Dynamic reconstruction of heterogeneous materials and microstructure evolution

Computational design of anisotropic stealthy hyperuniform composites with engineered directional scattering properties

Disordered hyperuniform materials are an emerging class of exotic amorphous states of matter that endow them with singular physical properties, including large isotropic photonic band gaps, superior resistance to fracture, and nearly optimal electrical and thermal transport properties, to name but a few. Here we generalize the Fourier-space-based numerical construction procedure for designing and generating digital realizations of isotropic disordered hyperuniform two-phase heterogeneous materials (i.e., composites) developed by Chen and Torquato [Acta Mater. 142, 152 (2018)1359-645410.1016/j.actamat.2017.09.053] to anisotropic microstructures with targeted spectral densities. Our generalized construction procedure explicitly incorporates the vector-dependent spectral density function χ[over ̃]_{_{V}}(k) of arbitrary form that is realizable. We demonstrate the utility of the procedure by generating a wide spectrum of anisotropic stealthy hyperuniform microstructures with χ[over ̃]_{_{V}}(k)=0 for k∈Ω, i.e., complete suppression of scattering in an "exclusion" region Ω around the origin in Fourier space. We show how different exclusion-region shapes with various discrete symmetries, including circular-disk, elliptical-disk, square, rectangular, butterfly-shaped, and lemniscate-shaped regions of varying size, affect the resulting statistically anisotropic microstructures as a function of the phase volume fraction. The latter two cases of Ω lead to directionally hyperuniform composites, which are stealthy hyperuniform only along certain directions and are nonhyperuniform along others. We find that while the circular-disk exclusion regions give rise to isotropic hyperuniform composite microstructures, the directional hyperuniform behaviors imposed by the shape asymmetry (or anisotropy) of certain exclusion regions give rise to distinct anisotropic structures and degree of uniformity in the distribution of the phases on intermediate and large length scales along different directions. Moreover, while the anisotropic exclusion regions impose strong constraints on the global symmetry of the resulting media, they can still possess structures at a local level that are nearly isotropic. Both the isotropic and anisotropic hyperuniform microstructures associated with the elliptical-disk, square, and rectangular Ω possess phase-inversion symmetry over certain range of volume fractions and a percolation threshold ϕ_{c}≈0.5. On the other hand, the directionally hyperuniform microstructures associated with the butterfly-shaped and lemniscate-shaped Ω do not possess phase-inversion symmetry and percolate along certain directions at much lower volume fractions. We also apply our general procedure to construct stealthy nonhyperuniform systems. Our construction algorithm enables one to control the statistical anisotropy of composite microstructures via the shape, size, and symmetries of Ω, which is crucial to engineering directional optical, transport, and mechanical properties of two-phase composite media.

Robust surface-correlation-function evaluation from experimental discrete digital images

Correlation functions (CFs) are universal structural descriptors; surface-surface F_{ss} and surface-void F_{sv} CFs are a subset containing additional information about the interface between the phases. The description of the interface between pores and solids in porous media is of particular importance and recently Ma and Torquato [Phys. Rev. E 98, 013307 (2018)2470-004510.1103/PhysRevE.98.013307] proposed an elegant way to compute these functions for a wide variety of cases. However, their "continuous" approach is not always applicable to digital experimental 2D and 3D images of porous media as obtained using x-ray tomography or scanning electron microscopy due to nonsingularities in chemical composition or local solid material's density and partial volume effects. In this paper we propose to use edge-detecting filters to compute surface CFs in the "digital" fashion directly in the images. Computed this way, surface correlation functions are the same as analytically known for Poisson disks in case the resolution of the image is adequate. Based on the multiscale image analysis we developed a C_{0.5} criterion that can predict if the imaging resolution is enough to make an accurate evaluation of the surface CFs. We also showed that in cases when the input image contains all major features, but do not pass the C_{0.5} criterion, it is possible with the help of image magnification to sample CFs almost similar to those obtained for high-resolution image of the same structure with high C_{0.5}. The computational framework as developed here is open source and available within the CorrelationFunctions.jl package developed by our group. Our "digital" approach was applied to a wide variety of real porous media images of different quality. We discuss critical aspects of surface correlation functions computations as related to different applications. The developed methodology allows applying surface CFs to describe the structure of porous materials based on their experimental images and enhance stochastic reconstructions or super-resolution procedures, or serve as an efficient metrics in machine learning applications due to computationally effective GPU implementation.

