universität BochumBochumGermany Robert Bosch LLC Research and Technology CenterWatertownMAUSA

Machine learning interatomic force fields are promising for combining high computational efficiency and accuracy in modeling quantum interactions and simulating atomistic *** learning methods have been recently developed to train force fields efficiently and *** them,Bayesian active learning utilizes principled uncertainty quantification to make data acquisition *** this work,we present a general Bayesian active learning workflow,where the force field is constructed from a sparse Gaussian process regression model based on atomic cluster expansion *** circumvent the high computational cost of the sparse Gaussian process uncertainty calculation,we formulate a high-performance approximate mapping of the uncertainty and demonstrate a speedup of several orders of *** demonstrate the autonomous active learning workflow by training a Bayesian force field model for silicon carbide(SiC)polymorphs in only a few days of computer time and show that pressure-induced phase transformations are accurately *** resulting model exhibits close agreement with both ab initio calculations and experimental measurements,and outperforms existing empirical models on vibrational and thermal *** active learning workflow readily generalizes to a wide range of material systems and accelerates their computational understanding.

关键词： computer thermal utilize

On-the-fly active learning of interpretable Bayesian force fields for atomistic rare events

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npj Computational Materials 2020年第1期6卷 1502-1512页

作者： jonathan vandermause Steven B.Torrisi Simon Batzner Yu Xie Lixin Sun Alexie M.Kolpak Boris Kozinsky Department of Physics Harvard UniversityCambridgeMA 02138USA John A.Paulson School of Engineering and Applied Sciences Harvard UniversityCambridgeMA 02138USA Center for Computational Engineering Massachusetts Institute of TechnologyCambridgeMA 02139USA Department of Mechanical Engineering Massachusetts Institute of TechnologyCambridgeMA 02139USA Bosch Research CambridgeMA 02139USA

Machine learned force fields typically require manual construction of training sets consisting of thousands of first principles calculations,which can result in low training efficiency and unpredictable errors when applied to structures not represented in the training set of the *** severely limits the practical application of these models in systems with dynamics governed by important rare events,such as chemical reactions and *** present an adaptive Bayesian inference method for automating the training of interpretable,low-dimensional,and multi-element interatomic force fields using structures drawn on the fly from molecular dynamics *** an active learning framework,the internal uncertainty of a Gaussian process regression model is used to decide whether to accept the model prediction or to perform a first principles calculation to augment the training set of the *** method is applied to a range of single-and multi-element systems and shown to achieve a favorable balance of accuracy and computational efficiency,while requiring a minimal amount of ab initio training *** provide a fully opensource implementation of our method,as well as a procedure to map trained models to computationally efficient tabulated force fields.

关键词： fields element typically

Gust response of an elasto-flexible morphing wing using fluid–structure interaction simulations

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Chinese Journal of Aeronautics 2024年第2期37卷 45-57页

作者： jonathan PFLÜGER Christian BREITSAMTER Department of Mechanical Engineering Technical University of MunichGarching 85748Germany

Small and micro unmanned aircraft are the focus of scientific interest due to their wide range of *** often operate in a highly unstable flight environment where the application of new morphing wing technologies offers the opportunity to improve flight *** investigated concept comprises port and starboard adjustable wings,and an adaptive elastoflexible membrane serves as the lifting *** focus is on the benefits of the deforming membrane during the impact of a one-minus-cosine type *** a low Reynolds number of Re=264000,the morphing wing model is investigated numerically by unsteady fluid-structure interaction ***,the numerical results are validated by experimental data from force and moment,flow field,and deformation ***,with the rigid wing as the baseline,the flexible case is investigated,focusing on the advantages of the elastic *** all configurations studied,the maximum amplitude of the lift coefficient under gust load shows good agreement between the experimental and numerical *** the decay of the gust,they differ more the higher the aspect ratio of the *** considering the flow field,the main differences are due to the separation behavior on the upper side of the *** flow reattaches earlier in the experiments than in the simulations,which explains the higher lift values observed in the *** at one intermediate configuration does the lift amplitude of the rigid configuration exceeds that of the flexible by about 12%,with the elastic membrane resulting in a smaller and more uniform peak load,which is also evident in the wing loading and hence in the root bending moment.

