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

1. Multi-parametric modeling of solid sample heating by nanosecond laser pulses in application for nano-ablation

Author: J.-L. Lacour, Michel Tabarant, Frédéric Chartier, Chirelle Jabbour, A. Semerok, S.V. Fomichev, Service d'études analytiques et de réactivité des surfaces ( SEARS ), Département de Physico-Chimie ( DPC ), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), National Research Centre 'Kurchatov Institute' ( NRC KI ), University of Moscow, Moscow Institute of Physics and Technology [Moscow] ( MIPT ), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Service d'études analytiques et de réactivité des surfaces (SEARS), Département de Physico-Chimie (DPC), CEA-Direction des Energies (ex-Direction de l'Energie Nucléaire) (CEA-DES (ex-DEN)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-CEA-Direction des Energies (ex-Direction de l'Energie Nucléaire) (CEA-DES (ex-DEN)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, National Research Center 'Kurchatov Institute' (NRC KI), and Moscow Institute of Physics and Technology [Moscow] (MIPT)
Subjects: Materials science, Field (physics), Near and far field, 02 engineering and technology, Thermal diffusivity, 01 natural sciences, 7. Clean energy, Analytical Chemistry, Optics, Thermal conductivity, Laser heating model, Nano, Laser nano-ablation, [PHYS.PHYS.PHYS-INS-DET]Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], Instrumentation, [ PHYS.PHYS.PHYS-INS-DET ] Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], Spectroscopy, [PHYS]Physics [physics], Range (particle radiation), [ PHYS ] Physics [physics], business.industry, 010401 analytical chemistry, Pulse duration, 021001 nanoscience & nanotechnology, Atomic and Molecular Physics, and Optics, 0104 chemical sciences, Near-field, Attenuation coefficient, 0210 nano-technology, business
Abstract: International audience; Multi-parametric theoretical studies to analyze the effect of both the matter properties (absorption coefficient, thermal conductivity and diffusivity) and the heating field parameters (spatial distribution and pulse duration) on the resulted temperature distribution are presented. For heating in sub-micrometric range (< 1 $\mu$m), a low dependence of heating temperature distribution on the sample thermal properties and,heating source duration was observed. Nano-ablation thresholds are found to be increasing inversely with heating source dimensions. The simulation results demonstrated a good agreement with the nanometer-size craters (100 nm diameters, 10 nm depth) obtained experimentally with a tip-enhanced near-field ablation (4 ns laser pulse duration, 266 nm wavelength) of Si- and Au-samples.
Published: 2017
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2. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment

Author: Eichiro Ichiishi, Dmitri Beglov, Bernard Maigret, Gyu Rie Lee, Artem B. Mamonov, Shoshana J. Wodak, Jonathan C. Fuller, Dima Kozakov, Jong Young Joung, Petr Popov, Xiaofeng Yu, Keehyoung Joo, João P. G. L. M. Rodrigues, Anna Vangone, Koen M. Visscher, Xiaoqin Zou, Paul A. Bates, Andriy Kryshtafovych, Shourya S. Roy Burman, Daisuke Kihara, Romina Oliva, Efrat Ben-Zeev, Jeffrey J. Gray, Yang Shen, Li C. Xue, Sameer Velankar, Emilie Neveu, Shruthi Viswanath, Dina Schneidman-Duhovny, Juan Esquivel-Rodríguez, Mieczyslaw Torchala, Amit Roy, Alexandre M. J. J. Bonvin, David R. Hall, Tanggis Bohnuud, Xusi Han, David W. Ritchie, Ron Elber, Daisuke Kuroda, Zhiwei Ma, Joan Segura, Carlos A. Del Carpio, Nicholas A. Marze, Jong Yun Kim, Andrej Sali, Petras J. Kundrotas, Ezgi Karaca, Neil J. Bruce, Chaok Seok, Panagiotis L. Kastritis, Shen You Huang, Ilya A. Vakser, Lim Heo, Sanbo Qin, Raphael A. G. Chaleil, Adrien S. J. Melquiond, Miguel Romero-Durana, Anisah W. Ghoorah, Surendra S. Negi, Andrey Tovchigrechko, Françoise Ochsenbein, Narcis Fernandez-Fuentes, Liming Qiu, Miriam Eisenstein, Mehdi Nellen, Marie-Dominique Devignes, Lenna X. Peterson, Jinchao Yu, Minkyung Baek, Brian G. Pierce, Hasup Lee, Toshiyuki Oda, Rebecca C. Wade, Raphael Guerois, Juan Fernández-Recio, Iain H. Moal, Edrisse Chermak, Sergei Grudinin, Sangwoo Park, Ivan Anishchenko, Chengfei Yan, Thom Vreven, Kentaro Tomii, Bing Xia, Hyung Rae Kim, Chiara Pallara, Jooyoung Lee, Kazunori D. Yamada, Xianjin Xu, Kenichiro Imai, Zhiping Weng, Luigi Cavallo, Tyler M. Borrman, Jianlin Cheng, Marc F. Lensink, Huan-Xiang Zhou, Jilong Li, Gydo C. P. van Zundert, Brian Jiménez-García, Tsukasa Nakamura, Scott E. Mottarella, Sandor Vajda, Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq] ( IRI ), Université de Lille, Sciences et Technologies-Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique ( CNRS ), European Molecular Biology Laboratory, European Bioinformatics Institute, Genome Center [UC Davis], University of California at Davis, Research Support Computing [Columbia], University of Missouri-Columbia, Bioinformatics Consortium and Department of Computer Science [Columbia], Department of Bioengineering and Therapeutic Sciences, University of California [San Francisco] ( UCSF ), Department of Pharmaceutical Chemistry, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, University of California [San Francisco] ( UCSF ) -California Institute for Quantitative Biosciences, GN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit, Centro Nacional de Biotecnología (CSIC), Institute of Biological, Environmental and Rural Sciences ( IBERS ), Institute for Computational Engineering and Sciences [Austin] ( ICES ), University of Texas at Austin [Austin], Department of Computer Science, Department of Chemistry, 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 ), Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Institut National Polytechnique de Grenoble ( INPG ), Moscow Institute of Physics and Technology [Moscow] ( MIPT ), Seoul National University [Seoul], Florida State University [Tallahassee] ( FSU ), 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 ), University of Mauritius, Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, G-INCPM, Weizmann Institute of Science, Chemical Research Support [Rehovot], Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch ( UTMB ), Program in Bioinformatics and Integrative Biology [Worcester], University of Massachusetts Medical School [Worcester] ( UMASS ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Bijvoet Center for Biomolecular Research [Utrecht], Utrecht University [Utrecht], Dalton Cardiovascular Research Center [Columbia], Department of Computer Science [Columbia], Informatics Intitute, Department of Biochemistry, University of Missouri, UNIVERSITY OF MISSOURI, Toyota Technological Institute at Chicago [Chicago] ( TTIC ), Department of Biological Sciences, Purdue University, Purdue University [West Lafayette], Department of Computer Science [Purdue], Bioinformatics and Computational Biosciences Branch, Rocky Mountain Laboratories, Molecular and Cellular Modeling Group, Heidelberg Institute of Theoretical Studies, Center for Molecular Biology ( ZMBH ), Universität Heidelberg [Heidelberg], Interdisciplinary Center for Scientiﬁc Computing ( IWR ), Department of Molecular Biosciences [Lawrence], University of Kansas [Lawrence] ( KU ), Computational Biology Research Center ( CBRC ), National Institute of Advanced Industrial Science and Technology ( AIST ), Graduate School of Frontier Sciences, The University of Tokyo, Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center - Centro Nacional de Supercomputacion ( BSC - CNS ), Center for In-Silico Protein Science, Korea Institute for Advanced Study ( KIAS ), Center for Advanced Computation, Department of Biomedical Engineering [Boston], Boston University [Boston] ( BU ), Institute of Biological Diversity, International Pacific Institute of Indiana, Drosophila Genetic Resource Center, Kyoto Institute of Technology, International University of Health and Welfare Hospital ( IUHW Hospital ), International University of Health and Welfare Hospital, Department of Chemical and Biomolecular Engineering [Baltimore], Johns Hopkins University ( JHU ), Program in Molecular Biophysics [Baltimore], King Abdullah University of Science and Technology ( KAUST ), University of Naples, J Craig Venter Institute, Structural Biology Research Center, VIB, 1050 Brussels, Belgium, Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq] (IRI), Université de Lille, Sciences et Technologies-Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique (CNRS), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), University of Missouri [Columbia] (Mizzou), University of Missouri System, University of California [San Francisco] (UC San Francisco), Centro Nacional de Biotecnología [Madrid] (CNB-CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institute of Biological, Environmental and Rural Sciences (IBERS), Institute for Computational Engineering and Sciences [Austin] (ICES), Algorithms for Modeling and Simulation of Nanosystems (NANO-D), 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), Seoul National University [Seoul] (SNU), Florida State University [Tallahassee] (FSU), Computational Algorithms for Protein Structures and Interactions (CAPSID), 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), Biomolecular Modelling Laboratory [London], The Francis Crick Institute [London], Weizmann Institute of Science [Rehovot, Israël], The University of Texas Medical Branch (UTMB), University of Massachusetts Medical School [Worcester] (UMASS), University of Massachusetts System (UMASS)-University of Massachusetts System (UMASS), 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), Assemblage moléculaire et intégrité du génome (AMIG), 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), University of Missouri System-University of Missouri System, Toyota Technological Institute at Chicago [Chicago] (TTIC), Department of Biological Sciences [Lafayette IN], Heidelberg Institute for Theoretical Studies (HITS ), Center for Molecular Biology (ZMBH), Universität Heidelberg [Heidelberg] = Heidelberg University, Interdisciplinary Center for Scientiﬁc Computing (IWR), University of Kansas [Lawrence] (KU), Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), The University of Tokyo (UTokyo), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Korea Institute for Advanced Study (KIAS), Boston University [Boston] (BU), International University of Health and Welfare Hospital (IUHW Hospital), Johns Hopkins University (JHU), King Abdullah University of Science and Technology (KAUST), University of Naples Federico II = Università degli studi di Napoli Federico II, J. Craig Venter Institute, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Droit et Santé-Université de Lille, Sciences et Technologies, University of California-University of California, University of California [San Francisco] (UCSF), 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), 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), University of Naples Federico II, Barcelona Supercomputing Center, NMR Spectroscopy, and Sub NMR Spectroscopy
Subjects: 0301 basic medicine, Protein Conformation, alpha-Helical, Protein Folding, Computer science, International Cooperation, Amino Acid Motifs, Oligomer state, Homoprotein, DATA-BANK, computer.software_genre, Molecular Docking Simulation, Biochemistry, CAPRI Round 30, DESIGN, Structural Biology, ALIGN, Blind prediction, AFFINITY, Protein interaction, Enginyeria biomèdica [Àrees temàtiques de la UPC], ZDOCK, Oligomer State, computer.file_format, Articles, Protein structure prediction, Proteïnes--Investigació, 3. Good health, WEB SERVER, CASP, Thermodynamics, Data mining, CAPRI, Protein docking, Molecular Biology, Algorithms, INTERFACES, Protein Binding, [ INFO.INFO-MO ] Computer Science [cs]/Modeling and Simulation, Bioinformatics, STRUCTURAL BIOLOGY, Computational biology, Molecular Dynamics Simulation, Article, 03 medical and health sciences, [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], Heteroprotein, Humans, Protein binding, Macromolecular docking, Protein Interaction Domains and Motifs, Homology modeling, ALGORITHM, Protein-protein docking, Internet, Binding Sites, Models, Statistical, 030102 biochemistry & molecular biology, Bacteria, Sequence Homology, Amino Acid, Computational Biology, Proteins, Protein Data Bank, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Protein Structure, Tertiary, 030104 developmental biology, Structural biology, Docking (molecular), Protein structure, Protein Conformation, beta-Strand, Protein Multimerization, oligomer state, blind prediction, protein interaction, protein docking, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Software
Abstract: We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein–protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy. We are most grateful to the PDBe at the European Bioinformatics Institute in Hinxton, UK, for hosting the CAPRI website. Our deepest thanks go to all the structural biologists and to the following structural genomics initiatives: Northeast Structural Genomics Consortium, Joint Center for Structural Genomics, NatPro PSI:Biology, New York Structural Genomics Research Center, Midwest Center for Structural Genomics, Structural Genomics Consortium, for contributing the targets for this joint CASP-CAPRI experiment. MFL acknowledges support from the FRABio FR3688 Research Federation “Structural & Functional Biochemistry of Biomolecular Assemblies.”
Published: 2016
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3. 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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4. The CO2 continuum absorption in the 1.10- and 1.18-μm windows on Venus from Maxwell Montes transits by SPICAV IR onboard Venus express

