Mutual information for examining correlations in DNA

This paper examines two methods for finding whether long-range correlations exist in DNA: a fractal measure and a mutual information technique. We evaluate the performance and implications of these methods in detail. In particular we explore their use comparing DNA sequences from a variety of sources. Using software for performing in silico mutations, we also consider evolutionary events leading to long range correlations and analyse these correlations using the techniques presented. Comparisons are made between these virtual sequences, randomly generated sequences, and real sequences. We also explore correlations in chromosomes from different species.Comment: 8 pages, 3 figure

Estimates of frequency-dependent compressibility from a quasistatic double-porosity model

Gassmann's relationship between the drained and undrained bulk modulus of a porous medium is often used to relate the dry bulk modulus to the saturated bulk modulus for elastic waves, because the compressibility of air is considered so high that the dry rock behaves in a drained fashion and the frequency of elastic waves is considered so high that the saturated rock behaves in an undrained fashion. The bulk modulus calculated from ultrasonic velocities, however, often does not match the Gassmann prediction. Mavko and Jizba examined how local flow effects and unequilibrated pore pressures can lead to greater stiffnesses. Their conceptual model consists of a distribution of porosities obtained from the strain-versus-confining-pressure behavior. Stiff pores that close at higher confining pressures are considered to remain undrained (unrelaxed) while soft pores drain even for high-frequency stress changes. If the pore shape distribution is bimodal, then the rock approximately satisfies the assumptions of a double-porosity, poroelastic material. Berryman and Wang [1995] established linear constitutive equations and identified four different time scales of ow behavior: (1) totally drained, (2) soft pores are drained but stiff pores are undrained, (3) soft and stiff pores are locally equilibrated, but undrained beyond the grain scale, and (4) both soft and stiff pores are undrained. The relative magnitudes of the four associated bulk moduli will be examined for all four moduli and illustrated for several sandstones

Characterization of two complete Isospora mitochondrial genomes from passerine birds: Isospora serinuse in a domestic canary and Isospora manorinae in a yellow-throated miner

The genus term Isospora is now applied specifically to parasites of birds, with the term Cystoisospora preferred for parasites which infect mammals. Isospora is a common parasitic coccidian in birds worldwide, especially in passerine birds, in which it can cause systemic coccidiosis. The complete mitochondrial genome sequences from two recently identified Isospora species; Isospora serinuse in a domestic canary and Isospora manorinae in a yellow-throated miner, were sequenced and compared with those of other closely related coccidian species. The complete mitochondrial genome sequence for Isospora serinuse is 6260. bp in size and 6223. bp for Isospora manorinae. The mitochondrial genomes of Isospora serinuse and Isospora manorinae include three protein-coding genes (COI, COIII and CytB), 19 LSU and 14 SSU rDNA fragments, including one newly identified putative LSU fragment in Isospora sp. The arrangement of coding regions in these two Isospora species were identical to that of available Isospora sp. and Eimeria spp. mitochondrial genomes and the start codon usage for protein coding genes was conservative. Phylogenetic analysis of the mt genome of the two Isospora species based on the three coding regions further support that the monophyletic nature of avian Isospora

Nonlinear equation for anomalous diffusion: unified power-law and stretched exponential exact solution

The nonlinear diffusion equation $\frac{\partial \rho}{\partial t}=D \tilde{\Delta} \rho^\nu$ is analyzed here, where $\tilde{\Delta}\equiv \frac{1}{r^{d-1}}\frac{\partial}{\partial r} r^{d-1-\theta} \frac{\partial}{\partial r}$, and $d$, $\theta$ and $\nu$ are real parameters. This equation unifies the anomalous diffusion equation on fractals ($\nu =1$) and the spherical anomalous diffusion for porous media ($\theta=0$). Exact point-source solution is obtained, enabling us to describe a large class of subdiffusion ($\theta > (1-\nu)d$), normal diffusion ($\theta= (1-\nu)d$) and superdiffusion ($\theta < (1-\nu)d$). Furthermore, a thermostatistical basis for this solution is given from the maximum entropic principle applied to the Tsallis entropy.Comment: 3 pages, 2 eps figure

Long-Term Variations in the Growth and Decay Rates of Sunspot Groups

Using the combined Greenwich (1874-1976) and Solar Optical Observatories Network (1977-2009) data on sunspot groups, we study the long-term variations in the mean daily rates of growth and decay of sunspot groups. We find that the minimum and the maximum values of the annually averaged daily mean growth rates are ~52% per day and ~183% per day, respectively, whereas the corresponding values of the annually averaged daily mean decay rates are ~21% per day and ~44% per day, respectively. The average value (over the period 1874-2009) of the growth rate is about 70% more than that of the decay rate. The growth and the decay rates vary by about 35% and 13%, respectively, on a 60-year time-scale. From the beginning of Cycle 23 the growth rate is substantially decreased and near the end (2007-2008) the growth rate is lowest in the past about 100 years.Comment: 1 table, 13 figures, accepted by Solar Physic

