DNA loop statistics and torsional modulus

The modelling of DNA mechanics under external constraints is discussed. Two analytical models are widely known, but disagree for instance on the value of the torsional modulus. The origin of this embarassing situation is located in the concept of writhe. This letter presents a unified model for DNA establishing a relation between the different approaches. I show that the writhe created by the loops of DNA is at the origin of the discrepancy. To take this into account, I propose a new treatment of loop statistics based on numerical simulations using the most general formula for the writhe, and on analytic calculations with only one fit parameter. One can then compute the value of the torsional modulus of DNA without the need of any cut-off.Comment: 8 pages, 1 figure. Accepted by Europhysics Letter

Non-equilibrium Lorentz gas on a curved space

The periodic Lorentz gas with external field and iso-kinetic thermostat is equivalent, by conformal transformation, to a billiard with expanding phase-space and slightly distorted scatterers, for which the trajectories are straight lines. A further time rescaling allows to keep the speed constant in that new geometry. In the hyperbolic regime, the stationary state of this billiard is characterized by a phase-space contraction rate, equal to that of the iso-kinetic Lorentz gas. In contrast to the iso-kinetic Lorentz gas where phase-space contraction occurs in the bulk, the phase-space contraction rate here takes place at the periodic boundaries

Efficiency of Free Energy Transduction in Autonomous Systems

We consider the thermodynamics of chemical coupling from the viewpoint of free energy transduction efficiency. In contrast to an external parameter-driven stochastic energetics setup, the dynamic change of the equilibrium distribution induced by chemical coupling, adopted, for example, in biological systems, is inevitably an autonomous process. We found that the efficiency is bounded by the ratio between the non-symmetric and the symmetrized Kullback-Leibler distance, which is significantly lower than unity. Consequences of this low efficiency are demonstrated in the simple two-state case, which serves as an important minimal model for studying the energetics of biomolecules.Comment: 4 pages, 4 figure

Force dependent fragility in RNA hairpins

We apply Kramers theory to investigate the dissociation of multiple bonds under mechanical force and interpret experimental results for the unfolding/refolding force distributions of an RNA hairpin pulled at different loading rates using laser tweezers. We identify two different kinetic regimes depending on the range of forces explored during the unfolding and refolding process. The present approach extends the range of validity of the two-states approximation by providing a theoretical framework to reconstruct free-energy landscapes and identify force-induced structural changes in molecular transition states using single molecule pulling experiments. The method should be applicable to RNA hairpins with multiple kinetic barriers.Comment: Latex file, 4 pages+3 figure

Radioisotopes demonstrate the contrasting bioaccumulation capacities of heavy metals in embryonic stages of cephalopod species

Cephalopods play a key role in many marine trophic food webs and also constitute alternative fishery resources in the context of the ongoing decline in finfish stocks. Most coastal cephalopod species of commercial importance migrate into shallow waters during the breeding season to lay their eggs, and are consequently subjected to coastal contamination. Eggs of common cuttlefish Sepia officinalis, European squid Loligo vulgaris, common octopus Octopus vulgaris and the sepiolid Rossia macrosoma were exposed during embryonic development to dissolved 110mAg, 109Cd, 60Co, 54Mn and 65Zn in order to determine their metal accumulation efficiencies and distribution among different egg compartments. Cuttlefish eggs, in which hard shells enclose the embryos, showed the lowest concentration factor (CF) values despite a longer duration of exposure. In contrast, octopus eggs, which are only protected by the chorionic membrane, accumulated the most metal. Uptake appears to be linked to the selective retention properties of the egg envelopes with respect to each element. The study also demonstrated that the octopus embryo accumulated 110mAg directly from the dissolved phase and also indirectly through assimilation of the contaminated yolk. These results raise questions regarding the potential contrasting vulnerability of early life stages of cephalopods to the metallic contamination of coastal water

A numerical approach to large deviations in continuous-time

We present an algorithm to evaluate the large deviation functions associated to history-dependent observables. Instead of relying on a time discretisation procedure to approximate the dynamics, we provide a direct continuous-time algorithm, valuable for systems with multiple time scales, thus extending the work of Giardin\`a, Kurchan and Peliti (PRL 96, 120603 (2006)). The procedure is supplemented with a thermodynamic-integration scheme, which improves its efficiency. We also show how the method can be used to probe large deviation functions in systems with a dynamical phase transition -- revealed in our context through the appearance of a non-analyticity in the large deviation functions.Comment: Submitted to J. Stat. Mec

