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1. Modulation of membrane permeability by carbon dioxide

Author: Wensheng Cai, Hong Zhang, François Dehez, Christophe Chipot, Xueguang Shao, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University (NKU), Laboratoire de Physique et Chimie Théoriques (LPCT), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire International Associé (LIA), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Illinois at Urbana-Champaign, USA], and University of Illinois System-University of Illinois System
Subjects: Membrane permeability, Lipid Bilayers, Molecular Dynamics Simulation, 010402 general chemistry, 01 natural sciences, Permeability, Trimethoprim, chemistry.chemical_compound, 0103 physical sciences, Ethanol, 010304 chemical physics, Cell Membrane, Biological membrane, General Chemistry, Carbon Dioxide, Permeation, 0104 chemical sciences, Bioavailability, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Computational Mathematics, Membrane, chemistry, 13. Climate action, Dideoxyadenosine, Drug delivery, Carbon dioxide, Phosphatidylcholines, Biophysics
Abstract: Promoting drug delivery across the biological membrane is a common strategy to improve bioavailability. Inspired by the observation that carbonated alcoholic beverages can increase the absorption rate of ethanol, we speculate that carbon dioxide (CO2 ) molecules could also enhance membrane permeability to drugs. In the present work, we have investigated the effect of CO2 on the permeability of a model membrane formed by 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine lipids to three drug-like molecules, namely, ethanol, 2',3'-dideoxyadenosine, and trimethoprim. The free-energy and fractional-diffusivity profiles underlying membrane translocation were obtained from μs-timescale simulations and combined in the framework of the fractional solubility-diffusion model. We find that addition of CO2 in the lipid environment results in an increase of the membrane permeability to the three substrates. Further analysis of the permeation events reveals that CO2 expands and loosens the membrane, which, in turn, facilitates permeation of the drug-like molecules. © 2019 Wiley Periodicals, Inc.
Published: 2019
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2. Skewness of mean transverse momentum fluctuations in heavy-ion collisions

Author: Fernando G. Gardim, Jean-Yves Ollitrault, Jacquelyn Noronha-Hostler, Giuliano Giacalone, Institut de Physique Théorique - UMR CNRS 3681 (IPHT), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Universidade Federal de Alfenas, Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, INCT-FNA grant 464898/201, FAPESP grant 2018/2472, USP-COFECUB (grant Uc Ph 160-16, 2015, and US-DOE Nuclear Science Grant No. de-sc0019
Subjects: Nuclear Theory, High Energy Physics::Lattice, FOS: Physical sciences, 01 natural sciences, High Energy Physics - Experiment, Nuclear Theory (nucl-th), High Energy Physics - Experiment (hep-ex), Mathematics::Group Theory, High Energy Physics - Phenomenology (hep-ph), 0103 physical sciences, Positive skewness, Statistical physics, Nuclear Experiment (nucl-ex), Nuclear Experiment, 010306 general physics, Nuclear theory, [PHYS]Physics [physics], Physics, 010308 nuclear & particles physics, High Energy Physics::Phenomenology, Skew, Collision, Nonlinear Sciences::Chaotic Dynamics, High Energy Physics - Phenomenology, Distribution (mathematics), MESH: Nuclear Theory (nucl-th), Skewness, Transverse momentum, Heavy ion
Abstract: We propose the skewness of mean transverse momentum, $\langle p_t \rangle$, fluctuations as a fine probe of hydrodynamic behavior in relativistic nuclear collisions. We describe how the skewness of the $\langle p_t \rangle$ distribution can be analyzed experimentally, and we use hydrodynamic simulations to predict its value. We predict in particular that $\langle p_t \rangle$ fluctuations have positive skew, which is significantly larger than if particles were emitted independently. We elucidate the origin of this result by deriving generic formulas relating the fluctuations of $\langle p_t \rangle$ to the fluctuations of the early-time thermodynamic quantities. We postulate that the large positive skewness of $\langle p_t \rangle$ fluctuations is a generic prediction of hydrodynamic models., 13 pages; 4 figures; v2: corrections in Sec IIIA and appendix A; v3: published version; improved baseline for stat. fluctuations in Fig 3; Expanded discussion in Sec. V
Published: 2021
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3. Direct Comparison of Many-Body Methods for Realistic Electronic Hamiltonians

Author: Mark van Schilfgaarde, Andrew J. Millis, George H. Booth, Li Chen, Jia Li, Bastien Mussard, Lan Nguyen Tran, Kiel T. Williams, Cyrus Umrigar, Yuan Yao, Hao Shi, Garnet Kin-Lic Chan, Junhao Li, Sheng Guo, Mario Motta, Robert J. Anderson, Lucas K. Wagner, Shiwei Zhang, Sandeep Sharma, Dominika Zgid, Fabien Bruneval, Chun-Yao Niu, Ushnish Ray, Chia-Nan Yeh, Emanuel Gull, Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Laboratory of Atomic and Solid State Physics [Ithaca] (LASSP), Cornell University [New York], Department of Physics [Ann Arbor], University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, Flatiron Institute, Simons Foundation, College of William and Mary [Williamsburg] (WM), IBM Almaden Research Center [San Jose], IBM, Zhengzhou University, California Institute of Technology (CALTECH), King‘s College London, Department of Chemistry [Ann Arbor], Department of Chemistry and Biochemistry [Boulder], University of Colorado [Boulder], Service de recherches de métallurgie physique (SRMP), Département des Matériaux pour le Nucléaire (DMN), 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, and Columbia University [New York]
Subjects: Condensed Matter - Materials Science, Strongly Correlated Electrons (cond-mat.str-el), 010304 chemical physics, Computer science, Physics, QC1-999, Materials Science (cond-mat.mtrl-sci), FOS: Physical sciences, General Physics and Astronomy, 7. Clean energy, 01 natural sciences, Many body, Condensed Matter - Strongly Correlated Electrons, Classical mechanics, 0103 physical sciences, [PHYS.COND.CM-SCE]Physics [physics]/Condensed Matter [cond-mat]/Strongly Correlated Electrons [cond-mat.str-el], 010306 general physics
Abstract: A large collaboration carefully benchmarks 20 first principles many-body electronic structure methods on a test set of 7 transition metal atoms, and their ions and monoxides. Good agreement is attained between the 3 systematically converged methods, resulting in experiment-free reference values. These reference values are used to assess the accuracy of modern emerging and scalable approaches to the many-electron problem. The most accurate methods obtain energies indistinguishable from experimental results, with the agreement mainly limited by the experimental uncertainties. Comparison between methods enables a unique perspective on calculations of many-body systems of electrons., Simons collaboration on the many-electron problem
Published: 2020
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4. Hepatitis C virus sequence divergence preserves p7 viroporin structural and dynamic features

