Eric Sembrat's Test Bonanza

From Four Wheels to Two

One group working to get more people on two-wheeled transportation is Starter Bikes, a student organization and campus co-op that lets members of the Tech community purchase and repair bikes at an affordable price.

“We want to reach those people who are on the fence, and those who may have never thought about biking,” said Alec Lindman, a graduate student in physics who is involved with Starter Bikes, as well as co-chair of BIIC and Bike GT, the central group of organizers for bike-related initiatives on campus. 

This year, Bike GT is updating its resources and creating new ones to make cycling more accessible. The group is revamping www.bike.gatech.edu, a digital starting point for all things bike-related, as well as working on a printed pocket guide that will outline cycling laws, guidelines, and campus resources. 

Many of those who use a bike as their main mode of transportation are eager to share the convenience and benefits with others.

“It gets you outside and in touch with your community,” said Mike Tennenbaum, also a graduate student in physics and part of Bike GT. “In the city, it actually gives you more mobility than being in a car.”

For students who don’t own a bike, Parking and Transportation Services (PTS) rents bikes on a semesterly basis through its BuzzBike program. Plans are also in the works for a campus bike share program, which would be open to students, faculty, and staff. PTS also periodically hosts educational classes that are free for the campus community; a bike safety class will take place in April.

Someday, Starter Bikes may have a home in the center of campus in a bike center — that’s one idea proposed in the Bicycle Master Plan. For now, Starter Bikes is located at the bottom of the Campus Recreation Center parking deck and is open Fridays from 4 to 6 p.m.
 

Other current Parking and Transportation Services initiatives include:

• Bike counting: PTS has started bike counting as a way to monitor usage trends in various areas of campus, particularly before and after infrastructure improvement projects. Cyclists may at times notice two parallel tubes in the road in various places on campus. Ride over these, not around them — they’re counting you.
• Clearing bike lanes: In Tech Square, Fifth Street now has dedicated parking spots for loading and unloading during peak delivery. These spots are located on the south side of the street, with the goal of keeping bike lanes clear of vehicles.
• Connecting the campus: PTS is in talks with the City of Atlanta about improving access to campus from the north and west. Discussions are underway and projects will soon be moving into the design phase.  Read more.

Related Links

Bike GT

Capital Planning and Space Management

Parking and Transportation Services

Parking and Transportation Services: Bicycling

Antibiotic resistance in bacteria is among the most critical public health threats today. As more existing antibiotics lose their ability to battle bacteria, there’s pressure to develop new drugs that can attack the bugs in different ways.

Key to that effort is understanding how bacteria operate so new compounds can be developed to attack the microorganisms at their weakest points. 

Georgia Tech researchers are modeling gram-negative bacteria such as E. coli, N. gonorrhoeae, and Salmonella to find gaps in their cellular defenses — specifically, their outer cell membranes. Having detailed models of these structures can help experimentalists understand what their research is showing and point to new areas of investigation.

“One of the helpful things about modeling is that often just having a detailed picture of the system shows you what questions you should be asking,” said J.C. Gumbart, a professor in Georgia Tech’s School of Physics. “It’s really important that we have very accurate models to understand how different bacteria interact with the immune system and with potential drugs in diverse ways.”

The bacteria that Gumbart studies are unusual in that they have two outer membranes, one on each side of the cell wall. These membranes are very different from those of other cells, and they have special features that may provide avenues for pharmaceutical attack.

But even the best experiments can’t show all of the factors involved in the membranes’ functions, which is why models can be useful. The models, which run on high-performance computers both locally and at national supercomputing centers such as the one at Oak Ridge National Laboratory, combine experimental data with basic principles of biophysics. “We have effectively infinite resolution, and we can present dynamic, atomistic resolution views of the processes going on there,” Gumbart said.

Georgia Tech researchers are working with colleagues at the National Institutes of Health, Caltech, Emory University, and other institutions to understand bacteria, including the critical protein BamA, which is responsible for protein insertion into the membrane and could therefore be a target for new ­antibiotics. 

