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We generate maximally random jammed (MRJ) packings of the four nontiling Platonic solids (tetrahedra, octahedra, dodecahedra, and icosahedra) using the adaptive-shrinking-cell method [S. Torquato and Y. Jiao, Phys. Rev. E 80, 041104 (2009)]. Such packings can be viewed as prototypical glasses in that they are maximally disordered while simultaneously being mechanically rigid. The MRJ packing fractions for tetrahedra, octahedra, dodecahedra, and icosahedra are, respectively, 0.763±0.005, 0.697±0.005, 0.716±0.002, and 0.707±0.002. We find that as the number of facets of the particles increases, the translational order in the packings increases while the orientational order decreases. Moreover, we show that the MRJ packings are hyperuniform (i.e., their infinite-wavelength local-number-density fluctuations vanish) and possess quasi-long-range pair correlations that decay asymptotically with scaling r(-4). This provides further evidence that hyperuniform quasi-long-range correlations are a universal feature of MRJ packings of frictionless particles of general shape. However, unlike MRJ packings of ellipsoids, superballs, and superellipsoids, which are hypostatic, MRJ packings of the nontiling Platonic solids are isostatic. We provide a rationale for the organizing principle that the MRJ packing fractions for nonspherical particles with sufficiently small asphericities exceed the corresponding value for spheres (∼0.64). We also discuss how the shape and symmetry of a polyhedron particle affects its MRJ packing fraction.

The degeneracy of two-phase disordered microstructures consistent with a specified correlation function is analyzed by mapping it to a ground-state degeneracy. We determine for the first time the associated density of states via a Monte Carlo algorithm. Our results are described in terms of the roughness of the energy landscape, defined on a hypercubic configuration space. The use of a Hamming distance in this space enables us to define a roughness metric, which is calculated from the correlation function alone and related quantitatively to the structural degeneracy. This relation is validated for a wide variety of disordered systems., Accepted for publication in Physical Review Letters

The densest binary sphere packings have historically been very difficult to determine. The only rigorously known packings in the alpha-x plane of sphere radius ratio alpha and relative concentration x are at the Kepler limit alpha = 1, where packings are monodisperse. Utilizing an implementation of the Torquato-Jiao sphere-packing algorithm [S. Torquato and Y. Jiao, Phys. Rev. E 82, 061302 (2010)], we present the most comprehensive determination to date of the phase diagram in (alpha,x) for the densest binary sphere packings. Unexpectedly, we find many distinct new densest packings., 5 pages, 2 figures. Accepted for publication in Physical Review Letters on August 9th, 2011

It is well known that two regular tetrahedra can be combined with a single regular octahedron to tile (complete fill) three-dimensional Euclidean space . This structure was called the “octet truss” by Buckminster Fuller. It was believed that such a tiling, which is the Delaunay tessellation of the face-centered cubic (fcc) lattice, and its closely related stacking variants, are the only tessellations of that involve two different regular polyhedra. Here we identify and analyze a unique family comprised of a noncountably infinite number of periodic tilings of whose smallest repeat tiling unit consists of one regular octahedron and six smaller regular tetrahedra. We first derive an extreme member of this unique tiling family by showing that the “holes” in the optimal lattice packing of octahedra, obtained by Minkowski over a century ago, are congruent tetrahedra. This tiling has 694 distinct concave (i.e., nonconvex) repeat units, 24 of which possess central symmetry, and hence is distinctly different and combinatorically richer than the fcc tetrahedra-octahedra tiling, which only has two distinct tiling units. Then we construct a one-parameter family of octahedron packings that continuously spans from the fcc to the optimal lattice packing of octahedra. We show that the “holes” in these packings, except for the two extreme cases, are tetrahedra of two sizes, leading to a family of periodic tilings with units composed four small tetrahedra and two large tetrahedra that contact an octahedron. These tilings generally possess 2,068 distinct concave tiling units, 62 of which are centrally symmetric.

Understanding tumor invasion and metastasis is of crucial importance for both fundamental cancer research and clinical practice. In vitro experiments have established that the invasive growth of malignant tumors is characterized by the dendritic invasive branches composed of chains of tumor cells emanating from the primary tumor mass. The preponderance of previous tumor simulations focused on non-invasive (or proliferative) growth. The formation of the invasive cell chains and their interactions with the primary tumor mass and host microenvironment are not well understood. Here, we present a novel cellular automaton (CA) model that enables one to efficiently simulate invasive tumor growth in a heterogeneous host microenvironment. By taking into account a variety of microscopic-scale tumor-host interactions, including the short-range mechanical interactions between tumor cells and tumor stroma, degradation of the extracellular matrix by the invasive cells and oxygen/nutrient gradient driven cell motions, our CA model predicts a rich spectrum of growth dynamics and emergent behaviors of invasive tumors. Besides robustly reproducing the salient features of dendritic invasive growth, such as least-resistance paths of cells and intrabranch homotype attraction, we also predict nontrivial coupling between the growth dynamics of the primary tumor mass and the invasive cells. In addition, we show that the properties of the host microenvironment can significantly affect tumor morphology and growth dynamics, emphasizing the importance of understanding the tumor-host interaction. The capability of our CA model suggests that sophisticated in silico tools could eventually be utilized in clinical situations to predict neoplastic progression and propose individualized optimal treatment strategies., Author Summary The goal of the present work is to develop an efficient single-cell based cellular automaton (CA) model that enables one to investigate the growth dynamics and morphology of invasive solid tumors. Recent experiments have shown that highly malignant tumors develop dendritic branches composed of tumor cells that follow each other, which massively invade into the host microenvironment and ultimately lead to cancer metastasis. Previous theoretical/computational cancer modeling neither addressed the question of how such chain-like invasive branches form nor how they interact with the host microenvironment and the primary tumor. Our CA model, which incorporates a variety of microscopic-scale tumor-host interactions (e.g., the mechanical interactions between tumor cells and tumor stroma, degradation of the extracellular matrix by the tumor cells and oxygen/nutrient gradient driven cell motions), can robustly reproduce experimentally observed invasive tumor evolution and predict a wide spectrum of invasive tumor growth dynamics and emergent behaviors in various different heterogeneous environments. Further refinement of our CA model could eventually lead to the development of a powerful simulation tool for clinical purposes capable of predicting neoplastic progression and suggesting individualized optimal treatment strategies.

