From sub-atomic to astronomical scales, we are working on the frontiers of science. A tradition of bridging boundaries has allowed us to probe fundamental questions at the intersections of different branches of science and mathematics and to create new fields of study. Because mathematics and the physical sciences are fundamental to many pursuits, including engineering, medicine and biology, we contribute to the education of most undergraduate students at UC San Diego.
An organization headed by UC San Diego physics professor Frank Würthwein recently received two HPCwire ‘Top Supercomputing Achievement’ awards for 2016, recognizing the use of high performance computing to verify Einstein’s theory of gravitational waves.
Würthwein, the current executive director of the Open Science Grid, worked in tandem with researchers to make these resources available to scientists working on the Laser Interferometer Gravitational-Wave Observatory over the course of several months to verify the statistical significance of the observed gravitational wave, thus leading to its unambiguous detection.
Würthwein is also the San Diego Supercomputer Center’s head of High Throughput Computing.
Funded by the U.S. Department of Energy and National Science Foundation, the Open Science Grid is a multi-disciplinary research partnership specializing in high throughput computational services.
The HPCwire awards were presented at the 2016 International Conference for High Performance Computing, Networking, Storage and Analysis (SC16), in Salt Lake City, Utah. The Open Science Grid won in both the online publication’s annual Readers’ Choice and Editors’ Choice categories. More information on the awards at: http://ucsdnews.ucsd.edu/pressrelease/sdsc_shares_hpcwires_top_supercomputing_achievement_awards1
Ruth Williams, a mathematician who analyzes math models associated with real-life problems, came to UC San Diego in 1983, attracted to the La Jolla campus by the strong science, engineering and mathematics faculty that she believed she could collaborate with to develop new theories and models in her field.
“I thought this was the place for me because I was, and am, still very motivated by applications,” said the professor of mathematics, who over the past three decades has developed fruitful collaborations with faculty on the campus in biology, cognitive science, electrical engineering and mechanical and aerospace engineering.
It was, in many ways, a prescient decision. As many academic disciplines have become more quantitative and data-driven, mathematical modeling and—especially her research on modeling “stochastic networks” to streamline the functioning of the congested Internet, sophisticated manufacturing systems and transportation networks running at capacity—has become an essential means by which researchers have been able to solve difficult problems.
UC San Diego News on the web at: http://ucsdnews.ucsd.edu
Graduate studies within any single scientific discipline are challenging endeavors on their own. But imagine combining graduate school-level training in physics and mathematics with advanced research in engineering and biology.
That’s the challenge of a new graduate program at UC San Diego that’s teaching Ph.D. students how to combine the power of physics and math-based reasoning with practical engineering skills and biology in an effort to unravel the fundamental principles of living systems—principles that will likely encompass concepts reaching well beyond those of traditional biology.
The goal of this ambitious program is to develop a new generation of scientists who are simultaneously fluent in biology, physics, mathematics and engineering. The program aims to train scientists who can not only develop instruments capable of quantifying the behaviors of living organisms but also develop and experimentally test their own theories based on these data. These young scientists are to be the foundation of an emerging discipline known as “quantitative biology”—or “qBio.”
Nine graduate students in the Division of Physical Sciences have been awarded fellowships provided to exceptional students pursuing research in the natural sciences, engineering and medicine from the San Diego chapter of the ARCS Foundation, Inc.
A national nonprofit organization led entirely by women, the ARCS Foundation is dedicated to boosting American leadership in science and technology by supporting promising undergraduate and graduate students. Since its inception in 1985, the San Diego chapter has awarded nearly $5 million to graduate students at UC San Diego.
The nine Division of Physical Sciences students were among 34 UC San Diego graduate students who this year received a total of $255,000 in fellowship awards from the ARCS Foundation.
They include five graduate students in the Department of Physics, three in the Department of Chemistry and Biochemistry and one in the Department of Mathematics.
The five physics graduate students are Frederick Matsuda, Emily Nardoni, David Leon and Aleksandra Shirman. The three chemistry graduate students are Michael Denny, Jr., Cassandra Callmann and Jessica Peters. The mathematics graduate student is Robert Snellman.
In addition to their financial awards, recognition as an ARCS Scholar gives students access to a network of talented researchers in academia and industry.