— John Toon

When an assembly of microgel particles includes one particle that's significantly larger than the rest, that oversized particle spontaneously shrinks to match the size of its smaller neighbors. This self-healing nature of the system allows the microparticles to form defect-free colloidal crystals, an unusual property not seen in systems made up of “hard” particles.

In 2009, Andrew Lyon, then a professor of chemistry at the Georgia Institute of Technology, observed this dynamic resizing in a microgel system he had created, but the mechanism behind the self-healing process remained uncertain. Now, researchers believe they've finally solved the mystery, and what they've learned could also have implications for biological systems made up of soft organic particles not unlike the polymer microgels.

Using small-angle X-ray and neutron scattering techniques, the researchers carefully studied the structures formed by dense concentrations of the microparticles. They also used tiny piezoelectric pressure transducers to measure osmotic pressure changes in the system. Their conclusion: In dense assemblies of microparticles, counter ions bound to the microgels by electrostatic attraction come to be shared by multiple particles, increasing the osmotic pressure which then works to shrink the oversized particle.

“When the particles are close enough together, there is a point at which the cloud of ions can no longer be associated with individual particles because they overlap other particles,” said Alberto Fernandez-Nieves, an associate professor in the School of Physics at the Georgia Institute of Technology. “The ions create an imbalance between osmotic pressure inside and outside the larger particles, pushing them to de-swell – expel solvent to change size – to match the pressure of the system given by these delocalized ions. This is only possible because the microgel particles are compressible.”

The research is reported April 25 in the early edition of the journal Proceedings of the National Academy of Sciences. The work was supported by the Swiss National Science Foundation, and the research partnership between Georgia Tech and Children’s Healthcare of Atlanta.

The presence of non-uniform particles normally creates point defects in the crystals or prevents the formation of crystalline structures altogether. That’s true for structures formed from atoms, but not those formed from the microgels, which are soft cross-linked polymer particles immersed in a solvent. The microgels, which range in size from about 100 nanometers up to several microns in diameter, can exist in either swollen or non-swollen states, depending on such external conditions as temperature.

Lyon and his research group reported the self-healing nature of the colloidal crystals in the journal Angewandte Chemie International in 2009. They initially believed that what they were seeing resulted from energetic issues associated with formation of the crystals.

“We interpreted the phenomenon in terms of the overall lattice energy – the propensity of the microgels to form an ordered array – perhaps being larger than the energy required to collapse the defect microgels,” he said. “In other words, we believed there was an energetic penalty associated with disruption of the crystalline lattice that was greater than the energetic penalty associated with individual microgel de-swelling.”

Fernandez-Nieves initially supported that hypothesis, but later came believe there was more at work. For instance, the shrunken microgels, which are identifiable because of their higher optical density, freely move about just like the smaller ones, suggesting that the shrinkage doesn’t result from being crowded by the smaller particles.

In a collaboration with Researcher Urs Gasser and Ph.D. student Andrea Scotti at the Laboratory for Neutron Scattering and Imaging at the Paul Scherrer Institut in Switzerland, the researchers used X-ray and neutron scattering techniques to study the structure of the suspended microgels and the degree of swelling in the large microparticles of the colloidal crystals. The work confirmed that these larger particles had indeed de-swollen, even at concentrations far larger than those initially used by Lyon’s research team.

“The system is able to make point defects disappear, and the mechanism we have proposed allows us to understand why this occurs,” said Fernandez-Nieves. “What we have proposed is a mechanism to explain what we see happening, and we think this is a general mechanism that could potentially apply to a wider range of soft particles.”

As a next step, the research group expects to determine the ionic structure to confirm what the existing research has suggested. Fernandez-Nieves believes the work will generate more research with soft particle suspensions, for both experimentalists and theoreticians.

“There is indeed much more theory and simulation work needed to confirm what we propose and to fully understand how this self-healing process occurs,” he said. “This principle could be at play in a large number of contexts, including biological systems, in which there is a subtle balance between rigidity, osmotic pressure and ionic balance. This is a mechanism that doesn’t really involve the other particles in the assembly. It involves the ions.”

