Conceptual Framework and Physical Implementation of a Systematic Design Strategy for Tissue-Engineered Devices

Tissue-engineered and biologically inspired devices promise to advance medical implants, robotic devices and diagnostic tools. Ideally, biohybrid constructs combine the versatility and fine control of traditional building substrates with dynamic properties of living tissues including sensory modalities and mechanisms of repair, plasticity and self-organization. These dynamic properties also complicate the design process as they arise from, and act upon, structure-function relationships across multiple spatiotemporal scales that need to be recapitulated in the engineered tissue. Biomimetic designs merely copying the structure of native organs and organisms, however, are likely to reflect evolutionary constraints, phenotypic variability and environmental factors rather than rendering optimal engineering solutions. This thesis describes an alternative to biomimetic design, i.e., a systematic approach to tissue engineering based on mechanistic analysis and a focus on functional, not structural, approximation of native and engineered system. As proof of concept, the design, fabrication and evaluation of a tissue-engineered jellyfish medusa with biomimetic propulsion and feeding currents is presented with an emphasis on reasoning and strategy of the iterative design process. A range of experimental and modeling approaches accomplishes mechanistic analysis at multiple scales, control of individual and emergent cell behavior, and quantitative testing of functional performance. The main achievement of this thesis lies in presenting both conceptual framework and physical implementation of a systematic design strategy for muscular pumps and other bioinspired and tissue-engineered applications.</p

Mixing and transport by ciliary carpets: a numerical study

We use a 3D computational model to study the fluid transport and mixing due to the beating of an infinite array of cilia. In accord with recent experiments, we observe two distinct regions: a fluid transport region above the cilia and a fluid mixing region below the cilia tip. The metachronal wave due to phase differences between neighboring cilia is known to enhance the fluid transport above the ciliary tip. In this work, we show that the metachronal wave also enhances the mixing rates in the sub-ciliary region, often simultaneously with the flow rate enhancement. Our results suggest that this simultaneous enhancement in transport and mixing is due to an enhancement in shear flow. As the flow above the cilia increases, shear rate in the fluid increases and such shear enhances stretching, which is an essential ingredient for mixing. Estimates of the mixing time scale indicate that, compared to diffusion, the mixing due to the cilia beat may be significant and sometimes dominates chemical diffusion.Comment: submitted to Journal of Fluid Mechanic

Induced drift by a self-propelled swimmer at intermediate Reynolds numbers

Swimming organisms have been proposed to contribute to the mixing of stratified water in the ocean, thereby facilitating the vertical transport of nutrients and dissolved gases. In general, mixing results from increasing the interface available for molecular diffusion between neighboring fluid volumes. At high Reynolds numbers (Re), swimmers generate such interfaces through their turbulent wake structures. At lower Re, however, turbulent mixing becomes ineffective as viscous effects dissipate small-scale fluid motions as heat, and diffusion is not significantly enhanced. In this regime, it appears that the dominant mechanism for mixing by a swimmer is induced drift, i.e., the propagation and stretching of a fluid volume by a moving body's pressure field, which increases the diffusion-enabling interface between the drift volume and surrounding fluid. The ratio of drift volume to body volume is called the “added-mass” coefficient and depends on the shape of the body. Importantly, previous computational analysis suggested that the total drift volume increases at low and intermediate Re, 3 implying that in contrast to turbulent mixing, mixing through induced drift becomes more efficient in viscous conditions. As pointed out by others, the limitation of previous numerical simulations, however, is that the simulated objects were towed through viscous fluid, which is dynamically distinct from a self-propelled swimmer. Using qualitative flow visualization, we here demonstrate the presence of induced drift in self-propelled swimmers operating at intermediate Re (1–100). In these experiments, the spatiotemporal pattern of a fluid volume initially surrounding a juvenile Moon jellyfish ( Aurelia aurita) is visualized using Fluorescein dye (see Fig. 1 ). For details on the experimental methods see supplemental material in Ref. 13

Design standards for engineered tissues

Traditional technologies are required to meet specific, quantitative standards of safety and performance. In tissue engineering, similar standards will have to be developed to enable routine clinical use and customized tissue fabrication. In this essay, we discuss a framework of concepts leading towards general design standards for tissue-engineering, focusing in particular on systematic design strategies, control of cell behavior, physiological scaling, fabrication modes and functional evaluation

Modeling of cardiac muscle thin films: Pre-stretch, passive and active behavior

Recent progress in tissue engineering has made it possible to build contractile bio-hybrid materials that undergo conformational changes by growing a layer of cardiac muscle on elastic polymeric membranes. Further development of such muscular thin films for building actuators and powering devices requires exploring several design parameters, which include the alignment of the cardiac myocytes and the thickness/Young's modulus of elastomeric film. To more efficiently explore these design parameters, we propose a 3-D phenomenological constitutive model, which accounts for both the passive deformation including pre-stretch and the active behavior of the cardiomyocytes. The proposed 3-D constitutive model is implemented within a finite element framework, and can be used to improve the current design of bio-hybrid thin films and help developing bio-hybrid constructs capable of complex conformational changes.Engineering and Applied Science