More information on this year’s fellowship awards to UC San Diego is available at: http://ucsdnews.ucsd.edu/pressrelease/arcs_foundation_awards_255000_in_fellowships_to_uc_san_diego_graduate_stude
Kim Prather has been named one of the “top 50 women in analytical science” by the Analytical Science magazine, which recently published its first ever all-women Power List, featuring “50 talented scientists who brilliantly represent the scope and impact of the analytical sciences.”
“As always, we don’t proclaim that our Power List is definitive – influence is subjective,” said Rich Whitworth, editor of the magazine. “But given its future-facing focus, we do hope it’s predictive.”
Prather, who holds the Distinguished Chair in Atmospheric Chemistry and is Director of the Center for Aerosol Impacts on Climate and the Environment, is a professor in the Department of Chemistry and Biochemistry and at Scripps Institution of Oceanography.
Nominations for the Analytical Scientist Power List were openly requested and reviewed by an expert judging panel consisting of well-respected scientists and the magazine’s editorial team to produce the final list of 50 women, which can be found online at https://theanalyticalscientist.com/power-list/2016/
Since it began publishing in 2013, the magazine has published two top 100 and a top 40 under 40 power list.
“Our Power Lists are intended to be a celebration of the whole analytical field – and our top 50 women list is no different in that respect; however, we do think it’s important for The Analytical Scientist to step up and highlight positive role models for young female scientists,” said Whitworth. “We also want to give the analytical community the opportunity to reflect on diversity and equality in general.”
As UC San Diego commemorated the groundbreaking of its new Biological and Physical Sciences Building this month, the campus also celebrated two gifts that will help shape the future of science, including $2 million in support from the Kavli Foundation and a legacy bequest from the Honorable Lynn A. Schenk.
The Biological and Physical Sciences Building is a much-needed facility constructed in response to the rapid growth of both the Division of Biological Sciences and the Division of Physical Sciences over the past 15 years. The new seven-story building, located near the Main Gym in the Revelle College area of campus, will provide 128,000 square feet of additional space for 20 research laboratories. Research inside the building will focus on brain activity mapping, advanced energy and drug discovery innovation.
Neal Devaraj, an associate professor of chemistry and biochemistry, has received $1.9 million from the National Institutes of Health to develop new imaging methods that will help the more than 1 million people in the United States living with type 1 diabetes, an autoimmune disease that destroys the insulin-secreting beta cells of the pancreas.
Molecular imaging tools are needed to monitor the progression of type 1 diabetes, the effectiveness of treatment and to track the viability of transplanted cells. Devaraj and his team of researchers will develop imaging methods to measure beta cell numbers in the pancreas.
Developing a tool that can measure cells that compromise one to two percent of the pancreas has been challenging, said Devaraj. Using existing positron emission tomography (PET) technology, he plans to capitalize on enzymes to amplify signals that sensitize beta cells for improved imaging. Before the onset of disease, this information could inform physicians if a patient is at risk of developing type 1 diabetes.
“This is a new and exciting direction for our lab,” said Devaraj. “The development of methods that amplify PET signals could lead to valuable imaging tools for monitoring beta cell mass. It could have an enormous impact on the diagnosis, treatment and understanding of type 1 diabetes. Moreover, the same concept might enable us to image very small targets like tumors when they may be invisible by other means. This method has potential to be more broadly applied to other diseases.”
Devaraj’s award is part of more than $5 million recently awarded by the NIH to UC San Diego researchers for type 1 diabetes research. More at: https://health.ucsd.edu/news/releases/Pages/2016-10-24-NIH-awards-type-1-diabetes-grants.aspx
Rommie Amaro, a professor of chemistry and biochemistry at UC San Diego, has won the 2016 Corwin Hansch Award, given by the Hansch-Fujita Foundation each year to a scholar under the age of 40 for significant contributions to the field of computer-aided drug design.
Amaro, who is the director of UC San Diego’s National Biomedical Computation Resource and a co-director of the Drug Design Data Resource, was presented with the award at the 2016 EuroQSAR meeting and the Gordon Research Conferences on Computer-Aided Drug Design in Verona, Italy.
The award, established in 2000, is named after the late honorary chair of the QSAR and Chemoinformatics Society and the pioneer of the interdisciplinary science of QSAR, Corwin Hansch.
