Five image processing algorithms are proposed to measure the average orientation, eccentricity and size of cells in images of biological tissue. These properties, which can be embodied by an elliptical 'composite cell', are crucial for biomechanical tissue models. To automatically determine these properties is challenging due to the diverse nature of the image data, with tremendous and unpredictable variability in illumination, cell pigmentation, cell shape and cell boundary visibility. One proposed algorithm estimates the composite cell properties directly from the input tissue image, while four others estimate the properties from frequency domain data. The accuracy and stability of the algorithms are quantitatively compared through application to a wide variety of real images. Based on these results, the best algorithm is selected.

This thesis presents a whole-embryo finite element model of neurulation -- the first of its kind. An advanced, multiscale finite element approach is used to capture the mechanical interactions that occur across cellular, tissue and whole-embryo scales. Cell-based simulations are used to construct a system of constitutive equations for embryonic tissue fabric evolution under different scenarios including bulk deformation, cell annealing, mitosis, and Lamellipodia effect. Experimental data are used to determine the parameters in these equations. Techniques for obtaining images of live embryos, serial sections of fixed embryo fabric parameters, and material properties of embryonic tissues are used. Also a spatial-temporal correlation system is introduced to organize and correlate the data and to construct the finite element model. Biological experiments have been conducted to verify the validity of this constitutive model. A full functional finite element analysis package has been written and is used to conduct computational simulations. A simplified contact algorithm is introduced to address the element permeability issue. Computational simulations of different cases have been conducted to investigate possible causes of neural tube defects. Defect cases including neural plate defect, non-neural epidermis defect, apical constriction defect, and convergent extension defect are compared with the case of normal embryonic development. Corresponding biological experiments are included to support these defect cases. A case with biomechanical feedbacks on non-neural epidermis is also discussed in detail with biological experiments and computational simulations. Its comparison with the normal case indicates that the introduction of biomechanical feedbacks can yield more realistic simulation results.

