The application of agent-based modeling and fuzzy-logic controllers for the study of magnesium biomaterials

Agent-based modeling (ABM) is a powerful approach for studying complex systems and their underlying properties by explicitly modeling the actions and interactions of individual agents. Over the past decade, numerous software programs have been developed to address the needs of the ABM community. However, these solutions often suffer from limitations in design, a lack of comprehensive documentation, or poor performance. As the first objective of this thesis, we introduce CppyABM-a general-purpose software for ABM that provides simulation tools in both Python and C++. CppyABM also enables ABM development using a combination of C++ and Python, taking advantage of the computational performance of C++ and the data analysis and visualization tools of Python. We demonstrate the capabilities of CppyABM through its application to various problems in ecology, virology, and computational biology. As the second objective of this thesis, we use ABM and fuzzy logic controllers (FLCs) to numerically study the effects of magnesium (Mg2+) ions on osteogenesis. Mg-based materials have emerged as the next generation of biomaterials that degrade in the body after implantation and eliminate the need for secondary surgery. We develop two computer models using ABM and FLC and calibrate them based on cell culture experiments. The models were able to capture the regulatory effects of Mg2+ ions and other important factors such as inflammatory cytokines on mesenchymal stem cells (MSC) activities. The models were also able to shed light on the fundamental differences in the cells cultured in different experiments such as proliferation capacity and sensitivity to environmental factors

The Resting Potential and K+ Currents in Primary Human Articular Chondrocytes

Human transplant programs provide significant opportunities for detailed in vitro assessments of physiological properties of selected tissues and cell types. We present a semi-quantitative study of the fundamental electrophysiological/biophysical characteristics of human chondrocytes, focused on K+ transport mechanisms, and their ability to regulate to the resting membrane potential, Em. Patch clamp studies on these enzymatically isolated human chondrocytes reveal consistent expression of at least three functionally distinct K+ currents, as well as transient receptor potential (TRP) currents. The small size of these cells and their exceptionally low current densities present significant technical challenges for electrophysiological recordings. These limitations have been addressed by parallel development of a mathematical model of these K+ and TRP channel ion transfer mechanisms in an attempt to reveal their contributions to Em. In combination, these experimental results and simulations yield new insights into: (i) the ionic basis for Em and its expected range of values; (ii) modulation of Em by the unique articular joint extracellular milieu; (iii) some aspects of TRP channel mediated depolarization-secretion coupling; (iv) some of the essential biophysical principles that regulate K+ channel function in “chondrons.” The chondron denotes the chondrocyte and its immediate extracellular compartment. The presence of discrete localized surface charges and associated zeta potentials at the chondrocyte surface are regulated by cell metabolism and can modulate interactions of chondrocytes with the extracellular matrix. Semi-quantitative analysis of these factors in chondrocyte/chondron function may yield insights into progressive osteoarthritis

Utilising marine collagen as a niche structure for enhanced osteoarthritic repair

Collagen is an abundant structural protein in the extracellular matrix and plays a role in both structural integrity and support that guides tissue formation and homeostasis. Collagen or matrix disruption, leading to altered cell-matrix interactions, is implicated in disease pathophysiology. Collagen has in turn become an attractive biomaterial in regenerative medicine, proving valuable in various long-term, robust repair strategies. Osteoarthritis (OA) is a multifactorial disease leading to the degeneration of articular cartilage, affecting approximately 8.5 million in the UK population. Current repair procedures require surgical interventions, with varying degrees of success, easing pain and recovery time. Future repair strategies are now being focused around the formation of new tissue for implantation, incorporating collagen scaffolds, donor cell populations and functional differentiation. This thesis presents a thorough characterization of a novel jellyfish (R.pulmo) source of collagen, benchmarked against mammalian collagen like material compatible with human and bovine chondroprogenitor cell invasion, proliferation, and differentiation. Significantly, no increased immune response was observed compared to research and clinical grade mammalian collagen sources during in vitro examination. Excitingly, jellyfish collagen (JCol) also demonstrated hallmarks of chondro-mimicry, enabling bovine chondroprogenitor cell invasion, proliferation and differentiation. Using a sponge scaffold design JCol provides adequate structural cell-matrix support appropriate for enhanced chondrogenesis in the presence of TGFβ1. The robust body of evidence presented supports the development of JCol, a seemingly inert collagen source, for tissue engineering and/or regenerative medicine applications. Analogous to native articular cartilage, this supports further development of jellyfish collagen as a biomaterial for matrix assisted chondrocyte implantation (MACI) approaches in OA repair. Jellagen, industrial sponsor for the project, have adopted central observations from this thesis and are now progressing with wider commercial and development activities to support market and clinical research expansion