We have previously shown that inverse statistical-mechanical techniques allow the determination of optimized isotropic pair interactions that self-assemble into low-coordinated crystal configurations in the d-dimensional Euclidean space R(d). In some of these studies, pair interactions with multiple extrema were optimized. In the present work, we attempt to find pair potentials that might be easier to realize experimentally by requiring them to be monotonic and convex. Encoding information in monotonic convex potentials to yield low-coordinated ground-state configurations in Euclidean spaces is highly nontrivial. We adapt a linear programming method and apply it to optimize two repulsive monotonic convex pair potentials, whose classical ground states are counterintuitively the square and honeycomb crystals in R(2). We demonstrate that our optimized pair potentials belong to two wide classes of monotonic convex potentials whose ground states are also the square and honeycomb crystal. We show that these unexpected ground states are stable over a nonzero number density range by checking their (i) phonon spectra, (ii) defect energies and (iii) self assembly by numerically annealing liquid-state configurations to their zero-temperature ground states.

We generate inherent structures, local potential-energy minima, of the "$k$-space overlap potential" in two-dimensional many-particle systems using a cooling and quenching simulation technique. The ground states associated with the $k$-space overlap potential are stealthy ({\it i.e.,} completely suppress single scattering of radiation for a range of wavelengths) and hyperuniform ({\it i.e.,} infinite wavelength density fluctuations vanish). However, we show via quantitative metrics that the inherent structures exhibit a range of stealthiness and hyperuniformity depending on the fraction of degrees of freedom that are constrained. Inherent structures in two dimensions typically contain five-particle rings, wavy grain boundaries, and vacancy-interstitial defects. The structural and thermodynamic properties of inherent structures are relatively insensitive to the temperature from which they are sampled, signifying that the energy landscape is relatively flat and devoid of deep wells. Using the nudged-elastic-band algorithm, we construct paths from ground-state configurations to inherent structures and identify the transition points between them. In addition, we use point patterns generated from a random sequential addition (RSA) of hard disks, which are nearly stealthy, and examine the particle rearrangements necessary to make the configurations absolutely stealthy. We introduce a configurational proximity metric to show that only small local, but collective, particle rearrangements are needed to drive initial RSA configurations to stealthy disordered ground states. These results lead to a more complete understanding of the unusual behaviors exhibited by the family of "collective-coordinate" potentials to which the $k$-space overlap potential belongs., 36 pages, 16 figures

A packing of spherical caps on the surface of a sphere (that is, a spherical code) is called rigid or jammed if it is isolated within the space of packings. In other words, aside from applying a global isometry, the packing cannot be deformed. In this paper, we systematically study the rigidity of spherical codes, particularly kissing configurations. One surprise is that the kissing configuration of the Coxeter-Todd lattice is not jammed, despite being locally jammed (each individual cap is held in place if its neighbors are fixed); in this respect, the Coxeter-Todd lattice is analogous to the face-centered cubic lattice in three dimensions. By contrast, we find that many other packings have jammed kissing configurations, including the Barnes-Wall lattice and all of the best kissing configurations known in four through twelve dimensions. Jamming seems to become much less common for large kissing configurations in higher dimensions, and in particular it fails for the best kissing configurations known in 25 through 31 dimensions. Motivated by this phenomenon, we find new kissing configurations in these dimensions, which improve on the records set in 1982 by the laminated lattices., 39 pages, 8 figures

We extend the results from the first part of this series of two papers by examining hyperuniformity in heterogeneous media composed of impenetrable anisotropic inclusions. Specifically, we consider maximally random jammed packings of hard ellipses and superdisks and show that these systems both possess vanishing infinite-wavelength local-volume-fraction fluctuations and quasi-long-range pair correlations. Our results suggest a strong generalization of a conjecture by Torquato and Stillinger [Phys. Rev. E. 68, 041113 (2003)], namely that all strictly jammed saturated packings of hard particles, including those with size- and shape-distributions, are hyperuniform with signature quasi-long-range correlations. We show that our arguments concerning the constrained distribution of the void space in MRJ packings directly extend to hard ellipse and superdisk packings, thereby providing a direct structural explanation for the appearance of hyperuniformity and quasi-long-range correlations in these systems. Additionally, we examine general heterogeneous media with anisotropic inclusions and show for the first time that one can decorate a periodic point pattern to obtain a hard-particle system that is not hyperuniform with respect to local-volume-fraction fluctuations. This apparent discrepancy can also be rationalized by appealing to the irregular distribution of the void space arising from the anisotropic shapes of the particles. Our work suggests the intriguing possibility that the MRJ states of hard particles share certain universal features independent of the local properties of the packings, including the packing fraction and average contact number per particle., Comment: 29 pages, 9 figures

The densest binary sphere packings in the alpha-x plane of small to large sphere radius ratio alpha and small sphere relative concentration x have historically been very difficult to determine. Previous research had led to the prediction that these packings were composed of a few known "alloy" phases including, for example, the AlB2 (hexagonal omega), HgBr2, and AuTe2 structures, and to XYn structures composed of close-packed large spheres with small spheres (in a number ratio of n to 1) in the interstices, e.g., the NaCl packing for n = 1. However, utilizing an implementation of the Torquato-Jiao sphere-packing algorithm [S. Torquato and Y. Jiao, Phys. Rev. E 82, 061302 (2010)], we have discovered that many more structures appear in the densest packings. For example, while all previously known densest structures were composed of spheres in small to large number ratios of one to one, two to one, and very recently three to one, we have identified densest structures with number ratios of seven to three and five to two. In a recent work [A. B. Hopkins, Y. Jiao, F. H. Stillinger, and S. Torquato, Phys. Rev. Lett. 107, 125501 (2011)], we summarized these findings. In this work, we present the structures of the densest-known packings and provide details about their characteristics. Our findings demonstrate that a broad array of different densest mechanically stable structures consisting of only two types of components can form without any consideration of attractive or anisotropic interactions. In addition, the novel structures that we have identified may correspond to currently unidentified stable phases of certain binary atomic and molecular systems, particularly at high temperatures and pressures., Comment: 45 pages, 23 figures, 1 table. Accepted for publication in Physical Review E on January 27th, 2012

