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88 results on '"Moscow Institute of Physics and Technology [Moscow] ( MIPT )"'

1. Demkov-kunike model for cold atom association: Weak interaction regime

Author

H. H. Azizbekyan, Claude Leroy, Ruzan Sokhoyan, Artur Ishkhanyan, Institute for Physical Research ( IPR ), National Academy of Sciences of Armenia, Laboratoire Interdisciplinaire Carnot de Bourgogne ( LICB ), Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de physique moléculaire et des collisions ( LPMC ), Université Paul Verlaine - Metz ( UPVM ), Moscow Institute of Physics and Technology [Moscow] ( MIPT ), Institute of Physical Research, Institute for Physical Research (IPR), National Academy of Sciences of the Republic of Armenia [Yerevan] (NAS RA), Laboratoire Interdisciplinaire Carnot de Bourgogne (LICB), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de physique moléculaire et des collisions (LPMC), Université Paul Verlaine - Metz (UPVM), and Moscow Institute of Physics and Technology [Moscow] (MIPT)

Subjects
[ PHYS.QPHY ] Physics [physics]/Quantum Physics [quant-ph], FOS: Physical sciences, General Physics and Astronomy, Weak interaction, level crossing, 01 natural sciences, 010305 fluids & plasmas, law.invention, weak interaction, [PHYS.QPHY]Physics [physics]/Quantum Physics [quant-ph], law, Ultracold atom, 0103 physical sciences, Statistical physics, 03.75.Nt, 33.80.Be, 010306 general physics, Scaling, Condensed Matter::Quantum Gases, Physics, Bose–Einstein condensate, Level crossing, Expression (computer science), Pulse (physics), Nonlinear system, Quantum Gases (cond-mat.quant-gas), Demkov–Kunike model, Condensed Matter - Quantum Gases
Abstract

We study the nonlinear mean-field dynamics of molecule formation at coherent photo- and magneto-association of an atomic Bose-Einstein condensate for the case when the external field configuration is defined by the quasi-linear level crossing Demkov-Kunike model, characterized by a bell-shaped pulse and finite variation of the detuning. We present a general approach to construct an approximation describing the temporal dynamics of the molecule formation in the weak interaction regime and apply the developed method to the nonlinear Demkov-Kunike problem. The presented approximation, written as a scaled solution to the linear problem associated to the nonlinear one we treat, contains fitting parameters which are determined through a variational procedure. Assuming that the parameters involved in the solution of the linear problem are not modified, we suggest an analytical expression for the scaling parameter., 6 pages, 4 figures

Published
2009
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2. Sb2Te3/graphite nanocomposite: A comprehensive study of thermal conductivity

Author

V. A. Kulbachinskii, S. Janaky, Sudip Mukherjee, Gangadhar Das, Ramzy Daou, Chandrabhas Narayana, A. K. Deb, Sylvie Hébert, P. Singha, Samir Kumar Bandyopadhyay, Vladimir G. Kytin, Aritra Banerjee, Subarna Das, Antoine Maignan, Laboratoire de cristallographie et sciences des matériaux (CRISMAT), École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche sur les Matériaux Avancés (IRMA), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), University of Calcutta, Moscow Institute of Physics and Technology [Moscow] (MIPT), Faculty of Physics [MSU, Moscow], Lomonosov Moscow State University (MSU), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Raiganj University, UGC-DAE Consortium for Scientific Research (UGC-DAE ), Bhabha Atomic Research Centre (BARC), and Government of India, Department of Atomic Energy-Government of India, Department of Atomic Energy

Subjects
Materials science, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, Specific heat measurements, Condensed Matter::Materials Science, symbols.namesake, Thermal conductivity, Thermoelectric effect, lcsh:TA401-492, Graphite, ComputingMilieux_MISCELLANEOUS, Nanocomposite, Condensed matter physics, Phonon scattering, Metals and Alloys, Thermoelectric systems, 021001 nanoscience & nanotechnology, Thermoelectric materials, 0104 chemical sciences, Surfaces, Coatings and Films, Electronic, Optical and Magnetic Materials, X-ray powder diffraction, Scattering rate, Raman spectroscopy, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], symbols, Phonons, lcsh:Materials of engineering and construction. Mechanics of materials, 0210 nano-technology
Abstract

International audience; Thermoelectric performance largely depends on the reduction of lattice thermal conductivity (κL). The study of the thermal conductivity (κ) of a Sb2Te3/graphite nanocomposite system demonstrates ∼40% reduction in κL with graphite incorporation. A plausible explanation of intrinsic low κL observed in Sb2Te3 based system is presented by modeling experimental specific heat (Cp) data. Raman spectroscopy measurement combined to X-Ray diffraction data confirms the presence of graphite as separate phase in the composite sample. It is found that phonon scattering dominates heat transport mechanism in the nanostructured Sb2Te3/graphite composite. Large reduction in κL is accomplished by intensifying scattering rate of phonons via various sources. Graphite introduces effective scattering sources, i.e., defects of different dimensionalities in synthesized nanocomposite sample. Furthermore, graphite mediates phonon-phonon coupling and enhances lattice anharmonicity, which causes an intrinsic scattering of phonons with all frequencies in the Sb2Te3/graphite nanocomposite sample. Dislocation density and phonon anharmonicity of the synthesized samples are estimated from in depth analysis of temperature dependent synchrotron powder diffraction and Raman spectroscopic data. κL value as low as 0.8 W m−1K−1 at 300 K, achieved with graphite dispersion in Sb2Te3 based composite system makes the present comprehensive study an interesting concept to be developed in thermoelectric materials.

Published
2021
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3. Tunable High Speed Atomic Rotor in Bi2Se3 Revealed by Current Noise

Author

Marco Aprili, F. Massee, Vasily S. Stolyarov, Léonard Desvignes, Laboratoire de Physique des Solides (LPS), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and Moscow Institute of Physics and Technology [Moscow] (MIPT)

Subjects
Materials science, FOS: Physical sciences, General Physics and Astronomy, 02 engineering and technology, 010402 general chemistry, 7. Clean energy, 01 natural sciences, law.invention, Condensed Matter - Strongly Correlated Electrons, Current noise, law, Condensed Matter::Superconductivity, Mesoscale and Nanoscale Physics (cond-mat.mes-hall), Physics::Atomic and Molecular Clusters, General Materials Science, Physics::Atomic Physics, ComputingMilieux_MISCELLANEOUS, Condensed Matter::Quantum Gases, Condensed Matter - Materials Science, Condensed Matter - Mesoscale and Nanoscale Physics, Strongly Correlated Electrons (cond-mat.str-el), business.industry, Rotor (electric), Atoms in molecules, General Engineering, Materials Science (cond-mat.mtrl-sci), 021001 nanoscience & nanotechnology, 0104 chemical sciences, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Optoelectronics, Scanning tunneling microscope, 0210 nano-technology, business
Abstract

The ability to manipulate individual atoms and molecules using a scanning tunnelling microscope (STM) has been crucial for the development of a vast array of atomic scale devices and structures ranging from nanoscale motors and switches to quantum corrals. Molecular motors in particular have attracted considerable attention in view of their potential for assembly into complex nanoscale machines. Whereas the manipulated atoms or molecules are usually on top of a substrate, motors embedded in a lattice can be very beneficial for bottom-up construction, and may additionally be used to probe the in uence of the lattice on the electronic properties of the host material. Here, we present the discovery of controlled manipulation of a rotor in Fe doped Bi$_{2}$Se$_{3}$. We find that the current into the rotor, which can be finely tuned with the voltage, drives omni-directional switching between three equivalent orientations, each of which can be frozen in at small bias voltage. Using current fluctuation measurements at 1MHz and model simulations, we estimate that switching rates of hundreds of kHz for sub-nA currents are achieved., Comment: Published in ACS Nano, this is the originally submitted manuscript prior to changes during the review process

Published
2021
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4. Modeling Thrombus Shell: Linking Adhesion Receptor Properties and Macroscopic Dynamics

Author

Dmitry Yu. Nechipurenko, Vitaly Volpert, Mikhail A. Panteleev, Fazoil Ataullahanov, Joanne L. Dunster, Valeriia N. Kaneva, Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences [Moscow] (RAS), University of Reading (UOR), Modélisation mathématique, calcul scientifique (MMCS), Institut Camille Jordan (ICJ), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Modélisation multi-échelle des dynamiques cellulaires : application à l'hématopoïese (DRACULA), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS)-Inria Lyon, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Peoples Friendship University of Russia [RUDN University] (RUDN), Dmitry Rogachev Federal Research and Clinical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Lomonosov Moscow State University (MSU), and Moscow Institute of Physics and Technology [Moscow] (MIPT)

Subjects
Blood Platelets, Platelet Aggregation, Biophysics, Shell (structure), 03 medical and health sciences, Platelet Adhesiveness, 0302 clinical medicine, Platelet adhesiveness, von Willebrand Factor, medicine, Humans, Platelet, Platelet activation, [MATH]Mathematics [math], Thrombus, 030304 developmental biology, 0303 health sciences, biology, New and Notable, Chemistry, Thrombosis, Platelet Glycoprotein GPIb-IX Complex, Adhesion, medicine.disease, Glycoprotein Ib, biology.protein, 030217 neurology & neurosurgery
Abstract

Damage to arterial vessel walls leads to the formation of platelet aggregate, which acts as a physical obstacle for bleeding. An arterial thrombus is heterogeneous; it has a dense inner part (core) and an unstable outer part (shell). The thrombus shell is very dynamic, being composed of loosely connected discoid platelets. The mechanisms underlying the observed mobility of the shell and its (patho)physiological implications are unclear. To investigate arterial thrombus mechanics, we developed a novel, to our knowledge, two-dimensional particle-based computational model of microvessel thrombosis. The model considers two types of interplatelet interactions: primary reversible (glycoprotein Ib (GPIb)-mediated) and stronger integrin-mediated interaction, which intensifies with platelet activation. At high shear rates, the former interaction leads to adhesion, and the latter is primarily responsible for stable platelet aggregation. Using a stochastic model of GPIb-mediated interaction, we initially reproduced experimental curves that characterize individual platelet interactions with a von Willebrand factor-coated surface. The addition of the second stabilizing interaction results in thrombus formation. The comparison of thrombus dynamics with experimental data allowed us to estimate the magnitude of critical interplatelet forces in the thrombus shell and the characteristic time of platelet activation. The model predicts moderate dependence of maximal thrombus height on the injury size in the absence of thrombin activity. We demonstrate that the developed stochastic model reproduces the observed highly dynamic behavior of the thrombus shell. The presence of primary stochastic interaction between platelets leads to the properties of thrombus consistent with in vivo findings; it does not grow upstream of the injury site and covers the whole injury from the first seconds of the formation. А simplified model, in which GPIb-mediated interaction is deterministic, does not reproduce these features. Thus, the stochasticity of platelet interactions is critical for thrombus plasticity, suggesting that interaction via a small number of bonds drives the dynamics of arterial thrombus shell.

Published
2021
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5. Small-RNA-mediated transgenerational silencing of histone genes impairs fertility in piRNA mutants

Author

Blaise Li, Martino Ugolini, Damarys Loew, Germano Cecere, Aleksei Samolygo, Céline Didier, Eric Cornes, Meetali Singh, Giorgia Barucci, Piergiuseppe Quarato, Florent Dingli, Mécanismes de l'Hérédité épigénétique / Mechanisms of epigenetic inheritance, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Scuola Normale Superiore di Pisa (SNS), Moscow Institute of Physics and Technology [Moscow] (MIPT), Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie [Paris], This project has received funding from the Institut Pasteur, the CNRS and the European Research Council (ERC) under the EU Horizon 2020 research and innovation programme under grant agreement no. ERC-StG- 679243. G.B. is part of the Pasteur–Paris University (PPU) International PhD Program and has received funding from the EU Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 665807. E.C. was supported by a Pasteur-Cantarini Fellowship program. F.D. and D.L. have received funding from Région Ile-de-France and Fondation pour la Recherche Médicale grants to support this study, We thank the members of the Cecere laboratory, D. Canzio, N. Iovino, R. Sawarkar and P. Andersen for discussions of the manuscript, the Miska, the Mello, the Kennedy, the Seydoux, the Claycomb, the Strome and the Dumont laboratories for sharing strains and/or antibodies. Some strains were provided by the CGC, funded by NIH Office of Research Infrastructure Programs (P40 OD010440)., and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
MESH: Gene Editing, MESH: CRISPR-Cas Systems, Small RNA, MESH: Argonaute Proteins / deficiency, MESH: Caenorhabditis elegans Proteins / metabolism, Inheritance Patterns, MESH: RNA, Small Interfering / genetics, MESH: Argonaute Proteins / metabolism, medicine.disease_cause, MESH: RNA, Antisense / genetics, MESH: Argonaute Proteins / genetics, Animals, Genetically Modified, Histones, 0302 clinical medicine, MESH: Histones / metabolism, MESH: Animals, RNA, Small Interfering, MESH: Caenorhabditis elegans / genetics, Caenorhabditis elegans, Gene Editing, 0303 health sciences, Mutation, MESH: RNA, Messenger / metabolism, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Biological Evolution, Cell biology, Histone, MESH: Fertility / genetics, 030220 oncology & carcinogenesis, Argonaute Proteins, Piwi RNAs, MESH: RNA, Messenger / genetics, MESH: Gene Silencing, Epigenetic memory, endocrine system, MESH: Mutation, MESH: Caenorhabditis elegans / metabolism, Piwi-interacting RNA, MESH: Biological Evolution, Biology, Article, MESH: Animals, Genetically Modified, 03 medical and health sciences, medicine, Animals, Gene silencing, RNA, Antisense, Gene Silencing, RNA, Messenger, MESH: RNA, Antisense / metabolism, Caenorhabditis elegans Proteins, Gene, Repetitive Sequences, Nucleic Acid, 030304 developmental biology, MESH: RNA, Small Interfering / metabolism, MESH: Repetitive Sequences, Nucleic Acid, MESH: Histones / genetics, urogenital system, RNA, Cell Biology, biology.organism_classification, Fertility, RNAi, biology.protein, MESH: Caenorhabditis elegans Proteins / genetics, MESH: Inheritance Patterns, CRISPR-Cas Systems
Abstract

International audience; PIWI-interacting RNAs (piRNAs) promote fertility in many animals. However, whether this is due to their conserved role in repressing repetitive elements (REs) remains unclear. Here, we show that the progressive loss of fertility in Caenorhabditis elegans lacking piRNAs is not caused by derepression of REs or other piRNA targets but, rather, is mediated by epigenetic silencing of all of the replicative histone genes. In the absence of piRNAs, downstream components of the piRNA pathway relocalize from germ granules and piRNA targets to histone mRNAs to synthesize antisense small RNAs (sRNAs) and induce transgenerational silencing. Removal of the downstream components of the piRNA pathway restores histone mRNA expression and fertility in piRNA mutants, and the inheritance of histone sRNAs in wild-type worms adversely affects their fertility for multiple generations. We conclude that sRNA-mediated silencing of histone genes impairs the fertility of piRNA mutants and may serve to maintain piRNAs across evolution.

