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PubMed2005

Numerical calculations of the phase diagram of cubic blue phases in cholesteric liquid crystals.

We study the static properties of cubic blue phases by numerically minimizing the three-dimensional, Landau-de Gennes free energy for a cholesteric liquid crystal close to the isotropic-cholesteric phase transition. Thus we are able to refine the powerful but approximate, semianalytic frameworks that have been used previously. We obtain the equilibrium phase diagram and discuss it in relation to previous results. We find that the value of the chirality above which blue phases appear is shifted by 20% (toward experimentally more accessible regions) with respect to previous estimates. We also find that the region of stability of the O5 structure-which has not been observed experimentally-shrinks, while that of blue phase I ( O-8 ) increases thus giving the correct order of appearance of blue phases at small chirality. We also study the approach to equilibrium starting from the infinite chirality solutions and we find that in some cases the disclination network has to assemble during the equilibration. In these situations disclinations are formed via the merging of isolated aligned defects.

Journal Article↗
PubMed2005

Quantitative phase-field modeling of two-phase growth.

A phase-field model that allows for quantitative simulations of low-speed eutectic and peritectic solidification under typical experimental conditions is developed. Its cornerstone is a smooth free-energy functional, specifically designed so that the stable solutions that connect any two phases are completely free of the third phase. For the simplest choice for this functional, the equations of motion for each of the two solid-liquid interfaces can be mapped to the standard phase-field model of single-phase solidification with its quartic double-well potential. By applying the thin-interface asymptotics and by extending the antitrapping current previously developed for this model, all spurious corrections to the dynamics of the solid-liquid interfaces linear in the interface thickness W can be eliminated. This means that, for small enough values of W, simulation results become independent of it. As a consequence, accurate results can be obtained using values of W much larger than the physical interface thickness, which yields a tremendous gain in computational power and makes simulations for realistic experimental parameters feasible. Convergence of the simulation outcome with decreasing W is explicitly demonstrated. Furthermore, the results are compared to a boundary-integral formulation of the corresponding free-boundary problem. Excellent agreement is found, except in the immediate vicinity of bifurcation points, a very sensitive situation where noticeable differences arise. These differences reveal that, in contrast to the standard assumptions of the free-boundary problem, out of equilibrium the diffuse trijunction region of the phase-field model can (i) slightly deviate from Young's law for the contact angles, and (ii) advance in a direction that forms a finite angle with the solid-solid interface at each instant. While the deviation (i) extrapolates to zero in the limit of vanishing interface thickness, the small angle in (ii) remains roughly constant, which indicates that it might be a genuine physical effect, present even for an atomic-scale interface thickness.

Journal Article↗
PubMed2006

Phase distribution and phase correlation of financial time series.

The scaling, phase distribution, and phase correlation of financial time series are investigated based on the Dow Jones Industry Average and NASDAQ 10-min intraday data for a period from 1 Aug. 1997 to 31 Dec. 2003. The returns of the two indices are shown to have nice scaling behaviors and belong to stable distributions according to the criterion of Lévy's alpha stable distribution condition. An approach catching characteristic features of financial time series based on the concept of instantaneous phase is further proposed to study the phase distribution and correlation. Analysis of the phase distribution concludes that return time series fall into a class which is different from other nonstationary time series. The correlation between returns of the two indices probed by the distribution of phase difference indicates that there was a remarkable change of trading activities after the event of the 9/11 attack, and this change persisted in later trading activities.

Journal Article↗
PubMed2001

Photoinduced phase transition to a new macroscopic spin-crossover-complex phase.

We clarified for the first time that the photoinduced phase is quite different in structure from the thermally induced phase by the resonant Raman spectroscopy in the spin-crossover complex, [Fe(2-pic)(3)]-Cl2EtOH. In the photoinduced phase we observed a number of additional lines assigned to infra-active vibrational modes which are strongly prohibited by selection rules in the thermally induced phase. These results indicate that a dramatic symmetry lowering should take place in the photoinduced phase. The cooperative Jahn-Teller transformation is a plausible candidate for the symmetry lowering in the photoinduced phase.

Journal Article↗
PubMed2002

Competing phases in the high field phase diagram of (TMTSF)(2)ClO(4).

