Various types of mammalian cells exhibit the remarkable ability to adapt to external applied mechanical stresses and strains. This ability allows cells to maintain a stable endogenous mechanical tension at a preferred (homeostatic) level, which is of great importance for normal physiological function of cells and tissues, and for a protection from various diseases, including atherosclerosis and cancer. Previous studies have shown that the cell ability to maintain tensional homeostasis is cell type-dependent. For example, isolated endothelial cell cannot maintain tensional homeostasis, whereas clusters of endothelial cells can, more so the greater the size of the cluster is. On the other hand, cell clustering does not affect tensional homeostasis of fibroblasts and vascular smooth muscle cells. Underlying mechanisms for these behaviors of different cell types are largely unknown. In this study, we combined theoretical analysis and mathematical modeling to investigate several biophysical factors, including cluster shape and size, magnitude and dynamics of cellular traction forces, and applied shear forces that may influence tensional homeostasis in cells and clusters. We developed two-dimensional models of cells clusters of different shapes and sizes. To simulate temporal fluctuations of cell-extracellular matrix traction forces, we used a Monte Carlo approach. We also applied physical forces obtained from previous experimental measurements to the models. Results of the analysis and modeling revealed that cluster size, magnitude and dynamics of focal adhesion traction forces have a major influence on traction field variability, whereas the influence of cluster shape appears to be minor. The dynamics of traction forces seems to be related to cell types and it can explain why in certain cell types, such as endothelial cells, cell clustering promotes tensional homeostasis, whereas in other cell types, such as fibroblasts, clustering has virtually no effect on homeostasis. To further investigate mechanisms that may affect tensional homeostasis, we investigated the effect of applied steady shear stress on the traction field dynamics of endothelial cells and clusters. We applied steady shear stress to our two-dimensional model of cell clusters and then computed ensuing changes in the traction force variability. These simulations mimicked the effect of flow-induced shear stress on tensional homeostasis of endothelial cells and clusters. We found that under steady shear stress, temporal fluctuations of the traction field of endothelial cells became attenuated. This result agrees with the viewpoint that steady shear flow promotes tensional homeostasis in the endothelium. Together, results of this study advance our understanding of biophysical mechanisms that contribute to the cell ability to maintain tensional homeostasis. Furthermore, these results will help us to modify our current experimental procedures, as well as to design new experiments for our investigation of tensional homeostasis. / 2020-10-22T00:00:00Z

Cell-cell adhesion is important to understanding the mechanics of cell-cell interactions. A recent study of cell adhesion was conducted by others using an Atomic Force Microscopy to measure forces when two cells are brought together and then pulled apart. When the two cells come in contact, the adhesion molecules of one cell bind to molecules of the other cell throughout the contact region. When the two cells are then pulled apart, some of these bonds break off while others lead to the formation of tethers which also eventually also break. These phenomena create a force-time curve, which is difficult to interpret. In order to model this experiment and understand details of the experiments, a series of modules were added to a 2D finite element model used previously to model cells and their mechanical interactions. These new modules were designed to replicate mechanical processes associated with molecular detachments at the cell-cell interface. The enhanced model includes several new types of elements including an InterfaceTruss, which characterizes individual adhesion bonds between two cells. Parametric studies carried out using the new finite element model showed that cytoplasmic viscosity, actin cortex stiffness, and the lifetime of the molecular attachments at the cell-cell interface all affect one or more portions of the force time curve. The model was able to model virtually all of the significant features of the experimental force-time curve, and when suitable parameter values are chosen, the model closely approximates the observed features of the experimental curves. The new finite element model provides an effective tool for investigating features of the cell-cell interface. It also provides a powerful tool for learning about the mechanical properties of the cells and their bonds and tethers and for the design of new cell adhesion experiments.

