Buffer transfer of cells is a critical process in many biomedical applications such as dielectrophoresis experiments, optical trapping, and flow cytometry. Existing methods for buffer transfer of cells are time consuming, require skilled technicians and involve expensive equipment such as centrifuge and bio safety hoods. Furthermore, even a minute error in transferring the cells can easily result in cell lysis and decrease in viability. In this work, a lab-on-a-chip device is proposed that uses a textit{passive microfluidic approach} to effectively transfer cells from a growth medium to a desired buffer for downstream cDEP analysis. This eliminates the need for any external fields, expensive equipment, and significantly reduces manual efforts. Computational studies were carried out to analyze the impact of device geometry, channel configuration, and flowrate on the effectiveness of buffer transfer. The proposed device was evaluated through a parametric sweep and the device configurations were identified that induce low values of fluid shear stress, support high throughput, and maintains minimal diffusion. Finally, a method for fabricating the device in the laboratory using PDMS was illustrated. The outcome of this study helps further the development of highly effective microfluidic devices capable of performing buffer transfer of multiple cell lines. / Master of Science / Prior to performing biomedical experiments, cells often need to be transferred from the chemical solution in which they are grown to a different buffer that is customized for the analysis technique. This process is called buffer transfer and it is a critical process that needs to be performed before running many cell experiments. The way in which buffer transfer is carried out in most labs is time consuming, requiring skilled technicians and expensive machines. Moreover, even a small error while performing buffer transfer can easily cause the cells to die and reduce the cell count available for performing experiments. In this work, we propose an easy-to-use device that can perform the buffer exchange process without the need for expensive technologies or skilled technicians. The device achieves this exchange by leveraging fluid flow the channel to filter the cells out of the growth medium and transferring the cells to the desired chemical solution while washing the unwanted chemical solution away. We used CAD modeling and computational analysis to develop the device. The performance of the device was enhanced through a parametric analysis such that the device induces low shear stress, supports high flow through the channels and limits the mixing between the growth medium and the buffer. Finally, we have also illustrated a method for building the device in the laboratory. The results of this research work would help in furthering current efforts in the buffer transfer of cells.

