Localization of Denaturation Bubbles in Random DNA Sequences

We study the thermodynamic and dynamic behaviors of twist-induced denaturation bubbles in a long, stretched random sequence of DNA. The small bubbles associated with weak twist are delocalized. Above a threshold torque, the bubbles of several tens of bases or larger become preferentially localized to \AT-rich segments. In the localized regime, the bubbles exhibit ``aging'' and move around sub-diffusively with continuously varying dynamic exponents. These properties are derived using results of large-deviation theory together with scaling arguments, and are verified by Monte-Carlo simulations.Comment: TeX file with postscript figure

Statistical Mechanics of Torque Induced Denaturation of DNA

A unifying theory of the denaturation transition of DNA, driven by temperature T or induced by an external mechanical torque Gamma is presented. Our model couples the hydrogen-bond opening and the untwisting of the helicoidal molecular structure. We show that denaturation corresponds to a first-order phase transition from B-DNA to d-DNA phases and that the coexistence region is naturally parametrized by the degree of supercoiling sigma. The denaturation free energy, the temperature dependence of the twist angle, the phase diagram in the T,Gamma plane and isotherms in the sigma, Gamma plane are calculated and show a good agreement with experimental data.Comment: 5 pages, 3 figures, model improve

Periodically driven stochastic un- and refolding transitions of biopolymers

Mechanical single molecule experiments probe the energy profile of biomolecules. We show that in the case of a profile with two minima (like folded/unfolded) periodic driving leads to a stochastic resonance-like phenomenon. We demonstrate that the analysis of such data can be used to extract four basic parameters of such a transition and discuss the statistical requirements of the data acquisition. As advantages of the proposed scheme, a polymeric linker is explicitly included and thermal fluctuations within each well need not to be resolved.Comment: 7 pages, 5 figures, submitted to EP

Nutritional composition of browse and diets fed to ungulates at the Breeding Centre for Endangered Arabian Wildlife

Captive browsing ruminants are particularly susceptible to gastrointestinal disorders, and inappropriate diets are an underlying factor. This study investigated the nutritional composition of browse and pelleted feedstuffs used in an Arabian facility and compared nutrient intake against current recommendations for exotic ungulates. Additionally, retrospective evaluation of post-mortem findings with regard to gastrointestinal pathologies was conducted (n = 497). Samples of browse from seven species of locally cultivated plants, as well as three brands of pelleted feeds, were submitted for laboratory analysis. Following a five-day feed intake study, nutrient intake was calculated. Only moderate variation was seen among browse species’ composition compared to previous reports. However, significant variation occurred between plant fractions (stem, leaves and seed pods) for neutral detergent fibre and several minerals. Browse comprised over half of the metabolisable energy (ME) intake of Arabian tahr (rabitragus jayakari), but only 11% of ME for Arabian gazelle (Gazella gazella cora) and Dorcas gazelle (G. gazella dorcas). However, no relationship could be detected between gastrointestinal disease and browse provision in these species. No nutrient deficiencies were identified, but the Arabian tahr diet exceeded the recommended amount of crude protein, and both gazelle diets provided excess iron, manganese, copper and zinc. These mineral excesses are the subject of on-going investigations in order to better balance the diets offered. Moreover, the high starch content of pelleted diets evaluated in the current study (22-29%, on a dry matter basis) indicates that a reduction in the proportional provision of pellets would improve the diet suitability, particularly for the gazelles. This study highlights a number of areas for potential improvement, although further research is required to fully understand the implications of these findings

Stretching Instability of Helical Spring

We show that when a gradually increasing tensile force is applied to the ends of a helical spring with sufficiently large ratios of radius to pitch and twist to bending rigidity, the end-to-end distance undergoes a sequence of discontinuous stretching transitions. Subsequent decrease of the force leads to step-like contraction and hysteresis is observed. For finite helices, the number of these transitions increases with the number of helical turns but only one stretching and one contraction instability survive in the limit of an infinite helix. We calculate the critical line that separates the region of parameters in which the deformation is continuous from that in which stretching instabilities occur, and propose experimental tests of our predictions.Comment: 5 pages, 4 figure

Getting DNA twist rigidity from single molecule experiments

We use an elastic rod model with contact to study the extension versus rotation diagrams of single supercoiled DNA molecules. We reproduce quantitatively the supercoiling response of overtwisted DNA and, using experimental data, we get an estimation of the effective supercoiling radius and of the twist rigidity of B-DNA. We find that unlike the bending rigidity, the twist rigidity of DNA seems to vary widely with the nature and concentration of the salt buffer in which it is immerged

Layering transitions for adsorbing polymers in poor solvents

An infinite hierarchy of layering transitions exists for model polymers in solution under poor solvent or low temperatures and near an attractive surface. A flat histogram stochastic growth algorithm known as FlatPERM has been used on a self- and surface interacting self-avoiding walk model for lengths up to 256. The associated phases exist as stable equilibria for large though not infinite length polymers and break the conjectured Surface Attached Globule phase into a series of phases where a polymer exists in specified layer close to a surface. We provide a scaling theory for these phases and the first-order transitions between them.Comment: 4 pages, 4 figure

The antiparallel loops in gal DNA

Interactions between proteins bound to distant sites along a DNA molecule require bending and twisting deformations in the intervening DNA. In certain systems, the sterically allowed protein–DNA and protein–protein interactions are hypothesized to produce loops with distinct geometries that may also be thermodynamically and biologically distinct. For example, theoretical models of Gal repressor/HU-mediated DNA-looping suggest that the antiparallel DNA loops, A1 and A2, are thermodynamically quite different. They are also biologically different, since in experiments using DNA molecules engineered to form only one of the two loops, the A2 loop failed to repress in vitro transcription. Surprisingly, single molecule measurements show that both loop trajectories form and that they appear to be quite similar energetically and kinetically

Thermal Fluctuations of Elastic Filaments with Spontaneous Curvature and Torsion

We study the effects of thermal flucutations on thin elastic filaments with spontaneous curvature and torsion. We derive analytical expressions for the orientational correlation functions and for the persistence length of helices, and find that this length varies non-monotonically with the strength of thermal fluctuations. In the weak fluctuation regime, the persistence length of a spontaneously twisted helix has three resonance peaks as a function of the twist rate. In the limit of strong fluctuations, all memory of the helical shape is lost.Comment: 1 figur

Single molecule experiments in biophysics: exploring the thermal behavior of nonequilibrium small systems

Biomolecules carry out very specialized tasks inside the cell where energies involved are few tens of k_BT, small enough for thermal fluctuations to be relevant in many biomolecular processes. In this paper I discuss a few concepts and present some experimental results that show how the study of fluctuation theorems applied to biomolecules contributes to our understanding of the nonequilibrium thermal behavior of small systems.Comment: Proceedings of the 22nd Statphys Conference 2004 (Bangalore,India). Invited contributio