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Yang Jiao

Publications and source records attributed to Yang Jiao.

At least 145 records · Page 8Linked to original sources

Improving Direct Physical Properties Prediction of Heterogeneous Materials from Imaging Data via Convolutional Neural Network and a Morphology-Aware Generative Model

Direct prediction of material properties from microstructures through statistical models has shown to be a potential approach to accelerating computational material design with large design spaces. However, statistical modeling of highly nonlinear mappings defined on high-dimensional microstructure spaces is known to be data-demanding. Thus, the added value of such predictive models diminishes in common cases where material samples (in forms of 2D or 3D microstructures) become costly to acquire either experimentally or computationally. To this end, we propose a generative machine learning model that creates an arbitrary amount of artificial material samples with negligible computation cost, when trained on only a limited amount of authentic samples. The key contribution of this work is the introduction of a morphology constraint to the training of the generative model, that enforces the resultant artificial material samples to have the same morphology distribution as the authentic ones. We show empirically that the proposed model creates artificial samples that better match with the authentic ones in material property distributions than those generated from a state-of-the-art Markov Random Field model, and thus is more effective at improving the prediction performance of a predictive structure-property model.

physics.comp-ph↗

Energy scaling law for nanostructured materials

The equilibrium binding energy is an important factor in the design of materials and devices. However, it presents great computational challenges for materials built up from nanostructures. Here we investigate the binding-energy scaling law from first-principles calculations. We show that the equilibrium binding energy per atom between identical nanostructures can scale up or down with nanostructure size. From the energy scaling law, we predict finite large-size limits of binding energy per atom. We find that there are two competing factors in the determination of the binding energy: Nonadditivities of van der Waals coefficients and center-to-center distance between nanostructures. To uncode the detail, the nonadditivity of the static multipole polarizability is investigated. We find that the higher-order multipole polarizability displays ultra-strong intrinsic nonadditivity, no matter if the dipole polarizability is additive or not.

cond-mat.mes-hall↗

Microstructure Representation and Reconstruction of Heterogeneous Materials via Deep Belief Network for Computational Material Design

Integrated Computational Materials Engineering (ICME) aims to accelerate optimal design of complex material systems by integrating material science and design automation. For tractable ICME, it is required that (1) a structural feature space be identified to allow reconstruction of new designs, and (2) the reconstruction process be property-preserving. The majority of existing structural presentation schemes rely on the designer's understanding of specific material systems to identify geometric and statistical features, which could be biased and insufficient for reconstructing physically meaningful microstructures of complex material systems. In this paper, we develop a feature learning mechanism based on convolutional deep belief network to automate a two-way conversion between microstructures and their lower-dimensional feature representations, and to achieves a 1000-fold dimension reduction from the microstructure space. The proposed model is applied to a wide spectrum of heterogeneous material systems with distinct microstructural features including Ti-6Al-4V alloy, Pb63-Sn37 alloy, Fontainebleau sandstone, and Spherical colloids, to produce material reconstructions that are close to the original samples with respect to 2-point correlation functions and mean critical fracture strength. This capability is not achieved by existing synthesis methods that rely on the Markovian assumption of material microstructures.

cond-mat.mtrl-sci↗

Assessment of two hybrid van der Waals density functionals for covalent and non-covalent binding of molecules

