Computer simulations of molecular probes binding weakly to target DNA suggests a new way to help detect diseases.
The current coronavirus crisis highlights the need for fast and accurate detection of infectious diseases. Both viral infections like coronavirus and bacterial infections like those associated with antimicrobial resistance (AMR) can be detected by screening for DNA in patient samples. However this is challenging because the amount of disease DNA is small and it has to be detected in the presence of other, non-disease DNA. Typically, scientists undertake this screening by designing molecular probes that bind strongly to the disease DNA but not to the non-disease DNA.
A new study, which is about to appear in the Proceedings of the National Academy of Sciences of the USA, uses computer simulations to suggest how this could be done better. The idea is that instead of designing molecular probes that bind strongly to one place on the target DNA, scientists should, counterintuitively, design probes that bind weakly all over the target DNA.
Experiments are required to test how well this works in practice – but it is exciting work, given the urgent need for fast, reliable disease detection methods, especially those that can be applied in countries with a weak health infrastructure.
This work was conducted by Prof Rosalind Allen at the University of Edinburgh, jointly with a multinational team of researchers in Cambridge, China, London and Slovenia.
Scientists have used a new technique to take the first-ever measurement of atmospheric wind speed outside the solar system.
A team of Astronomers, including the Institute for Astronomy’s Dr Beth Biller, have used NASA's Spitzer Space Telescope and the National Science Foundation's Karl G. Jansky Very Large Array (VLA) to take the first measurement of wind speed on a brown dwarf - an object intermediate in mass between a planet and a star.
Method of measurement
The method the team used is similar to that used to measure winds on Earth. To explain: imagine a cloud being blown by some wind. If you are looking down at Earth from space, you could measure the speed of a continent as it rotates in and out of view and a different speed for the cloud as it rotates in out of view. The difference in speed occurs because wind has pushed that cloud relative to the surface.
For planets and brown dwarfs outside of our solar system, we cannot see the clouds themselves, but when a cloud rotates into view or out of view, it changes the brightness of the planet. With that in mind, the team monitored the brightness of brown dwarf 2MASS J1047+21 and used periodic changes in its brightness to determine the rate at which the atmosphere was rotating.
Radio data
As continents on objects outside of our solar system cannot be observed, the team relied on observations at radio wavelengths to look at the rotation of a planet’s magnetic field below the atmosphere.
Since the magnetic field originates deep in the planet, or in this case brown dwarf, the radio data allowed the team to determine the interior period of rotation. Once they had an interior rotation rate and an atmospheric rotation rate, they could compare them to see how fast the wind was blowing.
The researchers measured a wind speed of 650 meters per second (1,450 miles per hour) for the brown dwarf they studied, which is 33.2 light years from earth.
Team collaboration
The team of collaborators, lead by Bucknell University‘s Professor Katelyn Allers also includes Dr Johanna Vos, from the American Museum of Natural History and Peter K. G. Williams, from the Center for Astrophysics and the American Astronomical Society.
Dr Beth Biller commented:
Pioneering this new technique is quite exciting, as it will enable future researchers to better understand the physics of atmospheres outside of our solar system.
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University of Edinburgh colleagues who are working on the LHCb (Large Hadron Collider beauty) experiment at CERN (the European Organization for Nuclear Research) have discovered a system of three particles interpreted as three new excited Xic0 states. The Xic0 state is a baryon composed of a charm-, a strange- and a down-quark (csd).
The lightest of all baryons, the proton, which is the nucleus of the hydrogen atom, is composed of two up- and one down-quark (uud) while its neutral partner the neutron is composed of two down- and one up-quark (ddu). If one (or more) light quark is replaced by either a charm c or a beauty b heavy quark we obtain heavier charmed or beauty baryon particles. The three quarks can also be formed in their lowest-energy quantum mechanical state: the ground state. Like electrons in atoms, the quarks can be rearranged into excited states with different values of angular momentum and quark spin orientation.
LHCb physicists searched for excited Xic0 states in their decay into a Λc+ baryon and a K- meson. Three new excited states of the Xic0 baryon have been observed and are named Ξc(2923)0, Ξc(2939)0 and Ξc(2965)0. The numbers in brackets represent the measured masses of each state.
Emmy Gabriel, PhD student within the Particle Physics Experiment Research Group at Edinburgh who was leading the analysis, said:
It has been incredibly interesting to perform an analysis in the field of baryon spectroscopy, and I am excited to see how the community will respond to this discovery.
The observed system seems to be related to another system of baryons observed a few years ago which drew a lot of attention from the scientific community.