We show for the first time that collectively jammed disordered packings of three-dimensional monodisperse frictionless hard spheres can be produced and tuned using a novel numerical protocol with packing density $\phi$ as low as 0.6. This is well below the value of 0.64 associated with the maximally random jammed state and entirely unrelated to the ill-defined ``random loose packing'' state density. Specifically, collectively jammed packings are generated with a very narrow distribution centered at any density $\phi$ over a wide density range $\phi \in [0.6,~0.74048\ldots]$ with variable disorder. Our results support the view that there is no universal jamming point that is distinguishable based on the packing density and frequency of occurence. Our jammed packings are mapped onto a density-order-metric plane, which provides a broader characterization of packings than density alone. Other packing characteristics, such as the pair correlation function, average contact number and fraction of rattlers are quantified and discussed., Comment: 19 pages, 4 figures

Results from a numerical study examining cross-property relations linking fluid permeability to diffusive and electrical properties are presented. Numerical solutions of the Stokes equations in three-dimensional consolidated granular packings are employed to provide a basis of comparison between different permeability estimates. Estimates based on the \ensuremath{\Lambda} parameter (a length derived from electrical conduction) and on ${\mathit{d}}_{\mathit{c}}$ (a length derived from immiscible displacement) are found to be considerably more reliable than estimates based on rigorous permeability bounds related to pore space diffusion. We propose two hybrid relations based on diffusion which provide more accurate estimates than either of the rigorous permeability bounds.

We determine, by first‐passage‐time simulations, the effective conductivity tensor σe of anisotropic suspensions of aligned spheroidal inclusions with aspect ratio b/a. This is a versatile model of composite media, containing the special limiting cases of aligned disks (b/a=0), spheres (b/a=1), and aligned needles (b/a=∞), and may be employed to model aligned, long‐ and short‐fiber composites, anisotropic sandstones, certain laminates, and cracked media. Data for σe are obtained for prolate cases (b/a=2, 5, and 10) and oblate cases (b/a=0.1, 0.2, and 0.5) over a wide range of inclusion volume fractions and selected phase conductivities (including superconducting inclusions and perfectly insulating ‘‘voids’’). The data always lie within second‐order rigorous bounds on σe due to Willis [J. Mech. Phys. Solids 25, 185 (1977)] for this model. We compare our data for prolate and oblate spheroids to our previously obtained data for spheres [J. Appl. Phys. 69, 2280 (1991)].

The boundary element method is applied to determine the effective elastic moduli of continuum models of composite materials. In this paper, we specialize to the idealized model of hexagonal arrays of infinitely long, aligned cylinders in a matrix (a model of a fiber‐reinforced material) or a thin‐plate composite consisting of hexagonal arrays of disks in a matrix. Thus, one need only consider two‐dimensional elasticity, i.e., either plane‐strain or plane‐stress elasticity. This paper examines a variety of cases in which the inclusions are either stiffer or weaker than the matrix for a wide range of inclusion volume fractions φ2. Our comprehensive set of simulation data for the elastic moduli are tabulated. Using the boundary element method, a key microstructural parameter η2 that arises in rigorous three‐point bounds on the effective shear modulus is also computed. Our numerical simulations of the elastic moduli for the hexagonal array are compared to rigorous two‐point and three‐point bounds on the respective effective properties. In the extreme instances of either superrigid particles or voids, we compare analytical relations for the elastic moduli near dilute and close packing limits to our simulation results.

The densest local packings of N three-dimensional identical nonoverlapping spheres within a radius Rmin(N) of a fixed central sphere of the same size are obtained for selected values of N up to N = 1054. In the predecessor to this paper [A.B. Hopkins, F.H. Stillinger and S. Torquato, Phys. Rev. E 81 041305 (2010)], we described our method for finding the putative densest packings of N spheres in d-dimensional Euclidean space Rd and presented those packings in R2 for values of N up to N = 348. We analyze the properties and characteristics of the densest local packings in R3 and employ knowledge of the Rmin(N), using methods applicable in any d, to construct both a realizability condition for pair correlation functions of sphere packings and an upper bound on the maximal density of infinite sphere packings. In R3, we find wide variability in the densest local packings, including a multitude of packing symmetries such as perfect tetrahedral and imperfect icosahedral symmetry. We compare the densest local packings of N spheres near a central sphere to minimal-energy configurations of N+1 points interacting with short-range repulsive and long-range attractive pair potentials, e.g., 12-6 Lennard-Jones, and find that they are in general completely different, a result that has possible implications for nucleation theory. We also compare the densest local packings to finite subsets of stacking variants of the densest infinite packings in R3 (the Barlow packings) and find that the densest local packings are almost always most similar, as measured by a similarity metric, to the subsets of Barlow packings with the smallest number of coordination shells measured about a single central sphere, e.g., a subset of the FCC Barlow packing. We additionally observe that the densest local packings are dominated by the spheres arranged with centers at precisely distance Rmin(N) from the fixed sphere's center., 45 pages, 18 figures, 2 tables

Bounded interactions are particularly important in soft-matter systems, such as colloids, microemulsions, and polymers. We derive new duality relations for a class of soft potentials, including three-body and higher-order functions, that can be applied to ordered and disordered classical ground states. These duality relations link the energy of configurations associated with a real-space potential to the corresponding energy of the dual (Fourier-transformed) potential. We apply the duality relations by demonstrating how information about the classical ground states of short-ranged potentials can be used to draw new conclusions about the ground states of long-ranged potentials and vice versa. The duality relations also lead to bounds on the T=0 system energies in density intervals of phase coexistence. Additionally, we identify classes of "self-similar" potentials, for which one can relate low- and high-density ground-state energies. We analyze the ground state configurations and thermodynamic properties of a one-dimensional system previously thought to exhibit an infinite number of structural phase transitions and comment on the known ground states of purely repulsive monotonic potentials in the context of our duality relations., 31 pages, 6 figures

