Isostatic phase transition and instability in stiff granular materials

In this letter, structural rigidity concepts are used to understand the origin of instabilities in granular aggregates. It is shown that: a) The contact network of a noncohesive granular aggregate becomes exactly isostatic in the limit of large stiffness-to-load ratio. b) Isostaticity is responsible for the anomalously large susceptibility to perturbation of these systems, and c) The load-stress response function of granular materials is critical (power-law distributed) in the isostatic limit. Thus there is a phase transition in the limit of intinitely large stiffness, and the resulting isostatic phase is characterized by huge instability to perturbation.Comment: RevTeX, 4 pages w/eps figures [psfig]. To appear in Phys. Rev. Let

The statistics of particle velocities in dense granular flows

We present measurements of the particle velocity distribution in the flow of granular material through vertical channels. Our study is confined to dense, slow flows where the material shears like a fluid only in thin layers adjacent to the walls, while a large core moves without continuous deformation, like a solid. We find the velocity distribution to be non-Gaussian, anisotropic, and to follow a power law at large velocities. Remarkably, the distribution is identical in the fluid-like and solid-like regions. The velocity variance is maximum at the core, defying predictions of hydrodynamic theories. We show evidence of spatially correlated motion, and propose a mechanism for the generation of fluctuational motion in the absence of shear.Comment: Submitted to Phys. Rev. Let

Force Distribution in a Granular Medium

We report on systematic measurements of the distribution of normal forces exerted by granular material under uniaxial compression onto the interior surfaces of a confining vessel. Our experiments on three-dimensional, random packings of monodisperse glass beads show that this distribution is nearly uniform for forces below the mean force and decays exponentially for forces greater than the mean. The shape of the distribution and the value of the exponential decay constant are unaffected by changes in the system preparation history or in the boundary conditions. An empirical functional form for the distribution is proposed that provides an excellent fit over the whole force range measured and is also consistent with recent computer simulation data.Comment: 6 pages. For more information, see http://mrsec.uchicago.edu/granula

Stresses in isostatic granular systems and emergence of force chains

Progress is reported on several questions that bedevil understanding of granular systems: (i) are the stress equations elliptic, parabolic or hyperbolic? (ii) how can the often-observed force chains be predicted from a first-principles continuous theory? (iii) How to relate insight from isostatic systems to general packings? Explicit equations are derived for the stress components in two dimensions including the dependence on the local structure. The equations are shown to be hyperbolic and their general solutions, as well as the Green function, are found. It is shown that the solutions give rise to force chains and the explicit dependence of the force chains trajectories and magnitudes on the local geometry is predicted. Direct experimental tests of the predictions are proposed. Finally, a framework is proposed to relate the analysis to non-isostatic and more realistic granular assemblies.Comment: 4 pages, 2 figures, Corrected typos and clkearer text, submitted to Phys. Rev. Let

PyCoM: a python library for large-scale analysis of residue-residue coevolution data

The version currently archived on this institutional repository is an accepted manuscript, the PDF version of the author’s final manuscript, as accepted for publication by the journal but prior to copyediting or typesetting. They can be cited using the author(s), article title, journal title, year of online publication, and DOI. They will be replaced by the final typeset articles, which may therefore contain changes. The DOI will remain the same throughout.Data availability The data underpinning this publication can be accessed from Brunel University London's data repository under CC BY license: Coevolution matrix database https://brunel.figshare.com/articles/dataset/PyCoM_ProCoM_Database_of_coevolu tion_matrices/23735613 and protein database https://brunel.figshare.com/articles/dataset/PyCoM_ProCoM_Curated_UniProt_pro tein_database/23733309 .Availability and implementation PyCoM code is freely available from https://github.com/scdantu/pycom and PyCoMdb and the Jupyter Notebook tutorials are freely available from https://pycom.brunel.ac.uk .Supplementary information: Supplementary data are available at Bioinformatics online at https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae166/7635577#supplementary-data .Motivation: Computational methods to detect correlated amino acid positions in proteins have become a valuable tool to predict intra and inter-residue protein contacts, protein structures, and effects of mutation on protein stability and function. While there are many tools and webservers to compute coevolution scoring matrices, there is no central repository of alignments and coevolution matrices for large-scale studies and pattern detection leveraging on structural and biological annotation already available in UniProt. Results: We present a Python library, PyCoM, which enables users to query and analyse coevolution matrices and sequence alignments of 457,622 proteins, selected from UniProtKB/Swiss-Prot database (length ≤ 500 residues), from a pre-compiled coevolution matrix database (PyCoMdb). PyCoM facilitates the development of statistical analyses of residue coevolution patterns using filters on structural and biological annotation from UniProtKB/Swiss-Prot, with simple access to PyCoMdb for both novice and advanced users, supporting Jupyter Notebooks, Python scripts, and a web API access. The resource is open source and will help in generating data-driven computational models and methods to study and understand protein structures, stability, function, and design.This project made use of time on HPC granted via the UK High-End Computing Consortium for Biomolecular Simulation, HECBioSim (http://hecbiosim.ac.uk), supported by EPSRC (grant no. EP/R029407/1). Philipp Bibik was funded by Department of Computer Science, Brunel University London, summer internship programme

