796 research outputs found
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
The impact of transport across the polar vortex edge on Match ozone loss estimates
The Match method for the quantification of polar chemical ozone loss is investigated mainly with respect to the impact of the transport of air masses across the vortex edge. For the winter 2002/03, we show that significant transport across the vortex edge occurred and was simulated by the Chemical Lagrangian Model of the Stratosphere. In-situ observations of inert tracers and ozone from HAGAR on the Geophysica aircraft and balloon-borne sondes, and remote observations from MIPAS on the ENVISAT satellite were reproduced well by CLaMS. The model even reproduced a small vortex remnant that remained a distinct feature until June 2003 and was also observed in-situ by a balloon-borne whole air sampler. We use this CLaMS simulation to quantify the impact of transport across the vortex edge on ozone loss estimates from the Match method. We show that a time integration of the determined vortex average ozone loss rates, as performed in Match, results in a larger ozone loss than the polar vortex average ozone loss in CLaMS. The determination of the Match ozone loss rates is also influenced by the transport of air across the vortex edge. We use the model to investigate how the sampling of the ozone sondes on which Match is based represents the vortex average ozone loss rate. Both the time integration of ozone loss and the determination of ozone loss rates for Match are evaluated using the winter 2002/2003 CLaMS simulation. These impacts can explain the majority of the differences between CLaMS and Match column ozone loss. While the investigated effects somewhat reduce the apparent discrepancy in January ozone loss rates reported earlier, a distinct discrepancy between simulations and Match remains. However, its contribution to the accumulated ozone loss over the winter is not large
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
The impact of mixing across the polar vortex edge on Match ozone loss estimates
The Match method for quantification of polar chemical ozone loss is investigated mainly with respect to the impact of mixing across the vortex edge onto this estimate. We show for the winter 2002/03 that significant mixing across the vortex edge occurred and was accurately modeled by the Chemical Lagrangian Model of the Stratosphere. Observations of inert tracers and ozone in-situ from HAGAR on the Geophysica aircraft and sondes and also remote from MIPAS on ENVISAT were reproduced well. The model even reproduced a small vortex remnant that was isolated until June 2003 and was observed in-situ by a balloon-borne whole air sampler. We use this CLaMS simulation to quantify the impact of cross vortex edge mixing on the results of the Match method. It is shown that a time integration of the determined vortex average ozone loss rates as performed in Match results in larger ozone loss than the polar vortex average ozone loss in CLaMS. Also, the determination of the Match ozone loss rates can be influenced by mixing. This is especially important below 430 K, where ozone outside the vortex is lower than inside and the vortex boundary is not a strong transport barrier. This effect and further sampling effects cause an offset between vortex average ozone loss rates derived from Match and deduced from CLaMS with an even sampling for the entire vortex. Both, the time-integration of ozone loss and the determination of ozone loss rates for Match are evaluated using the winter 2002/03 CLaMS simulation. These impacts can explain the differences between CLaMS and Match column ozone loss. While the investigated effects somewhat reduce the apparent discrepancy in January ozone loss rates, a discrepancy between simulations and Match remains. However, its contribution to the accumulated ozone loss over the winter is not large
Flow in linearly sheared two dimensional foams: from bubble to bulk scale
We probe the flow of two dimensional foams, consisting of a monolayer of
bubbles sandwiched between a liquid bath and glass plate, as a function of
driving rate, packing fraction and degree of disorder. First, we find that
bidisperse, disordered foams exhibit strongly rate dependent and inhomogeneous
(shear banded) velocity profiles, while monodisperse, ordered foams are also
shear banded, but essentially rate independent. Second, we introduce a simple
model based on balancing the averaged drag forces between the bubbles and the
top plate and the averaged bubble-bubble drag forces. This model captures the
observed rate dependent flows, and the rate independent flows. Third, we
perform independent rheological measurements, both for ordered and disordered
systems, and find these to be fully consistent with the scaling forms of the
drag forces assumed in the simple model, and we see that disorder modifies the
scaling. Fourth, we vary the packing fraction of the foam over a
substantial range, and find that the flow profiles become increasingly shear
banded when the foam is made wetter. Surprisingly, our model describes flow
profiles and rate dependence over the whole range of packing fractions with the
same power law exponents -- only a dimensionless number which measures the
ratio of the pre-factors of the viscous drag laws is seen to vary with packing
fraction. We find that , where , corresponding to the 2d jamming density, and suggest that this scaling
follows from the geometry of the deformed facets between bubbles in contact.