We reformulate the covering and quantizer problems as the determination of the ground states of interacting particles in $\mathbb{R}^d$ that generally involve single-body, two-body, three-body, and higher-body interactions. This is done by linking the covering and quantizer problems to certain optimization problems involving the "void" nearest-neighbor functions that arise in the theory of random media and statistical mechanics. These reformulations, which again exemplifies the deep interplay between geometry and physics, allow one now to employ theoretical and numerical optimization techniques to analyze and solve these energy minimization problems. The covering and quantizer problems have relevance in numerous applications, including wireless communication network layouts, the search of high-dimensional data parameter spaces, stereotactic radiation therapy, data compression, digital communications, meshing of space for numerical analysis, and coding and cryptography, among other examples. The connections between the covering and quantizer problems and the sphere-packing and number-variance problems are discussed. We also show that disordered saturated sphere packings provide relatively thin (economical) coverings and may yield thinner coverings than the best known lattice coverings in sufficiently large dimensions. In the case of the quantizer problem, we derive improved upper bounds on the quantizer error using sphere-packing solutions, which are generally substantially sharper than an existing upper bound in low to moderately large dimensions. We also demonstrate that disordered saturated sphere packings yield relatively good quantizers. Finally, we remark on possible applications of our results for the detection of gravitational waves., 52 pages, 9 figures, 8 tables; Changes reflect improvements made during the refereeing process

This review describes the diversity of jammed configurations attainable by frictionless convex nonoverlapping (hard) particles in Euclidean spaces and for that purpose it stresses individual-packing geometric analysis. A fundamental feature of that diversity is the necessity to classify individual jammed configurations according to whether they are locally, collectively, or strictly jammed. Each of these categories contains a multitude of jammed configurations spanning a wide and (in the large system limit) continuous range of intensive properties, including packing fraction $\phi$, mean contact number $Z$, and several scalar order metrics. Application of these analytical tools to spheres in three dimensions (an analog to the venerable Ising model) covers a myriad of jammed states, including maximally dense packings (as Kepler conjectured), low-density strictly-jammed tunneled crystals, and a substantial family of amorphous packings. With respect to the last of these, the current approach displaces the historically prominent but ambiguous idea of ``random close packing" (RCP) with the precise concept of ``maximally random jamming" (MRJ). This review also covers recent advances in understanding jammed packings of polydisperse sphere mixtures, as well as convex nonspherical particles, e.g., ellipsoids, ``superballs", and polyhedra. Because of their relevance to error-correcting codes and information theory, sphere packings in high-dimensional Euclidean spaces have been included as well. We also make some remarks about packings in (curved) non-Euclidean spaces. In closing this review, several basic open questions for future research to consider have been identified., Comment: 37 figures, 6 tables; Reviews of Modern Physics, in press

The determination of the densest packings of regular tetrahedra (one of the five Platonic solids) is attracting great attention as evidenced by the rapid pace at which packing records are being broken and the fascinating packing structures that have emerged. Here we provide the most general analytical formulation to date to construct dense periodic packings of tetrahedra with four particles per fundamental cell. This analysis results in six-parameter family of dense tetrahedron packings that includes as special cases recently discovered "dimer" packings of tetrahedra, including the densest known packings with density $\phi= 4000/4671 = 0.856347...$. This study strongly suggests that the latter set of packings are the densest among all packings with a four-particle basis. Whether they are the densest packings of tetrahedra among all packings is an open question, but we offer remarks about this issue. Moreover, we describe a procedure that provides estimates of upper bounds on the maximal density of tetrahedron packings, which could aid in assessing the packing efficiency of candidate dense packings., Comment: It contains 25 pages, 5 figures.

The densest local packings of N identical nonoverlapping spheres within a radius Rmin(N) of a fixed central sphere of the same size are obtained using a nonlinear programming method operating in conjunction with a stochastic search of configuration space. Knowledge of Rmin(N) in d-dimensional Euclidean space allows for the construction both of a realizability condition for pair correlation functions of sphere packings and an upper bound on the maximal density of infinite sphere packings. In this paper, we focus on the two-dimensional circular disk problem. We find and present the putative densest packings and corresponding Rmin(N) for selected values of N up to N = 348 and use this knowledge to construct such a realizability condition and upper bound. We additionally analyze the properties and characteristics of the maximally dense packings, finding significant variability in their symmetries and contact networks, and that the vast majority differ substantially from the triangular lattice even for large N. Our work has implications for packaging problems, nucleation theory, and surface physics., Comment: 35 pages, 33 figures, 2 tables. Supporting material available at http://cherrypit.princeton.edu/

Dense random packings of hard particles are useful models of granular media and are closely related to the structure of nonequilibrium low-temperature amorphous phases of matter. Most work has been done for random jammed packings of spheres and it is only recently that corresponding packings of nonspherical particles (e.g., ellipsoids) have received attention. Here we report a study of the maximally random jammed (MRJ) packings of binary superdisks and monodispersed superballs whose shapes are defined by |x1|2p+...+|xd|2por=1 with d=2 and 3, respectively, where p is the deformation parameter with values in the interval (0,infinity). As p increases from zero, one can get a family of both concave (0p0.5) and convex (por=0.5) particles with square symmetry (d=2), or octahedral and cubic symmetry (d=3). In particular, for p=1 the particle is a perfect sphere (circular disk) and for p--infinity the particle is a perfect cube (square). We find that the MRJ densities of such packings increase dramatically and nonanalytically as one moves away from the circular-disk and sphere point (p=1). Moreover, the disordered packings are hypostatic, i.e., the average number of contacting neighbors is less than twice the total number of degrees of freedom per particle, and yet the packings are mechanically stable. As a result, the local arrangements of particles are necessarily nontrivially correlated to achieve jamming. We term such correlated structures "nongeneric." The degree of "nongenericity" of the packings is quantitatively characterized by determining the fraction of local coordination structures in which the central particles have fewer contacting neighbors than average. We also show that such seemingly "special" packing configurations are counterintuitively not rare. As the anisotropy of the particles increases, the fraction of rattlers decreases while the minimal orientational order as measured by the tetratic and cubatic order parameters increases. These characteristics result from the unique manner in which superballs break their rotational symmetry, which also makes the superdisk and superball packings distinctly different from other known nonspherical hard-particle packings.

