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Ultra-fast interpretable machine-learning potentials

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npj Computational Materials 2023年第1期9卷 649-657页

作者： Stephen r.Xie Matthias rupp richard g.hennig Department of Materials Science and Engineering University of FloridaGainesvilleFLUSA Quantum Theory Project University of FloridaGainesvilleFLUSA Department of Computer and Information Science University of KonstanzKonstanzGermany Materials research and Technology Department Luxembourg Institute of Science and Technology(LIST)Esch-sur-AlzetteLuxembourg

All-atom dynamics simulations are an indispensable quantitative tool in physics,chemistry,and materials science,but large systems and long simulation times remain challenging due to the trade-off between computational efficiency and predictive *** address this challenge,we combine effective two-and three-body potentials in a cubic B-spline basis with regularized linear regression to obtain machine-learning potentials that are physically interpretable,sufficiently accurate for applications,as fast as the fastest traditional empirical potentials,and two to four orders of magnitude faster than state-of-the-art machine-learning *** data from empirical potentials,we demonstrate the exact retrieval of the *** data from density functional theory,the predicted energies,forces,and derived properties,including phonon spectra,elastic constants,and melting points,closely match those of the reference *** introduced potentials might contribute towards accurate all-atom dynamics simulations of large atomistic systems over long-time scales.

关键词： method spline faster

Heterogeneity of mature oligodendrocytes in the central nervous system

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Neural regeneration research 2025年第5期20卷 1336-1349页

作者： Chao Weng Adam M.r.groh Moein Yaqubi Qiao-Ling Cui Jo Anne Stratton g.r.Wayne Moore Jack P.Antel Neuroimmunology Unit Montreal Neurological Institute-HospitalDepartment of Neurology and NeurosurgeryMcGill UniversityMontrealQCCanada Department of Neurology Renmin Hospital of Wuhan UniversityWuhanHubei ProvinceChina

Mature oligodendrocytes form myelin sheaths that are crucial for the insulation of axons and efficient signal transmission in the central nervous *** evidence has challenged the classical view of the functionally static mature oligodendrocyte and revealed a gamut of dynamic functions such as the ability to modulate neuronal circuitry and provide metabolic support to *** the recognition of potential heterogeneity in mature oligodendrocyte function,a comprehensive summary of mature oligodendrocyte diversity is *** delve into early 20th-century studies by robertson and río-Hortega that laid the foundation for the modern identification of regional and morphological heterogeneity in mature ***,recent morphologic and functional studies call into question the long-assumed homogeneity of mature oligodendrocyte function through the identification of distinct subtypes with varying myelination ***,modern molecular investigations,employing techniques such as single cell/nucleus rNA sequencing,consistently unveil at least six mature oligodendrocyte subpopulations in the human central nervous system that are highly transcriptomically diverse and vary with central nervous system *** and disease related mature oligodendrocyte variation denotes the impact of pathological conditions such as multiple sclerosis,Alzheimer's disease,and psychiatric ***,caution is warranted when subclassifying mature oligodendrocytes because of the simplification needed to make conclusions about cell identity from temporally confined *** studies leveraging advanced techniques like spatial transcriptomics and single-cell proteomics promise a more nuanced understanding of mature oligodendrocyte *** research avenues that precisely evaluate mature oligodendrocyte heterogeneity with care to understand the mitigating influence of species,sex,central nervous system region,age,and disease,

关键词： aging central nervous system diseases electron microscopy heterogeneity immunohistochemistry myelin sheath natural history neuroglia oligodendroglia single-cell gene expression analysis

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Data-augmentation for graph neural network learning of the relaxed energies of unrelaxed structures

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npj Computational Materials 2022年第1期8卷 2037-2043页

作者： Jason gibson Ajinkya Hire richard g.hennig Department of Materials Science and Engineering University of FloridaGainesvilleFL32611USA Quantum Theory Project University of FloridaGainesvilleFL32611USA

Computational materials discovery has grown in utility over the past decade due to advances in computing power and crystal structure prediction algorithms(CSPA).However,the computational cost of the ab initio calculations required by CSPA limits its utility to small unit cells,reducing the compositional and structural space the algorithms can *** studies have bypassed unneeded ab initio calculations by utilizing machine learning to predict the stability of a ***,graph neural networks trained on large datasets of relaxed structures display high fidelity in predicting formation ***,the geometries of structures produced by CSPA deviate from the relaxed state,which leads to poor predictions,hindering the model’s ability to filter unstable *** remedy this behavior,we propose a simple,physically motivated,computationally efficient perturbation technique that augments training data,improving predictions on unrelaxed structures by 66%.Finally,we show how this error reduction can accelerate CSPA.

