Dense packing in the monodisperse hard-sphere system: A numerical study

We report a numerical study of the close packing of monodisperse hard spheres. The close packings of hard spheres are produced by the Lubachesky-Stillinger (LS) compression algorithm and span the range from the disordered states to the ordered states. We provide quantitative evidence for the claim that the density and structural order of the arrested close packing can be determined by the compression rate, i.e., with slower rates producing denser and more ordered structures. Through deeply analyzing the structure of the resulting arrested close packings, a transition region has been identified in the plane of density and reciprocal compression rate, in between what have been historically thought of as amorphous and crystalline packings. We also find clear system size dependences in studying the structural properties of the packings from the disordered ones to the ordered ones. These detailed investigations, on the structure of the arrested close packings, may provide a link between the glassy states and the crystalline states in the hard spheres.     

Jamming and crystallization in athermal polymer packings

Dense packings of chains of hard spheres possess characteristic features that do not have a counterpart in corresponding packings of monomeric spheres especially near the maximally random jammed (MRJ) state. From the modelling perspective the additional requirement that spheres keep their connectivity while maximizing the occupied volume fraction imposes severe constraints on generation algorithms of dense chain configurations. The extremely sluggish dynamics imposed by the uncrossability of chains precludes the use of deterministic or stochastic dynamics to generate all but dilute polymer packings. As a viable alternative, especially tailored chain-connectivity-altering Monte Carlo (MC) algorithms have been developed that bypass this kinetic hindrance and have actually been able to produce packings of hard-sphere chains in a volume fraction range spanning from infinite dilution up to the MRJ state. Such very dense athermal polymer packings share a number of structural features with packings of monomeric hard spheres, but also display unique characteristics due to the constraints imposed by connectivity. We give an overview of the most relevant results of our recent modeling work on packings of freely-jointed chains of tangent hard spheres about the MRJ state, local structure, chain dimensions and their scaling with density, topological constraints in the form of entanglements and knots, contact network at jamming, and entropically driven crystallization.     

Elegance of disordered granular packings: a validation of Edward's hypothesis

We have found a way to analyze Edwards' density of states for static granular packings in the special case of round, rigid, frictionless grains assuming a constant coordination number. It obtains the most entropic density of single grain states, which predicts several observables including the distribution of contact forces. We compare these results against empirical data obtained in dynamic simulations of granular packings. The agreement is quite good, helping validate the use of statistical mechanics methods in granular physics. The differences between theory and empirics are mainly related to the coordination number, and when the empirical data are sorted by that number we obtain several insights that suggest an underlying elegance in the density of states.     

Dense Packing on Uniform Lattices

We study the Hard Core Model on the graphs G obtained from Archimedean tilings i.e. configurations in {0,1} ^G with the nearest neighbor 1’s forbidden. Our particular aim in choosing these graphs is to obtain insight to the geometry of the densest packings in a uniform discrete set-up. We establish density bounds, optimal configurations reaching them in all cases, and introduce a probabilistic cellular automaton that generates the legal configurations. Its rule involves a parameter which can be naturally characterized as packing pressure. It can have a critical value but from packing point of view just as interesting are the noncritical cases. These phenomena are related to the exponential size of the set of densest packings and more specifically whether these packings are maximally symmetric, simple laminated or essentially random packings. Research partially supported by The Finnish Academy of Science and Letters.     

Structural transitions in granular packs: statistical mechanics and statistical geometry investigations

We investigate equal spheres packings generated from several experiments and from a large number of different numerical simulations. The structural organization of these disordered packings is studied in terms of the network of common neighbours. This geometrical analysis reveals sharp changes in the network’s clustering occurring at the packing fractions (fraction of volume occupied by the spheres respect to the total volume, ρ) corresponding to the so called Random Loose Packing limit (RLP, ρ ～ 0.555) and Random Close Packing limit (RCP, ρ ～ 0.645). At these packing fractions we also observe abrupt changes in the fluctuations of the portion of free volume around each sphere. We analyze such fluctuations by means of a statistical mechanics approach and we show that these anomalies are associated to sharp variations in a generalized thermodynamical variable which is the analogous for these a-thermal systems to the specific heat in thermal systems.     