With a new focus on flow regulation by the Tennessee Valley Authority (TVA) in reservoir tailwaters, it is now possible to recover many mussel species that once occurred in these reaches. Before flows can be modified to create habitat for freshwater mussels, suitable microhabitat conditions must be defined. In this study, I used multiple approaches to define suitable microhabitats for species in the free-flowing upper Clinch River, Virginia and Tennessee, where reproducing mussel populations persist. During summer low flows in 2003 and 2004, I measured flow and substrate conditions in over 1000 microhabitat patches (0.25 m² quadrat samples) across five river reaches. Flow characteristics and embeddedness were significantly different between microhabitats occupied and unoccupied by the most abundant species (MRPP, p < 0.05). Comparison of simple and multiple logistic regression models with Akaike's Information Criteria (AIC) demonstrated that increasing Fleisswasserstammtisch (FST) hemisphere number (a measure of shear stress), decreasing degree of embeddedness, and increasing mean column velocity best explained species occurrences in a microhabitat patch. Subtle differentiation in habitat use among species was observed; however, most species appeared to be microhabitat generalists. Species were grouped into three habitat guilds using corresponding canonical analysis and cluster analysis: fast-flow specialists (FFS), fast-flow generalists (FFG), and slow-flow tolerant (SFT). I used the same data set to develop and test transferability of Habitat Suitability Criteria (HSC) for three habitat guilds and seven species of adult freshwater mussels. Nonparametric tolerance limits were used to define the range of suitable and optimal habitat during summer low flows. Optimal habitat was defined as those ranges of FST hemisphere number, mean column velocity, and embeddedness occupied by the central 50% of independent observations for a species or guild, whereas suitable habitat was defined by those ranges occupied by the central 90% of observations. The transferability of criteria to other reaches of the Clinch River was assessed using one-sided Chi-square tests. Criteria developed for the fast-flow specialist (FFS) and fast-flow generalist (FFG) guilds, as well as most criteria for species in those guilds, transferred to destination reaches. In contrast, criteria developed for the slow-flow tolerant (SFT) guild and individual constituent species consistently failed to transfer. Criteria for FFS and FFG guilds and their constituent species should be incorporated into flow simulation models such as PHABSIM to gauge the effect of minimum flows on mussel habitat quality and quantity. These criteria could also be used to determine suitable sites for mussel translocations. However, my criteria require further testing in other rivers before they can be transferred beyond the Clinch River. Behavior and physiological responses to laboratory manipulations of flow velocity and substrate particle size were used to elucidate microhabitat preferences of Actinonaias pectorosa, Potamilus alatus, and Ptychobranchus subtentum. These species appeared less stressed in the fastest flow treatment, demonstrating significantly higher oxygen consumption and oxygen-to-nitrogen (O:N) ratios than in slower flow treatments. Only P. alatus demonstrated a preference for substrate particle size, and consistently selected finer particle sizes. Actinonaias pectorosa and P. subtentum demonstrated preference for fast-flow microhabitats by readily burrowing in those conditions, while abandoning slow-flow conditions. The lack of preference for substrate particle size demonstrated by A. pectorosa and P. subtentum supports conclusions of previous studies that substrate particle size is of little or secondary importance for explaining mussel microhabitat use. These results, along with previous studies in the Clinch River, demonstrate that the stable habitats of riffles and runs; characterized by fast flows during summer low flows, low percent bedrock, and low embeddedness, are the most suitable habitats for mussel assemblages. To create and maintain suitable habitat conditions in tailwaters, releases should maintain flow over riffles at a minimum depth of no less than 30 cm in riffles that provide higher shear stress conditions (FST number > 7) and velocities (> 0.70 m/s). Periodic releases that are sufficient to transport silt and sand, but not high enough to transport larger substrate should be adequate to maintain substrates with a low degree of embeddedness. Doing so would create suitable habitat for all mussels, from the most to least specialized. Additionally, HSC developed for FFS and FFG guilds can be used to determine suitable destination sites for translocations of species belonging to these guilds. / Master of Science

The multiangle submerged jet test device (JTD) provides a simple in situ method of measuring streambank critical shear stress (Ï c) and soil erodibility (kd). Previous research showed streambank kd and Ï c can vary by up to four orders of magnitude at a single site; therefore, it is essential to determine if the large range is due to natural variability in soil properties or errors due to the test method. The study objectives were to evaluate the repeatability of the JTD and determine how it compares to traditional flume studies. To evaluate the repeatability, a total of 21 jet tests were conducted on two remolded soils, a clay loam and clay, compacted at uniform moisture content to a bulk density of 1.53 g/cm^3 and 1.46 g/cm^3, respectively. To determine the similarity between JTD and a traditional measurement method, JTD Ï c and kd measurements were compared with measurements determined from flume tests. The JTD kd and Ï c ranged from 1.68-2.81 cm³/N-s and 0.28-0.79 Pa, respectively, for the clay loam and 1.36-2.69 cm³/N-s and 0.30-2.72 Pa, respectively, for the clay. The modest variation of kd and Ï c for the remolded soils suggests the JTD is repeatable, indicating the wide range of parameters measured in the field was a result of natural soil variability. The JTD median kd and Ï c, except clay loam kd (clay loam kd = 2.31 cm^3/N-s, Ï c = 0.45 Pa; clay kd = 2.18 cm^3/N-s, Ï c = 1.10 Pa) were significantly different than the flume values (clay loam kd = 2.43 cm³/N-s, Ï c = 0.23 Pa; clay kd = 4.59 cm³/N-s, Ï c = 0.16 Pa); however, considering the range of potential errors in both test methods, the findings indicate the multiangle submerged jet test provides reasonable measurement of erosion parameters in a field setting. / Master of Science

