Recently in Computers and computational physics Category

The tunable elasticity and porosity of colloidal gels lead to some interesting applications, among them tissue scaffolding and drug delivery. Conventionally, colloidal particles interact and assemble under entropic and electrostatic forces to form predictable structures. But greater control can be achieved from an approach developed by Paul Clegg, Michael Cates, and their collaborators at the University of Edinburgh in the UK. The researchers disperse silica particles in the single-phase region of two partially miscible solvents—water and the organic base 2,6-lutidine. When the solution is heated above a critical temperature, the solvents separate and the particles become trapped at the liquid–liquid interfaces. The bulky particle domains then jam together and arrest the solvent separation, forming a two-phase network the researchers call a bijel. But cool the solution and remix the solvents too soon and the distinct structure disappears, as shown in movie 1 and the two left images in which the colloids appear green, the water black, and the lutidine red. Now the researchers have discovered an approach to stabilize the bijel structure. When the phase-separated solution is allowed to sit for at least 24 hours before it is cooled, the bijel surprisingly keeps its shape, as shown in the two right images and movie 2. From Monte Carlo simulations, the researchers deduce how the resulting network of colloidal monolayers, or monogel, stays intact: the particles become compressed by capillary forces, remain attracted by van der Waals forces, and are kept from collapsing into each other by repulsive electrostatic forces. (E. Sanz et al., Phys. Rev. Lett., in press.) —Jermey N. A. Matthews

Movie 1

Movie 2

In a single cell, thousands of simultaneously occurring biochemical reactions carry out such functions as converting and storing energy and regulating nutrient levels; together, those processes make up the cell’s metabolic network. Computational biology involves, among other things, the linking of metabolic pathways to form a metabolic network model, a promising tool for preclinical drug studies and other medical research. However, such computational models do not traditionally include the function-determining structural details of a network’s macromolecules; for example, an enzyme’s ability to catalyze reactions and regulate the cell’s response to external stimuli is determined by its three-dimensional configuration. Now, an international team led by Adam Godzik at the Burnham Institute for Medical Research in California has taken a rare step and introduced atomic-level protein structural data to the metabolic network model of an ancient thermophilic bacterium, Thermotoga maritima, shown in this optical microscope image. The image also shows schematics of proteins in their 3D configurations, which, when they were expressed in the reconstructed metabolic network, helped the research team solve the puzzle of how proteins evolve when their cell networks grow larger.

It turns out that only 37% of T. maritima’s proteins are essential to the formation of its metabolic network; those “core-essential” proteins adopt the bulk—61%—of the bacterium’s relatively few unique 3D configurations. The finding suggests that the core-essential proteins evolved their structure to perform additional functions in distinct pathways. (Y. Zhang et al., Science 325, 1544, 2009.)—Jermey N.A. Matthews

When a person’s head strikes, or is struck by, another object, it accelerates. As it begins to decelerate, the brain slams into the skull, then bounces off and oscillates until the impact energy dissipates. The resulting shear and compressive strains can lead to brain damage. But in battlefield explosions, just the acoustic waves alone can cause soldiers traumatic brain injuries. To better understand that process, Lawrence Livermore National Laboratory's William Moss and Michael King and the University of Rochester’s Eric Blackman compared numerical simulations of a head colliding with a wall to one being struck by an explosion’s blast waves. Despite accelerating the head at less than half the rate of the wall collision, the simulated blast produced on the brain surprisingly comparable pressure spikes—ranging up to 3 bars—and even larger pressure gradients. Apparently, those mechanical loads are delivered by the skull, which ripples under the pressure of blast waves—the rippling motion is indicated in the image by velocity vectors. The researchers confirmed the role of the skull’s elasticity by making it 1000 times stiffer in their simulations and observing a fivefold drop in the pressure spikes. The simulations also revealed that helmets in contact with the head can impart an additional mechanical load to the skull and helmets that allow for an air cushion geometrically focus and increase the magnitude of blast waves. (W. C. Moss et al., Phys. Rev. Lett., in press.)—Jermey N. A. Matthews

Quantum computing is a goal that both excites and challenges researchers, who are working on a wide variety of physical realizations of the basic building block: the quantum bit, or qubit.

One type is the superconducting qubit made from one or more Josephson junctions. The biggest advantage of superconducting qubits is their strong coupling to microwave signals, which can control the qubits and mediate their interactions. The greatest limitation is their short coherence lifetime.

Despite that limitation, recent experiments have demonstrated the kind of precise control that will be needed to make progress toward a viable quantum computer.