Effects of atomic-scale contacts on transport properties through single molecules - ab initio study

Using the RTM/NEGF method, which is a first-principles calculation tool for the quantum transport through nanostructures between electrodes, we study the effects of atomic-scale contacts on the transport properties through single molecules. Electronic states and current-voltage (I-V) characteristics are investigated in various contact conditions with and without single molecules between electrodes. We find that similar nonlinear behaviors appear in the I-V characteristics. Such nonlinear behaviors are determined not only by the HOMO-LUMO electronic states of single molecules between electrodes, but also by the atomic-scale contact conditions. We show that the transitions from tunneling to ballistic regimes affect the I-V characteristics significantly.     

Modular and hierarchical structure of social contact networks

Social contact networks exhibit overlapping qualities of communities, hierarchical structure and spatial-correlated nature. We propose a mixing pattern of modular and growing hierarchical structures to reconstruct social contact networks by using an individual’s geospatial distribution information in the real world. The hierarchical structure of social contact networks is defined based on the spatial distance between individuals, and edges among individuals are added in turn from the modular layer to the highest layer. It is a gradual process to construct the hierarchical structure: from the basic modular model up to the global network. The proposed model not only shows hierarchically increasing degree distribution and large clustering coefficients in communities, but also exhibits spatial clustering features of individual distributions. As an evaluation of the method, we reconstruct a hierarchical contact network based on the investigation data of a university. Transmission experiments of influenza H1N1 are carried out on the generated social contact networks, and results show that the constructed network is efficient to reproduce the dynamic process of an outbreak and evaluate interventions. The reproduced spread process exhibits that the spatial clustering of infection is accordant with the clustering of network topology. Moreover, the effect of individual topological character on the spread of influenza is analyzed, and the experiment results indicate that the spread is limited by individual daily contact patterns and local clustering topology rather than individual degree.     

Force chain splitting in granular materials: A mechanism for large-scale pseudo-elastic behaviour

We investigate both numerically and analytically the effect of strong disorder on the large-scale properties of the hyperbolic equations for stresses proposed in J.-P. Bouchaud, M.E. Cates, P. Claudin, J. Phys. I 5, 639 (1995), and J.P. Wittmer, P. Claudin, M.E. Cates, J.-P. Bouchaud, Nature 382, 336 (1996); J.P. Wittmer, P. Claudin, M.E. Cates, J. Phys. I 7, 39 (1997). The physical mechanism that we model is the local splitting of the force chains (the characteristics of the hyperbolic equation) by packing defects. In analogy with the theory of light diffusion in a turbid medium, we propose a Boltzmann-like equation to describe these processes. We show that, for isotropic packings, the resulting large-scale effective equations for the stresses have exactly the same structure as those of an elastic body, despite the fact that no displacement field needs to be introduced at all. Correspondingly, the response function evolves from a two-peak structure at short scales to a broad hump at large scales. We find, however, that the Poisson ratio is anomalously large and incompatible with classical elasticity theory that requires the reference state to be thermodynamically stable. Received 13 November 2000 and Received in final form 3 January 2001     

Decomposition of symmetric tensor fields in the presence of a flat contact projective structure

Abstract

Let M be an odd-dimensional Euclidean space endowed with a contact 1-form α. We investigate the space of symmetric contravariant tensor fields over M as a module over the Lie algebra of contact vector fields, i.e. over the Lie subalgebra made up of those vector fields that preserve the contact structure defined by a. If we consider symmetric tensor fields with coefficients in tensor densities (also called symbols), the vertical cotangent lift of the contact form a defines a contact invariant operator. We also extend the classical contact Hamiltonian to the space of symbols. This generalized Hamiltonian operator on the space of symbols is invariant with respect to the action of the projective contact algebra sp(2n+2) the algebra of vector fields which preserve both the contact structure and the projective structure of the Euclidean space. These two operators lead to a decomposition of the space of symbols, except for some critical density weights, which generalizes a splitting proposed by V. Ovsienko in [18].     

