The packing of granular polymer chains

Rigid particles pack into structures, such as sand dunes on the beach, whose overall stability is determined by the average number of contacts between particles. However, when packing spatially extended objects with flexible shapes, additional concepts must be invoked to understand the stability of the resulting structure. Here we study the disordered packing of chains constructed out of flexibly-connected hard spheres. Using X-ray tomography, we find long chains pack into a low-density structure whose mechanical rigidity is mainly provided by the backbone. On compaction, randomly-oriented, semi-rigid loops form along the chain, and the packing of chains can be understood as the jamming of these elements. Finally we uncover close similarities between the packing of chains and the glass transition in polymers.Comment: 11 pages, 4 figure

Exact mean field inference in asymmetric kinetic Ising systems

We develop an elementary mean field approach for fully asymmetric kinetic Ising models, which can be applied to a single instance of the problem. In the case of the asymmetric SK model this method gives the exact values of the local magnetizations and the exact relation between equal-time and time-delayed correlations. It can also be used to solve efficiently the inverse problem, i.e. determine the couplings and local fields from a set of patterns, also in cases where the fields and couplings are time-dependent. This approach generalizes some recent attempts to solve this dynamical inference problem, which were valid in the limit of weak coupling. It provides the exact solution to the problem also in strongly coupled problems. This mean field inference can also be used as an efficient approximate method to infer the couplings and fields in problems which are not infinite range, for instance in diluted asymmetric spin glasses.Comment: 10 pages, 7 figure

First-principles investigation of spin polarized conductance in atomic carbon wire

We analyze spin-dependent energetics and conductance for one dimensional (1D) atomic carbon wires consisting of terminal magnetic (Co) and interior nonmagnetic (C) atoms sandwiched between gold electrodes, obtained employing first-principles gradient corrected density functional theory and Landauer's formalism for conductance. Wires containing an even number of interior carbon atoms are found to be acetylenic with sigma-pi bonding patterns, while cumulene structures are seen in wires containing odd number of interior carbon atoms, as a result of strong pi-conjugation. Ground states of carbon wires containing up to 13 C atoms are found to have anti-parallel spin configurations of the two terminal Co atoms, while the 14 C wire has a parallel Co spin configuration in the ground state. The stability of the anti-ferromagnetic state in the wires is ascribed to a super-exchange effect. For the cumulenic wires this effect is constant for all wire lengths. For the acetylenic wires, the super-exchange effect diminishes as the wire length increases, going to zero for the atomic wire containing 14 carbon atoms. Conductance calculations at the zero bias limit show spin-valve behavior, with the parallel Co spin configuration state giving higher conductance than the corresponding anti-parallel state, and a non-monotonic variation of conductance with the length of the wires for both spin configurations.Comment: revtex, 6 pages, 5 figure

Jamming in Systems Composed of Frictionless Ellipse-Shaped Particles

We study the structural and mechanical properties of jammed ellipse packings, and find that the nature of the jamming transition in these systems is fundamentally different from that for spherical particles. Ellipse packings are generically hypostatic with more degrees of freedom than constraints. The spectra of low energy excitations possess two gaps and three distinct branches over a range of aspect ratios. In the zero compression limit, the energy of the modes in the lowest branch increases {\it quartically} with deformation amplitude, and the density of states possesses a $\delta$-function at zero frequency. We identify scaling relations that collapse the low-frequency part of the spectra for different aspect ratios. Finally, we find that the degree of hypostaticity is determined by the number of quartic modes of the packing.Comment: 4 pages, 4 figure

Origin of Corrections to Mean-field at the Onset of Unjamming

We present a detailed analysis of the unjamming transition in 2D frictionless disk packings using a static correlation function that has been widely used to study disordered systems. We show that this point-to-set (PTS) correlation function exhibits a dominant length scale that diverges as the unjamming transition is approached through decompression. In addition, we identify deviations from meanfield predictions, and present detailed analysis of the origin of non-meanfield behavior. A mean-field bulk-surface argument is reviewed. Corrections to this argument are identified, which lead to a change in the functional form of the critical PTS boundary size. An entropic description of the origin of the correlations is presented, and simple rigidity assumptions are shown to predict the functional form of the critical PTS boundary size as a function of the pressure

