An electro-rheological study of the nematic liquid crystal 4-n-heptyl-4'-cyanobiphenyl

An experimental and theoretical study of the electro-rheological effects observed in the nematic phase of 4-n-heptyl-4'-cyanobiphenyl has been conducted. This liquid crystal appears to be a model system, in which the observed rheological behaviour can be interpreted by the Leslie-Ericksen continuum theory for low molecular weight liquid crystals. Flow curves are illustrated at different temperatures and under the influence of an external electric field ranging from 0 to 3 kV mm-1, applied perpendicular to the direction of flow. Also presented is the apparent viscosity as a function of temperature, over similar values of electric field, obtained at different shear rates. A master flow curve has been constructed for each temperature by dividing the shear rate by the square of the electric field and multiplying by the square of a reference value of electric field. In a log-log plot, two Newtonian plateaux are found to appear at low and high shear rates, connected by a shear-thinning region. We have applied the Leslie-Ericksen continuum theory, in which the director alignment angle is a function of the electric field and the flow field boundary conditions are neglected, to determine viscoelastic parameters and the dielectric anisotropy.

A 3-phase model for VIS/NIR mu C-Si : H p-i-n detectors

The spectral response and the photocurrent delivered by entirely microcrystalline p-i-n-Si:H detectors an analysed under different applied bias and light illumination conditions. The spectral response and the internal collection depend not only on the energy range but also on the illumination side. Under [p]- and [n]-side irradiation, the internal collection characteristics have an atypical shape. It is high for applied bias and lower than the open circuit voltage, shows a steep decrease near the open circuit voltage (higher under [n]-side illumination) and levels off for higher voltages. Additionally, the numerical modeling of the VIS/NIR detector, based on the band discontinuities near the grain boundaries and interfaces, complements the study and gives insight into the internal physical process.

Extraction of hemoglobin with calixarenes and biocatalysis in organic media of the complex with pseudoactivity of peroxidase

The present work involves the use of p-tert-butylcalix[4,6,8]arene carboxylic acid derivatives ((t)Butyl[4,6,8]CH2COOH) for selective extraction of hemoglobin. All three calixarenes extracted hemoglobin into the organic phase, exhibiting extraction parameters higher than 0.90. Evaluation of the solvent accessible positively charged amino acid side chains of hemoglobin (PDB entry 1XZ2) revealed that there are 8 arginine, 44 lysine and 30 histidine residues on the protein surface which may be involved in the interactions with the calixarene molecules. The hemoglobin-(t)Butyl[6]CH2COOH complex had pseudoperoxidase activity which catalysed the oxidation of syringaldazine in the presence of hydrogen peroxide in organic medium containing chloroform. The effect of pH, protein and substrate concentrations on biocatalysis was investigated using the hemoglobin-(t)Butyl[6]CH2COOH complex. This complex exhibited the highest specific activity of 9.92 x 10(-2) U mg protein(-1) at an initial pH of 7.5 in organic medium. Apparent kinetic parameters (V'(max), K'(m), k'(cat) and k'(cat)/K'(m)) for the pseudoperoxidase activity were determined in organic media for different pH values from a Michaelis-Menten plot. Furthermore, the stability of the protein-calixarene complex was investigated for different initial pH values and half-life (t(1/2)) values were obtained in the range of 1.96 and 2.64 days. Hemoglobin-calixarene complex present in organic medium was recovered in fresh aqueous solutions at alkaline pH, with a recovery of pseudoperoxidase activity of over 100%. These results strongly suggest that the use of calixarene derivatives is an alternative technique for protein extraction and solubilisation in organic media for biocatalysis.

