Forthcoming events in this series


Fri, 03 Mar 2017

14:45 - 15:30
L3

Regenerative Medicine from an Engineer's Perspective

Professor Cathy Ye
(Institute of Biomedical Engineering University of Oxford)
Abstract

Regenerative medicine offers great hope in curing many currently untreatable diseases. Tissue engineering and stem cell therapy are the two main components of regenerative medicine. In this talk, I will discuss how engineering can make contributions to this highly interdisciplinary field, including biomaterials as 3D scaffolds, bioreactor design, and stem cell bioprocessing.

Fri, 03 Mar 2017

14:00 - 14:45
L3

En route to mending broken hearts

Prof Paul Riley
(DPAG University of Oxford)
Abstract

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.

Fri, 24 Feb 2017

14:00 - 15:00
L3

Nanopore sequencing & informatic challenges

Dr Gordon Sanghera
(CEO of Oxford Nanopore Technologies)
Abstract

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.

Fri, 11 Nov 2016

14:00 - 15:00
L3

Multiscale modelling of biomolecules: from atomistic molecular dynamics to the continuum limit with fluctuating finite element analysis

Dr Sarah Harris
(School of Physics & Astronomy University of Leeds)
Abstract

Atomistic Molecular Dynamics is a well established biomolecular modelling tool that uses the wealth of information available in the Protein Data Bank (PDB). However, biophysical techniques that provide structural information at the mesoscale, such as cryo-electron microscopy and 3D tomography, are now sufficiently mature that they merit their own online repository called the EMDataBank (EMDB). We have developed a continuum mechanics description of proteins which uses this new experimental data as input to the simulations, and which we are developing into a software tool for use by the biomolecular science community. The model is a Finite Element algorithm which we have generalised to include the thermal fluctuations that drive protein conformational changes, and which is therefore known as Fluctuating Finite Element Analysis (FFEA) [1].

We will explain the physical principles underlying FFEA and provide a practical overview of how a typical FFEA simulation is set up and executed. We will then demonstrate how FFEA can be used to model flexible biomolecular complexes from EM and other structural data using our simulations of the molecular motors and protein self-assembly as illustrative examples. We then speculate how FFEA might be integrated with atomistic models to provide a multi-scale description of biomolecular structure and dynamics.

1. Oliver R., Read D. J., Harlen O. G. & Harris S. A. “A Stochastic finite element model for the dynamics of globular macromolecules”, (2013) J. Comp. Phys. 239, 147-165.

Fri, 06 May 2016

14:00 - 15:00
L3

Can puzzles self-assemble?

Professor Daan Frenkel
(Dept of Chemistry University of Cambridge)
Abstract

A holy grail of nano-technology is to create truly complex, multi-component structures by self assembly.
 

Most self-assembly has focused on the creation of `structural complexity'. In my talk, I will discuss `Addressable Complexity': the creation of structures that contain hundreds or thousands of
distinct building blocks that all have to find their place in a 3D structure.