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An Investigation Into Jamming Percolation Using Renormalization
An investigation into jamming percolation using renormalization group methods. Samuel Schoenholz Under the supervision of Professor Amy Bug and Professor Andrea Liu March 22, 2010 1 1 Overview Many systems in nature fail to satisfy the ergodic hypothesis and feature strong nonequilibrium behavior. These systems have proven remarkably difficult to study. In recent years theorists have studied a phase transition known as the jamming phase transition. The jamming phase transition unifies several far from equilibrium phase transitions including: the glass transition, the solidification of granular media in response to shearing forces, and the stiffening of colloids in response to increases in pressure. It has recently been shown that certain correlated percolation models can exhibit behavior analogous to the jamming phase transition. In particular this has been shown for two models, coined the spiral model and the force-balance model. The primary goal of this study was to determine whether or not the spiral model and the force-balance model reside in the same universality class. To investigate this issue we used the renormalization group to perform a numerical investigation of the spiral model and force balance model. There is evidence to suggest that both models feature exponential, as opposed to power-law scaling of the correlation function. It was therefore difficult to investigate, in a computationally feasible way, large enough systems so as to reduce the finite size effects. To do this we came up with a variety of algorithms including: a Monte-Carlo method, a binary search, and a linear time culling algorithm. The combination of these three strategies allowed us to investigate significantly larger systems than had been investigated in the past. -
Downloading Our Newsletter
Department of Chemistry Biochemistry& NEWSLETTER In This Issue Page Chair’s Message................2 Jorge Torres Discovers Key Role for a Motor Awards...........................2-5 Protein in Cancer Cell Proliferation Seaborg Symposium........6-7 Happenings....................7-10 Biochemistry Professor high-throughput genetic Distinguished Lectures....11-14 Jorge Torres discovered that screen that knocked the Research.......................15-17 suppressing STARD9, a proteins out one by one to In Memoriam................17-19 newly identified protein see how that affected involved in regulating cell spindle function. Calendar.........................19 division, could be a novel “The idea was to find strategy for fighting certain something that arrested the Spring 2012 cancers, as it stops malignant cells while they were Volume 31 - Number 2 cells from dividing and trying to divide and causes them to die quickly. injured them in such a way that cell death occurred quickly,” The study was published in Torres said. “We were looking for a way to attack the cancer the December 9, 2011 issue cells as they were dividing.” of Cell. From the screens, Torres and his team selected the most During the five-year promising protein. This was STARD9, a kinesin-like protein Jorge Torres study, designed to seek — a sort of molecular motor — that functions to form a targets for anti-cancer stable mitotic spindle. therapies, Torres and co-workers found that depleting “When STARD9 is depleted in the cancer cells, the STARD9 also helped the commonly used chemotherapy chromosomes attempt to align for transmission into the drug Taxol work more effectively against cancers such as daughter cells but fail,” he said. -
DNA Ejection from Bacteriophage: Towards a General Behavior for Osmotic Suppression Experiments Martin Castelnovo, Alex Evilevitch
