Measuring the Mechanical Forces of Disease

“All these complicated diseases that we don’t have a good handle on — they all have this mechanical component. Well why is that?”

Brent Hoffman is an assistant professor of biomedical engineering

Brent Hoffman is an assistant professor of biomedical engineering

This is exactly the question Brent Hoffman, Duke biomedical engineering assistant professor, is helping answer. Many of the common diseases that we fear have a mechanical component. In asthma attacks, a chemical or physical stimulus causes the air channels in the lung to shut as the muscles that control the width of the channel contract– the mechanical component.

Another example is atherosclerosis, commonly known as the hardening of the arteries, the leading killer in developed countries. Instead of air flow, blood flow is affected as the walls of the blood vessels get thicker. Factors such as smoking, being overweight, and having high cholesterol increase the chance of getting this disease. However, examining the mechanical portion, the plaques associated with atherosclerosis tend to occur at certain parts of the blood vessels, where they branch or curve. You can think of it like a hose. When you kink a hose or put your thumb over the nozzle, the fluid flows in a different way. Hoffman said there are similar stories concerning mechanical portions of major diseases, such as muscular dystrophy and breast cancer.

Hoffman's lab is building tension sensors to measure forces during collective cell migration.

Hoffman’s lab is building tension sensors to measure forces during collective cell migration.

This all sounds very biological, so why is he in the engineering department? As mechanobiology is a new field, there are few tools available for reporting a protein’s shape or its forces inside living cells. Hoffman makes the tools enabling the study of mechanobiology. During Hoffman’s postdoctoral research, he worked on recording forces across proteins in living cells, their natural environment. Now, he’s expanding that technology and using it to do basic science studies to understand mechanobiology.

Hoffman said he hadn’t planned this. From high school, he knew he wanted to be an engineer. As an undergraduate, Hoffman interned at IBM, where he worked on the production of chip carriers using copper-plating. Hoffman was able to apply knowledge, such as changing pH to get various amounts of copper, and make everything perform at optimal performance, but he wanted to know more about the processes.

So he set out to get his Ph.D in process control, which involves deciding how to set all the numbers and dials on the equipment, how large the tank should be, what pressure and temperature should be used, etc. in chemical plants. Hoffman was set on the path to become a chemical engineer. However, during the first week of graduate school, he attended a biophysics talk, in which he understood very little. Biophysics interested Hoffman, so he went from intending to do research on one of the most applied engineering projects on campus to arguably one of the least applied in a week. This was the beginning of his biophysics journey. However, as his Ph. D was much more heavily interested in the physics aspect, Hoffman chose to do his postdoc in cell biology to balance his training. Mixing everything together, he got biomedical engineering.

Hoffman reflects that his decisions were logical, but he had not planned to take the route he did. Hoffman cautions that it is better to have a plan than not because if you do not plan, you won’t know where you are going. However, he advises that since a person learns more about likes and dislikes as one proceeds on their route, students should not be afraid to incorporate what they learn into their plans.

Hoffman’s journey is characterized by finding and doing what he enjoyed. Trained in both the worlds of physics and biology, but never intending to pursue a future in either, Hoffman is uniquely suited for his current position in the revolutionary emerging field of mechanobiology. He is able to put his biology hat on and his physicist hat on for a bit, while the engineer in him is thinking, “is any of this practical?”
“If you had to pick out the key to my success, it would be doing that,” Hoffman said.

AmandaLi_100Guest Post by Amanda Li, a senior at the North Carolina School of Science and Math

 

Middle Schoolers Ask: What’s it Like to be a Scientist?

PostdocsWhen a group of local middle schoolers asked four Duke postdocs what it’s like to be a scientist, the answers they got surprised them.

For toxicologist Laura Maurer, it means finding out if the tiny silver particles used to keep socks and running shirts from getting smelly might be harmful to your health.

For physics researcher Andres Aragoneses, it means using lasers to stop hackers and make telecommunications more secure.

And for evolutionary anthropologist Noah Snyder-Mackler, it means handling a lot of monkey poop.

The end result is a series of short video interviews filmed and edited by 5th-8th graders in Durham, North Carolina. Read more about the project and the people behind it at http://sites.duke.edu/pdocs/, or watch the videos below:

Celebratory Bottles Mark the March of Time

The 50th anniversary of the Triangle University Nuclear Laboratory (TUNL) November 6-8 was a homecoming of sorts for hundreds of alumni, faculty and friends.

On the eve of the anniversary party, Chris Gould of NC State inspecting the trophy case at TUNL.

On the eve of the anniversary party, Chris Gould of NC State inspected the trophy case at TUNL.

