A virtual journal club for the general public, brought to you by a biophysics PhD candidate. The subject matter will be broad and cover many different areas of science. Come delve into the wonderful universe around us with me!
Credit: NASA, ESA, CSA, Jupiter ERS Team; image processing by Ricardo Hueso (UPV/EHU) and Judy Schmidt.
New JWST images of Jupiter highlight the planet's features, including its turbulent Great Red Spot (shown in white here), in amazing detail. These images were processed by citizen scientist Judy Schmidt.
The 60-hour crunch: working with xray free electron lasers
Imagine your job (or dream job). Imagine that job only being able to be conducted in five places worldwide at the time of this post. Five countries, five sites. Now imagine you can only go for a few days out of the year to complete months or years worth of work.
You would imagine that there would be a sense of urgency in the way you conduct the job. You’d have to be as efficient as possible, because those precious 48 to 60 hours are the only chances you’ll get for at least a year, possibly more, to do this work. On top of that, because of the nature of this job, there’s probably a lot of competition to get to choose who comes to the site in a given year. You pour hours into creating the perfect proposal, a demonstration of why you should be granted the opportunity.
This is the nature of working with X-ray Free Electron Lasers (XFELs). As of 2022, there are five operating in the world, each involved in cutting edge chemical, physical, and biological research. They are truly sites in the world where boundaries are being pushed, and processes being made more efficient. It opens the doors to collaborations where previously there wouldn’t have been any, and so this field of science flourishes and has a strong backbone in the form of the XFEL.
In my four years, I’ve been involved in four experiments at the XFELs. This is quite numerous — during 2020 we had two runs, completely virtual. This was its own challenge, of course, and I had also just joined my laboratory group, so needless to say most of the time I had no idea what was going on. That’s okay, though. It certainly planted a seed of anticipation for my first trip in person to such an instrument.
In August of 2021 I went to Menlo Park, California, where the national lab SLAC is located (the acronym actually has a weird story — let me know if you want to hear it. The S is of dubious status right now, but the LAC stands for ‘Linear Accelerator’).
I’d never been so far from the Midwest before, and this marked the first year I ever rode a plane — at age 25, no less!
At SLAC there’s the Linac Coherent Light Source (LCLS), and this is where the X-ray laser is generated and used for experiments.
You may ask me: ‘Why not just make an X-ray laser in an academic lab?’ Some people kind of have, but not nearly to this extent. When I write a post on it, I’ll be sure to link it here. X-ray generation for the doctor’s office is very different than the X-ray generation of these XFELs. For lower energy X-rays, a small x-ray tube is fine. But for the high-energy, high-intensity physical and chemical applications, a lot longer of a 'tube' is needed. This involves the acceleration of electrons through either a ring (like the particle accelerators at CERN in Switzerland) or through a long linear path. (The ring ones are called ‘synchrotrons’, and there are far more of these than there are x-ray lasers. Cooler word, though.)
Here is an article that talks about the basics of X-ray radiation generation from the Australian Radiation Protection and Nuclear Safety Agency. Please ask if any questions arise!
Because SLAC incorporates a linear path (hence the ‘linear accelerator part of it’s name), it means that the electrons are pushed through a 2km-long tunnel, all the while creating high-energy radiation. The electrons are pushed with magnets, since electrons have a negative charge. They are pushed so fast that they begin to emit radiation in the X-ray region of the electromagnetic spectrum. They are also pulsed, and these pulses of light are very intense, able to destroy the molecules that come in contact with it. It is very dangerous to be in the room with this laser on [1].
Electromagnetic radiation spans from long-wavelength radio waves to x-rays and gamma rays on the short-wavelength/higher-energy range. The shorter the wavelength, the higher the energy associated with the radiation. UV radiation, for example, tans and burns our skin because of the high energy associated with it. But it does good too -- it creates the vitamin D in our skin that is essential for health [2].
X-rays have more energy in them than the wavelengths of light that are visible. They have unique properties, such as being able to pass through soft matter like your skin and muscles when getting an X-ray done at the doctor's office.
