Three-dimensional phase-field study of crack-seal microstructures - insights from innovative post-processing techniques

Numerical simulations of vein evolution contribute to a better understanding of processes involved in their formation and possess the potential to provide invaluable insights into the rock deformation history and fluid flow pathways. The primary aim of the present article is to investigate the influence of a “realistic” boundary condition, i.e. an algorithmically generated “fractal” surface, on the vein evolution in 3-D using a thermodynamically consistent approach, while explaining the benefits of accounting for an extra dimensionality. The 3-D simulation results are supplemented by innovative numerical post-processing and advanced visualization techniques. The new methodologies to measure the tracking efficiency demonstrate the importance of accounting the temporal evolution; no such information is usually accessible in field studies and notoriously difficult to obtain from laboratory experiments as well. The grain growth statistics obtained by numerically post-processing the 3-D computational microstructures explain the pinning mechanism which leads to arrest of grain boundaries/multi-junctions by crack peaks, thereby, enhancing the tracking behavior

High spatial resolution optical imaging of the multiple T Tauri system LkH{\alpha} 262/LkH{\alpha} 263

We report high spatial resolution i' band imaging of the multiple T Tauri system LkH$\alpha$ 262/LkH$\alpha$ 263 obtained during the first commissioning period of the Adaptive Optics Lucky Imager (AOLI) at the 4.2 m William Herschel Telescope, using its Lucky Imaging mode. AOLI images have provided photometry for each of the two components LkH$\alpha$ 263 A and B (0.41 arcsec separation) and marginal evidence for an unresolved binary or a disc in LkH$\alpha$ 262. The AOLI data combined with previously available and newly obtained optical and infrared imaging show that the three components of LkH$\alpha$ 263 are co-moving, that there is orbital motion in the AB pair, and, remarkably, that LkH$\alpha$ 262-263 is a common proper motion system with less than 1 mas/yr relative motion. We argue that this is a likely five-component gravitationally bounded system. According to BT-settl models the mass of each of the five components is close to 0.4 M$_{\odot}$ and the age is in the range 1-2 Myr. The presence of discs in some of the components offers an interesting opportunity to investigate the formation and evolution of discs in the early stages of multiple very low-mass systems. In particular, we provide tentative evidence that the disc in 263C could be coplanar with the orbit of 263AB.Comment: 11 pages, 7 figures, Accepted 2016 May

Comparative Phylogenetic and Molecular Analysis of Plant TIR Domain Proteins

Toll/Interleukin 1 receptor (TIR) domains are found across kingdoms of life, where they serve as integral components in immune and cell death pathways. TIRs occur as single-domain proteins and parts of larger protein receptor complexes with common sets of associated domains. Self-association and enzymatic activity are common TIR features, conserved across kingdoms. In plants, TIRs constitute N-terminal signaling domains of intracellular nucleotide-binding leucine-rich repeat receptors (NLRs), which form an important part of the plant immune system to detect pathogen interference. Activated TIR-NLRs (TNLs) produce distinct enzymatic metabolites that serve as second messengers in immunity. While in plants, all studied TIR signaling requires the ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) protein family, TIR domains were predicted in plant species with an incomplete or missing EDS1 family. It remains unknown whether TIRs and EDS1 family members co-evolved in plants, and how TIRs evolved in plants without EDS1. The work presented here provides a large-scale phylogenetic analysis of TIR domains from 39 algae and land plant species, which identified four conserved TIR groups shared by multiple plant clades. Using the phylogeny, this study provides a comprehensive phylogeny-based nomenclature for plant TIRs. Among the conserved groups is a TIR-only group, which highly correlates with EDS1 in tested species and induces EDS1-dependent cell death. In contrast, a member of the most widespread group of TIR-NB-TPR (TNP) proteins, which persisted in plants without EDS1, induces EDS1-independent cell death. This is the first reported incidence of EDS1-independent cell death, induced by a plant TIR domain protein to date, and is in striking contrast to the majority of studied TIRs, including TNLs. This study furthermore provides a comprehensive set of conserved TIR-only and TNP mutants, generated by CRISPR/Cas9 mutagenesis, to study involvement of conserved TIRs in immune signaling pathways

