Photons map the atomic scale to help medicine and more | Science News for Students

Photons map the atomic scale to help medicine and more

Researchers at a gigantic lab — the Advanced Photon Source — are probing the world of the very small
Jun 14, 2018 — 6:45 am EST
Physicist Mary Upton at Argonne National Laboratory

Physicist Mary Upton lines up equipment just right in preparation for an experiment using X-rays emitted by the Advanced Photon Source.

Argonne National Laboratory

A giant ring-shaped research laboratory in Illinois is providing a new window into teeny, tiny molecules. What scientists learn there can help them study diseases, build better batteries, design bridges and aircraft, fight pollution and more.

Known as the Advanced Photon Source, or APS, it sprawls across 8.6 hectares (more than 21 acres) at Argonne National Laboratory, just west of Chicago. This research center is big, both in terms of its value to science and its size.

The outer diameter of its experiment hall spans 373 meters — the length of three and a half U.S. football fields. Within the building is a ring of narrow pipes that measure 1,104 meters (3,622 feet) around. You could fit a Major League Baseball stadium inside this ring!

This facility is one of several particle accelerators around the world. Their goal is to send a beam of subatomic particles into some target and then watch what happens. (Subatomic particles are bits of matter smaller than atoms.) Those collisions can provide detailed information about the structure of things too small to see — things almost too small to imagine.

Some accelerators shoot their particles down long, straight lines. Others, such as this one at Argonne, send particles around and around some giant ring-shaped structure. And at APS, it’s not the beam of electrons that the scientists want to use — at least not directly. Rather, they want to harness the high-energy particles of light, called photons, which its electron beam creates.

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Advanced Photon Source at Argonne National Laboratory
Lighting flashes in the sky over the Advanced Photon Source at Argonne National Laboratory in Argonne, Ill. The giant ring-shaped building houses a beam of tiny but powerful particles that helps scientists design better electronics, study disease and more.
Argonne National Laboratory (CC BY-NC-ND 2.0)

The photons’ high energy and tiny size are a powerful combo. Together they help scientists probe the properties of different molecules. In one recent study there, researchers showed how cooling a compound changes its ability to conduct electricity. In another, scientists revealed the point of attack for a disease-causing germ, called the Lassa virus. These teams and others can now use those findings for further work.

Clearly, argues APS physicist Mary Upton, this big, big facility is “a very special and unique tool” to understand the world of the very, very small.

Round and round they go

Left alone, a beam of electrons would travel in a straight line. Bending their path to go round and round takes some steering. At Advanced Photon Source, magnets do that job.

Equipment in a center building shoots out a beam of electrons. The accelerator then speeds up these electrons and steers them into a narrow pipe that runs through its large outer ring. Clusters of powerful magnets around the ring force these electrons to turn, a tiny bit at a time. Their path ends up making a big circle where they zoom around and around at nearly the speed of light. How nearly? Try more than 99.99999 percent of that ultimate speed limit.

chemist Karena Chapman
Chemist Karena Chapman peers inside a part of the Advanced Photon Source that transmits a selectable wavelength of light or other radiation.
Argonne National Laboratory (CC BY-NC-ND 2.0)

Other magnets around the ring steer the beam in more complex ways. These magnets are arranged with alternating pole positions. One steering magnet may have the north pole on top and the south pole on the bottom. The next would have the south pole on top and the north on the bottom. And so on. (The north and south poles tell which of the Earth’s magnetic poles the end of a magnet would seek if it were allowed to float freely. The north pole on a bar magnet would be attracted to Earth’s magnetic north pole.)

As a result, “you get an alternating magnetic field that forces the electron beam to deviate left and right,” explains Daniel West. He’s a former biology teacher who now gives tours at Argonne National Laboratory. “Any time you do that to a high-energy beam of any sort, it’s going to [lose] some energy.” He compares the effect to that of a bus swerving back and forth at high speed. If you were inside the bus, you would feel the energy from its movement pushing you from side to side.

