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Image credit: Steven McQuinn, Science Artist; Doug Smith, UCSD; Bonnie Draper and Venigalla Rao, Catholic University of America	Cutaway of virus with DNA being packaged within and a model of the DNA-packaging motor. News Release >>
Image Credit: Zeyun Yu, Postdoctoral Associate and Michael Holst, Professor Department of Mathematics, UCSD	Illustration of mesh generation for the bacterial chaperonin GroEL, a large molecular complex with seven-fold symmetry, fourteen identical subunits, and approximately 54,000 atoms. The tetrahedral mesh is used to perform physical simulations using the finite element method (FEM), which is a powerful numerical technique for solving partial differential equations (PDE) arising in biomedicine and other areas. A core part of all finite element simulations is the splitting of the complex physical domain into a number of nicely shaped tetrahedral (or other shaped) “elements” of sufficiently small size, so that simple polynomials defined on each element can accurately describe the solution to the PDE model. This splitting of the domain into elements is usually referred to as “mesh generation”, and is one of the most important and active areas of research in computational science. The mesh generation software used to generate the mesh above, called GAMer, is part of the Finite Element ToolKit (FETK), a software package developed and maintained by UCSD mathematicians. This software is designed for finite element analysis of a variety of biomedical simulation problems ranging from moelcular, cellular, to organ levels. The GAMer software is general in the sense that it can take as inputs a list of atoms, a 3D volume (e.g., reconstructed CT/MRI medical data), or a user-defined triangulated surface mesh that is generated in any other way and may have very low quality. There has been a critical need for this computational modeling tool for years. Research Website>> FETK website >> CSME Program >> Read research paper >>
Image Credit: Mike White, UCSD	It may look like mistletoe wrapped around a flexible candy cane. But this molecular model shows how some proteins form loops in DNA when they chemically attach, or bind, at separate sites to the double-helical molecule that carries life’s genetic blueprint. News Release >> Research Website >>
Image Credit: Peter G. Wolynes, Department of Chemistry & Biochemistry	Schematic representation of the "funneled" energy landscape of protein folding. Natural proteins are evolutionarily selected to be globally biased to become a well-defined folded structure as it descends down the energy landscape. Read research paper (PDF 2.2MB) >> Read "60 Seconds with Physical Biology Author" >>
Image Credit: Massimiliano Di Ventra, Department of Physics	DNA sequencing via transverse transport is essential in guiding experimentalists in providing detailed electronic and atomic information about the physical processes involved during transport of DNA in solid-state nanopores. Fast and low-cost DNA sequencing methods would usher in a real revolution in medicine. Read article >> News Release >> Watch Movie (MPEG 19.5 KB) >>
Jamie Matthews, graduate student (Chemistry) with laser apparatus used in study. Image Credit: UCSD	An innovative laser technique called “action spectroscopy” has enabled observation of minute quantities of radiation absorbed by a substance called methyl hydroperoxide. Methyl hydroperoxide is a naturally-occurring atmospheric chemical process which can absorb light in the lower UV spectrum, thus breaking down smog, pollutants and other damaging hydrocarbons after they absorb energy from sunlight. Read article >>
Image Credit: Leonid Butov	A photoluminescence pattern of cold excitons shows the exciton ring and macroscopically ordered exciton state. An exciton is an electron-hole bound pair in a semiconductor. It is a Bose quasi-particle, akin to the hydrogen atom. Exciton Bose-Einstein condensation occurs at temperatures many orders of magnitude higher than for atoms that makes cold excitons a paradigm system for studies of collective states and many-body phenomena. Read article >>
Image Credit: Eshel Ben-Jacob, Center for Theoretical Biological Physics	This picture is one of a series of remarkable patterns that bacteria form when grown in a petri dish. While the colors and shading are artistic additions, the image templates are actual colonies of tens of billions of these microorganisms. The colony structures form as adaptive responses to laboratory-imposed stresses that mimic hostile environments faced in nature. They illustrate the coping strategies that bacteria have learned to employ, strategies that involve cooperation through communication. Read article >>
	A gradient of pore sizes imparts a rainbow of colors to a porous silicon chip, one of a variety of new biosensor technologies in development around the world. The different colors correspond to different sized pores, ranging from a few nanometers to hundreds of nanometers in diameter. These pores help the device discriminate and detect proteins and other molecules based on their size. Michael Sailor's lab at UCSD is on the cutting edge of this research. Read article >> Image credit: Michael Sailor
	The intrigue of antimatter lies in its untouchability--its utter incompatibility with the stuff of our familiar world. Antimatter particles obey all the same physical laws as matter particles... or do they? UCSD Physicist Cliff Surko and other researchers are starting to discover it is not quite that simple.
