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The School of Science at Rensselaer Polytechnic Institute

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Oct. 2013
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Faculty News

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Student News

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Staff News
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Alumni/ae News
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Science Dean Laurie Leshin
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Message from
Dean Laurie Leshin

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Dear Colleagues and Friends,

Interdisciplinary research is a central theme that resonates throughout the School of Science. In the dynamic and complex world we live in, it is becoming more imperative to break down academic boundaries and reach across disciplines to design effective solutions to current and future challenges. Whether advancing human heath, harnessing technology for smarter environmental management, or leveraging the power of big data, the applications of interdisciplinary exploration are endless.

In order to develop and enhance interdisciplinary research as we seek to increase "Discovery Across Boundaries", we created the Dean's Seminar Series. The Series provides a forum for discussion and coordination in the areas of science, engineering, and connected fields. Each semester features a unique focus area, with the spotlight on "The Science of Big Data" for Fall 2013.

I invite all faculty members to attend a seminar and learn more about other disciplines - you never know what might pique your interest!

In the future we may try to record the talks to share with our alums and friends - if this would be of interest to you, tweet me @RPISciDean or leave a note on our Facebook page.

All the best,
Laurie Leshin

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science.rpi.edu

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Web version of this email

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tetraloop
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Researchers Create Accurate Computer Model of RNA Tetraloop

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A computational model developed by researchers at RPI is the first to accurately simulate the complex twists of a short sequence of RNA as it folds into a critical hairpin structure known as a "tetraloop." The research, published in Proceedings of the National Academy of Science, is a glimpse into RNA, found in all life on Earth, and could advance a variety of research areas, including the search for new antibiotics and cures for protein-related diseases.

Existing computational models, based on DNA rather than RNA, do not achieve the atomic level accuracy of the new model, said Angel Garcia, head of the department of Physics, Applied Physics, and Astronomy and senior constellation chaired professor in the Biocomputation and Bioinformatics Constellation, who co-wrote the paper with Alan Chen, a post-doctoral fellow at Rensselaer.


Full Article  |  Video

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Berman

International Research Data Alliance Facilitates Data Sharing

Is data the new gold? Data is certainly valuable, and properly shared, it can transform our lives.

Curioisiy

NASA Mars Rover Curiosity Finds Water in First Sample of Planet Surface

The first scoop of Martian soil analyzed reveals that fine materials on the surface of the planet contain several percent water by weight.
Dean Leshin talks with NPR (audio)

Asteroids

Researchers Propose New Theory To Explain Seeds of Life in Asteroids

A new look at the early solar system introduces an alternative theory to explain how biomolecules were once able to form inside of asteroids.

AMOS

Rensselaer at Petascale

Rensselaer has unveiled a new petascale supercomputing system, the Advanced Multiprocessing Optimized System, or AMOS.

AMOS

School of Science Retreat

A School of Science Retreat was held September 17-18 at the Heffner Alumni House.

Fall 2013 Dean's Seminar Series:
"The Science of Big Data"

October 30
John Mitchell, Prof., Mathematical Sciences
Barbara Cutler, Assoc. Prof., Computer Science

November 13
Fran Berman,
Edward G. Hamilton Distinguished Prof. of Computer Science
Karyn Rogers, Assist. Prof., Earth & Environmental Sciences

December 4
Heidi Newberg, Prof., Physics, Applied Physics, and Astronomy
Peter Fox, Prof. and Tetherless World Constellation Chair

For more information, please contact Amanda Thibault, thibaa2@rpi.edu.

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November 15, 2013; 9:00 a.m. to 10:30 a.m.
The National Press Club, 529 14th Street, NW, 13th Floor
Washington, DC

In the last half of the 20th century, the U.S. led the world in unprecedented exploration of space. Forty years after putting a man on the moon, the squeeze on federal spending places NASA in peril. Will the U.S. continue to lead? Can and should the private sector lead?

Join Dean of Science Laurie Leshin and other experts who'll explore what recent developments mean for our future in the final frontier... and on our own planet.