For half a century, the three Triangle universities have collaborated seamlessly on nuclear physics experiments using particle accelerators and other equipment too large and expensive for one university to effectively use on its own.

Key milestones in the lab’s history are marked by a dusty rank of empty champagne bottles marching across the top of a power supply cabinet in the basement lab.

Each trophy bottle records a moment of celebration, when faculty, researchers, technicians, and students gathered to savor an achievement made possible by years of working all hours of the day and night to design, build, measure, adjust, repair, monitor, and make sense of equipment and experiments. Each is labeled, typically in Wite-Out correction fluid, with a date and the event.

“The bottles represent technical milestones that either created new research opportunities at TUNL or increased the competitiveness of TUNL’s research activities in specific areas,” said Calvin Howell, who is a Duke professor and the director of TUNL.

December 29, 1968, the first beam of 30 MeV after two years of construction and assembly.

December 29, 1968, Roberson’s handwriting celebrates the first beam of 30 MeV, marking the end of two years of construction and assembly and the beginning of 50 years of science.

Russell Roberson, Duke professor emeritus and one-time TUNL director, started the tradition. On Sunday, December 29, 1968, TUNL physicists successfully coaxed a beam of particles out of the new equipment, marking the completion of  two years of constructing a new building behind Duke’s physics building and installing enormous equipment purchased with a $2.5 million grant from the Atomic Energy Commission.

“It was a pretty big deal to have that beam and it seemed like we ought to remember when we did it,” Roberson said.

Graduate student Chris Gould had just driven from Philadelphia to Duke between Christmas and New Year’s day to deliver a piece of equipment with colleague Steve Shafroth, who was beginning his TUNL career at UNC. “We arrived in the evening,” remembered Gould, who is now a professor of physics at NC State. “And came upon a bibulous celebration in the control room where bottles of Cold Duck were being cooled down with liquid nitrogen and drunk out of paper cups.”

Six months later, Gould began his career at TUNL.

In the coming years, they would collide this type of beam (and others) with targets of various compositions in their quest to unlock the secrets of subatomic structure and forces.

Here are a few trophies from over the years:

Worth Seagondollar

July 14, 1983 – “Polarized Target – Polarized Beam.” Worth Seagondollar, chair of physics at N.C. State. (Courtesy of David Haase, NCSU)

May 13, 1979 – “First pulsed polarized n”

In the mid-1970s, TUNL began producing polarized neutron beams, in which the neutrons were all spinning in the same direction. Knowing the spin direction of the particles in the beam made for more precise interpretation of the data when the beam hit the target. This bottle from 1979 marked a further enhancement—the beam was pulsed so that the speed of the neutrons in the beam could be calculated.

July 8, 1980 – “First data taken with the VAX”

TUNL was the first nuclear lab to take data with the new 32-bit VAX computer from the Digital Equipment Corporation. TUNL physicists built an operating system to go along with it, which was used by many other labs around the world. In fact, Gould and Roberson traveled to China and Saudi Arabia to help labs there set up the same system. (Before the VAX, TUNL “borrowed” computer power from the high-energy physics group at Duke, via cables that ran through a 4” pipe between the two labs.)

May 15, 1992 – “Lamb Shift Polarimeter Bump Bump Bump”

TUNL faculty and students designed a device called a “Lamb shift spin-filter polarimeter” that would characterize the distribution of spin directions of the particles in a polarized beam almost instantly — a task that had previously taken hours. “We had just collected the first spectrum which proved that the Lamb-shift polarimeter could be used to determine the beam polarization in the predicted way,” recalled UNC professor Tom Clegg. “It was a night for high-fives and celebration. We joyously popped the cork on this bottle late on Friday evening after a very difficult week.”

"Bump Bump Bump" signified three distinct signals from the new Lamb shift spin-filter polarimeter.

1992 “Bump Bump Bump”

October 26, 2006 – “First Beam Extracted from Booster”

TUNL operates the world’s most powerful Compton gamma-ray source, called HIGS (which stands for high intensity gamma-ray source). The gamma rays are produced in a free electron laser ring, which is housed in a 52,000-square-foot building adjacent to the original TUNL facility on Duke’s campus. In 2006, TUNL scientists added a booster ring called a synchrotron to increase the intensity of gamma rays that could be produced. Scientists from all over the world use the facility for experiments involving gamma rays at energies of 10 million to 100 million electron volts (MeV).

Mary-Russell RobersonGuest post by Mary-Russell Roberson

From Neutrinos to Nuclear Deals: Congressman Bill Foster

Hon. Bill Foster of the 11th District of Illinois is the only member of Congress to hold a Ph.D. in science. On November 5th, Congressman Foster visited Duke’s Initiative for Science and Society to discuss his unconventional path to politics and his consequent unique perspective. He lightheartedly delivered what he called a “recruiting speech” to a room full of scientists, hoping to persuade students with scientific background to become involved in public policy.

