Optimal Aeroacoustic Shape Design Using the Surrogate Management Framework

Shape optimization is applied to time-dependent trailing-edge flow in order to minimize aerodynamic noise. Optimization is performed using the surrogate management framework (SMF), a non-gradient based pattern search method chosen for its efficiency and rigorous convergence properties. Using SMF, design space exploration is performed not with the expensive actual function but with an inexpensive surrogate function. The use of a polling step in the SMF guarantees that the algorithm generates a convergent subsequence of mesh points in the parameter space. Each term of this subsequence is a weak local minimizer of the cost function on the mesh in a sense to be made precise later. We will discuss necessary optimality conditions for the design problem that are satisfied by the limit of this subsequence. Results are presented for an unsteady laminar flow past an acoustically compact airfoil. Constraints on lift and drag are handled within SMF by applying the filter pattern search method of Audet and Dennis, within which a penalty function is used to form and optimize a surrogate function. Optimal shapes that minimize noise have been identified for the trailing-edge problem in constrained and unconstrained cases. Results show a significant reduction (as much as 80%) in acoustic power with reasonable computational cost using several shape parameters. Physical mechanisms for noise reduction are discussed.     

Quasivelocities and symmetries in non-holonomic systems

This article is concerned with the theory of quasivelocities for non-holonomic systems. The equations of non-holonomic mechanics are derived using the Lagrange–d'Alembert principle written in an arbitrary configuration-dependent frame. The article also shows how quasivelocities may be used in the formulation of non-holonomic systems with symmetry. In particular, the use of quasivelocities in the analysis of symmetry that leads to unusual momentum conservation laws is investigated, as is the applications of these conservation laws and discrete symmetries to the qualitative analysis of non-holonomic dynamics. The relationship between asymptotic dynamics and discrete symmetries of the system is also elucidated.     

The alpha-synuclein Ala53Thr mutation is not a common cause of familial Parkinson''s disease: a study of 230 European cases. European Consortium on Genetic Susceptibility in Parkinson''s Disease

Deoxyguanosine kinase (dGK) is an enzyme responsible for the phosphorylation of purine deoxynucleosides in mitochondria of mammalian cells. Its role in activation of pharmacologically used nucleoside analogs is not well understood, because of the low levels of dGK found in tissue extracts and its inactivation during purification. The cDNA for dGK was recently cloned and expressed in Escherichia coli. Here we present an improved procedure for expression and purification of a highly active form of human recombinant dGK. The enzyme showed a broad substrate specificity toward natural purine and pyrimidine deoxynucleosides as well as toward important nucleoside analogs. The Km and Vmax values for deoxyguanosine, deoxyinosine, deoxyadenosine, and deoxycytidine were 4, 13, 460, 330 microM and 43, 330, 430 and 60 nmol/min/mg of protein, respectively. Antileukemic purine analogs such as arabinosyl guanine, 2-chloro-2'-deoxyadenosine, 2-chloro-2'-arabino-fluoro-2'-deoxyadenosine, and 2-fluoro-arabinosyl-adenine were phosphorylated as efficiently by dGK as the natural nucleoside substrates. This is the first report in which 2-fluoro-arabinosyl-adenine and 2-chloro-2'-arabino-fluoro-2'-deoxyadenosine were shown to be good substrates for dGK. The antiviral analogs dideoxyinosine and arabinosyl adenine also showed significant activity with dGK, as did several pyrimidine analogs (e.g., the cytostatic drugs 5-fluoro-2'-deoxycytidine and difluorodeoxycytidine). The broad specificity of dGK described here may change our understanding of the mechanisms responsible for the efficacy and mitochondrial toxicity of several nucleoside analogs.     

A comparison of outlet boundary treatments for prevention of backflow divergence with relevance to blood flow simulations

Simulation divergence due to backflow is a common, but not fully addressed, problem in three-dimensional simulations of blood flow in the large vessels. Because backflow is a naturally occurring physiologic phenomenon, careful treatment is necessary to realistically model backflow without artificially altering the local flow dynamics. In this study, we quantitatively compare three available methods for treatment of outlets to prevent backflow divergence in finite element Navier–Stokes solvers. The methods examined are (1) adding a stabilization term to the boundary nodes formulation, (2) constraining the velocity to be normal to the outlet, and (3) using Lagrange multipliers to constrain the velocity profile at all or some of the outlets. A modification to the stabilization method is also discussed. Three model problems, a short and long cylinder with an expansion, a right-angle bend, and a patient-specific aorta model, are used to evaluate and quantitatively compare these methods. Detailed comparisons are made to evaluate robustness, stability characteristics, impact on local and global flow physics, computational cost, implementation effort, and ease-of-use. The results show that the stabilization method offers a promising alternative to previous methods, with reduced effect on both local and global hemodynamics, improved stability, little-to-no increase in computational cost, and elimination of the need for tunable parameters.     

