Data for Synthesis and Analysis of Biomolecular Circuits using DNA Strand Displacement

Supplementary materials supporting PhD thesis submission titled "Synthesis and Analysis of Biomolecular Circuits using DNA Strand Displacement"<br><br>1. Chapter3.zip contains the relevant files that can be used to recreate the result of Chapter 3 of Synthesis and Analysis of Biomolecular Circuits using DNA Strand Displacement. In particular: - Codes for DSD leaks: the codes can be run using the Visual DSD executable, which can be downloaded from ph1ll1ps.github.io/project/visualdsd - TF-to-DSD compiler: the code can be run in MATLAB; the output file can be run in Visual DSD. 2.

Chapter4.zip contains the relevant files that can be used to recreate the result of Chapter 4 of Synthesis and Analysis of Biomolecular Circuits using DNA Strand Displacement. In particular: - Critical leaks detection: the automated MATLAB tool for identifying the most critical leak reactions in the TMT and FIT circuits together with the .txt files containing the list of reactions. The steps are listed inside the MATLAB-files. - Determining programmable time delay: MATLAB tool for identifying the concentration of the Delay complex needed to achieve the expected time delay. - SIMULINK models for the full leak TMT and FIT circuits.