Phase diagrams of particles with dissimilar patches: X-junctions and Y-junctions

We use Wertheim's first-order perturbation theory to investigate the phase behaviour and the structure of coexisting fluid phases for a model of patchy particles with dissimilar patches (two patches of type A and f(B) patches of type B). A patch of type alpha = {A, B} can bond to a patch of type beta = {A, B} in a volume nu(alpha beta), thereby decreasing the internal energy by epsilon(alpha beta). We analyse the range of model parameters where AB bonds, or Y-junctions, are energetically disfavoured (epsilon(AB) < epsilon(AA)/2) but entropically favoured (nu(AB) >> nu(alpha alpha)), and BB bonds, or X-junctions, are energetically favoured (epsilon(BB) > 0). We show that, for low values of epsilon(BB)/epsilon(AA), the phase diagram has three different regions: (i) close to the critical temperature a low-density liquid composed of long chains and rich in Y-junctions coexists with a vapour of chains; (ii) at intermediate temperatures there is coexistence between a vapour of short chains and a liquid of very long chains with X-and Y-junctions; (iii) at low temperatures an ideal gas coexists with a high-density liquid with all possible AA and BB bonds formed. It is also shown that in region (i) the liquid binodal is reentrant (its density decreases with decreasing temperature) for the lower values of epsilon(BB)/epsilon(AA). The existence of these three regions is a consequence of the competition between the formation of X- and Y-junctions: X-junctions are energetically favoured and thus dominate at low temperatures, whereas Y-junctions are entropically favoured and dominate at higher temperatures.

Phase diagrams of binary mixtures of patchy colloids with distinct numbers and types of patches: Theempty fluid regime

We investigate the effect of distinct bonding energies on the onset of criticality of low functionality fluid mixtures. We focus on mixtures ofparticles with two and three patches as this includes the mixture where "empty" fluids were originally reported. In addition to the number of patches, thespecies differ in the type of patches or bonding sites. For simplicity, we consider that the patches on each species are identical: one species has threepatches of type A and the other has two patches of type B. We have found a rich phase behavior with closed miscibility gaps, liquid-liquid demixing, and negative azeotropes. Liquid-liquid demixing was found to pre-empt the "empty" fluid regime, of these mixtures, when the AB bonds are weaker than the AA or BB bonds. By contrast, mixtures in this class exhibit "empty" fluid behavior when the AB bonds are stronger than at least one of the other two. Mixtureswith bonding energies epsilon(BB) = epsilon(AB) and epsilon(AA) < epsilon(BB), were found to exhibit an unusual negative azeotrope. (C) 2011 American Institute of Physics. [doi:10.1063/1.3561396]

Re-entrant phase behaviour of network fluids: A patchy particle model with temperature-dependent valence

We study a model consisting of particles with dissimilar bonding sites ("patches"), which exhibits self-assembly into chains connected by Y-junctions, and investigate its phase behaviour by both simulations and theory. We show that, as the energy cost epsilon(j) of forming Y-junctions increases, the extent of the liquid-vapour coexistence region at lower temperatures and densities is reduced. The phase diagram thus acquires a characteristic "pinched" shape in which the liquid branch density decreases as the temperature is lowered. To our knowledge, this is the first model in which the predicted topological phase transition between a fluid composed of short chains and a fluid rich in Y-junctions is actually observed. Above a certain threshold for epsilon(j), condensation ceases to exist because the entropy gain of forming Y-junctions can no longer offset their energy cost. We also show that the properties of these phase diagrams can be understood in terms of a temperature-dependent effective valence of the patchy particles. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3605703]

Reentrant Phase Diagram of Network Fluids

We introduce a microscopic model for particles with dissimilar patches which displays an unconventional "pinched'' phase diagram, similar to the one predicted by Tlusty and Safran in the context of dipolar fluids [Science 290, 1328 (2000)]. The model-based on two types of patch interactions, which account, respectively, for chaining and branching of the self-assembled networks-is studied both numerically via Monte Carlo simulations and theoretically via first-order perturbation theory. The dense phase is rich in junctions, while the less-dense phase is rich in chain ends. The model provides a reference system for a deep understanding of the competition between condensation and self-assembly into equilibrium-polymer chains.