Author: Latifah Almanea, Juan H. Bolivar, Nicole Zitzmann, François Dehez, Nicole Holzmann, Chris Chipot, Jolyon K. Claridge, Jason R. Schnell, Benjamin P. Oestringer, Oxford Glycobiology Institute, University of Oxford [Oxford], Department of Biochemistry [Oxford], Immunocore Limited, Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Structural Biology Research Center, VIB, 1050 Brussels, Belgium, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium]-VIB [Belgium], Laboratoire International Associé (LIA), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois System-University of Illinois System, Laboratoire de Physique et Chimie Théoriques (LPCT), and Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Genotype, Hepatitis C virus, lcsh:Medicine, Hepacivirus, Viral Nonstructural Proteins, medicine.disease_cause, Endoplasmic Reticulum, Ion Channels, Protein Structure, Secondary, Article, Viroporin Proteins, Viroporin, 03 medical and health sciences, Viral Proteins, medicine, Humans, Secretion, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, lcsh:Science, Protein secondary structure, Ion channel, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, 0303 health sciences, Multidisciplinary, Chemistry, Endoplasmic reticulum, lcsh:R, 030302 biochemistry & molecular biology, Hepatitis C, 3. Good health, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Transmembrane domain, lcsh:Q, Molecular modelling, Solution-state NMR
Abstract: The hepatitis C virus (HCV) viroporin p7 oligomerizes to form ion channels, which are required for the assembly and secretion of infectious viruses. The 63-amino acid p7 monomer has two putative transmembrane domains connected by a cytosolic loop, and has both N- and C- termini exposed to the endoplasmic reticulum (ER) lumen. NMR studies have indicated differences between p7 structures of distantly related HCV genotypes. A critical question is whether these differences arise from the high sequence variation between the different isolates and if so, how the divergent structures can support similar biological functions. Here, we present a side-by-side characterization of p7 derived from genotype 1b (isolate J4) in the detergent 6-cyclohexyl-1-hexylphosphocholine (Cyclofos-6) and p7 derived from genotype 5a (isolate EUH1480) in n-dodecylphosphocholine (DPC). The 5a isolate p7 in conditions previously associated with a disputed oligomeric form exhibits secondary structure, dynamics, and solvent accessibility broadly like those of the monomeric 1b isolate p7. The largest differences occur at the start of the second transmembrane domain, which is destabilized in the 5a isolate. The results show a broad consensus among the p7 variants that have been studied under a range of different conditions and indicate that distantly related HCVs preserve key features of structure and dynamics.
Published: 2019
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5. Structural Basis for Broad HIV-1 Neutralization by the MPER-Specific Human Broadly Neutralizing Antibody LN01

Author: Christophe Chipot, Timothée Bruel, Georgia D. Tomaras, Antonio Lanzavecchia, Dora Pinto, David C. Montefiori, Giuseppe Pantaleo, Winfried Weissenhorn, Sonia Barbieri, Agostino Riva, Craig Fenwick, Davide Corti, Maciej Tarkowski, Christophe Caillat, Olivier Schwartz, David Jarrossay, Andrea Minola, Michael S. Seaman, Jérémy Dufloo, Chiara Silacci, François Dehez, Serafima Guseva, Xiaoying Shen, Institute for Research in Biomedicine [Ticono, Suisse], Université de Lausanne = University of Lausanne (UNIL), Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Physique et Chimie Théoriques (LPCT), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Institute for Biomedicine [Bolzano, Italy] (Eurac Research), Affiliated Institute of the University of Lübeck, Humabs BioMed SA, Duke Human Vaccine Institute [Durham, North Carolina, USA], Université Paris Diderot - Paris 7 (UPD7), Luigi Sacco University Hospital [Milan], Rheumatology Unit, Milano (ASST Fatebenefratelli-Sacco), Virus et Immunité - Virus and immunity, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Vaccine Research Institute (VRI), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Université Sorbonne Paris Cité (USPC), Beth Israel Deaconess Medical Center, Beth Israel Deaconess Medical Center [Boston] (BIDMC), Harvard Medical School [Boston] (HMS)-Harvard Medical School [Boston] (HMS), Duke University Medical Center, Institute for Research in Biomedicine, ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), European Project: 681137,H2020,H2020-PHC-2015-single-stage_RTD,EAVI2020(2015), Université de Lausanne (UNIL), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Duke Human Vaccine Institute, and Duke School of Medicine
Subjects: Env, education, Mice, Transgenic, HIV Antibodies, Gp41, Microbiology, Neutralization, Epitope, Article, Cell Line, broadly neutralizing antibody, 03 medical and health sciences, Mice, 0302 clinical medicine, 10E8, Protein Domains, 4E10, Virology, Animals, Humans, membrane interaction, Amino Acid Sequence, 030304 developmental biology, AIDS Vaccines, 0303 health sciences, biology, Germinal center, Fusion protein, Antibodies, Neutralizing, gp41, Transmembrane protein, HIV Envelope Protein gp41, 3. Good health, Cell biology, MPER, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Disease Models, Animal, HEK293 Cells, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, biology.protein, HIV-1, [SDV.IMM]Life Sciences [q-bio]/Immunology, Parasitology, Paratope, Female, LN01, Antibody, 030217 neurology & neurosurgery
Abstract: Summary Potent and broadly neutralizing antibodies (bnAbs) are the hallmark of HIV-1 protection by vaccination. The membrane-proximal external region (MPER) of the HIV-1 gp41 fusion protein is targeted by the most broadly reactive HIV-1 neutralizing antibodies. Here, we examine the structural and molecular mechansims of neutralization by anti-MPER bnAb, LN01, which was isolated from lymph-node-derived germinal center B cells of an elite controller and exhibits broad neutralization breadth. LN01 engages both MPER and the transmembrane (TM) region, which together form a continuous helix in complex with LN01. The tilted TM orientation allows LN01 to interact simultaneously with the peptidic component of the MPER epitope and membrane via two specific lipid binding sites of the antibody paratope. Although LN01 carries a high load of somatic mutations, most key residues interacting with the MPER epitope and lipids are germline encoded, lending support for the LN01 epitope as a candidate for lineage-based vaccine development., Graphical Abstract, Highlights • bNAb LN01 neutralizes 92% of a 118-strain virus panel • LN01 targets the HIV-1 gp41 MPER, the TM region, and lipids • LN01-complexed MPER forms a continuous helix with TM • Most LN01 paratope residues interacting with MPER-TM and lipids are germline encoded, The gp41 membrane-proximal external region (MPER) is a highly conserved region of HIV-1 Env. Pinto et al. characterize the broadly neutralizing anti-MPER mAb LN01, which shows low autoreactivity. LN01 interacts with a complex epitope comprising MPER, the transmembrane region, and lipids, providing insights for vaccine design.
Published: 2019
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6. Molecular Basis of DNA Packaging in Bacteria Revealed by All-Atoms Molecular Dynamic Simulations: The case of histone like proteins in Borrelia burgdoferi

Author: Christophe Chipot, François Dehez, Cécilia Hognon, Antonio Monari, Joanna Timmins, Simon Garaude, Laboratoire de Physique et Chimie Théoriques (LPCT), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Groupe Infection virale et cancer (IBS-VIC), Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Laboratoire International Associé (LIA), University of Illinois System-University of Illinois System-Centre National de la Recherche Scientifique (CNRS), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0303 health sciences, biology, Chemistry, [SDV]Life Sciences [q-bio], 010402 general chemistry, biology.organism_classification, 01 natural sciences, 0104 chemical sciences, Cell biology, 03 medical and health sciences, Molecular dynamics, Histone, Dna compaction, Gene expression, biology.protein, [CHIM]Chemical Sciences, General Materials Science, Epigenetics, Physical and Theoretical Chemistry, Borrelia burgdorferi, Dna packaging, Bacteria, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract: DNA compaction is essential to ensure the packaging of the genetic material in living cells and also plays a key role in the epigenetic regulation of gene expression. In both humans and bacteria, D...
Published: 2019
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7. Induced Night-Vision by Singlet-Oxygen-Mediated Activation of Rhodopsin

