Histone H4 LRS mutations can attenuate UV mutagenesis without affecting PCNA ubiquitination or sumoylation.

UV is a significant environmental agent that damages DNA. Translesion synthesis (TLS) is a DNA damage tolerance pathway that utilizes specialized DNA polymerases to replicate through the damaged DNA, often leading to mutagenesis. In eukaryotic cells, genomic DNA is organized into chromatin that is composed of nucleosomes. To date, if and/or how TLS is regulated by a specific nucleosome feature has been undocumented. We found that mutations of multiple histone H4 residues mostly or entirely embedded in the nucleosomal LRS (loss of ribosomal DNA-silencing) domain attenuate UV mutagenesis in Saccharomyces cerevisiae. The attenuation is not caused by an alteration of ubiquitination or sumoylation of PCNA (proliferating cell nuclear antigen), the modifications well-known to regulate TLS. Also, the attenuation is not caused by decreased chromatin accessibility, or by alterations of methylation of histone H3 K79, which is at the center of the LRS surface. The attenuation may result from compromised TLS by both DNA polymerases ζ and η, in which Rad6 and Rad5 are but Rad18 is not implicated. We propose that a feature of the LRS is recognized or accessed by the TLS machineries either during/after a nucleosome is disassembled in front of a lesion-stalled replication fork, or during/before a nucleosome is reassembled behind a lesion-stalled replication fork.

Modelling viscous boundary layer dissipation effects in liquid surrounding individual solid nano and micro-particles in an ultrasonic field.

Upon application of ultrasonic waves to a suspension of solid particles in liquid, multiple scattering occurs at the particle/liquid interfaces leading to attenuation. It was recently shown through experimental verification that multiple scattering theory must include shear wave influences at the boundary between the liquid and solid particles in a nanofluid when the concentration of the scatterers is even as low as a few percent by volume. Herein, we consider silica spheres of 50-450 nm diameter in the long-wavelength regime to elucidate the form of the shear decay fields at the liquid/solid interface for individual particles. This is important because the overlap of these fields ultimately leads to the conversion of a compressional wave to shear waves and back into the compressional wave, the effect originating due to the density contrast between the particle and the liquid. Therefore, we examine in detail the velocity, vorticity and viscous dissipation in the shear wave field and around the silica spheres using finite element modelling, giving clarity to the viscous boundary effects. We also compare the numerical modelling to semi-analytical results.

The absorption of ultrasound in emulsions: computational modelling of thermal effects.

Around liquid particles in a fluid of contrasting properties (for example, oil in water) in ultrasonic fields there are small regions where thermal waves can propagate with relatively high amplitudes. Herein, we demonstrate the existence and character of these waveforms using three-dimensional finite element modelling based on linearised Navier-Stokes equations. We investigate single particles and small clusters of particles, validating the expected thermal wavelength and the power dissipation due to viscous and thermal effects around the particle. The energy lost due to thermal and viscous dissipation is explored as a function of the average separation distance between the particles (linking to concentration) as well as the applied frequency. The determination of energy loss provides a new method for calculating the attenuation in particle systems. We demonstrate that the effective attenuation of an emulsion in which particles exist in clusters is influenced by the interparticle separation within the cluster, even at the same total particle concentration. Thus, the finite element modelling provides evidence for thermal interactions and their effect in correlated particle systems.

Multiple scattering in random dispersions of spherical scatterers: Effects of shear-acoustic interactions.

The propagation of acoustic waves through a suspension of spherical particles in a viscous liquid is investigated, through application of a multiple scattering model. The model is based on the multiple scattering formulation of Luppé, Conoir, and Norris [J. Acoust. Soc. Am. 131, 1113-1120 (2012)] which incorporated the effects of thermal and shear wave modes on propagation of the acoustic wave mode. Here, the model is simplified for the case of solid particles in a liquid, in which shear waves make a significant contribution to the effective properties. The relevant scattering coefficients and effective wavenumber are derived in analytical form. The results of calculations are presented for a system of silica particles in water, illustrating the dependence of the scattering coefficients, effective wavenumber, speed, attenuation on particle size and frequency. The results demonstrate what has already been shown experimentally; that the shear-mediated processes have a very significant effect on the effective attenuation of acoustic waves, especially as the concentration of particles increases.

Whispering galleries and the control of artificial atoms.

Quantum computation using artificial-atoms, such as novel superconducting circuits, can be sensitively controlled by external electromagnetic fields. These fields and the self-fields attributable to the coupled artificial-atoms influence the amount of quantum correlation in the system. However, control elements that can operate without complete destruction of the entanglement of the quantum-bits are difficult to engineer. Here we investigate the possibility of using closely-spaced-linear arrays of metallic-elliptical discs as whispering gallery waveguides to control artificial-atoms. The discs confine and guide radiation through the array with small notches etched into their sides that act as scatterers. We focus on π-ring artificial-atoms, which can generate their own spontaneous fluxes. We find that the micro-discs of the waveguides can be excited by terahertz frequency fields to exhibit whispering-modes and that a quantum-phase-gate composed of π-rings can be operated under their influence. Furthermore, we gauge the level of entanglement through the concurrence measure and show that under certain magnetic conditions a series of entanglement sudden-deaths and revivals occur between the two qubits. This is important for understanding the stability and life-time of qubit operations using, for example, a phase gate in a hybrid of quantum technologies composed of control elements and artificial-atoms.

Experimental verification of nanofluid shear-wave reconversion in ultrasonic fields.