Contribución a la peligrosidad sísmica de las fallas activas de la zona intraplaca de Iberia: la Falla Alentejo-Plasencia

We present the earthquake potential characterisation of the Alentejo-Plasencia Fault (APF) in the intraplate area of the Iberian Peninsula. The APF displays clear deformation of geomorphic surfaces and sediments of Neogene and younger age and, thus, we consider it to be active within the current tectonic regime. APF fault slip rate values range from 0.01 to 0.1 mm/yr with a preferred value of 0.05 mm/yr. Mw associated to fault rupture ranges from 6.6 to 8.7 using different segmentation models (segments ranging from 20 to 500 km) and various fault scaling relationships. Recurrence intervals derived from slip rate and Mw range from 10 ka to 4 Ma, with preferred values between 20 and 30 ka. Other faults in the interior of Iberia present similar values. Hazard curves produced using all fault sources from the intraplate Iberia show that active faults of the intraplate Iberia do not contribute significantly to seismic hazard at short return periods typical of the building codes (~ 500 year return periods). However, they can be important contributors to hazard at critical facilities (high hazard dams, nuclear power plants, emergency response buildings) where return periods of interest may be 10,000 years or more. Our fault source characterisation is very preliminary (with large uncertainties) and further detailed studies of active faults across the whole plate boundary are required to confirm the values for the intraplate faults presented here.En este trabajo se presenta la caracterización del potencial sísmico de la falla Alentejo-Plasencia (APF) situada en la región intraplaca de la Península Ibérica. La APF muestra una clara deformación de superficies geomorfológicas y sedimentos de edad neógena y más reciente, de modo que la consideramos una falla activa dentro del régimen tectónico vigente. Los valores de velocidad de movimiento de la APF van de 0.01 a 0.1 mm/yr con un valor preferido de 0.05 mm/yr. El valor de magnitud Mw asociada a la falla oscila entre 6.6 y 8.7 utilizando diferentes modelos de segmentación (con longitudes de segmento que van de 20 a 500 km) y varias relaciones de escala. Los intervalos de recurrencia derivados de la velocidad de movimiento y de la Mw oscilan de 10 Ka a 4 Ma, estando los valores preferidos entre los 20 Ka y los 30 Ka. Otras fallas en el interior de Iberia presentan valores similares. Las curvas de peligrosidad generadas utilizando todas las fallas-fuente de la zona intraplaca de Iberia muestran que las fallas activas de esta zona no contribuyen de forma significativa a la peligrosidad sísmica para los cortos periodos de retorno generalmente considerados en los códigos de construcción (para períodos de retorno de ~ 500 años). Sin embargo, dichas fallas pueden contribuir de modo importante a la peligrosidad sísmica para instalaciones críticas (presas de elevado riesgo, centrales nucleares, edificios de servicios de emergencia) donde los periodos de retorno de interés pueden ser de 10.000 años o más. Nuestra caracterización de la falla como fuente sismogénica es muy preliminar (presenta importantes incertidumbres) y se requieren estudios detallados adicionales de las fallas activas a lo largo de todo el límite de placa para confirmar los valores de las fallas intraplaca presentados aquí

A Model for the Elasticity of Compressed Emulsions

We present a new model to describe the unusual elastic properties of compressed emulsions. The response of a single droplet under compression is investigated numerically for different Wigner-Seitz cells. The response is softer than harmonic, and depends on the coordination number of the droplet. Using these results, we propose a new effective inter-droplet potential which is used to determine the elastic response of a monodisperse collection of disordered droplets as a function of volume fraction. Our results are in excellent agreement with recent experiments. This suggests that anharmonicity, together with disorder, are responsible for the quasi-linear increase of $G$ and $\Pi$ observed at $\varphi_c$.Comment: RevTeX with psfig-included figures and a galley macr

Packing of Compressible Granular Materials

3D Computer simulations and experiments are employed to study random packings of compressible spherical grains under external confining stress. Of particular interest is the rigid ball limit, which we describe as a continuous transition in which the applied stress vanishes as (\phi-\phi_c)^\beta, where \phi is the (solid phase) volume density. This transition coincides with the onset of shear rigidity. The value of \phi_c depends, for example, on whether the grains interact via only normal forces (giving rise to random close packings) or by a combination of normal and friction generated transverse forces (producing random loose packings). In both cases, near the transition, the system's response is controlled by localized force chains. As the stress increases, we characterize the system's evolution in terms of (1) the participation number, (2) the average force distribution, and (3) visualization techniques.Comment: 4 pages, 7 figures, to appear in Phys. Rev. Let