Atlanta Area Molecular & Cellular Biophysics Symposium. Networking event will bring together graduate students, postdocs, and faculty from the greater Atlanta area with interests in biophysics, biological chemistry bioengineering, and cell and molecular biology on Saturday, December 7, 2013 from 9:00am - 6:00pm. The event will be held at PAIS 290 on the Emory University Campus. Registration is required. Go to bit.ly/ATLBPS.

Dr. Uzi Landman has been named the Distinguished Professor of Chemistry & Physics at the Indian Institute of Technology Madras for his contributions to the understanding of diverse areas such as nobel metal catalysis, surface diffusion, atomic-scale friction and lubrication, interfacial processes, confined complex fluids and several others.

Join us in congratulating Dr. Landman!

Structure of the SecY channel during initiation of protein translocation

Eunyong Park, Jean-François Ménétret, James C. Gumbart, Steven J. Ludtke, Weikai Li, Andrew Whynot, Tom A. Rapoport & Christopher W. Akey

Affiliations Contributions Corresponding authors Nature (2013) doi:10.1038/nature12720 

Water pours into a cup at about the same rate regardless of whether the water bottle is made of glass or plastic.

But at nanometer-size scales for water and potentially other fluids, whether the container is made of glass or plastic does make a significant difference. A new study shows that in nanoscopic channels, the effective viscosity of water in channels made of glass can be twice as high as water in plastic channels. Nanoscopic glass channels can make water flow more like ketchup than ordinary H₂O.

The effect of container properties on the fluids they hold offers yet another example of surprising phenomena at the nanoscale. And it also provides a new factor that the designers of tiny mechanical systems must take into account.

“At the nanoscale, viscosity is no longer constant, so these results help redefine our understanding of fluid flow at this scale,” said Elisa Riedo, an associate professor in the School of Physics at the Georgia Institute of Technology. “Anyone performing an experiment, developing a technology or attempting to understand a biological process that involves water or another liquid at this size scale will now have to take the properties of surfaces into account.”

Those effects could be important to designers of devices such as high resolution 3D printers that use nanoscale nozzles, nanofluidic systems and even certain biomedical devices.

Considering that nano-confined water is ubiquitous in animal bodies, in rocks, and in nanotechnology, this new understanding could have a broad impact.

Research into the properties of liquids confined by different materials was sponsored by the Department of Energy’s Office of Basic Sciences and the National Science Foundation. The results were reported September 19 in the journal Nature Communications.

The viscosity differences created by container materials are directly affected by the degree to which the materials are either hydrophilic – which means they attract water – or hydrophobic – which means they repel it. The researchers believe that in hydrophilic materials, the attraction for water – a property known as “wettability” – makes water molecules more difficult to move, contributing to an increase in the fluid’s effective viscosity. On the other hand, water isn’t as attracted to hydrophobic materials, making the molecules easier to move and producing lower viscosity.

In research reported in the journal, this water behavior appeared only when water was confined to spaces of a few nanometers or less – the equivalent of just a few layers of water molecules.  The viscosity continued to increase as the surfaces were moved closer together.

The research team studied water confined by five different surfaces: mica, graphene oxide, silicon, diamond-like carbon, and graphite. Mica, used in the drilling industry, was the most hydrophilic of the materials, while graphite was the most hydrophobic.  

“We saw a clear one-to-one relationship between the degree to which the confining material was hydrophilic and the viscosity that we measured,” Riedo said.

Experimentally, the researchers began by preparing atomically-smooth surfaces of the materials, then placing highly-purified water onto them. Next, an AFM tip made of silicon was moved across the surfaces at varying heights until it made contact. The tip – about 40 nanometers in diameter – was then lifted up and the measurements continued.

As the viscosity of the water increased, the force needed to move the AFM tip also increased, causing it to twist slightly on the cantilever beam used to raise and lower the tip. Changes in this torsion angle were measured by a laser bounced off the reflective cantilever, providing an indication of changes in the force exerted on the tip, the viscous resistance exerted – and therefore the water’s effective viscosity.