In this case, the high speed of the electron beam gives it lots of energy. It throws off that energy as it wiggles. As a result of the beam’s speed, the energy released is in the form of photons known as X-rays. These X-rays have short wavelengths of 0.01 to 10 billionths of a meter. The photons shoot off in bunches, or pulses, at rapid-fire speed.

This box-shaped room (at center) is a station where high-energy X-ray beams can shoot through samples at the Advanced Photon Source.
Argonne National Laboratory (CC BY-NC-ND 2.0)

The shape of the ring and the placement of the steering magnets means the rink can emit up to 70 of those X-ray beams, West says. Equipment directs some of those beams to more than one place. So there are more than 90 possible stations for experiments.

Remember how magnets bend the electron beam so that it curves into a circle? The emitted X-rays don’t do that. With nothing to curve the exiting beams, West explains, “the X-rays keep going straight.”

Depending on the work, equipment at these stations can filter or “tune” the X-rays to certain wavelengths, or energy levels. Different wavelengths work better for different types of experiments. Stations also can be set up to work with different types of materials. Some researchers work with metals or ceramics, for example. Other researchers may want to study proteins produced by living cells.

At some stations, the X-rays will bounce off the surface of a sample. “The way they are reflected can reveal exactly what kind of atom is present at each point on [the sample’s] surface,” West says, and precisely how far apart they are.

At other stations, X-rays will pass through a sample. As they do, they scatter or spread out. As these X-ray photons come out the other side, they produce different patterns. This gives clues to the arrangement of atoms within the sample. Computers analyze the X-ray exit patterns. With those data, scientists can measure energy loss from atoms in a sample. Such knowledge can help scientists and engineers make materials that last longer, work better or have new uses. 

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Here’s a tour around the ring at the Advanced Photon Source — by tricycle!
Janet Smith Lab/YouTube

Using the beam

The Advanced Photon Source is a U.S. government research lab. But scientists and engineers come from all over the world to use it. For most of the year, its stations are used around the clock, six days a week.

“A huge part of my job is to set these experiments up for success,” Upton says. Seeing the first results from a sample sometimes feels “really magical,” she adds. “You never know if it’s going to work.”

A lot of her work deals with energy and electronics. For example, one project showed how a crystal material that contained nickel changed its electrical properties at different temperatures. Scientists knew that at different temperatures, the material could either act like a metal, conducting electricity, or become an insulator. What they didn’t know was why.

Nickel compound
This model shows the crystal structure of a nickel material that changes its physical properties depending on the temperature. Work at the Advanced Photon Source helps explain how cooling the compound switches it from an electrical conductor to an insulator.
Argonne National Laboratory

Upton’s team used three X-ray-beam stations to compare a material’s properties at different temperatures. Equipment at each station gave different measurements about the material. Think of it, she says, as “a bottle of liquid and you want to know what it is. You can use your eyes to tell the color and your nose to determine the smell,” Upton says.

In this case, one station might measure a material’s structure very accurately. Another might give information about what was going on with a nickel atom’s electrons as they moved to different energy levels. (Electrons orbiting an atom may jump up or down based on their energies.)

In fact, Upton found, at low temperatures the crystal had slightly fewer electrons on its nickel atoms. Meanwhile, when colder, the material’s atoms of neodymium (another metallic element) showed a small increase in how many electrons they hosted.

“These two measurements make researchers think that electrons are moving from the nickel atoms to the neodymium atoms as the crystal changes from a [conductor] to an insulator,” Upton says. Scientists hadn’t seen such a shift by electrons before.

Why do they care about this? The more scientists understand about what goes on inside a material — such as this crystal — the more likely they are to discover new uses that depend on these properties.

Explains Upton: “The goal of this type of experiment is to be able to design custom electronic components.” For instance, a device might need a part that will conduct electricity well at 21° Celsius (70° Fahrenheit) and even better at 27 °C (80 °F).

