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CMNS e-News November 2011

Vol. 2, No. 2
Please submit items to the editor, Mary Kearney.



Tony Busalacchi (AOSC and ESSIC) has been appointed Chair of the new UMD Council on the Environment, which will operate as an advisory group on research, education, outreach and economic development related to the environment. As chair, Busalacchi will coordinate and oversee strategic efforts to place the University of Maryland at the forefront of environmental and earth system science. Busalacchi will help promote the unique strengths that distinguish UMD from its peers, and develop new partnerships with federal and state government agencies and laboratories, corporations and academic institutions.

Michael Hicks (Computer Science and UMIACS) has been named director of UMD’s Cybersecurity Center (MC2). Hicks' research focuses primarily on developing and evaluating techniques to improve software reliability and security. MC2 was created last year to provide an interdisciplinary, comprehensive approach to educating a new generation of cyber leaders and developing advanced cyber policy and technology. The Center aims to partner with government and industry on advanced research and educational initiatives.

The Department of Physics is holding a Memorial for John S. Toll on Tuesday, December 13, at 4:00 p.m. Toll was the former Chair of the Department, President of the University of Maryland College Park, and the first Chancellor of the University System of Maryland. The Memorial will take place in Room 1410 Physics Building, with refreshments being served prior to the event.  The department would welcome anecdotes and memories of Dr. Toll, so please feel free to send your recollections to or Joe Sucher ( Toll, who passed away on July 15, 2011, was a gifted physicist, a dedicated and highly effective higher education leader and an exemplary public servant.

Book Talk: Image Registration for Remote Sensing
Thursday, December 15, 2011
Reception at 4:30 p.m. in the Lobby of the Computer Science Instructional Center
Talk at 5:00 p.m. in Room 1121
Alumni Roger D. Eastman (1984 M.S. and 1990 Ph.D. Computer Science, advisor Larry Davis) and Nathan S. Netanyahu (1989 M.S. and 1992 Ph.D. Computer Science, advisors David Mount and Azriel Rosenfeld) with Jacqueline Le Moigne, are editors of the book which addresses the main issues involved in the registration of multiple remotely sensed images, a very important and topical subject because of the current availability of data from many heterogeneous satellite sensors.

Honors and Awards

Two faculty members have been elected 2011 Fellows of the Institute of Electrical and Electronics Engineers (IEEE):

  • Thomas Antonsen (Physics and IREAP) for contributions to the theory of magnetically confined plasmas, laser-plasma interactions and high power coherent radiation sources.
  • Ben Shneiderman (Computer Science and UMIACS) for contributions to human-computer interaction and information visualization.

Ben Bederson (Computer Science and UMIACS) has been recognized as a Distinguished Scientist by the Association for Computing Machinery (ACM) for his significant accomplishments in Human-Computer Interaction (HCI) and his impact on the field of computing.

James Gates (Physics) has been elected a Fellow of the Institute of Physics (UK). The Institute works to advance physics research, application and education; and engages with policy makers and the public to develop awareness and understanding of physics. Its publishing company, IOP Publishing, is a world leader in professional scientific communications.

Mohammad Hajiaghayi (Computer Science and UMIACS) has been selected as an Office of Naval Research (ONR) Young Investigator. The program is designed to attract young scientists and engineers who show exceptional promise for outstanding research and teaching careers. Out of a group of 270 applicants, Hajiaghayi was one of 21 investigators selected because of his ".... academic achievements [and] his ability to contribute to the strength of the Nation's research and development."

Roberta Rudnick (Geology) has been elected a Foreign Member of the Chinese Academy of Sciences (CAS). Founded in Beijing on November 1, 1949, the Academy is a leading academic institution and comprehensive research and development center in natural science, technological science and high-tech innovation in China.


Catherine Fenselau (Chemistry and Biochemistry) with Bettina Warscheid (University of Freiberg), "Analyzing and Distinguishing Organisms Such as Bacterial Spores by their Soluble Polypeptides."