Bien que reconnu comme une étape importante vers une meilleur compréhension de l’évolution des tumeurs, de la morphogénèse des tissus et des tests hauts débits de médicaments, l’utilisation de tests cellulaires in vitro en trois dimensions est toujours limitée et ce surtout par la difficulté d’établir un protocole simple et robuste pour leur formation. Dans ce travail, nous présentons d'abord une nouvelle méthode microfluidique pour la formation des sphéroïdes multicellulaires. Cette technologie des Capsules cellulaire est basée sur l'encapsulation et la croissance des cellules à l'intérieur de micro- sphères creuses, perméable, élastiques. Deuxièmement, nous montrons que ces microcapsules servent de capteurs mécaniques pour mesurer la pression exercée par les sphéroïdes expansion. En imagerie en temps réel multi- photons, on observe en outre que le confinement induit une organisation cellulaire stratifiée, avec un noyau nécrotique, solide et dense, entouré d'un rebord de cellules périphériques hyper-mobiles, qui présentent des propriétés invasives. Troisièmement, nous avons adapté la technologie des capsules cellulaires pour former des tubes creux. Cette géométrie cylindrique nous permet d'étudier l'impact de la libération partielle de confinement (le long de l'axe du tube principal) sur la cinétique de croissance d’agrégats cellulaires pseudo-unidimensionnel (nommé cylindroids). Nos données de microscopie et l’analyse d'images suggèrent un mécanisme de croissance par pointe et la prouvent la génération d’une contrainte radiale. La combinaison des configurations sphériques et cylindriques tend vers l'image globale du confinement qui déclenche la motilité cellulaire et l'invasion par la périphérie de l'agrégat cellulaire tandis que la prolifération des cellules est inhibée dans le noyau lorsque la pression augmente. Quatrièmement, nous utilisons l’alginate comme moule pour concevoir des coquilles et tubes multicouches perméables. En particulier, une légère adaptation du protocole nous permet d'ancrer une fine couche de Matrigel (utilisé comme une membrane basale artificielle) sur la paroi interne de l'alginate. Par l'utilisation de ces capsules sphériques décorés de Matrigel, nous montrons que les monocouches sphériques fermés de cellules épithéliales, ou des kystes, peuvent être facilement conçus avec des tailles qui sont imposées par la taille des capsules. De même, les capsules tubulaires décorées de Matrigel sont utilisées pour la formation des organoïds cultivés à partir de cellules extraites des cryptes du côlon de la souris. Enfin, notre technologie offre une nouvelle voie pour produire dans les tests cellulaires in vitro utiles pour développer de nouvelles thérapies anticancéreuses ou des approches d'ingénierie tissulaire et d'étudier l'interaction entre la mécanique et de la croissance dans les agrégats cellulaires in vitro. / Although recognized as an important step towards better understanding of tumor progression, tissue morphogenesis and high throughput screening of drugs, the use of three dimensional in vitro cellular assays is still limited, especially due to the difficulty in establishing simple and robust protocols for their formation. In this work, we first present a novel microfluidics-assisted method for multicellular spheroids formation. This Cellular Capsules technology is based on the encapsulation and growth of cells inside permeable, elastic, hollow micro-spheres. Second, we show that these microcapsules serve as unique mechanical sensors to measure the pressure exerted by the expanding spheroids. By multiphoton live imaging, we additionally observe that confinement induces a layered cellular organization, with a dense, solid, necrotic core surrounded by a rim of hyper-motile peripheral cells, which exhibit enhanced invasive properties. Third, we adapt the Cellular Capsules technology to form hollow tubes. This cylindrical geometry allows us to investigate the impact of partial confinement release (along the main tube axis) on the growth kinetics of pseudo-one dimensional cellular aggregates (named cylindroids). Our microscopy data and image analyses suggest a tip-growing mechanism and evidence radial stress generation. The combination of the spherical and cylindrical configurations leads to the overall picture that confinement triggers cell motility and invasion at the periphery of the cellular aggregate while cell proliferation is inhibited in the core as pressure builds up. Fourth, we use alginate as a template to design multilayered permeable shells and tubes. In particular, slight adaptation of the protocol allows us to anchor a thin layer of Matrigel (used as an artificial basement membrane) to the alginate inner wall. Using these Matrigel-decorated spherical capsules, we show that closed spherical monolayers of epithelial cells, or cysts, can be readily engineered with sizes that are imposed by the size of the capsules. Similarly, Matrigel-decorated tubular capsules are shown to be convenient for the formation of organoids grown from cells extracted from the cypts of mouse colon. Finally, our technology offers a new avenue to produce in vitro cell-based assays useful for developing new anti-cancer therapies or tissue engineering approaches and to investigate the interplay between mechanics and growth of in vitro cellular assemblies.

<p dir="ltr">Subcutaneous injection for self-administration of biotherapeutics, such as monoclonal antibodies (mAbs), is becoming increasingly prominent within the pharmaceutical sector due to its benefits in patient compliance and cost-effectiveness. The success of this drug delivery process depends on the coupled mechanical and transport phenomena within the subcutaneous tissue, both during and after the injection. Yet, the details of these processes are not well-elucidated, sparking a surge in computational efforts to fill this knowledge gap. Remarkably, there are very few computational studies on subcutaneous injection into three-dimensional porous media that account for large tissue deformations, drug transport and absorption, the use medical devices, and human factors. Here, we develop a high-fidelity computational framework to study large-volume subcutaneous injection of mAbs. Our investigation begins with a linear poroelastic model without drug transport, which we employ to study the effect of tissue deformation on injection dynamics. We progressively enhance this model, advancing to a nonlinear porohyperelastic framework that include drug transport and absorption. To capture the anisotropy of subcutaneous tissue, we employ a fibril-reinforced porohyperelastic model. Furthermore, we integrate the multi-layered structure of skin tissue by creating data-driven geometrical models of the tissue layers derived from histological data. Our analysis explores the impact of different handheld autoinjectors on the injection dynamics for various patient-applied forces. We investigate the effect of different pre-injection techniques, such as the pinch and stretch methods, on the drug transport and absorption. Additionally, we evaluate the impact of several physiological variables, including flow rate, injection depth, and body mass index. Our simulations yield crucial insights essential for comprehending and improving subcutaneous drug administration of mAbs. Additionally, they offer a deeper understanding of the human aspect of the injection procedure, thereby paving the way for advancements in the development of patient-centered injection devices and techniques.</p>

