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Physics in the pandemic: ‘Routines are important’

Usually I ride my bike to work. From my front door to my office at the Danish Centre for Particle Therapy it takes me about ten minutes. These days I walk. The trip can take anywhere from five to thirty minutes and it takes me from my front door and back to my front door.

A friend and fellow PhD student told me about this habit in one of our recent “I can’t believe this is real” phone conversations. It’s supposed to be a way of separating at-work time from at-home time when your workplace is in your home. Ever since the Danish state mandated that all non-essential public employees must work from home, my workplace has become a little desk about a metre away from my bed. And while I am happy to stay home and keep from inadvertently spreading this scary new virus to all the doctors, nurses, radiation therapists and – most importantly – cancer patients I normally share the building with, this situation takes some getting used to.

Routines are important when every day could easily become a lazy Sunday at home. So I get up at 6:30, shower, have breakfast, walk to work, make coffee, go sit at my desk, and log on to my research group’s newly established office chat. In the afternoon I walk home from work, and in theory the desk should be off-limits for the remainder of the day. This doesn’t always work out, but that’s not really a new issue. Even in pre-coronavirus times I often took my work home with me in the evenings. Any PhD student will understand: You just need this last bit of code to run, to fine-polish this last figure, to rehearse your presentation for tomorrow one last time. In that way not much has changed.

I am one of the fortunate ones. My work does not demand that I be in a laboratory and perform experiments. I only need my computer and access to the right drives and databases. My biggest problem was getting permission to establish a VPN connection to our hospital systems (not as simple as one should think).

Physics in the pandemic: ‘Work will always be there’

I have friends who were forced to shut down experiments and postpone critical work, though. The shutdown of all Danish universities was announced on a Wednesday evening around seven. That evening, the friend I mentioned earlier stayed at her lab until two in the morning, feverishly collecting data so she would have enough to keep her occupied for at least a few weeks’ worth of forced home office work.

I guess in the end all I can say is that, for me personally, it could really have been much worse. Yes, a few conferences were postponed, as was my planned six months’ research stay abroad in the Netherlands. But I can still do my work, my PhD probably won’t have to be extended, and I guess I can use the quiet and isolation to finally get around to writing up that paper I’ve been meaning to get around to for the last few months… In any disaster it’s important to look for the silver lining. Stay safe out there (hopefully at home, if you can)!

Ask me anything: Sadik Hafizovic

What skills do you use every day in your job?

The fundamental concepts that I acquired in academia, during my engineering and physics studies, PhD and postdoc time, are the foundation upon which I judge technological decisions. This understanding is priceless and feels indispensable to me. Zurich Instruments participates in government-funded projects such as OpenSuperQ, where we are helping build an open superconducting quantum computer. Even though I am not personally much involved in the project, I do need to understand where it can take us.

Communication is a skill that I wouldn’t say I lacked, but as the company now has 100 people, with offices in China, France, Italy, South Korea and the US, it is becoming pivotal and the requirements on communication are growing. Likewise, organization development and change-management are topics that I wasn’t confronted with in my education, but are key for me in mastering today’s challenges.

What do you like best and least about your job?

An outstanding feature of my job that I enjoy is getting to help, and learn from, many scientists all over the world, in many different disciplines. Over time, I have built up lasting relationships that go beyond the provider–customer relationship, which I find very rewarding. My circle of outreach seems much bigger than the one I had during my postdoc days in my research community. Of course, this also has a flip-side: in a research community one can strive for in-depth knowledge; now my technical knowledge has become shallower, as I cannot afford to go into too much depth in technical and scientific matters anymore. Nonetheless, the fact that I can be entrepreneurial and still stay close to science is wonderful.

What do you know today that you wish you knew when you were starting out in your career?

I can share what has worked for me: if you want to start a company, don’t do it by yourself; find one or two friends to embark on that adventure together. If possible, don’t do it as a side project, make it your main job. If you are currently in academia, build your company outside of the university if possible. Don’t be afraid of competition. The world is a large place with many niches – find yours.

Thread-like defects in 3D active crystals get a closer look

Flocks of birds, schools of fish and swarms of insects are all examples of “active matter” – systems of particles that move on their own without recourse to external forces. Scientists have long sought to replicate such behaviour in the laboratory, with the aim of producing synthetic materials that mimic biological functionalities such as self-healing or cell mobility and division. A team of researchers in California, US, has now moved closer to this goal by obtaining the first detailed, three-dimensional views of a type of active matter known as nematic liquid crystals.