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International Research Data Alliance Facilitates Data Sharing at First U.S. Meeting

September 18, 2013

Is data the new gold? Data is certainly valuable, and properly shared, it can transform our lives through improved disaster management prediction, health care, and environmental stewardship. But unlike gold or other commodities, data is inexhaustible. It is the rich and growing renewable resource of the information age and with proper management, data can be harnessed to our advantage.

Top leaders from the White House and our nation's science agencies understand the importance of data management. From September 16-18, they are gathering at the National Academy of Sciences in Washington as part of a major meeting of the international Research Data Alliance (RDA). Francine Berman, distinguished professor of computer science at Rensselaer Polytechnic Institute, is co-chair of the RDA Council and opened the conference.

The RDA is supported by a $2.5 million grant from the National Science Foundation, as well as financial support from the European Commission and the Australian government. RDA was officially launched in March 2013 in Gothenburg, Sweden. Since that time, membership has grown to more than 1,200 international researchers and data experts from 52 countries who focus on the development and adoption of common tools, harmonized standards, and infrastructure needed for data sharing by practicing researchers, as well as the application of policy and best practices to facilitate data-driven research. RDA members work across dozens of disciplines to tackle data topics pertaining to global agricultural research and innovation, history and ethnography, human health, and others.

"Science is global. Researchers all over the world are addressing today's toughest problems by combining data from many sources in innovative ways," said Berman. "The international Research Data Alliance community builds infrastructure that scientists can use to share and exchange data, create new discoveries, and facilitate innovation."

More than 400 participants from 22 countries are expected to attend. Speakers include: Farnam Jahanian, assistant director of the NSF Computer and Information Science and Engineering; Tom Kalil, deputy director of the White House Office of Science & Technology Policy Technology & Innovation Division; Mark Suskin, deputy director of the NSF Office of Cyberinfrastructure; and Michael Stebbins, assistant director of the Science Division of the White House Office of Science and Technology Policy

To view the full program, please visit http://rd-alliance.org.

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NASA Mars Rover Curiosity Finds Water in First Sample of Planet Surface

September 26, 2013

The first scoop of soil analyzed by the analytical suite in the belly of NASA's Curiosity rover reveals that fine materials on the surface of the planet contain several percent water by weight. The results were published today in Science as one article in a five-paper special section on the Curiosity mission. Rensselaer Polytechnic Institute Dean of Science Laurie Leshin is the study's lead author.

"One of the most exciting results from this very first solid sample ingested by Curiosity is the high percentage of water in the soil," said Leshin. "About 2 percent of the soil on the surface of Mars is made up of water, which is a great resource, and interesting scientifically." The sample also released significant carbon dioxide, oxygen, and sulfur compounds when heated.

Curiosity landed in Gale Crater on the surface of Mars on August 6, 2012, charged with answering the question "Could Mars have once harbored life?" To do that, Curiosity is the first rover on Mars to carry equipment for gathering and processing samples of rock and soil. One of those instruments was employed in the current research: Sample Analysis at Mars (SAM) includes a gas chromotograph, a mass spectrometer, and a tunable laser spectrometer enabling it to identify a wide range of chemical compounds and determine the ratios of different isotopes of key elements.

"This work not only demonstrates that SAM is working beautifully on Mars, but also shows how SAM fits into Curiosity's powerful and comprehensive suite of scientific instruments," said Paul Mahaffy, principal investigator for SAM at NASA's Goddard Space Flight Center in Maryland. "By combining analyses of water and other volatiles from SAM with mineralogical, chemical, and geological data from Curiosity's other instruments, we have the most comprehensive information ever obtained on martian surface fines. These data greatly advance our understanding of surface processes and the action of water on Mars."

"This is the first solid sample that we've analyzed with the instruments on Curiosity. It's the very first scoop of stuff that's been fed into the analytical suite. Although this is only the beginning of the story, what we've learned is substantial," said Leshin, who co-wrote the article, titled "Volatile, Isotope and Organic Analysis of Martian Fines with the Mars Curiosity Rover." Thirty-four researchers, all members of the Mars Science Laboratory Science Team, contributed to the paper.

