School of Physics and Astronomy

By combining our knowledge of polymer physics and molecular biology, scientists can craft DNA-based soft materials that can change properties over time.

DNA is essentially a long polymer consisting of four different types of monomers – the nucleotides A, T, C and G, which stack together into base pairs. Like all polymers, DNA chains can get entangled at high concentrations. In fact, they get so tied up that a single human cell can store up to 2m of DNA crammed into its nucleus, an object just 10μm in size.

If DNA molecules stayed horribly entangled, there would be a problem: it would be impossible for chromosomes – long pieces of DNA containing millions of base pairs – to be constantly read and copied. And if that didn’t happen, cells would be unable to make proteins and multiply. Nature has got round this problem by “engineering” special proteins that can change DNA’s shape, or “topology”, to get rid of the entanglements.

Dr Davide Michieletto, who is based in the School’s Institute for Condensed Matter and Complex Systems claims that DNA’s ability to morph its architecture means that it behaves a bit like soap:

The link between DNA and soap is certainly surprising. But by combining our knowledge of polymer physics and molecular biology, we can exploit this soapy feature to craft DNA-based soft materials that change topology over time. And by tweaking their topology, we can control their physical properties in unusual ways.

Soaps consists of “amphiphilic” molecules, one part of which loves water and another part that hates it. These molecules don’t exist in isolation but group together to form structures, known as “micelles”. At low concentrations, they are usually spherical, but at higher concentrations, the molecules can form long, tube-like structures, with the water-hating parts of the molecules facing inside.

These elongated, multi-molecule objects do strange things at high concentrations. In particular, just like DNA, they get entangled, increasing the fluid’s friction and making it harder to deform. In fact, the entanglements between worm-like micelles are what give soap, shampoo, face cream or hair gel that pleasant, smooth hand-feel.

Just like DNA, worm-like micelles can also disentangle themselves by constantly getting broken up and glued back together again with a new topology. But there’s one big difference: the DNA inside cells needs to preserve its genetic sequence otherwise cells might die or diseases could be triggered. In soap, there’s no precise sequence of monomers in micelles so they can be put back together in any order. This has a fundamental impact on how topological operations are performed on DNA: they have to happen at the right place and the right time.

To break DNA you need “restriction enzymes”, which cut the chain only where a certain DNA sequence is recognized. Topoisomerase proteins, meanwhile, have to be precisely positioned at certain locations on chromosomes where entanglements and mechanical stress often accumulate. Similarly, when two pieces of DNA reconnect and recombine – the process is tightly regulated in space and time to avoid aberrant chromosomes in cells. It’s almost as if DNA (thanks to proteins) behaved as a smart worm-like micelle.

Davide is definitely not the only person to see the potential of DNA as an advanced polymer, rather than just as genetic material. Over the last two decades, researchers have developed lots of new, DNA-based materials, such as hydrogels and nano-scaffolds, that could, for example, grow bones, tissues, skin and cells, using the unique properties of DNA to encode information.

What excites me about this line of research is that solutions of DNA, functionalized by the presence of proteins that can change DNA’s topology in time, may yield novel “topologically active” complex fluids that respond to external stimuli. For example, adding restriction enzymes that can cut the DNA at specific sequences could allow stiff and robust DNA-based scaffolds to be degraded as soon as they are no longer needed.

At the same time, adding topoisomerase to an ensemble of DNA plasmids (circular DNA) can create a gel, in which the rings of DNA are joined together like the rings on the logo of the modern-day Olympic Games. These “Olympic gels” have proved very difficult to synthesize chemically in the lab despite decades of trying, yet nature has been doing so for millions of years.

Apart from their intrinsic scientific interest, studying such biological structures will also help scientists design a new generation of self-assembled topological materials. These complex, DNA-based materials hold great technological promise, but to make progress, multidisciplinary teams of physicists, chemists and biologists are required.

Davide adds:

We still need more top-quality journals that recognize high-value interdisciplinary research of this kind, while research centres that cut across traditional academic disciplines will be vital too. It is an exhilarating field to be in, where everyone – no matter where they are in their career – learns something new every day. My hope is that in 10 or 20 years’ time, scientists who are starting out in their careers will no longer feel obliged to explore only one specific discipline or to choose between theoretical and experimental work. Instead, it would be great if they could simply satisfy their scientific curiosity no matter what background they are from. For if they do that, who knows what we might find next?

