Dr Nicola Beer heads up the Department of Stem Cell Engineering at the new Novo Nordisk Research Centre Oxford. Her team will use human stem cells to derive metabolically-relevant cells and tissues such as islets, hepatocytes, and adipocytes todiscover novel secreted factors and corresponding signalling pathways which modify cell function, health, and viability. Bycombining in vitro-differentiated human stem cell-derived models with CRISPR and other genomic targeting techniques, the teamassay cell function from changes in a single gene up to a genome-wide scale. Understanding the genes and pathways underlying cell function (and dysfunction) highlights potential targets for new Type 2 Diabetes therapeutics. Dr Beer will talk about the work ongoing in her team, as well as more broadly about the role of human stem cells in drug discovery and patient treatment.

Please note that this seminar will take place at the Physical and Theoretical Chemistry Laboratory within the
Department of Chemistry, room, PTCL lecture theatre.

The ability of cells to sense and respond to the mechanical properties of their environments is fundamental to cellular behaviour, with stiffness found to be a key control parameter. The physical mechanisms underpinning mechanosensing are, however, not well understood. I here consider the key physical cellular behaviours of active contractility of the internal cytoskeleton and cell growth, coupling these into mechanical models. These models suggest new distinct mechanisms of mechanotransduction in cells and tissues.

I will discuss a new theoretical approach to information and decisions in signalling systems and relate this to new experimental results about the NF-kappaB signalling system. NF-kappaB is an exemplar system that controls inflammation and in different contexts has varying effects on cell death and cell division. It is commonly claimed that it is information processing hub, taking in signals about the infection and stress status of the tissue environment and as a consequence of the oscillations, transmitting higher amounts of information to the hundreds of genes it controls. My aim is to develop a conceptual and mathematical framework to enable a rigorous quantifiable discussion of information in this context in order to follow Francis Crick's counsel that it is better in biology to follow the flow of information than those of matter or energy. In my approach the value of the information in the signalling system is defined by how well it can be used to make the "correct decisions" when those "decisions" are made by molecular networks. As part of this I will introduce a new mathematical method for the analysis and simulation of large stochastic non-linear oscillating systems. This allows an analytic analysis of the stochastic relationship between input and response and shows that for tightly-coupled systems like those based on current models for signalling systems, clocks, and the cell cycle this relationship is highly constrained and non-generic.

Multivariate cryptography is one of a handful of proposals for post-quantum cryptographic schemes, i.e. cryptographic schemes that are secure also against attacks carried on with a quantum computer. Their security relies on the assumption that solving a system of multivariate (quadratic) equations over a finite field is computationally hard. 

Groebner bases allow us to solve systems of polynomial equations. Therefore, one of the key questions in assessing the robustness of multivariate cryptosystems is estimating how long it takes to compute the Groebner basis of a given system of polynomial equations. 

After introducing multivariate cryptography and Groebner bases, I will present a rigorous method to estimate the complexity of computing a Groebner basis. This approach is based on techniques from commutative algebra and is joint work with Alessio Caminata (University of Barcelona).

In this talk I will review recent results on the analysis of shock-capturing-type methods applied to convection-dominated problems. The method of choice is a variant of the Algebraic Flux-Correction (AFC) scheme. This scheme has received some attention over the last two decades due to its very satisfactory numerical performance. Despite this attention, until very recently there was no stability and convergence analysis for it. Thus, the purpose of the works reviewed in this talk was to bridge that gap. The first step towards the full analysis of the method is a rewriting of it as a nonlinear edge-based diffusion method. This writing makes it possible to present a unified analysis of the different variants of it. So, minimal assumptions on the components of the method are stated in such a way that the resulting scheme satisfies the Discrete Maximum Principle (DMP) and is convergence. One property that will be discussed in detail is the linearity preservation. This property has been linked to the good performance of methods of this kind. We will discuss in detail its role and the impact of it in the overall convergence of the method. Time permitting, some results on a posteriori error estimation will also be presented. 
This talk will gather contributions with A. Allendes (UTFSM, Chile), E. Burman (UCL, UK), V. John (WIAS, Berlin), F. Karakatsani (Chester, UK), P. Knobloch (Prague, Czech Republic), and 
R. Rankin (U. of Nottingham, China).

The development of reduced order models for complex applications, offering the promise for rapid and accurate evaluation of the output of complex models under parameterized variation, remains a very active research area. Applications are found in problems which require many evaluations, sampled over a potentially large parameter space, such as in optimization, control, uncertainty quantification and applications where near real-time response is needed.

However, many challenges remain to secure the flexibility, robustness, and efficiency needed for general large-scale applications, in particular for nonlinear and/or time-dependent problems.

After giving a brief general introduction to reduced order models, we discuss developments in two different directions. In the first part, we discuss recent developments of reduced methods that conserve chosen invariants for nonlinear time-dependent problems. We pay particular attention to the development of reduced models for Hamiltonian problems and propose a greedy approach to build the basis. As we shall demonstrate, attention to the construction of the basis must be paid not only to ensure accuracy but also to ensure stability of the reduced model. Time permitting, we shall also briefly discuss how to extend the approach to include more general dissipative problems through the notion of port-Hamiltonians, resulting in reduced models that remain stable even in the limit of vanishing viscosity and also touch on extensions to Euler and Navier-Stokes equations.

The second part of the talk discusses the combination of reduced order modeling for nonlinear problems with the use of neural networks to overcome known problems of on-line efficiency for general nonlinear problems. We discuss the general idea in which training of the neural network becomes part of the offline part and demonstrate its potential through a number of examples, including for the incompressible Navier-Stokes equations with geometric variations.

This work has been done with in collaboration with B.F. Afkram (EPFL, CH), N. Ripamonti EPFL, CH) and S. Ubbiali (USI, CH).