-The Model page has 7 sections-

Modeling Overview

Overview

We utilized modeling for our project through the following four approaches.

  1. Supporting the build phase of the project through modeling based on previous research.

  2. Using data obtained from wet lab experiments to describe the system with mathematical equations and facilitate understanding of the system.

  3. Using modeling based on data obtained from wet lab experiments to predict the behavior of more complex systems.

  4. Phenomena on a natural scale, rather than a laboratory scale, cannot be directly measured; therefore, they are simulated on a computer.

The first approach was incorporated into Part 4, the second approach into Parts 1 and 6, the third approach into Parts 2 and 3, and the fourth approach into Part 5.

This Overview page presents a summary of the modeling conducted in each Part. A figure about model overview is summarized below.

Figure

You can navigate to each part of the modeling using the buttons labeled "Part 1," etc., at the top of the page.

Part1 Transcription by T7 RNA Polymerase

In this chapter, we simulated the transcription of T7 RNAP based on previous studies by modeling the time-dependent T7 RNAP transcription using ordinary differential equations (ODE). Specifically, we performed fitting using data obtained from wet experiments to accurately reproduce the time-dependent transcription behavior. Additionally, we considered improvements of the model based on data from wet lab.

Part2 Ammonium Sensor

In this chapter, based on the results of the modeling in Part 1 and literature data of the proteins used in the nitrogen sensor, we conducted modeling to simulate the behavior of the ammonium sensor.

Part3 Threshold

In this chapter, we modeled the mechanism we devised to create a "threshold" in the sensing output based on previous research. Although we were unable to obtain actual functional data due to wet lab limitations, we introduce this as one potential approach to establishing a threshold in bio-sensor.

Part4 Protein Structure Prediction

In this chapter, we introduce the approach we took when designing modified proteins by fusing existing proteins. After meetings with experts, the process of carefully designing the artificial proteins was documented in detail on the Wiki, as we believe it will serve as a valuable reference for future iGEM teams.

Part5 Nitrogen Modeling

In this chapter, we shifted the scale from test tubes to ecosystems and modeled the dynamics of ammonia and nitrate in soil and rivers based on previous research to deepen our understanding of nitrogen issues.

Part6 Split reconstruction on RNA and two hybrid system

In this chapter, we conducted modeling to describe questions that arose during the experimental process using mathematical equations. Specifically, we addressed the question, "Does the reconstitution of split proteins on RNA not necessarily lead to an increase in luminescence according to RNA concentration?" as well as "What is the relationship between DNA-binding proteins and transcription rate in the two-hybrid system?". We answered these questions using mathematical equations, utilizing data from previous studies and wet lab experiments for model construction.