arXiv subjects

Yuliang Jin

Publications and source records attributed to Yuliang Jin.

51 records · Page 3Linked to original sources

arXiv2016

Growing timescales and lengthscales characterizing vibrations of amorphous solids

Low-temperature properties of crystalline solids can be understood using harmonic perturbations around a perfect lattice, as in Debye's theory. Low-temperature properties of amorphous solids, however, strongly depart from such descriptions, displaying enhanced transport, activated slow dynamics across energy barriers, excess vibrational modes with respect to Debye's theory (i.e., a Boson Peak), and complex irreversible responses to small mechanical deformations. These experimental observations indirectly suggest that the dynamics of amorphous solids becomes anomalous at low temperatures. Here, we present direct numerical evidence that vibrations change nature at a well-defined location deep inside the glass phase of a simple glass former. We provide a real-space description of this transition and of the rapidly growing time and length scales that accompany it. Our results provide the seed for a universal understanding of low-temperature glass anomalies within the theoretical framework of the recently discovered Gardner phase transition.

cond-mat.soft↗

arXiv2016

A first-order phase transition at the random close packing of hard spheres

Randomly packing spheres of equal size into a container consistently results in a static configuration with a density of ~64%. The ubiquity of random close packing (RCP) rather than the optimal crystalline array at 74% begs the question of the physical law behind this empirically deduced state. Indeed, there is no signature of any macroscopic quantity with a discontinuity associated with the observed packing limit. Here we show that RCP can be interpreted as a manifestation of a thermodynamic singularity, which defines it as the "freezing point" in a first-order phase transition between ordered and disordered packing phases. Despite the athermal nature of granular matter, we show the thermodynamic character of the transition in that it is accompanied by sharp discontinuities in volume and entropy. This occurs at a critical compactivity, which is the intensive variable that plays the role of temperature in granular matter. Our results predict the experimental conditions necessary for the formation of a jammed crystal by calculating an analogue of the "entropy of fusion". This approach is useful since it maps out-of-equilibrium problems in complex systems onto simpler established frameworks in statistical mechanics.

cond-mat.soft↗

arXiv2015

Numerical detection of the Gardner transition in a mean-field glass former

Recent theoretical advances predict the existence, deep into the glass phase, of a novel phase transition, the so-called Gardner transition. This transition is associated with the emergence of a complex free energy landscape composed of many marginally stable sub-basins within a glass metabasin. In this study, we explore several methods to detect numerically the Gardner transition in a simple structural glass former, the infinite-range Mari-Kurchan model. The transition point is robustly located from three independent approaches: (i) the divergence of the characteristic relaxation time, (ii) the divergence of the caging susceptibility, and (iii) the abnormal tail in the probability distribution function of cage order parameters. We show that the numerical results are fully consistent with the theoretical expectation. The methods we propose may also be generalized to more realistic numerical models as well as to experimental systems.

cond-mat.dis-nn↗

arXiv2015

Dimensional study of the dynamical arrest in a random Lorentz gas

The random Lorentz gas is a minimal model for transport in heterogeneous media. Upon increasing the obstacle density, it exhibits a growing subdiffusive transport regime and then a dynamical arrest. Here, we study the dimensional dependence of the dynamical arrest, which can be mapped onto the void percolation transition for Poisson-distributed point obstacles. We numerically determine the arrest in dimensions d=2-6. Comparing the results with standard mode-coupling theory reveals that the dynamical theory prediction grows increasingly worse with $d$. In an effort to clarify the origin of this discrepancy, we relate the dynamical arrest in the RLG to the dynamic glass transition of the infinite-range Mari-Kurchan model glass former. Through a mixed static and dynamical analysis, we then extract an improved dimensional scaling form as well as a geometrical upper bound for the arrest. The results suggest that understanding the asymptotic behavior of the random Lorentz gas may be key to surmounting fundamental difficulties with the mode-coupling theory of glasses.

cond-mat.dis-nn↗

arXiv2014

Hopping and the Stokes-Einstein relation breakdown in simple glass formers

One of the most actively debated issues in the study of the glass transition is whether a mean-field description is a reasonable starting point for understanding experimental glass formers. Although the mean-field theory of the glass transition -- like that of other statistical systems -- is exact when the spatial dimension $d\rightarrow\infty$, the evolution of systems properties with $d$ may not be smooth. Finite-dimensional effects could dramatically change what happens in physical dimensions, $d=2,3$. For standard phase transitions finite-dimensional effects are typically captured by renormalization group methods, but for glasses the corrections are much more subtle and only partially understood. Here, we investigate hopping between localized cages formed by neighboring particles in a model that allows to cleanly isolate that effect. By bringing together results from replica theory, cavity reconstruction, void percolation, and molecular dynamics, we obtain insights into how hopping induces a breakdown of the Stokes--Einstein relation and modifies the mean-field scenario in experimental systems. Although hopping is found to supersede the dynamical glass transition, it nonetheless leaves a sizable part of the critical regime untouched. By providing a constructive framework for identifying and quantifying the role of hopping, we thus take an important step towards describing dynamic facilitation in the framework of the mean-field theory of glasses.

