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Erratum: Search for anomalous production in the highly-boosted all-hadronic final state

Journal of High Energy Physics 2014年第3期2014卷 1-18页

作者： Chatrchyan, S. Khachatryan, V. Sirunyan, A. M. Tumasyan, A. Adam, W. Bergauer, T. Dragicevic, M. Erö, J. Fabjan, C. Friedl, M. Frühwirth, R. Ghete, V. M. Hammer, J. Hörmann, N. Hrubec, J. Jeitler, M. Kiesenhofer, W. Krammer, M. Liko, D. Mikulec, I. Pernicka, M. Rahbaran, B. Rohringer, C. Rohringer, H. Schöfbeck, R. Strauss, J. Taurok, A. Teischinger, F. Wagner, P. Waltenberger, W. Walzel, G. Widl, E. Wulz, C.-E. Mossolov, V. Shumeiko, N. Gonzalez, J. Suarez Bansal, S. Cerny, K. Cornelis, T. De Wolf, E. A. Janssen, X. Luyckx, S. Maes, T. Mucibello, L. Ochesanu, S. Roland, B. Rougny, R. Selvaggi, M. Van Haevermaet, H. Van Mechelen, P. Van Remortel, N. Van Spilbeeck, A. Blekman, F. Blyweert, S. D’Hondt, J. Suarez, R. Gonzalez Kalogeropoulos, A. Maes, M. Olbrechts, A. Van Doninck, W. Van Mulders, P. Van Onsem, G. P. Villella, I. Charaf, O. Clerbaux, B. De Lentdecker, G. Dero, V. Gay, A. P. R. Hreus, T. Léonard, A. Marage, P. E. Reis, T. Thomas, L. Velde, C. Vander Vanlaer, P. Adler, V. Beernaert, K. Cimmino, A. Costantini, S. Garcia, G. Grunewald, M. Klein, B. Lellouch, J. Marinov, A. Mccartin, J. Rios, A. A. Ocampo Ryckbosch, D. Strobbe, N. Thyssen, F. Tytgat, M. Vanelderen, L. Verwilligen, P. Walsh, S. Yazgan, E. Zaganidis, N. Basegmez, S. Bruno, G. Ceard, L. Delaere, C. du Pree, T. Favart, D. Forthomme, L. Giammanco, A. Hollar, J. Lemaitre, V. Liao, J. Militaru, O. Nuttens, C. Pagano, D. Pin, A. Piotrzkowski, K. Schul, N. Beliy, N. Caebergs, T. Daubie, E. Hammad, G. H. Alves, G. A. Junior, M. Correa Martins De Jesus Damiao, D. Martins, T. Pol, M. E. Souza, M. H. G. Júnior, W. L. Aldá Carvalho, W. Custódio, A. Da Costa, E. M. De Oliveira Martins, C. De Souza, S. Fonseca Figueiredo, D. Matos Mundim, L. Nogima, H. Oguri, V. Da Silva, W. L. Prado Santoro, A. Amaral, S. M. Silva Do Jorge, L. Soares Sznajder, A. Anjos, T. S. Bernardes, C. A. Dias, F. A. Tomei, T. R. Fernandez Perez Gregores, E. M. Lagana, C. Marinho, F. Mercadante, P. G. Novaes, S. F. Padula, Sandra S. Genchev, V. Iaydjiev, P. Piperov, S. Rodozov, M. St Yerevan Physics Institute Yerevan Armenia Institut für Hochenergiephysik der OeAW Wien Austria CERN European Organization for Nuclear Research Geneva Switzerland National Centre for Particle and High Energy Physics Minsk Belarus Universiteit Antwerpen Antwerpen Belgium Vrije Universiteit Brussel Brussel Belgium Université Libre de Bruxelles Bruxelles Belgium Ghent University Ghent Belgium Université Catholique de Louvain Louvain-la-Neuve Belgium National Institute of Chemical Physics and Biophysics Tallinn Estonia Université de Mons Mons Belgium Centro Brasileiro de Pesquisas Fisicas Rio de Janeiro Brazil Universidade do Estado do Rio de Janeiro Rio de Janeiro Brazil Instituto de Fisica Teorica Universidade Estadual Paulista Sao Paulo Brazil Universidade Federal do ABC Santo Andre Brazil California Institute of Technology Pasadena U.S.A Institute for Nuclear Research and Nuclear Energy Sofia Bulgaria University of Sofia Sofia Bulgaria Institute of High Energy Physics Beijing China State Key Lab. of Nucl. Phys. and Tech. Peking University Beijing China Universidad de Los Andes Bogota Colombia Technical University of Split Split Croatia Laboratoire Leprince-Ringuet Ecole Polytechnique IN2P3-CNRS Palaiseau France University of Split Split Croatia Institute Rudjer Boskovic Zagreb Croatia University of Cyprus Nicosia Cyprus Charles University Prague Czech Republic Academy of Scientific Research and Technology of the Arab Republic of Egypt Egyptian Network of High Energy Physics Cairo Egypt Suez Canal University Suez Egypt Cairo University Cairo Egypt British University Cairo Egypt Fayoum University El-Fayoum Egypt Ain Shams University Cairo Egypt Department of Physics University of Helsinki Helsinki Finland Helsinki Institute of Physics Helsinki Finland Lappeenranta University of Technology Lappeenranta Finland Laboratoire d’Annecy-le-Vieux de Physique des Particules IN2P3-CNRS Annecy-le-Vieux France DSM/IRFU CEA/Saclay Gif-sur-Yvette

