Hayden Tronnolone

Thin-film flow in helically wound rectangular channels with small torsion

Laminar gravity-driven thin-film flow down a helically wound channel of rectangular cross-section with small torsion in which the fluid depth is small is considered. Neglecting the entrance and exit regions we obtain the steady-state solution that is independent of position along the axis of the channel, so that the flow, which comprises a primary flow in the direction of the axis of the channel and a secondary flow in the cross-sectional plane, depends only on position in the two-dimensional cross-section of the channel. A thin-film approximation yields explicit expressions for the fluid velocity and pressure in terms of the free-surface shape, the latter satisfying a nonlinear ordinary differential equation that has a simple exact solution in the special case of a channel of rectangular cross-section. The predictions of the thin-film model are shown to be in good agreement with much more computationally intensive solutions of the small-helix-torsion Navier–Stokes equations. The present work has particul...

Quantifying the dominant growth mechanisms of dimorphic yeast using a lattice-based model

A mathematical model is presented for the growth of yeast that incorporates both dimorphic behaviour and nutrient diffusion. The budding patterns observed in the standard and pseudohyphal growth modes are represented by a bias in the direction of cell proliferation. A set of spatial indices is developed to quantify the morphology and compare the relative importance of the directional bias to nutrient concentration and diffusivity on colony shape. It is found that there are three different growth modes: uniform growth, diffusion-limited growth (DLG) and an intermediate region in which the bias determines the morphology. The dimorphic transition due to nutrient limitation is investigated by relating the directional bias to the nutrient concentration, and this is shown to replicate the behaviour observed in vivo. Comparisons are made with experimental data, from which it is found that the model captures many of the observed features. Both DLG and pseudohyphal growth are found to be capable of generating observed experimental morphologies.

Diffusion-Limited Growth of Microbial Colonies

The emergence of diffusion-limited growth (DLG) within a microbial colony on a solid substrate is studied using a combination of mathematical modelling and experiments. Using an agent-based model of the interaction between microbial cells and a diffusing nutrient, it is shown that growth directed towards a nutrient source may be used as an indicator that DLG is influencing the colony morphology. A continuous reaction–diffusion model for microbial growth is employed to identify the parameter regime in which DLG is expected to arise. Comparisons between the model and experimental data are used to argue that the bacterium Bacillus subtilis can undergo DLG, while the yeast Saccharomyces cerevisiae cannot, and thus the non-uniform growth exhibited by this yeast must be caused by the pseudohyphal growth mode rather than limited nutrient availability. Experiments testing directly for DLG features in yeast colonies are used to confirm this hypothesis.

Characterizing the shape patterns of dimorphic yeast pseudohyphae

Pseudohyphal growth of the dimorphic yeast Saccharomyces cerevisiae is analysed using two-dimensional top-down binary images. The colony morphology is characterized using clustered shape primitives (CSPs), which are learned automatically from the data and thus do not require a list of predefined features or a priori knowledge of the shape. The power of CSPs is demonstrated through the classification of pseudohyphal yeast colonies known to produce different morphologies. The classifier categorizes the yeast colonies considered with an accuracy of 0.969 and standard deviation 0.041, demonstrating that CSPs capture differences in morphology, while CSPs are found to provide greater discriminatory power than spatial indices previously used to quantify pseudohyphal growth. The analysis demonstrates that CSPs provide a promising avenue for analysing morphology in high-throughput assays.

Pinch-off masses of very viscous fluids extruded from dies of arbitrary shape

The extrusion of slender very viscous fluid cylinders from dies of arbitrary geometry is modeled to approximate the mass of the first drop to pinch off. The model neglects inertia, which, although important to the dynamics near pinch-off, does not have a significant impact on the drop mass. Extrudate swell is also assumed to be negligible. The model is able to compute the pinch-off mass for fluid cylinders with cross-sectional geometries of any connectivity. By way of illustration, pinch-off masses are computed for epicycloidal cross sections, two touching circular rods, and circular cylinders with a single circular hole placed both centrally and off-centre. It is shown that the drop mass may be controlled by altering either the extrusion conditions or the die geometry.The extrusion of slender very viscous fluid cylinders from dies of arbitrary geometry is modeled to approximate the mass of the first drop to pinch off. The model neglects inertia, which, although important to the dynamics near pinch-off, does not have a significant impact on the drop mass. Extrudate swell is also assumed to be negligible. The model is able to compute the pinch-off mass for fluid cylinders with cross-sectional geometries of any connectivity. By way of illustration, pinch-off masses are computed for epicycloidal cross sections, two touching circular rods, and circular cylinders with a single circular hole placed both centrally and off-centre. It is shown that the drop mass may be controlled by altering either the extrusion conditions or the die geometry.