DNA ejection from bacteriophage: towards a general behavior for osmotic suppression experiments Martin Castelnovo, Alex Evilevitch To cite this version: Martin Castelnovo, Alex Evilevitch. DNA ejection from bacteriophage: towards a general behavior for osmotic suppression experiments. European Physical Journal E: Soft matter and biological physics, EDP Sciences: EPJ, 2007, 24, pp.9-18. 10.1140/epje/i2007-10205-5. hal-00196724 HAL Id: hal-00196724 https://hal.archives-ouvertes.fr/hal-00196724 Submitted on 13 Dec 2007 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. DNA ejection from bacteriophage: towards a general behavior for osmotic suppression experiments M. Castelnovo∗ and A. Evilevitch† (Dated: December 18, 2007) We present in this work in vitro measurements of the force ejecting DNA from two distinct bacteriophages (T5 and λ) using the osmotic ejection suppression technique. Our datas are analyzed by revisiting the current theories of DNA packaging in spherical capsids. In particular we show that a simplified analytical model based on bending considerations only is able to account quantitatively for the experimental findings. Physical and biological consequences are discussed. I. INTRODUCTION Viruses have developped various specific strategies over the evolution in order to infect higher organisms. -
Two-Stage Dynamics of in Vivo Bacteriophage Genome Ejection
View metadata, citation and similar papers at core.ac.uk brought to you by CORE PHYSICAL REVIEW X 8, 021029 (2018) provided by Caltech Authors Two-Stage Dynamics of In Vivo Bacteriophage Genome Ejection † ‡ Yi-Ju Chen,1,* David Wu,2, William Gelbart,3 Charles M. Knobler,3 Rob Phillips,2,4, and Willem K. Kegel5,§ 1Department of Physics, California Institute of Technology, Pasadena, California 91125, USA 2Division of Engineering and Applied Sciences, California Institute of Technology, Pasadena, California 91125, USA 3Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, USA 4Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA 5Van ’t Hoff Laboratory for Physical and Colloid Chemistry, Debye Institute, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands (Received 1 July 2017; revised manuscript received 27 January 2018; published 1 May 2018) Biopolymer translocation is a key step in viral infection processes. The transfer of information-encoding genomes allows viruses to reprogram the cell fate of their hosts. Constituting 96% of all known bacterial viruses [A. Fokine and M. G. Rossmann, Molecular architecture of tailed double-stranded DNA phages, Bacteriophage 4, e28281 (2014)], the tailed bacteriophages deliver their DNA into host cells via an “ejection” process, leaving their protein shells outside of the bacteria; a similar scenario occurs for mammalian viruses like herpes, where the DNA genome is ejected into the nucleus of host cells, while the viral capsid remains bound outside to a nuclear-pore complex. In light of previous experimental measurements of in vivo bacteriophage λ ejection, we analyze here the physical processes that give rise to the observed dynamics. -
Biosoft Frontiers: Physics of Soft And
BioSoft Frontiers: Physics of Soft and Biological Matter Research Workshop of the Israel Science Foundation September 18-21, 2016 Weizmann Institute and Tel Aviv University Sponsors Israel Science Foundation Weizmann Institute of Science Tel Aviv University Chorafas Institute for Scientific Exchange, Weizmann Institute Clore Center for Biological Physics, Weizmann Institute Schmidt Minerva Center, Weizmann Institute Department of Materials and Interfaces, Weizmann Institute Faculty of Exact Sciences, Tel Aviv University School of Physics & Astronomy, Tel Aviv University School of Chemistry, Tel Aviv University Sackler Institute of Solid State Physics, Tel Aviv University Sackler Institute of Chemical Physics, Tel Aviv University 1 Scientific Program 18/9/16 Weizmann Institute (Lopatie Center) 12:00-13:45 Arrival and Lunch 13:45-14:00 Opening 14:00-15:25 Session 1. Chair: Jacques Prost (Institut Curie, Paris) 14:00-14:30 Fred MacKintosh (VU University, Amsterdam) Phase transitions and non-equilibrium behavior in living systems 14:30-14:50 Ayelet Lesman (Tel Aviv University) The influence of contractile forces on biological processes 14:50-15:05 Xingpeng Xu (Weizmann Institute) Nonlinear elastic responses of biopolymer gels under compression 15:05-15:35 Tsvi Tlusty (IAS, Princeton) Proteins as learning amorphous matter: dimension and spectrum of the genotype-to-phenotype map 15:35-16:20 Coffee 16:20-17:25 Session 2. Chair: Nihat Berker (Sabanci University, Istanbul) 16:20-16:50 Christoph Schmidt (Universitaet Goettingen) Active soft matter builds life 16:50-17:05 Kinjal Dasbiswas (University of Chicago) Mechanobiological induction of long-range contractility by diffusing biomolecules and size scaling in cell assemblies 17:05-17:25 Yoram Burak (Hebrew University) Encoding of an animal's trajectory by grid cells in the entorhinal cortex 18:00 Dinner (Lopatie Center) 2 19/9/16 Weizmann Institute (Lopatie Center) 09:00-09:30 Arrival and coffee 09:30-10:35 Session 3. -
