Numerical simulation of the von Kármán sodium dynamo experiment

We present hydrodynamic and magnetohydrodynamic (MHD) simulations of liquid sodium flows in the von Kármán sodium (VKS) set-up. The counter-rotating impellers made of soft iron that were used in the successful 2006 experiment are represented by means of a pseudo-penalty method. Hydrodynamic simulations are performed at high kinetic Reynolds numbers using a large eddy simulation technique. The results compare well with the experimental data: the flow is laminar and steady or slightly fluctuating at small angular frequencies; small scales fill the bulk and a Kolmogorov-like spectrum is obtained at large angular frequencies. Near the tips of the blades the flow is expelled and takes the form of intense helical vortices. The equatorial shear layer acquires a wavy shape due to three coherent co-rotating radial vortices as observed in hydrodynamic experiments. MHD computations are performed: at fixed kinetic Reynolds number, increasing the magnetic permeability of the impellers reduces the critical magnetic Reynolds number for dynamo action; at fixed magnetic permeability, increasing the kinetic Reynolds number also decreases the dynamo threshold. Our results support the conjecture that the critical magnetic Reynolds number tends to a constant as the kinetic Reynolds number tends to infinity. The resulting dynamo is a mostly axisymmetric axial dipole with an azimuthal component concentrated near the impellers as observed in the VKS experiment. A speculative mechanism for dynamo action in the VKS experiment is proposed

Small-angle neutron scattering and Molecular Dynamics structural study of gelling DNA nanostars

DNA oligomers with properly designed sequences self-assemble into well defined constructs. Here, we exploit this methodology to produce bulk quantities of tetravalent DNA nanostars (each one composed by 196 nucleotides) and to explore the structural signatures of their aggregation process. We report small-angle neutron scattering experiments focused on the evaluation of both the form factor and the temperature evolution of the scattered intensity at a nano star concentration where the system forms a tetravalent equilibrium gel. We also perform molecular dynamics simulations of one isolated tetramer to evaluate the form factor theoretically, without resorting to any approximate shape. The numerical form factor is found to be in very good agreement with the experimental one. Simulations predict an essentially temperature independent form factor, offering the possibility to extract the effective structure factor and its evolution during the equilibrium gelation.Comment: 9 pages, 5 figure

Investigation of the Multiple Method Adaptive Control (MMAC) method for flight control systems

The stochastic adaptive control of the NASA F-8C digital-fly-by-wire aircraft using the multiple model adaptive control (MMAC) method is presented. The selection of the performance criteria for the lateral and the longitudinal dynamics, the design of the Kalman filters for different operating conditions, the identification algorithm associated with the MMAC method, the control system design, and simulation results obtained using the real time simulator of the F-8 aircraft at the NASA Langley Research Center are discussed

CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping.

Broad-scale protein-protein interaction mapping is a major challenge given the cost, time, and sensitivity constraints of existing technologies. Here, we present a massively multiplexed yeast two-hybrid method, CrY2H-seq, which uses a Cre recombinase interaction reporter to intracellularly fuse the coding sequences of two interacting proteins and next-generation DNA sequencing to identify these interactions en masse. We applied CrY2H-seq to investigate sparsely annotated Arabidopsis thaliana transcription factors interactions. By performing ten independent screens testing a total of 36 million binary interaction combinations, and uncovering a network of 8,577 interactions among 1,453 transcription factors, we demonstrate CrY2H-seq's improved screening capacity, efficiency, and sensitivity over those of existing technologies. The deep-coverage network resource we call AtTFIN-1 recapitulates one-third of previously reported interactions derived from diverse methods, expands the number of known plant transcription factor interactions by three-fold, and reveals previously unknown family-specific interaction module associations with plant reproductive development, root architecture, and circadian coordination

Migration of Zebrafish Primordial Germ Cells: A Role for Myosin Contraction and Cytoplasmic Flow

SummaryThe molecular and cellular mechanisms governing cell motility and directed migration in response to the chemokine SDF-1 are largely unknown. Here, we demonstrate that zebrafish primordial germ cells whose migration is guided by SDF-1 generate bleb-like protrusions that are powered by cytoplasmic flow. Protrusions are formed at sites of higher levels of free calcium where activation of myosin contraction occurs. Separation of the acto-myosin cortex from the plasma membrane at these sites is followed by a flow of cytoplasm into the forming bleb. We propose that polarized activation of the receptor CXCR4 leads to a rise in free calcium that in turn activates myosin contraction in the part of the cell responding to higher levels of the ligand SDF-1. The biased formation of new protrusions in a particular region of the cell in response to SDF-1 defines the leading edge and the direction of cell migration

Direct numerical simulation of the axial dipolar dynamo in the Von Kármán Sodium experiment

For the first time, a direct numerical simulation of the incompressible, fully nonlinear, magnetohydrodynamic (MHD) equations for the Von Kármán Sodium (VKS) experiment is presented with the two counter-rotating impellers realistically represented. Dynamo thresholds are obtained for various magnetic permeabilities of the impellers and it is observed that the threshold decreases as the magnetic permeability increases. Hydrodynamic results compare well with experimental data in the same range of kinetic Reynolds numbers: at small impeller rotation frequency, the flow is steady; at larger frequency, the fluctuating flow is characterized by small scales and helical vortices localized between the blades. MHD computations show that two distinct magnetic families compete at small kinetic Reynolds number and these two families merge at larger kinetic Reynolds number. In both cases, using ferromagnetic material for the impellers decreases the dynamo threshold and enhances the axisymmetric component of the magnetic field: the resulting dynamo is a mostly axisymmetric axial dipole with an azimuthal component concentrated in the impellers as observed in the VKS experiment

Characterization of Selective Antibacterial Peptides by Polarity Index

In the recent decades, antibacterial peptides have occupied a strategic position for pharmaceutical drug applications and became subject of intense research activities since they are used to strengthen the immune system of all living organisms by protecting them from pathogenic bacteria. This work proposes a simple and easy statistical/computational method through a peptide polarity index measure by which an antibacterial peptide subgroup can be efficiently identified, that is, characterized by a high toxicity to bacterial membranes but presents a low toxicity to mammal cells. These peptides also have the feature not to adopt to an alpha-helicoidal structure in aqueous solution. The double-blind test carried out to the whole Antimicrobial Peptide Database (November 2011) showed an accuracy of 90% applying the polarity index method for the identification of such antibacterial peptide groups