The scope of this operation is huge, and this size is required. It is no mystery now that you can’t just build this in your backyard, nor in an academic lab. Universities can have x-ray sources… but nothing like this. This laser is capable of creating ultra-intense, ultra-bright pulses of X-rays, which lends itself well to applications such as finding structures of proteins or dynamics of molecular motion.
In particular, my group is interested in ‘molecular movies’, and x-ray lasers can help provide some of the answers of how molecules move physically in response to light. We went to the LCLS to study vitamin B-12’s response to light, and overall it was very productive.
Yes, you can only go for a few hours out of the year, and getting in is highly competitive because of the demand for the cutting-edge technology. But if you plan those 60 hours well, you can have data to last an entire dissertation. I am currently working on analyzing data that was taken in 2017. So there is a lot of information that can be gathered, and the perk is that you get to travel!
Soon I will travel to Hamburg, Germany to do an experiment at the European XFEL. It’ll be my fifth XFEL experiment overall that I have been involved in, including collaborations. I'll keep this blog updated with the goings-on of the work and fun I'll have while there! And if you have any questions, please send an ask or message!
References
Overview of X-ray Lasers from LCLS
Sofferman, D. Journal of Chemical Physics, (2021), 154(9).
Images:
Locations of XFELs: Chemical and Engineering News, ACS
SLAC sign picture: taken by me during my visit in 2021
Overhead view of LCLS: LCLS website
View of x-ray tunnel: LCLS website
Electromagnetic spectrum: Encyclopaedia Britannica
Snailfish With Anti-Freeze In It's Veins Found Beneath Greenland Iceberg
A snailfish (Liparis gibbus) with the "highest expressions levels" of bioluminescent green anti-freeze proteins in its veins has been found by scientists drilling into an iceberg off Greenland.
The anti-freeze proteins work the same way that anti-freeze in cars works. It regulates the temperature of the organism . How, you say? Well, the proteins stick to the surface of ice crystals and slow them, preventing them for growing larger. Fish, unlike other cold blooded organisms, cannot survive when bodily fluids freeze, so grains of ice form in their cells, freezing them from the inside out. The anti-freeze stops this.
Even more extraordinary than the snailfish's ability to produce the anti-freeze, it exhibits biofluorescence (the ability to convert blue light into green, red, or yellow light, typically used during extended periods of darkness, like those at the poles). This characteristic is normally found in fish swimming in warmer waters, and this is the first reported case of an arctic fish species displaying it.
However, due to warming water temperatures caused by climate change, warmer water species can migrate further north now, creating more competition for the snailfish, making it's anti-freeze proteins slightly unnecessary.
This extraordinary little creature certainly has provided us with some food for thought about how organisms adapt to their environments.
Source: LiveScience, written by Jennifer Nalewicki, and, Burns, J. et al. (2022). Transcriptomics of a Greenlandic Snailfish Reveals Exceptionally High Expression of Antifreeze Protein Transcripts. Evolutionary Bioinformatics, 18 . Available at: https://journals.sagepub.com/doi/10.1177/11769343221118347. Accessed: 17th August 2022
Here's another post just to get the introductions out of the way!
If you've read my introductory post, you may know that I am a fourth-year PhD candidate studying biophysics. I currently attend the University of Michigan in the United States. While I have not published a first-author paper yet, I have recently been involved with Chapter 13 in the book Methods in Enzymology. I love writing in general, and I write novels and short stories as a hobby. I want to synergize my love of writing and my love of science. I think a science writing career would be a great fit for me if I can hone my skills, get practice, and make the right connections.
While I am in the biophysics program, I actually work more in the field of physical chemistry and spectroscopy, studying a biological sample. Specifically, I study vitamin B-12, an essential molecule for human function. I study how this vitamin responds to light from an intense and powerful short-pulsed laser over time. interesting applications can spring forth from this, though I would describe my area of research more as being 'basic science' than strictly working towards a particular application. This in contrast to research where the hope is to create a product immediately usable by people. My research lays the fundamental groundwork for people to then create useful applications with the knowledge we have provided.
I get to work with my favorite experimental instrument every day -- huge ultrafast laser systems. They can be a pain because of their sensitivity and 'temper tantrums', as I like to call it. Even so, I love every day of learning how they work and making light magic happen. I'll do a post soon on these lasers alone, since I think it is one of the coolest things out there. Here's just a piece of it. These are huge lasers. Like 'they take up half an entire room' huge. I love it.