The team made their observations using a technique called light-sheet microscopy, which was originally developed to visualize how living organisms acquire their shape and architecture. According to co-team leader Zvonimir Dogic of the University of California, Santa Barbara, these observations represent the first step towards real-world applications for active crystals, as previous studies had mostly focused on simpler two-dimensional systems.

Non-equilibrium state

Nematic liquid crystals get their name from the Greek word nema, meaning “thread” – a reference to their characteristic thread-like topological defects. These defects are called disclination lines, and they can be made of elongated molecules or colloidal particles. Within a given area, they will on average point in the same direction, along a localized preferential axis known as the director.

In ordinary, passive, nematics, homogenously aligned states are favoured over deformations that cause the material to bend. In active nematics, however, the situation is different, because the active components provide energy on the microscale throughout the structure. This energy drives internal stresses that distort the fluid, with the result that even the smallest deformations can amplify exponentially.

This non-equilibrium state cannot be described in the framework of conventional thermodynamics, and it leads to unsteady, active turbulent flows in the bulk of the material. In contrast to turbulence in normal fluids, the chaotic flow in active nematics does not contain regular patterns and can give rise to large-scale coherent motion, producing emergent structures, such as phase boundaries and topological defects, in which local order has broken down.

Bending instabilities and bulk flows

In their new work, Dogic and his colleagues, together with a team led by Daniel Beller from the University of California, Merced, made their active nematic fluids from bacteriophage virus particles. The rigid rods of the virus provide the nematic liquid crystal phase at room temperature.

Building on earlier work in Dogic’s lab, the teams dispersed two basic components of biological cells – microtubules and kinesin motors – into the nematic phase to create their active material. Microtubules are filaments of long, semi-flexible protein assemblies, while kinesin is a protein that can convert chemical energy (in the form of adenosine triphosphate, or ATP) to mechanical energy.

When fuelled with ATP, the molecular motors elongated the microtubule bundles, which in turn induced active stresses that created bending instabilities and bulk flows throughout the entire sample, including the nematic phase.

Tracking the motion of defects in real time

To study this behaviour, the team turned to light-sheet microscopy. In this technique, a micron-thin sheet of light is used to image a sample of molecules labelled with a fluorescent marker. By rapidly scanning the sheet along the z-direction of the sample, the researchers could image their active nematic crystals with molecular-scale resolution and track the motion of defects in real time. This approach provides a quantitative measure of the local director field over the entire 3D volume of the active material.

The researchers found that their nematics contain both disclination lines and loops, including Möbius-strip-like objects that can nucleate, shrink, open and merge to form spatially extended structures. These disclinations can be thought of as rubber-band-like loops that are continuously being pulled and stretched by internal forces, they say.

To understand how the dynamics of these loops depends on the material’s local topological structure, Dogic says that he and his colleagues will need to develop visualization techniques with improved temporal resolution as well as new methods to isolate single loops. “We would also like to gain a detailed appreciation of how an isolated loop appears in a perfectly aligned material,” he tells Physics World.

The new work, which is detailed in Science, is an important example of how to make and study 3D active crystals, Dogic adds. In a related Perspectives article, Dennis Bartolo, a researcher at the University of Lyon, France, who was not involved in the work, called it “a formidable experimental platform” for future observations of these complex materials.

Gamma rays and gravitational lensing provide hints of dark matter

A comparison of data from gravitational lensing and gamma-ray observations has revealed that regions of the sky with greater concentrations of matter emit more gamma rays. The researchers who carried out the work conclude that much of the correlation is likely due to the action of supermassive black holes, but they say that some of the emission may be due to dark matter.

When light travels to Earth from a distant object it can be affected by the warping of space caused by the gravity of massive objects that it passes on the way. This results in a distortion of the image of the object that we see — and the type and degree of distortion reveals the distribution of mass along the light’s path. After accounting for all the visible foreground objects, what remains in the mass distribution is assumed to be dark matter – a still undetected substance that is reckoned to make up about 25% of the universe’s energy/mass content.

