BBH-LS: An algorithm for computing positional homologs using sequence and gene context similarity

10.1186/1752-0509-6-S1-S22BMC Systems Biology6SUPPL.1

GaN hemispherical micro-cavities

published_or_final_versio

Faraday instability on viscous ferrofluids in a horizontal magnetic field: Oblique rolls of arbitrary orientation

A linear stability analysis of the free surface of a horizontally unbounded ferrofluid layer of arbitrary depth subjected to vertical vibrations and a horizontal magnetic field is performed. A nonmonotonic dependence of the stability threshold on the magnetic field is found at high frequencies of the vibrations. The reasons of the decrease of the critical acceleration amplitude caused by a horizontal magnetic field are discussed. It is revealed that the magnetic field can be used to select the first unstable pattern of Faraday waves. In particular, a rhombic pattern as a superposition of two different oblique rolls can occur. A scaling law is presented which maps all data into one graph for the tested range of viscosities, frequencies, magnetic fields and layer thicknesses.Comment: 8 pages, 6 figures, RevTex

Parametrically Excited Surface Waves: Two-Frequency Forcing, Normal Form Symmetries, and Pattern Selection

Motivated by experimental observations of exotic standing wave patterns in the two-frequency Faraday experiment, we investigate the role of normal form symmetries in the pattern selection problem. With forcing frequency components in ratio m/n, where m and n are co-prime integers, there is the possibility that both harmonic and subharmonic waves may lose stability simultaneously, each with a different wavenumber. We focus on this situation and compare the case where the harmonic waves have a longer wavelength than the subharmonic waves with the case where the harmonic waves have a shorter wavelength. We show that in the former case a normal form transformation can be used to remove all quadratic terms from the amplitude equations governing the relevant resonant triad interactions. Thus the role of resonant triads in the pattern selection problem is greatly diminished in this situation. We verify our general results within the example of one-dimensional surface wave solutions of the Zhang-Vinals model of the two-frequency Faraday problem. In one-dimension, a 1:2 spatial resonance takes the place of a resonant triad in our investigation. We find that when the bifurcating modes are in this spatial resonance, it dramatically effects the bifurcation to subharmonic waves in the case of forcing frequencies are in ratio 1/2; this is consistent with the results of Zhang and Vinals. In sharp contrast, we find that when the forcing frequencies are in ratio 2/3, the bifurcation to (sub)harmonic waves is insensitive to the presence of another spatially-resonant bifurcating mode.Comment: 22 pages, 6 figures, late

Novel tau filament fold in chronic traumatic encephalopathy encloses hydrophobic molecules

Chronic traumatic encephalopathy (CTE) is a neurodegenerative tauopathy that is associated with repetitive head impacts or exposure to blast waves. First described as punch-drunk syndrome and dementia pugilistica in retired boxers1-3, CTE has since been identified in former participants of other contact sports, ex-military personnel and after physical abuse4-7. No disease-modifying therapies currently exist, and diagnosis requires an autopsy. CTE is defined by an abundance of hyperphosphorylated tau protein in neurons, astrocytes and cell processes around blood vessels8,9. This, together with the accumulation of tau inclusions in cortical layers II and III, distinguishes CTE from Alzheimer's disease and other tauopathies10,11. However, the morphologies of tau filaments in CTE and the mechanisms by which brain trauma can lead to their formation are unknown. Here we determine the structures of tau filaments from the brains of three individuals with CTE at resolutions down to 2.3 Å, using cryo-electron microscopy. We show that filament structures are identical in the three cases but are distinct from those of Alzheimer's and Pick's diseases, and from those formed in vitro12-15. Similar to Alzheimer's disease12,14,16-18, all six brain tau isoforms assemble into filaments in CTE, and residues K274-R379 of three-repeat tau and S305-R379 of four-repeat tau form the ordered core of two identical C-shaped protofilaments. However, a different conformation of the β-helix region creates a hydrophobic cavity that is absent in tau filaments from the brains of patients with Alzheimer's disease. This cavity encloses an additional density that is not connected to tau, which suggests that the incorporation of cofactors may have a role in tau aggregation in CTE. Moreover, filaments in CTE have distinct protofilament interfaces to those of Alzheimer's disease. Our structures provide a unifying neuropathological criterion for CTE, and support the hypothesis that the formation and propagation of distinct conformers of assembled tau underlie different neurodegenerative diseases

Oscillating flames in open tubes

When a flame passes along a tube that is open at both ends a self induced fluctuating pressure/flow field is created which the flame has to traverse. Here fuel rich (1.1 < ϕ < 1.4) propane-air flames have been filmed travelling along a 20 mm internal diameter quartz tube. Fluctuations in the flame’s progression were observed to increase as the flame propagated, achieving a maximum oscillation amplitude of ±10 mm at 220 Hz that decayed as the flame progressed further towards the end of the tube. The impact of the periodic pressure gradients on the flame shape could be discerned with tongues of unburned reactants pushed into the products as well as the corresponding rapid acceleration of the flame into the unburned mixture. The impact of the fluctuations on flame chemistry was monitored by capturing the CH∗ and C2 chemiluminescence using a high speed colour camera. The CH∗/C2∗ ratio was observed to decrease as the flame was pulled back towards the burned mixture; and increased when the flame was pushed forwards. This was consistent throughout the flame progress even when small oscillations in the flame position were measured. This could be a significant feature of flames in this environment

Failure Analysis of Geomaterials under Dynamic Loading Conditions

Department of Engineering Machanics, State Key Laboratory of Structural Analysis and Industrial Equipment, Dalian University of Technology, ChinaPromoting Environmental Pesearch in Pan-Japan Sea Area : Young Researchers\u27 Network, Schedule: March 8-10,2006,Kanazawa Excel Hotel Tokyu, Japan, Organized by: Kanazawa University 21st-Century COE Program, Environmental Monitoring and Prediction of Long- & Short- Term Dynamics of Pan-Japan Sea Area ; IICRC(Ishikawa International Cooperation Research Centre), Sponsors : Japan Sea Research ; UNU-IAS(United Nations University Institute of Advanced Studies)+Ishikawa Prefecture Government ; City of Kanazaw

Universality and scaling study of the critical behavior of the two-dimensional Blume-Capel model in short-time dynamics

In this paper we study the short-time behavior of the Blume-Capel model at the tricritical point as well as along the second order critical line. Dynamic and static exponents are estimated by exploring scaling relations for the magnetization and its moments at early stage of the dynamic evolution. Our estimates for the dynamic exponents, at the tricritical point, are $z= 2.215(2)$ and $\theta= -0.53(2)$.Comment: 12 pages, 9 figure

Fullerene graphs have exponentially many perfect matchings

A fullerene graph is a planar cubic 3-connected graph with only pentagonal and hexagonal faces. We show that fullerene graphs have exponentially many perfect matchings.Comment: 7 pages, 3 figure