Published
2020
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6. The Dichotomy of Mn–H Bond Cleavage and Kinetic Hydricity of Tricarbonyl Manganese Hydride Complexes

Author

Elena S. Osipova, Sergey A. Kovalenko, Ekaterina S. Gulyaeva, Nikolay V. Kireev, Alexander A. Pavlov, Oleg A. Filippov, Anastasia A. Danshina, Dmitry A. Valyaev, Yves Canac, Elena S. Shubina, Natalia V. Belkova, A. N. Nesmeyanov Institute of Organoelement Compounds (INEOS), Russian Academy of Sciences [Moscow] (RAS), Laboratoire de chimie de coordination (LCC), Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Bauman Moscow State Technical University, Moscow Institute of Physics and Technology [Moscow] (MIPT), Russian Science Foundation, and CNRS

Subjects
Hydrogen bond, Hydricity, Non-covalent interactions, Organic Chemistry, Pharmaceutical Science, Hydride transfer, Proton transfer, manganese hydrides, hydrogen bond, non-covalent interactions, proton transfer, hydride transfer, hydricity, Analytical Chemistry, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Manganese hydrides, Chemistry (miscellaneous), Drug Discovery, Molecular Medicine, [CHIM.COOR]Chemical Sciences/Coordination chemistry, Physical and Theoretical Chemistry
Abstract

Acid-base characteristics (acidity, pKa, and hydricity, ΔG°H− or kH−) of metal hydride complexes could be a helpful value for forecasting their activity in various catalytic reactions. Polarity of the M–H bond may change radically at the stage of formation of a non-covalent adduct with an acidic/basic partner. This stage is responsible for subsequent hydrogen ion (hydride or proton) transfer. Here, the reaction of tricarbonyl manganese hydrides mer,trans–[L2Mn(CO)3H] (1; L = P(OPh)3, 2; L = PPh3) and fac–[(L–L′)Mn(CO)3H] (3, L–L′ = Ph2PCH2PPh2 (dppm); 4, L–L′ = Ph2PCH2–NHC) with organic bases and Lewis acid (B(C6F5)3) was explored by spectroscopic (IR, NMR) methods to find the conditions for the Mn–H bond repolarization. Complex 1, bearing phosphite ligands, features acidic properties (pKa 21.3) but can serve also as a hydride donor (ΔG≠298K = 19.8 kcal/mol). Complex 3 with pronounced hydride character can be deprotonated with KHMDS at the CH2–bridge position in THF and at the Mn–H position in MeCN. The kinetic hydricity of manganese complexes 1–4 increases in the order mer,trans–[(P(OPh)3)2Mn(CO)3H] (1) < mer,trans–[(PPh3)2Mn(CO)3H] (2) ≈ fac–[(dppm)Mn(CO)3H] (3) < fac–[(Ph2PCH2NHC)Mn(CO)3H] (4), corresponding to the gain of the phosphorus ligand electron-donor properties.

Published
2023
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7. True-atomic-resolution insights into the structure and functional role of linear chains and low-barrier hydrogen bonds in proteins

Author

Valentin Borshchevskiy, Kirill Kovalev, Ekaterina Round, Rouslan Efremov, Roman Astashkin, Gleb Bourenkov, Dmitry Bratanov, Taras Balandin, Igor Chizhov, Christian Baeken, Ivan Gushchin, Alexander Kuzmin, Alexey Alekseev, Andrey Rogachev, Dieter Willbold, Martin Engelhard, Ernst Bamberg, Georg Büldt, Valentin Gordeliy, Moscow Institute of Physics and Technology [Moscow] (MIPT), Institute of Complex Systems (ICS), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association-Helmholtz-Gemeinschaft = Helmholtz Association, European X-ray Free Electron Laser GmbH, Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), DESY, European Mol Biol Lab, D-22607 Hamburg, Germany, Institute of Biological Information Processing [Jülich] (IBI-7), Institute for Biophysical Chemistry, Hannover Medical School [Hannover] (MHH), Jülich Center for Structural Biology [Jülich] (JuStruct), Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow, Institut für Physikalische Biologie [Düsseldorfd], Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], Max Planck Institute of Molecular Physiology, Max-Planck-Gesellschaft, and Department of Structural Biology, Max-Planck-Institute of Biophysics, Frankfurt, Germany

Subjects
[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Structural Biology, Proteins, MESH: Proteins, Hydrogen Bonding, MESH: Hydrogen Bonding, MESH: Protons, Protons, Molecular Biology
Abstract

International audience; Hydrogen bonds are fundamental to the structure and function of biological macromolecules and have been explored in detail. The chains of hydrogen bonds (CHBs) and low-barrier hydrogen bonds (LBHBs) were proposed to play essential roles in enzyme catalysis and proton transport. However, high-resolution structural data from CHBs and LBHBs is limited. The challenge is that their 'visualization' requires ultrahigh-resolution structures of the ground and functionally important intermediate states to identify proton translocation events and perform their structural assignment. Our true-atomic-resolution structures of the light-driven proton pump bacteriorhodopsin, a model in studies of proton transport, show that CHBs and LBHBs not only serve as proton pathways, but also are indispensable for long-range communications, signaling and proton storage in proteins. The complete picture of CHBs and LBHBs discloses their multifunctional roles in providing protein functions and presents a consistent picture of proton transport and storage resolving long-standing debates and controversies.

Published
2021
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8. An efficient pseudo-polynomial algorithm for finding a lower bound on the makespan for the Resource Constrained Project Scheduling Problem

Author

Dmitry I. Arkhipov, Alexander A. Lazarev, Olga Battaïa, Institut Supérieur de l'Aéronautique et de l'Espace - ISAE-SUPAERO (FRANCE), Moscow Institute of Physics and Technology - MIPT (RUSSIA), Lomonosov Moscow State University - MSU (RUSSIA), Trapeznikov Institute of Control Sciences (RUSSIA), National Research University Higher School of Economics (RUSSIA), Département d'Ingénierie des Systèmes Complexes - DISC (Toulouse, France), Trapeznikov Institute of Control Sciences (ICS RAS), Russian Academy of Sciences [Moscow] (RAS), Lomonosov Moscow State University (MSU), National Research University Higher School of Economics [St. Petersburg], Moscow Institute of Physics and Technology [Moscow] (MIPT), Département d'Ingénierie des Systèmes Complexes (DISC), and Institut Supérieur de l'Aéronautique et de l'Espace (ISAE-SUPAERO)

Subjects
Information Systems and Management, General Computer Science, Computer science, Resource constrained, 0211 other engineering and technologies, 02 engineering and technology, Management Science and Operations Research, Upper and lower bounds, Industrial and Manufacturing Engineering, Scheduling (computing), Project scheduling problem, 0502 economics and business, Constraint programming, 050210 logistics & transportation, RCPSP, 021103 operations research, Job shop scheduling, Scheduling, 05 social sciences, Workload, [INFO.INFO-RO]Computer Science [cs]/Operations Research [cs.RO], Lower bounds, Schedule (project management), Pseudo-polynomial time, Pseudo-polynomial algorithms, Modeling and Simulation, Project scheduling, Recherche opérationnelle, Algorithm
Abstract

International audience; Several algorithms for finding a lower bound on the makespan for the Resource Constrained Project Scheduling Problem (RCPSP) were proposed in the literature. However, fast computable lower bounds usually do not provide the best estimations and the methods that obtain better bounds are mainly based on the cooperation between linear and constraint programming and therefore are time-consuming. In this paper, a new pseudo-polynomial algorithm is proposed to find a makespan lower bound for RCPSP with time-dependent resource capacities. Its idea is based on a consecutive evaluation of pairs of resources and their cumulated workload. Using the proposed algorithm, several bounds for the PSPLIB benchmark were improved. The results for industrial applications are also presented where the algorithm could provide good bounds even for very large problem instances.

Published
2019
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9. Accelerated Directional Search with Non-Euclidean Prox-Structure

Author

Eduard Gorbunov, Evgeniya Vorontsova, Alexander Gasnikov, Calcul des Variations, Géométrie, Image (CVGI ), Laboratoire Jean Kuntzmann (LJK ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Far Eastern Federal University (FEFU), and Moscow Institute of Physics and Technology [Moscow] (MIPT)

Subjects
0209 industrial biotechnology, Mathematical optimization, convex optimization, Optimization problem, ускоренные методы первого порядка, Computer science, G.1.6, Structure (category theory), first-order accelerated methods, 02 engineering and technology, non-Euclidean prox-structure, 01 natural sciences, методлинейного каплинга, 020901 industrial engineering & automation, Non-Euclidean geometry, Euclidean geometry, FOS: Mathematics, Point (geometry), 0101 mathematics, Electrical and Electronic Engineering, linear coupling method, Mathematics - Optimization and Control, Descent (mathematics), 90C25, 90C30, 68Q25, 65K05, 65Y20, 68W40, 010102 general mathematics, концентрация равномерной меры на единичной евклидовойсфере, неевклидова прокс-структура, выпуклая оптимизация, Rate of convergence, Optimization and Control (math.OC), Control and Systems Engineering, Convex optimization, uniform measure concentration on a single Euclidean sphere, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC]
Abstract

In the paper we propose an accelerated directional search method with non-euclidian prox-structure. We consider convex unconstraint optimization problem in $\mathbb{R}^n$. For simplicity we start from the zero point. We expect in advance that 1-norm of the solution is close enough to its 2-norm. In this case the standard accelerated Nesterov's directional search method can be improved. In the paper we show how to make Nesterov's method $n$-times faster (up to a $\log n$-factor) in this case. The basic idea is to use linear coupling, proposed by Allen-Zhu & Orecchia in 2014, and to make Grad-step in 2-norm, but Mirr-step in 1-norm. We show that for constrained optimization problems this approach stable upon an obstacle., in Russian, 13 pages, 3 figures

Published
2019
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10. Germanium Nanoparticles Prepared by Laser Ablation in Low Pressure Helium and Nitrogen Atmosphere for Biophotonic Applications

Author

Anastasiya A. Fronya, Sergey V. Antonenko, Nikita V. Karpov, Nikolay S. Pokryshkin, Anna S. Eremina, Valery G. Yakunin, Alexander Yu. Kharin, Alexander V. Syuy, Valentin S. Volkov, Yaroslava Dombrovska, Alexander A. Garmash, Nikolay I. Kargin, Sergey M. Klimentov, Victor Yu. Timoshenko, Andrei V. Kabashin, The National Research Nuclear University MEPhI (Moscow Engineering Physics Institute) [Moscow, Russia], Lomonosov Moscow State University (MSU), Moscow Institute of Physics and Technology [Moscow] (MIPT), Laboratoire Lasers, Plasmas et Procédés photoniques (LP3), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
theranostics, [SPI]Engineering Sciences [physics], nanostructured germanium (Ge), nanoparticles, Ge nanocrystals, laser ablation, pulsed laser deposition, photoluminescence, phototherapy, nanostructured germanium (Ge) nanoparticles Ge nanocrystals laser ablation pulsed laser deposition photoluminescence phototherapy theranostics, General Materials Science
Abstract

International audience; Due to particular physico-chemical characteristics and prominent optical properties, nanostructured germanium (Ge) appears as a promising material for biomedical applications, but its use in biological systems has been limited so far due to the difficulty of preparation of Ge nanostructures in a pure, uncontaminated state. Here, we explored the fabrication of Ge nanoparticles (NPs) using methods of pulsed laser ablation in ambient gas (He or HeN 2 mixtures) maintained at low residual pressures (1-5 Torr). We show that the ablated material can be deposited on a substrate (silicon wafer in our case) to form a nanostructured thin film, which can then be ground in ethanol by ultrasound to form a stable suspension of Ge NPs. It was found that these formed NPs have a wide size dispersion, with sizes between a few nm and hundreds of nm, while a subsequent centrifugation step renders possible the selection of one or another NP size fraction. Structural characterization of NPs showed that they are composed of aggregations of Ge crystals, covered by an oxide shell. Solutions of the prepared NPs exhibited largely dominating photoluminescence (PL) around 450 nm, attributed to defects in the germanium oxide shell, while a separated fraction of relatively small (5-10 nm) NPs exhibited a red-shifted PL band around 725 nm under 633 nm excitation, which could be attributed to quantum confinement effects. It was also found that the formed NPs exhibit high absorption in the visible and near-IR spectral ranges and can be strongly heated under photoexcitation in the region of relative tissue transparency, which opens access to phototherapy functionality. Combining imaging and therapy functionalities in the biological transparency window, laser-synthesized Ge NPs present a novel promising object for cancer theranostics.

Published
2022
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11. Cluster-size constrained network partitioning

Author

Konstantin Avrachenkov, Maksim Mironov, Network Engineering and Operations (NEO ), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), and Moscow Institute of Physics and Technology [Moscow] (MIPT)

Subjects
Theoretical computer science, Degree (graph theory), business.industry, Computer science, Node (networking), 05 social sciences, 050801 communication & media studies, 020206 networking & telecommunications, 02 engineering and technology, [INFO.INFO-SI]Computer Science [cs]/Social and Information Networks [cs.SI], Scheduling (computing), Task (project management), [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], 0508 media and communications, [STAT.ML]Statistics [stat]/Machine Learning [stat.ML], Stochastic block model, Synchronization (computer science), 0202 electrical engineering, electronic engineering, information engineering, Unsupervised learning, Artificial intelligence, business, Clustering coefficient
Abstract

International audience; In this paper we consider a graph clustering problem with a given number of clusters and approximate desired sizes of the clusters. One possible motivation for such task could be the problem of databases or servers allocation within several given large computational clusters, where we want related objects to share the same cluster in order to minimize latency and transaction costs. This task differs from the original community detection problem. To solve this task, we adopt some ideas from Glauber Dynamics and Label Propagation Algorithm. At the same time we consider no additional information about node labels, so the task has the nature of unsupervised learning. We propose an algorithm for the problem, show that it works well for a large set of parameters of Stochastic Block Model (SBM) and theoretically show that its running time complexity for achieving almost exact recovery is of O(n·d·ω) for the mean-field SBM with d being the average degree and ω tending to infinity arbitrary slow. Other significant advantage of the proposed approach is its local nature, which means it can be efficiently distributed with no scheduling or synchronization.