关键词： material relaxed utilizing

The revolution of the biology of the genome

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Cell research 2004年第1期14卷 1-7页

作者： WoIfgang hennig 320 Yue Yang road China. Chinese Academy of Sciences german Academic Exchange Service (DAAD) Laboratory Shanghai 200031 Shanghai Institutes for Biological Sciences

Sequence data of entire eukaryotic genomes and their detailed comparison have provided new evidence on genome evolution. The major mechanisms involved in the increase of genome sizes are polyploidization and gene duplication. Subsequent gene silencing or mutations, preferentially in regulatory sequences of genes, modify the genome and permit the development of genes with new properties. Mechanisms such as lateral gene transfer, exon shuffling or the creation of new genes by transposition contribute to the evolution of a genome, but remain of relatively restricted relevance. Mechanisms to decrease genome sizes and, in particular, to remove specific DNA sequences, such as blocks of satellite DNAs, appear to involve the action of rNA interference (rNAi). rNAi mechanisms have been proven to be involved in chromatin packaging related with gene inactivation as well as in DNA excision during the macronucleus development in ciliates.

关键词： genome structure gene duplication rNAi gene silencing chromatin.

An SPH Framework for Earthquake-Induced Liquefaction Hazard Assessment of geotechnical Structures

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Computer Modeling in Engineering & Sciences 2025年第1期142卷 251-277页

作者： Sourabh Mhaski g.V.ramana Department of Civil Engineering Indian Institute of Technology DelhiNew Delhi110016India

Earthquake-induced soil liquefaction poses significant risks to the stability of geotechnical structures *** understanding of the liquefaction triggering,and the post-failure large deformation behaviour is essential for designing resilient *** present study develops a Smoothed Particle Hydrodynamics(SPH)framework for earthquake-induced liquefaction hazard assessment of geotechnical *** coupled flowdeformation behaviour of soils subjected to cyclic loading is described using the PM4Sand model implemented in a three-phase,single-layer SPH framework.A staggered discretisation scheme based on the stress particle SPH approach is adopted to minimise numerical inaccuracies caused by zero-energy modes and tensile ***,non-reflecting boundary conditions for seismic analysis of semi-infinite soil domains using the SPH method are *** numerical framework is employed for the analysis of cyclic direct simple shear test,seismic analysis of a level ground site,and liquefaction-induced failure of the Lower San Fernando *** agreement for liquefaction triggering and post-failure behaviour demonstrates that the SPH framework can be utilised to assess the effect of seismic loading on field-scale geotechnical *** present study also serves as the basis for future advancements of the SPH method for applications related to earthquake geotechnical engineering.

关键词： Earthquake seismic liquefaction stress particle PM4Sand smoothed particle hydrodynamics(SPH)

Design of small-scale gradient coils in magnetic resonance imaging by using the topology optimization method

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Chinese Physics B 2018年第5期27卷 91-100页

作者： Hui Pan Feng Jia Zhen-Yu Liu Maxim Zaitsev Juergen hennig Jan g Korvink Changchun Institute of Optics Fine Mechanics and PhysicsChinese Academy of SciencesChangchun 130033China University of Chinese Academy of Sciences Beijing 100049China Deptartment of radiology Medical PhysicsMedical Center University of FreihurgFaculty of MedicineUniversity of FreiburgFreiburg 79106Germany Institute of Microstructure Technology Karlsruhe Institute of Technology(KIT)Karlsruhe 76344Germany

A topology optimization method based on the solid isotropic material with penalization interpolation scheme is utilized for designing gradient coils for use in magnetic resonance *** the popular stream function method,the proposed method has design variables that are the distribution of conductive material.A voltage-driven transverse gradient coil is proposed to be used as micro-scale magnetic resonance imaging(MrI)gradient coils,thus avoiding introducing a coil-winding pattern and simplifying the coil *** proposed method avoids post-processing errors that occur when the continuous current density is approximated by discrete wires in the stream function *** feasibility and accuracy of the method are verified through designing the z-gradient and y-gradient coils on a cylindrical *** design results show that the proposed method can provide a new coil layout in a compact design space.