Actually, once upon a time, I thought I hated optics and never wanted to do anything regarding lasers and mirrors and lenses again... how wrong I was!
I study a biologically-relevant form of vitamin B-12 and how it responds to light in different environments. This can mean water vs. a more 'goopy' solvent, or a solution vs. protein environment. In organisms, like ourselves, vitamin B-12 is a helper for proteins carrying out important biological reactions. In addition, some of these proteins need vitamin B-12 and light to do the right thing for the organism at a particular time. Therefore, knowing the way vitamin B-12 responds to light in a protein environment is important, though it can be difficult to study. My work helps bridge some of these challenges and answer these questions, as well as push the boundaries of the techniques used to study them. Of course, I can always explain more if anybody is interested!
I hope this was interesting, if not brief! I can explain more in the future, and will be happy to unfold the story for you. My first few posts will go more in-depth about some of the travel I do for my PhD research, including updates on my upcoming trip to Hamburg, Germany! I'm excited -- I've never been out of the US before.
Outside of the realm of science, I write in my free time. I really enjoy writing creative fiction, and I'm currently working on a few ventures. I like taking walks, spending time in nature, taking train rides, and I play the viola. The star of my life is my beautiful cat Oolong who helps me through these tough graduate school years -- I'll have to acknowledge him in my defense!
-Eilidh -- Interesting thing about my name is that this is actually a nickname! I will publish under the name 'Taylor' but Eilidh is a nickname I gained when I moved to my graduate school city. New city, fresh start, I guess! Now I can't imagine being called anything else.
My name is Eilidh, and I am a PhD student studying biophysics. I have a goal of becoming a scientific communicator when I graduate in a couple of years, and I thought a tumblr blog would be a wonderful place to start thinking about this. As the title implies, I have a passion for making science accessible to people who aren't in science fields but still like to read about it. I think learning about science can be a wonderful hobby no matter what your job or lifestyle is!
Considering the ongoing COVID-19 pandemic and the initial challenges associated with how the public received information and recommendations concerning the virus, clear scientific communication seems to be rather lacking in today's political, economic, and social climate. I think it's of great importance to be able to communicate science effectively to anyone, and that is my goal for this blog. Of course, I will be learning on the way, so feedback and engagement is much appreciated!
I don't really believe that 'science is hard'. Sometimes it's just explained in a rather non-intuitive way. I used to struggle with science and math when I was younger -- I was always better with reading and writing. I do enjoy math and science, though I find I have to work really hard at it to gain a good understanding. I've had great teachers and professors throughout the years who have helped explain things in terms I found more accessible. I am grateful for them.
Science, above all, isn't just a compendium of facts. It's a process that is used to figure out how the world works. I think that's beautiful, and I hope it can be beautiful for you too.
What this blog will be about (at least in the beginning)
The sun the scientific world revolves around is the journal article. Estimated over a million published per year, the scientific article provides the backbone for advancement and understanding. Without them, science would progress in a vacuum, which would make it slower and the creative environment wouldn't flourish. Sometimes one article can entirely change the course of a PhD (I've seen it happen)! If you wanted to put science learning down to a basic unit, the journal article is it.
My goal with this blog is to help demystify journal articles I and you find interesting, as well as provide updates on the research experiences I go through as a upper-year PhD candidate. I will do my best to explain articles in an accessible way, and it'll help with my goal of reading more, too! If you have recommendations or curiosities, please send them my way! If you'd like information about graduate school in the sciences in general, I'd be happy to answer questions to the best of my ability as well.
If anybody is interested in guest-writing an article for this blog or having an article edited, please let me know via messages! I really like editing work too. I love writing in general and do creative writing as a hobby. I am hoping to turn writing into my career.
I hope everyone who see this will enjoy what the blog has to offer! Apart from the introductory posts, my tentative post schedule will be once per week -- three general posts and one journal article dissection to start. I will let everyone know if this changes due to other circumstance.
Thanks for joining this journey with me, and please consider giving this blog a follow if it piques your interest!
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