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Reversals and collisions optimize protein exchange in bacterial swarms

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Physical Review E 2017年第3期95卷 032408-032408页

作者： Aboutaleb Amiri Cameron Harvey Amy Buchmann Scott Christley Joshua D. Shrout Igor S. Aranson Mark Alber Department of Applied and Computational Mathematics and Statistics University of Notre Dame Notre Dame Indiana 46556 USA and Department of Mathematics University of California Riverside California 92521 USA

Swarming groups of bacteria coordinate their behavior by self-organizing as a population to move over surfaces in search of nutrients and optimal niches for colonization. Many open questions remain about the cues used by swarming bacteria to achieve this self-organization. While chemical cue signaling known as quorum sensing is well-described, swarming bacteria often act and coordinate on time scales that could not be achieved via these extracellular quorum sensing cues. Here, cell-cell contact-dependent protein exchange is explored as a mechanism of intercellular signaling for the bacterium Myxococcus xanthus. A detailed biologically calibrated computational model is used to study how M. xanthus optimizes the connection rate between cells and maximizes the spread of an extracellular protein within the population. The maximum rate of protein spreading is observed for cells that reverse direction optimally for swarming. Cells that reverse too slowly or too fast fail to spread extracellular protein efficiently. In particular, a specific range of cell reversal frequencies was observed to maximize the cell-cell connection rate and minimize the time of protein spreading. Furthermore, our findings suggest that predesigned motion reversal can be employed to enhance the collective behavior of biological synthetic active systems.

关键词： Biological complexity Collective behavior

Numerical aspect of large-scale electronic state calculation for flexible device material

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arXiv 2018年

作者： Hoshi, Takeo Imachi, Hiroto Kuwata, Akiyoshi Kakuda, Kohsuke Fujita, Takatoshi Matsui, Hiroyuki Department of Applied Mathematics and Physics Tottori University 4-101 Koyama-Minami Tottori680-8552 Japan Department of Theoretical and Computational Molecular Science Institute for Molecular Science Japan Research Center of Organic Electronics Yamagata University Japan

Numerical aspects of large-scale electronic state calculation are explored on flexible organic device materials. Physical theory, numerical method and real application studies are discussed in the context of application-algorithmarchitecture co-design. An application study was carried out for disordered organic thin film. Participation ratio, a measure for the spatial extension of electronic wavefunction is focused on, since it is crucial for device property. A data scientific research is reported for a classification problem of disordered organic polymers, in which participation ratio is used as descriptor. These application studies indicate the potential need of purpose-specific solvers for internal eigenpairs. Copyright © 2018, The Authors. All rights reserved.

关键词： Numerical methods

Light Localization in Local Isomorphism Classes of Quasicrystals

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Physical Review Letters 2018年第24期120卷 247401-247401页

作者： Chaney Lin Paul J. Steinhardt Salvatore Torquato Department of Physics Princeton University Princeton New Jersey 08544 USA Princeton Center for Theoretical Science Princeton University Princeton New Jersey 08544 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Program of Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA

We study a continuum of photonic quasicrystal heterostructures derived from local isomorphism (LI) classes of pentagonal quasicrystal tilings. These tilings are obtained by direct projection from a five-dimensional hypercubic lattice. We demonstrate that, with the sole exception of the Penrose LI class, all other LI classes result in degenerate, effectively localized states, with precisely predictable and tunable properties (frequencies, frequency splittings, and densities). We show that localization and tunability are related to a mathematical property of the pattern known as “restorability,” i.e., whether the tiling can be uniquely specified given only a set of rules that fix all allowed clusters smaller than some bound.

关键词： Photonic crystals Photonics Quasicrystals

The influence of numerical error on an inverse problem methodology in PDE models

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arXiv 2018年

作者： Nardini, John T. Bortz, D.M. Department of Applied Mathematics 526 UCB BoulderCO80309-0526 United States Interdisciplinary Quantitative Biology Graduate Program University of Colorado BoulderCO80309-0596 United States

The inverse problem methodology is a commonly-used framework in the sciences for parameter estimation and inference. It is typically performed by fitting a mathematical model to noisy experimental data. There are two significant sources of error in the process: 1. Noise from the measurement and collection of experimental data and 2. numerical error in approximating the true solution to the mathematical model. Little attention has been paid to how this second source of error alters the results of an inverse problem. As a first step towards a better understanding of this problem, we present a modeling and simulation study using a simple advection-driven PDE model. We present both analytical and computational results concerning how the different sources of error impact the least squares cost function as well as parameter estimation and uncertainty quantification. We investigate residual patterns to derive an autocorrelative statistical model that can improve parameter estimation and confidence interval computation for first order methods. Building on the results of our investigation, we provide guidelines for practitioners to determine when numerical or experimental error is the main source of error in their inference, along with suggestions of how to efficiently improve their results. Copyright © 2018, The Authors. All rights reserved.

