Accelerating Your Particles: So Where Does My Beam Come From Anyway?

This week's guest blogger is Kellen McGee, 1^st year graduate student in Physics (specializing in nuclear and accelerator physics) at the National Superconducting Cyclotron Laboratory/Facility for Rare Isotope Beams at Michigan State University. 

Big particle accelerators and colliders have long been some of the most visible physics experiments. Many of us going through graduate school these days remember when CERN, the 27-km around circular particle collider in Geneva, Switzerland, turned on. This event brought great excitement over what the new physics experiment was about to uncover (notably the much anticipated detection of the Higgs boson), and also anxiety about whether or not it would accidentally create a black hole, This is but the latest example of how various particle acceleration technologies have, since the turn of the century, been almost entirely responsible for us having figured out and validated as much as we have about the laws of the physical world at the subatomic level. 

Physicists, both theorists and experimentalists, drove the hunt for the particles and laws of the Standard Model: physicists’ current, and beautifully proven, understanding of the fundamental particles and the three fundamental forces. These forces are the the weak, the strong, and the electromagnetic forces. Gravity is, alas, not included; if you’d like to try to incorporate gravity into the Standard Model, there’s at least a PhD in it for you, if not a Nobel Prize. The particles of the Standard Model are all the known fundamental particles that can’t be made up of each other–the various flavors of quarks, gluons, leptons and neutrinos that make up all other particles we know of.

However, quite apart from knowing the physics that told you about the particles, and how they would behave, or be identified in detectors, you also need physicists who know how to speed up the particles to the energies you would need to collide or smash them into detectors to learn about the particles’ insides, be they protons, electrons, neutrons, or even atomic nuclei.

How does this work?

The history of particle accelerating devices is a long and interesting one. You might not know that you have a few particle accelerators in your very own house. If you have an older-model television or computer, for example, (the kind that isn’t flat), the screen is illuminated by something called a cathode-ray tube (CRT). This is essentially an electron accelerator, using a voltage source to accelerate electrons that then zoom off and hit a phosphorescent screen, causing it to glow wherever electrons hit. This is an example of the simplest type of what’s called an “electrostatic” accelerator- two plates, one negatively charged, the other one positively charged, cause electrons to fly off of one, accelerate in the electric field, and land on the other plate.

This type of accelerator works because electrons are charged particles, and will get pushed (“kicked” in accelerator jargon) by an electric field. Now, it’s cool to zoom electrons around, but there’s only so much you can do with them because they’re light, and to get them going fast  enough to smash into things and expect any interesting particles to get created (or other interesting physics effects) you have to give them more energy than we really know how to, (really long accelerators being really expensive and energy-hungry). Fortunately for us, other particles have charges. Protons, for example, have positive charge, and were smashed into each other at CERN (technically, it was a proton-antiproton collision with the antiproton having negative charge) for their famous Higgs experiments.

While there historically has been fame in colliders and particle accelerators aiming for higher and higher energies, Nuclear physicists, people who are interested in the structure and behavior of nuclei, their interrelationship in the periodic table of elements, their relative stabilities (how easily their clusters of protons and neutrons fall apart) and other properties, have been turning to accelerator experiments as well. Accelerators, either linear or circular (cyclotrons) are also used in the creation of medical isotopes for cancer treatments. Your local hospital might just have one of these in their basement, and be looking for newer and more efficient ways of making these medically critical materials.

Nuclei that are missing electrons have a net positive charge, and thus can be kicked along an electric field just like the electrons in a CRT, or the protons at CERN. By accelerating whole nuclei, and smashing them into carefully engineered targets, nuclear physicists can start addressing some of the questions above. However, after you get beyond electrons at slow speeds, acceleration becomes much harder than just setting up two plates and putting one at positive and the other at negative voltage. The only way to make those electrons go faster in that setup would be to increase the voltage, which will always, eventually, lead to an electric discharge (boring name for shock!) before you get your electrons up to interesting speeds.

