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Observatory Catches Neutrinos in a South Pole Block of Ice

Tuesday, December 17, 2013

Scientists are using a one cubic kilometer block of ice at the South Pole to help unravel one of the great scientific mysteries of our time.

The block is part of IceCube, an observatory built in one of the most inhospitable parts of the world to study neutrinos zipping through the Earth from outer space. These subatomic particles normally pass through the Earth as easily as light passes through a pane of glass.But a few of them crash into the ultra-clear ice of IceCube. When they do, they produce secondary particles that can create a faint bluish light called Cherenkov radiation.

Scientists like Ignacio Taboada, an assistant professor in the Georgia Tech School of Physics, are using information from that glow to learn more about these neutrinos – including, perhaps, where in the universe they came from. Using data collected between May 2010 and May 2012, IceCube has measured 28 neutrinos that likely originated outside our solar system, the first time such very-high-energy cosmic neutrinos have been observed.

As the IceCube Neutrino Observatory celebrates the third anniversary of the end of construction on Dec. 18th, it is receiving the “Breakthrough of the Year” award from the British journal Physics World for observing these cosmic visitors.

“We now know that neutrinos from outside our planet are there, and we saw roughly as many as we had expected,” said Taboada, who has been part of the IceCube Collaboration team for 14 years and was a co-author of the Nov. 22 paper in the journal Science that reported the neutrino findings. “We have learned some things about neutrinos, but there are still other things that we still don’t understand.”

The centerpiece of IceCube is a matrix of 86 strings of basketball-sized optical detectors placed one and a half kilometers beneath the Antarctic snow. Each string includes 60 optical detectors that are so sensitive they can register a single photon. Dug into the ice by a special hot-water drill, the strings are arranged in a pattern designed to use the Cherenkov radiation to map the path of neutrinos through the ice.

By observing the path of the particles through the ice block, scientists had hoped to learn where the particles originated in space. But from the 28 neutrino events observed, that hasn’t yet been possible.

“So far, we are not seeing individual sources for the neutrinos,” said Taboada. “We are not seeing any place in the sky that we can point to and say that we see even three or four of the neutrinos coming from. It is very diffuse. It may be that the sources are very weak, or that we have a detector that is not large enough.”

Neutrinos are nearly-massless particles that carry no electrical charge and originate from a variety of sources, including radioactive decay, our own Sun, cosmic rays and events such as exploding stars. From May 2010 to May 2012, IceCube recorded 28 neutrinos with very high energy levels – above 30 trillion electron volts – suggesting they were from beyond our own solar system.

One challenge for the nearly 300 scientists involved in the program is separating cosmic neutrinos from those that originate on Earth. Cosmic neutrinos tend to have much higher energy levels, which can be measured by the amount of light they produce in the ice. Their direction also gives a clue; only cosmic neutrinos can pass through the Earth into the ice.

Built with funds from the National Science Foundation and scientific organizations from three European countries, IceCube was also designed to measure cosmic rays, which accompany the formation of neutrinos. The existence of cosmic rays has been known for more than a hundred years, but their sources are also unknown.

“This is essentially the birth of a new branch of astrophysics,” said Taboada. “We’ve observed the universe with photons, and now we can observe using neutrinos.”

IceCube is also facilitating Taboada’s own research on gamma-ray bursts, which is being conducted with Ph.D. students James Casey and Jacob Daughhetee.

“Gamma ray bursts are gigantic explosions that last for only a few seconds,” Taboada said. “Over those few seconds, they are so bright that they can outshine the rest of the universe combined. They are brief, but they are very powerful while they last.”

Scientists believe that there are at least two kinds of gamma ray bursts: those associated with supernovas that eject jets of matter and radiation, and neutron stars that spiral together and eventually merge. Neutrinos from gamma ray bursts can also be detected by IceCube.

IceCube was built at the South Pole to take advantage of the very clear ice available there and the darkness within the ice. “We used Antarctic ice because we needed a highly transparent material to observe the Cherenkov radiation,” explained Taboada. “The ice allows us to see evidence of these secondary particles.”

But that transparency has a cost. The South Pole experiences extremely cold temperatures, and everything used there must be flown in. Taboada has been to the South Pole three times, each time for a month during the Antarctic summer – when temperatures can still be as low as 45 degrees below zero Celsius (minus 49 degrees Fahrenheit).

“It’s a very work-oriented place,” he said. “Because it is so difficult to get there, you work every day, 12 and 15 hours a day. At the end of a month, you are exhausted.”

During the summer – November through February – as many as 150 people work at the South Pole facilities, known officially as the Amundsen-Scott South Pole Station. During the Antarctic winter, only 50 or 60 people work there, and aircraft don’t land except in extreme emergencies.

While space is tight, the station does have a music room, gymnasium and basketball court, along with a greenhouse for growing fresh vegetables. Water is precious because it is obtained by melting ice, so researchers are limited to two two-minute showers per week.

Construction of IceCube began in 2005, and the facility – now managed by the University of Wisconsin – was turned on in December 2010. With participation from 41 institutions in 12 countries, IceCube is expected to operate for at least ten years. Already, however, there is discussion about enhancing its capabilities – and perhaps expanding it to capture more neutrinos.