Improved surgical procedures and implant developments for ligament or tendon repair require an in-depth understanding of tissue load-deformation and fatigue properties. Cyclic testing will provide crucial information on the behavior of these materials under reoccurring loads and on fatigue strength. Sparse data are available describing soft tissue behavior under cyclic loading. To examine fatigue strength, a new technology was trialed deploying 3D-printing to facilitate and standardize cyclic tests aiming to determine tendon fatigue behavior. Cadaveric flexor digitorum tendons were harvested and mounted for tensile testing with no tapering being made, using 3Dprinted clamps and holder arms, while ensuring a consistent testing length. Loads ranging between 200 to 510 N were applied at a frequency of 4 Hz, and cycles to failure ranged between 8 and >260,000. S–N curves (Woehler curves) were generated based on the peak stresses and cycles to failure. Power regression yielded a combined coefficient of determination of stress and cycles to failure of R 2 = 0.65, while the individual coefficients for tissues of single donors ranged between R 2 = 0.54 and R 2 = 0.88. The here-presented results demonstrate that S–N curves of human tendons can be obtained using a standardized setting deploying 3D-printing technology

During development of tissues, cells collectively organize to form complex patterns and morphologies. A general feature of many developing epithelia is their distinct organization into cellular compartments of different cell lineages. The interfaces between these compartments, called compartment boundaries, maintain straight and sharp morphologies. The interfaces play key roles in tissue development and pattern formation. An important model system to study the morphology of compartment boundaries during development is the wing disc of the fruit fly. Two compartment boundaries exist in the fly wing disc, the anteroposterior (AP) boundary and the dorsoventral (DV) boundary. A crucial question is how compartment boundaries are shaped and remain stable during growth. In this work, we discuss the dynamics and mechanisms of compartment boundaries in developing epithelia. We analyze the general features of interfacial phenomena in coarse- grained models of passive and active fluids. We introduce a continuum description of tissues with two cell types. This model allows us to study the propagation of interfaces due to the interplay of cell dynamics and tissue mechanics. We also use a vertex model to describe cellular compartments in growing epithelia. The vertex model accounts for cell mechanics and describes a 2D picture of tissues where the network of adherens junctions characterizes cell shapes. We use this model to study the general physical mechanisms by which compartment boundaries are shaped. We quantify the stresses in the cellular network and discuss how cell mechanics and growth influence the stress profile. With the help of the anisotropic stress profile near the interfaces we calculate the interfacial tension. We show that cell area pressure, cell proliferation rate, orientation of cell division, cell elongation created by external stress, and cell bond tension all have distinct effects on the morphology of interfaces during tissue growth. Furthermore, we investigate how much different mechanisms contribute to the effective interfacial tension. We study the mechanisms shaping the DV boundary in wing imaginal disc at different stages during the development. We analyze the images of wing discs to quantify the roughness of the DV boundary and average cell elongation in its vicinity. We quantify increased cell bond tension along the boundary and analyze the role of localized reduction in cell proliferation on the morphology of the DV boundary. We use experimentally determined values for cell bond tension, cell elongation and bias in orientation of cell division in simulations of tissue growth in order to reproduce the main features of the time-evolution of the DV boundary shape.