Two hybrid van der Waals density functionals (vdW-DFs) are constructed using 25%, Fock exchange with i) the consistent-exchange vdW-DF-cx functional and ii) with the vdW-DF2 functional. The ability to describe covalent and non-covalent binding properties of molecules are assessed. For properties related to covalent binding, atomization energies (G2-1 set), molecular reaction energies (G2RC set), as well as ionization energies (G21IP set) are benchmarked against experimental reference values. We find that hybrid-vdW-DF-cx yields results that are rather similar to those of the standard non-empirical hybrid PBE0 [JCP 110, 6158 (1996)]. Hybrid vdW-DF2 follows somewhat different trends, showing on average significantly larger deviations from the reference energies, with a MAD of 14.5 kcal/mol for the G2-1 set. Non-covalent binding properties of molecules are assessed using the S22 benchmark set of non-covalently bonded dimers and the X40 set of dimers of small halogenated molecules, using wavefunction-based quantum chemistry results for references. For the S22 set, hybrid-vdW-DF-cx performs better than standard vdW-DF-cx for the mostly hydrogen-bonded systems. Hybrid-vdW-DF2 offers a slight improvement over standard vdW-DF2. Similar trends are found for the X40 set, with hybrid-vdW-DF-cx performing particularly well for binding involving the strongly polar hydrogen halides, but poorly for systems with tiny binding energies. Our study of the X40 set reveals both the potential of mixing Fock exchange with vdW-DF, but also highlights shortcomings of the hybrids constructed here. The solid performance of hybrid-vdW-DF-cx for covalent-bonded systems, as well as the strengths and issues uncovered for non-covalently bonded systems, makes this study a good starting point for developing even more precise hybrid vdW-DFs.

physics.chem-ph↗

Algorithms for Automatic Ranking of Participants and Tasks in an Anonymized Contest

We introduce a new set of problems based on the Chain Editing problem. In our version of Chain Editing, we are given a set of anonymous participants and a set of undisclosed tasks that every participant attempts. For each participant-task pair, we know whether the participant has succeeded at the task or not. We assume that participants vary in their ability to solve tasks, and that tasks vary in their difficulty to be solved. In an ideal world, stronger participants should succeed at a superset of tasks that weaker participants succeed at. Similarly, easier tasks should be completed successfully by a superset of participants who succeed at harder tasks. In reality, it can happen that a stronger participant fails at a task that a weaker participants succeeds at. Our goal is to find a perfect nesting of the participant-task relations by flipping a minimum number of participant-task relations, implying such a "nearest perfect ordering" to be the one that is closest to the truth of participant strengths and task difficulties. Many variants of the problem are known to be NP-hard. We propose six natural $k$-near versions of the Chain Editing problem and classify their complexity. The input to a $k$-near Chain Editing problem includes an initial ordering of the participants (or tasks) that we are required to respect by moving each participant (or task) at most $k$ positions from the initial ordering. We obtain surprising results on the complexity of the six $k$-near problems: Five of the problems are polynomial-time solvable using dynamic programming, but one of them is NP-hard.

cs.DS↗

Novel dense crystalline packings of ellipsoids

An ellipsoid, the simplest non-spherical shape, has been extensively used as models for elongated building blocks for a wide spectrum of molecular, colloidal and granular systems. Yet the densest packing of congruent hard ellipsoids, which is intimately related to the high-density phase of many condensed matter systems, is still an open problem. We discover a novel dense crystalline packing of ellipsoids containing 24 particles with a quasi-square-triangular (SQ-TR) tiling arrangement, whose packing density ϕ exceeds that of the SM2 crystal for aspect ratios α in (1.365, 1.5625), attaining a maximal ϕ about 0.75806 at α = 93/64. We show that SQ-TR phase is thermodynamically stable at high densities over the aforementioned α range and report a novel phase diagram for self-dual ellipsoids. The discovery of SQ-TR crystal suggests novel organizing principles for non-spherical particles and self-assembly of colloidal systems.

