DSpace Community: Department of Chemical Engineering

An error-controlled adaptive chemistry method for reacting flow simulations

Sat, 29 Oct 2005 22:58:59 GMT

Title: An error-controlled adaptive chemistry method for reacting flow simulations

Authors: Oluwole, Oluwayemisi

Abstract: Many technologically important processes in the chemical and mechanical industries involve coupled interactions of heat and mass transfer with chemical reactions - e.g. commercial burners, gas turbines, internal combustion engines, etc. However, detailed computational studies of such processes remain difficult at best, particularly due to the large reaction mechanisms that describe the chemical kinetics over the relevant range of reaction conditions. As a result, reduced models that contain fewer reactions and/or species while still capturing the "important" kinetics are often used in place of the full comprehensive reaction model in modeling complex reacting flows. "Adaptive Chemistry" - a method that uses several smaller locally-accurate reduced reaction models rather than a single "catch-all" model - has been shown in the combustion literature to be a viable option for improving computational efficiency in such studies. However, several outstanding challenges have prevented the adoption of this method in mainstream studies, most notably the difficulty of determining the accuracy of a solution obtained using Adaptive Chemistry. The focus of this research was to develop methods to enable efficient and accurate implementation of Adaptive Chemistry for reacting flow simulations.; (cont.) A method was developed for determining how much error may be tolerated in each reduced model in order to achieve a desired accuracy in Adaptive Chemistry solutions at steady-state. A novel model reduction method was also developed to obtain automatically reduced models (based on reaction elimination) that are guaranteed to satisfy the imposed error tolerances at all conditions in a user-specified range. In order to enable point-validated reduced models to be used accurately over ranges, an iterative method was developed for identifying ranges of reaction conditions over which such reduced models are guaranteed to remain valid. An Adaptive Chemistry method that demonstrates the application of these methods is presented. Efficient implementations of construction, storage and retrieval of reduced models that are appropriate for the reaction conditions encountered during Adaptive Chemistry simulations are presented, including an algorithm that adapts the library of reduced models to the solution trajectory "on the fly".; (cont.) The error-controlled Adaptive Chemistry method developed here is the first method that enables rigorous control of the model reduction error in steady-state Adaptive Chemistry solutions, as demonstrated in 1-D and 2-D premixed and partially premixed flame simulations. Results of a collaborative effort to facilitate engine research by developing the necessary cyberinfrastructure to provide remote access to the model reduction tools developed here are also discussed. Finally, methods are described for extending the error control criteria developed and demonstrated for reduced reaction models to reduced-species models and suggestions are made for future research in Adaptive Chemistry.

Description: Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2006.; Includes bibliographical references (p. 251-257).

Integrated characterization of cellular physiology underlying hepatic metabolism

Sat, 29 Oct 2005 22:58:59 GMT

Title: Integrated characterization of cellular physiology underlying hepatic metabolism

Authors: Wong, Matthew Sing

Abstract: The macroscopic metabolic phenotype of a cellular system, such as insulin resistance, is the result of the integration of many hundreds or thousands of preceding cellular events, which culminates in the cell's final response to a perturbation in the environment. The data provided by DNA microarrays and multiple types of metabolic measurements can be integrated to reconstruct the actions taken by a cellular system to arrive at a particular metabolic response to a stimulus, elucidating the underlying physiology. We employed this integrated approach for the characterization of hepatic metabolism. First, we implemented a novel method for functional genomics. The metabolic response of hepatoma cells to the depletion and repletion of glutamine was characterized in time course measurements of metabolic fluxes and metabolite pool sizes. DNA microarrays characterized the expression profiles. The metabolic data were correlated with the microarray data to identify coregulated clusters of genes. This study contributed to our understanding of glutamine metabolism in hepatomas, and advanced the field of functional genomics. Next, we identified the hexosamine biosynthetic pathway (HBP) as a mechanism for hyperglycemia-induced hepatic insulin resistance.; (cont.) Glycogen deposition and glucose production data in mouse hepatocytes confirmed that HBP activity was negatively correlated with insulin sensitivity. Metabolite profiling data confirmed that prolonged incubation in hyperglycemic conditions raised the levels of hexosamine intermediates by saturating upper glycolysis. Our data, along with previous work in muscle and adipose tissue, underline the increasingly important role of the HBP in regulating insulin action and energy homeostasis. A dysfunctional HBP may contribute to the pathophysiology of Type 2 diabetes. Finally, we analyzed the control structure of the glucose production bioreaction network. We systematically perturbed the network and analyzed the effects on the fluxes. We found that gluconeogenesis was the dominant flux, and therefore regulation of gluconeogenesis determined the glucose production phenotype. G6Pase was identified as the enzyme in gluconeogenesis controlling the glucose production phenotype, whereas PEPCK played a secondary role. Our conclusions here give insight into the physiology underlying the regulation and dysregulation of hepatic glucose production with possible application to the treatment of Type 2 diabetes.