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Search for supersymmetry with razor variables in pp collisions at s=7 TeV

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physical Review D 2014年第11期90卷 112001-112001页

作者： S. Chatrchyan V. Khachatryan A. M. Sirunyan A. Tumasyan W. Adam T. Bergauer M. Dragicevic J. Erö C. Fabjan M. Friedl R. Frühwirth V. M. Ghete C. Hartl N. Hörmann J. Hrubec M. Jeitler W. Kiesenhofer V. Knünz M. Krammer I. Krätschmer D. Liko I. Mikulec D. Rabady B. Rahbaran H. Rohringer R. Schöfbeck J. Strauss A. Taurok W. Treberer-Treberspurg W. Waltenberger C.-E. Wulz V. Mossolov N. Shumeiko J. Suarez Gonzalez S. Alderweireldt M. Bansal S. Bansal T. Cornelis E. A. De Wolf X. Janssen A. Knutsson S. Luyckx S. Ochesanu B. Roland R. Rougny H. Van Haevermaet P. Van Mechelen N. Van Remortel A. Van Spilbeeck F. Blekman S. Blyweert J. D’Hondt N. Heracleous A. Kalogeropoulos J. Keaveney T. J. Kim S. Lowette M. Maes A. Olbrechts Q. Python D. Strom S. Tavernier W. Van Doninck P. Van Mulders G. P. Van Onsem I. Villella C. Caillol B. Clerbaux G. De Lentdecker L. Favart A. P. R. Gay A. Léonard P. E. Marage A. Mohammadi L. Perniè T. Reis T. Seva L. Thomas C. Vander Velde P. Vanlaer J. Wang V. Adler K. Beernaert L. Benucci A. Cimmino S. Costantini S. Crucy S. Dildick G. Garcia B. Klein J. Lellouch J. Mccartin A. A. Ocampo Rios D. Ryckbosch S. Salva Diblen M. Sigamani N. Strobbe F. Thyssen M. Tytgat S. Walsh E. Yazgan N. Zaganidis S. Basegmez C. Beluffi G. Bruno R. Castello A. Caudron L. Ceard G. G. Da Silveira C. Delaere T. du Pree D. Favart L. Forthomme A. Giammanco J. Hollar P. Jez M. Komm V. Lemaitre J. Liao O. Militaru C. Nuttens D. Pagano A. Pin K. Piotrzkowski A. Popov L. Quertenmont M. Selvaggi M. Vidal Marono J. M. Vizan Garcia N. Beliy T. Caebergs E. Daubie G. H. Hammad G. A. Alves M. Correa Martins Junior T. Dos Reis Martins M. E. Pol W. L. Aldá Júnior W. Carvalho J. Chinellato A. Custódio E. M. Da Costa D. De Jesus Damiao C. De Oliveira Martins S. Fonseca De Souza H. Malbouisson M. Malek D. Matos Figueiredo L. Mundim H. Nogima W. L. Prado Da Silva J. Santaolalla A. Santoro A. Sznajder E. J. Tonelli Manganote A. Vilela Pereira C. A. Bernardes F. A. Dias T. R. Fernandez Perez Tomei E. M. Gregores P. G. Mercadante S. F. Yerevan Physics Institute Yerevan Armenia Institut für Hochenergiephysik der OeAW Wien Austria National Centre for Particle and High Energy Physics Minsk Belarus Universiteit Antwerpen Antwerpen Belgium Vrije Universiteit Brussel Brussel Belgium Université Libre de Bruxelles Bruxelles Belgium Ghent University Ghent Belgium Université Catholique de Louvain Louvain-la-Neuve Belgium Université de Mons Mons Belgium Centro Brasileiro de Pesquisas Fisicas Rio de Janeiro Brazil Universidade do Estado do Rio de Janeiro Rio de Janeiro Brazil Universidade Federal do ABC São Paulo Brazil Universidade Estadual Paulista São Paulo Brazil Institute for Nuclear Research and Nuclear Energy Sofia Bulgaria University of Sofia Sofia Bulgaria Institute of High Energy Physics Beijing China State Key Laboratory of Nuclear Physics and Technology Peking University Beijing China Rice University Houston Texas 77005 USA Vanderbilt University Nashville Tennessee 37235 USA Universidad de Los Andes Bogota Colombia Technical University of Split Split Croatia University of Split Split Croatia Institute Rudjer Boskovic Zagreb Croatia University of Cyprus Nicosia Cyprus Charles University Prague Czech Republic Academy of Scientific Research and Technology of the Arab Republic of Egypt Egyptian Network of High Energy Physics Cairo Egypt National Institute of Chemical Physics and Biophysics Tallinn Estonia Department of Physics University of Helsinki Helsinki Finland Helsinki Institute of Physics Helsinki Finland Lappeenranta University of Technology Lappeenranta Finland DSM/IRFU CEA/Saclay Gif-sur-Yvette France Laboratoire Leprince-Ringuet Ecole Polytechnique IN2P3-CNRS Palaiseau France Institut Pluridisciplinaire Hubert Curien Université de Strasbourg Université de Haute Alsace Mulhouse CNRS/IN2P3 Strasbourg France Centre de Calcul de l’Institut National de Physique Nucleaire et de Physique des Particules CNRS/IN2P3 Villeurbanne France Université de Lyon Université Cl

