Past

In my talk I will discuss the use of topological methods in the analysis of neural data. I will show how to obtain good state spaces for Head Direction Cells and Grid Cells. Topological decoding shows how neural firing patterns determine behaviour. This is a local to global situation which gives rise to some reflections.

This week's Fridays@2 will be a panel discussion focusing on what it is like to pursue a research degree. The panel will share their thoughts and experiences in a question-and-answer session, discussing some of the practicalities of being a postgraduate student, and where a research degree might lead afterwards. Participants include:

Jono Chetwynd-Diggle (Smith Institute)

Victoria Patel (PDE CDT, Mathematical Institute)

Robin Thompson (Christ Church)

Rosemary Walmsley (DPhil student Health Economics Research Centre, Oxford) 

The spatial coordination of cellular differentiation enables functional organogenesis. How coordination results in specific patterns of differentiation in a robust manner is a fundamental question for all developmental systems in biology. Theoreticians such as Turing and Wolpert have proposed the importance of specific mechanisms that enable certain types of patterns to emerge, but these mechanisms are often difficult to identify in natural systems. Therefore, we have started using synthetic biology to ask whether specific mechanisms of pattern formation can be engineered into a simple cellular background. In this talk, I will show several examples of emergent spatial patterning that results from the insertion of synthetic signalling pathways and transcriptional logic into E. coli. In all cases, we use computational modelling to initially design circuits with a desired outcome, and improve the selection of biological components (DNA sub-sequences) that achieve this outcome according to a quantifiable measure. In the specific case of Turing patterns, we have yet to produce a functional system in vivo, but I will describe new analytical tools that are helping to guide the design of synthetic circuits that can produce a Turing instability.

Optical super-resolution microscopy enables the observations of individual bio-molecules. The arrangement and dynamic behaviour of such molecules is studied to get insights into cellular processes which in turn lead to various application such as treatments for cancer diseases. STFC's Central Laser Facility provides (among other) public access to super-resolution microscope techniques via research grants. The access includes sample preparation, imaging facilities and data analysis support. Data analysis includes single molecule tracking algorithms that produce molecule traces or tracks from time series of molecule observations. While current algorithms are gradually getting away from "connecting the dots" and using probabilistic methods, they often fail to quantify the uncertainties in the results. We have developed a method that samples a probability distribution of tracking solutions using the Metropolis-Hastings algorithm. Such a method can produce likely alternative solutions together with uncertainties in the results. While the method works well for smaller data sets, it is still inefficient for the amount of data that is commonly collected with microscopes. Given the observations of the molecules, tracking solutions are discrete, which gives the proposal distribution of the sampler a peculiar form. In order for the sampler to work efficiently, the proposal density needs to be well designed. We will discuss the properties of tracking solutions and the problems of the proposal function design from the point of view of discrete mathematics, specifically in terms of graphs. Can mathematical theory help to design a efficient proposal function?

Recently, Joyce constructed a Ringel-Hall style graded vertex algebra on the homology of moduli stacks of objects in certain categories of algebro-geometric and representation-theoretic origin. The construction is most natural for 2n-Calabi-Yau categories. We present this construction and explain the geometric reason why it exists. If time permits, we will explain how to compute the homology of the moduli stack of objects in the derived category of a smooth complex projective variety and to identify it with a lattice-type vertex algebra.

We study a class of non linear integro-differential equations on the Wasserstein space related to the optimal control of McKean-Vlasov jump-diffusions. We develop an intrinsic notion of viscosity solutions that does not rely on the lifting to an Hilbert space and prove a comparison theorem for these solutions. We also show that the value function is the unique viscosity solution. Based on a joint work with V. Ignazio, M. Reppen and H. M. Soner

Let n be a random integer (sampled from {1,..,X} for some large X). It is a classical fact that, typically, n will have around (log n)^{log 2} divisors. Must some of these be close together? Hooley's Delta function Delta(n) is the maximum, over all dyadic intervals I = [t,2t], of the number of divisors of n in I. I will report on joint work with Kevin Ford and Dimitris Koukoulopoulos where we conjecture that typically Delta(n) is about (log log n)^c for some c = 0.353.... given by an equation involving an exotic recurrence relation, and then prove (in some sense) half of this conjecture, establishing that Delta(n) is at least this big almost surely.

The dynamics of many physical systems often evolve to asymptotic states that exhibit periodic spatial and temporal variations in their properties such as density, temperature, etc. Such regular patterns look the same when moved by a basic unit and/or rotated by certain special angles. They possess both translational and rotational symmetries giving rise to discrete spatial Fourier transforms. In contrast, an aperiodic crystal displays long range spatial order but no translational symmetry. 