Basic science done in facilities like IceCube is really all about human curiosity – which often ends up having a more practical benefit.

“Basic science is not always about finding a cure for cancer,” Taboada said. “But if you look at the last 400 years of basic scientific discovery, research and basic science have time and again resulted in a better life for humans. Satisfying that human curiosity often turns out to be a very long-term, very high-risk and very high payoff investment. That’s a basic reason to do science.”

Research News

Georgia Institute of Technology

177 North Avenue

Atlanta, Georgia  30332-0181  USA

 

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

 

Media Contact: 

John Toon

Research News

jtoon@gatech.edu

(404) 894-6986

Summary: 

Located at the South Pole, the IceCube Neutrino Observatory is helping unravel one of the key scientific mysteries of our time: the question of where cosmic neutrinos originate.

Intro: 

Located at the South Pole, the IceCube Neutrino Observatory is helping unravel one of the key scientific mysteries of our time: the question of where cosmic neutrinos originate.

Alumni: 

Congratulations APS Fellows and NSF CAREER Proposals!

Tuesday, December 10, 2013

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.

 

Summary: 

Claire Berger, Chandra Raman, Elisa Riedo, Mike Schatz and Deirdre Shoemaker have been named Fellows of the American Physical Society

Intro: 

Claire Berger, Chandra Raman, Elisa Riedo, Mike Schatz and Deirdre Shoemaker have been named Fellows of the American Physical Society

Alumni: 

Congratulations to Andy Zangwill

Monday, December 2, 2013

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

Summary: 

Congratulations to Andy Zangwill

Intro: 

Congratulations to Andy Zangwill

Alumni: 

Biophysics Symposium

Monday, November 18, 2013

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.

Summary: 

Atlanta Area Molecular & Cellular Biophysics Symposium

Intro: 

Atlanta Area Molecular & Cellular Biophysics Symposium

Alumni: 

Congratulations to Dr. Uzi Landman

Thursday, November 14, 2013

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!

Summary: 

Dr. Uzi Landman has been named the Distinguished Professor of Chemistry & Physics at the Indian Institute of Technology Madras.

Intro: 

Dr. Uzi Landman has been named the Distinguished Professor of Chemistry & Physics at the Indian Institute of Technology Madras.

Alumni: 

Structure of the SecY channel during initiation of protein translocation

Monday, October 28, 2013

 

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 doi:10.1038/nature12720 

Received Accepted Published online

Many secretory proteins are targeted by signal sequences to a protein-conducting channel, formed by prokaryotic SecY or eukaryotic Sec61 complexes, and are translocated across the membrane during their synthesis1, 2. Crystal structures of the inactive channel show that the SecY subunit of the heterotrimeric complex consists of two halves that form an hourglass-shaped pore with a constriction in the middle of the membrane and a lateral gate that faces the lipid phase3, 4, 5. The closed channel has an empty cytoplasmic funnel and an extracellular funnel that is filled with a small helical domain, called the plug. During initiation of translocation, a ribosome–nascent chain complex binds to the SecY (or Sec61) complex, resulting in insertion of the nascent chain. However, the mechanism of channel opening during translocation is unclear. Here we have addressed this question by determining structures of inactive and active ribosome–channel complexes with cryo-electron microscopy. Non-translating ribosome–SecY channel complexes derived from Methanocaldococcus jannaschii or Escherichia coli show the channel in its closed state, and indicate that ribosome binding per se causes only minor changes. The structure of an active E. coli ribosome–channel complex demonstrates that the nascent chain opens the channel, causing mostly rigid body movements of the amino- and carboxy-terminal halves of SecY. In this early translocation intermediate, the polypeptide inserts as a loop into the SecY channel with the hydrophobic signal sequence intercalated into the open lateral gate. The nascent chain also forms a loop on the cytoplasmic surface of SecY rather than entering the channel directly.

 

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12720.html

Summary: 

Structure of the SecY channel during initiation of protein translocation

Intro: 

Structure of the SecY channel during initiation of protein translocation

Alumni: 

Glass or Plastic? Container’s Properties Affect the Viscosity of Nanoscale Water

Thursday, September 19, 2013

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
177 North Avenue
Atlanta, Georgia  30332-0181 USA

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

 

Media Contact: 

John Toon

Research News

jtoon@gatech.edu

(404) 894-6986

Summary: 

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.

Intro: 

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.

Alumni: 

Researchers Determine Protein Structure for New Antimicrobial Target

Friday, September 6, 2013

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

Media Contact: 

John Toon

Research News

jtoon@gatech.edu

(404) 894-6986

Summary: 

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.

Intro: 

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.

Alumni: 

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

Thursday, August 29, 2013

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

 

Summary: 

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

Intro: 

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

Alumni: 

Quantum Inverted Pendulum

Wednesday, August 28, 2013

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

Summary: 

Quantum Inverted Pendulum: Dynamically Maintaining an Unstable Quantum System

Intro: 

Quantum Inverted Pendulum: Dynamically Maintaining an Unstable Quantum System

Alumni: 

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