Published
2021
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12. Electronic Structure and Coexistence of Superconductivity with Magnetism in RbEuFe4As4

Author

Kim, T.K., Pervakov, K.S., Evtushinsky, D.V., Jung, S.W., Poelchen, G., Kummer, K., Vlasenko, V.A., Sadakov, A.V., Usoltsev, A.S., Pudalov, V.M., Roditchev, D., Stolyarov, V.S., Vyalikh, D.V., Borisov, V., Valentí, R., Ernst, A., Eremeev, S.V., Chulkov, E.V., DIAMOND Light source, P. N. Lebedev Physical Institute of the Russian Academy of Sciences [Moscow] (LPI RAS), Russian Academy of Sciences [Moscow] (RAS), Ecole Polytechnique Fédérale de Lausanne (EPFL), Technische Universität Dresden = Dresden University of Technology (TU Dresden), European Synchrotron Radiation Facility (ESRF), Laboratoire de Physique et d'Etude des Matériaux (UMR 8213) (LPEM), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Moscow Institute of Physics and Technology [Moscow] (MIPT), Ikerbasque - Basque Foundation for Science, Goethe-Universität Frankfurt am Main, Johannes Kepler Universität Linz (JKU), the Russian Academy of Sciences [Moscow, Russia] (RAS), and Saint Petersburg State University (SPBU)

Subjects
[PHYS]Physics [physics], Electronic structure, Magnetic order, Magnetic phase transitions, spectra, Multiband superconductivity, scattering, band-structure, Superconducting gap, Condensed Matter::Superconductivity, dichroism, Superconducting phase transition, order, photoemission
Abstract

In the novel stoichiometric iron-based material RbEuFe4As4, superconductivity coexists with a peculiar long-range magnetic order of Eu 4f states. Using angle-resolved photoemission spectroscopy, we reveal a complex three-dimensional electronic structure and compare it with density functional theory calculations. Multiple super-conducting gaps were measured on various sheets of the Fermi surface. High-resolution resonant photoemission spectroscopy reveals magnetic order of the Eu 4f states deep into the superconducting phase. Both the absolute values and the anisotropy of the superconducting gaps are remarkably similar to the sibling compound without Eu, indicating that Eu magnetism does not affect the pairing of electrons. A complete decoupling between Fe-and Eu-derived states was established from their evolution with temperature, thus unambiguously demonstrating that superconducting and a long-range magnetic orders exist independently from each other. The established electronic structure of RbEuFe4As4 opens opportunities for the future studies of the highly unorthodox electron pairing and phase competition in this family of iron-based superconductors with doping. We thank Matthew Watson for his critical reading of the manuscript. We thank Diamond Light Source for access to beamline I05 (Proposal No. SI15074 and No. SI19041) that contributed to the results presented here. Work was done using equipment from the LPI Shared Facility Center. K.S.P. and V.M.P. acknowledge support by the Russian Scientific Foundation (RSF Project No. 21-12-00394). A.V.S. and A.S.U. acknowledge support by the Russian Foundation for Basic Research (Project No. 21-52-12043). E.V.C. acknowledges funding by Saint Petersburg State University project for scientific investigations (ID No. 73028629). S.V.E. acknowledges support from the government research assignment for ISPMS SB RAS (Project FWRW-2019-0032). R.V. acknowledges funding by the Deutsche Forschungsgemeinschaft (DFG) TRR 288 (Project A05). V.B. thanks the Goethe University Frankfurt for computational resources and Daniel Guterding for providing the FS plotting software. K.K. thanks M. Valvidares, J. Herrero, H. B. Vasili, S. Agrestini, and N. Brookes for their support during the XMCD experiment at ALBA via IHR Proposal 2019063615. D.V.V. also acknowledges support from the Spanish Ministry of Economy (MAT-2017-88374-P)

Published
2021
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13. Foldover-free maps in 50 lines of code

Author

Liudmila Kudryavtseva, Igor Kaporin, V. A. Garanzha, Dmitry Sokolov, François Protais, Nicolas Ray, Computing Centre of the Russian Academy of Sciences (CCRAS), Russian Academy of Sciences [Moscow] (RAS), Moscow Institute of Physics and Technology [Moscow] (MIPT), Structurer des formes géométriques (PIXEL), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Algorithms, Computation, Image and Geometry (LORIA - ALGO), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), This work is supported by the Ministry of Science and Higher Education of the Russian Federation, project No 075-15-2020-799, Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), and Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)

Subjects
Computational Geometry (cs.CG), FOS: Computer and information sciences, Source lines of code, Computer science, Parameterization, 02 engineering and technology, [INFO.INFO-CG]Computer Science [cs]/Computational Geometry [cs.CG], 01 natural sciences, Domain (software engineering), mesh untangling, 0202 electrical engineering, electronic engineering, information engineering, 0101 mathematics, computer.programming_language, 010102 general mathematics, 020207 software engineering, Geometry processing, injective mapping, Python (programming language), Surface (topology), Computer Graphics and Computer-Aided Design, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Injective function, 010101 applied mathematics, Mesh generation, Computer Science - Computational Geometry, Element (category theory), Algorithm, computer
Abstract

International audience; Mapping a triangulated surface to 2D space (or a tetrahedral mesh to 3D space) is the most fundamental problem in geometry processing. In computational physics, untangling plays an important role in mesh generation: it takes a mesh as an input, and moves the vertices to get rid of foldovers. In fact, mesh untangling can be considered as a special case of mapping where the geometry of the object is to be defined in the map space and the geometric domain is not explicit, supposing that each element is regular. In this paper, we propose a mapping method inspired by the untangling problem and compare its performance to the state of the art.The main advantage of our method is that the untangling aims at producing locally injective maps, which is the major challenge of mapping. In practice, our method produces locally injective maps in very difficult settings, and with less distortion than the previous work, both in 2D and 3D. We demonstrate it on a large reference database as well as on more difficult stress tests. For a better reproducibility, we publish the code in Python for a basic evaluation, and in C++ for more advanced applications.

Published
2021
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14. Nanosphere Photolithography: The Influence of Nanopore Arrays Disorder on Extraordinary Optical Transmission

Author

Jean-Yves Michalon, Isabelle Verrier, Olivier Dellea, Andrei Ushkov, Yves Jourlin, Thomas Kämpfe, Alexey A. Shcherbakov, Laboratoire Hubert Curien [Saint Etienne] (LHC), Institut d'Optique Graduate School (IOGS)-Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS), Moscow Institute of Physics and Technology [Moscow] (MIPT), CEA-Grenoble, ITMO Univiversity, Laboratoire Hubert Curien (LHC), and Institut d'Optique Graduate School (IOGS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], Materials science, business.industry, NPL, EOT, Nanosphere Photolithohraphy, Extraordinary Optical Transmission, Extraordinary optical transmission, Diffraction Graing, Numerical Simulations, law.invention, [SPI]Engineering Sciences [physics], Nanopore, law, Disorder, Plasmonics, Optoelectronics, Photolithography, business, Nanopore Array
Abstract

International audience; We analyze both experimentally and numerically the influence of nanopore arrays disorder on extraordinary optical transmission in samples, fabricated via nanosphere photolithography. Two measures of disorder are considered, the correlations between them are discussed using experimental and numerical data. We propose a theoretical model which takes explicitly the disorder into account, and show how the concurrence between nanopore depth and disorder level defines the quality of EOT excitation. Simulated spectra are in a good agreement with experimental ones. Our results reveal the possibilities of NPL for EOT-based applications and pave the way toward plasmonic devices with a polycrystalline design.

Published
2021
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15. THz Spectroscopy, Holographic Approach and Phantoms Design for the Diagnostics of Socially Significant Diseases

Author

Vladimir L. Vaks, Nikolay V. Petrov, M. M. Nazarov, Patrick Mounaix, Alexander P. Shkurinov, Yu. V. Kistenev, J-P. Guillet, O. A. Smolyanskaya, Olga P. Cherkasova, ITMO University [Russia], Novosibirsk State University (NSU), Laboratoire de l'intégration, du matériau au système (IMS), Université Sciences et Technologies - Bordeaux 1-Institut Polytechnique de Bordeaux-Centre National de la Recherche Scientifique (CNRS), and Moscow Institute of Physics and Technology [Moscow] (MIPT)

Subjects
Materials science, Human blood, business.industry, Terahertz radiation, Holography, 01 natural sciences, law.invention, Optics, law, 0103 physical sciences, [SPI.OPTI]Engineering Sciences [physics]/Optics / Photonic, 010306 general physics, Spectroscopy, business, 010303 astronomy & astrophysics, Refractive index, ComputingMilieux_MISCELLANEOUS, Thz spectroscopy
Abstract

This work describes the promising approach for the diagnostic of diseases, such as diabetes, by using the THz spectroscopy and THz holography method. In this paper, dry pellets consisting of human blood plasma (normal and diabetic) were designed; these objects were analyzed in various THz Russian laboratories, PCA-analysis of THz spectra was applied to separate the normal and diabetic groups; the holographic approach was proposed that provides sufficient information to reconstruct the spatial distribution of complex refractive index of the samples.

Published
2020
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16. Controlling Charge Transfer from Quantum Dots to Polyelectrolyte Layers Extends Prospective Applications of Magneto-Optical Microcapsules

Author

Pavel Samokhvalov, Galina Nifontova, Igor I. Agapov, Sergei Zarubin, O. I. Agapova, E. V. Korostylev, Igor Nabiev, Maria Zvaigzne, Victor Krivenkov, Alexander Karaulov, Anton E. Efimov, Alyona Sukhanova, The National Research Nuclear University MEPhI (Moscow Engineering Physics Institute) [Moscow, Russia], Shumakov National Medical Research Center of Transplantology and Artificial Organs [Moscow, Russia], Moscow Institute of Physics and Technology [Moscow] (MIPT), Sechenov First Moscow State Medical University, Laboratoire de Recherche en Nanosciences - EA 4682 (LRN), Université de Reims Champagne-Ardenne (URCA)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-SFR Condorcet, and Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Plasmonic nanoparticles, Materials science, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, Layer by layer, Nanotechnology, 02 engineering and technology, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, Polyelectrolyte, 0104 chemical sciences, Quantum dot, Photodarkening, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Magnetic nanoparticles, Surface modification, Deposition (phase transition), General Materials Science, 0210 nano-technology, ComputingMilieux_MISCELLANEOUS
Abstract

The layer-by-layer (LbL) deposition approach allows combined incorporation of fluorescent, magnetic, and plasmonic nanoparticles into the shell of polyelectrolyte microcapsules to obtain stimulus-responsive systems whose imaging and drug release functions can be triggered by external stimuli. The combined use of fluorescent quantum dots (QDs) and magnetic nanoparticles (MNPs) yields magnetic-field-driven imaging tools that can be tracked and imaged even deep in tissue when the appropriate type of QDs and wavelength of their excitation are used. QDs are excellent photonic labels for microcapsule encoding due to their close-to-unity photoluminescence (PL) quantum yields, narrow PL emission bands, and tremendous one- and two-photon extinction coefficients. However, the presence of MNPs and electrically charged polyelectrolyte molecules used for the LbL fabrication of magneto-optical microcapsules provokes alterations of the QD optical properties because of the photoinduced charge and energy transfer resulting in QD photodarkening or photobrightening. These lead to variation of the microcapsule PL signal under illumination, which hampers their tracking and quantitative analysis in cells and tissues. Here, we have studied the effects of the structure and spatial arrangement of the nanoparticles within the microcapsule polyelectrolyte shell, the total shell thickness, and the shell surface charge on their PL properties under continuous illumination. The roles of the charge transfer and its main driving forces in the stability of the microcapsules PL signal have been established, and the design of the microcapsules dually encoded with QDs and MNPs providing the strongest and most stable PL has been determined. Controlling the energy transfer from the QDs and MNPs and the charge transfer from QDs to polyelectrolyte layers in the engineering of magneto-optical microcapsules with a bright and stable PL signal extends their applications to long-lasting quantitative fluorescence imaging.

Published
2020
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17. VoroCNN: Deep convolutional neural network built on 3D Voronoi tessellation of protein structures

Author

Česlovas Venclovas, Kliment Olechnovič, Sergei Grudinin, Maria Kadukova, Ilia Igashov, Moscow Institute of Physics and Technology [Moscow] (MIPT), Données, Apprentissage et Optimisation (DAO), Laboratoire Jean Kuntzmann (LJK), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Vilnius University [Vilnius], Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Kuntzmann (LJK), and Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )

Subjects
Statistics and Probability, 0303 health sciences, Computational model, 010304 chemical physics, Computer science, 030302 biochemistry & molecular biology, [INFO.INFO-CG]Computer Science [cs]/Computational Geometry [cs.CG], 01 natural sciences, Biochemistry, Convolutional neural network, Computer Science Applications, 03 medical and health sciences, Computational Mathematics, Protein structure, [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], Computational Theory and Mathematics, 0103 physical sciences, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Voronoi diagram, Molecular Biology, Algorithm, 030304 developmental biology
Abstract

Motivation Effective use of evolutionary information has recently led to tremendous progress in computational prediction of three-dimensional (3D) structures of proteins and their complexes. Despite the progress, the accuracy of predicted structures tends to vary considerably from case to case. Since the utility of computational models depends on their accuracy, reliable estimates of deviation between predicted and native structures are of utmost importance. Results For the first time, we present a deep convolutional neural network (CNN) constructed on a Voronoi tessellation of 3D molecular structures. Despite the irregular data domain, our data representation allows us to efficiently introduce both convolution and pooling operations and train the network in an end-to-end fashion without precomputed descriptors. The resultant model, VoroCNN, predicts local qualities of 3D protein folds. The prediction results are competitive to state of the art and superior to the previous 3D CNN architectures built for the same task. We also discuss practical applications of VoroCNN, for example, in recognition of protein binding interfaces. Availability and implementation The model, data and evaluation tests are available at https://team.inria.fr/nano-d/software/vorocnn/. Supplementary information Supplementary data are available at Bioinformatics online.

Published
2020
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18. Novel isatin-derived molecules activate p53 via interference with Mdm2 to promote apoptosis

Author

Alexey Petukhov, Nickolai A. Barlev, Gerry Melino, Vyacheslav G. Tribulovich, Burhan Uyanik, Oleg Shuvalov, Olga A. Fedorova, Oleg N. Demidov, Ekaterina Lomert, Darya Kriger, Pavel B. Davidovich, Victor Kartsev, Alexandra Daks, Varvara Petrova, Larissa Lezina, Dmitry Tentler, Institute of Cytology and Genetics, Russian Academy of Sciences [Moscow] (RAS), MRC Toxicology Unit, University of Leicester, Almazov National Medical Research Centre (St. Petersburg), Departments laboratory of Molecular Pharmacology (St Petersburg), Saint Petersburg State Institute of Technology (Technical University), Interbioscreen (Chernogolovka), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM), and Moscow Institute of Physics and Technology [Moscow] (MIPT)

Subjects
Isatin, 0301 basic medicine, Programmed cell death, Cell cycle checkpoint, Antineoplastic Agents, Apoptosis, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Piperazines, Histones, Mice, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Nutlin, Cell Line, Tumor, Proto-Oncogene Proteins, Animals, Humans, Molecular Biology, chemistry.chemical_classification, DNA ligase, Imidazoles, ISMBDs, Proto-Oncogene Proteins c-mdm2, Cell Biology, p53-activating molecules, Cell biology, 030104 developmental biology, chemistry, Proteasome, 030220 oncology & carcinogenesis, biology.protein, Mdm2, Puma, Tumor Suppressor Protein p53, Apoptosis Regulatory Proteins, automated microscopy system Operetta, Research Paper, Developmental Biology
Abstract

International audience; The p53 protein is a key tumor suppressor in mammals. In response to various forms of genotoxic stress p53 stimulates expression of genes whose products induce cell cycle arrest and/or apoptosis. An E3-ubiquitin ligase, Mdm2 (mouse-double-minute 2) and its human ortholog Hdm2, physically interact with the amino-terminus of p53 to mediate its ubiquitin-mediated degradation via the proteasome. Thus, pharmacological inhibition of the p53-Mdm2 interaction leads to overall stabilization of p53 and stimulation of its anti-tumorigenic activity. In this study we characterize the biological effects of a novel class of non-genotoxic isatin Schiff and Mannich base derivatives (ISMBDs) that stabilize p53 on the protein level. The likely mechanism behind their positive effect on p53 is mediated via the competitive interaction with Mdm2. Importantly, unlike Nutlin, these compounds selectively promoted p53-mediated cell death. These novel pharmacological activators of p53 can serve as valuable molecular tools for probing p53-positive tumors and set up the stage for development of new anti-cancer drugs.