A model is presented for the high field phase diagram of (TMTSF)(2)ClO(4), taking into account the anion ordering, which splits the Fermi surface into two bands. For strong enough field, the largest metal spin density wave critical temperature corresponds to the N=0 phase, which originates from two intraband nesting processes. At lower temperature, the competition between these processes puts at disadvantage the N=0 phase vs the N=1 phase, which is due to interband nesting. A first order transition then takes place from the N=0 to N=1 phase. We ascribe to this effect the experimentally observed phase diagrams.

Journal Article↗
PubMed2003

Ab initio protein phasing at 1.4 A resolution: the new phasing approach of SIR2003-N.

New algorithms for solving ab initio protein crystal structures have been identified and implemented in a modified version of the program SIR2002. They succeed in solving numerous protein structures diffracting at atomic resolution; the solution was also attained when data were cut at 1.4 A resolution. The direct-space refinement procedure of SIR2003-N takes advantage of using the envelope of the protein, calculated during the phasing process from the current phases. The electron-density map is modified by assuming different weights for pixels within the envelope or out of it, so tentatively depleting the intensities of the false peaks. The map is then inverted and the resulting phase sets may improve their values. The new phasing strategy is also based on an optimal use of some figures of merit, one of which may be successfully applied in the early stages of the phasing process: only the most promising trials are submitted to the complete phasing procedure, so saving computing time. SIR2003-N has been successfully applied also in solving some protein structures diffracting at 1.4-1.5 A resolution.

Algorithms↗
PubMed2006

The low-temperature phase III structure and phase transition behaviour of cyclohexanone.

The crystal structure of phase III of perdeuterocyclohexanone, C(6)D(10)O, has been determined at 5 K using high-resolution neutron powder diffraction. Below its melting point of 245 K cyclohexanone forms a plastic crystal in the space group Fm3m. On cooling below 225 K the crystal transforms to the monoclinic phase III structure in the space group P2(1)/n. The orthorhombic phase II structure exists under high pressure, but the triple point for all three phases is close to atmospheric pressure. Details of the phase II structure are also reported at 4.8 kbar (273 K) and ambient pressure. The phase behaviour of the compound and isotope effects are discussed.

Journal Article↗
PubMed1993

Direct-space methods in phase extension and phase determination. II. Developments of low-density elimination.

The low-density elimination method for phase extension and refinement [Shiono & Woolfson (1992). Acta Cryst. A48, 451-456] has been improved by substituting a smoother density-modification procedure for the original sharp cut-off function. In addition, better criteria have been found for limiting the number of refinement cycles, which gives a better final result for much less work. The effectiveness of the process has been illustrated by phase refinement for a protein with high-resolution (1.17 A) data containing 808 independent non-H atoms plus 83 water molecules in the asymmetric unit; the unweighted mean-phase error was reduced from 74 to 39.3 degrees. Phase extension and refinement was also demonstrated for pig 2Zn insulin starting with multiple isomorphous replacement (MIR) phases at 1.9 A and extending out to 1.5 A. There was a significant improvement of phases and the final map had a correlation coefficient of 0.540.

Journal Article↗
PubMed1982

Electronic pacemaker models of parasystole. With special reference to artificial intermittent parasystole with phase 3 and phase 4 protection and to parasystolic modulation.

This study deals with a method of analysis of artificial pacemaker function which can be used to understand the electrocardiographic manifestations of some spontaneous rhythms. The modes of operation of 11 normally-functioning QRS-inhibited (VVI) pacemakers resembled those of spontaneous automatic nonprotected (nonparasystolic) rhythms. The function of 11 continuous asynchronous (fixed rate or VOO) pacemakers was similar to that of continuous-parasystolic rhythms. In 12 patients with malfunctioning QRS-inhibited (VVI) pacemakers, an abnormally-prolonged pacemaker refractory period was equivalent to intermittent parasystole with phase 3 protection; and non-sensing during the terminal portions of the cycle was the iatrogenic counterpart of intermittent parasystole with phase 4 protection. Premature beats occurring within the periods of phase 3 and phase 4 protection were "encompassed" by ectopic intervals equalling the ectopic cycle length, or twice the ectopic cycle length. Therefore, they were manifested differently from the "decelerating" and "accelerating" phases of modulation since premature beats occurring during the letter phases may be encompassed by ectopic intervals which are longer and shorter, respectively, than the ectopic cycle length. Because in previous reports the search for these phenomena was based on premises established "a priori," future studies should be designed to analyze tracings of "group beating" where no previous conclusions have been reached.