The vicinity of an equilibrium three-phase contact line using density-functional theory: density profiles normal to the fluid interface

The paper by Nold et al. [Phys. Fluids 26 (7), 072001 (2014)] examined density profiles and the micro-scale structure of an equilibrium three-phase (liquid–vapour–solid) contact line in the immediate vicinity of the wall using elements from the statistical mechanics of classical fluids, namely density-functional theory. The present research note, building on the above work, further contributes to our understanding of the nanoscale structure of a contact line by quantifying the strong dependence of the liquid–vapour density profile on the normal distance to the interface, when compared to the dependence on the vertical distance to the substrate. A recent study by Benet et al. [J. Phys. Chem. C 118 (38), 22079 (2014)] has shown that this could explain the emergence of a film-height-dependent surface tension close to the wall, with implications for the Frumkin–Derjaguin theory.     

Force networks and elasticity in granular silos

We have made experimental observations of the force networks within a two-dimensional granular silo similar to the classical system of Janssen. Models like that of Janssen predict that pressure within a silo saturates with depth as the result of vertical forces being redirected to the walls of the silo where they can then be carried by friction. We use photoelastic particles to obtain information not available in previous silo experiments --the internal force structure. We directly compare various predictions with the results obtained by averaging ensembles of experimentally obtained force networks. We identify several differences between the mean behavior in our system and that predicted by Janssen-like models: We find that the redirection parameter describing how the force network transfers vertical forces to the walls varies with depth. We find that changes in the preparation of the material can cause the pressure within the silo to either saturate or to continue building with depth. Most strikingly, we observe a nonlinear response to overloads applied to the top of the material in the silo. For larger overloads we observe the previously reported “giant overshoot” effect where overload pressure decays only after an initial increase (G. Ovarlez et al., Phys. Rev. E 67, 060302(R) (2003)). For smaller overloads we find that additional pressure propagates to great depth. Analysis of the differences between the inter-grain contact and force networks suggests that, for our system, when the load and the particle weight are comparable, particle elasticity acts to stabilize the force network, allowing deep propagation. For larger loads, the force network rearranges, resulting in the expected, Janssen-like behavior. Thus, a meso-scale network phenomenon results in an observable nonlinearity in the mean pressure profile.     

Phase transitions in granular packings

We describe the contact network of granular packings by a frustrated lattice gas that contains steric frustration as esential ingredient. Two transitions are identified, a spin glass transition at the onset of Reynolds dilatancy and at lower densities a percolation transition. We describe the correlation functions that give rise to the singularities and propose some dynamical experiments.     

Spectral Analysis for Systems of Atoms and Molecules Coupled to the Quantized Radiation Field

We consider systems of static nuclei and electrons – atoms and molecules – coupled to the quantized radiation field. The interactions between electrons and the soft modes of the quantized electromagnetic field are described by minimal coupling, p→p−e A (x), where A(x) is the electromagnetic vector potential with an ultraviolet cutoff. If the interactions between the electrons and the quantized radiation field are turned off, the atom or molecule is assumed to have at least one bound state. We prove that, for sufficiently small values of the fine structure constant α, the interacting system has a ground state corresponding to the bottom of its energy spectrum. For an atom, we prove that its excited states above the ground state turn into metastable states whose life-times we estimate. Furthermore the energy spectrum is absolutely continuous, except, perhaps, in a small interval above the ground state energy and around the threshold energies of the atom or molecule. Received: 3 September 1998 / Accepted: 17 March 1999     

Electron-energy-loss spectroscopy and X-ray absorption spectroscopy as complementary probes for complex f-electron metals: cerium and plutonium

In this paper, we demonstrate the power of electron-energy-loss spectroscopy (EELS) in a transmission electron microscope by investigating the electron structure of two f-electron metals: Ce and Pu. It is shown that EELS in a transmission electron microscope may be used to circumvent the difficulty of producing single-phase or single-crystal samples owing to its high spatial resolution, and that diffraction patterns and images can be acquired, providing unambiguous phase determination when acquiring spectra. EELS results are supported by synchrotron-radiation-based X-ray absorption, multielectron atomic spectral simulations, and local density approximation calculations based on density-functional theory with the generalized gradient approximation. For Ce, it is shown that changes in {111} stacking sequences can drive substantial modifications in the electronic structure of close-packed phases of Ce that have similar atomic volumes, contrary to previous assumptions in literature. For Pu, it is shown that Russell–Saunders (L–S) coupling fails for the 5f states and that either a j–j or an intermediate scheme must be used for the actinides because of the considerable spin–orbit interaction in the 5f states. We present a model showing how the 5f states behave along the light actinide series.     

