# Team:NTU-Taida/Modeling

(Difference between revisions)
 Revision as of 10:30, 26 September 2012 (view source)Lbwang (Talk | contribs)← Older edit Revision as of 12:00, 26 September 2012 (view source)Lbwang (Talk | contribs) Newer edit → Line 3: Line 3: ==Single Cell Model== ==Single Cell Model== - To get started, we designed a single cell model based on ordinary differential equations  to simulate the function of our circuit in a single E.coli cell. With the single cell model, we can predict the behavior of our sensor, high pass filter and quorum sensing system reliably. + To get started, we designed a single cell model based on ordinary differential equations  to simulate the function of our circuit in a single E.coli cell. With the single cell model, we can predict the behavior of our sensor, high pass filter and quorum sensing system reliably. + + [[FIle:NTU-Taida-Model-Single-DEs.png|450px|thumb|right]] + [[FIle:NTU-Taida-Model-Single-Overview-Time-Response.png|450px|thumb|right]] + + ==System Analysis== ==System Analysis== To have better understanding of the roles each parameter plays in our single cell model, we performed system analysis, which explores extensively into the parameter space. With the help of the system analysis, we are able to determine which parameters should be adjusted in order to achieve our expected circuit response. To have better understanding of the roles each parameter plays in our single cell model, we performed system analysis, which explores extensively into the parameter space. With the help of the system analysis, we are able to determine which parameters should be adjusted in order to achieve our expected circuit response. + + [[FIle:NTU-Taida-Model-System-Overview.png|450px|thumb|right]] + ==Fatty Acid Reaction Absorption Model== ==Fatty Acid Reaction Absorption Model== In parallel to these effort we created a two dimensional dynamic reaction- absorption model , using the mechanical engineering software platform COMSOL, to describe the spatial-temporal change of fatty acid level in the extracellular environment after a meal. In parallel to these effort we created a two dimensional dynamic reaction- absorption model , using the mechanical engineering software platform COMSOL, to describe the spatial-temporal change of fatty acid level in the extracellular environment after a meal. + + [[FIle:NTU-Taida-Model-FA-Overview.png|450px|thumb|right]] + + ==Cell Population Response Model== ==Cell Population Response Model== To move further from single cell response to the response of a cell population, we conducted another two dimensional spatial-temporal model in COMSOL, which simulate the communication of cells through quorum sensing in our synthetic system. To move further from single cell response to the response of a cell population, we conducted another two dimensional spatial-temporal model in COMSOL, which simulate the communication of cells through quorum sensing in our synthetic system. + + [[FIle:NTU-Taida-Model-Cell-Overview.png|450px|thumb|right]] + + ==Partition System Model== ==Partition System Model== Last but not least, ____(partition system) Last but not least, ____(partition system)

# Modeling Overview

To evaluate the synthetic network designs in our pepdex system, we performed thorough analysis of ___ by created a series of computational models describing the circuit in our E.coli cells, the communications between cells, and the dynamic change in their extracellular environment.

## Single Cell Model

To get started, we designed a single cell model based on ordinary differential equations to simulate the function of our circuit in a single E.coli cell. With the single cell model, we can predict the behavior of our sensor, high pass filter and quorum sensing system reliably.

## System Analysis

To have better understanding of the roles each parameter plays in our single cell model, we performed system analysis, which explores extensively into the parameter space. With the help of the system analysis, we are able to determine which parameters should be adjusted in order to achieve our expected circuit response.

## Fatty Acid Reaction Absorption Model

In parallel to these effort we created a two dimensional dynamic reaction- absorption model , using the mechanical engineering software platform COMSOL, to describe the spatial-temporal change of fatty acid level in the extracellular environment after a meal.

## Cell Population Response Model

To move further from single cell response to the response of a cell population, we conducted another two dimensional spatial-temporal model in COMSOL, which simulate the communication of cells through quorum sensing in our synthetic system.

## Partition System Model

Last but not least, ____(partition system)

These modeling were valuable in the decision process on how to design our synthetic network. With the interactive talk between the biologists and modelers, we are able to avoid problems in advance and gain further insights into our pepdex system.