Recovery of reaction pathways under the DCSC framework.

# Past Junior Applied Mathematics Seminar

Structure from Motion (SfM) is a problem which asks: given photos of an object from different angles, can we reconstruct the object in 3D? This problem is important in computer vision, with applications including urban planning and autonomous navigation. A key part of SfM is bundle adjustment, where initial estimates of 3D points and camera locations are refined to match the images. This results in a high-dimensional nonlinear least-squares problem. In this talk, I will discuss how dimensionality reduction methods such as block coordinates and sketching can be used to improve solver scalability for bundle adjustment problems.

Calcination describes the heat treatment of anthracite particles in a furnace to produce a partially-graphitised material which is suitable for use in electrodes and for other met- allurgical applications. Electric current is passed through a bed of anthracite particles, here referred to as a coke bed, causing Ohmic heating and high temperatures which result in the chemical and structural transformation of the material.

Understanding the behaviour of such mechanisms on the scale of a single particle is often dealt with through the use of computational models such as DEM (Discrete Element Methods). However, because of the great discrepancy between the length scale of the particles and the length scale of the furnace, we can exploit asymptotic homogenisation theory to simplify the problem.

In this talk, we will present some results relating to the electrical and thermal conduction through granular material which define effective quantities for the conductivities by considering a microscopic representative volume within the material. The effective quantities are then used as parameters in the homogenised macroscopic model to describe calcination of anthracite.

It is known that in steady-state potential flows, the separation of a gravity-driven free-surface from a solid exhibits a number of peculiar characteristics. For example, it can be shown that the fluid must separate from the body so as to form one of three possible in-fluid angles: (i) 180°, (ii) 120°, or (iii) an angle such that the surface is locally perpendicular to the direction of gravity. These necessary separation conditions were notably remarked by Dagan & Tulin (1972) in the context of ship hydrodynamics [J. Fluid Mech., 51(3) pp. 520-543], but they are of crucial importance in many potential flow applications. It is not particularly well understood why there is such a drastic change in the local separation behaviours when the global flow is altered. The question that motivates this work is the following: outside a formal balance-of-terms arguments, why must (i) through (iii) occur and furthermore, what is the connections between them?

In this work, we seek to explain the transitions between the three cases in terms of the singularity structure of the associated solutions once they are extended into the complex plane. A numerical scheme is presented for the analytic continuation of a vertical jet (or alternatively a rising bubble). It will be shown that the transition between the three cases can be predicted by observing the coalescence of singularities as the speed of the jet is modified. A scaling law is derived for the coalescence rate of singularities.

Over the past decade, the randomized singular value decomposition (RSVD)

algorithm has proven to be an efficient, reliable alternative to classical

algorithms for computing low-rank approximations in a number of applications.

However, in cases where no information is available on the singular value

decay of the data matrix or the data matrix is known to be close to full-rank,

the RSVD is ineffective. In recent years, there has been great interest in

randomized algorithms for computing full factorizations that excel in this

regime. In this talk, we will give a brief overview of some key ideas in

randomized numerical linear algebra and introduce a new randomized algorithm for

computing a full, rank-revealing URV factorization.

Collective neural crest (NC) cell migration determines the formation of peripheral tissues during vertebrate development. If NC cells fail to reach a target or populate an incorrect location, improper cell differentiation or uncontrolled cell proliferation can occur. Therefore, knowledge of embryonic cell migration is important for understanding birth defects and tumour formation. However, the response of NC cells to different stimuli, and their ability to migrate to distant targets, are still poorly understood. Recently, experimental and computational studies have provided evidence that there are at least two subpopulations of NC cells, namely “leading” and “trailing” cells, with potential further differentiation between the cells in these subpopulations [1,2]. The main difference between these two cell types is the mechanism driving motility and invasion: the leaders follow the gradient of a chemoattractant, while the trailing cells follow “gradients” of the leaders. The precise mechanisms underlying these leader-follower interactions are still unclear.

We develop and apply innovative multi-scale modelling frameworks to analyse signalling effects on NC cell dynamics. We consider different potential scenarios and investigate them using an individual-based model for the cell motility and reaction-diffusion model to describe chemoattractant dynamics. More specifically, we use a discrete self-propelled particle model [3] to capture the interactions between the cells and incorporate volume exclusion. Streaming migration is represented using an off-lattice model to generate realistic cell arrangements and incorporate nonlinear behaviour of the system, for example the coattraction between cells at various distances. The simulations are performed using Aboria, which is a C++ library for the implementation of particle-based numerical methods [4]. The source of chemoattractant, the characteristics of domain growth, and types of boundary conditions are some other important factors that affect migration. We present results on how robust/sensitive cells invasion is to these key biological processes and suggest further avenues of experimental research.

[1] R. McLennan, L. Dyson, K. W. Prather, J. A. Morrison, R.E. Baker, P. K. Maini and P. M. Kulesa. (2012). Multiscale mechanisms of cell migration during development: theory and experiment, Development, 139, 2935-2944.

[2] R. McLennan, L. J. Schumacher, J. A. Morrison, J. M. Teddy, D. A. Ridenour, A. C. Box, C. L. Semerad, H. Li, W. McDowell, D. Kay, P. K. Maini, R. E. Baker and P. M. Kulesa. (2015). Neural crest migration is driven by a few trailblazer cells with a unique molecular signature narrowly confined to the invasive front, Development, 142, 2014-2025.

[3] G. Grégoire, H. Chaté and Y Tu. (2003). Moving and staying together without a leader, Physica D: Nonlinear Phenomena, 181, 157-170.

[4] M. Robinson and M. Bruna. (2017). Particle-based and meshless methods with Aboria, SoftwareX, 6, 172-178. Online documentation https://github.com/martinjrobins/Aboria.

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.

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.