Quantifying microstructural evolution via time-dependent reduced-dimension metrics based on hierarchical n-point polytope functions

We devise reduced-dimension metrics for effectively measuring the distance between two points (i.e., microstructures) in the microstructure space and quantifying the pathway associated with microstructural evolution, based on a recently introduced set of hierarchical n-point polytope functions P_{n}. The P_{n} functions provide the probability of finding particular n-point configurations associated with regular n polytopes in the material system, and are a special subset of the standard n-point correlation functions S_{n} that effectively decompose the structural features in the system into regular polyhedral basis with different symmetries. The nth order metric Ω_{n} is defined as the L_{1} norm associated with the P_{n} functions of two distinct microstructures. By choosing a reference initial state (i.e., a microstructure associated with t_{0}=0), the Ω_{n}(t) metrics quantify the evolution of distinct polyhedral symmetries and can in principle capture emerging polyhedral symmetries that are not apparent in the initial state. To demonstrate their utility, we apply the Ω_{n} metrics to a two-dimensional binary system undergoing spinodal decomposition to extract the phase separation dynamics via the temporal scaling behavior of the corresponding Ω_{n}(t), which reveals mechanisms governing the evolution. Moreover, we employ Ω_{n}(t) to analyze pattern evolution during vapor deposition of phase-separating alloy films with different surface contact angles, which exhibit rich evolution dynamics including both unstable and oscillating patterns. The Ω_{n} metrics have potential applications in establishing quantitative processing-structure-property relationships, as well as real-time processing control and optimization of complex heterogeneous material systems.

Three-dimensional reconstruction of porous media using super-dimension-based adjacent block-matching algorithm

As porous media play an essential role in a variety of industrial applications, it is essential to understand their physical properties. Nowadays, the super-dimensional (SD) reconstruction algorithm is used to stochastically reconstruct a three-dimensional (3D) structure of porous media from a given two-dimensional image. This algorithm exhibits superiority in accuracy compared with classical algorithms because it learns information from the real 3D structure. However, owing to the short development time of the SD algorithm, it also has some limitations, such as inexact porosity characterization, long run time, blocking artifacts, and suboptimal accuracy that may be improved. To mitigate these limitations, this study presents the design of a special template that contains two parts of data (i.e., adjacent blocks and a central block); the proposed method matches adjacent blocks during reconstruction and assigns the matched central block to the area to be reconstructed. Furthermore, we design two important mechanisms during reconstruction: one for block matching and the other for porosity control. To verify the effectiveness of the proposed method compared with an existing SD method, both methods were tested on silica particle material and three homogeneous sandstones with different porosities; meanwhile, we compared the proposed method with a multipoint statistics method and a simulated annealing method. The reconstructed results were then compared with the target both visually and quantitatively. The experimental results indicate that the proposed method can overcome the aforementioned limitations and further improve the accuracy of existing methods. This method achieved 4-6 speedup factor compared with the traditional SD method.

Adaptive phase-retrieval stochastic reconstruction with correlation functions: Three-dimensional images from two-dimensional cuts