Roadmap to a vaccine

Erica Ollmann Saphire is a molecular biologist at the Scripps Research Institute in La Jolla, Calif. She used the Advanced Photon Source to learn more about the virus responsible for Lassa fever. Its victims develop breathing problems, stomachaches, vomiting, diarrhea, heart problems, seizures and more. They also can bleed from the gums, nose, eyes and other body parts. Each year, this nasty infection sickens some 300,000 people, mostly in West Africa.

People tend to pick up the potentially lethal virus after making contact with infected rats or with bodily fluids from sick people. Pregnant women are especially likely to die from Lassa fever. Of those who survive, many end up deaf.

“There are no vaccines or treatments yet available for Lassa virus,” Saphire says. To help change that, her team conducted research using the Advanced Photon Source. Specifically, they probed the germ’s means of attack.

The virus attaches to and invades new host cells using a protein on its surface called GP. Patients who survive the disease will have antibodies to that protein. Scientists want to now create a vaccine that would trigger the body to make those same antibodies. Then it could prevent new cases of the disease.

Lassa protein
Each blue or green portion of this image shows a separate copy of a protein that the Lassa virus uses to invade human cells. Like triplets, the copies work together as a three-part molecule.
Scripps Research Institute

But no one knew what the protein looked like. So they didn’t know how to make a vaccine to target it. “Without the structure of GP, they were hunting blindly,” Saphire explains.

The GP protein usually wants to fall apart and change shape, she explains. So her group spent 10 years trying to stabilize this protein so that wouldn’t happen. Researchers in Africa helped with that effort. Eventually, the team brought their stable protein to the Advanced Photon Source. It let them see, for the first time, this molecule’s tripod-like structure.

That structure is now “the roadmap to make a vaccine against Lassa virus,” Saphire says. Similar techniques might help work toward targeting proteins in other viruses as well. Her group shared its findings in the June 2, 2017 issue of Science.

A brighter future

Argonne National Laboratory is currently planning a $770 million upgrade of the Advanced Photon Source. This will make its X-rays brighter, somewhat “like switching from a 60-watt to a 120-watt bulb,” Upton explains. Other improvements will bring the X-rays more in sync with each other, giving it a sharper focus. That will allow it to peer into smaller samples.

Work on the upgrade could be finished as early as 2023. One day, perhaps you or your classmates might even work on a project there. “If they like math and they like tinkering, they should join us!” Upton says.

Reporting for this piece was made possible by an MBL Logan Science Journalism Fellowship in Chicago. It was arranged by the Marine Biological Laboratory in Woods Hole, Mass., and the University of Chicago.

Power Words

(more about Power Words)

accelerator     (in physics) Also known as a particle accelerator, this massive machine revs up the motion of subatomic particles to great speed, and then beams them at targets. Sometimes the beams are used to deliver radiation at a tissue for cancer treatment. Other times, scientists crash the particles into solid targets in hopes of breaking the particles into their building blocks.

Argonne National Laboratory     A federal laboratory owned by the U.S. Department of Energy, outside of Chicago, Ill. It was formally created on July 1, 1946. Today, its roughly 1,400 scientists and engineers (and 1,000 students) conduct research across a broad range of fields, from biology and physics to materials science, energy development and climate studies.

atom     The basic unit of a chemical element. Atoms are made up of a dense nucleus that contains positively charged protons and uncharged neutrons. The nucleus is orbited by a cloud of negatively charged electrons.

biology     The study of living things. The scientists who study them are known as biologists.

cell     The smallest structural and functional unit of an organism. Typically too small to see with the unaided eye, it consists of a watery fluid surrounded by a membrane or wall. Depending on their size, animals are made of anywhere from thousands to trillions of cells. Most organisms, such as yeasts, molds, bacteria and some algae, are composed of only one cell.