Dr Marco Pappagallo, LHCb research assistant within the Particle Physics Experiment Group reported:
This discovery probes the internal structure of the baryons and helps us to understand how quarks bind together inside the hadrons.
An upgrade of the LHCb experiment is ongoing with the contribution of the Edinburgh group into commissioning the Cherenkov detector, which is essential to identify the different types of particles involved in this discovery. The LHCb experiment plans to collect a much larger dataset in the upcoming years which will allow physicists to study the properties of these new states by measuring their spin and parities.
Prof Franz Muheim, leader of the LHCb team at the University of Edinburgh said:
With this avalanche of discoveries of new baryons with charmed and b-quarks, LHCb has established charmed and beauty baryon spectroscopy as an experimental topic.
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The COVID-19 situation represents an unusual circumstance for all students. The basic principle of no semester 2 exams for Pre-Hons students, and online exams for Honours students was decreed at University level. During the past week, the School has been working to develop arrangements to ensure students learn and can be assessed in as fair a way as possible.
Coursework and teaching
Remote teaching will take place from Monday 23 March.
We ask that students:
- Try to engage with the last two weeks of the teaching term online.
- Complete all remaining coursework assignments and finish your project work to the highest standard you can. We have extended deadlines to take some account of all the problems we know you are facing.
- Check your coursesʼ LEARN pages for other guidance, the Student Website (link below) and read carefully messages sent by the Director of Teaching, Dr Ross Galloway.
Special Circumstances
The Boards of Examiners will automatically be taking into account the disruption in all cases. Accordingly, please only submit Special Circumstances for matters that extend beyond the general COVID-19 disruption, e.g. personal illness, illness of a person close to you, any of the specific problems for which you would likely have submitted Special Circumstances in a 'normal' year, or if you have difficulties with the technical aspects of on-line assessment - for example poor internet performance inhibiting upload/download.
You should also please note that the University has relaxed the evidence required for Special Circumstances such that you need not provide third-party support for cases submitted (e.g. you do not need to obtain medical notes).
Exams
Honours Students
Our aim in offering the Honours exams is to give you, as far as possible, the opportunity to take the exams you were expecting at the end of many months/years of hard work. We think that to deny you that opportunity, and the possible chance to improve your grade average, would be unfair. At the same time we want to reassure you that you will not be disadvantaged by these exams, should there be any problems - technical, logistical or personal.
These exams will provide a minority of the marks that contribute towards your final degree, so the exam boards already have (or will have) a lot of information about your performance across the programme. We also of course have information of performance on comparable exams by previous cohorts, and the exam boards have a lot of power to make sure you are treated fairly and sympathetically in light of the current unusually difficult circumstances.
We will be asking you to do the expected honours exams, according to the published exam timetable, but remotely. Further technical details will be released in due course, but so you know what to expect: you will be allowed the normal exam time + 1 extra hour to photograph or scan your written solutions and upload them to Learn as a single pdf file. We will provide all of you with a trial run of this online process well in advance of the first exam, to identify and correct any issues.
If you have learning adjustments for extra time, that will be added on, and more complex learning profiles will be catered for on an individual basis.
We realise for some of you who have returned home across the world this may mean taking some exams at a somewhat unusual time of day - we apologise for this, but we need to release the exam at the same time everywhere to maintain academic standards. So the exams will commence according the the British Summer Time (GMT+1 hr) exam timetable you have already received.
Pre-honours Students
As already stated there will be no 1st or 2nd year exams in April & May this year. You should therefore focus simply on the remaining coursework.
Please see the following points with regards to resits and progression:
- For Second-semester courses, where you are not getting the opportunity to sit exams, we will adopt your coursework mark as your mark for each course. Pre-hons students who have already passed their 1st-semester courses, and who pass 2nd-semester courses with their coursework marks, can therefore expect to progress with no further assessments.
- For students who fail either coursework for 2nd-semester courses, or who already anticipate summer resits for failed 1st-semester courses, we will provide online assessments later in the summer. This is required to enable us to gather enough evidence to be confident you can progress and cope with the next level of your degree course.
- Some students are expecting to take a 2nd Semester exam as a resit for a course failed last year - for example, Dynamics & Vector Calculus in 2nd year. In this situation we will use your coursework from this year (if you are retaking in attendance) or from last year (if you are retaking exam only), to assess your performance. A reassessment in the summer will only be required if you do not have a pass in the coursework from either year.
- In the specific case of Practical Physics, which runs over both semesters, you will not be required to pass the Experimental Physics component in addition to passing the course overall (given the unavoidable early closure of our labs).