Published
2018
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19. Dynamics of the stress-mediated magnetoelectric memory cell N×(TbCo2/FeCo)/PMN-PT

Author

Théo Mathurin, Yannick Dusch, Alexander Sigov, Philippe Pernod, Stefano Giordano, Vladimir Preobrazhensky, Alexey Klimov, Nicolas Tiercelin, Anton Churbanov, Laboratoire International associé sur les phénomènes Critiques et Supercritiques en électronique fonctionnelle, acoustique et fluidique (LIA LICS/LEMAC), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), A. M. Prokhorov General Physics Institute (GPI), Russian Academy of Sciences [Moscow] (RAS), Russian Technological University (MIREA), Kotelnikov Institute of Radio Engineering and Electronics (IRE), Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), Acoustique Impulsionnelle & Magnéto-Acoustique Non linéaire - Fluides, Interfaces Liquides & Micro-Systèmes - IEMN (AIMAN-FILMS-IEMN), Institut d’Électronique, de Microélectronique et de Nanotechnologie - Département Opto-Acousto-Électronique - UMR 8520 (IEMN-DOAE), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-INSA Institut National des Sciences Appliquées Hauts-de-France (INSA Hauts-De-France)-Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-INSA Institut National des Sciences Appliquées Hauts-de-France (INSA Hauts-De-France), Moscow Institute of Physics and Technology [Moscow] (MIPT), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), Acoustique Impulsionnelle & Magnéto-Acoustique Non linéaire - Fluides, Interfaces Liquides & Micro-Systèmes - IEMN (AIMAN-FILMS - IEMN), AcknowledgementsThe work was supported by the grant RFBR 16-29-14022 and the StartAirr program MELRAM of the Région Hauts de France.Technological developments are supported by the french RENATECH network., and RENATECH network

Subjects
Wheatstone bridge, Materials science, Magnetoelectric Memory, Magnetoelectric effect, 02 engineering and technology, 7. Clean energy, 01 natural sciences, [SPI.MAT]Engineering Sciences [physics]/Materials, law.invention, Stress (mechanics), Extra-low energy, law, Memory cell, 0103 physical sciences, [SPI.NANO]Engineering Sciences [physics]/Micro and nanotechnologies/Microelectronics, Straintronics, 010302 applied physics, Condensed matter physics, Reading (computer), Heterojunction, Magnetostriction, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Electronic, Optical and Magnetic Materials, Magnetoelectric readout, 0210 nano-technology, Realization (systems), MELRAM
Abstract

Stress-mediated magnetoelectric heterostructures represent a very promising approach for the realization of ultra-low energy Random Access Memories. The magnetoelectric writing of information has been extensively studied in the past, but it was demonstrated only recently that the magnetoelectric effect can also provide means for reading the stored information. We hereby theoretically study the dynamic behaviour of a magnetoelectric random access memory cell (MELRAM) typically composed of a magnetostrictive multilayer N × ( TbCo 2 / FeCo ) that is elastically coupled with a 〈0 1 1〉 PMN-PT ferroelectric crystal and placed in a Wheatstone bridge-like configuration. The numerical resolution of the LLG and electrodynamics equation system demonstrates high speed write and read operations with an associated extra-low energy consumption. In this model, the reading energy for a 50 nm cell size is estimated to be less than 5 aJ/bit.

Published
2018
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20. Analytical symmetry detection in protein assemblies. I. Cyclic symmetries

Author

Guillaume Pagès, Sergei Grudinin, Elvira Kinzina, Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Laboratoire Jean Kuntzmann (LJK ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), and Moscow Institute of Physics and Technology [Moscow] (MIPT)

Subjects
0301 basic medicine, Cyclic symmetry in three dimensions, Protein Structure, Computer science, Protein Assemblies, Topology, Machine epsilon, 03 medical and health sciences, Structural Biology, Position (vector), Euclidean geometry, Molecular symmetry, Databases, Protein, Continuous Optimization, Point-Group Symmetry, Proteins, computer.file_format, Function (mathematics), Protein Data Bank, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, 030104 developmental biology, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Symmetry (geometry), computer, Algorithms, Software
Abstract

International audience; Symmetry in protein, and, more generally, in macromolecular assemblies is a key point to understand their structure, stability and function. Many symmetrical assemblies are currently present in the Protein Data Bank (PDB) and some of them are among the largest solved structures, thus an efficient computational method is needed for the exhaustive analysis of these. The cyclic symmetry groups represent the most common assemblies in the PDB. These are also the building blocks for higher-order symmetries. This paper presents a mathematical formulation to find the position and the orientation of the symmetry axis in a cyclic symmetrical protein assembly, and also to assess the quality of this symmetry. Our method can also detect symmetries in partial assemblies. We provide an efficient C++ implementation of the method and demonstrate its efficiency on several examples including partial assemblies and pseudo symmetries. We also compare the method with two other published techniques and show that it is significantly faster on all the tested examples. Our method produces results with a machine precision, its cost function is solely based on 3D Euclidean geometry, and most of the operations are performed analytically. The method is available at http://team.inria.fr/nano-d/software/ananas. The graphical user interface of the method built for the SAMSON platform is available at http://samson-connect.net.

Published
2018
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21. Synthesis and characterization of poly(ester amide amide)s of different alkylene chain lengths

Author

Manisha Gupta, Azaliya F. Akhyamova, Kseniia N. Grafskaya, A. P. Melnikov, Clément Girard, Abdelaziz Lallam, Ekaterina D. Shabratova, Dimitri A. Ivanov, A. A. Rychkov, Xiaomin Zhu, Alexander I. Rodygin, Polina V. Bovsunovskaya, Denis V. Anokhin, Martin Möller, Alexey A. Piryazev, Laboratoire de Physique et Mécanique Textiles (LPMT), ENSITM-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Moscow Institute of Physics and Technology [Moscow] (MIPT), Goethe-Universität Frankfurt am Main, Institut de Science des Matériaux de Mulhouse (IS2M), Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, and Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)

Subjects
Materials science, Condensation polymer, Polymers and Plastics, 02 engineering and technology, 010402 general chemistry, Biodegradable polymers, 01 natural sciences, Melt polycondensation, chemistry.chemical_compound, Amide, Polymer chemistry, Materials Chemistry, Thermal stability, Wide-angle X-ray scattering, chemistry.chemical_classification, Small-angle X-ray scattering, General Chemistry, Polymer, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Biodegradable polymer, 0104 chemical sciences, Poly(ester amide amide)s, [CHIM.POLY]Chemical Sciences/Polymers, chemistry, Melting point, 0210 nano-technology
Abstract

International audience; In this work, a series of aliphatic biodegradable poly(ester amide amide) polymers was synthesized by melt polycondensation of a tailor-made amide-containing monomer based on 1,4-diaminobutane and ε-caprolactone and different dicarboxylic acid methyl esters with even number of methylene groups. The synthesized polymers were characterized by 1H NMR, FT-IR spectroscopy, GPC, SAXS and WAXS. DSC results show that the melting point is located at about 150 °C for all polymers. X-ray scattering experiments in small and wide angles reveal formation of crystals with extended-chain conformation resulting in strict periodicity of electron density along the main chain. TGA data indicate the high thermal stability of polymers to temperatures above 350 °C, which are much above the melting point. The obtained characteristics of the newly synthesized PEAAs can open new perspectives for melt processing to fabricate films, highly oriented fibers and injection-molded parts with good thermal stability and mechanical performance

Published
2018
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22. Plasmonic Si@Au core-satellite nanoparticles prepared by laser-assisted synthesis for photothermal therapy

Author

Gleb Tselikov, Ahmed Al-Kattan, Anton A. Popov, Andrei V. Kabashin, Aix Marseille Université (AMU), Moscow Institute of Physics and Technology [Moscow] (MIPT), and The National Research Nuclear University MEPhI (Moscow Engineering Physics Institute) [Moscow, Russia]

Subjects
History, Materials science, biology, business.industry, Nanoparticle, Photothermal therapy, biology.organism_classification, Laser assisted, Computer Science Applications, Education, Core (optical fiber), [SPI]Engineering Sciences [physics], Optoelectronics, Satellite (biology), business, Plasmon
Abstract

We describe a laser-assisted methodology for the fabrication of Si@Au core-satellite nanostructures for photothermal therapy applications. The methodology consists in laser ablative synthesis of Si and Au NPs in water/ethanol solutions, followed by a chemical modification of the Si NPs by APTMS and their subsequent decoration by the Au NPs. We show that despite a relatively small size (< 40 nm) the formed core-satellites exhibit a strong plasmonic absorption peak centred around 610 nm and having a large tail over 700 nm overlapping with the first optical window of relative tissue transparency. Being relatively small and exempt of any toxic impurity due to ultraclean laser synthesis, the fabricated nanoparticles promise a major advancement of imaging and phototherapy modalities based on plasmonic properties of nanomatererials.

Published
2021
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23. Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization

Author

Sergei Grudinin, Maria Kadukova, Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Laboratoire Jean Kuntzmann (LJK ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), and Moscow Institute of Physics and Technology [Moscow] (MIPT)

Subjects
0301 basic medicine, Optimization problem, Protein Conformation, Computer science, Knowledge Bases, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Protein-ligand interactions, Ligands, computer.software_genre, Structure-Activity Relationship, 03 medical and health sciences, Polynomial basis, Knowledge-based potential, Scoring functions for docking, Software, Machine learning, Drug Discovery, Humans, Physical and Theoretical Chemistry, Databases, Protein, Binding Sites, Molecular Structure, business.industry, Regular polygon, Proteins, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Computer Science Applications, Molecular Docking Simulation, 030104 developmental biology, Docking (molecular), Drug Design, Molecular docking, Convex optimization, Data mining, Scoring function, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, Algorithm, computer, Algorithms, [CHIM.CHEM]Chemical Sciences/Cheminformatics, Protein Binding, Protein ligand
Abstract

We present a novel optimization approach to train a free-shape distance-dependent protein-ligand scoring function called Convex-PL. We do not impose any functional form of the scoring function. Instead, we decompose it into a polynomial basis and deduce the expansion coefficients from the structural knowledge base using a convex formulation of the optimization problem. Also, for the training set we do not generate false poses with molecular docking packages, but use constant RMSD rigid-body deformations of the ligands inside the binding pockets. This allows the obtained scoring function to be generally applicable to scoring of structural ensembles generated with different docking methods. We assess the Convex-PL scoring function using data from D3R Grand Challenge 2 submissions and the docking test of the CASF 2013 study. We demonstrate that our results outperform the other 20 methods previously assessed in CASF 2013. The method is available at http://team.inria.fr/nano-d/software/Convex-PL/ .

Published
2017
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24. Infimal Convolution and Optimal Time Control Problem II: Limiting Subdifferential

Author

Grigorii Evgen'evich Ivanov, Lionel Thibault, Moscow Institute of Physics and Technology [Moscow] (MIPT), Institut Montpelliérain Alexander Grothendieck (IMAG), and Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Statistics and Probability, Infimal convolution, Mathematics::Optimization and Control, 0211 other engineering and technologies, Banach space, 02 engineering and technology, Subderivative, 01 natural sciences, Convolution, Minimal time projection, Continuation, Lower regular function, Fréchet subdifferential, Applied mathematics, [MATH]Mathematics [math], 0101 mathematics, Mathematics, Mathematics::Functional Analysis, Numerical Analysis, 021103 operations research, Applied Mathematics, 010102 general mathematics, Mathematical analysis, Regular polygon, Minimal time function, Function (mathematics), Infimum and supremum, Geometry and Topology, Constant (mathematics), Mordukhovich limiting subdifferential, Analysis
Abstract

International audience; This paper is the continuation of our study of a general minimal time problem with a convex constant dynamics and a lower semicontinuous extended real-valued target function defined on a Banach space. We study several properties of the limiting subdifferential for the infimum time function and we provide explicit expressions of the limiting subdifferential. Necessary and sufficient conditions for the infimum time function to be lower regular are presented. The sharpness of assumptions is shown through diverse examples.

Published
2017
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25. High-order parametric generation of coherent XUV radiation

Author

E. Mével, Ondrej Hort, Frédéric Burgy, V. Strelkov, M. A. Khokhlova, Antoine Dubrouil, Eric Constant, Stéphane Petit, Dominique Descamps, Centre d'Etudes Lasers Intenses et Applications (CELIA), Université de Bordeaux (UB)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Institut fur Photonik (TU WIEN), Vienna University of Technology (TU Wien), ELI Beamlines, Institute of Physics of the Czech Academy of Sciences (FZU / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Max-Born Institute for Nonlinear Optics and Short Pulse Spectroscopy (MBI), Blackett Laboratory, Imperial College London, Structure et dynamique multi-échelle des édifices moléculaires (DYNAMO), Institut Lumière Matière [Villeurbanne] (ILM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), A. M. Prokhorov General Physics Institute (GPI), Russian Academy of Sciences [Moscow] (RAS), Moscow Institute of Physics and Technology [Moscow] (MIPT), ANR-09-BLAN-0031,ATTO-WAVE(2009), European Project: 657272,H2020,H2020-MSCA-IF-2014,COFFEE(2015), Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Bordeaux (UB), Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, and Prokhorov General Physics Institute of the Russian Academy of Sciences

Subjects
Photon, Terahertz radiation, Atomic Physics (physics.atom-ph), Attosecond, FOS: Physical sciences, 02 engineering and technology, Radiation, 7. Clean energy, 01 natural sciences, Physics - Atomic Physics, 010309 optics, Optics, Physics::Plasma Physics, Ionization, 0103 physical sciences, Physics::Atomic and Molecular Clusters, High harmonic generation, ComputingMilieux_MISCELLANEOUS, Physics, [PHYS]Physics [physics], business.industry, 021001 nanoscience & nanotechnology, Atomic and Molecular Physics, and Optics, Extreme ultraviolet, Astrophysics::Earth and Planetary Astrophysics, 0210 nano-technology, business, Ultrashort pulse, Physics - Optics, Optics (physics.optics)
Abstract

We observe a new regime of coherent XUV radiation generation in noble gases induced by femtosecond pulses at very high intensities. This XUV emission has both a reduced divergence and spectral width as compared to high-order harmonic generation (HHG). It is not emitted at a moderate intensity of the driving pulses where only high-order harmonics are generated. At high driving intensities, the additional XUV comb appears near all harmonic orders and even exceeds the HHG signal on the axis. The peaks are observed in several gases and their frequencies do not depend on the driving intensity or gas pressure. We analyze the divergence, spectral width and spectral shift of this XUV emission. We show that these specific features are well explained by high-order parametric generation (HPG) involving multiphoton absorption and combined emission of an idler THz radiation and an XUV beam with remarkably smooth spatial and spectral characteristics., Comment: 18 pages, 12 figures. To be published in a peer-reviewed scientific journal

Published
2020
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26. Actin polymerization downstream of integrins: signaling pathways and mechanotransduction

Author

Christophe Le Clainche, Alexis Gautreau, Stéphane Romero, Laboratoire de Biologie Structurale de la Cellule (BIOC), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Dynamique du cytosquelette et motilité (ACTIN), Département Biochimie, Biophysique et Biologie Structurale (B3S), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Moscow Institute of Physics and Technology [Moscow] (MIPT), ANR-16-CE13-0007,PHAGOMECANO,Mécanotransduction associée à la phagocytose dépendante des intégrines(2016), and ANR-18-CE13-0026,RECAMECA,Etude des liens moléculaires entre la force du cytosquelette d'actomyosine, la régulation des intégrines et les propriétés de la matrice extracellulaire grâce à une reconstitution in vitro(2018)

Subjects
Integrins, [SDV]Life Sciences [q-bio], Integrin, Formins, macromolecular substances, Biochemistry, Mechanotransduction, Cellular, Actin-Related Protein 2-3 Complex, Polymerization, Extracellular matrix, 03 medical and health sciences, Mice, 0302 clinical medicine, Cell Adhesion, Animals, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Mechanotransduction, Cell adhesion, Molecular Biology, Actin, 030304 developmental biology, 0303 health sciences, Durotaxis, biology, Chemistry, Cell Biology, VASP, Actin cytoskeleton, Actins, Cell biology, Extracellular Matrix, DNA-Binding Proteins, biology.protein, Arp2/3, actin, 030217 neurology & neurosurgery
Abstract

International audience; A cell constantly adapts to its environment. Cell decisions to survive, to proliferate or to migrate are dictated not only by soluble growth factors, but also through the direct interaction of the cell with the surrounding extracellular matrix (ECM). Integrins and their connections to the actin cytoskeleton are crucial for monitoring cell attachment and the physical properties of the substratum. Cell adhesion dynamics are modulated in complex ways by the polymerization of branched and linear actin arrays, which in turn reinforce ECM-cytoskeleton connection. This review describes the major actin regulators, Ena/VASP proteins, formins and Arp2/3 complexes, in the context of signaling pathways downstream of integrins. We focus on the specific signaling pathways that transduce the rigidity of the substrate and which control durotaxis, i.e. directed migration of cells towards increased ECM rigidity. By doing so, we highlight several recent findings on mechanotransduction and put them into a broad integrative perspective that is the result of decades of intense research on the actin cytoskeleton and its regulation.