Author: Colin Wilson, Jean-Loup Bertaux, Oleg Korablev, Bruno Bézard, Anna Fedorova, Space Research Institute of the Russian Academy of Sciences ( IKI ), Russian Academy of Sciences [Moscow] ( RAS ), Moscow Institute of Physics and Technology [Moscow] ( MIPT ), 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 Diderot - Paris 7 ( UPD7 ) -Centre National de la Recherche Scientifique ( CNRS ), IMPEC - 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 ), Department of Atmospheric, Oceanic and Planetary Physics [Oxford] ( AOPP ), University of Oxford [Oxford], Space Research Institute of the Russian Academy of Sciences (IKI), Russian Academy of Sciences [Moscow] (RAS), Moscow Institute of Physics and Technology [Moscow] (MIPT), 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), 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), Department of Atmospheric, Oceanic and Planetary Physics [Oxford] (AOPP), and University of Oxford
Subjects: Atmospheres, Opacity, [PHYS.ASTR.EP]Physics [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], Continuum (design consultancy), [SDU.ASTR.EP]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], Venus, Astrophysics, Atmospheric sciences, Atmosphere, Altitude, Radiative transfer, Emissivity, Mixing ratio, Physics, Venus Express, biology, Infrared observations, Astronomy and Astrophysics, biology.organism_classification, [ SDU.ASTR.EP ] Sciences of the Universe [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], [ PHYS.ASTR.EP ] Physics [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], 13. Climate action, Space and Planetary Science, Composition
Abstract: One of the difficulties in modeling Venus' nightside atmospheric windows is the need to apply CO2 continuum opacity due to collision-induced CO2 bands and/or extreme far wings of strong allowed CO2 bands. Characterizing the CO2 continuum absorption at near-IR wavelengths as well as searching for a possible vertical gradient of minor species near the surface require observations over different surface elevations. The largest change in altitude occurs during a passage above Maxwell Montes at high northern latitudes. In 2011, 2012 and 2013 the SPICAV instrument aboard the Venus Express satellite performed three sets of observations over Maxwell Montes with variation of surface altitude from -2 to 9 km in the 1.10, 1.18 and 1.28-μm windows. The retrieved CO2 continuum absorption for the 1.10- and 1.18-μm windows varies from 0.29 to 0.66×10-9 cm-1 amagat-2 and from 0.30 to 0.78×10-9 cm-1 amagat-2, respectively, depending on the assumed input parameters. The retrieval is sensitive to possible variations of the surface emissivity. Our values fall between the results of Bezard et al., (2009, 2011) based on VIRTIS-M observations and laboratory measurements by Snels et al. (2014). We can also conclude that the continuum absorption at 1.28 μm can be constrained below 2.0×10-9 cm-1 amagat-2. Based on the 1.18 μm window the constant H2O mixing ratio varying from 25.7+1.4 -1.2 ppm to 29.4+1.6 -1.4 ppm has been retrieved assuming the surface emissivity of 0.95 and 0.6, respectively. No firm conclusion from SPICAV data about the vertical gradient of water vapor content at 10-20 km altitude could be drawn because of low signal-to-noise ratio and uncertainties in the surface emissivity. © 2014 Elsevier Ltd. All rights reserved.
Published: 2015
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5. Bone conducted responses in the neonatal rat auditory cortex

Author: Makarov, Roman, Sintsov, Mikhail, Valeeva, Guzel, Starikov, Pavel, Negrov, Dmitriy, Khazipov, Roustem, Kazan Federal University (KFU), Moscow Institute of Physics and Technology [Moscow] (MIPT), Institut de Neurobiologie de la Méditerranée [Aix-Marseille Université] (INMED - INSERM U1249), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Kazan Federal University #0671-2020-0059 and the Institut National de la Sante et de la Recherche Medicale (Laboratoire International Associe INSERM-KFU), and pellegrino, Christophe
Subjects: Auditory Cortex, Physiology, Science, Electric Stimulation, Inferior Colliculi, Article, Cochlea, Rats, Animals, Newborn, Developmental biology, otorhinolaryngologic diseases, Animals, Medicine, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], [SDV.NEU] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Rats, Wistar, Bone Conduction, Neuroscience
Abstract: International audience; Rats are born deaf and start hearing at the end of the second postnatal week, when the ear canals open and low-intensity sounds start to evoke responses in the auditory cortex. Here, using μECoG electrode arrays and intracortical silicon probe recordings, we found that bone-conducted (BC) sounds evoked biphasic responses in the auditory cortex starting from postnatal day (P) 8. The initial phase of these responses, generated by thalamocortical input, was followed by intracortical propagation within supragranular layers. BC-evoked responses co-localized with the responses evoked by electrical stimulation of the cochlea and the deepest layers of the inferior colliculus prior to onset of low-threshold hearing (P13), as well as with the responses evoked by high-frequency (30 kHz) lowintensity (70 dB) air-conducted sounds after that. Thus, BC signals reach high-frequency processing regions of the auditory cortex well before the onset of low-threshold hearing, reflecting early integrity of the auditory system.
Published: 2021
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6. The structure of groups of circle diffeomorphisms with the property of nonexpandable points being fixed

Author: Filimonov, Dmitry A., Kleptsyn, Victor A., Moscow Institute of Physics and Technology [Moscow] ( MIPT ), Institut de Recherche Mathématique de Rennes ( IRMAR ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST-École normale supérieure - Rennes ( ENS Rennes ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National des Sciences Appliquées ( INSA ) -Université de Rennes 2 ( UR2 ), Université de Rennes ( UNIV-RENNES ) -Centre National de la Recherche Scientifique ( CNRS ), Moscow Institute of Physics and Technology [Moscow] (MIPT), Institut de Recherche Mathématique de Rennes (IRMAR), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], [ MATH.MATH-DS ] Mathematics [math]/Dynamical Systems [math.DS], group action, dynamical system, circle diffeomorphism, Markov partition, 37E10, 37E30
Abstract: Translated from Funktsionalnyi Analiz i Ego Prilozheniya, Vol. 46, No. 3, pp. 38-61, 2012; International audience
Published: 2012
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7. Optimization in complex spaces with the Mixed Newton Method

Author: Bakhurin, Sergey, Hildebrand, Roland, Alkousa, Mohammad, Titov, Alexander, Huawei Technologies Co., Ltd [Moscow], 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), and Moscow Institute of Physics and Technology [Moscow] (MIPT)
Subjects: 32-08, 90C26, 65K05, 90C53, Optimization and Control (math.OC), FOS: Mathematics, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], Mathematics - Optimization and Control
Abstract: We propose a second-order method for unconditional minimization of functions $f(z)$ of complex arguments. We call it the Mixed Newton Method due to the use of the mixed Wirtinger derivative $\frac{\partial^2f}{\partial\bar z\partial z}$ for computation of the search direction, as opposed to the full Hessian $\frac{\partial^2f}{\partial(z,\bar z)^2}$ in the classical Newton method. The method has been developed for specific applications in wireless network communications, but its global convergence properties are shown to be superior on a more general class of functions $f$, namely sums of squares of absolute values of holomorphic functions. In particular, for such objective functions minima are surrounded by attraction basins, while the iterates are repelled from other types of critical points. We provide formulas for the asymptotic convergence rate and show that in the scalar case the method reduces to the well-known complex Newton method for the search of zeros of holomorphic functions. In this case, it exhibits generically fractal global convergence patterns., 20 pages
Published: 2022

8. 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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9. E-site drug specificity of the human pathogen Candida albicans ribosome

Author: Yury Zgadzay, Olga Kolosova, Artem Stetsenko, Cheng Wu, David Bruchlen, Konstantin Usachev, Shamil Validov, Lasse Jenner, Andrey Rogachev, Gulnara Yusupova, Matthew S. Sachs, Albert Guskov, Marat Yusupov, Yusupova, Gulnara, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Kazan Federal University (KFU), University of Groningen [Groningen], Texas A&M University [College Station], Kazan Scientific Centre of the Russian Academy of Sciences, Moscow Institute of Physics and Technology [Moscow] (MIPT), Joint Institute for Nuclear Research (JINR), and X-ray Crystallography
Subjects: Multidisciplinary, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], [SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], [SDV.MP.MYC] Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology
Abstract: Candida albicans is a widespread commensal fungus with substantial pathogenic potential and steadily increasing resistance to current antifungal drugs. It is known to be resistant to cycloheximide (CHX) that binds to the E–transfer RNA binding site of the ribosome. Because of lack of structural information, it is neither possible to understand the nature of the resistance nor to develop novel inhibitors. To overcome this issue, we determined the structure of the vacant C. albicans 80 S ribosome at 2.3 angstroms and its complexes with bound inhibitors at resolutions better than 2.9 angstroms using cryo–electron microscopy. Our structures reveal how a change in a conserved amino acid in ribosomal protein eL42 explains CHX resistance in C. albicans and forms a basis for further antifungal drug development.
Published: 2022
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10. Synthesis of Titanium Nitride Nanoparticles by Pulsed Laser Ablation in Different Aqueous and Organic Solutions

Author: Anton A. Popov, Gleb V. Tikhonowski, Pavel V. Shakhov, Elena A. Popova-Kuznetsova, Gleb I. Tselikov, Roman I. Romanov, Andrey M. Markeev, Sergey M. Klimentov, Andrei V. Kabashin, The National Research Nuclear University MEPhI (Moscow Engineering Physics Institute) [Moscow, Russia], 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: laser ablation in aqueous and organic solutions, [SPI]Engineering Sciences [physics], pulsed laser ablation in liquids, titanium nitride nanoparticles, XPS, EDX, General Chemical Engineering, General Materials Science
Abstract: International audience; Owing to a strong photothermal response in the near-IR spectral range and very low toxicity, titanium nitride (TiN) nanoparticles (NPs) synthesized by pulsed laser ablation in liquids (PLAL) present a novel appealing object for photo-induced therapy of cancer, but the properties of these NPs still require detailed investigation. Here, we have elaborated methods of femtosecond laser ablation from the TiN target in a variety of liquid solutions, including acetonitrile, dimethylformamide, acetone, water, and H2O2, to synthesize TiN NPs and clarify the effect of liquid type on the composition and properties of the formed NPs. The ablation in all solvents led to the formation of spherical NPs with a mean size depending on the liquid type, while the composition of the NPs ranged from partly oxidized TiN to almost pure TiO2, which conditioned variations of plasmonic peak in the region of relative tissue transparency (670–700 nm). The degree of NP oxidation depended on the solvent, with much stronger oxidation for NPs prepared in aqueous solutions (especially in H2O2), while the ablation in organic solvents resulted in a partial formation of titanium carbides as by-products. The obtained results contribute to better understanding of the processes in reactive PLAL and can be used to design TiN NPs with desired properties for biomedical applications.
Published: 2022
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11. 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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12. 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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13. Molecular mechanism of light-driven sodium pumping

