An Adaptive Viscoelastic Fluid Solver: Formulation, Verification, and Applications to Fluid-Structure Interaction

Many biological fluids exhibit non-Newtonian responses to stresses, and, as such, the Navier-Stokes equations are inadequate to properly model these fluids. To model the polymeric, visco-elastic fluids encountered in biological systems, we often turn to Oldroyd-B type models, where the immersed polymers are modeled using a linear Hooke's law for the restoring force. However, theory for how these models behave is severely lacking, and obtaining convergence in numerical simulations of these fluid models remains a significant challenge. These hyperbolic fluid models yield stress concentrations near large extensional flows. Sufficient spatial resolution is required to accurately resolve highly localized stress concentrations. However, away from such regions, lower computational resolution often suffices. This thesis presents a novel adaptive viscoelastic fluid solver that allows for the use of high spatial resolution where needed but permits the use of a coarser resolution away from areas of interest. The fluid solver is built into the open-source Immersed Boundary Adaptive Mesh Refinement (IBAMR) library to utilize recent adaptations of the immersed boundary method. We present applications of the fluid solver with an immersed interface method for complex fluids and a twirling flagellum in non-Newtonian fluids.Doctor of Philosoph

Tangible UI by object and material classification with radar

Radar signals penetrate, scatter, absorb and reflect energy into proximate objects and ground penetrating and aerial radar systems are well established. We describe a highly accurate system based on a combination of a monostatic radar (Google Soli), supervised machine learning to support object and material classification based Uls. Based on RadarCat techniques, we explore the development of tangible user interfaces without modification of the objects or complex infrastructures. This affords new forms of interaction with digital devices, proximate objects and micro-gestures.Postprin

Roles and mechanisms of DNA repair factors and pathways in Maintaining Seed Quality.

Successful germination is a major determinant of crop yields and survival of plants in the natural environment. Our knowledge of molecular factors important to seed quality is far from complete, yet such understanding is vital in the endeavour of mitigating the detrimental effects of extended storage on seed vigour and viability. Genome integrity is crucial for cellular survival and transmission of genetic information. A number of pre-genomic era studies identified strong correlations between DNA damage accumulated in the quiescent seed and seed ageing. If unrepaired, DNA damage results in delayed growth, mutagenesis and cell death. Damage products incurred by DNA are remarkably heterologous and plants have evolved multiple pathways to facilitate the repair of specific damage products. Through the isolation and analysis of knockout Arabidopsis mutants, this work identifies and characterises DNA repair genes whose action is required during seed imbibition. These studies examined the importance of four major DNA repair pathways in germination and seed quality. Mutants deficient in non-homologues end joining (KU70 and KU80), homologues recombination (XRCC2) and base excision repair (ARP) DNA repair pathways were all found to be hypersensitive to accelerated ageing treatment but those deficient in nucleotide excision repair (ERCC1) were not. Therefore this work establishes roles for multiple DNA repair pathways in seed longevity. Comparative analysis also defined non-homologues end joining as the most important DNA repair pathway to seed quality. LIG6 encodes a unique plant specific DNA ligase with roles in seed longevity and implicated in repair of DSBs but remains largely uncharacterised to date. Here studies using extra-chromosomal recombination assays demonstrate LIG6 functions in the promotion of recombination activities in Arabidopsis protoplasts. Further studies demonstrate the involvement of LIG6 in the maintenance of root meristem genome stability. Collectively, this work provides an increased understanding of the early events central to the germination process and seed longevity

Flagellum Pumping Efficacy in Shear-Thinning Viscoelastic Fluids

Microorganism motility often takes place within complex, viscoelastic fluid environments, e.g., sperm in cervicovaginal mucus and bacteria in biofilms. In such complex fluids, strains and stresses generated by the microorganism are stored and relax across a spectrum of length and time scales and the complex fluid can be driven out of its linear response regime. Phenomena not possible in viscous media thereby arise from feedback between the "swimmer" and the complex fluid, making swimming efficiency co-dependent on the propulsion mechanism and fluid properties. Here we parameterize a flagellar motor and filament properties together with elastic relaxation and nonlinear shear-thinning properties of the fluid in a computational immersed boundary model. We then explore swimming efficiency over this parameter space. One exemplary insight is that motor efficiency (measured by the volumetric flow rate) can be boosted vs.\ degraded by moderate vs.\ strong shear-thinning of the viscoelastic environment.Comment: 15 pages, 8 figure

Multi-scale gestural interaction for augmented reality

We present a multi-scale gestural interface for augmented reality applications. With virtual objects, gestural interactions such as pointing and grasping can be convenient and intuitive, however they are imprecise, socially awkward, and susceptible to fatigue. Our prototype application uses multiple sensors to detect gestures from both arm and hand motions (macro-scale), and finger gestures (micro-scale). Micro-gestures can provide precise input through a belt-worn sensor configuration, with the hand in a relaxed posture. We present an application that combines direct manipulation with microgestures for precise interaction, beyond the capabilities of direct manipulation alone.Postprin

Book Reviews

Book reviews by Edward F. Barrett, Alfred L. Scanlan, Robert T. Molloy, Aaron I. Abell, and Robert E. Sullivan

A Model of Fluid-Structure and Biochemical Interactions for Applications to Subclinical Leaflet Thrombosis

Subclinical leaflet thrombosis (SLT) is a potentially serious complication of aortic valve replacement with a bioprosthetic valve in which blood clots form on the replacement valve. SLT is associated with increased risk of transient ischemic attacks and strokes and can progress to clinical leaflet thrombosis. SLT following aortic valve replacement also may be related to subsequent structural valve deterioration, which can impair the durability of the valve replacement. Because of the difficulty in clinical imaging of SLT, models are needed to determine the mechanisms of SLT and could eventually predict which patients will develop SLT. To this end, we develop methods to simulate leaflet thrombosis that combine fluid-structure interaction and a simplified thrombosis model that allows for deposition along the moving leaflets. Additionally, this model can be adapted to model deposition or absorption along other moving boundaries. We present convergence results and quantify the model's ability to realize changes in valve opening and pressures. These new approaches are an important advancement in our tools for modeling thrombosis in which they incorporate both adhesion to the surface of the moving leaflets and feedback to the fluid-structure interaction.Comment: 29 pages, 11 figure