Arrhythmias, Cardiac↗
PubMed1990

Binaural masking experiments using noise maskers with frequency-dependent interaural phase differences. II: Influence of frequency and interaural-phase uncertainty.

This study investigates whether binaural signal detection is improved by the listener's previous knowledge about the interaural phase relations of masker and test signal. Binaural masked thresholds were measured for a 500-ms dichotic noise masker that had an interaural phase difference of 0 below 500 Hz and of pi above 500 Hz. The thresholds for two difference 20-ms test signals were determined within the same measurement using an interleaved adaptive 3-interval forced-choice (3IFC) procedure. In each 3IFC trial, both signals could occur with equal probability (uncertainty). The two signals differed in frequency and interaural phase in such a way that one signal always had a frequency above the masker edge frequency (500 Hz) and no interaural phase difference (So), whereas the other signal frequency was below 500 Hz and the interaural phase difference was pi (S pi). The frequencies of a signal pair remained fixed during the whole 3IFC track. These two signals thus lead to two different binaural conditions, i.e., NoS pi for the low-frequency signal and N pi So for the high-frequency signal. For comparison, binaural masked thresholds were measured with the same masker for fixed signal frequency and phase. The binaural masking level differences (BMLDs) resulting from the two experimental conditions show no significant difference. This indicates that the binaural system is able to apply different internal transformations or processing strategies simultaneously in different critical bands and even within the same critical band.

Attention↗
PubMed1970

Penicillinase Studies on L-Phase Variants, G-Phase Variants, and Reverted Strains of Staphylococcus aureus.

L-phase variants and small colony (G-phase) variants derived from penicillinase-producing Staphylococcus aureus strains were tested for penicillinase (beta lactamase) production. A refined variation of the modified Gots test for penicillinase was used to demonstrate penicillinase synthesis. Penicillinase synthesis was reduced in L-phase variants and G-phase variants when compared to parental strains. After reversion of variants to vegetative stages had been induced, revertants were tested for production of penicillinase, coagulase, and alpha hemolysin, mannitol fermentation, and pigment production, and comparisons were made between parent and reverted vegetative forms. All revertants of G-phase variants retained penicillinase activity. Most revertants of L-phase variants showed reduction or loss of penicillinase activity. Retention of coagulase activity, alpha hemolysin production, mannitol fermentation, pigmentation, and phage type varied among revertants.

Journal Article↗
PubMed2002

Staphylococcus aureus aconitase inactivation unexpectedly inhibits post-exponential-phase growth and enhances stationary-phase survival.

Staphylococcus aureus preferentially catabolizes glucose, generating pyruvate, which is subsequently oxidized to acetate under aerobic growth conditions. Catabolite repression of the tricarboxylic acid (TCA) cycle results in the accumulation of acetate. TCA cycle derepression coincides with exit from the exponential growth phase, the onset of acetate catabolism, and the maximal expression of secreted virulence factors. These data suggest that carbon and energy for post-exponential-phase growth and virulence factor production are derived from the catabolism of acetate mediated by the TCA cycle. To test this hypothesis, the aconitase gene was genetically inactivated in a human isolate of S. aureus, and the effects on physiology, morphology, virulence factor production, virulence for mice, and stationary-phase survival were examined. TCA cycle inactivation prevented the post-exponential growth phase catabolism of acetate, resulting in premature entry into the stationary phase. This phenotype was accompanied by a significant reduction in the production of several virulence factors and alteration in host-pathogen interaction. Unexpectedly, aconitase inactivation enhanced stationary-phase survival relative to the wild-type strain. Aconitase is an iron-sulfur cluster-containing enzyme that is highly susceptible to oxidative inactivation. We speculate that reversible loss of the iron-sulfur cluster in wild-type organisms is a survival strategy used to circumvent oxidative stress induced during host-pathogen interactions. Taken together, these data demonstrate the importance of the TCA cycle in the life cycle of this medically important pathogen.

Acetates↗
PubMed1997

Stationary-phase mutants of Sinorhizobium meliloti are impaired in stationary-phase survival or in recovery to logarithmic growth.