Lyon, now dean of the Schmid College of Science and Technology at Chapman University, believes the findings might go beyond creating better colloidal systems to provide insights into how living cells operate.

“By obtaining a deeper insight into microgel assemblies, we may be able to take advantage of the subtle energetic balances that determine the overall structures to create more complex, defect-tolerant assemblies,” he said. “The physics we uncovered here could be relevant for other crowded, soft-materials systems, such as the interior of the eukaryotic cells. Perhaps an extension of this knowledge will provide a better understanding of how the interior of a cell is organized, and how material is transported through this complex and crowded environment.”

CITATION: A. Scotti, et al., “Self-healing colloidal crystals: Why soft particles feel the squeeze,” Proceedings of the National Academy of Sciences, 2016).

Research News
Georgia Institute of Technology
177 North Avenue
Atlanta, Georgia 30332-0181 USA

Media Relations Contacts: John Toon (404-894-6986) (jtoon@gatech.edu) or Ben Brumfield (404-385-1933) (ben.brumfield@comm.gatech.edu).

Writer: John Toon

Graduate

Curtis Balusek, Bonnie B. and Charles K. Rice, Jr. Fellowship

James Waters, Bonnie B. and Charles K. Rice, Jr. Fellowship

Pak Hong Leung, Amelio Fellowship Award

Greg Richards, Amelio Award for Excellence in Research by a Graduate Student

Undergraduate

Alexander Covington, Roger M. Wartell and Stephen E. Brossette Award for Multidisciplinary Studies in Biology, Physics, and Mathematics, Hitohiro Fukuyo Outstanding Physics Undergraduate Award

Zixin (Wendy) Jiang , the A. Joyce Nickelson and John C. Sutherland Undergraduate Research Award, Hitohiro Fukuyo Memorial Scholarship Award

Mary Elizabeth Lee, Leddy Family Scholarship

Krishma Singal, Mehta Phingbodhipakkiya Undergraduate Memorial Scholarship, Joyce M. and Glenn A. Burdick Prize

Sai Naga Manoj Paladugu, Hitohiro Fukuyo Memorial Scholarship Award

Rebecca Zane Wolf, Hitohiro Fukuyo Outstanding Physics Undergraduate Award

Have a close-up look at DNA; you’ll see it wiggles in the oddest way.

Put more scientifically, a piece of DNA’s movements are often counterintuitive to those of objects in our everyday grasp.  Take a rod of rubber, for example. Bend it until its ends meet, and you can count on the elastic tension to snap it back straight when you let go, said biological physicist Harold Kim.

“That doesn’t always work that way with a piece of DNA. When you bend it into a loop, the elastic energy more often than not wants to bend the chain further in instead of pushing it back out,” said Kim, an associate professor at the Georgia Institute of Technology.

At the School of Physics, Kim is fine-tuning the observation of how biopolymers behave, in particular DNA at short lengths. He published his latest results on “Force distribution in a semiflexible loop” in the journal Physical Review E on April 18, 2016.  The research is funded by National Institutes of Health. Georgia Tech’s James T. Waters coauthored the research paper.

In complex simulations, Kim studied the motions of DNA chains at lengths where they still have springy qualities, in order to understand their mechanochemical properties, or how they work as microscopic objects. In particular, he has illuminated the forces acting upon DNA bound up in short loops.

That’s a common and important shape that keeps DNA from expressing when it shouldn’t and then possibly messing up cell functioning.

Kim’s most significant counterintuitive find could improve understanding of how DNA snaps free from the proteins that bind them into those loops. He has observed that looped DNA, though on average very gentle in its motions, is beset by moments of unusually high force. 

“It would be a little like a chaotic spring drawn up to a loop making pretty even jumbly movements then suddenly whipping out violently,” Kim said.

The range of observed forces on DNA loops breaks the bounds of what thermodynamics predicts. Even though the mean of the force distribution does indeed equal the thermodynamic force, the distribution of forces pushes past the anticipated norm, falling broadly outside a Gaussian distribution on both ends.

That’s a key determination.