cond-mat.dis-nn↗

arXiv2014

Structural properties of dense hard spheres near random close packing

We numerically study structural properties of mechanically stable packings of hard spheres (HS), in a wide range of packing fractions $0.53 \le ϕ\le 0.72$. Detailed structural information is obtained from the analysis of orientational order parameters, which clearly reveals a disorder-order phase transition at the random close packing (RCP) density, $ϕ_{\rm c} \simeq 0.64$. Above $ϕ_{\rm c}$ the crystalline nuclei form 3D-like clusters, which upon further desification, transform into alternating planar-like layers. We also find that particles with icosahedral symmetry survive only in a narrow density range in the vicinity of the RCP transition.

cond-mat.soft↗

arXiv2014

Statistical theory of correlations in random packings of hard particles

A random packing of hard particles represents a fundamental model for granular matter. Despite its importance, analytical modeling of random packings remains difficult due to the existence of strong correlations which preclude the development of a simple theory. Here, we take inspiration from liquid theories for the $n$-particle angular correlation function to develop a formalism of random packings of hard particles from the bottom-up. A progressive expansion into a shell of particles converges in the large layer limit under a Kirkwood-like approximation of higher-order correlations. We apply the formalism to hard disks and predict the density of two-dimensional random close packing (RCP), $ϕ_{\rm rcp} = 0.85\pm0.01$, and random loose packing (RLP), $ϕ_{\rm rlp} = 0.67\pm0.01$. Our theory also predicts a phase diagram and angular correlation functions that are in good agreement with experimental and numerical data.

cond-mat.soft↗

arXiv2013

Dimensional dependence of the Stokes--Einstein relation and its violation

We generalize to higher spatial dimensions the Stokes--Einstein relation (SER) and the leading correction to diffusivity in periodic systems, and validate them using numerical simulations. Using these results, we investigate the evolution of the SER violation with dimension in simple hard sphere glass formers. The analysis suggests that the SER violation disappears around dimension d=8, above which SER is not violated. The critical exponent associated to the violation appears to evolve linearly in 8-d below d=8, as predicted by Biroli and Bouchaud [J. Phys.: Cond. Mat. 19, 205101 (2007)], but the linear coefficient is not consistent with their prediction. The SER violation evolution with d establishes a new benchmark for theory, and a complete description remains an open problem.

cond-mat.stat-mech↗

arXiv2013

The evolutionary dynamics of protein-protein interaction networks inferred from the reconstruction of ancient networks

Cellular functions are based on the complex interplay of proteins, therefore the structure and dynamics of these protein-protein interaction (PPI) networks are the key to the functional understanding of cells. In the last years, large-scale PPI networks of several model organisms were investigated. Methodological improvements now allow the analysis of PPI networks of multiple organisms simultaneously as well as the direct modeling of ancestral networks. This provides the opportunity to challenge existing assumptions on network evolution. We utilized present-day PPI networks from integrated datasets of seven model organisms and developed a theoretical and bioinformatic framework for studying the evolutionary dynamics of PPI networks. A novel filtering approach using percolation analysis was developed to remove low confidence interactions based on topological constraints. We then reconstructed the ancient PPI networks of different ancestors, for which the ancestral proteomes, as well as the ancestral interactions, were inferred. Ancestral proteins were reconstructed using orthologous groups on different evolutionary levels. A stochastic approach, using the duplication-divergence model, was developed for estimating the probabilities of ancient interactions from today's PPI networks. The growth rates for nodes, edges, sizes and modularities of the networks indicate multiplicative growth and are consistent with the results from independent static analysis. Our results support the duplication-divergence model of evolution and indicate fractality and multiplicative growth as general properties of the PPI network structure and dynamics.

q-bio.MN↗

arXiv2010

Application of Edwards' statistical mechanics to high dimensional jammed sphere packings

The isostatic jamming limit of frictionless spherical particles from Edwards' statistical mechanics [Song \emph{et al.}, Nature (London) {\bf 453}, 629 (2008)] is generalized to arbitrary dimension $d$ using a liquid-state description. The asymptotic high-dimensional behavior of the self-consistent relation is obtained by saddle-point evaluation and checked numerically. The resulting random close packing density scaling $ϕ\sim d\,2^{-d}$ is consistent with that of other approaches, such as replica theory and density functional theory. The validity of various structural approximations is assessed by comparing with three- to six-dimensional isostatic packings obtained from simulations. These numerical results support a growing accuracy of the theoretical approach with dimension. The approach could thus serve as a starting point to obtain a geometrical understanding of the higher-order correlations present in jammed packings.

