It is hypothesized that exposing endothelial cells to steady or non-reversing pulsatile shear stress produces a healthy, anti-atherogenic endothelium, whereas a reversing pulsatile shear stress promotes an unhealthy, pro-atherogenic endothelium. To further investigate this hypothesis, a novel parallel plate flow chamber system was used to expose human endothelial cells to a pro-atherogenic reversing shear stress waveform designed to simulate the wall shear stress at the carotid sinus, a region prone to atherosclerosis. Cells exposed to this reversing shear stress were compared to cells exposed to high levels of steady shear stress (15 dynes/cm²), low steady shear stress (1 dyne/cm², the time-average of the carotid shear stress), and static culture conditions. Functional analysis confirmed previous findings that reversing shear stress increases cell proliferation and monocyte adhesion. Microarray results indicate that although there are unique sets of genes controlled by both low average shear stress and by reversing flow, more genes were controlled by low average shear stress. We propose that low-time average shear stress, and not fluid reversal/oscillation, may be the more significant mechanical force. The reversing shear stress system was also used to investigate two shear stress-responsive genes, CYP1A1 and CYP1B1. Both were maximally up-regulated at arterial steady shear stresses of at least 15 dynes/cm² and reversing pulsatile shear stress attenuated expression of both genes. Furthermore, AhR nuclear localization and CYP1A1 protein expression correlate with the flow patterns in the mouse aortic arch. The data strongly suggest that the AhR/CYP1 pathway promotes an anti-atherogenic phenotype in the endothelium. Changes in free zinc were measured under different shear stresses. High steady shear stress dramatically increases the levels of free zinc in endothelial cells as compared to cells grown in static culture. This increase in free zinc is attenuated under reversing shear stress and low steady shear stress, which correlates with an increase in zinc-binding metallothinein proteins and zinc exporter Znt-1. Overall, the findings provide further insight into endothelial responses to mechanical forces and may be important in understanding mechanisms of atherosclerotic development and localization to regions of disturbed flow.

Atherosclerosis is a multifactoral inflammatory disease that occurs in predisposed locations in the vasculature where blood flow is disturbed. In vitro studies have implicated reactive oxygen species as mediators of mechanotransduction leading to inflammatory protein expression and ultimately atherogenesis. While these cell culture-based studies have provided enormous insight into the effects of WSS on endothelial biology, the applicability to the in vivo setting is questionable. We hypothesized that low magnitude oscillatory WSS acts through reactive oxygen species (ROS) to increase expression of inflammatory cell adhesion molecules leading to the development of atherosclerotic lesions. The overall objective for this thesis was to develop an in vivo flow model that produces low magnitude oscillatory WSS which could be used to investigate the in vivo molecular mechanisms of mechanotransduction. We created a novel aortic coarctation model using a shape memory nitinol clip. The clip reproducibly constricts the aorta creating a narrowing of the lumen resulting in a stenosis. This mechanical constraint produces a region of flow separation downstream from the coarctation. We have characterized the coarctation in terms of the efficacy, pressure loss, and fluid dynamics. We then measured the endothelial response of shear sensitive redox and inflammatory markers. Lastly, we utilized genetically modified mice and mice treated with pharmacological inhibitors to investigate the mechanisms involved in the expression of WSS induced inflammatory and redox markers. We found that inducing a coarctation of the aorta using a nitinol clip uniquely created a hemodynamic environment of low magnitude oscillatory WSS without a significant change in blood pressure. Using this model we found that the in vivo endothelial phenotype associated with acutely disturbed flow was characterized by increased production of superoxide and increased expression of select inflammatory proteins. In comparison, the phenotype associated with chronically disturbed flow was characterized by a more modest increase in superoxide and increased levels of multiple inflammatory proteins. We determined that in regions of acutely disturbed flow in vivo, VCAM-1 expression was not modulated by reactive oxygen species. Additionally, p47 phox-dependent NADPH Oxidase activity does not have a functional role in WSS induced superoxide generation in the endothelium. In summary, we have created a novel murine model of low magnitude oscillatory WSS that can be used to investigate the in vivo molecular mechanisms associated with atherogenesis. While previous data obtained in vitro indicated that depletion of an individual ROS was sufficient to inhibit flow-induced inflammatory protein expression, our findings, to the contrary, showed that antioxidant treatment in vivo does not inhibit shear-dependent inflammatory protein expression. Our results suggest that atherogenesis in the in vivo environment is significantly more complicated than the in vitro environment and that parallel pathways and compensatory mechanisms are likely activated in vivo in response to WSS. These results could have significant implications in the efficacy of antioxidant treatment of atherosclerosis and could explain the complexity of results observed in clinical trials.

