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Life Sciences

2009

Articles 1 - 6 of 6

Full-Text Articles in Numerical Analysis and Computation

Biological Simulations And Biologically Inspired Adaptive Systems, Edgar Alfredo Duenez-Guzman Dec 2009

Biological Simulations And Biologically Inspired Adaptive Systems, Edgar Alfredo Duenez-Guzman

Doctoral Dissertations

Many of the most challenging problems in modern science lie at the interface of several fields. To study these problems, there is a pressing need for trans-disciplinary research incorporating computational and mathematical models. This dissertation presents a selection of new computational and mathematical techniques applied to biological simulations and problem solving: (i) The dynamics of alliance formation in primates are studied using a continuous time individual-based model. It is observed that increasing the cognitive abilities of individuals stabilizes alliances in a phase transition-like manner. Moreover, with strong cultural transmission an egalitarian regime is established in a few generations. (ii) A …

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Modeling In Microbial Batch Culture And Its Parameter Identification, Zhaohua Gong, Chongyang Liu, Enmin Feng Nov 2009

Modeling In Microbial Batch Culture And Its Parameter Identification, Zhaohua Gong, Chongyang Liu, Enmin Feng

Chongyang Liu

In this paper, the nonlinear dynamical system of batch fermentation is investigated in the bioconversion of glycerol to 1,3-propanediol(1,3-PD) by Klebsiella pneumoniae. Taking account of the kinetic behavior and experimental results in the batch cultures, we propose a two-stage dynamical system to formulate the fermentation process. Then some properties of the proposed system are proved. In view of the big errors between observations and numerical simulation results, we subsequently establish a parameter identification model to identify parameters in the system. The identifiability of the model is also discussed. Finally, in order to find the optimal parameters of the identification model, …

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Computational Method For Inferring Objective Function Of Glycerol Metabolism In Klebsiella Pneumoniae, Zhaohua Gong, Chongyang Liu, Enmin Feng, Qingrui Zhang Jan 2009

Computational Method For Inferring Objective Function Of Glycerol Metabolism In Klebsiella Pneumoniae, Zhaohua Gong, Chongyang Liu, Enmin Feng, Qingrui Zhang

Chongyang Liu

Flux balance analysis (FBA) is an effective tool in the analysis of metabolic network. It can predict the flux distribution of engineered cells, whereas the accurate prediction depends on the reasonable objective function. In this work, we propose two nonlinear bilevel programming models on anaerobic glycerol metabolism in Klebsiella pneumoniae (K. pneumoniae) for 1,3-propanediol (1,3-PD) production. One intends to infer the metabolic objective function, and the other is to analyze the robustness of the objective function. In view of the models’ characteristic an improved genetic algorithm is constructed to solve them, where some techniques are adopted to guarantee all chromosomes …

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Modelling And Optimal Control For Nonlinear Multistage Dynamical System Of Microbial Fed-Batch Culture, Chongyang Liu, Zhaohua Gong, Enmin Feng, Hongchao Yin Jan 2009

Modelling And Optimal Control For Nonlinear Multistage Dynamical System Of Microbial Fed-Batch Culture, Chongyang Liu, Zhaohua Gong, Enmin Feng, Hongchao Yin

Chongyang Liu

In this paper, we propose a new controlled multistage system to formulate the fed-batch culture process of glycerol bio-dissimilation to 1,3-propanediol (1,3-PD) by regarding the feeding rate of glycerol as a control function. Compared with the previous systems, this system doesn’t take the feeding process as an impulsive form, but a time-continuous process, which is much closer to the actual culture process. Some properties of the above dynamical system are then proved. To maximize the concentration of 1,3-PD at the terminal time, we develop an optimal control model subject to our proposed controlled multistage system and continuous state inequality constraints. …

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Optimal Control And Properties Of Nonlinear Multistage Dynamical System For Planning Horizontal Well Paths, Zhaohua Gong, Chongyang Liu, Enmin Feng Jan 2009

Optimal Control And Properties Of Nonlinear Multistage Dynamical System For Planning Horizontal Well Paths, Zhaohua Gong, Chongyang Liu, Enmin Feng

Chongyang Liu

The goal of planning a horizontal well path is to obtain a trajectory that arrives at a given target subject to various constraints. In this paper, the optimal control problem subject to a nonlinear multistage dynamical system (NMDS) for horizontal well paths is investigated. Some properties of the multistage system are proved. In order to derive the optimality conditions, we transform the optimal control problem into one with control constraints and inequality-constrained trajectories by defining some functions. The properties of these functions are then discussed and optimality conditions for optimal control problem are also given. Finally, an improved simplex method …

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Optimal Control For Nonlinear Dynamical System Of Microbial Fed-Batch Culture, Chongyang Liu Jan 2009

Optimal Control For Nonlinear Dynamical System Of Microbial Fed-Batch Culture, Chongyang Liu

Chongyang Liu

In fed-batch culture of glycerol bio-dissimilation to 1, 3-propanediol (1, 3-PD), the aim of adding glycerol is to obtain as much 1, 3-PD as possible. So a proper feeding rate is required during the process. Taking the concentration of 1, 3-PD at the terminal time as the performance index and the feeding rate of glycerol as the control function, we propose an optimal control model subject to a nonlinear dynamical system and constraints of continuous state and non-stationary control. A computational approach is constructed to seek the solution of the above model in two aspects. On the one hand we …

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