Amaro received both her bachelor’s degree in chemical engineering and her PhD in chemistry at the University of Illinois at Urbana-Champaign. She was an assistant professor of pharmaceutical sciences, computer science and chemistry at UC Irvine for two years before being recruited to the faculty at UC San Diego in 2011.
Five physicists at the University of California San Diego have been named 2016 Fellows of the American Physical Society, a distinct honor of professional achievement from the nation’s largest society of physicists.
Richard Averitt, Jose Boedo, Brian Keating, Wouter-Jan Rappel and Massimo Vergassola were honored by the society this week for “exceptional contributions to the physics enterprise,” which can include “outstanding physics research, important applications of physics, leadership in or service to physics, or significant contributions to physics education.”
Surfers have a very intimate connection to the ocean. Their skin is bathed in the rushing tide, and crashing waves send salty seawater into their ears, eyes and throat. Inside and out, they are saturated with diverse molecules and bacteria to which the average person is not exposed. This prompts the question: How do these unique bacteria and chemicals impact human health? Cliff Kapono, UC San Diego chemistry doctoral student, is embarking on a worldwide quest to find out.
A native of the Big Island of Hawaii, Kapono is passionate about his heritage and promoting the well-being of people and our planet. As a scientist, he seeks to tap into the microscopic world of bacteria, fungi, viruses and other microbes. These microbiomes, or communities of microorganisms and their gene products, live in our bodies and on our skin and pervade much of the world around us. And scientists are just beginning to discover their impact on human and environmental health.
By Kim McDonald
Photo Credit: Denise Applewhite, Princeton U
F. Duncan Haldane, the Princeton University physicist who was awarded 2016 Nobel Prize in Physics this week for his research into the properties of matter in extreme states, was a professor of physics at UC San Diego from 1986 to 1992.
Haldane, who joined the Princeton faculty after he left the La Jolla campus, shared the Nobel Prize with David Thouless of the University of Washington and J. Michael Kosterlitz of Brown University “for theoretical discoveries of topological phase transitions and topological phases of matter.”
“They have used advanced mathematical methods to study unusual phases, or states, of matter, such as superconductors, superfluids or thin magnetic films,” the Royal Swedish Academy of Sciences said in announcing the award.
Haldane said in an interview publicized by Princeton University on the day he was informed of his Nobel Prize that “My work was a kind of sleeper. It was a very theoretical thing. ... It didn't become such a big deal until my work got extended” by other scientists.
On the nature of discovery, he added, “All these things are things that no one expects. You stumble over something and then you find the big picture after.”
Elizabeth Villa, a biophysicist who is an assistant professor of chemistry and biochemistry, received a $2.325 million New Innovator Award from the National Institutes of Health.
She was one of only 48 researchers nationwide this year to receive the prestigious award, which was established in 2007 and is designed to support unusually innovative research from early career investigators who are within 10 years of their final degree or clinical residency and have not yet received a research project grant or equivalent NIH grant.
Villa, who will use her award for her research project on “Opening Windows into the Cell: Revealing the Molecular Architecture of the Nuclear Periphery,” received her Ph.D. in Biophysics from the University of Illinois at Urbana-Champaign working with Klaus Schulten on multiscale simulations of biomolecular complexes, where she worked closely with Joachim Frank developing computational tools for cryo-electron microscopy.
She was a Marie Curie postdoctoral fellow in the lab of Wolfgang Baumeister at the Max Planck Institute of Biochemistry in Munich. Her lab develops tools to observe macromolecular complexes in their natural environment, the cell. Her goal is to transform cryo-electron tomography into a high-resolution technique to unveil the structural dynamics of these complexes that is directly compatible with other biophysics experiments. She combines cell biology and cryo-electron microscopy to generate data, and use computational analysis and physical modeling to understand these data. Her current research is focused on studying the nuclear periphery, one of the most exciting and structurally uncharted territories in the cell.
San Diego Magazine's Celebrating Women event honored dynamic San Diego women committed to creating positive change with power networking, a compelling panel discussion, and the announcement of special award winners at the Museum of Contemporary Art La Jolla on September 28.