Mohammad Hajiaghayi (Computer Science and UMIACS), Cambridge-MIT Institute, $105,000, "Frameworks for Efficient Algorithms in Planar Networks and Beyond."

Xin-Zhong Liang (AOSC and ESSIC), EPA, $259,778, "Impacts of Global Climate and Emissions Changes on U.S. Air Quality (Ozone, Particulate Matter, Mercury) and Projection Uncertainty."

Xin-Zhong Liang (AOSC and ESSIC), University of Illinois-Urbana Champaign, $118,316, "Linking Regional Aerosol Emission Changes with Multiple Impact Measures through Direct and Cloud-related Forcing Estimates."

Arpita Upadhyaya (Physics and IPST), NSF, $150,235, "Collaborative Research: Regulation of Cellular Mechanics by Crosslinked Actin Networks - Role of Palladin and Alpha-actinin."

Wade Winkler (Cell Biology & Molecular Genetics), NSF, $181,084, "Investigation of Antitermination in Firmicutes."

What's New

The UMD-NCI Partnership for Cancer Technology workshop was held on November 10, at the National Institutes of Health, Bethesda, Maryland.  The workshop’s goal was to foster interactions between NCI and UMD in biophysics, systems biology, bioengineering, and bioinformatics, and to highlight results from ongoing collaborative projects.  Participating CMNS faculty included Wael Abd-Almageed (UMIACS), Hector Corrada Bravo (Computer Science), Larry Davis (Computer Science and UMIACS), David Fushman (Chemistry & Biochemistry), Michelle Girvan (Physics, IPST & IREAP), Anthony Jose (Cell Biology & Molecular Genetics) Ed Ott (Physics & IREAP) and Arpita Upadhyaya (Physics and IPST).

The Department of Physics held their annual PALS Yard and Bake Sale on November 9, raising over $1,000.00.  This year, PALS donated the monies raised to the PALS Scholarship for Physics Undergraduate Students.  For more information, please contact Tom Gleason, Assistant Director, Undergraduate Office.

The Center for Bioinformatics & Computational Biology (CBCB) has just released version 1.2.0 of the transcript assembly software Cufflinks, a collaborative effort between the Laboratory for Mathematical Computational Biology (Lior Pachter, UC Berkeley), Caltech (Barbara Wold’s Lab) and CBCB.  Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.  It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts.  Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols. 

Dennis Bodewits and Stefan Immler (Astronomy) were part of a team studying Asteroid 2005 YU55 during its recent close approach to Earth using NASA's Swift satellite. The Swift team studied the asteroid's ultraviolet light to learn more about its surface composition;  the results may improve our ability to predict the asteroid's future orbit.

James Gates (Physics) will give a public lecture about the frontiers of physics at Montana State University’s Museum of the Rockies, December 8.  Gates also was an invited speaker at the Annual Biomedical Research Conference for Minority Students, St. Louis, MO on November 11, with a presentation entitled “Is Our Reality in The Matrix.”

Jonathan Dinman (Chemistry and Biochemistry) served as a judge for the Siemens Competition in Math, Science and Technology for High School Students, held at Princeton University on October 14-18.  The judges reviewed and ranked approximately 200 applications in the Biochemistry group from all over the US, identifying the top 3 individuals and teams from each region.  Subsequently, and after meeting with counterparts in other disciplines, the judges picked the top 5 individuals and teams overall (e.g. biochemistry, biology, mathematics, physics, astronomy, chemistry, geology, etc) for each region.  The National Finals will be held at George Washington University on December 1-5.

William Goldman (Mathematics) is the Distinguished Lecturer, Texas A&M, Department of Mathematics, December 5-7.  Goldman will present three lectures, with his last lecture entitled “Classification of Margulis Spacetimes.”  Goldman is also co-organizing a special trimester, Geometry and Analysis of Surface Group Representations, at the Institut Henri Poincare, Paris, France, January-March 2012.

