Competing Alignments of Nematic Liquid Crystals on Square Patterned Substrates

A theoretical analysis is presented of a nematic liquid crystal confined between substrates pat- terned with squares that promote vertical and planar alignment. Two approaches are used to eluci- date the behavior across a wide range of length scales: Monte Carlo simulation of hard particles and Frank-Oseen continuum theory. Both approaches predict bistable degenerate azimuthal alignment in the bulk along the edges of the squares; the continuum calculation additionally reveals the possi- bility of an anchoring transition to diagonal alignment if the polar anchoring energy associated with the pattern is sufficiently weak. Unlike the striped systems previously analyzed, the Monte Carlo simulations suggest that there is no "bridging" transition for sufficiently thin cells. The extent to which these geometrically patterned systems resemble topographically patterned substrates, such as square wells, is also discussed.Comment: 11 pages, 12 figure

Saturation mutagenesis reveals manifold determinants of exon definition.

To illuminate the extent and roles of exonic sequences in the splicing of human RNA transcripts, we conducted saturation mutagenesis of a 51-nt internal exon in a three-exon minigene. All possible single and tandem dinucleotide substitutions were surveyed. Using high-throughput genetics, 5560 minigene molecules were assayed for splicing in human HEK293 cells. Up to 70% of mutations produced substantial (greater than twofold) phenotypes of either increased or decreased splicing. Of all predicted secondary structural elements, only a single 15-nt stem-loop showed a strong correlation with splicing, acting negatively. The in vitro formation of exon-protein complexes between the mutant molecules and proteins associated with spliceosome formation (U2AF35, U2AF65, U1A, and U1-70K) correlated with splicing efficiencies, suggesting exon definition as the step affected by most mutations. The measured relative binding affinities of dozens of human RNA binding protein domains as reported in the CISBP-RNA database were found to correlate either positively or negatively with splicing efficiency, more than could fit on the 51-nt test exon simultaneously. The large number of these functional protein binding correlations point to a dynamic and heterogeneous population of pre-mRNA molecules, each responding to a particular collection of binding proteins

Independent control of polar and azimuthal anchoring

Monte Carlo simulation, experiment and continuum theory are used to examine the anchoring exhibited by a nematic liquid crystal at a patterned substrate comprising a periodic array of rectangles that, respectively, promote vertical and planar alignment. It is shown that the easy axis and effective anchoring energy promoted by such surfaces can be readily controlled by adjusting the design of the pattern. The calculations reveal rich behavior: for strong anchoring, as exhibited by the simulated system, for rectangle ratios $\geq 2$ the nematic aligns in the direction of the long edge of the rectangles, the azimuthal anchoring coefficient changing with pattern shape. In weak anchoring scenarios, however, including our experimental systems, preferential anchoring is degenerate between the two rectangle diagonals. Bistability between diagonally-aligned and edge-aligned arrangement is predicted for intermediate combinations of anchoring coefficient and system length-scale.Comment: 12 pages, 12 figure

Automatic generation of software interfaces for supporting decision-making processes. An application of domain engineering and machine learning

Information dashboards are sophisticated tools. Although they enable users to reach useful insights and support their decisionmaking challenges, a good design process is essential to obtain powerful tools. Users need to be part of these design processes, as they will be the consumers of the information displayed. But users are very diverse and can have different goals, beliefs, preferences, etc., and creating a new dashboard for each potential user is not viable. There exist several tools that allow users to configure their displays without requiring programming skills. However, users might not exactly know what they want to visualize or explore, also becoming the configuration process a tedious task. This research project aims to explore the automatic generation of user interfaces for supporting these decisionmaking processes. To tackle these challenges, a domain engineering, and machine learning approach is taken. The main goal is to automatize the design process of dashboards by learning from the context, including the end-users and the target data to be displayed

Transformation-based Refactorings: a First Analysis

International audienceRefactorings are behavior preserving transformations. Little work exists on the analysis of their implementation and in particular how refactorings could be composed from smaller, reusable, parts (being simple transformations or other refactorings) and how (non behavior preserving) transformations could be used in isolation or to compose new refactoring operators. In this article we study the seminal implementation and evolution of Refactorings as proposed in the PhD of D. Roberts. Such an implementation is available as the Refactoring Browser package in Pharo. In particular we focus on the possibilities to reuse transformations independently from the behavior preserving aspect of a refactoring. The long term question we want to answer is: Is it possible to have more atomic transformations and refactorings composed out of such transformations? We study preconditions of existing refactorings and identify several families. We identify missed opportunities of reuse in the case of implicit composite refactorings. We analyze the refactorings that are explicitly composed out of other refactorings to understand whether the composition could be expressed at another level of abstraction. This analysis should be the basis for a more systematic expression of composable refactorings as well as the reuse of logic between transformations and refactorings

