Chris H. Rycroft

VORO++: A three-dimensional Voronoi cell library in C++

6 Customized output 9 6.1 Particle-related entries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 6.2 Vertex-related entries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 6.3 Edge-related entries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 6.4 Face-related entries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 6.5 Volume-related entries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

In silico screening of carbon-capture materials

One of the main bottlenecks to deploying large-scale carbon dioxide capture and storage (CCS) in power plants is the energy required to separate the CO(2) from flue gas. For example, near-term CCS technology applied to coal-fired power plants is projected to reduce the net output of the plant by some 30% and to increase the cost of electricity by 60-80%. Developing capture materials and processes that reduce the parasitic energy imposed by CCS is therefore an important area of research. We have developed a computational approach to rank adsorbents for their performance in CCS. Using this analysis, we have screened hundreds of thousands of zeolite and zeolitic imidazolate framework structures and identified many different structures that have the potential to reduce the parasitic energy of CCS by 30-40% compared with near-term technologies.

Analysis of granular flow in a pebble-bed nuclear reactor

Pebble-bed nuclear reactor technology, which is currently being revived around the world, raises fundamental questions about dense granular flow in silos. A typical reactor core is composed of graphite fuel pebbles, which drain very slowly in a continuous refueling process. Pebble flow is poorly understood and not easily accessible to experiments, and yet it has a major impact on reactor physics. To address this problem, we perform full-scale, discrete-element simulations in realistic geometries, with up to 440,000 frictional, viscoelastic 6-cm-diam spheres draining in a cylindrical vessel of diameter 3.5m and height 10 m with bottom funnels angled at 30 degrees or 60 degrees. We also simulate a bidisperse core with a dynamic central column of smaller graphite moderator pebbles and show that little mixing occurs down to a 1:2 diameter ratio. We analyze the mean velocity, diffusion and mixing, local ordering and porosity (from Voronoi volumes), the residence-time distribution, and the effects of wall friction and discuss implications for reactor design and the basic physics of granular flow.

Rapid disorganization of mechanically interacting systems of mammary acini

Significance Tissue mechanics are important in differentiation and development but also in diseases like breast cancer. Most breast cancers start in mammary acini, which are basic anatomical units of the mammary gland. We found in a model system that mammary acini can coordinate their disorganization toward a malignant phenotype through long-range mechanical interactions. When two or more contractile acini are sufficiently close together, they can interact via collagen lines that form between them due to acinar contractility and the nonlinearity of collagen mechanics. Disorganization of interacting acini is more probable, rapid, and extensive than that of noninteracting acini. The results may help to better understand how extrinsic factors such as tissue architecture and mechanics contribute to tumor initiation and progression. Cells and multicellular structures can mechanically align and concentrate fibers in their ECM environment and can sense and respond to mechanical cues by differentiating, branching, or disorganizing. Here we show that mammary acini with compromised structural integrity can interconnect by forming long collagen lines. These collagen lines then coordinate and accelerate transition to an invasive phenotype. Interacting acini begin to disorganize within 12.5 ± 4.7 h in a spatially coordinated manner, whereas acini that do not interact mechanically with other acini disorganize more slowly (in 21.8 ± 4.1 h) and to a lesser extent (P < 0.0001). When the directed mechanical connections between acini were cut with a laser, the acini reverted to a slowly disorganizing phenotype. When acini were fully mechanically isolated from other acini and also from the bulk gel by box-cuts with a side length <900 μm, transition to an invasive phenotype was blocked in 20 of 20 experiments, regardless of waiting time. Thus, pairs or groups of mammary acini can interact mechanically over long distances through the collagen matrix, and these directed mechanical interactions facilitate transition to an invasive phenotype.

A mathematical model of fluid and gas flow in nanoporous media

The mathematical modeling of the flow in nanoporous rocks (e.g., shales) becomes an important new branch of subterranean fluid mechanics. The classic approach that was successfully used in the construction of the technology to develop oil and gas deposits in the United States, Canada, and the Union of Soviet Socialist Republics becomes insufficient for deposits in shales. In the present article a mathematical model of the flow in nanoporous rocks is proposed. The model assumes the rock consists of two components: (i) a matrix, which is more or less an ordinary porous or fissurized-porous medium, and (ii) specific organic inclusions composed of kerogen. These inclusions may have substantial porosity but, due to the nanoscale of pores, tubes, and channels, have extremely low permeability on the order of a nanodarcy () or less. These inclusions contain the majority of fluid: oil and gas. Our model is based on the hypothesis that the permeability of the inclusions substantially depends on the pressure gradient. At the beginning of the development of the deposit, boundary layers are formed at the boundaries of the low-permeable inclusions, where the permeability is strongly increased and intensive flow from inclusions to the matrix occurs. The resulting formulae for the production rate of the deposit are presented in explicit form. The formulae demonstrate that the production rate of deposits decays with time following a power law whose exponent lies between and . Processing of experimental data obtained from various oil and gas deposits in shales demonstrated an instructive agreement with the prediction of the model.