“When the AFM tip was about one nanometer away from the surface, we began to see an increase of the viscous force acting on the tip for the hydrophilic surfaces,” Riedo said. “We had to use larger forces to move the tip at this point, and the closer we got to the surface, the more dramatic this became.”

Those differences can be explained by understanding how water behaves differently on different surfaces.

“At the nanoscale, liquid-surface interaction forces become important, particularly when the liquid molecules are confined in tiny spaces,” Riedo explained. “When the surfaces are hydrophilic, the water sticks to the surface and does not want to move. On hydrophobic surfaces, the water is slipping on the surfaces. With this study, not only have we observed this nanoscale wetting-dependent viscosity, but we have also been able to explain quantitatively the origin of the observed changes and relate them to boundary slip. This new understanding was able to explain previous unclear results of energy dissipation during dynamic AFM studies in water.”

While the researchers have so far only studied the effect of the material properties in water channels, Riedo expects to perform similar experiments on other fluids, including oils. Beyond simple fluids, she hopes to study complex fluids composed of nanoparticles in suspension to determine how the phenomenon changes with particle size and chemistry.

“There is no reason why this should not be true for other liquids, which means that this could redefine the way that fluid dynamics is understood at the nanoscale,” she said. “Every technology and natural process that uses liquids confined at the nanoscale will be affected.”

In addition to Riedo, co-authors of the paper included Deborah Ortiz-Young, Hsiang-Chih Chiu and Suenne Kim, who were at Georgia Tech when the research was done, and Kislon Voitchovsky of the Ecole Polytechnique Federale de Lausanne in Switzerland.

CITATION: Deborah Ortiz-Young, Hsiang-Chih Chiu, Suenne Kim, Kislon Voitchovsky and Elisa Riedo, “The interplay between apparent viscosity and wettability in nanoconfined water," (Nature Communications, 2013). http://www.nature.com/ncomms/2013/130919/ncomms3482/full/ncomms3482.html

This research was supported by the Office of Basic Energy Sciences of the U.S. Department of Energy (DOE) under grant DE-FG02-06ER46293 and by the National Science Foundation (NSF) under grants DMR-0120967, DMR-0706031 and CMMI-1100290. Any opinions or conclusions are those of the authors and do not necessarily reflect the official views of the DOE or NSF.

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Growing concern about bacterial resistance to existing antibiotics has created strong interest in new approaches for therapeutics able to battle infections. The work of an international team of researchers that recently solved the structure of a key bacterial membrane protein could provide a new target for drug and vaccine therapies able to battle one important class of bacteria.

The researchers determined the structure of BamA, a key component of the cellular machinery that controls insertion of beta-barrel proteins into the outer membranes of Gram-negative bacteria, organisms that cause a range of respiratory, gastrointestinal, urinary and other infections.

Beta-barrel membrane proteins transport substrates ranging from small molecules to large proteins into and out of the Gram-negative bacteria. These transport proteins help maintain the structure and composition of the outer membrane. Responsible for the virulence of pathogenic strains, the proteins are also essential to the viability of the bacteria – making them of interest for the development of new therapeutics.

“Because BamA is required for viability in all Gram-negative bacteria, it is a promising candidate for vaccines and drugs targeting bacterial infections,” said Susan Buchanan, a senior investigator in the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), part of the National Institutes of Health (NIH) in Bethesda, Md. “Knowing the structure and understanding how BamA works will likely help advance vaccine and drug design, and could result in novel antibiotics.”

The research team solved BamA structures from two bacteria: Neisseria gonorrhoeae and Haemophilus ducreyi. Buchanan, the paper’s principal author, said several biotechnology companies are already interested in understanding the structure of the protein and how it functions.  

The team reported its findings September 1 in the journal Nature. The research was led by NIH scientists and included researchers from the Georgia Institute of Technology, Monash University in Australia and Diamond Light Source in the United Kingdom.

“Learning how individual amino acid residues are organized into three-dimensional protein structures helps us understand features that are not apparent by any other type of analysis,” Buchanan said. “With a crystal structure, we essentially have a snapshot of what the protein looks like in 3D, which is a huge advantage in determining how a particular protein functions and in designing therapeutics.”