If you can’t make one “kick” really strong, your next option is to line up a series of kicks, that each increase the speed of the charged particle by a certain amount. Imagine being a whitewater rafter, rafting down a series of waterfalls- this is similar to what happens if a charged particle travels across a series of kicks- it gets more and more energy, regardless of how fast it’s going (before relativity starts kicking in, of course!).

We want to build a nuclear science accelerator to accelerate ions to interesting energies, about 65% the speed of light. CERN, a high-energy physics facility aims for 99.999…% the speed of light, for comparison. To do this, we have to figure out how to line up enough kicks to accelerate the particles to the speed we want to study.  This is exactly the problem currently being tackled by FRIB, the Facility for Rare Isotope Beams at Michigan State University.

In the picture below, you see a plan of the FRIB linear accelerator (“linac”) under construction. Each of the little boxes along the straight parts make the particles (the nuclei) go faster by a certain amount. The little boxes are called cryomodules and in real life are taller than a person and several meters long. These house the true engines of the accelerator- the structures that allow us to set up and maintain many, extremely strong (2-5 megavolt-per-meter) electric fields that kick the nuclei along.

The best way to set up these electric fields is still very much a field of open development. For FRIB’s application, making a number of different kinds of ions go fast, FRIB decided to use pure niobium superconducting RF (radio frequency) cavities. This is a mouthful. Let’s break those words down, a little out of order.

RF: radio frequency. An oscillating electric and magnetic field. It would at first seem counterintuitive that we would be using RF, since “oscillating” means the direction the fields are pointing changes by 180 degrees every half period. Physically this means if we used RF at 650 megahertz (650 million cycles per second) to make an electric field in one direction, half the time the electric field is pointing in the other direction (backwards). This problem is controlled by making sure that the particles are timed to be in the electric field when it’s pointing forwards and out of the electric field when it is pointing backwards.

Cavities: this RF has to live somewhere. Cavities are metal,
cylindrical objects with special geometric properties that you
can stick an antenna inside of and pump RF inside.
Image copyright FRIB, P. Ostroumov, SRF Group et. al.

This is a model of a five-cell prototype cavity for FRIB. The upper half shows the distribution of the magnetic field (strongest in the red regions) and the bottom photo shows the distribution of the electric field. The series of kicks we see now are the series of spaces that are the orange-yellow color. The isotope we want to accelerate enters the tube, then sees five electric fields that make it go faster and faster. The gaps (blue spaces on the axis of the pipe) are where the particle is traveling during the time that the electric field in the orange region is pointed backwards.

 

Superconducting Niobium: The rainbow pictures, again, are depictions of what happens to the electric and magnetic fields when an antenna is put into the cavity and RF is piped in at certain frequencies. The RF waving along the walls of the cavity can generate resistance that has to be dissipated as heat, and also constitutes a power drain on the RF, causing less energy to go into moving the particle forward, and more energy to go into heating the cavity walls. Ideally, we want a low-resistance material. Fortunately, Niobium, an element, is a relatively workable metal and goes superconducting at 9.6 degrees above absolute zero. Thus FRIB and many similar facilities have chosen to engineer their superconducting cavities from either pure niobium, or some variety of niobium compound, and cool these in the cryomodules to superconducting temperatures using liquid nitrogen and liquid helium.

Though the above is only the briefest description, it shows how accelerators demand a variety of specialists- you can receive a PhD in any number of accelerator-related subfields including cryogenic systems, superconducting RF, particle beam dynamics, test diagnostic equipment design and implementation, controls programming…the list goes on and on. The simple task of accelerating particles, or nuclei, for science is thus, itself, a science.

The Story of Green Fluorescent Protein

This is a special guest blog article by Joel Lusk, a third-year PhD student in Biological Design at Arizona State University and a member of the Science on Main group. His research involves the study of photoacoustic contrast agents in the imaging and detection of cells. He can be reached at jlusk@asu.edu.