关键词： topology optimization method gradient coils solid isotropic material with penalization magnetic resonance imaging

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A Structural Bisulfite Assay to Identify DN Cruciforms

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Molecular Plant 2016年第9期9卷 1328-1336页

作者： Matthew gentry Lars hennig Department of Plant Biology Uppsala BioCenter Swedish University of Agricultural Sciences and Linnean Center for Plant Biology 75007 Uppsala Sweden

In the half century since the discovery of the double-helix structure of DNA, it has become increasingly clear that DNA functionality is based on much more than its sequence in a double-helical structure. Further advances have highlighted the importance of additional aspects of DNA structure： its packaging in the higher order chromatin structure, positioning of nucleosomes along the DNA, and the occurrence of non-helical DNA structures. Of these, the latter has been problematic to prove empirically. Here, we describe a method that uses non-denaturing bisulfite sequencing on isolated Arabidopsis thaliana nuclei to determine the location of cytosines positioned outside the double helix as a result of non-B-form DNA structures. We couple this with computational methods and S1 nuclease digest to reliably identify stable, non-B-form, cruciform structures. This enables us to identify a palindrome in the promoter of FLOWErINg LOCUS T that forms a stable non-B-form structure. The stronger conservation of the ability to form a nonhelical secondary structure than of the sequence suggests that this structure is biologically relevant.

关键词： DNA structure cruciform DNA genome organization

Machine Learning Techniques in Predicting Hot Deformation Behavior of Metallic Materials

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Computer Modeling in Engineering & Sciences 2025年第1期142卷 713-732页

作者： Petr Opela Josef Walek Jaromír Kopecek Department of Metallurgical Technologies Faculty of Materials Science and TechnologyVSB–Technical University of OstravaOstrava70800Czech Republic FZU—Institute of Physics of the Czech Academy of Sciences Prague18200Czech Republic

In engineering practice,it is often necessary to determine functional relationships between dependent and independent *** relationships can be highly nonlinear,and classical regression approaches cannot always provide sufficiently reliable ***,Machine Learning(ML)techniques,which offer advanced regression tools to address complicated engineering issues,have been developed and widely *** study investigates the selected ML techniques to evaluate their suitability for application in the hot deformation behavior of metallic *** ML-based regression methods of Artificial Neural Networks(ANNs),Support Vector Machine(SVM),Decision Tree regression(DTr),and gaussian Process regression(gPr)are applied to mathematically describe hot flow stress curve datasets acquired experimentally for a medium-carbon *** the gPr method has not been used for such a regression task before,the results showed that its performance is the most favorable and practically unrivaled;neither the ANN method nor the other studied ML techniques provide such precise results of the solved regression analysis.

关键词： Machine learning gaussian process regression artificial neural networks support vector machine hot deformation behavior

Stepping up after spinal cord injury:negotiating an obstacle during walking

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Neural regeneration research 2025年第7期20卷 1919-1929页

作者： Alain Frigon Charly g.Lecomte Department of Pharmacology-Physiology Faculty of Medicine and Health SciencesUniversitéde SherbrookeCentre de recherche du Centre Hospitalier Universitaire de SherbrookeSherbrookeQCCanada

Every day walking consists of frequent voluntary modifications in the gait pattern to negotiate *** spinal cord injury,stepping over an obstacle becomes *** over an obstacle requires sensorimotor transformations in several structures of the brain,including the parietal cortex,premotor cortex,and motor *** information and planning are transformed into motor commands,which are sent from the motor cortex to spinal neuronal circuits to alter limb trajectory,coordinate the limbs,and maintain *** spinal cord injury,bidirectional communication between the brain and spinal cord is disrupted and animals,including humans,fail to voluntarily modify limb trajectory to step over an ***,in this review,we discuss the neuromechanical control of stepping over an obstacle,why it fails after spinal cord injury,and how it recovers to a certain extent.

关键词： biomechanics locomotion neurophysiology obstacle negotiation spinal cord injury

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