Precise characterization of three-dimensional (3D) heterogeneous media is indispensable in finding the relationships between structure and macroscopic physical properties (permeability, conductivity, and others). The most widely used experimental methods (electronic and optical microscopy) provide high-resolution bidimensional images of the samples of interest. However, 3D material inner microstructure registration is needed to apply numerous modeling tools. Numerous research areas search for cheap and robust methods to obtain the full 3D information about the structure of the studied sample from its 2D cuts. In this work, we develop an adaptive phase-retrieval stochastic reconstruction algorithm that can create 3D replicas from 2D original images, APR. The APR is free of artifacts characteristic of previously proposed phase-retrieval techniques. While based on a two-point S_{2} correlation function, any correlation function or other morphological metrics can be accounted for during the reconstruction, thus, paving the way to the hybridization of different reconstruction techniques. In this work, we use two-point probability and surface-surface functions for optimization. To test APR, we performed reconstructions for three binary porous media samples of different genesis: sandstone, carbonate, and ceramic. Based on computed permeability and connectivity (C_{2} and L_{2} correlation functions), we have shown that the proposed technique in terms of accuracy is comparable to the classic simulated annealing-based reconstruction method but is computationally very effective. Our findings open the possibility of utilizing APR to produce fast or crude replicas further polished by other reconstruction techniques such as simulated annealing or process-based methods. Improving the quality of reconstructions based on phase retrieval by adding additional metrics into the reconstruction procedure is possible for future work.

Generation and structural characterization of Debye random media

In their seminal paper on scattering by an inhomogeneous solid, Debye and coworkers proposed a simple exponentially decaying function for the two-point correlation function of an idealized class of two-phase random media. Such Debye random media, which have been shown to be realizable, are singularly distinct from all other models of two-phase media in that they are entirely defined by their one- and two-point correlation functions. To our knowledge, there has been no determination of other microstructural descriptors of Debye random media. In this paper, we generate Debye random media in two dimensions using an accelerated Yeong-Torquato construction algorithm. We then ascertain microstructural descriptors of the constructed media, including their surface correlation functions, pore-size distributions, lineal-path function, and chord-length probability density function. Accurate semianalytic and empirical formulas for these descriptors are devised. We compare our results for Debye random media to those of other popular models (overlapping disks and equilibrium hard disks) and find that the former model possesses a wider spectrum of hole sizes, including a substantial fraction of large holes. Our algorithm can be applied to generate other models defined by their two-point correlation functions, and their other microstructural descriptors can be determined and analyzed by the procedures laid out here.

Probing information content of hierarchical n-point polytope functions for quantifying and reconstructing disordered systems

Disordered systems are ubiquitous in physical, biological, and material sciences. Examples include liquid and glassy states of condensed matter, colloids, granular materials, porous media, composites, alloys, packings of cells in avian retina, and tumor spheroids, to name but a few. A comprehensive understanding of such disordered systems requires, as the first step, systematic quantification, modeling, and representation of the underlying complex configurations and microstructure, which is generally very challenging to achieve. Recently, we introduced a set of hierarchical statistical microstructural descriptors, i.e., the "n-point polytope functions" P_{n}, which are derived from the standard n-point correlation functions S_{n}, and successively included higher-order n-point statistics of the morphological features of interest in a concise, explainable, and expressive manner. Here we investigate the information content of the P_{n} functions via optimization-based realization rendering. This is achieved by successively incorporating higher-order P_{n} functions up to n=8 and quantitatively assessing the accuracy of the reconstructed systems via unconstrained statistical morphological descriptors (e.g., the lineal-path function). We examine a wide spectrum of representative random systems with distinct geometrical and topological features. We find that, generally, successively incorporating higher-order P_{n} functions and, thus, the higher-order morphological information encoded in these descriptors leads to superior accuracy of the reconstructions. However, incorporating more P_{n} functions into the reconstruction also significantly increases the complexity and roughness of the associated energy landscape for the underlying stochastic optimization, making it difficult to convergence numerically.

Quantifying accuracy of stochastic methods of reconstructing complex materials by deep learning

