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Numerical modeling of ureagenesis in a microfluidic channel mimicking a liver lobule
, Article 2015 22nd Iranian Conference on Biomedical Engineering, ICBME 2015, 25 November 2015 through 28 November 2015 ; 2015 , Pages 54-59 ; 9781467393515 (ISBN) ; Firoozabadi, B ; Saidi, M. S ; Firoozbakhsh, K ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2015
Abstract
Ammonia detoxification is one of the main functions of the liver results in production of urea. In this study ammonia elimination and urea production was simulated in a microchannel mimicking the hepatic porto central axis. Navier- Stockes equations along with convection equations were solved for the related species in the entire domain. Since the Reynolds number was small (~1) the fluid flow regime was laminar. Urea cycle was modeled regarding its four main enzymes. Twelve rate equations were also solved in order to obtain the concentration of each metabolites participating in urea cycle. Concentration of the urea reached its maximum ca. 1.2e-5 M at the end of the channel which is in good...
Numerical Simulation of Glucose Metabolism and Hepatocyte Viability within a Microfluidic
, M.Sc. Thesis Sharif University of Technology ; Firoozabadi, Bahar (Supervisor)
Abstract
The advent of microfluidics as suitable environments for culturing cells is associated with some challenges such as shear stresses applied on the cells. In fact, hepatocytes lose their function as exposed to high shear stresses similar to other cell types. Moreover, among all factors needed for cell viability, feeding hepatocytes with adequate oxygen is of great importance due to their high demand for oxygen compared the other cells. In this thesis, different types of cultures including 2D and 3D has been used in order that shear stresses would be in allowed range and provision of hepatocytes with sufficient oxygen concentrations has been ensured as well. In addition to supplying hepatocytes...
Theoretical and Experimental Simulation of Hepatic Cells and their Functionalities On-a-chip
, Ph.D. Dissertation Sharif University of Technology ; Firoozabadi, Bahar (Supervisor) ; Firoozbakhsh, Keikhosrow (Supervisor)
Abstract
Liver is the largest internal organ of the human body which serves many vital functionalities. Recently, liver-on-a-chip systems have been used to model some of the vital liver specific-functions and to investigate its related diseases. The purpose of the present study was simulation of some of these liver specific functionalities on-a-chip and using the obtained results in predicting hepatocellular functionalities i.e. production of some metabolites and modeling some of the liver-related diseases which have been done numerically and experimentally. Numerical simulations have been developed in two-dimensional and three-dimensional forms. In the 2D simulation, the governing equations i.e....
A numerical model for predicting hepatocytes ureagenesis and its related inborn enzyme deficiencies: case studies
, Article Scientia Iranica ; Volume 26, Issue 1B , 2019 , Pages 408-420 ; 10263098 (ISSN) ; Firoozabadi, B ; Saidi, M. S ; Firoozbakhsh, K ; Sharif University of Technology
Sharif University of Technology
2019
Abstract
One important functionality of liver cells is ammonia detoxification and urea production. In this study, a numerical model of the urea cycle in hepatocytes was developed. Navier Stokes and convection equations were employed to study the process of ammonia elimination and urea production using a microfluidic channel. The concentration of urea and ammonia throughout the channel was obtained. Furthermore, the urea cycle was modelled with respect to its four main enzymes. This resulted in twelve rate equations that were solved to determine the concentration of each metabolite participating in the urea cycle. Application of results implied common disorders such as hyperammonemia types I and II...