<p>Phase-contrast magnetic resonance imaging (PC-MRI) is a powerful tool for measuring blood flow and has a wide range of cardiovascular applications. Simulation of PC-MRI from numerical flow data would be useful for addressing the data quality of PC-MRI measurements and to study and understand different artifacts. It would also make it possible to optimize imaging parameters prior to the PC-MRI measurements and to evaluate different methods for measuring wall shear stress.</p><p>Based on previous studies a PC-MRI simulation tool was developed. An Eulerian-Lagrangian approach was used to solve the problem. Computational fluid dynamics (CFD) data calculated on a fix structured mesh (Eulerian point of view) were used as input. From the CFD data spin particle trajectories were computed. The magnetization of the spin particle is then evaluated as the particle travels along its trajectory (Lagrangian point of view).</p><p>The simulated PC-MRI data were evaluated by comparison with PC-MRI measurements on an in vitro phantom. Results indicate that the PC-MRI simulation tool functions well. However, further development is required to include some of the artifacts. Decreasing the computation time will make more accurate and powerful simulations possible. Several suggestions for improvements are presented in this report.</p>

Atherosclerosis is an inflammatory disease of the arterial walls and is the major cause of heart attack and stroke. Atherosclerosis is localized to curves or branches in the vasculature where disturbed blood flow alters endothelial cell (EC) gene expression and induces EC dysfunction. Epigenetics controls aberrant gene expression in many diseases, but the mechanism of flow-induced epigenetic gene regulation in ECs via DNA methylation has not been well studied until very recently. The goal of this project was to determine how the DNA methylome responds to flow, causes altered gene expression, and regulates atherosclerosis development. Here, we found that d-flow increases DNA Methyltransferase 1 (DNMT1) expression in ECs, and we hypothesized that this causes a shift in the EC methylome and transcriptome towards a pro-inflammatory, pro-atherosclerotic gene expression program, and further that this leads to atherosclerosis development. To test this hypothesis, we employed both in vitro and in vivo experimental approaches combined with genome-wide studies of the transcriptome and DNA methylome according to the following three specific aims: 1) to elucidate the role of DNA Methyltransferase 1 in EC function, 2) to uncover the DNA methylation-dependent EC gene expression response to flow, and 3) to discover and examine master regulators of EC function that are controlled by DNA methylation. The work presented here has resulted in new knowledge about the epigenetic EC shear response, details the previously unstudied EC methylome, and implicates specific loci within the genome for additional studies on their role in EC biology and atherosclerosis. This work provides a foundation for novel and more targeted therapeutic strategies for CVD.

Major advances in highly active antiretroviral therapies (ARVs) have extended the lives of people living with HIV, but there still remains an increased risk of death by cardiovascular diseases (CVD). HIV proteins and ARVs have been shown to contribute to cardiovascular dysfunction with effects on the different cell types that comprise the arterial wall. In particular, HIV-1 transactivating factor, Tat, is a cationic polypeptide that binds to endothelial cells, inducing a range of responses that have been shown to contribute to vascular dysfunction. It is well established that hemodynamics also play an important role in endothelial cell mediated atherosclerotic development where upon exposure to low or oscillatory shear stress, such as that found at branches and bifurcations, endothelial cells contribute to proteolytic vascular remodeling, by upregulating cathepsins, potent elastases and collagenases. The results of this work demonstrate that upregulation of cathepsins in vivo and in vitro is caused by a synergism between pro-atherogenic shear stress and HIV-1 proteins, elucidates pathways that are activated by HIV-1 Tat and pro-atherogenic shear stress - leading to cathepsin-mediated ECM degradation, and identifies cathepsins as novel biomarkers to monitor the adherence of patients on efavirenz- and tenofovir-containing antiretroviral regimens.