	Calculations have convinced physicists that matter-antimatter hybrids exist, though no one has yet worked out a way to test for their presence. Image Credit: MagicTorch
	"Stable organic molecules with just a few hundred electrons acted like dynamite when they encountered antimatter. It was a clear sign something was wrong." Image Credit: MagicTorch Read article in New Scientist, April 2004 >>
	UCSD Scientist Arthur M. Wolfe looks back in time for clues to how the first stars formed. Today's most powerful telescopes can take us back to about a billion years after the big bang. "We're looking very far back in time," he says. "I'm not sure these are the first stars, (but) they're very early stars." Read news release >> Using sources from UCSD, Cal Tech, NASA, Goddard Space Flight Center, American Scientist, Don't Know Much About the Universe, and The Universal Book of Astronomy. Credit: Paul Horn, San Diego Union Tribune.
	Astronomers are examining quasar light produced billions of years ago to look back to a time when some of the first stars illuminated a young, dark universe.
	The Design Of Composite Materials That Detect Terahertz Rays May Make Possible A New Generation Of Imaging Tools. Read news releases >> More on left-handed materials >> Scanning electron microscope image of the metamaterial. Credit: Ta-Jen Yen UCLA
Credit: Ingrid Castro-Rodriguez, UCSD	Snapshots of a catalytic process in action taken by researchers at the University of California, San Diego provide important information for the first time about the chemical action of catalysis, and could have implications for improving the energy efficiency and environmental safety of the reactions involved in the refinement of the hydrocarbons in petroleum. read news release >> Molecular model of catalyst with uranium atom shown in pink.
Photo sequence from top left to bottom right showing high energy electrons in yellow and red approaching Earth. Sun is at the center of the photo. Image Credit: “Bernard Jackson, Paul Hicks and Andrew Buffington, UCSD”	Using an orbiting camera designed to block the light from the sun and stars, an international team of solar physicists has been able for the first time to directly image clouds of electrons surrounding Earth that travel from the sun during periods of solar flare activity. These electron clouds, a part of the solar atmosphere that extends millions of miles from the sun, cause geomagnetic storms that can disrupt communications satellites, expose high-flying aircraft to excess radiation and even damage ground-based power-generating facilities. The images taken by this new camera, which will be discussed at a scientific session and news conference at the fall meeting in San Francisco of the American Geophysical Union, should allow space weather forecasters to substantially improve their predictions of geomagnetic storms. read news release movies of auroras: hammer fisheye
Image Credit: “Bernard Jackson, Paul Hicks and Andrew Buffington, UCSD” High altitude aurora is seen as bright light in the center of these sequential images taken two minutes apart.
Image Credit: Rebecca Phillips, UCSD Image showing Pseudomonas bacteria toxin (green) localized to the cell membrane. The nucleus of the cell is blue.	Pseudomonas aeruginosa, a common bacterium, can infect nearly every part of the body and produces toxins that damage tissues. In the study to be published in the October 17th issue of the Journal of Biological Chemistry, the researchers report that when the bacterium injects a toxin called “ExoU” with a tiny needle-like structure into cells, the toxin degrades phospholipids—greasy molecules that are a key component of cell membranes. They also found that chemicals known to block proteins that degrade phospholipids could save cells that would otherwise die. An earlier on-line version of the paper is available here >> “We have found that the toxin, which is associated with 90 percent of the severe cases of Pseudomonas infections, kills cells by targeting a component of the cell membrane,” says Partho Ghosh, a professor of chemistry and biochemistry in UCSD’s Division of Physical Sciences who headed the research team. “We have been able to identify chemicals that protect cells from the effects of the toxin, raising the possibility of a novel mode of treatment for these infections.” Read news release >>
Image of mammalian cell showing bacterial toxin (green spots) at the cell membrane.
The films are broken up into particles about the size of a human hair. With the chemistry at left, the particles seek out and attach themselves to an oil drop, presenting their red surface to the outside world and their green surface towards the inside of the drop. Image credit: Sailor Research Group	Targeted Smart Dust: How It Works: In order to spontaneously assemble and orient the micron-sized porous Si "smart dust," we couple chemical modification with the electrochemical machining process used to prepare the nanostructures. The process involves two steps, see the scheme below. In the first step, a porous photonic structure is produced by etching silicon with an electrochemical machining process. This step imparts a highly reflective and specific color-code to the material, that acts like an address, or identifying bar-code for the particles. The second step involves chemically modifying the porous silicon photonic structure so that it will find and stick to the desired target. In the present case, we use chemistry that will target the interface between a drop of oil in water, but we hope to be able to apply the methodology to pollution particles, pathogenic bacteria, and cancer cells. The two steps (etch and modify) are repeated with a different color and a different chemistry, yielding two-sided films. click here for news articles more images of smart dust Sailor Research Group
	Chemists at the University of California, San Diego have developed a novel method of detecting molecules with a conventional compact disk player that provides scientists with an inexpensive way to screen for molecular interactions and a potentially cheaper alternative to medical diagnostic tests. click here for article Discode Project Photo credit: Photo Credit: Nina Seiler, UCSD

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