Student support
We hope you are all safe and well. We know that many of you have left Edinburgh to be back with family and loved ones, and hope this journey has gone ok. We want to reiterate to you that we have support here in the School and the University if there are people you would like to talk to: in particular please keep in touch with your Personal Tutor. You are also welcome to direct questions or queries to kristel.torokoff [at] ed.ac.uk (Kristel Torokoff )(Senior Personal Tutor), ross.galloway [at] ed.ac.uk (Ross Galloway )(Director of Teaching), your lecturers, or James.Dunlop [at] ed.ac.uk (Jim Dunlop) (Head of School).
Congratulations to Adam who will have the opportunity to work with Nobel Laureates and young scientists at this meeting, which aims to foster exchanges among scientists of different generations, cultures, and disciplines.
The Council for the Lindau Nobel Laureate Meetings has selected 600 young scientists to come together with 70 Nobel Laureates in Lindau, Germany from 28 June to 3 July 2020. This year marks the 70th Lindau Nobel Laureate Meeting, which is focused on interdisciplinary exchanges between those working in physical sciences and medicine.
The selected young scientists are outstanding undergraduates, postgraduate students and postdocs under the age of 35. They have successfully passed a multi-stage international selection process, with Adam’s application having been supported by Edinburgh University and the Royal Society.
The scientific programme will include lectures, discussions, masterclasses and panel discussions – all designed to facilitate the exchange of knowledge, ideas and experience between Nobel Laureates and young scientists across a range of disciplines.
Adam commented:
I am very excited to have been selected, and thank Edinburgh University and the Royal Society for supporting my application. I am looking forward to the opportunity to meet several figures who have inspired me throughout my life, and to develop new connections with other young scientists from across the globe.
Following a message delivered by Prof Peter Mathieson, the Principal and Vice-Chancellor, on University developments regarding Coronavirus (COVID-19), there will be no further in-person gatherings of students for the remainder of the semester. However, we would like to emphasise that the university is not closed, and teaching is not terminated. Teaching is paused for the week commencing 16 March 2020, and will resume in distant mode thereafter.
Further information
Classes
There will be no classes of any type this week: no lectures, no labs, no workshops/tutorials. Please do not attend university buildings for these classes, as they will not be running. We will provide information later in the week on how we will move to distant provision from next week.
Coursework
Coursework tasks continue. If you have coursework that is normally submitted electronically, you should continue to submit it electronically by the originally published deadline. If you have coursework that is normally submitted in person (e.g. on paper) then continue to complete the coursework, but do not attempt to submit it. Do not come in to university buildings to hand it in, and do not email it to lecturers or the Teaching Office. We will provide further updates on how the coursework will be handled later in the week.
Presentations
Presentations and other oral forms of assessment will not go ahead in person. The relevant course organisers will contact affected students during the week to let them know the alternative forms of assessment that will be replacing these presentations.
Project work
Since projects do not involve gatherings of large groups of people, essential project work can still go ahead in person. Students conducting experimental projects should take steps this week to ensure that they will no longer have to come in to the building after Friday 20 March. Students may meet with project supervisors this week and should take steps to ensure that, from Friday 20th at the latest, any further such meetings can be carried out remotely, e.g. via Skype or phone/email.
Exams
As has already been announced, there will be effects on examinations. School staff will be working this week to determine the approaches that will be used. Please do not email staff with questions about exams; they will not be able to answer. We will communicate full information to you as soon as we are able.
Support and School communications
We appreciate that this is a stressful and confusing time. Please do communicate with your Personal Tutor if you need advice or assistance.
However, we would ask you also to appreciate that all university staff are receiving high volumes of communication right now, and to be patient in waiting for responses, particularly if your query is not critically urgent.
The School and University is pulling together to address the inevitable disruption being caused by COVID-19, and I am confident that we will be able to put suitable alternatives in place. We appreciate everyone's cooperation at this time.
Please remember that your university email account is our primary means of communicating with you. It is essential that you continue to regularly check your university email.
Additional guidance
The FAQs on the University website provide general information on travel and self-isolation, health and hygiene, along with additional guidance for applicants, students and staff.
Prof Rosalind Allen is included in the 64 new fellows announced from across sciences, arts, education, business and public life.
The Royal Society of Edinburgh (The RSE), Scotland’s National Academy has announced its newly elected 2020 Fellows. These new Fellows comprise leading thinkers and experts from Scotland and around the world whose work has a significant impact on our nation.