cond-mat.stat-mech↗

arXiv2010

Jamming I: A volume function for jammed matter

We introduce a "Hamiltonian"-like function, called the volume function, indispensable to describe the ensemble of jammed matter such as granular materials and emulsions from a geometrical point of view. The volume function represents the available volume of each particle in the jammed systems. At the microscopic level, we show that the volume function is the Voronoi volume associated to each particle and in turn we provide an analytical formula for the Voronoi volume in terms of the contact network, valid for any dimension. We then develop a statistical theory for the probability distribution of the volumes in 3d to calculate an average volume function coarse-grained at a mesoscopic level. The salient result is the discovery of a mesoscopic volume function inversely proportional to the coordination number. Our analysis is the first step toward the calculation of macroscopic observables and equations of state using the statistical mechanics of jammed matter, when supplemented by the condition of mechanical equilibrium of jamming that properly defines jammed matter at the ensemble level.

cond-mat.soft↗

arXiv2010

Jamming in two-dimensional packings

We investigate the existence of random close and random loose packing limits in two-dimensional packings of monodisperse hard disks. A statistical mechanics approach-- based on several approximations to predict the probability distribution of volumes-- suggests the existence of the limiting densities of the jammed packings according to their coordination number and compactivity. This result has implications for the understanding of disordered states in the disk packing problem as well as the existence of a putative glass transition in two dimensional systems.

cond-mat.soft↗

arXiv2010

Jamming II: Edwards' statistical mechanics of random packings of hard spheres

The problem of finding the most efficient way to pack spheres has an illustrious history, dating back to the crystalline arrays conjectured by Kepler and the random geometries explored by Bernal in the 60's. This problem finds applications spanning from the mathematician's pencil, the processing of granular materials, the jamming and glass transitions, all the way to fruit packing in every grocery. There are presently numerous experiments showing that the loosest way to pack spheres gives a density of ~55% (RLP) while filling all the loose voids results in a maximum density of ~63-64% (RCP). While those values seem robustly true, to this date there is no physical explanation or theoretical prediction for them. Here we show that random packings of monodisperse hard spheres in 3d can pack between the densities 4/(4 + 2 \sqrt 3) or 53.6% and 6/(6 + 2 \sqrt 3) or 63.4%, defining RLP and RCP, respectively. The reason for these limits arises from a statistical picture of jammed states in which the RCP can be interpreted as the ground state of the ensemble of jammed matter with zero compactivity, while the RLP arises in the infinite compactivity limit. We combine an extended statistical mechanics approach 'a la Edwards' (where the role traditionally played by the energy and temperature in thermal systems is substituted by the volume and compactivity) with a constraint on mechanical stability imposed by the isostatic condition. Ultimately, our results lead to a phase diagram that provides a unifying view of the disordered hard sphere packing problem.

cond-mat.soft↗

arXiv2010

Distribution of volumes and coordination number in jammed matter: mesoscopic ensemble

We investigate the distribution of the volume and coordination number associated to each particle in a jammed packing of monodisperse hard sphere using the mesoscopic ensemble developed in Nature 453, 606 (2008). Theory predicts an exponential distribution of the orientational volumes for random close packings and random loose packings. A comparison with computer generated packings reveals deviations from the theoretical prediction in the volume distribution, which can be better modeled by a compressed exponential function. On the other hand, the average of the volumes is well reproduced by the theory leading to good predictions of the limiting densities of RCP and RLP. We discuss a more exact theory to capture the volume distribution in its entire range. The available data suggests a plausible order/disorder transition defining random close packings. Finally, we consider an extended ensemble to calculate the coordination number distribution which is shown to be of an exponential and inverse exponential form for coordinations larger and smaller than the average, respectively, in reasonable agreement with the simulated data.

cond-mat.soft↗

arXiv2010

Model of random packings of different size balls

We develop a model to describe the properties of random assemblies of polydisperse hard spheres. We show that the key features to describe the system are (i) the dependence between the free volume of a sphere and the various coordination numbers between the species, and (ii) the dependence of the coordination numbers with the concentration of species; quantities that are calculated analytically. The model predicts the density of random close packing and random loose packing of polydisperse systems for a given distribution of ball size and describes packings for any interparticle friction coefficient. The formalism allows to determine the optimal packing over different distributions and may help to treat packing problems of non-spherical particles which are notoriously difficult to solve.

cond-mat.dis-nn↗