Universal dynamics of biological pattern formation in spatio-temporal morphogen variations

In biological systems, chemical signals termed morphogens self-organize into patterns that are vital for many physiological processes. As observed by Turing in 1952, these patterns are in a state of continual development, and are usually transitioning from one pattern into another. How do cells robustly decode these spatio-temporal patterns into signals in the presence of confounding effects caused by unpredictable or heterogeneous environments? Here, we answer this question by developing a general theory of pattern formation in spatio-temporal variations of ‘pre-pattern’ morphogens, which determine gene-regulatory network parameters. Through mathematical analysis, we identify universal dynamical regimes that apply to wide classes of biological systems. We apply our theory to two paradigmatic pattern-forming systems, and predict that they are robust with respect to non-physiological morphogen variations. More broadly, our theoretical framework provides a general approach to classify the emergent dynamics of pattern-forming systems based on how the bifurcations in their governing equations are traversed

Motility-induced phase separation mediated by bacterial quorum sensing

We study motility-induced phase separation (MIPS) in living active matter, in which cells interact through chemical signaling, or quorum sensing. In contrast to previous theories of MIPS, our multiscale continuum model accounts explicitly for genetic regulation of signal production and motility. Through analysis and simulations, we derive a new criterion for the onset of MIPS that depends on features of the genetic network. Furthermore, we identify and characterize a new type of oscillatory instability that occurs when gene regulation inside cells promotes motility in higher signal concentrations

Understanding how porosity gradients can make a better filter using homogenization theory

Filters whose porosity decreases with depth are often more efficient at removing solute from a fluid than filters with a uniform porosity. We investigate this phenomenon via an extension of homogenization theory that accounts for a macroscale variation in microstructure. In the first stage of the paper, we homogenize the problems of flow through a filter with a near-periodic microstructure and of solute transport owing to advection, diffusion and filter adsorption. In the second stage, we use the computationally efficient homogenized equations to investigate and quantify why porosity gradients can improve filter efficiency. We find that a porosity gradient has a much larger effect on the uniformity of adsorption than it does on the total adsorption. This allows us to understand how a decreasing porosity can lead to a greater filter efficiency, by lowering the risk of localized blocking while maintaining the rate of total contaminant removal

Mathematical modelling of chemical agent removal by reaction with an immiscible cleanser

When a hazardous chemical agent has soaked into a porous medium, such as concrete, it can be difficult to neutralise. One removal method is chemical decontamination, where a cleanser is applied to react with and neutralise the agent, forming less harmful reaction products. There are often several cleansers that could be used to neutralise the same agent, so it is important to identify the cleanser features associated with fast and effective decontamination. As many cleansers are aqueous solutions while many agents are immiscible with water, the decontamination reaction often takes place at the interface between two phases. In this paper, we develop and analyse a mathematical model of a decontamination reaction between a neat agent and an immiscible cleanser solution. We assume that the reaction product is soluble in both the cleanser phase and the agent phase. At the moving boundary between the two phases, we obtain coupling conditions from mass conservation arguments and the oil–water partition coefficient of the product. We analyse our model using both asymptotic and numerical methods, and investigate how different features of a cleanser affect the time taken to remove the agent. Our results reveal the existence of two regimes characterised by different rate-limiting transport processes, and we identify the key parameters that control the removal time in each regime. In particular, we find that the oil–water partition coefficient of the reaction product is significantly more important in determining the removal time than the effective reaction rate

Upscaling diffusion through first-order volumetric sinks: a homogenization of bacterial nutrient uptake

In mathematical models that include nutrient delivery to bacteria, it is prohibitively expensive to include a pointwise nutrient uptake within small bacterial regions over bioreactor length-scales, and so such models often impose an effective uptake instead. In this paper, we systematically investigate how the effective uptake should scale with bacterial size and other microscale properties under first-order uptake kinetics. We homogenize the unsteady problem of nutrient diffusing through a locally periodic array of spherical bacteria, within which it is absorbed. We introduce a general model that could also be applied to other single-cell microorganisms, such as cyanobacteria, microalgae, protozoa, and yeast and we consider generalizations to arbitrary bacterial shapes, including some analytic results for ellipsoidal bacteria. We explore in detail the three distinguished limits of the system on the timescale of diffusion over the macroscale. When the bacterial size is of the same order as the distance between them, the effective uptake has two limiting behaviours, scaling with the bacterial volume for weak uptake and with the bacterial surface area for strong uptake. We derive the function that smoothly transitions between these two behaviours as the system parameters vary. Additionally, we explore the distinguished limit in which bacteria are much smaller than the distance between them and have a very strong uptake. In this limit, we find that the effective uptake is bounded above as the uptake rate grows without bound; we are able to quantify this and characterise the transition to the other limits we consider