Time and cost are two main hurdles to acquiring a large number of digital image I of the microstructure of materials. Thus, use of stochastic methods for producing plausible realizations of materials' morphology based on one or very few images has become an increasingly common practice in their modeling. The accuracy of the realizations is often evaluated using two-point microstructural descriptors or physics-based modeling of certain phenomena in the materials, such as transport processes or fluid flow. In many cases, however, two-point correlation functions do not provide accurate evaluation of the realizations, as they are usually unable to distinguish between high- and low-quality reconstructed models. Calculating flow and transport properties of the realization is an accurate way of checking the quality of the realizations, but it is computationally expensive. In this paper a method based on machine learning is proposed for evaluating stochastic approaches for reconstruction of materials, which is applicable to any of such methods. The method reduces the dimensionality of the realizations using an unsupervised deep-learning algorithm by compressing images and realizations of materials. Two criteria for evaluating the accuracy of a reconstruction algorithm are then introduced. One, referred to as the internal uncertainty space, is based on the recognition that for a reconstruction method to be effective, the differences between the realizations that it produces must be reasonably wide, so that they faithfully represent all the possible spatial variations in the materials' microstructure. The second criterion recognizes that the realizations must be close to the original I and, thus, it quantifies the similarity based on an external uncertainty space. Finally, the ratio of two uncertainty indices associated with the two criteria is considered as the final score of the accuracy of a stochastic algorithm, which provides a quantitative basis for comparing various realizations and the approaches that produce them. The proposed method is tested with images of three types of heterogeneous materials in order to evaluate four stochastic reconstruction algorithms.

Reconstruction of porous media from extremely limited information using conditional generative adversarial networks

Porous media are ubiquitous in both nature and engineering applications. Therefore, their modeling and understanding is of vital importance. In contrast to direct acquisition of three-dimensional (3D) images of this type of medium, obtaining its subregion (s) such as 2D images or several small areas can be feasible. Therefore, reconstructing whole images from limited information is a primary technique in these types of cases. Given data in practice cannot generally be determined by users and may be incomplete or only partially informed, thus making existing reconstruction methods inaccurate or even ineffective. To overcome this shortcoming, in this study we propose a deep-learning-based framework for reconstructing full images from their much smaller subareas. In particular, conditional generative adversarial network is utilized to learn the mapping between the input (a partial image) and output (a full image). To ensure the reconstruction accuracy, two simple but effective objective functions are proposed and then coupled with the other two functions to jointly constrain the training procedure. Because of the inherent essence of this ill-posed problem, a Gaussian noise is introduced for producing reconstruction diversity, thus enabling the network to provide multiple candidate outputs. Our method is extensively tested on a variety of porous materials and validated by both visual inspection and quantitative comparison. It is shown to be accurate, stable, and even fast (∼0.08 s for a 128×128 image reconstruction). The proposed approach can be readily extended by, for example, incorporating user-defined conditional data and an arbitrary number of object functions into reconstruction, while being coupled with other reconstruction methods.

Hierarchical Optimization: Fast and Robust Multiscale Stochastic Reconstructions with Rescaled Correlation Functions

Stochastic reconstructions based on universal correlation functions allow obtaining spatial structures based on limited input data or to fuse multiscale images from different sources. Current application of such techniques is severely hampered by the computational cost of the annealing optimization procedure. In this study we propose a novel hierarchical annealing method based on rescaled correlation functions, which improves both accuracy and computational efficiency of reconstructions while not suffering from disadvantages of existing speeding-up techniques. A significant order of magnitude gains in computational efficiency now allows us to add more correlation functions into consideration and, thus, to further improve the accuracy of the method. In addition, the method provides a robust multiscale framework to solve the universal upscaling or downscaling problem. The novel algorithm is extensively tested on binary (two-phase) microstructures of different genesis. In spite of significant improvements already in place, the current implementation of the hierarchical annealing method leaves significant room for additional accuracy and computational performance tweaks. As described here, (multiscale) stochastic reconstructions will find numerous applications in material and Earth sciences. Moreover, the proposed hierarchical approach can be readily applied to a wide spectrum of constrained optimization problems.

