The classifying space of a bound quiver

We associate to a bound quiver (Q,I) a CW-complex which we denote by B(Q,I), and call the classifying space of (Q,I). We show that the fundamental group of B(Q,I) is isomorphic to the fundamental group of (Q,I). Moreover, we show that this construction behaves well with respect to coverings. On the other hand, we study the (co)homology groups of B(Q,I), and compare them with the simplicial and the Hochschild (co)homology groups of the algebra A=kQ/I. More precisely, we give sufficient conditions for these groups to be isomorphic. This generalizes a theorem due to Gerstenhaber and Schack.Comment: Revised version. To appear in J. Algebra. 22 pages, 3 postscript figure

Force induced stretched state: Effects of temperature

A model of self avoiding walks with suitable constraint has been developed to study the effect of temperature on a single stranded DNA (ssDNA) in the constant force ensemble. Our exact calculations for small chains show that the extension (reaction co-ordinate) may increase or decrease with the temperature depending upon the applied force. The simple model developed here which incorporates semi-microscopic details of base direction provide an explanation of the force induced transitions in ssDNA as observed in experiments.Comment: 5 pages, 8 figures, RevTex

The response of Musa cultivar root systems to a tree shade gradient

Poster presented at Tropentag 2011 - Development on the Margin. Bonn (Germany), 3-7 Oct 2011

Effects of Eye-phase in DNA unzipping

The onset of an "eye-phase" and its role during the DNA unzipping is studied when a force is applied to the interior of the chain. The directionality of the hydrogen bond introduced here shows oscillations in force-extension curve similar to a "saw-tooth" kind of oscillations seen in the protein unfolding experiments. The effects of intermediates (hairpins) and stacking energies on the melting profile have also been discussed.Comment: RevTeX v4, 9 pages with 7 eps figure

Condensation transition in DNA-polyaminoamide dendrimer fibers studied using optical tweezers

When mixed together, DNA and polyaminoamide (PAMAM) dendrimers form fibers that condense into a compact structure. We use optical tweezers to pull condensed fibers and investigate the decondensation transition by measuring force-extension curves (FECs). A characteristic plateau force (around 10 pN) and hysteresis between the pulling and relaxation cycles are observed for different dendrimer sizes, indicating the existence of a first-order transition between two phases (condensed and extended) of the fiber. The fact that we can reproduce the same FECs in the absence of additional dendrimers in the buffer medium indicates that dendrimers remain irreversibly bound to the DNA backbone. Upon salt variation FECs change noticeably confirming that electrostatic forces drive the condensation transition. Finally, we propose a simple model for the decondensing transition that qualitatively reproduces the FECs and which is confirmed by AFM images.Comment: Latex version, 4 pages+3 color figure

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

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

Evaluation of Eta Model seasonal precipitation forecasts over South America

International audienceSeasonal forecasts run by the Eta Model over South America were evaluated with respect to precipitation predictability at different time scales, seasonal, monthly and weekly for one-year period runs. The model domain was configured over most of South America in 40km horizontal resolution and 38 layers. The lateral boundary conditions were taken from CPTEC GCM forecasts at T62L28. The sea surface temperature was updated daily with persisted anomaly during the integrations. The total time integration length was 4.5 months. The Eta seasonal forecasts represented reasonably well the large scale precipitation systems over South America such as the Intertropical Convergence Zone and the South Atlantic Convergence Zone. The total amounts were comparable to observations. The season total precipitation forecasts from the driver model exhibited large overestimate. In general, the largest precipitation errors were found in ASON season and the smallest in FMAM. The major error areas were located along the northern and northeastern coast and over the Andes. These areas were present in both models. The monthly precipitation totals indicated that the intra-seasonal variability, such as the monsoonal onset, was reasonably captured by the model. The equitable threat score and the bias score showed that the Eta Model forecasts had higher precipitation predictability over the Amazon Region and lower over Northeast Brazil. The evaluation of the precipitation forecast range showed that at the fourth month the forecast skill was still comparable to the first month of integration. Comparisons with the CPTEC GCM forecasts showed that the Eta improved considerably the forecasts from the driver model. Five-member ensemble runs were produced for the NDJF rainy season. Both driver model and Eta Model forecasts showed some internal variability in the SACZ and over the Andes regions. Comparison of the Eta Model seasonal forecasts against climatology showed that in general the model produced additional useful information over the climatology. Transient variability was evaluated by tracking the frontal passages along the eastern coast. The frontal timing was no longer captured by the model but some indication of the frequency and of the northward movement was given by the model forecast. Weekly precipitation totals were evaluated for the São Francisco Basin. Some parameters, such as the mean and the standard deviation of the 7-day total precipitation, were comparable to observations. The correlations between the forecast and the observed 7-day series were positive, but low

A charged particle in a magnetic field - Jarzynski Equality

We describe some solvable models which illustrate the Jarzynski theorem and related fluctuation theorems. We consider a charged particle in the presence of magnetic field in a two dimensional harmonic well. In the first case the centre of the harmonic potential is translated with a uniform velocity, while in the other case the particle is subjected to an ac force. We show that Jarzynski identity complements Bohr-van Leeuwen theorem on the absence of diamagnetism in equilibrium classical system.Comment: 5 pages, minor corrections made and journal reference adde