Star Hughes-Gorup, Director of Hughes Marino, received the Young Leader Award. Randa Coniglio, CEO and President of Port of San Diego, was recognized with the Executive Trailblazer Award. Dr. Mimi Guarneri , Medical Director of Guarneri Integrative Health, Inc., was named the Health and Wellness Pioneer. Celia Lanning, Greater San Diego Region President of Wells Fargo, earned the Mentoring Maverick Award. Kim Perell, President of Amobee, took home the Industry Innovator Award. Barbara Sawrey, Associate Vice Chancellor and Dean of Undergraduate Education of University of California San Diego, was heralded as Academic Champion.
The awards presentation culminated with the announcement of the 2016 Woman of the Year. This honor went to Diana Kelly, Regional Vice President of The Home Depot. Congratulations to all 120 finalists!
This coupling between electrons and phonons determines how efficiently solar cells convert sunlight into electricity. It also plays key roles in superconductors that transfer electricity without losses, topological insulators that conduct electricity only on their surfaces, materials that drastically change their electrical resistance when exposed to a magnetic field, and more.
At the Department of Energy’s SLAC National Accelerator Laboratory, scientists can study these coupled motions in unprecedented detail with the world’s most powerful X-ray laser, the Linac Coherent Light Source (LCLS). LCLS is a DOE Office of Science User Facility.
Using a unique computational approach to rapidly sample, in millisecond time intervals, proteins in their natural state of gyrating, bobbing, and weaving, a research team from UC San Diego and Monash University in Australia has identified promising drug leads that may selectively combat heart disease, from arrhythmias to cardiac failure.
Reported in the September 5, 2016 Proceedings of the National Academy of Sciences (PNAS) Early Edition, the researchers used the computing power of Gordon andComet, based at the San Diego Supercomputer Center (SDSC) at UC San Diego; and Stampede, at the Texas Advanced Computing Center at the University of Texas at Austin, to perform an unprecedented survey of protein structures using accelerated molecular dynamics or aMD – a method that performs a more complete sampling of the myriad shapes and conformations that a target protein molecule may go through.
Biochemists at the University of California San Diego have uncovered patterns in the outer protein coat of group AStreptococcus that could finally lead to a vaccine against this highly infectious bacteria—responsible for more than 500,000 deaths a year, including toxic shock syndrome and necrotizing fasciitis or “flesh-eating disease.”
In a paper published in this week’s issue of Nature Microbiology, the researchers report that they had uncovered “hidden sequence patterns in the major surface protein and virulence factor” of group A Strep, called the M protein, that limit the body’s immune response against these bacteria.
J. Andrew McCammon, a distinguished professor of chemistry, biochemistry and pharmacology at the University of California San Diego, has won this year’s most prestigious university-based prize in theoretical chemistry.
McCammon, who holds the Joseph E. Mayer Chair of Theoretical Chemistry at UC San Diego, was today named the winner of the 2016-17 Joseph O. Hirschfelder Prize in Theoretical Chemistry, awarded by the Theoretical Chemistry Institute at the University of Wisconsin-Madison.
A chemistry professor at the University of California San Diego has won two prestigious national prizes awarded by the American Chemical Society.
Neal Devaraj, an associate professor of chemistry and biochemistry, is the recipient of the 2017 ACS Award in Pure Chemistry, which recognizes outstanding fundamental research in pure chemistry carried out in North America by chemists early in their careers, and the 2016 National Fresenius Award, which annually recognizes “an outstanding young scientist who has attained national recognition in the areas of research, teaching and/or administration.”
Mark Thiemens, a former dean and professor of chemistry and biochemistry at UC San Diego, has won the most prestigious prize awarded in the field of meteoritics —the scientific discipline concerned with the study of solar system origin, evolution and history.
Migratory birds often use warm, rising atmospheric currents to gain height with little energy expenditure when flying over long distances.
It’s a behavior known as thermal soaring that requires complex decision-making within the turbulent environment of a rising column of warm air from the sun baked surface of the earth. But exactly how birds navigate within this ever-changing environment to optimize their thermal soaring was unknown until a team of physicists and biologists at the University of California San Diego took an exacting computational look at the problem.
Biochemists at the University of California San Diego have developed artificial cell membranes that grow and remodel themselves in a manner similar to that of living mammalian cells.
The achievement, detailed in a paper published in this week’s issue of the Proceedings of the National Academy of Sciences, follows the successful design last year in the same laboratory of artificial, or synthetic, cell membranes capable of sustaining continual growth. The two developments now bring the researchers closer to mimicking all of the properties of living mammalian cell membranes with synthetic components.
