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Exploring Synthetic Biology Logic Gates with Chemical Equations and Simulink

Explore biological and digital logic gates using chemical equations, kinetic constants, and Simulink simulations to understand gene expression control mechanisms. Implement various circuits, modify kinetics for optimal performance, and investigate oscillatory behavior.

deborah-velazquez
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Exploring Synthetic Biology Logic Gates with Chemical Equations and Simulink

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  1. SYNTHETIC BIOLOGY Guillermo RODRIGO Alfonso JARAMILLO

  2. LOGIC GATES OR NOT AND NOR NAND

  3. INVERTER • Biological Inverter: High input concentration, low output concentration (vv) • Digital gate: NOT • True table

  4. Chemical equations

  5. PROBLEM 1 1.- Using chemical equations and kinetic constants, obtain differential equations. Which is the general expression of reaction velocity with R reactifs and P products of stechiometry ni? 2.- Using Simulink, implement the differential system. 3.- Obtain the concentrations when the drive (mRNA) is 1 between 10 and 20 (x100) s. Is it really a NOT gate? 4.- Try to modify some kinetic constant to reduce the delay.

  6. PROBLEM 2 1.- Which biological circuit is designed by this DNA sequence (in parts)? 2.- Implement that with logic gates and use Simulink to show the protein concentrations. Note: proteins are not the input/output of the subsystems, it is mRNA, namely, RNA Polymerase. 3.- Study the form of the curves and play with the time scale.

  7. PROBLEM 2’ (version) 1.- Using the NOT gate, implement a NAND gate with Simulink. 2.- Implement the RS Latch with NAND gates and show the protein concentrations. 3.- What is your opinion of this sequence (in parts)?

  8. PROBLEM 3 1.- Obtain the biologic circuit of the following genetic sequence. 2.- Obtain the logic circuit. 3.- Implement it with Simulink and show the graphics of the protein concentrations. What is happen? 4.- Try to solve this problem to obtain an oscillator. Can we lose the symmetric behavior?

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