Published
2019
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27. Corrigendum: Spatial Lymphocyte Dynamics in Lymph Nodes Predicts the Cytotoxic T Cell Frequency Needed for HIV Infection Control

Author

Gennady Bocharov, Vitaly Volpert, N. Bessonov, Andreas Meyerhans, Anass Bouchnita, Dmitry Grebennikov, Moscow Institute of Physics and Technology [Moscow] (MIPT), Modélisation mathématique, calcul scientifique (MMCS), Institut Camille Jordan (ICJ), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Multi-scale modelling of cell dynamics : application to hematopoiesis (DRACULA), Centre de génétique et de physiologie moléculaire et cellulaire (CGPhiMC), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut Camille Jordan (ICJ), Institute of Mechanical Engineering Problems [St. Petersburg] (IPME), Russian Academy of Sciences [Moscow] (RAS), Department of Virology [Homburg], Saarland University [Saarbrücken], Institute of Numerical Mathematics [Moscou] (INM-RAS), Institut Camille Jordan [Villeurbanne] (ICJ), Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre de génétique et de physiologie moléculaire et cellulaire (CGPhiMC), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
CD4-Positive T-Lymphocytes, 0301 basic medicine, lcsh:Immunologic diseases. Allergy, Lymphoid tissue, Lymphocyte, Cell, Immunology, Motility, HIV Infections, Cell motility, Cytotoxic T cell scanning, Biology, cell motility, dissipative particle dynamics, 03 medical and health sciences, 0302 clinical medicine, Immune system, In vivo, medicine, Humans, Cytotoxic T cell, [MATH.MATH-AP]Mathematics [math]/Analysis of PDEs [math.AP], multicellular dynamics, Immunology and Allergy, HIV vaccine, lymphoid tissue, Original Research, Stochastic differential equation, Models, Immunological, Correction, Dissipative particle dynamics, HIV infection, 3. Good health, Multicellular dynamics, 030104 developmental biology, medicine.anatomical_structure, Lymphatic system, cytotoxic T cell scanning, HIV-1, Lymph Nodes, lcsh:RC581-607, Neuroscience, T-Lymphocytes, Cytotoxic, 030215 immunology
Abstract

The surveillance of host body tissues by immune cells is central for mediating their defense function. In vivo imaging technologies have been used to quantitatively characterize target cell scanning and migration of lymphocytes within lymph nodes (LNs). The translation of these quantitative insights into a predictive understanding of immune system functioning in response to various perturbations critically depends on computational tools linking the individual immune cell properties with the emergent behavior of the immune system. By choosing the Newtonian second law for the governing equations, we developed a broadly applicable mathematical model linking individual and coordinated T-cell behaviors. The spatial cell dynamics is described by a superposition of autonomous locomotion, intercellular interaction, and viscous damping processes. The model is calibrated using in vivo data on T-cell motility metrics in LNs such as the translational speeds, turning angle speeds, and meandering indices. The model is applied to predict the impact of T-cell motility on protection against HIV infection, i.e., to estimate the threshold frequency of HIV-specific cytotoxic T cells (CTLs) that is required to detect productively infected cells before the release of viral particles starts. With this, it provides guidance for HIV vaccine studies allowing for the migration of cells in fibrotic LNs. This work is supported by the Russian Science Foundation (grant 18-11-00171). VV was supported by a grant from the RUDN University Program 5-100. AM is also supported by a grant from the Spanish Ministry of Economy, Industry and Competitiveness and FEDER grant no. SAF2016-75505-R (AEI/MINEICO/FEDER, UE) and the María de Maeztu Programme for Units of Excellence in R&D (MDM-2014-0370).

Published
2019
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28. Assessment of chemical-crosslink-assisted protein structure modeling in CASP13

Author

Bohdan Monastyrskyy, Juri Rappsilber, Krzysztof Fidelis, J. Eduardo Fajardo, Mikhail Karasikov, Alexander Leitner, Agnieszka S. Karczyńska, Andras Fiser, Adam Belsom, Silvia Crivelli, Emilia A. Lubecka, Celina Sikorska, Andriy Kryshtafovych, Nelson Gil, Cezary Czaplewski, Rojan Shrestha, Esben Trabjerg, Sergei Grudinin, Guillaume Pagès, Adam Liwo, Adam K. Sieradzan, Department of Systems & Computational Biology [New York], Albert Einstein College of Medicine [New York], Department of Biochemistry [New York], Institut für Biotechnologie [berlin], Technische Universität Berlin (TU), Department of Computer Science [Davis] (UC Davis), University of California [Davis] (UC Davis), University of California-University of California, Department of Environmental Analytics [Univ Gdańsk], Faculty of Chemistry [Univ Gdańsk], University of Gdańsk (UG)-University of Gdańsk (UG), Genome Center [UC Davis], Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Laboratoire Jean Kuntzmann (LJK ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Moscow Institute of Physics and Technology [Moscow] (MIPT), Skolkovo Institute of Science and Technology [Moscow] (Skoltech), Department of Computer Science [ETH Zürich] (D-INFK), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Institute of Molecular Systems Biology [Zurich], Korea Institute for Advanced Study (KIAS), Institute of Mathematics [Univ Gdańsk], University of Gdańsk (UG), Wellcome Trust Centre for Cell Biology, University of Edinburgh, Technical University of Berlin / Technische Universität Berlin (TU), Department of Computer Science [Univ California Davis] (CS - UC Davis), University of California (UC)-University of California (UC), Algorithms for Modeling and Simulating Nanosystems [2018-...] (NANO-D-POST [2018-2020]), and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)

Subjects
CASP13, Models, Molecular, Computer science, Protein Conformation, Context (language use), Computational biology, Routine practice, 010402 general chemistry, Mass spectrometry, Machine learning, computer.software_genre, 01 natural sciences, Biochemistry, Article, [PHYS.PHYS.PHYS-COMP-PH]Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], 03 medical and health sciences, Protein structure, chemical-crosslink-assisted protein structure modeling, Structural Biology, Tandem Mass Spectrometry, Molecular Biology, 030304 developmental biology, 0303 health sciences, Chemistry, business.industry, 030302 biochemistry & molecular biology, Model protein, Computational Biology, Proteins, Reproducibility of Results, 0104 chemical sciences, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Workflow, Cross-Linking Reagents, Models, Chemical, chemical crosslinking/mass spectrometry, Critical assessment, Artificial intelligence, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, Protein structure modeling, computer, Function (biology), Algorithms, Chromatography, Liquid
Abstract

International audience; With the advance of experimental procedures obtaining chemical crosslinking information is becoming a fast and routine practice. Information on crosslinks can greatly enhance the accuracy of protein structure modeling. Here, we review the current state of the art in modeling protein structures with the assistance of experimentally determined chemical crosslinks within the framework of the 13th meeting of Critical Assessment of Structure Prediction approaches. This largest‐to‐date blind assessment reveals benefits of using data assistance in difficult to model protein structure prediction cases. However, in a broader context, it also suggests that with the unprecedented advance in accuracy to predict contacts in recent years, experimental crosslinks will be useful only if their specificity and accuracy further improved and they are better integrated into computational workflows.

Published
2019
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29. Multiblock Thermoplastic Polyurethanes: In Situ Studies of Structural and Morphological Evolution under Strain

Author

Ainur F. Abukaev, Denis V. Anokhin, Dimitri A. Ivanov, Marina A. Gorbunova, Talrose Institute for Energy Problems of Chemical Physics of the RAS, Russian Academy of Sciences [Moscow] (RAS), Lomonosov Moscow State University (MSU), Moscow Institute of Physics and Technology [Moscow] (MIPT), Institut de Science des Matériaux de Mulhouse (IS2M), Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), and Ivanov, Dimitri

Subjects
Technology, synchrotron SAXS/WAXS, Materials science, 02 engineering and technology, Plasticity, lamellar morphology, 010402 general chemistry, 01 natural sciences, Article, law.invention, Thermoplastic polyurethane, Crystallinity, poly(1,4-butylene adipate), law, [CHIM] Chemical Sciences, poly-ε-caprolactone, [CHIM]Chemical Sciences, General Materials Science, Lamellar structure, poly(1, Crystallization, Composite material, Elastic modulus, thermoplastic polyurethane ureas, polymer deformation, Microscopy, QC120-168.85, shape memory materials, QH201-278.5, Engineering (General). Civil engineering (General), 021001 nanoscience & nanotechnology, TK1-9971, 0104 chemical sciences, Descriptive and experimental mechanics, 4-butylene adipate), Electrical engineering. Electronics. Nuclear engineering, TA1-2040, Deformation (engineering), 0210 nano-technology, Necking
Abstract

International audience; The structural evolution of multiblock thermoplastic polyurethane ureas based on two polydiols, poly(1,4-butylene adipate (PBA) and poly-ε-caprolactone (PCL), as soft blocks and two diisocyanites, 2,4-toluylene diisocyanate (TDI) and 1,6-hexamethylene diisocyanate (HMDI), as hard blocks is monitored during in situ deformation by small- and wide-angle X-ray scattering. It was shown that the urethane environment determines the crystal structure of the soft block. Consequently, two populations of crystalline domains of polydiols are formed. Aromatic TDI forms rigid domains and imposes constrains on the crystallization of bounded polydiol. During stretching, the TDI–polydiol domains reveal limited elastic deformation without reorganization of the crystalline phase. The constrained lamellae of polydiol form an additional physical network that contributes to the elastic modulus and strength of the material. In contrast, polydiols connected to the linear semi-flexible HMDI have a higher crystallization rate and exhibit a more regular lamellar morphology. During deformation, the HMDI-PBA domains show a typical thermoplastic behavior with plastic flow and necking because of the high degree of crystallinity of PBA at room temperature. Materials with HMDI-PCL bonding exhibit elastic deformation due to the low degree of crystallinity of the PCL block in the isotropic state. At higher strain, hardening of the material is observed due to the stress-induced crystallization of PCL

Published
2021
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30. Information Processing Using Three-Qubit and Qubit–Qutrit Encodings of Noncomposite Quantum Systems

Author

Aleksey Popov, Vladimir I. Man’ko, Aleksey Fedorov, Evgeniy O. Kiktenko, Bauman Moscow State Technical University, Russian Quantum Center, Laboratoire de Physique Théorique et Modèles Statistiques (LPTMS), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11), Moscow Institute of Physics and Technology [Moscow] (MIPT), P. N. Lebedev Physical Institute of the Russian Academy of Sciences [Moscow] (LPI RAS), and Russian Academy of Sciences [Moscow] (RAS)

Subjects
Quantum Physics, Computer science, Information processing, FOS: Physical sciences, Parity (physics), Bit array, Topology, 01 natural sciences, Atomic and Molecular Physics, and Optics, 010305 fluids & plasmas, [PHYS.QPHY]Physics [physics]/Quantum Physics [quant-ph], Qubit, 0103 physical sciences, Subadditivity, Qutrit, Quantum information, Quantum Physics (quant-ph), 010306 general physics, Engineering (miscellaneous), Quantum
Abstract

We study quantum information properties of a seven-level system realized by a particle in an one-dimensional square-well trap. Features of encodings of seven-level systems in a form of three-qubit or qubit-qutrit systems are discussed. We use the three-qubit encoding of the system in order to investigate subadditivity and strong subadditivity conditions for the thermal state of the particle. The qubit-qutrit encoding is employed to suggest a single qudit algorithm for calculation of parity of a bit string. Obtained results indicate on the potential resource of multilevel systems for realization of quantum information processing., Comment: 6 pages, 3 figures; published version

Published
2016
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31. PEPSI-Dock: a detailed data-driven protein–protein interaction potential accelerated by polar Fourier correlation

Author

Petr Popov, David W. Ritchie, Emilie Neveu, Sergei Grudinin, Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Laboratoire Jean Kuntzmann (LJK ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Computational Algorithms for Protein Structures and Interactions (CAPSID), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Complex Systems, Artificial Intelligence & Robotics (LORIA - AIS), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), and Moscow Institute of Physics and Technology [Moscow] (MIPT)

Subjects
0301 basic medicine, Statistics and Probability, Binding free energy, Protein Conformation, Computer science, Molecular Conformation, Docking proteines, Machine learning, computer.software_genre, Biochemistry, Molecular Docking Simulation, Molecular conformation, Protein–protein interaction, Machine Learning, 03 medical and health sciences, Protein structure, DOCK, Native state, Macromolecular docking, Protein Interactions, Molecular Biology, business.industry, Proteins, Models, Theoretical, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Computer Science Applications, Computational Mathematics, 030104 developmental biology, Computational Theory and Mathematics, Docking (molecular), Artificial intelligence, business, computer, Algorithm, Algorithms, Protein Binding
Abstract

Motivation Docking prediction algorithms aim to find the native conformation of a complex of proteins from knowledge of their unbound structures. They rely on a combination of sampling and scoring methods, adapted to different scales. Polynomial Expansion of Protein Structures and Interactions for Docking (PEPSI-Dock) improves the accuracy of the first stage of the docking pipeline, which will sharpen up the final predictions. Indeed, PEPSI-Dock benefits from the precision of a very detailed data-driven model of the binding free energy used with a global and exhaustive rigid-body search space. As well as being accurate, our computations are among the fastest by virtue of the sparse representation of the pre-computed potentials and FFT-accelerated sampling techniques. Overall, this is the first demonstration of a FFT-accelerated docking method coupled with an arbitrary-shaped distance-dependent interaction potential. Results First, we present a novel learning process to compute data-driven distant-dependent pairwise potentials, adapted from our previous method used for rescoring of putative protein–protein binding poses. The potential coefficients are learned by combining machine-learning techniques with physically interpretable descriptors. Then, we describe the integration of the deduced potentials into a FFT-accelerated spherical sampling provided by the Hex library. Overall, on a training set of 163 heterodimers, PEPSI-Dock achieves a success rate of 91% mid-quality predictions in the top-10 solutions. On a subset of the protein docking benchmark v5, it achieves 44.4% mid-quality predictions in the top-10 solutions when starting from bound structures and 20.5% when starting from unbound structures. The method runs in 5–15 min on a modern laptop and can easily be extended to other types of interactions. Availability and Implementation https://team.inria.fr/nano-d/software/PEPSI-Dock. Contact sergei.grudinin@inria.fr

Published
2016
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32. Knodle: A Support Vector Machines-Based Automatic Perception of Organic Molecules from 3D Coordinates

Author

Sergei Grudinin, Maria Kadukova, Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Laboratoire Jean Kuntzmann (LJK ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), and Moscow Institute of Physics and Technology [Moscow] (MIPT)

Subjects
0301 basic medicine, Informatics, Support Vector Machine, Computer science, protein ligand docking, SVM, General Chemical Engineering, Library and Information Sciences, Ligands, computer.software_genre, 01 natural sciences, Set (abstract data type), Automation, 03 medical and health sciences, Software, [STAT.ML]Statistics [stat]/Machine Learning [stat.ML], 3D structure perception, 0103 physical sciences, Organic Chemicals, 010304 chemical physics, business.industry, Atom (order theory), General Chemistry, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Computer Science Applications, Molecular Weight, Data set, Support vector machine, machine learning, 030104 developmental biology, Protein–ligand docking, Benchmark (computing), Data mining, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, Algorithm, computer, Algorithms
Abstract

International audience; Here we address the problem of the assignment of atom types and bond orders in low molecular weight compounds. For this purpose, we have developed a prediction model based on nonlinear Support Vector Machines (SVM), implemented in a KNOwledge-Driven Ligand Extractor called Knodle, a software library for the recognition of atomic types, hybridization states, and bond orders in the structures of small molecules. We trained the model using an excessive amount of structural data collected from the PDBbindCN database. Accuracy of the results and the running time of our method is comparable with other popular methods, such as NAOMI, fconv, and I-interpret. On the popular Labute’s benchmark set consisting of 179 protein–ligand complexes, Knodle makes five to six perception errors, NAOMI makes seven errors, I-interpret makes nine errors, and fconv makes 13 errors. On a larger set of 3,000 protein–ligand structures collected from the PDBBindCN general data set (v2014), Knodle and NAOMI have a comparable accuracy of approximately 3.9% and 4.7% of errors, I-interpret made 6.0% of errors, while fconv produced approximately 12.8% of errors. On a more general set of 332,974 entries collected from the Ligand Expo database, Knodle made 4.5% of errors. Overall, our study demonstrates the efficiency and robustness of nonlinear SVM in structure perception tasks. Knodle is available at https://team.inria.fr/nano-d/software/Knodle.

