A Brownian ratchet model for DNA loop extrusion by the cohesin complex.

The cohesin complex topologically encircles DNA to promote sister chromatid cohesion. Alternatively, cohesin extrudes DNA loops, thought to reflect chromatin domain formation. Here, we propose a structure-based model explaining both activities. ATP and DNA binding promote cohesin conformational changes that guide DNA through a kleisin N-gate into a DNA gripping state. Two HEAT-repeat DNA binding modules, associated with cohesin’s heads and hinge, are now juxtaposed. Gripping state disassembly, following ATP hydrolysis, triggers unidirectional hinge module movement, which completes topological DNA entry by directing DNA through the ATPase head gate. If head gate passage fails, hinge module motion creates a Brownian ratchet that, instead, drives loop extrusion. Molecular-mechanical simulations of gripping state formation and resolution cycles recapitulate experimentally observed DNA loop extrusion characteristics. Our model extends to asymmetric and symmetric loop extrusion, as well as z-loop formation. Loop extrusion by biased Brownian motion has important implications for chromosomal cohesin function

Molybdenum sputtering film characterization for high gradient accelerating structures

Technological advancements are strongly required to fulfill the demands of new accelerator devices with the highest accelerating gradients and operation reliability for the future colliders. To this purpose an extensive R&D regarding molybdenum coatings on copper is in progress. In this contribution we describe chemical composition, deposition quality and resistivity properties of different molybdenum coatings obtained via sputtering. The deposited films are thick metallic disorder layers with different resistivity values above and below the molibdenum dioxide reference value. Chemical and electrical properties of these sputtered coatings have been characterized by Rutherford backscattering, XANES and photoemission spectroscopy. We will also present a three cells standing wave section coated by a molybdenum layer $\sim$ 500 nm thick designed to improve the performance of X-Band accelerating systems.Comment: manuscript has been submitted and accepted by Chinese Physics C (2012

Molecular motion in cell membranes: analytic study of fence-hindered random walks

A theoretical calculation is presented to describe the confined motion of transmembrane molecules in cell membranes. The study is analytic, based on Master equations for the probability of the molecules moving as random walkers, and leads to explicit usable solutions including expressions for the molecular mean square displacement and effective diffusion constants. One outcome is a detailed understanding of the dependence of the time variation of the mean square displacement on the initial placement of the molecule within the confined region. How to use the calculations is illustrated by extracting (confinement) compartment sizes from experimentally reported published observations from single particle tracking experiments on the diffusion of gold-tagged G-protein coupled mu-opioid receptors in the normal rat kidney cell membrane, and by further comparing the analytical results to observations on the diffusion of phospholipids, also in normal rat kidney cells.Comment: 10 pages, 5 figure

Quantum-well states in ultrathin Ag(111) films deposited onto H-passivated Si(111)-(1x1) surfaces

Ag(111) films were deposited at room temperature onto H-passivated Si(111)-(1x1) substrates, and subsequently annealed at 300 C. An abrupt non-reactive Ag/Si interface is formed, and very uniform non-strained Ag(111) films of 6-12 monolayers have been grown. Angle resolved photoemission spectroscopy has been used to study the valence band electronic properties of these films. Well-defined Ag sp quantum-well states (QWS) have been observed at discrete energies between 0.5-2eV below the Fermi level, and their dispersions have been measured along the GammaK, GammaMM'and GammaL symmetry directions. QWS show a parabolic bidimensional dispersion, with in-plane effective mass of 0.38-0.50mo, along the GammaK and GammaMM' directions, whereas no dispersion has been found along the GammaL direction, indicating the low-dimensional electronic character of these states. The binding energy dependence of the QWS as a function of Ag film thickness has been analyzed in the framework of the phase accumulation model. According to this model, a reflectivity of 70% has been estimated for the Ag-sp states at the Ag/H/Si(111)-(1x1) interface.Comment: 6 pages, 6 figures, submitted to Phys. Rev.

Effects of disorder in location and size of fence barriers on molecular motion in cell membranes

The effect of disorder in the energetic heights and in the physical locations of fence barriers encountered by transmembrane molecules such as proteins and lipids in their motion in cell membranes is studied theoretically. The investigation takes as its starting point a recent analysis of a periodic system with constant distances between barriers and constant values of barrier heights, and employs effective medium theory to treat the disorder. The calculations make possible, in principle, the extraction of confinement parameters such as mean compartment sizes and mean intercompartmental transition rates from experimentally reported published observations. The analysis should be helpful both as an unusual application of effective medium theory and as an investigation of observed molecular movements in cell membranes.Comment: 9 pages, 5 figure

Current status of the CLIO project

CLIO (Cryogenic Laser Interferometer Observatory) is a Japanese gravitational wave detector project. One of the main purposes of CLIO is to demonstrate thermal-noise suppression by cooling mirrors for a future Japanese project, LCGT (Large-scale Cryogenic Gravitational Telescope). The CLIO site is in Kamioka mine, as is LCGT. The progress of CLIO between 2005 and 2007 (room- and cryogenic-temperature experiments) is introduced in this article. In a room-temperature experiment, we made efforts to improve the sensitivity. The current best sensitivity at 300 K is about $6 \times 10^{-21} /\sqrt{\rm Hz}$ around 400 Hz. Below 20 Hz, the strain (not displacement) sensitivity is comparable to that of LIGO, although the baselines of CLIO are 40-times shorter (CLIO: 100m, LIGO: 4km). This is because seismic noise is extremely small in Kamioka mine. We operated the interferometer at room temperature for gravitational wave observations. We obtained 86 hours of data. In the cryogenic experiment, it was confirmed that the mirrors were sufficiently cooled (14 K). However, we found that the radiation shield ducts transferred 300K radiation into the cryostat more effectively than we had expected. We observed that noise caused by pure aluminum wires to suspend a mirror was suppressed by cooling the mirror.Comment: 8 pages, 9 figures. Amaldi7 proceedings, J. Phys.: Conf. Ser. (accepted

Ising Universality in Three Dimensions: A Monte Carlo Study

We investigate three Ising models on the simple cubic lattice by means of Monte Carlo methods and finite-size scaling. These models are the spin-1/2 Ising model with nearest-neighbor interactions, a spin-1/2 model with nearest-neighbor and third-neighbor interactions, and a spin-1 model with nearest-neighbor interactions. The results are in accurate agreement with the hypothesis of universality. Analysis of the finite-size scaling behavior reveals corrections beyond those caused by the leading irrelevant scaling field. We find that the correction-to-scaling amplitudes are strongly dependent on the introduction of further-neighbor interactions or a third spin state. In a spin-1 Ising model, these corrections appear to be very small. This is very helpful for the determination of the universal constants of the Ising model. The renormalization exponents of the Ising model are determined as y_t = 1.587 (2), y_h = 2.4815 (15) and y_i = -0.82 (6). The universal ratio Q = ^2/ is equal to 0.6233 (4) for periodic systems with cubic symmetry. The critical point of the nearest-neighbor spin-1/2 model is K_c=0.2216546 (10).Comment: 25 pages, uuencoded compressed PostScript file (to appear in Journal of Physics A