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Critical pore radius and transport properties of disordered hard- And overlapping-sphere models

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arXiv 2021年

作者： Klatt, Michael A. Ziff, Robert M. Torquato, Salvatore Department of Physics Princeton University PrincetonNJ08544 United States Institut für Theoretische Physik FAU Erlangen-Nürnberg Staudtstr. 7 Erlangen91058 Germany Center for the Study of Complex Systems Department of Chemical Engineering University of Michigan Ann ArborMI48109 United States Department of Physics Princeton University PrincetonNJ08544 United States Department of Chemistry Princeton Institute for the Science and Technology of Materials Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

Transport properties of porous media are intimately linked to their pore-space microstructures. We quantify geometrical and topological descriptors of the pore space of certain disordered and ordered distributions of spheres, including pore-size functions and the critical pore radius δc. We focus on models of porous media derived from maximally random jammed sphere packings, overlapping spheres, equilibrium hard spheres, "quantizer" sphere packings, and crystalline sphere packings. For precise estimates of the percolation thresholds, we use a strict relation of the void percolation around sphere configurations to weighted bond percolation on the corresponding Voronoi networks. We use the Newman-Ziff algorithm to determine the percolation threshold using universal properties of the cluster size distribution. The critical pore radius δc is often used as the key characteristic length scale that determines the fluid permeability k. A recent study [Torquato. Adv. Wat. Resour. 140,103565 (2020)] suggested for porous media with a well-connected pore space an alternative estimate of k based on the second moment of the pore size hδ2i, which is easier to determine than δc. Here, we compare δc to the second moment of the pore size hδ2i, and indeed confirm that, for all porosities and all models considered, δc2 is to a good approximation proportional to hδ2i. However, unlike hδ2i, the permeability estimate based on δc2 does not predict the correct ranking of k for our models. Thus, we confirm hδ2i to be a promising candidate for convenient and reliable estimates of the fluid permeability for porous media with a well-connected pore space. Moreover, we compare the fluid permeability of our models with varying degrees of order, as measured by the τ order metric. We find that (effectively) hyperuniform models tend to have lower values of k than their nonhyperuniform counterparts. Our findings could facilitate the design of porous media with desirable transport properties via target

关键词： Porous materials

Riccati conditioning and sensitivity for a MinMax controlled cable-mass system

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Riccati conditioning and sensitivity for a MinMax controlled...

IEEE Conference on Decision and Control

作者： Lizette Zietsman Katie A. Evans J. Teye Brown Richard A. Idowu Faculty of the Interdisciplinary Center for Applied Mathematics Virginia Technology Blacksburg VA USA Faculty of Mathematics and Statistics Louisiana Tech University Ruston LA USA Computational Analysis and Modeling Program Louisiana Tech University Ruston LA USA

ISBN: (纸本)9781424431236

In this paper we present a numerical study that investigates the relationship between the parameter q, used in the design of the MinMax controller, and the conditioning of the approximate algebraic Riccati equations, the sensitivity of the eigenvalues of I-¿ 2 P¿ to ¿ as well as the effect of q on the stability radia and the stability margin of the system. In order to guarantee accurate numerical solutions to the approximate Riccati equations, the Riccati equations must remain well-conditioned for the values of ¿ that are considered. This condition number reflects the combined sensitivity of the Riccati equations to the system inputs A, B, R, C and ¿. In addition, we also consider the sensitivity of the eigenvalues of I-¿ 2 P¿ to ¿. We study the possibility of these sensitivities serving as an indication of the largest value of ¿ for which I-¿ 2 P¿ remains positive definite. This sensitivity could also serve as an indication of the accuracy of the computation of I-¿ 2 P¿. Lastly, in order to design efficient low order controllers, it is important to ensure the robustness of the design. Stability radius and stability margin serve as measures of the robustness of the controller. A one-dimensional nonlinear cable mass system is considered to illustrate these ideas and numerical results are presented.

关键词： Riccati equations Minimax techniques Control systems Eigenvalues and eigenfunctions Robust control Robust stability Optimal control Contracts mathematics Military computing

Elastohydrodynamic study of actin filaments using fluorescence microscopy

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Physical Review E 1997年第2期56卷 R1330(R)-R1330(R)页

作者： D. Riveline C. H. Wiggins R. E. Goldstein A. Ott Laboratoire PhysicoChimie Curie Section de Recherche Institut Curie 11 rue Pierre et Marie Curie 75231 Paris Cedex 05 France Department of Physics Joseph Henry Laboratories Princeton University Princeton New Jersey 08544 Department of Physics and Program in Applied Mathematics University of Arizona Tucson Arizona 85721

We probed the bending of actin subject to external forcing and viscous drag. Single actin filaments were moved perpendicular to their long axis in an oscillatory way by means of an optically tweezed latex bead attached to one end of the filaments. Shapes of these polymers were observed by epifluorescence microscopy. They were found to be in agreement with predictions of semiflexible polymer theory and slender-body hydrodynamics. A persistence length of 7.4±0.2 μm could be extracted.