The razor approach to search for R–parity conserving supersymmetric particles is described in detail. Two analyses are considered: an inclusive search for new heavy particle pairs decaying to final states with at least two jets and missing transverse energy, and a dedicated search for final states with at least one jet originating from a bottom quark. For both the inclusive study and the study requiring a bottom-quark jet, the data are examined in exclusive final states corresponding to all-hadronic, single-lepton, and dilepton events. The study is based on the data set of proton-proton collisions at s=7 TeV collected with the CMS detector at the LHC in 2011, corresponding to an integrated luminosity of 4.7 fb−1. The study consists of a shape analysis performed in the plane of two kinematic variables, denoted MR and R2, that correspond to the mass and transverse energy flow, respectively, of pair-produced, heavy, new-physics particles. The data are found to be compatible with the background model, defined by studying event simulations and data control samples. Exclusion limits for squark and gluino production are derived in the context of the constrained minimal supersymmetric standard model (CMSSM) and also for simplified-model spectra (SMS). Within the CMSSM parameter space considered, squark and gluino masses up to 1350 GeV are excluded at 95% confidence level, depending on the model parameters. For SMS scenarios, the direct production of pairs of top or bottom squarks is excluded for masses as high as 400 GeV.

关键词： SUPERSYMMETRY (Physics) PROTON-proton interactions BOTTOM quark STANDARD model (Nuclear physics) DILEPTON production

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Gripper synthesis for indirect manipulation of cells using Holographic Optical Tweezers

Gripper synthesis for indirect manipulation of cells using H...

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IEEE International Conference on Robotics and Automation (ICRA)

作者： Sagar Chowdhury Petr Svec Chenlu Wang Wolfgang Losert Satyandra K. Gupta Department of Mechanical Engineering and The Institute for Systems Research University of Maryland College Park MD USA Department of Mechanical Engineering University of Maryland College Park MD USA Biophysics Program University of Maryland College Park MD USA Department of Physics Institute for Physical Science and Technology and the Institute forResearch in Electronics and Applied Physics University of Maryland College Park MD USA

Optical Tweezers (OT) are used for highly accurate manipulations of biological cells. However, the direct exposure of cells to focused laser beam may negatively influence their biological functions. In order to overcome this problem, we generate multiple optical traps to grab and move a 3D ensemble of inert particles such as silica microspheres to act as a reconfigurable gripper for a manipulated cell. The relative positions of the microspheres are important in order for the gripper to be robust against external environmental forces and the exposure of high intensity laser on the cell to be minimized. In this paper, we present results of different gripper configurations, experimentally tested using our OT setup, that provide robust gripping as well as minimize laser intensity experienced by the cell. We developed a computational approach that allowed us to perform preliminary modeling and synthesis of the gripper configurations. The gripper synthesis is cast as a multi-objective optimization problem.