Surface-Only Simulation of Fluids

Surface-only simulation methods for fluid dynamics are those that perform computation only on a surface representation, without relying on any volumetric discretization. Such methods have superior asymptotic complexity in time and memory than the traditional volumetric discretization approaches, and thus are more tractable for simulation of complex fluid phenomena. Although for most computer graphics applications and many engineering applications, the interior flow inside the fluid phases is typically not of interest, the vast majority of existing numerical techniques still rely on discretization of the volumetric domain. My research first tackles the mesh-based surface tracking problem in the multimaterial setting, and then proposes surface-only simulation solutions for two scenarios: the soap-films and bubbles, and the general 3D liquids. Throughout these simulation approaches, all computation takes place on the surface, and volumetric discretization is entirely eliminated

The interaction ‘Supply’, ‘Demand’, and ‘Technological Capabilities’ in terms of Medical Subject Headings: A triple helix model of medical innovations

We develop a model of innovation that enables us to trace the interplay among three key dimensions of the innovation process: (i) demand of and (ii) supply for innovation, and (iii) technological capabilities available to generate innovation in the forms of products, processes, and services. Building on Triple Helix research, we use entropy statistics to elaborate an indicator of mutual information among these dimensions that can provide indication of reduction of uncertainty. To do so, we focus on the medical context, where uncertainty poses significant challenges to the governance of innovation. The Medical Subject Headings (MeSH) of MEDLINE/PubMed provide us with publication records classified within the categories “Diseases” (C), “Drugs and Chemicals” (D), “Analytic, Diagnostic, and Therapeutic Techniques and Equipment” (E) as knowledge representations of demand, supply, and technological capabilities, respectively. Three case-studies of medical research areas are used as representative ‘entry perspectives’ of the medical innovation process. These are: (i) Human Papilloma Virus, (ii) RNA interference, and (iii) Magnetic Resonance Imaging. We find statistically significant periods of synergy among demand, supply, and technological capabilities (C-D-E) that points to three-dimensional interactions as a fundamental perspective for the understanding and governance of the uncertainty associated with medical innovation. Among the pairwise configurations in these contexts, the demand-technological capabilities (C-E) provided the strongest link, followed by the supply-demand (D-C) and the supply-technological capabilities (D-E) channels

Clusters and Innovation in the Life Sciences

The paper presents a conceptual framework which faces clusters, or localized networks, in the life-science domains. Amongst the various lenses, it focuses on the relationship -if any- interlacing structural settings (clusters) and innovation by referring to the broader field of network theory approach. The final aim of the paper is to contribute to the extant literature by creating a theoretical framework able to describe the effects of intra-cluster and inter-cluster structural and nodal network characteristics upon the clusters' innovative performance. The work sheds light on the factors influencing different innovative performance across different domains in the life-science field