The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection

The 19th annual Database Issue of Nucleic Acids Research features descriptions of 92 new online databases covering various areas of molecular biology and 100 papers describing recent updates to the databases previously described in NAR and other journals. The highlights of this issue include, among others, a description of neXtProt, a knowledgebase on human proteins; a detailed explanation of the principles behind the NCBI Taxonomy Database; NCBI and EBI papers on the recently launched BioSample databases that store sample information for a variety of database resources; descriptions of the recent developments in the Gene Ontology and UniProt Gene Ontology Annotation projects; updates on Pfam, SMART and InterPro domain databases; update papers on KEGG and TAIR, two universally acclaimed databases that face an uncertain future; and a separate section with 10 wiki-based databases, introduced in an accompanying editorial. The NAR online Molecular Biology Database Collection, available at http://www.oxfordjournals.org/nar/database/a/, has been updated and now lists 1380 databases. Brief machine-readable descriptions of the databases featured in this issue, according to the BioDBcore standards, will be provided at the http://biosharing.org/biodbcore web site. The full content of the Database Issue is freely available online on the Nucleic Acids Research web site (http://nar.oxfordjournals.org/)

Serum Cholesterol and Nigrostriatal R2* Values in Parkinson's Disease

The occurrence of Parkinson's disease (PD) is known to be associated both with increased nigrostriatal iron content and with low serum cholesterol and PD, but there has been no study to determine a potential relationship between these two factors.High-resolution MRI (T1-, T2, and multiple echo T2*-weighted imaging) and fasting lipid levels were obtained from 40 patients with PD and 29 healthy controls. Iron content was estimated from mean R2* values (R2* = 1/T2*) calculated for each nigrostriatal structure including substantia nigra, caudate, putamen, and globus pallidus. This was correlated with serum cholesterol levels after controlling for age, gender, and statin use.In patients with PD, higher serum cholesterol levels were associated with lower iron content in the substantia nigra (R = -0.43, p = 0.011 for total-cholesterol, R = -0.31, p = 0.080 for low-density lipoprotein) and globus pallidus (R = -0.38, p = 0.028 for total-cholesterol, R = -0.27, p = 0.127 for low-density lipoprotein), but only a trend toward significant association of higher total-cholesterol with lower iron content in the striatum (R = -0.34, p = 0.052 for caudate; R = -0.32, p = 0.061 for putamen). After adjusting for clinical measures, the cholesterol-iron relationships held or became even stronger in the substantia nigra and globus pallidus, but weaker in the caudate and putamen. There was no significant association between serum cholesterol levels and nigrostriatal iron content for controls.The data show that higher serum total-cholesterol concentration is associated with lower iron content in substantia nigra and globus pallidus in Parkinson's disease patients. Further studies should investigate whether this is mechanistic or epiphenomenological relationship

Constraints and vibrations in static packings of ellipsoidal particles

We numerically investigate the mechanical properties of static packings of ellipsoidal particles in 2D and 3D over a range of aspect ratio and compression $\Delta \phi$. While amorphous packings of spherical particles at jamming onset ($\Delta \phi=0$) are isostatic and possess the minimum contact number $z_{\rm iso}$ required for them to be collectively jammed, amorphous packings of ellipsoidal particles generally possess fewer contacts than expected for collective jamming ($z < z_{\rm iso}$) from naive counting arguments, which assume that all contacts give rise to linearly independent constraints on interparticle separations. To understand this behavior, we decompose the dynamical matrix $M=H-S$ for static packings of ellipsoidal particles into two important components: the stiffness $H$ and stress $S$ matrices. We find that the stiffness matrix possesses $N(z_{\rm iso} - z)$ eigenmodes ${\hat e}_0$ with zero eigenvalues even at finite compression, where $N$ is the number of particles. In addition, these modes ${\hat e}_0$ are nearly eigenvectors of the dynamical matrix with eigenvalues that scale as $\Delta \phi$, and thus finite compression stabilizes packings of ellipsoidal particles. At jamming onset, the harmonic response of static packings of ellipsoidal particles vanishes, and the total potential energy scales as $\delta^4$ for perturbations by amplitude $\delta$ along these `quartic' modes, ${\hat e}_0$. These findings illustrate the significant differences between static packings of spherical and ellipsoidal particles.Comment: 18 pages, 21 figure

Onset of Irreversibility in Cyclic Shear of Granular Packings

021309Biological and Soft Matter Physic