498 citations · 3.5k across the 66 of their papers we have counts for
66 papers
Recurrent neural chemical reaction networks trained to switch dynamical behaviours through learned bifurcations
Alexander Dack, Tomislav Plesa, Thomas E. Ouldridge
Both natural and synthetic chemical systems not only exhibit a range of non-trivial dynamics, but also transition between qualitatively different dynamical behaviours as environmen…
Design of DNA Strand Displacement Reactions
Križan Jurinović, Merry Mitra, Rakesh Mukherjee +1
DNA strand displacement (SD) reactions are central to the operation of many synthetic nucleic acid systems, including molecular circuits, sensors, and machines. Over the years, a b…
Bit reset protocols that obey activity-constrained speed limits do not minimize work for a given speed
Daan Mulder, Thomas E. Ouldridge, Pieter Rein ten Wolde
The goal of thermodynamic optimal control theory is to find protocols to change the state of a system from an initial to a desired final distribution, within a finite time, with th…
The Interplay of Heterogeneity and Product Detachment in Templated Polymer Copying
Jeremy E. B. Guntoro, Benjamin J. Qureshi, Thomas E. Ouldridge
Templated copolymerization, in which information stored in the sequence of a heteropolymer template is copied into another polymer product, is the mechanism behind all known method…
Recurrent neural chemical reaction networks that approximate arbitrary dynamics
Alexander Dack, Benjamin Qureshi, Thomas E. Ouldridge +1
Many important phenomena in biochemistry and biology exploit dynamical features such as multi-stability, oscillations, and chaos. Construction of novel chemical systems with such r…
Thermodynamic limits on general far-from-equilibrium molecular templating networks
Benjamin Qureshi, Jenny M. Poulton, Thomas E. Ouldridge
Cells produce RNA and proteins via molecular templating networks. We show that information transmission in such networks is bounded by functions of a simple thermodynamic property…