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Exploitation of symmetry in periodic Self-Consistent-Field ab initio calculations: application to large three-dimensional compounds

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Science China Chemistry 2014年第10期57卷 1418-1426页

作者： de la pierre marco ORlaNDO Roberto FERRABONE Matteo ZICOVICH-WILSON Claudio M. DOVESI Roberto Dipartimento di Chimica Università di Torino and NIS Nanostructured Interfaces and Surfaces Centre of Excellence Via P. Giuria 7 10125 Torino Italy Nanochemistry Research Institute Department of Chemistry Curtin University GPO Box U1987 Perth WA 6845 Australia Facultad de Ciencias Universidad Autónoma del Estado de Morelos Av. Universidad 1001 Col. Chamilpa 62209 Cuernavaca (Morelos) Mexico

Symmetry can dramatically reduce the computational cost （running time and memory allocation） of Self-Consistent-Field ab initio calculations for crystalline systems. Crucial for running time is use of symmetry in the evaluation of one- and two-electron integrals, diagonalization of the Fock matrix at selected points in reciprocal space, reconstruction of the density matrix. As regards memory allocation, full square matrices （overlap, Fock and density） in the Atomic Orbital （AO） basis are avoided and a direct transformation from the packed AO to the SACO （Symmetry Adapted Crystalline Orbital） basis is per- formed, so that the largest matrix to be handled has the size of the largest sub-block in the latter basis. We here illustrate the effectiveness of this scheme, following recent advancements in the CRYSTAL code, concerning memory allocation and direct basis set transformation. Quantitative examples are given for large unit cell systems, such as zeolites （all-silica faujasite and silicalite MF1） and garnets （pyrope）. It is shown that the full SCF of 3D systems containing up to 576 atoms and 11136 Atomic Orbitals in the cell can be run with a hybrid functional on a single core PC with 500 MB RAM in about 8 h.

关键词： point symmetry Symmetry Adapted Crystalline Orbitals Fock matrix density matrix CPU time memory allocation quantum-mechanical calculations CRYSTAL code

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Additive neurorestorative effects of exercise and docosahexaenoic acid intake in a mouse model of Parkinson’s disease

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Neural Regeneration Research 2025年第2期20卷 574-586页

作者： Olivier Kerdiles Méryl-Farelle Oye Mintsa Mi-mba Katherine Coulombe Cyntia Tremblay VincentÉmond Martine Saint-pierre Clémence Rouxel Line Berthiaume pierre Julien Francesca Cicchetti Frédéric Calon Facultéde pharmacie UniversitéLaval1050 Avenue de la MédecineQuebecQCCanada Axe Neuroscience Centre de recherche du CHU de Québec-UniversitéLaval(Pavillon CHUL)2705 Boulevard LaurierQuebecQCCanada Institute of Nutrition and Functional Foods QuebecQCCanada Optinutribrain International Associated laboratory(NutriNeuro FranceINAFCanada)QuebecQCCanada Axe Endocrinologie et Néphrologie Centre de recherche du CHU de Québec-UniversitéLavalQuebecQCCanada Département de Médecine Facultéde MédecineUniversitéLavalQuebecQCCanada Département de Psychiatrie et Neurosciences Facultéde MédecineQuebecQCCanada

There is a need to develop interventions to slow or reverse the degeneration of dopamine neurons in Parkinson’s disease after *** that preclinical and clinical studies suggest benefits of dietary n-3 polyunsaturated fatty acids,such as docosahexaenoic acid,and exercise in Parkinson’s disease,we investigated whether both could synergistically interact to induce recovery of the dopaminergic ***,mice received a unilateral stereotactic injection of 6-hydroxydopamine into the striatum to establish an animal model of nigrostriatal *** weeks after lesion,animals were fed a docosahexaenoic acid-enriched or a control diet for the next 8 *** this period,the animals had access to a running wheel,which they could use or *** acid treatment,voluntary exercise,or the combination of both had no effect on(i)distance traveled in the open field test,(ii)the percentage of contraversive rotations in the apomorphine-induction test or(iii)the number of tyrosine-hydroxylase-positive cells in the substantia nigra pars ***,the docosahexaenoic acid diet increased the number of tyrosine-hydroxylase-positive terminals and induced a rise in dopamine concentrations in the lesioned *** to docosahexaenoic acid treatment or exercise alone,the combination of docosahexaenoic acid and exercise(i)improved forelimb balance in the stepping test,(ii)decreased the striatal DOPAC/dopamine ratio and(iii)led to increased dopamine transporter levels in the lesioned *** present results suggest that the combination of exercise and docosahexaenoic acid may act synergistically in the striatum of mice with a unilateral lesion of the dopaminergic system and provide support for clinical trials combining nutrition and physical exercise in the treatment of Parkinson’s disease.

