Recently in Statistical physics & thermodynamics Category

Lactose isn't present in our guts all the time. To ingest it and other occasional sources of nutrition, Escherichia coli (see figure) must detect the molecules and then make the proteins that help harvest them. That process of on-demand protein production is called gene regulation. It's the subject of a new quantitative analysis by physicists Ulrich Gerland of the University of Munich, Germany and Terence Hwa of the University of California, San Diego. E. coli uses two modes of gene regulation. In (+ +) control, proteins called transcription factors float freely in the cell. When a TF molecule meets its molecular target—lactose, say—it locks onto the appropriate region of the bacterium's DNA and triggers the production of the appropriate protein. In (− −) control, the TF is usually bound to the DNA and blocks protein production until TF's molecular target arrives to detach the TF and lift the block. Both modes are equally effective. When does evolution favor one over the other? The answer, according to Gerland and Hwa, depends on a tug of war between two competing selection principles. The use-it-or-lose-it principle favors (+ +) control during feasts and (− −) control during famines, whereas the wear-and-tear principle favors the opposite. Both selection principles mitigate the adverse effects of genetic mutation but, as Gerland and Hwa found, whether one prevails over the other depends on the size and age of the colony and on how rapidly the food supply fluctuates. Besides quantifying gene regulation, Gerland and Hwa's analysis might help pharmacologists understand and combat the resistance of bacteria to antibiotics. One strain of E. coli, called mar, is resistant to tetracycline, an otherwise potent antibiotic, due to the working of two transcription factors. (U. Gerland, T. Hwa, Proc. Natl. Acad. Sci. USA 106, 8841, 2009.) —Charles Day

The Indus Valley civilization, in what is now eastern Pakistan and northwestern India, flourished circa 2500-1900 BCE. To this day its writing, as in the figure, has not been deciphered. Indeed, scholars are unsure if the Indus script represents a language. Other, superficially similar ancient texts are thought to be either rigidly prescribed strings, such as a hierarchical list of deities, or nonlinguistic strings in which order is unimportant. Now computer scientist Rajesh Rao (University of Washington) and colleagues from several Indian institutions have studied the correlations of neighboring tokens (symbols or words) with a statistical tool—the conditional entropy—that reliably distinguishes natural languages from token strings in which the ordering is rigid or unimportant. The Indus script, they conclude, has the structure of a language. Like the conventional entropy, the conditional entropy involves the logarithm of a probability—in this case the conditional probability that a specified token appears, given its immediate antecedent. Rao and colleagues identified the N most common tokens in the Indus script, various languages, and nonlinguistic systems and plotted the conditional entropy against N. The curves for the Indus system and the natural languages bunched in the middle and were clearly distinct from those corresponding to rigid or unimportant orderings. And the conditional entropy of the Indus system seemed especially closely related to Old Tamil, consistent with the conclusions of scholars who have analyzed the Indus script with more conventional means. (R. P. N. Rao et al., Science, 2009, doi:10.1126/science.1170391. Photo courtesy of J. M. Kenoyer / Harappa.com.) — Steven K. Blau

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Ancient Scripts: Indus Script

In his "Milkdrop Coronet," strobe-photography pioneer Harold Edgerton famously captured the splash produced by a milk droplet falling into a saucer. But our understanding of the underlying physics remains poor. It's known that before a liquid droplet splashes upward from a surface, a thin sheet of liquid spreads out from the impact point. Four years ago experiments by Sidney Nagel and colleagues at the University of Chicago showed, surprisingly, that splashing on a dry surface can be suppressed by reducing the ambient air pressure. The researchers concluded that compressible effects in the air are responsible for the splashing (L. Xu, W. W. Zhang, S. R. Nagel, Phys. Rev. Lett. 94, 184505, 2005). Now Michael Brenner and coworkers at Harvard University have further looked into the air's role in how droplets splash on a dry surface. Taking into account the compressibility and viscosity of the gas and the surface tension of the liquid, they modeled the behavior of the approaching droplet as it reaches the surface. They find that instead of spreading out over the surface, the liquid spreads over a very thin film of air. When the droplet nears the surface, pressure builds beneath it and the bottom of the droplet deforms by flattening and then becoming dimpled. The droplet's bottom perimeter develops a kink that, still over a layer of air, moves out and creates capillary waves. The calculations don't, however, show any indications of splashing; the researchers suggest that other parameters, such as the droplet viscosity and thermal transfer, must become important after the initial spreading phase. (S. Mandre, M. Mani, M. P. Brenner, Phys. Rev. Lett., in press.) — Richard J. Fitzgerald

