Dynamics and Control of Oscillatory Bioreactors

Bioreactors are widely used in many industries to generate a range of products using various host cells e.g., yeast, insect, and mammalian cells. Depending on the process, product, and host cell, some bioreactors exhibit sustained periodic behavior in key process variables such as metabolite concentrations, biomass, and product titer. Such dynamical behavior can arise from different mechanisms, including predator-prey dynamics, substrate inhibition, and cell sub-population synchrony. Oscillatory dynamical behavior is undesirable as it can impact downstream processes, especially in a continuous operation, and can make process operations and product quality control more challenging. This article provides an overview of oscillatory dynamics. The mechanisms that give rise to the oscillations and process control strategies for suppressing the oscillations are discussed, while providing insights that go beyond past studies. Alternative process configurations are proposed for bypassing the mechanisms that generate oscillations.Comment: Submitted to Biotechnology Progress, ICB V Special Issue (invited). Pavan Inguva and Krystian Ganko contributed equally to this work. Corresponding author: Richard D. Braat

Feedback Linearizing Control Strategies for Chemical Engineering Applications.

Two widely studied control techniques which compensate for process nonlinearities are feedback linearization (FBL) and nonlinear model predictive control (NMPC). Feedback linearization has a low computational requirement but provides no means to explicitly handle constraints which are important in the chemical process industry. Nonlinear model predictive control provides explicit constraint compensation but only at the expense of high computational requirements. Both techniques suffer from the need for full-state feedback and may have high sensitivities to disturbances. The main work of this dissertation is to eliminate some of the disadvantages associated with FBL techniques. The computation time associated with solving a nonlinear programming problem at each time step restricts the use of NMPC to low-dimensional systems. By using linear model predictive control on top of a FBL controller, it is found that explicit constraint compensation can be provided without large computational requirements. The main difficulty is the required constraint mapping. This strategy is applied to a polymerization reactor, and stability results for discrete-time nonlinear systems are established. To alleviate the need for full-state feedback in FBL techniques it is necessary to construct an observer, which is very difficult for general nonlinear systems. A class of nonlinear systems is studied for which the observer construction is quite easy in that the design mimics the linear case. The class of systems referred to are those in which the unmeasured variables appear in an affine manner. The same observer construction can be used to estimate unmeasured disturbances, thereby providing a reduction in the controller sensitivity to those disturbances. Another contribution of this work is the application of feedback linearization techniques to two novel biotechnological processes. The first is a mixed-culture bioreactor in which coexistence steady states of the two cell populations must be stabilized. These steady states are unstable in the open-loop system since each population competes for the same substrate, and each has a different growth rate. The requirement of a pulsatile manipulated input complicates the controller design. The second process is a bioreactor described by a distributed parameter model in which undesired oscillations must be damped without the use of distributed control

The mathematical model of Schizosaccharomyces pombe : Batch and repeated batch simulations.

Mathematical models are playing an important part in the current developments in engineering, science and biotechnology. Within this field the most fashionable and representative organisms are the ones who are genetically and physiologically tractable. Since the fission yeast Schizosaccharomyces pombe plays a role model among them and its behaviour has medical, genetic and industrial links (related to cancer research, metabolic pathways and beer production), this makes it a particularly interesting organism for study. This dissertation presents the first physiological model ever developed for the yeast S. pombe. The model allows for the simulation and prediction of batch and repeated batch experiments which are an important engineering tool in terms of optimization of industrial processes improving yield in bioreactors by predicting precise values of harvest fraction (HF) and dilution cycle times (DCT). The model has been developed within the generic modelling framework of CelCyMUS (Cell Cycle Model University of Surrey). As part of the research being carried out CelCyMUS has been up-dated by introducing the new Fortran 95 features and utilities in order to exploit its powerful new features and to keep the generic model in pace with technological software advancements. The model is a one-dimensional age-based population balance for the fission yeast S. pombe. It includes the four typical phases (S, G2, M and G1) with the G2 phase divided into two phases (G2A, G2B) and two checkpoints that govern the movement of cells between G1 and S, and G2B and M phases. The transitions (movement of cells between phases) are determined by a probability function related to the consumption of glucose. The G2B-M transition is also dependent on cell size, but since individual growth of cells is related to the consumption of the carbon source (in this case glucose), cell size is dependent upon the amount of glucose consumed per cell. The model also includes a phase for cells facing starvation before going into a meiotic cycle, with some chance of coming back to the mitotic cycle, and a death phase that accounts for cells dying with no chance of recovering at all. Parameters in the S. pombe model have been gathered from experimental data in batch culture reported in literature. Data generated from this specific model have been compared with data from experiments (Fotuhi, 2002) in batch and repeated batch cultures of S. pombe following the behaviour of population balance, consumption of nutrients, and production of metabolites. The new code was tested by successftilly reproducing data from mm-321 hybridoma cell line, the first specific model of a cell line developed in CelCyMUS. As a new feature a model of mass transfer has been incorporated in the generic framework. This mass transfer module accounts for interactions of metabolites (oxygen and carbon dioxide) in the gas and liquid phase of bioreactors. The new S. pombe model was fitted to the experiments of Creanor (1992) on synchronised cultures where the consumption of oxygen was being measured. Such experiments identify two points (G2B and G1) where the rate of oxygen uptake increased in the cycle, doubling the consumption at the end of every cycle. With the model fitted to experimental results in synchronised cultures of S. pombe the model was then used to simulate desynchronised cultures. S. pombe was successfully tested when reproducing experimental data generated by Fotuhi (2002) in S.pombe for batch and repeated batch bioreactors. The S. pombe model was able to simulate cell number, oxygen and glucose consumption. Carbon dioxide and ATP production were predicted by the model however there was no experimental data to compare with. Now that the S. pombe model has been tested against experimental data it will be applied in a model-based observer strategy for the online control of bioreactors

