Parallel linear equation solvers for finite element computations

The overall objective of this research is to develop efficient methods for the solution of linear and nonlinear systems of equations on parallel and supercomputers, and to apply these methods to the solution of problems in structural analysis. Attention has been given so far only to linear equations. The methods considered for the solution of the stiffness equation Kx=f have been Choleski factorization and the conjugate gradient iteration with SSOR and Incomplete Choleski preconditioning. More detail on these methods will be given on subsequent slides. These methods have been used to solve for the static displacements for the mast and panel focus problems in conjunction with the CSM testbed system based on NICE/SPAR

Self-adaptive combination of global tabu search and local search for nonlinear equations

Solving systems of nonlinear equations is a very important task since the problems emerge mostly through the mathematical modeling of real problems that arise naturally in many branches of engineering and in the physical sciences. The problem can be naturally reformulated as a global optimization problem. In this paper, we show that a self-adaptive combination of a metaheuristic with a classical local search method is able to converge to some difficult problems that are not solved by Newton-type methodsFundação para a Ciência e a Tecnologia (FCT

Automatic differentiation for gradient-based optimization of radiatively heated microelectronics manufacturing equipment

Automatic differentiation is applied to the optimal design of microelectronic manufacturing equipment. The performance of nonlinear, least-squares optimization methods is compared between numerical and analytical gradient approaches. The optimization calculations are performed by running large finite-element codes in an object-oriented optimization environment. The Adifor automatic differentiation tool is used to generate analytic derivatives for the finite-element codes. The performance results support previous observations that automatic differentiation becomes beneficial as the number of optimization parameters increases. The increase in speed, relative to numerical differences, has a limited value and results are reported for two different analysis codes

Making Automatic Differentiation Truly Automatic: Coupling PETSc with ADIC

Despite its name, automatic differentiation (AD) is often far from an automatic process. often one must specify independent and dependent variables, indicate the derivative quantities to be computed, and perhaps even provide information about the structure of the Jacobians or Hessians being computed. However, when AD is used in conjunction with a toolkit with well-defined interfaces, many of these issues do not arise. They describe recent research into coupling the ADIC automatic differentiation tool with PETSc, a toolkit for the parallel numerical solution of PDEs. This research leverages the interfaces and objects of PETSc to make the AD process very nearly transparent

Site-Specific Bioconjugation of a Murine Dihydrofolate Reductase Enzyme by Copper(I)-Catalyzed Azide-Alkyne Cycloaddition with Retained Activity

Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) is an efficient reaction linking an azido and an alkynyl group in the presence of copper catalyst. Incorporation of a non-natural amino acid (NAA) containing either an azido or an alkynyl group into a protein allows site-specific bioconjugation in mild conditions via CuAAC. Despite its great potential, bioconjugation of an enzyme has been hampered by several issues including low yield, poor solubility of a ligand, and protein structural/functional perturbation by CuAAC components. In the present study, we incorporated an alkyne-bearing NAA into an enzyme, murine dihydrofolate reductase (mDHFR), in high cell density cultivation of Escherichia coli, and performed CuAAC conjugation with fluorescent azide dyes to evaluate enzyme compatibility of various CuAAC conditions comprising combination of commercially available Cu(I)-chelating ligands and reductants. The condensed culture improves the protein yield 19-fold based on the same amount of non-natural amino acid, and the enzyme incubation under the optimized reaction condition did not lead to any activity loss but allowed a fast and high-yield bioconjugation. Using the established conditions, a biotin-azide spacer was efficiently conjugated to mDHFR with retained activity leading to the site-specific immobilization of the biotin-conjugated mDHFR on a streptavidin-coated plate. These results demonstrate that the combination of reactive non-natural amino acid incorporation and the optimized CuAAC can be used to bioconjugate enzymes with retained enzymatic activityope

Preparation of Precise Bioconjugates Using Atom Transfer Radical Polymerization

This thesis shows the development of atom transfer radical polymerization (ATRP) for the preparation of biohybrid materials. The general flow of the thesis is an introduction to the field of bioconjugates (Chapter 1), then research that involved growing polymers from biomolecule initiators is covered (Chapter 2-4), followed by projects that conjugated preformed polymers to biomolecules. (Chapters 5 and 6). Chapter 7 covers unique class of biohybrids called polyplexes that are formed by electrostatic interaction between the polymer and biomolecules. Chapter 1 is a broad overview of the field of polymer bioconjugates (i.e. biohybrids) that are prepared using reversible deactivator radical polymerization methods (RDRP) and thebiomolecules covered are proteins, DNA and RNA. Chapter 2 describes the preparation of protein polymer hybrids by “grafting from” a genetically encoded non-canonical amino acid ATRP initiator expressed at the 134 amino acid residue in the green fluorescent protein using normal ATRP (Chapter 2A) and activators generated by electron transfer (AGET) ATRP (Chapter 2B). The development of ATRP under biologically relevant conditions (BRC) for the synthesis of welldefined protein polymer hybrids by “by grafting from” a protein initiator using both normal and AGET ATRP was explored in Chapter 3. DNA is a versatile biomolecules that is synthetically prepared using solid phase synthesis using phosphoramidite coupling chemistry. To incorporatean ATRP initiator into DNA a phosphoramidite ATRP initiator was synthesized and incorporated into DNA and polymers could be “blocked from” DNA both on and of the solid phase bead (Chapter 4). The preparation of reversible DNA mediated star-polymer assemblies is described in Chapter 5. A self-transfecting nuclease resistant siRNA delivery system was developed by coupling a polymer to both the 5’ and 3’ ends of a passenger RNA strand followed by guide strand aneling (Chapter 6). A cationic nanogel was prepared, using AGET ATRP in inverse miniemulsion, and used to form polyplexes with siRNA. The nanogels were capable of binding and delivering siRNA to knockdown a protein of interest (Chapter 7). <br

Evaluation Of Large-Scale Optimization Problems On Vector And Parallel Architectures

. We examine the importance of problem formulation for the solution of large-scale optimization problems on high-performance architectures. We use limited memory variable metric methods to illustrate performance issues. We show that the performance of these algorithms is drastically affected by application implementation. Model applications are drawn from the MINPACK-2 test problem collection, with numerical results from a super-scalar architecture (IBM RS6000/370), a vector architecture (CRAY-2), and a massively parallel architecture (Intel DELTA). Key words. optimization, large-scale, limited memory, variable metric, performance evaluation, vector architecture, parallel architecture. AMS subject classifications. 65Y05, 65Y20, 65K05, 65K10, 90C06, 90C30 1. Introduction. Our aim is to explore performance issues associated with the solution of large-scale optimization problems on high-performance architectures. The solution of these problems, where the number of variables ranges betwe..