关键词： 6-hydroxydopamine dopamine dopamine transporter exercise neurorestoration Parkinson’s disease polyunsaturated fatty acids omega-3

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Materials property prediction for limited datasets enabled by feature selection and joint learning with MODNet

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npj Computational Materials 2021年第1期7卷 731-738页

作者： pierre-Paul de Breuck Geoffroy Hautier Gian-marco Rignanese UCLouvain Institute of Condensed Matter and Nanosciences(IMCN)Louvain-la-NeuveBelgium Dartmouth College Thayer School of EngineeringHanoverNHUSA

In order to make accurate predictions of material properties,current machine-learning approaches generally require large amounts of data,which are often not available in *** this work,MODNet,an all-round framework,is presented which relies on a feedforward neural network,the selection of physically meaningful features,and when applicable,*** to being faster in terms of training time,this approach is shown to outperform current graph-network models on small *** particular,the vibrational entropy at 305 K of crystals is predicted with a mean absolute test error of 0.009 meV/K/atom(four times lower than previous studies).Furthermore,joint learning reduces the test error compared to single-target learning and enables the prediction of multiple properties at once,such as temperature ***,the selection algorithm highlights the most important features and thus helps to understand the underlying physics.

关键词： learning prediction property

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A simple denoising approach to exploit multi-fidelity data for machine learning materials properties

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npj Computational Materials 2022年第1期8卷 2226-2238页

作者： Xiaotong Liu pierre-Paul de Breuck Linghui Wang Gian-marco Rignanese Beijing Advanced Innovation Center for Materials Genome Engineering Beijing Information Science and Technology UniversityNo.35 Beisihuan Middle RoadBeijing100101BeijingP.R.China School of Computer Beijing Information Science and Technology UniversityNo.35 Beisihuan Middle RoadBeijing100101BeijingP.R.China Institute of Condensed Matter and Nanosciences UCLouvainChemin desÉtoiles 8Louvain-la-Neuve1348Belgium School of Materials Science and Engineering Northwestern Polytechnical UniversityNo.127 Youyi West RoadXi’an710072ShaanxiP.R.China

Machine-learning models have recently encountered enormous success for predicting the properties of *** are often trained based on data that present various levels of accuracy,with typically much less high-than low-fidelity *** order to extract as much information as possible from all available data,we here introduce an approach which aims to improve the quality of the data through *** investigate the possibilities that it offers in the case of the prediction of the band gap using both limited experimental data and density-functional theory relying on different exchange-correlation *** analyzing the raw data thoroughly,we explore different ways to combine the data into training sequences and analyze the effect of the chosen *** also study the effect of applying the denoising procedure several times until ***,we compare our approach with various existing methods to exploit multi-fidelity data and show that it provides an interesting improvement.

关键词： approach learning exploit

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A porous puckered V_(2)O_(5) polymorph as new high performance cathode material for aqueous rechargeable zinc batteries

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Journal of Energy Chemistry 2021年第10期30卷 459-468,I0012页

作者： Dauren Batyrbekuly Barbara laïk Jean-pierre Pereira-Ramos Zhumabay Bakenov Rita Baddour-Hadjean Institut de Chimie et des Matériaux Paris Est(ICMPE) UMR 7182 CNRS et UniversitéParis Est Créteil2 rue Henri Dunant94320 ThiaisFrance School of Engineering National Laboratory AstanaNazarbayev University53 Kabanbay Batyr AvenueAstana 010000Kazakhstan