cond-mat.stat-mech↗

Heterogeneous Force Chains in Cellularized Biopolymer Network

Biopolymer Networks play an important role in coordinating and regulating collective cellular dynamics via a number of signaling pathways. Here, we investigate the mechanical response of a model biopolymer network due to the active contraction of embedded cells. Specifically, a graph (bond-node) model derived from confocal microscopy data is used to represent the network microstructure, and cell contraction is modeled by applying correlated displacements at specific nodes, representing the focal adhesion sites. A force-based stochastic relaxation method is employed to obtain force-balanced network under cell contraction. We find that the majority of the forces are carried by a small number of heterogeneous force chains emitted from the contracting cells. The force chains consist of fiber segments that either possess a high degree of alignment before cell contraction or are aligned due to the reorientation induced by cell contraction. Large fluctuations of the forces along different force chains are observed. Importantly, the decay of the forces along the force chains is significantly slower than the decay of radially averaged forces in the system. These results suggest that the fibrous nature of biopolymer network structure can support long-range force transmission and thus, long-range mechanical signaling between cells.

cond-mat.soft↗

Schottky barrier formation and band bending revealed by first principles calculations

An atomistic insight into potential barrier formation and band bending at the interface between a metal and an n-type semiconductor is achieved by ab initio simulations and model analysis of a prototype Schottky diode, i.e., niobium doped rutile titania in contact with gold (Au/Nb:TiO$_2$). The local Schottky barrier height is found to vary between 0 and 1.26 eV depending on the position of the dopant. The band bending is caused by a dopant induced dipole field between the interface and the dopant site, whereas the pristine Au/TiO$_2$ interface does not show any band bending. These findings open the possibility for atomic scale optimization of the Schottky barrier and light harvesting in metal-semiconductor nanostructures.

cond-mat.mes-hall↗

A Cellular Automaton Model for Tumor Dormancy: Emergence of a Proliferative Switch

Malignant cancers that lead to fatal outcomes for patients may remain dormant for very long periods of time. Although individual mechanisms such as cellular dormancy, angiogenic dormancy and immunosurveillance have been proposed, a comprehensive understanding of cancer dormancy and the "switch" from a dormant to a proliferative state still needs to be strengthened from both a basic and clinical point of view. Computational modeling enables one to explore a variety of scenarios for possible but realistic microscopic dormancy mechanisms and their predicted outcomes. The aim of this paper is to devise such a predictive computational model of dormancy with an emergent "switch" behavior. Specifically, we generalize a previous cellular automaton (CA) model for proliferative growth of solid tumor that now incorporates a variety of cell-level tumor-host interactions and different mechanisms for tumor dormancy, for example the effects of the immune system. Our new CA rules induce a natural "competition" between the tumor and tumor suppression factors in the microenvironment. This competition either results in a "stalemate" for a period of time in which the tumor either eventually wins (spontaneously emerges) or is eradicated; or it leads to a situation in which the tumor is eradicated before such a "stalemate" could ever develop. We also predict that if the number of actively dividing cells within the proliferative rim of the tumor reaches a critical, yet low level, the dormant tumor has a high probability to resume rapid growth. Our findings may shed light on the fundamental understanding of cancer dormancy.

physics.bio-ph↗

Equilibrium Phase Behavior and Maximally Random Jammed State of Truncated Tetrahedra

Systems of hard nonspherical particles exhibit a variety of stable phases with different degrees of translational and orientational order, including isotropic liquid, solid crystal, rotator and a variety of liquid crystal phases. In this paper, we employ a Monte Carlo implementation of the adaptive-shrinking-cell (ASC) numerical scheme and free-energy calculations to ascertain with high precision the equilibrium phase behavior of systems of congruent Archimedean truncated tetrahedra over the entire range of possible densities up to the maximal nearly space-filling density. In particular, we find that the system undergoes two first-order phase transitions as the density increases: first a liquid-solid transition and then a solid-solid transition. The isotropic liquid phase coexists with the Conway-Torquato (CT) crystal phase at intermediate densities. At higher densities, we find that the CT phase undergoes another first-order phase transition to one associated with the densest-known crystal. We find no evidence for stable rotator (or plastic) or nematic phases. We also generate the maximally random jammed (MRJ) packings of truncated tetrahedra, which may be regarded to be the glassy end state of a rapid compression of the liquid. We find that such MRJ packings are hyperuniform with an average packing fraction of 0.770, which is considerably larger than the corresponding value for identical spheres (about 0.64). We conclude with some simple observations concerning what types of phase transitions might be expected in general hard-particle systems based on the particle shape and which would be good glass formers.

