Non-Linear Damping of Surface Alfvén Waves Due to Uniturbulence

This investigation is concerned with uniturbulence associated with surface Alfvén waves that exist in a Cartesian equilibrium model with a constant magnetic field and a piece-wise constant density. The surface where the equilibrium density changes in a discontinuous manner are the source of surface Alfvén waves. These surface Alfvén waves create uniturbulence because of the variation of the density across the background magnetic field. The damping of the surface Alfvén waves due to uniturbulence is determined using the Elsässer formulation. Analytical expressions for the wave energy density, the energy cascade, and the damping time are derived. The study of uniturbulence due to surface Alfvén waves is inspired by the observation that (the fundamental radial mode of) kink waves behave similarly to surface Alfvén waves. The results for this relatively simple case of surface Alfvén waves can help us understand the more complicated case of kink waves in cylinders. We perform a series of 3D ideal MHD simulations for a numerical demonstration of the non-linearly self-cascading model of unidirectional surface Alfvén waves using the code MPI-AMRVAC. We show that surface Alfvén waves damping time in the numerical simulations follows well our analytical prediction for that quantity. Analytical theory and the simulations show that the damping time is inversely proportional to the amplitude of the surface Alfvén waves and the density contrast. This unidirectional cascade may play a role in heating the coronal plasma.

Optimized Method for Pseudomonas aeruginosa Integrative Filamentous Bacteriophage Propagation

Filamentous bacteriophages frequently infect Pseudomonas aeruginosa and alter its phenotypic traits, including virulence factors. The first step in examination of these phages is to obtain suspensions with high virus titer, but as there are no methods for integrative filamentous phage multiplication, the aim was to design, describe, and compare two methods for this purpose. As models, three strains of Pseudomonas aeruginosa, containing (pro)phages Pf4, Pf5, and PfLES were used (PAO1, UCBPP-PA14, and LESB58, respectively). Method 1 comprised propagation of phages in 6 L of bacterial culture for 48 h, and method 2 applied 600 mL culture and incubation for 6 days with centrifugation and addition of new medium and inoculum at 2-day intervals. In method 1, phages were propagated by culture agitation, followed by centrifugation and filtration (0.45 and 0.22 μm), and in method 2, cultures were agitated and centrifuged several times to remove bacteria without filtration. Regardless of the propagation method, supernatants were subjected to concentration by PEG8000 and CsCl equilibrium density gradient centrifugation, and phage bands were removed after ultracentrifugation and dialyzed. In the obtained suspensions, phage titer was determined, and concentration of isolated ssDNA from virions was measured. When propagation method 2 was compared with method 1, the phage bands in CsCl were much thicker, phage number was 3.5–7.4 logs greater, and concentration of ssDNA was 7.6–22.4 times higher. When phage count was monitored from days 2 to 6, virion numbers increased for 1.8–5.6 logs, depending on phage. We also observed that filamentous phage plaques faded after 8 h of incubation when the double layer agar spot method was applied, whereas the plaques were visible for 24 h on single-layer agar. Finally, for the first time, we confirmed existence of replicative form and virions of PfLES (pro)phage as well as its ability to produce plaques. Similarly, for the first time, we confirmed plaque production of Pf5 (pro)phage present in P. aeruginosa strain UCBPP-PA14. The described method 2 has many advantages and can be further improved and adopted for filamentous phages of other hosts.

Determination of human DNA replication origin position and efficiency reveals principles of initiation zone organisation

Replication of the human genome initiates within broad zones of ~ 150 kb. The extent to which firing of individual DNA replication origins within initiation zones is spatially stochastic or localised at defined sites remains a matter of debate. A thorough characterisation of the dynamic activation of origins within initiation zones is hampered by the lack of a high-resolution map of both their position and efficiency. To address this shortcoming, we describe a modification of initiation site sequencing (ini-seq) based on density substitution. Newly-replicated DNA is rendered heavy-light (HL) by incorporation of BrdUTP, unreplicated DNA remaining light-light (LL). Replicated HL-DNA is separated from unreplicated LL-DNA by equilibrium density gradient centrifugation, then both fractions are subjected to massive parallel sequencing. This allows precise mapping of 23,905 replication origins simultaneously with an assignment of a replication initiation efficiency score to each. We show that origin firing within initiation zones is not randomly distributed. Rather, origins are arranged hierarchically with a set of very highly efficient origins marking zone boundaries. We propose that these origins explain much of the early firing activity arising within initiation zones, helping to unify the concept of replication initiation zones with the identification of discrete replication origin sites.