Description: Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2006.; Includes bibliographical references (p. 187-207).

Analysis of complex viscoelastic flows using a finite element method

Sat, 29 Oct 2005 22:58:59 GMT

Title: Analysis of complex viscoelastic flows using a finite element method

Authors: Phillips, Scott David, Ph. D. Massachusetts Institute of Technology

Abstract: The field of computational fluid mechanics of viscoelastic flows has been well explored in the three decades since its inception. Still, even with the vast amount of work detailed in the literature, much remains to be done towards the improvement of models of viscoelastic fluids and the improvement of the numerical methods used to solve the set of governing equations. The work contained in this document is concentrated in the latter of these areas. The main goal of this body of work is to develop a robust, efficient simulation package to model three-dimensional viscoelastic flows. In order to accomplish this goal, improvements to the numerical methods and equation formulation were necessary to help reduce the overall size of the equation set used to describe viscoelastic flows in three-dimensional geometries. In order to test their viability for use in reducing the overall size of the problem, concepts involving changing the formulation of the equations and the numerical methods used to find the solution to the equations were first implemented and analyzed in a previously developed two-dimensional finite element simulation package. Implementation and analysis is discussed of a formulation change involving decoupling the calculation of the velocity gradient interpolant equation and the momentum and mass continuity equations in the DEVSS-G formulation.; (cont.) Two different decoupled methods for computing the velocity gradient, one using a global least squares approximation and the other a local patch algorithm, are explored. While both methods reduce to the true velocity gradient with mesh refinement, the patch algorithm is shown to require significantly more mesh refinement than the global least squares approximation to order to attain equivalent refinement of the solution. Comparison of the two methods taking into account the additional refinement requirements of the local patch algorithm makes clear the superiority of the decoupled global least squares approximation for calculation of the velocity gradient interpolant. The versatility and robustness of the decoupled form of the DEVSS-G equations are demonstrated through the addition and modification of the evolution equations describing the stress of the polymer as well as new physical quantities of the flow. A time-dependent, free-surface finite element method is developed in which an evolution equation derived from the kinematic boundary condition is used to describe the height of the free surface as a function of time.; (cont.) This new evolution equation is incorporated into the decoupled formulation by simply adding an additional step to the time integration to evaluate the change in the height of the surface during the current timestep and then updating the element locations in the deformable region of the mesh. Application of the new equation in this manner requires no knowledge of the direct dependence of the system on changes in the new quantity, allowing for quick and easy implementation. Incorporation of more advanced constitutive equations is used as further example of the utility of the decoupled form of the DEVSS-G equations. For most continuum based constitutive equations, the dependence of the equations on the flow variables can be expressed explicitly, allowing for the coupled set of equations to be solved with Newton's method. However, the dependence of the stress on the flow cannot be explicitly written for more advanced constitutive equations such as those derived from kinetic theory or those employing Brownian dynamics, greatly hindering the performance of Newton's method in locating the solution to the system. As an illustrative example, incorporation into the decoupled equation formulation of the closed form of the Adaptive-Length-Scale model (ALS-C) is presented.; (cont.) Simulations are presented capturing for the first time the pressure drop enhancement with increasing viscoelasticity of the model of the flow of a Boger fluid in the 4:1:4 axisymmetric contraction-expansion geometry observed experimentally (Rothstein et al., 2001). Simulations of the flow of a 4-mode FENE-P model fluid within the geometry are also presented. Though its dependence on the flow field can be expressed analytically, the cost of computation using multimode models is typically prohibitive when using fully coupled equation sets as the overall problem size grows considerably with the addition of each new mode. Incorporation of the 4-mode model within the decoupled equation formulation adds relatively little computational cost to the overall calculation. Employing the formulation and numerical methods developed herein, a new three-dimensional finite element package is described for simulating confined viscoelastic flows. To make the package more robust, a number of different boundary conditions are included for modeling different geometries used in polymer processing. To help reduce the burden associated with mesh refinement in three-dimensional meshes, a commercial meshing package utilizing o-grid refinement for localization of refinement is employed.; (cont.) Furthermore, to allow for computation of the large equation sets typically associated with three-dimensional geometries, a parallel implementation of the three-dimensional simulation package is developed based on the two-dimensional parallel method developed by Caola et al. ((Caola et al., 2001), (Caola et al., 2002)). Simulation results demonstrating the accuracy and performance of the method are presented. As a test of the robustness of the three-dimensional method, simulations of the flow of Newtonian and Oldroyd-B fluids through a periodic, linear array of cylinders are presented. Comparisons with previous calculations for the Oldroyd-B flow in an infinitely wide domain with no variations in the direction of the width show the same trend in the drag force on the cylinder with increasing viscoelasticity as well as in the size and shape of the vortices formed in the gap between the cylinders. The study of this flow includes effects of modeling the cross section of the flow as an infinite domain with no variation in the direction of the width, an infinite domain of periodic computational width, an infinite domain of periodic computational width and a symmetric flow above and below the cylinders, and a bounded domain with solid walls located 4 cylinder radii apart.