Author: Hugo Gattuso, Antonio Monari, Miriam Navarrete-Miguel, Christophe Chipot, Wensheng Cai, Hong Zhang, Daniel Roca-Sanjuán, Angelo Giussani, Marco Marazzi, François Dehez, Laboratoire de Physique et Chimie Théoriques (LPCT), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Universidad de Alcalá - University of Alcalá (UAH), Instituto de Ciencia Molecular (ICMol), Universitat de València (UV), Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University (NKU), Laboratoire International Associé (LIA), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Illinois at Urbana-Champaign, USA], and University of Illinois System-University of Illinois System
Subjects: genetic structures, biology, 010405 organic chemistry, Singlet oxygen, Photoreceptor protein, Retinal, 010402 general chemistry, 01 natural sciences, Visual sensitivity, eye diseases, Transmembrane protein, 0104 chemical sciences, chemistry.chemical_compound, chemistry, Rhodopsin, Night vision, biology.protein, Biophysics, [CHIM]Chemical Sciences, General Materials Science, Physical and Theoretical Chemistry, ComputingMilieux_MISCELLANEOUS, Visual phototransduction
Abstract: In humans, vision is limited to a small fraction of the whole electromagnetic spectrum. One possible strategy for enhancing vision in deep-red or poor-light conditions consists of recruiting chlorophyll derivatives in the rod photoreceptor cells of the eye, as suggested in the case of some deep-sea fish. Here, we employ all-atom molecular simulations and high-level quantum chemistry calculations to rationalize how chlorin e6 (Ce6), widely used in photodynamic therapy although accompanied by enhanced visual sensitivity, mediates vision in the dark, shining light on a fascinating but largely unknown molecular mechanism. First, we identify persistent interaction sites between Ce6 and the extracellular loops of rhodopsin, the transmembrane photoreceptor protein responsible for the first steps in vision. Triggered by Ce6 deep-red light absorption, the retinal within rhodopsin can be isomerized thus starting the visual phototransduction cascade. Our data largely exclude previously hypothesized energy-transfer mechanisms while clearly lending credence to a retinal isomerization indirectly triggered by singlet oxygen, proposing an alternative mechanism to rationalize photosensitizer-mediated night vision.
Published: 2019
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8. Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors

Author: Audrey Hessel, Katharina Weinhäupl, Adrián Velázquez-Campoy, Christophe Chipot, Cécile Morlot, Paul Schanda, Jan Felix, François Dehez, Olga Abian, Hugo Pacheco de Freitas Fraga, Irina Gutsche, Diego F. Gauto, Instituto de Investigação e Inovação em Saúde, Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry, Physiology and Microbiology, Universiteit Gent = Ghent University [Belgium] (UGENT), Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique et Chimie Théoriques (LPCT), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Laboratoire International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France., Unidad Asociada IQFR-CSIC-BIFI [Zaragoza, Spain], University of Zaragoza - Universidad de Zaragoza [Zaragoza]-Instituto de Biocomputación y Física de Sistemas Complejos - BIFI [Zaragoza, Spain], Grenoble Partnership for Structural Biology (PSB), Innovative EM/NMR approach for the characterization of the drug target ClpP APPID: 301, ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), Centre National de la Recherche Scientifique (France), Agence Nationale de la Recherche (France), Ministerio de Economía y Competitividad (España), Instituto de Salud Carlos III, European Science Foundation, European Commission, SCOAP, Universiteit Gent = Ghent University (UGENT), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and University of Illinois System
Subjects: DYNAMICS, [SDV]Life Sciences [q-bio], medicine.medical_treatment, Crystallography, X-Ray, Biochemistry, 01 natural sciences, Serine, Structural Biology, Catalytic Domain, CRYSTAL-STRUCTURE, Research Articles, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, 0303 health sciences, Multidisciplinary, biology, Chemistry, Thermus thermophilus / enzymology, SciAdv r-articles, Endopeptidase Clp, Bacterial Proteins / chemistry, 3. Good health, INSIGHTS, Drug development, ESCHERICHIA-COLI, NMR-SPECTROSCOPY, Endopeptidase Clp / antagonists & inhibitors, Research Article, medicine.drug, PROTEINS, Protein subunit, Allosteric regulation, TUBERCULOSIS, 010402 general chemistry, 03 medical and health sciences, Bacterial Proteins, Allosteric Regulation, medicine, Protease Inhibitors, Bacterial Proteins / antagonists & inhibitors, 030304 developmental biology, COMPLEX, Protease, 010405 organic chemistry, Thermus thermophilus, Biology and Life Sciences, Active site, Isothermal titration calorimetry, 0104 chemical sciences, MODEL, SERINE-PROTEASE, Enzyme, Endopeptidase Clp / chemistry, Chaperone (protein), Proteasome inhibitor, biology.protein, Biophysics, Protease Inhibitors / chemistry
Abstract: 18 pags., 6 figs., 1 tab. -- Open Access funded by Creative Commons Atribution Licence 4.0, Coordinated conformational transitions in oligomeric enzymatic complexes modulate function in response to substrates and play a crucial role in enzyme inhibition and activation. Caseinolytic protease (ClpP) is a tetradecameric complex, which has emerged as a drug target against multiple pathogenic bacteria. Activation of different ClpPs by inhibitors has been independently reported from drug development efforts, but no rationale for inhibitor-induced activation has been hitherto proposed. Using an integrated approach that includes x-ray crystallography, solid- and solution-state nuclear magnetic resonance, molecular dynamics simulations, and isothermal titration calorimetry, we show that the proteasome inhibitor bortezomib binds to the ClpP active-site serine, mimicking a peptide substrate, and induces a concerted allosteric activation of the complex. The bortezomib-activated conformation also exhibits a higher affinity for its cognate unfoldase ClpX. We propose a universal allosteric mechanism, where substrate binding to a single subunit locks ClpP into an active conformation optimized for chaperone association and protein processive degradation., This work used the platforms of the Grenoble Instruct center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) with support from INSTRUCT (“Innovative EM/NMR approach for the characterization of the drug target ClpP APPID: 301“), FRISBI (ANR-10-INSB-05-02), and GRAL (ANR-10-LABX-49-01) within the Grenoble Partnership for Structural Biology (PSB). We thank the ESRF for beamtime at ID30A and ID23-1. Funding: This work was supported by Spanish Ministerio de Economia y Competitividad (BFU2016-78232-P) and Instituto de Salud Carlos III co-funded by European Union (PI15/00663 and PI18/00349, ERDF/ ESF, “Investing in your future”). This work was financially supported by the European Research Council (ERC-Stg-2012-311318 to P.S.). J.F. is supported by an EMBO long-term post-doctoral fellowship (ALTF441-2017).
Published: 2019
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9. Changes in Microenvironment Modulate the B- to A-DNA Transition