Representative Bill Foster, Ph.D., doing what politicians must.

Bill Foster started his first business with his brother at the age of 19 out of his family basement. His earnest, innovative efforts to use computers to control lighting manifested in the company Electronic Theatre Controls, which powered Disneyland and Disneyworld’s Parade of Lights in the 1980s, the 2012 London Olympic Stadium, Chicago’s Millenium Park, and a large portion of shows on Broadway.

Foster then transitioned into his career in physics. He undertook the IMB Proton Decay Experiment for his Ph.D. thesis under Larry Sulak; Foster did not observe proton decay, but he did observe neutrinos from a supernova. Foster continued his physics career at the Fermi National Accelerator Lab in suburban Chicago, where he smashed protons and anti-protons together at high speeds and later worked on the particle accelerators themselves.

In the midst of discovering Big Bang particles, Foster also fell into politics by maintaining an active civil engagement. He volunteered for Patrick Murphy’s campaign in 2006, where he says he “learned business on the factory floor,” a philosophy he has maintained since his days at Electronic Theatre Controls. He began the 110th Congress as an intern for Rep. Patrick Murphy, and ended it sitting as a Congressman.

Hon. Foster graphs the relative numbers of scientists and engineers, lawyers, and career politicians in Congress. The U.S. Congress consists mostly of career politicians, explains Foster, while China, for example, consists mostly of engineers.

Rep. Foster plots the relative numbers of scientists and engineers, lawyers, and career politicians in international governing bodies. The U.S. Congress consists mostly of career politicians, explains Foster, while China, for example, consists mostly of engineers.

Since winning his seat in 2012, Foster has introduced a scientific perspective to Congress, even if he’s careful not to conflate that with his political stance. He makes a point to clarify technical details of issues like the Iran nuclear deals, human genetic engineering, and public key cryptography on cell phones, to ensure that Congress makes the most informed decisions possible on highly complicated ethical issues. On genetic engineering, he noted, “Our ethical paradigm is not set up for it,” as the notion of “All men are created equal” fundamentally cannot handle humans whose genetic traits are pre-picked. Clearly, scientific expertise will be invaluable in such consequential issues.

Life in Washington, Foster stated, is unromantic. Foster lives in efficiency apartments and grounds himself by holding “Congress on your Corner” events, where he answers any constituent questions, like why grout isn’t working on a driveway.

Political customs, such as the dilemma of which tie to wear to promote his campaign, still bewilder his scientific mind. Most of the votes he makes, like renaming a post office, or voting on an issue the President will inevitably veto, don’t really matter, he said.

But what makes politics worth it for him, Foster explained as he passed around his voting card, is the power to make a positive difference in issues that impact millions of people. Such ambitions transcend the boundaries between science and policy.

By Olivia Zhu Olivia_Zhu_100

Star Wars and Space Travel: The Study of Science through Popular Movies

Who says class has to be all about lectures and labs? Andrés Aragoneses, a quantum optics researcher at Duke, has created a class called “Science & Science Fiction” in conjunction with the Osher Lifelong Learning Institute at Duke (OLLI). The course explores hot science fiction topics through the study of famous movies – from Star Wars, to Independence Day, to The Martian.

Professor Aragoneses teaching the class about the Big Bang Expansion

Professor Aragoneses teaching the class about the Big Bang Expansion

The unconventional idea to use movies as the primary medium for the class was born during Professor Aragoneses’s time teaching in Spain. Physics professors at his university had found that in order to get students to follow their classes, they had to do more than just explain Newton’s law and demonstrate practice problems. So, they began to relate these complex topics to media that the students were familiar with — news, cinema, and comics.

Each week, the OLLI group watches small scenes of movies that use scientific concepts in their production, and then learns the true theories behind these concepts. Most movies are quite fantastic when it comes to their scientific aspects, and this leads to incorrect representations of cosmological, physical, and astronomical phenomena on the screen. Focusing on a single concept each class, Aragoneses debunks Hollywood myths about natural disasters, comets, solar flares, neutrinos, and magnetic fields (to name a few).

Astronauts traveling with fuel packing in "Mission to Mars"

Astronauts traveling with jet packs in “Mission to Mars”

One week, the class focused on the dynamics of travel in space, calling on “Mission to Mars” to provide them with their screen reference. In one particular scene, astronauts are walking on Mars, propelled by air coming out of their backs and pushing them forward. The class learned that due to the lack of frictional force in space, the astronauts would, in reality, never run out of fuel since they would not need to push as hard as the movie suggested, using up much less fuel. The popular movie reference allowed Aragoneses to easily segue into the topics of friction, Newton’s laws, and the reality of space travel for the remainder of the class, while still holding the students’ attention. The group also analyzed the scientifically impossible behavior of deadly neutrinos in scenes from “2012” to learn about their true movement, and watched parts of “Independence Day” to better understand meteors and atmospheric interferences.