Elasticity model of a supercoiled DNA molecule

Within a simple elastic theory, we study the elongation versus force characteristics of a supercoiled DNA molecule at thermal equilibrium in the regime of small supercoiling. The partition function is mapped to the path integral representation for a quantum charged particle in the field of a magnetic monopole with unquantized charge. We show that the theory is singular in the continuum limit and must be regularised at an intermediate length scale. We find good agreement with existing experimental data, and point out how to measure the twist rigidity accurately.Comment: Latex, 4 pages. The figure contains new experimental data, giving a new determination of the twist rigidit

Global assessment of nitrogen deposition effects on terrestrial plant diversity : a synthesis

Atmospheric nitrogen (N) deposition is it recognized threat to plant diversity ill temperate and northern parts of Europe and North America. This paper assesses evidence from field experiments for N deposition effects and thresholds for terrestrial plant diversity protection across a latitudinal range of main categories of ecosystems. from arctic and boreal systems to tropical forests. Current thinking on the mechanisms of N deposition effects on plant diversity, the global distribution of G200 ecoregions, and current and future (2030) estimates of atmospheric N-deposition rates are then used to identify the risks to plant diversity in all major ecosystem types now and in the future. This synthesis paper clearly shows that N accumulation is the main driver of changes to species composition across the whole range of different ecosystem types by driving the competitive interactions that lead to composition change and/or making conditions unfavorable for some species. Other effects such its direct toxicity of nitrogen gases and aerosols long-term negative effects of increased ammonium and ammonia availability, soil-mediated effects of acidification, and secondary stress and disturbance are more ecosystem, and site-specific and often play a supporting role. N deposition effects in mediterranean ecosystems have now been identified, leading to a first estimate of an effect threshold. Importantly, ecosystems thought of as not N limited, such as tropical and subtropical systems, may be more vulnerable in the regeneration phase. in situations where heterogeneity in N availability is reduced by atmospheric N deposition, on sandy soils, or in montane areas. Critical loads are effect thresholds for N deposition. and the critical load concept has helped European governments make progress toward reducing N loads on sensitive ecosystems. More needs to be done in Europe and North America. especially for the more sensitive ecosystem types. including several ecosystems of high conservation importance. The results of this assessment Show that the Vulnerable regions outside Europe and North America which have not received enough attention are ecoregions in eastern and Southern Asia (China, India), an important part of the mediterranean ecoregion (California, southern Europe). and in the coming decades several subtropical and tropical parts of Latin America and Africa. Reductions in plant diversity by increased atmospheric N deposition may be more widespread than first thought, and more targeted Studies are required in low background areas, especially in the G200 ecoregions

Inferring the effective thickness of polyelectrolytes from stretching measurements at various ionic strengths: applications to DNA and RNA

By resorting to the thick-chain model we discuss how the stretching response of a polymer is influenced by the self-avoidance entailed by its finite thickness. The characterization of the force versus extension curve for a thick chain is carried out through extensive stochastic simulations. The computational results are captured by an analytic expression that is used to fit experimental stretching measurements carried out on DNA and single-stranded RNA (poly-U) in various solutions. This strategy allows us to infer the apparent diameter of two biologically-relevant polyelectrolytes, namely DNA and poly-U, for different ionic strengths. Due to the very different degree of flexibility of the two molecules, the results provide insight into how the apparent diameter is influenced by the interplay between the (solution-dependent) Debye screening length and the polymers' ``bare'' thickness. For DNA, the electrostatic contribution to the effective radius, $\Delta$, is found to be about 5 times larger than the Debye screening length, consistently with previous theoretical predictions for highly-charged stiff rods. For the more flexible poly-U chains the electrostatic contribution to $\Delta$ is found to be significantly smaller than the Debye screening length.Comment: iopart, 14 pages, 13 figures, to appear in J. Phys.: Condens. Matte

Sequence Effects on DNA Entropic Elasticity

DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by this method is a combination of bend stiffness and intrinsic bend effects reflecting sequence information, just as at zero stretching force. This observation resolves the discrepancy between the value of A measured in these experiments and the larger ``dynamic persistence length'' measured by other means. On the other hand, the twist persistence length deduced from torsionally-constrained stretching experiments suffers no such correction. Our calculation is very simple and analytic; it applies to DNA and other polymers with weak intrinsic disorder.Comment: LaTeX; postscript available at http://dept.physics.upenn.edu/~nelson/index.shtm