Aqueous rechargeable zinc batteries are getting increasing attention for large-scale energy storage owing to their advantages in terms of cost,environmental friendliness and ***,the layered puckeredγ’-V_(2)O_(5) polymorph with a porous morphology is firstly introduced as cathode for an aqueous zinc battery system in a binary Zn^(2+)/Li^(+)*** Zn‖γ’-V_(2)O_(5) cell delivers high capacities of 240 and190 mAh g^(-1) at current densities of 29 and 147 mA g^(-1),respectively,and remarkable cycling stability in the 1.6 V-0.7 V voltage window(97%retention after 100 cycles at 0.15 A g^(-1)).The detailed structural evolution during first discharge-charge and subsequent cycling is investigated using X-ray diffraction and Raman *** demonstrate a reaction mechanism based on a selective Li insertion in the1.6 V-1.0 V voltage *** involves a reversible exchange of 0.8 Li^(+)in γ’-V_(2)O_(5) and the same structural response as the one reported in lithiated organic ***,in the extended 1.6 V-0.7 V voltage range,this work puts forward a concomitant and gradual phase transformation from γ’-V_(2)O_(5) to zinc pyrovanadate Zn_(3)V_(2)O_(7)(OH)2.2 H_(2)O(ZVO)during *** mechanism involving the in-situ formation of ZVO,known as an efficient Zn and Li intercalation material,explains the high electrochemical performance here reported for the Zn‖γ’-V_(2)O_(5) *** work highlights the peculiar layered-puckeredγ’-V_(2)O_(5) polymorph outperforms the conventionalα-V_(2)O_(5) with a huge improvement of capacity of 240 mAh g^(-1)vs 80 mAh g^(-1) in the same electrolyte and voltage window.

关键词： Vanadium pentoxide γ-V_(2)O_(5) Cathode Aqueous zinc battery High performance layered structure Energy storage Renewable energy

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Phonon-limited mobility for electrons and holes in highly-strained silicon

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npj Computational Materials 2024年第1期10卷 673-683页

作者： Nicolas Roisin Guillaume Brunin Gian-marco Rignanese denis Flandre Jean-pierre Raskin Samuel Poncé Institute of Information and Communication Technologies Electronics and Applied MathematicsUniversitécatholique de LouvainLouvain-la-NeuveBelgium European Theoretical Spectroscopy Facility Institute of Condensed Matter and NanosciencesUniversitécatholique de LouvainLouvain-la-NeuveBelgium Matgenix A6K Advanced Engineering CenterCharleroiBelgium WEL Research Institute WavreBelgium

Strain engineering is a widely used technique for enhancing the mobility of charge carriers in semiconductors,but its effect is not fully *** this work,we perform first-principles calculations to explore the variations of the mobility of electrons and holes in silicon upon deformation by uniaxial strain up to 2%in the[100]crystal direction.

关键词： mobility strained electrons

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The interaction of versican with its binding partners

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Cell Research 2005年第7期15卷 483-494页

作者： David P. la pierre,Albert J. YEE,Burton B. YANG Sunnybrook & Women’s College Health Sciences Centre 2075 Bayview Avenue Toronto M4N 3M5 Canada department of laboratory Medicine and Pathobiology University of Toronto Canada Sunnybrook & Women’s College Health Sciences Centre 2075 Bayview Avenue Toronto M4N 3M5 Canada Sunnybrook & Women’s College Health Sciences Centre 2075 Bayview Avenue Toronto M4N 3M5 Canada department of laboratory Medicine and Pathobiology University of Toronto Canada

Versican belongs to the family of the large aggregating chondroitin sulfate proteoglycans located primarily within theextracellular matrix (ECM). Versican, like other members of its family, has unique N- and C-terminal globular regions,each with multiple motifs. A large glycosaminoglycan-binding region lies between them. This review will begin byoutlining these structures, in the context of ECM proteoglycans. The diverse binding partners afforded to versican byvirtue of its modular design will then be examined. These include ECM components, such as hyaluronan, type Icollagen, tenascin-R, fibulin-1, and -2, fibrillin-1, fibronectin, P- and L-selectins, and chemokines. Versican also binds tothe cell surface proteins CD44, integrin β1, epidermal growth factor receptor, and P-selectin glycoprotein *** multiple interactors play important roles in cell behaviour, and the roles of versican in modulating such processesare discussed.