Supersolid phase of a spin-orbit-coupled Bose-Einstein condensate: A perturbation approach

The phase diagram of a Bose-Einstein condensate with Raman-induced spin-orbit coupling includes a stripe phase with supersolid features. In this work we develop a perturbation approach to study the ground state and the Bogoliubov modes of this phase, holding for small values of the Raman coupling. We obtain analytical predictions for the most relevant observables (including the periodicity of stripes, sound velocities, compressibility, and magnetic susceptibility) which are in excellent agreement with the exact (non perturbative) numerical results, obtained for significantly large values of the coupling. We further unveil the nature of the two gapless Bogoliubov modes in the long-wavelength limit. We find that the spin branch of the spectrum, corresponding in this limit to the dynamics of the relative phase between the two spin components, describes a translation of the fringes of the equilibrium density profile, thereby providing the crystal Goldstone mode typical of a supersolid configuration. Finally, using sum-rule arguments, we show that the superfluid density can be experimentally accessed by measuring the ratio of the sound velocities parallel and perpendicular to the direction of the spin-orbit coupling.

The effect of interference time in a predator–prey–nonprey system

In this paper, we propose a three-species model consisting of two competing (prey and nonprey) species and a predator species. Here, nonprey species are not included in the predator’s food choice. The competition process follows Holling type II competitive response to interference time. Basic results include the stability of the system. First, it is established that an increasing number of interference time stabilizes the system. Second, it is shown that the interference time has an impact on the predator equilibrium density. Third, we develop the criterion of persistence of all the species. It is also shown that the system may not be persistent when multiple steady states appear. We examine the global stability of the coexistence equilibrium point. Numerical experiments are carried out to understand the analytical outcomes.

Differential thermopower images as a probe of many-body effects in quantum point contacts

Mesoscopic circuit elements such as quantum dots and quantum point contacts (QPCs) offer a uniquely controllable platform for engineering complex quantum devices, whose tunability makes them ideal for generating and investigating interacting quantum systems. However, the conductance measurements commonly employed in mesoscopics experiments are poorly suited to discerning correlated phenomena from those of single-particle origin. Here, we introduce non-equilibrium thermopower measurements as a novel approach to probing the local density of states (LDOS), offering an energy-resolved readout of many-body effects. We combine differential thermopower measurements with non-equilibrium density functional theory (DFT) to both confirm the presence of a localized state at the saddle point of a QPC and reveal secondary states that emerge wherever the reservoir chemical potential intersects the gate-induced potential barrier. These experiments establish differential thermopower imaging as a robust and general approach to exploring quantum many-body effects in mesoscopic circuits.

Quantum properties of dielectric losses in nanometer layers of solid dielectrics at ultra-low temperatures