In one experiment, Max Hofheinz, John Martinis, Andrew Cleland and colleagues from the University of California, Santa Barbara, showed that they could impose on a microwave resonator any desired superposition of photon-number states. (M. Hofheinz et al., Nature 459, 546, 2009.)—Barbara Goss Levi

In an effort to reduce the pervasive smog in Beijing (see photo), Chinese authorities imposed measures to restrict traffic and close factories around the city during the 2008 Olympics. Were those efforts successful in reducing total atmospheric aerosol? Climate scientists Jan Cermak and Reto Knutti at ETH Zürich in Switzerland attempted to find out. They began by comparing absolute values of aerosol optical thickness—transmittance measurements from the Moderate-Resolution Imaging Spectroradiometer aboard NASA's Terra satellite—for the years 2002–08. They found that within a 150-km radius of Beijing, the average 2008 AOT value was more than 14% lower than the previous years. But what would it have been without the mandated emissions reductions? To answer that question, the researchers used a neural network approach: With data from the preceding six summers, they trained a model to predict AOT as a function of relative humidity, wind velocity, and precipitation. The model then predicted that within a 500-km radius of the city, AOTs in 2008 would have been 10%–14% higher than the actual observed values; the model was less accurate when larger regions were analyzed. Although the magnitude of the reductions was lower than expected, the emissions restrictions did have a statistically significant local impact. (J. Cermak, R. Knutti, Geophys. Res. Lett. 36, L10806, 2009, doi:10.1029/2009GL038572. Photo by Michael Silverman, 6 August 2006.)—Jermey N. A. Matthews

Before they form snowflakes and other hexagonal crystals, water molecules nucleate in smaller configurations. Determining the structure of those precursors—even in the outwardly simple case of water on a clean metal surface—is an area of ongoing interest and controversy. For example, at submonolayer coverage on a copper (110) surface, water molecules form chains that can grow to many tens of nanometers in length but are just 1 nm wide. The chains’ structure has been a mystery, since no arrangement of water molecules into hexagonal units entirely explains the experimental data. Now, Andrew Hodgson and colleagues of the University of Liverpool in the UK have collaborated with Angelos Michaelides’ group at University College London to find the structure. Michaelides and postdoc Javier Carrasco ran calculations on some 50 possible chain structures; they found that the most energetically stable one also gave the best fit to the Liverpool group’s high-resolution scanning tunneling microscopy images (as shown in the top panel) and vibrational spectra. That structure (bottom panel) is an arrangement of pentagons, not hexagons. The water molecules shown in red and yellow are perpendicular to the Cu surface—the hydrogen atoms pointing up are responsible for the bright spots in the STM images, and the ones pointing down (not visible in the figure) interact with the Cu atoms. The researchers suggest that nonhexagon arrangements might be involved at other water–metal interfaces where the structure of water is unknown. (J. Carrasco et al., Nat. Mater., doi:10.1038/nmat2403.) — Johanna Miller

Soft biological tissue is often subjected to forces that affect the tissue’s geometry, and finite elasticity provides a robust theoretical framework for analyzing the mechanical behavior of those tissues. Although the theory can accommodate anisotropic, nonlinear, and inhomogeneous processes subjected to large stresses and strains, its complexity makes many problems intractable. For growing tissue, though, the slow addition of cells generates shape- or size-changing stresses that are small enough to model successfully (see PHYSICS TODAY, April 2007, page 20). So, too, are simple geometries for tissues in equilibrium, even after those tissues are subjected to large stresses. Two recent papers have looked at applying the theory to those cases in thin elastic disks. In one recent study, Julien Dervaux and Martine Ben Amar (both of École Normale Supérieure, Paris) looked at anisotropic growth rates: If growth was faster in the radial than in the circumferential direction, the disk became conelike, while a reversal of rates generated saddle shapes. A separate study by Jemal Guven (National Autonomous University of Mexico) along with Martin Müller (ENS) and Ben Amar looked at excessively large circumferences for a given radius. Using the fully nonlinear theory, the researchers found an infinity of quantized equilibrium states for an ever-increasing perimeter at fixed radius. The ripples around the edge grew in size and number—not unlike the flower petals shown here—eventually crowding together enough to touch, like the ruffled collar in a portrait by Rembrandt. For more on the elasticity of thin sheets, see the article in PHYSICS TODAY, February 2007, page 33. (J. Dervaux, M. Ben Amar, Phys. Rev. Lett. 101, 068101, 2008; M. M. Mueller, M. Ben Amar, J. Guven, Phys. Rev. Lett., in press.) — Stephen G. Benka

In plasma physics as in fluid dynamics, turbulence remains one of the most challenging fundamental problems to understand. The nonlinear processes that lead to characteristic turbulence power spectra observed in the solar wind—the plasma that flows from the Sun out through the solar system—are poorly understood. So too are the dissipation mechanisms by which plasma turbulence transfers its energy to plasma electrons and ions. Most research in plasma turbulence has assumed that dissipation is weak and the plasma may be approximated as a fluid. But interest has increased in the so-called short-wavelength regime, in which dissipation plays out. Recently, an international team performed the first kinetic, particle-in-cell simulations of decaying short-wavelength whistler-mode turbulence in a collisionless plasma, using parameters similar to those of the solar wind near Earth. (Whistlers acquired their name from World War I radio operators who frequently heard what they thought were outgoing artillery shells, brief whistling sounds that decreased in frequency.) Limited not by any approximations but only by computing resources, the researchers found steep power-law magnetic fluctuation spectra consistent with those observed in space. In addition, they found and analyzed anisotropies in the turbulence whereby stronger initial fluctuations generated more magnetic energy perpendicular to the background magnetic field than along it. Because of the anisotropies, the whistlers were found to be more compressible than expected. The physicists also demonstrated the first simulation results of whistler turbulence dissipation by showing signatures of two well-known types of wave–particle interactions. (S. Saito et al., Phys. Plasmas, in press.) —Stephen G. Benka