Lyle Isaacs' group (Chemistry and Biochemistry), in collaboration with Professor Volker Briken's group (Department of Cell Biology and Molecular Genetics), won the Professor Venture Fair for best invention for their creation of "Molecular Containers that Solubilize and Deliver Insoluble Pharmaceutical Agents." Dr. Isaacs' invention was chosen as the top from the six inventions selected by the University's Office of Technology Commercialization to compete in this year's Bioscience Day: Next Generation Research in Infectious Diseases.

Arthur Popper (Biology) has recently published several books. The “Effects of Noise on Aquatic Life”A. N. Popper and A. Hawkins, eds, Springer Science & Business Media, Inc is the extended proceedings from a meeting organized by the editors in Cork, Ireland, in 2010.  In addition, Popper and colleagues have several new books in his Springer Handbook of Auditory Research Series:  “Noise-Induced Hearing Loss: Scientific Advances,” Le Prell, C. G., Henderson, D., Fay, R. R., and Popper, A. N. (eds). (2012), “Synaptic Mechanisms in the Auditory System,” Trussell, L. O., Popper, A. N., and Fay, R. R. (eds). (2012) and “Auditory Prostheses: New Horizons,” Zeng, F.-G., Popper, A. N., and Fay, R. R. (eds). (2011).

Scott Wolpert (Mathematics) was an invited speaker at the Hyperbolic and Riemannian Geometry of Surfaces and Other Manifolds conference, held in Ascona, Switzerland, October 31-November 4. 

In The News

John Weeks (Chemistry and Biochemistry and IPST) was co-editor and also co-authored, with Graduate Student Richard Remsing (Chemistry and Biochemistry, Chemical Physics) and Jocelyn Rodgers (2008 Ph.D. Chemical Physics, advisor John Weeks), one of the articles in a special issue of the Journal of Statistical Physics on water and associated liquids.  The article, on deconstructing classical water models at interfaces and in bulk, focused on the anomalous behavior of the internal pressure and the temperature dependence of the density of bulk water. 

Mikhail Anisimov (IPST and Chemical & Biomolecular Engineering) published a Letter to the Editor in the International Journal of Thermophysics, [DOI 10.1007/s10765-011-1073-0], August 2011 on the occasion of Jan Sengers 80th birthday.  The letter discussed the 1961 breakthrough experiments, conducted by Sengers and Alexander Voronel, which challenged commonly accepted views on critical phenomena in fluids.

Volker Briken and David M. Mosser (Cell Biology & Molecular Genetics and MPRI) published an editorial in the Journal of Leukocyte Biology, November issue, on research conducted by Claire Whyte et al. on the suppressor of cytokine signaling (SOCS) 1 being a key determinant of differential macrophage activation and function.

Jonathan Dinman (Cell Biology and Molecular Genetics) led an interdisciplinary team from UMD, the University of California San Francisco, and the University of Alabama Birmingham, focusing on the role of ribosomal RNA (rRNA) pseudouridylation.  How this most common and evolutionarily conserved modification of rRNA regulates ribosome activity is poorly understood.  Medically, it is important because the rRNA synthase, DKC1, is mutated in X-linked dyskeratosis congenita (X-DC) and Hoyeraal-Hreidarsson (HH) syndrome.  Their findings, published in the November 18 issue of Molecular Cell, uncover specific roles for rRNA pseudouridylation in ribosome-ligand interactions that are conserved in yeast, mouse, and humans.

Tom Holtz (Geology) appeared on a Brazilian science news show, Espaco Aberto Ciencia e Tecnologia (Open Space for Science and Technology), Globo News, in an episode on the collaboration between scientists and artists in creating accurate representations of dinosaurs. Holtz’ section begins at 13:00 and can be viewed at

James Gates (Physics) was interviewed by the Washington Post, November 7 about the PBS documentary “The Fabric of the Cosmos,” in which he appeared.   The documentary, a miniseries about space, time and the multiverse, premiered on November 2nd.

