Dynamic Environments as a Tool to Preserve Desired Output in a Chemical Reaction Network

Abstract

Currente fforts to design functional molecular systems have overlooked the importance of coupling out-ofequilibrium behaviour with changes in the environment. Here, the authors use an oscillating reaction network and demonstrate that the application of environmental forcing, in the form of periodic changes in temperature and in the inflow of the concentrationo fo ne of the network components, removes the dependency of the periodicity of this network on temperature or flow rates and enforces as table periodicity across aw ide range of conditions. Coupling a system to ad ynamic environmentc an thusb eu sed as a simple tool to regulate the output of an etwork. In addition, the authors show that coupling can also induce an increase in behavioural complexity to include quasi-periodic oscillations. Institute for Molecules and Materials, RadboudU niversity Heyendaalseweg 135, 6525 AJ Supporting information and the ORCID identification number(s) for the author(s) of this articlecan be found under: https://doi.

Early warning signals in chemical reaction networks

“…The universality of this broadening, in that it occurs irrespective of whether the temperature is raised/lowered or whether flow rates are increased/ decreased, demonstrates the increase in FWHM can act as an early warning signal. In addition to the effect of temperature on the FWHM, an examination of some of our previously reported experimental results 24 confirmed that as the flow rate is changed and the system approaches the edge of the sustained oscillation region an increase in FWHM occurred (Fig. S6, ESI †).…”

“…We complemented the experimental data by modelling the effect of perturbations upon the recovery time using the previously reported temperature dependent rate equations (see ESI † Section 4 for details). 24 A comparison between the experimental and modelled results showed reasonable agreement (Fig. 2c).…”

“…8 Which behaviour is produced depends upon the concentrations of reagents used and upon the conditions of the environment, namely temperature and flow rate. 24 Within the temperature range 15-38 1C and flow rates 0.05-0.8 h À1 the system produces sustained oscillations in trypsin concentration. Outside of this optimum range the system produces dampened oscillations that lead to a steady state concentration.…”

Programming properties of transient hydrogels by an enzymatic reaction

“…To induce a pH change, the autocatalytic reaction between urea and urease was developed by Taylor et al [55][56][57] and also used by Walther et al 58,59 and other research groups. 16,[60][61][62][63] Under aqueous conditions, urea reacts with urease to produce ammonia, which is responsible for the increase of the pH of the medium. [64][65][66][67][68] The reaction itself is highly dependent on the initial reaction conditions such as pH and the reagent concentrations, 57,64,65 which enables us to exercise precise control over the rate of pH change and subsequent transitions between the energy states.…”

A Bayesian Approach to Extracting Kinetic Information from Artificial Enzymatic Networks

“… 4 − 8 Previous work has shown the development of small network motifs 9 by autocatalysis and delayed inhibition, 10 photochemical control of oscillations by reversible photoinhibitors, 11 coupling to DNA-based circuits, 12 logic-gate responses, 13 pattern-formation, 14 adaptive responses to environmental perturbations, 15 and coupling to dynamic environments. 16 While these networks can show complex behavior, such as oscillations and adaptation, scaling up their size toward metabolic scales remains a significant challenge. To construct complex, yet functional ERNs, estimating the mechanisms and kinetics of the enzymatic reactions in these systems is essential in order to reliably predict the relevant experimental regimes in which a desired functional output will be observed.…”