Arrow Plot: a new graphical tool for selecting up and down regulated genes and genes differentially expressed on samples subgroups

Background: A common task in analyzing microarray data is to determine which genes are differentially expressed across two (or more) kind of tissue samples or samples submitted under experimental conditions. Several statistical methods have been proposed to accomplish this goal, generally based on measures of distance between classes. It is well known that biological samples are heterogeneous because of factors such as molecular subtypes or genetic background that are often unknown to the experimenter. For instance, in experiments which involve molecular classification of tumors it is important to identify significant subtypes of cancer. Bimodal or multimodal distributions often reflect the presence of subsamples mixtures. Consequently, there can be genes differentially expressed on sample subgroups which are missed if usual statistical approaches are used. In this paper we propose a new graphical tool which not only identifies genes with up and down regulations, but also genes with differential expression in different subclasses, that are usually missed if current statistical methods are used. This tool is based on two measures of distance between samples, namely the overlapping coefficient (OVL) between two densities and the area under the receiver operating characteristic (ROC) curve. The methodology proposed here was implemented in the open-source R software. Results: This method was applied to a publicly available dataset, as well as to a simulated dataset. We compared our results with the ones obtained using some of the standard methods for detecting differentially expressed genes, namely Welch t-statistic, fold change (FC), rank products (RP), average difference (AD), weighted average difference (WAD), moderated t-statistic (modT), intensity-based moderated t-statistic (ibmT), significance analysis of microarrays (samT) and area under the ROC curve (AUC). On both datasets all differentially expressed genes with bimodal or multimodal distributions were not selected by all standard selection procedures. We also compared our results with (i) area between ROC curve and rising area (ABCR) and (ii) the test for not proper ROC curves (TNRC). We found our methodology more comprehensive, because it detects both bimodal and multimodal distributions and different variances can be considered on both samples. Another advantage of our method is that we can analyze graphically the behavior of different kinds of differentially expressed genes. Conclusion: Our results indicate that the arrow plot represents a new flexible and useful tool for the analysis of gene expression profiles from microarrays.

Computing the phase diagram of binary mixtures: A patchy particle case study

We investigate the phase behaviour of 2D mixtures of bi-functional and three-functional patchy particles and 3D mixtures of bi-functional and tetra-functional patchy particles by means of Monte Carlo simulations and Wertheim theory. We start by computing the critical points of the pure systems and then we investigate how the critical parameters change upon lowering the temperature. We extend the successive umbrella sampling method to mixtures to make it possible to extract information about the phase behaviour of the system at a fixed temperature for the whole range of densities and compositions of interest. (C) 2013 AIP Publishing LLC.

Phase growth control in low temperature PLD Co: TiO2 films by pressure

This paper reports on the structural and optical properties of Co-doped TiO2 thin films grown onto (0001)Al2O3 substrates by non-reactive pulsed laser deposition (PLD) using argon as buffer gas. It is shown that by keeping constant the substrate temperature at as low as 310 degrees C and varying only the background gas pressure between 7 Pa and 70 Pa, it is possible to grow either epitaxial rutile or pure anatase thin films, as well as films with a mixture of both polymorphs. The optical band gaps of the films are red shifted in comparison with the values usually reported for undoped TiO2, which is consistent with n-type doping of the TiO2 matrix. Such band gap red shift brings the absorption edge of the Co-doped TiO2 films into the visible region, which might favour their photocatalytic activity. Furthermore, the band gap red shift depends on the films' phase composition, increasing with the increase of the Urbach energy for increasing rutile content. (C) 2012 Elsevier B.V. All rights reserved.

SCANNERS: constraining the phase diagram of a complex scalar singlet at the LHC

We present the first version of a new tool to scan the parameter space of generic scalar potentials, SCANNERS (Coimbra et al., SCANNERS project., 2013). The main goal of SCANNERS is to help distinguish between different patterns of symmetry breaking for each scalar potential. In this work we use it to investigate the possibility of excluding regions of the phase diagram of several versions of a complex singlet extension of the Standard Model, with future LHC results. We find that if another scalar is found, one can exclude a phase with a dark matter candidate in definite regions of the parameter space, while predicting whether a third scalar to be found must be lighter or heavier. The first version of the code is publicly available and contains various generic core routines for tree level vacuum stability analysis, as well as implementations of collider bounds, dark matter constraints, electroweak precision constraints and tree level unitarity.