Using theoretical and experimental analysis, researchers aim to better understand the novel and intriguing magnetic properties of 2D materials for the next generation of information technologies.

Since the discovery of graphene in 2004 - which won its inventors the Nobel Prize and launched a new field of materials research - two dimensional (2D) materials that are one atom thick have promised to revolutionized technology as a result of their unique and sometimes bizarre properties.

However, one crucial property to data storage and electronics has, for a long time, remained elusive in these materials: magnetism.

For a while, many experts thought that 2D magnetism existed only in theory, but in 2017, a breakthrough came with the first measurements of ferromagnetism were made in chromium triiodide (CrI₃) and Cr₂Ge₂Te₆ compounds. This discovery sparked a renewed interest in the magnetism of these materials, for which many unknowns still remain. "For one," said Dr Elton Santos from the School of Physics and Astronomy, "it is still unclear how magnetism develops in 2D."

Dr Santos is part of a collaborative team of researchers who suggest that as a result of magnetic domains found in 2D CrI₃, this material shows properties that may go beyond those in conventional magnets, with quantum effects playing an important role in large area and denser amounts of information that may be stored. The researcher’s findings have recently featured the cover of Advanced Materials.

The interplay between different interactions usually align the spins of the atoms in small spatial regions on the material, with different orientations forming what are called ‘magnetic domains’. In the case of monolayer CrI₃, however, we observed that the domains cluster themselves in patches that can be large enough to cover the material’s entire surface, like in a single-domain particle but with no magnetic fields. Materials that show such a large area of magnetism can be used in different magnetic processes, such as information storage, but in a much finer fashion—in an area about 10,000 times thinner than the human hair.

When first discovered in 2017, 2D materials like CrI₃ were initially classified as Ising magnets, which is the simplest mathematical model that may describe magnets in a honeycomb lattice of spins, where each site can be either spin up or spin down. Each spin acts like a mini magnet with its own magnetic moment; if all the spins are aligned, then the whole lattice behaves like a big magnet with a net magnetic moment.

But Santos and his colleagues felt this classification did not fully capture the properties of these materials, as they had observed some contradictory phenomenon.

CrI3 was assigned as an Ising magnet, but at the same time it shows properties that would not be compatible with this characteristic, i.e., spin-waves—continuous variations of the orientation of the spins in a wave form. Spin waves have been measured by different techniques, including neutron scattering and Raman spectroscopy, and by different groups worldwide. So, we thought something was not quite right.

What Santos and his group uncovered is the presence of domain walls within the 2D materials, which evolve following the low-dimensionality of the layer, which is not commonly found. To give an example, in conventional magnets like Fe (iron), the domain walls just separate the magnetic domains but they don’t change. They are mostly static in time.

The team now is working on the implementation of these thin magnets in different device-platforms. For instance, where the control of magnetic domain walls is mediated by electrical currents. Initially designed by Stuart Parkin and his team at IBM in 2008, this phenomenon was used to build what are called racetrack memories, which organize data in a 3D microchip and may someday replace conventional data storage.

Dr Santos commented:

We believe that the implementation of our findings in racetrack structures is a matter of time. Since the domain wall is very narrow in these 2D magnets, it is ideal for such processes, and they can also be transferred on different surfaces which facilitates integration with current semiconductor components. This could result in devices that are practically unbreakable because the 2D material is so flexible, as well as light and thin enough to be carried around in your pocket but with the capacity to store thousands of huge files on the go. However, we would need to be cautious since there is a long way before we will reach that level in terms of application.

Attend Postgraduate Virtual Open Days to find out about our MSc programmes.

The School of Physics & Astronomy will take part in the University of Edinburgh Postgraduate Virtual Open Days 23-25 March 2021. 

Academic and professional staff together with students will be involved in a number of online information sessions.

MSc programme

Presentations and Q&A sessions

• Tuesday 23rd March: Introduction to MSc Theoretical Physics and Mathematical Physics 11:00-12:00 UK time
• Tuesday 23rd March: Introduction to MSc Particle and Nuclear Physics  13:00-14:00 UK time
• Wednesday 24th March: Introduction to MSc Theoretical Physics and Mathematical Physics  16:00-17:00 UK time, repeat of the Tuesday session

Exhibitor booths

• Tuesday 23rd March: text chat live with a member of School's recruitment team 15.00-17.00 UK time
• Thursday 25th March: text chat live with a member of School's recruitment team 9.00-11.00 UK time

To book a place visit the Virtual Postgraduate Open Days 2021 page on the University of Edinburgh website.