关键词： Parameter estimation

Using natural travel paths to infer and compare primate cognition in the wild

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iScience 2021年第4期24卷 102343页

作者： Janmaat, Karline R.L. de Guinea, Miguel Collet, Julien Byrne, Richard W. Robira, Benjamin van Loon, Emiel Jang, Haneul Biro, Dora Ramos-Fernández, Gabriel Ross, Cody Presotto, Andrea Allritz, Matthias Alavi, Shauhin Van Belle, Sarie Evolutionary and Population Biology Institute for Biodiversity and Ecosystem Dynamics University of Amsterdam Amsterdam Netherlands Department of Cognitive Psychology Faculty of Social Sciences Leiden University Leiden Netherlands ARTIS Amsterdam Royal zoo Amsterdam Netherlands Department of Social Sciences Oxford Brookes University Oxford United Kingdom Oxford Navigation Group Department of Zoology Oxford University Oxford United Kingdom Centre for Social Learning and Cognitive Evolution School of Psychology and Neuroscience University of St Andrews St Andrew United Kingdom Scottish Primate Research Group Scotland United Kingdom Centre d’Écologie Fonctionnelle et Évolutive Université de Montpellier Montpellier France Eco-anthropologie Muséum National d'Histoire Naturelle CNRS Université de Paris Paris France Theoretical and Computational Ecology Institute for Biodiversity and Ecosystem Dynamics University of Amsterdam Amsterdam Netherlands Department of Human Behavior Ecology and Culture Max Planck Institute for Evolutionary Anthropology Leipzig Germany Department of Brain and Cognitive Sciences University of Rochester Rochester United States Department of Mathematical Modelling of Social Systems Institute for Research on Applied Mathematics and Systems Universidad Nacional Autónoma de México Mexico City Mexico Center for Complexity Sciences Universidad Nacional Autónoma de México Mexico City Mexico Department of Geography and Geosciences Salisbury University Salisbury MA United States School of Psychology and Neuroscience University of St Andrews Scotland United Kingdom Department for the Ecology of Animal Societies Max Planck Institute of Animal Behaviour Konstanz Germany Centre for the Advanced Study of Collective Behaviour University of Konstanz Konstanz Germany Department of Biology University of Konstanz Konstanz Germany Department of Anthropology University of Austin at Texas Austin TX United States

Within comparative psychology, the evolution of animal cognition is typically studied either by comparing indirect measures of cognitive abilities (e.g., relative brain size) across many species or by conducting batteries of decision-making experiments among (typically) a few captive species. Here, we propose a third, complementary approach: inferring and comparing cognitive abilities through observational field records of natural information gradients and the associated variation in decision-making outcomes, using the ranging behavior of wild animals. To demonstrate the feasibility of our proposal, we present the results of a global survey assessing the availability of long-term ranging data sets from wild primates and the willingness of primatologists to share such data. We explore three ways in which such ranging data, with or without the associated behavioral and ecological data often collected by primatologists, might be used to infer and compare spatial cognition. Finally, we suggest how ecological complexity may be best incorporated into comparative analyses. © 2021 The Authors

关键词： Biological Sciences Cognitive Neuroscience Neuroscience

An adaptive high order direct solution technique for elliptic boundary value problems

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arXiv 2017年

作者： Geldermans, P. Gillman, A. Department of Computational and Applied Mathematics Rice University United States

This manuscript presents an adaptive high order discretization technique for elliptic boundary value problems. The technique is applied to an updated version of the Hierarchical Poincaré-Steklov (HPS) method. Roughly speaking, the HPS method is based on local pseudospectral discretizations glued together with Poincaré-Steklov operators. The new version uses a modified tensor product basis which is more efficient and stable than previous versions. The adaptive technique exploits the tensor product nature of the basis functions to create a criterion for determining which parts of the domain require additional refinement. The resulting discretization achieves the user prescribed accuracy and comes with an efficient direct solver. The direct solver increases the range of applicability to time dependent problems where the cost of solving elliptic problems previously limited the use of implicit time stepping schemes. Copyright © 2017, The Authors. All rights reserved.