Author: Kovalev, Kirill, Astashkin, Roman, Gushchin, Ivan, Orekhov, Philipp, Volkov, Dmytro, Zinovev, Egor, Marin, Egor, Rulev, Maksim, Alekseev, Alexey, Royant, Antoine, Carpentier, Philippe, Vaganova, Svetlana, Zabelskii, Dmitrii, Baeken, Christian, Sergeev, Ilya, Balandin, Taras, Bourenkov, Gleb, Carpena, Xavier, Boer, Roeland, Maliar, Nina, Borshchevskiy, Valentin, Büldt, Georg, Bamberg, Ernst, Gordeliy, Valentin, 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), Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow, Moscow Institute of Physics and Technology [Moscow] (MIPT), Biocatalyse (BIOCAT), Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-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)-Université Grenoble Alpes (UGA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), European Synchrotron Radiation Facility (ESRF), Institute of Complex Systems (ICS), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association-Helmholtz-Gemeinschaft = Helmholtz Association, European Molecular Biology Laboratory [Hamburg] (EMBL), Max-Planck-Institut für Biophysik - Max Planck Institute of Biophysics (MPIBP), Max-Planck-Gesellschaft, and ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017)
Subjects: Protein Folding, Rhodopsin, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Science, Sodium, Molecular Dynamics Simulation, Crystallography, X-Ray, Article, Bacterial Proteins, X-Ray Diffraction, Escherichia coli, lcsh:Q, ddc:500, Sodium-Potassium-Exchanging ATPase, lcsh:Science, Flavobacteriaceae, Ion transport, X-ray crystallography
Abstract: Nature Communications 11(1), 2137 (2020). doi:10.1038/s41467-020-16032-y, The light-driven sodium-pumping rhodopsin KR2 from Krokinobacter eikastus is the only non-proton cation active transporter with demonstrated potential for optogenetics. However, the existing structural data on KR2 correspond exclusively to its ground state, and show no sodium inside the protein, which hampers the understanding of sodium-pumping mechanism. Here we present crystal structure of the O-intermediate of the physiologically relevant pentameric form of KR2 at the resolution of 2.1 Å, revealing a sodium ion near the retinal Schiff base, coordinated by N112 and D116 of the characteristic NDQ triad. We also obtained crystal structures of D116N and H30A variants, conducted metadynamics simulations and measured pumping activities of putative pathway mutants to demonstrate that sodium release likely proceeds alongside Q78 towards the structural sodium ion bound between KR2 protomers. Our findings highlight the importance of pentameric assembly for sodium pump function, and may be used for rational engineering of enhanced optogenetic tools., Published by Nature Publishing Group UK, [London]
Published: 2020
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14. 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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15. Laser-Ablative Synthesis of Ultrapure Magneto-Plasmonic Core-Satellite Nanocomposites for Biomedical Applications

Author: Anton A. Popov, Zaneta Swiatkowska-Warkocka, Marta Marszalek, Gleb Tselikov, Ivan V. Zelepukin, Ahmed Al-Kattan, Sergey M. Deyev, Sergey M. Klimentov, Tatiana E. Itina, Andrei V. Kabashin, Moscow State Engineering Physics Institute (MEPhI), Laboratoire Lasers, Plasmas et Procédés photoniques (LP3), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), H. Niewodniczanski Institute of Nuclear Physics, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Moscow Institute of Physics and Technology [Moscow] (MIPT), Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry (IBCh RAS), Russian Academy of Sciences [Moscow] (RAS), 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: core-satellite, IR hyperthermia, iron, General Chemical Engineering, nanoparticles, laser ablation in liquids, gold, modeling, [SDV.IB]Life Sciences [q-bio]/Bioengineering, General Materials Science, [SPI.MAT]Engineering Sciences [physics]/Materials
Abstract: International audience; The combination of magnetic and plasmonic properties at the nanoscale promises the development of novel synergetic image-guided therapy strategies for the treatment of cancer and other diseases, but the fabrication of non-contaminated magneto-plasmonic nanocomposites suitable for biological applications is difficult within traditional chemical methods. Here, we describe a methodology based on laser ablation from Fe target in the presence of preliminarily ablated water-dispersed Au nanoparticles (NPs) to synthesize ultrapure bare (ligand-free) core-satellite nanostructures, consisting of large (several tens of nm) Fe-based core decorated by small (mean size 7.5 nm) Au NPs. The presence of the Fe-based core conditions a relatively strong magnetic response of the nanostructures (magnetization of >12.6 emu/g), while the Au NPs-based satellite shell provides a broad extinction peak centered at 550 nm with a long tale in the near-infrared to overlap with the region of relative tissue transparency (650–950 nm). We also discuss possible mechanisms responsible for the formation of the magnetic-plasmonic nanocomposites. We finally demonstrate a protocol to enhance colloidal stability of the core-satellites in biological environment by their coating with different polymers. Exempt of toxic impurities and combining strong magnetic and plasmonic responses, the formed core-satellite nanocomposites can be used in biomedical applications, including photo- and magneto-induced therapies, magnetic resonance imaging or photoacoustic imaging.
Published: 2022
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16. Structure and dynamics of the SARS‐CoV ‐2 envelope protein monomer

Author: Alexander Kuzmin, Philipp Orekhov, Roman Astashkin, Valentin Gordeliy, Ivan Gushchin, Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow, Moscow Institute of Physics and Technology [Moscow] (MIPT), 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), Institute of Biological Information Processing [Jülich] (IBI-7), and Jülich Center for Structural Biology [Jülich] (JuStruct)
Subjects: MESH: Humans, glycosylation, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], SARS-CoV-2, COVID-19, Biochemistry, molecular dynamics, Coronavirus Envelope Proteins, envelope protein, Protein Domains, Viral Envelope Proteins, MESH: Coronavirus Envelope Proteins, Structural Biology, ddc:570, MESH: Viral Envelope Proteins, membrane curvature, Humans, MESH: COVID-19, MESH: Protein Domains, membrane protein, palmitoylation, MESH: SARS-CoV-2, Molecular Biology
Abstract: International audience; Coronaviruses, especially severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), present an ongoing threat to human wellbeing. Consequently, elucidation of molecular determinants of their function and interaction with the host is an important task. Whereas some of the coronaviral proteins are extensively characterized, others remain understudied. Here, we use molecular dynamics simulations to analyze the structure and dynamics of the SARS-CoV-2 envelope (E) protein (a viroporin) in the monomeric form. The protein consists of the hydrophobic α-helical transmembrane domain (TMD) and amphiphilic α-helices H2 and H3, connected by flexible linkers. We show that TMD has a preferable orientation in the membrane, while H2 and H3 reside at the membrane surface. Orientation of H2 is strongly influenced by palmitoylation of cysteines Cys40, Cys43, and Cys44. Glycosylation of Asn66 affects the orientation of H3. We also observe that the monomeric E protein both generates and senses the membrane curvature, preferably localizing with the C-terminus at the convex regions of the membrane; the protein in the pentameric form displays these properties as well. Localization to curved regions may be favorable for assembly of the E protein oligomers, whereas induction of curvature may facilitate the budding of the viral particles. The presented results may be helpful for a better understanding of the function of the coronaviral E protein and viroporins in general, and for overcoming the ongoing SARS-CoV-2 pandemic.
Published: 2022
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17. 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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18. A versatile technology for colloidal crystal transfer using parylene coatings and hydrosoluble polymers

Author: Andrei A Ushkov, Olivier Dellea, Olivier Lebaigue, Olivier Poncelet, Isabelle Verrier, Yaya Lefkir, Yves Jourlin, Laboratoire Hubert Curien (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), Laboratoire d'Innovation pour les Technologies des Energies Nouvelles et les nanomatériaux (LITEN), Institut National de L'Energie Solaire (INES), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)
Subjects: Mechanics of Materials, Mechanical Engineering, digestive, oral, and skin physiology, [SPI.OPTI]Engineering Sciences [physics]/Optics / Photonic, General Materials Science, Bioengineering, General Chemistry, Electrical and Electronic Engineering, [SPI.NANO]Engineering Sciences [physics]/Micro and nanotechnologies/Microelectronics, complex mixtures, [SPI.MAT]Engineering Sciences [physics]/Materials
Abstract: We propose a novel versatile colloidal crystal transfer technique compatible with a wide range of water-insoluble substrates regardless of their size, material, and wettability. There are no inherent limitations on colloidal particles material and size. The method possibilities are demonstrated via the colloidal transfer on quartz, glass substrates with a flat and curved surface, and via the fabrication of 3D colloidal structure with 5 overlaid colloidal monolayers. The process occurs at a room temperature in water and is independent from the illumination conditions, which makes it ideal for experimental manipulations with sensitive functional substrates. We performed the nanosphere photolithography process on a photosensitive substrate with a transferred colloidal monolayer. The metallized hexagonal arrays of nanopores demonstrated a clear resonant plasmonic behavior. We believe that due to its high integration possibilities the proposed transfer technique will find applications in a large-area surface nanotexturing, plasmonics, and will speed up a device fabrication process.
Published: 2022
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19. Transition metal dichalcogenide nanospheres for high-refractive-index nanophotonics and biomedical theranostics

Author: Gleb I. Tselikov, Georgy A. Ermolaev, Anton A. Popov, Gleb V. Tikhonowski, Daria A. Panova, Alexey S. Taradin, Andrey A. Vyshnevyy, Alexander V. Syuy, Sergey M. Klimentov, Sergey M. Novikov, Andrey B. Evlyukhin, Andrei V. Kabashin, Aleksey V. Arsenin, Kostya S. Novoselov, Valentyn S. Volkov, Moscow Institute of Physics and Technology [Moscow] (MIPT), The National Research Nuclear University MEPhI (Moscow Engineering Physics Institute) [Moscow, Russia], Institute of Quantum Optics, Liebniz University Hannover, 30167 Hannover, Germany, Laboratoire Lasers, Plasmas et Procédés photoniques (LP3), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and University of Manchester [Manchester]
Subjects: [PHYS]Physics [physics], Molybdenum, Condensed Matter - Materials Science, Multidisciplinary, Condensed Matter - Mesoscale and Nanoscale Physics, Dewey Decimal Classification::500 | Naturwissenschaften::570 | Biowissenschaften, Biologie, Dewey Decimal Classification::000 | Allgemeines, Wissenschaft::000 | Informatik, Wissen, Systeme, transition metal dichalcogenides, Materials Science (cond-mat.mtrl-sci), FOS: Physical sciences, Water, 2D materials, [SPI]Engineering Sciences [physics], Refractometry, nanooptics, ddc:570, Mesoscale and Nanoscale Physics (cond-mat.mes-hall), ddc:000, laser ablation, ddc:500, Precision Medicine, Nanospheres, Dewey Decimal Classification::500 | Naturwissenschaften, Optics (physics.optics), Physics - Optics
Abstract: Recent developments in the area of resonant dielectric nanostructures has created attractive opportunities for the concentrating and manipulating light at the nanoscale and the establishment of new exciting field of all-dielectric nanophotonics. Transition metal dichalcogenides (TMDCs) with nanopatterned surfaces are especially promising for these tasks. Still, the fabrication of these structures requires sophisticated lithographic processes, drastically complicating application prospects. To bridge this gap and broaden the application scope of TMDC nanomaterials, we report here femtosecond laser-ablative fabrication of water-dispersed spherical TMDC (MoS2 and WS2) nanoparticles (NPs) of variable size (5 - 250 nm). Such nanoparticles demonstrate exciting optical and electronic properties inherited from TMDC crystals, due to preserved crystalline structure, which offers a unique combination of pronounced excitonic response and high refractive index value, making possible a strong concentration of electromagnetic field in the nanoparticles. Furthermore, such nanoparticles offer additional tunability due to hybridization between the Mie and excitonic resonances. Such properties bring to life a number of nontrivial effects, including enhanced photoabsorption and photothermal conversion. As an illustration, we demonstrate that the nanoparticles exhibit a very strong photothermal response, much exceeding that of conventional dielectric nanoresonators based on Si. Being in a mobile colloidal state and exhibiting superior optical properties compared to other dielectric resonant structures, the synthesized TMDC nanoparticles offer opportunities for the development of next-generation nanophotonic and nanotheranostic platforms, including photothermal therapy and multimodal bioimaging., 18 pages, 4 figures
Published: 2022
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20. 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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21. Superconducting Long-Range Proximity Effect through the Atomically Flat Interface of a Bi 2 Te 3 Topological Insulator