ceramic     A hard but brittle material made by firing clay or some other non-metal-based mineral at a high temperature. Bricks, porcelain and other types of earthenware are examples of ceramics. Many high-performance ceramics are used in industry where materials must withstand harsh conditions.

component     Something that is part of something else (such as pieces that go on an electronic circuit board or ingredients that go into a cookie recipe).

compound     (often used as a synonym for chemical) A compound is a substance formed when two or more chemical elements unite (bond) in fixed proportions. For example, water is a compound made of two hydrogen atoms bonded to one oxygen atom. Its chemical symbol is H2O.

conductor     (in physics and engineering) A material through which an electrical current can flow.

crystal     (adj. crystalline) A solid consisting of a repeating symmetrical, ordered, three-dimensional arrangement of atoms or molecules. It’s the organized structure taken by most minerals. Apatite, for example, forms six-sided crystals. The mineral crystals that make up rock are usually too small to be seen with the unaided eye.

diameter     The length of a straight line that runs through the center of a circle or spherical object, starting at the edge on one side and ending at the edge on the far side.

diarrhea     (adj. diarrheal) Loose, watery stool (feces) that can be a symptom of many types of microbial infections affecting the gut.

electricity     A flow of charge, usually from the movement of negatively charged particles, called electrons.

electron     A negatively charged particle, usually found orbiting the outer regions of an atom; also, the carrier of electricity within solids.

electronics     Devices that are powered by electricity but whose properties are controlled by the semiconductors or other circuitry that channel or gate the movement of electric charges.

element     A building block of some larger structure. (in chemistry) Each of more than one hundred substances for which the smallest unit of each is a single atom. Examples include hydrogen, oxygen, carbon, lithium and uranium.(in chemistry) Each of more than one hundred substances for which the smallest unit of each is a single atom. Examples include hydrogen, oxygen, carbon, lithium and uranium.

engineer     A person who uses science to solve problems. As a verb, to engineer means to design a device, material or process that will solve some problem or unmet need.

field     An area of study, as in: Her field of research was biology. Also a term to describe a real-world environment in which some research is conducted, such as at sea, in a forest, on a mountaintop or on a city street. It is the opposite of an artificial setting, such as a research laboratory. (in physics) A region in space where certain physical effects operate, such as magnetism (created by a magnetic field), gravity (by a gravitational field), mass (by a Higgs field) or electricity (by an electrical field).

filter     (in chemistry and environmental science) A device or system that allows some materials to pass through but not others, based on their size or some other feature. (in physics) A screen, plate or layer of a substance that absorbs light or other radiation or selectively prevents the transmission of some of its components.

football field     The field on which athletes play American football. Owing to its size and familiarity, many people use this field as a measure of how big something is. A regulation field (including its end zones) runs 360 feet (almost 110 meters) long and 160 feet (almost 49 meters) wide.

force     Some outside influence that can change the motion of a body, hold bodies close to one another, or produce motion or stress in a stationary body.

germ     Any one-celled microorganism, such as a bacterium or fungal species, or a virus particle. Some germs cause disease. Others can promote the health of more complex organisms, including birds and mammals. The health effects of most germs, however, remain unknown.

host      (in biology and medicine) The organism (or environment) in which some other thing resides. Humans may be a temporary host for food-poisoning germs or other infective agents.

infection     A disease that can spread from one organism to another. It’s usually caused by some type of germ.

insulator     A substance or device that does not readily conduct electricity.

magnet     A material that usually contains iron and whose atoms are arranged so they attract certain metals.

magnetic field     An area of influence created by certain materials, called magnets, or by the movement of electric charges.

matter     Something that occupies space and has mass. Anything on Earth with matter will have a property described as "weight."

metal     Something that conducts electricity well, tends to be shiny (reflective) and malleable (meaning it can be reshaped with heat and not too much force or pressure). 