Fracture toughness of metallic glasses: annealing-induced embrittlement.

Quantitative understanding of the fracture toughness of metallic glasses, including the associated ductile-to-brittle (embrittlement) transitions, is not yet available. Here, we use a simple model of plastic deformation in glasses, coupled to an advanced Eulerian level set formulation for solving complex free-boundary problems, to calculate the fracture toughness of metallic glasses as a function of the degree of structural relaxation corresponding to different annealing times near the glass temperature. Our main result indicates the existence of an elastoplastic crack tip instability for sufficiently relaxed glasses, resulting in a marked drop in the toughness, which we interpret as annealing-induced embrittlement transition similar to experimental observations.

Characterization and comparison of pore landscapes in crystalline porous materials.

Crystalline porous materials have many applications, including catalysis and separations. Identifying suitable materials for a given application can be achieved by screening material databases. Such a screening requires automated high-throughput analysis tools that characterize and represent pore landscapes with descriptors, which can be compared using similarity measures in order to select, group and classify materials. Here, we discuss algorithms for the calculation of two types of pore landscape descriptors: pore size distributions and stochastic rays. These descriptors provide histogram representations that encode the geometrical properties of pore landscapes. Their calculation involves the Voronoi decomposition as a technique to map and characterize accessible void space inside porous materials. Moreover, we demonstrate pore landscape comparisons for materials from the International Zeolite Association (IZA) database of zeolite frameworks, and illustrate how the choice of pore descriptor and similarity measure affects the perspective of material similarity exhibiting a particular emphasis and sensitivity to certain aspects of structures.

High accuracy geometric analysis of crystalline porous materials

A number of algorithms to analyze crystalline porous materials and their porosities employ the Voronoi tessellation, whereby the space in the material is divided into irregular polyhedral cells that can be analyzed to determine the pore topology and structure. However, the Voronoi tessellation is only appropriate when atoms all have equal radii, and the natural generalization to structures with unequal radii leads to cells with curved boundaries, which are computationally expensive to compute. Therefore, high-throughput structure analysis codes utilize the radical Voronoi tessellation, which approximates the curved cells by polyhedra. In this study, we investigate the errors arising from this approximation reflected in the predicted values of two important porosity descriptors, the largest included and free sphere diameters. The maximum observed errors amount to ca. 0.6 A for a test set comprised of zeolite and metal–organic framework materials. Following the work of Phillips et al. (Soft Matter, 2010, 6, 1693–1703), we describe a strategy to systematically decrease observed errors, and demonstrate that high accuracy (errors below 0.1 A) can be obtained within the same algorithmic framework and at the expense of only an order of magnitude increase in computational cost.

Coarse graining atomistic simulations of plastically deforming amorphous solids

The primary mode of failure in disordered solids results from the formation and persistence of highly localized regions of large plastic strains known as shear bands. Continuum-level field theories capable of predicting this mechanical response rely upon an accurate representation of the initial and evolving states of the amorphous structure. We perform molecular dynamics simulations of a metallic glass and propose a methodology for coarse graining discrete, atomistic quantities, such as the potential energies of the elemental constituents. A strain criterion is established and used to distinguish the coarse-grained degrees-of-freedom inside the emerging shear band from those of the surrounding material. A signal-to-noise ratio provides a means of evaluating the strength of the signal of the shear band as a function of the coarse graining. Finally, we investigate the effect of different coarse graining length scales by comparing a two-dimensional, numerical implementation of the effective-temperature description in the shear transformation zone (STZ) theory with direct molecular dynamics simulations. These comparisons indicate the coarse graining length scale has a lower bound, above which there is a high level of agreement between the atomistics and the STZ theory, and below which the concept of effective temperature breaks down.

Multicellular Architecture of Malignant Breast Epithelia Influences Mechanics

Cell–matrix and cell–cell mechanosensing are important in many cellular processes, particularly for epithelial cells. A crucial question, which remains unexplored, is how the mechanical microenvironment is altered as a result of changes to multicellular tissue structure during cancer progression. In this study, we investigated the influence of the multicellular tissue architecture on mechanical properties of the epithelial component of the mammary acinus. Using creep compression tests on multicellular breast epithelial structures, we found that pre-malignant acini with no lumen (MCF10AT) were significantly stiffer than normal hollow acini (MCF10A) by 60%. This difference depended on structural changes in the pre-malignant acini, as neither single cells nor normal multicellular acini tested before lumen formation exhibited these differences. To understand these differences, we simulated the deformation of the acini with different multicellular architectures and calculated their mechanical properties; our results suggest that lumen filling alone can explain the experimentally observed stiffness increase. We also simulated a single contracting cell in different multicellular architectures and found that lumen filling led to a 20% increase in the “perceived stiffness” of a single contracting cell independent of any changes to matrix mechanics. Our results suggest that lumen filling in carcinogenesis alters the mechanical microenvironment in multicellular epithelial structures, a phenotype that may cause downstream disruptions to mechanosensing.