In typical loudspeakers, a coil surrounds the apex of a flexible cone; when a varying current flows through the coil, the cone moves toward and away from a fixed permanent magnet and produces pressure waves we hear as sound. But researchers from Tsinghua University and Beijing Normal University have demonstrated a radically simpler loudspeaker design based on nanotubes: They showed that a thin film of nanotubes can reproduce sounds over a wide frequency range--including the full human audible range--with high sound pressure level, low total harmonic distortion, and no magnets. The team created the film by drawing nanotubes from a so-called superaligned array grown on a wafer, a technique the group introduced six years ago (see also PHYSICS TODAY, October 2005, page 23). The resulting film, only tens of nanometers thick but up to 10 cm wide, is transparent and has a nearly purely resistive impedance. When electrodes are placed along its ends and an alternating current is applied, the film produces clear tones that can be as loud as a conventional speaker. Moreover, since the film is flexible, the nanotube speaker can be configured into arbitrary shapes or mounted onto curved substrates; the figure shows an omnidirectional cylindrical loudspeaker 9 cm in diameter and 8.5 cm high. The film can even be stretched with essentially no degradation of the sound reproduction. The researchers attribute the sound generation not to vibration but to a thermoacoustic effect first proposed nearly a century ago: Thanks to the nanotube film's extremely low heat capacity per unit area, changes in the current flowing through the film are reflected in the film's temperature, and those temperature changes excite pressure waves in the surrounding air. The mechanism is independent of the sign of the current, which leads to a frequency doubling of the input signal, but that drawback can be overcome by applying a constant current bias. The movie shows a nanotube loudspeaker being periodically stretched with almost no noticeable effect on the sound intensity. (L. Xiao et al., Nano Lett., in press, doi:10.1021/nl802750z.) -- Richard J. Fitzgerald

Sodium is volatile. It easily burns and boils and diffuses. Meteorites are hardy, and the type known as chondrites are also primitive, dating back to the very early solar system. Chondrites contain a high density of so-called chondrules—roughly millimeter-sized spheres like the one shown here in polarized light—that were flash-melted at temperatures around 2000 K and subsequently cooled and incorporated into a meteorite's parent object, typically an asteroid. The heating mechanism is unknown but could involve shocks or lightning. Mostly made of silicate minerals such as olivine and pyroxene and of the metals iron and nickel, chondrules are expected to be deficient in volatile elements like sodium. But researchers at the Carnegie Institution of Washington, the US Geological Survey, and the American Museum of Natural History say it isn't so. Using electron microprobe spectroscopy, they studied 26 chondrules from the Semarkona meteorite that fell in India in 1940 and found significant sodium throughout. The only way that could happen, they say, is if the chondrules formed as closed systems at densities in the solar nebula (the disk of gas and dust from which the planets formed) that were far higher than previously thought. That way, the cooling droplets would be crowded together in an area of saturated sodium vapor. The required ambient densities range from 10 to hundreds of grams per cubic meter, far exceeding the standard assumption of 0.1 g/m³ or less. At the much higher densities, astronomically tiny regions just a few thousand kilometers across can collapse under their own gravity. Thus chondrule formation seems to be intimately linked to planetesimal formation, the first step in making planets like Earth. (C. M. O'D. Alexander et al., Science 320, 1617, 2008 [MEDLINE].) — Stephen G. Benka

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Department of Terrestrial Magnetism

At the May Conference on Lasers and Electro-Optics in San Jose, California, University of Colorado graduate student Mark Siemens reported on studying how tiny parcels of heat, called phonons, spread in a crystal. He and his colleagues used a near-IR laser to heat a grating of nickel lines—each 20 nm high and 1 µm
wide—grown on a sapphire substrate that acted as a heat sink. Then, by recording the transient diffraction of 10-fs pulses of coherent soft x rays from the sample, the researchers could monitor with picometer (10^-12 m) precision the displacement of the heated nickel nanostructure. The transport of heat is considered "ballistic" if the characteristic distance over which a phonon moves—about a micron in this case—is smaller than its mean free path before scattering off another phonon. At room temperature a typical phonon's mean free path in sapphire is a mere 150 nm but grows to more than a micron when the sample is cooled below 130 K. At that temperature the data show a clear transition from thermally diffusive to ballistic behavior. One reason for trying to understand how heat moves away from a nanoscale interface, says Siemens, is to manage the thermal environment of future advanced high-speed transistors. — Phillip F. Schewe

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Nanoscale Probes of Materials

In conventional superconductivity, electrons combine into Cooper pairs, and those pairs collectively enter into a single quantum state in which current can flow with zero electrical resistivity; there is no current dissipation and no Joule heating of the material. A multinational collaboration led by Valerii Vinokur of Argonne National Laboratory in the US and Tatyana Baturina of the Institute of Semiconductor Physics in Russia recently reported on an analogous but opposite situation in which electrical current is vanishingly small, effectively zero. The group studied a thin film of superconducting titanium nitride. Below critical values of temperature and applied voltage, the system went through an abrupt transition from an insulator with normal, linear resistivity to one with apparently infinite resistivity. What's more, the transition could be crossed by tuning a magnetic field for a given threshold voltage, as shown in the figure. As with a superconductor, the superinsulator has zero Joule loss—but now because there is no current rather than no resistance. The experimental system was successfully modeled and analyzed as an array of superconducting islands or droplets connected by Josephson weak links. The researchers conjecture that such a network is also essential to the superconductor-to-insulator transition in thin films. (V. M. Vinokur et al., Nature 452, 613, 2008 [MEDLINE].) — Phillip F. Schewe