关键词： Grippers Laser beams Biomedical optical imaging Silicon compounds Robustness Force Holography

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Automated indirect transport of biological cells with optical tweezers using planar gripper formations

Automated indirect transport of biological cells with optica...

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IEEE International Conference on Automation science and Engineering (CASE)

作者： Sagar Chowdhury Atul Thakur Chenlu Wang Petr Svec Wolfgang Losert Satyandra K. Gupta The Department of Mechanical Engineering and the Institute for Systems Research University of Maryland College Park MD USA The Department of Mechanical Engineering University of Maryland College Park MD USA The Biophysics Program University of Maryland College Park MD USA The Department of Physics Institute for Physical Science and Technology and the Institute for Research in Electronics and Applied Physics University of Maryland College Park MD USA

Optical tweezers are used for manipulation of micron-sized dielectric beads and cells. Some biological cells are vulnerable to photo damage if subjected to laser-based direct manipulation. In such cases, precise manipulation of these cells can be accomplished by using gripper formations made up of silica beads, which are actuated by optical tweezers. Manual indirect manipulation of cells using grippers made of optically trapped beads is a time consuming process or sometimes just impossible. This paper presents an approach for automated micromanipulation using gripper formations and heuristic based path planning for collision-free transport of biological cells. The objective of the developed planner is to transport target cells to their respective goal positions in the minimum time. we evaluated the performance of different gripper formations in terms of gripper stability, speed of transport, and required laser power using experiments.

关键词： Grippers Charge carrier processes Biomedical optical imaging Laser stability Laser beams Educational institutions

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Erratum to: Study protocol: differential effects of diet and physical activity based interventions in pregnancy on maternal and fetal outcomes: individual patient data (IPD) meta-analysis and health economic evaluation

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Systematic reviews 2015年第1期4卷 101页

作者： Anneloes E Ruifrok Ewelina Rogozinska Mireille N M van Poppel Girish Rayanagoudar Sally Kerry Christianne J M de Groot SeonAe Yeo Emma Molyneaux Ruben Barakat Carballo Maria Perales Annick Bogaerts Jose G Cecatti Fernanda Surita Jodie Dodd Julie Owens Nermeen El Beltagy Roland Devlieger Helena Teede Cheryce Harrison Lene Haakstad Garry X Shen Alexis Shub Narges Motahari Janette Khoury Serena Tonstad Riitta Luoto Tarja I Kinnunen Kym Guelfi Fabio Facchinetti Elisabetta Petrella Suzanne Phelan Tânia T Scudeller Kathrin Rauh Hans Hauner Kristina Renault Linda Reme Sagedal Ingvild Vistad Signe Nilssen Stafne Siv Mørkved Kjell Åsmund Salvesen Christina Vinter Marcia Vitolo Arne Astrup Nina Rica Wium Geiker Fionnuala McAuliffe Lucilla Poston Tracy Roberts Richard D Riley Arri Coomarasamy Khalid S Khan Ben Willem Mol Shakila Thangaratinam Department of Obstetrics and Gynecology Academic Medical Centre Amsterdam The Netherlands. anneloesruifrok@***. Department of Obstetrics and Gynaecology Faculty of Medicine VU University Medical Center Amsterdam The Netherlands. anneloesruifrok@***. Women's Health Research Unit Barts and The London School of Medicine and Dentistry Queen Mary University of London London UK. e.a.rogozinska@qmul.ac.uk. Multidisciplinary Evidence Synthesis Hub (mEsh) Barts and The London School of Medicine and Dentistry Queen Mary University of London London UK. e.a.rogozinska@qmul.ac.uk. Department of Public and Occupational Health EMGO+ Institute for Health and Care Research VU University Medical Center Amsterdam The Netherlands. mnm.vanpoppel@vumc.nl. Women's Health Research Unit Barts and The London School of Medicine and Dentistry Queen Mary University of London London UK. g.rayanagoudar@qmul.ac.uk. Multidisciplinary Evidence Synthesis Hub (mEsh) Barts and The London School of Medicine and Dentistry Queen Mary University of London London UK. s.m.kerry@qmul.ac.uk. Department of Obstetrics and Gynaecology Faculty of Medicine VU University Medical Center Amsterdam The Netherlands. cj.degroot@vumc.nl. University of North Carolina at Chapel Hill School of Nursing Chapel Hill NC USA. syeo@email.unc.edu. Section of Women's Mental Health Health Service and Population Research Department Institute of Psychiatry King's College London London UK. emma.molyneaux@kcl.ac.uk. Facultad de Ciencias de la Actividad Fısica y del Deporte-INEF Universidad Politecnica de Madrid Madrid Spain. rubenomar.barakat@upm.es. Facultad de Ciencias de la Actividad Fısica y del Deporte-INEF Universidad Politecnica de Madrid Madrid Spain. m.perales.santaella@***. Division of Mother and Child Department of Obstetrics and Gynaecology University Colleges Leuven-Limburg Hasselt and University Hospitals KU Leuven Leuven Belgium. Annick.Bogaerts@khlim.be. Department of Obstetrics and Gynecology School of Medical Scienc

