Protein interaction networks (PINs) allow the representation and analysis of biological processes in cells. Because cells are dynamic and adaptive, these processes change over time. Thus far, research has focused either on the static PIN analysis or the temporal nature of gene expression. By analysing temporal PINs using multilayer networks, we want to link these efforts. The analysis of temporal PINs gives insights into how proteins, individually and in their entirety, change their biological functions. We present a general procedure that integrates temporal gene expression information with a monolayer PIN to a temporal PIN and allows the detection of modular structure using multilayer modularity maximisation.

# Past Junior Applied Mathematics Seminar

We are all familiar with the need for continuum mechanics-based models in physical applications. In this case, we are interested in large-scale water-wave problems, such as coastal flows and dam breaks.

When modelling these problems, we inevitably wish to solve them on a finite domain, and require boundary conditions to do so. Ideally, we would recreate the semi-infinite nature of a coastline by allowing any generated waves to flow out of the domain, as opposed to them reflecting off the far-field boundary and disrupting the remainder of our simulation. However, applying an appropriate boundary condition is not as straightforward as we might think.

In this talk, we aim to evaluate alternatives to so-called 'active boundary condition' absorption. We will derive a toy model of a shallow-water wavetank, and consider the implementation and efficacy of two 'passive' absorption techniques.

Snap-through buckling is a type of instability in which an elastic object rapidly jumps from one state to another, just as an umbrella flips upwards in a gust of wind. While snap-through under dry, mechanical loads has already been harnessed in engineering to generate fast motions between two states, the mechanisms underlying snapping in bulk fluid flows remain relatively unexplored. In this talk we demonstrate how elastic snap-through may be used to passively control fluid flows at low Reynolds number, in contrast to some pre-existing valves that rely on active control. We study viscous flow through a channel in which one of the bounding walls is an elastic arch. By performing experiments at the macroscopic scale, we show that snap-through of the arch rapidly changes the channel from a constricted to an unconstricted state, increasing the hydraulic conductivity by up to an order of magnitude. We also observe nonlinear pressure-flux characteristics away from snapping due to the coupling between the driving flow and elasticity. This behaviour is confirmed by a mathematical model that also shows the device may readily be scaled down for microfluidic applications. Finally, we demonstrate that such a device may be used to create a fluidic analogue of a fuse: the fluid flux through a channel may not rise above a given value.

Many species of insects adhere to vertical and inverted surfaces using footpads that secrete thin films of a mediating fluid. The fluid bridges the gap between the foot and the target surface. The precise role of this liquid is still subject to debate, but it is thought that the contribution of surface tension to the adhesive force may be significant. It is also known that the footpad is soft, suggesting that capillary forces might deform its surface. Inspired by these physical ingredients, we study a model problem in which a thin, deformable membrane under tension is adhered to a flat, rigid surface by a liquid droplet. We find that there can be multiple possible equilibrium states, with the number depending on the applied tension and aspect ratio of the system. The presence of elastic deformation significantly enhances the adhesion force compared to a rigid footpad. A mathematical model shows that the equilibria of the system can be controlled via two key parameters depending on the imposed separation of the foot and target surface, and the tension applied to the membrane. We confirm this finding experimentally and show that the system may transition rapidly between two states as the two parameters are varied. This suggests that different strategies may be used to adhere strongly and then detach quickly.

Many metallurgical processes involve the heat treatment of granular material due to large alternating currents. To understand how the current propagates through the material, one must understand the bulk resistivity, that is, the resistivity of the granular material as a whole. The literature suggests that the resistance due to contacts between particles contributes significantly to the bulk resistivity, therefore one must pay particular attention to these contacts.

My work is focused on understanding the precise impact of small contacts on the current propagation. The scale of the contacts is several order of magnitude smaller than that of the furnace itself, therefore we apply matched asymptotics methods to study how the current varies with the size of the contact.

One of the greatest challenges in developing renewable energy sources is finding an efficient energy storage solution to smooth out the inherently fluctuating supply. One cheap solution is lead-acid batteries, which are used to provide off-grid solar energy in developing countries. However, modelling of this technology has fallen behind other types of battery; the state-of-the-art models are either overly simplistic, fitting black-box functions to current and voltage data, or overly complicated, requiring complex and time-consuming numerical simulations. Neither of these methods offers great insight into the chemical behaviour at the micro-scale.

In our research, we use asymptotic methods to explore the Newman porous-electrode model for a constant-current discharge at low current densities, a good estimate for real-life applications. In this limit, we obtain a simple yet accurate formula for the cell voltage as a function of current density and time. We also gain quantitative insight into the effect of various parameters on this voltage. Further, our model allows us to quantitatively investigate the effect of ohmic resistance and mass transport limitations, as a correction to the leading order cell voltage. Finally, we explore the effect on cell voltage of other secondary phenomena, such as growth of a discharge-product layer in the pores and reaction-induced volume changes in the electrolyte.

In this talk we consider the limiting behaviour of the strong solution of the Navier--Stokes equation as the viscosity goes to zero, on a three--dimensional region with curved boundary. Under the Navier and kinematic boundary conditions, we show that the solution converges to that of the Euler equation (in suitable topologies). The proof is based on energy estimates and differential--geometric considerations. This is a joint work with Profs. Gui-Qiang Chen and Zhongmin Qian, both at Oxford.

Multi-agent systems in nature oftentimes exhibit emergent behaviour, i.e. the formation of patterns in the absence of a leader or external stimuli such as light or food sources. We present a non-local two species crossinteraction model with cross-diffusion and explore its long-time behaviour. We observe a rich zoology of behaviours exhibiting phenomena such as mixing and/or segregation of both species and the formation of travelling pulses.

In this presentation, we give an overview of the numerical methods used in commercial oil and gas reservoir simulation. The models are described by flow through porous media and are solved using a series of nested numerical methods. Most of the computational effort resides in solving large linear systems resulting from Newton iterations. Therefore, we will go in greater detail about the iterative linear solvers and preconditioning techniques.

Note: This talk will cover similar topics to the InFoMM group meeting talks on Friday 28th April, but I will discuss more mathematical details for this JAMS talk.