Experimental and theoretical studies of sequence effects on the fluctuation and melting of short DNA molecules

Understanding the melting of short DNA sequences probes DNA at the scale of the genetic code and raises questions which are very different from those posed by very long sequences, which have been extensively studied. We investigate this problem by combining experiments and theory. A new experimental method allows us to make a mapping of the opening of the guanines along the sequence as a function of temperature. The results indicate that non-local effects may be important in DNA because an AT-rich region is able to influence the opening of a base pair which is about 10 base pairs away. An earlier mesoscopic model of DNA is modified to correctly describe the time scales associated to the opening of individual base pairs well below melting, and to properly take into account the sequence. Using this model to analyze some characteristic sequences for which detailed experimental data on the melting is available [Montrichok et al. 2003 Europhys. Lett. {\bf 62} 452], we show that we have to introduce non-local effects of AT-rich regions to get acceptable results. This brings a second indication that the influence of these highly fluctuating regions of DNA on their neighborhood can extend to some distance.Comment: To be published in J. Phys. Condensed Matte

A Novel Multi-parameter Family of Quantum Systems with Partially Broken N-fold Supersymmetry

We develop a systematic algorithm for constructing an N-fold supersymmetric system from a given vector space invariant under one of the supercharges. Applying this algorithm to spaces of monomials, we construct a new multi-parameter family of N-fold supersymmetric models, which shall be referred to as "type C". We investigate various aspects of these type C models in detail. It turns out that in certain cases these systems exhibit a novel phenomenon, namely, partial breaking of N-fold supersymmetry.Comment: RevTeX 4, 28 pages, no figure

Clustering transition in a system of particles self-consistently driven by a shear flow

We introduce a simple model of active transport for an ensemble of particles driven by an external shear flow. Active refers to the fact that the flow of the particles is modified by the distribution of particles itself. The model consists in that the effective velocity of every particle is given by the average of the external flow velocities felt by the particles located at a distance less than a typical radius, $R$. Numerical analysis reveals the existence of a transition to clustering depending on the parameters of the external flow and on $R$. A continuum description in terms of the number density of particles is derived, and a linear stability analysis of the density equation is performed in order to characterize the transitions observed in the model of interacting particles.Comment: 11 pages, 2 figures. To appear in PR

Source identification and quantification of particulate matter emitted from livestock houses

There is need to identify and quantify the contribution of different sources to airborne particulate matter (PM) emissions from animal houses. To this end, we compared the chemical and morphological characteristics of fine and coarse PM from known sources collected from animal houses with the characteristics of on-farm fine and coarse airborne PM using two methods: classification rules based on decision trees and multiple linear regression. Fourteen different farms corresponding to seven different housing systems for poultry and pigs were sampled during winter. A total of 28 fine and 28 coarse on-farm airborne PM samples were collected, together with a representative sample of each known source per farm (56 known source samples in total). Source contributions were calculated as relative percentage contributions in particle numbers and then estimated in particle mass. Based on particle numbers, results showed that in poultry houses, most on-farm airborne PM originated from feathers (ranging from 4% to 43% in fine PM and from 6% to 35% in coarse PM) and manure (ranging from 9% to 85% in fine PM and from 30% to 94% in coarse PM). For pigs, most on-farm airborne PM originated from manure (ranging from 70% to 98% in fine PM and from 41% to 94% in coarse PM). Based on particle mass, for poultry most on-farm airborne PM still originated from feathers and manure; for pigs, however, most PM originated from skin and manure. Feed had a negligible contribution to on-farm airborne PM compared with other sources. Results presented in this study improve the understanding of sources of PM in different animal housing systems, which may be valuable when choosing optimal PM reduction technique

Morpho-kinematic analysis of the point-symmetric, bipolar planetary nebulae Hb 5 and K 3-17, a pathway to poly-polarity

The kinematics of the bipolar planetary nebulae Hb~5 and K 3-17 are investigated in detail by means of a comprehensive set of spatially resolved high spectral resolution, long-slit spectra. Both objects share particularly interesting characteristics, such as a complex filamentary, rosette-type nucleus, axial point-symmetry and very fast bipolar outflows. The kinematic information of Hb~5 is combined with {\it HST} imagery to construct a detailed 3D model of the nebula using the code SHAPE. The model shows that the large scale lobes are growing in a non-homologous way. The filamentary loops in the core are proven to actually be secondary lobes emerging from what appears to be a randomly punctured, dense, gaseous core and the material that forms the point symmetric structure flows within the lobes with a distinct kinematic pattern and its interaction with the lobes has had a shaping effect on them. Hb~5 and K~3-17 may represent a class of fast evolving planetary nebulae that will develop poly-polar characteristics once the nebular core evolves and expands.Comment: 19 pages, 8 figures. To appear in The Astrophysical Journa

Scaling Approach to Calculate Critical Exponents in Anomalous Surface Roughening

We study surface growth models exhibiting anomalous scaling of the local surface fluctuations. An analytical approach to determine the local scaling exponents of continuum growth models is proposed. The method allows to predict when a particular growth model will have anomalous properties ($\alpha \neq \alpha_{loc}$) and to calculate the local exponents. Several continuum growth equations are examined as examples.Comment: RevTeX, 4 pages, no figs. To appear in Phys. Rev. Let