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Dark matter constraints from observations of 25 Milky Way satellite galaxies with the Fermi Large Area Telescope

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physical Review D 2014年第4期89卷 042001-042001页

作者： M. Ackermann A. Albert B. Anderson L. Baldini J. Ballet G. Barbiellini D. Bastieri K. Bechtol R. Bellazzini E. Bissaldi E. D. Bloom E. Bonamente A. Bouvier T. J. Brandt J. Bregeon M. Brigida P. Bruel R. Buehler S. Buson G. A. Caliandro R. A. Cameron M. Caragiulo P. A. Caraveo C. Cecchi E. Charles A. Chekhtman J. Chiang S. Ciprini R. Claus J. Cohen-Tanugi J. Conrad F. D’Ammando A. de Angelis C. D. Dermer S. W. Digel E. do Couto e Silva P. S. Drell A. Drlica-Wagner R. Essig C. Favuzzi E. C. Ferrara A. Franckowiak Y. Fukazawa S. Funk P. Fusco F. Gargano D. Gasparrini N. Giglietto M. Giroletti G. Godfrey G. A. Gomez-Vargas I. A. Grenier S. Guiriec M. Gustafsson M. Hayashida E. Hays J. Hewitt R. E. Hughes T. Jogler T. Kamae J. Knödlseder D. Kocevski M. Kuss S. Larsson L. Latronico M. Llena Garde F. Longo F. Loparco M. N. Lovellette P. Lubrano G. Martinez M. Mayer M. N. Mazziotta P. F. Michelson W. Mitthumsiri T. Mizuno A. A. Moiseev M. E. Monzani A. Morselli I. V. Moskalenko S. Murgia R. Nemmen E. Nuss T. Ohsugi E. Orlando J. F. Ormes J. S. Perkins F. Piron G. Pivato T. A. Porter S. Rainò R. Rando M. Razzano S. Razzaque A. Reimer O. Reimer S. Ritz M. Sánchez-Conde N. Sehgal C. Sgrò E. J. Siskind P. Spinelli L. Strigari D. J. Suson H. Tajima H. Takahashi J. B. Thayer L. Tibaldo M. Tinivella D. F. Torres Y. Uchiyama T. L. Usher J. Vandenbroucke G. Vianello V. Vitale M. Werner B. L. Winer K. S. Wood M. Wood G. Zaharijas S. Zimmer Deutsches Elektronen Synchrotron DESY D-15738 Zeuthen Germany W. W. Hansen Experimental Physics Laboratory Kavli Institute for Particle Astrophysics and Cosmology Department of Physics and SLAC National Accelerator Laboratory Stanford University Stanford California 94305 USA Department of Physics Stockholm University AlbaNova SE-106 91 Stockholm Sweden The Oskar Klein Centre for Cosmoparticle Physics AlbaNova SE-106 91 Stockholm Sweden Università di Pisa and Istituto Nazionale di Fisica Nucleare Sezione di Pisa I-56127 Pisa Italy Laboratoire AIM CEA-IRFU/CNRS/Université Paris Diderot Service d’Astrophysique CEA Saclay 91191 Gif sur Yvette France Istituto Nazionale di Fisica Nucleare Sezione di Trieste I-34127 Trieste Italy Dipartimento di Fisica Università di Trieste I-34127 Trieste Italy Istituto Nazionale di Fisica Nucleare Sezione di Padova I-35131 Padova Italy Dipartimento di Fisica e Astronomia “G. Galilei ” Università di Padova I-35131 Padova Italy Istituto Nazionale di Fisica Nucleare Sezione di Pisa I-56127 Pisa Italy Istituto Nazionale di Fisica Nucleare Sezione di Trieste and Università di Trieste I-34127 Trieste Italy Istituto Nazionale di Fisica Nucleare Sezione di Perugia I-06123 Perugia Italy Dipartimento di Fisica Università degli Studi di Perugia I-06123 Perugia Italy Santa Cruz Institute for Particle Physics Department of Physics and Department of Astronomy and Astrophysics University of California at Santa Cruz Santa Cruz California 95064 USA NASA Goddard Space Flight Center Greenbelt Maryland 20771 USA Dipartimento di Fisica “M. Merlin” dell’Università e del Politecnico di Bari I-70126 Bari Italy Istituto Nazionale di Fisica Nucleare Sezione di Bari 70126 Bari Italy Laboratoire Leprince-Ringuet École polytechnique CNRS/IN2P3 Palaiseau France INAF-Istituto di Astrofisica Spaziale e Fisica Cosmica I-20133 Milano Italy Center for Earth Observing and Space Research College of Science George Mason University Fairfax Virginia 22030

