Slow dynamics in a turbulent von K\'arm\'an swirling flow

We present an experimental study of a turbulent von K\'arm\'an flow produced in a cylindrical container using two propellers. The mean flow is stationary up to $Re = 10^4$, where a bifurcation takes place. The new regime breaks some symmetries of the problem, and is time-dependent. The axisymmetry is broken by the presence of equatorial vortices with a precession movement, being the velocity of the vortices proportional to the Reynolds number. The reflection symmetry through the equatorial plane is broken, and the shear layer of the mean flow appears displaced from the equator. These two facts appear simultaneously. In the exact counterrotating case, a bistable regime appears between both mirrored solutions and spontaneous reversals of the azimuthal velocity are registered. This evolution can be explained using a three-well potential model with additive noise. A regime of forced periodic response is observed when a very weak input signal is applied.Comment: Improved model, additional results and figures, accepted in PR

In-situ early age hydration of cement-based materials by synchrotron X-ray powder diffraction

Cement based binders are building materials of worldwide importance. Since these samples are very complex, the knowledge/control of their mineralogical composition are essential to design and predict materials with specific/improved performance. Rietveld quantitative phase analysis (RQPA) allows the quantification of crystalline phases and, when combined with specific methodologies, as the addition of an internal standard or the external standard approach (G-factor), amorphous and non-crystalline phases can also be quantified. However, to carry out a proper RQPA in hydrated cementitious-materials, a good powder diffraction pattern is necessary. In this work, synchrotron X-ray powder diffraction (SXRPD) has been used, allowing in-situ measurements during the early-age hydration process. This work deals with the early hydration study of cement-based materials. The studied samples were: a laboratory-prepared belite calcium sulphoaluminate (BCSAF) clinker (non-active) mixed with 10wt% gypsum, labelled G10B0; two active laboratory-prepared BCSAF clinkers (activated with 2wt% borax), one mixed with 10wt% gypsum and the other one with 10wt% monoclinic-bassanite, hereafter named G10B2 and B10B2, respectively; and an environmentally-friendly cement sample from Henkel, composed of bassanite mixed with 15wt% Portland cement and 10wt% Metakaolin, labelled H1. Anhydrous G10B0 contains beta-belite and orthorhombic-ye'elimite as main phases, while alpha'H-belite and pseudo-cubic-ye'elimite are stabilized in G10B2 and B10B2, with the corresponding sulphate source. Anhydrous H1 contains monoclinic and hexagonal bassanite and alite as main phases. Ye'elimite, in the non-active BCSAF cement pastes, dissolves at a higher pace than in the active one (degree of reaction is α~25% and α~10% at 1 h, respectively) (both prepared with gypsum), with the corresponding differences in ettringite crystallisation (degree of precipitation is α~30% and α~5%, respectively). Moreover, the type of sulphate source has important consequences on the hydration of the active BCSAF cement pastes. Bassanite is quickly dissolved and it precipitates as gypsum within the first hour of hydration (in B10B2). At that time, ettringite starts to crystallize, and after 12 hours is almost fully crystallized, similar to G10B2. In H1, bassanite transforms into gypsum within the first hour, being the principal hydration product; ettringite starts to be formed just after few hydration minutes. These results are crucial in the understanding and development of improved cement materials.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Envelope Exchange for the Generation of Live-Attenuated Arenavirus Vaccines