Once they had determined the three-dimensional structure of the protein, the researchers still needed to understand how the BamA-mediated insertion mechanism worked. To develop clues to the protein’s function, a Georgia Tech researcher carried out molecular dynamics simulations to provide a hypothesis that could be tested experimentally.

“When we looked at the structure, it wasn’t obvious to us how BamA helps proteins insert into the membrane,” said J.C. Gumbart, an assistant professor in the Georgia Tech School of Physics. “What my simulations revealed is that the barrel spontaneously opens and closes laterally to the membrane. We could actually see the opening of the barrel in the simulations, and based on that, came up with a hypothesis for how it could assist insertion of proteins into the outer membrane of the bacteria.”

For example, the crystalline structure of the protein showed that one side of the membrane-spanning beta-barrel domain is shorter than the other side, a feature that, according to the simulations, compresses the lipid bilayer and locally destabilizes the lipids in that region. The structure provides a potential route for inserting newly-synthesized outer-membrane proteins.

In conducting the simulations, Gumbart used the special-purpose Anton supercomputer at the Pittsburgh Supercomputing Center. The machine, developed by D.E. Shaw Research, allows simulations to attain microsecond-per-day computation rates, which was essential because the BamA simulations needed to be unusually long for researchers to observe its conformational flexibility.

The simulations will next have to be validated by experimental research, which could provide additional information about how the membrane proteins are inserted. In turn, that may lead to further simulations and additional experiments.

“Simulations and experiments often work hand-in-hand to attack very difficult problems,” Gumbart said. “We can have a give-and-take in which I make a prediction based on the simulations, and the other members of the team work to verify it experimentally.”

The new work adds significantly to the understanding of how BamA proteins operate in Gram-negative bacteria.

“Gram-negative bacteria have an unusual outer membrane that differs from other species and had not been well studied before,” Gumbart noted. “Many people are aware of the protein folding problem generally, but fewer people know about the membrane protein issues. This is a really distinct, but critical biophysical question that we need to address to better understand how these bacteria function.”

Ultimately, the work may lead to new approaches for addressing the challenge posed by bacterial resistance to existing drugs.

“We need completely new thinking about antimicrobials and antibacterial agents to get ideas on how better to kill these bacteria,” Gumbart added. “Any time you develop a better understanding of how a process works in a cell, you can begin to predict ways to interfere with that process. Inserting proteins into the outer membranes of bacteria is one of the most fundamental processes taking place in these microorganisms, so it offers a significant target for therapeutic development.”

In addition to those already mentioned, the paper’s authors included Nicholas Noinaj, Adam J. Kuszak, Hoshing Chang and Nicole C. Easley from the NIH; Petra Lukacik from Diamond Light Source, and Trevor Lithgow from Monash University.

CITATION: Nicholas Noinaj, et al., “Structural insight into the biogenesis of beta-barrel membrane proteins,” (Nature 2013). http://dx.doi.org/10.1038/nature12521

The research was supported by the NIDDK Intramural Research Program of the National Institutes of Health (NIH) and by NIH grants K22-AI100927 and R01-GM067887. The opinions and conclusions are those of the authors and do not necessary reflect the official views of the NIH.

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Media Relations Contacts: John Toon (jtoon@gatech.edu)(404-894-6986) or Brett Israel (brett.israel@comm.gatech.edu)(404-385-1933).

Writer: John Toon

John Wise's Award Winning Visualizations of the First Stars are Stunning!!

Dr. John Wise (Center for Relativistic Astrophysics and School of Physics), in conjunction with his collaborators, won the Best Visualization Prize in the XSEDE13 conference that showcases a diverse collection of computational driven sciences made possible by the NSF XSEDE computing resource. Their winning visualization depicts simulated data of the birth and death of the first stars in the universe and was made with the open-source analysis toolkit, yt.

