Fourier transform to analyse reaction-diffusion dynamics in a microsystem

Front speed and pattern selection of a propagating chemical front in an active fluid

Spontaneous pattern formation in living systems is driven by reaction-diffusion chemistry and active mechanics. The feedback between chemical and mechanical forces is often essential to robust pattern formation, yet it remains poorly understood in general. In this analytical and numerical paper, we study an experimentally motivated minimal model of coupling between reaction-diffusion and active matter: a propagating front of an autocatalytic and stress-generating species. In the absence of activity, the front is described by the well-studied Kolmogorov, Petrovsky, and Piskunov equation. We find that front propagation is maintained even in active systems, with crucial differences: an extensile stress increases the front speed beyond a critical magnitude of the stress, while a contractile stress has no effect on the front speed but can generate a periodic instability in the high-concentration region behind the front. We expect our results to be useful in interpreting pattern formation in active systems with mechanochemical coupling in vivo and in vitro.

Multicomponent diffusion coefficients from microfluidics using Raman microspectroscopy

Diffusion is slow. Thus, diffusion experiments are intrinsically time-consuming and laborious. Additionally, the experimental effort is multiplied for multicomponent systems as the determination of multicomponent diffusion coefficients typically requires several experiments. To reduce the experimental effort, we present the first microfluidic diffusion measurement method for multicomponent liquid systems. The measurement setup combines a microfluidic chip with Raman microspectroscopy. Excellent agreement between experimental results and literature data is achieved for the binary system cyclohexane + toluene and the ternary system 1-propanol + 1-chlorobutane + heptane. The Fick diffusion coefficients are obtained from fitting a multicomponent convection-diffusion model to the mole fractions measured in experiments. Ternary diffusion coefficients can be obtained from a single experiment; high accuracy is already obtained from two experiments. Advantages of the presented measurement method are thus short measurement times, reduced sample consumption, and less experiments for the determination of a multicomponent diffusion coefficient.

Identification of two-step chemical mechanisms using small temperature oscillations and a single tagged species

In order to identify two-step chemical mechanisms, we propose a method based on a small temperature modulation and on the analysis of the concentration oscillations of a single tagged species involved in the first step. The thermokinetic parameters of the first reaction step are first determined. Then, we build test functions that are constant only if the chemical system actually possesses some assumed two-step mechanism. Next, if the test functions plotted using experimental data are actually even, the mechanism is attributed and the obtained constant values provide the rate constants and enthalpy of reaction of the second step. The advantage of the protocol is to use the first step as a probe reaction to reveal the dynamics of the second step, which can hence be relieved of any tagging. The protocol is anticipated to apply to many mechanisms of biological relevance. As far as ligand binding is considered, our approach can address receptor conformational changes or dimerization as well as competition with or modulation by a second partner. The method can also be used to screen libraries of untagged compounds, relying on a tracer whose concentration can be spectroscopically monitored.

Spatial waves in synthetic biochemical networks

We report the experimental observation of traveling concentration waves and spirals in a chemical reaction network built from the bottom up. The mechanism of the network is an oscillator of the predator-prey type, and this is the first time that predator-prey waves have been observed in the laboratory. The molecular encoding of the nonequilibrium behavior relies on small DNA oligonucleotides that enforce the network connectivity and three purified enzymes that control the reactivity. Wave velocities in the range 80-400 μm min(-1) were measured. A reaction-diffusion model in quantitative agreement with the experiments is proposed. Three fundamental parameters are easy to tune in nucleic acid reaction networks: the topology of the network, the rate constants of the individual reactions, and the diffusion coefficients of the individual species. For this reason, we expect such networks to bring unprecedented opportunities for assaying the principles of spatiotemporal order formation in chemistry.

A nanoliter-scale open chemical reactor

An open chemical reactor is a container that exchanges matter with the exterior. Well-mixed open chemical reactors, called continuous stirred tank reactors (CSTR), have been instrumental for investigating the dynamics of out-of-equilibrium chemical processes, such as oscillations, bistability, and chaos. Here, we introduce a microfluidic CSTR, called μCSTR, that reduces reagent consumption by six orders of magnitude. It consists of an annular reactor with four inlets and one outlet fabricated in PDMS using multi-layer soft lithography. A monolithic peristaltic pump feeds fresh reagents into the reactor through the inlets. After each injection the content of the reactor is continuously mixed with a second peristaltic pump. The efficiency of the μCSTR is experimentally characterized using a bromate, sulfite, ferrocyanide pH oscillator. Simulations accounting for the digital injection process are in agreement with experimental results. The low consumption of the μCSTR will be advantageous for investigating out-of-equilibrium dynamics of chemical processes involving biomolecules. These studies have been scarce so far because a miniaturized version of a CSTR was not available.