Macroscopic loop formation in circular DNA denaturation

The statistical mechanics of DNA denaturation under fixed linking number is qualitatively different from that of the unconstrained DNA. Quantitatively different melting scenarios are reached from two alternative assumptions, namely, that the denatured loops are formed in expense of 1) overtwist, 2) supercoils. Recent work has shown that the supercoiling mechanism results in a BEC-like picture where a macroscopic loop appears at Tc and grows steadily with temperature, while the nature of the denatured phase for the overtwisting case has not been studied. By extending an earlier result, we show here that a macroscopic loop appears in the overtwisting scenario as well. We calculate its size as a function of temperature and show that the fraction of the total sum of microscopic loops decreases above Tc, with a cusp at the critical point.Comment: 5 pages, 3 figures, submitted for publicatio

A two-state model for helicase translocation and unwinding of nucleic acids

Helicases are molecular motors that unwind double-stranded nucleic acids (dsNA), such as DNA and RNA). Typically a helicase translocates along one of the NA single strands while unwinding and uses adenosine triphosphate (ATP) hydrolysis as an energy source. Here we model of a helicase motor that can switch between two states, which could represent two different points in the ATP hydrolysis cycle. Our model is an extension of the earlier Betterton-J\"ulicher model of helicases to incorporate switching between two states. The main predictions of the model are the speed of unwinding of the dsNA and fluctuations around the average unwinding velocity. Motivated by a recent claim that the NS3 helicase of Hepatitis C virus follows a flashing ratchet mechanism, we have compared the experimental results for the NS3 helicase with a special limit of our model which corresponds to the flashing ratchet scenario. Our model accounts for one key feature of the experimental data on NS3 helicase. However, contradictory observations in experiments carried out under different conditions limit the ability to compare the model to experiments.Comment: minor modification

Wrapping Transition and Wrapping-Mediated Interactions for Discrete Binding along an Elastic Filament: An Exact Solution

The wrapping equilibria of one and two adsorbing cylinders are studied along a semi-flexible filament (polymer) due to the interplay between elastic rigidity and short-range adhesive energy between the cylinder and the filament. We show that statistical mechanics of the system can be solved exactly using a path integral formalism which gives access to the full effect of thermal fluctuations, going thus beyond the usual Gaussian approximations which take into account only the contributions from the minimal energy configuration and small fluctuations about this minimal energy solution. We obtain the free energy of the wrapping-unwrapping transition of the filament around the cylinders as well as the effective interaction between two wrapped cylinders due to thermal fluctuations of the elastic filament. A change of entropy due to wrapping of the filament around the adsorbing cylinders as they move closer together is identified as an additional source of interactions between them. Such entropic wrapping effects should be distinguished from the usual entropic configuration effects in semi-flexible polymers. Our results may be applicable to the problem of adsorption of proteins as well as synthetic nano-particles on semi-flexible polymers such as DNA.Comment: 24 pages, 12 figure

Average-case analysis of dynamic graph algorithms

We present a model for edge updates with restricted randomness in dynamic graph algorithms and a general technique for analyzing the expected running time of an update operation. This model is able to capture the average case in many applications, since (1) it allows restrictions on the set of edges which can be used for insertions and (2) the type (insertion or deletion) of each update operation is arbitrary, i.e., not random. We use our technique to analyze existing and new dynamic algorithms for the following problems: maximum cardinality matching, minimum spanning forest, connectivity, 2- edge connectivity, k-edge connectivity, k-vertex connectivity, and bipartiteness. Given a random graph G with m0 edges and n vertices and a sequence of l update operations such that the graph contains mi edges after operation i, the expected time for performing the updates for any l is O(l log(n) + sum(i=1 to l) n/sqrt(m_i)) in the case of minimum spanning forests, connectivity, 2-edge connectivity, and bipartiteness. The expected time per update operation is O(n) in the case of maximum matching. We also give improved bounds for k-edge and k-vertex connectivity. Additionally we give an insertions-only algorithm for maximum cardinality matching with worst- case O(n) amortized time per insertion

Submm/mm Galaxy Counterpart Identification Using a Characteristic Density Distribution

We present a new submm/mm galaxy counterpart identification technique which builds on the use of Spitzer IRAC colors as discriminators between likely counterparts and the general IRAC galaxy population. Using 102 radio- and SMA-confirmed counterparts to AzTEC sources across three fields (GOODS-N, GOODS-S, and COSMOS), we develop a non-parametric IRAC color-color characteristic density distribution (CDD), which, when combined with positional uncertainty information via likelihood ratios, allows us to rank all potential IRAC counterparts around SMGs and calculate the significance of each ranking via the reliability factor. We report all robust and tentative radio counterparts to SMGs, the first such list available for AzTEC/COSMOS, as well as the highest ranked IRAC counterparts for all AzTEC SMGs in these fields as determined by our technique. We demonstrate that the technique is free of radio bias and thus applicable regardless of radio detections. For observations made with a moderate beamsize (~18"), this technique identifies ~85 per cent of SMG counterparts. For much larger beamsizes (>30"), we report identification rates of 33-49 per cent. Using simulations, we demonstrate that this technique is an improvement over using positional information alone for observations with facilities such as AzTEC on the LMT and SCUBA-2 on JCMT.Comment: 30 pages, 9 figures, 5 tables. Accepted for publication in MNRA

Growth and Mycotoxin Production by Chaetomium globosum Is Favored in a Neutral pH

Chaetomium globosum is frequently isolated in water-damaged buildings and produces two mycotoxins called chaetoglobosins A and C when cultured on building material. In this study, the influence of ambient pH on the growth of C. globosum was examined on an artificial medium. This fungus was capable of growth on potato dextrose agar ranging in pH from 4.3 to 9.4 with optimal growth and chaetoglobosin C production occurring at a neutral pH. In addition, our results show that sporulation is favored in an acidic environment

Fluctuation-Induced Interactions between Rods on a Membrane

We consider the interaction between two rods embedded in a fluctuating surface. The modification of fluctuations by the rods leads to an attractive long-range interaction between them. We consider fluctuations governed by either surface tension (films) or bending rigidity (membranes). In both cases the interaction falls off with the separation of the rods as $1/R^4$. The orientational part of the interaction is proportional to $\cos^2\left[ \theta_1+\theta_2 \right]$ in the former case, and to $\cos^2\left[ 2\left(\theta_1+\theta_2\right) \right]$ in the latter, where $\theta_1$ and $\theta_2$ are angles between the rods and the line joining them. These interactions are somewhat reminiscent of dipolar forces and will tend to align collections of such rods into chains.Comment: REVTEX, 14 pages, with 2 Postscript figure