Published
2016
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33. Kelvin’s Dissymmetric Models and Consistency Conditions of Multicomponent Gas-Liquid Equilibrium and Capillary Condensation

Author

Alexandre Koldoba, Mikhail Panfilov, Laboratoire Énergies et Mécanique Théorique et Appliquée (LEMTA ), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), and Moscow Institute of Physics and Technology [Moscow] (MIPT)

Subjects
Article Subject, Capillary condensation, Chemistry, Phase equilibrium, Capillary action, 0208 environmental biotechnology, Biophysics, General Physics and Astronomy, Thermodynamics, Binary number, 02 engineering and technology, 020801 environmental engineering, Mathematical theory, [SPI]Engineering Sciences [physics], 020401 chemical engineering, Consistency (statistics), Phase (matter), 0204 chemical engineering, Physical and Theoretical Chemistry, Ternary operation
Abstract

International audience; To describe phase equilibrium of mixtures, we develop a nonclassical approach based on using different equations of state for gas and liquid. We show that not all the types of EOS are admissible but only those which verify some specific conditions of consistency. We developed the mathematical theory of this new approach for pure cores and for mixtures, in presence and absence of capillary forces, which leads to explicit analytical relationships for phase concentrations of chemical components. Several examples of comparison with experimental data for binary and ternary mixtures illustrate the feasibility of the suggested approach.

Published
2016
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34. Principal Component Analysis of Lipid Molecule Conformational Changes in Molecular Dynamics Simulations

Author

Ivan Gushchin, Sergei Grudinin, Valentin Gordeliy, Pavel Buslaev, Moscow Institute of Physics and Technology [Moscow] (MIPT), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Laboratoire Jean Kuntzmann (LJK ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Principal Component Analysis, Physics::Biological Physics, 010304 chemical physics, Chemistry, Bilayer, Molecular Conformation, Molecular Dynamics Simulation, Lipids, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, 01 natural sciences, Molecular conformation, Computer Science Applications, 03 medical and health sciences, Molecular dynamics, 030104 developmental biology, Chemical physics, Computational chemistry, 0103 physical sciences, Principal component analysis, Molecule, Lipid molecule, Physical and Theoretical Chemistry, Lipid bilayer
Abstract

International audience; Molecular dynamics simulations of lipid bilayers are ubiquitous nowadays. Usually, either global properties of the bilayer or some particular characteristics of each lipid molecule are evaluated in such simulations, but the structural properties of the molecules as a whole are rarely studied. Here, we show how a comprehensive quantitative description of conformational space and dynamics of a single lipid molecule can be achieved via the principal component analysis (PCA). We illustrate the approach by analyzing and comparing simulations of DOPC bilayers obtained using eight different force fields: all-atom generalized AMBER, CHARMM27, CHARMM36, Lipid14 and Slipids, and united-atom Berger, GROMOS43A1-S3 and GROMOS54A7. Similarly to proteins, most of the structural variance of a lipid molecule can be described by only a few principal components. These major components are similar in different simulations, although there are notable distinctions between the older and newer force fields, and between the all-atom and united-atom force fields. The DOPC molecules in the simulations generally equilibrate on the timescales of tens to hundreds of nanoseconds. The equilibration is the slowest in the GAFF simulation, and the fastest in the Slipids simulation. Somewhat unexpectedly, the equilibration in the united-atom force fields is generally slower than in the all-atom force fields. Overall, there is a clear separation between the more variable previous generation force fields, and significantly more similar new generation force fields (CHARMM36, Lipid14, Slipids). We expect that the presented approaches will be useful for quantitative analysis of conformations and dynamics of individual lipid molecules in other simulations of lipid bilayers.

Published
2016
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35. Compensation of disorder for extraordinary optical transmission effect in nanopore arrays fabricated by nanosphere photolithography

Author

Olivier Dellea, Jean-Yves Michalon, Alexey A. Shcherbakov, Andrei A. Ushkov, Thomas Kämpfe, Isabelle Verrier, Yves Jourlin, Laboratoire Hubert Curien [Saint Etienne] (LHC), Institut d'Optique Graduate School (IOGS)-Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS), CEA/DRT/LITEN, Moscow Institute of Physics and Technology [Moscow] (MIPT), National Research University of Information Technologies, Mechanics and Optics [St. Petersburg] (ITMO), Laboratoire Hubert Curien (LHC), and Institut d'Optique Graduate School (IOGS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], Materials science, Computer simulation, business.industry, Extraordinary optical transmission, 02 engineering and technology, 021001 nanoscience & nanotechnology, 01 natural sciences, Atomic and Molecular Physics, and Optics, law.invention, Compensation (engineering), 010309 optics, Nanopore, Optics, law, 0103 physical sciences, Phenomenological model, Optoelectronics, Photolithography, Thin film, 0210 nano-technology, business, Electron-beam lithography
Abstract

International audience; The work considers the effect of extraordinary optical transmission (EOT) in polycrystalline arrays of nanopores fabricated via nanosphere photolithography (NPL). The use of samples with different qualities of polycrystalline structure allows us to reveal the role of disorder for EOT. We propose a phenomenological model which takes the disorder into account in numerical simulations and validate it using experimental data. Due to the NPL flexibility for the structure geometry control, we demonstrate the possiblity to partially compensate the disorder influence on EOT by the nanopore depth adjustments. The proposed experimental and theoretical results are promising to reveal the NPL limits for EOT-based devices and stimulate systematic studies of disorder compensation designs.

Published
2020
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36. Smooth orientation-dependent scoring function for coarse-grained protein quality assessment

Author

Sergei Grudinin, Guillaume Pagès, Mikhail Karasikov, Moscow Institute of Physics and Technology [Moscow] (MIPT), Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Laboratoire Jean Kuntzmann (LJK ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Algorithms for Modeling and Simulating Nanosystems [2018-...] (NANO-D-POST [2018-2020]), and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)

Subjects
Statistics and Probability, Models, Molecular, 0303 health sciences, Computer science, Hydrogen bond, Protein Conformation, 030302 biochemistry & molecular biology, Protein design, Atomic coordinates, Function (mathematics), Protein structure prediction, Biochemistry, Computer Science Applications, 03 medical and health sciences, Computational Mathematics, Structural bioinformatics, Protein structure, Computational Theory and Mathematics, Grain Proteins, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Molecular Biology, Algorithm, 030304 developmental biology
Abstract

Motivation Protein quality assessment (QA) is a crucial element of protein structure prediction, a fundamental and yet open problem in structural bioinformatics. QA aims at ranking predicted protein models to select the best candidates. The assessment can be performed based either on a single model or on a consensus derived from an ensemble of models. The latter strategy can yield very high performance but substantially depends on the pool of available candidate models, which limits its applicability. Hence, single-model QA methods remain an important research target, also because they can assist the sampling of candidate models. Results We present a novel single-model QA method called SBROD. The SBROD (Smooth Backbone-Reliant Orientation-Dependent) method uses only the backbone protein conformation, and hence it can be applied to scoring coarse-grained protein models. The proposed method deduces its scoring function from a training set of protein models. The SBROD scoring function is composed of four terms related to different structural features: residue–residue orientations, contacts between backbone atoms, hydrogen bonding and solvent–solute interactions. It is smooth with respect to atomic coordinates and thus is potentially applicable to continuous gradient-based optimization of protein conformations. Furthermore, it can also be used for coarse-grained protein modeling and computational protein design. SBROD proved to achieve similar performance to state-of-the-art single-model QA methods on diverse datasets (CASP11, CASP12 and MOULDER). Availability and implementation The standalone application implemented in C++ and Python is freely available at https://gitlab.inria.fr/grudinin/sbrod and supported on Linux, MacOS and Windows. Supplementary information Supplementary data are available at Bioinformatics online.

Published
2018
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37. Direct S -matrix calculation for diffractive structures and metasurfaces

Author

Yves Jourlin, Alexey A. Shcherbakov, Denis F. Baidin, Yury V. Stebunov, Thomas Kämpfe, Moscow Institute of Physics and Technology [Moscow] (MIPT), Laboratoire Hubert Curien [Saint Etienne] (LHC), and Institut d'Optique Graduate School (IOGS)-Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
FOS: Physical sciences, Physics::Optics, 02 engineering and technology, Grating, 01 natural sciences, law.invention, 010309 optics, Planar, law, 0103 physical sciences, Cartesian coordinate system, ComputingMilieux_MISCELLANEOUS, Plasmon, S-matrix, Physics, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], Curvilinear coordinates, Numerical analysis, Mathematical analysis, Computational Physics (physics.comp-ph), 021001 nanoscience & nanotechnology, Reflection (mathematics), 0210 nano-technology, Physics - Computational Physics, Physics - Optics, Optics (physics.optics)
Abstract

The paper presents a derivation of analytical components of S-matrices for arbitrary planar diffractive structures and metasurfaces in the Fourier domain. Attained general formulas for S-matrix components can be applied within both formulations in the Cartesian and curvilinear metric. A numerical method based on these results can benefit from all previous improvements of the Fourier domain methods. In addition, we provide expressions for S-matrix calculation in case of periodically corrugated layers of 2D materials, which are valid for arbitrary corrugation depth-to-period ratios. As an example the derived equations are used to simulate resonant grating excitation of graphene plasmons and an impact of silica interlayer on corresponding reflection curves., Comment: 21 pages, 5 figures

Published
2018
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38. Sulfur dioxide in the Venus atmosphere: I. Vertical distribution and variability

Author

Franklin P. Mills, Sanjay S. Limaye, Oleg Korablev, Tony Roman, Ann Carine Vandaele, Daria Evdokimova, Arnaud Mahieux, Franck Lefèvre, Kandis Lea Jessup, Valérie Wilquet, Christopher D. Parkinson, Emmanuel Marcq, Th. Encrenaz, Aurélien Stolzenbach, Brad J. Sandor, Colin Wilson, Séverine Robert, S. Chamberlain, Larry W. Esposito, Franck Montmessin, Denis Belyaev, Belgian Institute for Space Aeronomy / Institut d'Aéronomie Spatiale de Belgique (BIRA-IASB), Moscow Institute of Physics and Technology [Moscow] (MIPT), Space Research Institute of the Russian Academy of Sciences (IKI), Russian Academy of Sciences [Moscow] (RAS), Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Laboratory for Atmospheric and Space Physics [Boulder] (LASP), University of Colorado [Boulder], Department of Space Studies [Boulder], Southwest Research Institute [Boulder] (SwRI), PLANETO - LATMOS, Laboratoire Atmosphères, Milieux, Observations Spatiales (LATMOS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Space Science and Engineering Center [Madison] (SSEC), University of Wisconsin-Madison, Fonds National de la Recherche Scientifique [Bruxelles] (FNRS), Fenner School of Environment and Society, Australian National University (ANU), Space Science Institute [Boulder] (SSI), Department of Atmospheric, Oceanic, and Space Sciences [Ann Arbor] (AOSS), University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, Space Telescope Science Institute (STSci), Clarendon Laboratory [Oxford], University of Oxford [Oxford], and University of Oxford

Subjects
Haze, 010504 meteorology & atmospheric sciences, biology, [SDU.ASTR.SR]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Solar and Stellar Astrophysics [astro-ph.SR], [SDU.ASTR.EP]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], Astronomy and Astrophysics, Venus, Atmospheric model, biology.organism_classification, Atmospheric sciences, 01 natural sciences, Sulfur oxide, Mesosphere, Atmosphere, Atmosphere of Venus, Altitude, 13. Climate action, Space and Planetary Science, 0103 physical sciences, 010303 astronomy & astrophysics, 0105 earth and related environmental sciences
Abstract

International audience; Recent observations of sulfur containing species (SO2, SO, OCS, and H2SO4) in Venus’ mesosphere have generated controversy and great interest in the scientific community. These observations revealed unexpected spatial patterns and spatial/temporal variability that have not been satisfactorily explained by models. Sulfur oxide chemistry on Venus is closely linked to the global-scale cloud and haze layers, which are composed primarily of concentrated sulfuric acid. Sulfur oxide observations provide therefore important insight into the on-going chemical evolution of Venus’ atmosphere, atmospheric dynamics, and possible volcanism.This paper is the first of a series of two investigating the SO2 and SO variability in the Venus atmosphere. This first part of the study will focus on the vertical distribution of SO2, considering mostly observations performed by instruments and techniques providing accurate vertical information. This comprises instruments in space (SPICAV/SOIR suite on board Venus Express) and Earth-based instruments (JCMT). The most noticeable feature of the vertical profile of the SO2 abundance in the Venus atmosphere is the presence of an inversion layer located at about 70–75 km, with VMRs increasing above. The observations presented in this compilation indicate that at least one other significant sulfur reservoir (in addition to SO2 and SO) must be present throughout the 70–100 km altitude region to explain the inversion in the SO2 vertical profile. No photochemical model has an explanation for this behaviour. GCM modelling indicates that dynamics may play an important role in generating an inflection point at 75 km altitude but does not provide a definitive explanation of the source of the inflection at all local times or latitudesThe current study has been carried out within the frame of the International Space Science Institute (ISSI) International Team entitled ‘SO2 variability in the Venus atmosphere’.