Estimates of bank erosion typically require field measurements to determine the soil erodibility since soil characteristics are highly variable between sites, especially for cohesive soils. The submerged jet test device is an in situ method of determining the critical shear stress and soil erodibility of cohesive soils. A constant velocity jet, applied perpendicular to the soil surface, creates a scour hole which is measured at discrete time intervals. While the results of these tests are able to provide values of critical shear stress and soil erodibility, the results are often highly variable and do not consider certain aspects of scour phenomena found in cohesive soils. Jet test measurements taken on the lower Roanoke River showed that the results varied for samples from similar sites and bulk failures of large areas of soil were common on the clay banks. Computational Fluid Dynamics (CFD) can be used to determine the effect of scour hole shape changes on the applied shear stress. Previous calculation methods assumed that the depth of the scour hole was the only parameter that affected the applied shear stress. The analysis of the CFD models showed that depth did heavily influence the maximum shear stress applied to the soil boundary. However, the scour hole shape had an impact on the flow conditions near the jet centerline and within the scour hole. Wide, shallow holes yielded results that were similar to the flat plate, therefore it is recommended that field studies only use jet test results from wide, shallow holes to determine the coefficient of erodibility and the critical shear stress of cohesive soils. / Master of Science

No / This paper proposes that the changes which occur in composition of the bed load during the transport of mixed-grain-size sediments are largely controlled by the distributions of critical entrainment shear stress for the various size fractions. This hypothesis is examined for a unimodal sediment mixture by calculating these distributions with a discrete particle model and using them in a probabilistic calculation of bed-load composition. The estimates of bed-load composition compare favorably with observations of fractional transport rates made in a laboratory flume for the same sediment, suggesting that the hypothesis is reasonable. The analysis provides additional insight, in terms of grain mechanics, into the processes that determine bed-load composition. These insights strongly suggest that better prediction methods will result from taking account of the variation of threshold within size fractions, something that most previous studies have neglected.

Due to the fact that bone cells are highly responsive to mechanical stimuli, shear stress has been extensively studied for its ability to enhance osteogenic differentiation through mechanotransduction. In addition, thermal stress has also been explored as a conditioning method to stimulate cellular proliferation, differentiation, and cytoprotection through heat shock protein induction. Despite the beneficial effects observed with individual stress on cells, there has been little focus on the potential of a combination of stresses to improve cellular response. Therefore, the aim of this study was to investigate the effect of combined shear and thermal stress on preosteoblasts to stimulate an enhanced osteogenic response. To achieve this, MC3T3-E1 cells were exposed to one of the following protocols for an hour: no stress (control), shear stress at 1 dyne/cm2 using a parallel plate flow chamber, thermal stress in a 42°C incubator, or combined shear and thermal stress (1 dyne/cm2 at 42°C). Stress treatments were applied on Day 2, Day 6, and Day 10. To assess the early response of cells to stress treatments, we measured metabolic activity, expression of signaling factors, and HSPs following stress on Day 2. Despite an initial decrease in metabolism, combined stress stimulated a strong response in VEGF (12.49 RFI) COX-2 (12.32 RFI), HSPs (2-4 RFI) and increased PGE accumulation. The long-term cellular response to stress treatments was measured on Day 15 by evaluating the ability of combined stress to stimulate late stage markers of differentiation. Combined stress increased OPN gene and protein expression, yet OCN was minimally affected by stress treatments. However, mineralization was significantly decreased with combined stress. Overall, combined stress was able to stimulate an enhanced effect across a majority of the bone-related markers measured, whereas individual shear stress or thermal stress were limited in their response. This suggests that combined stress can provide the appropriate cues to modify osteoblast differentiation and generate an enhanced osteogenic response. / Master of Science

