Lyapunov exponent and natural invariant density determination of chaotic maps: An iterative maximum entropy ansatz

We apply the maximum entropy principle to construct the natural invariant density and Lyapunov exponent of one-dimensional chaotic maps. Using a novel function reconstruction technique that is based on the solution of Hausdorff moment problem via maximizing Shannon entropy, we estimate the invariant density and the Lyapunov exponent of nonlinear maps in one-dimension from a knowledge of finite number of moments. The accuracy and the stability of the algorithm are illustrated by comparing our results to a number of nonlinear maps for which the exact analytical results are available. Furthermore, we also consider a very complex example for which no exact analytical result for invariant density is available. A comparison of our results to those available in the literature is also discussed.Comment: 16 pages including 6 figure

Conveyance of texture signals along a rat whisker

Neuronal activities underlying a percept are constrained by the physics of sensory signals. In the tactile sense such constraints are frictional stick-slip events, occurring, amongst other vibrotactile features, when tactile sensors are in contact with objects. We reveal new biomechanical phenomena about the transmission of these microNewton forces at the tip of a rat’s whisker, where they occur, to the base where they engage primary afferents. Using high resolution videography and accurate measurement of axial and normal forces at the follicle, we show that the conical and curved rat whisker acts as a sign-converting amplification filter for moment to robustly engage primary afferents. Furthermore, we present a model based on geometrically nonlinear Cosserat rod theory and a friction model that recreates the observed whole-beam whisker dynamics. The model quantifies the relation between kinematics (positions and velocities) and dynamic variables (forces and moments). Thus, only videographic assessment of acceleration is required to estimate forces and moments measured by the primary afferents. Our study highlights how sensory systems deal with complex physical constraints of perceptual targets and sensors

Role of magnetic dopants in the phase diagram of Sm1111 pnictides: The Mn case

The deliberate insertion of magnetic Mn dopants in the Fe sites of the optimally-doped SmFeAsO0.88-F0.12 iron-based superconductor can modify in a controlled way its electronic properties. The resulting phase diagram was investigated across a wide range of manganese contents (x) by means of muon-spin spectroscopy (muSR), both in zero- and in transverse fields, respectively, to probe the magnetic and the superconducting order. The pure superconducting phase (at x < 0.03) is replaced by a crossover region at intermediate Mn values (0.03 =< x < 0.08), where superconductivity coexists with static magnetic order. After completely suppressing superconductivity for x = 0.08, a further increase in Mn content reinforces the natural tendency towards antiferromagnetic correlations among the magnetic Mn ions. The sharp drop of Tc and the induced magnetic order in the presence of magnetic disorder/dopants, such as Mn, are both consistent with a recent theoretical model of unconventional superconductors [M. Gastiasoro et al., ArXiv 1606.09495], which includes correlation-enhanced RKKY-couplings between the impurity moments.Comment: 10 pages, 13 figures. Accepted on Physical Review

Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD

BACKGROUND: The Rat Genome Database (RGD) ( http://rgd.mcw.edu/) is the premier site for comprehensive data on the different strains of the laboratory rat (Rattus norvegicus). The strain data are collected from various publications, direct submissions from individual researchers, and rat providers worldwide. Rat strain, substrain designation and nomenclature follow the Guidelines for Nomenclature of Mouse and Rat Strains, instituted by the International Committee on Standardized Genetic Nomenclature for Mice. While symbols and names aid in identifying strains correctly, the flat nature of this information prohibits easy search and retrieval, as well as other data mining functions. In order to improve these functionalities, particularly in ontology-based tools, the Rat Strain Ontology (RS) was developed. RESULTS: The Rat Strain Ontology (RS) reflects the breeding history, parental background, and genetic manipulation of rat strains. This controlled vocabulary organizes strains by type: inbred, outbred, chromosome altered, congenic, mutant and so on. In addition, under the chromosome altered category, strains are organized by chromosome, and further by type of manipulations, such as mutant or congenic. This allows users to easily retrieve strains of interest with modifications in specific genomic regions. The ontology was developed using the Open Biological and Biomedical Ontology (OBO) file format, and is organized on the Directed Acyclic Graph (DAG) structure. Rat Strain Ontology IDs are included as part of the strain report (RS: ######). CONCLUSIONS: As rat researchers are often unaware of the number of substrains or altered strains within a breeding line, this vocabulary now provides an easy way to retrieve all substrains and accompanying information. Its usefulness is particularly evident in tools such as the PhenoMiner at RGD, where users can now easily retrieve phenotype measurement data for related strains, strains with similar backgrounds or those with similar introgressed regions. This controlled vocabulary also allows better retrieval and filtering for QTLs and in genomic tools such as the GViewer. The Rat Strain Ontology has been incorporated into the RGD Ontology Browser ( http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=RS:0000457#s) and is available through the National Center for Biomedical Ontology ( http://bioportal.bioontology.org/ontologies/1150) or the RGD ftp site ( ftp://rgd.mcw.edu/pub/ontology/rat_strain/)

Magnetic and Transport Properties in CoSr2Y1−xCaxCu2O7CoSr_2Y_{1-x}Ca_xCu_2O_7 (xx=0∼\sim0.4)