The Dynamics Is Encoded in the Pair Correlation Function François Landes, Giulio Biroli, Olivier Dauchot, Andrea Liu, David Reichman
Attractive versus truncated repulsive supercooled liquids: The dynamics is encoded in the pair correlation function François Landes, Giulio Biroli, Olivier Dauchot, Andrea Liu, David Reichman To cite this version: François Landes, Giulio Biroli, Olivier Dauchot, Andrea Liu, David Reichman. Attractive versus truncated repulsive supercooled liquids: The dynamics is encoded in the pair correlation function. Physical Review E , American Physical Society (APS), 2020, 101 (1), 10.1103/PhysRevE.101.010602. hal-02439295 HAL Id: hal-02439295 https://hal.inria.fr/hal-02439295 Submitted on 14 Jan 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Attractive versus truncated repulsive supercooled liquids: The dynamics is encoded in the pair correlation function Fran¸coisP. Landes,1, 2, 3, 4 Giulio Biroli,2 Olivier Dauchot,5 Andrea J. Liu,3 and David R. Reichman4 1LRI, AO team, B^at660 Universit´eParis Sud, Orsay 91405, France∗ 2Laboratoire de Physique de l'Ecole´ normale sup´erieure, ENS, Universit´ePSL, CNRS, Sorbonne Universit´e, Universit´eParis-Diderot, Sorbonne Paris Cit´e,Paris, France 3Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104 4Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA 5UMR Gulliver 7083 CNRS, ESPCI ParisTech, PSL Research University, 10 rue Vauquelin, 75005 Paris, France We compare glassy dynamics in two liquids that differ in the form of their interaction poten- tials. -
How a Virus Circumvents Energy Barriers to Form Symmetric Shells Sanaz Panahandeh, Siyu Li, Laurent Marichal, Rafael Leite Rubim, Guillaume Tresset, Roya Zandi
How a Virus Circumvents Energy Barriers to Form Symmetric Shells Sanaz Panahandeh, Siyu Li, Laurent Marichal, Rafael Leite Rubim, Guillaume Tresset, Roya Zandi To cite this version: Sanaz Panahandeh, Siyu Li, Laurent Marichal, Rafael Leite Rubim, Guillaume Tresset, et al.. How a Virus Circumvents Energy Barriers to Form Symmetric Shells. ACS Nano, American Chemical Society, 2020, 14 (3), pp.3170-3180. 10.1021/acsnano.9b08354. hal-03035711 HAL Id: hal-03035711 https://hal.archives-ouvertes.fr/hal-03035711 Submitted on 4 Jan 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. How a virus circumvents energy barriers to form symmetric shells Sanaz Panahandeh,y Siyu Li,y Laurent Marichal,z Rafael Leite Rubim,z Guillaume Tresset,z and Roya Zandi∗,y yDepartment of Physics and Astronomy, University of California, Riverside, California 92521, USA zLaboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France E-mail: [email protected] Abstract Previous self-assembly experiments on a model icosahedral plant virus have shown that, under physiological conditions, capsid proteins initially binds to the genome through an en masse mechanism and form nucleoprotein complexes in a disordered state, which raises the questions as to how virions are assembled into a highly or- dered structure in the host cell. -
From the President's Desk
