Numerical simulation tools for fluid and solid mechanics are often based on the discretisation of coupled systems of partial differential equations, which can easily be identified in terms of physical
conservation laws.  In contrast, much physical insight is often gained from the equivalent formulation of the relevant energy or free-energy functional, possibly subject to constraints.  Motivated by the
nonlinear static and dynamic behaviour of nematic liquid crystals and of magnetosensitive elastomers, we propose a finite-element framework for minimising these free-energy functionals, using Lagrange multipliers to enforce additional constraints.  This talk will highlight challenges, limitations, and successes, both in the formulation of these models and their use in numerical simulation.
This is joint work with PhD students Thomas Benson, David Emerson, and Dong Han, and with James Adler, Timothy Atherton, and Luis Dorfmann.

As the fundamental unit of life, the biological cell is a natural focus for computational simulations of growing cell population and tissues. However, models developed at the cellular scale can also be integrated into more complex multiscale models in order to examine complex biological and physical process that scan scales from the molecule to the organ.

This seminar will present a selection of the cellular scale agent-based modelling that has taken place at the University of Sheffield (where one software agent represents one biological cell) and how such models can be used to examine collective behaviour in cellular systems. Finally some of the issues in extending to multiscale models and the theoretical and computational methodologies being developed in Sheffield and by the wider community in this area will be presented.

Data in many areas of science and sociology is now routinely represented in the form of networks. A fundamental task often required is to compare two datasets (networks) to assess the level of similarity between them. In the context of biological sciences, networks often represent either direct or indirect molecular interactions and an active research area is to assess the level of conservation of interaction patterns across species.

Currently biological network comparison software largely relies on the concept of alignment where close matches between the nodes of two or more networks are sought. These node matches are based on sequence similarity and/or interaction patterns. However, because of the incomplete and error-prone datasets currently available, such methods have had limited success. Moreover, the results of network alignment are in general not amenable for distance-based evolutionary analysis of sets of networks. In this talk I will describe Netdis, a topology-based distance measure between networks, which offers the possibility of network phylogeny reconstruction.

Sudden cardiac arrhythmic death remains a major health challenge in Western Society. Recent advances in computational methods and technologies have made clinically-based cardiac modelling a reality. An important current focus is the use of modelling to understand the nature of arrhythmias in the setting of different forms of structural heart disease. However, many challenges remain regarding the best use of these models to inform clinical decision making and guide therapies. In this talk, I will introduce a diverse sample of applications of modelling in this context, ranging from basic science studies which aim to leverage a fundamental mechanistic understanding of different aspects of pathological cardiac function, to direct clinical-application projects which aim to use modelling to immediately inform a clinical therapy. I will also discuss the challenges involved in clinically-driven modelling, and how to both engage, and manage, the expectations of clinicians at the same time, particularly with respect to the potential uses of 'patient-specific' modelling.

I this talk I will try to give an overview of recent progress in
spatial stochastic modeling within the reaction-diffusion
framework. While much of the initial motivation for this work came
from problems in cell biology, I will also highlight some examples
from epidemics and neuroscience.

As a motivating introduction, some newly discovered properties of
optimal controls in stochastic enzymatic reaction networks will be
presented. I will next detail how diffusive and subdiffusive reactive
processes in realistic geometries at the cellular scale may be modeled
mesoscopically. Along the way, some different means by which these
models may be analyzed with respect to consistency and convergence
will also be discussed. These analytical techniques hint at how
effective (i.e. parallel) numerical implementations can be
designed. Large-scale simulations will serve as illustrations.

I present a new method for optimizing quadratic functions subject to simple bound constraints.  If the problem happens to be strictly convex, the algorithm reduces to a highly efficient method by Dostal and Schoberl.  Our algorithm, however, is also able to efficiently solve nonconcex problems. During this talk I will present the algorithm, a sketch of the convergence theory, and numerical results for convex and nonconvex problems.

We will begin by discussing the risk parity portfolio selection problem, which aims to find  portfolios for which the contributions of risk from all assets are equally weighted. The risk parity may be satisfied over either individual assets or groups of assets. We show how convex optimization techniques can find a risk parity solution in the nonnegative  orthant, however, in general cases the number of such solutions can be anywhere between zero and  exponential in the dimension. We then propose a nonconvex least-squares formulation which allows us to consider and possibly solve the general case. 

Motivated by this problem we present several alternating direction schemes for specially structured nonlinear nonconvex problems. The problem structure allows convenient 2-block variable splitting.  Our methods rely on solving convex subproblems at each iteration and converge to a local stationary point. Specifically, discuss approach  alternating directions method of multipliers and the alternating linearization method and we provide convergence rate results for both classes of methods. Moreover, global optimization techniques from polynomial optimization literature are applied to complement our local methods and to provide lower bounds.