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Register a new userAnalysis of the spatial and dynamical properties of a multiscale model of intestinal crypts
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Publication date
2013
fields
Informatics Engineering
and research's language is
English
Authors
Giulio Caravagna
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The preliminary analyses on a multiscale model of intestinal crypt dynamics are here presented. The model combines a morphological model, based on the Cellular Potts Model (CPM), and a gene regulatory network model, based on Noisy Random Boolean Networks (NRBNs). Simulations suggest that the stochastic differentiation process is itself sufficient to ensure the general homeostasis in the asymptotic states, as proven by several measures.
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Multiscale models of materials, consisting of upscaling discrete simulations to continuum models, are unique in their capability to simulate complex materials behavior. The fundamental limitation in multiscale models is the presence of uncertainty in the computational predictions delivered by them. In this work, a sequential multiscale model has been developed, incorporating discrete dislocation dynamics (DDD) simulations and a strain gradient plasticity (SGP) model to predict the size effect in plastic deformations of metallic micro-pillars. The DDD simulations include uniaxial compression of micro-pillars with different sizes and over a wide range of initial dislocation densities and spatial distributions of dislocations. An SGP model is employed at the continuum level that accounts for the size-dependency of flow stress and hardening rate. Sequences of uncertainty analyses have been performed to assess the predictive capability of the multiscale model. The variance-based global sensitivity analysis determines the effect of parameter uncertainty on the SGP model prediction. The multiscale model is then constructed by calibrating the continuum model using the data furnished by the DDD simulations. A Bayesian calibration method is implemented to quantify the uncertainty due to microstructural randomness in discrete dislocation simulations (density and spatial distributions of dislocations) on the macroscopic continuum model prediction (size effect in plastic deformation). The outcomes of this study indicate that the discrete-continuum multiscale model can accurately simulate the plastic deformation of micro-pillars, despite the significant uncertainty in the DDD results. Additionally, depending on the macroscopic features represented by the DDD simulations, the SGP model can reliably predict the size effect in plasticity responses of the micropillars with below 10% of error
In this chapter, we discuss applications of topological data analysis (TDA) to spatial systems. We briefly review the recently proposed level-set construction of filtered simplicial complexes, and we then examine persistent homology in two cases studies: street networks in Shanghai and hotspots of COVID-19 infections. We then summarize our results and provide an outlook on TDA in spatial systems.
We develop the pruned continuous Haar transform and the fast continuous Fourier series, two fast and efficient algorithms for rectilinear polygons. Rectilinear polygons are used in VLSI processes to describe design and mask layouts of integrated circuits. The Fourier representation is at the heart of many of these processes and the Haar transform is expected to play a major role in techniques envisioned to speed up VLSI design. To ensure correct printing of the constantly shrinking transistors and simultaneously handle their increasingly large number, ever more computationally intensive techniques are needed. Therefore, efficient algorithms for the Haar and Fourier transforms are vital. We derive the complexity of both algorithms and compare it to that of discrete transforms traditionally used in VLSI. We find a significant reduction in complexity when the number of vertices of the polygons is small, as is the case in VLSI layouts. This analysis is completed by an implementation and a benchmark of the continuous algorithms and their discrete counterpart. We show that on tested VLSI layouts the pruned continuous Haar transform is 5 to 25 times faster, while the fast continuous Fourier series is 1.5 to 3 times faster.
A general-purpose computational homogenization framework is proposed for the nonlinear dynamic analysis of membranes exhibiting complex microscale and/or mesoscale heterogeneity characterized by in-plane periodicity that cannot be effectively treated by a conventional method, such as woven fabrics. The framework is a generalization of the finite element squared (or FE2) method in which a localized portion of the periodic subscale structure is modeled using finite elements. The numerical solution of displacement driven problems involving this model can be adapted to the context of membranes by a variant of the Klinkel-Govindjee method[1] originally proposed for using finite strain, three-dimensional material models in beam and shell elements. This approach relies on numerical enforcement of the plane stress constraint and is enabled by the principle of frame invariance. Computational tractability is achieved by introducing a regression-based surrogate model informed by a physics-inspired training regimen in which FE$^2$ is utilized to simulate a variety of numerical experiments including uniaxial, biaxial and shear straining of a material coupon. Several alternative surrogate models are evaluated including an artificial neural network. The framework is demonstrated and validated for a realistic Mars landing application involving supersonic inflation of a parachute canopy made of woven fabric.
Systematic enumeration and identification of unique 3D spatial topologies of complex engineering systems such as automotive cooling layouts, hybrid-electric power trains, and aero-engines are essential to search their exhaustive design spaces to identify spatial topologies that can satisfy challenging system requirements. However, efficient navigation through discrete 3D spatial topology options is a very challenging problem due to its combinatorial nature and can quickly exceed human cognitive abilities at even moderate complexity levels. Here we present a new, efficient, and generic design framework that utilizes mathematical spatial graph theory to represent, enumerate, and identify distinctive 3D topological classes for an abstract engineering system, given its system architecture (SA) -- its components and interconnections. Spatial graph diagrams (SGDs) are generated for a given SA from zero to a specified maximum crossing number. Corresponding Yamada polynomials for all the planar SGDs are then generated. SGDs are categorized into topological classes, each of which shares a unique Yamada polynomial. Finally, for each topological class, one 3D geometric model is generated for an SGD with the fewest interconnect crossings. Several case studies are shown to illustrate the different features of our proposed framework. Design guidelines are also provided for practicing engineers to aid the utilization of this framework for application to different types of real-world problems.
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