关键词： extracellular matrix proteoglycan G3 domain glycosaminoglycan interaction.

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determination of the Apparent Gas Permeability in a Macrocracked Concrete

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Engineering 2022年第10期17卷 93-98页

作者： pierre Rossi Univ Gustave Eiffel French Institute of Science and Technology for TransportDevelopment and Networks(IFSTTAR)Marne-la-Vallée F-77447France

This paper reports on analysis of an expermental study that armed to determine the apparent gas permeability in cracked *** is a lack of research on this topic in the international literature,due to the difficulty of performing reliable experimental testing for gas *** principal interest of this work is to present new and reliable experimental *** functions between the evolution of the apparent crack permeability and the apparent crack opening are also *** functions appear to be relevant in consideration of Poiseuille theory.

关键词： Concrete Macrocrack Gas transfer Permeability

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Active Matter, Microreversibility, and Thermodynamics

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Research 2020年第1期2020卷 1921-1940页

作者： pierre Gaspard Raymond Kapral Center for Nonlinear Phenomena and Complex Systems UniversitéLibre de Bruxelles(U.L.B.)Code Postal 231Campus PlaineB-1050 BrusselsBelgium Chemical Physics Theory Group Department of ChemistryUniversity of TorontoTorontoOntarioCanada M5S 3H6

Active matter,comprising many active agents interacting and moving in fluids or more complex environments,is a commonly occurring state of matter in biological and physical *** its very nature,active matter systems exist in nonequilibrium *** this paper,the active agents are small Janus colloidal particles that use chemical energy provided by chemical reactions occurring on their surfaces for propulsion through a diffusiophoretic *** a result of interactions among these colloids,either directly or through fluid velocity and concentration fields,they may act collectively to form structures such as dynamic clusters.A general nonequilibrium thermodynamics framework for the description of such systems is presented that accounts for both self-diffusiophoresis and diffusiophoresis due to external concentration gradients,and is consistent with *** predicts the existence of a reciprocal effect of diffusiophoresis back onto the reaction rate for the entire collection of colloids in the system,as well as the existence of a clustering instability that leads to nonequilibrium inhomogeneous system states.

关键词： mechanism nonequilibrium system

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Chemical reproductive traits of diploid Bombus terrestris males： Consequences on bumblebee conservation

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Insect Science 2017年第4期24卷 623-630页

作者： Thomas Lecocq Maxence Gerard Kevin Maebe Nicolas Brasero lauren dehon Guy Smagghe Irena Valterova Thibaut de Meulemeester pierre Rasmont denis Michez laboratory of Zoology Research Institute of Biosciences University of Mons Mons France Research Unit Animal and Functionalities of Animal Products (URAFPA) University of Lorraine - INRA Avenue de la Foret de Haye BP 172 F-54505 Vandoeuvre-les-Nancy France department of Crop Protection Faculty of Bioscience Engineering Ghent University Coupure links 653 B-9000 Ghent Belgium Academy of Sciences of the Czech Republic Institute of Organic Chemistry and Biochemistry Flamingovo nam 2 CZ 166 10 Prague Czech Republic Naturalis Biodiversity Center Darwinweg 2 Postbus 9517 2300 RA Leiden the Netherlands

The current bumblebee decline leads to inbreeding in populations that fosters a loss of allelic diversity and diploid male production. As diploid males are viable and their offspring are sterile, bumblebee populations can quickly fall in a vortex of extinction. In this article, we investigate for the first time a potential premating mechanism through a major chemical reproductive trait （male cephalic labial gland secretions） that could prevent monandrous virgin queens from mating with diploid males. We focus our study on the cephalic labial gland secretions of diploid and haploid males ofBombus terrestris （L.）. Contrary to initial expectations, our results do not show any significant differentiation of cephalic labial gland secretions between diploid and haploid specimens. Queens seem therefore to be unable to avoid mating with diploid males based on their compositions of cephalic labial gland secretions. This suggests that the vortex of extinction of diploid males could not be stopped through premating avoidance based on the cephalic labial gland secretions but other mechanisms could avoid mating between diploid males and queens.

关键词： bee decline bumblebees conservation diploid males premating recogni-tion reproductive traits

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