Author: Vasily S. Stolyarov, Sergio Vlaic, Evgueni V. Chulkov, Yuriy E. Lozovik, S. V. Remizov, Tatiana V. Menshchikova, Christophe Brun, D. S. Shapiro, Sergey I. Bozhko, Tristan Cren, Dimitri Roditchev, Stéphane Pons, W. V. Pogosov, Moscow Institute of Physics and Technology [Moscow] (MIPT), 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), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Superconductivity, Range (particle radiation), Materials science, Condensed matter physics, 02 engineering and technology, 021001 nanoscience & nanotechnology, 01 natural sciences, law.invention, Amorphous solid, [PHYS.COND.CM-S]Physics [physics]/Condensed Matter [cond-mat]/Superconductivity [cond-mat.supr-con], law, Condensed Matter::Superconductivity, Topological insulator, 0103 physical sciences, Proximity effect (superconductivity), [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], General Materials Science, Physical and Theoretical Chemistry, Scanning tunneling microscope, 010306 general physics, 0210 nano-technology, Spectroscopy, Layer (electronics), ComputingMilieux_MISCELLANEOUS
Abstract: We report on structural and electronic properties of superconducting nanohybrids made of Pb grown in the ultrahigh vacuum on the atomically clean surface of single crystals of topological Bi2Te3. In situ scanning tunneling microscopy and spectroscopy demonstrated that the resulting network is composed of Pb-nanoislands dispersed on the surface and linked together by an amorphous atomic layer of Pb, which wets Bi2Te3. As a result, the superconducting state of the system is characterized by a thickness-dependent superconducting gap of Pb-islands and by a very unusual position-independent proximity gap between them. Furthermore, the data analysis and DFT calculations demonstrate that the Pb-wetting layer leads to significant modifications of both topological and trivial electronic states of Bi2Te3, which are responsible for the observed long-range proximity effect.
Published: 2021
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22. Convex-PL-R - Revisiting affinity predictions and virtual screening using physics-informed machine learning

Author: Kadukova, Maria, Chupin, Vladimir, Grudinin, Sergei, 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), and Moscow Institute of Physics and Technology [Moscow] (MIPT)
Subjects: SAS - Solvent-Accessible Surface, CASF - Comparative Assessment of Scoring Functions, CASF -Comparative Assessment of Scoring Functions, PDB - Protein Data Bank, SAS -Solvent-Accessible Surface, SVM - Support Vector Machines, [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], RMSD - Root Mean Squared Deviation, SASA - Solvent-Accessible Surface Area, PDB -Protein Data Bank, SVM -Support Vector Machines, SASA -Solvent-Accessible Surface Area, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], RMSD -Root Mean Squared Deviation
Abstract: Virtual screening is an essential part of the modern drug design pipeline, which significantly accelerates the discovery of new drug candidates. Structure-based virtual screening involves ligand conformational sampling, which is often followed by re-scoring of docking poses. A great variety of scoring functions have been designed for this purpose. The advent of structural and affinity databases and the progress in machinelearning methods have recently boosted scoring function performance. Nonetheless, the most successful scoring functions are typically designed for specific tasks or systems. All-purpose scoring functions still perform poorly on the virtual screening tests, compared to precision with which they are able to predict co-crystal binding poses. Another limitation is the low interpretability of the heuristics being used. We analyzed scoring functions' performance in the CASF benchmarks and discovered that the vast majority of them have a strong bias towards predicting larger binding interfaces. This motivated us to develop a physical model with additional entropic terms with the aim of penalizing such a preference. We parameterized the new model using affinity and structural data, solving a classification problem followed by regression. The new model, called Convex-PL-R , demonstrated high-quality results on multiple tests and a substantial improvement over its predecessor Convex-PL. Convex-PL-R can be used for molecular docking together with VinaCPL, our version of AutoDock Vina, with Convex-PL integrated as a scoring function. Convex-PL-R , Convex-PL, and VinaCPL are available at https://team.inria.fr/nano-d/convex-pl/.
Published: 2021

23. Insertion and activation of functional Bacteriorhodopsin in a floating bilayer

Author: Jean-Luc Pellequer, Thierry Charitat, Arnaud Hemmerle, Jean Daillant, Kirill Kovalev, Yuri Gerelli, Jean-Marie Teulon, Alexandros Koutsioubas, Giovanna Fragneto, Tetiana Mukhina, Institut Laue-Langevin (ILL), Institut Charles Sadron (ICS), Université de Strasbourg (UNISTRA)-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)-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, 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), Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), Jülich Centre for Neutron Science (JCNS), Forschungszentrum Jülich GmbH at Heinz Maier-Leibnitz Zentrum (MLZ), 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), Grenoble Instruct-ERIC Center (ISBG), Thomas, Frank, ILL, Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-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))-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)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Polytechnic University of Marche [Ancona, Italy], Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, 85748 Garching, Institute of Biological Information Processing [Jülich] (IBI-7), Moscow Institute of Physics and Technology [Moscow] (MIPT), Institute of Crystallography [Aachen], and Rheinisch-Westfälische Technische Hochschule Aachen (RWTH)
Subjects: Materials science, X-ray reflectometry, [SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Lipid Bilayers, Protein reconstitution, Phospholipid, Bacteriorhodopsin, Physique [physics]/Matière Condensée [cond-mat], 02 engineering and technology, 010402 general chemistry, 01 natural sciences, Biomaterials, chemistry.chemical_compound, Colloid and Surface Chemistry, Bilayer, Lipid bilayer, Neutrons, Neutron reflectometry, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Membrane, Quartz crystal microbalance, 021001 nanoscience & nanotechnology, Transmembrane protein, 0104 chemical sciences, Surfaces, Coatings and Films, Electronic, Optical and Magnetic Materials, [PHYS.COND.CM-SCM] Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft], chemistry, Bacteriorhodopsins, ddc:540, Quartz Crystal Microbalance Techniques, biology.protein, Biophysics, 0210 nano-technology, [PHYS.COND.CM-SCM]Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft]
Abstract: International audience; The proton pump transmembrane protein bacteriorhodopsin was successfully incorporated into planar floating lipid bilayers in gel and fluid phases, by applying a detergent-mediated incorporation method. The method was optimized on single supported bilayers by using quartz crystal microbalance, atomic force and fluorescence microscopy techniques. Neutron and X-ray reflectometry were used on both single and floating bilayers with the aim of determining the structure and composition of this membrane-protein system before and after protein reconstitution at sub-nanometer resolution. Lipid bilayer integrity and protein activity were preserved upon the reconstitution process. Reversible structural modifications of the membrane, induced by the bacteriorhodopsin functional activity triggered by visible light, were observed and characterized at the nanoscale.
Published: 2021
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24. Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment

Author: Kryshtafovych, Andriy, Moult, John, Billings, Wendy, Della Corte, Dennis, Fidelis, Krzysztof, Kwon, Sohee, Olechnovič, Kliment, Seok, Chaok, Venclovas, Česlovas, Won, Jonghun, Adhikari, Badri, Adiyaman, Recep, Aguirre-Plans, Joaquim, Anishchenko, Ivan, Baek, Minkyung, Baker, David, Baldassarre, Frederico, Barger, Jacob, Bhattacharya, Sutanu, Bhattacharya, Debswapna, Bitton, Mor, Cao, Renzhi, Cheng, Jianlin, Christoffer, Charles, Czaplewski, Cezary, Elofsson, Arne, Faraggi, Eshel, Feig, Michael, Fernandez-Fuentes, Narcis, Grishin, Nick, Grudinin, Sergei, Guo, Zhiye, Hanazono, Yuya, Hassabis, Demis, Hedelius, Bryce, Heo, Lim, Hiranuma, Naozumi, Hunt, Cassandra, Igashov, Ilia, Ishida, Takashi, Jernigan, Robert, Jones, David, Jumper, John, Kadukova, Maria, Kandathil, Shaun, Keasar, Chen, Kihara, Daisuke, Kinch, Lisa, Kiyota, Yasuomi, Kloczkowski, Andrzje, Kohli, Pushmeet, Kogut, Mateusz, Laine, Elodie, Lilley, Cade, Liu, Jian, Liwo, Adam, Lubecka, Emilia, Mondal, Arup, Morris, Connor, Mcguffin, Liam, Molina, Alexis, Nakamura, Tsukasa, Oliva, Baldo, Perez, Alberto, Pozzati, Gabriele, Sarkar, Daipayan, Sato, Rin, Schwede, Torsten, Shrestha, Bikash, Sidi, Tomer, Studer, Gabriel, Shuvo, Md Hossain, Takeda-Shitaka, Mayuko, Takei, Yuma, Terashi, Genki, Tomii, Kentaro, Tsuchiya, Yuko, Tunyasuvunakool, Kathryn, Waliner, Björn, Wu, Tianqi, Xu, Jinbo, Yamamori, Yu, Zhang, Chengxin, Zhang, Yang, Zheng, Wei, University of California [Davis] (UC Davis), University of California (UC), Institute for Bioscience and Biotechnology Research [Rockville, MD, États-Unis] (IBBR), University of Maryland [College Park], University of Maryland System-University of Maryland System, Brigham Young University (BYU), Seoul National University [Seoul] (SNU), Vilnius University [Vilnius], University of Missouri [St. Louis], University of Missouri System, University of Reading (UOR), Universitat Pompeu Fabra [Barcelona] (UPF), Biorobotics Lab (University of Washington), University of Washington [Seattle], Royal Institute of Technology [Stockholm] (KTH ), Auburn University (AU), Ben-Gurion University of the Negev (BGU), Pacific Lutheran University [Tacoma] (PLU), University of Missouri [Columbia] (Mizzou), Purdue University [West Lafayette], University of Gdańsk (UG), Stockholm University, Indiana University - Purdue University Indianapolis (IUPUI), Indiana University System, Michigan State University [East Lansing], Michigan State University System, Aberystwyth University, University of Texas Southwestern Medical Center [Dallas], 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), National Institutes for Quantum and Radiological Science and Technology (QST), DeepMind [London], DeepMind Technologies, Moscow Institute of Physics and Technology [Moscow] (MIPT), Tokyo Institute of Technology [Tokyo] (TITECH), Iowa State University (ISU), University College of London [London] (UCL), Kitasato University, Ohio State University [Columbus] (OSU), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Florida [Gainesville] (UF), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Tohoku University [Sendai], University of Basel (Unibas), National Institute of Advanced Industrial Science and Technology (AIST), Linköping University (LIU), Toyota Technological Institute at Chicago [Chicago] (TTIC), University of Michigan [Ann Arbor], University of Michigan System, University of California, University of Maryland [Baltimore], 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: Models, Molecular, 2019-20 coronavirus outbreak, Research groups, Protein Conformation, Computer science, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Model accuracy, Genome, Viral, computer.software_genre, Biochemistry, SARS‐CoV‐2, Viroporin Proteins, Domain (software engineering), Viral Proteins, 03 medical and health sciences, Protein Domains, Structural Biology, EMA, Humans, CASP, Molecular Biology, Research Articles, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, COVID, 0303 health sciences, SARS-CoV-2, 030302 biochemistry & molecular biology, COVID-19, Protein structure prediction, Model quality, Critical assessment, Data mining, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Research Article
Abstract: International audience; Critical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on 10 proteins. The resulting models were released to the public. CASP community members also worked together to provide estimates of local and global accuracy and identify structure-based domain boundaries for some proteins. Subsequently, two of these structures (ORF3a and ORF8) have been solved experimentally, allowing assessment of both model quality and the accuracy estimates. Models from the AlphaFold2 group were found to have good agreement with the experimental structures, with main chain GDT_TS accuracy scores ranging from 63 (a correct topology) to 87 (competitive with experiment).
Published: 2021
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25. Inverse Conformational Selection in Lipid–Protein Binding