Cell-cell adhesion is important to understanding the mechanics of cell-cell interactions. A recent study of cell adhesion was conducted by others using an Atomic Force Microscopy to measure forces when two cells are brought together and then pulled apart. When the two cells come in contact, the adhesion molecules of one cell bind to molecules of the other cell throughout the contact region. When the two cells are then pulled apart, some of these bonds break off while others lead to the formation of tethers which also eventually also break. These phenomena create a force-time curve, which is difficult to interpret. In order to model this experiment and understand details of the experiments, a series of modules were added to a 2D finite element model used previously to model cells and their mechanical interactions. These new modules were designed to replicate mechanical processes associated with molecular detachments at the cell-cell interface. The enhanced model includes several new types of elements including an InterfaceTruss, which characterizes individual adhesion bonds between two cells. Parametric studies carried out using the new finite element model showed that cytoplasmic viscosity, actin cortex stiffness, and the lifetime of the molecular attachments at the cell-cell interface all affect one or more portions of the force time curve. The model was able to model virtually all of the significant features of the experimental force-time curve, and when suitable parameter values are chosen, the model closely approximates the observed features of the experimental curves. The new finite element model provides an effective tool for investigating features of the cell-cell interface. It also provides a powerful tool for learning about the mechanical properties of the cells and their bonds and tethers and for the design of new cell adhesion experiments.

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In this thesis, we develop a new computational method using Voronoi vertex model and energy to describe the cell-cell interaction among the epithelial tissue. Several studies and simulations will be showed such as equilibrium states, wound closure process, and abnormal growth. We also perform analysis on circular epithelial wound closure process.

In this thesis, we develop a new computational method using Voronoi vertex model and energy to describe the cell-cell interaction among the epithelial tissue. Several studies and simulations will be showed such as equilibrium states, wound closure process, and abnormal growth. We also perform analysis on circular epithelial wound closure process.

In this thesis I explore how migratory properties of the model organism Dictyostelium discoideum are influenced by dimensionality and topology of the environment that surrounds the cell. Additionally, I sought to develop a microfluidic device able to measure mechanical properties of single cells with a sufficient throughput to account for the inherent heterogeneity of biological samples. Throughout this thesis I made use of microfabrication methods such as photo-lithography and soft-lithography, to develop ad hoc microstructured substrates. These tools enabled me to tackle different biological and biomedical questions related to cell migration and cell mechanics. Confining cells into channels with low dimensionality appeared to regulate the velocity of cellular locomotion, as well as the migration strategy adopted by the cell. Spatial confinement induced an altered arrangement of the acto-myosin cytoskeleton and microtubules. Moreover, the spatial constraint resulted in a simplified, mono-dimensional migration, characterised by constant average speed. Additionally, some cellular processes tended to occur in a periodic fashion, upon confinement. Interestingly, if Dictyostelium cells migrated through asymmetric bifurcating micro- channels, they appeared to be able to undergo a ’decision-making’ process leading to a directional bias. Although the biophysical mechanism underlying this response is yet to be understood, the data shown in this thesis suggest that Dictyostelium cells respond to differences in local concentrations of chemoattractants. The speed of a cell that crawls in a channel also depends on the cell’s stiffness, that in turn represents a measure of the density and structure of its cytoskeleton. To date, only a few methods have been developed to investigate cell mechanics with sufficient throughput. This motivated my interest in developing a microfluidic-based device that, exploiting the recording capabilities of a modern high speed camera, enabled me to assess the cellular mechanical properties at a rate greater than 10,000 cells per second, without the need for cell labelling. In this thesis I presented an example of how this method can be employed to detect differences between healthy and cancerous prostate cells, as well as to differentiate between prostate and bladder cancer cells based on their mechanical response. In conclusion, the work presented in this thesis highlights the interdisciplinarity required to investigate complex biological and biomedical problems. Specifically, the use of quantitative approaches that span from microtechnology, live imaging, computer vision and computational modelling enabled me to investigate novel biological processes as well as to explore new diagnostic technologies that aim to promote the improvement of the future healthcare.

