An Arduino-based constant pressure fluid pump.

Constant pressure pumps are an invaluable yet underutilized resource for microfluidic flow systems. In particular, constant pressure pumps are able to stabilize the fluid pressure in systems where the viscosity may change due to chemical reactions or the flow rate may vary due to deformations of the channels. The constant pressure pump presented here is designed on the premise of creating and maintaining a pressure differential between the laboratory and a pressure reservoir. This pressure reservoir is then used to drive the input fluid at the specified gauge pressure. The pump design presented here is perfect for primarily undergraduate institutions and other laboratories with modest research budgets as it can be built for under US$100 and construction is within the scope of an advanced undergraduate. The pump consists of an Arduino-compatible microcontroller, Adafruit electronic components, low-voltage air pump, Nalgene water bottle, and various fluid components. A complete parts list is included in the appendix. Comparable commercial pumps have a retail price in excess of US$5000. Multiple pump designs were constructed and tested with the ability to hold a constant pressure of up to 14 psig (97 kPa-gauge) with a maximum flow rate of 65 [Formula: see text]L/s for water.

Dynamics of Reaction-Diffusion Oscillators in Star and other Networks with Cyclic Symmetries Exhibiting Multiple Clusters.

We experimentally and theoretically investigate the dynamics of inhibitory coupled self-driven oscillators on a star network in which a single central hub node is connected to k peripheral arm nodes. The system consists of water-in-oil Belousov-Zhabotinsky ∼100 µm emulsion drops contained in storage wells etched in silicon wafers. We observed three dynamical attractors by varying the number of arms in the star graph and the coupling strength: (i) unlocked, uncorrelated phase shifts between all oscillators; (ii) locked, arm hubs synchronized in phase with a k-dependent phase shift between the arm and central hub; and (iii) center silent, a central hub stopped oscillating and the arm hubs oscillated without synchrony. We compare experiment to theory. For case (ii), we identified a logarithmic dependence of the phase shift on star degree, and were able to discriminate between contributions to the phase shift arising from star topology and oscillator chemistry.

A Model for Link Pruning to Establish Correctly Polarized and Oriented Tip Links in Hair Bundles.

Tip links are thought to gate the mechanically sensitive transduction channels of hair cells, but how they form during development and regeneration remains mysterious. In particular, it is unclear how tip links are strung between stereocilia so that they are oriented parallel to a single axis; why their polarity is uniform despite their constituent molecules' intrinsic asymmetry; and why only a single tip link is present at each tip-link position. We present here a series of simple rules that reasonably explain why these phenomena occur. In particular, our model relies on each of the two ends of the tip link having distinct Ca2+-dependent stability and being connected to different motor complexes. A simulation employing these rules allowed us to explore the parameter space for the model, demonstrating the importance of the feedback between transduction channels and angled links, links that are 60° off-axis with respect to mature tip links. We tested this key aspect of the model by examining angled links in chick cochlea hair cells. As implied by the assumptions used to generate the model, we found that angled links were stabilized if there was no tip link at the tip of the upper stereocilium, and appeared when transduction channels were blocked. The model thus plausibly explains how tip-link formation and pruning can occur.

Testing Turing's theory of morphogenesis in chemical cells.

Alan Turing, in "The Chemical Basis of Morphogenesis" [Turing AM (1952) Philos Trans R Soc Lond 237(641):37-72], described how, in circular arrays of identical biological cells, diffusion can interact with chemical reactions to generate up to six periodic spatiotemporal chemical structures. Turing proposed that one of these structures, a stationary pattern with a chemically determined wavelength, is responsible for differentiation. We quantitatively test Turing's ideas in a cellular chemical system consisting of an emulsion of aqueous droplets containing the Belousov-Zhabotinsky oscillatory chemical reactants, dispersed in oil, and demonstrate that reaction-diffusion processes lead to chemical differentiation, which drives physical morphogenesis in chemical cells. We observe five of the six structures predicted by Turing. In 2D hexagonal arrays, a seventh structure emerges, incompatible with Turing's original model, which we explain by modifying the theory to include heterogeneity.

An inexpensive programmable illumination microscope with active feedback.

We have developed a programmable illumination system capable of tracking and illuminating numerous objects simultaneously using only low-cost and reused optical components. The active feedback control software allows for a closed-loop system that tracks and perturbs objects of interest automatically. Our system uses a static stage where the objects of interest are tracked computationally as they move across the field of view allowing for a large number of simultaneous experiments. An algorithmically determined illumination pattern can be applied anywhere in the field of view with simultaneous imaging and perturbation using different colors of light to enable spatially and temporally structured illumination. Our system consists of a consumer projector, camera, 35-mm camera lens, and a small number of other optical and scaffolding components. The entire apparatus can be assembled for under $4,000.

Tunable diffusive lateral inhibition in chemical cells.

The Belousov-Zhabotinsky (BZ) reaction has become the prototype of nonlinear chemical dynamics. Microfluidic techniques provide a convenient method for emulsifying BZ solutions into monodispersed drops with diameters of tens to hundreds of microns, providing a unique system in which reaction-diffusion theory can be quantitatively tested. In this work, we investigate monolayers of microfluidically generated BZ drops confined in close-packed two-dimensional (2D) arrays through experiments and finite element simulations. We describe the transition from oscillatory to stationary chemical states with increasing coupling strength, controlled by independently varying the reaction chemistry within a drop and diffusive flux between drops. For stationary drops, we studied how the ratio of stationary oxidized to stationary reduced drops varies with coupling strength. In addition, using simulation, we quantified the chemical heterogeneity sufficient to induce mixed stationary and oscillatory patterns.

Creation and perturbation of planar networks of chemical oscillators.

Methods for creating custom planar networks of diffusively coupled chemical oscillators and perturbing individual oscillators within the network are presented. The oscillators consist of the Belousov-Zhabotinsky (BZ) reaction contained in an emulsion. Networks of drops of the BZ reaction are created with either Dirichlet (constant-concentration) or Neumann (no-flux) boundary conditions in a custom planar configuration using programmable illumination for the perturbations. The differences between the observed network dynamics for each boundary condition are described. Using light, we demonstrate the ability to control the initial conditions of the network and to cause individual oscillators within the network to undergo sustained period elongation or a one-time phase delay.