Author: Matti Javanainen, Salla I. Virtanen, Fernando Favela-Rosales, Chris Papadopoulos, Antonio Peón, Amélie Bacle, Anne M. Kiirikki, Patrick F.J. Fuchs, O. H. Samuli Ollila, Pavel Buslaev, Ángel Piñeiro, Rebeca García-Fandiño, Paula Milán Rodríguez, Tiago Mendes Ferreira, Markus S. Miettinen, Jesper J. Madsen, Josef Melcr, Ivan Gushchin, Thomas J. Piggot, Lipotoxicity and Channelopathies - ConicMeds (LitCh), Signalisation et Transports Ioniques Membranaires (STIM), Université de Poitiers-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Nanoscience Center [Jyväskylä Univ] (NSC@JYU), University of Jyväskylä (JYU), Moscow Institute of Physics and Technology [Moscow] (MIPT), Centro de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS ), Universidade de Santiago de Compostela [Spain] (USC ), Universidade do Porto = University of Porto, Tecnológico Nacional de México (TecNM), Martin-Luther-University Halle-Wittenberg, Laboratoire des biomolécules (LBM UMR 7203), Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), UFR Sciences du Vivant [Sciences] - Université Paris Cité (UFR SDV UPCité), Université Paris Cité (UPCité), Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences (IOCB / CAS), Czech Academy of Sciences [Prague] (CAS), HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, University of Chicago, University of South Florida [Tampa] (USF), Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen [Groningen], Max Planck Institute of Colloids and Interfaces, Max-Planck-Gesellschaft, 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), University of Southampton, Molecular Dynamics, Institute of Biotechnology, Biophysical chemistry, Gestionnaire, Hal Sorbonne Université, Université Paris Cité - UFR Sciences du Vivant [Sciences] (UPCité - UFR SDV), Université de Poitiers-Université de Tours-Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Universidade do Porto, Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, 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)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Paris - UFR Sciences du Vivant [Sciences] (UP - UFR SDV), Université de Paris (UP), University of Helsinki-University of Helsinki, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), and Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: DYNAMICS, ELECTRIC CHARGE, BILAYERS, PHOSPHATIDYLCHOLINE HEADGROUP, Membrane lipids, DEUTERIUM, Plasma protein binding, Molecular Dynamics Simulation, lipidit, 010402 general chemistry, 01 natural sciences, Biochemistry, biomolekyylit, Catalysis, 03 medical and health sciences, Molecular dynamics, kemialliset sidokset, Colloid and Surface Chemistry, Protein structure, PHOSPHOLIPID-BINDING, MAGNETIC-RESONANCE, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, SEGMENTAL ORDER, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Conformational ensembles, Nuclear Magnetic Resonance, Biomolecular, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Chemistry, Biomolecule, MEMBRANE-LIPIDS, Proteins, Phosphatidylglycerols, General Chemistry, computer.file_format, Protein Data Bank, Lipids, 0104 chemical sciences, Biophysics, Phospholipid Binding, Phosphatidylcholines, MAS NMR, 1182 Biochemistry, cell and molecular biology, lipids (amino acids, peptides, and proteins), proteiinit, computer, Protein Binding
Abstract: International audience; Interest in lipid interactions with proteins and other biomolecules is emerging not only in fundamental biochemistry but also in the field of nanobiotechnology where lipids are commonly used, for example, in carriers of mRNA vaccines. The outward-facing components of cellular membranes and lipid nanoparticles, the lipid headgroups, regulate membrane interactions with approaching substances, such as proteins, drugs, RNA, or viruses. Because lipid headgroup conformational ensembles have not been experimentally determined in physiologically relevant conditions, an essential question about their interactions with other biomolecules remains unanswered: Do headgroups exchange between a few rigid structures, or fluctuate freely across a practically continuous spectrum of conformations? Here, we combine solid-state NMR experiments and molecular dynamics simulations from the NMRlipids Project to resolve the conformational ensembles of headgroups of four key lipid types in various biologically relevant conditions. We find that lipid headgroups sample a wide range of overlapping conformations in both neutral and charged cellular membranes, and that differences in the headgroup chemistry manifest only in probability distributions of conformations. Furthermore, the analysis of 894 protein-bound lipid structures from the Protein Data Bank suggests that lipids can bind to proteins in a wide range of conformations, which are not limited by the headgroup chemistry. We propose that lipids can select a suitable headgroup conformation from the wide range available to them to fit the various binding sites in proteins. The proposed inverse conformational selection model will extend also to lipid binding to targets other than proteins, such as drugs, RNA, and viruses.
Published: 2021
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26. 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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27. 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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28. 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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29. Convex optimization

Author: Vorontsova, Evgeniya, Hildebrand, Roland, Gasnikov, Alexander, Stonyakin, Fedor, Université Catholique de Louvain = Catholic University of Louvain (UCL), 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), Moscow Institute of Physics and Technology [Moscow] (MIPT), and V.I. Vernadsky Crimean Federal University
Subjects: [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC]
Abstract: 364 pages, in Russian; International audience; This textbook is based on lectures given by the authors at MIPT (Moscow), HSE (Moscow), FEFU (Vladivostok), V.I. Vernadsky KFU (Simferopol), ASU (Republic of Adygea), and the University of Grenoble-Alpes (Grenoble, France). First of all, the authors focused on the program of a two-semester course of lectures on convex optimization, which is given to students of MIPT. The first chapter of this book contains the materials of the first semester ("Fundamentals of convex analysis and optimization"), the second and third chapters contain the materials of the second semester ("Numerical methods of convex optimization"). The textbook has a number of features. First, in contrast to the classic manuals, this book does not provide proofs of all the theorems mentioned. This allowed, on one side, to describe more themes, but on the other side, made the presentation less self-sufficient. The second important point is that part of the material is advanced and is published in the Russian educational literature, apparently for the first time. Third, the accents that are given do not always coincide with the generally accepted accents in the textbooks that are now popular. First of all, we talk about a sufficiently advanced presentation of conic optimization, including robust optimization, as a vivid demonstration of the capabilities of modern convex analysis.
Published: 2021

30. The resonance properties of Superconductor/Ferroelectric/Superconductor heterostructure

Author: Rahmonov, Ilhom, Chtchelkatchev, Nikolay, Sjukrinov, Yury, Joint Institute for Nuclear Research (JINR), Institute for High Pressure Physics of the RAS (HPPI), Russian Academy of Sciences [Moscow] (RAS), Moscow Institute of Physics and Technology [Moscow] (MIPT), Ural Federal University [Ekaterinburg] (UrFU), and Université de Lorraine
Subjects: Condensed Matter::Materials Science, resonance branch, Devonshire theory, Condensed Matter::Superconductivity, Ferroelectric layer, Josephson junction, [SPI.NRJ]Engineering Sciences [physics]/Electric power, Josephson effect, Landau, Condensed Matter::Mesoscopic Systems and Quantum Hall Effect
Abstract: International audience; The phase dynamics of the Superconductor/Ferroelectric/Superconductor hetero structure, which can be considered as the Josephson junction with the ferroelectric barrier, is investigated. The dynamics of the Josephson junction is described based on the Resistively and Capacitively Shunted Junction model, and the Landau- Devonshire theory is used to describe the dynamics of polarization in ferroelectric layer. The current – voltage characteristic and the voltage dependence of polarization amplitude are calculated. It is shown that, when the Josephson frequency reaches the polarization eigenfrequency as a result of the resonance an increase in the polarization amplitude is observed and an additional resonance branch appears on the current – voltage characteristi
Published: 2021

31. On Local Invertibility and Quality of Free-boundary Deformations

Author: Garanzha, Vladimir, Kaporin, Igor, Kudryavtseva, Liudmila, Protais, François, Ray, Nicolas, Sokolov, Dmitry, 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), 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: polyconvex functional, penalty technique, mesh untangling, [INFO.INFO-CG]Computer Science [cs]/Computational Geometry [cs.CG], variational method
Abstract: Mesh untangling is still a hot topic in applied mathematics. Tangled or folded meshes appear in many applications involving mappings or deformations. Despite the fact that a large number of mesh untangling strategies was proposed during the last decades, this problem still persists. Recently we have proposed a numerical optimization scheme [1] that provably untangles 2d and 3d meshes with inverted elements by partially solving a finite number of unconditional minimization problems. The method is robust for fixed boundary mesh untangling problems, and it can be applied to some extent to free boundary untangling. The problem, however, is that the absence of inverted elements does not guarantee invertibility of the deformation (map). The invertibility is lost if the mesh gets caught in a k-covering trap, i.e. in a local minimum of the deformation energy where all mesh elements are not inverted but total angle around certain vertex is above 2πfor 2D and above 4πfor 3D. This problem is particularly vexing when partially constrained mesh deformation problems are considered. In this paper we show how to improve the method suggested in [1]. Namely, we show the way to guarantee absence of k-covering folds, and so, the local invertibility is assured. We demonstrate enhanced stability of suggested untangling technique which has a potential to make untangling a routine operation over meshes.
Published: 2021

32. Effect of Controlled Artificial Disorder on the Magnetic Properties of EuFe2(As1−xPx)2 Ferromagnetic Superconductor

Author: Tsuyoshi Tamegai, Kyuil Cho, Makariy A. Tanatar, Marcin Konczykowski, Daniele Torsello, Ivan Veshchunov, Gianluca Ghigo, Sunil Ghimire, Ruslan Prozorov, Ames Laboratory [Ames, USA], Iowa State University (ISU)-U.S. Department of Energy [Washington] (DOE), Laboratoire des Solides Irradiés (LSI), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Politecnico di Torino = Polytechnic of Turin (Polito), Moscow Institute of Physics and Technology [Moscow] (MIPT), Department of Applied Physics, The University of Tokyo, The University of Tokyo (UTokyo), Department of Applied Science and Technology [Politecnico di Torino] (DISAT), Istituto Nazionale di Fisica Nucleare, Sezione di Torino (INFN, Sezione di Torino), Istituto Nazionale di Fisica Nucleare (INFN), The Ames Laboratory (Ameslab), Iowa State University (ISU)-U.S. Department of Energy, Department of Physics and Astronomy [Ames, Iowa], Iowa State University (ISU), and the EMIR SIRIUS team
Subjects: Technology, Materials science, Proton, tunnel diode resonator (TDR), iron-based superconductors (IBS), FOS: Physical sciences, 02 engineering and technology, Electron, 01 natural sciences, Article, Superconductivity (cond-mat.supr-con), 0103 physical sciences, General Materials Science, Irradiation, 010306 general physics, tunnel diode resonator (TDR, Superconductivity, Microscopy, QC120-168.85, Coplanar waveguide resonator (CPWR), Iron-based superconductors (IBS), Tunnel diode resonator (TDR), Condensed matter physics, Condensed Matter - Superconductivity, QH201-278.5, Engineering (General). Civil engineering (General), 021001 nanoscience & nanotechnology, Ferromagnetic superconductor, TK1-9971, Magnetic field, [PHYS.COND.CM-S]Physics [physics]/Condensed Matter [cond-mat]/Superconductivity [cond-mat.supr-con], Descriptive and experimental mechanics, Ferromagnetism, coplanar waveguide resonator (CPWR), Diamagnetism, Electrical engineering. Electronics. Nuclear engineering, TA1-2040, 0210 nano-technology
Abstract: Static (DC) and dynamic (AC, at 14 MHz and 8 GHz) magnetic susceptibilities of single crystals of a ferromagnetic superconductor, EuFe2(As1−xPx)2 (x = 0.23), were measured in pristine state and after different doses of 2.5 MeV electron or 3.5 MeV proton irradiation. The superconducting transition temperature, Tc(H), shows an extraordinarily large decrease. It starts at Tc(H=0)≈24K in the pristine sample for both AC and DC measurements, but moves to almost half of that value after moderate irradiation dose. Remarkably, after the irradiation not only Tc moves significantly below the FM transition, its values differ drastically for measurements at different frequencies, ≈16 K in AC measurements and ≈12 K in a DC regime. We attribute such a large difference in Tc to the appearance of the spontaneous internal magnetic field below the FM transition, so that the superconductivity develops directly into the mixed spontaneous vortex-antivortex state where the onset of diamagnetism is known to be frequency-dependent. We also examined the response to the applied DC magnetic fields and studied the annealing of irradiated samples, which almost completely restores the superconducting transition. Overall, our results suggest that in EuFe2(As1−xPx)2 superconductivity is affected by local-moment ferromagnetism mostly via the spontaneous internal magnetic fields induced by the FM subsystem. Another mechanism is revealed upon irradiation where magnetic defects created in ordered Eu2+ lattice act as efficient pairbreakers leading to a significant Tc reduction upon irradiation compared to other 122 compounds. On the other hand, the exchange interactions seem to be weakly screened by the superconducting phase leading to a modest increase of Tm (less than 1 K) after the irradiation drives Tc to below Tm. Our results suggest that FM and SC phases coexist microscopically in the same volume.
Published: 2021
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33. Manifold Topology Divergence: a Framework for Comparing Data Manifolds

