L3

We adopt the paradigm of understanding how the heart develops during pregnancy as a first principal to inform on adult heart repair and regeneration. Our target for cell-based repair is the epicardium and epicardium-derived cells (EPDCs) which line the outside of the forming heart and contribute vascular endothelial and smooth muscle cells to the coronary vasculature, interstitial fibroblasts and cardiomyocytes. The epicardium can also act as a source of signals to condition the growth of the underlying embryonic heart muscle. In the adult heart, whilst the epicardium is retained, it is effectively quiescent. We have sought to extrapolate the developmental potential of the epicardium to the adult heart following injury by stimulating dormant epicardial cells to give rise to new muscle and vasculature. In parallel, we seek to modulate the local environment into which the new cells emerge: a cytotoxic mixture of inflammation and fibrosis which prevents cell engraftment and integration with survived heart tissue. To this end we manipulate the lymphatic vessels in the heart given that, elsewhere in the body, the lymphatics survey the immune system and modulate inflammation at peripheral injury sites. We recently described the development of the cardiac lymphatic vasculature and revealed in the adult heart that they undergo increased vessel sprouting (lymphangiogenesis) in response to injury, to improve function, remodelling and fibrosis. We are currently investigating whether increased lymphangiogenesis functions to clear immune cells and constrain the reparative response for optimal healing.

Oxford Nanopore Technologies aim to enable the analysis of any living thing, by any person, in any environment. The world's first and only nanopore DNA
sequencer, the MinION is a portable, real time, long-read, low cost device that has been designed to bring easy biological analyses to anyone, whether in
scientific research, education or a range of real world applications such as disease/pathogen surveillance, environmental monitoring, food chain
surveillance, self-quantification or even microgravity biology. Gordon will talk the about the technology, applications and future direction.
Stuart will talk about the nanopore signal, computational methods and informatics challenges associated with reading DNA directly.

Soft active materials are largely employed to realize devices (actuators), where deformations and displacements are triggered by a wide range of external stimuli such as electric field, pH, temperature, and solvent absorption. The effectiveness of these actuators critically depends on the capability of achieving prescribed changes in their shape and size and on the rate of changes. In particular, in gel–based actuators, the shape of the structures can be related to the spatial distribution of the solvent inside the gel, to the magnitude and the rate of solvent uptake.

In the talk, I am going to discuss some results obtained by my group regarding surface patterns arising in the transient dynamics of swelling gels [1,2], based on the stress diffusion model we presented a few years ago [3]. I am also going to show our extended stress diffusion model suited for investigating swelling processes in fiber gels, and to discuss shape formation issues in presence of fiber gels [4-6].

[1]   A. Lucantonio, M. Rochè, PN, H.A. Stone. Buckling dynamics of a solvent-stimulated stretched elastomeric sheet. Soft Matter 10, 2014.

[2]   M. Curatolo, PN, E. Puntel, L. Teresi. Full computational analysis of transient surface patterns in swelling hydrogels. Submitted, 2017.

[3]   A. Lucantonio, PN, L. Teresi. Transient analysis of swelling-induced large deformations in polymer gels. JMPS 61, 2013.

[4]   PN, M. Pezzulla, L. Teresi. Anisotropic swelling of thin gel sheets. Soft Matter 11, 2015.

[5]   PN, M. Pezzulla, L. Teresi. Steady and transient analysis of anisotropic swelling in fibered gels. JAP 118, 2015.

[6]   PN, L. Teresi. Actuation performances of anisotropic gels. JAP 120, 2016.

Bubble Dynamics

We shall discuss certain generalisations of the Rayleigh Plesset equation for bubble dynamics

Self-assembly of a filament by curvature-inducing proteins

We explore a simplified macroscopic model of membrane shaping by means of curvature-sensing proteins. Equations describing the interplay between the shape of a freely floating filament in a fluid and the adhesion kinetics of proteins are derived from mechanical principles. The constant curvature solutions that arise from this system are studied using weakly nonlinear analysis. We show that the stability of the filament’s shape is completely characterized by the parameters associated with protein recruitment and establish that in the bistable regime, proteins aggregate on the filament forming regions of high and low curvatures. This pattern formation is then followed by phase-coarsening that resolves on a time-scale dependent on protein diffusion and drift across the filament, which contend to smooth and maintain the pattern respectively. The model is generalized for multiple species of proteins and we show that the stability of the assembled shape is determined by a competition between proteins attaching on opposing sides.

In recent years, ideas from the world of partial differential equations (PDEs) have found their way into the arena of graph and network problems. In this talk I will discuss how techniques based on nonlinear PDE models, such as the Allen-Cahn equation and the Merriman-Bence-Osher threshold dynamics scheme can be used to (approximately) detect particular structures in graphs, such as densely connected subgraphs (clustering and classification, minimum cuts) and bipartite subgraphs (maximum cuts). Such techniques not only often lead to fast algorithms that can be applied to large networks, but also pose interesting theoretical questions about the relationships between the graph models and their continuum counterparts, and about connections between the different graph models.

Stochastic Hamiltonian systems with multiplicative noise are a mathematical model for many physical systems with uncertainty. For example, they can be used to describe synchrotron oscillations of a particle in a storage ring. Just like their deterministic counterparts, stochastic Hamiltonian systems possess several important geometric features; for instance, their phase flows preserve the canonical symplectic form. When simulating these systems numerically, it is therefore advisable that the numerical scheme also preserves such geometric structures. In this talk we propose a variational principle for stochastic Hamiltonian systems and use it to construct stochastic Galerkin variational integrators. We show that such integrators are indeed symplectic, preserve integrals of motion related to Lie group symmetries, demonstrate superior long-time energy behavior compared to nonsymplectic methods, and they include stochastic symplectic Runge-Kutta methods as a special case. We also analyze their convergence properties and present the results of several numerical experiments.