Author: Xueguang Shao, Haohao Fu, Wensheng Cai, Hong Zhang, Christophe Chipot, François Dehez, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University (NKU), Laboratoire de Physique et Chimie Théoriques (LPCT), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire International Associé (LIA), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois System-University of Illinois System, and Collaborative Innovation Center of Chemical Science and Engineering [Tianjin, China]
Subjects: Models, Molecular, General Chemical Engineering, Salt (chemistry), DNA, A-Form, Library and Information Sciences, 01 natural sciences, chemistry.chemical_compound, 0103 physical sciences, Molecule, A-DNA, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, 010304 chemical physics, Transition (genetics), Dose-Response Relationship, Drug, Ethanol, digestive, oral, and skin physiology, General Chemistry, 0104 chemical sciences, Computer Science Applications, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, 010404 medicinal & biomolecular chemistry, chemistry, Biophysics, Nucleic Acid Conformation, Chemical equilibrium, DNA, B-Form, DNA
Abstract: B- to A-DNA transition is known to be sensitive to the macroscopic properties of the solution, such as salt and ethanol concentrations. Microenvironmental effects on DNA conformational transition have been broadly studied. Providing an intuitive picture of how DNA responds to environmental changes is, however, still needed. Analyzing the chemical equilibrium of B-to-A DNA transition at critical concentrations, employing explicit-solvent simulations, is envisioned to help understand such microenvironmental effects. In the present study, free-energy calculations characterizing the B- to A-DNA transition and the distribution of cations were carried out in solvents with different ethanol concentrations. With the addition of ethanol, the most stable structure of DNA changes from the B- to A-form, in agreement with previous experimental observation. In 60% ethanol, a chemical equilibrium is found, showing reversible transition between B- and A-DNA. Analysis of the microenvironment around DNA suggests that with the increase of ethanol concentration, the cations exhibit a significant tendency to move toward the backbone, and mobility of water molecules around the major groove and backbone decreases gradually, leading eventually to a B-to-A transition. The present results provide a free-energy view of DNA microenvironment and of the role of cation motion in the conformational transition.
Published: 2019
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10. Enthalpy-Entropy Interplay in π-Stacking Interaction of Benzene Dimer in Water

Author: Christophe Chipot, François Dehez, Hankyul Lee, Hyung-Kyu Lim, Hyungjun Kim, Korea Advanced Institute of Science and Technology (KAIST), Laboratoire de Physique et Chimie Théoriques (LPCT), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire International Associé (LIA), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Illinois at Urbana-Champaign, USA], and University of Illinois System-University of Illinois System
Subjects: chemistry.chemical_classification, 010304 chemical physics, Chemistry, Dimer, Enthalpy, Supramolecular chemistry, Stacking, 01 natural sciences, Computer Science Applications, Hydrophobic effect, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, chemistry.chemical_compound, Molecular dynamics, Chemical physics, 0103 physical sciences, Non-covalent interactions, Physical and Theoretical Chemistry, ComputingMilieux_MISCELLANEOUS, Entropy (order and disorder)
Abstract: Aromatic groups can engage in an interesting class of noncovalent interactions termed π-π interactions, which play a pivotal role in stabilizing a variety of molecular architectures, including nucleic acids, proteins, and supramolecular assemblies. When the aromatic compounds interact with each other in an aqueous environment, their association is facilitated by the hydrophobic effect-the trend of nonpolar solutes to aggregate in a polar solution. To develop an in-depth understanding of hydrophobic association, we investigate in the present work π-π interactions in water, employing as a paradigm the benzene dimer. Using DFT-CES, a mean-field QM/MM method recently developed by our group, we describe the benzene solute at a quantum-mechanical level. Full consideration of detailed solute-electron density enables an optimal description of the solute-solvent interactions, leading to an accurate prediction of hydration free energies. In π-stacking of benzene, we find an entropic stabilization associated with the shrinkage of the solvent-excluded volume, which agrees with the theory of hydrophobic effect at subnanoscales. However, at the equilibrium binding distance of the benzene dimer, we find that the entropic stabilization nearly cancels out due to the enthalpic cost required for dewetting the internal space. Such an enthalpy-entropy compensation leads the association free energy to be predominantly dictated by the solute-solute interaction enthalpy. The present work offers new insight into the mechanistic role of water and the primary thermodynamic driving force of hydrophobic association.
Published: 2019
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11. Triggering Tautomerization of Curcumin by Confinement into Liposomes

Author: Ewa Rogalska, Stéphane Parant, Maxime Girardon, Antonio Monari, Christophe Chipot, Andreea Pasc, Nadia Canilho, François Dehez, Laboratoire Lorrain de Chimie Moléculaire (L2CM), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique et Chimie Théoriques (LPCT), Laboratoire International Associé (LIA), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois System-University of Illinois System, PhotoNS, and Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Liposome, food.ingredient, 010304 chemical physics, Organic Chemistry, 02 engineering and technology, 021001 nanoscience & nanotechnology, Photochemistry, 01 natural sciences, Fluorescence, Tautomer, Lecithin, Analytical Chemistry, chemistry.chemical_compound, food, chemistry, 0103 physical sciences, Curcumin, [CHIM]Chemical Sciences, Physical and Theoretical Chemistry, 0210 nano-technology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2019
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12. Conformational transitions of the serotonin 5-HT3 receptor

Author: Emmanuelle Neumann, Ghérici Hassaine, Hugues Nury, Jonathan Perot, Anders A. Jensen, François Dehez, Christophe Chipot, Jacques Neyton, Lucie Polovinkin, Pierre-Jean Corringer, Guy Schoehn, Solène N Lefebvre, Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Theranyx SA (Theranyx), Department of Drug Design and Pharmacology [Copenhagen] (ILF), Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Récepteurs Canaux - Channel Receptors, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Laboratoire de Physique et Chimie Théoriques (LPCT), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Laboratoire International Associé (LIA), University of Illinois System-University of Illinois System-Centre National de la Recherche Scientifique (CNRS), The work was funded by the Marie Curie CIG NeuroPenta and ERC Starting grant 637733 (to H.N.). It used the platforms of the Grenoble Instruct-ERIC Center (ISBG: UMS 3518 CNRS-CEA-UGA-EMBL) with support from FRISBI (ANR-10 INSB-05-02) and GRAL (ANR-10-LABX-49-01) within the Grenoble PSB. The electron microscopy facility is supported by the Rhône-Alpes Region, the FRM, the FEDER and the GIS-IBISA., ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), European Project: 637733,H2020,ERC-2014-STG,PentaBrain(2015), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Multidisciplinary, Allosteric modulator, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Allosteric regulation, Gating, 03 medical and health sciences, chemistry.chemical_compound, 030104 developmental biology, 0302 clinical medicine, chemistry, Biophysics, Serotonin, Binding site, Neurotransmitter, Receptor, 030217 neurology & neurosurgery, Ion channel
Abstract: International audience; The serotonin 5-HT3 receptor is a pentameric ligand-gated ion channel (pLGIC). It belongs to a large family of receptors that function as allosteric signal transducers across the plasma membrane1,2; upon binding of neurotransmitter molecules to extracellular sites, the receptors undergo complex conformational transitions that result in transient opening of a pore permeable to ions. 5-HT3 receptors are therapeutic targets for emesis and nausea, irritable bowel syndrome and depression3. In spite of several reported pLGIC structures4-8, no clear unifying view has emerged on the conformational transitions involved in channel gating. Here we report four cryo-electron microscopy structures of the full-length mouse 5-HT3 receptor in complex with the anti-emetic drug tropisetron, with serotonin, and with serotonin and a positive allosteric modulator, at resolutions ranging from 3.2 Å to 4.5 Å. The tropisetron-bound structure resembles those obtained with an inhibitory nanobody5 or without ligand9. The other structures include an 'open' state and two ligand-bound states. We present computational insights into the dynamics of the structures, their pore hydration and free-energy profiles, and characterize movements at the gate level and cation accessibility in the pore. Together, these data deepen our understanding of the gating mechanism of pLGICs and capture ligand binding in unprecedented detail.
Published: 2018
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13. Dynamics and interactions of AAC3 in DPC are not functionally relevant

Author: Christophe Chipot, Vilius Kurauskas, François Dehez, Beate Bersch, Paul Schanda, Audrey Hessel, Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Physique et Chimie Théoriques (LPCT), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire International Associé (LIA), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois System-University of Illinois System, Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, biology, Membrane transport protein, Dynamics (mechanics), Nuclear magnetic resonance spectroscopy, 010402 general chemistry, 01 natural sciences, 0104 chemical sciences, 03 medical and health sciences, chemistry.chemical_compound, Adenosine diphosphate, 030104 developmental biology, chemistry, Structural Biology, biology.protein, Biophysics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Adenosine triphosphate, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2018
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14. α-Helix Unwinding as Force Buffer in Spectrins

