SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures.

Structural Classification of Proteins-extended (SCOPe, http://scop.berkeley.edu) is a database of protein structural relationships that extends the SCOP database. SCOP is a manually curated ordering of domains from the majority of proteins of known structure in a hierarchy according to structural and evolutionary relationships. Development of the SCOP 1.x series concluded with SCOP 1.75. The ASTRAL compendium provides several databases and tools to aid in the analysis of the protein structures classified in SCOP, particularly through the use of their sequences. SCOPe extends version 1.75 of the SCOP database, using automated curation methods to classify many structures released since SCOP 1.75. We have rigorously benchmarked our automated methods to ensure that they are as accurate as manual curation, though there are many proteins to which our methods cannot be applied. SCOPe is also partially manually curated to correct some errors in SCOP. SCOPe aims to be backward compatible with SCOP, providing the same parseable files and a history of changes between all stable SCOP and SCOPe releases. SCOPe also incorporates and updates the ASTRAL database. The latest release of SCOPe, 2.03, contains 59 514 Protein Data Bank (PDB) entries, increasing the number of structures classified in SCOP by 55% and including more than 65% of the protein structures in the PDB

Multi-Gigabit Wireless data transfer at 60 GHz

In this paper we describe the status of the first prototype of the 60 GHz wireless Multi-gigabit data transfer topology currently under development at University of Heidelberg using IBM 130 nm SiGe HBT BiCMOS technology. The 60 GHz band is very suitable for high data rate and short distance applications as for example needed in the HEP experments. The wireless transceiver consist of a transmitter and a receiver. The transmitter includes an On-Off Keying (OOK) modulator, an Local Oscillator (LO), a Power Amplifier (PA) and a BandPass Filter (BPF). The receiver part is composed of a BandPass- Filter (BPF), a Low Noise Amplifier (LNA), a double balanced down-convert Gilbert mixer, a Local Oscillator (LO), then a BPF to remove the mixer introduced noise, an Intermediate Amplifier (IF), an On-Off Keying demodulator and a limiting amplifier. The first prototype would be able to handle a data-rate of about 3.5 Gbps over a link distance of 1 m. The first simulations of the LNA show that a Noise Figure (NF) of 5 dB, a power gain of 21 dB at 60 GHz with a 3 dB bandwidth of more than 20 GHz with a power consumption 11 mW are achieved. Simulations of the PA show an output referred compression point P1dB of 19.7 dB at 60 GHz.Comment: Proceedings of the WIT201

The fractional Keller-Segel model

The Keller-Segel model is a system of partial differential equations modelling chemotactic aggregation in cellular systems. This model has blowing up solutions for large enough initial conditions in dimensions d >= 2, but all the solutions are regular in one dimension; a mathematical fact that crucially affects the patterns that can form in the biological system. One of the strongest assumptions of the Keller-Segel model is the diffusive character of the cellular motion, known to be false in many situations. We extend this model to such situations in which the cellular dispersal is better modelled by a fractional operator. We analyze this fractional Keller-Segel model and find that all solutions are again globally bounded in time in one dimension. This fact shows the robustness of the main biological conclusions obtained from the Keller-Segel model

Gradient discretization of Hybrid Dimensional Darcy Flows in Fractured Porous Media with discontinuous pressures at the matrix fracture interfaces

We investigate the discretization of Darcy flow through fractured porous media on general meshes. We consider a hybrid dimensional model, invoking a complex network of planar fractures. The model accounts for matrix-fracture interactions and fractures acting either as drains or as barriers, i.e. we have to deal with pressure discontinuities at matrix-fracture interfaces. The numerical analysis is performed in the general framework of gradient discretizations which is extended to the model under consideration. Two families of schemes namely the Vertex Approximate Gradient scheme (VAG) and the Hybrid Finite Volume scheme (HFV) are detailed and shown to satisfy the gradient scheme framework, which yields, in particular, convergence. Numerical tests confirm the theoretical results. Gradient Discretization; Darcy Flow, Discrete Fracture Networks, Finite Volum

Effect of sampling rate and record length on the determination of stability and control derivatives

Flight data from five aircraft were used to assess the effects of sampling rate and record length reductions on estimates of stability and control derivatives produced by a maximum likelihood estimation method. Derivatives could be extracted from flight data with the maximum likelihood estimation method even if there were considerable reductions in sampling rate and/or record length. Small amplitude pulse maneuvers showed greater degradation of the derivative maneuvers than large amplitude pulse maneuvers when these reductions were made. Reducing the sampling rate was found to be more desirable than reducing the record length as a method of lessening the total computation time required without greatly degrading the quantity of the estimates

Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium

Microbial consortia form when multiple species colocalize and communally generate a function that none is capable of alone. Consortia abound in nature, and their cooperative metabolic activities influence everything from biodiversity in the global food chain to human weight gain. Here, we present an engineered consortium in which the microbial members communicate with each other and exhibit a “consensus” gene expression response. Two colocalized populations of Escherichia coli converse bidirectionally by exchanging acyl-homoserine lactone signals. The consortium generates the gene-expression response if and only if both populations are present at sufficient cell densities. Because neither population can respond without the other's signal, this consensus function can be considered a logical AND gate in which the inputs are cell populations. The microbial consensus consortium operates in diverse growth modes, including in a biofilm, where it sustains its response for several days

Damped finite-time-singularity driven by noise

We consider the combined influence of linear damping and noise on a dynamical finite-time-singularity model for a single degree of freedom. We find that the noise effectively resolves the finite-time-singularity and replaces it by a first-passage-time or absorbing state distribution with a peak at the singularity and a long time tail. The damping introduces a characteristic cross-over time. In the early time regime the probability distribution and first-passage-time distribution show a power law behavior with scaling exponent depending on the ratio of the non linear coupling strength to the noise strength. In the late time regime the behavior is controlled by the damping. The study might be of relevance in the context of hydrodynamics on a nanometer scale, in material physics, and in biophysics.Comment: 9 pages, 4 eps-figures, revtex4 fil

Thermomechanical properties of graphene: valence force field model approach

Using the valence force field model of Perebeinos and Tersoff [Phys. Rev. B {\bf79}, 241409(R) (2009)], different energy modes of suspended graphene subjected to tensile or compressive strain are studied. By carrying out Monte Carlo simulations it is found that: i) only for small strains ($|\varepsilon| \lessapprox 0.02$) the total energy is symmetrical in the strain, while it behaves completely different beyond this threshold; ii) the important energy contributions in stretching experiments are stretching, angle bending, out-of-plane term and a term that provides repulsion against $\pi-\pi$ misalignment; iii) in compressing experiments the two latter terms increase rapidly and beyond the buckling transition stretching and bending energies are found to be constant; iv) from stretching-compressing simulations we calculated the Young modulus at room temperature 350$\pm3.15$\,N/m, which is in good agreement with experimental results (340$\pm50$\,N/m) and with ab-initio results [322-353]\,N/m; v) molar heat capacity is estimated to be 24.64\,J/mol$^{-1}$K$^{-1}$ which is comparable with the Dulong-Petit value, i.e. 24.94\,J/mol$^{-1}$K$^{-1}$ and is almost independent of the strain; vi) non-linear scaling properties are obtained from height-height correlations at finite temperature; vii) the used valence force field model results in a temperature independent bending modulus for graphene, and viii) the Gruneisen parameter is estimated to be 0.64.Comment: 8 pages, 5 figures. To appear in J. Phys.: Condens. Matte

Thermal diffusion by Brownian motion induced fluid stress

The Ludwig-Soret effect, the migration of a species due to a temperature gradient, has been extensively studied without a complete picture of its cause emerging. Here we investigate the dynamics of DNA and spherical particles sub jected to a thermal gradient using a combination of Brownian dynamics and the lattice Boltzmann method. We observe that the DNA molecules will migrate to colder regions of the channel, an observation also made in the experiments of Duhr, et al[1]. In fact, the thermal diffusion coefficient found agrees quantitatively with the experimental value. We also observe that the thermal diffusion coefficient decreases as the radius of the studied spherical particles increases. Furthermore, we observe that the thermal fluctuations-fluid momentum flux coupling induces a gradient in the stress which leads to thermal migration in both systems.Comment: 6 pages, 5 figue

Radio-frequency operation of a double-island single-electron transistor

We present results on a double-island single-electron transistor (DISET) operated at radio-frequency (rf) for fast and highly sensitive detection of charge motion in the solid state. Using an intuitive definition for the charge sensitivity, we compare a DISET to a conventional single-electron transistor (SET). We find that a DISET can be more sensitive than a SET for identical, minimum device resistances in the Coulomb blockade regime. This is of particular importance for rf operation where ideal impedance matching to 50 Ohm transmission lines is only possible for a limited range of device resistances. We report a charge sensitivity of 5.6E-6 e/sqrt(Hz) for a rf-DISET, together with a demonstration of single-shot detection of small (<=0.1e) charge signals on microsecond timescales.Comment: 6 pages, 6 figure