Some aspects of electrical conduction in granular systems of various dimensions

We report on measurements of the electrical conductivity in both a 2D triangular lattice of metallic beads and in a chain of beads. The voltage/current characteristics are qualitatively similar in both experiments. At low applied current, the voltage is found to increase logarithmically in a good agreement with a model of widely distributed resistances in series. At high enough current, the voltage saturates due to the local welding of microcontacts between beads. The frequency dependence of the saturation voltage gives an estimate of the size of these welded microcontacts. The DC value of the saturation voltage (~ 0.4 V per contact) gives an indirect measure of the number of welded contact carrying the current within the 2D lattice. Also, a new measurement technique provides a map of the current paths within the 2D lattice of beads. For an isotropic compression of the 2D granular medium, the current paths are localized in few discrete linear paths. This quasi-onedimensional nature of the electrical conductivity thus explains the similarity between the characteristics in the 1D and 2D systems.Comment: To be published in The European Physical Journal

Force distributions in 3D granular assemblies: Effects of packing order and inter-particle friction

We present a systematic investigation of the distribution of normal forces at the boundaries of static packings of spheres. A new method for the efficient construction of large hexagonal-close-packed crystals is introduced and used to study the effect of spatial ordering on the distribution of forces. Under uniaxial compression we find that the form for the probability distribution of normal forces between particles does not depend strongly on crystallinity or inter-particle friction. In all cases the distribution decays exponentially at large forces and shows a plateau or possibly a small peak near the average force but does not tend to zero at small forces.Comment: 9 pages including 8 figure

Force correlations and arches formation in granular assemblies

In the context of a simple microscopic schematic scalar model we study the effects of spatial correlations in force transmission in granular assemblies. We show that the parameters of the normalized weights distribution function, $P(v)\sim v^{\alpha}\exp(-v/\phi)$, strongly depend on the spatial extensions, $\xi_V$, of such correlations. We show, then, the connections between measurable macroscopic quantities and microscopic mechanisms enhancing correlations. In particular we evaluate how the exponential cut-off, $\phi(\xi_V)$, and the small forces power law exponent, $\alpha(\xi_V)$, depend on the correlation length, $\xi_V$. If correlations go to infinity, weights are power law distributed.Comment: 6 page

Properties of layer-by-layer vector stochastic models of force fluctuations in granular materials

We attempt to describe the stress distributions of granular packings using lattice-based layer-by-layer stochastic models that satisfy the constraints of force and torque balance and non-tensile forces at each site. The inherent asymmetry in the layer-by-layer approach appears to lead to an asymmetric force distribution, in disagreement with both experiments and general symmetry considerations. The vertical force component probability distribution is robust and in agreement with predictions of the scalar q model while the distribution of horizontal force components is qualitatively different and depends on the details of implementation.Comment: 18 pages, 12 figures (with subfigures), 1 table. Uses revtex, epsfig,subfigure, and cite. Submitted to PRE. Plots have been bitmapped. High-resolution version is available. Email [email protected] or download from http://rainbow.uchicago.edu/~mbnguyen/research/vm.htm