Using the methods of quasi-classical kinetic theory, continuum electrodynamics, and non-relativistic quantum theory, we construct and study the quantum kinetic equation of proton relaxation, which, together with the Poisson operator equation describes the mechanism of diffusion tunneling transport of hydrogen ions (protons) in the potential field of a crystal lattice perturbed by a polarizing field (quantum diffusion polarization) in crystals with hydrogen bonds. Using the apparatus of the density matrix (statistical matrix), by complete quantum-mechanical averaging of the polarization operator, studies are carried out of the experimental value of the polarization of the dielectric, as a function of the parameters of the external electric field (amplitude, frequency of electromotive force) and temperature. When calculating the equilibrium density matrix for an ensemble of basic relaxers (hydrogen ions), the proton-proton and proton-phonon interactions are not taken into account, and the Hamilton operator for the phonon subsystem is assumed to be a numerical constant for a given crystal under given experimental conditions (calculated by computer method as a parameter for comparing the theory with the experiment). The influence of the phonon subsystem on the kinetics of the relaxation process is reduced to a weak spatially homogeneous force field acting on protons moving in the field of the main forces of hydrogen bonds. The Hamilton of the proton subsystem is constructed for the model of an ideal proton gas in equilibrium with the ionic subsystem of the crystal lattice, and the equilibrium statistical operator of the proton subsystem is written using the Boltzmann quantum statistics. Theoretically, the size effects are found to be manifested in shifts of the low-temperature (50–100 K) maxima of the dielectric loss angle tangent towards ultra-low temperatures (4–25 K) with a decrease in the amplitudes of the maxima by 3-4 orders of magnitude, with a reduction in the thickness of the crystal layer from 1–10 microns to 1–10 nm. The effect of anomalous displacements of low-temperature maxima, which is explained by the abnormally high quantum transparency of the potential barrier for protons (0.8-0.9) in thin films of a crystal with hydrogen bonds (1-10 nm), causes, near the temperatures of the shifted maxima of dielectric losses (4–25 K), a quasi-ferroelectric state, which is also characterized by abnormally high values of the real component of the complete dielectric permittivity (2.5–3.5millions).

Proof-of-concept for the yadokari nature: a capsidless replicase-encoding but replication-dependent (+)ssRNA virus hosted by an unrelated dsRNA virus

We have previously proposed a new virus lifestyle or yadokari/yadonushi nature exhibited by a positive-sense ssRNA virus, yadokari virus 1 (YkV1), and an unrelated dsRNA virus, yadonushi virus 1 (YnV1) in a phytopathogenic ascomycete, Rosellinia necatrix . We have proposed that YkV1 diverts the YnV1 capsid to trans-encapsidate YkV1 RNA and RNA-dependent RNA polymerase (RdRp) and replicate in the heterocapsid. However, it remains uncertain whether YkV1 replicates using its own RdRp, and whether YnV1 capsid co-packages both YkV1 and YnV1 components. To address these questions, we first took advantage of the reverse genetics tools available for YkV1. Mutations in the GDD RdRp motif, one of the two identifiable functional motifs on the YkV1 polyprotein, abolished its replication competency. Mutations were also introduced in the conserved 2A-like peptide motif, hypothesized to cleave the YkV1 polyprotein co-translationally. Interestingly, the replication proficiency of YkV1 mutants in the host fungus agreed with the cleavage activity of the 2A-like peptide tested using a baculovirus expression system. Cesium chloride equilibrium density gradient centrifugation allowed for the separation of particles, with a subset of YnV1 capsid solely packaging YkV1 dsRNA and RdRp. These results provide proof-of-concept that a capsidless (+)ssRNA virus is hosted by an unrelated dsRNA virus. Importance Viruses typically encode their own capsids that encase their genomes. However, a capsidless (+)ssRNA virus, YkV1, depends on an unrelated dsRNA virus, YnV1, for encapsidation and replication. We have previously shown that YkV1 highjacks the capsid of YnV1 for trans-encapsidation of its own RNA and RdRp. YkV1 was hypothesized to divert the hetero-capsid as the replication site, as is commonly observed for dsRNA viruses. Herein, mutational analyses showed that the RdRp and 2A-like domains on the YkV1 polyprotein are important for its replication. The active RdRp must be cleaved by a 2A-like peptide from the C-proximal protein. Cesium chloride equilibrium density gradient centrifugation allowed for the separation of particles, with YnV1 capsid solely packaging YkV1 dsRNA and RdRp. This study provides proof-of-concept of a virus neo-lifestyle where a (+)ssRNA virus snatches capsids from an unrelated dsRNA virus to replicate with its own RdRp, thereby mimicking the typical dsRNA virus lifestyle.