Sharif Digital Repository

There are many limitations to determine relationships within biological systems. Among the limitations of these systems, one can consider the lack of sufficient information about them, such as the complete knowledge of many networks, the lack of reaction information, the complexity of the analysis of these reactions, etc. One of the methods to analyze these systems is called flux balance analysis. This method consists of three parts: objective function, equal constraints and unequal constraints. Among the features available in this method, we can mention less need for experimental information and no need for high processing systems. In order to determine the objective functions in this... 

For the simulation of microbial systems, constraint-based models have been proposed. The most famous constraint-based model is the flux balance analysis, in which to apply extra-molecular effects into the system, the dynamism of the problem is also introduced to generate the dynamic flux balance analysis. In this thesis, the bee colony optimization algorithm is used as an optimization engine. To increase the simulation accuracy and obtain more accurate solutions, this method was further developed and tested with thirteen benchmark functions. Better results were obtained compared to other proposed algorithms. Then the proposed algorithm was developed with four methods for constrained... 

In this thesis, a typical dynamic model of syngas fermentation, refered as hybrid method for biofuels production, coupled with a distillation column is developed in SimDFBA. The bioreactor is simulated in MATLAB/Simulink by using Clostridium ljungdahlii acetogenic micro-organism metabolic network. Bioreactor modeling is accomplished with a bubble column reactor in both liquid and gas phases, while the separator was simulated with ASPEN. PDE equiations of bioreactor modeing are dicretized to ODE equation by using QUICK scheme of finite volume method. A new econometric optimization study for outlet gas purification through a pressure swing adsorption unit to recycle relatively pure hydrogen is... 

Optimization and control of complex bioprocesses require accurate modeling. The application of flux balance analysis has gained considerable attention. In this approach, structured modeling is constructed based on metabolic genome networks. Although flux balance analysis provides an accurate model, applying it in optimization and control schemes especially model predictive control strategies often lead to bilevel optimization problems with significant computational cost. Therefore, we require a faster approach. The aim of this work is to use hybrid neural networks as a substitute for the optimization problem embedded in the dynamic model of a fermenter. In this work by proposing a hybrid... 

More than 80% of desalination units in the Persian Gulf use multi-stage flash (MSF) technology. The discharge of effluent from these units sometimes causes severe impacts to the marine environment due to the increase in temperature and salinity around the discharge point. In the current thesis, the geometrical, mixing and turbulence characteristics of the discharge of thermal-saline inclined jets under the water surface, similar to the effluent of MSF units, are numerically investigated by developing the buoyantBoussinesqPimpleFoam solver in the OpenFoam open-source software, using the LES turbulence model and the dynamic Smagorinsky subgrid scale and the UNESCO equation of state. The...