The list includes the School of Physics and Astronomy’s Professor Rosalind Allen, whose work contributes to our understanding of antibiotic resistance. Prof Allen's research focuses on biological and soft condensed matter physics, using simulations, theory and experiments. She is particularly interested in applying ideas and methods from physics to the important emerging biological question of how microbial populations develop, interact and function as ecosystems. She has also contributed to the development of advanced computer simulation methods, to our understanding of the kinetics of protein aggregation, and to understanding the behaviour of non-equilibrium active matter.
The new intake of 64 fellows joins the current roll of around 1,600, representing the full range of physical and life sciences, arts, humanities, social sciences, education, professions, industry, business and public life. Those who are nominated, and then invited to join, have undergone rigorous assessment of their achievements, professional standing and societal contribution. Fellows, who give of their time freely, play a fundamental role in enabling the RSE to deliver its mission ‘Knowledge Made Useful’, contributing to the cultural, economic and social well-being of Scotland and the wider world.
Prof Allen commented:
I am delighted to be joining as a fellow of the Royal Society of Edinburgh. I am looking forward to working with the Society and to have the opportunity to be part of such an esteemed network.
Europlanet 2024 Research Infrastructure (RI) will provide open access to the world’s largest collection of planetary simulation and analysis facilities, as well as a global network of small telescopes, data services, and community support activities.
Europlanet 2024 RI aims to widen participation in planetary science and provides the infrastructure to address key scientific and technological challenges facing the planetary research community.
The project is funded through the European Commission’s Horizon 2020 programme and will run for four years from February 2020 until January 2024. The Europlanet 2024 RI consortium is led by the University of Kent, and has 53 beneficiary institutions from 21 countries in Europe and around the world, with a further 44 affiliated partners. The University of Edinburgh’s Dr Colin Snodgrass chairs the advisory board on using small telescopes to support planetary science.
Dr Snodgrass reported:
Europlanet 2024 RI has created a unique opportunity for scientists to develop our planetary research, as well as forge a global community and support sustainable development around new facilities.
Europlanet 2024 RI will provide the planetary community with free ‘transnational access’ to 24 laboratories in Europe and five field sites worldwide to carry out research projects. The five field sites stretch from Africa to the Arctic Circle and provide terrestrial analogues for planetary environments past and present, including the icy environments of Europa and Ganymede, geothermally active regions of Venus, Io and ancient Mars, and lava caves on the Moon or Mars that may house human habitats in the future.
Eleven laboratories provide simulation facilities for atmospheric and surface environments that do not exist on Earth, from the scorching surface conditions of Mercury and Venus, to low-pressure dust-storms on Mars, or the extreme cold of Uranus, Neptune and comets, as well as dust and particle accelerators to study impact and irradiation effects. A further 13 facilities offer capabilities to analyse the composition of planetary samples with high precision and using non-destructive techniques, and to detect and sequence microbial communities found living in hostile conditions on Earth.
Europlanet 2024 RI builds on the heritage of EU-funded projects dating back over 15 years. To harness collaborations developed between professional and amateur astronomers, Europlanet 2024 RI is launching a coordinated network of small telescope facilities around the world that can provide rapid response observations to support planetary missions.
The project will expand virtual access services to include a geological mapping portal, GMAP, and to exploit machine learning for automatic recognition and analysis of planetary data sets.
Over 30 databases will be added to the VESPA virtual observatory portal, which currently provides access to 54 planetary science data services derived from space missions, observation campaigns, modelling projects and laboratory experiments. Europlanet 2024 RI will also extend its planetary space weather service, SPIDER, to provide predictions and alerts for spacecraft operations in response to solar activity and support science data analysis.
To bring in new users, support the community and raise awareness of planetary science, Europlanet 2024 RI will organise training and workshops to engage industry, policy makers, early career professionals and researchers from countries that are under-represented in planetary science, both in Europe and around the world. The project will also trial a reciprocal access agreement with Chinese and Korean research facilities.
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The School welcomes applications from both external and internal scientists interested in applying for latest round of UKRI Future Leader Fellowships.
We are keen to attract outstanding researchers from Edinburgh and across the world to join us as Research Fellows. We offer a high quality research environment and support for you in your fellowship application process.
Fellowship opportunities
The School operates an internal review process for the UKRI Future Leaders Fellowships with deadline:
Noon on Friday 6th March 2020.
Applications are also welcomed for other fellowship opportunities, which will be part of a later review process.
Application information
Candidates are expected to have a PhD in Physics, Astronomy or a related discipline, and in most cases a few years research experience, as well as the ability to present clear evidence of their potential to undertake leading research.
