Dependence on temperature and GC content of bubble length distributions in DNA

We present numerical results on the temperature dependence of the distribution of bubble lengths in DNA segments of various guanine-cytosine (GC) concentrations. Base-pair openings are described by the Peyrard-Bishop-Dauxois model and the corresponding thermal equilibrium distributions of bubbles are obtained through Monte Carlo calculations for bubble sizes up to the order of a hundred base pairs. The dependence of the parameters of bubble length distribution on temperature and the GC content is investigated. We provide simple expressions which approximately describe these relations. The variation of the average bubble length is also presented. We find a temperature dependence of the exponent c that appears in the distribution of bubble lengths. If an analogous dependence exists in the loop entropy exponent of real DNA, it may be relevant to understand overstretching in force-extension experiments.Comment: 8 pages, 6 figures. Published on The Journal of Chemical Physic

Entanglement in fermionic chains with finite range coupling and broken symmetries

We obtain a formula for the determinant of a block Toeplitz matrix associated with a quadratic fermionic chain with complex coupling. Such couplings break reflection symmetry and/or charge conjugation symmetry. We then apply this formula to compute the Renyi entropy of a partial observation to a subsystem consisting of $X$ contiguous sites in the limit of large $X$. The present work generalizes similar results due to Its, Jin, Korepin and Its, Mezzadri, Mo. A striking new feature of our formula for the entanglement entropy is the appearance of a term scaling with the logarithm of the size of $X$. This logarithmic behaviour originates from certain discontinuities in the symbol of the block Toeplitz matrix. Equipped with this formula we analyse the entanglement entropy of a Dzyaloshinski-Moriya spin chain and a Kitaev fermionic chain with long range pairing.Comment: 27 pages, 5 figure

On the M\"obius transformation in the entanglement entropy of fermionic chains

There is an intimate relation between entanglement entropy and Riemann surfaces. This fact is explicitly noticed for the case of quadratic fermionic Hamiltonians with finite range couplings. After recollecting this fact, we make a comprehensive analysis of the action of the M\"obius transformations on the Riemann surface. We are then able to uncover the origin of some symmetries and dualities of the entanglement entropy already noticed recently in the literature. These results give further support for the use of entanglement entropy to analyse phase transition.Comment: 29 pages, 5 figures. Final version published in JSTAT. Two new figures. Some comments and references added. Typos correcte

Million frames per second infrared imaging system

An infrared imaging system has been developed for measuring the temperature increase during the dynamic deformation of materials. The system consists of an 8×8 HgCdTe focal plane array, each with its own preamplifier. Outputs from the 64 detector/preamplifiers are digitized using a row-parallel scheme. In this approach, all 64 signals are simultaneously acquired and held using a bank of track and hold amplifiers. An array of eight 8:1 multiplexers then routes the signals to eight 10 MHz digitizers, acquiring data from each row of detectors in parallel. The maximum rate is one million frames per second. A fully reflective lens system was developed, consisting of two Schwarszchild objectives operating at infinite conjugation ratio. The ratio of the focal lengths of the objectives determines the lens magnification. The system has been used to image the distribution of temperature rise near the tip of a notch in a high strength steel sample (C-300) subjected to impact loading by a drop weight testing machine. The results show temperature rises at the crack tip up to around 70 K. Localization of temperature, and hence, of deformation into "U" shaped zones emanating from the notch tip is clearly seen, as is the onset of crack propagation