Synthetic vascular grafts are useful to bypass diseased arteries. The long-term failure of synthetic grafts is primarily due to intimal hyperplasia at the anastomotic sites. The accelerated intimal hyperplasia may stem from a compliance mismatch between the host artery and the graft since commercially available synthetic conduits are much stiffer than an artery. The objective of this thesis is to design a method for fabricating a vascular graft that mechanically matches the patients native artery over the expected physiologic range of pressures. The creation of an optimized mechanical graft will hopefully lead to an improvement in patency rates. The mechanical equivalency between the graft and the host artery is defined locally by several criteria including the diameter upon inflation, the elasticity at mean pressure, and axial force. A single parameter mathematical for a thin-walled tube is used to describe of the final mechanical behavior of a synthetic graft. For the general problem, the objective would be to fabricate a mechanics-matching vascular graft for each host artery. Typically, fabrication parameters are set initially and the properties of the fabricated graft are measured. However, by modeling the entire fabrication process and final mechanical properties, it is possible to invert the situation and let the typical output mechanical values be used to define the fabrication parameters. The resultant fabricated graft will then be mechanically matching. As a proof-of-concept, several prototype synthetic grafts were manufactured and characterized by a single Invariant to match a canine artery. The resultant graft equaled the diameter upon inflation, the elasticity at mean pressure, and axial force of the native canine artery within 6%. An alternative to making an individual graft for each artery is also presented. A surgeon may choose the best graft from a set of pre-manufactured grafts, using a computer program algorithm for best fit using two parameters in a neighborhood. The design optimization problem was solved for both canine carotid and human coronary arteries. In conclusion, the overall process of design, fabrication and selection of a mechanics matching synthetic vascular graft is shown to be reliable and robust.

Calcific aortic valve disease (CAVD) is one of the most common causes of cardiovascular disease in North America. Mechanical factors have been closely linked to the pathogenesis of CAVD and may contribute to the disease by actively regulating the mechanobiology of valve interstitial cells (VICs). Mechanical forces affect VIC function through interactions between the VIC and the extracellular matrix (ECM). Studies have shown that the transfer of mechanical stimulus during cell-ECM interaction depends on the local material properties at hierarchical length scales encompassing tissue, cell and cytoskeleton. In this thesis, biomechanical tools were developed and applied to investigate hierarchical cell-ECM interactions, using VICs and valve tissue as a model system. Four topics of critical importance to understanding VIC-ECM interactions were studied: focal biomechanical material properties of aortic valve tissue; viscoelastic properties of VICs; transduction of mechanical deformation from the ECM to the cytoskeletal network; and the impact of altered cell-ECM interactions on VIC survival. To measure focal valve tissue properties, a micropipette aspiration (MA) method was implemented and validated. It was found that nonlinear elastic properties of the top layer of a multilayered biomaterial can be estimated by MA by using a pipette with a diameter smaller than the top layer thickness. Using this approach, it was shown that the effective stiffness of the fibrosa layer is greater than that of the ventricularis layer in intact aortic valve leaflets (p<0.01). To characterize the viscoelastic properties of VICs, an inverse FE method of single cell MA was developed and compared with the analytical half-space model. It was found that inherent differences in the half-space and FE models of single cell MA yield different cell viscoelastic material parameters. However, under particular experimental conditions, the parameters estimated by the half-space model are statistically indistinguishable from those predicted by the FE model. To study strain transduction from the ECM to cytoskeleton, an improved texture correlation algorithm and a uniaxial tension release device were developed. It was found that substrate strain fully transfers to the cytoskeletal network via focal adhesions in live VICs under large strain tension release. To study the effects of cell-ECM interactions on VIC survival, two mechanical stimulus systems that can simulate the separate effects of cell contraction and cell monolayer detachment were developed. It was found that cell sheet detachment and disrupted cell-ECM signaling is likely responsible for the apoptosis of VICs grown in culture on thin collagen matrices, leading to calcification. The studies presented in this thesis refine existing biomechanical tools and provide new experimental and analytical tools with which to study cell-ECM interactions. Their application resulted in an improved understanding of hierarchical valve biomechanics, mechanotransduction, and mechanobiology.