Magnetic and transport properties of $Co Sr_2 Y_{1-x} Ca_x Cu_2 O_7$ ($x=0 \sim 0.4$) system have been investigated. A broad maximum in M(T) curve, indicative of low-dimensional antiferromagnetic ordering originated from $CoO_{1+\delta}$ layers, is observed in Ca-free sample. With increasing Ca doping level up to 0.2, the M(T) curve remains almost unchanged, while resistivity is reduced by three orders. Higher Ca doping level leads to a drastic change of magnetic properties. In comparison with the samples with $x=0.0 \sim 0.2$, the temperature corresponding to the maximum of M(T) is much lowered for the sample $x$=0.3. The sample $x$=0.4 shows a small kink instead of a broad maximum and a weak ferromagnetic feature. The electrical transport behavior is found to be closely related to magnetic properties for the sample $x$=0.2, 0.25, 0.3, 0.4. It suggests that $CoO_{1+\delta}$ layers are involved in charge transport in addition to conducting $CuO_2$ planes to interpret the correlation between magnetism and charge transport. X-ray photoelectron spectroscopy studies give an additional evidence of the the transfer of the holes into the $CoO_{1+\delta}$ charge reservoir

Superconducting order parameter in heavily overdoped Bi2Sr2CaCu2O8+δBi_2 Sr_2 Ca Cu_2 O_{8+\delta}: a global quantitative analysis

A systematic analysis of the complex lineshape at $(\pi,0)$ of heavily overdoped Bi$_2$Sr$_2$CaCu$_2$O$_{8+\delta}$ is presented. We show that a coherent component in the quasi-particle excitation is correlated with the superfluid density throughout the entire doping range and suggest it is a direct measure of the order parameter of high temperature superconductors.Comment: 4 RevTex4 pages, 4 eps figures (Fig. 3 revised after publication on PRB

Conveyance of texture signals along a rat whisker

Neuronal activities underlying a percept are constrained by the physics of sensory signals. In the tactile sense such constraints are frictional stick–slip events, occurring, amongst other vibrotactile features, when tactile sensors are in contact with objects. We reveal new biomechanical phenomena about the transmission of these microNewton forces at the tip of a rat’s whisker, where they occur, to the base where they engage primary afferents. Using high resolution videography and accurate measurement of axial and normal forces at the follicle, we show that the conical and curved rat whisker acts as a sign-converting amplification filter for moment to robustly engage primary afferents. Furthermore, we present a model based on geometrically nonlinear Cosserat rod theory and a friction model that recreates the observed whole-beam whisker dynamics. The model quantifies the relation between kinematics (positions and velocities) and dynamic variables (forces and moments). Thus, only videographic assessment of acceleration is required to estimate forces and moments measured by the primary afferents. Our study highlights how sensory systems deal with complex physical constraints of perceptual targets and sensors

Predicting protein decomposition: the case of aspartic-acid racemization kinetics

The increase in proportion of the non-biological (D-) isomer of aspartic acid (Asp) relative to the L- isomer has been widely used in archaeology and geochemistry as a tool for dating. The method has proved controversial, particularly when used for bones. The non-linear kinetics of Asp racemization have prompted a number of suggestions as to the underlying mechanism(s) and have led to the use of mathe- matical transformations which linearize the increase in D-Asp with respect to time. Using one example, a suggestion that the initial rapid phase of Asp racemization is due to a contribution from asparagine (Asn), we demonstrate how a simple model of the degradation and racemization of Asn can be used to predict the observed kinetics. A more complex model of peptide bound Asx (Asn+Asp) racemization, which occurs via the formation of a cyclic succinimide (Asu), can be used to correctly predict Asx racemi- zation kinetics in proteins at high temperatures (95-140 °C). The model fails to predict racemization kinetics in dentine collagen at 37 °C. The reason for this is that Asu formation is highly conformation dependent and is predicted to occur extremely slowly in triple helical collagen. As conformation strongly in£uences the rate of Asu formation and hence Asx racemization, the use of extrapolation from high temperatures to estimate racemization kinetics of Asx in proteins below their denaturation temperature is called into question. In the case of archaeological bone, we argue that the D:L ratio of Asx re£ects the proportion of non- helical to helical collagen, overlain by the e¡ects of leaching of more soluble (and conformationally unconstrained) peptides. Thus, racemization kinetics in bone are potentially unpredictable, and the proposed use of Asx racemization to estimate the extent of DNA depurination in archaeological bones is challenged

The Rat Genome Database curation tool suite: a set of optimized software tools enabling efficient acquisition, organization, and presentation of biological data

The Rat Genome Database (RGD) is the premier repository of rat genomic and genetic data and currently houses over 40 000 rat gene records as well as human and mouse orthologs, 1771 rat and 1911 human quantitative trait loci (QTLs) and 2209 rat strains. Biological information curated for these data objects includes disease associations, phenotypes, pathways, molecular functions, biological processes and cellular components. A suite of tools has been developed to aid curators in acquiring and validating data objects, assigning nomenclature, attaching biological information to objects and making connections among data types. The software used to assign nomenclature, to create and edit objects and to make annotations to the data objects has been specifically designed to make the curation process as fast and efficient as possible. The user interfaces have been adapted to the work routines of the curators, creating a suite of tools that is intuitive and powerful