A screening method was used to identify Sinorhizobium meliloti mutants which are affected in stationary-phase survival. Of 20,000 individual colonies mutagenized with transposon Tn5-B20, 10 mutant strains which showed poor or no survival in the stationary phase were identified. Analyses of expression patterns of the promoterless lacZ genes in the mutant strains revealed individual induction patterns. Most strains were induced in stationary phase as well as under carbon limitation and in pure H2O, but none of the mutants was induced under heat, alkali stress conditions, or low oxygen tension. Plant inoculation tests revealed that the symbiotic proficiency of the mutants was not affected. Two mutants, however, showed gene induction not only in the stationary phase under free-living conditions but also in the bacteroid state. A long-term starvation test was carried out to examine the ability of the 10 mutants to survive prolonged stationary-phase conditions. All mutants showed a clear decrease in the colony-forming ability under the chosen experimental conditions. Staining with green and red fluorescent nucleic acid stain showed that the mutants fell into two different classes. Seven mutants died during stationary phase; the three other mutants remained viable but did not resume growth after prolonged starvation. Five of the ten Tn5-B20 insertions were cloned from the genomes of the mutant strains. Nucleotide sequence analyses established that the transposon had inserted in five distinctive genes. Database searches revealed that four of the tagged loci corresponded to already characterized genes whose gene products are involved in important cellular processes such as amino acid metabolism or aerobic respiration.

Alleles↗
PubMed2004

Ribosomal protein S1 specifically binds to the 5' untranslated region of the Pseudomonas aeruginosa stationary-phase sigma factor rpoS mRNA in the logarithmic phase of growth.

The rpoS gene encodes the stationary-phase sigma factor (RpoS or sigma(s)), which was identified in several gram-negative bacteria as a central regulator controlling the expression of genes involved in cell survival in response to cessation of growth (stationary phase) and providing cross-protection against various stresses. In Pseudomonas aeruginosa, the levels of sigma(s) increase dramatically at the onset of the stationary phase and are regulated at the transcriptional and posttranscriptional levels. The P. aeruginosa rpoS gene is transcribed as a monocistronic rpoS mRNA transcript comprised of an unusually long 373-bp 5' untranslated region (5' UTR). In this study, the 5' UTR and total protein extracts from P. aeruginosa logarithmic and stationary phases of growth were used in order to investigate the protein-RNA interactions that may modulate the translational process. It was observed that a 69-kDa protein, which corresponded to ribosomal protein S1, preferentially binds the 5' UTR of the rpoS mRNA in the logarithmic phase and not in the stationary phase. This is the first report of a protein-rpoS mRNA 5' UTR interaction in P. aeruginosa, and the possible involvement of protein S1 in translation regulation of rpoS is discussed.

5' Untranslated Regions↗
PubMed1996

Adrenal masses: correlation between CT attenuation value and chemical shift ratio at MR imaging with in-phase and opposed-phase sequences.

PURPOSE: To correlate attenuation values at computed tomography (CT) with signal intensity at chemical-shift magnetic resonance (MR) imaging in adrenal masses. MATERIALS AND METHODS: Thirty-eight patients with 47 adrenal lesions underwent MR imaging and unenhanced CT examinations. MR examinations, performed at 1.5 T, included T1-weighted imaging with fat and water in phase and gradient-echo imaging with fat and water out of phase (repetition time, 45-180 msec; echo time, 1.4-3.1 msec). Lesion-to-spleen signal intensity ratios were calculated for the in-phase and opposed-phase images. The chemical-shift ratio, a measure of signal intensity loss between in-phase and opposed-phase images, and the CT attenuation value (in Hounsfield units) were determined for each lesion. RESULTS: A statistically significant correlation (0.85) was found between attenuation and chemical-shift-ratio values (P < .000001). Attenuation in six benign lesions was within 2 standard deviations of the mean attenuation in malignant lesions, and the chemical-shift ratio in eight benign lesions was within 2 standard deviations of the mean chemical-shift ratio in malignant lesions. Six of these eight lesions were misclassified on the basis of both attenuation and chemical-shift-ratio values. CONCLUSION: CT attenuation values are highly correlated with chemical-shift ratios. Both values were indeterminate for a similar subset of benign lesions.

Adrenal Gland Neoplasms↗
PubMed2002

Lipolytic and metabolic response to glucagon in fasting king penguins: phase II vs. phase III.

