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Hypostatic jammed packings of frictionless nonspherical particles

Physical Review E 2018年第1期97卷 012909-012909页

作者： Kyle VanderWerf Weiwei Jin Mark D. Shattuck Corey S. O'Hern Department of Physics Yale University New Haven Connecticut 06520 USA Department of Mechanics and Engineering Science Peking University Beijing 100871 China Department of Mechanical Engineering & Materials Science Yale University New Haven Connecticut 06520 USA Benjamin Levich Institute and Physics Department The City College of New York New York New York 10031 USA Department of Applied Physics Yale University New Haven Connecticut 06520 USA Graduate Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut 06520 USA

We perform computational studies of static packings of a variety of nonspherical particles including circulo-lines, circulo-polygons, ellipses, asymmetric dimers, dumbbells, and others to determine which shapes form packings with fewer contacts than degrees of freedom (hypostatic packings) and which have equal numbers of contacts and degrees of freedom (isostatic packings), and to understand why hypostatic packings of nonspherical particles can be mechanically stable despite having fewer contacts than that predicted from naive constraint counting. To generate highly accurate force- and torque-balanced packings of circulo-lines and cir-polygons, we developed an interparticle potential that gives continuous forces and torques as a function of the particle coordinates. We show that the packing fraction and coordination number at jamming onset obey a masterlike form for all of the nonspherical particle packings we studied when plotted versus the particle asphericity A, which is proportional to the ratio of the squared perimeter to the area of the particle. Further, the eigenvalue spectra of the dynamical matrix for packings of different particle shapes collapse when plotted at the same A. For hypostatic packings of nonspherical particles, we verify that the number of “quartic” modes along which the potential energy increases as the fourth power of the perturbation amplitude matches the number of missing contacts relative to the isostatic value. We show that the fourth derivatives of the total potential energy in the directions of the quartic modes remain nonzero as the pressure of the packings is decreased to zero. In addition, we calculate the principal curvatures of the inequality constraints for each contact in circulo-line packings and identify specific types of contacts with inequality constraints that possess convex curvature. These contacts can constrain multiple degrees of freedom and allow hypostatic packings of nonspherical particles to be mechanically stable.

关键词： Granular materials Granular packing Jamming

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The role of deformability in determining the structural and mechanical properties of bubbles and emulsions

arXiv

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arXiv 2019年

作者： Boromand, Arman Signoriello, Alexandra Lowensohn, Janna Orellana, Carlos S. Weeks, Eric R. Ye, Fangfu Shattuck, Mark D. O’Hern, Corey S. Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Beijing National Laboratory for Condensed Matter Physics CAS Key Laboratory of Soft Matter Physics Institute of Physics Chinese Academy of Sciences Beijing China Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Department of Physics Emory University AtlantaGA30322 United States School of Physical Sciences University of Chinese Academy of Sciences Beijing China Benjamin Levich Institute and Physics Department City College of New York New YorkNY10031 United States Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States

We perform computational studies of jammed particle packings in two dimensions undergoing isotropic compression using the well-characterized soft particle (SP) model and deformable particle (DP) model that we developed for bubbles and emulsions. In the SP model, circular particles are allowed to overlap, generating purely repulsive forces. In the DP model, particles minimize their perimeter, while deforming at fixed area to avoid overlap during compression. We compare the structural and mechanical properties of jammed packings generated using the SP and DP models as a function of the packing fraction ρ, instead of the reduced number density φ. We show that near jamming onset the excess contact number ∆z = z−zJ and shear modulus G scale as ∆ρ0.5 in the large system limit for both models, where ∆ρ = ρ−ρJ and zJ ≈4 and ρJ ≈0.842 are the values at jamming onset. ∆z and G for the SP and DP models begin to differ for ρ & 0.88. In this regime, ∆z∼G can be described by a sum of two power-laws in ∆ρ, i.e. ∆z∼G ∼C0∆ρ0.5+C1∆ρ1.0 to lowest order. We show that the ratio C1/C0 is much larger for the DP model compared to to that for the SP model. We also characterize the void space in jammed packings as a function of ρ. We find that the DP model can describe the formation of Plateau borders as ρ → 1. We further show that the results for z and the shape factor A versus ρ for the DP model agree with recent experimental studies of foams and emulsions. Copyright © 2019, The Authors. All rights reserved.

