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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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Interactions between species introduce spurious associations in microbiome studies

arXiv

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arXiv 2017年

作者： Menon, Rajita Ramanan, Vivek Korolev, Kirill S. Department of Physics Boston University BostonMA United States BRITE Bioinformatics REU Program Boston University BostonMA United States Graduate Program in Bioinformatics Boston University BostonMA United States Department of Biology and Computer Science Swarthmore College SwarthmorePA United States

Microbiota contribute to many dimensions of host phenotype, including disease. To link specific microbes to specific phenotypes, microbiome-wide association studies compare microbial abundances between two groups of samples. Abundance differences, however, reflect not only direct associations with the phenotype, but also indirect effects due to microbial interactions. We found that microbial interactions could easily generate a large number of spurious associations that provide no mechanistic insight. Using techniques from statistical physics, we developed a method to remove indirect associations and applied it to the largest dataset on pediatric inflammatory bowel disease. Our method corrected the inflation of p-values in standard association tests and showed that only a small subset of associations is directly linked to the disease. Direct associations had a much higher accuracy in separating cases from controls and pointed to immunomodulation, butyrate production, and the brain-gut axis as important factors in the inflammatory bowel disease. Copyright © 2017, The Authors. All rights reserved.

关键词： Association reactions

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Chirality provides a direct fitness advantage and facilitates intermixing in cellular aggregates

arXiv

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arXiv 2017年

作者： George, Ashish B. Korolev, Kirill S. Department of Physics Boston University BostonMA02215 United States Department of Physics Graduate Program in Bioinformatics Boston University BostonMA02215 United States

Short Abstract: Is it better to be left- or right-handed? The answer depends on whether the goal is making a handshake or winning a boxing match. The need for coordination favors the handedness of the majority, but being different could also provide an advantage. The same rules could apply to microbial colonies and cancer tumors. Like humans, cells often have handedness (chirality) that reflects the lack of mirror symmetry in their shapes or movement patterns. We find that cells gain a substantial fitness advantage by either increasing the magnitude of their chirality or switching to the opposite handedness. Selection for specific chirality is mediated by the formation of bulges along the colony edge in regions where cells with different chiralities meet. Long Abstract: Chirality in shape and motility can evolve rapidly in microbes and cancer cells. To determine how chirality affects cell fitness, we developed a model of chiral growth in compact aggregates such as microbial colonies and solid tumors. Our model recapitulates previous experimental findings and shows that mutant cells can invade by increasing their chirality or switching their handedness. The invasion results either in a takeover or stable coexistence between the mutant and the ancestor depending on their relative chirality. For large chiralities, the coexistence is accompanied by strong intermixing between the cells, while spatial segregation occurs otherwise. We show that the competition within the aggregate is mediated by bulges in regions where the cells with different chiralities meet. The two-way coupling between aggregate shape and natural selection is described by the chiral Kardar-Parisi-Zhang equation coupled to the Burgers' equation with multiplicative noise. We solve for the key features of this theory to explain the origin of selection on chirality. Overall, our work suggests that chirality could be an important ecological trait that mediates competition, invasion, and spatial structure in

关键词： Chirality

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Housing and husbandry factors affecting zebrafish novel tank test responses: a global multi-laboratory study

Lab animal

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Lab animal 2025年第6期54卷 2025 May 26页