Recently, quasicrystals which are related to aperiodic crystals have been observed to form in diverse physical systems such as metallic alloys (atomic scale) and dendritic-, star-, and block co-polymers (molecular scale). Such quasicrystals lack the lattice symmetries of regular crystals, yet have discrete Fourier spectra. We look to understand the minimal mechanism which promotes the formation of such quasicrystalline structures using a phase field crystal model. Direct numerical simulations combined with weakly nonlinear analysis highlight the parameter values where the quasicrystals are the global minimum energy state and help determine the phase diagram. 

By locating parameter values where multiple patterned states possess the same free energy (Maxwell points), we obtain states where a patch of one type of pattern (for example, a quasicrystal) is present in the background of another (for example, the homogeneous liquid state) in the form of spatially localized dodecagonal (in 2D) and icosahedral (in 3D) quasicrystals. In two dimensions, we compute several families of spatially localized quasicrystals with dodecagonal structure and investigate their properties as a function of the system parameters. The presence of such meta-stable localized quasicrystals is significant as they may affect the dynamics of the crystallisation in soft matter.

The fully coupled numerical simulation of different physical processes, which can typically occur
at variable time and space scales, is often a very challenging task. A common feature of such models is that
their discretization gives rise to systems of linearized equations with an inherent block structure, which
reflects the properties of the set of governing PDEs. The efficient solution of a sequence of systems with
matrices in a block form is usually one of the most time- and memory-demanding issue in a coupled simulation.
This effort can be carried out by using either iteratively coupled schemes or monolithic approaches, which
tackle the problem of the system solution as a whole.

This talk aims to discuss recent advances in the monolithic solution of coupled multi-physics problems, with
application to poromechanical simulations in fractured porous media. The problem is addressed either by proper
sparse approximations of the Schur complements or special splittings that can partially uncouple the variables
related to different physical processes. The selected approaches can be included in a more general preconditioning
framework that can help accelerate the convergence of Krylov subspace solvers. The generalized preconditioner
relies on approximately decoupling the different processes, so as to address each single-physics problem
independently of the others. The objective is to provide an algebraic framework that can be employed as a
general ``black-box'' tool and can be regarded as a common starting point to be later specialized for the
particular multi-physics problem at hand.

Numerical experiments, taken from real-world examples of poromechanical problems and fractured media, are used to
investigate the behaviour and the performance of the proposed strategies.

In the twentieth century we leant that the theory of communication is a mathematical theory. Mathematics is able to add to the value of data, for example by removing redundancy (compression) or increasing robustness (error correction). More famously mathematics can add value to data in the presence of an adversary which is my personal definition of cryptography. Cryptographers talk about properties of confidentiality, integrity, and authentication, though modern cryptography also facilitates transparency (distributed ledgers), plausible deniability (TrueCrypt), and anonymity (Tor).
Modern cryptography faces new design challenges as people demand more functionality from data. Some recent requirements include homomorphic encryption, efficient zero knowledge proofs for smart contracting, quantum resistant cryptography, and lightweight cryptography. I'll try and cover some of the motivations and methods for these.
 

In the seminar, I will talk about a parabolic toy-model for the incompressible Navier-Stokes equations, that satisfies the same energy inequality, same scaling symmetry and which is also super-critical in dimension 3. I will present some partial regularity results that this model shares with the incompressible model and other results that occur only for our model.

When Gromov defined non-positively curved cube complexes no one knew what they would be useful for.
Decades latex they played a key role in the resolution of the Virtual Haken conjecture.
In one of the early forays into experimenting with cube complexes, Aitchison, Matsumoto, and Rubinstein produced some nice results about certain "cubed" manifolds, that in retrospect look very prescient.
I will define non-positively curved cube complexes, what it means for a 3-manifold to be cubed, and discuss what all this Haken business is about.
 

This session will discuss how Douglas Hartree and Arthur Porter used Meccano — a child’s toy and an engineer’s tool — to build an analogue computer, the Hartree Differential Analyser in 1934. It will explore the wider historical and social context in which this model computer was rooted, before providing an opportunity to engage with the experiential aspects of the 'Kent Machine,' a historically reproduced version of Hartree and Porter's original model, which is also made from Meccano.

The 'Kent Machine' sits at a unique intersection of historical research and educational engagement, providing an alternative way of teaching STEM subjects, via a historic hands-on method. The session builds on the work and ideas expressed in Otto Sibum's reconstruction of James Joule's 'Paddle Wheel' apparatus, inviting attendees to physically re-enact the mathematical processes of mechanical integration to see how this type of analogue computer functioned in reality. The session will provide an alternative context of the history of computing by exploring the tacit knowledge that is required to reproduce and demonstrate the machine, and how it sits at the intersection between amateur and professional science.