Author: Hirohide Takahashi, Felix Rico, Simon Scheuring, Christophe Chipot, BIO-AFM-LAB Bio Atomic Force Microscopy Laboratory (Bio-AFM-Lab), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Weill Medical College of Cornell University [New York], Laboratoire International Associé Centre National de la Recherche Scientifique, University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Department of Physics [Illinois at Urbana-Champaign, USA], Laboratoire de Physique et Chimie Théoriques (LPCT), and Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], General Physics and Astronomy, macromolecular substances, Spring (mathematics), 01 natural sciences, 03 medical and health sciences, Molecular dynamics, unwinding, 0103 physical sciences, General Materials Science, Spectrin, Cytoskeleton, High-Speed Force Spectroscopy, Actin, unfolding, 010304 chemical physics, Chemistry, General Engineering, Force spectroscopy, 030104 developmental biology, Membrane, Helix, Biophysics, Force Spectroscopy, AFM
Abstract: Spectrins are cytoskeletal proteins located at the inner face of the plasma membrane, making connections between membrane anchors and the actin cortex, and between actin filaments. Spectrins share a common structure forming a bundle of 3 α-helices and play a major role during cell deformation. Here, we used high-speed force spectroscopy and steered molecular dynamics simulations to understand the mechanical stability of spectrin, revealing a molecular force buffering function. We find that spectrin acts as a soft spring at short extensions (70-100 Å). Under continuous external stretching, its α-helices unwind, leading to a viscous mechanical response over larger extensions (100-300 Å), represented by a constant-force plateau in force/extension curves. This viscous force buffering emerges from a quasi-equilibrium competition between disruption and re-formation of α-helical hydrogen bonds. Our results suggest that, in contrast to β-sheet proteins, which unfold in a catastrophic event, α-helical spectrins dominantly unwind, providing a viscous force buffer over extensions about 5 times their folded length.
Published: 2018
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15. Thermodynamics of DNA: sensitizer recognition. Characterizing binding motifs with all-atom simulations

Author: Hugo Gattuso, Elise Dumont, Antonio Monari, Christophe Chipot, François Dehez, Structure et Réactivité des Systèmes Moléculaires Complexes (SRSMC), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie - UMR5182 (LC), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon)-Institut de Chimie du CNRS (INC), Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Laboratoire International Associé (LIA), University of Illinois System-University of Illinois System-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Models, Molecular, Binding free energy, Binding energy, General Physics and Astronomy, 010402 general chemistry, 01 natural sciences, Molecular dynamics, chemistry.chemical_compound, Competitive binding, 0103 physical sciences, Atom, Benzophenone, Animals, Humans, [CHIM]Chemical Sciences, Computer Simulation, Physical and Theoretical Chemistry, ComputingMilieux_MISCELLANEOUS, 010304 chemical physics, Chemistry, Intercalating Agents, 0104 chemical sciences, Crystallography, Chemical physics, Nucleic Acid Conformation, Thermodynamics, DNA, B-Form, DNA, Minor groove
Abstract: We report the investigation of the thermochemical properties of benzophenone interacting with B-DNA studied by all-atom molecular dynamic simulations. In particular, we determine the binding free energy for two competitive binding modes, minor groove binding and double insertion. Our results allow us to quantitatively resolve for the first time the mode of binding of this paradigmatic photosensitizer, indicating a marked preference for minor groove binding. Furthermore, we have settled a protocol allowing for the determination of binding energies in the case of non-covalent interaction with DNA, in particular, tackling the non-trivial problem of the strong reorganization of the DNA imposing extended statistical sampling. Our contribution paves the way to the systematic determination of the thermochemical properties of drugs or pollutants interacting with DNA.
Published: 2016
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16. Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins with Non-native Affinity

Author: Christophe Chipot, François Dehez, Edmund R.S. Kunji, Martin S. King, Paul Schanda, Laboratoire International Associé Centre National de la Recherche Scientifique, University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge [UK] (CAM), King, Martin [0000-0001-6030-5154], Kunji, Edmund [0000-0002-0610-4500], Apollo - University of Cambridge Repository, Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire International Associé (LIA), University of Illinois System-University of Illinois System-Centre National de la Recherche Scientifique (CNRS), Structure et Réactivité des Systèmes Moléculaires Complexes (SRSMC), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL), MRC Mitochondrial Biology Unit, Dunn Human Nutrition Unit, Medical Research Council, and Department of Physics [Illinois at Urbana-Champaign, USA]
Subjects: 0301 basic medicine, Cardiolipins, Phosphorylcholine, Biophysics, Biology, Article, 03 medical and health sciences, Molecular dynamics, Protein structure, [CHIM]Chemical Sciences, Binding selectivity, ComputingMilieux_MISCELLANEOUS, reproductive and urinary physiology, 030102 biochemistry & molecular biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Yeast, Mitochondria, 030104 developmental biology, Membrane protein, Biochemistry, Solubilization, embryonic structures, ATP–ADP translocase, Mitochondrial ADP, ATP Translocases, Protein Binding
Abstract: International audience; Biophysical investigation of membrane proteins generally requires their extraction from native sources using detergents, a step that can lead, possibly irreversibly, to protein denaturation. The propensity of dodecylphosphocholine (DPC), a detergent widely utilized in NMR studies of membrane proteins, to distort their structure has been the subject of much controversy. It has been recently proposed that the binding specificity of the yeast mitochondrial ADP/ATP carrier (yAAC3) toward cardiolipins is preserved in DPC, thereby suggesting that DPC is a suitable environment in which to study membrane proteins. In this communication, we used all-atom molecular dynamics simulations to investigate the specific binding of cardiolipins to yAAC3. Our data demonstrate that the interaction interface observed in a native-like environment differs markedly from that inferred from an NMR investigation in DPC, implying that in this detergent, the protein structure is distorted. We further investigated yAAC3 solubilized in DPC and in the milder dodecylmaltoside with thermal-shift assays. The loss of thermal transition observed in DPC confirms that the protein is no longer properly folded in this environment.
Published: 2017
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17. A central cavity within the holo-translocon suggests a mechanism for membrane protein insertion