关键词： Elastohydrodynamics

ON THE MOTION OF CURVED DISLOCATIONS IN THREE DIMENSIONS: SIMPLIFIED LINEARIZED ELASTICITY

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arXiv 2020年

作者： Fonseca, Irene Ginster, Janusz Wojtowytsch, Stephan Department of Mathematical Sciences Carnegie-Mellon University 5000 Forbes Avenue PittsburghPA15213 United States Institut für Mathematik Humboldt-Universität zu Berlin Rudower Chaussee 25 Berlin12489 Germany Program in Applied and Computational Mathematics Princeton University 205 Fine Hall PrincetonNJ08544 United States

It is shown that in core-radius cutoff regularized simplified elasticity (where the elastic energy depends quadratically on the full displacement gradient rather than its symmetrized version), the force on a dislocation curve by the negative gradient of the elastic energy asymptotically approaches the mean curvature of the curve as the cutoff radius converges to zero. Rigorous error bounds in Hölder spaces are provided. As an application, convergence of dislocations moving by the gradient flow of the elastic energy to dislocations moving by the gradient flow of the arclength functional, when the motion law is given by an H1-type dissipation, and convergence to curve shortening flow in co-dimension 2 for the usual L2-dissipation is established. In the second scenario, existence and regularity are assumed while the H1-gradient flow is treated in full generality (for short time). The methods developed here are a blueprint for the more physical setting of linearized isotropic *** Codes 35K93, 35Q74, 74N05 Copyright © 2020, The Authors. All rights reserved.

关键词： Elasticity

Periodicity Scoring of Time Series Encodes Dynamical Behavior of the Tumor Suppressor p53 ⁎ ⁎

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IFAC-PapersOnLine 2021年第9期54卷 488-495页

作者： Caroline Moosmüller Christopher J. Tralie Mahdi Kooshkbaghi Zehor Belkhatir Maryam Pouryahya José Reyes Joseph O. Deasy Allen R. Tannenbaum Ioannis G. Kevrekidis C. Moosmüller and C. Tralie contributed equally to this work Department of Mathematics University of California San Diego La Jolla CA 92093 USA Department of Medical Physics Memorial Sloan-Kettering Cancer Center NY USA Department of Chemical and Biomolecular Engineering Johns Hopkins University Baltimore MD 21218 USA Department of Mathematics and Computer Science Ursinus College Collegeville PA USA Program in Applied and Computational Mathematics Princeton University NJ USA School of Engineering and Sustainable Development De Montfort University Leicester UK Cancer Biology and Genetics Program and Computational and Systems Biology Program Memorial Sloan-Kettering Cancer Center New York NY 10065 USA and Department of Systems Biology Harvard Medical School Boston MA 02115 USA Departments of Computer Science and Applied Mathematics & Statistics Stony Brook University NY USA

In this paper we analyze the dynamical behavior of the tumor suppressor protein p53, an essential player in the cellular stress response, which prevents a cell from dividing if severe DNA damage is present. When this response system is malfunctioning, e.g. due to mutations in p53, uncontrolled cell proliferation may lead to the development of cancer. Understanding the behavior of p53 is thus crucial to prevent its failing. It has been shown in various experiments that periodicity of the p53 signal is one of the main descriptors of its dynamics, and that its pulsing behavior (regular vs. spontaneous) indicates the level and type of cellular stress. In the present work, we introduce an algorithm to score the local periodicity of a given time series (such as the p53 signal), which we call Detrended Autocorrelation Periodicity Scoring (DAPS). It applies pitch detection (via autocorrelation) on sliding windows of the entire time series to describe the overall periodicity by a distribution of localized pitch scores. We apply DAPS to the p53 time series obtained from single cell experiments and establish a correlation between the periodicity scoring of a cell’s p53 signal and the number of cell division events. In particular, we show that high periodicity scoring of p53 is correlated to a low number of cell divisions and vice versa. We show similar results with a more computationally intensive state-of-the-art periodicity scoring algorithm based on topology known as Sw1PerS. This correlation has two major implications: It demonstrates that periodicity scoring of the p53 signal is a good descriptor for cellular stress, and it connects the high variability of p53 periodicity observed in cell populations to the variability in the number of cell division events.

关键词： Systems biology cellular systems time series modeling bioinformatics computational biology

Oscillator models and collective motion

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IEEE Control Systems Magazine

IEEE Control Systems Magazine 2007年第4期27卷 89-105页

作者： Paley, Derek A. Leonard, Naomi Ehrich Sepulchre, Rodolphe Grünbaum, Daniel Parrish, Julia K. Princeton University Department of Mechanical and Aerospace Engineering Princeton NJ 08544 United States Department of Mechanical and Aerospace Engineering Program in Applied and Computational Mathematics Princeton University Princeton NJ 08544 United States Department Electrical Engineering and Computer Science University of Liège Liège Belgium School of Oceanography Department of Biology University of Washington Seattle WA United States Biology Department School of Aquatic and Fishery Sciences University of Washington Seattle WA United States

A description of the so called "particles with coupled oscillator dynamics" (PCOD) is presented which is used to model, analyze and synthesize collective motion. An oscillator model with spatial dynamics is presented to help describe how to design steering control laws while it is being used to study biological collectives. Lastly, both engineering and biological analysis were described.