作者： Courtney Hillman Barbara D Fontana Tamara G Amstislavskaya Maria A Gorbunova Stefani Altenhofen Karissa Barthelson Leonardo M Bastos João V Borba Carla D Bonan Caroline H Brennan Amaury Farías-Cea Austin Cooper Jamie Corcoran Eduardo R Dondossola Luis M Martinez-Duran Matheus Gallas-Lopes David S Galstyan Ella O Garcia Ewan Gerken Robert Hindges Justin W Kenney Maxim A Kleshchev Tatiana O Kolesnikova Adele Leggieri Sergey L Khatsko Michael Lardelli Guilherme Lodetti Giulia Lombardelli Ana C Luchiari Stefani M Portela Violeta Medan Lirane M Moutinho Evgeny V Nekhoroshev Barbara D Petersen Maureen L Petrunich-Rutherford Angelo Piato Maurizio Porfiri Emily Read Cássio M Resmim Eduardo P Rico Denis B Rosemberg Murilo S de Abreu Catia A Salazar Thailana Stahlhofer-Buss Júlia R Teixeira Ana M Valentim Alexander V Zhdanov Patricio Iturriaga-Vásquez Xian Wang Ryan Y Wong Allan V Kalueff Matthew O Parker Surrey Sleep Research Centre Department of Clinical and Experimental Medicine School of Biosciences University of Surrey Surrey UK. Laboratory of Experimental Neuropsychobiology Department of Biochemistry and Molecular Biology Natural and Exact Sciences Center Federal University of Santa Maria Santa Maria Brazil. Department of Biological Sciences Wayne State University Detroit MI USA. Laboratory of Experimental Models of Neuropsychiatric Disorders Scientific Research Institute of Neurosciences and Medicine Novosibirsk State University Novosibirsk Russia. Ural Federal University Yekaterinburg Russia. Laboratório de Neuroquímica e Psicofarmacologia Escola de Ciências da Saúde e da Vida Pontifícia Universidade Católica do Rio Grande do Sul Porto Alegre Brazil. Alzheimer's Disease Genetics Laboratory School of Biological Sciences Faculty of Sciences Engineering and Technology The University of Adelaide Adelaide South Australia Australia. Childhood Dementia Research Group College of Medicine and Public Health Flinders Health and Medical Research Institute Flinders University Adelaide South Australia Australia. Laboratório de Psicofarmacologia e Comportamento Departamento de Farmacologia Instituto de Ciências Básicas da Saúde Universidade Federal do Rio Grande do Sul Porto Alegre Brazil. School of Biological and Behavioural Sciences Queen Mary University of London London UK. Molecular Pharmacology and Medicinal Chemistry Lab Facultad de Ingeniería y Ciencias Universidad de la Frontera Temuco Chile. Department of Psychology University of Nebraska at Omaha Omaha NE USA. Translational Psychiatry Laboratory Graduate Program in Health Sciences University of Southern Santa Catarina Criciúma Brazil. St. Petersburg State University St. Petersburg Russia. Department of Psychology Indiana University Northwest Gary IN USA. Centre for Developmental Neurobiology and MRC Centre for Neurodevelopmental Disorders King's College London London UK. Neurobiology Program Sir

The reproducibility crisis in bioscience, characterized by inconsistent study results, impedes our understanding of biological processes. Global collaborative studies offer a unique solution to this problem. Here, we present a global collaboration using the zebrafish (Danio rerio) novel tank test, a popular behavioral assay for anxiety-like responses. We analyzed data from 20 laboratories worldwide, focusing on housing conditions and experimental setups. Our study included 488 adult zebrafish, tested for 5 min, focusing on a variety of variables. Key findings show that female zebrafish exhibit more anxiety-like behavior than males, highlighting sex as a critical variable. Housing conditions, including higher stocking densities and specific feed types, also influenced anxiety levels. Optimal conditions (5 fish/L) and nutritionally rich feeds (for example, rotifers) mitigated anxiety-like behaviors. Environmental stressors, such as noise and transportation, significantly impacted behavior. We recommend standardizing testing protocols to account for sex differences, optimal stocking densities, nutritionally rich feeds and minimizing stressors to improve the reliability of zebrafish behavioral studies.

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Evolutionary computation and swarm intelligence for the inference of gene regulatory networks

Evolutionary computation and swarm intelligence for the infe...

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作者： Hattori, Leandro Takeshi Lopes, Heitor Silvério Lopes, Fabrício Martins Graduate Program in Electrical and Computer Engineering Federal University of Technology ParanáCuritiba Brazil Graduate Program in Bioinformatics Federal University of Technology ParanáCornélio Procópio Brazil

The inference of gene regulatory networks (GRNs) from expression profiles is still an important challenge in bioinformatics research. The main difficulty of this problem is associated to the huge number of genes and the small number of samples available, as well as the intrinsic noise in the data acquisition process. In this context, this paper presents a feature selection approach to the identification of GRNs using optimisation strategies from evolutionary computation and swarm intelligence. As a case-study we used an artificial gene network (AGN) based on the scale-free topology. This AGN has 1,000 genes and was simulated with 500 temporal expression samples. The methods compared were: differential evolution (DE), bat algorithm (BAT) and artificial bee colony (ABC) algorithms. All algorithms used their standard control parameters and the same criterion function: the mean conditional entropy (MCE). This is an information theory measure, commonly adopted for various feature selection problems in the pattern recognition research field. The results showed that DE algorithm leaded to the best results than BAT and ABC in all comparisons, and the inferred network was more similar to the original network. Copyright © 2016 Inderscience Enterprises Ltd.

