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

Exact extreme value statistics at mixed order transitions

We study extreme value statistics (EVS) for spatially extended models exhibiting mixed order phase transitions (MOT). These are phase transitions which exhibit features common to both first order (discontinuity of the order parameter) and second order (diverging correlation length) transitions. We consider here the truncated inverse distance squared Ising (TIDSI) model which is a prototypical model exhibiting MOT, and study analytically the extreme value statistics of the domain lengths. The lengths of the domains are identically distributed random variables except for the global constraint that their sum equals the total system size $L$. In addition, the number of such domains is also a fluctuating variable, and not fixed. In the paramagnetic phase, we show that the distribution of the largest domain length $l_{\max}$ converges, in the large $L$ limit, to a Gumbel distribution. However, at the critical point (for a certain range of parameters) and in the ferromagnetic phase, we show that the fluctuations of $l_{\max}$ are governed by novel distributions which we compute exactly. Our main analytical results are verified by numerical simulations.Comment: 25 pages, 6 figures, 1 tabl

Fabrication of Nano-Scale Gaps in Integrated Circuits

Nano-size objects like metal clusters present an ideal system for the study of quantum phenomena and for constructing practical quantum devices. Integrating these small objects in a macroscopic circuit is, however, a difficult task. So far the nanoparticles have been contacted and addressed by highly sophisticated techniques which are not suitable for large scale integration in macroscopic circuits. We present an optical lithography method that allows for the fabrication of a network of electrodes which are separated by gaps of controlled nanometer size. The main idea is to control the gap size with subnanometer precision using a structure grown by molecular beam epitaxy.Comment: 4 pages, 3 figure

Denaturation of Circular DNA: Supercoil Mechanism

The denaturation transition which takes place in circular DNA is analyzed by extending the Poland-Scheraga model to include the winding degrees of freedom. We consider the case of a homopolymer whereby the winding number of the double stranded helix, released by a loop denaturation, is absorbed by \emph{supercoils}. We find that as in the case of linear DNA, the order of the transition is determined by the loop exponent $c$. However the first order transition displayed by the PS model for $c>2$ in linear DNA is replaced by a continuous transition with arbitrarily high order as $c$ approaches 2, while the second-order transition found in the linear case in the regime $1<c\le2$ disappears. In addition, our analysis reveals that melting under fixed linking number is a \emph{condensation transition}, where the condensate is a macroscopic loop which appears above the critical temperature.Comment: 9 pages, 4 figure