cond-mat.soft↗

Maximally dense packings of two-dimensional convex and concave noncircular particles

Dense packings of hard particles have important applications in many fields, including condensed matter physics, discrete geometry and cell biology. In this paper, we employ a stochastic search implementation of the Torquato-Jiao Adaptive-Shrinking-Cell optimization scheme [Nature 460, 876 (2009)] to find maximally dense particle packings in d-dimensional Euclidean space $\mathbb{R}^d$. While the original implementation was designed to study spheres and convex polyhedra in $d\ge3$, our implementation focuses on $d=2$ and extends the algorithm to include both concave polygons and certain convex or concave non-polygonal particle shapes. We verify the robustness of this packing protocol by successfully reproducing the known putative optimal packings of congruent copies of regular pentagons and octagons, then employ it to suggest dense packing arrangements of congruent copies of certain families of concave crosses, convex and concave curved triangles (incorporating shapes resembling the Mercedes-Benz logo), and "moon-like" shapes. Analytical constructions are determined subsequently to obtain the densest known packings of these particle shapes. For the examples considered, we find that the densest packings of both convex and concave particles with central symmetry are achieved by their corresponding optimal Bravais lattice packings; for particles lacking central symmetry, the densest packings obtained are non-lattice periodic packings, which are consistent with recently-proposed general organizing principles for hard particles. Moreover, we find that the densest known packings of certain curved triangles are periodic with a four-particle basis, and we find that the densest known periodic packings of certain moon-like shapes possess no inherent symmetries. Our work adds to the growing evidence that particle shape can be used as a tuning parameter to achieve a diversity of packing structures.

cond-mat.stat-mech↗

Dense periodic packings of tori

Dense packings of nonoverlapping bodies in three-dimensional Euclidean space are useful models of the structure of a variety of many-particle systems that arise in the physical and biological sciences. Here we investigate the packing behavior of congruent ring tori, which are multiply connected nonconvex bodies of genus 1, as well as horn and spindle tori. We analytically construct a family of dense periodic packings of unlinked tori guided by the organizing principles originally devised for simply connected solid bodies [Torquato and Jiao, PRE 86, 011102 (2012)]. We find that the horn tori as well as certain spindle and ring tori can achieve a packing density higher than the densest known packing of both sphere and ellipsoids. In addition, we study dense packings of cluster of pair-linked ring tori (i.e., Hopf links).

cond-mat.stat-mech↗

Avian photoreceptor patterns represent a disordered hyperuniform solution to a multiscale packing problem

Optimal spatial sampling of light rigorously requires that identical photoreceptors be arranged in perfectly regular arrays in two dimensions. Examples of such perfect arrays in nature include the compound eyes of insects and the nearly crystalline photoreceptor patterns of some fish and reptiles. Birds are highly visual animals with five different cone photoreceptor subtypes, yet their photoreceptor patterns are not perfectly regular. By analyzing the chicken cone photoreceptor system consisting of five different cell types using a variety of sensitive microstructural descriptors, we find that the disordered photoreceptor patterns are ``hyperuniform'' (exhibiting vanishing infinite-wavelength density fluctuations), a property that had heretofore been identified in a unique subset of physical systems, but had never been observed in any living organism. Remarkably, the photoreceptor patterns of both the total population and the individual cell types are simultaneously hyperuniform. We term such patterns ``multi-hyperuniform'' because multiple distinct subsets of the overall point pattern are themselves hyperuniform. We have devised a unique multiscale cell packing model in two dimensions that suggests that photoreceptor types interact with both short- and long-ranged repulsive forces and that the resultant competition between the types gives rise to the aforementioned singular spatial features characterizing the system, including multi-hyperuniformity.