Citrate Binding to the Membrane Protein Proteorhodopsin

Proteorhodopsin (pR) is an intrinsic membrane protein with an important role in solar-energy storage of the biosphere. Earlier work in our lab has shown that polyhistidine-tagged pR can be purified by means of selective precipitation with citrate under specific conditions, as can a number of mutants based on this His6-tagged pR. Purification of a heterologously-expressed trans-membrane protein by a simple salt such as citrate is novel. However, such a phenomenon leads to several questions: How does citrate cause pR precipitation? Does the polyhistidine-tag assist in such a precipitation? Is this precipitation pH-specific? Does citrate affect the function of pR? Does citrate-induced pR precipitation have any biological significance? Are there other ions that could cause pR precipitation? This dissertation focuses on understanding the nature of the interaction of pR with citrate and other anions, and in particular on trying to take advantage of this interaction in order to develop a novel membrane protein purification method. The end goal that branches out of these two aims is to utilize the compact citrate interaction site identified in pR, by incorporating it into other membrane proteins and using it to permit their purification by similar simple procedures. In Chapter 1, I briefly provide some background information on the wide variety of structurally-similar proteins as rhodopsins that include pR. I also describe the general importance of developing purification methods for 7-helix membrane proteins, including pR. Chapter 2 focuses on the investigation of the nature of citrate-binding site of pR. To address the main question of how citrate aids in pR purification, site-directed mutagenesis technique was applied to generate several single, double, triple or quadruple mutants of pR in a histidine-tag free background, which were then tested for their reactivity to citrate. Several different anions were tested to examine if precipitation of pR was specific to citrate or whether the precipitation is susceptible to other negatively charged salts. Photocycle of pR progresses through several intermediates, each with a distinct absorption maximum (described in subsection 1.3.1). M-intermediate is detected at pH ≥ 8 with λmax = 410 nm. Flash spectroscopy involves excitation of pR at a particular wavelength that leads to transient absorption, thus, signaling the formation of the corresponding intermediate. Flash-induced transient visible absorption measurements were used to assay the effect of exposing pR to citrate on its physiological function. Chapter 3 describes the development of a method of purification of pR using simple salts, citrate and phosphate. Chapter 4 begins an exploration of a future direction. The ultimate objective is to apply the above techniques for the general purpose of 7-helix membrane protein purification, especially for the important class of pharmacological receptors known as GPCRs. An attempt at heterologous expression in E. coli, and purification, of a mammalian GPCR, is described therein. Such a method would be desirable for obtaining proteins for structural, functional and pharmacological studies

On the diversity and statistical properties of protostellar discs (article)

This is the final version of the article. Available from OUP via the DOI in this record.The dataset associated with this article is in ORE: http://hdl.handle.net/10871/31266We present results from the first population synthesis study of protostellar discs. We analyse the evolution and properties of a large sample of protostellar discs formed in a radiation hydrodynamical simulation of star cluster formation. Due to the chaotic nature of the star formation process, we find an enormous diversity of young protostellar discs, including misaligned discs, and discs whose orientations vary with time. Star–disc interactions truncate discs and produce multiple systems. Discs may be destroyed in dynamical encounters and/or through ram-pressure stripping, but reform by later gas accretion. We quantify the distributions of disc mass and radii for protostellar ages up to ≈105 yr. For low-mass protostars, disc masses tend to increase with both age and protostellar mass. Disc radii range from of order 10 to a few hundred au, grow in size on time-scales ≲ 104 yr, and are smaller around lower mass protostars. The radial surface density profiles of isolated protostellar discs are flatter than the minimum mass solar nebula model, typically scaling as Σ ∝ r−1. Disc to protostar mass ratios rarely exceed two, with a typical range of Md/M* = 0.1–1 to ages ≲ 104 yr and decreasing thereafter. We quantify the relative orientation angles of circumstellar discs and the orbit of bound pairs of protostars, finding a preference for alignment that strengths with decreasing separation. We also investigate how the orientations of the outer parts of discs differ from the protostellar and inner disc spins for isolated protostars and pairs.This work was by the European Research Council under the European Commission's Seventh Framework Programme (FP7/2007-2013 Grant Agreement No. 339248). The calculation discussed in this paper was performed on the University of Exeter Supercomputer, a DiRAC Facility jointly funded by STFC, the Large Facilities Capital Fund of BIS, and the University of Exeter, and on the DiRAC Complexity system, operated by the University of Leicester IT Services, which forms part of the STFC DiRAC HPC Facility (www.dirac.ac.uk). The latter equipment is funded by BIS National E-Infrastructure capital grant ST/K000373/1 and STFC DiRAC Operations grant ST/K0003259/1. DiRAC is part of the National E-Infrastructure. The calculation was conducted as part of the award ‘The formation of stars and planets: Radiation hydrodynamical and magnetohydrodynamical simulations’ made under the European Heads of Research Councils and European Science Foundation EURYI (European Young Investigator) Awards scheme, was supported by funds from the Participating Organisations of EURYI and the EC Sixth Framework Programme