Have you ever seen the stories in the news where scientists make plants or animals glow? These stories are fascinating and amazing, and scientists accomplish these feats by using a protein that was originally found in a jellyfish! This protein is called Green Fluorescent Protein (GFP for short), and the story of its discovery and the scientists that originally pioneered its use is an interesting one. The protein itself has been used in science in a wide variety of applications to study plants, biological processes, and even the things that make up our cells.

Two mice expressing enhanced GFP with one non-GFP mouse in the
center. Source: Moen et al., 2012, BMC Cancer 12.1: 21.

 In 1960, a scientist named Osamu Shimomura started studying the bioluminescence of the jellyfish species Aequorea victoria. When the rings of these jellyfish are squeezed, they produce a glowing liquid. Shimomura claimed to have squeezed over a million jellyfish to collect this liquid and study it for his research. In 1962, he and his colleagues was the first to identify a protein in this jellyfish that he named aequorin. The aequorin first emits blue light, which is then absorbed by the GFP, causing it to glow.

The Aequorea victoria jellyfish. Copyright: Sierra Blakely.

Now that the protein that was responsible for the jellyfish's glow was identified, several other scientists became interested in cloning the gene responsible for it. If the gene for the fluorescent protein could be cloned and inserted into other organisms, it could revolutionize biology. In 1992 a biologist named Douglas Prasher suggested that this glowing protein could trace the way proteins moved in cells and was the first to clone the GFP gene. Unfortunately, the funding for his lab ran out and he left academia. Before he left, Prasher sent several samples of GFP to other scientists so they could continue his work.

After the genetic sequence was found for this glowing protein and it had been successfully cloned, the doors opened to a world of new possibilities for GFP. Prasher had predicted that this protein could be used as a reporter molecule in cells. This means that when a scientist wanted to know if a cell was producing a protein, they could just add the gene for GFP next to the gene for the other protein into the genetic code. When the cell produced that protein, it would also produce GFP, causing the cell to glow. This allowed scientists to undertake all sorts of amazing experiments, including the work of Martin Chalfie, who produced these proteins in E. coli bacteria and worms called C. elegans.

Neurons imaged from a "Brainbow" mouse. Source: Smith
(2007), Opinion article in Neurobiology 17.5: 601–608.

Another scientist, Roger Tsien, took the GFP and augmented it to be many different colors. He did this by changing the shape of the protein so it absorbed and emitted light at different wavelengths. This allowed scientists to not just label cells and animals with a green protein, but with an entire rainbow of colors! This has been applied to every part of the field of biology, allowing scientists to understand and see processes they never could before. Shimomura, Chalfie, and Tsien all shared the 2008 Nobel Prize in Chemistry for their work with GFP. Unfortunately, Prasher, the man who first cloned the protein, was not awarded the prize as three people maximum can share the prize. To honor him, all three recipients mentioned him in their acceptance speeches as even invited Prasher to the ceremony.

So now we know the history of GFP, but what are some of the cool things that scientists can do with it? Mainly scientists have used the protein to tag and visualize processes in cells. One amazing application of GFP and other fluorescent proteins was the production of a "Brainbow" mouse. This mouse produces a variety of colors in its neurons, allowing scientists to see the way the neurons interact with each other. Not only does this tell scientists a lot about how the brain works, it also creates a beautiful image!

The story of GFP is one that shows the usefulness of a fundamental science. Who would have thought that a protein first found in a jellyfish would go on to revolutionize the way we understand and see cells? Research into fluorescent proteins is still going strong, and scientists are currently looking at new fluorescent proteins that have been isolated from other sources such as bacteria and coral. Further work with the fluorescent proteins might reveal even more about the inner workings of our cells and our bodies. In the meantime, we can have a little fun with these proteins, and even paint pictures using bacteria who produce these fluorescent proteins across the visible light spectrum!

A picture painted on an agar plate with bacterial colonies expressing a
variety of fluorescent proteins. Source: Tsien Lab. Artwork: Nathan Shaner.
Photographer: Paul Steinbach.