First-principles calculations employing density functional theory (DFT) were performed on the energetic materials PETN, HMX, RDX, nitromethane, and a recently discovered material, nitrate ester 1 (NEST-1). The aims of the study were to accurately predict the isothermal equation of state for each material, improve the description of these molecular crystals in DFT by introducing a correction for dispersion interactions, and perform uniaxial compressions to investigate physical properties that might contribute to anisotropic sensitivity. For each system, hydrostatic-compression simulations were performed. Important properties calculated from the simulations such as the equilibrium structure, isothermal equation of state, and bulk moduli were compared with available experimental data to assess the agreement of the calculation method. The largest contribution to the error was believed to be caused by a poor description of van der Waals (vdW) interactions within the DFT formalism. An empirical van der Waals correction to DFT was added to VASP to increase agreement with experiment. The average agreement of the calculated unit-cell volumes for six energetic crystals improved from approximately 9% to 2%, and the isothermal EOS showed improvement for PETN, HMX, RDX, and nitromethane. A comparison was made between DFT results with and without the vdW correction to identify possible advantages and limitations.  Uniaxial compressions perpendicular to seven low-index crystallographic planes were performed on PETN, HMX, RDX, nitromethane, and NEST-1. The principal stresses, shear stresses, and band gaps for each direction were compared with available experimental information on shock-induced sensitivity to determine possible correlations between physical properties and sensitivity. The results for PETN, the only system for which the anisotropic sensitivity has been thoroughly investigated by experiment, indicated a possible correlation between maximum shear stress and sensitivity. The uniaxial compressions that corresponded to the greatest maximum shear stresses in HMX, RDX, solid nitromethane, and NEST-1 were identified and predicted as directions with possibly greater sensitivity. Experimental data is anticipated for comparison with the predictions.

Indentation is used as a technique for mechanical characterization of materials for a long time. In the last few decades, new techniques of mechanical characterization at micro and nano level using indentation have been developed. Mechanical character-ization of thin films has become an important area of research because of their crucial role in modern technological applications. Theoretical and computational models of indentation are less time consuming,cost effective, and flexible. Many researchers have investigated mechanical properties of thin films using theoretical and computational models. In this study, an indentation model for a thin layer-substrate geometry with the possibility of nonhomogeneous or homogeneous interface of finite thickness between layer and substrate has been developed. The layer and substrate can be nonhomogeneous or homogeneous. Three types of indenters are modeled: 1) Uniform pressure indenter 2) Flat indenter 3) Smooth indenter. Contact depth, maximum interfacial normal stress and maximum interfacial shear stress play an important role in design and mechanical characterization of thin films using indentation and the effect of modeling the interface as homogeneous and nonhomogeneous on these parameters is studied. A sensitivity analysis is also conducted to find the effect of indentation area, substrate to layer Young's modulus ratio, layer to interface thickness ratio on contact depth and critical interfacial stresses.

<p>The adaptive response of vascular endothelial cells to shear stress alteration induced by global hemodynamic changes is an essential component of normal endothelial physiology in vivo; and an understanding of the transient regulation of endothelial phenotype during adaptation will advance our understanding of endothelial biology and yield new insights into the mechanism of atherogenesis. The objective of this study was to characterize the adaptive response of arterial endothelial cells to acute increases in shear stress magnitude and frequency in well-defined in vitro settings. Porcine endothelial cells were preconditioned by a basal level shear stress of ±15dynes/cm^2 at 1 Hz for 24 hours, and an acute increase in shear stress magnitude (30 ±15 dynes/cm^2) or frequency (2 Hz) was then applied. Endothelial permeability to bovine serum albumin was measured and gene expression profiling was performed using microarrays at multiple time points during a period of 6 hours after the shear stress alteration. The instantaneous endothelial permeability was found to increase rapidly in response to the acute increase in shear stress magnitude. Endothelial permeability nearly doubled after 40 minutes exposure to the elevated shear magnitude, and then decreased gradually. However, less dependency of endothelial permeability on shear stress frequency was observed. Endothelial permeability increased slowly from 120 minutes to 6 hours after exposure to the elevated shear frequency, but the increase was not statistically significant and was relatively small (1.2 fold increase at 6 hours). The transcriptomics studies identified 86 genes that were sensitive to the elevated shear magnitude and 37 genes sensitive to the elevated frequency. A significant number of the identified genes are previously unknown as sensitive to shear stress. The acute increase in shear magnitude promoted the expression of a group of anti-inflammatory and anti-oxidative genes; while the acute increase in shear frequency upregulated a set of cell-cycle regulating genes and angiogenesis genes. The adaptive response of global gene expression profile to the elevated shear magnitude is found to be triphasic, consisting of an induction period, an early adaptive response (ca. 45 minutes) and a late remodeling response. However, no apparent temporal regulation pattern of global gene expression was found during the adaptation to the elevated shear frequency. The results from this dissertation suggest that endothelial cells exhibit a specific phenotype during the adaptive response to changes in shear stress; and the transient phenotype is different than that of fully-adapted endothelial cells and may alter arterial atherosusceptibility.</p> / Dissertation

