401 research outputs found
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
Amplitude equations and pattern selection in Faraday waves
We present a systematic nonlinear theory of pattern selection for parametric
surface waves (Faraday waves), not restricted to fluids of low viscosity. A
standing wave amplitude equation is derived from the Navier-Stokes equations
that is of gradient form. The associated Lyapunov function is calculated for
different regular patterns to determine the selected pattern near threshold.
For fluids of large viscosity, the selected wave pattern consists of parallel
stripes. At lower viscosity, patterns of square symmetry are obtained in the
capillary regime (large frequencies). At lower frequencies (the mixed
gravity-capillary regime), a sequence of six-fold (hexagonal), eight-fold, ...
patterns are predicted. The regions of stability of the various patterns are in
quantitative agreement with recent experiments conducted in large aspect ratio
systems.Comment: 12 pages, 1 figure, Revte
Topography and instability of monolayers near domain boundaries
We theoretically study the topography of a biphasic surfactant monolayer in
the vicinity of domain boundaries. The differing elastic properties of the two
phases generally lead to a nonflat topography of ``mesas'', where domains of
one phase are elevated with respect to the other phase. The mesas are steep but
low, having heights of up to 10 nm. As the monolayer is laterally compressed,
the mesas develop overhangs and eventually become unstable at a surface tension
of about K(dc)^2 (dc being the difference in spontaneous curvature and K a
bending modulus). In addition, the boundary is found to undergo a
topography-induced rippling instability upon compression, if its line tension
is smaller than about K(dc). The effect of diffuse boundaries on these features
and the topographic behavior near a critical point are also examined. We
discuss the relevance of our findings to several experimental observations
related to surfactant monolayers: (i) small topographic features recently found
near domain boundaries; (ii) folding behavior observed in mixed phospholipid
monolayers and model lung surfactants; (iii) roughening of domain boundaries
seen under lateral compression; (iv) the absence of biphasic structures in
tensionless surfactant films.Comment: 17 pages, 9 figures, using RevTeX and epsf, submitted to Phys Rev
Amplitude measurements of Faraday waves
A light reflection technique is used to measure quantitatively the surface
elevation of Faraday waves. The performed measurements cover a wide parameter
range of driving frequencies and sample viscosities. In the capillary wave
regime the bifurcation diagrams exhibit a frequency independent scaling
proportional to the wavelength. We also provide numerical simulations of the
full Navier-Stokes equations, which are in quantitative agreement up to
supercritical drive amplitudes of 20%. The validity of an existing perturbation
analysis is found to be limited to 2.5% overcriticaly.Comment: 7 figure
Thermodynamics and structure of self-assembled networks
We study a generic model of self-assembling chains which can branch and form
networks with branching points (junctions) of arbitrary functionality. The
physical realizations include physical gels, wormlike micells, dipolar fluids
and microemulsions. The model maps the partition function of a solution of
branched, self-assembling, mutually avoiding clusters onto that of a Heisenberg
magnet in the mathematical limit of zero spin components. The model is solved
in the mean field approximation. It is found that despite the absence of any
specific interaction between the chains, the entropy of the junctions induces
an effective attraction between the monomers, which in the case of three-fold
junctions leads to a first order reentrant phase separation between a dilute
phase consisting mainly of single chains, and a dense network, or two network
phases. Independent of the phase separation, we predict the percolation
(connectivity) transition at which an infinite network is formed that partially
overlaps with the first-order transition. The percolation transition is a
continuous, non thermodynamic transition that describes a change in the
topology of the system. Our treatment which predicts both the thermodynamic
phase equilibria as well as the spatial correlations in the system allows us to
treat both the phase separation and the percolation threshold within the same
framework. The density-density correlation correlation has a usual
Ornstein-Zernicke form at low monomer densities. At higher densities, a peak
emerges in the structure factor, signifying an onset of medium-range order in
the system. Implications of the results for different physical systems are
discussed.Comment: Submitted to Phys. Rev.
