School of Physics and Astronomy

A team of researchers from the Institute of Condensed Matter and Complex Systems and EPCC has been awarded £297,000 by EPSRC to develop software for simulating rare events in soft matter and biological systems.

The grant was awarded to Kevin Stratford, Rosalind Allen and Davide Marenduzzo, who will work with postdoc Juho Lintuvuori on the 2-year project.

Rare events are processes that happen unpredictably and infrequently, but may be very important when they do happen. Examples include computer system failures, earthquakes and disease outbreaks. Despite their importance, rare events are notoriously difficult to study in computer simulations, because of the long waiting times between events. A method developed by Rosalind Allen and coworkers, called Forward Flux Sampling, alleviates this problem by allowing simulations to sample only the interesting trajectories where the event happens, and not the waiting times.

This EPSRC High Performance Computing grant will allow the team to implement the Forward Flux Sampling method in two widely used simulation packages: the Edinburgh-developed Ludwig code for Lattice-Boltzmann simulations and the LAMMPS Molecular dynamics simulation code, in order to study transitions between different liquid crystal phases, and the nucleation of chiral crystals under shear. Eventually the researchers hope to develop a version of the method that is portable to a wide variety of different simulation packages, opening the door to applications across condensed matter and biological physics.

Dr Bartlomiej Waclaw (Bartek), an Institute of Condensed Matter and Complex Systems (ICMCS) researcher, has been awarded a  Leverhulme Trust Early Career Research Fellowship.

The Fellowship will support Bartek's work on the development of statistical physics models to understand biological evolution, in collaboration with Rosalind Allen and Martin Evans. Bartek's Leverhulme Fellowship will start in April 2012 and run for 2 years.

Bartek's project focuses on the evolution of microbes. Microbes are tiny, single-celled living organisms which exist in huge numbers in almost every possible habitat, including the human body. Understanding how microbial populations in connected habitats evolve is crucial to developing better ways to tackle the emergence of new diseases as well as the spread of
resistance to known treatments (such as antibiotics).

Microbial evolution is also very interesting from a physics point of view as an example of a far-from-equilibrium process. In particular, in his previous work published with Dr Allen and Prof. Evans in Physical Review Letters in 2010, Bartek showed that migration between different habitats can not only have profound effects on the genetic composition of microbes, but it also leads to the existence of a dynamical, non-equilibrium phase transition at a critical value of the migration rate.

Bartek will now build on this work to discover how the results change when microbes can exchange genes by horizontal gene transfer (a key factor in the spread of antibiotic resistance) and to develop realistic models for the spread of antibiotic resistance through spatially structured human populations.

Bartek has been a postdoctoral researcher at ICMCS since 2009, funded by the group's EPSRC programme grant, led by Mike Cates. From 2007 to 2009 he worked as a postdoctoral researcher with Prof. Wolfhard Janke at the University of Leipzig, following a PhD in theoretical physics at the Jagellonian University in Krakow, in his native Poland, with Prof. Zdzislaw Burda. In his spare time Bartek enjoys 3d graphics programming and (since his move to Scotland) golf.

Early Career Fellowships

Early Career Fellowships aim to provide career development opportunities for those who are at a relatively early stage of their academic careers but with a proven record of research. It is anticipated that a Fellowship will lead to a more permanent academic position. Applications are welcomed in any discipline, and approximately 70 Fellowships will be available in 2011. Fellowships can be held at universities or at other institutions of higher education in the UK.

Nuclear Physics Group student wins the annual SUPA presentation award.

Congratulations to Helena David, of the Edinburgh Nuclear Physics group, who won the competition to find the best student talk at the annual SUPA General Meeting this spring.

As part of the day’s events, postgraduate students from eight Scottish universities presented their work in a competition to find the best student talk, with a first prize of £500 to be spent on a conference of the winner's choice. The panel of judges - Prof. Charles Cockell (Ex-OU and new PaLS Chair), Dr. Allan Colquhoun (SELEX Galileo) and Margaret McGarry (Lambie McGarry) - made comments after each presentation, and the winner was chosen by the audience. Entrants represented the diversity of physics areas covered by SUPA: from protein synthesis to star formation and the LHC.