关键词： Evolutionary algorithms

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Plant biotic interactions

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Journal of Integrative Plant Biology 2016年第4期58卷 282-283页

作者： Hailing Jin Special Issue EditorUC President's Chair Director of Genetics Genomics and Bioinformatics Graduate ProgramCenter for Plant Cell BiologyInstitute for Integrative Genome BiologyUniversity of CaliforniaRiversideUSA

Plants are constantly under attack by pathogens,pests,and parasites,resulting in severe consequences on global food production and human *** pathogens and pests find their ways to invade and communicate with their hos... 详细信息

关键词： communicate constantly sophisticated consequences microbial fight biotic evolved pathogen volatile

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Correction to: Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions

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Genome medicine 2021年第1期13卷 151页

作者： Indhu-Shree Rajan-Babu Junran J Peng Readman Chiu Chenkai Li Arezoo Mohajeri Egor Dolzhenko Michael A Eberle Inanc Birol Jan M Friedman Department of Medical Genetics University of British Columbia and Children's & Women's Hospital Vancouver BC V6H3N1 Canada. indhu.babu@bcchr.ca. Department of Medical and Molecular Genetics King's College London Strand London WC2R 2LS UK. indhu.babu@bcchr.ca. Department of Medical Genetics University of British Columbia and Children's & Women's Hospital Vancouver BC V6H3N1 Canada. Canada's Michael Smith Genome Sciences Centre BC Cancer Agency Vancouver BC V5Z4S6 Canada. Bioinformatics Graduate Program University of British Columbia Vancouver BC V6T1Z4 Canada. Illumina Inc. San Diego CA 92121 USA.

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A27 Exploring novel mechanisms of HIV-2 mutagenesis

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Virus Evolution 2018年第SUPPL_1期4卷

作者： Meissner, M E Baliga, S Roth, M Baller, J Mansky, L M Institute for Molecular Virology Madison WI USA Molecular Cellular Developmental Biology and Genetics Graduate Program Saint-Paul MN USA Bioinformatics and Computational Biology Graduate Program Minneapolis MN USA Minnesota Supercomputing Institute Minneapolis MN USA University of Minnesota Minneapolis MN USA

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Front Cover: Synthesis and Immunomodulatory Activity of Fluorine-Containing Bisphosphonates (ChemMedChem 4/2019)

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ChemMedChem 2019年第4期14卷 360-360页

作者： Dr. Satoshi Mizuta Mohammed S. O. Tagod Dr. Masashi Iwasaki Prof. Yoichi Nakamura Dr. Hiroaki Senju Prof. Hiroshi Mukae Prof. Craig T. Morita Prof. Yoshimasa Tanaka Center for Bioinformatics and Molecular Medicine Graduate School of Biomedical Sciences Nagasaki University 1-12-4 Sakamoto Nagasaki 852-8523 Japan Program for Nurturing Global Leaders in Tropical and Emerging Infectious Diseases Graduate School of Biomedical Sciences Nagasaki University 1-12-4 Sakamoto Nagasaki 852-8523 Japan Center for Innovation in Immunoregulative Technology and Therapeutics Graduate School of Medicine Kyoto University Yoshidakonoe-cho Kyoto 606-8501 Japan Department of Respiratory Medicine Nagasaki University School of Medicine 1-7-1 Sakamoto Nagasaki 852-8501 Japan Department of Internal Medicine and the Interdisciplinary Graduate Program in Immunology University of Iowa Carver College of Medicine Iowa City Veterans Affairs Health Care System Iowa City IA 52246 USA Hyogo College of Medicine 1-1 Mukogawa Nishinomiya Hyogo 663-8501 Japan

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Author Correction: African-centric TP53 variant increases iron accumulation and bacterial pathogenesis but improves response to malaria toxin

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Nature communications 2020年第1期11卷 1541页

作者： Kumar Sachin Singh Julia I-Ju Leu Thibaut Barnoud Prashanthi Vonteddu Keerthana Gnanapradeepan Cindy Lin Qin Liu James C Barton Andrew V Kossenkov Donna L George Maureen E Murphy Farokh Dotiwala Vaccine and Immunotherapy Center The Wistar Institute Philadelphia PA 19104 USA. Department of Genetics The Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania Philadelphia PA 19104 USA. Program in Molecular and Cellular Oncogenesis The Wistar Institute Philadelphia PA 19104 USA. Graduate Group in Biochemistry and Molecular Biophysics The Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania Philadelphia PA 19104 USA. Program in Immunology Microenvironment and Metastasis The Wistar Institute Philadelphia PA 19104 USA. Southern Iron Disorders Center Birmingham AL 35209 USA and Department of Medicine University of Alabama at Birmingham Birmingham AL 35294 USA. Bioinformatics Facility The Wistar Institute Philadelphia PA 19104 USA. Department of Genetics The Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania Philadelphia PA 19104 USA. georged@pennmedicine.upenn.edu. Program in Molecular and Cellular Oncogenesis The Wistar Institute Philadelphia PA 19104 USA. mmurphy@***. Vaccine and Immunotherapy Center The Wistar Institute Philadelphia PA 19104 USA. fdotiwala@***.

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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