Mathematics Professor James McKernan has been named by the Simons Foundation as a Simons Investigator, an honor that will provide him with an award of $100,000 per year in research support over the next five years.
In announcing his selection as a 2016 Simons Investigator, the foundation said that “McKernan, in collaboration with Caucher Birkar, Paolo Cascini, and Christopher D. Hacon, has established one of the cornerstones of the Minimal Model Program: the finite generation of canonical rings in all dimensions.”
McKernan, who received his doctorate in mathematics from Harvard University in 1991, was a professor at UC Santa Barbara and MIT before coming to UC San Diego and currently holds the Charles Lee Powell Endowed Chair in Mathematics.
His research is focused on birational geometry and his work has been recognized by professional organizations with numerous awards: the Clay Research Award in 2007 and the Cole Prize in Algebra in 2009. In 2011, he was elected to the Royal Society in the UK. He was also honored by being invited to and delivering a lecture at the International Congress of Mathematicians in Hyderabad in 2010.
A team of physicists that visualized the internal nanostructure of an intact butterfly wing has discovered two physical attributes that make those structures so bright and colorful.
“Over millions of years, butterflies have evolved sophisticated cellular mechanisms to grow brightly colored structures, normally for the purpose of camouflage as well as mating,” says Oleg Shpyrko, an associate professor of physics at UC San Diego, who headed the research effort. “It’s been known for a century that the wings of these beautiful creatures contain what are called photonic crystals, which can reflect light of only a particular color.”
Scientists at UC San Diego, MIT and Harvard University have engineered “topological plexcitons,” energy-carrying particles that could help make possible the design of new kinds of solar cells and miniaturized optical circuitry.
The researchers report their advance in an article published in the current issue of Nature Communications.
Within the Lilliputian world of solid state physics, light and matter interact in strange ways, exchanging energy back and forth between them.
“When light and matter interact, they exchange energy,” explained Joel Yuen-Zhou, an assistant professor of chemistry and biochemistry at UC San Diego and the first author of the paper. “Energy can flow back and forth between light in a metal (so called plasmon) and light in a molecule (so called exciton). When this exchange is much faster than their respective decay rates, their individual identities are lost, and it is more accurate to think about them as hybrid particles; excitons and plasmons marry to form plexcitons.”
Tehseen Lazzouni, Recharge Analyst in the Chemistry and Biochemistry Business Office, has been selected as a recipient of the 2016 Exemplary Staff Employee of the Year Award. This annual campus award recognizes professional and support staff from across all Vice Chancellor and Health System areas, who have demonstrated exemplary service and made other significant contributions to the UC San Diego and San Diego communities.
Since joining the Department of Chemistry and Biochemistry in 2015, Tehseen has been committed to excellence through her attention to detail, unsurpassed customer service skills, keen problem solving, collaborative spirit, integrity and creativity. She has gained a mastery of the recharge facility operations despite often dealing with ambiguous information and conflicting priorities. Her optimistic attitude is infectious and often serves as a catalyst for improved relationships with many stakeholders, both internal and external.
In addition to her work in Chem/Biochem Tehseen is being honored for her previous work with the NASA California Space Grant Consortium. There she worked creatively and tirelessly to improve the consortium by reaching out to groups to promote diversity in Science, Technology, Engineering and Math (STEM). Some examples of her work included working with MESA directors at over a dozen state-wide community colleges to improve their STEM programs. In an effort to promote gender diversity in STEM at UCSD, Tehseen presented California Space Grant projects and opportunities to the UCSD chapter of the Society of Women Engineers (SWE) and developed two scholarship programs for them. Together these programs have provided 23 scholarships.
We are extremely fortunate and honored to have Tehseen as a member of our team in the Department of Chemistry and Biochemistry and Division of Physical Sciences!
Kimberly Prather, distinguished chair in atmospheric chemistry at the University of California San Diego, will receive the Haagen-Smit Clean Air Award from the California Air Resources Board May 18. The awards have since their inception in 2001 recognized individuals for career accomplishments in improving air quality in a number of categories.
Board officials said they bestowed the award upon Prather in its Atmospheric Chemistry Research category to acknowledge her “pioneering work that has transformed our understanding of atmospheric aerosols and their impacts on atmospheric chemistry, climate, and the hydrologic cycle.”