Helena's talk - entitled “Measurements of exotic nuclei for explosive nuclear astrophysics” - described her work with the Argonne National Laboratory near Chicago, which involves using the GAMMASPHERE gamma-ray detector array to obtain precise structure information of exotic nuclei that are important in explosive astrophysical scenarios, like X-ray bursts.

The Edinburgh-Argonne collaboration has developed a new detection system that uses a highly segmented double-sided silicon strip detector (DSSD) to allow gamma-rays from exotic beta-unstable nuclei to be measured with a high degree of selectivity, greatly suppressing background from unwanted isobars. Exotic nuclei of interest in X-ray bursters are often characterised by a very short beta-decay half-life. The system takes advantage of this by making clean correlations between the exotic nuclei and their subsequent beta-decay. The effectiveness of the new method is demonstrated in figure 1. Note that a previously obscured peak in the more exotic nucleus ⁶²Ga at 276 keV becomes prominent when using the new system.

SUPA (Scottish Universities Physics Alliance) is an alliance of the physics departments of eight Scottish universities.

Two papers from the Soft, Biological and Statistical Physics group appeared in the 22nd April edition of Physical Review Letters.

Both papers relate to nonequilibrium statistical physics, which is a central research theme of the group. In essence, this concerns fundamental theories for forms of condensed matter that exhibit a current or flow of some kind. Although these systems are ubiquitous in nature, theories are still in their infancy. Both papers reveal surprising new information.

In the first - "Diffusion with Stochastic Resetting" by M. R. Evans and S. N. Majumdar, Phys. Rev. Lett. 106 160601 - the fundamental process of diffusion was re-examined when the diffusing particles returned at random times to the initial position. One way to visualise this is to imagine the process of looking for a lost item in a room by taking steps in a random direction, periodically returning to the starting position to begin the search anew.  Evans and Majumdar found that this strategy of going back to the beginning can in fact drastically improve the time to locate the object.

The second paper - "Noise-induced dynamical transition in systems with symmetric absorbing states" by D. I. Russell and R. A. Blythe, Phys. Rev. Lett. 106 165702 - shows that the way in which regions of magnetic alignment grow in time depends on the scale of local fluctuations. The model discussed in this paper can also be used to describe the spread of behaviour (like language or fashions) in a human population. In this model, fluctuations increase with the willingness to forget one's existing behaviour, showing that behaviours might spread in a fundamentally different way in populations of culturally forgetful individuals than in those who have a long cultural memory.

 

'SOUND in a man-made environment' is a project that considers the effects of background noise produced by technology. The 'Sound' exhibition has been shown in leading exhibition centres around the world and has featured on both radio and television. It is now supported by a dedicated website where visitors can read about the scientific and environmental aspects of noise, see images from the exhibition and play clips from its soundscapes. You are also invited to contribute your own comments to the site.

The public engagement project 'SOUND in a man-made environment' is funded at the School of Physics and Astronomy by the Engineering and Physical Sciences Research Council in partnership with the National Physical Laboratory.

If you are interested in applying for the MSc in High Performance Computing at the School of Physics & Astronomy, the Open Days are a good opportunity to:

• Talk to staff from the MSc in HPC
• Discuss career opportunities and financial support
• Meet current students.

Upcoming MSc in HPC Virtual Open Days

Thursday 28th April, 12:00-13:00 BST
Thursday 5th May, 13:00-14:00 BST

Live sessions in the chat rooms and virtual space will allow you to talk to staff and current students about applying for the MSc, studying in the University, living in Edinburgh and any other aspect of studying with us.