Astrophysicist searching for new planets by analyzing star movements.

Astrophysicist searching for new planets by analyzing star movements.

Occasionally, Aragoneses uses scientifically sound movies to study different concepts. One scene in Star Wars features Obi-Wan searching for a planet he is not able to find in existing maps. Yoda explains to him that the movement of the other stars in the sky is suspicious, and reasons that something must exist in between, although Obi-Wan cannot see it. The scene demonstrates the true manner in which astrophysicists search for new planets; since they are so tiny, they analyze movements of surrounding stars to detect their presence rather than searching for the planets themselves. Clearly the Grand Jedi Master knew a thing or two about the real universe!

Aragoneses’s idea to teach the class in such a unique fashion has evidently captivated his students; they often return after the week with new questions, suggestions for future movie references, and an excitement to continue their exploration of elaborate scientific concepts. The class has been a learning experience for Aragoneses as well, as he has had the chance to watch movies he hadn’t previously seen, and develop a deeper understanding of the concepts he teaches. He has so thoroughly enjoyed his work on the class in fact, that he is considering continuing to teach for OLLI in the future.

For those who are interested in enrolling in one of Aragoneses’s future classes, or another class hosted by OLLI, please visit their website. The Institute teaches about 100 different courses that range in topic from history, to science, to politics, to religion. The courses are taught both by Duke professors, and by other individuals from the Durham area.

Anika Ayyar_100Post by Anika Ayyar

Visualizing Crystals of the Cosmos

The beautiful mathematical structure of Penrose patterns have advanced our understanding of quasicrystals, a new breed of high-tech physical materials discovered in meteorites. Like all physical materials, these are collections of one or a few types of “particles” – atoms, molecules, or larger units – that are arranged in some pattern. The most familiar patterns are crystalline arrangements in which a simple unit is repeated in a regular way.

Periodic pattern of the honeycomb

During last Friday’s Visualization Forum, Josh Socolar, a Duke physics professor, conveyed his enthusiasm for the exotic patterns generated by non-periodic crystalline structures to a large audience munching on barbecue chicken and Alfredo pasta in the LSRC (Levine Science Research Center). Unlike many of the previous talks on visualizing data, Professor Socolar is not trying to find a new technique of visualization, but rather aims to emphasize the importance of visualizing certain structures.

Equations in chemistry for calculating vibrations when a material is heated are often based on the assumption that the material has a uniform structure such as the honeycomb pattern above. However, the atoms of a non-periodic crystalline object will behave differently when heated, making it necessary to revise the simplified mathematical models – since they can no longer be applied to all physical materials.

Quasicrystals, one type of non-periodic structured material, can be represented by the picture below. The pattern contains features with 5-fold symmetry of various sizes (highlighted in red, magenta, yellow, and green).

Quasicrystal structure with 5-fold symmetry

Quasicrystal structure with 5-fold symmetry

Drawing straight lines within each tile – as shown on the bottom half of the diagram below – produces lines running straight through the material with various lengths. Professor Socolar computed the lengths of these line segments and was amazed to discover that they follow the Fibonacci sequence. This phenomenon was recently discovered to occur naturally in icosahedrite, a rare and exotic mineral found in outer space.

Lines drawn through a quasicrystal structure

Lines drawn through a quasicrystal structure

By using software programs like Mathematica, we can create 3D images and animations for the expansion of such quasicrystal structures (a) as well as computing Sierpinski patterns formed when designing other types of non-periodic tile shapes (b).

Still of animation of expanding quasicrystal tiles - that looks like a cup of coffee.

(a) Still of animation of expanding quasicrystal tiles – that looks like a cup of coffee.

(b)

(b) Sierpinski triangle pattern drawn for other non-periodic tile shapes

(b) Recolored diagram of

(b) Recolored diagram of Sierpinski triangle pattern

Most importantly, Professor Socolar concludes, neither the Fibonacci nor non-periodic Penrose patterns would have been identified in quasicrystal structures without the visualization tools we have today. With Fibonacci sequence patterns discovered in the sunflower seed spiral as well as in the structure of the icosahedrite meteorite, we have found yet another mathematical point of unity between our world and the rest of the cosmos.

Professor Socolar taking questions from the audience.

Professor Socolar taking questions from the audience.

Post by Anika Radiya-Dixit