关键词： Boundary value problems

Mid-Range Science Objectives for the Event Horizon Telescope

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arXiv 2024年

作者： Akiyama, Kazunori Albentosa-Ruíz, Ezequiel Alberdi, Antxon Alef, Walter Algaba, Juan Carlos Anantua, Richard Asada, Keiichi Azulay, Rebecca Bach, Uwe Baczko, Anne-Kathrin Ball, David Balokovi, Mislav Bandyopadhyay, Bidisha Barrett, John Baubck, Michi Benson, Bradford A. Bintley, Dan Blackburn, Lindy Blundell, Raymond Bouman, Katherine L. Bower, Geoffrey C. Bremer, Michael Brissenden, Roger Britzen, Silke Broderick, Avery E. Broguiere, Dominique Bronzwaer, Thomas Bustamante, Sandra Carlstrom, John E. Chael, Andrew Chan, Chi-Kwan Chang, Dominic O. Chatterjee, Koushik Chatterjee, Shami Chen, Ming-Tang Chen, Yongjun Cheng, Xiaopeng Cho, Ilje Christian, Pierre Conroy, Nicholas S. Conway, John E. Crawford, Thomas M. Crew, Geoffrey B. Cruz-Osorio, Alejandro Cui, Yuzhu Curd, Brandon Dahale, Rohan Davelaar, Jordy De Laurentis, Mariafelicia Deane, Roger Dempsey, Jessica Desvignes, Gregory Dexter, Jason Dhruv, Vedant Dihingia, Indu K. Doeleman, Sheperd S. Dzib, Sergio A. Eatough, Ralph P. Emami, Razieh Falcke, Heino Farah, Joseph Fish, Vincent L. Fomalont, Edward Ford, H. Alyson Foschi, Marianna Fraga-Encinas, Raquel Freeman, William T. Friberg, Per Fromm, Christian M. Fuentes, Antonio Galison, Peter Gammie, Charles F. García, Roberto Gentaz, Olivier Georgiev, Boris Goddi, Ciriaco Gold, Roman Gómez-Ruiz, Arturo I. Gómez, JoséL Gu, Minfeng Gurwell, Mark Hada, Kazuhiro Haggard, Daryl Hesper, Ronald Heumann, Dirk Ho, Luis C. Ho, Paul Honma, Mareki Huang, Chih-Wei L. Huang, Lei Hughes, David H. Ikeda, Shiro Impellizzeri, C.M. Violette Inoue, Makoto Issaoun, Sara James, David J. Jannuzi, Buell T. Janssen, Michael Jeter, Britton Jiang, Wu Jiménez-Rosales, Alejandra Johnson, Michael D. Jorstad, Svetlana Jones, Adam C. Joshi, Abhishek V. Jung, Taehyun Karuppusamy, Ramesh Kawashima, Tomohisa Keating, Garrett K. Kettenis, Mark Kim, Dong-Jin Kim, Jae-Young Kim, Jongsoo Kim, Junhan Kino, Motoki Koay, Jun Yi Kocherlakota, Prashant Kofuji, Yutaro Koch, Patrick M. Koyama, Shoko Kramer, Carsten Kramer, Joana A. Kramer, Michael Krichbaum, T Massachusetts Institute of Technology Haystack Observatory 99 Millstone Road WestfordMA01886 United States National Astronomical Observatory of Japan 2-21-1 Osawa Mitaka Tokyo181-8588 Japan Black Hole Initiative Harvard University 20 Garden Street CambridgeMA02138 United States Departament d’Astronomia i Astrofísica Universitat de València C. Dr. Moliner 50 Burjassot ValènciaE-46100 Spain Instituto de Astrofísica de Andalucía-CSIC Glorieta de la Astronomía s/n GranadaE-18008 Spain Max-Planck-Institut für Radioastronomie Auf dem Hügel 69 BonnD-53121 Germany Department of Physics Faculty of Science Universiti Malaya Kuala Lumpur50603 Malaysia Center for Astrophysics Harvard & Smithsonian 60 Garden Street CambridgeMA02138 United States Department of Physics & Astronomy The University of Texas at San Antonio One UTSA Circle San AntonioTX78249 United States Institute of Astronomy and Astrophysics Academia Sinica 11F of Astronomy-Mathematics Building AS/NTU No. 1 Sec. 4 Roosevelt Rd. Taipei106216 Taiwan Observatori Astronòmic Universitat de València C. Catedrático JoséBeltrán 2 Paterna ValènciaE-46980 Spain Department of Space Earth and Environment Chalmers University of Technology Onsala Space Observatory OnsalaSE-43992 Sweden Steward Observatory Department of Astronomy University of Arizona 933 N. Cherry Ave. TucsonAZ85721 United States Yale Center for Astronomy & Astrophysics Yale University 52 Hillhouse Avenue New HavenCT06511 United States Astronomy Department Universidad de Concepción Casilla 160-C Concepción Chile Department of Physics University of Illinois 1110 West Green Street UrbanaIL61801 United States Fermi National Accelerator Laboratory MS209 P.O. Box 500 BataviaIL60510 United States Department of Astronomy and Astrophysics University of Chicago 5640 South Ellis Avenue ChicagoIL60637 United States East Asian Observatory 660 N. A’ohoku Place HiloHI96720 United States 660 N. A’ohoku Place HiloHI