Coronary tortuosity is the abnormal curving and twisting of the coronary arteries. Although the phenomenon of coronary tortuosity is frequently encountered by cardiologists its clinical significance is unclear. It is known that coronary tortuosity has significant influence on the hemodynamics inside the coronary arteries, but it is difficult to draw definite conclusions due to the lack of patient-specific studies and an absence of a clear definition of tortuosity. In this work, in order to investigate a relation of coronary tortuosity to such diseases as atherosclerosis, ischemia, and angina, a numerical investigation of coronary tortuosity was performed. First, we studied a correlation between a degree of tortuosity and flow parameters in three simplified vessels with curvature and zero torsion. Next, a statistical analysis based on flow calculations of 23 patient-based real tortuous arteries was performed in order to investigate a correlation between tortuosity and flow parameters, such as pressure drop, wall shear stress distribution, and a strength of helical flow, represented by a helicity intensity, and concomitant risks. Results of both idealized and patient-specific studies indicate that a risk of perfusion defects grows with an increased degree of tortuosity due to an increased pressure drop downstream an artery. According to the results of the patient-specific study, a risk of atherosclerosis decreases in more tortuous arteries - a result different from an outcome of the idealized study of arteries with zero torsion. Consequently, a modeling of coronary tortuosity should take into account all aspects of tortuosity including a heart shape that introduces additional torsion to arteries. Moreover, strength of a helical flow was shown to depend strongly on a degree of tortuosity and affect flow alterations and accompanying risks of developing atherosclerosis and perfusion defects. A corresponding quantity, helicity intensity, might have a potential to be implemented in future studies as a universal single parameter to describe tortuosity and assess congruent impact on the health of a patient. / Master of Science

Yes / The bed slope and the tailwater depth are two important ones among the factors that affect the propagation of the dam-break flood and Favre waves. Most previous studies have only focused on the macroscopic characteristics of the dam-break flows or Favre waves under the condition of horizontal bed, rather than the internal movement characteristics in sloped channel. The present study applies two numerical models, namely, large eddy simulation (LES) and shallow water equations (SWEs) models embedded in the CFD software package FLOW-3D to analyze the internal movement characteristics of the dam-break flows and Favre waves, such as water level, the velocity distribution, the fluid particles acceleration and the bed shear stress, under the different bed slopes and water depth ratios. The results under the conditions considered in this study show that there is a flow state transition in the flow evolution for the steep bed slope even in water depth ratio α = 0.1 (α is the ratio of the tailwater depth to the reservoir water depth). The flow state transition shows that the wavefront changes from a breaking state to undular. Such flow transition is not observed for the horizontal slope and mild bed slope. The existence of the Favre waves leads to a significant increase of the vertical velocity and the vertical acceleration. In this situation, the SWEs model has poor prediction. Analysis reveals that the variation of the maximum bed shear stress is affected by both the bed slope and tailwater depth. Under the same bed slope (e.g., S0 = 0.02), the maximum bed shear stress position develops downstream of the dam when α = 0.1, while it develops towards the end of the reservoir when α = 0.7. For the same water depth ratio (e.g., α = 0.7), the maximum bed shear stress position always locates within the reservoir at S0 = 0.02, while it appears in the downstream of the dam for S0 = 0 and 0.003 after the flow evolves for a while. The comparison between the numerical simulation and experimental measurements shows that the LES model can predict the internal movement characteristics with satisfactory accuracy. This study improves the understanding of the effect of both the bed slope and the tailwater depth on the internal movement characteristics of the dam-break flows and Favre waves, which also provides a valuable reference for determining the flood embankment height and designing the channel bed anti-scouring facility. / National Natural Science Foundation of China (Grant No: 51879179, 52079081), the Open Fund from the State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University (SKHL1809) and the Sichuan Science and Technology Program (No. 2019JDTD0007)

Yes / Bridge pier is a common feature in hydraulic structure. Its impact to the river usually occurs in group form rather than single pier, so this challenging piers-group influence towards river hydraulics and turbulence needs to be explored. In this paper, the measurements were conducted using an Acoustic doppler velocimeter (ADV) to study velocities in three dimensions (longitudinal, transversal, and vertical). Based on the experimental data, we have observed reversed depth-averaged velocity vector after each pier in the group of three-pier. The analysis has been conducted on the contribution of each bursting event to Reynolds shear stress (RSS) generation, in order to identify the critical events and turbulence structures around the piers. In the upstream near-wake flow in the bed-wall layer, strong sweep and ejection events have been observed; while at downstream, sweeps were more dominant. The pattern of burst changed in the outer layer of flow, where ejections were more dominant. Furthermore, the contribution fractional ratio to RSS variation at hole size H = 0 indicates that sweeps and ejections were significantly generated at the near wake-flow in upstream.