Clustering in Cell Cycle Dynamics with General Response/Signaling Feedback

Motivated by experimental and theoretical work on autonomous oscillations in yeast, we analyze ordinary differential equations models of large populations of cells with cell-cycle dependent feedback. We assume a particular type of feedback that we call Responsive/Signaling (RS), but do not specify a functional form of the feedback. We study the dynamics and emergent behaviour of solutions, particularly temporal clustering and stability of clustered solutions. We establish the existence of certain periodic clustered solutions as well as "uniform" solutions and add to the evidence that cell-cycle dependent feedback robustly leads to cell-cycle clustering. We highlight the fundamental differences in dynamics between systems with negative and positive feedback. For positive feedback systems the most important mechanism seems to be the stability of individual isolated clusters. On the other hand we find that in negative feedback systems, clusters must interact with each other to reinforce coherence. We conclude from various details of the mathematical analysis that negative feedback is most consistent with observations in yeast experiments.Comment: To appear in J. Theoretical Biology 292 (2012), 103-11

Methods in Computational Biology

Modern biology is rapidly becoming a study of large sets of data. Understanding these data sets is a major challenge for most life sciences, including the medical, environmental, and bioprocess fields. Computational biology approaches are essential for leveraging this ongoing revolution in omics data. A primary goal of this Special Issue, entitled “Methods in Computational Biology”, is the communication of computational biology methods, which can extract biological design principles from complex data sets, described in enough detail to permit the reproduction of the results. This issue integrates interdisciplinary researchers such as biologists, computer scientists, engineers, and mathematicians to advance biological systems analysis. The Special Issue contains the following sections:•Reviews of Computational Methods•Computational Analysis of Biological Dynamics: From Molecular to Cellular to Tissue/Consortia Levels•The Interface of Biotic and Abiotic Processes•Processing of Large Data Sets for Enhanced Analysis•Parameter Optimization and Measuremen

Microgravity science and applications bibliography, 1989 revision

This edition of the Microgravity Science and Applications (MSA) Bibliography is a compilation of government reports, contractor reports, conference proceedings, and journal articles dealing with flight experiments utilizing a low gravity environment to elucidate and control various processes, or with ground based activities that provide supported research. It encompasses literature published but not cited in the 1988 Revision and that literature which has been published in the past year. Subdivisions of the Bibliography include: electronic materials, metals, alloys, and composites; fluids, interfaces, and transport; glasses and ceramics; biotechnology; combustion science; experimental technology, facilities, and instrumentation. Also included are publications from the European, Soviet, and Japanese programs

NASA's Microgravity Research Program

This fiscal year (FY) 1997 annual report describes key elements of the NASA Microgravity Research Program (MRP) as conducted by the Microgravity Research Division (MRD) within NASA's Office of Life and Microgravity, Sciences and Applications. The program's goals, approach taken to achieve those goals, and program resources are summarized. All snapshots of the program's status at the end of FY 1997 and a review of highlights and progress in grounds and flights based research are provided. Also described are major space missions that flew during FY 1997, plans for utilization of the research potential of the International Space Station, the Advanced Technology Development (ATD) Program, and various educational/outreach activities. The MRP supports investigators from academia, industry, and government research communities needing a space environment to study phenomena directly or indirectly affected by gravity

Computational Design of Synthetic Microbial Communities

In naturally occurring microbial systems, species rarely exist in isolation. There is strong ecological evidence for a positive relationship between species diversity and the functional output of communities. The pervasiveness of these communities in nature highlights that there may be advantages for engineered strains to exist in cocultures as well. Building synthetic microbial communities allows us to create distributed systems that mitigate issues often found in engineering a monoculture, especially when functional complexity is increasing. The establishment of synthetic microbial communities is a major challenge we must overcome in order to implement coordinated multicellular systems. Here I present computational tools that help us design engineering strategies for establishing synthetic microbial communities. Using these tools I identify promising candidates for several design scenarios. This work highlights the importance of parameter inference and model selection to build robust communities. The findings highlight important interaction motifs that provide stability, and identify requirements for selecting genetic parts and tuning the community composition. Additionally, I show that fundamental interactions in small synthetic communities can produce chaotic behaviour that is unforecastable. Together these findings have important ramifications for how we build synthetic communities in the lab, and the considerations of interactions in microbiomes we manipulate