Astrophysicists also study emissions of gamma rays from places that are believed to contain lots of dark matter – such as the centre of the Milky Way. This radiation could be generated when hypothetical dark matter called weakly interacting massive particles (WIMPs) collide and annihilate one another. To date, however, those studies have been inconclusive as to the existence of WIMPs.

Unresolved sources

The latest work scrutinizes nine years’ worth of gamma-ray data from the Large Area Telescope onboard NASA’s Fermi satellite. Those data have previously revealed many individual gamma-ray sources, such as the remnants of supernova explosions or blazars – jets of ionized matter produced when supermassive black holes at the centre of some galaxies accrete surrounding material. However, those sources cannot account for all the detected radiation. Instead, objects too faint to be revealed individually generate what is known as the unresolved gamma-ray background.

The study was done by Simone Ammazzalorso at the University of Turin in Italy and colleagues, who have compared gamma-ray background measurements with the first year of data from the Dark Energy Survey – optical snapshots of 40 million galaxies obtained by the Dark Energy Camera on the 4 m Victor M Blanco Telescope in Chile. Their aim was to establish whether there is any correlation between the positions of gravitational lenses – deduced from the stretching of distant galaxies – and gamma-ray photons, as is predicted. As they report in Physical Review Letters, the answer is yes.

Scrutinizing the two sets of data for common patterns, the researchers found that regions of the sky containing more matter also emit more gamma rays and that, conversely, there are fewer gamma rays from less dense regions. Specifically, they confirmed the existence of such a correlation at high energies and small angular scales – less than 0.3°– with statistical significance of greater than 5σ, a value that is generally considered to indicate a discovery.

Blazars in the frame

To establish what might be responsible for that emission, the team plugged the data into computer models that simulate how various celestial objects generate gamma rays. Doing so, they concluded that most of the correlation is likely due to blazars, which are essentially point-like objects.

However, the researchers found that an extra ingredient was probably needed to account for a second, weaker, correlation at larger angular scales. They established at the level of 3σ that their models reproduce the observed data, including energy and red-shift components, more faithfully when they include dark matter among the gamma-ray emitters than when they don’t.

“This result is exciting as it marks one of the few hints at the existence of dark matter via indirect detection methods, and it opens up new possibilities for probing dark matter particle models,” according to Francesca Calore, an astroparticle physicist at Annecy-le-Vieux Theoretical Physics Lab in France, who wrote a commentary piece to accompany the paper describing the research.

However, Calore cautions that scientists do not completely understand the physics of blazars, arguing it is still possible that even the correlation at large angular scales “comes entirely” from these objects. Getting a firmer idea of dark matter’s contribution to the unresolved gamma-ray background, she says, will require fresh data.

Indeed, the Dark Energy Survey is due to release an enlarged data set, containing observations of 100 million galaxies, in the summer. Beyond that, the Legacy Survey of Space and Time at the Vera Rubin Observatory in Chile should provide data on billions of galaxies over a larger area of the sky after it opens for business in 2022. That year should also see the launch of the European Space Agency’s Euclid telescope, designed to better understand dark energy and dark matter by comparing the shape and redshift of galaxies.

“With deeper redshift coverage and a better angular resolution, future instruments will enable scientists to better understand the sources behind the universe’s gamma-ray glow and, potentially, uncover the nature of dark matter,” says Calore.

Physics in the pandemic: ‘Work will always be there’

I’m writing this on my typewriter. She’s a trusty Corona Standard that has seen everything from the Great Depression to the rise of the Internet. And I’m writing on her today (20 March) because my screen time is through the roof.

I’m one week into an isolation of indeterminate length to limit the spread of the novel coronavirus and its resultant disease, COVID-19, and it’s been hard for me to ignore the incessant barrage of media updates.

This time last week, I was loading books from work into my car. I had a feeling that I wouldn’t be returning to my cubicle anytime soon.

Two days later, in part a response to Wisconsin Governor Tony Evers’ declaration of a public health emergency, University of Wisconsin-Madison chancellor Rebecca Blank announced that university employees should work from home, when possible. Two days after that, Blank said that in-person classes, which had originally been cancelled through 10 April, would remain online through semester’s end.

In the days that followed, cancellations and closures piled up. University buildings closed to all but essential personnel, and research activities involving human participants were suspended until further notice. Life as I knew it had ground to a halt.