Author: Ian Collinson, Aurélien Deniaud, Juri Rappsilber, Patrick Schultz, Nathan R. Zaccai, Manikandan Karuppasamy, Remy Martin, Kèvin Knoops, Juan Zou, Christiane Schaffitzel, Klaus Schulten, Giuseppe Zaccai, Imre Berger, Gabor Papai, Qiyang Jiang, Mathieu Botte, Jelger A. Lycklama a Nijeholt, Abhishek Roy, Laboratoire européen de biologie moléculaire - European Molecular Biology Laboratory (EMBL Grenoble), European Molecular Biology Laboratory [Grenoble] (EMBL), School of Biochemistry, University of Bristol [Bristol], 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), Wellcome Trust Centre for Cell Biology, University of Edinburgh, Department of Physics, University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Department of Physics [Illinois at Urbana-Champaign, USA], Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Thomas, Frank, Zaccai, Nathan [0000-0002-1476-2044], and Apollo - University of Cambridge Repository
Subjects: Models, Molecular, Protein Conformation, alpha-Helical, 0301 basic medicine, Methanocaldococcus, [SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Genetic Vectors, Gene Expression, membrane proteins, Article, Substrate Specificity, 03 medical and health sciences, Scattering, Small Angle, biophysical chemistry, Escherichia coli, Protein Interaction Domains and Motifs, Cloning, Molecular, Binding Sites, Multidisciplinary, electron microscopy, 030102 biochemistry & molecular biology, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Escherichia coli Proteins, Thermus thermophilus, Cryoelectron Microscopy, Membrane Transport Proteins, SAXS, Periplasmic space, biology.organism_classification, Translocon, Recombinant Proteins, Transport protein, Neutron Diffraction, Protein Transport, 030104 developmental biology, Biochemistry, Membrane protein, Structural Homology, Protein, Chaperone (protein), ddc:000, biology.protein, Biophysics, Protein Conformation, beta-Strand, SEC Translocation Channels, Protein Binding, Biophysical chemistry
Abstract: The conserved SecYEG protein-conducting channel and the accessory proteins SecDF-YajC and YidC constitute the bacterial holo-translocon (HTL), capable of protein-secretion and membrane-protein insertion. By employing an integrative approach combining small-angle neutron scattering (SANS), low-resolution electron microscopy and biophysical analyses we determined the arrangement of the proteins and lipids within the super-complex. The results guided the placement of X-ray structures of individual HTL components and allowed the proposal of a model of the functional translocon. Their arrangement around a central lipid-containing pool conveys an unexpected, but compelling mechanism for membrane-protein insertion. The periplasmic domains of YidC and SecD are poised at the protein-channel exit-site of SecY, presumably to aid the emergence of translocating polypeptides. The SecY lateral gate for membrane-insertion is adjacent to the membrane ‘insertase’ YidC. Absolute-scale SANS employing a novel contrast-match-point analysis revealed a dynamic complex adopting open and compact configurations around an adaptable central lipid-filled chamber, wherein polytopic membrane-proteins could fold, sheltered from aggregation and proteolysis.
Published: 2017
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18. Light Harvesting by Lamellar Chromatophores in Rhodospirillum photometricum

Author: Danielle E. Chandler, Melih Sener, Simon Scheuring, Johan Strümpfer, Klaus Schulten, Beckman Institute [Illinois at Urbana-Champaign, USA], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Center for Biophysics and Computational Biology [Illinois at Urbana-Champaign, USA], BIO-AFM-LAB Bio Atomic Force Microscopy Laboratory (Bio-AFM-Lab), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Physics [Illinois at Urbana-Champaign, USA], and Aix-Marseille Université, U1006
Subjects: Rhodospirillum, Rhodospirillum photometricum, Atomic force microscopy, Molecular Sequence Data, Light-Harvesting Protein Complexes, Biophysics, Bacterial Chromatophores, Molecular Dynamics Simulation, Biology, Chromatophore, Protein Structure, Tertiary, Bacterial protein, Absorption, Physicochemical, Bacterial Proteins, Biochemistry, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Lamellar structure, Amino Acid Sequence, Photosynthetic bacteria, Proteins and Nucleic Acids
Abstract: International audience; Purple photosynthetic bacteria harvest light using pigment-protein complexes which are often arranged in pseudo-organelles called chromatophores. A model of a chromatophore from Rhodospirillum photometricum was constructed based on atomic force microscopy data. Molecular-dynamics simulations and quantum-dynamics calculations were performed to characterize the intercomplex excitation transfer network and explore the interplay between close-packing and light-harvesting efficiency.
Published: 2014
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19. Resolution Dependence of Magnetorotational Turbulence in the Isothermal Stratified Shearing Box

Author: Benjamin R. Ryan, Pierre Kestener, Sebastien Fromang, Charles F. Gammie, Astrophysique Interprétation Modélisation (AIM (UMR_7158 / UMR_E_9005 / UM_112)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Maison de la Simulation (MDLS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Sud - Paris 11 (UP11)-Institut National de Recherche en Informatique et en Automatique (Inria)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut National de Recherche en Informatique et en Automatique (Inria)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Laboratoire AIM, Université Paris Diderot - Paris 7 ( UPD7 ) -Centre d'Etudes de Saclay, Maison de la Simulation ( MDLS ), Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université de Versailles Saint-Quentin-en-Yvelines ( UVSQ ), and Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Paris-Sud - Paris 11 (UP11)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)
Subjects: Angular momentum, 010504 meteorology & atmospheric sciences, [ PHYS.ASTR ] Physics [physics]/Astrophysics [astro-ph], FOS: Physical sciences, 01 natural sciences, accretion, Magnetorotational instability, 0103 physical sciences, Shear stress, 010303 astronomy & astrophysics, 0105 earth and related environmental sciences, Shearing (physics), Physics, High Energy Astrophysical Phenomena (astro-ph.HE), Turbulence, accretion disks, turbulence, Astronomy and Astrophysics, Scale height, Computational physics, Space and Planetary Science, Magnetohydrodynamics, Astrophysics - High Energy Astrophysical Phenomena, magnetohydrodynamics, [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph], Dimensionless quantity
Abstract: Magnetohydrodynamic (MHD) turbulence driven by the magnetorotational instability can provide diffusive transport of angular momentum in astrophysical disks, and a widely studied computational model for this process is the ideal, stratified, isothermal shearing box. Here we report results of a convergence study of such boxes up to a resolution of $N = 256$ zones per scale height, performed on blue waters at NCSA with ramses-gpu. We find that the time and vertically integrated dimensionless shear stress $\overline{\alpha} \sim N^{-1/3}$, i.e. the shear stress is resolution dependent. We also find that the magnetic field correlation length decreases with resolution, $\lambda \sim N^{-1/2}$. This variation is strongest at the disk midplane. We show that our measurements of $\alpha$ are consistent with earlier studies. We discuss possible reasons for the lack of convergence., Comment: 35 pages, 9 figures, submitted to ApJ. Comments welcome
Published: 2017
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20. Adaptive Multilevel Splitting Method for Molecular Dynamics Calculation of Benzamidine-Trypsin Dissociation Time

Author: Christopher G. Mayne, Tony Lelièvre, Ivan Teo, Klaus Schulten, Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, The Beckman Institute for Advanced Science and Technology, Centre d'Enseignement et de Recherche en Mathématiques et Calcul Scientifique (CERMICS), École des Ponts ParisTech (ENPC), MATHematics for MatERIALS (MATHERIALS), École des Ponts ParisTech (ENPC)-École des Ponts ParisTech (ENPC)-Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), European Project: 614492,EC:FP7:ERC,ERC-2013-CoG,MSMATH(2014), Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre d'Enseignement et de Recherche en Mathématiques et Calcul Scientifique (CERMICS), and École des Ponts ParisTech (ENPC)-École des Ponts ParisTech (ENPC)
Subjects: 0301 basic medicine, Field (physics), Computer science, Monte Carlo method, Molecular Dynamics Simulation, Ligands, 01 natural sciences, Article, Dissociation (chemistry), Benzamidine, 03 medical and health sciences, Search engine, Molecular dynamics, chemistry.chemical_compound, 0103 physical sciences, Trypsin, Rare Event Sampling, Statistical physics, Physical and Theoretical Chemistry, Simulation, 010304 chemical physics, Sampling (statistics), Benzamidines, Computer Science Applications, 030104 developmental biology, chemistry, Monte Carlo Method, Algorithms, [MATH.MATH-NA]Mathematics [math]/Numerical Analysis [math.NA], Protein Binding
Abstract: International audience Adaptive multilevel splitting (AMS) is a rare event sampling method that requires minimal parameter tuning and allows unbiased sampling of transition pathways of a given rare event. Previous simulation studies have verified the efficiency and accuracy of AMS in the calculation of transition times for simple systems in both Monte Carlo and molecular dynamics (MD) simulations. Now, AMS is applied for the first time to an MD simulation of protein–ligand dissociation, representing a leap in complexity from the previous test cases. Of interest is the dissociation rate, which is typically too low to be accessible to conventional MD. The present study joins other recent efforts to develop advanced sampling techniques in MD to calculate dissociation rates, which are gaining importance in the pharmaceutical field as indicators of drug efficacy. The system investigated here, benzamidine bound to trypsin, is an example common to many of these efforts. The AMS estimate of the dissociation rate was found to be (2.6 ± 2.4) × 102 s–1, which compares well with the experimental value.
Published: 2016
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21. Orientation discrimination of single-stranded DNA inside the α-hemolysin membrane channel