Here we present the verification of shear-mediated contributions to multiple scattering of ultrasound in suspensions. Acoustic spectroscopy was carried out with suspensions of silica of differing particle sizes and concentrations in water to find the attenuation at a broad range of frequencies. As the particle sizes approach the nanoscale, commonly used multiple scattering models fail to match experimental results. We develop a new model, taking into account shear mediated contributions, and find excellent agreement with the attenuation spectra obtained using two types of spectrometer. The results determine that shear-wave phenomena must be considered in ultrasound characterisation of nanofluids at even relatively low concentrations of scatterers that are smaller than one micrometre in diameter.

Shear-mediated contributions to the effective properties of soft acoustic metamaterials including negative index.

Here we show that, for sub-wavelength particles in a fluid, viscous losses due to shear waves and their influence on neighbouring particles significantly modify the effective acoustic properties, and thereby the conditions at which negative acoustic refraction occurs. Building upon earlier single particle scattering work, we adopt a multiple scattering approach to derive the effective properties (density, bulk modulus, wavenumber). We show,through theoretical prediction, the implications for the design of "soft" (ultrasonic) metamaterials based on locally-resonant sub-wavelength porous rubber particles, through selection of particle size and concentration, and demonstrate tunability of the negative speed zones by modifying the viscosity of the suspending medium. For these lossy materials with complex effective properties, we confirm the use of phase angles to define the backward propagation condition in preference to "single-" and "double-negative" designations.

Arrays of coupled chemical oscillators.

Oscillating chemical reactions result from complex periodic changes in the concentration of the reactants. In spatially ordered ensembles of candle flame oscillators the fluctuations in the ratio of oxygen atoms with respect to that of carbon, hydrogen and nitrogen produces an oscillation in the visible part of the flame related to the energy released per unit mass of oxygen. Thus, the products of the reaction vary in concentration as a function of time, giving rise to an oscillation in the amount of soot and radiative emission. Synchronisation of interacting dynamical sub-systems occurs as arrays of flames that act as master and slave oscillators, with groups of candles numbering greater than two, creating a synchronised motion in three-dimensions. In a ring of candles the visible parts of each flame move together, up and down and back and forth, in a manner that appears like a "worship". Here this effect is shown for rings of flames which collectively empower a central flame to pulse to greater heights. In contrast, situations where the central flames are suppressed are also found. The phenomena leads to in-phase synchronised states emerging between periods of anti-phase synchronisation for arrays with different columnar sizes of candle and positioning.

Self-assembled multi-ring formations of glutamine and a possible link to erythema gyratum repens.

In the body L-glutamine is abundant and required for the proliferation of cells. Indeed human physiology is dependent upon having and maintaining the correct glutamine levels for a range of functions including neurological signalling and a healthy immune system. However, during tumourigenesis cell proliferation demands elevated levels of glutamine, which can ultimately lead to muscle atrophy. In some cases the skin provides the first indications of the underlying disease and erupts in a wave of complicated pattern formations. One such skin marker is erythema gyratum repens. We investigated the pattern formations associated with concentrations of glutamine in aqueous solutions at levels higher than that of a normal biological functionality. We find remarkable similarities between the patterns of erythema gyratum repens and the unusual self-assembled patterns of glutamine. The findings may lead to new therapeutics and understanding for those working in oncology and toxicology. Utilising the formations associated with glutamine could also assist in bio-functionalising micro and nanoparticles for high efficacy.

Designing magnetic superlattices that are composed of single domain nanomagnets.

BACKGROUND: The complex nature of the magnetic interactions between any number of nanosized elements of a magnetic superlattice can be described by the generic behavior that is presented here. The hysteresis characteristics of interacting elliptical nanomagnets are described by a quasi-static method that identifies the critical boundaries between magnetic phases. A full dynamical analysis is conducted in complement to this and the deviations from the quasi-static analysis are highlighted. Each phase is defined by the configuration of the magnetic moments of the chain of single domain nanomagnets and correspondingly the existence of parallel, anti-parallel and canting average magnetization states. RESULTS: We give examples of the phase diagrams in terms of anisotropy and coupling strength for two, three and four magnetic layers. Each phase diagrams character is defined by the shape of the magnetic hysteresis profile for a system in an applied magnetic field. We present the analytical solutions that enable one to define the "phase" boundaries between the emergence of spin-flop, anti-parallel and parallel configurations. The shape of the hysteresis profile is a function of the coupling strength between the nanomagnets and examples are given of how it dictates a systems magnetic response. Many different paths between metastable states can exist and this can lead to instabilities and fluctuations in the magnetization. CONCLUSION: With these phase diagrams one can find the most stable magnetic configurations against perturbations so as to create magnetic devices. On the other hand, one may require a magnetic system that can easily be switched between phases, and so one can use the information herein to design superlattices of the required shape and character by choosing parameters close to the phase boundaries. This work will be useful when designing future spintronic devices, especially those manipulating the properties of CoFeB compounds.

Graphene levitons and anti-levitons in magnetic fields.

The leviton is an electron or hole wavepacket that rides the surface of the Fermi sea. When a series of Lorentzian or Gaussian time dependent pulses are applied to an ultracold system a soliton-like excitation with only one electron and no localised hole emerges. Graphene is a unique system where the Fermi surface may arise from a Dirac point and therewith the levitons character may display many interesting features. For example, the leviton formation may be associated with a chiral anomaly, and inside a single potential step an anti-leviton forms. We show that the application of weak magnetic fields may switch on and off the leviton Klein tunnelling. Also, in a moderate field negative refraction arises along a curved trajectory, whereas with a stronger field a new elementary excitation - the levity vortex - in the reflected wavefunction occurs. Herein we describe these phenomena in detail along with a complete explanation of the transmission of graphene levitons at a step potential in terms of the probability densities and a series of phase diagrams and the tunnelling times.