The Remote3 project based at the University of Edinburgh was invited by the Muslim Scout Fellowship to run a space night for their scouts (aged 10-14 years), with the aim of achieving the Scout Astronautics Activity badge.

The Remote³ project, or ‘Remote sensing by remote schools in remote environments’, is an STFC (Science and Technology Facilities Council) Spark Award Project aiming to deliver much-needed STEM outreach to some of the most remote areas of Scotland.

The Remote³ team worked with the Muslim Scout Fellowship to complete one requirement of the Astronautics Activity Badge - debate about life elsewhere in the universe. Along with team members from the Rutherford Appleton Laboratory and the Boulby Underground Laboratory we discussed what alien life might it look like. How do we search for life on other planets and moons? And how would the human race react to the discovery of life elsewhere in the universe? 

The evening was broadcast live to social media, generating close to 1000 comments and questions during the event, and garnering more than 8000 views since. All attendees were able to complete the badge requirement.

The Remote³ project will continue to work closely with the Muslim Scout Fellowship in future events, including their 2022 summer Jamboree, as well as with many other public engagement teams across Scotland, the UK and beyond.

Scientists are developing vital software to exploit the large data sets collected by the next-generation experiments in high energy physics (HEP), predominantly those at the Large Hadron Collider (LHC).

Over the years, the existing code has struggled to meet rising output levels from large-scale experiments. The new and optimised software will have the capability to crunch the masses of data that the LHC at CERN and next-generation neutrino experiments such as DUNE (Deep Underground Neutrino Experiment) and Hyper-Kamiokande will produce this decade.  

The project, known as SWIFT-HEP (SoftWare InFrastructure and Technology for High Energy Physics), involves the School’s Particle Physics Experiment researchers Professors Peter Clarke, Philip Clark, Sinead Farrington, Christos Leonidopoulos and Drs Yanyan Gao, Akanksha Vishwakarma and Ben Wynne. This work is in collaboration with a number of universities across the UK, partners from the Science and Technology Facilities Council’s (STFC) Rutherford Appleton Laboratory, and in co-operation with CERN and other international stakeholders.

As part of a precursor project to SWIFT-HEP, Professor Farrington, Dr Vishwakarma and UK colleagues coordinated a workshop on Efficient Computing in High Energy Physics where the community met to formulate ideas and plans for the future and to engage with industry invitees. Professors Clarke and Farrington are members of the Advisory Board which led to the eventual SWIFT-HEP proposal. 

If scientists used everyday computers to store one exabyte of data they would need almost one million powerful home computers to do it. Without a software upgrade the need of computing resources for the LHC would be expected to grow six times in size in the next decade. This is not only too expensive in hardware costs and software inefficiencies, but would also imply an increased consumption of electricity. The more efficient software the team will develop will help reduce the usage of computing resources and the carbon footprint of data centre across the world. The project is to ensure scientists can exploit the physics capabilities of future HEP experiments, while keeping computing costs affordable.

The project’s key milestone for 2024 is to evolve from proof-of-concept studies to deployment, ready for the start of data-taking at the HL-LHC and next generation neutrino experiments, which are expected to dominate the particle physics scene in the second half of the decade.

Merons are a type of topological spin texture, with relevance for both fundamental and technological problems. In this theoretical work, scientists show that a new family of van der Waals (vdW) CrCl3 ferromagnet can host merons and anti-merons, and goes on to explore their dynamics and interactions.

Magnetic moments in magnetic materials can organise themselves in different forms of spin structures. From usual ferromagnetic and anti-ferromagnetic materials where spins of neighbouring atoms tend to align parallel or antiparallel to each other, respectively, up to more intricate configurations where spins can assume complex orientations composing a quasiparticle on their own (Figure 1). 

Such spin quasiparticles hold promises in several aspects of information technologies from cheaper, lighter devices, up to ultra-compact spin-based electronic (spintronics). In particular, these quasiparticles offer energy-efficient current-driven phenomena useful in the next generation of low-energy device applications (i.e. computer memory, logic, etc.). Despite their importance, direct observation of spin textures, such as merons and anti-merons, is rare and has been limited to femtosecond transient states, and a few complex chiral magnets. On a recent paper led by the School’s Dr Elton Santos published in Nature Communications, and featured at the Editor’s Highlight section, reports evidence that recently exfoliated vdW CrCl₃ hosts merons and antimerons in its magnetic structure. This finding may revolutionise how to integrate fundamental spin-textures in two-dimensional device platforms. 