Like many PhD students, I am now reflecting on my priorities and research project. To be honest, I hadn’t truly felt connected to my project – developing quantitative ultrasound imaging parameters for stroke risk assessment – until a few months ago, when I returned to Madison from an internship and received my committee’s OK to defend in fall. With that “OK”, I felt a renewed determination to finish my project, complete the degree.

Earlier today, I realized I can’t start my final aim until the university reopens…Does it really matter?

My advisers say that the university closure is temporary, that it won’t last more than two months, that my degree is not on hold. I disagree…Does that matter?

I’m more fortunate than many graduate students. I have a reliable Internet connection, computer workstation and an office space at home, and I have enough food and supplies to last a while. I have a car. I don’t have to prelim or defend virtually.

But I’m also concerned: for my friends and family, friends’ families, colleagues and their families, myself. We’re spread out across the globe, some still trying to make it home. Some of us are considered essential and are working throughout this pandemic in hospitals and clinics, bakeries and law offices.

I’m tired. I’m frustrated at those who do not heed requests to stay home. I’m angry at those who hoard supplies and spread misinformation. I’m disappointed and grieving for events and conferences that were cancelled. I wonder what will happen if people, desperate for necessities and actionable change, start looting.

Needless to say, finding a routine hasn’t been in the cards. Not this week, at least. In spite of external pressures to continue working, I’m treating myself gently and encouraging my friends and colleagues who can afford to, to do the same. Work will always be there.

For now, I read, cook, watch my neighbours’ dogs play outside, and chat and vent frustrations with friends. For now, it’s finally the weekend, although it doesn’t feel like it. For now, I’m going to watch Avenue 5 on HBO. Space cruise escapism, anyone?

Radiomics-based MR image analysis can predict brain tumour prognosis

MRI prognostic features — Example MRI scans showing prognostic features for short-term and long-term survival. (Courtesy: Case Western Reserve University)

Glioblastoma is the most common primary malignant brain tumour. It is aggressive and rapidly fatal, with a median survival time of only 15 months after diagnosis. Glioblastoma cells’ genetic profiles are extremely heterogenous, which is one reason for the generally poor prognosis. It also means that disease progression and response to treatment can vary greatly between patients.

A group of researchers from Case Western Reserve University has now developed a model that links radiomics features to tumour biology. This could greatly improve prognostic accuracy and help in the design of patient-specific treatments for glioblastoma (Clin. Cancer Res. 10.1158/1078-0432.CCR-19-2556).

Gene expression as a prognostic tool

In recent years, researchers have identified several characteristic genetic markers in glioblastoma that influence the disease prognosis. These markers can be used as predictors of a patient’s survival time or even to predict which treatment a patient is most likely to respond well to. Discovering a tumour’s gene profile requires a biopsy, however – an invasive procedure that carries risks of its own.

MRI provides a non-invasive way of analysing a tumour and its surroundings. Using radiomics methods, one can extract image information, so-called “features”, that are hard or impossible to detect by the naked eye. The group, led by Pallavi Tiwari, has developed a prognostic model based on pre-treatment MRI radiomics features – and, importantly, connected the features used in this model to biological processes in the tumour. In this way, the researchers not only show that their model can predict survival, but they also explain why it does.

Niha Beig and Pallavi Tiwari — First author Niha Beig (left) and group leader Pallavi Tiwari.

Tiwari and colleagues built their model using pre-treatment MR image sets of 130 patients. For each of these, they extracted 2850 radiomics features and finally identified 25 as being especially prognostic of a patient’s progression-free survival. These features describe image properties such as “wavy, ripple and spot-like patterns”, the authors explain, or the sphericity of the oedema (swelling) surrounding the tumour. They combined these features into a model to calculate a radiomic risk score (RRS) and validated the model’s prognostic ability in an independent patient cohort.

Tiwari’s team then showed that these radiomics features correlate with certain gene expressions in the tumour. These genes control biological processes such as the rate of cell division or the growth of new blood vessels to transport nutrients to the tumour. In this way, the researchers established a direct connection between the radiomics features and the biological processes leading to disease progression.