molecule     An electrically neutral group of atoms that represents the smallest possible amount of a chemical compound. Molecules can be made of single types of atoms or of different types. For example, the oxygen in the air is made of two oxygen atoms (O2), but water is made of two hydrogen atoms and one oxygen atom (H2O).

neodymium     A chemical element which appears as a soft, silvery metal when it is pure. It is found in some minerals, and can be used to trace the source of mineral grains carried long distances by water or wind. Its scientific symbol is Nd.

nickel     Number 28 on the periodic table of elements, this hard, silvery element resists oxidation and corrosion. That makes it a good coating for many other elements or for use in multi-metal alloys.

particle     A minute amount of something.

peer      (verb) To look into something, searching for details.

photon     A particle representing the smallest possible amount of light or other type of electromagnetic radiation.

physicist     A scientist who studies the nature and properties of matter and energy.

protein     A compound made from one or more long chains of amino acids. Proteins are an essential part of all living organisms. They form the basis of living cells, muscle and tissues; they also do the work inside of cells. Among the better-known, stand-alone proteins are the hemoglobin (in blood) and the antibodies (also in blood) that attempt to fight infections. Medicines frequently work by latching onto proteins.

ray     (in mathematics) A line that has a defined endpoint on one side, but the other side continues on forever.

rays     (in biology) Members of the shark family, these kite-shaped fish species resemble a flattened shark with wide fins that resemble wings.

seizure     A sudden surge of electrical activity within the brain. Seizures are often a symptom of epilepsy and may cause dramatic spasming of muscles.

speed of light     A constant often used in physics, corresponding to 1.08 billion kilometers (671 million miles) per hour.

subatomic     Anything smaller than an atom, which is the smallest bit of matter that has all the properties of whatever chemical element it is (like hydrogen, iron or calcium).

tripod     A three-legged stand for supporting a camera or other device.

tune     (in engineering) Adjust to the right level.

unique     Something that is unlike anything else; the only one of its kind.

vaccine     (v. vaccinate) A biological mixture that resembles a disease-causing agent. It is given to help the body create immunity to a particular disease. The injections used to administer most vaccines are known as vaccinations.

virus     Tiny infectious particles consisting of RNA or DNA surrounded by protein. Viruses can reproduce only by injecting their genetic material into the cells of living creatures. Although scientists frequently refer to viruses as live or dead, in fact no virus is truly alive. It doesn’t eat like animals do, or make its own food the way plants do. It must hijack the cellular machinery of a living cell in order to survive.

watt     A measure of the rate of energy use, flux (or flow) or production. It is equivalent to one joule per second. It describes the rate of energy converted from one form to another — or moved — per unit of time. For instance, a kilowatt is 1,000 watts, and household energy use is typically measured and quantified in terms of kilowatt-hours, or the number of kilowatts used per hour.

wavelength     The distance between one peak and the next in a series of waves, or the distance between one trough and the next. Visible light — which, like all electromagnetic radiation, travels in waves — includes wavelengths between about 380 nanometers (violet) and about 740 nanometers (red). Radiation with wavelengths shorter than visible light includes gamma rays, X-rays and ultraviolet light. Longer-wavelength radiation includes infrared light, microwaves and radio waves.

X-ray     A type of radiation analogous to gamma rays, but having somewhat lower energy.


Journal: K. Hastie et al. Structural basis for antibody-mediated neutralization of Lassa virus. Science. Vol. 356, June 2, 2017, p. 923. doi: 10.1126/science.aam7260.

Journal: M. Upton et al. Novel electronic behavior driving NdNiO3 metal-insulator transition. Physical Review Letters. Vol. 115, July 13, 2015. doi: 10.1103/PhysRevLett.115.036401.  

Further Reading

Chemist Karena Chapman talks about her work at the Advanced Photon Source.
Video: “Argonne National Laboratory employee spotlight: Karena Chapman.”  

I. Peterson. “Bright x-rays to illuminate a new frontier.” Science News. May 4, 1996.