The concept of merons and antimerons originated in classical field theory dated from the 1970s, and later applied to particle physics, and more recently in condensed matter physics. In merons and antimerons, which are also called vortex and antivortex, the spins at the core region point either up or down, but those around the perimeter align parallel to the plane of the material with a gradual variation of the orientation of the spins as they move towards or backwards the centre (Figure 1).  Some studies have confirmed the existence of merons and antimerons in chiral magnets, but their complex chemistry and synthesis require additional protocols that ramp up further progress. With the discovery of meron quasiparticles in a relatively simpler vdW layered material, it opens the prospect of explorations of a number of other 2D magnets where such spin textures could be observed. Indeed, the researchers also give some guidelines for looking into materials that may develop topological non-trivial spin textures such as weak out-of-plane anisotropy, and potential competitions between next-nearest neighbour interactions. With the discovery of graphene in 2004 via a handy scotch-tape exfoliation technique, different nanosheets have been isolated up to date. This has generated a broad and fast-pace increased library of 2D compounds for applications. Similar methods have been applied to layered magnetic materials which have contributed to rapidly popularise the field.

The multiscale theoretical methods developed also provide a general framework for a rapid computational screening ahead of lab experimentation on compounds that may stabilise merons and antimerons. The authors unveil the complete evolution of these spin quasiparticles from pair creation, their subsequent motion over magnetic domains (Figure 2), and annihilation via collisions. These results push the boundary to what is currently known about the most concise and fundamental localized spin structures in 2D magnets and open exciting opportunities to explore magnetic domain control via topological spin textures.

A collaboration of nuclear physicists from the Universities of Edinburgh and Liverpool, and mechanical engineers from the Science and Technology Facilities Council (STFC) have designed a vacuum chamber for use in nuclear and atomic physics experiments.

The camber, known as CARME (CRYRING Array for Reaction Measurements), is unique in that it can work in extremely high vacuum conditions. The camber has been produced for CRYRING – a heavy ion storage ring at the Facility for Antiproton Research (FAIR) in Germany.

Experiments with CARME

CARME will initially be used for detecting charged particles for nuclear astrophysics experiments. Elements heavier than helium are created by nuclear reactions taking place in stars. Nuclear astrophysics aims to study these key nuclear reactions to understand the origin of the elements.

In stellar explosions such as novae and supernovae, nuclear reactions involving short-lived radioactive isotopes play a key role in the synthesis of new elements. Producing these radioisotopes in Earth-based laboratories is a major challenge. CRYRING at FAIR offers the unique possibility to recreate the conditions in which nuclear reactions occur in stellar explosions, such as novae and supernovae, using pure beams of radioisotopes inaccessible elsewhere in the world.

The first experiment approved for CARME will be led by Dr Carlo Bruno from the School’s Nuclear Physics research group, and will aim at improving our understanding of the expected composition of cosmic dust formed in nova explosions.

Whilst the initial focus will be on detecting charged particles, CARME is special in that it will also be able to detect gamma rays and X-rays, making it very flexible. In the longer term this will be advantageous because to mount/unmount a system like this is very time consuming, not least because when you break the vacuum it can take weeks or months to recover those specific conditions.

Creating CARME

In order to create CARME, the scientists and engineers had to calculate the number of pumps required to reach extremely high vacuum (XHV) and find the necessary space inside the chamber to make it pump at the required speed. They then created a complete set of construction specifications, from mechanical requirements to what material to weld CARME.

When it came to building CARME’s vessels, they were manufactured in the UK and delivered back to the lab. Each element had to be dismounted, cleaned, fired to high temperatures, rebuilt and then checked for leaks. Finally, before being carefully packaged for delivery to Germany, CARME was re-assembled and tested.

Professor Alexander Morozov’s New Horizons funding will examine phenomena in the microbial world to enrich our understanding of non-equilibrium physics.

New Horizons is a ground-breaking new programme designed to support adventurous, high-risk research in mathematical sciences and physical sciences, with grants of up to £200,000 covering a maximum of two years’ work.

Lattice Models of Bacterial Turbulence

Professor Alexander Morozov has received such funds to study bacterial turbulence to better understand non-equilibrium physics.  