Author: Barannikov, Serguei, Trofimov, Ilya, Sotnikov, Grigorii, Trimbach, Ekaterina, Korotin, Alexander, Filippov, Alexander, Burnaev, Evgeny, Université Paris Diderot - Paris 7 (UPD7), Institut de Mathématiques de Jussieu - Paris Rive Gauche (IMJ-PRG), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Skolkovo Institute of Science and Technology [Moscow] (Skoltech), Moscow Institute of Physics and Technology [Moscow] (MIPT), Huawei Noah's Ark Lab, and Huawei Technologies [Shenzhen]
Subjects: FOS: Computer and information sciences, generative neural networks, Computer Science - Machine Learning, Computer Science - Artificial Intelligence, Computer Vision and Pattern Recognition (cs.CV), data manifolds, Computer Science - Computer Vision and Pattern Recognition, deep learning, Metric Geometry (math.MG), [INFO.INFO-NE]Computer Science [cs]/Neural and Evolutionary Computing [cs.NE], 55N31, 68T07, persistent homology, Machine Learning (cs.LG), [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], [MATH.MATH-SG]Mathematics [math]/Symplectic Geometry [math.SG], topological data analysis, Artificial Intelligence (cs.AI), Mathematics - Metric Geometry, [MATH.MATH-AT]Mathematics [math]/Algebraic Topology [math.AT], FOS: Mathematics, Algebraic Topology (math.AT), Mathematics - Algebraic Topology, [MATH.MATH-AG]Mathematics [math]/Algebraic Geometry [math.AG]
Abstract: International audience; We develop a framework for comparing data manifolds, aimed, in particular, towards the evaluation of deep generative models. We describe a novel tool, Cross-Barcode(P,Q), that, given a pair of distributions in a high-dimensional space, tracks multiscale topology spacial discrepancies between manifolds on which the distributions are concentrated. Based on the Cross-Barcode, we introduce the Manifold Topology Divergence score (MTop-Divergence) and apply it to assess the performance of deep generative models in various domains: images, 3D-shapes, time-series, and on different datasets: MNIST, Fashion MNIST, SVHN, CIFAR10, FFHQ, chest X-ray images, market stock data, ShapeNet. We demonstrate that the MTop-Divergence accurately detects various degrees of mode-dropping, intra-mode collapse, mode invention, and image disturbance. Our algorithm scales well (essentially linearly) with the increase of the dimension of the ambient high-dimensional space. It is one of the first TDA-based practical methodologies that can be applied universally to datasets of different sizes and dimensions, including the ones on which the most recent GANs in the visual domain are trained. The proposed method is domain agnostic and does not rely on pre-trained networks.
Published: 2021

34. Foreword to the Special Issue 'Inverse problems and nonlinear phenomena'

Author: Roman Novikov, Alemdar Hasanov Hasanoğlu, A. A. Shananin, Iskander A. Taimanov, Kocaeli University [Turkey], Centre de Mathématiques Appliquées - Ecole Polytechnique (CMAP), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Moscow Institute of Physics and Technology [Moscow] (MIPT), Sobolev Institute of Mathematics, and Siberian Branch of the Russian Academy of Sciences (SB RAS)
Subjects: Nonlinear phenomena, Computer science, Applied Mathematics, 010103 numerical & computational mathematics, Inverse problem, [MATH.MATH-FA]Mathematics [math]/Functional Analysis [math.FA], 01 natural sciences, 010101 applied mathematics, [MATH.MATH-MP]Mathematics [math]/Mathematical Physics [math-ph], Applied mathematics, [MATH.MATH-AP]Mathematics [math]/Analysis of PDEs [math.AP], [NLIN]Nonlinear Sciences [physics], 0101 mathematics, ComputingMilieux_MISCELLANEOUS, [MATH.MATH-NA]Mathematics [math]/Numerical Analysis [math.NA], [MATH.MATH-SP]Mathematics [math]/Spectral Theory [math.SP]
Abstract: International audience
Published: 2021
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35. Bicontinuous Gyroid Phase of a Water-Swollen Wedge-Shaped Amphiphile: Studies with In-Situ Grazing-Incidence X-ray Scattering and Atomic Force Microscopy

Author: Dimitri A. Ivanov, K. N. Grafskaia, Denis S. Kotlyarskiy, Denis V. Anokhin, Diego Pontoni, Azaliia F. Akhkiamova, Dmitry V. Vashurkin, Xiaomin Zhu, Moscow Institute of Physics and Technology [Moscow] (MIPT), Institute of Problems of Chemical Physics of RAS, Russian Academy of Sciences [Moscow] (RAS), ESRF-The European Synchrotron, Lomonosov Moscow State University (MSU), Leibniz Institute, Universitätsklinikum RWTH Aachen - University Hospital Aachen [Aachen, Germany] (UKA), RWTH Aachen University, 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: Technology, business.product_category, Materials science, wedge-shaped amphiphile, grazing-incidence X-ray scattering, Supramolecular chemistry, vapor annealing, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, Phase (matter), Amphiphile, [CHIM]Chemical Sciences, General Materials Science, Thin film, Microscopy, QC120-168.85, Scattering, Communication, Mesogen, QH201-278.5, double gyroid phase, 021001 nanoscience & nanotechnology, Engineering (General). Civil engineering (General), Wedge (mechanical device), 0104 chemical sciences, TK1-9971, environmental atomic force microscopy, Descriptive and experimental mechanics, Chemical physics, Electrical engineering. Electronics. Nuclear engineering, TA1-2040, 0210 nano-technology, business, ddc:600, Gyroid
Abstract: Materials 14(11), 2892 (2021). doi:10.3390/ma14112892 special issue: "Special Issue "X-ray Diffraction of Functional Materials" / Special Issue Editors: Dr. Thomas Walter Cornelius, Guest Editor", Published by MDPI, Basel
Published: 2021
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36. The Mass Distribution of Transit Exoplanets from the Mass–Radius Relationships: the Structurization within Planetary Systems

Author: O. Ya. Yakovlev, Inna Shashkova, Jean-Loup Bertaux, V. I. Ananyeva, A. V. Tavrov, A. E. Ivanova, Andrey Yudaev, Space Research Institute of the Russian Academy of Sciences (IKI), Russian Academy of Sciences [Moscow] (RAS), Moscow Institute of Physics and Technology [Moscow] (MIPT), HELIOS - LATMOS, Laboratoire Atmosphères, Milieux, Observations Spatiales (LATMOS), and 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)
Subjects: Physics, 010504 meteorology & atmospheric sciences, Mass distribution, mass distribution, mass–radius relationship, Astronomy and Astrophysics, Radius, Astrophysics, Planetary system, 01 natural sciences, Power law, Exoplanet, Radial velocity, Spitzer Space Telescope, exoplanets, statistical analysis, Space and Planetary Science, Planet, transit method, [SDU]Sciences of the Universe [physics], 0103 physical sciences, Astrophysics::Earth and Planetary Astrophysics, 010303 astronomy & astrophysics, 0105 earth and related environmental sciences
Abstract: International audience; Most transit exoplanets (85%) were discovered with the Kepler space telescope. However, the mass, which was measured mainly with the radial velocity method, is known only for ~15% of them. The mass of an exoplanet may be estimated by its radius from the statistical dependences based on the observational data, though no unambiguous interrelation between the mass and the radius of planets exists. Here, we calculate the earlier unknown masses of exoplanets from four statistical mass–radius relationships (Bashi et al., 2017; Chen and Kipping, 2017; Ning et al., 2018, and the averaged dependence derived) and added the results to the distribution of planets with known masses. The mass distributions of transit exoplanets obtained in this way are analyzed with taking into account the observational selection effect inherent in the transit method. The distributions are approximated by the power law ∂N/∂M ~ Mα, where the exponent (α < 0) is determined by the maximum likelihood estimation for the samplings acquired with four mass–radius relationships: α = –2.12 ± 0.03, –2.09 ± 0.03, –1.94 ± 0.03, and –2.27 ± 0.04. Moreover, for one of these distributions, we determine the parameters of the power law, the exponent of which differs on three intervals (with the boundaries at 0.025, 0.28, and 1.34 Jupiter masses): –1.99, –0.62, and –2.88. We also conclude that there is no evidence of the interrelation between the mass of an exoplanet and its average distance to the host star (the structurization within planetary systems), if this distance is smaller than 1 AU; besides, the dependence of the exponent α on the considered mass interval is analyzed. The above estimates appertain to exoplanets detected by the space telescopes: Kepler Space Telescope and Transiting Exoplanet Survey Satellite (TESS) (these exoplanets compose group 1). The masses of the other transit exoplanets, which were detected by ground-based instruments, were known (they compose group 2). For the latter group, the exponent α is estimated at –2.21 ± 0.04. In general, the results of our analysis agree with those of the earlier statistical and theoretic studies. A key idea of the present paper is to apply the model interrelations between the mass and the radius of exoplanets to the analysis of the mass distribution of exoplanets on the basis of the recent data of observations.
Published: 2021
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37. Thermal relaxation in metal films limited by diffuson lattice excitations of amorphous substrates