We report the first experimental demonstration of photonic bandgaps (PBGs) in 2D hyperuniform disordered materials and show that is possible to obtain isotropic, disordered, photonic materials of arbitrary size with complete PBGs.

Theoretical and computational tools that can be used in the clinic to predict neoplastic progression and propose individualized optimal treatment strategies to control cancer growth is desired. To develop such a predictive model, one must account for the complex mechanisms involved in tumor growth. Here we review resarch work that we have done toward the development of an "Ising model" of cancer. The review begins with a description of a minimalist four-dimensional (three in space and one in time) cellular automaton (CA) model of cancer in which healthy cells transition between states (proliferative, hypoxic, and necrotic) according to simple local rules and their present states, which can viewed as a stripped-down Ising model of cancer. This model is applied to model the growth of glioblastoma multiforme, the most malignant of brain cancers. This is followed by a discussion of the extension of the model to study the effect on the tumor dynamics and geometry of a mutated subpopulation. A discussion of how tumor growth is affected by chemotherapeutic treatment is then described. How angiogenesis as well as the heterogeneous and confined environment in which a tumor grows is incorporated in the CA model is discussed. The characterization of the level of organization of the invasive network around a solid tumor using spanning trees is subsequently described. Then, we describe open problems and future promising avenues for future research, including the need to develop better molecular-based models that incorporate the true heterogeneous environment over wide range of length and time scales (via imaging data), cell motility, oncogenes, tumor suppressor genes and cell-cell communication. The need to bring to bear the powerful machinery of the theory of heterogeneous media to better understand the behavior of cancer in its microenvironment is presented., Comment: 55 pages, 21 figures and 3 tables. To appear in Physical Biology. Added references

We have formulated the problem of generating periodic dense paritcle packings as an optimization problem called the Adaptive Shrinking Cell (ASC) formulation [S. Torquato and Y. Jiao, Phys. Rev. E {\bf 80}, 041104 (2009)]. Because the objective function and impenetrability constraints can be exactly linearized for sphere packings with a size distribution in $d$-dimensional Euclidean space $\mathbb{R}^d$, it is most suitable and natural to solve the corresponding ASC optimization problem using sequential linear programming (SLP) techniques. We implement an SLP solution to produce robustly a wide spectrum of jammed sphere packings in $\mathbb{R}^d$ for $d=2,3,4,5$ and $6$ with a diversity of disorder and densities up to the maximally densities. This deterministic algorithm can produce a broad range of inherent structures besides the usual disordered ones with very small computational cost by tuning the radius of the {\it influence sphere}. In three dimensions, we show that it can produce with high probability a variety of strictly jammed packings with a packing density anywhere in the wide range $[0.6, 0.7408...]$. We also apply the algorithm to generate various disordered packings as well as the maximally dense packings for $d=2,3, 4,5$ and 6. Compared to the LS procedure, our SLP protocol is able to ensure that the final packings are truly jammed, produces disordered jammed packings with anomalously low densities, and is appreciably more robust and computationally faster at generating maximally dense packings, especially as the space dimension increases., Comment: 34 pages, 6 figures

The phase behavior of hard superballs is examined using molecular dynamics within a deformable periodic simulation box. A superball's interior is defined by the inequality $|x|^{2q} + |y|^{2q} + |z|^{2q} \leq 1$, which provides a versatile family of convex particles ($q \geq 0.5$) with cube-like and octahedron-like shapes as well as concave particles ($q < 0.5$) with octahedron-like shapes. Here, we consider the convex case with a deformation parameter q between the sphere point (q = 1) and the cube (q = 1). We find that the asphericity plays a significant role in the extent of cubatic ordering of both the liquid and crystal phases. Calculation of the first few virial coefficients shows that superballs that are visually similar to cubes can have low-density equations of state closer to spheres than to cubes. Dense liquids of superballs display cubatic orientational order that extends over several particle lengths only for large q. Along the ordered, high-density equation of state, superballs with 1 < q < 3 exhibit clear evidence of a phase transition from a crystal state to a state with reduced long-ranged orientational order upon the reduction of density. For $q \geq 3$, long-ranged orientational order persists until the melting transition. The width of coexistence region between the liquid and ordered, high-density phase decreases with q up to q = 4.0. The structures of the high-density phases are examined using certain order parameters, distribution functions, and orientational correlation functions. We also find that a fixed simulation cell induces artificial phase transitions that are out of equilibrium. Current fabrication techniques allow for the synthesis of colloidal superballs, and thus the phase behavior of such systems can be investigated experimentally., 33 pages, 14 figures

We provide numerical constructions of one-dimensional hyperuniform many-particle distributions that exhibit unusual clustering and asymptotic local number density fluctuations growing more slowly than the volume of an observation window but faster than the surface area. By targeting a specified form of the structure factor at small wavenumbers using collective density variables, we are able to tailor the form of asymptotic local density fluctuations while simultaneously measuring the effect of imposing weak and strong constraints on the available degrees of freedom within the system. Even in one dimension, the long-range effective interactions induce clustering and nontrivial phase transitions in the resulting ground-state configurations. We provide an analytical connection between the fraction of contrained degrees of freedom within the system and the disorder-order phase transition for a class of target structure factors by examining the realizability of the constrained contribution to the pair correlation function. Our results explicitly demonstrate that disordered hyperuniform many-particle ground states, and therefore also point distributions, with substantial clustering can be constructed. We directly relate the local coordination structure of our point patterns to the distribution of the void space external to the particles, and we provide a scaling argument for the configurational entropy of the systems when only a small fraction of the degrees of freedom are constrained. By emphasizing the intimate connection between geometrical constraints on the particle distribution and structural regularity, our work has direct implications for higher-dimensional systems, including an understanding of the appearance of hyperuniformity and quasi-long-range pair correlations in maximally random strictly jammed packings of hard spheres., Comment: 34 pages, 11 figures

