Dear School of Physics Community,

Please join me congratulating Claire Berger, Chandra Raman, Elisa Riedo, Mike Schatz and Deirdre Shoemaker. They have been named Fellows of the American Physical Society (citations below). APS Fellowship is a recognition by their peers of their exceptional contributions to physics. This is a distinct honor as the number of Fellows of the APS is limited to no more than one half of one percent of the membership.

CITATIONS:

Claire Berger (Division of Material Physics) “For seminal contributions to the development of epitaxial graphene electronics”

Mike Schatz (Topical Group on Statistical and Nonlinear Physics) “For pioneering and creative experimental contributions to the characterization and control of complex fluid and pattern formation phenomena”

Deirdre Shoemaker (Division of Computational Physics) “For her leading role in the investigation of dynamical and black-hole space-times and their observational signatures”

Elisa Riedo (Division of Condensed Matter Physics) "For atomic force microscopy studies of nanoscale friction, liquid structure and nanoscale elasticity, and the invention of thermochemical nanolithography.”  
 

NSF CAREER Proposal

Shina Tan’s NSF CAREER proposal on "Few-body and many-body theory of ultracold atoms and molecules” has been recommended for funding.

Congratulations to Andy Zangwill for his book on Modern Electrodynamics and the rave reviews it's received.

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.

Research News
Georgia Institute of Technology
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Media Relations Assistance: John Toon (jtoon@gatech.edu)(404-894-6986) or Brett Israel (brett.israel@comm.gatech.edu)(404-385-1933)

Writer: John Toon

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.

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

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.