Regulation of antioxidant enzymes gene expression in the yeast Saccharomyces cerevisiae during stationary phase

Gene expression of three antioxidant enzymes, Mn superoxide dismutase (MnSOD), Cu,Zn superoxide dismutase (Cu,ZnSOD), and glutathione reductase (GR) was investigated in stationary phase Saccharomyces cerevisiae during menadione-induced oxidative stress. Both GR and Cu,ZnSOD mRNA steady state levels increased, reaching a plateau at about 90 min exposure to menadione. GR mRNA induction was higher than that of Cu,ZnSOD (about 14-fold and 9-fold after 90 min, respectively). A different pattern of response was obtained for MnSOD mRNA, with a peak at about 15 min (about 8-fold higher) followed by a decrease to a plateau approximately 4-fold higher than the control value. However, these increased mRNA levels did not result in increased protein levels and activities of these enzymes. Furthermore, exposure to menadione decreased MnSOD activity to half its value, indicating that the enzyme is partially inactivated due to oxidative damage. Cu,ZnSOD protein levels were increased 2-fold, but MnSOD protein levels were unchanged after exposure to menadione in the presence of the proteolysis inhibitor phenylmethylsulfonyl fluoride. These results indicate that the rates of Cu,ZnSOD synthesis and proteolysis are increased, while the rates of MnSOD synthesis and proteolysis are unchanged by exposure to menadione. Also, the translational efficiency for both enzymes is probably decreased, since increases in protein levels when proteolysis is inhibited do not reflect the increases in mRNA levels. Our results indicate that oxidative stress modifies MnSOD, Cu,ZnSOD, and GR gene expression in a complex way, not only at the transcription level but also at the post-transcriptional, translational, and post-translational levels.

Shear-induced lamellar phase of an ionic liquid crystal at room temperature

The phase behaviour of a number of N-alkylimidazolium salts was studied using polarizing optical microscopy, differential scanning calorimetry and X-ray diffraction. Two of these compounds exhibit lamellar mesophases at temperatures above 50 degrees C. In these systems, the liquid crystalline behaviour may be induced at room temperature by shear. Sheared films of these materials, observed between crossed polarisers, have a morphology that is typical of (wet) liquid foams: they partition into dark domains separated by brighter (birefringent) walls, which are approximately arcs of circle and meet at "Plateau borders" with three or more sides. Where walls meet three at a time, they do so at approximately 120 degrees angles. These patterns coarsen with time and both T1 and T2 processes have been observed, as in foams. The time evolution of domains is also consistent with von Neumann's law. We conjecture that the bright walls are regions of high concentration of defects produced by shear, and that the system is dominated by the interfacial tension between these walls and the uniform domains. The control of self-organised monodomains, as observed in these systems, is expected to play an important role in potential applications.

How foam-like is the shear-induced lamellar phase of an ionic liquid crystal?

Philosophical Magazine Letters Volume 88, Issue 9-10, 2008 Special Issue: Solid and Liquid Foams. In commemoration of Manuel Amaral Fortes

Arrow plot and CA maps on microarray preprocessing methods

Microarray allow to monitoring simultaneously thousands of genes, where the abundance of the transcripts under a same experimental condition at the same time can be quantified. Among various available array technologies, double channel cDNA microarray experiments have arisen in numerous technical protocols associated to genomic studies, which is the focus of this work. Microarray experiments involve many steps and each one can affect the quality of raw data. Background correction and normalization are preprocessing techniques to clean and correct the raw data when undesirable fluctuations arise from technical factors. Several recent studies showed that there is no preprocessing strategy that outperforms others in all circumstances and thus it seems difficult to provide general recommendations. In this work, it is proposed to use exploratory techniques to visualize the effects of preprocessing methods on statistical analysis of cancer two-channel microarray data sets, where the cancer types (classes) are known. For selecting differential expressed genes the arrow plot was used and the graph of profiles resultant from the correspondence analysis for visualizing the results. It was used 6 background methods and 6 normalization methods, performing 36 pre-processing methods and it was analyzed in a published cDNA microarray database (Liver) available at http://genome-www5.stanford.edu/ which microarrays were already classified by cancer type. All statistical analyses were performed using the R statistical software.