Target search on a dynamic DNA molecule

We study a protein-DNA target search model with explicit DNA dynamics applicable to in vitro experiments. We show that the DNA dynamics plays a crucial role for the effectiveness of protein "jumps" between sites distant along the DNA contour but close in 3D space. A strongly binding protein that searches by 1D sliding and jumping alone, explores the search space less redundantly when the DNA dynamics is fast on the timescale of protein jumps than in the opposite "frozen DNA" limit. We characterize the crossover between these limits using simulations and scaling theory. We also rationalize the slow exploration in the frozen limit as a subtle interplay between long jumps and long trapping times of the protein in "islands" within random DNA configurations in solution.Comment: manuscript and supplementary material combined into a single documen

Charmonium suppression from purely geometrical effects

The extend to which geometrical effects contribute to the production and suppression of the $J/\psi$ and $q\bar{q}$ minijet pairs in general is investigated for high energy heavy ion collisions at SPS, RHIC and LHC energies. For the energy range under investigation, the geometrical effects referred to are shadowing and anti-shadowing, respectively. Due to those effects, the parton distributions in nuclei deviate from the naive extrapolation from the free nucleon result; $f_{A}\neq A f_{N}$. The strength of the shadowing/anti-shadowing effect increases with the mass number. The consequences of gluonic shadowing effects for the $x_F$ distribution of $J/\psi$'s at $\sqrt s =20$ GeV, $\sqrt s =200$ GeV and $\sqrt s =6$ TeV are calculated for some relevant combinations of nuclei, as well as the $p_T$ distribution of minijets at midrapidity for $N_f=4$ in the final state.Comment: corrected some typos, improved shadowing ratio

Exact steady-state velocity of ratchets driven by random sequential adsorption

We solve the problem of discrete translocation of a polymer through a pore, driven by the irreversible, random sequential adsorption of particles on one side of the pore. Although the kinetics of the wall motion and the deposition are coupled, we find the exact steady-state distribution for the gap between the wall and the nearest deposited particle. This result enables us to construct the mean translocation velocity demonstrating that translocation is faster when the adsorbing particles are smaller. Monte-Carlo simulations also show that smaller particles gives less dispersion in the ratcheted motion. We also define and compare the relative efficiencies of ratcheting by deposition of particles with different sizes and we describe an associated "zone-refinement" process.Comment: 11 pages, 4 figures New asymptotic result for low chaperone density added. Exact translocation velocity is proportional to (chaperone density)^(1/3

Contribution of deformation to sea-ice mass balance: a case study from an N-ICE2015 storm

The fastest and most efficient process of gaining sea ice volume is through the mechanical redistribution of mass as a consequence of deformation events. During the ice growth season divergent motion produces leads where new ice grows thermodynamically, while convergent motion fractures the ice and either piles the resultant ice blocks into ridges or rafts one floe under the other. Here we present an exceptionally detailed airborne dataset from a 9km2 area of first and second year ice in the Transpolar Drift north of Svalbard that allowed us to estimate the redistribution of mass from an observed deformation event. To achieve this level of detail we analyzed changes in sea ice freeboard acquired from two airborne laser scanner surveys just before and right after a deformation event brought on by a passing low pressure system. A linear regression model based on divergence during this storm can explain 64% of freeboard variability. Over the survey region we estimated that about 1.3% of level sea ice volume was pressed together into deformed ice and the new ice formed in leads in a week after the deformation event would increase the sea ice volume by 0.5%. As the region is impacted by about 15 storms each winter a simple linear extrapolation would result in about 7% volume increase and 20% deformed ice fraction at the end of the seaso

Black carbon in the atmosphere and snow, from pre-industrial times until present

The distribution of black carbon (BC) in the atmosphere and the deposition of BC on snow surfaces since pre-industrial time until present are modelled with the Oslo CTM2 model. The model results are compared with observations including recent measurements of BC in snow in the Arctic. The global mean burden of BC from fossil fuel and biofuel sources increased during two periods. The first period, until 1920, is related to increases in emissions in North America and Europe, and the last period after 1970 are related mainly to increasing emissions in East Asia. Although the global burden of BC from fossil fuel and biofuel increases, in the Arctic the maximum atmospheric BC burden as well as in the snow was reached in 1960s, with a slight reduction thereafter. The global mean burden of BC from open biomass burning sources has not changed significantly since 1900. With current inventories of emissions from open biomass sources, the modelled burden of BC in snow and in the atmosphere north of 65° N is small compared to the BC burden of fossil fuel and biofuel origin. From the concentration changes radiative forcing time series due to the direct aerosol effect as well as the snow-albedo effect is calculated for BC from fossil fuel and biofuel. The calculated radiative forcing in 2000 for the direct aerosol effect is 0.35 W m<sup>−2</sup> and for the snow-albedo effect 0.016 W m<sup>−2</sup> in this study. Due to a southward shift in the emissions there is an increase in the lifetime of BC as well as an increase in normalized radiative forcing, giving a change in forcing per unit of emissions of 26 % since 1950

Force-induced unfolding of a homopolymer on fractal lattice: exact results vs. mean field predictions

We study the force-induced unfolding of a homopolymer on the three dimensional Sierpinski gasket. The polymer is subject to a contact energy between nearest neighbour sites not consecutive along the chain and to a stretching force. The hierarchical nature of the lattice we consider allows for an exact treatment which yields the phase diagram and the critical behaviour. We show that for this model mean field predictions are not correct, in particular in the exact phase diagram there is {\em not} a low temperature reentrance and we find that the force induced unfolding transition below the theta temperature is second order.Comment: 15 pages, 5 eps figure

Probing coherent charmonium photoproduction off light nuclei at medium energies

We demonstrate how the elementary amplitudes $\gamma N\to \Psi N$, the amplitude of the nondiagonal $J/\psi N\Leftrightarrow \psi' N$ transition, and the total $J/\psi N$ and $\psi' N$ cross sections can be determined from measurements of the coherent $J/\psi$ and $\psi'$ photoproduction off light nuclei at moderate energies. For this purpose we provide a detailed numerical analysis of the coherent charmonium photoproduction off silicon within the generalized vector dominance model (GVDM) adjusted to account for the physics of charmonium models and color transparency phenomenon.Comment: 8 pages, 5 figures (color