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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

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

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.

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

可去除染料--N-聚糖多方法深入分析中的缺失环节

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Engineering 2023年第7期26卷 132-150,I0006页

作者： Samanta Cajic Renéhennig Valerian Grote Udo Reichl Erdmann Rapp Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg 39106Germany glyXera GmbH Magdeburg 39120Germany Otto-von-Guericke University Chair of Bioprocess EngineeringMagdeburg 39106Germany

As the roles of glycans in health and disease continue to be unraveled,it is becoming apparent that glycans’immense complexity cannot be *** fully delineate glycan structures,we developed an integrative approach combining a set of cost-effective,widespread,and easy-to-handle analytical *** key feature of our workflow is the exploitation of a removable fluorescent label—exemplified by 9-fluorenylmethyl chloroformate(Fmoc)—to bridge the gap between diverse glycoanalytical methods,especially multiplexed capillary gel electrophoresis with laser-induced fluorescence detection(xCGELIF)and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry(MALDI-TOFMS).Through the detailed structural analysis of selected,dauntingly complex N-glycans from chicken ovalbumin,horse serum,and bovine transferrin,we illustrate the capabilities of the presented ***,this approach“visualizes”N-glycans that have been difficult to identify thus far—such as the sulfated glycans on human immunoglobulin A—including minute changes in glycan structures,potentially providing useful new targets for biomarker discovery.

关键词： Glycoproteins N-glycans Reversible labeling Hydrophilic interaction liquid chromatography Capillary gel electrophoresis Mass spectrometry

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NEW ADVANCES IN HUMAN MR

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波谱学杂志 2002年第1期19卷 88-89页

作者： Jurgen hennig Abt.Rontgendiagnostik Section of Medical PhysicsHugstetterstr.5579106 REIBURGGermany

MR Tomography has entered clinical practice in the early 1980 s with the introduction of the first commercial scanner. In its twenty years of history it went through several developmental cycles.

关键词： NEW ADVANCES IN HUMAN MR

Lost Memories of Winter： Breaking the FLC Silence

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Molecular Plant 2017年第12期10卷 1477-1479页

作者： Miyuki Nakamura Iva Mozgova Lars hennig Department of Plant Biology Uppsala BioCenter Swedish University of Agricultural Sciences and Linnean Center for Plant Biology 75007 Uppsala Sweden Institute of Microbiology of the Czech Academy of Sciences Centre Algatech Opatovický mlýn 37981 Třeboň Czech Republic Faculty of Science University of South Bohemia in Ceske Budejovice 37005 Ceske Budejovice Czech Republic

Vernalization, the acquisition of competence to flower after extended cold treatment, has puzzled researchers throughout the last century. Great progress in understanding the molecular mechanisms of vernalization in Arabidopsis has been made in the course of the last 20 years, placing the flowering repressor- encoding gene FLOWERING LOCUS C （FLC） in the limelight （Bouch6 et al., 2017）. In vernalization-dependent accessions, FRIGIDA （FRI） ensures strong expression of FLC that delays flowering, and extended exposure to low temperatures such as during winter leads to stable repression of FLC, which in turn clears the way for induction of flowering.

关键词： FLOWERING-LOCUS-C TRANSCRIPTION FACTOR VERNALIZATION INHERITANCE ARABIDOPSIS EXPRESSION

The chromosome as a dynamic structure of the cell nucleus

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Cell Research 1993年第1期3卷 1-9页

作者： Wolfgang hennig Deparment of Molecular and Developmental Genetics University of Nijmegen Faculty of Science Toernooiveld The Netherlands Maχ-PlanckGuest Laboratory Shanghai Institute of Cell Biology Academia Sinica Shanghai China

Our view of eukaryotic chromosomes is still very much dictated by the classic ideas of geneticists and cytologists considering the chromosome just as a vehicle for genes. This one-sided view of chromosomes may have been strongly influenced by the many cytological observations made on polytene chromosomes. They, in particular, revealed that the activation of genes for transcription is accompanied by local decondensation of the chromosome as it becomes evident in the formation of puffs in polytene chromosomes. The studies of chromosomes have for many years been focused on the relationship between genes and bands or interbands as they are seen in polytene chromosomes (or in the supposed equivalents, the chromomeres, of meiotic prophase chromosomes). This has yielded much fruitful informations such as the first direct evidence for the relationship between differential gene activity and cellular differentiation by the demonstration by Clever that steroid hormones directly regulate gene activity at the chromosomal level.

关键词： Cell The chromosome as a dynamic structure of the cell nucleus cell

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：潘辉贾峰刘震宇 Maxim Zaitsev Juergen hennig Jan G Korvink Changchun Institute of Optics Fine Mechanics and Physics Chinese Academy of Sciences Changchun 130033 China University of Chinese Academy of Sciences Beijing 100049 China Deptartment of Radiology Medical Physics Medical Center University of Freiburg Faculty of Medicine University of Freiburg Freiburg 79106 Germany Institute of Microstructure Technology Karlsruhe Institute of Technology (KIT) Karlsruhe 76344 Germany

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 microscopy. Unlike 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 configuration. The proposed method avoids post-processing errors that occur when the continuous current density is approximated by discrete wires in the stream function approach. The 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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