Most women die of ovarian metastasis rather than the effects of the primary tumor. However, little is known about the factors that support the survival and secondary outgrowth of exfoliated ovarian cancer cells. In addition to genetic and molecular factors, the unique environment of the peritoneal cavity exposes ovarian cells to biophysical forces, particularly fluid shear stress (FSS). These biomechanical forces, only recently identified as a hallmark of cancer, induce rapid signaling events in attached and aggregated cells, a process termed mechanotransduction. The cellular responses to these forces and their impact on tumor initiation, progression, and metastasis are not understood. In order to delineate these phenomena, dynamic and syngeneic cell models are needed that represent the development of the disease and can be used in relevant engineered testing platforms. Thus, in an interdisciplinary approach, this work bridges molecular and cancer biology, device engineering, fluid mechanics, and biophysics strategies. The results demonstrated that even a low level of continual FSS significantly and differentially affected the viability of epithelial ovarian cancer cells of various stages of progression over time, and enhanced their aggregation, adhesion, and cellular architecture, traits of more aggressive disease. Furthermore, benign cells that survived FSS displayed phenotypic and genotypic changes resembling more aggressive stages of the disease, suggesting an impact of FSS on early stages of tumor development. After identifying a biological affect, we designed an in vitro testing platform for controlled FSS investigations, and we modeled the system fluid mechanics to understand the platform's performance capability. A cylindrical platform divided into annular sections with lid-driven flow was selected to allow continuous experiments sustainable for long durations. Tuning of the lid speed or fluid height resulted in a wide range of FSS magnitudes (0- 20 N/m2) as confirmed by analytical and numerical modeling. Further, detailed numerical modeling uncovered that FSS magnitudes experienced by cell aggregates were larger than previously observed, suggesting an even larger role of FSS in ovarian cancer. Finally, we built and engineered the designed platform to investigate changes in benign and cancer cells as a function of time and FSS magnitude. Device precision was balanced with biological consistency needs, and a novel platform was built for controlled FSS investigations. This work provides a foundational understanding of the physical environment and its potential links to ovarian cancer progression and metastatic potential. / Ph. D. / Most women die of ovarian metastasis rather than the effects of the primary tumor. However, little is known about the factors that support the survival and secondary outgrowth of exfoliated ovarian cancer cells. In addition to genetic and molecular factors, the unique environment of the peritoneal cavity exposes ovarian cells to biophysical forces, particularly fluid shear stress (FSS). These biomechanical forces, only recently identified as a hallmark of cancer, induce rapid signaling events in attached and aggregated cells, a process termed mechanotransduction. The cellular responses to these forces and their impact on tumor initiation, progression, and metastasis are not understood. In order to delineate these phenomena, dynamic and syngeneic cell models are needed that represent the development of the disease and can be used in relevant engineered testing platforms. Thus, in an interdisciplinary approach, this work bridges molecular and cancer biology, device engineering, fluid mechanics, and biophysics strategies. The results demonstrated that even a low level of continual FSS significantly and differentially affected the viability of epithelial ovarian cancer cells of various stages of progression over time, and enhanced their aggregation, adhesion, and cellular architecture, traits of more aggressive disease. Furthermore, benign cells that survived FSS displayed phenotypic and genotypic changes resembling more aggressive stages of the disease, suggesting an impact of FSS on early stages of tumor development. After identifying a biological affect, we designed an in vitro testing platform for controlled FSS investigations, and we modeled the system fluid mechanics to understand the platform’s performance capability. A cylindrical platform divided into annular sections with lid-driven flow was selected to allow continuous experiments sustainable for long durations. Tuning of the lid speed or fluid height resulted in a wide range of FSS magnitudes (0 − 20 N/m² ) as confirmed by analytical and numerical modeling. Further, detailed numerical modeling uncovered that FSS magnitudes experienced by cell aggregates were larger than previously observed, suggesting an even larger role of FSS in ovarian cancer. Finally, we built and engineered the designed platform to investigate changes in benign and cancer cells as a function of time and FSS magnitude. Device precision was balanced with biological consistency needs, and a novel platform was built for controlled FSS investigations. This work provides a foundational understanding of the physical environment and its potential links to ovarian cancer progression and metastatic potential.