How to apply
Candidates must submit information including a 2 page Case for Support, CV and list of publications by Noon, 6th March 2020.
Submissions should be emailed to: fellowships-panel [at] ph.ed.ac.uk
If you have any queries concerning Fellowships please contact the Director of Research, Martin Evans (m.evans [at] ed.ac.uk).
Professor Neil Turok, a world-leading researcher in theoretical physics and fundamental cosmology has been appointed as the Inaugural Higgs Chair by the University of Edinburgh. Professor Turok will be joining the Higgs Centre for Theoretical Physics in the School of Physics and Astronomy starting July 2020.
Neil Turok
Neil Turok (PhD Imperial College London, 1983) was Director of Perimeter Institute in Canada from 2008 to 2019. Under his leadership the institute grew into one of the strongest centres for theoretical physics worldwide. Earlier in his career Turok was Professor of Physics at Princeton University and Chair of Mathematical Physics at the University of Cambridge.
Born in South Africa, Turok founded the African Institute for Mathematical Sciences (AIMS) in Cape Town in 2003. AIMS has since graduated over 2000 students at Masters level and above and has expanded to a network of centres spanning the African continent.
Turok has made numerous contributions to theoretical physics and cosmology. His work is highly original and addresses some of physics’ most profound problems, such as the quantum mechanical formulation of gravity and the nature and origin of large-scale structure, dark energy and dark matter. Much of Turok’s theoretical work connects directly to experiment and observation. He predicted correlations between polarisation and temperature anisotropies of the cosmic background radiation, confirmed by the WMAP and Planck satellites. He helped verify the existence of dark energy through an independent test involving the correlation between galaxies and the cosmic microwave background.
The Higgs Centre for Theoretical Physics
The Higgs Centre for Theoretical Physics was established in 2012 following the discovery of the Higgs boson at CERN, building on the legacy of Peter Higgs and Edinburgh’s outstanding tradition. Its purpose is to promote research excellence in theoretical physics, aiming to answer fundamental questions about Nature by developing new ideas and concepts. Our vision is to create bridges between disciplines and combine graduate-school education in synergy with cutting-edge research. Accordingly, the Higgs Centre has launched highly successful masters programmes in theoretical and mathematical physics. In parallel, the Centre runs a diverse programme of workshops and schools, through which it has established itself as a global focal point in theoretical physics.
Turok’s joining the Higgs Centre will be associated with a considerable expansion of its activities, including new faculty positions and fellowships, details of which will be announced later this year.
New focus on the quantum universe
Turok brings to the Higgs Centre several new and highly promising research directions. This includes an ambitious research programme formulating quantum mechanical theories, in particular general relativity, using real-time path integrals. Turok recently proposed one of the simplest yet solutions to the problem of dark matter in cosmology, in terms of right-handed neutrinos. These research directions and others will see a new level of investment by the University, further enhancing theoretical physics in Edinburgh.
Professor Turok said:
I am deeply honoured to be taking up the Higgs Chair. Theoretical physics is one of science’s most fruitful disciplines: when our ideas work, their impact can be extraordinary. The field stands at an exciting juncture. A combination of observational advances and theoretical clues are guiding us towards a transformation in our understanding of the universe. The Higgs Centre’s excellent direction and the quality and scope of its programmes, within Edinburgh’s exhilarating setting and its outstanding scientific community, create opportunities to foster and develop brilliant new talent and to make major discoveries.
Professor Peter Mathieson, Principal and Vice-Chancellor of the University of Edinburgh reported:
We are delighted to appoint Neil Turok, one of the world’s foremost theoretical physicists, to our inaugural Higgs Chair. The University of Edinburgh has a proud record in fundamental physics, including the fabulous work of the eponymous Peter Higgs. I am confident that Neil can build on that legacy and lead us to further success.
Professor James Dunlop, Physics and Astronomy Head of School commented:
This is a landmark appointment for the School of Physics & Astronomy at the University of Edinburgh. Neil Turok is an internationally renowned physicist, also well known for his science outreach and educational work. We are very excited to welcome him to the School and the wider University. Neil will further enhance the already strong international reputation of the School and, with his breadth of expertise and research interests, can help forge new links between different areas of theoretical physics. We also look forward to developing new connections with Africa.
Professor Einan Gardi, Director of the Higgs Centre for Theoretical Physics said:
We are excited to welcome Neil Turok as the inaugural Higgs Chair. We believe that he will find a natural new home in the Higgs Centre for Theoretical Physics. His scientific vision, energy and enthusiasm, will help us promote excellence and generate a thriving environment in which a new generation of leading researchers can develop.