Towards personalized treatments

Despite being the most common primary brain cancer, glioblastoma remains a relatively rare disease. It would likely take a prohibitively long time to collect enough patients for a study such as this in a single institution. Tiwari and her colleagues circumvented this issue by using open-source data sets from The Cancer Imaging Archive and the Ivy Glioblastoma Atlas Project, in addition to data from their collaborating institution, the Cleveland Clinic. Data pooling efforts such as these are essential for building increasingly stronger predictive disease models.

In the future, the group will work on extending the image correlates found to be prognostic of overall survival and demonstrate that the RRS model can be predictive of response to chemotherapy in particular, says Tiwari. “This could have huge clinical implications in terms of identifying glioblastoma patients who may not respond favourably to chemotherapy and may be more suited for genomically-driven treatments to improve their quality of life as well as overall survival times,” she explains.

Ask me anything: Helen Margolis

What skills do you use every day in your job?

As the UK’s national metrology institute, NPL’s mission is to provide the measurement capability that underpins the UK’s prosperity and quality of life. In my department, we operate the national time scale, using it to contribute to global timekeeping and to disseminate accurate time and frequency to users across the UK. This work underpins many technologies that are part of our daily lives, such as mobile phones, the Internet and satellite navigation systems. Of the topics I studied during my undergraduate physics degree, I have probably made most use of the atomic physics, laser physics and optics. The practical and coding skills developed during my doctoral research have also been vital to me during my career at NPL. Equally important is being inquisitive and curious, not being afraid to ask questions, and paying attention to detail. This last point is absolutely critical to succeeding as a metrologist.

As I have progressed into more senior roles, skills such as planning, prioritization, communication and collaboration have become increasingly important. I am currently co-ordinating a three-year European project that involves 15 organizations from eight countries. This is a challenge at times, but one I enjoy. Mentoring is also an important part of my job, and for this effective listening is key.

What do you like best and least about your job?

One of the best things about my job is its variety, which means I am always learning new things, and never get bored. One day I might be deep in detailed discussions about the development of an ultra-stable laser source, or drafting a paper describing the results of an international clock comparison campaign. The next I might find myself discussing the future strategic direction of my department with a member of NPL’s executive team, or giving a lab tour to a government chief scientific adviser. I also work with a diverse and dedicated team of people who are passionate about what they do, and bring a wide range of skills and experience to the team. As head of science my role is to maximize their potential by inspiring them to work effectively together to achieve our goals.

My job does involve quite a bit of international travel, which may not appeal to everyone, but it has taken me to some interesting places that I would probably never have visited otherwise.

What do you know today that you wish you knew when you were starting out in your career?

I wish I’d known that there were places like NPL. I started my research career as a DPhil student at the University of Oxford, working on spectroscopic experiments to test the theory of quantum electrodynamics. This taught me many important things, not least the importance of setting ambitious goals, which increases the likelihood of generating significant results, even if you don’t achieve everything you originally set out to. While I enjoyed my time in Oxford, I always felt challenged when friends asked, “but what is the point of your research?”

Once I moved to NPL, which sits at the intersection between academia, government and industry, this became a much easier question to answer, as the work we do has a direct impact on people’s lives. As in academia, we carry out leading-edge, fundamental research – our work on next-generation optical atomic clocks and related technology fits into this category. However, a key difference is that we always have an end use in mind, even if it is many years away.

Blue energy: innovative ways of harnessing energy from the oceans

This three-minute video introduces two innovative approaches to harnessing energy from ocean waves from Eco Wave Power and AW Energy. Water covers about 70% of the planet, and much of it, driven by the Sun, is in constant motion. For at least 200 years, visionaries have dreamt of harnessing this “blue energy” and using it to power the world. But engineering challenges in these environments – especially at sea – can be vast. Another big hurdle is convincing investors to back these projects in the face of current uncertainty.

Find out more about the researchers and hi-tech business pioneers offering ways to harness blue energy – read this feature by science writer Stephen Ornes, originally published in the March 2020 issue of Physics World.

Ask me anything: James McKenzie

What skills do you use every day in your job?

Communication of ideas is one of the main skills I am using at the moment. The challenge is to communicate complex ideas simply without them becoming misleading. Given I work in a physics-based business that has rather complex markets and technology, this is a challenge – keeping it to a level that doesn’t baffle the audience, bore them or patronize them is difficult. I think I have learnt this from explaining to my mother, who is very smart but is a historian, what I am doing over a number of years.