关键词： Jamming

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Corrigendum to: Impact of Acute HIV Infection and Early Antiretroviral Therapy on the Human Gut Microbiome

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Open forum infectious diseases 2020年第9期7卷 ofaa381页

作者： Ornella Sortino Nittaya Phanuphak Alexandra Schuetz Alexandra M Ortiz Nitiya Chomchey Yasmine Belkaid Jacquice Davis Harry A Mystakelis Mariam Quiñones Claire Deleage Brian Ingram Rungsun Rerknimitr Suteeraporn Pinyakorn Adam Rupert Merlin L Robb Jintanat Ananworanich Jason Brenchley Irini Sereti Clinical Research Directorate Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute. National Institute of Allergy and Infectious Diseases National Institutes of Health Bethesda Maryland. SEARCH/Thai Red Cross AIDS Research Centre Bangkok Thailand. The Henry M. Jackson Foundation for the Advancement of Military Medicine Bethesda Maryland. United States Military HIV Research Program Walter Reed Army Institute of Research Silver Spring Maryland. Armed Forces Research Institute of Medical Sciences Bangkok Thailand. Metaorganism Immunity Section Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health Bethesda Maryland. Microbiome Program National Institute of Allergy and Infectious Diseases National Institutes of Health Bethesda Maryland. Bioinformatics and Computational Biosciences Branch Office of Cyber Infrastructure and Computational Biology National Institute of Allergy and Infectious Diseases National Institutes of Health Bethesda Maryland. Metabolon Inc. Research Triangle Park North Carolina. Department of Global Health University of Amsterdam Amsterdam the Netherlands.

[This corrects the article DOI: 10.1093/ofid/ofz367.].

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Publisher Correction: Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery

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Nature communications 2021年第1期12卷 4318页

作者： Bahar Behsaz Edna Bode Alexey Gurevich Yan-Ni Shi Florian Grundmann Deepa Acharya Andrés Mauricio Caraballo-Rodríguez Amina Bouslimani Morgan Panitchpakdi Annabell Linck Changhui Guan Julia Oh Pieter C Dorrestein Helge B Bode Pavel A Pevzner Hosein Mohimani Bioinformatics and Systems Biology Program University of California San Diego La Jolla CA USA. Center for Microbiome Innovation University of California at San Diego La Jolla CA USA. Computational Biology Department School of Computer Science Carnegie Mellon University Pittsburgh PA USA. Molecular Biotechnology Department of Biosciences Goethe University Frankfurt Frankfurt am Main Germany. Center for Algorithmic Biotechnology Institute of Translational Biomedicine St. Petersburg State University St Petersburg Russia. Tiny Earth Chemistry Hub University of Wisconsin-Madison Madison WI USA. Collaborative Mass Spectrometry Innovation Center Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego La Jolla CA USA. The Jackson Laboratory of Medical Genomics Farmington CT USA. Molecular Biotechnology Department of Biosciences Goethe University Frankfurt Frankfurt am Main Germany. helge.bode@mpi-marburg.mpg.de. Buchmann Institute for Molecular Life Sciences (BMLS) Goethe University Frankfurt & Senckenberg Research Institute Frankfurt am Main Germany. helge.bode@mpi-marburg.mpg.de. Max-Planck-Institute for Terrestrial Microbiology Department for Natural Products in Organismic Interactions Marburg Germany. helge.bode@mpi-marburg.mpg.de. Department of Computer Science and Engineering University of California San Diego La Jolla CA USA. ppevzner@ucsd.edu. Computational Biology Department School of Computer Science Carnegie Mellon University Pittsburgh PA USA. hoseinm@andrew.cmu.edu.

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"RETRACTED ARTICLE: Vibrio parahaemolyticus RhsP represents a widespread group of pro-effectors for type VI secretion systems

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Nature Communications 2018年第1期9卷 1-14页

作者： Nan Jiang Le Tang Ruiqiang Xie Zhi Li Brianne Burkinshaw Xiaoye Liang Dylan Sosa L. Aravind Tao Dong Dapeng Zhang Jun Zheng Faculty of Health Sciences University of Macau Macau SAR China Department of Ecosystem and Public Health University of Calgary Calgary Canada Department of Biochemistry and Molecular Biology University of Calgary Calgary Canada Snyder Institute for Chronic Diseases University of Calgary Calgary Canada State Key Laboratory of Microbial Metabolism Joint International Laboratory on Metabolic and Developmental Sciences School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai China Program of Bioinformatics and Computational Biology College of Arts and Sciences Saint Louis University Saint Louis USA National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda USA Department of Biology College of Arts and Sciences Saint Louis University Saint Louis USA