cond-mat.stat-mech↗

Effect of Dimensionality on the Percolation Thresholds of Various $d$-Dimensional Lattices

We show analytically that the $[0,1]$, $[1,1]$ and $[2,1]$ Pad{é} approximants of the mean cluster number $S(p)$ for site and bond percolation on general $d$-dimensional lattices are upper bounds on this quantity in any Euclidean dimension $d$, where $p$ is the occupation probability. These results lead to certain lower bounds on the percolation threshold $p_c$ that become progressively tighter as $d$ increases and asymptotically exact as $d$ becomes large. These lower-bound estimates depend on the structure of the $d$-dimensional lattice and whether site or bond percolation is being considered. We obtain explicit bounds on $p_c$ for both site and bond percolation on five different lattices: $d$-dimensional generalizations of the simple-cubic, body-centered-cubic and face-centered-cubic Bravais lattices as well as the $d$-dimensional generalizations of the diamond and kagom{é} (or pyrochlore) non-Bravais lattices. These analytical estimates are used to assess available simulation results across dimensions (up through $d=13$ in some cases). It is noteworthy that the tightest lower bound provides reasonable estimates of $p_c$ in relatively low dimensions and becomes increasingly accurate as $d$ grows. We also derive high-dimensional asymptotic expansions for $p_c$ for the ten percolation problems and compare them to the Bethe-lattice approximation. Finally, we remark on the radius of convergence of the series expansion of $S$ in powers of $p$ as the dimension grows.

cond-mat.stat-mech↗

Effect of Dimensionality on the Percolation Threshold of Overlapping Nonspherical Hyperparticles

A set of lower bounds on the continuum percolation threshold $η_c$ of overlapping convex hyperparticles of general nonspherical (anisotropic) shape with a specified orientational probability distribution in $d$-dimensional Euclidean space have been derived [S. Torquato, J. Chem. Phys. {\bf 136}, 054106 (2012)]. The simplest of these lower bounds is given by $η_c \ge v/v_{ex}$, where $v_{ex}$ is the $d$-dimensional exclusion volume of a hyperparticle and $v$ is its $d$-dimensional volume. In order to study the effect of dimensionality on the threshold $η_c$ of overlapping nonspherical convex hyperparticles with random orientations here, we obtain a scaling relation for $η_c$ that is based on this lower bound and a conjecture that hyperspheres provide the highest threshold among all convex hyperparticle shapes for any $d$. This scaling relation exploits the principle that low-dimensional continuum percolation behavior encodes high-dimensional information. We derive a formula for the exclusion volume $v_{ex}$ of a hyperparticle in terms of its $d$-dimensional volume $v$, surface area $s$ and {\it radius of mean curvature} ${\bar R}$ (or, equivalently, {\it mean width}). These basic geometrical properties are computed for a wide variety of nonspherical hyperparticle shapes with random orientations across all dimensions, including, among other shapes, various polygons for $d=2$, Platonic solids, spherocylinders, parallepipeds and zero-volume plates for $d=3$ and their appropriate generalizations for $d \ge 4$. We then compute the lower bound and scaling relation for $η_c$ for this comprehensive set of continuum percolation models across dimensions. We show that the scaling relation provides accurate {\it upper-bound} estimates of the threshold $η_c$ across dimensions and becomes increasingly accurate as the space $d$ increases.

cond-mat.stat-mech↗

Effect of Dimensionality on the Continuum Percolation of Overlapping Hyperspheres and Hypercubes: II. Simulation Results and Analyses

