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From sub-atomic to astronomical scales, we are working on the frontiers of science. Founded by Nobel laureates and members of the National Academy of Sciences, our departments have all played a central role in UC San Diego’s rapid rise to national and international prominence.

A tradition of bridging boundaries long before interdisciplinary research became fashionable has allowed us to probe fundamental questions at the intersections 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.

News from the Physical Sciences

Rommie Amaro$9M for biomedical computation

UC San Diego's National Biomedical Computation Resource has received $9 million in funding from the National Institutes of Health to continue its work connecting biomedical scientists with supercomputing power and emerging information technologies. 

As scientists, we are very good at looking at particular components of the human body within a single scale, but we ultimately need to connect across three or four scales in order to model and understand complex biological phenomena from the molecular level all the way up to the whole organ,” says director Rommie Amaro, associate professor of chemisty and biochemistry. 

Amaro cites the example of cross-disciplinary work of Michael Holst in mathematics, Mark Ellisman in neurosciences, Andrew McCammon in chemistry and Andrew McCulloch in bioengineering, as well as visualization specialists at The Scripps Research Institute who are collaborating to develop new technologies that will help scientists understand the causes of heart failure. 

The team develops models of patients' hearts to analyze what happens at the organ level when a heartbeat becomes irregular. These models are connected to images of the macroscopic units that regulate calcium (and thus heart beats). Delving more deeply reveals defects in molecular components that interact with calcium. They visualize these models at multiple scales using state-of-the-art software. 

“The tools allow researchers to follow a hypothesis all the way from the whole organ, through to the level of cells, and, deeper still, connecting all the way down to the protein or small molecule level,” Amaro says. Read more.

a collision with

Dark matter: the next big challenge for particle physics

Now that we've found the Higgs boson, what's next, ABC Radio's Robyn Williams asked physics professor Frank Wuerthwein. 

"I look at it as a closure of a 50-year story on understanding the normal stuff that things are made out of. And now the next big question is what is the universe made out of, what else is in there? And within the last 10, 20 years we almost went through a Copernican revolution. Suddenly we realize this makes up only 5% or 4.5% of the universe. So what is all this other stuff? And so the big next thing in my mind is really what is dark matter, what is dark energy, what is the rest of the universe, the other 95%, made out of? As we close one chapter, a whole new set of questions begin," Wuerthwein said. Listen to the whole conversation on ABC Radio's The Science Show.

strain on a single particle of an electrode in a lithium ion battery as it dischargesStrain mapped on the surface of a single nanoparticle of a lithium nickel manganese oxide electrode while the battery discharges. The greatest strain occurs just before the particle changes structure as the ions depart.

Imaging reveals strain of charge cycles in single particles of electrode

Using a novel technique called coherent X-ray diffractive imaging, Andrew Ulvestad, Andrej Singer and colleagues mapped the three-dimensional strain in nanoparticles in within the electrodes of operating coin cell batteries, like those found in watches. In two papers recently published in Nano Letters, they report evidence that the history of charge cycles alters the patterns of strain in single particles of the electrode material.

This new approach will help to reveal fundamental processes underlying the transfer of electrical charge, insight that could help to guide the design of economical batteries with longer useful lives. Read more.

Pleiades star cluster

Radio telescopes settle controversy over distance to star cluster

A satellite called Hipparcos, launched in 1989, measured the distances to clusters of stars and found that one cluster, familiar to stargazers as the Pleiades, was 10 percent closer than everyone had thought. That suggested its stars must be fainter than stellar models predict. A debate ensued about whether the model or the measure was wrong.

Now Carl Melis, a research scientist with the Center for Astrophysics and Space Sciences, and colleagues from other institutions have seemingly put the matter to rest. In the August 29th issue of Science, they report a distance derived from very-long-baseline radio interferometry that agrees well with previous ground-based determinations — and not with Hipparcos. Read more at Sky and Telescope.

Elizabeth Villa and Ryan Anderson with the FEI SCIOS microscope
Elizabeth Villa, who is helping to develop a new kind of telescope, and Ryan Anderson, nanofabrication engineer

Chemist helps to develop new microscope for detailed look inside cells

Elizabeth Villa, a new assistant professor in the Department of Chemistry and Biochemistry, along with her colleagues at Germany’s Max Planck Institute of Biochemistry, adapted a focused-ion-beam microscope for biological applications during her postdoctoral studies. The design was adopted by the Dutch company FEI into a first-of-a-kind prototype that Villa will further develop at UC San Diego in collaboration with the company.

“With cryo-electron tomography techniques, we can create 3D pictures of the cells called tomograms,” Villa says. “What I do is exactly equivalent to a CT (computed tomography) scan, except the cells are a million times smaller."

Villa adds that another benefit of cryo-electron microscopy is the ability to infer cellular dynamics over time, “or what we call in physics ‘ergodicity.’ I can look at 3,000 nuclear pores frozen at different times to infer the cellular dynamics, classify all of this information and then make predictions. We can then do a light microscopy experiment in vivo and correlate what we see with the previous data we’ve gathered.”  Read more.

Quantitative Biology approach reveals the importance of physical constraints on critical DNA interaction

visualization of numerical simulation

Our immune system copes with a multitude of threats using a mix-and-match system to create millions of different antibodies.

The white blood cells that produce these antibodies assemble their specific versions by selecting three gene segments from among multiple variants.

Joseph Lucas, a graduate student working with Cornelis Murre, a professor of biology at UC San Diego, tagged individual gene segments in live cells to track their movement in three dimensions.

To better understand what they observed, the biologists turned to Yaojun Zhang, a graduate student in physics and her advisor, Olga Dudko, a professor of physics at UC San Diego, who analyzed the movements. They recognized the patterns as ‘fractional Langevin motion.’

 Read more.


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Recent Awards

Charles Perrin, Professor of Chemistry and Biochemistry, will receive the 2015 James Flack Norris Award in Physical Organic Chemistry from the American Chemical Society. Perrin will receive this national recognition for his contributions to the field at the spring meeting of the society in March. 

David Kleinfeld, Professor of Physics, has been awarded an Early Concept Grant for Exploratory Research from the National Science Foundation for his project with Ehud Ahissar of the Weizmann Institute in Israel, "Closed Loop Computing in the Brainstem." The collaboration will be supported by a coordinating grant from the U.S.-Israel Binational Science Foundation.