We show that quasi-long-range (QLR) pair correlations that decay asymptotically with scaling $r^{-(d+1)}$ in $d$-dimensional Euclidean space $\mathbb{R}^d$, trademarks of certain quantum systems and cosmological structures, are a universal signature of maximally random jammed (MRJ) hard-particle packings. We introduce a novel hyperuniformity descriptor in MRJ packings by studying local-volume-fraction fluctuations and show that infinite-wavelength fluctuations vanish even for packings with size- and shape-distributions. Special void statistics induce hyperuniformity and QLR pair correlations., Comment: 10 pages, 3 figures; changes to figures and text based on review process; accepted for publication at Phys. Rev. Lett

We present designs of 2D isotropic, disordered photonic materials of arbitrary size with complete band gaps blocking all directions and polarizations. The designs with the largest gaps are obtained by a constrained optimization method that starts from a hyperuniform disordered point pattern, an array of points whose number variance within a spherical sampling window grows more slowly than the volume. We argue that hyperuniformity, combined with uniform local topology and short-range geometric order, can explain how complete photonic band gaps are possible without long-range translational order. We note the ramifications for electronic and phononic band gaps in disordered materials., Comment: 8 pages, 6 figures

Cross‐property relations linking the fluid permeability k associated with viscous flow through a porous medium to effective diffusion properties of the medium have recently been derived. Torquato [Phys. Rev. Lett. 64, 2644 (1990)] found that k≤Dφ1τ, where τ is the ‘‘mean survival time’’ associated with steady‐state diffusion of ‘‘reactants’’ in the fluid region of diffusion coefficient D and porosity φ1 of a porous medium containing absorbing walls (i.e., trap boundaries). Subsequently, Avellaneda and Torquato [Phys. Fluids A 3, 2529 (1991)] related k to the electrical formation factor F (inverse of the dimensionless effective electrical conductivity) and the principal (largest) diffusion relaxation time T1 associated with the time‐dependent trapping problem, namely, k≤DT1/F. In this study, we compute the aforementioned bounds, using an efficient first‐passage‐time algorithm, for grain‐consolidation models of porous media and compare them to exact results for these models. We also conjecture a new relatio...

An accurate first‐passage simulation technique formulated by the authors [J. Appl. Phys. 68, 3892 (1990)] is employed to compute the effective conductivity σe of distributions of penetrable (or overlapping) spheres of conductivity σ2 in a matrix of conductivity σ1. Clustering of particles in this model results in a generally intricate topology for virtually the entire range of sphere volume fractions φ2 (i.e., 0≤φ2≤1). Results for the effective conductivity σe are presented for several values of the conductivity ratio α=σ2/σ1, including superconducting spheres (α=∞) and perfectly insulating spheres (α=0), and for a wide range of volume fractions. The data are shown to lie between rigorous three‐point bounds on σe for the same model. Consistent with the general observations of Torquato [J. Appl. Phys. 58, 3790 (1985)] regarding the utility of rigorous bounds, one of the bounds provides a good estimate of the effective conductivity, even in the extreme contrast cases (α≫1 or α≂0), depending upon whether the system is below or above the percolation threshold.

Improved rigorous bounds on the effective elastic moduli of a transversely isotropic fiber-reinforced material composed of aligned, infinitely long, equisized, circular cylinders distributed throughout a matrix are evaluated for cylinder volume fractions up to 70 percent. The bounds are generally shown to provide significant improvement over the Hill-Hashin bounds which incorporate only volume-fraction information. For cases in which the cylinders are stiffer than the matrix, the improved lower bounds provide relatively accurate estimates of the elastic moduli, even when the upper bound diverges from it (i.e., when the cylinders are substantially stiffer than the matrix). This last statement is supported by accurate, recently obtained Monte Carlo computer-simulation data of the true effective axial shear modulus.

The effective diffusion coefficient De for porous media composed of identical obstacles of radius R in which the diffusing particles have finite radius βR (β≥0) is determined by an efficient Brownian motion simulation technique. This is accomplished by first computing De for diffusion of ‘‘point’’ Brownian particles in a certain system of interpenetrable spherical obstacles and then employing an isomorphism between De for this interpenetrable sphere system and De for the system of interest, i.e., the one in which the Brownian particles have radius βR. [S. Torquato, J. Chem. Phys. 95, 2838 (1991)]. The diffusion coefficient is computed for the cases β=1/9 and β=1/4 for a wide range of porosities and compared to previous calculations for point Brownian particles (β=0). The effect of increasing the size of the Brownian particle is to hinder the diffusion, especially at low porosities. A simple scaling relation enables one to compute the effective diffusion coefficient De for finite β given the result of De f...

An amorphous or ‘glass’ structure can be created when a liquid is cooled quickly. It has long been debated whether this transition involves an underlying thermodynamic or kinetic change. A model system of hard spheres supports the second view.

An in silico tool that can be utilized in the clinic to predict neoplastic progression and propose individualized treatment strategies is the holy grail of computational tumor modeling. Building such a tool requires the development and successful integration of a number of biophysical and mathematical models. In this paper, we work toward this long-term goal by formulating a cellular automaton model of tumor growth that accounts for several different inter-tumor processes and host-tumor interactions. In particular, the algorithm couples the remodeling of the microvasculature with the evolution of the tumor mass and considers the impact that organ-imposed physical confinement and environmental heterogeneity have on tumor size and shape. Furthermore, the algorithm is able to account for cell-level heterogeneity, allowing us to explore the likelihood that different advantageous and deleterious mutations survive in the tumor cell population. This computational tool we have built has a number of applications in its current form in both predicting tumor growth and predicting response to treatment. Moreover, the latent power of our algorithm is that it also suggests other tumor-related processes that need to be accounted for and calls for the conduction of new experiments to validate the model's predictions.

We present a method to calculate upper bounds on the photonic band gaps of two-component photonic crystals. The method involves calculating both upper and lower bounds on the frequency bands for a given structure, and then maximizing over all possible two-component structures. We apply this method to a number of examples, including a one-dimensional photonic crystal (or ``Bragg grating'') and two-dimensional photonic crystals (in both the TM and TE polarizations) with both four and sixfold rotational symmetries. We compare the bounds to band gaps of numerically optimized structures and find that the bounds are extremely tight. We prove that the bounds are ``sharp'' in the limit of low dielectric contrast ratio between the two components. This method and the bounds derived here have important implications in the search for optimal photonic band-gap structures.