Type VI secretion systems (T6SSs) translocate effector proteins, such as Rhs toxins, to eukaryotic cells or prokaryotic competitors. All T6SS Rhs-type effectors characterized thus far contain a PAAR motif or a similar structure. Here, we describe a T6SS-dependent delivery mechanism for a subset of Rhs proteins that lack a PAAR motif. We show that the N-terminal Rhs domain of protein RhsP (or VP1517) fromVibrio parahaemolyticusinhibits the activity of the C-terminal DNase domain. Upon auto-proteolysis, the Rhs fragment remains inside the cells, and the C-terminal region interacts with PAAR2 and is secreted by T6SS2; therefore, RhsP acts as a pro-effector. Furthermore, we show that RhsP contributes to the control of certain “social cheaters” (opaRmutants). Genes encoding proteins with similar Rhs and PAAR-interacting domains, but diverse C-terminal regions, are widely distributed amongVibriospecies.

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Learning binary latent variable models: A tensor eigenpair approach

arXiv

引用

arXiv 2018年

作者： Jaffe, Ariel Weiss, Roi Carmi, Shai Kluger, Yuval Nadler, Boaz Dept. of Computer Science and Applied Mathematics Weizmann Institute of Science Rehovot7610001 Israel Braun School of Public Health and Community Medicine Hebrew University of Jerusalem Jerusalem9112102 Israel Interdepartmental Program in Computational Biology and Bioinformatics Yale University New HavenCT06511 United States Dept. of Pathology Yale Cancer Center Yale University School of Medicine New HavenCT06520 United States Program of Applied Mathematics Yale University New HavenCT06511 United States

Latent variable models with hidden binary units appear in various applications. Learning such models, in particular in the presence of noise, is a challenging computational problem. In this paper we propose a novel spectral approach to this problem, based on the eigenvectors of both the second order moment matrix and third order moment tensor of the observed data. We prove that under mild non-degeneracy conditions, our method consistently estimates the model parameters at the optimal parametric rate. Our tensor-based method generalizes previous orthogonal tensor decomposition approaches, where the hidden units were assumed to be either statistically independent or mutually exclusive. We illustrate the consistency of our method on simulated data and demonstrate its usefulness in learning a common model for population mixtures in genetics. Copyright © 2018, The Authors. All rights reserved.

关键词： Tensors

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Correction to: Genes associated with survival of female bovine blastocysts produced in vivo

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Cell and tissue research 2020年第3期382卷 679页

作者： A M Zolini J Block M B Rabaglino G Rincon M Hoelker J J Bromfield D Salilew-Wondim P J Hansen Department of Animal Sciences D.H. Barron Reproductive and Perinatal Biology Research Program and Genetics Institute University of Florida PO Box 110910 Gainesville FL 32611-0910 USA. Zoetis Inc. Kalamazoo MI 49007 USA. Instituto de Investigación en Ciencias de La Salud CONICET Córdoba Argentina. Quantitative Genetics Bioinformatics and Computational Biology Group Department of Applied Mathematics and Computer Science Technical University of Denmark Kemitorvet 2800 Kgs. Lyngby Denmark. Institute of Animal Science Animal Breeding and Husbandry University of Bonn Bonn Germany. Teaching and Research Station Frankenforst Faculty of Agriculture University of Bonn Königswinter Germany. Center of Integrated Dairy Research University of Bonn Bonn Germany. Department of Animal Sciences D.H. Barron Reproductive and Perinatal Biology Research Program and Genetics Institute University of Florida PO Box 110910 Gainesville FL 32611-0910 USA. pjhansen@ufl.edu.

The first error is on page 5. A sentence lists two genes as SCNA1A and SCNA2A but they should be SCN1A and SCN2A.

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Using LICHeE and BAMSE for Reconstructing Cancer Phylogenetic Trees

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Current Protocols in bioinformatics 2018年第1期62卷 e49-e49页

作者： Ricketts, Camir Popic, Victoria Toosi, Hosein Hajirasouliha, Iman Tri-I Computational Biology & Medicine Graduate Program Cornell University New York NY United States Institute for Computational Biomedicine Department of Physiology and Biophysics Weill Cornell Medicine New York NY United States Illumina Inc. Illumina Mission Bay San Francisco CA United States Department of Bioinformatics Institute for Biochemistry and Biophysics University of Tehran Iran Englander Institute for Precision Medicine The Meyer Cancer Center Weill Cornell Medicine New York United States

The reconstruction of cancer phylogeny trees and quantifying the evolution of the disease is a challenging task. LICHeE and BAMSE are two computational tools designed and implemented recently for this purpose. They both utilize estimated variant allele fraction of somatic mutations across multiple samples to infer the most likely cancer phylogenies. This unit provides extensive guidelines for installing and running both LICHeE and BAMSE. © 2018 by John Wiley & Sons, Inc. © 2018 John Wiley & Sons, Inc.

