A new algorithm for extended nonequilibrium molecular dynamics simulations of mixed flow

In this work, we develop a new algorithm for nonequilibrium molecular dynamics of fluids under planar mixed flow, a linear combination of planar elongational flow and planar Couette flow. To date, the only way of simulating mixed flow using nonequilibrium molecular dynamics techniques was to impose onto the simulation box irreversible transformations. This would bring the simulation to an end as soon as the minimum lattice space requirements were violated. In practical terms, this meant repeating the short simulations to improve statistics and extending the box dimensions to increase the total simulation time. Our method, similar to what has already been done for pure elongational flow, allows a cuboid box to deform in time following the streamlines of the mixed flow and, after a period of time determined by the elongational field, to be mapped back and recover its initial shape. No discontinuity in physical properties is present during the mapping and the simulation can, in this way, be extended indefinitely. We also show that the most general form of mixed flow, in which the angle between the expanding (or contracting) direction and the velocity gradient axis varies, can be cast in a so-called canonical form, in which the angle assumes values that are multiples of π (when a mixed flow exists), by an appropriate choice of the field parameters

Circlator: automated circularization of genome assemblies using long sequencing reads

The assembly of DNA sequence data is undergoing a renaissance thanks to emerging technologies capable of producing reads tens of kilobases long. Assembling complete bacterial and small eukaryotic genomes is now possible, but the final step of circularizing sequences remains unsolved. Here we present Circlator, the first tool to automate assembly circularization and produce accurate linear representations of circular sequences. Using Pacific Biosciences and Oxford Nanopore data, Circlator correctly circularized 26 of 27 circularizable sequences, comprising 11 chromosomes and 12 plasmids from bacteria, the apicoplast and mitochondrion of Plasmodium falciparum and a human mitochondrion. Circlator is available at http://sanger-pathogens.github.io/circlator/

Randomised controlled study comparing two psychological therapies for Posttraumatic Stress Disorder (PTSD): Emotional Freedom Techniques (EFT) vs. Narrative Exposure Therapy (NET)

Background: Post-Traumatic Stress Disorder (PTSD) is a common psychological reaction after traumatic events. The aim of this study was to evaluate the efficacy of Emotional Freedom Techniques (EFT) and Narrative Exposure Therapy (NET) as treatments for PTSD with traumatised people. Methods: A randomized controlled trial design was used. Sixty Iraqi students were selected who met the DSM-IV PTSD criteria. Participants were male students who were aged between 16-19 years. Participants were randomly divided into three groups, with 20 participants in each group. Those in the EFT and NET groups received 4 therapy sessions, while the control group received no treatment. One person from the NET group withdrew. All participants were assessed on PTSD symptoms, anxiety and depression, social support. Results: The results showed that the participants who received EFT reported a significant difference in all PTSD cluster at pre-test and post-test from T1 to T2 (p>0.05). However, although the NET group reported a significant difference between pre-test and posttest in avoidance and re-experience, no significant difference was found in hyper arousal (p<0.05). However, no significant differences were found in the experiential group with social support, coping strategies, and religious coping (p<0.05). These changes of PTSD, PTSD clusters, anxiety and depression remained stable for 3, 6 and 12 month follow-ups in EFT group, while these changes were unstable during the follow-ups. Measures of coping strategies showed that seeking support and active coping improved since the interventions. In conclusion, both EFT and NET showed their effectiveness among traumatised Iraqi people