High-resolution three-dimensional extracellular recording of neuronal activity with microfabricated electrode arrays

Microelectrode array recordings of neuronal activity present significant opportunities for studying the brain with single-cell and spike-time precision. However, challenges in device manufacturing constrain dense multisite recordings to two spatial dimensions, whereas access to the three-dimensional (3D) structure of many brain regions appears to remain a challenge. To overcome this limitation, we present two novel recording modalities of silicon-based devices aimed at establishing 3D functionality. First, we fabricated a dual-side electrode array by patterning recording sites on both the front and back of an implantable microstructure. We found that the majority of single-unit spikes could not be simultaneously detected from both sides, suggesting that in addition to providing higher spatial resolution measurements than that of single-side devices, dual-side arrays also lead to increased recording yield. Second, we obtained recordings along three principal directions with a multilayer array and demonstrated 3D spike source localization within the enclosed measurement space. The large-scale integration of such dual-side and multilayer arrays is expected to provide massively parallel recording capabilities in the brain

A tissue-engineered jellyfish with biomimetic propulsion

Reverse engineering of biological form and function requires hierarchical design over several orders of space and time. Recent advances in the mechanistic understanding of biosynthetic compound materials, computer-aided design approaches in molecular synthetic biology and traditional soft robotics, and increasing aptitude in generating structural and chemical microenvironments that promote cellular self-organization have enhanced the ability to recapitulate such hierarchical architecture in engineered biological systems. Here we combined these capabilities in a systematic design strategy to reverse engineer a muscular pump. We report the construction of a freely swimming jellyfish from chemically dissociated rat tissue and silicone polymer as a proof of concept. The constructs, termed 'medusoids', were designed with computer simulations and experiments to match key determinants of jellyfish propulsion and feeding performance by quantitatively mimicking structural design, stroke kinematics and animal-fluid interactions. The combination of the engineering design algorithm with quantitative benchmarks of physiological performance suggests that our strategy is broadly applicable to reverse engineering of muscular organs or simple life forms that pump to survive

Motile cilia create fluid-mechanical microhabitats for the active recruitment of the host microbiome

We show that mucociliary membranes of animal epithelia can create fluid-mechanical microenvironments for the active recruitment of the specific microbiome of the host. In terrestrial vertebrates, these tissues are typically colonized by complex consortia and are inaccessible to observation. Such tissues can be directly examined in aquatic animals, providing valuable opportunities for the analysis of mucociliary activity in relation to bacteria recruitment. Using the squid–vibrio model system, we provide a characterization of the initial engagement of microbial symbionts along ciliated tissues. Specifically, we developed an empirical and theoretical framework to conduct a census of ciliated cell types, create structural maps, and resolve the spatiotemporal flow dynamics. Our multiscale analyses revealed two distinct, highly organized populations of cilia on the host tissues. An array of long cilia (∼25 μm) with metachronal beat creates a flow that focuses bacteria-sized particles, at the exclusion of larger particles, into sheltered zones; there, a field of randomly beating short cilia (∼10 μm) mixes the local fluid environment, which contains host biochemical signals known to prime symbionts for colonization. This cilia-mediated process represents a previously unrecognized mechanism for symbiont recruitment. Each mucociliary surface that recruits a microbiome such as the case described here is likely to have system-specific features. However, all mucociliary surfaces are subject to the same physical and biological constraints that are imposed by the fluid environment and the evolutionary conserved structure of cilia. As such, our study promises to provide insight into universal mechanisms that drive the recruitment of symbiotic partners

Conceptual Framework and Physical Implementation of a Systematic Design Strategy for Tissue-Engineered Devices

Foremost, I would like to thank my family and friends who have provided support and encouragement during good and bad times. I am particularly grateful to my mother who, along with my aunts and other close relatives, has laid the foundation for my passion for science and the con dence to persue an academic career. My dear friend and colleague Kamila Naxerova deserves particular gratefulness for her e ective mix of endless patience and tough love that has carried me through more than one icy Boston winter full of frustration and failed experiments. My advisor Professor John Dabiri has o ered me his continuous support and advice. His creativity, focus, and enthusiasm have been a great source of inspiration and encouragement. Through his example and guidance I have developed the con dence and humility needed to form a broader perspective on science that goes beyond the boundaries of classical disciplines and yet remain focused on concrete projects and tangible progress. I also would like to express my gratitude to my other mentors on this project, Professors Kevin Kit Parker, Bruce Hay, Paul Sternberg, Scott Fraser, Mory Gharib, an