Published
2018
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39. The Atmospheric Chemistry Suite (ACS) of three spectrometers for the ExoMars 2016 Trace Gas Orbiter

Author

Korablev, O., Montmessin, F., Trokhimovskiy, A., Fedorova, A. A., Shakun, A. V., Grigoriev, A. V., Moshkin, B. E., Ignatiev, N. I., Forget, F., Lefèvre, F., Anufreychik, K., Dzuban, I., Ivanov, Y. S., Kalinnikov, Y. K., Kozlova, T. O., Kungurov, A., Makarov, V., Martynovich, F., Maslov, I., Merzlyakov, D., Moiseev, P. P., Nikolskiy, Y., Patrakeev, A., Patsaev, D., Santos-Skripko, A., Sazonov, O., Semena, N., Semenov, A., Shashkin, V., Sidorov, A., Stepanov, A. V., Stupin, I., Timonin, D., Titov, A. Y., Viktorov, A., Zharkov, A., Altieri, F., Arnold, G., Belyaev, D. A., Bertaux, J. L., Betsis, D. S., Duxbury, N., Encrenaz, T., Fouchet, T., Gérard, J.-C., Grassi, D., Guerlet, S., Hartogh, P., Kasaba, Y., Khatuntsev, I., Krasnopolsky, V. A., Kuzmin, R. O., Lellouch, E., Lopez-Valverde, M. A., Luginin, M., Määttänen, A., Marcq, E., Martin Torres, J., Medvedev, A. S., Millour, E., Olsen, K. S., Patel, M. R., Quantin-Nataf, C., Rodin, A. V., Shematovich, V. I., Thomas, I., Thomas, N., Vazquez, L., Vincendon, M., Wilquet, V., Wilson, C. F., Zasova, L. V., Zelenyi, L. M., Zorzano, M. P., Space Research Institute of the Russian Academy of Sciences (IKI), Russian Academy of Sciences [Moscow] (RAS), IMPEC - LATMOS, Laboratoire Atmosphères, Milieux, Observations Spatiales (LATMOS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Météorologie Dynamique (UMR 8539) (LMD), Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-École des Ponts ParisTech (ENPC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département des Géosciences - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris), Main Astronomical Observatory of NAS of Ukraine (MAO), National Academy of Sciences of Ukraine (NASU), National Research Institute for Physical-technical and Radiotechnical Measurements (VNIIFTRI), Scientific Production Enterprise Astron Electronics, Faculty of Physics [MSU, Moscow], Lomonosov Moscow State University (MSU), Istituto di Astrofisica e Planetologia Spaziali - INAF (IAPS), Istituto Nazionale di Astrofisica (INAF), Deutsches Zentrum für Luft- und Raumfahrt [Berlin] (DLR), Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA (UMR_8109)), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique Atmosphérique et Planétaire (LPAP), Université de Liège, Max-Planck-Institut für Sonnensystemforschung (MPS), Max-Planck-Gesellschaft, Tohoku University [Sendai], Moscow Institute of Physics and Technology [Moscow] (MIPT), Catholic University of America, Vernadsky Institute of Geochemistry and Analytical Chemistry (GEOKHI), Instituto de Astrofísica de Andalucía (IAA), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Department of Computer Science [Kiruna], Luleå University of Technology (LUT), Instituto Andaluz de Ciencias de la Tierra (IACT), Consejo Superior de Investigaciones Científicas [Spain] (CSIC)-Universidad de Granada (UGR), The Open University [Milton Keynes] (OU), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] (LGL-TPE), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon), Institute of Astronomy of the Russian Academy of Sciences (INASAN), Belgian Institute for Space Aeronomy / Institut d'Aéronomie Spatiale de Belgique (BIRA-IASB), Universität Bern [Bern], Facultad de Informática [Madrid], Universidad Complutense de Madrid [Madrid] (UCM), Institut d'astrophysique spatiale (IAS), Université Paris-Sud - Paris 11 (UP11)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Oxford], University of Oxford [Oxford], Centro de Astrobiologia [Madrid] (CAB), Consejo Superior de Investigaciones Científicas [Spain] (CSIC)-Instituto Nacional de Técnica Aeroespacial (INTA), PLANETO - LATMOS, Sorbonne Université (SU)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Universidad de Granada (UGR), Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Instituto Nacional de Técnica Aeroespacial (INTA), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Max-Planck-Institut für Sonnensystemforschung = Max Planck Institute for Solar System Research (MPS), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Universidad de Granada = University of Granada (UGR), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Universität Bern [Bern] (UNIBE), Université Paris-Sud - Paris 11 (UP11)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National d’Études Spatiales [Paris] (CNES), University of Oxford, and Instituto Nacional de Técnica Aeroespacial (INTA)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)

Subjects
Cross-dispersion, [SDU.ASTR]Sciences of the Universe [physics]/Astrophysics [astro-ph], Atmosphere, 520 Astronomy, Mars, Echelle, Fourier-spectrometer, 620 Engineering, High-resolution spectrometer, [PHYS.PHYS.PHYS-SPACE-PH]Physics [physics]/Physics [physics]/Space Physics [physics.space-ph]
Abstract

International audience; The Atmospheric Chemistry Suite (ACS) package is an element of the Russian contribution to the ESA-Roscosmos ExoMars 2016 Trace Gas Orbiter (TGO) mission. ACS consists of three separate infrared spectrometers, sharing common mechanical, electrical, and thermal interfaces. This ensemble of spectrometers has been designed and developed in response to the Trace Gas Orbiter mission objectives that specifically address the requirement of high sensitivity instruments to enable the unambiguous detection of trace gases of potential geophysical or biological interest. For this reason, ACS embarks a set of instruments achieving simultaneously very high accuracy (ppt level), very high resolving power (>10,000) and large spectral coverage (0.7 to 17 μm—the visible to thermal infrared range). The near-infrared (NIR) channel is a versatile spectrometer covering the 0.7–1.6 μm spectral range with a resolving power of ∼20,000. NIR employs the combination of an echelle grating with an AOTF (Acousto-Optical Tunable Filter) as diffraction order selector. This channel will be mainly operated in solar occultation and nadir, and can also perform limb observations. The scientific goals of NIR are the measurements of water vapor, aerosols, and dayside or night side airglows. The mid-infrared (MIR) channel is a cross-dispersion echelle instrument dedicated to solar occultation measurements in the 2.2–4.4 μm range. MIR achieves a resolving power of >50,000. It has been designed to accomplish the most sensitive measurements ever of the trace gases present in the Martian atmosphere. The thermal-infrared channel (TIRVIM) is a 2-inch double pendulum Fourier-transform spectrometer encompassing the spectral range of 1.7–17 μm with apodized resolution varying from 0.2 to 1.3 cm−1. TIRVIM is primarily dedicated to profiling temperature from the surface up to ∼60 km and to monitor aerosol abundance in nadir. TIRVIM also has a limb and solar occultation capability. The technical concept of the instrument, its accommodation on the spacecraft, the optical designs as well as some of the calibrations, and the expected performances for its three channels are described.

Published
2018
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40. ACS experiment for atmospheric studies on 'ExoMars-2016' Orbiter

Author

Anna Fedorova, Alexei Grigoriev, Nikolai Ignatiev, Alexander Trokhimovskiy, K. A. Anufreichik, Franck Montmessin, Oleg Korablev, Alexei Shakun, T. O. Kozlova, Moscow Institute of Physics and Technology [Moscow] (MIPT), Space Research Institute of the Russian Academy of Sciences (IKI), Russian Academy of Sciences [Moscow] (RAS), PLANETO - LATMOS, Laboratoire Atmosphères, Milieux, Observations Spatiales (LATMOS), and Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Fourier spectrometer, 010504 meteorology & atmospheric sciences, Solar occultations, [SDU.ASTR.EP]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], High-resolution spectrometer, 01 natural sciences, 7. Clean energy, Astrobiology, law.invention, Atmosphere, Orbiter, Mars atmosphere, law, Cross dispersion, 0103 physical sciences, Nadir, 010303 astronomy & astrophysics, 0105 earth and related environmental sciences, Remote sensing, Astronomy and Astrophysics, Mars Exploration Program, Atmosphere of Mars, Acousto-optical filter, [SDU.ASTR.IM]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Instrumentation and Methods for Astrophysic [astro-ph.IM], Trace gas, Planetary science, 13. Climate action, Space and Planetary Science, Atmospheric chemistry, Echelle grating, Environmental science, Methane isotopes
Abstract

International audience; ACS is a set of spectrometers for atmospheric studies (Atmospheric Chemistry Suite). It is one of the Russian instruments for the Trace Gas Orbiter (TGO) of the Russian-European “ExoMars” program. The purpose of the experiment is to study the Martian atmosphere by means of two observations regimes: sensitive trace gases measurements in solar occultations and by monitoring the atmospheric state during nadir observations. The experiment will allow us to approach global problems of Mars research such as current volcanism, and the modern climate status and its evolution. Also, the experiment is intended to solve the mystery of methane presence in the Martian atmosphere. Spectrometers of the ACS set cover the spectral range from the near IR-range (0.7 μm) to the thermal IR-range (17 μm) with spectral resolution λ/Δλ reaching 50000. The ACS instrument consists of three independent IR spectrometers and an electronics module, all integrated in a single unit with common mechanical, electrical and thermal interfaces. The article gives an overview of scientific tasks and presents the concept of the experiment.

Published
2015
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41. Coherent long-range magnetic bound states in a superconductor

Author

Dimitri Roditchev, Gerbold Menard, François Debontridder, Pascal Simon, Matthieu V. Leclerc, Sébastien Guissart, Christophe Brun, Etienne Janod, Tristan Cren, Laurent Cario, Vasily S. Stolyarov, Stéphane Pons, Institut des Nanosciences de Paris (INSP), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Spectroscopie des nouveaux états quantiques (INSP-E2), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique des Solides d'Orsay (LPS), Universirté d'Orsay, Laboratoire de Physique et d'Etude des Matériaux (UMR 8213) (LPEM), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Moscow Institute of Physics and Technology [Moscow] (MIPT), Institut des Matériaux Jean Rouxel (IMN), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Université de Nantes (UN)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Ecole Polytechnique de l'Université de Nantes (EPUN), and Université de Nantes (UN)-Université de Nantes (UN)

Subjects
Physics, Superconductivity, Range (particle radiation), Condensed matter physics, Niobium, General Physics and Astronomy, chemistry.chemical_element, [PHYS.COND.CM-S]Physics [physics]/Condensed Matter [cond-mat]/Superconductivity [cond-mat.supr-con], chemistry.chemical_compound, chemistry, Condensed Matter::Superconductivity, Selenide, Bound state, Physics::Atomic Physics, Atomic physics, ComputingMilieux_MISCELLANEOUS
Abstract

International audience; The quantum coupling of fully different degrees of freedom is a challenging path towards new functionalities for quantum electronics [1–3]. Here we show that the localized classical spin of a magnetic atom immersed in a superconductor with a two-dimensional electronic band structure gives rise to a long range coherent magnetic quantum state. We experimentally evidence coherent bound states with spatially oscillating particle-hole asymmetry extending tens of nanometers from individual iron atoms embedded in a 2H-NbSe 2 crystal. We theoretically elucidate how reduced dimensionality enhances the spatial extent of these bound states and describe their energy and spatial structure. These spatially extended magnetic states could be used as building blocks for coupling coherently distant magnetic atoms in new topological superconducting phases [4–11].

Published
2015
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42. Thermal structure of Venus nightside upper atmosphere measured by stellar occultations with SPICAV/Venus Express

Author

Denis Belyaev, Ann Carine Vandaele, Jean-Loup Bertaux, Franck Montmessin, Arnaud Mahieux, Anna Fedorova, Oleg Korablev, Emmanuel Marcq, Silvia Tellmann, Arianna Piccialli, Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), IMPEC - LATMOS, Laboratoire Atmosphères, Milieux, Observations Spatiales (LATMOS), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Moscow Institute of Physics and Technology [Moscow] (MIPT), Space Research Institute of the Russian Academy of Sciences (IKI), Russian Academy of Sciences [Moscow] (RAS), Fonds National de la Recherche Scientifique (FNRS), Université de Liège, Belgian Institute for Space Aeronomy / Institut d'Aéronomie Spatiale de Belgique (BIRA-IASB), Rhenish Institute for Environmental Research (RIU), University of Cologne, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), PLANETO - LATMOS, and Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Atmospheres, 010504 meteorology & atmospheric sciences, [SDU.ASTR.EP]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], Venus, Atmospheric sciences, 01 natural sciences, Atmosphere of Venus, Atmosphere, Altitude, 0103 physical sciences, 010303 astronomy & astrophysics, Spectroscopy, 0105 earth and related environmental sciences, Morning, biology, Structure, Astronomy and Astrophysics, biology.organism_classification, Warm front, 13. Climate action, Space and Planetary Science, Local time, Mesopause, Occultations, Geology
Abstract

International audience; The thermal structure of Venus upper atmosphere (90–140 km) was investigated using stellar occultation measurements acquired by the SPICAV experiment on board Venus Express. The SPICAV ultraviolet channel provides CO2 local density and temperature vertical profiles with a vertical resolution of View the MathML source of both the southern and the northern hemispheres on the nightside (18:00-06:00 hr local time). A permanent layer of warm air is observed at the mesopause in the altitude range 90–100 km. Temperature then decreases with increasing altitude reaching a minimum value around 125 km. Spatial and temporal changes in the thermal structure have been analyzed. Local time variations dominate the structure of Venus atmosphere at these altitudes: temperatures show an increase of View the MathML source on the morning side compared to the evening side. The homopause altitude was also determined; it varies between 119 and 138 km of altitude, increasing from the evening side to the morning side. SPICAV temperature profiles were compared to several literature results from ground-based observations, previous spacecraft missions and the Venus Express mission.

Published
2015
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43. Mars’ water vapor mapping by the SPICAM IR spectrometer: Five martian years of observations

Author

Franck Montmessin, Jean-Loup Bertaux, Michael D. Smith, Anna Fedorova, Alexander Rodin, Alexander Trokhimovskiy, Oleg Korablev, Space Research Institute of the Russian Academy of Sciences (IKI), Russian Academy of Sciences [Moscow] (RAS), Moscow Institute of Physics and Technology [Moscow] (MIPT), PLANETO - LATMOS, Laboratoire Atmosphères, Milieux, Observations Spatiales (LATMOS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), and NASA Goddard Space Flight Center (GSFC)

Subjects
[PHYS.PHYS.PHYS-AO-PH]Physics [physics]/Physics [physics]/Atmospheric and Oceanic Physics [physics.ao-ph], Martian, Atmosphere, Mars, Astronomy and Astrophysics, Atmosphere of Mars, Mars Exploration Program, Albedo, Atmospheric sciences, Aerosol, 13. Climate action, Space and Planetary Science, Dust storm, Environmental science, Abundances, Spectroscopy, Water vapor
Abstract

The SPICAM IR instrument on the Mars Express mission continuously observes the water vapor in the martian atmosphere starting from 2004 in the 1.38-μm spectral band. The water vapor column abundance is retrieved from nadir observations to characterize its spatial, seasonal and interannual variations. A reference set of SPICAM water vapor column abundances (zonally averaged) covering the time period from 2004 to 2013 (martian years 27–31) is available for a grid of 2° Ls × 2° latitude, along with an average reference map of water vapor abundance combining all the martian years of Mars Express observations. Compared to the previous data retrieval by Fedorova et al. (Fedorova, A., Korablev, O., Bertaux, J.L., Rodin, A., Kiselev, A., Perrier, S. [2006]. J. Geophys. Res. 111, E09S08) the new processing algorithm includes many improvements concerning the calibration and assumed parameters. A major improvement is the account for aerosol scattering based on dust and water ice cloud optical depths measured by THEMIS/Mars Odyssey (Smith, M.D. [2009]. Icarus 202, 444–452). The account for multiple scattering by aerosol particles increases the retrieved water vapor amount by ∼10% in polar areas during summer, and up to 60–70% for large solar zenith angles. The sensitivity of the results to aerosol properties, surface albedo, solar spectrum, and water vapor vertical distribution has also been studied. The retrieved water vapor reveals nominal annual cycle with maximum abundance of about 60–70 pr. μm for the Northern summer and ∼20 pr. μm for the Southern summer. The annual average amount of water has been estimated to be of 10–20 pr. μm, in agreement with other measurements. From year to year the seasonal cycle of water vapor abundance is very stable. An observed decrease during the MY 28 global dust storm cannot be fully attributed to the masking effect of dust, and indicates a real decrease of water amount near or above the surface. No evidence of diurnal variation of column water vapor amount was found, even though the 1.38-μm measurements are sensitive to the few lowermost kilometers above the surface.

