Bubble statistics and positioning in superhelically stressed DNA

We present a general framework to study the thermodynamic denaturation of double-stranded DNA under superhelical stress. We report calculations of position- and size-dependent opening probabilities for bubbles along the sequence. Our results are obtained from transfer-matrix solutions of the Zimm-Bragg model for unconstrained DNA and of a self-consistent linearization of the Benham model for superhelical DNA. The numerical efficiency of our method allows for the analysis of entire genomes and of random sequences of corresponding length ($10^6-10^9$ base pairs). We show that, at physiological conditions, opening in superhelical DNA is strongly cooperative with average bubble sizes of $10^2-10^3$ base pairs (bp), and orders of magnitude higher than in unconstrained DNA. In heterogeneous sequences, the average degree of base-pair opening is self-averaging, while bubble localization and statistics are dominated by sequence disorder. Compared to random sequences with identical GC-content, genomic DNA has a significantly increased probability to open large bubbles under superhelical stress. These bubbles are frequently located directly upstream of transcription start sites.Comment: to be appeared in Physical Review

Large-Scale Structure Shocks at Low and High Redshifts

Cosmological simulations show that, at the present time, a substantial fraction of the gas in the intergalactic medium (IGM) has been shock-heated to T>10^5 K. Here we develop an analytic model to describe the fraction of shocked, moderately overdense gas in the IGM. The model is an extension of the Press & Schechter (1974) description for the mass function of halos: we assume that large-scale structure shocks occur at a fixed overdensity during nonlinear collapse. This in turn allows us to compute the fraction of gas at a given redshift that has been shock-heated to a specified temperature. We show that, if strong shocks occur at turnaround, our model provides a reasonable description of the temperature distribution seen in cosmological simulations at z~0, although it does overestimate the importance of weak shocks. We then apply our model to shocks at high redshifts. We show that, before reionization, the thermal energy of the IGM is dominated by large-scale structure shocks (rather than virialized objects). These shocks can have a variety of effects, including stripping ~10% of the gas from dark matter minihalos, accelerating cosmic rays, and creating a diffuse radiation background from inverse Compton and cooling radiation. This radiation background develops before the first stars form and could have measurable effects on molecular hydrogen formation and the spin temperature of the 21 cm transition of neutral hydrogen. Finally, we show that shock-heating will also be directly detectable by redshifted 21 cm measurements of the neutral IGM in the young universe.Comment: 12 pages, 8 figures, submitted to Ap

Generalization of hysteresis modeling to anisotropic materials

An extension to the model of hysteresis has been presented earlier which included the effect of anisotropy in the modeling of the anhysteretic magnetization curves of uniaxially anisotropic single crystalline materials. Further exploration of this extension shown here considers different kinds of crystal anisotropy in materials. Theory considers that the differential susceptibility at any given field is determined by the displacement of the prevailing magnetization from the anhysteretic magnetization. Thus, it has been shown that the effect of anisotropy on magnetic hysteresis in materials can be incorporated into the model of hysteresis through the anisotropic anhysteretic. This extension is likely to be particularly useful in the case of hard magnetic materials which exhibit high anisotropy

The Essence of Nested Composition

Calculi with disjoint intersection types support an introduction form for intersections called the merge operator, while retaining a coherent semantics. Disjoint intersections types have great potential to serve as a foundation for powerful, flexible and yet type-safe and easy to reason OO languages. This paper shows how to significantly increase the expressive power of disjoint intersection types by adding support for nested subtyping and composition, which enables simple forms of family polymorphism to be expressed in the calculus. The extension with nested subtyping and composition is challenging, for two different reasons. Firstly, the subtyping relation that supports these features is non-trivial, especially when it comes to obtaining an algorithmic version. Secondly, the syntactic method used to prove coherence for previous calculi with disjoint intersection types is too inflexible, making it hard to extend those calculi with new features (such as nested subtyping). We show how to address the first problem by adapting and extending the Barendregt, Coppo and Dezani (BCD) subtyping rules for intersections with records and coercions. A sound and complete algorithmic system is obtained by using an approach inspired by Pierce\u27s work. To address the second problem we replace the syntactic method to prove coherence, by a semantic proof method based on logical relations. Our work has been fully formalized in Coq, and we have an implementation of our calculus

Epigenetic Chromatin Silencing: Bistability and Front Propagation

The role of post-translational modification of histones in eukaryotic gene regulation is well recognized. Epigenetic silencing of genes via heritable chromatin modifications plays a major role in cell fate specification in higher organisms. We formulate a coarse-grained model of chromatin silencing in yeast and study the conditions under which the system becomes bistable, allowing for different epigenetic states. We also study the dynamics of the boundary between the two locally stable states of chromatin: silenced and unsilenced. The model could be of use in guiding the discussion on chromatin silencing in general. In the context of silencing in budding yeast, it helps us understand the phenotype of various mutants, some of which may be non-trivial to see without the help of a mathematical model. One such example is a mutation that reduces the rate of background acetylation of particular histone side-chains that competes with the deacetylation by Sir2p. The resulting negative feedback due to a Sir protein depletion effect gives rise to interesting counter-intuitive consequences. Our mathematical analysis brings forth the different dynamical behaviors possible within the same molecular model and guides the formulation of more refined hypotheses that could be addressed experimentally.Comment: 19 pages, 5 figure

Random Walks for Spike-Timing Dependent Plasticity

Random walk methods are used to calculate the moments of negative image equilibrium distributions in synaptic weight dynamics governed by spike-timing dependent plasticity (STDP). The neural architecture of the model is based on the electrosensory lateral line lobe (ELL) of mormyrid electric fish, which forms a negative image of the reafferent signal from the fish's own electric discharge to optimize detection of sensory electric fields. Of particular behavioral importance to the fish is the variance of the equilibrium postsynaptic potential in the presence of noise, which is determined by the variance of the equilibrium weight distribution. Recurrence relations are derived for the moments of the equilibrium weight distribution, for arbitrary postsynaptic potential functions and arbitrary learning rules. For the case of homogeneous network parameters, explicit closed form solutions are developed for the covariances of the synaptic weight and postsynaptic potential distributions.Comment: 18 pages, 8 figures, 15 subfigures; uses revtex4, subfigure, amsmat

Far-infrared optical properties of the pyrochlore spin ice compound Dy2Ti2O4

Near normal incident far-infrared reflectivity spectra of [111] dysprosium titanate (Dy2Ti2O4) single crystal have been measured at different temperatures. Seven phonon modes (eight at low temperature) are identified at frequency below 1000 cm-1. Optical conductivity spectra are obtained by fitting all the reflectivity spectra with the factorized form of the dielectric function. Both the Born effective charges and the static optical primitivity are found to increase with decreasing temperature. Moreover, phonon linewidth narrowering and phonon modes shift with decreasing temperature are also observed, which may result from enhanced charge localization. The redshift of several low frequency modes is attributed to the spin-phonon coupling. All observed optical properties can be explained within the framework of nearest neighbor ferromagnetic(FM) spin ice model

Characterising epithelial tissues using persistent entropy

In this paper, we apply persistent entropy, a novel topological statistic, for characterization of images of epithelial tissues. We have found out that persistent entropy is able to summarize topological and geometric information encoded by \alpha-complexes and persistent homology. After using some statistical tests, we can guarantee the existence of significant differences in the studied tissues.Comment: 12 pages, 7 figures, 4 table