Overall, our work suggests a route to rationalize aspects of the ubiquitous
Herschel-Bulkley (power law) rheology observed in a wide range of disordered
materials.Comment: 16 pages, 14 figures, submitted to Phys. Rev. E. High quality version
available at: http://www.physics.leidenuniv.nl/sections/cm/gr
The Effect of Air on Granular Size Separation in a Vibrated Granular Bed
Using high-speed video and magnetic resonance imaging (MRI) we study the
motion of a large sphere in a vertically vibrated bed of smaller grains. As
previously reported we find a non-monotonic density dependence of the rise and
sink time of the large sphere. We find that this density dependence is solely
due to air drag. We investigate in detail how the motion of the intruder sphere
is influenced by size of the background particles, initial vertical position in
the bed, ambient pressure and convection. We explain our results in the
framework of a simple model and find quantitative agreement in key aspects with
numerical simulations to the model equations.Comment: 14 pages, 16 figures, submitted to PRE, corrected typos, slight
change
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
A quasi-Lagrangian coordinate system based on high resolution tracer observations: implementation for the Antarctic polar vortex
In order to quantitatively analyse the chemical and dynamical evolution of the polar vortex it has proven extremely useful to work with coordinate systems that follow the vortex flow. We propose here a two-dimensional quasi-Lagrangian coordinate system {X i, delta X i}, based on the mixing ratio of a long-lived stratospheric trace gas i, and its systematic use with i = N2O, in order to describe the structure of a well-developed Antarctic polar vortex. In the coordinate system {X i, delta X i} the mixing ratio X i is the vertical coordinate and delta X i = X i(theta) - X i vort(theta) is the meridional coordinate (X i vort(theta) being a vertical reference profile in the vortex core). The quasi-Lagrangian coordinates {X i, delta X i} persist for much longer time than standard isentropic coordinates, potential temperature theta and equivalent latitude Phi e, do not require explicit reference to geographic space, and can be derived directly from high-resolution in situ measurements. They are therefore well-suited for studying the evolution of the Antarctic polar vortex throughout the polar winter with respect to the relevant chemical and microphysical processes. By using the introduced coordinate system {X N2O, delta X N2O} we analyze the well-developed Antarctic vortex investigated during the APE-GAIA (Airborne Polar Experiment – Geophysica Aircraft in Antarctica – 1999) campaign (Carli et al., 2000). A criterion, which uses the local in-situ measurements of X i=X i(theta) and attributes the inner vortex edge to a rapid change (delta-step) in the meridional profile of the mixing ratio X i, is developed to determine the (Antarctic) inner vortex edge. In turn, we suggest that the outer vortex edge of a well-developed Antarctic vortex can be attributed to the position of a local minimum of the X H2O gradient in the polar vortex area. For a well-developed Antarctic vortex, the delta X N2O-parametrization of tracer-tracer relationships allows to distinguish the tracer inter-relationships in the vortex core, vortex boundary region and surf zone and to examine their meridional variation throughout these regions. This is illustrated by analyzing the tracer-tracer relationships X i : X N2O obtained from the in-situ data of the APE-GAIA campaign for i = CFC-11, CFC-12, H-1211 and SF6. A number of solitary anomalous points in the CFC-11 : N2O correlation, observed in the Antarctic vortex core, are interpreted in terms of small-scale cross-isentropic dispersion
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