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Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures…

Biomolecules · Quantitative Biology 2025-05-27 Sotirios Touliopoulos , Nicholas M. Glykos

The streaming instability is an efficient method for overcoming the barriers to planet formation in protoplanetary discs. The streaming instability has been extensively modelled by hydrodynamic simulations of gas and a single dust size.…

Earth and Planetary Astrophysics · Physics 2025-03-19 Jip Matthijsse , Hossam Aly , Sijme-Jan Paardekooper

Amorphous materials as diverse as foams, emulsions, colloidal suspensions and granular media can jam into a rigid, disordered state where they withstand finite shear stresses before yielding. Here we review the current understanding of the…

Soft Condensed Matter · Physics 2015-05-14 M van Hecke

We model the packing structure of a marginally jammed bulk ensemble of polydisperse spheres using an extended granocentric mode explicitly taking into account rattlers. This leads to a relation- ship between the characteristic parameters of…

Jamming in hard-particle packings has been the subject of considerable interest in recent years. In a paper by Torquato and Stillinger [J. Phys. Chem. B, 105 (2001)], a classification scheme of jammed packings into hierarchical categories…

Materials Science · Physics 2007-05-23 Aleksandar Donev , Salvatore Torquato , Frank H. Stillinger , Robert Connelly

Segregation patterns of size-bidisperse particle mixtures in a fully-three-dimensional flow produced by alternately rotating a spherical tumbler about two perpendicular axes are studied over a range of particle sizes and volume ratios using…

Soft Condensed Matter · Physics 2019-07-03 Mengqi Yu , Paul B. Umbanhowar , Julio M. Ottino , Richard M. Lueptow

We consider a system of hard spheres close to jamming, where translation invariance is broken by pinning a randomly chosen set of particles. Using two different protocols, we generate two kinds of packings at the jamming point, isostatic…

Disordered Systems and Neural Networks · Physics 2013-08-20 Carolina Brito , Giorgio Parisi , Francesco Zamponi

We study the fragment size distributions after crushing of single and many particles under uniaxial compression inside a cylindrical container by means of numerical simulations. Under the assumption that breaking goes through the bulk of…

Soft Condensed Matter · Physics 2019-01-16 Pavel S. Iliev , Falk K. Wittel , Hans J. Herrmann

Consider the system of particles on ${\Bbb Z}^d$ where particles are of two types, $A$ and $B$, and execute simple random walks in continuous time. Particles do not interact with their own type, but when a type $A$ particle meets a type $B$…

Mathematical Physics · Physics 2007-05-23 M. Bramson , J. L. Lebowitz

In bidisperse particle mixtures varying in size or density alone, large particles rise (driven by percolation) and heavy particles sink (driven by buoyancy). When the two particle species differ from each other in both size and density, the…

Soft Condensed Matter · Physics 2021-06-09 Yifei Duan , Paul B. Umbanhowar , Richard M. Lueptow

A new type of quasi-two-dimensional complex plasma system was observed which consisted of monodisperse microspheres and their binary agglomerations (dimers). The particles and their dimers levitated in a plasma sheath at slightly different…

Plasma Physics · Physics 2016-05-25 M. Chaudhuri , I. Semenov , V. Nosenko , H. M. Thomas

This work analyzes the distribution and size of interparticle gaps arising in an ensemble of hexagonal unit structures in the xy plane when packing disks with a Gaussian distribution of radii with mean (r) and standard deviation $\Delta r$.…

Statistical Mechanics · Physics 2007-11-29 Daniel P. Snowman

Previous studies have suggested a conundrum in the relaxation dynamics of polydisperse supercooled liquids. It has been shown that in two dimensions, the relative relaxation times of particles of different sizes become more similar as the…

Soft Condensed Matter · Physics 2025-03-06 Ilian Pihlajamaa , Lotte van Gessel , Corentin Laudicina , Luc van Burik , Liesbeth Janssen

Jammed particulate systems, such as granular media, colloids, and foams, interact via one-sided forces that are nonzero only when particles overlap. We find that systems with one-sided repulsive interactions possess no linear response…

Soft Condensed Matter · Physics 2011-08-29 Carl F. Schreck , Thibault Bertrand , Corey S. O'Hern , M. D. Shattuck

For the binary discs packed in two dimensions, the packing fraction of disc assembly becomes lower than that of the monodisperse system when the size ratio is close to unity. We show that the suppressed packing fraction is caused by an…

Disordered Systems and Neural Networks · Physics 2007-10-24 Takashi Odagaki , Tsuyoshi Okubo , Ryusei Ogata , Keiji Okazaki

We examine the jamming transition in a two-dimensional granular polymer system using compressional simulations. The jamming density \phi_c decreases with increasing length of the granular chain due to the formation of loop structures, in…

Soft Condensed Matter · Physics 2015-05-14 L. M. Lopatina , C. J. Olson Reichhardt , C. Reichhardt

Hyperuniformity characterizes a state of matter for which density fluctuations diminish towards zero at the largest length scales. However, the task of determining whether or not an experimental system is hyperuniform is experimentally…

Soft Condensed Matter · Physics 2015-06-22 Remi Dreyfus , Ye Xu , Tim Still , Lawrence A. Hough , A. G. Yodh , Salvatore Torquato

We study properties of jammed packings of frictionless spheres over a wide range of volume fractions. There exists a crossover volume fraction which separates deeply jammed solids from marginally jammed solids. In deeply jammed solids, all…

Soft Condensed Matter · Physics 2011-03-25 Cang Zhao , Kaiwen Tian , Ning Xu

The jamming transition of particles with finite-range interactions is characterized by a variety of critical phenomena, including power law distributions of marginal contacts. We numerically study a recently proposed simple model of…

Statistical Mechanics · Physics 2016-01-20 Yoav Kallus

We numerically study the distributions of global pressure that are found in ensembles of statically jammed and quasistatically sheared systems of bidisperse, frictionless, disks at fixed packing fraction $\phi$ in two dimensions. We use…

Disordered Systems and Neural Networks · Physics 2015-06-17 Daniel Vagberg , Yegang Wu , Peter Olsson , S. Teitel