This study aims to determine how glucagon intervenes in the regulation of fuel metabolism, especially lipolysis, at two stages of a spontaneous long-term fast characterized by marked differences in lipid and protein availability and/or utilization (phases II and III). Changes in the plasma concentration of various metabolites and hormones, and in lipolytic fluxes as determined by continuous infusion of [2-3H]glycerol and [1-14C]palmitate, were examined in vivo in a subantarctic bird (king penguin) before, during, and after a 2-h glucagon infusion. In the two fasting phases, glucagon infusion at a rate of 0.025 microg. kg(-1). min(-1) induced a three- to fourfold increase in the plasma concentration and in the rate of appearance (Ra) of glycerol and nonesterified fatty acids, the percentage of primary reesterification remaining unchanged. Infusion of glucagon also resulted in a progressive elevation of the plasma concentration of glucose and beta-hydroxybutyrate and in a twofold higher insulinemia. These changes were not significantly different between the two phases. The plasma concentrations of triacylglycerols and uric acid were unaffected by glucagon infusion, except for a 40% increase in plasma uric acid in phase II birds. Altogether, these results indicate that glucagon in a long-term fasting bird is highly lipolytic, hyperglycemic, ketogenic, and insulinogenic, these effects, however, being similar in phases II and III. The maintenance of the sensitivity of adipose tissue lipolysis to glucagon could suggest that the major role of the increase in basal glucagonemia observed in phase III is to stimulate gluconeogenesis rather than fatty acid delivery.

3-Hydroxybutyric Acid↗
PubMed2004

Thermodynamics and phase equilibria involving nano phases in the Cu-Ag system.

The surface tensions of the Cu-Ag system have been evaluated using Butler's equations. Since the evaluation is dependent on the thermodynamic properties of the surface phases, they are calculated based on the first and second order differentials of the surface tension at infinite dilution. The present study establishes significant differences in the properties between the surface phase and bulk phases of the system. The study of the adsorption behaviour finds silver to be surface active relative to copper, which results in the preferential adsorption of silver in the alloys. Furthermore, in view of the differences in terms of fundamental thermodynamic properties between the two phases coupled with the volume-to-radius ratio as depicted by the Thomson-Freundlich concept, the nano phases of the system exhibit a pronounced increase in the adsorption behaviour relative to that of the planar interface of the system. As expected based on the above combined effect of the surface properties, present research shows a considerable decrease in the melting points of the metals, solid-solid, solid-liquid transition and eutectic temperature with a consequent increase in the solubilities of the terminal phases of the system.

Adsorption↗
PubMed1993

Opposite, phase-dependent effects of 3,4,5-trimethoxybenzoic acid 8-(diethylamino) octyl ester or tetracaine on islet function during three phases of glucose-stimulated insulin secretion.

The spontaneous decline of insulin secretion which occurs under a variety of secretory conditions is well documented and suggests a general desensitization of the secretory process distal to signal recognition. Accordingly, we have investigated the effects of agents thought to mobilize intracellular Ca++ on insulin secretion over 24 h, which includes periods of rising secretory activity (second phase) and desensitized secretory activity (third phase). During the first 3 h of glucose stimulation of freshly isolated rat islets, insulin secretion was strongly inhibited by 30 microM 3,4,5-trimethoxybenzoic acid 8-(diethylamino) octyl ester (TMB) or 300 microM tetracaine hydrochloride (TC). However, when either of these agents was added for the first time to islets at h 20 when insulin secretion was at a low steady rate (third phase), insulin secretion was greatly enhanced. Both these inhibitory and stimulatory effects declined with continued administration. Removal of TMB and rechallenge with high glucose plus forskolin uncovered a residual inhibition in both chronically and acutely treated islets. Coadministration of forskolin with either TMB or TC blunted both inhibitory and stimulatory effects. Pertussis toxin pretreatment, however, did not alter subsequent response of islets to either agent. Thus TMB or TC have opposite, phase-dependent effects on glucose-stimulated insulin secretion. We postulate that potentiators of glucose-stimulated insulin secretion, which are increased during second phase, are most sensitive to inhibitory effects of TMB or TC, and that the low steady rate of third phase permits their stimulatory component(s) to become apparent.

Animals↗