Strain Coupled Domains in BaTiO3(111)-CoFeB Heterostructures

Domain pattern transfer from ferroelectric to ferromagnetic materials is a critical step for the electric field control of magnetism and has the potential to provide new schemes for low-power data storage and computing devices. Here we investigate domain coupling in BaTiO$_3$(111)/CoFeB heterostructures by direct imaging in a wide-field Kerr microscope. The magnetic easy axis is found to locally change direction as a result of the underlying ferroelectric domains and their polarisation. By plotting the remanent magnetisation as a function of angle in the plane of the CoFeB layer, we find that the magnetic easy axes in adjacent domains are angled at 60$^\circ$ or 120$^\circ$, corresponding to the angle of rotation of the polarisation from one ferroelectric domain to the next, and that the magnetic domain walls may be charged or uncharged depending on the magnetic field history. Micromagnetic simulations show that the properties of the domain walls vary depending on the magnetoelastic easy axis configuration and the charged or uncharged nature of the wall. The configuration where the easy axis alternates by 60$^\circ$ and a charged wall is initialised exhibits the largest change in domain wall width from 192 nm to 119 nm as a function of in-plane magnetic field. Domain wall width tuning provides an additional degree of freedom for devices that seek to manipulate magnetic domain walls using strain coupling to ferroelectrics.Comment: 7 pages, 8 figure

Bifenthrin Baseline Susceptibility and Evaluation of Simulated Aerial Applications in \u3ci\u3eStriacosta albicosta\u3c/i\u3e (Lepidoptera: Noctuidae)

Striacosta albicosta (Smith) is a maize pest that has recently expanded its geographical range into the eastern United States and southeastern Canada. Aerial application of pyrethroids, such as bifenthrin, has been a major practice adopted to manage this pest. Reports of field failure of pyrethroids have increased since 2013. Striacosta albicosta populations were collected in 2016 and 2017 from maize fields in Nebraska, Kansas, and Canada and screened with bifenthrin active ingredient in larval contact dose-response bioassays. Resistance ratios estimated were generally low in 2016 (1.04- to 1.32-fold) with the highest LC50 in North Platte, NE (66.10 ng/cm2) and lowest in Scottsbluff, NE (50.10 ng/cm2). In 2017, O’Neill, NE showed the highest LC50 (100.66 ng/cm2) and Delhi, Canada exhibited the lowest (6.33 ng/cm2), resulting in a resistance ratio variation of 6.02- to 15.90-fold. Implications of bifenthrin resistance levels were further investigated by aerial application simulations. Experiments were conducted with a spray chamber where representative S. albicosta populations were exposed to labeled rates of a commercial bifenthrin formulation. Experiments resulted in 100% mortality for all populations, instars, insecticide rates, and carrier volumes, suggesting that levels of resistance estimated for bifenthrin active ingredient did not seem to impact the efficacy of the correspondent commercial product under controlled conditions. Results obtained from this research indicate that control failures reported in Nebraska could be associated with factors other than insecticide resistance, such as issues with the application technique, environmental conditions during and/or after application, or the insect’s natural behavior. Data generated will assist future S. albicosta resistance management programs

An Analytical Construction of the SRB Measures for Baker-type Maps

For a class of dynamical systems, called the axiom-A systems, Sinai, Ruelle and Bowen showed the existence of an invariant measure (SRB measure) weakly attracting the temporal average of any initial distribution that is absolutely continuous with respect to the Lebesgue measure. Recently, the SRB measures were found to be related to the nonequilibrium stationary state distribution functions for thermostated or open systems. Inspite of the importance of these SRB measures, it is difficult to handle them analytically because they are often singular functions. In this article, for three kinds of Baker-type maps, the SRB measures are analytically constructed with the aid of a functional equation, which was proposed by de Rham in order to deal with a class of singular functions. We first briefly review the properties of singular functions including those of de Rham. Then, the Baker-type maps are described, one of which is non-conservative but time reversible, the second has a Cantor-like invariant set, and the third is a model of a simple chemical reaction $R \leftrightarrow I \leftrightarrow P$. For the second example, the cases with and without escape are considered. For the last example, we consider the reaction processes in a closed system and in an open system under a flux boundary condition. In all cases, we show that the evolution equation of the distribution functions partially integrated over the unstable direction is very similar to de Rham's functional equation and, employing this analogy, we explicitly construct the SRB measures.Comment: 53 pages, 10 figures, to appear in CHAO