Sources:

https://www.conncoll.edu/ccacad/zimmer/GFP-ww/shimomura.html

Chalfie, Martin, et al. "Green fluorescent protein as a marker for gene expression." Science 263.5148 (1994): 802-805.

Moen, Ingrid, et al. "Gene expression in tumor cells and stroma in dsRed 4T1 tumors in eGFP-expressing mice with and without enhanced oxygenation." BMC cancer 12.1 (2012): 21

Tsien, Roger Y. "Constructing and exploiting the fluorescent protein paintbox (Nobel Lecture)." Angewandte Chemie International Edition 48.31 (2009): 5612-5626.

Smith, Stephen J. "Circuit reconstruction tools today." Current opinion in neurobiology 17.5 (2007): 601-608.

http://www.tsienlab.ucsd.edu/Images.htm

"What's your Day Like?"

This blog article was written by Dr. Christina Forbes, co-founder of Science on Main. She earned her PhD in chemistry and is currently a post-doctoral researcher at Arizona State University. 

I was recently matched through Skype a Scientist with a 6th grade classroom at St. Hubert Catholic School in Minnesota. Some 40 students and their teacher got a chance to Skype with me while I was in my lab in Tempe, Arizona. I showed them around the lab a bit, but we spent most of the time just chatting about my work.

I met with 3 different class periods, and all three classes asked me a question that is surprisingly hard to answer: "What's your day like?" Since it was one of the burning-est questions these students had for me, I wanted to bring it up to Science on Main. After all, our aim with Science on Main is to answer your questions!

This question sometimes follows the classic "What do you do?" that comes up in polite conversation. I've learned that the attitude towards my accurate-but-short answer, "chemist," can range from excitement to disgust. Some people think that's cool, others think that sounds pretentious, and even others seem uncomfortable or unsettled with my answer.

Only the very curious, or confident, have asked me the follow-up: "So what's your day like?" 

Indeed, this is just my job, and it's a job I like and I worked hard to get to, but it doesn't endow me with any particular superpowers. I don't know how much people in other professions are asked this question, but I hope everyone is. There is so much fascinating stuff that can go into one person's workday. What does a software engineer do on a day-to-day basis? Or an investment banker? Or an event coordinator?

Nonetheless, these 6th graders were very curious. If you are also very curious, then I can give you a detailed approximation of my answer to "What's your Day Like?"

[Get on with it!]

On an average day, I don't function well for the first hour, so I sit at my laptop with my coffee before I attempt any chemistry. Yup, even scientists have morning commutes and laptops. I deal with emails, follow up on other emails, check my calendar for scheduled meetings, update my calendar based on the emails I got that morning, and other desk-stuff that I have to do to keep my life in order. I might edit a peer's manuscript for a paper they want to publish, or I might finish writing a draft of something that I'm working on. I might catch up on reading recent literature, like reading the news but it's only the chemistry section, written with all the jargon. When the coffee has kicked in and I think I'm a little more ready to face my day, then I'll pull out my lab notebook, put on safety glasses, and go into the lab.

My day in lab will focus on a different part of a project that I might be working on. To save chemistry jargon, I will use an analogy for my project: making a batch of THE BEST cookies for a friend. Let's say I chose, with some reasoning, to make chocolate chip cookies for my friend.

Troubleshooting a reaction:
I'll need a good recipe for the cookies. I probably looked up recipes online, maybe chose a few recipes based on reviews or ingredients that I have on hand. Maybe I asked a buddy in another lab what recipe they use, or if they have feedback on a recipe they tried. Once I have a recipe I feel good about, I do a test reaction, or a small batch. I look at the product (in this case, the cookies) to see if I could have done the reaction differently, or if this recipe is terrible and I need to try a completely different one. I'll do a series of these test reactions until I obtain the cookies I want, then I scale up the reaction and try a larger batch. Sometimes I'll have to adjust the recipe a bit more when I make a larger batch, like a longer baking time or less salt. All the while, I make notes on how I set up each batch of cookies, and how the cookies came out. What was my baking time? Baking temperature? How much sugar? Should I use honey instead of sugar? Were the cookies undercooked? Burned? Too salty? I might spend a month or more testing and perfecting a recipe for cookies in these batches.
For those of you trying this at home, this might look like running reactions, refluxing reactions, distilling materials, running a purification column, mixing chemicals, etc.