Arenaviruses such as Lassa fever virus cause significant mortality in endemic areas and represent potential bioterrorist weapons. The occurrence of arenaviral hemorrhagic fevers is largely confined to Third World countries with a limited medical infrastructure, and therefore live-attenuated vaccines have long been sought as a method of choice for prevention. Yet their rational design and engineering have been thwarted by technical limitations. In addition, viral genes had not been identified that are needed to cause disease but can be deleted or substituted to generate live-attenuated vaccine strains. Lymphocytic choriomeningitis virus, the prototype arenavirus, induces cell-mediated immunity against Lassa fever virus, but its safety for humans is unclear and untested. Using this virus model, we have developed the necessary methodology to efficiently modify arenavirus genomes and have exploited these techniques to identify an arenaviral Achilles' heel suitable for targeting in vaccine design. Reverse genetic exchange of the viral glycoprotein for foreign glycoproteins created attenuated vaccine strains that remained viable although unable to cause disease in infected mice. This phenotype remained stable even after extensive propagation in immunodeficient hosts. Nevertheless, the engineered viruses induced T cell–mediated immunity protecting against overwhelming systemic infection and severe liver disease upon wild-type virus challenge. Protection was established within 3 to 7 d after immunization and lasted for approximately 300 d. The identification of an arenaviral Achilles' heel demonstrates that the reverse genetic engineering of live-attenuated arenavirus vaccines is feasible. Moreover, our findings offer lymphocytic choriomeningitis virus or other arenaviruses expressing foreign glycoproteins as promising live-attenuated arenavirus vaccine candidates

Hydrodynamic modelling of protein conformation in solution: ELLIPS and HYDRO

The last three decades has seen some important advances in our ability to represent the conformation of proteins in solution on the basis of hydrodynamic measurements. Advances in theoretical modeling capabilities have been matched by commensurate advances in the precision of hydrodynamic measurements. We consider the advances in whole-body (simple ellipsoid-based) modeling—still useful for providing an overall idea of molecular shape, particularly for those systems where only a limited amount of data is available—and outline the ELLIPS suite of algorithms which facilitates the use of this approach. We then focus on bead modeling strategies, particularly the surface or shell–bead approaches and the HYDRO suite of algorithms. We demonstrate how these are providing great insights into complex issues such as the conformation of immunoglobulins and other multi-domain complexes

Many-particle Brownian and Langevin Dynamics Simulations with the Brownmove package

<p>Abstract</p> <p>Background</p> <p>Brownian Dynamics (BD) is a coarse-grained implicit-solvent simulation method that is routinely used to investigate binary protein association dynamics, but due to its efficiency in handling large simulation volumes and particle numbers it is well suited to also describe many-protein scenarios as they often occur in biological cells.</p> <p>Results</p> <p>Here we introduce our "brownmove" simulation package which was designed to handle many-particle problems with varying particle numbers and allows for a very flexible definition of rigid and flexible protein and polymer models. Both a Brownian and a Langevin dynamics (LD) propagation scheme can be used and hydrodynamic interactions are treated efficiently with our recently introduced TEA-HI ansatz [Geyer, Winter, JCP 130 (2009) 114905]. With simulations of constrained polymers and flexible models of spherical proteins we demonstrate that it is crucial to include hydrodynamics when multi-bead models are used in BD or LD simulations. Only then both the translational and the rotational diffusion coefficients and the timescales of the internal dynamics can be reproduced correctly. In the third example project we show how constant density boundary conditions [Geyer et al, JCP 120 (2004) 4573] can be used to set up a non-equilibrium simulation of diffusional transport across an array of fixed obstacles. Finally, we demonstrate how the agglomeration dynamics of multiple particles with attractive patches can be analysed conveniently with the help of a dynamic interaction network.</p> <p>Conclusions</p> <p>Combining BD and LD propagation, fast hydrodynamics, a flexible protein model, and interfaces for "open" simulation settings, our freely available "brownmove" simulation package constitutes a new platform for coarse-grained many-particle simulations of biologically relevant diffusion and transport processes.</p

The conceptual and practical ethical dilemmas of using health discussion board posts as research data.