Accurate and reliable modeling of cardiovascular hemodynamics has the potential to improve understanding of the localization and progression of heart diseases, which are currently the most common cause of death in Western countries. However, building a detailed, realistic model of human blood flow is a formidable mathematical and computational challenge. The simulation must combine the motion of the fluid, the intricate geometry of the blood vessels, continual changes in flow and pressure driven by the heartbeat, and the behavior of suspended bodies such as red blood cells. Such simulations can provide insight into factors like endothelial shear stress that act as triggers for the complex biomechanical events that can lead to atherosclerotic pathologies. Currently, it is not possible to measure endothelial shear stress in vivo, making these simulations a crucial component to understanding and potentially predicting the progression of cardiovascular disease. In this thesis, an approach for efficiently modeling the fluid movement coupled to the cell dynamics in real-patient geometries while accounting for the additional force from the expansion and contraction of the heart will be presented and examined. First, a novel method to couple a mesoscopic lattice Boltzmann fluid model to the microscopic molecular dynamics model of cell movement is elucidated. A treatment of red blood cells as extended structures, a method to handle highly irregular geometries through topology driven graph partitioning, and an efficient molecular dynamics load balancing scheme are introduced. These result in a large-scale simulation of the cardiovascular system, with a realistic description of the complex human arterial geometry, from centimeters down to the spatial resolution of red-blood cells. The computational methods developed to enable scaling of the application to 294,912 processors are discussed, thus empowering the simulation of a full heartbeat. Second, further extensions to enable the modeling of fluids in vessels with smaller diameters and a method for introducing the deformational forces exerted on the arterial flows from the movement of the heart by borrowing concepts from cosmodynamics are presented. These additional forces have a great impact on the endothelial shear stress. Third, the fluid model is extended to not only recover Navier-Stokes hydrodynamics, but also a wider range of Knudsen numbers, which is especially important in micro- and nano-scale flows. The tradeoffs of many optimizations methods such as the use of deep halo level ghost cells that, alongside hybrid programming models, reduce the impact of such higher-order models and enable efficient modeling of extreme regimes of computational fluid dynamics are discussed. Fourth, the extension of these models to other research questions like clogging in microfluidic devices and determining the severity of co-arctation of the aorta is presented. Through this work, a validation of these methods by taking real patient data and the measured pressure value before the narrowing of the aorta and predicting the pressure drop across the co-arctation is shown. Comparison with the measured pressure drop in vivo highlights the accuracy and potential impact of such patient specific simulations. Finally, a method to enable the simulation of longer trajectories in time by discretizing both spatially and temporally is presented. In this method, a serial coarse iterator is used to initialize data at discrete time steps for a fine model that runs in parallel. This coarse solver is based on a larger time step and typically a coarser discretization in space. Iterative refinement enables the compute-intensive fine iterator to be modeled with temporal parallelization. The algorithm consists of a series of prediction-corrector iterations completing when the results have converged within a certain tolerance. Combined, these developments allow large fluid models to be simulated for longer time durations than previously possible. / Engineering and Applied Sciences

Development of shear databases attracted a great deal of attention in the shear research community within the last decade. Although a few shear databases have already been developed by several research groups, there is no comprehensive shear database that is focused on prestressed concrete members. This thesis aims to develop a shear database for prestressed concrete members with an intensive literature review. This literature review resulted in a database that contained a total of 1,696 tests reported in North America, Japan, and Europe from 1954 to 2010. The database was used to evaluate shear design provisions available in North America, Japan, and Europe. The variations in measured versus calculated shear strength using twelve shear design equations were analyzed. The analysis results indicated that design expressions based on the Modified Compression Filed Theory (MCFT) produced the best performance to estimate the shear strength of prestressed concrete members with sufficient shear reinforcement. The MCFT-based design expressions, however, provided unconservative strength estimations for members that failed in shear but exhibited signs of horizontal shear damage and/or anchorage zone distress. The ACI 318-08 detailed method was found to be less conservative than the MCFT-based design expressions. Additionally, on the basis of a careful examination of test results included in the database, a new limit for the minimum shear reinforcement was proposed. The database was also used to investigate the shear behavior of prestressed concrete members. This investigation revealed that there was no evidence of size effect in the shear strength of prestressed concrete members with sufficient shear reinforcement. Additionally, it was found that prestress force and shear reinforcement increased the shear strength although there was an upper limit on the effectiveness of shear reinforcement. / text