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News from the Physical Sciences

enzymes modify DNA and the proteins it wraps around

Program predicts placement of chemical tags that control gene activity

Biochemists have developed a program that predicts the placement of chemical marks that control the activity of genes based on sequences of DNA. Read more.

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.

visiting students explore physics demonstrations

Native American students explore physics on visit to UC San Diego

More than two dozen Native American students explored light, sound, momentum and more in a morning of physics in Mayer Hall this summer.

The visit was part of a program called Intertribal Youth that seeks to empower Native American youth by providing access to world-class universities, environments, professionals and mentors. Ramin Skibba, a postdoc with UC San Diego’s Center for Astrophysics and Space Sciences and a volunteer for the event, provides this account.

strain on a single particle of an electrode in a lithium ion battery as it discharges

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 individual nanoparticles in within the electrodes of working batteries. 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. The greatest strain occurs just before the particle changes structure as the ions depart. 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.

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.

Sulfur signals in Antarctic snow reveal clues to climate, past and future

Robina Shaheen
Robina Shaheen measured sulfur isotopes from snow.

Sulfur signals in the Antarctic snow have revealed the importance of overlooked atmospheric chemistry for understanding climate, past and future.

Eruptions of huge volcanoes, the disruptive weather pattern known as El Niño, and a fire season from hell each left distinctive chemical marks in layers of snow excavated near the South Pole, researchers from the University of California, San Diego and France report in the Proceedings of the National Academy of Sciences the week of August 4.

Sorting out the chemical reactions that must have led to those traces revealed a process, known but overlooked, that should be included in models of climate, both forecasts of climate to come and those built to understand Earth’s early history.

“We observed huge signals from ENSO driven changes like extreme dry weather and ensuing biomass burning, which surprised me,” said Robina Shaheen, a project scientist in chemistry at UC San Diego and lead author of the report. “The pattern we saw fits signals that have been observed in pre-Cambrian rocks, which prompted us to take another look at which molecules play a role in this chemistry.” Read more.

A superfluid gas formed in layers of 2D crystals could induce superconductivity at high temperatures

stack of 2D crystalsAn elusive state of matter called superconductivity could be realized in stacks of sheetlike crystals just a few atoms thick, a trio of physicists has determined.

Superconductivity, the flow of electrical current without resistance, is usually found in materials chilled to the most frigid temperatures, which is impractical for most applications. It's been observed at higher temperatures–higher being about 100 kelvin or minus 280 degrees below zero Fahrenheit–in copper oxide materials called cuprate superconductors. But those materials are brittle and unsuitable for fabricating devices like circuits.

In a paper published in Nature Communications, Michael Fogler and Leonid Butov, professors of physics at the University of California, San Diego, and Konstantin Novoselov, Nobel laureate in physics and professor at the University of Manchester, propose a design for an artificially structured material that should support superconductivity at temperatures rivaling those seen for cuprates. Read more.

embryonic stem cells become neural
Image: JACS

Sugar mimic guides stem cells toward neural fate

Long chains of sugars dangle from proteins on the surface of embryonic stem cells and play an important role in how the cells develop into specific cell types. Kamil Godula, an assistant professor of chemistry and biochemistry, and his research group have now synthesized a molecular mimic of these sugar-decorated proteins that helps direct mouse embryonic stem cells down the path toward nerve cells they report in the Journal of the American Chemical Society. The researchers hope others can easily adopt their method to explore how these cell surface sugars influence stem cell differentiation. Read more about these molecular mimics in Chemical and Engineering News.

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