Author: Aleksei Aksimentiev, Jérôme Mathé, David R. Nelson, Amit Meller, Klaus Schulten, Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois at Urbana-Champaign [Urbana], and University of Illinois System-University of Illinois System
Subjects: Models, Molecular, Stereochemistry, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Diffusion, Bacterial Toxins, Biophysics, DNA, Single-Stranded, 02 engineering and technology, In Vitro Techniques, 010402 general chemistry, Hemolysin Proteins, 01 natural sciences, Biophysical Phenomena, Ion Channels, Ion, Motion, Molecular dynamics, chemistry.chemical_compound, Molecule, Ion channel, Multidisciplinary, Base Sequence, Biological Sciences, 021001 nanoscience & nanotechnology, 0104 chemical sciences, chemistry, Nucleic Acid Conformation, Thermodynamics, Membrane channel, Poly A, 0210 nano-technology, DNA
Abstract: International audience; We characterize the voltage-driven motion and the free motion of single-stranded DNA (ssDNA) molecules captured inside the Ϸ1.5-nm ␣-hemolysin pore, and show that the DNA-channel interactions depend strongly on the orientation of the ssDNA molecules with respect to the pore. Remarkably, the voltage-free diffusion of the 3-threaded DNA (in the trans to cis direction) is two times slower than the corresponding 5-threaded DNA having the same poly(dA) sequence. Moreover, the ion currents flowing through the blocked pore with either a 3-threaded DNA or 5 DNA differ by Ϸ30%. All-atom molecular dynamics simulations of our system reveal a microscopic mechanism for the asymmetric behavior. In a confining pore, the ssDNA straightens and its bases tilt toward the 5 end, assuming an asymmetric conformation. As a result, the bases of a 5-threaded DNA experience larger effective friction and forced reorientation that favors co-passing of ions. Our results imply that the translocation process through a narrow pore is more complicated than previously believed and involves base tilting and stretching of ssDNA molecules inside the confining pore. asymmetry ͉ DNA translocation ͉ DNA hairpin T he transport of biomolecules across cell walls is a ubiquitous process in biology, controlled by membrane proteins that act as selective channels and transporters (1, 2). These processes usually involve the passage of a biopolymer through a narrow proteinic confinement that, in the case of polynucleic acids, can result in temporary structural deformations of the molecules. The ability of membrane proteins to sort single molecules, and in particular polynucleic acids, is also of great interest in bioengineering. In the past few years membrane channels like the bacterial ␣-hemolysin (␣-HL) have been adapted as in vitro devices for rapid, single-molecule nucleic acid characterization (3-7). In these experiments the negatively charged single-stranded DNA (ssDNA) or RNA molecules were electrophoreti-cally driven through a single, membrane-embedded pore having dimensions that are only slightly larger than the size of a nucleotide (8). The passage time of each individual molecule was measured by monitoring the residual ion current f lowing through the pore during the transport of the biopolymer. One of the important findings has been that the translocation dynamics is dominated by the nucleic acid interactions with the pore walls, and that these interactions are substantially stronger for purine-rich DNA sequences as compared with pyrimidine-rich molecules (5, 9). However, the microscopic source for this sequence selectivity as well as the exact shape of the interaction potential between the DNA and the pore have not yet been resolved. In particular, it was unclear whether the asymmetric structure of ␣-HL (8) coupled with the directionality of ssDNA can lead to asymmetric polynucleotide dynamics, with and without an external biasing potential. To address these questions, we have carried out extensive DNA translocation experiments, which take advantage of the finding that ssDNA can enter the trans membrane pore of the ␣-HL, but double-stranded DNA cannot (8, 10-12). Thus, DNA hairpin molecules with a long single-stranded overhang only enter the ␣-HL pore with the single-stranded part, either the 3Ј or the 5Ј end, depending on the DNA construct. As a result, the blockade currents and the DNA transport resulting from either 3Ј or 5Ј entries can be unambiguously discriminated and characterized. Moreover, by taking advantage of the dynamic voltage control method (13), the escape dynamics of molecules from the pore can be measured at a finite voltage level, as well as at V ϭ 0. Previous DNA translocation experiments have revealed two peaks in the translocation time distribution (3) as well as in the blockade current histogram (5, 7, 13) comprised of several hundred translocation events from identical molecules. The two peaks have been associated with the direction of polynucleotide translocation, either 3Ј or 5Ј end first (5, 7, 14). However, it remained unclear which of the two orientations produce the shorter blockade times and the lower blockade current. Here, we show that 3Ј end DNA entries induce a larger current blockade as compared with the 5Ј end threading, and measure the fundamental, voltage-free diffusion constants associated with either 3Ј or 5Ј threading of ssDNA through the pore. Remarkably , we found that the voltage-free dynamics of the 3Ј-threaded molecules (entering and exiting from the same side of the pore) is two times slower than the corresponding diffusion of the 5Ј threading. To delineate the underlying mechanism responsible for the observed dynamics, we carried out all-atom molecular dynamics (MD) simulations, using the known structures of the ␣-HL pore and the DNA. The MD simulations independently confirmed the experimental results, indicating that the 3Ј threading blocks the ion current more effectively and will result in stronger interactions. Moreover, the MD data allow us to pinpoint a mechanistic explanation for the observed asymmetry in DNA dynamics based on a microscopic picture. We find that the confinement of the ssDNA in the ␣-HL pore results in straightening of the DNA backbone and, consequently, in a collective tilt of the bases with respect to the DNA backbone in the direction of the 5Ј end of the molecule, and that this tilt can create an asymmetric DNA-pore interaction. Noteworthy is the fact that the MD simulations were performed without any a priori knowledge of the experimental data (i.e., which orientation is faster or causes larger ion current blockade). Our results agree with a theoretical model that describes the DNA-pore interactions by using a different asymmetric sawtooth potential for each orientation (14). These potentials yield asymmetric dynamics of the threaded DNA even at zero applied voltage, as observed in our experiments. Methods Experiments. PAGE-purified ssDNA and DNA hairpins (Euro-gentec, San Diego) were buffered in 10 mM Tris͞1 mM EDTA (pH 8.5) solution. Before each measurement the samples were heated to 75°C for 10 min and then quenched to 4°C. The hairpins are constituted of a single-stranded overhang of 50
Published: 2005
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22. Stability of Glassy and Ferroelectric States in the Relaxors PbMg1/3Nb2/3O3 and PbMg1/3Nb2/3O3-12% PbTiO3