关键词： Membrane wing Morphing wing Flexible wing surface Computational fluid dynam-ics Fluid-structure interaction Unsteady inflow condition Gust response

NLRP3 inflammasome plays a vital role in the pathogenesis of age-related diseases in the eye and brain

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Neural Regeneration Research 2024年第7期19卷 1425-1426页

作者： Jack jonathan Maran Odunayo Omolola Mugisho Buchanan Ocular Therapeutics Unit Department of OphthalmologyNew Zealand National Eye CentreUniversity of AucklandAucklandNew Zealand

Key points:With aging,there is increased nucleotide-binding oligomerization domain-(NOD-)like receptor(NLR) protein-3(NLRP3) activation in neural and ocular *** of the NLRP3 inflammasome appears to be a common denominator in the pathogenesis of age-related diseases of the eye and *** inhibition of the NLRP3 inflammasome may be a potent therapy for preventing the development and progression of age-related eye and brain diseases.

关键词： NLRP3 pathogenesis inflam

DNA G-Quadruplexes as Targets for Natural Product Drug Discovery

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Engineering 2024年第7期38卷 39-51页

作者： Kai-Bo Wang Yingying Wang jonathan Dickerhoff Danzhou Yang Borch Department of Medicinal Chemistry and Molecular Pharmacology College of PharmacyPurdue UniversityWest LafayetteIN 47907USA Purdue Center for Cancer Research Purdue UniversityWest LafayetteIN 47907USA Department of Chemistry Purdue UniversityWest LafayetteIN 47907USA Purdue Institute for Drug Discovery Purdue UniversityWest LafayetteIN 47907USA Jiangsu Key Laboratory of Bioactive Natural Product Research&State Key Laboratory of Natural Medicines China Pharmaceutical UniversityNanjing 210009China

DNA guanine(G)-quadruplexes(G4s)are unique secondary structures formed by two or more stacked Gtetrads in G-rich DNA *** structures have been found to play a crucial role in highly transcribed genes,especially in cancer-related oncogenes,making them attractive targets for cancer ***,targeting oncogene promoter G4 structures has emerged as a promising strategy to address the challenge of undruggable and drug-resistant proteins,such as MYC,BCL2,KRAS,and *** products have long been an important source of drug discovery,particularly in the fields of cancer and infectious *** progress has recently been made in the discovery of naturally occurring DNA G4-targeting *** DNA G4s,such as MYC-G4,BCL2-G4,KRAS-G4,PDGFR-b-G4,VEGF-G4,and telomeric-G4,have been identified as potential targets of natural products,including berberine,telomestatin,quindoline,sanguinarine,isaindigotone,and many ***,we summarize and evaluate recent advancements in natural and nature-derived DNA G4 binders,focusing on understanding the structural recognition of DNA G4s by small molecules derived from *** also discuss the challenges and opportunities associated with developing drugs that target DNA G4s.

关键词： G-quadruplex Natural products Alkaloids Cancer Promoter

Treatment of Helicobacter pylori with potassium competitive acid blockers:A systematic review and meta-analysis

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World Journal of Gastroenterology 2024年第9期30卷 1213-1223页

作者： Joseph Edwin Kanu jonathan Soldera Post Graduate Program at Acute Medicine and Gastroenterology University of South WalesCardiff CF371DLUnited Kingdom