Check out the movie at:

http://www.youtube.com/watch?v=tTilF_hbrHE

Researchers in the Chapman Lab have demonstrated a way to stabilize an unstable quantum system by applying bursts of microwave radiation to control the spin dynamics in a Bose-Einstein condensate. http://www.sciencedaily.com/releases/2013/08/130827135032.htm

First Sight: Black Holes and the Epic Effort to Detect Gravitational Radiation

For the past 50 years physicists have been trying, without success, to build a device that allows us to detect gravitational waves. But rather than looking for the minuscule gravitational waves produced by everyday occurrences, we have to focus on truly massive objects such as black holes and neutron starts. But what do we hope to learn? How hard is it, and why does it matter?

Lionel will discuss what we hope to learn from detecting gravitational waves. He will describe the breadth of current detection efforts.

Join Lionel London fro this student talk at the Atlanta Science Tavern on Wednesday, September 11th at 7pm. The address to the Atlanta Science Tavern is at Java Vino, 579 N Highland Ave., Atlanta, GA.

A simple pendulum has two equilibrium points: hanging in the “down” position and perfectly inverted in the “up” position. While the “down” position is a stable equilibrium, the inverted position is definitely not stable. Any infinitesimal deviation from perfectly inverted is enough to cause the pendulum to eventually swing down.

It has been known for more than 100 years, though, that an inverted pendulum can be stabilized by vibrating the pivot point. This non-intuitive phenomenon is known as dynamic stabilization, and it has led to a broad range of applications including charged particle traps, mass spectrometers and high-energy particle accelerators.

Many-body quantum systems can also be placed into unstable non-equilibrium states, and like the inverted pendulum of classical physics, they typically evolve away from these states. Now, researchers at the Georgia Institute of Technology have demonstrated a way to maintain an unstable quantum system by applying bursts of microwave radiation – a quantum analog to vibrating the inverted pendulum.

In an experiment that could have implications for quantum computers and quantum simulators, the researchers used microwave pulses of varying amplitudes and frequencies to control a quantum system composed of a cloud of approximately 40,000 rubidium atoms cooled nearly to absolute zero.

The research, sponsored by the National Science Foundation and reported online August 27 by the journal Physical Review Letters, experimentally demonstrated dynamical stabilization of a non-equilibrium many-body quantum system. The paper is scheduled to appear in the journal's August 30 print issue.

“In this work, we have demonstrated that we can control the quantum dynamics of a cloud of atoms to maintain them in a non-equilibrium configuration analogous to the inverted pendulum,” said Michael Chapman, a professor in the Georgia Tech School of Physics. “What we actually control is the internal spins of the atoms that give each atom a small magnetic moment. The spins are oriented in an external magnetic field against their will such that they would prefer to flip their orientation to the equilibrium position.”

Mathematically, the state of the rubidium atoms is virtually identical to that of the simple mechanical pendulum, meaning that Chapman and his students have controlled what could be called a “quantum inverted pendulum.”

In their experiment, the researchers began with a spin-1 atomic Bose-Einstein condensate (BEC) that is initialized in an unstable, fixed point of the spin-nematic phase space – comparable to an inverted pendulum. If allowed to freely evolve, interactions between the atoms would give rise to squeezing, quantum spin mixing and eventually relaxation to a stable state – comparable to a pendulum hanging straight down from a pivot point.

By periodically applying bursts of microwave radiation, the researchers rotated the spin-nematic many-body fluctuations, halting the squeezing and the relaxation toward stability. The researchers investigated a range of pulse periods and phase shifts to map a stability diagram that compares well with what they expected theoretically.

“The net effect is that the many-body system basically returns to the original state,” said Chapman. “We reverse the squeezing of the condensate, and after it again evolves toward squeezing, we cause it to return. If we do this periodically, we can maintain the Bose-Einstein condensate in this unstable point indefinitely.”

The control technique differs from active feedback, which measures the direction in which a system is moving and applies a force counter to that direction. The open-loop technique used by Chapman’s group applies a constant input that doesn’t vary with the activity of the system being controlled.

“We are periodically kicking the system to keep it in a state where it doesn’t want to be,” he said. “This is the first time we have been able to make a many-body spin system that we can stabilize against its natural evolution.”