In this study, scientists used the rover's scoop to collect dust, dirt, and finely grained soil from a sandy patch known as "Rocknest." Researchers fed portions of the fifth scoop into SAM. Inside SAM, the "fines"-as the dust, dirt, and fine soil is known-were heated to 835 degrees Celsius.

Baking the sample also revealed a compound containing chlorine and oxygen, likely chlorate or perchlorate, previously known only from high-latitude locations on Mars. This finding at Curiosity's equatorial site suggests more global distribution. The analysis also suggests the presence of carbonate materials, which form in the presence of water.

In addition to determining the amount of the major gases released, SAM also analyzed ratios of isotopes of hydrogen and carbon in the released water and carbon dioxide. Isotopes are variants of the same chemical element with different numbers of neutrons, and therefore different atomic weights. SAM found that the ratio of isotopes in the soil is similar to that found in the atmosphere analyzed earlier by Curiosity, indicating that the surface soil has interacted heavily with the atmosphere.

"The isotopic ratios, including hydrogen-to-deuterium ratios and carbon isotopes, tend to support the idea that as the dust is moving around the planet, it's reacting with some of the gases from the atmosphere," Leshin said.

SAM can also search for trace levels of organic compounds. Although several simple organic compounds were detected in the experiments at Rocknest, they aren't clearly martian in origin. Instead, it is likely that they formed during the heating experiments, as the non-organic compounds in Rocknest samples reacted with terrestrial organics already present in the SAM instrument background.

"We find that organics are not likely preserved in surface soils, which are exposed to harsh radiation and oxidants," said Leshin. "We didn't necessarily expect to find organic molecules in the surface fines, and this supports Curiosity's strategy of drilling into rocks to continue the search for organic compounds. Finding samples with a better chance of organic preservation is key."

The results shed light on the composition of the planet's surface, while offering direction for future research, said Leshin.

"Mars has kind of a global layer, a layer of surface soil that has been mixed and distributed by frequent dust storms. So a scoop of this stuff is basically a microscopic Mars rock collection," said Leshin. "If you mix many grains of it together, you probably have an accurate picture of typical martian crust. By learning about it in any one place, you're learning about the entire planet."

These results have implications for future Mars explorers. "We now know there should be abundant, easily accessible water on Mars," said Leshin. "When we send people, they could scoop up the soil anywhere on the surface, heat it just a bit, and obtain water."

In addition to her work research as part of the Mars Science Laboratory Team, Leshin is Dean of the School of Science at Rensselaer Polytechnic Institute, where she leads the scientific academic and research enterprise at the nation's first technological university.

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Rensselaer Researchers Propose New Theory To Explain Seeds of Life in Asteroids

September 30, 2013

A new look at the early solar system introduces an alternative to a long-taught, but largely discredited, theory that seeks to explain how biomolecules were once able to form inside of asteroids. In place of the outdated theory, researchers at Rensselaer Polytechnic Institute propose a new theory - based on a richer, more accurate image of magnetic fields and solar winds in the early solar system, and a mechanism known as multi-fluid magneto-hydrodynamics - to explain the ancient heating of the asteroid belt.

Although today the asteroid belt between Mars and Jupiter is cold and dry, scientists have long known that warm, wet conditions, suitable to formation of some biomolecules, the building blocks of life, once prevailed. Traces of bio-molecules found inside meteorites - which originated in the asteroid belt -could only have formed in the presence of warmth and moisture. One theory of the origin of life proposes that some of the biomolecules that formed on asteroids may have reached the surfaces of planets, and contributed to the origin of life as we know it.

"The early sun was actually dimmer than the sun today, so in terms of sunlight, the asteroid belt would have been even colder than it is now. And yet we know that some asteroids were heated to the temperature of liquid water, the ‘goldilocks zone,' which enabled some of these interesting biomolecules to form," said Wayne Roberge, a professor of physics within the School of Science at Rensselaer, and member of the New York Center for Astrobiology, who co-authored a paper on the subject with Ray Menzel, a graduate student in physics. "Here's the question: How could that have happened? How could that environment have existed inside an asteroid?"