Author: V. S. Khrapai, A. I. Kardakova, A. V. Semenov, Gregory Goltsman, Louis Veyrat, N.A. Titova, Elmira M. Baeva, Benjamin Sacépé, Moscow City Pedagogical University, Nano-Electronique Quantique et Spectroscopie (QuNES), Institut Néel (NEEL), 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)-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), Moscow Institute of Physics and Technology [Moscow] (MIPT), and institute of solide state physics, Moscow
Subjects: Condensed Matter - Materials Science, Materials science, Condensed matter physics, Phonon, Mean free path, Lattice (group), Materials Science (cond-mat.mtrl-sci), FOS: Physical sciences, General Physics and Astronomy, 02 engineering and technology, Substrate (electronics), 021001 nanoscience & nanotechnology, Coupling (probability), 01 natural sciences, Amorphous solid, [PHYS.COND.CM-S]Physics [physics]/Condensed Matter [cond-mat]/Superconductivity [cond-mat.supr-con], Condensed Matter::Materials Science, Thermal conductivity, 0103 physical sciences, 010306 general physics, 0210 nano-technology, Diffuson, [PHYS.COND.CM-MSQHE]Physics [physics]/Condensed Matter [cond-mat]/Mesoscopic Systems and Quantum Hall Effect [cond-mat.mes-hall]
Abstract: Here we examine the role of the amorphous insulating substrate in the thermal relaxation in thin NbN, InO$_x$, and Au/Ni films at temperatures above 5 K. The studied samples are made up of metal bridges on an amorphous insulating layer lying on or suspended above a crystalline substrate. Noise thermometry was used to measure the electron temperature $T_e$ of the films as a function of Joule power per unit of area $P_{2D}$. In all samples, we observe the dependence $P_{2D}\propto T_e^n$ with the exponent $n\simeq 2$, which is inconsistent with both electron-phonon coupling and Kapitza thermal resistance. In suspended samples, the functional dependence of $P_{2D}(T_e)$ on the length of the amorphous insulating layer is consistent with the linear $T$-dependence of the thermal conductivity, which is related to lattice excitations (diffusons) for the phonon mean free path smaller than the dominant phonon wavelength. Our findings are important for understanding the operation of devices embedded in amorphous dielectrics., 9 pages, 5 figures
Published: 2021
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38. Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors

Author: Lucy R. Forrest, Antoniya A. Aleksandrova, René Staritzbichler, Marcus Stamm, Kamil Khafizov, Emily Yaklich, Edoardo Sarti, Leipzig University, National Institutes of Health [Bethesda] (NIH), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Max-Planck-Institut für Biophysik - Max Planck Institute of Biophysics (MPIBP), Max-Planck-Gesellschaft, Moscow Institute of Physics and Technology [Moscow] (MIPT), Gestionnaire, Hal Sorbonne Université, and Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Protein Structure Comparison, Protein Folding, Computer science, [SDV]Life Sciences [q-bio], Cell Membranes, Sequence assembly, Biochemistry, Database and Informatics Methods, Mice, 0302 clinical medicine, Protein structure, Sequence Analysis, Protein, Macromolecular Structure Analysis, Integral membrane protein, chemistry.chemical_classification, 0303 health sciences, Sequence, Multidisciplinary, Amino acid, [SDV] Life Sciences [q-bio], Medicine, Drosophila, Cellular Structures and Organelles, Sequence Analysis, Hydrophobic and Hydrophilic Interactions, Algorithm, Algorithms, Research Article, Protein Structure, Bioinformatics, Science, Context (language use), Sequence alignment, Research and Analysis Methods, Molecular Evolution, 03 medical and health sciences, Robustness (computer science), Sequence Motif Analysis, Animals, Humans, Amino Acid Sequence, Molecular Biology, 030304 developmental biology, Evolutionary Biology, Sequence Homology, Amino Acid, Biology and Life Sciences, Proteins, Membrane Proteins, Reproducibility of Results, Cell Biology, Membrane protein, chemistry, Pairwise comparison, Sequence Alignment, Software, 030217 neurology & neurosurgery
Abstract: The alignment of primary sequences is a fundamental step in the analysis of protein structure, function, and evolution, and in the generation of homology-based models. Integral membrane proteins pose a significant challenge for such sequence alignment approaches, because their evolutionary relationships can be very remote, and because a high content of hydrophobic amino acids reduces their complexity. Frequently, biochemical or biophysical data is available that informs the optimum alignment, for example, indicating specific positions that share common functional or structural roles. Currently, if those positions are not correctly matched by a standard pairwise sequence alignment procedure, the incorporation of such information into the alignment is typically addressed in an ad hoc manner, with manual adjustments. However, such modifications are problematic because they reduce the robustness and reproducibility of the aligned regions either side of the newly matched positions. Previous studies have introduced restraints as a means to impose the matching of positions during sequence alignments, originally in the context of genome assembly. Here we introduce position restraints, or “anchors” as a feature in our alignment tool AlignMe, providing an aid to pairwise global sequence alignment of alpha-helical membrane proteins. Applying this approach to realistic scenarios involving distantly-related and low complexity sequences, we illustrate how the addition of anchors can be used to modify alignments, while still maintaining the reproducibility and rigor of the rest of the alignment. Anchored alignments can be generated using the online version of AlignMe available at www.bioinfo.mpg.de/AlignMe/.
Published: 2021
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39. Paramagnetic intrinsic point defects in alkali phosphate glasses: unraveling the $P_3$ center origin and local environment effects

Author: Mikhail E. Povarnitsyn, Shinji Kohara, Matjaž Valant, Nadège Ollier, Layla Martin-Samos, Nicolas Richard, Luigi Giacomazzi, Nikita S. Shcheblanov, University of Nova Gorica, Laboratoire des Solides Irradiés (LSI), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), DEmocritos MOdeling Center for Research In aTOmistic Simulation (DEMOCRITOS), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Moscow Institute of Physics and Technology [Moscow] (MIPT), Japan Synchrotron Radiation Research Institute [Hyogo] (JASRI), DAM Île-de-France (DAM/DIF), Direction des Applications Militaires (DAM), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: Electron paramagnetic resonance spectroscopy, [PHYS]Physics [physics], Materials science, 02 engineering and technology, 010402 general chemistry, 021001 nanoscience & nanotechnology, Alkali metal, Phosphate, 01 natural sciences, Crystallographic defect, 0104 chemical sciences, Surfaces, Coatings and Films, Electronic, Optical and Magnetic Materials, Amorphous solid, chemistry.chemical_compound, Paramagnetism, General Energy, chemistry, Chemical physics, Local environment, Physical and Theoretical Chemistry, 0210 nano-technology
Abstract: International audience; In this work, we carry out a first-principles investigation of intrinsic paramagnetic point defects in P$_2$O$_5$ and in Na$_2$O−P$_2$O$_5$ glasses as a representative of alkali phosphate glasses. Glass models are generated by combining classical molecular dynamics and Monte Carlo simulations and validated by comparing their corresponding structure factors with the available X-ray and neutron scattering experiments. We use density functional theory to calculate the electron paramagnetic resonance parameters for a large set of paramagnetic oxygen-vacancy configurations. Our investigation, also by unveiling the effect of the local environment and disorder on the hyperfine tensor, enables us to propose a new model for the much debated P$_3$ center. In particular, we establish the occurrence of two variants, which we name P$_3^a$ and P$_3^b$ centers, that are instrumental to explaining the experimental shifts of the hyperfine splittings observed in alkali phosphate glasses as a function of the alkali content x in the phosphate glass. Our scenario predicts that for low to intermediate alkali contents (0 < x < 50%), a mixture of P$_1$ and P$_3^a$ centers should be generated under irradiation. For x > 50%, essentially only P$_3^a$ and P$_3^b$ centers would be generated, while P$_1$ will be absent. Therefore, our findings, by providing an improved mapping of P centers in phosphate glasses, pave the way for fine-controlling/tuning the optical absorption in a wide range of technological applications.
Published: 2021
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40. Disorder-Promoted Splitting in Quasiparticle Interference at Nesting Vectors

Author: Sergio Vlaic, Eugene V. Chulkov, R. S. Akzyanov, V. A. Sheina, Tatiana V. Menshchikova, Hervé Aubin, T. Cren, Andrey S. Vasenko, Alexandre Avraamovitch Golubov, Vasily S. Stolyarov, Stéphane Pons, Dimitri Roditchev, D. A. Khokhlov, Moscow Institute of Physics and Technology [Moscow] (MIPT), 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), Saint Petersburg State University (SPBU), MESA+ Institute, and Interfaces and Correlated Electron Systems
Subjects: трехмерные топологические изоляторы, 02 engineering and technology, Interference (wave propagation), Condensed Matter::Disordered Systems and Neural Networks, 01 natural sciences, Quantum mechanics, 0103 physical sciences, General Materials Science, Physical and Theoretical Chemistry, 010306 general physics, Quantum, когерентное рассеяние, ComputingMilieux_MISCELLANEOUS, Condensed Matter::Quantum Gases, Friedel oscillations, Physics, [PHYS]Physics [physics], Condensed Matter::Mesoscopic Systems and Quantum Hall Effect, 021001 nanoscience & nanotechnology, квантовые осцилляции, квазичастицы, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Quasiparticle, амплитуда расщепления, Nesting (computing), High Energy Physics::Experiment, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], 0210 nano-technology
Abstract: Inelastic interactions of quantum systems with the environment usually wash coherent effects out. In the case of Friedel oscillations, the presence of disorder leads to a fast decay of the oscillation amplitude. Here we show both experimentally and theoretically that in three-dimensional topological insulator Bi2Te3 there is a nesting-induced splitting of coherent scattering vectors which follows a peculiar evolution in energy. The effect becomes experimentally observable when the lifetime of quasiparticles shortens due to disorder. The amplitude of the splitting allows an evaluation of the lifetime of the electrons. A similar phenomenon should be observed in any system with a well-defined scattering vector regardless of its topological properties.
Published: 2021
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41. Renormalization flow of a weak extended backscattering Hamiltonian in a non-chiral Tomonaga-Luttinger liquid

Author: Thomas Martin, Jérôme Rech, A Lebedev, Laurent Raymond, A. Popoff, Thibaut Jonckheere, Centre de Physique Théorique - UMR 7332 (CPT), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Collège Tinomana Ebb de Teva I Uta, Moscow Institute of Physics and Technology [Moscow] (MIPT), CPT - E6 Nanophysique, and 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)
Subjects: FOS: Physical sciences, Scalar potential, 02 engineering and technology, 01 natural sciences, Renormalization, Condensed Matter - Strongly Correlated Electrons, symbols.namesake, Luttinger liquid, Quantum mechanics, 0103 physical sciences, Mesoscale and Nanoscale Physics (cond-mat.mes-hall), Coulomb, General Materials Science, 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, Strongly Correlated Electrons (cond-mat.str-el), Fermion, Renormalization group, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Imaginary time, [PHYS.COND.CM-S]Physics [physics]/Condensed Matter [cond-mat]/Superconductivity [cond-mat.supr-con], symbols, renormalization group, 0210 nano-technology, Hamiltonian (quantum mechanics), extended backscattering
Abstract: We consider a non-chiral Luttinger liquid in the presence of a backscattering Hamiltonian which has an extended range. Right/left moving fermions at a given location can thus be converted as left/right moving fermions at a different location, within a specific range. We perform a momentum shell renormalization group treatment which gives the evolution of the relative degrees of freedom of this Hamiltonian contribution under the renormalization flow, and we study a few realistic examples of this extended backscattering Hamiltonian. We find that, for repulsive Coulomb interaction in the Luttinger liquid, any such Hamiltonian contribution evolves into a delta-like scalar potential upon renormalization to a zero temperature cutoff. On the opposite, for attractive couplings, the amplitude of this kinetic Hamiltonian is suppressed, rendering the junction fully transparent. As the renormalization procedure may have to be stopped because of experimental constraints such as finite temperature, we predict the actual spatial shape of the kinetic Hamiltonian at different stages of the renormalization procedure, as a function of the position and the Luttinger interaction parameter, and show that it undergoes structural changes. This renormalized kinetic Hamiltonian has thus to be used as an input for the perturbative calculation of the current, for which we provide analytic expressions in imaginary time. We discuss the experimental relevance of this work by looking at one-dimensional systems consisting of carbon nanotubes or semiconductor nanowires., Comment: 27 pages, 8 figures
Published: 2021
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42. Spherical convolutions on molecular graphs for protein model quality assessment