A numerical model for predicting hepatocytes ureagenesis and its related inborn enzyme deficiencies: Case studies
, Article Scientia Iranica ; Volume 26, Issue 1B , 2019 , Pages 408-420 ; 10263098 (ISSN) ; Firoozabadi, B ; Saidi, M. S ; Firoozbakhsh, K ; Sharif University of Technology
Sharif University of Technology
2019
Abstract
One important functionality of liver cells is ammonia detoxification and urea production. In this study, a numerical model of the urea cycle in hepatocytes was developed. Navier Stokes and convection equations were employed to study the process of ammonia elimination and urea production using a microfluidic channel. The concentration of urea and ammonia throughout the channel was obtained. Furthermore, the urea cycle was modelled with respect to its four main enzymes. This resulted in twelve rate equations that were solved to determine the concentration of each metabolite participating in the urea cycle. Application of results implied common disorders such as hyperammonemia types I and II...
Selection and simulation of a proper microfluidic for hepatocyte culture
, Article 2015 22nd Iranian Conference on Biomedical Engineering, ICBME 2015, 25 November 2015 through 28 November 2015 ; 2015 , Pages 65-69 ; 9781467393515 (ISBN) ; Firoozabadi, B ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2015
Abstract
The advent of microfluidics as suitable environments for culturing cells is associated with some challenges as shear stresses applied on the cells. Moreover, among all factors needed for cell viability, feeding hepatocytes with adequate oxygen is of great importance due to their high demand for oxygen compared the other cell types. In this paper three kinds of geometries has been studied in order that shear stresses would be in allowed range and provision of hepatocytes with sufficient oxygen concentrations has been ensured as well. In addition to supplying hepatocytes with oxygen, the range of its concentration has been adjusted in physiologic value so that it would be practical for further...
Numerical investigations of hepatic spheroids metabolic reactions in a perfusion bioreactor
, Article Frontiers in Bioengineering and Biotechnology ; Volume 7 , 2019 ; 22964185 (ISSN) ; Firoozabadi, B ; Firoozbakhsh, K ; Sharif University of Technology
Frontiers Media S.A
2019
Abstract
Miniaturized culture systems of hepatic cells are emerging as a strong tool facilitating studies related to liver diseases and drug discovery. However, the experimental optimization of various parameters involved in the operation of these systems is time-consuming and expensive. Hence, developing numerical tools predicting the function of such systems can significantly reduce the associated cost. In this paper, a perfusion-based three dimensional (3D) bioreactor comprising encapsulated human liver hepatocellular carcinoma (HepG2) spheroids are analyzed. The flow and mass transfer equations for oxygen as well as different metabolites such as albumin, glucose, glutamine, ammonia, and urea were...
A mechanobiological mathematical model of liver metabolism
, Article Biotechnology and Bioengineering ; Volume 117, Issue 9 , 5 June , 2020 , Pages 2861-2874 ; Firoozabadi, B ; Munn, L. L ; Sharif University of Technology
John Wiley and Sons Inc
2020
Abstract
The liver plays a complex role in metabolism and detoxification, and better tools are needed to understand its function and to develop liver-targeted therapies. In this study, we establish a mechanobiological model of liver transport and hepatocyte biology to elucidate the metabolism of urea and albumin, the production/detoxification of ammonia, and consumption of oxygen and nutrients. Since hepatocellular shear stress (SS) can influence the enzymatic activities of liver, the effect of SS on the urea and albumin synthesis are empirically modeled through the mechanotransduction mechanisms. The results demonstrate that the rheology and dynamics of the sinusoid flow can significantly affect...
Nonparametric simulation of signal transduction networks with semi-synchronized update
, Article PLoS ONE ; Volume 7, Issue 6 , 2012 ; 19326203 (ISSN) ; Masoudi Nejad, A ; Jalili, M ; Moeini, A ; Sharif University of Technology
2012
Abstract
Simulating signal transduction in cellular signaling networks provides predictions of network dynamics by quantifying the changes in concentration and activity-level of the individual proteins. Since numerical values of kinetic parameters might be difficult to obtain, it is imperative to develop non-parametric approaches that combine the connectivity of a network with the response of individual proteins to signals which travel through the network. The activity levels of signaling proteins computed through existing non-parametric modeling tools do not show significant correlations with the observed values in experimental results. In this work we developed a non-parametric computational...