In the paper, titled "Reexamination of Induction Heating of Primitive Bodies in Protoplanetary Disks" and published today in The Astrophysical Journal, Menzel and Roberge revisit and refute one of two theories proposed decades ago to explain how asteroids could have been heated in the early solar system. Both of the established theories - one involving the same radioactive process that heats the interior of Earth, and the other involving the interaction of plasma (super-heated gases that behave somewhat like fluids) and a magnetic field - are still taught to students of astrobiology. Although radioactive heating of asteroids was undoubtedly important, current models of radioactive heating make some predictions about temperatures in the asteroid belt that are inconsistent with observations.

Motivated by this, Roberge and Menzel reviewed the second of the two theories, which is based on an early assessment of the young sun and the premise that an object moving through a magnetic field will experience an electric field. According to this theory, as an asteroid moves through the magnetic field of the solar system, it will experience an electric field, which will in turn push electrical currents through the asteroid, heating the asteroid in the same way that electrical currents heat the wires in a toaster.

"It's a very clever idea, and the mechanism is viable, but the problem is that they made a subtle error in how it should be applied, and that's what we correct in this paper," said Roberge. "In our work, we correct the physics, and also apply it to a more modern understanding of the young solar system."

Menzel said the researchers have now definitively refuted the established theory.

"The mechanism requires some extreme assumptions about the young solar system," Menzel said. "They assumed some things about what the young sun was doing which are just not believed to be true today. For example, the young sun would have had to produce a powerful solar wind which blew past the asteroids, and that's just no longer believed to be true."

The solar wind, and the plasma stream it produced, was not as powerful as early theorists assumed, and the researchers have corrected those calculations based on the current understanding of the young sun. Roberge said the early theorists also incorrectly calculated the position of the electric field asteroids would have experienced. Roberge said that, in reality, an electric field would have permeated the asteroid and the space around it, a mistake very few researchers would have realized.

"We've calculated the electric field everywhere, including the interior of the asteroid," Roberge said. "How that electric field comes about is a very specialized thing; about 10 people in the world study that kind of physics. Fortunately, two of them are here at RPI working together."

What emerges, Menzel and Roberge said, is a new possibility, based on the corrected understanding of the electric fields the asteroids would have experienced, the solar wind and plasma conditions that would have prevailed, and a mechanism known as multi-fluid magneto-hydrodynamics.

Magneto-hydrodynamics is the study of how charged fluids - including plasmas - interact with magnetic fields. The magnetic fields can influence the motion of the charged fluid, or plasma, and vice versa. Magneto-hydrodynamics had a moment of fame as the propulsion system for an experimental nuclear submarine in the 1990 movie The Hunt for Red October.

Multi-fluid magneto-hydrodynamics are an even more specialized variation of the mechanism that apply in situations where the plasma is very weakly ionized, and the neutral particles behave distinctly from the charged particles.

"The neutral particles interact with the charged particles by friction," Menzel said. "So this creates a complex problem of treating the dynamics of the neutral gas and allowing for the presence of the small number of charged particles interacting with the magnetic field."

Menzel and Roberge said their new theory is promising, but it raises many questions that merit further exploration.

"We're just at the beginning of this. It would be wrong to assert that we've solved this problem," Roberge said. "What we've done is to introduce a new idea. But through observations and theoretical work, we know have a pretty good paradigm."

And much as Menzel and Roberge benefited from recent progress in understanding the physical conditions in an emerging planetary system, they hope their own work will advance the field of astrophysics.

"There are a lot of byproducts of this work because, in the course of doing this, we had to really zero in on how an asteroid interacts with the plasma of the young solar system," said Roberge. "There are a lot of physical processes that we had to consider that have not been considered in this context before."

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Rensselaer at Petascale: AMOS Among the World's Fastest and Most Powerful Supercomputers

October 3, 2013

Rensselaer Polytechnic Institute today unveiled a new petascale supercomputing system, the Advanced Multiprocessing Optimized System, or AMOS.