The dwarf spheroidal satellite galaxies of the Milky Way are some of the most dark-matter-dominated objects known. Due to their proximity, high dark matter content, and lack of astrophysical backgrounds, dwarf spheroidal galaxies are widely considered to be among the most promising targets for the indirect detection of dark matter via γ rays. Here we report on γ-ray observations of 25 Milky Way dwarf spheroidal satellite galaxies based on 4 years of Fermi Large Area Telescope (LAT) data. None of the dwarf galaxies are significantly detected in γ rays, and we present γ-ray flux upper limits between 500 MeV and 500 GeV. We determine the dark matter content of 18 dwarf spheroidal galaxies from stellar kinematic data and combine LAT observations of 15 dwarf galaxies to constrain the dark matter annihilation cross section. We set some of the tightest constraints to date on the annihilation of dark matter particles with masses between 2 GeV and 10 TeV into prototypical standard model channels. We find these results to be robust against systematic uncertainties in the LAT instrument performance, diffuse γ-ray background modeling, and assumed dark matter density profile.

关键词： DWARF galaxies MILKY Way DARK matter (Astronomy) ANNIHILATION reactions TELESCOPES

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Noise associated with nonconservative forces in optical traps

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physical Review E 2011年第3期84卷 031108-031108页

作者： Michel de Messieres Natalia A. Denesyuk Arthur La Porta []Department of Physics Institute for Physical Science and Technology Biophysics Program University of Maryland College Park Maryland 20742 USA

It is known that for a particle held in an optical trap the interaction of thermal fluctuations with a nonconservative scattering force can cause a persistent nonequilibrium probability flux in the particle position. We investigate position fluctuations associated with this nonequilibrium flux analytically and through simulation. We introduce a model which reproduces the nonequilibrium effects, and in which the magnitude of additional position fluctuations can be calculated in closed form. The ratio of additional nonconservative fluctuations to direct thermal fluctuations scales inversely with the square root of trap power, and is small for typical experimental parameters. In a simulated biophysical experiment the nonconservative scattering force does not significantly increase the observed fluctuations in the length of a double-stranded DNA tether.

关键词： NOISE SCATTERING (Physics) EQUILIBRIUM DNA DOUBLE-stranded RNA

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MDMap: A system for data-driven layout and exploration of molecular dynamics simulations

MDMap: A system for data-driven layout and exploration of mo...

