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Physics News Update
Number 633, April 16, 2003 by Phillip F. Schewe, Ben Stein, and James Riordon


The First Single-Molecule, Single-Base-Resolution DNA Sequencing

The first single-molecule, single-base-resolution DNA sequencing has been carried out by a Caltech group. In this new approach, the bases forming the backbone of the typical DNA molecule are viewed one by one in the act of replicating. To be more exact, a DNA polymerase molecule, acting as a genetic xerox machine, copies a single strand of DNA by adding complementary base units to it; the "fuel" for this process, the base molecules being added, were fluorescently labeled beforehand (by attaching site-specific, light-producing fluorophore molecules), so the DNA sequence could be observed by microscope observations (schematic setup figure). Sequencing single-molecule DNA strands is intrinsically difficult because of the high linear data storage density: the bases are only about 3.4 angstroms apart along the DNA helix. Past efforts to sequence bases through their fluorescence have been complicated by background noise, a problem avoided by the Caltech scientists through careful use of two laser pulses, one for producing pinpoint fluorescence and another for nulling or "bleaching" the fluorescence in order to prepare for the next base identification.

Stephen Quake and his colleagues can currently identify no more than about 6 bases in a row, so this research is still at the proof-of-principle stage. However, within about two years or so, Quake believes, his process should be a factor of ten faster than standard gel-electrophoresis techniques used to sequence DNA molecules on a wholesale level, and several orders of magnitude cheaper. (Braslavsky et al., Proc. Natl. Acad. Sci., 1 April 2003.)

 

Charge Symmetry Breaking

Charge symmetry breaking has been observed in two experiments reported at the recent American Physical Society meeting in Philadelphia. In the 1930s, physicist Werner Heisenberg proposed that the neutron and proton are simply slightly different manifestations of the same particle, called the "nucleon." Modern nuclear physics endorses this view: plenty of nuclear reactions proceed exactly the same way if a proton takes the place of a neutron, or vice versa. However, this close similarity breaks down in some cases, leading to a situation known as "charge symmetry breaking" (CSB). In separate experiments at the Indiana University Cyclotron Facility (IUCF) and the TRIUMF cyclotron in Canada, researchers have made groundbreaking new measurements of CSB (which, incidentally, is a nuclear-physics phenomenon completely different from charge [C] conjugation in particle physics). Such CSB measurements can provide deep insights into why nature gave the neutron and proton slightly different masses. At an even more fundamental level, the CSB measurements can potentially yield more precise values of the mass difference between the up and down quarks that make up protons and neutrons. Nuclear theorists are busily analyzing these new experimental results to put tighter constraints on the up-down mass difference.

At the APS meeting, Ed Stephenson of Indiana University announced the first unambiguous identification of a rare process: the fusion of two nuclei of heavy hydrogen to form a nucleus of helium and an uncharged pion, one of the subatomic particles responsible for the strong force that binds nuclei together. This process would not exist at all were it not that nature allowed a small violation of charge symmetry. Over a two-month period, researchers observed this rare reaction several dozen times, giving physicists enough data to test theories of charge-symmetry breaking.

Representing a collaboration at TRIUMF, Allena Opper of Ohio University discussed the detection of CSB in another nuclear reaction: the fusion of a proton and neutron, which produces a charged pion as one of its products. Viewed from a perspective or ("reference frame") at which the proton and neutron meet at the center, the reaction, repeated man times, produces a small excess of pions (0.17%) in a preferred direction. Such an asymmetry is a hallmark of CSB. Taken together, these new CSB results promise a wealth of information on such things as the slightly different electromagnetic fields inside each nucleon. As it turns out, such fields may contribute to the proton-neutron mass difference, as they carry energy which convert into a small amount of mass.

Tunable Photonic Crystals

Photonic crystals affect the flow of photons in much the same way that electronic devices affect the flow of electrons. Most photonic crystals, however, have specific properties that cannot be varied once the crystals are made. A few types of photonic crystals, such as fluid suspensions of colloidal silica, can be modified on the fly, but the time required to change configurations is inconveniently long. Researchers at Brown University have now made photonic crystals that can be modified in milliseconds. The tunable photonic crystals consist of a class of materials known as holographic-polymer dispersed liquid crystals (H-PDLCs). Complex structures are defined in the material by exposing it to an interference pattern produced by a set of four laser beams. Liquid crystal droplets form in regions where the laser light interferes coherently; these droplets constitute a photonic crystal. An electric field applied to the suspension of liquid crystals modifies the refraction index of the droplets, which changes the spectrum of light that the photonic crystals transmits. The new photonic crystals are easily constructed on a wide range of scales, which allows them to affect a wide spectrum of light, and can replicate sophisticated structures including diamond lattices as well as anisotropic lattices that affect light differently depending on the direction of propagation through the crystal. Potential applications of the tunable photonic crystals include filters to selectively block certain light frequencies. With further improvement, they may also lead other optical devices such as to novel lasers and optical waveguides. Jun Qi of Brown University (401-863-3078) described the tunable photonic crystals in a paper he presented recently at the Optical Fiber and Communication Conference in Atlanta.