The first images of the black holes in Sgr A∗ and M87∗ have created a wide range of new scientific opportunities in gravitational physics, compact objects, and relativistic astrophysics. We discuss here the scientific opportunities that arise from the rich data sets that have already been obtained and the new data sets that will be obtained, exploiting a wide range of technical advances, including observational agility, receiver upgrades, and the addition of new stations. This document provides a 5-year framework for Event Horizon Telescope (EHT) science structured around four fundamental questions that are used to prioritize the analysis of existing data, guide technical upgrades, and determine the optimal use of future observational opportunities with EHT, ALMA, and multi-wavelength facilities. Through enhancements over this period, the EHT will create the first movie of M87∗ connecting black hole and jet physics, provide detailed studies of the structure and dynamics of Sgr A∗, characterize the magnetospheres of both systems through polarimetric imaging, and explore the spacetime properties of black holes with greater precision and range. © 2024, CC BY.

关键词： Astrophysics

Multiphase flows of N immiscible incompressible fluids: A reduction-consistent and thermodynamically-consistent formulation and associated algorithm

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arXiv 2017年

作者： Dong, S. Center for Computational and Applied Mathematics Department of Mathematics Purdue University West LafayetteIN United States

We present a reduction-consistent and thermodynamically consistent formulation and an associated numerical algorithm for simulating the dynamics of an isothermal mixture consisting of N (N ≥ 2) immiscible incompressible fluids with different physical properties (densities, viscosities, and pair-wise surface tensions). By reduction consistency we refer to the property that if only a set of M (1 ≤ M ≤ N−1) fluids are present in the system then the N-phase governing equations and boundary conditions will exactly reduce to those for the corresponding M-phase system. By theromdynamic consistency we refer to the property that the formulation honors the thermodynamic principles. Our N-phase formulation is developed based on a more general method that allows for the systematic construction of reduction-consistent formulations, and the method suggests the existence of many possible forms of reduction-consistent and thermodynamically consistent N-phase formulations. Extensive numerical experiments have been presented for flow problems involving multiple fluid components and large density ratios and large viscosity ratios, and the simulation results are compared with the physical theories or the available physical solutions. The comparisons demonstrate that our method produces physically accurate results for this class of problems. Copyright © 2017, The Authors. All rights reserved.

关键词： Multiphase flow

A pseudo knockoff filter for correlated features

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arXiv 2017年

作者： Chen, Jiajie Hou, Anthony Hou, Thomas Y. Applied and Computational Mathematics Caltech Department of Statistics Harvard University

In [3], the authors introduced a new variable selection procedure called the knockoff filter to control the false discovery rate (FDR) and proved that this method achieves exact FDR control. Inspired by the work of [3], we propose a pseudo-knockoff filter that inherits some advantages of the original knockoff filter and has more flexibility in constructing its knockoff matrix. Moreover, we perform a number of numerical experiments that seem to suggest that the pseudo knockoff filter with the half Lasso statistic has FDR control and offers more power than the original knockoff filter with the Lasso Path or the half Lasso statistic for the numerical examples that we consider in this paper. Although we cannot establish rigorous FDR control for the pseudo knockoff filter, we provide some partial analysis of the pseudo knockoff filter with the half Lasso statistic and establish a uniform FDP bound and an expectation inequality. Copyright © 2017, The Authors. All rights reserved.

关键词： Machine learning