Zhanqing Li (AOSC and ESSIC), with co-authors Feng Niu, Yanni Ding (both Graduate Students, AOSC), Jiwen Fan (Pacific Northwest National Laboratory), Yangang Liu (Brookhaven National laboratory) and Daniel Rosenfeld (The Hebrew University of Jerusalem), published an article in Nature-Geoscience, November 13 showing that increases in air pollution and other particulate matter in the atmosphere can strongly affect cloud development in ways that reduce precipitation in dry regions or seasons, while increasing, rain, snowfall and the intensity of severe storms in wet regions or seasons.  The study is the first systematic assessment of aerosol’s climate affect using long-term and global data.  Media coverage included ScienceNews, Discovery News, RedOrbit, Daily News and analysis, International Business Times, MSN-India, ScienceDaily and the Pakistan Observer.

Research conducted by Karen Lips (Biology) was mentioned in MongoBay, November 9, in an article on amphibian die-offs in Mexico and Central America due to Batrachyochytrium dendrobatidis (bd). 

Bill McDonough (Geology) gave a radio interview on defining and explaining the nature and use of electron anti-neutrinos as well as the research being conducted worldwide on neutrinos/anti-neutrinos for Marfa Public Radio’s Talk At Ten program, November 22.

Roald Sagdeev (Physics and IPST) was interviewed for a Nature article, November 4, on the November 8 launch of the Russian probe, Phobus-Grunt.  On November 17, he was again interviewed by Nature on the probe’s failure.

Ben Shneiderman (Computer Science and UMIACS) published a Feature Special Topic in ACM Interactions, November/December issue, on improving electronic health records (EHR) user-interface designs that offer healthcare providers shorter learning times, faster performance and lower interface error rates.

Dan Stein (Cell Biology and Molecular Genetics) and Phil DeShong (Chemistry and Biochemistry) appeared on the History Channel’s program “Modern Marvels” on November 7.  They performed biochemical and microbiological analysis of lint found in pockets in the episode "Is That a ... in Your Pocket?"

Kai Sun (JQI) and Sankar Das Sarma (Physics and JQI), with colleagues W. Vincent Liu (University of Pittsburgh) and Andreas Hemmerich (University of Hamburg) published a letter in Nature Physics [DOI: 10.1038/NPHYS2134], online edition, showing that an optical lattice system exhibits a never-before-seen quantum state called a topological semimetal.  The semimetal can undergo a new type of phase transition to a topological insulator.

Dave Thirumalai (Chemistry and Biochemistry and IPST), with S. Vaitheeswaran (IPST) and Jie Chen (IPST) also published an article in the special issue of the Journal of Statistical Physics on water and associated liquids, on hydrophobic and ionic-interactions in bulk and confined water with implications for collapse and folding of proteins.  They demonstrated that, using simulations in explicit water, that ordered states of generic amphiphilic peptide sequences should be stabilized in cylindrical nanopores.

Kaci Thompson (Dean’s Office) was quoted in Chemical and Engineering News, November 21, in an article on NEXUS (National Experiment in Undergraduate Science Education).  NEXUS,  focuses on the interfaces between biology and the other sciences, with CMNS focusing on physics and piloting a revamped physics class tailored to premed students.

Alumni News

Sergey Brin (1993 B.S. Computer Science and Mathematics) was quoted in the New York Times, November 13, in an article on Google's top secret lab, Google X.

Judy Che-Casaldo (2011 Ph.D. Behavioral, Ecology, Evolution, and Systematics) with advisor David Inouye (Biology), published, an article in Ecosphere, the new online-only open-access journal of the Ecological Society of America. Using a 35-year dataset from an ongoing study, they described the population dynamics of Frasera speciosa (Gentianaceae), a long-lived monocarpic plant, using matrix projection models, addressed how many years of data are needed to estimate population growth and elasticity values consistently, and examined the effects of mast seeding on demographic parameter estimates. Their results indicated that the demography of F. speciosa is similar to that of other long-lived monocarps without mast seeding, that long datasets may be needed to capture the variation in demographic rates even for stable populations, and that life history stages with low elasticity values can still be very important to population growth. This work was supported by an NSF grant, Drivers and consequences of phenological change at high altitudes, for long-term research

Chul 'Eddy' Chung (1999 Ph.D. Meteorology, advisor Sumant Nigam) with colleagues published an article in Nature, November 2 on their research, reporting an increase in the intensity of pre-monsoon Arabian Sea tropical cyclones (1979-2010), and showing that this change in storm strength is a consequence of a simultaneous upward trend in black carbon and sulphate emissions.