Author: Colla, Eugene V., Vigil, D., Timmerwilke, J., Weissman, Michael B., Viehland, Dwight D., Dkhil, B., Laboratoire Structures, Propriétés et Modélisation des solides (SPMS), CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Department of Materials Science and Engineering [Blacksburg] (MSE), Virginia Tech [Blacksburg], Institut de Chimie du CNRS (INC)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Materials Science and Engineering (MSE), and Virginia Tech
Subjects: Condensed Matter - Materials Science, Phase transitions, Polarization, Physics, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Materials Science (cond-mat.mtrl-sci), FOS: Physical sciences, PACS: 77.80.-e, 75.10.Nr, 77.84.-s, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph]
Abstract: The stability of the disordered glassy phase in the relaxors PbMg1/3Nb2/3O3 and (PbMg1/3Nb2/3O3)0.88(PbTiO3)0.12, called PMN and PMN-PT, was investigated by preparing partially polarized samples and allowing them to age at zero field in the temperature range for which the phase is history-dependent. The PMN-PT polarization would spontaneously increase until long-range order formed, first appearing as giant polarization noise. Thus the thermodynamically stable phase in PMN-PT appears to be ferroelectric. In contrast, a PMN sample lacking the sharp first-order field-driven transition found in some other samples spontaneously depolarized, consistent with its glassy state being thermodynamically stable. Detailed thermal depolarization results in PMN show two distinct broad peaks as well as a small fraction of material with a distribution of abrupt melting transitions., submitted to Phys. Rev. B. 9 text pages + 10 figs
Published: 2007
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23. Quasivertical line in the phase diagram of single crystals of Pb Mg1 3 Nb2 3 O3 -x PbTiO3 (x=0.00, 0.06, 0.13, and 0.24) with a giant piezoelectric effect

Author: Raevskaya, S.I., Emelyanov, A.S., Savenko, F.I., Panchelyuga, M.S., Raevski, I.P., Prosandeev, S.A., Colla, E.V., Chen, H., Lu, S.G., Blinc, R., Kutnjak, Z., Gemeiner, P., Dkhil, B., Kamzina, L.S., Southern Federal University [Rostov-on-Don] (SFEDU), University of Arkansas for Medical Sciences (UAMS), Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Tunghai University [Taichung], City University of Hong Kong [Hong Kong] (CUHK), Jozef Stefan Institute [Ljubljana] (IJS), Laboratoire Structures, Propriétés et Modélisation des solides (SPMS), Institut de Chimie du CNRS (INC)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), A.F. Ioffe Physical-Technical Institute, and Russian Academy of Sciences [Moscow] (RAS)
Subjects: [SPI.MAT]Engineering Sciences [physics]/Materials
Abstract: We show that the phase diagram of the (001) Pb Mg1 3 Nb2 3 O3 -x PbTiO3 (PMN- x PT) (x=0.00, 0.06, 0.13, and 0.24) and (111) PMN-0.24PT lead-magnesium niobate mixed with lead titanate possesses a quasivertical line in the E electric field - T temperature plot, which hardly depends on the field. The existence of this line has been confirmed by independent studies of single crystals grown in different laboratories, by measuring the dielectric permittivity, compliances, and optical transmission, also in different laboratories. A thermal hysteresis inherent to first order phase transitions complicates the phase diagram. The piezoelectric coefficients of the (001) PMN- x PT (x = 0.06 and 0.13) have two peaks versus temperature, at finite fields. The first peak is due to the quasivertical phase boundary. The second is in the vicinity of a turning point of the Tm (E) temperature of the dielectric permittivity diffuse maximum. We show that the second peak prevails at reasonable fields, and the piezoelectric coefficients have comparatively large values at this peak, even at small x. © 2007 The American Physical Society.
Published: 2007
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24. Arctic curves of the octahedron equation

Author: Philippe Di Francesco, Rodrigo Soto-Garrido, Department of Mathematics [Urbana], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Institut de Physique Théorique - UMR CNRS 3681 (IPHT), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and Department of Physics [Illinois at Urbana-Champaign, USA]
Subjects: Statistics and Probability, Phase transition, exact solution, Dimer, [PHYS.MPHY]Physics [physics]/Mathematical Physics [math-ph], FOS: Physical sciences, General Physics and Astronomy, Probability density function, chemistry.chemical_compound, [MATH.MATH-MP]Mathematics [math]/Mathematical Physics [math-ph], arctic curve, Aztec diamond, [PHYS.COND.CM-SM]Physics [physics]/Condensed Matter [cond-mat]/Statistical Mechanics [cond-mat.stat-mech], Condensed Matter - Statistical Mechanics, Mathematical Physics, Physics, Statistical Mechanics (cond-mat.stat-mech), Mathematical analysis, Statistical and Nonlinear Physics, Mathematical Physics (math-ph), dimer, Exact solutions in general relativity, Arctic, chemistry, Octahedron, phase transition, Modeling and Simulation, Thermodynamic limit, tiling
Abstract: We study the octahedron relation (also known as the $A_{\infty}$ $T$-system), obeyed in particular by the partition function for dimer coverings of the Aztec Diamond graph. For a suitable class of doubly periodic initial conditions, we find exact solutions with a particularly simple factorized form. For these, we show that the density function that measures the average dimer occupation of a face of the Aztec graph, obeys a system of linear recursion relations with periodic coefficients. This allows us to explore the thermodynamic limit of the corresponding dimer models and to derive exact "arctic" curves separating the various phases of the system., Comment: 39 pages, 21 figures; typos fixed, four references and an appendix added
Published: 2014
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24 results on '"Department of Physics [Illinois at Urbana-Champaign, USA]"'

1. Modulation of membrane permeability by carbon dioxide

2. Skewness of mean transverse momentum fluctuations in heavy-ion collisions

3. Direct Comparison of Many-Body Methods for Realistic Electronic Hamiltonians

4. Hepatitis C virus sequence divergence preserves p7 viroporin structural and dynamic features

5. Structural Basis for Broad HIV-1 Neutralization by the MPER-Specific Human Broadly Neutralizing Antibody LN01

6. Molecular Basis of DNA Packaging in Bacteria Revealed by All-Atoms Molecular Dynamic Simulations: The case of histone like proteins in Borrelia burgdoferi

7. Induced Night-Vision by Singlet-Oxygen-Mediated Activation of Rhodopsin

8. Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors

9. Changes in Microenvironment Modulate the B- to A-DNA Transition

10. Enthalpy-Entropy Interplay in π-Stacking Interaction of Benzene Dimer in Water

11. Triggering Tautomerization of Curcumin by Confinement into Liposomes

12. Conformational transitions of the serotonin 5-HT3 receptor

13. Dynamics and interactions of AAC3 in DPC are not functionally relevant

14. α-Helix Unwinding as Force Buffer in Spectrins

15. Thermodynamics of DNA: sensitizer recognition. Characterizing binding motifs with all-atom simulations

16. Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins with Non-native Affinity

17. A central cavity within the holo-translocon suggests a mechanism for membrane protein insertion

18. Light Harvesting by Lamellar Chromatophores in Rhodospirillum photometricum

19. Resolution Dependence of Magnetorotational Turbulence in the Isothermal Stratified Shearing Box

20. Adaptive Multilevel Splitting Method for Molecular Dynamics Calculation of Benzamidine-Trypsin Dissociation Time

21. Orientation discrimination of single-stranded DNA inside the α-hemolysin membrane channel

22. Stability of Glassy and Ferroelectric States in the Relaxors PbMg1/3Nb2/3O3 and PbMg1/3Nb2/3O3-12% PbTiO3

23. Quasivertical line in the phase diagram of single crystals of Pb Mg1 3 Nb2 3 O3 -x PbTiO3 (x=0.00, 0.06, 0.13, and 0.24) with a giant piezoelectric effect

24. Arctic curves of the octahedron equation

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24 results on '"Department of Physics [Illinois at Urbana-Champaign, USA]"'

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