Author: Ilia Igashov, Nikita Pavlichenko, Sergei Grudinin, Moscow Institute of Physics and Technology [Moscow] (MIPT), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria), This work was partially supported by the Inria International Partnership program BIOTOOLS., Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-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)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), and Université Grenoble Alpes (UGA)
Subjects: FOS: Computer and information sciences, Computer Science - Machine Learning, Computer science, Coordinate system, Image processing, Topology (electrical circuits), Quantitative Biology - Quantitative Methods, Convolutional neural network, Convolution, Machine Learning (cs.LG), 03 medical and health sciences, 0302 clinical medicine, [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], Artificial Intelligence, CASP, Quantitative Methods (q-bio.QM), 030304 developmental biology, Structure (mathematical logic), 0303 health sciences, rotational equivariance, Spherical harmonics, spherical harmonics, structural bioinformatics, Graph Convolutional Network, Human-Computer Interaction, 030220 oncology & carcinogenesis, FOS: Biological sciences, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Algorithm, Software
Abstract: Processing information on three-dimensional (3D) objects requires methods stable to rigid-body transformations, in particular rotations, of the input data. In image processing tasks, convolutional neural networks achieve this property using rotation-equivariant operations. However, contrary to images, graphs generally have irregular topology. This makes it challenging to define a rotation-equivariant convolution operation on these structures. In this work, we propose spherical graph convolutional network that processes 3D models of proteins represented as molecular graphs. In a protein molecule, individual amino acids have common topological elements. This allows us to unambiguously associate each amino acid with a local coordinate system and construct rotation-equivariant spherical filters that operate on angular information between graph nodes. Within the framework of the protein model quality assessment problem, we demonstrate that the proposed spherical convolution method significantly improves the quality of model assessment compared to the standard message-passing approach. It is also comparable to state-of-the-art methods, as we demonstrate on critical assessment of structure prediction benchmarks. The proposed technique operates only on geometric features of protein 3D models. This makes it universal and applicable to any other geometric-learning task where the graph structure allows constructing local coordinate systems. The method is available at https://team.inria.fr/nano-d/software/s-gcn/.
Published: 2021
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43. 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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44. XFEL and HHG interaction with matter: Effects of ultrashort pulses and random spikes

Author: Valery A. Astapenko, F. B. Rosmej, E. S. Khramov, Laboratoire pour l'utilisation des lasers intenses (LULI), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Moscow Institute of Physics and Technology [Moscow] (MIPT)
Subjects: Nuclear and High Energy Physics, Free electron lasers, QC770-798, Photoionization, Expectation value, 01 natural sciences, 010305 fluids & plasmas, law.invention, law, Nuclear and particle physics. Atomic energy. Radioactivity, Ionization, 0103 physical sciences, Physics::Atomic and Molecular Clusters, Spontaneous emission, Physics::Atomic Physics, Electrical and Electronic Engineering, 010306 general physics, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], Laser, Atomic and Molecular Physics, and Optics, Computational physics, Nonlinear system, Nuclear Energy and Engineering, Orders of magnitude (time), Fermi's golden rule, Fermi Gamma-ray Space Telescope
Abstract: International audience; The theory of photoionization describing the interaction of x-ray free-electron laser (XFEL) pulses and high-harmonic-generated (HHG) radiation is generalized to ultrashort laser pulses, where the concept of the standard ionization probability per unit time in Fermi’s golden rule and in Einstein’s theory breaks down. Numerical calculations carried out in terms of a generalized photoionization probability for the total duration of pulses in the near-threshold regime demonstrate essentially nonlinear behavior, while absolute values may change by orders of magnitude for typical XFEL and HHG pulses. XFEL self-amplified spontaneous emission pulses are analyzed to reveal general features of photoionization for random and regular spikes: the dependences of the nonlinear photoionization probability on carrier frequency and spike duration are very similar, allowing an analytical expectation value approach that is valid even when there is only limited knowledge of random and regular parameters. Numerical simulations carried out for typical parameters demonstrate excellent agreement.
Published: 2021
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45. New point compression method for elliptic Fq2-curves of j-invariant 0

Author: Koshelev, Dmitrii I., Laboratoire de Mathématiques de Versailles (LMV), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institute for Information Transmission Problems, Russian Academy of Sciences [Moscow] (RAS), Moscow Institute of Physics and Technology [Moscow] (MIPT), and This work was supported by a public grant as part of the FMJH project.
Subjects: Rationality problems, Point compression, Generalized Kummer surfaces, Conic bundles, Weil restriction, Pairing-based cryptography, Elliptic curves of j=0, Cubic roots, Singular cubic surfaces, [MATH.MATH-NT]Mathematics [math]/Number Theory [math.NT]
Abstract: International audience; In the article we propose a new compression method (to 2⌈log2⁡(q)⌉+3 bits) for the Fq2-points of an elliptic curve Eb:y2=x3+b (for b∈Fq2⁎) of j-invariant 0. It is based on Fq-rationality of some generalized Kummer surface GKb. This is the geometric quotient of the Weil restriction Rb:=RFq2/Fq(Eb) under the order 3 automorphism restricted from Eb. More precisely, we apply the theory of conic bundles (i.e., conics over the function field Fq(t)) to obtain explicit and quite simple formulas of a birational Fq-isomorphism between GKb and A2. Our point compression method consists in computation of these formulas. To recover (in the decompression stage) the original point from Eb(Fq2)=Rb(Fq) we find an inverse image of the natural map Rb→GKb of degree 3, i.e., we extract a cubic root in Fq. For q≢1(mod27) this is just a single exponentiation in Fq, hence the new method seems to be much faster than the classical one with x-coordinate, which requires two exponentiations in Fq.
Published: 2021
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46. 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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47. Gravity wave activity in the Martian atmosphere at altitudes 20‐160 km from ACS/TGO occultation measurements

Author: Alexander S. Medvedev, Oleg Korablev, Juan Alday, Anna Fedorova, Paul Hartogh, Alexander Trokhimovskiy, Denis Belyaev, Erdal Yiğit, Ekaterina D. Starichenko, Franck Montmessin, Space Research Institute of the Russian Academy of Sciences (IKI), Russian Academy of Sciences [Moscow] (RAS), Moscow Institute of Physics and Technology [Moscow] (MIPT), Max-Planck-Institut für Sonnensystemforschung (MPS), Max-Planck-Gesellschaft, Department of Physics and Astronomy [Fairfax], George Mason University [Fairfax], Department of Physics [Oxford], University of Oxford [Oxford], PLANETO - LATMOS, Laboratoire Atmosphères, Milieux, Observations Spatiales (LATMOS), and 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)
Subjects: Gravity (chemistry), 010504 meteorology & atmospheric sciences, Spectrometer, Astrophysics::Cosmology and Extragalactic Astrophysics, Atmosphere of Mars, Geophysics, 01 natural sciences, Occultation, Space and Planetary Science, Geochemistry and Petrology, [SDU]Sciences of the Universe [physics], Atmospheric chemistry, 0103 physical sciences, Earth and Planetary Sciences (miscellaneous), Gravity wave, Astrophysics::Earth and Planetary Astrophysics, Nuclear Experiment, 010303 astronomy & astrophysics, Physics::Atmospheric and Oceanic Physics, Astrophysics::Galaxy Astrophysics, Geology, 0105 earth and related environmental sciences, Communication channel
Abstract: International audience; The paper presents observations of gravity wave-induced temperature disturbances in the Martian atmosphere obtained with the mid-infrared (MIR) spectrometer, a channel of the Atmospheric Chemistry Suite instrument on board the Trace Gas Orbiter (ACS/TGO). Solar occultation measurements of a CO2absorption band at 2.7 µm were used for retrieving density and temperature profiles between heights of 20 and 160 km with vertical resolution sufficient for deriving small-scale structures associated with gravity waves. Several techniques for distinguishing disturbances from the background temperature have been explored and compared. Instantaneous temperature profiles, amplitudes of wave packets and potential energy have been determined. Horizontal momentum fluxes and associated wave drag have been estimated. The analyzed data set of 144 profiles encompasses the measurements made over the second half of Martian Year 34, from the Solar longitude 165° through 355°. We observe enhanced gravity wave dissipation/breaking in the mesopause region of 100-130 km. Our analysis shows no direct correlation between the wave amplitude and Brunt-Väisälä frequency. It may indicate that convective instability may not be the main mechanism limiting gravity wave growth in the middle atmosphere of Mars.
Published: 2021
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48. The Arp1/11 minifilament of dynactin primes the endosomal Arp2/3 complex

Author: Frédéric Saudou, Emmanuel Derivery, Ksenia Oguievetskaia, Andrew P. Carter, Maria-Victoria Hinckelmann, Nathalie Rocques, Christophe Le Clainche, Guillaume Romet-Lemonne, Véronique Henriot, Nicolas Molinie, Artem I. Fokin, Alexis Gautreau, Violaine David, Luyan Cao, Magali Aumont-Nicaise, Caroline E. Stone, 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), Mesures d'interactions protéine-protéine (PIM), Département Plateforme (PF 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)-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), Dynamique du cytosquelette et motilité (ACTIN), Département Biochimie, Biophysique et Biologie Structurale (B3S), Laboratoire de Biologie Structurale de la Cellule (BIOC), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), MRC Laboratory of Molecular Biology [Cambridge, UK] (LMB), University of Cambridge [UK] (CAM)-Medical Research Council, Institut Jacques Monod (IJM (UMR_7592)), Université de Paris (UP)-Centre National de la Recherche Scientifique (CNRS), [GIN] Grenoble Institut des Neurosciences (GIN), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA), Moscow Institute of Physics and Technology [Moscow] (MIPT), Le Clainche, Christophe, and Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)
Subjects: Endosome, Protein subunit, [SDV]Life Sciences [q-bio], Mutant, Arp2/3 complex, macromolecular substances, Biochemistry, WASH complex, Protein filament, 03 medical and health sciences, 0302 clinical medicine, Research Articles, Actin, 030304 developmental biology, 0303 health sciences, Multidisciplinary, biology, urogenital system, Chemistry, fungi, SciAdv r-articles, 3. Good health, [SDV] Life Sciences [q-bio], Dynactin, biology.protein, Biophysics, 030217 neurology & neurosurgery, Research Article
Abstract: Dendritic actin networks grow in an autocatalytic manner starting from the uncapped minifilament of dynactin., Dendritic actin networks develop from a first actin filament through branching by the Arp2/3 complex. At the surface of endosomes, the WASH complex activates the Arp2/3 complex and interacts with the capping protein for unclear reasons. Here, we show that the WASH complex interacts with dynactin and uncaps it through its FAM21 subunit. In vitro, the uncapped Arp1/11 minifilament elongates an actin filament, which then primes the WASH-induced Arp2/3 branching reaction. In dynactin-depleted cells or in cells where the WASH complex is reconstituted with a FAM21 mutant that cannot uncap dynactin, formation of branched actin at the endosomal surface is impaired. Our results reveal the importance of the WASH complex in coordinating two complexes containing actin-related proteins.
Published: 2021
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49. 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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50. Les rayons extrêmes du cône copositif de taille 6x6

Author: Afonin, Andrey, Hildebrand, Roland, Dickinson, Peter, 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), University of Twente, and University of Twente [Netherlands]
Subjects: non-convex optimization, extreme ray, minimal zero, MSC 2020: 90C26, 15B48, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], copositive matrix
Abstract: International audience; We provide a complete classification of the extreme rays of the 6 × 6 copositive cone COP^6. We proceed via a coarse intermediate classification of the possible minimal zero support set of an exceptional extremal matrix A ∈ COP^6. To each such minimal zero support set we construct a stratified semi-algebraic manifold in the space of real symmetric 6 × 6 matrices S^6 , parameterized in a semi-trigonometric way, which consists of all exceptional extremal matrices A ∈ COP^6 having this minimal zero support set. Each semi-algebraic stratum is characterized by the supports of the minimal zeros u as well as the supports of the corresponding matrix-vector products Au. The analysis uses recently and newly developed methods that are applicable also to copositive matrices of arbitrary order.
Published: 2021
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