With the ability to perform more than one quadrillion calculations per second, AMOS is the most powerful university-based supercomputer in New York state and the Northeast, and among the most powerful in the world. In addition to massive computational power, AMOS has high-performance networking capabilities with a bandwidth of more than four terabytes per second-more than the combined bandwidth of 2 million home Internet subscribers.

This combination of speed and networking is unique among the world's university-based supercomputing systems, and will enable Rensselaer and its partners in academia and industry to better tackle highly complex, data-rich research challenges ranging from personalized health care, to smart grids, to economic modeling.

AMOS is a five-rack IBM Blue Gene/Q supercomputer with additional equipment, and represents the latest milestone in the decades-long close collaboration between IBM and Rensselaer. In January of this year, IBM provided a Watson cognitive computing system to Rensselaer, Watson at Rensselaer, making it the first university to receive such a system.

Both AMOS (a reference to Rensselaer co-founder Amos Eaton) and Watson (named for IBM founder Thomas J. Watson Sr.) are housed in the Rensselaer supercomputing center which has been renamed the Center for Computational Innovations (CCI). This combination of AMOS's balanced supercomputing power and Watson at Rensselaer's ability to understand the subtle nuances of human language and sift through vast amounts of data uniquely positions Rensselaer as a world leader in data-related research, innovation, and education.

"Amos Eaton would be very proud today of the school he helped to establish, as we celebrate with our partners at IBM the arrival of yet another key element in the unique computational ecosystem that is coalescing at Rensselaer Polytechnic Institute. This ecosystem is a combination of remarkable infrastructure, crucial partnerships, and towering talent that is allowing Rensselaer to lead the way in a new era of computation," said Rensselaer President Shirley Ann Jackson. "The combination of AMOS and Watson in the CCI will help Rensselaer further achieve the overarching goal we have set for ourselves as we approach the 200th anniversary of our founding with The Rensselaer Plan 2024: to be a transformative force with global impact."

"This new petascale system will enable Rensselaer researchers to easily explore and analyze massive amounts of data empowering discovery and creating new opportunities for breakthroughs," said John E. Kelly III, senior vice president and director of IBM Research, who was recently elected a member for the National Academy of Engineering for his extraordinary contributions to the United States semiconductor industry. "Together, Rensselaer and IBM are strengthening our commitment to leading at the critical intersection of Big Data, high performance computing, and the new era of cognitive systems."

"If every person in the world performed one simple mathematical calculation per second continuously without sleep or any breaks, it would take the whole of humanity nearly two days to compute what AMOS could do in a single second," said Christopher Carothers, director of CCI and a professor in the Department of Computer Science at Rensselaer. "It is such an exciting time to be at Rensselaer. By entering the petascale with AMOS, we are better positioned than ever before to change the world."

AMOS is a critical cornerstone of the Rensselaer Institute for Data Exploration and Applications-known as The Rensselaer IDEA-which serves as a hub for Rensselaer faculty, staff, and students engaged in data-driven discovery and innovation. The institute is anchored in the strength of Rensselaer in six primary areas: high performance computing, web science, data science, network science, cognitive computing, and immersive technologies.

Working across disciplines and sectors, The Rensselaer IDEA empowers students and researchers with new tools and technologies to access, aggregate, and analyze data from multiple sources and in multiple formats. Related projects and programs span the entire spectrum of high-impact global challenges and opportunities, including basic research, environment and energy, water resources, health care and biomedicine, business and finance, public policy, and national security.

The Rensselaer IDEA connects three of the university's critical research platforms: the CCI supercomputing center (AMOS and Watson at Rensselaer), the Curtis R. Priem Experimental Media and Performing Arts Center, and the Center for Biotechnology and Interdisciplinary Studies.

Rensselaer Polytechnic Institute, founded in 1824, is the nation's oldest technological research university. The university offers bachelor's, master's, and doctoral degrees in engineering, the sciences, information technology, architecture, management, and the humanities and social sciences. Institute programs serve undergraduates, graduate students, and working professionals around the world.

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