BACKGROUND Helicobacter pylori(***)infects over half the global population,causing gastrointestinal diseases like dyspepsia,gastritis,duodenitis,peptic ulcers,GMALT lymphoma,and gastric *** *** is crucial for treating and preventing these *** conventional proton pump inhibitor(PPI)-based triple therapy is effective,there’s growing interest in longer acid suppression *** competitive acid blocker(P-CAB)triple and dual therapy are new regimens for *** *** used in Asian populations,vonoprazan(VPZ)has been recently Food and Drug Administration-approved for *** *** To assess the efficacy of regimens containing P-CABs in eradicating *** *** This study,following PRISMA 2020 guidelines,conducted a systematic review and meta-analysis by searching MEDLINE and Scopus libraries for randomized clinical trials(RCTs)or observational studies with the following command:[("Helicobacter pylori"OR"H pylori")AND("Treatment"OR"Therapy"OR"Eradication")AND("Vonaprazan"OR"Potassium-Competitive Acid Blocker"OR"P-CAB"OR"PCAB"OR"Revaprazan"OR"Linaprazan"OR"Soraprazan"OR"Tegoprazan")].Studies comparing the efficacy of P-CABs-based treatment to classical PPIs in eradicating *** were *** criteria included case reports,case series,unpublished trials,or conference *** variables encompassed age,diagnosis method,sample sizes,study duration,intervention and control,and *** eradication method were gathered by two independent ***-analysis was performed in R software,and forest plots were *** A total of 256 references were initially retrieved through the search ***,fifteen studies(7 RCTs,7 retrospective observational studies,and 1 comparative unique study)were included,comparing P-CAB triple therapy to PPI triple *** intention-to-treat analysis involved 8049 patients,with 4471 in the P-CAB intervention g

关键词： Helicobacter pylori infection Potassium competitive acid blockers Proton pump inhibitors Vonoprazan Amoxicillin

Formadinium Cation Doping Stabilized Ultra-deep-blue Lead Halide Perovskite Nanocrystal Light-emitting Diodes

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Chemical Research in Chinese Universities 2024年第3期40卷 556-560页

作者： Pui Kei KO jonathan E.HALPERT Department of Chemistry The Hong Kong University of Science and TechnologyKowloonHong Kong 999077P.R.China

The halide migration effect in mixed-halide lead-based perovskite is a serious problem hindering the development of its display *** this study,we have successfully addressed this issue by reporting formadinium(FA)doped mixed-halide perovskite nanocrystals(NCs)with ultra-deep-blue emission of 450 nm,narrow bandwidth of 16 nm,and a high photoluminescence quantum yield(PLQY)of 66%.The perovskite nanocrystal light-emitting diodes(NC-LEDs)using this nanocrystal as an active layer achieved a maximum external quantum efficiency(EQE)of 0.32%,30-fold improved compared to that of pristine and stable electroluminescence(EL)spectra at 450 nm under a 4.9–8.0 V *** findings demonstrate the potential of our approach in developing stable and efficient deep blue perovskite NC-LEDs.

关键词： Halide perovskite Light-emitting diode Deep-blue

On the calibration of a shear stress criterion for rock joints to represent the full stress-strain profile

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Journal of Rock Mechanics and Geotechnical Engineering 2024年第2期16卷 379-392页

作者： Akram Deiminiat jonathan D.Aubertin Yannic Ethier Department of Construction Engineering École de Technologie Supérieure(ÉTS)MontréalCanada

Conventional numerical solutions developed to describe the geomechanical behavior of rock interfaces subjected to differential load emphasize peak and residual shear *** detailed analysis of preand post-peak shear stress-displacement behavior is central to various time-dependent and dynamic rock mechanic problems such as rockbursts and structural instabilities in highly stressed *** complete stress-displacement surface(CSDS)model was developed to describe analytically the pre-and post-peak behavior of rock interfaces under differential *** formulations of the CSDS model required extensive curve-fitting iterations which limited its practical applicability and transparent integration into engineering *** present work proposes modifications to the CSDS model aimed at developing a comprehensive and modern calibration protocol to describe the complete shear stressdisplacement behavior of rock interfaces under differential *** proposed update to the CSDS model incorporates the concept of mobilized shear strength to enhance the post-peak ***’s concepts of joint roughness coefficient(JRC)and joint compressive strength(JCS)are incorporated to facilitate empirical estimations for peak shear stress and normal closure ***/uniaxial compression test and direct shear test results are used to validate the updated model and exemplify the proposed calibration *** results illustrate that the revised model successfully predicts the post-peak and complete axial stressestrain and shear stressedisplacement curves for rock joints.

关键词： Full shear profile Post-peak shear behavior Rock joint Joint roughness coefficient(JRC) Axial stress-strain curve