Synthesizing a molecule I need:
In the midst of testing my cookie recipe, I run out of chocolate chips. Nope, the store doesn't sell any chocolate chips, but the store does have a lot of cheap cocoa beans. After a little more internet searching, I learn how to make chocolate chips from the beans, and find that I have the equipment to roast, winnow, grind, and, generally, make chocolate. Since I've never done this before, I may have to borrow some techniques I know about about making coffee from the beans, or borrow equipment from a neighboring group. Much like the cookies, I practice making the chocolate from the beans in small batches, but it comes out gritty and yucky. I work on refining my chocolate to get the grittiness out before I can make it into chips. Once I have a few chocolate chips that are right for putting into cookies, I'll make a bigger batch so that I have plenty to use for testing out my cookie recipes. All the while, I've made notes on each step of the process to make the chocolate. That way, I've built a recipe that I can follow if I need more chocolate chips.
This might look a lot like troubleshooting reactions. I bring this up because sometimes there are materials that I can't buy, and I have to take a step back in my project to make what I need for myself. So much of this stuff is self-taught.

Something as simple as removing liquid from a solution requires this contraption.

Drying a purified product under vacuum.
Imagine chocolate chips, I guess.

Characterizing:
Remember, I'm trying to make these cookies so that my friend thinks they're THE BEST. To do that, my friend will need some other cookies to compare against mine (think control experiments). Maybe they have another friend with jerk chocolate chip cookies, and another friend that made some ginger snaps. After trying all these different sample cookies, my friend thinks that mine are THE BEST, but we should probably check again another day, just to be sure. More cookies are made, and each sample cookie is brought to the friend the next day, and they still think mine are THE BEST. But, there's a rule of three in replicating results, so we should check again next Monday.
I'm using a person and their sense of taste as an analogy for taking a measurement for making comparisons.
This is where the edge of science really happens, and it can depend on the project. It could be taking a spectroscopic measurement, or it could be comparing different reaction rates. This is often in front of a computer that it attached to some very expensive instrumentation. Knowing if your method or product is THE BEST is revealed by a number that the instrument tells you. It could be a simple as taking a measurement of a sample, and the number 550 means that a month's worth of tireless hours of work has paid off. It's very exciting, but it probably doesn't look as exciting as other parts of my work.

Sample preparation for a spectroscopic measurement.

Measuring pH in a series of samples. UV-Vis spectroscopy came a little later.

Squiggly-lines and peaks coming from instruments is sometimes the most exciting part.

Fixing equipment:
Naturally, the following Monday, my friend has the flu, so I spend every day for a week with my friend. I need to get them back to good health so they can try all the cookies a third time. When my friend tries the cookies a third time, they think those other jerk chocolate chip cookies are THE BEST. This seems weird, since it's not consistent with our earlier tests. I have my friend try the sample cookies the next day, for a fourth time. My friend now likes ginger snaps, and they seem very confused and disoriented. I might spend a few days studying human anatomy, and realize that my friend probably has a blood sugar problem, and now it's time to call a doctor. Since doctors can be really expensive, my boss asks me to correct my friend's blood sugar problem myself. I might have to study human anatomy for two more days, only to realize that my friend is having a calcium deficiency, which effects their ability to taste anything. I give them milk, and my friend is immediately feeling better. My friend tries the cookie samples, and mine are THE BEST. For good measure, I ask my friend to try the cookie samples three additional times over three different days, just to be extra sure of the result.
A frustrating part of my job is when I've had to spend whole days away from my projects just fixing instrumentation. We need our instruments to be accurate, well calibrated, and well maintained. In my lab, these instruments include spectrometers, chromatographs (gas or liquid), or potentiostats. A service technician can be expensive for on-site service (e.g. house call), so we often learn how to do repairs and maintenance ourselves. These repairs can range from cleaning sample holders to needing replacement parts that you can only describe with picture messages.

