Synchronization of Chemical Reaction Networks Based on DNA Strand Displacement Circuits

Robustness analysis of a nucleic acid controller for a dynamic biomolecular process using the structured singular value

“…Since we wish to verify the robustness results by checking the local stability with Lyapunov's indirect method, we may need to linearise the dynamics around unstable equilibria, which cannot be found by integrating the dynamics (35).…”

“…This leads to variability on the reaction rates and uncertainty in the implemented network. Moreover, in the case of the nonlinear system (35), the equilibrium moves depending on the parameterisation [27]. Hence, the linearisation depends on the uncertainty both through A and x 0 .…”

“…Robustness levels are independent of scaling for feasibility of DNA implementation So far we have focused on the analysis of the CRN representation of the biomolecular control system, without addressing the implementation using DSD reactions, which has its own challenges. In particular, there is a physical limit for the bimolecular rate η, which is usually set close to the maximum hybridisation rate around 10 6 (Ms) −1 [33,35]. This, together with limits in concentrations, can impose constraints incompatible with the parameterisation of the CRN.…”

Solving 0–1 Integer Programming Problem Based on DNA Strand Displacement Reaction Network

“…DSD has the characteristics of product predictability, programmability, and simple operation. It has been widely used to construct computational models such as chemical reaction networks (CRNs), logic gates, neural networks, and DNA nanorobots. − In the DSD reaction, the reaction rate increases exponentially with the length of the toehold domain in the range of 6 nt, and the reaction rate reaches the maximum when the toehold domain length reaches 6 nt. , This feature makes it easy for the DSD reaction to act as a threshold and very easy to use for building the AND gate circuit based on DSD. − Complex CRNs based on DSD reaction modules often have cascading and programmable advantages. − NP-complete and combinatorial problems are mathematical problems that are difficult to solve by traditional algorithms. The reason is that the solution space of such problems increases exponentially as the variables increase.…”

Construction of a Genetic Comparator in Escherichia Coli

“…In the last decade, numerous biomolecular computing devices for in vitro and in vivo applications have been developed with the rapid advancement of biotechnology [1]- [3]. These biomolecular computing devices have demonstrated a wide range of applications, such as bistability [4], oscillation [5], counter [6], logic capabilities [7]- [9], memory [10]- [12], state machine [13], sensor [14], NP-problem [15], information storage [16], [17], arithmetic logic unit [18], and reaction controller [19].…”