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1st IEEE Symposium on Biological Data Visualization, BioVis 2011

作者： Patro, Robert Ip, Cheuk Yiu Bista, Sujal Thirumalai, D. Cho, Samuel S. Varshney, Amitabh Department of Computer Science Institute for Advanced Computer Studies University of Maryland College Park United States Biophysics Program Institute for Physical Sciences and Technology University of Maryland College Park United States Departments of Physics and Computer Science Wake Forest University United States

ISBN: (纸本)9781467300025

Contemporary molecular dynamics simulations result in a glut of simulation data, making analysis and discovery a difficult and burdensome task. We present MDMap, a system designed to summarize long-running molecular dynamics (MD) simulations. We represent a molecular dynamics simulation as a state transition graph over a set of intermediate (stable and semi-stable) states. The transitions amongst the states together with their frequencies represent the flow of a biomolecule through the trajectory space. MDMap automatically determines potential intermediate conformations and the transitions amongst them by analyzing the conformational space explored by the MD simulation. MDMap is an automated system to visualize MD simulations as state-transition diagrams, and can replace the current tedious manual layouts of biomolecular folding landscapes with an automated tool. The layout of the representative states and the corresponding transitions among them is presented to the user as a visual synopsis of the long-running MD simulation. We compare and contrast multiple presentations of the state transition diagrams, such as conformational embedding, and spectral, hierarchical, and force-directed graph layouts. We believe this system could provide a road-map for the visualization of other stochastic time-varying simulations in a variety of different domains. © 2011 IEEE.

关键词： Visualization

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Measurements of tt spin correlations and top-quark polarization using dilepton final states in pp collisions at sqrt[s]=7 TeV

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physical Review Letters [Phys Rev Lett] 2014年第18期112卷 182001-182001页

作者： Chatrchyan Khachatryan Sirunyan A Tumasyan Adam Bergauer Dragicevic Erö Fabjan Friedl Frühwirth Ghete V Hartl Hörmann Hrubec Jeitler Kiesenhofer Knünz Krammer Krätschmer Liko Mikulec Rabady Rahbaran Rohringer Schöfbeck Strauss Taurok Treberer-Treberspurg Waltenberger Wulz C Mossolov Shumeiko Suarez Gonzalez Alderweireldt Bansal Cornelis De Wolf E Janssen Knutsson Luyckx Mucibello Ochesanu Roland Rougny Van Haevermaet Van Mechelen Van Remortel Van Spilbeeck Blekman Blyweert D''Hondt Heracleous Kalogeropoulos Keaveney Kim T Lowette Maes Olbrechts Strom Tavernier Van Doninck Van Mulders Van Onsem G Villella Caillol Clerbaux De Lentdecker Favart Gay A Hreus Léonard Marage P Mohammadi Perniè Reis Seva Thomas Vander Velde Vanlaer Wang Adler Beernaert Benucci Cimmino Costantini Dildick Garcia Klein Lellouch Mccartin Ocampo Rios A Ryckbosch Sigamani Strobbe Thyssen Tytgat Walsh Yazgan Zaganidis Basegmez Beluffi Bruno Castello Caudron Ceard Da Silveira G Delaere du Pree Forthomme Giammanco Hollar Jez Komm Lemaitre Liao Militaru Nuttens Pagano Pin Piotrzkowski Popov Quertenmont Selvaggi Vidal Marono Vizan Garcia J Beliy Caebergs Daubie Hammad G Alves G Correa Martins Junior Martins Pol M Souza M Aldá Júnior W Carvalho Chinellato Custódio Da Costa E De Jesus Damiao De Oliveira Martins Fonseca De Souza Malbouisson Malek Matos Figueiredo Mundim Nogima Prado Da Silva W Santaolalla Santoro Sznajder Tonelli Manganote E Vilela Pereira Bernardes C Dias F Fernandez Perez Tomei T Gregores E Lagana Mercadante P Novaes S Padula S Genchev Iaydjiev Marinov Piperov Rodozov Sultanov Vutova Dimitrov Glushkov Hadjiiska Kozhuharov Litov Pavlov Petkov Bian J Chen G Chen H Chen Du Jiang C Liang Meng Plestina Tao Asawatangtrakuldee Ban Guo Li Liu Mao Qian S Zhang Zou Avila Carrillo Montoya C Chaparro Sierra L Florez Gomez J Gomez Moreno Sanabria J Godinovic Lelas Polic Puljak Antunovic Kovac Brigljevic Kadija Luetic Mekterovic Morovic Tikvica Attikis Mavromanolakis Mousa Nicolaou Ptochos Razis P Finger Finger M J Abdelalim A Assran Elgammal Ell Yerevan Physics Institute Yerevan Armenia Institut für Hochenergiephysik der OeAW Wien Austria National Centre for Particle and High Energy Physics Minsk Belarus Universiteit Antwerpen Antwerpen Belgium Massachusetts Institute of Technology Cambridge USA Vrije Universiteit Brussel Brussel Belgium Kangwon National University Chunchon Korea Université Libre de Bruxelles Bruxelles Belgium Université Catholique de Louvain Louvain-la-Neuve Belgium Rutgers The State University of New Jersey Piscataway USA Purdue University West Lafayette USA Ghent University Ghent Belgium RWTH Aachen University I. Physikalisches Institut Aachen Germany Deutsches Elektronen-Synchrotron Hamburg Germany RWTH Aachen University III. Physikalisches Institut A Aachen Germany Institute for Theoretical and Experimental Physics Moscow Russia INFN Sezione di Bari Bari Italy and Università di Bari Bari Italy Université de Mons Mons Belgium Centro Brasileiro de Pesquisas Fisicas Rio de Janeiro Brazil Universidade do Estado do Rio de Janeiro Rio de Janeiro Brazil Universidade Federal do ABC São Paulo Brazil Universidade Estadual Paulista São Paulo Brazil Institute for Nuclear Research and Nuclear Energy Sofia Bulgaria University of Sofia Sofia Bulgaria Institute of High Energy Physics Beijing China Florida State University Tallahassee USA University of Bristol Bristol United Kingdom State Key Laboratory of Nuclear Physics and Technology Peking University Beijing China Rice University Houston USA University of California Riverside Riverside USA Vanderbilt University Nashville USA Northeastern University Boston USA Universidad de Los Andes Bogota Colombia University of Maryland College Park USA Technical University of Split Split Croatia University of Split Split Croatia Institute Rudjer Boskovic Zagreb Croatia University of Cyprus Nicosia Cyprus Charles University Prague Czech Republic Academy of Scientific Research and Technology of the Arab Republic of Egypt Egypt