In the past I have run some large and diverse teams as chief executive and in this role you need to know enough about everything to be respected, or have people around you whom you trust and are able to cover the gaps. Communication skills therefore include asking the right questions. The skills and knowledge gained from studying physics represent a solid foundation to build on. Much of the detail of the physics I learnt at university is gone, but the logic and framework remains and that’s key to your view of the world. When working in industry, rapid problem-solving is about knowing what to focus on and how to eliminate dead ends. People management is by far the biggest challenge in my job: how to motivate and encourage is tricky and something that comes with practice.

What do you like best and least about your job?

One of the things I like most is taking scientific ideas and turning them into business ideas in the form of products or services. To do this, you need to do an in-depth study and weigh the pros and cons of any idea, to build confidence in it. That’s the fun part for me, but there are a number of necessary evils – paperwork, documentation, referencing and report writing – which are less fun but need to be done.

Travelling to meet customers, investors and suppliers is part of the job. In my early career I liked it – it gave me a chance to see the world – but now I am less bothered about it, as it’s easier to communicate via e-mail and video conferencing. Legal paperwork is my least favourite thing in the world. I used to run a public company that was AIM listed and on the London stock exchange. This sounded impressive but the amount of paperwork and regulation was overwhelming. Everything was audited, annual reports were 100 pages long. One investment I was involved in had five legal teams working on it and took five months to finalize from the offer of money to getting the money in the bank, and the legal fees were £250,000.

Being at the top of a company is a really lonely place – everything you say has consequences. You are never really able to have many friends in the businesses you work in – it’s best to build a network of peers and mentors you can talk to about challenges and issues.

What do you know today that you wish you knew when you were starting out in your career?

Have confidence in your abilities – you are probably better equipped to deal with things than you think. There are plenty of options out there – you may as well do something you enjoy (rather than do it for just the money). Getting out of bed every day with a love of what you do is the secret to a happy life and you are more likely to be successful doing what you love.

Pitch of birdsong is determined by body size

The characteristics of the white-tipped plantcutter’s song are directly linked to its body size, a new study shows. A team of physicists and ornithologists in Argentina and Germany, including Gonzalo Uribarri at the University of Buenos Aires, discovered the relationship through a detailed analysis of recordings and museum specimens of the birds. Their findings could lead to new insights into the intriguing acoustics of birds that develop their songs independently.

Birds can convey a rich array of sounds through their song. Around half of species are “vocal learners” that develop their complex, specific songs by copying older members of their species. In contrast, “non-learners” develop their vocal characteristics by themselves. These birds have evolved a diverse variety of biomechanical mechanisms for enriching the sounds they make.

Uribarri’s team has explored these mechanisms in detail and have concluded that the physical characteristics of non-learners – particularly their body sizes – can impact their songs.

Rusty door hinge

The researchers tested this idea by analysing recordings of the white-tipped plantcutter: a non-learner native to South America, whose song resembles a long, rough creak like a rusty door hinge. To predict the sizes of the birds making the recordings, the team used museum specimens to show that the bird’s body size tends to increase with altitude, making them better adapted to colder environments. This then allowed the team to plot the frequencies of the recordings against the altitudes at which they were made – confirming that the larger the bird, the deeper their song.

Uribarri’s team also performed acoustic analysis on the recordings to create mathematical models of the bird’s call. This revealed that their songs begin with sudden, sharp vibrations, and then taper off exponentially. Therefore, the researchers deduced that rather than pushing air straight through its vocal folds, as is the case for most birds, the white-tipped plantcutter builds up air inside its vocal folds, which escapes in sudden, explosive energy pulses when the pressure becomes high enough.

After a burst, the sound resonates inside a cavity in the oesophagus of the bird. The cavity then dissipates these vibrations, producing the exponential decay in sound. Ultimately, the frequency of the resulting song depends on the fundamental frequency of this cavity, which directly depends on its size. Uribarri and colleagues now believe that this mechanism is likely to apply to other non-learner bird species. With future research, this could lead to a better understanding of the rich variety of sounds such birds produce.

The research is described in Physical Review Letters.

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Physics in the pandemic: ‘Routines are important’

Physics in the pandemic: ‘Work will always be there’

Ask me anything: Sadik Hafizovic

What skills do you use every day in your job?

What do you like best and least about your job?

What do you know today that you wish you knew when you were starting out in your career?