Unifying thermodynamic and kinetic descriptions of single-molecule processes: RNA unfolding under tension

We use mesoscopic non-equilibrium thermodynamics theory to describe RNA unfolding under tension. The theory introduces reaction coordinates, characterizing a continuum of states for each bond in the molecule. The unfolding considered is so slow that one can assume local equilibrium in the space of the reaction coordinates. In the quasi-stationary limit of high sequential barriers, our theory yields the master equation of a recently proposed sequential-step model. Non-linear switching kinetics is found between open and closed states. Our theory unifies the thermodynamic and kinetic descriptions and offers a systematic procedure to characterize the dynamics of the unfolding processComment: 13 pages, 3 figure

Comparison of the Ultra-High Energy Cosmic Ray Flux Observed by AGASA, HiRes and Auger

The current measurements of the cosmic ray energy spectrum at ultra-high energies ($\text{E}>10^{19}$ eV) are characterized by large systematic errors and poor statistics. In addition, the experimental results of the two experiments with the largest published data sets, AGASA and HiRes, appear to be inconsistent with each other, with AGASA seeing an unabated continuation of the energy spectrum even at energies beyond the GZK cutoff energy at $10^{19.6}$ eV. Given the importance of the related astrophysical questions regarding the unknown origin of these highly energetic particles, it is crucial that the extent to which these measurements disagree be well understood. Here we evaluate the consistency of the two measurements for the first time with a model-independent method that accounts for the large statistical and systematic errors of current measurements. We further compare the AGASA and HiRes spectra with the recently presented Auger spectrum. The method directly compares two measurements, bypassing the introduction of theoretical models for the shape of the energy spectrum. The inconsistency between the observations is expressed in terms of a Bayes Factor, a standard statistic defined as the ratio of a separate parent source hypothesis to a single parent source hypothesis. Application to the data shows that the two-parent hypothesis is disfavored. We expand the method to allow comparisons between an experimental flux and that predicted by any model.Comment: accepted by Phys. Rev.

Geo-scientific characterisation of the Boom Clay in the Netherlands in light of permanent confinement of radio-active waste

Recently, the OPERA research program has been initiated in the Netherlands. Its central objective is to develop initial, conditional safety cases for repositories in the Boom Clay and Zechstein rocksalt formations. TNO Geological Survey of the Netherlands has been granted two projects that deal with the geoscientific characterisation of the Tertiairy Boom Clay in the Netherlands, one of which is in cooperation with Utrecht University. The set-up of these projects is presented..

Langevin dynamics with dichotomous noise; direct simulation and applications

We consider the motion of a Brownian particle moving in a potential field and driven by dichotomous noise with exponential correlation. Traditionally, the analytic as well as the numerical treatments of the problem, in general, rely on Fokker-Planck description. We present a method for direct numerical simulation of dichotomous noise to solve the Langevin equation. The method is applied to calculate nonequilibrium fluctuation induced current in a symmetric periodic potential using asymmetric dichotomous noise and compared to Fokker-Planck-Master equation based algorithm for a range of parameter values. Our second application concerns the study of resonant activation over a fluctuating barrier.Comment: Accepted in Journal of Statistical Mechanics: Theory and Experimen

Calibration of the Milagro Cosmic Ray Telescope

The Milagro detector is an air shower array which uses the water Cherenkov technique and is capable of continuously monitoring the sky at energies near 1 TeV. The detector consists of 20000 metric tons of pure water instrumented with 723 photo-multiplier tubes (PMTs). The PMTs are arranged in a two-layer structure on a lattice of 3 m spacing covering 5000 $m^2$ area. The direction of the shower is determined from the relative timing of the PMT signals, necessitating a common time reference and amplitude slewing corrections to improve the time resolution. The calibration system to provide these consists of a pulsed laser driving 30 diffusing light sources deployed in the pond to allow cross-calibration of the PMTs. The system is capable of calibrating times and the pulse-heights from the PMTs using the time-over-threshold technique. The absolute energy scale is provided using single muons passing through the detector. The description of the calibration system of the Milagro detector and its prototype Milagrito will be presented.Comment: 4 pages, submitted to the XXVI International Cosmic Ray Conferenc

Study of the Shadows of the Moon and the Sun with VHE Cosmic Rays

Milagrito, a prototype for the Milagro detector, operated for 15 months in 1997-8 and collected 8.9 billion events. It was the first extensive air shower (EAS) array sensitive to showers intiated by primaries with energy below 1 TeV. The shadows of the sun and moon observed with cosmic rays can be used to study systematic pointing shifts and measure the angular resolution of EAS arrays. Below a few TeV, the paths of cosmic rays coming toward the earth are bent by the helio- and geo-magnetic fields. This is expected to distort and displace the shadows of the sun and the moon. The moon shadow, offset from the nominal (undeflected) position, has been observed with high statistical significance in Milagrito. This can be used to establish energy calibrations, as well as to search for the anti-matter content of the VHE cosmic ray flux. The shadow of the sun has also been observed with high significance.Comment: 4 pages, submitted to XXVI International Cosmic Ray Conference, Salt Lake Cit