Optimal flexibility for conformational transitions in macromolecules

Conformational transitions in macromolecular complexes often involve the reorientation of lever-like structures. Using a simple theoretical model, we show that the rate of such transitions is drastically enhanced if the lever is bendable, e.g. at a localized "hinge''. Surprisingly, the transition is fastest with an intermediate flexibility of the hinge. In this intermediate regime, the transition rate is also least sensitive to the amount of "cargo'' attached to the lever arm, which could be exploited by molecular motors. To explain this effect, we generalize the Kramers-Langer theory for multi-dimensional barrier crossing to configuration dependent mobility matrices.Comment: 4 pages, 4 figure

Intruders in the Dust: Air-Driven Granular Size Separation

Using MRI and high-speed video we investigate the motion of a large intruder particle inside a vertically shaken bed of smaller particles. We find a pronounced, non-monotonic density dependence, with both light and heavy intruders moving faster than those whose density is approximately that of the granular bed. For light intruders, we furthermore observe either rising or sinking behavior, depending on intruder starting height, boundary condition and interstitial gas pressure. We map out the phase boundary delineating the rising and sinking regimes. A simple model can account for much of the observed behavior and show how the two regimes are connected by considering pressure gradients across the granular bed during a shaking cycle.Comment: 5 pages, 4 figure

Dielectric susceptibility of the Coulomb-glass

We derive a microscopic expression for the dielectric susceptibility $\chi$ of a Coulomb glass, which corresponds to the definition used in classical electrodynamics, the derivative of the polarization with respect to the electric field. The fluctuation-dissipation theorem tells us that $\chi$ is a function of the thermal fluctuations of the dipole moment of the system. We calculate $\chi$ numerically for three-dimensional Coulomb glasses as a function of temperature and frequency

Kinetic Accessibility of Buried DNA Sites in Nucleosomes

Using a theoretical model for spontaneous partial DNA unwrapping from histones, we study the transient exposure of protein-binding DNA sites within nucleosomes. We focus on the functional dependence of the rates for site exposure and reburial on the site position, which is measurable experimentally and pertinent to gene regulation. We find the dependence to be roughly described by a random walker model. Close inspection reveals a surprising physical effect of flexibility-assisted barrier crossing, which we characterize within a toy model, the "semiflexible Brownian rotor."Comment: final version as published in Phys. Rev. Let

Corrigendum to "Fractional release factors of long-lived halogenated organic compounds in the tropical stratosphere" published in Atmos. Chem. Phys., 10, 1093–1103, 2010

We have noted a computational error in the calculation of the averaged Fractional Release Factors (FRFs) relative to the averaged FRF of CFCl3 (CFC-11). ..

Observation of mesospheric air inside the arctic stratospheric polar vortex in early 2003

During several balloon flights inside the Arctic polar vortex in early 2003, unusual trace gas distributions were observed, which indicate a strong influence of mesospheric air in the stratosphere. The tuneable diode laser (TDL) instrument SPIRALE (Spectroscopie InFrarouge par Absorption de Lasers Embarqués) measured unusually high CO values (up to 600 ppb) on 27 January at about 30 km altitude. The cryosampler BONBON sampled air masses with very high molecular Hydrogen, extremely low SF6 and enhanced CO values on 6 March at about 25 km altitude. Finally, the MIPAS (Michelson Interferometer for Passive Atmospheric Sounding) Fourier Transform Infra-Red (FTIR) spectrometer showed NOy values which are significantly higher than NOy* (the NOy derived from a correlation between N2O and NOy under undisturbed conditions), on 21 and 22 March in a layer centred at 22 km altitude. Thus, the mesospheric air seems to have been present in a layer descending from about 30 km in late January to 25 km altitude in early March and about 22 km altitude on 20 March. We present corroborating evidence from a model study using the KASIMA (KArlsruhe Simulation model of the Middle Atmosphere) model that also shows a layer of mesospheric air, which descended into the stratosphere in November and early December 2002, before the minor warming which occurred in late December 2002 lead to a descent of upper stratospheric air, cutting of a layer in which mesospheric air is present. This layer then descended inside the vortex over the course of the winter. The same feature is found in trajectory calculations, based on a large number of trajectories started in the vicinity of the observations on 6 March. Based on the difference between the mean age derived from SF6 (which has an irreversible mesospheric loss) and from CO2 (whose mesospheric loss is much smaller and reversible) we estimate that the fraction of mesospheric air in the layer observed on 6 March, must have been somewhere between 35% and 100%

Proton endor study of the photoexcited triplet state PT in Rps. sphaeroides R-26 photosynthetic reaction centres

The photoexcited triplet state PT of Rhodopseudomonas sphaeroides R-26 has been investigated by ENDOR measurements performed on frozen photosynthetic reaction centre solutions. For the first time hyperfine data could be obtained for PT. These data indicate a delocalisation of the triplet state over two bacteriochlorophyll a molecules

Optimization by thermal cycling

Thermal cycling is an heuristic optimization algorithm which consists of cyclically heating and quenching by Metropolis and local search procedures, respectively, where the amplitude slowly decreases. In recent years, it has been successfully applied to two combinatorial optimization tasks, the traveling salesman problem and the search for low-energy states of the Coulomb glass. In these cases, the algorithm is far more efficient than usual simulated annealing. In its original form the algorithm was designed only for the case of discrete variables. Its basic ideas are applicable also to a problem with continuous variables, the search for low-energy states of Lennard-Jones clusters.Comment: Submitted to Proceedings of the Workshop "Complexity, Metastability and Nonextensivity", held in Erice 20-26 July 2004. Latex, 7 pages, 3 figure

Comparative monolayer investigations of surface properties of negatively charged glycosphingolipids from vertebrates (gangliosides) and invertebrates (SGL-II, lipid IV).

The surface properties of four negatively charged glycosphingolipids from vertebrates, the sialo-glycosphingolipids (=gangliosides) GM1, GD1a, GT1b and a sulfo-glycosphingolipid (=sulfatide), and of the two negatively charged glycosphingolipids from lower invertebrates, the glucurono-glycosphingolipid Lipid IV and the aminophosphono-glycosphingo-lipid SGL-II were investigated in monolayers at the air/water interface. The molecular peculiarities under investigation were surface pressure (π) and surface potential (ΔV) which are described for Lipid IV and SGL-II for the first time. The surface pressure/area isotherms of all glycosphingolipids were typical of a liquid-expanded monolayer and, with the exception of SGL-II, exhibited a phase transition to a liquid-condensed state at surface pressures above 20 mN/m. The surface potential/molecular area data found for gangliosides in the closely packed state at π=30 mN/m (GM1: ΔV = −17 mV; GD1a: ΔV = −35 mV; GT1b: ΔV = −39 mV) showed only a slight influence of the additional number of negatively charged residues. For Lipid IV, the surface behavior was very similar to GM1 both possessing one negative group per molecule, whereas in SGL-II also the surface potential data (ΔV = −173 mV) were different compared with GD1a both possessing two negative groups per molecule. The addition of Ca2+ condensed the monolayers of all glycolipids and increased the potential in the direction to more positive values, but these findings were less effective in SGL-II films. On the basis of monolayer results presented here, in biological membranes of invertebrates especially Lipid IV might play a similar role as the ganglioside GM1 in vertebrate cells