Competition of lattice and basis for alignment of nematic liquid crystals

Due to elastic anisotropy, two-dimensional patterning of substrates can promote weak azimuthal alignment of adjacent nematic liquid crystals. Here we consider how such alignment can be achieved using a periodic square lattice of circular or elliptical motifs. In particular, we examine ways in which the lattice and motif can combine to favor differing orientations. Using Monte Carlo simulation and continuum elasticity we find, for circular motifs, that the coverage fraction controls both the polar anchoring angle and a transition in the azimuthal orientation. If the circles are generalized to ellipses, arbitrary control of the effective easy axis and effective anchoring potential becomes achievable by appropriate tuning of the ellipse motif relative to the periodic lattice patterning. This has possible applications in both monostable and bistable liquid crystal device contexts

Neural-network approach to modeling liquid crystals in complex confinement

Finding the structure of a confined liquid crystal is a difficult task since both the density and order parameter profiles are non-uniform. Starting from a microscopic model and density-functional theory, one has to either (i) solve a non-linear, integral Euler-Lagrange equation, or (ii) perform a direct multi-dimensional free energy minimisation. The traditional implementations of both approaches are computationally expensive and plagued with convergence problems. Here, as an alternative, we introduce an unsupervised variant of the Multi-Layer Perceptron (MLP) artificial neural network for minimising the free energy of a fluid of hard non-spherical particles confined between planar substrates of variable penetrability. We then test our algorithm by comparing its results for the structure (density-orientation profiles) and equilibrium free energy with those obtained by standard iterative solution of the Euler-Lagrange equations and with Monte Carlo simulation results. Very good agreement is found and the MLP method proves competitively fast, flexible and refinable. Furthermore, it can be readily generalised to the richer experimental patterned-substrate geometries that are now experimentally realisable but very problematic to conventional theoretical treatments

Nematic liquid crystal alignment on chemical patterns

Patterned Self-Assembled Monolayers (SAMs) promoting both homeotropic and planar degenerate alignment of 6CB and 9CB in their nematic phase, were created using microcontact printing of functionalised organothiols on gold films. The effects of a range of different pattern geometries and sizes were investigated, including stripes, circles and checkerboards. EvanescentWave Ellipsometry was used to study the orientation of the liquid crystal (LC) on these patterned surfaces during the isotropic-nematic phase transition. Pretransitional growth of a homeotropic layer was observed on 1 ¹m homeotropic aligning stripes, followed by a homeotropic mono-domain state prior to the bulk phase transition. Accompanying Monte-Carlo simulations of LCs aligned on nano-patterned surfaces were also performed. These simulations also showed the presence of the homeotropic mono-domain state prior to the transition.</p

Saturation mutagenesis reveals manifold determinants of exon definition.

To illuminate the extent and roles of exonic sequences in the splicing of human RNA transcripts, we conducted saturation mutagenesis of a 51-nt internal exon in a three-exon minigene. All possible single and tandem dinucleotide substitutions were surveyed. Using high-throughput genetics, 5560 minigene molecules were assayed for splicing in human HEK293 cells. Up to 70% of mutations produced substantial (greater than twofold) phenotypes of either increased or decreased splicing. Of all predicted secondary structural elements, only a single 15-nt stem-loop showed a strong correlation with splicing, acting negatively. The in vitro formation of exon-protein complexes between the mutant molecules and proteins associated with spliceosome formation (U2AF35, U2AF65, U1A, and U1-70K) correlated with splicing efficiencies, suggesting exon definition as the step affected by most mutations. The measured relative binding affinities of dozens of human RNA binding protein domains as reported in the CISBP-RNA database were found to correlate either positively or negatively with splicing efficiency, more than could fit on the 51-nt test exon simultaneously. The large number of these functional protein binding correlations point to a dynamic and heterogeneous population of pre-mRNA molecules, each responding to a particular collection of binding proteins

Simulation Modifies Prehension: Evidence for a Conjoined Representation of the Graspable Features of an Object and the Action of Grasping It

Movement formulas, engrams, kinesthetic images and internal models of the body in action are notions derived mostly from clinical observations of brain-damaged subjects. They also suggest that the prehensile geometry of an object is integrated in the neural circuits and includes the object's graspable characteristics as well as its semantic properties. In order to determine whether there is a conjoined representation of the graspable characteristics of an object in relation to the actual grasping, it is necessary to separate the graspable (low-level) from the semantic (high-level) properties of the object. Right-handed subjects were asked to grasp and lift a smooth 300-g cylinder with one hand, before and after judging the level of difficulty of a “grasping for pouring” action, involving a smaller cylinder and using the opposite hand. The results showed that simulated grasps with the right hand exert a direct influence on actual motor acts with the left hand. These observations add to the evidence that there is a conjoined representation of the graspable characteristics of the object and the biomechanical constraints of the arm