关键词： Oscillators (mechanical)

Hard convex lens-shaped particles: Characterization of dense disordered packings

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arXiv 2019年

作者： Cinacchi, Giorgio Torquato, Salvatore Instituto de Ciencias de Materiales "Nicolás Cabrera" Universidad Autónoma de Madrid Ciudad Universitaria de Cantoblanco MadridE-28049 Spain Department of Chemistry Department of Physics Institute for the Science and Technology of Materials Program for Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

Among the family of hard convex lens-shaped particles (lenses), the one with aspect ratio equal to 2/3 is ‘optimal’ in the sense that the maximally random jammed (MRJ) packings of such lenses achieve the highest packing fraction φMRJ ' 0.73. This value is only a few percent lower than φDKP = 0.76210 . . . , the packing fraction of the corresponding densest-known crystalline (degenerate) packings. By exploiting the appreciably reduced propensity that a system of such optimal lenses has to positionally and orientationally order, disordered packings of them are progressively generated by a Monte Carlo method-based procedure from the dilute equilibrium isotropic fluid phase to the dense nonequilibrium MRJ state. This allows one to closely monitor how the (micro)structure of these packings changes in the process of formation of the MRJ state. The gradual changes undergone by the many structural descriptors calculated can coherently and consistently be traced back to the gradual increase in contacts between the hard particles until the isostatic mean value of 10 contact neighbors per lens is reached at the effectively hyperuniform MRJ state. Compared to the MRJ state of hard spheres, the MRJ state of such optimal lenses is denser (less porous), more disordered, and rattler-free. This set of characteristics makes them good glass formers. It is possible that this conclusion may also hold for other hard convex uniaxial particles with a correspondingly similar aspect ratio, be they oblate or prolate, and that, by using suitable biaxial variants of them, that set of characteristics might further improve. Copyright © 2019, The Authors. All rights reserved.

关键词： Aspect ratio

Deep potentials for materials science

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材料展望（英文）

材料展望（英文） 2022年第2期 89-115页

作者： Tongqi Wen Linfeng Zhang Han Wang Weinan E David J Srolovitz Department of Mechanical Engineering The University of Hong KongHong KongHong Kong Special Administrative Region of China DP Technology BeijingPeople's Republic of China AI for Science Institute BeijingPeople's Republic of China Laboratory of Computational Physics Institute of Applied Physics and Computational MathematicsBeijingPeople's Republic of China HEDPS CAPTCollege of EngineeringPeking UniversityBeijingPeople's Republic of China AI for Science Institute BeijingPeople's Republic of China School of Mathematical Sciences Peking UniversityBeijingPeople's Republic of China Department of Mathematics and Program in Applied and Computational Mathematics Princeton UniversityPrincetonNJUnited States of America Department of Mechanical Engineering The University of Hong KongHong KongHong Kong Special Administrative Region of China International Digital Economy Academy(IDEA) ShenzhenPeople's Republic of China

To fill the gap between accurate(and expensive)ab initio calculations and efficient atomistic simulations based on empirical interatomic potentials,a new class of descriptions of atomic interactions has emerged and been widely applied;*** learning potentials(MLPs).One recently developed type of MLP is the deep potential(DP)*** this review,we provide an introduction to DP methods in computational materials *** theory underlying the DP method is presented along with a step-by-step introduction to their development and *** also review materials applications of DPs in a wide range of materials *** DP Library provides a platform for the development of DPs and a database of extant *** discuss the accuracy and efficiency of DPs compared with ab initio methods and empirical potentials.

关键词： deep potential atomistic simulation machine learning potential neural network

CONVERGENCE SPEED AND APPROXIMATION ACCURACY OF NUMERICAL MCMC

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arXiv 2022年

作者： Cui, Tiangang Dong, Jing Jasra, Ajay Tong, Xin T. School of Mathematics Monash University Australia Graduate School of Business Columbia University United States Applied Mathematics and Computational Science Program Computer Electrical Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Saudi Arabia Department of Mathematics National University of Singapore Singapore

When implementing Markov Chain Monte Carlo (MCMC) algorithms, perturbation caused by numerical errors is sometimes inevitable. This paper studies how perturbation of MCMC affects the convergence speed and Monte Carlo estimation accuracy. Our results show that when the original Markov chain converges to stationarity fast enough and the perturbed transition kernel is a good approximation to the original transition kernel, the corresponding perturbed sampler has similar convergence speed and high approximation accuracy as well. We discuss two different analysis frameworks: ergodicity and spectral gap, both are widely used in the literature. Our results can be easily extended to obtain non-asymptotic error bounds for MCMC estimators. We also demonstrate how to apply our convergence and approximation results to the analysis of specific sampling algorithms, including Random walk Metropolis and Metropolis adjusted Langevin algorithm with perturbed target densities, and parallel tempering Monte Carlo with perturbed densities. Finally we present some simple numerical examples to verify our theoretical claims. Copyright © 2022, The Authors. All rights reserved.

关键词： Inverse problems