We introduce an optimization method to design examples of photonic quasicrystals with substantial, complete photonic band gaps; that is, a range of frequencies over which electromagnetic wave propagation is forbidden for all directions and polarizations. The method can be applied to photonic quasicrystals with arbitrary rotational symmetry; here, we illustrate the results for fivefold and eightfold symmetric quasicrystals. The optimized band gaps are highly isotropic, which may offer advantages over photonic crystals for certain applications.

We formulate the problem of generating dense packings of nonoverlapping, non-tiling polyhedra within an adaptive fundamental cell subject to periodic boundary conditions as an optimization problem, which we call the Adaptive Shrinking Cell (ASC) scheme. This novel optimization problem is solved here (using a variety of multi-particle initial configurations) to find the dense packings of each of the Platonic solids in three-dimensional Euclidean space R3 , except for the cube, which is the only Platonic solid that tiles space. We find the densest known packings of tetrahedra, icosahedra, dodecahedra, and octahedra with densities 0.823, 0.836, 0.904, and 0.947, respectively. It is noteworthy that the densest tetrahedral packing possesses no long-range order. Unlike the densest tetrahedral packing, which must not be a Bravais lattice packing, the densest packings of the other non-tiling Platonic solids that we obtain are their previously known optimal (Bravais) lattice packings. We also derive a simple upper bound on the maximal density of packings of congruent nonspherical particles, and apply it to Platonic solids, Archimedean solids, superballs and ellipsoids. Our simulation results, rigorous upper bounds, and other theoretical arguments lead us to the conjecture that the densest packings of Platonic and Archimedean solids with central symmetry are given by their corresponding densest lattice packings. In addition, we conjecture that the optimal packing of any convex, congruent polyhedron without central symmetry generally is not a lattice packing., To appear in Phys. Rev. E. The paper is a sequel of a recent Nature paper, i.e., Nature 460, 876 (2009). In this paper, we reported a new packing of tetrahedra with higher density 0.823 than that reported in Nature (0.782). The paper is 52 pages, including 14 figures and 4 tables

We have shown that any pair potential function v(r) possessing a Fourier transform V(k) that is positive and has compact support at some finite wave number K yields classical disordered ground states for a broad density range [R. D. Batten, F. H. Stillinger, and S. Torquato, J. Appl. Phys. 104, 033504 (2008)]. By tuning a constraint parameter chi (defined in the text), the ground states can traverse varying degrees of local order from fully disordered to crystalline ground states. Here, we show that in two dimensions, the " k -space overlap potential," where V(k) is proportional to the intersection area between two disks of diameter K whose centers are separated by k , yields anomalous low-temperature behavior, which we attribute to the topography of the underlying energy landscape. At T=0 , for the range of densities considered, we show that there is continuous energy degeneracy among Bravais-lattice configurations. The shear elastic constant of ground-state Bravais-lattice configurations vanishes. In the harmonic regime, a significant fraction of the normal modes for both amorphous and Bravais-lattice ground states have vanishing frequencies, indicating the lack of an internal restoring force. Using molecular-dynamics simulations, we observe negative thermal-expansion behavior at low temperatures, where upon heating at constant pressure, the system goes through a density maximum. For all temperatures, isothermal compression reduces the local structure of the system unlike typical single-component systems.

Point configurations have been widely used as model systems in condensed matter physics, materials science and biology. Statistical descriptors such as the $n$-body distribution function $g_n$ is usually employed to characterize the point configurations, among which the most extensively used is the pair distribution function $g_2$. An intriguing inverse problem of practical importance that has been receiving considerable attention is the degree to which a point configuration can be reconstructed from the pair distribution function of a target configuration. Although it is known that the pair-distance information contained in $g_2$ is in general insufficient to uniquely determine a point configuration, this concept does not seem to be widely appreciated and general claims of uniqueness of the reconstructions using pair information have been made based on numerical studies. In this paper, we introduce the idea of the distance space, called the $\mathbb{D}$ space. The pair distances of a specific point configuration are then represented by a single point in the $\mathbb{D}$ space. We derive the conditions on the pair distances that can be associated with a point configuration, which are equivalent to the realizability conditions of the pair distribution function $g_2$. Moreover, we derive the conditions on the pair distances that can be assembled into distinct configurations. These conditions define a bounded region in the $\mathbb{D}$ space. By explicitly constructing a variety of degenerate point configurations using the $\mathbb{D}$ space, we show that pair information is indeed insufficient to uniquely determine the configuration in general. We also discuss several important problems in statistical physics based on the $\mathbb{D}$ space., 28 pages, 8 figures

We show that classical many-particle systems interacting with certain soft pair interactions in two dimensions exhibit novel low-temperature behaviors. Ground states span from disordered to crystalline. At some densities, a large fraction of normal-mode frequencies vanish. Lattice ground-state configurations have more vanishing frequencies than disordered ground states at the same density and exhibit vanishing shear moduli. For the melting transition from a crystal, the thermal expansion coefficient is negative. These unusual results are attributed to the topography of the energy landscape.

Due to their ability to control the most fundamental properties of light, photonic band gap (PBG) materials open a new frontier in both basic science and technology [1,2]. Until now, the only materials known to have complete photonic band gaps were photonic crystals, periodic structures. We show that there exists a more general class of systems, called hyperuniform photonic structures, which exhibit large and complete photonic band gaps. The common feature of hyperuniform photonic structures considered here is that they are derived from hyperuniform point patterns [3]. Hyperuniform point patterns are those whose number variance within a spherical sampling window of radius R (in d dimensions) grows more slowly than the window volume for large R, i.e., 〈N R 2〉 − 〈N R 〉2 ∼ Rp, where p ≪ d. This classification includes all crystals and quasicrystals [4], as well as a special subset of disordered structures.

