"A quantitative understanding of the complex interactions between cells, soluble factors, and the biological and mechanical properties of biomaterials is required to guide cell remodeling towards regeneration of healthy tissue rather than fibrocontractive tissue. The goal of this thesis was to elucidate the interactions between the boundary stiffness of three-dimensional (3D) matrix and soluble factors on valvular interstitial cell (VIC) phenotype with a quantitative approach. The first part of the work presented in this thesis was to characterize the combined effects of boundary stiffness and transforming growth factor-β1 (TGF-β1) on cell-generated forces and collagen accumulation. We first generated a quantitative map of cell-generated tension in response to these factors by culturing VICs within micro-scale fibrin gels between compliant posts (0.15-1.05 nN/nm) in chemically-defined media with TGF-β1 (0-5 ng/mL). The VICs generated 100 to 3000 nN/cell after one week of culture, and multiple regression modeling demonstrated, for the first time, quantitative interaction (synergy) between these factors in a 3D culture system. We then isolated passive and active components of tension within the micro-tissues and found that cells cultured with high levels of stiffness and TGF-β1 expressed myofibroblast markers and generated substantial residual tension in the matrix yet, surprisingly, were not able to generate additional tension in response to membrane depolarization signifying a state of continual maximal contraction. In contrast, negligible residual tension was stored in the low stiffness and TGF-β1 groups indicating a lower potential for shrinkage upon release. We then studied if ECM could be generated under the low tension environment and found that TGF-β1, but not EGF, increased de novo collagen accumulation in both low and high tension environments roughly equally. Combined, these findings suggest that isometric cell force, passive retraction, and collagen production can be tuned by independently altering boundary stiffness and TGF-β1 concentration. In the second part, by using the quantitative information obtained from the first part, we investigated the effects of dynamic changes in stiffness on cell phenotype in a 3D protein matrix, quantitatively. Our novel method utilizing magnetic force to constrain the motion of one of two flexible posts between which VIC-populated micro-tissues were cultured effectively doubled the boundary stiffness and resulted in a significant increase in cell-generated forces. When the magnetic force was removed, the effective boundary stiffness was halved and the tissue tension dropped to 65-87% of the peak value. Surprisingly, following release the cell-generated forces continued to increase for the next two days rather than reducing down to the homeostatic tension level of the control group with identical (but constant) boundary stiffness. The rapid release of tension with the return to baseline boundary stiffness did not result in a decrease in number of cells with α-SMA positive stress fibers or an increase in apoptosis. When samples were entirely released from the boundaries and cultured free floating (where tension is minimal but cannot be measured), the proportion of apoptotic cells in middle region of the micro-tissues increased more than five-fold to 31%. Together, these data indicate that modest temporary changes in boundary stiffness can have lasting effects on myofibroblast activation and persistence in 3D matrices, and that a large decrease in the ability of the cells to generate tension is required to trigger de-differentiation and apoptosis. "

Successful field waterflood is a crucial prerequisite for improving the performance before EOR methods, such as ASP, SP, and P flooding, are applied in the field. Excess water production is a major problem in mature waterflooded oil fields that leads to early well abandonment and unrecoverable hydrocarbon. Gel treatments at the injection and production wells to preferentially plug the thief zones are cost-effective methods to improve sweep efficiency in reservoirs and reduce excess water production during hydrocarbon recovery. There are extensive experimental studies performed by some researchers in the past to investigate the performance of gels in conformance control and decreasing water production in mature waterflooded reservoirs, but no substantial modeling work has been done to simulate these experiments and predict the results for large field cases. We developed a novel, 3-dimensional chemical compositional and robust general reservoir simulator (UTGEL) to model gel treatment processes. The simulator has the capability to model different types of microgels, such as preformed particle gels (PPG), thermally active polymers (TAP), pH-sensitive microgels, and colloidal dispersion gels (CDG). The simulator has been validated for gel flooding using laboratory and field scale data. The simulator helps to design and optimize the flowing gel injection for conformance control processes in larger field cases. The gel rheology, adsorption, resistance factor and residual resistance factor with salinity effect, gel viscosity, gel kinetics, and swelling ratio were implemented in UTGEL. Several simulation case studies in fractured and heterogeneous reservoirs were performed to illustrate the effect of gel on production behavior and water control. Laboratory results of homogeneous and heterogeneous sandpacks, and Berea sandstone corefloods were used to validate the PPG transport models. Simulations of different heterogeneous field cases were performed and the results showed that PPG can improve the oil recovery by 5-10% OOIP compared to waterflood. For recovery from fractured reservoirs by waterflooding, injected water will flow easily through fractures and most part of reservoir oil will remain in matrix blocks unrecovered. Recovery from these reservoirs depends on matrix permeability, wettability, fracture intensity, temperature, pressure, and fluid properties. Chemical processes such as polymer flooding (P), surfactant/polymer (SP) flooding and alkali/surfactant/polymer (ASP) flooding are being used to enhance reservoir energy and increase the recovery. Chemical flooding has much broader range of applicability than in the past. These include high temperature reservoirs, formations with extreme salinity and hardness, naturally fractured carbonates, and sandstone reservoirs with heavy and viscous crude oils. The recovery from fractured carbonate reservoirs is frequently considered to be dominated by spontaneous imbibition. Therefore, any chemical process which can enhance the rate of imbibition has to be studied carefully. Wettability alteration using chemicals such as surfactant and alkali has been studied by many researchers in the past years and is recognized as one of the most effective recovery methods in fractured carbonate reservoirs. Injected surfactant will alter the wettability of matrix blocks from oil-wet to water-wet and also reduce the interfacial tension to ultra-low values and consequently more oil will be recovered by spontaneous co-current or counter-current imbibition depending on the dominant recovery mechanism. Accurate and reliable up-scaling of chemical enhanced oil recovery processes (CEOR) are among the most important issues in reservoir simulation. The important challenges in up-scaling CEOR processes are predictability of developed dimensionless numbers and also considering all the required mechanisms including wettability alteration and interfacial tension reduction. Thus, developing new dimensionless numbers with improved predictability at larger scales is of utmost importance in CEOR processes. There are some scaling groups developed in the past for either imbibition or coreflood experiments but none of them were predictive because all the physics related to chemical EOR processes (interfacial tension reduction and wettability alteration) were not included. Furthermore, most of commercial reservoir simulators do not have the capability to model imbibition tests due to lack of some physics, such as surfactant molecular diffusion. The modeling of imbibition cell tests can aid to understand the mechanisms behind wettability alteration and consequently aid in up-scaling the process. Also, modeling coreflood experiments for fractured vuggy carbonates is challenging. Different approaches of random permeability distribution and explicit fractures were used to model the experiments which demonstrate the validity and ranges of applicability of upscaled procedures, and also indicate the importance of viscous and capillary forces in larger scales. The simulation models were then used to predict the recovery response times for larger cores.