16,503 research outputs found
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 ( base pairs). We show that, at physiological
conditions, opening in superhelical DNA is strongly cooperative with average
bubble sizes of 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
- …