关键词： cancer phylogeny deep sequencing next-generation sequencing somatic variations tumor heterogeneity

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Publisher Correction: Integrating yeast chemical genomics and mammalian cell pathway analysis

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Acta pharmacologica Sinica 2020年第5期41卷 729页

作者： Fu-Lai Zhou Sheena C Li Yue Zhu Wan-Jing Guo Li-Jun Shao Justin Nelson Scott Simpkins De-Hua Yang Qing Liu Yoko Yashiroda Jin-Biao Xu Yao-Yue Fan Jian-Min Yue Minoru Yoshida Tian Xia Chad L Myers Charles Boone Ming-Wei Wang The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research Shanghai Institute of Materia Medica Chinese Academy of Sciences (CAS) Shanghai 201203 China. University of Chinese Academy of Sciences Beijing 100049 China. RIKEN Center for Sustainable Resource Science Wako Saitama 3510198 Japan. Bioinformatics and Computational Biology Program University of Minnesota-Twin Cities Minneapolis Minnesota 55455 USA. The State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China. Department of Biology The University of Tokyo Bunkyo-ku Tokyo 1138657 Japan. Collaborative Research for Innovative Microbiology The University of Tokyo Bunkyo-ku Tokyo 1138657 Japan. Department of Electronics and Information Engineering Huazhong University of Science and Technology Wuhan 430074 China. Bioinformatics and Computational Biology Program University of Minnesota-Twin Cities Minneapolis Minnesota 55455 USA. chadm@umn.edu. RIKEN Center for Sustainable Resource Science Wako Saitama 3510198 Japan. charlie.boone@utoronto.ca. Donnelly Centre and Department of Molecular Genetics University of Toronto Ontario M5S 3E1 Canada. charlie.boone@utoronto.ca. The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research Shanghai Institute of Materia Medica Chinese Academy of Sciences (CAS) Shanghai 201203 China. mwwang@***. University of Chinese Academy of Sciences Beijing 100049 China. mwwang@***.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Ten simple rules for reproducible research in jupyter notebooks

arXiv

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arXiv 2018年

作者： Rule, Adam Birmingham, Amanda Zuniga, Cristal Altintas, Ilkay Huang, Shih-Cheng Knight, Rob Moshiri, Niema Nguyen, Mai H. Rosenthal, Sara Brin Pérez, Fernando Rose, Peter W. Design Lab UC San Diego San DiegoCA United States Center for Computational Biology and Bioinformatics UC San Diego San DiegoCA United States Department of Pediatrics UC San Diego San DiegoCA United States Data Science Hub San Diego Supercomputer Center UC San Diego San DiegoCA United States Departments of Bioengineering and Computer Science and Engineering Center for Microbiome Innovation UC San Diego San DiegoCA United States Bioinformatics and Systems Biology Graduate Program UC San Diego San DiegoCA United States Department of Statistics Berkeley Institute for Data Science UC Berkeley Lawrence Berkeley National Laboratory BerkeleyCA United States Biomedical Informatics Graduate Program Stanford University StanfordCA United States

Reproducibility of computational studies is a hallmark of scientific methodology. It enables researchers to build with confidence on the methods and findings of others, reuse and extend computational pipelines, and thereby drive scientific progress. Since many experimental studies rely on computational analyses, biologists need guidance on how to set up and document reproducible data analyses or simulations. In this paper, we address several questions about reproducibility. For example, what are the technical and non-technical barriers to reproducible computational studies? What opportunities and challenges do computational notebooks offer to overcome some of these barriers? What tools are available and how can they be used effectively? We have developed a set of rules to serve as a guide to scientists with a specific focus on computational notebook systems, such as Jupyter Notebooks, which have become a tool of choice for many applications. Notebooks combine detailed workflows with narrative text and visualization of results. Combined with software repositories and open source licensing, notebooks are powerful tools for transparent, collaborative, reproducible, and reusable data analyses. Copyright © 2018, The Authors. All rights reserved.

关键词： Digital storage

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