Engineering Commons^™

Modeling The Interplay Between Photosynthesis, Co2 Fixation, And The Quinone Pool In A Purple Non-Sulfur Bacterium, Adil Alsiyabi

Department of Chemical and Biomolecular Engineering: Theses and Student Research

Rhodopseudomonas palustris CGA009 is a purple non-sulfur bacterium (PNSB) that can fix CO₂ and nitrogen or break down organic compounds for its carbon and nitrogen requirements. Light, inorganic, and organic compounds can all be used for its source of energy. Excess electrons produced during its metabolic processes can be exploited to produce hydrogen gas or biodegradable polyesters (polyhydroxybutyrate). A genome-scale metabolic model of the bacterium was reconstructed to study the interactions between photosynthesis, carbon dioxide fixation, and the redox state of the quinone pool. A comparison of model-predicted flux values with published in vivo MFA fluxes resulted in predicted …

Spatiotemporal Modeling And Model Restructuration Approaches In Studies Of Intracellular Signalling Pathways, Md Shahinuzzaman

Doctoral Dissertations

"The main focus of the research is to understand the complex phenomena of cell transduction pathways and cell biology in a single cell. Mathematical modeling and experimental evaluation are widely used approaches for this kind of research. Firstly, A multiscale framework for protein-protein interaction has been established using Brownian dynamics algorithm. Sit specific feature, steric collision, diffusion, co-localization and complex formation with time and space has been included in this spatial modeling framework. By implementation of the time adaptive feature in this framework, the computation time reduces in an order of magnitude compared with traditional modeling framework. This multiscale Brownian …

Multiscale Spatio-Temporal Modeling Of Cell Population In Tissue Architecture And Drug Delivery Nanoparticles, Mohammad Aminul Islam

Doctoral Dissertations

"Multiscale nature of a biological system span at many order of magnitudes in time and space. Molecular interaction at lower scale is connected with the higher scale behavior of tissue or organism. Integrating the dynamics and information at different time and space can give a fundamental physiological understanding of the higher level phenomena. But complex features, functions, interconnectivity between different scales and lack of information on the fundamental physiological property make the model difficult and computationally challenging. The multiscale modeling approach can bridge the gap between different scale by a systemic integration of the complex dynamic behavior.

Here, the focus …