Discovery Seminar Series 2025

Host: Prof Simon Arthur

Venue: MSI Small Lecture Theatre, SLS

In person seminar 

All staff/students are encouraged to attend in support of the school seminar series

I am a Professor of Respiratory Medicine, University of Edinburgh, Honorary Consultant Physician, NHS Lothian, Dean of Medical Research and a Director of the Edinburgh Clinical Academic Training Scheme. I undertook my medical training at the University of Edinburgh graduating in 1997, and an MRC training fellowship at the University of Cambridge with award of my PhD in 2004. My specialist training in Respiratory Medicine was in Sheffield, where I also held a Wellcome Intermediate Fellowship, prior to my move to Edinburgh as a Wellcome Senior Clinical Fellow. During this time, I had two periods of maternity leave. I am currently based in the Centre for Inflammation Research in the Institute for Regeneration and Repair in Edinburgh. My work is focused on understanding how local oxygen and nutrient availability in the inflamed environment can reprogram neutrophil behaviour in both acute and chronic inflammatory lung disease states.

Host : Professor Geoff Barton

Venue: MSI Small Lecture Theatre, SLS

Abstract: 

In this talk, David will first introduce P2Rank, a protein binding site prediction method developed within our group. He will then discuss how the development and evaluation of this tool led us to explore the conformational flexibility of binding pockets in known experimental structures. Finally, David will show how this exploration paved the way for the development of new benchmarks and methods to identify more dynamic types of binding sites, such as cryptic binding sites. 

The method of fundamental solutions (MFS) is a numerical method for solving  boundary value problems involving linear partial differential equations. It is well known that it can be very effective assuming regularity of the domain and boundary conditions. The main drawback of the MFS is that the matrices involved are typically  ill-conditioned and this may prevent the method from achieving high accuracy. In   this talk, we will present some new approaches involving tools from numerical linear algebra such as the singular value decomposition and Arnoldi iteration for reducing the ill conditioning in the MFS. Several numerical examples show that these approaches are much   superior to the classical MFS in terms of conditioning and accuracy.

Venue: Fulton Building, Room G20

Breast cancer is a leading cause of death among women. X-rays mammography is considered to be the gold standard for breast imaging. However, most cancerous lesions are missed for women with dense breast, due to poor sensitivity of a mammographic exam in the case of breast with moderate/high density. Together with the ionizing character of the x-ray radiation, this hampers the widespread use of x-ray mammography as a population screening tool. In this seminar, I will review recent attempts at detecting breast cancer with ultrasound computed tomography, with a particular emphasis on the deterministic and stochastic iterative imaging algorithms that employ the framework of a pde-constrained numerical optimization problem. The seminar will discuss the mathematics and the physics aspects of the acoustic wave equation and of the associated inverse problem, and it will briefly touch the engineering aspects of an ultrasound sensing device.

Venue: Fulton Building, Room G20