Description: Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2006.; Includes bibliographical references (v. 2, leaves 259-268).

Genomic analysis of hepatic insulin resistance

Sat, 29 Oct 2005 22:58:59 GMT

Title: Genomic analysis of hepatic insulin resistance

Authors: Raab, R. Michael

Abstract: Type II Diabetes mellitus is a genetically complex disease characterized by insulin resistance in peripheral tissues, which results in simultaneous hyperglycemia and hyperinsulinemia. Because of the prevalence of type II diabetes, many researchers are investigating the genetics of glucose homeostasis, however, traditional mapping techniques have not been successful in determining all of the genes that regulate glycemia. To complement these efforts, we used DNA microarrays to find differentially expressed genes and combinatorial siRNA screening to investigate the effects of hepatic gene transcription during periods of high and low glucose production. This strategy provides a new approach to studying the molecular mechanisms of disease pathogenesis. Our investigations focused on discovering new genes that influence hepatic metabolism and glucose production. Hepatocytes help maintain whole body glycemia by providing glucose and other substrates during non-feeding periods. DNA microarrays containing 17,000 unique gene probes were used to study hepatic gene transcription during normal, insulin resistant, and fasting states in C57/BL/6J mice. We analyzed this data set using a combination of statistical and multivariate techniques to determine 41 different, genes that are differentially expressed and highly discriminatory of the treatment groups.; (cont.) Hepatocytes perform many physiological roles, thus to investigate which genes from the microarray analysis affected hepatic metabolism, we developed combinatorial RNA-interference (RNAi) based gene silencing techniques. Using combinatorial siRNA screening, we silenced genes that were over-expressed within the microarray data set to study loss of function effects on hepatic metabolism, which was quantified by measuring intracellular metabolite concentrations in relevant metabolic pathways. Based upon the metabolite dependent clustering of experimental and control samples using Fisher Discriminant Analysis, four of the silenced genes had a significant effect on key metabolites involved in hepatic glucose output. Of these four genes, three were shown to influence hepatic glucose output in our primary cell model.

Description: Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, February 2006.; Includes bibliographical references (leaves 159-191).