Increasing numbers of people living with a long-term health condition are putting personal health information online, including on discussion boards. Many discussion boards contain material of potential use to researchers; however, it is unclear how this information can and should be used by researchers. To date there has been no evaluation of the views of those individuals sharing health information online regarding the use of their shared information for research purposes

Temporal Modulation of the Control Parameter in Electroconvection in the Nematic Liquid Crystal I52

I report on the effects of a periodic modulation of the control parameter on electroconvection in the nematic liquid crystal I52. Without modulation, the primary bifurcation from the uniform state is a direct transition to a state of spatiotemporal chaos. This state is the result of the interaction of four, degenerate traveling modes: right and left zig and zag rolls. Periodic modulations of the driving voltage at approximately twice the traveling frequency are used. For a large enough modulation amplitude, standing waves that consist of only zig or zag rolls are stabilized. The standing waves exhibit regular behavior in space and time. Therefore, modulation of the control parameter represents a method of eliminating spatiotemporal chaos. As the modulation frequency is varied away from twice the traveling frequency, standing waves that are a superposition of zig and zag rolls, i.e. standing rectangles, are observed. These results are compared with existing predictions based on coupled complex Ginzburg-Landau equations

FLOWERING REPRESSOR AAA(+) ATPase 1 is a novel regulator of perennial flowering in Arabis alpina

Arabis alpina is a polycarpic perennial, in which PERPETUAL FLOWERING1 (PEP1) regulates flowering and perennial traits in a vernalization-dependent manner. Mutagenesis screens of the pep1 mutant established the role of other flowering time regulators in PEP1-parallel pathways. Here we characterized three allelic enhancers of pep1 (eop002, 085 and 091) which flower early. We mapped the causal mutations and complemented mutants with the identified gene. Using quantitative reverse transcriptase PCR and reporter lines, we determined the protein spatiotemporal expression patterns and localization within the cell. We also characterized its role in Arabidopsis thaliana using CRISPR and in A. alpina by introgressing mutant alleles into a wild-type background. These mutants carried lesions in an AAA(+) ATPase of unknown function, FLOWERING REPRESSOR AAA(+) ATPase 1 (AaFRAT1). AaFRAT1 was detected in the vasculature of young leaf primordia and the rib zone of flowering shoot apical meristems. At the subcellular level, AaFRAT1 was localized at the interphase between the endoplasmic reticulum and peroxisomes. Introgression lines carrying Aafrat1 alleles required less vernalization to flower and reduced number of vegetative axillary branches. By contrast, A. thaliana CRISPR lines showed weak flowering phenotypes. AaFRAT1 contributes to flowering time regulation and the perennial growth habit of A. alpina

Displacement of the Scholar? Participatory Action Research under COVID-19

The impact of COVID-19 on conducting research is far-reaching, especially for those scholars working for or alongside communities. As the pandemic continues to create and exacerbate many of the issues that communities at the margins faced pre-pandemic, such as health disparities and access to resources, it also creates particular difficulties in collaborative, co-developed participatory research and scholar-activism. These forms of community engagement require the commitment of researchers to look beyond the purview of the racialized capitalist and neoliberal structures and institutions that tend to limit the scope of our research and engagement. Both the presence of the researcher within the community as well as deep community trust in the researcher is required in order to identify and prioritize local, often counter-hegemonic forms of knowledge production, resources, and support networks. The pandemic and similar conditions of crises has likely limited opportunities for building long-term, productive relationships of mutual trust and reciprocity needed for PAR while communities refocus on meeting basic needs. The pandemic has now not only exacerbated existing disparities and made the need for engaged, critical and co-creative partnerships even greater, it has also abruptly halted opportunities for partnerships to occur, and further constrained funds to support communities partnering with researchers. In this paper we highlight accomplishments and discuss the many challenges that arise as participatory action researchers are displaced from the field and classroom, such as funding obstacles and working remotely. An analysis of experiences of the displacement of the scholar exposes the conflicts of conducting PAR during crises within a state of academic capitalism. These experiences are drawn from our work conducting PAR during COVID-19 around the globe, both in urban and rural settings, and during different stages of engagement. From these findings the case is made for mutual learning from peer-experiences and institutional support for PAR. As future crises are expected, increased digital resources and infrastructure, academic flexibility and greater consideration of PAR, increased funding for PAR, and dedicated institutional support programs for PAR are needed