Spin correlations and polarization in the top quark-antiquark system are measured using dilepton final states produced in pp collisions at the LHC at sqrt[s]=7 TeV. The data correspond to an integrated luminosity of 5.0 fb(-1) collected with the CMS detector. The measurements are performed using events with two oppositely charged leptons (electrons or muons), a significant imbalance in transverse momentum, and two or more jets, where at least one of the jets is identified as originating from a b quark. The spin correlations and polarization are measured through asymmetries in angular distributions of the two selected leptons, unfolded to the parton level. All measurements are found to be in agreement with predictions of the standard model.

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Prediction of mitochondrial proteins of malaria parasite using improved hybrid method and reduced amino acid alphabet

Prediction of mitochondrial proteins of malaria parasite usi...

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2011 4th International Conference on Biomedical Engineering and Informatics, BMEI 2011

作者： Chen, Ying-Li Li, Qian-Zhong Zhang, Li-Qing Laboratory of Theoretical Biophysics School of Physical Science and Technology Inner Mongolia University Hohhot China Department of Computer Science Virginia Tech Blacksburg VA United States Program in Genetics Bioinformatics and Computational Biology Virginia Tech Blacksburg VA United States

ISBN: (纸本)9781424493524

The rate of human death and morbidity due to malaria is increasing in many parts of the developing countries. Thus, there is a great need to understand the critical pathways in malaria parasite in order to develop effective drugs and vaccines. In this work, based on the measure of diversity definition, we introduce the increment of diversity fusion (IDF), an improved hybrid method to predict mitochondrial proteins of malaria parasite. We conduct our experiment on an expanded protein dataset where we require the pairwise identity between two proteins is less than 25%. By choosing amino acids composition as the only input vector, we are able to achieve 65.4% accuracy with 0.32 Mathew's correlation coefficient (MCC) for the jackknife test. Further, incorporting the compositions of the N-terminal and C-terminal regions into the input vector, we show that the prediction results are improved to 82.0% accuracy with 0.64 MCC in the jackknife test. In addition, by combining with the several reduced amino acid alphabet and the hydropathy distribution along protein sequence, we achieve maximum 83.4% accuracy with 0.67 MCC in the jackknife test by using the 64 dipeptide compositions of the reduced amino acid alphabet obtained from Protein Blocks method. © 2011 IEEE.

关键词： Proteins

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