Realizations of highly heterogeneous collagen networks via stochastic reconstruction for micromechanical analysis of tumor cell invasion

Three-dimensional (3D) collective cell migration in a collagen-based extracellular matrix (ECM) is among one of the most significant topics in developmental biology, cancer progression, tissue regeneration, and immune response. Recent studies have suggested that collagen-fiber mediated force transmission in cellularized ECM plays an important role in stress homeostasis and regulation of collective cellular behaviors. Motivated by the recent in vitro observation that oriented collagen can significantly enhance the penetration of migrating breast cancer cells into dense Matrigel which mimics the intravasation process in vivo [Han et al. Proc. Natl. Acad. Sci. USA 113, 11208 (2016)PNASA60027-842410.1073/pnas.1610347113], we devise a procedure for generating realizations of highly heterogeneous 3D collagen networks with prescribed microstructural statistics via stochastic optimization. Specifically, a collagen network is represented via the graph (node-bond) model and the microstructural statistics considered include the cross-link (node) density, valence distribution, fiber (bond) length distribution, as well as fiber orientation distribution. An optimization problem is formulated in which the objective function is defined as the squared difference between a set of target microstructural statistics and the corresponding statistics for the simulated network. Simulated annealing is employed to solve the optimization problem by evolving an initial network via random perturbations to generate realizations of homogeneous networks with randomly oriented fibers, homogeneous networks with aligned fibers, heterogeneous networks with a continuous variation of fiber orientation along a prescribed direction, as well as a binary system containing a collagen region with aligned fibers and a dense Matrigel region with randomly oriented fibers. The generation and propagation of active forces in the simulated networks due to polarized contraction of an embedded ellipsoidal cell and a small group of cells are analyzed by considering a nonlinear fiber model incorporating strain hardening upon large stretching and buckling upon compression. Our analysis shows that oriented fibers can significantly enhance long-range force transmission in the network. Moreover, in the oriented-collagen-Matrigel system, the forces generated by a polarized cell in collagen can penetrate deeply into the Matrigel region. The stressed Matrigel fibers could provide contact guidance for the migrating cell cells, and thus enhance their penetration into Matrigel. This suggests a possible mechanism for the observed enhanced intravasation by oriented collagen.

Markov prior-based block-matching algorithm for superdimension reconstruction of porous media

A superdimension reconstruction algorithm is used for the reconstruction of three-dimensional (3D) structures of a porous medium based on a single two-dimensional image. The algorithm borrows the concepts of "blocks," "learning," and "dictionary" from learning-based superresolution reconstruction and applies them to the 3D reconstruction of a porous medium. In the neighborhood-matching process of the conventional superdimension reconstruction algorithm, the Euclidean distance is used as a criterion, although it may not really reflect the structural correlation between adjacent blocks in an actual situation. Hence, in this study, regular items are adopted as prior knowledge in the reconstruction process, and a Markov prior-based block-matching algorithm for superdimension reconstruction is developed for more accurate reconstruction. The algorithm simultaneously takes into consideration the probabilistic relationship between the already reconstructed blocks in three different perpendicular directions (x, y, and z) and the block to be reconstructed, and the maximum value of the probability product of the blocks to be reconstructed (as found in the dictionary for the three directions) is adopted as the basis for the final block selection. Using this approach, the problem of an imprecise spatial structure caused by a point simulation can be overcome. The problem of artifacts in the reconstructed structure is also addressed through the addition of hard data and by neighborhood matching. To verify the improved reconstruction accuracy of the proposed method, the statistical and morphological features of the results from the proposed method and traditional superdimension reconstruction method are compared with those of the target system. The proposed superdimension reconstruction algorithm is confirmed to enable a more accurate reconstruction of the target system while also eliminating artifacts.

Reconstruction of a digital core containing clay minerals based on a clustering algorithm

It is difficult to obtain a core sample and information for digital core reconstruction of mature sandstone reservoirs around the world, especially for an unconsolidated sandstone reservoir. Meanwhile, reconstruction and division of clay minerals play a vital role in the reconstruction of the digital cores, although the two-dimensional data-based reconstruction methods are specifically applicable as the microstructure reservoir simulation methods for the sandstone reservoir. However, reconstruction of clay minerals is still challenging from a research viewpoint for the better reconstruction of various clay minerals in the digital cores. In the present work, the content of clay minerals was considered on the basis of two-dimensional information about the reservoir. After application of the hybrid method, and compared with the model reconstructed by the process-based method, the digital core containing clay clusters without the labels of the clusters' number, size, and texture were the output. The statistics and geometry of the reconstruction model were similar to the reference model. In addition, the Hoshen-Kopelman algorithm was used to label various connected unclassified clay clusters in the initial model and then the number and size of clay clusters were recorded. At the same time, the K-means clustering algorithm was applied to divide the labeled, large connecting clusters into smaller clusters on the basis of difference in the clusters' characteristics. According to the clay minerals' characteristics, such as types, textures, and distributions, the digital core containing clay minerals was reconstructed by means of the clustering algorithm and the clay clusters' structure judgment. The distributions and textures of the clay minerals of the digital core were reasonable. The clustering algorithm improved the digital core reconstruction and provided an alternative method for the simulation of different clay minerals in the digital cores.