Registration

To book your place, please send an email with your name and the session you would like to attend to msc [at] epcc.ed.ac.uk (subject: MSc%20in%20HPC%20Virtual%20Open%20Day)

The School's Institute for Condensed Matter & Complex Systems and Oxford University have received £477,000 from EPSRC to study the molecular structure and function of novel protein fragments (peptides) designed to have potent anti-microbial activity. The work is an international collaboration and involes the UK's National Physical Laboratory (NPL) as an industrial co-funder and IBM Research in New York. Jason Crain will be the Edinburgh project leader.

The project seeks to understand how short protein fragments are effective in combating infection from bacteria and viruses and to reveal the molecular mechanisms by which they function. The aim is to design new and more effective molecules in collaboration with industrial partners.

The project combines synthesis of new materials with state-of-the-art experiment and computer simulations implemented on the Blue Gene supercomputers at IBM's Watson Research Labs and on facilities at EPCC. A particular aim is to understand the interactions of antimicrobial peptides with cellular membranes.

The work is relevant to the issue of antimicrobial resistance, which is recognised as a growing global concern with wide-ranging ramifications to the extent that the problem has been selected by the WHO as the theme for World Health Day 2011.

The project is part of a major collaboration between the partners funded by NPL and SUPA. Edinburgh's work, which spans both the experimental and computational aspects, is part of its growing research activities in biophysics with applications in healthcare.
 

'Hunting the Higgs Boson' is the theme of the Particle Physics For Scottish Schools (PP4SS) exhibition at this year's Edinburgh International Science Festival. Honorary Fellow and PP4SS director Alan Walker will represent the School at the event in the Discover Science Zone in the National Museum of Scotland. 

PP4SS aims to support physics teachers by introducing particle physics to school pupils, encouraging them to become engaged with the subject.

'Hunting the Higgs Boson' runs from 13-22 April at 10am-5pm each day.

Physics wins for innovative teaching and best postgraduate tutor.

Two members of the Physics teaching team have been recognised in the 2011 EUSA Teaching Awards. The Vitae Award for Best Postgraduate Who Tutors went to Robert Concannon. Two other Physics postgraduates - Adam Apostoli and Kate Slaughter - were also nominated. For Adam, this was the third time in a row.

Simon Bates - who was a runner-up in the two previous years - picked up the Teach First Innovative Teaching Award.

This is the third year that EUSA has made the awards. A record 5,168 student nominations were received for 777 teachers, with 11 awards presented to outstanding members of University staff and postgraduate tutors.

Here are just a few of the comments left by students making nominations.

 

Simon Bates: award for Innovative Teaching

"Professor Bates puts a lot of energy into his lectures and interacts with the students extremely well... His use of clicker questions keeps his lectures interesting and fun, and allows the students to engage with the lecture content... One of the main aspects of why I think Simon was a good teacher is the fact that every week he would take the time to make screencasts for webCT. These would range from overall advice with studies to specific problems with the subject. This became very helpful as it was able to cover a lot of problems that couldn't be answered in lectures... This interaction outside lectures shows students that Professor Bates has a genuine interest in us all doing well in this course."

 

Robert Concannon: Best Postgraduate Who Tutors

"He has most definitely given me a deeper understanding of the course material... Rob has always been enthusiastic and incredibly encouraging even when I have been despairing that I would never understand and be able to get through the course material and problems set... He makes maths funny and the tutorials so much more enjoyable. He also readily gave up more of his time if you needed more help... He is brilliant at spotting where you are struggling with a question and diligently makes sure you actually understand everything... I honestly feel that without all his support, patience and determination I would not have managed to pass the course... I was so lucky to have him as a tutor."

The MSc in HPC Virtual Open Days are live, online interactive sessions where you will meet course staff in chat rooms and virtual spaces. You do not need to attend the University campus, as these events are hosted online.

The next MSc in HPC Virtual Open Days are on:

- Monday 28 March 14:00–15:00 BST
- Wednesday 6 April 11:00–12:00 BST

To book your place, please email your name and the session you would like to attend to: msc [at] epcc.ed.ac.uk.