That time we had a problem with a part that isn't normally part of the wear&tear kit and doesn't have a part number... 20 emails, 3 manuals, and many pictures later, I managed to communicate to the service tech that I needed a new needle port tube.

Because a degree in chemistry sometimes means that you've had to figure out how to disassemble, diagnose, and service an injector for an HPLC. (Really, what does that even mean?!?)

The tube had been mangled--not sure how, or how long it was like this.
The guide did not fit on the old tube, thereby ruining the fluid seal, thereby disrupting sample injection for analysis, and grossly ruining the data.
A reminder that scientist does more than just experiments and mixing chemicals!

Publishing:
Since my cookies are THE BEST, now I need to publish my recipe. I write out my recipe, with pictures of what they look like and a picture of my friend eating each sample cookie (they're happy only when they're eating my cookies). I attach a supplemental document that describes how I made the chocolate chips from cocoa beans, with some information about my friend who tried and judged the cookies. I send all of this to a bakery owner, and they send my recipe to other bakers. These other bakers submit feedback about my recipe, asking me to have my friend try some other cookie types. These other bakers also think that my cookie baking time is a little weird. I spend some time doing what the bakers ask, subjecting my friend to more cookies, and refining the cookie-making process. I send a revised recipe and more photos of my friend eating all these other cookies, and the bakery owner agrees to publish my recipe in their next book.
This is a very broad brush-stroke of the peer-review process. This is often a background think to my work, but dealing with reviews and doing new experiments can become part of my average day.

Copyright prevents me from posting my papers, so instead you get a picture of my dissertation.
For the record, a doctoral dissertation should not be this long.

Training new colleagues
While I'm working away at perfecting my cookie recipes, my boss walks in with a college student and says "this new student wants to learn how to make cookies. By the way, they've never been in a kitchen before, but it would be great if they had a batch of cookies by the end of the week." My boss leaves, and the student looks at me with excitement and fear. We may as well start with the batch I'm working on, and I show the student how to use a spoon to stir the dough. I step out of the kitchen for a moment, and when I return, I find the dough on the floor. Maybe this new student was stirring the batch too fast and lost control of the spoon and the bowl. I tell the student that it's ok, but now they'll have to help me start over. It's a part of the learning experience, and if they pay attention, they'll get better with time.
As I explain the recipe and how to stir the dough, the student seems to think I know everything about cookies. I explain that I wasn't born with cookie knowledge, but I just worked with cookies for a long time. I tell them that if they work with cookies long enough, and learn from their own mistakes, then they'll know a lot about cookies, too.
As you gain more experience in your project or techniques, you're expected to help train new people. You learn a lot of patience when you train new people, but it's crucial to the learning process. I sure know that I tested people's patience when I was still learning this stuff! 


Each day in lab can be very different, since each day might be part of this overall process of making and testing THE BEST cookies. At some point during the day, I eat lunch (maybe). Sometimes I might meet briefly with my boss, and we talk about how cookie-making is going. Maybe not; I've earned some independence with cookie-making.

By the end of the day, and when I've brought my work to a natural close, I catch up on my emails or whatever else happened at my desk while I was in lab. I write out a new to-do list for the next day, hopefully with notes to myself like "make another lb. of chips" or "try the recipe on page 42 with more butter." I close up my laptop and go home. I try throw together dinner. Maybe I look at a colleague's manuscript while my husband works on his own homework, or maybe I work up and analyze some new data that I can't wait to see the next day. Or maybe I'll just read a book or watch Netflix. Scientists just need to chill sometimes, too.