Calcific aortic valve disease (CAVD) is one of the most common causes of cardiovascular disease in North America. Mechanical factors have been closely linked to the pathogenesis of CAVD and may contribute to the disease by actively regulating the mechanobiology of valve interstitial cells (VICs). Mechanical forces affect VIC function through interactions between the VIC and the extracellular matrix (ECM). Studies have shown that the transfer of mechanical stimulus during cell-ECM interaction depends on the local material properties at hierarchical length scales encompassing tissue, cell and cytoskeleton. In this thesis, biomechanical tools were developed and applied to investigate hierarchical cell-ECM interactions, using VICs and valve tissue as a model system. Four topics of critical importance to understanding VIC-ECM interactions were studied: focal biomechanical material properties of aortic valve tissue; viscoelastic properties of VICs; transduction of mechanical deformation from the ECM to the cytoskeletal network; and the impact of altered cell-ECM interactions on VIC survival. To measure focal valve tissue properties, a micropipette aspiration (MA) method was implemented and validated. It was found that nonlinear elastic properties of the top layer of a multilayered biomaterial can be estimated by MA by using a pipette with a diameter smaller than the top layer thickness. Using this approach, it was shown that the effective stiffness of the fibrosa layer is greater than that of the ventricularis layer in intact aortic valve leaflets (p<0.01). To characterize the viscoelastic properties of VICs, an inverse FE method of single cell MA was developed and compared with the analytical half-space model. It was found that inherent differences in the half-space and FE models of single cell MA yield different cell viscoelastic material parameters. However, under particular experimental conditions, the parameters estimated by the half-space model are statistically indistinguishable from those predicted by the FE model. To study strain transduction from the ECM to cytoskeleton, an improved texture correlation algorithm and a uniaxial tension release device were developed. It was found that substrate strain fully transfers to the cytoskeletal network via focal adhesions in live VICs under large strain tension release. To study the effects of cell-ECM interactions on VIC survival, two mechanical stimulus systems that can simulate the separate effects of cell contraction and cell monolayer detachment were developed. It was found that cell sheet detachment and disrupted cell-ECM signaling is likely responsible for the apoptosis of VICs grown in culture on thin collagen matrices, leading to calcification. The studies presented in this thesis refine existing biomechanical tools and provide new experimental and analytical tools with which to study cell-ECM interactions. Their application resulted in an improved understanding of hierarchical valve biomechanics, mechanotransduction, and mechanobiology.

During development of tissues, cells collectively organize to form complex patterns and morphologies. A general feature of many developing epithelia is their distinct organization into cellular compartments of different cell lineages. The interfaces between these compartments, called compartment boundaries, maintain straight and sharp morphologies. The interfaces play key roles in tissue development and pattern formation. An important model system to study the morphology of compartment boundaries during development is the wing disc of the fruit fly. Two compartment boundaries exist in the fly wing disc, the anteroposterior (AP) boundary and the dorsoventral (DV) boundary. A crucial question is how compartment boundaries are shaped and remain stable during growth. In this work, we discuss the dynamics and mechanisms of compartment boundaries in developing epithelia. We analyze the general features of interfacial phenomena in coarse- grained models of passive and active fluids. We introduce a continuum description of tissues with two cell types. This model allows us to study the propagation of interfaces due to the interplay of cell dynamics and tissue mechanics. We also use a vertex model to describe cellular compartments in growing epithelia. The vertex model accounts for cell mechanics and describes a 2D picture of tissues where the network of adherens junctions characterizes cell shapes. We use this model to study the general physical mechanisms by which compartment boundaries are shaped. We quantify the stresses in the cellular network and discuss how cell mechanics and growth influence the stress profile. With the help of the anisotropic stress profile near the interfaces we calculate the interfacial tension. We show that cell area pressure, cell proliferation rate, orientation of cell division, cell elongation created by external stress, and cell bond tension all have distinct effects on the morphology of interfaces during tissue growth. Furthermore, we investigate how much different mechanisms contribute to the effective interfacial tension. We study the mechanisms shaping the DV boundary in wing imaginal disc at different stages during the development. We analyze the images of wing discs to quantify the roughness of the DV boundary and average cell elongation in its vicinity. We quantify increased cell bond tension along the boundary and analyze the role of localized reduction in cell proliferation on the morphology of the DV boundary. We use experimentally determined values for cell bond tension, cell elongation and bias in orientation of cell division in simulations of tissue growth in order to reproduce the main features of the time-evolution of the DV boundary shape.