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Autonomous Learning of Generative Models with Chemical Reaction Network Ensembles
Can a micron sized sack of interacting molecules autonomously learn an internal model of a complex and fluctuating environment?
A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results
The oxDNA model of DNA has been applied widely to systems in biology, biophysics and nanotechnology.
Integral feedback in synthetic biology: Negative-equilibrium catastrophe
A central goal of synthetic biology is the design of molecular controllers that can manipulate the dynamics of intracellular networks in a stable and accurate manner.
Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts
These effective catalytic reactions are typically realised through one or more of the following: many-stranded gate complexes to coordinate the catalysis, indirect interaction between the catalyst and its substrate, and the recovery of a distinct ``catalyst'' strand from the one that triggered the reaction.
Optimizing enzymatic catalysts for rapid turnover of substrates with low enzyme sequestration
We analyse the mechanism of enzyme-substrate catalysis from the perspective of minimizing the load on the enzymes through sequestration, whilst maintaining at least a minimum reaction flux.