Self-Consistent Field study of Polyelectrolyte Brushes
We formulate a self-consistent field theory for polyelectrolyte brushes in
the presence of counterions. We numerically solve the self-consistent field
equations and study the monomer density profile, the distribution of
counterions, and the total charge distribution. We study the scaling relations
for the brush height and compare them to the prediction of other theories. We
find a weak dependence of the brush height on the grafting density.We fit the
counterion distribution outside the brush by the Gouy-Chapman solution for a
virtual charged wall. We calculate the amount of counterions outside the brush
and find that it saturates as the charge of the polyelectrolytes increases
MiDRMpol: A High-Throughput Multiplexed Amplicon Sequencing Workflow to Quantify HIV-1 Drug Resistance Mutations against Protease, Reverse Transcriptase, and Integrase Inhibitors
The detection of drug resistance mutations (DRMs) in minor viral populations is of potential clinical importance. However, sophisticated computational infrastructure and competence for analysis of high-throughput sequencing (HTS) data lack at most diagnostic laboratories. Thus, we have proposed a new pipeline, MiDRMpol, to quantify DRM from the HIV-1 pol region. The gag-vpu region of 87 plasma samples from HIV-infected individuals from three cohorts was amplified and sequenced by Illumina HiSeq2500. The sequence reads were adapter-trimmed, followed by analysis using in-house scripts. Samples from Swedish and Ethiopian cohorts were also sequenced by Sanger sequencing. The pipeline was validated against the online tool PASeq (Polymorphism Analysis by Sequencing). Based on an error rate of <1%, a value of >1% was set as reliable to consider a minor variant. Both pipelines detected the mutations in the dominant viral populations, while discrepancies were observed in minor viral populations. In five HIV-1 subtype C samples, minor mutations were detected at the <5% level by MiDRMpol but not by PASeq. MiDRMpol is a computationally as well as labor efficient bioinformatics pipeline for the detection of DRM from HTS data. It identifies minor viral populations (<20%) of DRMs. Our method can be incorporated into large-scale surveillance of HIV-1 DRM
Draft genome sequence of Sclerospora graminicola, the pearl millet downy mildew pathogen:Genome sequence of pearl millet downy mildew pathogen
Sclerospora graminicola pathogen is one of the most important biotic production constraints of pearl millet worldwide. We report a de novo whole genome assembly and analysis of pathotype 1. The draft genome assembly contained 299,901,251 bp with 65,404 genes. Pearl millet [Pennisetum glaucum (L.) R. Br.], is an important crop of the semi-arid and arid regions of the world. It is capable of growing in harsh and marginal environments with highest degree of tolerance to drought and heat among cereals (1). Downy mildew is the most devastating disease of pearl millet caused by Sclerospora graminicola (sacc. Schroet), particularly on genetically uniform hybrids. Estimated annual grain yield loss due to downy mildew is approximately 10?80 % (2-7). Pathotype 1 has been reported to be the highly virulent pathotype of Sclerospora graminicola in India (8). We report a de novo whole genome assembly and analysis of Sclerospora graminicola pathotype 1 from India. A susceptible pearl millet genotype Tift 23D2B1P1-P5 was used for obtaining single-zoospore isolates from the original oosporic sample. The library for whole genome sequencing was prepared according to the instructions by NEB ultra DNA library kit for Illumina (New England Biolabs, USA). The libraries were normalised, pooled and sequenced on Illumina HiSeq 2500 (Illumina Inc., San Diego, CA, USA) platform at 2 x100 bp length. Mate pair (MP) libraries were prepared using the Nextera mate pair library preparation kit (Illumina Inc., USA). 1 ?g of Genomic DNA was subject to tagmentation and was followed by strand displacement. Size selection tagmented/strand displaced DNA was carried out using AmpureXP beads. The libraries were validated using an Agilent Bioanalyser using DNA HS chip. The libraries were normalised, pooled and sequenced on Illumina MiSeq (Illumina Inc., USA) platform at 2 x300 bp length. The whole genome sequencing was performed by sequencing of 7.38 Gb with 73,889,924 paired end reads from paired end library, and 1.15 Gb with 3,851,788 reads from mate pair library generated from Illumina HiSeq2500 and Illumina MiSeq, respectively. The sequences were assembled using various assemblers like ABySS, MaSuRCA, Velvet, SOAPdenovo2, and ALLPATHS-LG. The assembly generated by MaSuRCA (9) algorithm was observed superior over other algorithms and hence used for scaffolding using SSPACE. Assembled draft genome sequence of S. graminicola pathotype 1 was 299,901,251 bp long, with a 47.2 % GC content consisting of 26,786 scaffolds with N50 of 17,909 bp with longest scaffold size of 238,843 bp. The overall coverage was 40X. The draft genome sequence was used for gene prediction using AUGUSTUS. The completeness of the assembly was investigated using CEGMA and revealed 92.74% proteins completely present and 95.56% proteins partially present, while BUSCO fungal dataset indicated 64.9% complete, 12.4% fragmented, 22.7% missing out of 290 BUSCO groups. A total of 52,285 predicted genes were annotated using BLASTX and 38,120 genes were observed with significant BLASTX match. Repetitive element analysis in the assembly revealed 8,196 simple repeats, 1,058 low complexity repeats and 5,562 dinucleotide to hexanucleotide microsatellite repeats.publishersversionPeer reviewe
Growth of Long Range Forward-Backward Multiplicity Correlations with Centrality in Au+Au Collisions at = 200 GeV
Forward-backward multiplicity correlation strengths have been measured with
the STAR detector for Au+Au and collisions at =
200 GeV. Strong short and long range correlations (LRC) are seen in central
Au+Au collisions. The magnitude of these correlations decrease with decreasing
centrality until only short range correlations are observed in peripheral Au+Au
collisions. Both the Dual Parton Model (DPM) and the Color Glass Condensate
(CGC) predict the existence of the long range correlations. In the DPM the
fluctuation in the number of elementary (parton) inelastic collisions produces
the LRC. In the CGC longitudinal color flux tubes generate the LRC. The data is
in qualitative agreement with the predictions from the DPM and indicates the
presence of multiple parton interactions.Comment: 6 pages, 3 figures The abstract has been slightly modifie
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