Cell shape is important to understanding the mechanics of three-dimensional (3D) cell aggregates. When an aggregate of embryonic cells is compressed between parallel plates, the cell mass and the cells of which it is composed flatten. Over time, the cells typically move past one another and return to their original, spherical shapes, even during sustained compression, although the profile of the aggregate changes little once plate motion stops. Although the surface and interfacial tensions of cells have been attributed to driving these internal movements, measurements of these properties have largely eluded researchers. Here, an existing 3D finite element model, designed specifically for the mechanics of cell-cell interactions, is enhanced so that it can be used to investigate aggregate compression. The formulation of that model is briefly presented and enhancements made to its rearrangement algorithms discussed. Simulations run using the model show that the rounding of interior cells is governed by the ratio between the interfacial tension and cell viscosity, whereas the shape of cells in contact with the medium or the compression plates is dominated by their respective cell-medium or cell-plate surface tensions. The model also shows that as an aggregate compresses, its cells elongate more in the circumferential direction than the radial direction. Since experimental data from compressed aggregates are anticipated to consist of confocal sections, geometric characterization methods are devised to quantify the anisotropy of cells and to relate cross sections to 3D properties. The average anisotropy of interior cells as found using radial cross sections corresponds more closely with the 3D properties of the cells than data from series of parallel sections. A basis is presented for estimating cell-cell interfacial tensions from the cell shape histories they exhibit during the cell reshaping phase of an aggregate compression test.

Cell shape is important to understanding the mechanics of three-dimensional (3D) cell aggregates. When an aggregate of embryonic cells is compressed between parallel plates, the cell mass and the cells of which it is composed flatten. Over time, the cells typically move past one another and return to their original, spherical shapes, even during sustained compression, although the profile of the aggregate changes little once plate motion stops. Although the surface and interfacial tensions of cells have been attributed to driving these internal movements, measurements of these properties have largely eluded researchers. Here, an existing 3D finite element model, designed specifically for the mechanics of cell-cell interactions, is enhanced so that it can be used to investigate aggregate compression. The formulation of that model is briefly presented and enhancements made to its rearrangement algorithms discussed. Simulations run using the model show that the rounding of interior cells is governed by the ratio between the interfacial tension and cell viscosity, whereas the shape of cells in contact with the medium or the compression plates is dominated by their respective cell-medium or cell-plate surface tensions. The model also shows that as an aggregate compresses, its cells elongate more in the circumferential direction than the radial direction. Since experimental data from compressed aggregates are anticipated to consist of confocal sections, geometric characterization methods are devised to quantify the anisotropy of cells and to relate cross sections to 3D properties. The average anisotropy of interior cells as found using radial cross sections corresponds more closely with the 3D properties of the cells than data from series of parallel sections. A basis is presented for estimating cell-cell interfacial tensions from the cell shape histories they exhibit during the cell reshaping phase of an aggregate compression test.

Out of the growing body of evidence demonstrating the role of higher-order chromatin organization within the nucleus in regulating the functions of the linear sequence of DNA emerges the genome as a physical entity. DNA packs into hierarchical levels of chromatin condensation, which then tailor accessibility to the linear sequence for nuclear processes while also serving as a central feature of nuclear organization. Further, varying condensation state alters the physical properties of the chromatin fiber. These may then exert or facilitate forces aiding in the spatial organization within the nucleus. Yet, this complex concept of nuclear structure even neglects the dynamic aspects of the genome continuously fluctuating and undergoing structural remodeling within the nucleus. Thus, while chromatin position within the nucleus is critical for biological functions including transcription, we must reconcile a particular position of a gene locus with the dynamic and physical nature of chromatin. Here we characterize the physical aspects of the genome associated with its dynamic properties that aid in regulation. We focus on developing techniques that measure the evolution of physical properties associated with nuclear processes. We leverage these techniques, capable of quantifying and spatially resolving its structural state within the nucleus and elucidating the underlying physics of its dynamics, to illuminate physical features associated with cellular processes. Specifically, we investigate the nuclear structural changes associated with growth factor stimulation on primary human cells known to impact large scale gene expression pathways. We also demonstrate dysfunction associated with these physical mechanisms accompany disease pathologies. Thus, we unify the biological understanding of cellular processes within the context of physical features of genome structure, organization and dynamics that are critical to human health and disease.