Donaldson-Thomas invariants of a Calabi-Yau 3-fold Y are related to Pandharipande-Thomas invariants via a wall-crossing formula known as the DT/PT correspondence, proved by Bridgeland and Toda. The same relation holds for the “local invariants”, those encoding the contribution of a fixed smooth curve in Y. We show how to lift the local DT/PT correspondence to the motivic level and provide an explicit formula for the local motivic invariants, exploiting the critical structure on certain Quot schemes acting as our local models. Our strategy is parallel to the one used by Behrend, Bryan and Szendroi in their definition and computation of degree zero motivic DT invariants. If time permits, we discuss a further (conjectural) cohomological upgrade of the local DT/PT correspondence.
Joint work with Ben Davison.
 

We describe the main geometric tools required to work on the manifold of fixed-rank symmetric positive-semidefinite matrices: we present expressions for the Riemannian logarithm and the injectivity radius, to complement the already known Riemannian exponential. This manifold is particularly relevant when dealing with low-rank approximations of large positive-(semi)definite matrices. The manifold is represented as a quotient of the set of full-rank rectangular matrices (endowed with the Euclidean metric) by the orthogonal group. Our results allow understanding the failure of some curve fitting algorithms, when the rank of the data is overestimated. We illustrate these observations on a dataset made of covariance matrices characterizing a wind field.

Topology optimisation finds the optimal material distribution of a fluid or solid in a domain, subject to PDE and volume constraints. There are many formulations and we opt for the density approach which results in a PDE, volume and inequality constrained, non-convex, infinite-dimensional optimisation problem without a priori knowledge of a good initial guess. Such problems can exhibit many local minima or even no minima. In practice, heuristics are used to obtain the global minimum, but these can fail even in the simplest of cases. In this talk, we will present an algorithm that solves such problems and systematically discovers as many of these local minima as possible along the way.  

Spreading processes on geometric networks are often influenced by a network’s underlying spatial structure, and it is insightful to study the extent to which a spreading process follows that structure. In particular, considering a threshold contagion on a network whose nodes are embedded in a manifold and which has both 'geometric edges' that respect the geometry of the underlying manifold, as well as 'non-geometric edges' that are not constrained by the geometry of the underlying manifold, one can ask whether the contagion propagates as a wave front along the underlying geometry, or jumps via long non-geometric edges to remote areas of the network. 
Taylor et al. developed a methodology aimed at determining the spreading behaviour of threshold contagion models on such 'noisy geometric networks' [1]. This methodology is inspired by nonlinear dimensionality reduction and is centred around a so-called 'contagion map' from the network’s nodes to a point cloud in high dimensional space. The structure of this point cloud reflects the spreading behaviour of the contagion. We apply this methodology to a family of noisy-geometric networks that can be construed as being embedded in a torus, and are able to identify a region in the parameter space where the contagion propagates predominantly via wave front propagation. This consolidates contagion map as both a tool for investigating spreading behaviour on spatial network, as well as a manifold learning technique. 
[1] D. Taylor, F. Klimm, H. A. Harrington, M. Kramar, K. Mischaikow, M. A. Porter, and P. J. Mucha. Topological data analysis of contagion maps for examining spreading processes on networks. Nature Communications, 6(7723) (2015)

In this talk I will explain (a) what observations speak for the
hypothesis of dark matter, (b) what observations speak for
the hypothesis of modified gravity, and (c) why it is a mistake
to insist that either hypothesis on its own must
explain all the available data. The right explanation, I will argue,
is instead a suitable combination of dark matter and modified
gravity, which can be realized by the idea that dark matter
has a superfluid phase.

Given a prime p and an elliptic curve E (say over Q), one can associate a "mod p Galois representation" of the absolute Galois group of Q by considering the natural action on p-torsion points of E.

In 1972, Serre showed that if the endomorphism ring of E is "minimal", then there exists a prime P(E) such that for all p>P(E), the mod p Galois representation is surjective. This raised an immediate question (now known as Serre's uniformity conjecture) on whether P(E) can be bounded as E ranges over elliptic curves over Q with minimal endomorphism rings.

I'll sketch a proof of this result, the current status of the conjecture, and (time permitting) some extensions of this result (e.g. to abelian varieties with appropriately analogous endomorphism rings).

The translation method for constructing quasiconvex lower bound of a given function in the calculus of variations and the notion of compensated convex transforms for tightly approximate functions in Euclidean spaces will be briefly reviewed. By applying the upper compensated convex transform to the finite maximum function we will construct computable quasiconvex functions with finitely many point wells contained in a subspace with rank-one matrices. The complexity for evaluating the constructed quasiconvex functions is O(k log k) with k the number of wells involved. If time allows, some new applications of compensated convexity will be briefly discussed.