Title:

Modelling of biological systems using multidimensional population balances

Biological systems are intrinsically heterogeneous and, consequently, their mathematical descriptions should account for this heterogeneity as it often influences the dynamic behaviour of the individual cells. For example, in the cell cycle dependent production ofproteins, it is necessary to account for the distribution of the individual cells with respect to their position in the cell cycle as this has a strong influence on protein production. A second notable example is the formation of cancerous cells. In this case, the failure of regulatory mechanisms results in the transition of somatic cells to their cancerous state. Therefore, in developing the corresponding mathematical model, it is necessary to consider both the different states of the cells as well as their regulation. In this regard, the population balance equation is the ideal mathematical framework to capture cell population heterogeneity as it elegantly takes into account the distribution of cell populations with respect to their intracellular state together with the phenomena of cell birth, division, differentiation and recombination. Recent developments in solution algorithms together with the exponential increase in computational abilities now permit the efficient solution of onedimensional population balance models which attribute the heterogeneity of cell populations to differences in the age or mass of individual cells. The inherent complexity of biological systems implies that the differentiation of cells based on a single characteristic alone may not be sufficient to capture the underlying biological phenomena. Therefore, current research is focussing on the development of multidimensional population balances that consider the differentiation of cells based on multiple characteristics, most notably, the state of cells with respect to key intracellular metabolites. However, conventional numerical techniques are inefficient for the solution of the formulated population balance models and this warrants the development of novel, tailormade algorithms. This thesis presents one such solution algorithm and demonstrates its application to the study of several biological systems. The algorithm developed herein employs a finitevolume technique to convert the partialdifferential equation comprising the population balance model into a set of ordinary differential equations. A twotier technique based on the solution technique for inhomogeneous differential equations is then developed to solve the system of ordinary differential equations. This approach has two main advantages: (a) the decomposition technique considerably reduces the stiffness of the system of equations enabling more efficient solution, and (b) semianalytical solutions for the integrals employed in the modelling of cell division and differentiation can be obtained further reducing computation times. Further improvements in solution efficiency are obtained by the formulation of a twolevel discretisation algorithm. In this approach, processes such as cell growth which are more sensitive to the discretisation are solved using a fine grid whereas less sensitive processes such as cell' division  which are usually more computationally expensive  are solved using a coarse grid at a higher level. Thus, further improvements are obtained in the efficiency of the technique. The solution algorithm is applied to various multidimensional population balance models of biological systems. The technique is first demonstrated on models of oscillatory dynamics in yeast glycolysis, cellcycle related oscillations in eukaryotes, and circadian oscillations in crayfish. A model of cell division and proliferation control in eukaryotes is an example of a second class of problems where extracellular phenomena influence the behaviour of cells. As a third case for demonstration, a hybrid model of biopolymer accumulation in bacteria is formulated. In this case, cybernetic modelling principles are used to account for intracellular competitions while the population balance framework takes into consideration the heterogeneity of the cell population. Another important aspect in the formulation ofmultidimensional population balances is the development of the intracellular models themselves. While research in the biological sciences is permitting the formulation of detailed dynamic models of various bioprocesses, the accurate estimation of the kinetic parameters in these models can be difficult due to the unavailability of sufficient experimental data. This can result in considerable parametric uncertainty as is demonstrated on a simple cybernetic' model of biopolymer accumulation in bacteria. However, it is shown that, via the use of systems engineering tools, experiments can be designed that permit the accurate estimation of all model parameters even when measurements pertaining to all modelled quantities are unavailable.