Analysis of protein folds using protein contact networks

Proteins are important biomolecules, which perform diverse structural and functional roles in living systems. Starting from a linear chain of amino acids, proteins fold to different secondary structures, which then fold through short- and long-range interactions to give rise to the final three-dimensional shapes useful to carry out the biophysical and biochemical functions. Proteins are defined as having a common ‘fold’ if they have major secondary structural elements with same topological connections. It is known that folding mechanisms are largely determined by a protein’s topology rather than its interatomic interactions. The native state protein structures can, thus, be modelled, using a graph-theoretical approach, as coarse-grained networks of amino acid residues as ‘nodes’ and the inter-residue interactions/contacts as ‘links’. Using the network representation of protein structures and their 2D contact maps, we have identified the conserved contact patterns (groups of contacts) representing two typical folds — the EF-hand and the ubiquitin-like folds. Our results suggest that this direct and computationally simple methodology can be used to infer about the presence of specific folds from the protein’s contact map alone.      

Force indeterminacy in the jammed state of hard disks

Granular packings of hard disks are investigated by means of contact dynamics which is an appropriate technique to explore the allowed force realizations in the space of contact forces. Configurations are generated for given friction coefficients, and then an ensemble of equilibrium forces is found for fixed contacts. We study the force fluctuations within this ensemble. In the limit of zero friction, the fluctuations vanish in accordance with the isostaticity of the packing. The magnitude of the fluctuations has a nonmonotonous friction dependence. The increase for small friction can be attributed to the opening of the angle of the Coulomb cone, while the decrease as friction increases is due to the reduction of connectivity of the contact network, leading to local, independent clusters of indeterminacy. We discuss the relevance of indeterminacy to packings of deformable particles and to the mechanical response properties.     

Social dynamics with peer support on heterogeneous networks

Human behavior often exhibits a scheme in which individuals adopt indifferent, neutral, or radical positions on a given topic. The mechanisms leading to community formation are strongly related with social pressure and the topology of the contact network. Here, we discuss an approach to model social behavior which accounts for the protection by alike peers proportional to their relative abundance in the closest neighborhood. We explore the ensuing non-linear dynamics emphasizing the role of the specific structure of the social network, modeled by scale-free graphs. We find that both coexistence of opinions and consensus on the default position are possible stationary states of the model. In particular, we show how these states critically depend on the heterogeneity of the social network and the specific distribution of external control elements.     

Set Voronoi diagrams of 3D assemblies of aspherical particles

Abstract

Several approaches to quantitative local structure characterization for particulate assemblies, such as structural glasses or jammed packings, use the partition of space provided by the Voronoi diagram. The conventional construction for spherical mono-disperse particles, by which the Voronoi cell of a particle is that of its centre point, cannot be applied to configurations of aspherical or polydisperse particles. Here, we discuss the construction of a Set Voronoi diagram for configurations of aspherical particles in three-dimensional space. The Set Voronoi cell of a given particle is composed of all points in space that are closer to the surface (as opposed to the centre) of the given particle than to the surface of any other; this definition reduces to the conventional Voronoi diagram for the case of mono-disperse spheres. An algorithm for the computation of the Set Voronoi diagram for convex particles is described, as a special case of a Voronoi-based medial axis algorithm, based on a triangulation of the particles’ bounding surfaces. This algorithm is further improved by a pre-processing step based on morphological erosion, which improves the quality of the approximation and circumvents the problems associated with small degrees of particle–particle overlap that may be caused by experimental noise or soft potentials. As an application, preliminary data for the volume distribution of disordered packings of mono-disperse oblate ellipsoids, obtained from tomographic imaging, is computed.