Microstructure and mechanical properties of hyperuniform heterogeneous materials

A hyperuniform random heterogeneous material is one in which the local volume fraction fluctuations in an observation window decay faster than the reciprocal window volume as the window size increases. Recent studies show that this class of materials are endowed with superior physical properties such as large isotropic photonic band gaps and optimal transport properties. Here we employ a stochastic optimization procedure to systematically generate realizations of hyperuniform heterogeneous materials with controllable short-range order, which is partially quantified using the two-point correlation function S_{2}(r) associated with the phase of interest. Specifically, our procedure generalizes the widely used Yeong-Torquato reconstruction procedure by including an additional constraint for hyperuniformity, i.e., the volume integral of the autocovariance function χ(r)=S_{2}(r)-ϕ^{2} over the whole space is zero. In addition, we only require the reconstructed S_{2} to match the target function up to a certain cutoff distance γ, in order to give the system sufficient degrees of freedom to satisfy the hyperuniform condition. By systematically increasing the γ value for a given S_{2}, one can produce a spectrum of hyperuniform heterogeneous materials with varying degrees of partial short-range order compatible with the specified S_{2}. The mechanical performance including both elastic and brittle fracture behaviors of the generated hyperuniform materials is analyzed using a volume-compensated lattice-particle method. For the purpose of comparison, the corresponding nonhyperuniform materials with the same short-range order (i.e., with S_{2} constrained up to the same γ value) are also constructed and their mechanical performance is analyzed. Here we consider two specific S_{2} including the positive exponential decay function and the correlation function associated with an equilibrium hard-sphere system. For the constructed systems associated with these two specific functions, we find that although the hyperuniform materials are softer than their nonhyperuniform counterparts, the former generally possess a significantly higher brittle fracture strength than the latter. This superior mechanical behavior is attributed to the lower degree of stress concentration in the material resulting from the hyperuniform microstructure, which is crucial to crack initiation and propagation.

Heterogeneous force network in 3D cellularized collagen networks

Collagen networks play an important role in coordinating and regulating collective cellular dynamics via a number of signaling pathways. Here, we investigate the transmission of forces generated by contractile cells in 3D collagen-I networks. Specifically, the graph (bond-node) representations of collagen networks with collagen concentrations of 1, 2 and 4 mg ml^-1 are derived from confocal microscopy data and used to model the network microstructure. Cell contraction is modeled by applying correlated displacements at specific nodes of the network, representing the focal adhesion sites. A nonlinear elastic model is employed to characterize the mechanical behavior of individual fiber bundles including strain hardening during stretching and buckling under compression. A force-based relaxation method is employed to obtain equilibrium network configurations under cell contraction. We find that for all collagen concentrations, the majority of the forces are carried by a small number of heterogeneous force chains emitted from the contracting cells, which is qualitatively consistent with our experimental observations. The force chains consist of fiber segments that either possess a high degree of alignment before cell contraction or are aligned due to fiber reorientation induced by cell contraction. The decay of the forces along the force chains is significantly slower than the decay of radially averaged forces in the system, suggesting that the fibreous nature of biopolymer network structure can support long-range force transmission. The force chains emerge even at very small cell contractions, and the number of force chains increases with increasing cell contraction. At large cell contractions, the fibers close to the cell surface are in the nonlinear regime, and the nonlinear region is localized in a small neighborhood of the cell. In addition, the number of force chains increases with increasing collagen concentration, due to the larger number of focal adhesion sites in collagen networks with high concentrations.