Lateral and vertical distribution of downstream migrating juvenile sea lamprey

Sea lamprey is considered an invasive and nuisance species in the Laurentian Great Lakes, Lake Champlain, and the Finger Lakes of New York and is a major focus of control efforts. Currently, management practices focus on limiting the area of infestation using barriers to block migratory adults, and lampricides to kill ammocoetes in infested tributaries. No control efforts currently target the downstream-migrating post-metamorphic life stage which could provide another management opportunity. In order to apply control methods to this life stage, a better understanding of their downstream movement patterns is needed. To quantify spatial distribution of downstream migrants, we deployed fyke and drift nets laterally and vertically across the stream channel in two tributaries of Lake Champlain. Sea lamprey was not randomly distributed across the stream width and lateral distribution showed a significant association with discharge. Results indicated that juvenile sea lamprey is most likely to be present in the thalweg and at midwater depths of the stream channel. Further, a majority of the catch occurred during high flow events, suggesting an increase in downstream movement activity when water levels are higher than base flow. Discharge and flow are strong predictors of the distribution of out-migrating sea lamprey, thus managers will need to either target capture efforts in high discharge areas of streams or develop means to guide sea lamprey away from these areas.     

The visualization of hepatic vasculature by X-ray micro-computed tomography

In this study, X-ray micro-computed tomography (CT) was used to reconstruct the fine structure macro- and microvasculature in three dimensions in contrast-enhanced rat liver samples. The subsequent application in the experimental CC531s colorectal cancer model was concurrent with results obtained from confocal microscopy in earlier studies. The en bloc stains osmium tetroxide in combination with uranyl acetate provided an excellent contrasting result for hepatic tissue after a trial of several contrasting agents. X-ray micro-CT allowed us to image the large blood vessels together with the branching sinusoids of hepatic tissue in three dimensions. Furthermore, interruption of the microvasculature was noted when rats were injected with CC531s colorectal cancer cells indicating the presence of hepatic metastases.     

The history and future of Lake Champlain's fishes and fisheries

In the last two centuries, physical, chemical, and biological alterations of Lake Champlain have resulted in the loss of two species, addition of 15 fish species, and listing of 16 species as endangered, threatened or of special concern. The lake currently supports 72 native fish species; lake trout (Salvelinus namaycush) and Atlantic salmon (Salmo salar) were extirpated by 1900, American eel (Anguilla rostrata) and lake sturgeon (Acipenser fulvescens) populations are extremely low, and walleye (Sander vitreum) are declining. Dams on several rivers, and ten causeways constructed in the mid 1800s to early 1900s, cut off access to critical spawning areas and may have limited fish movements. Siltation and sediment loading from agricultural activity and urban growth have degraded substrates and led to noxious algal blooms in some bays. A commercial fishery targeting spawning grounds of lake whitefish (Coregonus clupeaformis), lake trout, and walleye probably reduced numbers of these species prior to its closure in 1912. Non-native species introductions have had ecosystem-wide impacts. Sea lamprey (Petromyzon marinus) populations were very high prior to successful control, possibly as a consequence of ecological imbalance and habitat changes. A paucity of historic survey data or accurate species accounts limits our understanding of the causes of current fish population trends and status; in particular, the effects of habitat fragmentation within the lake and between the lake and its watershed are poorly understood. Holistic, ecosystem management, including pollution reduction and examination of habitat impacts, is necessary to restore the general structure of native biological assemblages.     

Constrained optimization of an idealized Y-shaped baffle for the Fontan surgery at rest and exercise

Coupling shape optimization to three-dimensional unsteady cardiovascular simulations poses several key challenges, including high computational cost, a need to handle constraints, and a need for automatic generation of parameterized vessel geometry. In this work we extend our previous framework for cardiovascular optimization to include constraints, pulsatile flow under both rest and exercise conditions, and multiple geometric parameters. Optimization is performed using a derivative-free algorithm called the surrogate management framework, with constraints enforced using a filter method. In this work, we examine a specific surgery called the Fontan, which is performed to treat single-ventricle heart patients. These patients typically undergo a series of three surgeries, the last of which connects the inferior vena cava to the pulmonary arteries. Our group and others have recently proposed and evaluated a new Y-graft modification of the Fontan operation that replaces the current tube shaped baffle. Preliminary simulations have shown that the Y-graft modification is a promising design that increases energy efficiency and improves flow distribution to the pulmonary arteries. In this work, we perform optimization on a model Y-graft design problem. This work represents the first use of formal design optimization methods for the Fontan surgery, and also demonstrates the applicability of the optimization framework on a pulsatile flow problem with multiple design parameters and constraints. The idealized Y-graft model was parameterized with six geometric parameters including graft diameter and anastomosis locations, and the optimization procedure, including model construction, meshing, and simulation, was executed automatically. Energy efficiency was chosen as the objective function. A constraint on the wall shear stress (WSS), a presumed correlate to thrombosis risk, was added to the problem using a filter method, which allowed for exploration of the trade-offs between WSS and energy efficiency. Optimization was performed at two exercise levels with effects of respiration incorporated, and differences in optimal solutions were examined. It was shown that optimal shapes differed between rest and exercise, as well as steady and pulsatile flow conditions, with wide-span branches and decreasing graft branch size favored with increasing exercise level. The optimization method was found to be robust for different polling strategies, and computationally efficient both with and without constraints.