An efficient stochastic algorithm for studying coagulation dynamics and gelation phenomena

A new class of efficient stochastic algorithms for the numerical treatment of coagulation processes is proposed. The algorithms are based on the introduction of fictitious jumps combined with an acceptance-rejection technique for distributions depending on particle size. The increased efficiency is demonstrated by numerical experiments. In particular, gelation phenomena are studied

Coagulation and Fragmentation Models

Analysis of coagulation and fragmentation is crucial to understanding many processes of scientific and industrial importance. In recent years this has led to intensified research activities in the areas of differential equations, probability theory, and combinatorics. The purpose of the workshop was to bring together people from these different areas working on various aspects of coagulation and fragmentation. We believe that the insights resulting from the interactions which have been stimulated that week should lead to further advances both in the development of mathematical techniques and in new applications

Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics

We revisit two basic Direct Simulation Monte Carlo Methods to model aggregation kinetics and extend them for aggregation processes with collisional fragmentation (shattering). We test the performance and accuracy of the extended methods and compare their performance with efficient deterministic finite-difference method applied to the same model. We validate the stochastic methods on the test problems and apply them to verify the existence of oscillating regimes in the aggregation-fragmentation kinetics recently detected in deterministic simulations. We confirm the emergence of steady oscillations of densities in such systems and prove the stability of the oscillations with respect to fluctuations and noise.Comment: 19 pages, 2 figures, 4 table

Stochastic weighted particle methods for population balance equations

A class of stochastic algorithms for the numerical treatment of population balance equations is introduced. The algorithms are based on systems of weighted particles, in which coagulation events are modelled by a weight transfer that keeps the number of computational particles constant. The weighting mechanisms are designed in such a way that physical processes changing individual particles (such as growth, or other surface reactions) can be conveniently treated by the algorithms. Numerical experiments are performed for complex laminar premixed flame systems. Two members of the class of stochastic weighted particle methods are compared to each other and to a direct simulation algorithm. One weighted algorithm is shown to be consistently better than the other with respect to the statistical noise generated. Finally, run times to achieve fixed error tolerances for a real flame system are measured and the better weighted algorithm is found to be up to three times faster than the direct simulation algorithm

Stochastic weighted particle methods for population balance equations

A class of stochastic algorithms for the numerical treatment of population balance equations is introduced. The algorithms are based on systems of weighted particles, in which coagulation events are modelled by a weight transfer that keeps the number of computational particles constant. The weighting mechanisms are designed in such a way that physical processes changing individual particles (such as growth, or other surface reactions) can be conveniently treated by the algorithms. Numerical experiments are performed for complex laminar premixed flame systems. Two members of the class of stochastic weighted particle methods are compared to each other and to a direct simulation algorithm. One weighted algorithm is shown to be consistently better than the other with respect to the statistical noise generated. Finally, run times to achieve fixed error tolerances for a real flame system are measured and the better weighted algorithm is found to be up to three times faster than the direct simulation algorithm

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 one-dimensional 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 multi-dimensional 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, tailor-made 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 finite-volume technique to convert the partial-differential equation comprising the population balance model into a set of ordinary differential equations. A two-tier 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 two-level 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 multi-dimensional population balance models of biological systems. The technique is first demonstrated on models of oscillatory dynamics in yeast glycolysis, cell-cycle 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 ofmulti-dimensional 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.Imperial Users onl

Multi-Scale Fluctuations in Non-Equilibrium Systems: Statistical Physics and Biological Application

Understanding how fluctuations continuously propagate across spatial scales is fundamental for our understanding of inanimate matter. This is exemplified by self-similar fluctuations in critical phenomena and the propagation of energy fluctuations described by the Kolmogorov-Law in turbulence. Our understanding is based on powerful theoretical frameworks that integrate fluctuations on intermediary scales, as in renormalisation group or coupled mode theory. In striking contrast to typical inanimate systems, living matter is typically organised into a hierarchy of processes on a discrete set of spatial scales: from biochemical processes embedded in dynamic subcellular compartments to cells giving rise to tissues. Therefore, the understanding of living matter requires novel theories that predict the interplay of fluctuations on multiple scales of biological organisation and the ensuing emergent degrees of freedom. In this thesis, we derive a general theory of the multi-scale propagation of fluctuations in non-equilibrium systems and show that such processes underlie the regulation of cellular behaviour. Specifically, we draw on paradigmatic systems comprising stochastic many-particle systems undergoing dynamic compartmentalisation. We first derive a theory for emergent degrees of freedom in open systems, where the total mass is not conserved. We show that the compartment dynamics give rise to the localisation of probability densities in phase space resembling quasi-particle behaviour. This emergent quasi-particle exhibits fundamentally different response kinetics and steady states compared to systems lacking compartment dynamics. In order to investigate a potential biological function of such quasi-particle dynamics, we then apply this theory to the regulation of cell death. We derive a model describing the subcellular processes that regulate cell death and show that the quasi-particle dynamics gives rise to a kinetic low-pass filter which suppresses the response of the cell to fast fluituations in cellular stress signals. We test our predictions experimentally by quantifying cell death in cell cultures subject to stress stimuli varying in strength and duration. In closed systems, where the total mass is conserved, the effect of dynamic compartmentalisation depends on details of the kinetics on the scale of the stochastic many-particle dynamics. Using a second quantisation approach, we derive a commutator relation between the kinetic operators and the change in total entropy. Drawing on this, we show that the compartment dynamics alters the total entropy if the kinetics of the stochastic many-particle dynamics violate detailed balance. We apply this mechanism to the activation of cellular immune responses to RNA-virus infections. We show that dynamic compartmentalisation in closed systems gives rise to giant density fluctuations. This facilitates the emergence of gelation under conditions that violate theoretical gelation criteria in the absence of compartment dynamics. We show that such multi-scale gelation of protein complexes on the membranes of dynamic mitochondria governs the innate immune response. Taken together, we provide a general theory describing the multi-scale propagation of fluctuations in biological systems. Our work pioneers the development of a statistical physics of such systems and highlights emergent degrees of freedom spanning different scales of biological organisation. By demonstrating that cells manipulate how fluctuations propagate across these scales, our work motivates a rethinking of how the behaviour of cells is regulated

Study of industrial titania synthesis using a hybrid particle-number and detailed particle model

We apply a hybrid particle model to study synthesis of particulate titania under representative industrial conditions. The hybrid particle model employs a particle-number description for small particles, and resolves complicated particle morphology where required using a detailed particle model. This enables resolution of particle property distributions under fast process dynamics. Robustness is demonstrated in a network of reactors used to simulate the industrial process. The detailed particle model resolves properties of the particles that determine end product quality and post-processing efficiency, including primary particle size and degree of aggregate cohesion. Sensitivity of these properties to process design choices is quantified, showing that higher temperature injections produce more sintered particles; more frequent injections narrow the geometric standard deviation of primary particle diameter; and chlorine dilution reduces particle size and size variance. Structures of a typical industrial particle are compared visually with simulated particles, illustrating similar aggregate features with slightly larger primary particles