Published
2015
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44. Random Migration Assays of Mammalian Cells and Quantitative Analyses of Single Cell Trajectories

Author

Irene Dang, Alexis Gautreau, Laboratoire de Biochimie de l'Ecole polytechnique (BIOC), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Department of Systems Pharmacology and Translational Therapeutics (DSPTT), University of Pennsylvania [Philadelphia], Department of Biological and Medical Physics, and Moscow Institute of Physics and Technology [Moscow] (MIPT)

Subjects
0301 basic medicine, Cell, Motility, [SDV.CAN]Life Sciences [q-bio]/Cancer, Speed, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Directionality, Biology, Random migration, Persistence, Extracellular matrix, MSD, 03 medical and health sciences, 0302 clinical medicine, medicine, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Cell migration, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Immune surveillance, Cell biology, Cell tracking, 030104 developmental biology, medicine.anatomical_structure, Autocorrelation, Wound healing, 030217 neurology & neurosurgery
Abstract

International audience; Cell migration is essential to many biological processes such as embryonic development, immune surveillance and wound healing. Random cell migration refers to the intrinsic ability of cells to migrate, often called cell motility. This basal condition contrasts with directed cell migration, where cells migrate toward a chemical or physical cue. Unlike Brownian particles, however, randomly migrating cells exhibit a directional persistence, i.e., they are more likely to sustain the movement in the direction they previously took than to change, even if this direction is randomly chosen in an isotropic environment. Here we describe how to set up time-lapse recording of mammalian cells freely moving on a two-dimensional surface coated with extracellular matrix proteins, how to acquire single cell trajectories from movies and how to extract key parameters that characterize cell motility, such as cell speed, directionality, mean square displacement, and directional persistence.

Published
2018
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45. Scale magnetic effect in quantum electrodynamics and the Wigner-Weyl formalism

Author

M. A. Zubkov, M. N. Chernodub, Laboratoire de Mathématiques et Physique Théorique (LMPT), Université de Tours-Centre National de la Recherche Scientifique (CNRS), Laboratory of Physics of Living Matter [Vladivostok], School of Biomedicine [Vladivostok], Far Eastern Federal University (FEFU)-Far Eastern Federal University (FEFU), Institute of Theoretical and Experimental Physics [Moscow] (ITEP), National Research Center 'Kurchatov Institute' (NRC KI), Moscow Institute of Physics and Technology [Moscow] (MIPT), and Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
High Energy Physics - Theory, Conformal anomaly, FOS: Physical sciences, Conformal map, General Relativity and Quantum Cosmology (gr-qc), 01 natural sciences, General Relativity and Quantum Cosmology, Hall effect, Quantum mechanics, Mesoscale and Nanoscale Physics (cond-mat.mes-hall), Quantum Anomalies, 0103 physical sciences, 010306 general physics, [PHYS.COND.CM-MSQHE]Physics [physics]/Condensed Matter [cond-mat]/Mesoscopic Systems and Quantum Hall Effect [cond-mat.mes-hall], Physics, Condensed Matter - Mesoscale and Nanoscale Physics, 010308 nuclear & particles physics, Space time, Fermion, Magnetic field, Massless particle, High Energy Physics - Theory (hep-th), [PHYS.HPHE]Physics [physics]/High Energy Physics - Phenomenology [hep-ph], Quantum electrodynamics, Transport properties, Quantum Electrodynamics, [PHYS.GRQC]Physics [physics]/General Relativity and Quantum Cosmology [gr-qc], Electric current
Abstract

The Scale Magnetic Effect (SME) is the generation of electric current due to conformal anomaly in external magnetic field in curved spacetime. The effect appears in a vacuum with electrically charged massless particles. Similarly to the Hall effect, the direction of the induced anomalous current is perpendicular to the direction of the external magnetic field $\bf B$ and to the gradient of the conformal factor $\tau$, while the strength of the current is proportional to the beta function of the theory. In massive electrodynamics the SME remains valid, but the value of the induced current differs from the current generated in the system of massless fermions. In the present paper we use the Wigner--Weyl formalism to demonstrate that in accordance with the decoupling property of heavy fermions the corresponding anomalous conductivity vanishes in the large-mass limit with $m^2 \gg |e {\bf B}|$ and $m \gg |\nabla \tau|$., Comment: 12 pages, accepted for publication in Phys.Rev.D

Published
2017
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46. RapidRMSD: rapid determination of RMSDs corresponding to motions of flexible molecules

Author

Grégoire Danoy, Petr Popov, Angelo Migliosi, Emilie Neveu, Pascal Bouvry, Xavier Besseron, Sergei Grudinin, Alexandre Hoffmann, Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Laboratoire Jean Kuntzmann (LJK ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Université de Lausanne = University of Lausanne (UNIL), Moscow Institute of Physics and Technology [Moscow] (MIPT), Computer Science and Communications Research Unit [Luxembourg] (CSC), Laboratory of Advanced Software SYstems [Luxembourg] (LASSY), Université du Luxembourg (Uni.lu)-Université du Luxembourg (Uni.lu), and Université de Lausanne (UNIL)

Subjects
0301 basic medicine, Statistics and Probability, Computer science, Protein Conformation, Initialization, Molecular Dynamics Simulation, 01 natural sciences, Biochemistry, Molecular conformation, 03 medical and health sciences, Molecular dynamics, Motion, Protein structure, 0103 physical sciences, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Cluster analysis, Pliability, Molecular Biology, Quantitative Biology::Biomolecules, Principal Component Analysis, 010304 chemical physics, Computational Biology, Proteins, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Computer Science Applications, Computational Mathematics, 030104 developmental biology, Computational Theory and Mathematics, Structural biology, Docking (molecular), Principal component analysis, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Algorithm, Algorithms, Software
Abstract

Motivation The root mean square deviation (RMSD) is one of the most used similarity criteria in structural biology and bioinformatics. Standard computation of the RMSD has a linear complexity with respect to the number of atoms in a molecule, making RMSD calculations time-consuming for the large-scale modeling applications, such as assessment of molecular docking predictions or clustering of spatially proximate molecular conformations. Previously, we introduced the RigidRMSD algorithm to compute the RMSD corresponding to the rigid-body motion of a molecule. In this study, we go beyond the limits of the rigid-body approximation by taking into account conformational flexibility of the molecule. We model the flexibility with a reduced set of collective motions computed with e.g. normal modes or principal component analysis. Results The initialization of our algorithm is linear in the number of atoms and all the subsequent evaluations of RMSD values between flexible molecular conformations depend only on the number of collective motions that are selected to model the flexibility. Therefore, our algorithm is much faster compared to the standard RMSD computation for large-scale modeling applications. We demonstrate the efficiency of our method on several clustering examples, including clustering of flexible docking results and molecular dynamics (MD) trajectories. We also demonstrate how to use the presented formalism to generate pseudo-random constant-RMSD structural molecular ensembles and how to use these in cross-docking. Availability and implementation We provide the algorithm written in C++ as the open-source RapidRMSD library governed by the BSD-compatible license, which is available at http://team.inria.fr/nano-d/software/RapidRMSD/. The constant-RMSD structural ensemble application and clustering of MD trajectories is available at http://team.inria.fr/nano-d/software/nolb-normal-modes/. Supplementary information Supplementary data are available at Bioinformatics online.

Published
2017
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47. Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2

Author

Sergei Grudinin, Maria Kadukova, Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Laboratoire Jean Kuntzmann (LJK ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), and Moscow Institute of Physics and Technology [Moscow] (MIPT)

Subjects
0301 basic medicine, Computer science, Protein Conformation, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Receptors, Cytoplasmic and Nuclear, Computational biology, Crystallography, X-Ray, Ligands, 01 natural sciences, ensemble docking, Autodock vina, Small Molecule Libraries, 03 medical and health sciences, Computational chemistry, Drug Discovery, scoring function, Humans, Physical and Theoretical Chemistry, Receptor, Databases, Protein, Lead Finder, Binding Sites, protein-ligand docking, Small molecule, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, 0104 chemical sciences, Computer Science Applications, Molecular Docking Simulation, 010404 medicinal & biomolecular chemistry, 030104 developmental biology, Protein–ligand docking, Searching the conformational space for docking, Docking (molecular), Drug Design, Computer-Aided Design, Farnesoid X receptor, flexible docking, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], D3R, Software, Protein Binding
Abstract

International audience; The 2016 D3R Grand Challenge 2 provided an opportunity to test multiple protein-ligand docking protocols on a set of ligands bound to farnesoid X receptor that has many available experimental structures. We participated in the Stage 1 of the Challenge devoted to the docking pose predictions, with the mean RMSD value of our submission poses of 2.9 Å. Here we present a thorough analysis of our docking predictions made with AutoDock Vina and the Convex-PL rescoring potential by reproducing our submission protocol and running a series of additional molecular docking experiments. We conclude that a correct receptor structure, or more precisely, the structure of the binding pocket, plays the crucial role in the success of our docking studies. We have also noticed the important role of a local ligand geometry, which seems to be not well discussed in literature. We succeed to improve our results up to the mean RMSD value of 2.15 – 2.33 Å dependent on the models of the ligands, if docking these to all available homologous receptors. Overall, for docking of ligands of diverse chemical series we suggest to perform docking of each of the ligands to a set of multiple receptors that are homologous to the target.

Published
2017
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48. Asymptotics of Green function for the linear waves equations in a domain with a non-uniform bottom

Author

A. Yu. Anikin, Michel Rouleux, S. Yu. Dobrokhotov, Vladimir E. Nazaikinskii, Moscow Institute of Physics and Technology [Moscow] (MIPT), institute for Problems in Mechanics [Moscow], Russian Academy of Sciences [Moscow] (RAS), CPT - E8 Dynamique quantique et analyse spectrale, Centre de Physique Théorique - UMR 7332 (CPT), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), and Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Physics, Operator (physics), [PHYS.MPHY]Physics [physics]/Mathematical Physics [math-ph], 010102 general mathematics, Mathematical analysis, FOS: Physical sciences, Harmonic (mathematics), Mathematical Physics (math-ph), 01 natural sciences, Electronic mail, 010101 applied mathematics, Quadratic equation, Free surface, Boundary value problem, 0101 mathematics, Constant (mathematics), Mathematical Physics, Convergent series
Abstract

International audience; We consider the linear problem for water-waves created by sources on the bottom and the free surface in a 3-D basin having slowly varying profile $z=-D(x)$. The fluid verifies Euler-Poisson equations. These (non-linear) equations have been given a Hamiltonian form by Zakharov, involving canonical variables $(\xi(x,t),\eta(x,t))$ describing the dynamics of the free surface; variables $(\xi,\eta)$ are related by the free surface Dirichlet-to-Neumann (DtN) operator. For a single variable $x\in{\bf R}$ and constant depth, DtN operator was explicitely computed in terms of a convergent series. Here we neglect quadratic terms in Zakharov equations, and consider the linear response to a disturbance of $D(x)$ harmonic in time when the wave-lenght is small compared to the depth of the basin. We solve the Green function problem for a matrix-valued DtN operator, at the bottom and the free-surface.

Published
2017
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49. HermiteFit: fast-fitting atomic structures into a low-resolution density map using three-dimensional orthogonal Hermite functions

Author

Georgy Derevyanko, Sergei Grudinin, Institute of Complex Systems (ICS), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association-Helmholtz-Gemeinschaft = Helmholtz Association, Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Moscow Institute of Physics and Technology [Moscow] (MIPT), Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Kuntzmann (LJK), Centre National de la Recherche Scientifique (CNRS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Université Joseph Fourier - Grenoble 1 (UJF)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Centre National de la Recherche Scientifique (CNRS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Université Joseph Fourier - Grenoble 1 (UJF)-Université Pierre Mendès France - Grenoble 2 (UPMF), ANR-11-MONU-0006,PEPSI,Expansions Polynomiales de Structures de Protéines et Interactions(2011), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Laboratoire Jean Kuntzmann (LJK ), and Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])

Subjects
Hermite spline, Protein Conformation, Fast Fourier transform, Basis function, density fitting, Cubic Hermite spline, symbols.namesake, [INFO.INFO-TS]Computer Science [cs]/Signal and Image Processing, Structural Biology, Hermite interpolation, HermiteFit, [CHIM.CRIS]Chemical Sciences/Cristallography, Cryo-EM, [INFO.INFO-MS]Computer Science [cs]/Mathematical Software [cs.MS], Mathematics, Crystallography, Hermite polynomials, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], spherical harmonics, Spherical harmonics, Chaperonin 60, General Medicine, fast Fourier transform, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Hermite orthogonal polynomials, Fourier transform, symbols, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Conotoxins, Algorithm, Algorithms
Abstract

HermiteFit, a novel algorithm for fitting a protein structure into a low-resolution electron-density map, is presented. The algorithm accelerates the rotation of the Fourier image of the electron density by using three-dimensional orthogonal Hermite functions. As part of the new method, an algorithm for the rotation of the density in the Hermite basis and an algorithm for the conversion of the expansion coefficients into the Fourier basis are presented.HermiteFitwas implemented using the cross-correlation or the Laplacian-filtered cross-correlation as the fitting criterion. It is demonstrated that in the Hermite basis the Laplacian filter has a particularly simple form. To assess the quality of density encoding in the Hermite basis, an analytical way of computing the crystallographicRfactor is presented. Finally, the algorithm is validated using two examples and its efficiency is compared with two widely used fitting methods,ADP_EMandcoloresfrom theSituspackage.HermiteFitwill be made available at http://nano-d.inrialpes.fr/software/HermiteFit or upon request from the authors.

Published
2014
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50. Collapse of superconductivity in a hybrid tin–graphene Josephson junction array

Author

Hadi Arjmandi-Tash, Vincent Bouchiat, Adrien Allain, Konstantin S. Tikhonov, Benjamin Sacépé, Zheng Han, Mikhail Feigel'man, Systèmes hybrides de basse dimensionnalité (HYBRID), Institut Néel (NEEL), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Dept of Condensed Matter Physics, Weizmann Institute of Science, Weizmann Institute of Science [Rehovot, Israël], L.D. Landau Institute for Theoretical Physics of RAS, Russian Academy of Sciences [Moscow] (RAS), Moscow Institute of Physics and Technology [Moscow] (MIPT), and Nano-Electronique Quantique et Spectroscopie (QuNES)

Subjects
Quantum phase transition, Physics, Superconductivity, Josephson effect, Condensed matter physics, Condensed Matter - Superconductivity, graphene, FOS: Physical sciences, General Physics and Astronomy, Superconductivity (cond-mat.supr-con), Phase qubit, Pi Josephson junction, josephson junction, SIT, Condensed Matter::Superconductivity, Superconducting tunnel junction, Superconducting quantum computing, Critical field, [PHYS.COND.CM-MSQHE]Physics [physics]/Condensed Matter [cond-mat]/Mesoscopic Systems and Quantum Hall Effect [cond-mat.mes-hall]
Abstract

When a Josephson junction array is built with hybrid superconductor/metal/superconductor junctions, a quantum phase transition from a superconducting to a two-dimensional (2D) metallic ground state is predicted to happen upon increasing the junction normal state resistance. Owing to its surface-exposed 2D electron gas and its gate-tunable charge carrier density, graphene coupled to superconductors is the ideal platform to study the above-mentioned transition between ground states. Here we show that decorating graphene with a sparse and regular array of superconducting nanodisks enables to continuously gate-tune the quantum superconductor-to-metal transition of the Josephson junction array into a zero-temperature metallic state. The suppression of proximity-induced superconductivity is a direct consequence of the emergence of quantum fluctuations of the superconducting phase of the disks. Under perpendicular magnetic field, the competition between quantum fluctuations and disorder is responsible for the resilience at the lowest temperatures of a superconducting glassy state that persists above the upper critical field. Our results provide the entire phase diagram of the disorder and magnetic field-tuned transition and unveil the fundamental impact of quantum phase fluctuations in 2D superconducting systems., 25 pages, 6 figures

Published
2014
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