David Horowitz (2006 B.S. Computer Science and Economics) recently launched a new startup called, which, with one click, searches for movies and TV shows on Netflix, iTunes, Amazon, Redbox, Hulu, Comcast XFINITY, and more. Horowitz started Watchily in response to Netflix' recent price increases, after realizing that frustrated subscribers would be looking for alternative sources of movies and TV shows. He is also a software developer at The World Bank responsible for the iSimulate collaborative economic simulation platform.

Richard Kreminski (1990 M.A. and 1994 Ph.D. Applied Mathematics, advisor Paul Green), previously Dean of the College of Science and Mathematics, Colorado State University-Pueblo, Pueblo CO has been named interim provost at the university. The co-author of "Applied Abstract Algebra," with W. David Joyner (1983 Ph.D. Mathematics, advisor John Benedetto) and JoAnn Turisco, Kreminski earned a Juris Doctorate from the Dedman School of Law, Southern Methodist University, in 2008.

Jennifer Mattei (1982 B.S. Zoology), has been named the director of the Professional Science Master's Program in Environmental Systems Analysis and Management at Sacred Heart University, Fairfield, CT. Mattei earned her doctorate at SUNY-Stony Brook, and her Master of Forest Science degree at Yale University.

Mike Mayo (1985 B.S. Computer Science), a bank-stock analyst for Credit Agricole Securities USA, published his memoir, Exile on Wall Street: One Analyst's Fight to Save the Big Banks from Themselves on November 15. Media coverage included, but is not limited to, MarketWatch, Bloomberg Television's Surveillance Midday, MoneyIndex, Motley Fool, Istockanalyst, WorldNews, The Ledger and The News Tribune.

Kshemendra Paul (1984 B.S. Mathematics and Engineering and 1987 M.S. Electrical Engineering) is the Program Manager for the Information Sharing Environment (ISE), having government-wide authority to plan, oversee the build-out, and manage use of the ISE. The Program Manager also co-chairs the White House's Information Sharing and Access Inter-agency Policy Committee (ISA-IPC). Prior to his appointment by President Obama, Paul served as the Federal Chief Architect in the Office of management and Budget where he led Federal enterprise architecture activities and chaired committees responsible for leading initiatives.

D.J. Patil (1999 M.A., 2001 Ph.D. Applied Mathematics, advisor James Yorke) was interviewed on NPR's Morning Edition, November 30 on the demand by businesses for mathematicians and the resultant recruiting wars. Patil, previously the Chief Scientist at LinkedIn, is the Data Scientist in Residence, Greylock Partners, Menlo Park, CA.

Sriram Ramaswamy (1977 B.S. Physics) was the subject of an article in The Hindu, November 21. Ramaswamy, the winner of the Infosys prize 2011, is a professor of Physics, Centre for Condensed Matter Theory, Indian Institute of Science, Bangalore. Presently he is working on what governs the movement of small organisms like bacteria or large schools of fish in the medium in which they live.

Roberto Vilarrubi (1994 Ph.D. Mathematics, advisor Mark Freidlin) was interviewed by the Montgomery County Gazette, November 30, on using visual images to connect with students. Vilarrubi is a math teacher at the Barrie School, Silver Spring, MD.

David Wheeler (1972 B.S. Zoology) is the Director of Cancer Genomics and Assistant Director of the Human Genome Sequencing Center at Baylor College of Medicine, Houston, TX. He leads the development of methods for discovery of genome variation in human and animal populations using DNA sequencing technologies with the goal of relating polymorphism to human disease. Wheeler received his Ph.D. in Molecular Genetics from the George Washington University and conducted postdoctoral research in behavioral genetics at Brandeis University.