APRIL 2005 From the President’s desk: The sequence of the human genome underscores the necessity for genetic analysis to define gene function and validates the importance of genomic and genetic approaches in model organisms for gene discovery. The GSA promotes genetic research in model organisms and its application to human genetics via our journal Genetics, supporting public education and congressional lobbying through the Joint Steering Committee for Public Policy (www.jscpp.org) and in its sponsorship of scientific meetings. The GSA support of scientific meetings includes providing the crucial infrastructure, organization, administration, and financial foundation, as well as recognition for students and postdocs through the awards we sponsor. The society’s sponsorship of model organisms meetings in C. elegans, Drosophila, Fungi, Yeast and Zebrafish has enabled those research communities to hold conferences that are particularly accessible to students and postdocs who are our future. The support of the GSA has been key in enabling these very successful meetings while permitting each of the model organism communities the independence to organize the meeting according to their needs. In recognition of the importance of genomics in our field, this year the GSA will support a new meeting of biocurators and database developers with the goal of bringing together developers of these bioinformatics tools for a variety of organisms. Your membership in the GSA entitles you to a reduced registration fee for all of these meetings. The GSA will organize its own meeting “Genetic Analysis: Model Organisms to Human Biology,” Jan. 5-7, 2006 in San Diego to draw together the entire constituency of our society and to promote interactions with our colleagues directly studying human disease. -
Arxiv:2006.09592V4 [Cond-Mat.Soft] 21 Apr 2021 13]
Mean-Field Predictions of Scaling Prefactors Match Low-Dimensional Jammed Packings James D. Sartor∗, Sean A. Ridout†, Eric I. Corwin∗ ∗Department of Physics and Materials Science Institute, University of Oregon, Eugene, Oregon 97403, USA †Department of Physics and Astronomy University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA (Dated: April 22, 2021) No known analytic framework precisely explains all the phenomena observed in jamming. The replica theory for glasses and jamming is a mean-field theory which attempts to do so by working in the limit of infinite dimensions, such that correlations between neighbors are negligible. As such, results from this mean-field theory are not guaranteed to be observed in finite dimensions. However, many results in mean field for jamming have been shown to be exact or nearly exact in low dimensions. This suggests that the infinite dimensional limit is not necessary to obtain these results. In this Letter, we perform precision measurements of jamming scaling relationships between pressure, excess packing fraction, and number of excess contacts from dimensions 2–10 in order to extract the prefactors to these scalings. While these prefactors should be highly sensitive to finite dimensional corrections, we find the mean-field predictions for these prefactors to be exact in low dimensions. Thus the mean-field approximation is not necessary for deriving these prefactors. We present an exact, first-principles derivation for one, leaving the other as an open question. Our results suggest that mean-field theories of critical phenomena may compute more for d du than has been previously appreciated. ≥ Introduction – Granular materials exhibit universal these results. -
Jamming Phase Diagram, Effective Temperature, and Heterogeneous Dynamics of Model Glass-Forming Liquids
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations Summer 2010 Jamming Phase Diagram, Effective Temperature, and Heterogeneous Dynamics of Model Glass-Forming Liquids Thomas K. Haxton University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Condensed Matter Physics Commons Recommended Citation Haxton, Thomas K., "Jamming Phase Diagram, Effective Temperature, and Heterogeneous Dynamics of Model Glass-Forming Liquids" (2010). Publicly Accessible Penn Dissertations. 235. https://repository.upenn.edu/edissertations/235 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/235 For more information, please contact [email protected]. Jamming Phase Diagram, Effective Temperature, and Heterogeneous Dynamics of Model Glass-Forming Liquids Abstract We establish that the behavior of fluids consisting of epulsivr e spheres under the combined effects of pressure p, temperature T, and applied shear stress s can be organized in a jamming phase diagram parameterized by the dimensionless quantities T/pd^3, s/p, and pd^3/e, where d is the diameter of the spheres and e is the interaction energy scale. The jamming phase diagram describes the three- dimensional parameter space as the product of an equilibrium plane at s/p=0 and a hard sphere plane at pd^3/e=0. Near the hard sphere plane, the jamming phase diagram is universal in the sense that material properties are insensitive to the details of the interaction potential. We demonstrate that within the universal regime, the conventional approach to the dynamic glass transition along a decreasing temperature trajectory is equivalent to the colloidal glass transition approach along an increasing pressure trajectory. -