In the first paper of this series [S. Torquato, J. Chem. Phys. {\bf 136}, 054106 (2012)], analytical results concerning the continuum percolation of overlapping hyperparticles in $d$-dimensional Euclidean space $\mathbb{R}^d$ were obtained, including lower bounds on the percolation threshold. In the present investigation, we provide additional analytical results for certain cluster statistics, such as the concentration of $k$-mers and related quantities, and obtain an upper bound on the percolation threshold $η_c$. We utilize the tightest lower bound obtained in the first paper to formulate an efficient simulation method, called the {\it rescaled-particle} algorithm, to estimate continuum percolation properties across many space dimensions with heretofore unattained accuracy. This simulation procedure is applied to compute the threshold $η_c$ and associated mean number of overlaps per particle ${\cal N}_c$ for both overlapping hyperspheres and oriented hypercubes for $ 3 \le d \le 11$. These simulations results are compared to corresponding upper and lower bounds on these percolation properties. We find that the bounds converge to one another as the space dimension increases, but the lower bound provides an excellent estimate of $η_c$ and ${\cal N}_c$, even for relatively low dimensions. We confirm a prediction of the first paper in this series that low-dimensional percolation properties encode high-dimensional information. We also show that the concentration of monomers dominate over concentration values for higher-order clusters (dimers, trimers, etc.) as the space dimension becomes large. Finally, we provide accurate analytical estimates of the pair connectedness function and blocking function at their contact values for any $d$ as a function of density.

cond-mat.stat-mech↗

Organizing Principles for Dense Packings of Nonspherical Hard Particles: Not All Shapes Are Created Equal

We have recently devised organizing principles to obtain maximally dense packings of the Platonic and Archimedean solids, and certain smoothly-shaped convex nonspherical particles [Torquato and Jiao, Phys. Rev. E 81, 041310 (2010)]. Here we generalize them in order to guide one to ascertain the densest packings of other convex nonspherical particles as well as concave shapes. Our generalized organizing principles are explicitly stated as four distinct propositions. We apply and test all of these organizing principles to the most comprehensive set of both convex and concave particle shapes to date, including Catalan solids, prisms, antiprisms, cylinders, dimers of spheres and various concave polyhedra. We demonstrate that all of the densest known packings associated with this wide spectrum of nonspherical particles are consistent with our propositions. Among other applications, our general organizing principles enable us to construct analytically the densest known packings of certain convex nonspherical particles, including spherocylinders, "lens-shaped" particles, square pyramids and rhombic pyramids. Moreover, we show how to apply these principles to infer the high-density equilibrium crystalline phases of hard convex and concave particles. We also discuss the unique packing attributes of maximally random jammed packings of nonspherical particles.

cond-mat.stat-mech↗

Microstructural Degeneracy associated with a Two-Point Correlation Function and its Information Content

Two-point correlation functions provide crucial yet incomplete characterization of microstructures because different microstructures may have the same correlation function. In an earlier Letter [Phys. Rev. Lett. 108, 080601 (2012)], we addressed the degeneracy question: What is the number of microstructures compatible with a specified correlation function? We computed this degeneracy, i.e., configurational entropy, in the framework of reconstruction methods, which enabled us to map the problem to the determination of ground-state degeneracies. Here, we provide a more comprehensive presentation and additional results. Since the configuration space of a reconstruction problem is a hypercube on which a Hamming distance is defined, we can calculate analytically an energy profile corresponding to the average energy of all microstructures at a given Hamming distance from a ground state. The steepness of this profile is a measure of the roughness of the energy landscape, which can be used as a proxy for ground-state degeneracy. The relationship between roughness metric and ground-state degeneracy is calibrated using a Monte Carlo algorithm for determining the degeneracy of a variety of microstructures, including hard disks and Poisson point processes as well as those with known degeneracies (single disks of various sizes and a particular crystalline microstructure). We show that our results can be expressed in terms of the information content of the two-point correlation functions. From this perspective, the a priori condition for a reconstruction to be accurate is that the information content, expressed in bits, should be comparable to the number of pixels in the unknown microstructure. We provide a formula to calculate the information content of any two-point correlation function, which makes our results broadly applicable to any field in which correlation functions are employed.

cond-mat.stat-mech↗