In an effort to probe the first few moments of time after the Big Bang some 13.8 billion years ago, a consortium of researchers, including astrophysicists from the University of California San Diego, is planning a new observatory in Chile’s Atacama Desert to measure the cosmic microwave background, or CMB.
The $40 million initiative, known as the Simons Observatory, was announced on Thursday and is being funded by grants from the Simons Foundation and the Heising-Simons Foundation.
An international group of mathematicians at UC San Diego and other institutions has produced a new kind of online resource to help discover uncharted mathematical worlds.
The “L-functions and Modular Forms Database,” or LMFDB, is an intricate catalog of mathematical objects and the connections between them. Both beautiful and functional like an atlas, the LMFDB reveals deep relationships in the abstract universe of mathematics. This coordinated effort is part of a massive collaboration of researchers around the globe, and includes developing new algorithms and performing large calculations on an extensive network of computers.
Neal Devaraj named Camille Dreyfus Teacher-Scholar
Neal Devaraj, an assistant professor of chemistry and biochemistry, has been named a Camille Dreyfus Teacher-Scholar by the Camille and Henry Dreyfus Foundation, one of 13 faculty members nationwide to receive the honor.
Criteria for selection include an independent body of scholarship attained in the early years of a faculty member’s appointment, and a demonstrated commitment to education, signaling the promise of continuing outstanding contributions to both research and teaching.
The award provides an unrestricted research grant of $75,000. Devaraj will receive his award for his research project “Site-Specific Covalent Tagging of RNA for Live Cell Imaging and Affinity Purification.” He is the sixth faculty member at UC San Diego to receive the prestigious award.
The foundation said the 13 faculty members receiving awards this year “are within the first five years of their academic careers, have each created an outstanding independent body of scholarship, and are deeply committed to education.”
“The Camille Dreyfus Teacher-Scholar Award is the Dreyfus Foundation’s flagship program,” said Mark Cardillo, executive director of The Camille and Henry Dreyfus Foundation. “The award supports exceptional young academic researchers at an early and crucial stage of their careers. They are selected based on their independent contributions to both research in the chemical sciences and education.”
Since its inception in 1970, the Teacher-Scholar program has awarded over $45 million to support emerging young leaders in the chemical sciences.
The Camille and Henry Dreyfus Foundation is a leading non-profit organization devoted to the advancement of the chemical sciences. It was established in 1946 by chemist, inventor and businessman Camille Dreyfus in honor of his brother Henry. The Foundation's purpose is “to advance the science of chemistry, chemical engineering and related sciences as a means of improving human relations and circumstances around the world.” More information on the foundation and award is at: http://www.dreyfus.org
Guy Bertrand, a distinguished professor of chemistry and biochemistry at UC San Diego, has been named this year’s winner of the Royal Society of Chemistry’s Sir Geoffrey Wilkinson Award.
Bertrand received the award for “for his discovery of stable carbenes and their applications in organometallic synthesis and catalysis.”
Bertrand studied chemistry at the National School of Chemistry in Montpellier and received his PhD from the University Paul Sabatier in Toulouse. After being a CNRS group leader (French National Center for Scientific Research) at the University of Toulouse, and then at the Laboratoire de Chimie de Coordination du CNRS, he served as director of the Laboratoire d'Hétérochimie Fondamentale et Appliquée at the University Paul Sabatier from 1998 to 2005.
From 2001 to 2012 he also was director of the UCR/CNRS Joint Research Chemistry Laboratory that he created and since arriving on the La Jolla campus in 2012, he has been the director of UCSD/CNRS Joint Research Chemistry Laboratory.
Bertrand is a member of the French Academy of Technology (2000), the Academia Europaea (2002), the European Academy of Sciences (2003), the French Academy of Sciences (2004) and is a Fellow of the American Association for Advancement of Sciences (2006). He has recently received the Sir Ronald Nyholm Medal of the RSC (2009), the Grand Prix Le Bel of the French Chemical Society (2010) and the American Chemical Society Award in Inorganic Chemistry (2014).
He is one of the associate editors of Chemical Reviews and serves as a member of the editorial board of several professional journals, including the Royal Society’s Chemical Science and Organic Chemistry Frontiers.