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SYNTHETIC BIOLOGY

SYNTHETIC BIOLOGY. Guillermo RODRIGO Alfonso JARAMILLO. LOGIC GATES. OR. NOT. AND. NOR. NAND. INVERTER. Biological Inverter: High input concentration, low output concentration (vv) Digital gate: NOT True table. Chemical equations. PROBLEM 1.

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SYNTHETIC BIOLOGY

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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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