Controlling and manipulating single-particle quantum systems or simple collections of atoms, electrons and photons has been a focus of the physics community over recent decades. These capabilities have formed the foundation for technologies such as lasers, magnetic resonance imaging, atomic clocks and new atomic sensors for magnetic fields and inertial guidance.

Now, researchers are studying more complex systems that involve many additional interacting particles, perhaps thousands of them. Chapman and his group hope to help extend their knowledge of these more complex many-body systems, which could lead to developments in quantum computing, quantum simulations and improved measurements.

“The long-range goal of our work is to further the understanding of quantum mechanics and to develop new technologies that exploit the often counterintuitive realities of the quantum world,” Chapman said. “Quantum many-body systems are being actively explored, and one of the things you’d like to do is be able to control them. I think this is one of the cleanest examples of being able to control a quantum many-body system in a manifestly unstable configuration.”

In addition to Chapman, other co-authors of the paper include T.M. Hoang, C.S. Gerving, B.J. Land, M. Anquez and C.D. Hamley.

This research is supported by the National Science Foundation (NSF) under Award PHY-1208828. Any conclusions or opinions are those of the authors and do not necessarily represent the official views of the NSF.

CITATION: T.M. Hoang, et at., “Dynamic stabilization of a quantum many-body spin system, (Physical Review Letters, 2013). http://link.aps.org/doi/10.1103/PhysRevLett.111.090403

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Having videos available so that she could learn at her own pace — that’s what Theresa Sorrentino enjoyed most about her recent online class experience.

“The video lectures helped me to better understand the course material because I  could watch and pause each one whenever I needed to,” added Sorrentino, a third-year Biomedical Engineering student.

Sorrentino was one of 11 Georgia Tech students who made up an on-campus contingent of this summer’s Introductory Physics I massive open online course (MOOC). (There were a total of 17,000 students around the world enrolled in the course.) The on-campus students actually took the course through Tech and earned credit.

“This flipped classroom model allowed the Tech students to watch lectures and complete homework assignments online, which freed up class time to work on problems and do other activities together,” said Mike Schatz, the physics professor who led the MOOC.

For example, as part of the course, students were asked to complete five video labs where they recorded a moving object, analyzed it using software, and created a five-minute lab report to share with the class.

When on campus, students were able to do a dry run of their lab reports during the face-to-face time with Schatz, allowing for them to get feedback before uploading their final videos to YouTube.

“This exercise was valuable, because we were able to catch some wrong turns and help students improve along the way,” Schatz said.    

Sorrentino is quick to share that being part of the small cohort of on-campus students was a plus.

“There was good camaraderie among us,” she said. “Also, there was greater accountability. If you didn’t get your work done, it was easily noticed, which was a good incentive to keep up with the class.”   

Aside from the flipped model and the video labs, this course experimented with video white board illustrations as another way to teach the material. The illustrations cover everything from the differences between length and time measurements to friction.

“I thought they were great,” Sorrentino said. “I don’t know if it was because they were a novelty or if I am just a visual learner, but the video illustrations made it easier to understand the information being taught.”

The five- to 15-minute videos were primarily created by several undergraduate students, which allowed the students to become engaged in the teaching process, Schatz said.

From writing the script and creating the storyboard to editing the footage, each video took about eight to 10 hours to complete. The team is still producing videos, with the goal being to have a library of about 100.   

The MOOC will be offered again beginning Aug. 19, and will run for 16 weeks. Schatz’s approach to teaching the course will be similar but with a few changes.

One change will include more frequent testing. This summer, peer-evaluated lab reports, homework, and a final exam contributed to the students’ final grades. In the fall, there will be more frequent testing (weekly quizzes and a midterm) and less weight placed on the lab reports.

“Testing will be spread out, so students will know where they stand in the course, and we will be able to see if they’re grasping the material,” Schatz said.

Also, the number of on-campus students taking the course will increase to six sections of 30.
“We want to find out what it takes to successfully scale up the course to handle all the Tech students who may want to take the course,” Schatz said.

For more information, email Schatz.