It could help scientists in various disciplines predict the lifespans of many DNA loops and understand the frequency and likelihood of their undoing.

The forces contributing to those momentary jerks and snaps work on the whole contrary to one another. While that elastic energy works on DNA pieces in its ways, the forces of entropy push hard in their own ways.

Reflective of the universe overall, in Kim’s observations of springy DNA loops, entropy, here too, wins. Entropic forces slightly outdo the elastic forces.

And they, too, defy intuition.

To understand how, let’s take a look back at that rubber bar. When a short DNA chain is not looped but only bent, it acts more like the rubber bar. The elastic force dominates and mostly wants to push it back straight, while entropy mostly wants to keep it curvy.

Then, as the DNA chain lengthens a bit and loops: That relation starkly turns on its head.

The elastic force then pulls inward with vehemence, and the entropic force then pushes the chain outward with even more vigor.

The length of a DNA loop appears to contribute strongly to how likely these intermittent extreme forces are to destabilize its bond with the protein holding it shut.

That, incidentally, plays right into many scientists’ current discussions on other biopolymers.

“There’s a lot of speculation right now that the kinds of force-peaks we observed actually regulate the length of some biopolymers, so, in an interesting way, our observations and methods may help colleagues explore this idea more closely,” Kim said.

Kim’s group augmented thermodynamic calculations with a novel simulation method, “phase-space sampling.” It not only establishes the positon of molecular components in space but also their momentum at a given time.

This took into account the constant bombardment by water molecules, i.e. the “heat bath.”

This way, Kim was better able to access the fluctuating forces on looped DNA chains – and see more closely how they really wriggle.

The work is funded by the National Institutes of Health, grant number R01GM112882. Any conclusions or opinions are those of the authors and do not necessarily represent the official views of the NIH.

Research News

Georgia Insitute of Technology

177 North Avenue

Atlanta, Georgia 30032-0181

Media Relations Contacts: Ben Brumfield (ben.brumfield@comm.gatech.edu) (404-385-1933)

Writer: Ben Brumfield

Another view of the universe is becoming available as the facility known as HAWC gathers data. Analysis of the data by scientists, including Georgia Tech physicist Ignacio Taboada, is revealing astronomical objects never known before. 

HAWC is the High-Altitude Water Cherenkov Observatory, nestled at 14,000 feet above sea level between two mountains – Pico de Orizaba and Sierra Negra – in Mexico. It was constructed to locate sources of gamma rays by detecting the secondary particles resulting from the interaction of gamma rays in Earth’s upper atmosphere. Gamma rays are made in extreme environments in the universe, such as supernova explosions, pulsars, and supermassive black holes

HAWC uses light sensors inside 50,000-gallon water tanks to detect the secondary particles of gamma rays. As these particles travel through the water tanks, they produce faint blue light, known as Cherenkov radiation. A total of 300 tanks covers an area of about four football fields.

More than 120 scientists in Europe, Mexico, and the U.S. are involved in the HAWC collaboration.  Construction of the gamma ray observatory was completed in March 2015, and results of the first year of operation are now available. At the meeting of the American Physical Society on April 16-19, in Salt Lake City, Utah, scientists will report the first discoveries made possible by HAWC.

Among several findings to be reported at the APS meeting is the discovery of several new sources of gamma rays several thousands of light years away in our very own galaxy, the Milky Way. Discovering many new distant objects in so short a time is evidence of HAWC’s sensitivity, Taboada says. It is about 15 times as sensitive as the best previous instruments to survey the sky for gamma rays.

A unique capability of HAWC is that is operates day and night and observes a much larger fraction of the sky than is possible with other instruments, making HAWC an ideal survey detector, Taboada says. “HAWC will help us draw a fuller picture of the universe than we’ve known before.”

Construction of HAWC was funded by the National Science Foundation (NSF) and the U.S. Department of Energy and by Mexico’s Consejo Nacional de Ciencia y Tecnologia. Taboada’s HAWC research in Georgia Tech is funded by NSF and National Aeronautics and Space Administration (NASA).