Optimising the flow through a concertinaed filtration membrane

Membrane filtration is a vital industrial process, with applications including air purification and blood filtration. In this paper, we study the optimal design for a concertinaed filtration membrane composed of angled porous membranes and dead-ends. We examine how the filter performance depends on the angle, position, thickness, and permeance of the membrane, through a combination of numerical and asymptotic approaches, the latter in the limit of a slightly angled membrane. We find that, for a membrane of fixed angle and physical properties, there can exist multiple membrane positions that maximise the flux for an applied pressure difference. More generally, we show that while the maximal flux achievable depends on the membrane thickness and permeance, the optimal membrane configuration is always in one of two setups: centred and diagonal across the full domain; or angled and in the corner of the domain.Comment: 24 pages, 10 figure

Motility-induced phase separation mediated by bacterial quorum sensing

We study motility-induced phase separation (MIPS) in living active matter, in which cells interact through chemical signalling, or quorum sensing. In contrast to previous theories of MIPS, our multiscale continuum model accounts explicitly for genetic regulation of signal production and motility. Through analysis and simulations, we derive a new criterion for the onset of MIPS that depends on features of the genetic network. Furthermore, we identify and characterise a new type of oscillatory instability that occurs when gene regulation inside cells promotes motility in higher signal concentrations

Emergent three-dimensional dynamics of rapidly spinning, self-propelled particles in shear flow. Part II: Chiral objects

In the second part of this two-part study, we investigate the motion of three-dimensional, rigid, active particles in shear Stokes flow, focusing on bodies that induce rapid rotation as part of their activity. We consider the general class of objects with helicoidal symmetry, focusing on chiral objects without reflectional fore-aft symmetry, significantly broadening the class of objects studied in Part I. We perform an intricate multiple-scales asymptotic analysis to systematically derive emergent equations of motion for the angular and translational dynamics of the object that explicitly account for the significant effects of fast spinning. We show that the emergent dynamics due to rapid rotation can be described by generalized Jeffery's equations for the wide class of objects that exhibit helicoidal symmetry, significantly expanding the scope of Jeffery's seminal study. Furthermore, we use our analytic results to characterise and quantify the explicit effect of rotation on the effective hydrodynamic shape of the objects

Generalised Jeffery's equations for rapidly spinning particles. Part 1: Spheroids

The observed behaviour of passive objects in simple flows can be surprisingly intricate, and is complicated further by object activity. Inspired by the motility of bacterial swimmers, in this two-part study we examine the three-dimensional motion of rigid active particles in shear Stokes flow, focusing on bodies that induce rapid rotation as part of their activity. Here, in Part 1, we develop a multiscale framework to investigate these emergent dynamics and apply it to simple spheroidal objects. In Part 2 (arXiv:2301.11032), we apply our framework to understand the emergent dynamics of more complex shapes; helicoidal objects with chirality. Via a multiple-scales asymptotic analysis for nonlinear systems, we systematically derive emergent equations of motion for long-term trajectories that explicitly account for the strong (leading-order) effects of fast spinning. Supported by numerical examples, we constructively link these effective dynamics to the well-known Jeffery's orbits for passive spheroids, deriving an explicit closed-form expression for the effective shape of the active particle, broadening the scope of Jeffery's seminal study to spinning spheroids

The effect of weak inertia in rotating high-aspect-ratio vessel bioreactors

One method to grow artificial body tissue is to place a porous scaffold seeded with cells, known as a tissue construct, into a rotating bioreactor filled with a nutrient-rich fluid. The flow within the bioreactor is affected by the movement of the construct relative to the bioreactor which, in turn, is affected by the hydrodynamical and gravitational forces the construct experiences. The construct motion is thus coupled to the flow within the bioreactor. Over the timescale of a few hours, the construct appears to move in a periodic orbit but, over tens of hours, the construct drifts from periodicity. In the biological literature, this effect is often attributed to the change in density of the construct that occurs via tissue growth. In this paper, we show that weak inertia can cause the construct to drift from its periodic orbit over the same timescale as tissue growth. We consider the coupled flow and construct motion problem within a rotating high-aspect- ratio vessel bioreactor. Using an asymptotic analysis, we investigate the case where the Reynolds number is large but the geometry of the bioreactor yields a small reduced Reynolds number, resulting in a weak inertial effect. In particular, to accurately couple the bioreactor and porous flow regions, we extend the nested boundary layer analysis of Dalwadi et al. (J. Fluid Mech. vol. 798, pp. 88–139, 2016) to include moving walls and the thin region between the porous construct and the bioreactor wall. This allows us to derive a closed system of nonlinear ordinary differential equations for the construct trajectory, from which we show that neglecting inertia results in periodic orbits; we solve the inertia-free problem analytically, calculating the periodic orbits in terms of the system parameters. Using a multiple-scale analysis, we then systematically derive a simpler system of nonlinear ordinary differential equations that describe the long-time drift of the construct due to the effect of weak inertia. We investigate the bifurcations of the construct trajectory behaviour, and the limit cycles that appear when the construct is less dense than the surrounding fluid and the rotation rate is large enough. Thus, we are able to predict when the tissue construct will drift towards a stable limit cycle within the bioreactor and when it will drift out until it hits the bioreactor edg