Dense hard-particle packings are intimately related to the structure of low-temperature phases of matter and are useful models of heterogeneous materials and granular media. Most studies of the densest packings in three dimensions have considered spherical shapes, and it is only more recently that nonspherical shapes (e.g., ellipsoids) have been investigated. Superballs (whose shapes are defined by |x1|^2p + |x2|^2p + |x3|^2p = 0.5) with both cubic- and octahedral-like shapes as well as concave particles (0 < p < 0.5) with octahedral-like shapes. In this paper, we provide analytical constructions for the densest known superball packings for all convex and concave cases. The candidate maximally dense packings are certain families of Bravais lattice packings. The maximal packing density as a function of p is nonanalytic at the sphere-point (p = 1) and increases dramatically as p moves away from unity. The packing characteristics determined by the broken rotational symmetry of superballs are similar to but richer than their two-dimensional "superdisk" counterparts, and are distinctly different from that of ellipsoid packings. Our candidate optimal superball packings provide a starting point to quantify the equilibrium phase behavior of superball systems, which should deepen our understanding of the statistical thermodynamics of nonspherical-particle systems., 28 pages, 16 figures

Understanding the transport properties of a porous medium from a knowledge of its microstructure is a problem of great interest in the physical, chemical and biological sciences. Using a first-passage time method, we compute the mean survival time $\tau$ of a Brownian particle among perfectly absorbing traps for a wide class of triply-periodic porous media, including minimal surfaces. We find that the porous medium with an interface that is the Schwartz P minimal surface maximizes the mean survival time among this class. This adds to the growing evidence of the multifunctional optimality of this bicontinuous porous medium. We conjecture that the mean survival time (like the fluid permeability) is maximized for triply periodic porous media with a simply connected pore space at porosity $\phi=1/2$ by the structure that globally optimizes the specific surface. We also compute pore-size statistics of the model microstructures in order to ascertain the validity of a "universal curve" for the mean survival time for these porous media. This represents the first nontrivial statistical characterization of triply periodic minimal surfaces., Comment: 14 pages, 5 figures, 1 table

A rigorous expression is derived that relates exactly the static fluid permeability k for flow through porous media to the electrical formation factor F (inverse of the dimensionless effective conductivity) and an effective length parameter L, i.e., k=L2/8F. This length parameter involves a certain average of the eigenvalues of the Stokes operator and reflects information about electrical and momentum transport. From the exact relation for k, a rigorous upper bound follows in terms of the principal viscous relation time Θ1 (proportional to the inverse of the smallest eigenvalue): k≤νΘ1/F, where ν is the kinematic viscosity. It is also demonstrated that νΘ1≤DT1, where T1 is the diffusion relaxation time for the analogous scalar diffusion problem and D is the diffusion coefficient. Therefore, one also has the alternative bound k≤DT1/F. The latter expression relates the fluid permeability on the one hand to purely diffusional parameters on the other. Finally, using the exact relation for the permeability, a ...

Diffusion and reaction in heterogeneous media plays an important role in a variety of processes arising in the physical and biological sciences. The determination of the relaxation times Tn (n=1,2,...) and the mean survival time τ is considered for diffusion and reaction among partially absorbing traps with dimensionless surface rate constant κ. The limits κ=∞ and κ=0 correspond to the diffusion‐controlled case (i.e., perfect absorbers) and reaction‐controlled case (i.e., perfect reflectors), respectively. Rigorous lower bounds on the principal (or largest) relaxation time T1 and mean survival time τ for arbitrary κ are derived in terms of the pore size distribution P(δ). Here P(δ)dδ is the probability that a randomly chosen point in the pore region lies at a distance δ and δ+dδ from the nearest point on the pore–trap interface. The aforementioned moments and hence the bounds on T1 and τ are evaluated for distributions of interpenetrable spherical traps. The length scales 〈δ〉 and 〈δ2〉1/2, under certai...

It is shown that the trapping of finite‐sized spherical Brownian particles of radius βR in a system of interpenetrable spherical traps of radius R is isomorphic to the trapping of ‘‘point’’ Brownian particles (β=0) in a particular system of interpenetrable spherical traps of radius (1+β)R. This isomorphism in conjunction with previous trapping‐rate data for β=0 is employed to compute the trapping rate for the case β=1/4 in a system of hard spherical traps as a function of trap volume fraction. The effect of increasing the size of the Brownian particles is to increase the trapping rate relative to the instance of point Brownian particles.

The Lagrangian transport of a passive scalar in a class of incompressible, random stationary velocity fields, termed ‘‘random‐vortex’’ models, is studied. These fields generally consist of random distributions of finite‐sized elementary vortices in space with zero mean velocity in the presence of molecular diffusion D. The effects of vortex density, vortex strength, and sign of the vorticity on the Lagrangian history of a fluid particle [i.e., mean‐square displacement σ2(t) and velocity autocorrelation function R(t)] on the specific random‐vortex models which possess identical energy spectra but different higher‐order statistics for a Peclet number of 100 are investigated. This is done by a combination of Monte Carlo simulations of the Langevin equations and analysis. It is found that the Lagrangian autocorrelation R(t) and the mean‐square displacement σ2(t) can be significantly different as the density of the vortices increases and when there are long‐range correlations in the sign of the vorticity. A simple theory based on a model for R(t) agrees strikingly well with the present simulations. It is found that D* increases with vortex density, suggesting that Gaussian fields are maximally dissipative among a wide class of vortex flows with given energy spectra.

A two-dimensional model of a two-phase solid which undergoes a reaction at its surface is used to study the fragmentation of reactive materials in which the marphalagi- CBI hindering of fragment release is considered. Scaling concepts of cluster percolation theory are used to evaluate Monte Carlo data generated from a Simulation of the hindered fragmentation process. By defining a hierarchy of fragmentation objects, different scaling exponents arc computed for each of these objects as measured by the number of sub-objects they contain. In addition, it appears that each of the different measures of object size exhibits optimum scaling at a different critical reactive-phase mas fraction; simulation data indicate that the critical mass fractions follow a trend consistent with expected physical behaviour of the system. In addition, the critical mass fractions reported correspond to 'virtual' criticalities, i.e. the critical points cannot result in actual divergences in size, but rather are properties of the scaling fundion.