Assembly and Disassembly of Viral Capsids
Journal of Theoretical Medicine, Vol. 6, No. 2, June 2005, 69–72 Assembly and disassembly of viral capsids ROYA ZANDI†*, DAVID REGUERA†, ROBIJN BRUINSMA‡, WILLIAM GELBART† and JOSEPH RUDNICK‡{ †Department of Chemistry, University of California, Los Angeles, LA 90095, USA ‡Department of Physics, University of California, Los Angeles, LA 90095, USA We address here a theoretical basis for the icosahedral symmetry that is observed so commonly for viral capsids, i.e., the single-protein-thick rigid shells that protect the viral genome. In particular, we outline the phenomenological hamiltonian approach developed recently (see Zandi, R., Reguera, D., Bruinsma, R., Gelbart, W.M. and Rudnick, J. (2004), Original of icosahedral symmetry in viruses, Proc. Natl. Acad. Sci., 101, 15556–15560) to account for the overwhelming prevalence of the Caspar-Klug “T- number” structures that are found for “spherical” viruses. We feature the role of “conformational switching energies” defining the competing multimeric states of the protein subunits. The results of Monte Carlo simulation of this model are argued to shed light as well on the mechanical properties and genome release mechanism for these viruses. Keywords: Viral self-assembly; Icosahedral symmetry; Structural transitions; T-number 1. Introduction believed to describe the generic structure of protein shells.§ However, with current computational capabilities The cowpea rotic mottle virus (CCMV) is a classical it is neither possible to verify this claim through all-atom T ¼ 3 RNA virus with a shell composed of 180 identical molecular dynamics simulations nor can we design subunits, [2] see also A. Zlotnick, this volume. Figure 1(a) artificial protein shells by all-atom simulations. -
Assembly from Atoms to Life October 3 to 5, 2016
Self-assembly from atoms to life October 3 to 5, 2016. Tuxtla Gutiérrez, Chiapas, México. Organizers: Prof. Charles M. Knobler / University of California Los Angeles (USA) Prof. Alexander J. Levine / University of California Los Angeles (USA) Prof. Jaime Ruiz García / Universidad Autónoma de San Luis Potosí (México) Dr. Elías Castellano Alcantara / Mesoamerican Centre for Theoretical Physics (MCTP) Sponsor: UCLA Center for Biological Physics, UCLA College of Letters and Sciences, UCLA ICAM branch, ICAM, 12 ICAM (http://icam-i2cam.org/), ICTP, MCTP, UNACH and CONACYT. The three-day October 2016 workshop in Mexico will honor of Professor William Gelbart’s 70th birthday. The "Self-assembly from atoms to life" workshop will bring together both young and senior scientists from around the world and it covers research areas that match UCLA physical chemistry professor Gelbart's broad range of interests that he has pursued over a 45- year career in research. It will take place October 3-5, 2016, at the Mesoamerican Centre for Theoretical Physics in Tuxtla Gutiérrez, Chiapas, Mexico. To facilitate travel to and from the event, the Marriott Tuxtla Gutiérrez Hotel has reserved a block a rooms at the special conference rate for October 2 through October 6. The workshop organizers are Profs. Alex Levine and Chuck Knobler from the UCLA Department of Chemistry and Biochemistry and Prof. Jaime Ruiz-Garcia, of the Physics Institute of the University of San Luis Potosi, in Mexico. One archetypal example of emergent phenomena in nature is found in the self-assembly of complex spatio-temporal structures, either in the relaxation of many-body systems toward their thermal equilibrium or in non-equilibrium steady states characterized by continuous energy throughput.