Studies of the behaviour of fish, flocks or birds or insects has transformed our understanding of animal behaviour, biology of groups of organisms, and social interactions. Surprisingly, such phenomena have had a strong impact on statistical and soft matter physics by stimulating the development of what is now called the field of active matter. In the attempt to distil what aspects of such collective behaviour can be attributed to physical interactions, a new direction in non-equilibrium physics emerged that seeks to understand the unique states of matter formed by particles that extract energy from their environment and transform it into self-propulsion.

Professor Morozov’s project will focus on dilute solutions of swimming bacteria - an archetypal model for swimming microorganisms. Such solutions often exhibit a unique dynamical state, known as "bacterial turbulence".

Professor Morozov said:

At very low densities, bacterial suspensions appear featureless and disordered, while at higher, yet still sufficiently low densities, collective motion sets in on the scale of the system. We propose a high-risk, high-gain research programme that will establish a novel class of lattice models describing collective motion in microscopic self-propelled particles suspended in a fluid. Similar in spirit to other non-equilibrium lattice models, our model is simple enough to allow for detailed studies into the exact nature of collective motion.

If successful, the model will gain the status similar to, say, the Ising model in condensed matter physics, and will establish itself as a new archetypal class of active matter systems, ultimately enriching the understanding of non-equilibrium physics and fascinating collective phenomena in nature.

New Horizons

The Engineering and Physical Sciences Research Council (EPSRC), part of UK Research and Innovation (UKRI), has allocated almost £25.5 million of funding to 126 adventurous projects in the mathematical and physical sciences through this pilot programme.

Science Minister Amanda Solloway said: 

It is critical we give the UK’s best researchers the resources to drive forward their revolutionary ideas so they can focus on identifying solutions to some of the world’s greatest challenges, such as climate change. This government funding will allow some of our brightest mathematicians and physicists to channel all their creative ingenuity into achieving potentially life-changing scientific breakthroughs – from mathematics informing how we save our rainforests to robotics that will help track cancer faster.

The School has achieved an excellent outcome in the latest round of grants awarded by the Science and Technology Facilities Council’s Astronomy Grants Panel.

The new Astronomy and Astrophysics Consolidated Grant, led by Professor Philip Best, will support 11 theoretically and observationally-focussed postdoctoral researchers at the Institute for Astronomy from April 2021, on research topics ranging from exoplanet studies to cosmology. This is an increase of funding from seven researchers, which was received at the last submission three years ago.

Support for two further postdoctoral researchers in solar system and planetary science was successful through the Astrobiology-focussed Consolidated Grant led by Professor Charles Cockell. These two grants were complemented by a successful Consortium Grant in Nuclear Astrophysics, with Edinburgh-lead Professor Alex Murphy.

Combined, these grants represent a success rate of just over 60% for Edinburgh researchers, roughly double the national average of 30%.
 

Dr Jean-Christophe Denis received an External Engagement and Impact Award from the School of Biological Sciences in December 2020 for engagement work he undertook last year.

He was involved in the delivery of boxes containing science experiments to around 2000 children in the Craigmillar, Moredun and Gilmerton areas of Edinburgh. He also helped run weekly online science clubs during the school term, providing all the necessary equipment and running online live sessions to pupils from six primary schools in the same area.

Dr Jean-Christophe Denis (or JC as he is known) is the School’s Ogden Outreach Officer, and he received the award alongside Dr Janet Paterson, Public Engagement Officer at the School of Biological Sciences, and Dr Cathy Southworth, Community Engagement Manager at the Bioquarter who were also involved in the work.

Dr JC Denis commented:

Having worked closely with the Craigmillar and Moredun communities over the past year, I felt it was vital to maintain our relationships despite the challenging conditions, and to support pupils and their families during a tough year. Together with Cathy and Janet, we decided to provide science kits to all primary school aged children in the area, an initiative which met a lot of success and enthusiasm from children, parents and schools alike. We then offered online live science  clubs to pupils in these communities. We originally feared it would not be an effective way to deliver science and build relationships, but it ran very smoothly and the children enjoyed the sessions very much, and clearly built their enthusiasm for science further. This success is largely due to the Physics undergraduate students, Annabelle Avery and Cristina Cortes, who led these online session, and to whom I am extremely grateful.

2020 is the first year the School of Biological Sciences has granted External Engagement and Impact Awards. Dr JC Denis said:

I am very grateful and honoured to have received this Award alongside my colleagues Cathy and Janet. 2020 has been a very challenging year for Public Engagement and Outreach, as we have had to totally change the way we work, so it was heart-warming to receive such an Award in recognition for our work in these difficult times.