101 research outputs found
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
Growing length scale in gravity-driven dense granular flow
We report simulations of a two-dimensional, dense, bidisperse system of
inelastic hard disks falling down a vertical tube under the influence of
gravity. We examine the approach to jamming as the average flow of particles
down the tube is slowed by making the outlet narrower. Defining coarse-grained
velocity and stress fields, we study two-point temporal and spatial correlation
functions of these fields in a region of the tube where the time-averaged
velocity is spatially uniform. We find that fluctuations in both velocity and
stress become increasingly correlated as the system approaches jamming. We
extract a growing length scale and time scale from these correlations.Comment: 21 pages, 13 figure
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
QUALITATIVE ANALYSIS AND ANTHELMINTIC ACTIVITY OF HYDRO-ALCOHOLIC EXTRACT OF TABERNAEMONTANA DIVARICATA
Tabernaemontana divaricata is a common shrub found in the tropical regions and is often used for medicinal purposes, particularly the flowers of the plant. The present study is conducted to compare and identify the phytochemical constituents by Thin Layer Chromatography (TLC) and Qualitative Phytochemical analysis and to determine the anthelmentic activity of fresh and dried flower extract of Tabernaemontana divaricata. The extract is obtained using two different methods like cold maceration and hot solvent extraction by using soxhlet apparatus, first with petroleum ether followed by hydroalcohol as solvents. The preliminary phytochemical analysis of the extract indicated the presence of Alkaloids, Flavanoids, Steroids, Proteins, Carbohydrates and Tannins. The Rf value of TLC is calculated and compared with standard values and analysis proved the presence of the phytochemical constituents. The anthelmentic activity studies are performed using Indian earth worms. For this, the concentrated extract is diluted to various concentrations, and the effect of each solution is studied by measuring the time taken for paralysis and death of the earth worms. It is found to show significant anthelmentic activity at various concentrations compared with that of the standard drug Metronidazole
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
Development of Stresses in Cohesionless Poured Sand
The pressure distribution beneath a conical sandpile, created by pouring sand
from a point source onto a rough rigid support, shows a pronounced minimum
below the apex (`the dip'). Recent work of the authors has attempted to explain
this phenomenon by invoking local rules for stress propagation that depend on
the local geometry, and hence on the construction history, of the medium. We
discuss the fundamental difference between such approaches, which lead to
hyperbolic differential equations, and elastoplastic models, for which the
equations are elliptic within any elastic zones present .... This displacement
field appears to be either ill-defined, or defined relative to a reference
state whose physical existence is in doubt. Insofar as their predictions depend
on physical factors unknown and outside experimental control, such
elastoplastic models predict that the observations should be intrinsically
irreproducible .... Our hyperbolic models are based instead on a physical
picture of the material, in which (a) the load is supported by a skeletal
network of force chains ("stress paths") whose geometry depends on construction
history; (b) this network is `fragile' or marginally stable, in a sense that we
define. .... We point out that our hyperbolic models can nonetheless be
reconciled with elastoplastic ideas by taking the limit of an extremely
anisotropic yield condition.Comment: 25 pages, latex RS.tex with rspublic.sty, 7 figures in Rsfig.ps.
Philosophical Transactions A, Royal Society, submitted 02/9
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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
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
Vector lattice model for stresses in granular materials
A vector lattice model for stresses in granular materials is proposed. A two
dimensional pile built by pouring from a point is constructed numerically
according to this model. Remarkably, the pile violates the Mohr Coulomb
stability criterion for granular matter, probably because of the inherent
anisotropy of such poured piles. The numerical results are also compared to the
earlier continuum FPA model and the (scalar) lattice -model
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