bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of protein profiles of genetically modified potato tubers by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry
Authors: Careri M. , Elviri L. , Mangia A. , Zagnoni I. , Agrimonti C. , Visioli G. , Marmiroli N.
Published: February 2003

Traceability of genetically modified (GM) foods demands the development of appropriate reliable techniques in order to identify and quantify peptide or nucleic acid residues in GM plants and food products through the food chain. In this study the applicability of matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS) was demonstrated for the characterization of proteins of transformed and untransformed potato (Solanum Tuberosum L.) tubers. In GM tubers the expression level of the G1‐1 gene, which regulates transition from dormancy to sprouting tubers, was inhibited by antisense technology. The analysis of antisense transformed lines showed that several of them exhibited a significant delay in sprouting relative to the control lines, in accordance with a decrease in the transcript level. Preliminary attempts to compare the protein patterns obtained from transformed and control lines using traditional electrophoresis were not able to reveal differences in the low‐kDa range. Instead, MALDI‐TOFMS applied to total peptide extract without any purification was able to distinguish spectral patterns of transformed and untransformed lines. In particular, several characteristic peaks from m/z 4373 to 4932 were detected only in the mass spectra of GM tuber samples. Copyright © 2003 John Wiley & Sons, Ltd.
Stability of multivariable fractional polynomial models with selection of variables and transformations: a bootstrap investigation
Authors: Royston P. , Sauerbrei W.
Published: February 2003

Sauerbrei and Royston have recently described an algorithm, based on fractional polynomials, for the simultaneous selection of variables and of suitable transformations for continuous predictors in a multivariable regression setting. They illustrated the approach by analyses of two breast cancer data sets. Here we extend their work by considering how to assess possible instability in such multivariable fractional polynomial models. We first apply the algorithm repeatedly in many bootstrap replicates. We then use log‐linear models to investigate dependencies among the inclusion fractions for each predictor and among the simplified classes of fractional polynomial function chosen in the bootstrap samples. To further evaluate the results, we define measures of instability based on a decomposition of the variability of the bootstrap‐selected functions in relation to a reference function from the original model. For each data set we are able to identify large, reasonably stable subsets of the bootstrap replications in which the functional forms of the predictors appear fairly stable. Despite the considerable flexibility of the family of fractional polynomials and the consequent risk of overfitting when several variables are considered, we conclude that the multivariable selection algorithm can find stable models. Copyright © 2003 John Wiley & Sons, Ltd.
Confidence intervals for the binomial parameter: some new considerations
Authors: Reiczigel Jenö
Published: February 2003

Several methods have been proposed to construct confidence intervals for the binomial parameter. Some recent papers introduced the ‘mean coverage’ criterion to evaluate the performance of confidence intervals and suggested that exact methods, because of their conservatism, are less useful than asymptotic ones. In these studies, however, exact intervals were always represented by the Clopper–Pearson interval (C–P). Now we focus on Sterne's interval, which is also exact and known to be better than the C–P in the two‐sided case. Introducing a computer intensive level‐adjustment procedure which allows constructing intervals that are exact in terms of mean coverage, we demonstrate that Sterne's interval performs better than the best asymptotic intervals, even in the mean coverage context. Level adjustment improves the C–P as well, which, with an appropriate level adjustment, becomes equivalent to the mid‐P interval. Finally we show that the asymptotic behaviour of the mid‐P method is far poorer than is generally expected. Copyright © 2003 John Wiley & Sons, Ltd.
Generalized covariance‐adjusted canonical correlation analysis with application to psychiatry
Authors: Kowalski J. , Tu X. M. , Jia G. , Perlis M. , Frank E. , Crits‐Christoph P. , Kupfer D. J.
Published: February 2003

The lack of control over covariates in practice motivates the need for their adjustment when measuring the degree of association between two sets of variables, for which canonical correlation is traditionally used. In most studies however, there is also a lack of control over the attributes of responses for the sets of variables of interest. In particular, a portion of the response variable may be continuous and the other discrete. For such settings, the traditional partial canonical correlation approach is restrictive, since a covariate‐adjustment for a set of continuous variables is assumed. By ignoring the assumption of continuous variates and proceeding with a partial canonical correlation analysis in the presence of continuous and discrete variates, results in canonical correlation estimates that are not consistent. In this paper we generalize the traditional partial canonical correlation approach to covariate‐adjustment by allowing the response variables to contain continuous, as well as discrete, variates. The methodology is illustrated with a psychiatric application for examining which sleep variables relate to which depressive symptoms, as measured by commonly used constructs that presents with both continuous and discrete outcomes. Copyright © 2003 John Wiley & Sons, Ltd.
Methods for categorizing a prognostic variable in a multivariable setting
Authors: Mazumdar Madhu , Smith Alex , Bacik Jennifer
Published: February 2003

The literature is filled with examples of categorization of a continuous prognostic variable in a univariable setting followed by the addition of this categorical variable to an existing multivariable model. Typically, an ‘optimal’ cutpoint for a new prognostic variable is obtained through a systematic search relating the variable to the outcome in an univariable manner. The corresponding categorical variable is then fitted in a multivariable model along with other already established prognostic covariates to assess the additional value of the new variable. This prompts the question whether the cutpoint search should have been performed in the same multivariable setting where it will ultimately be used. In this paper, we extend the univariable cutpoint search methods (split‐sample approach and two‐fold cross‐validation approach) to the multivariable setting using ‐2×log‐likelihood statistic as the correlative measure. A Monte Carlo simulation study demonstrates that both methods are more efficient in detecting the true cutpoint and in estimating the effect size under the multivariable setting as opposed to the univariable setting. The cross‐validation method performs better than the split‐sample method in univariable as well as multivariable scenarios. For the cross‐validation method in the multivariable setting, there is still a substantial loss of power when a cutpoint model is used in cases where there is a continuous relationship between the covariate and the outcome. An example is provided to illustrate the value of the multivariable cross‐validation approach. Copyright © 2003 John Wiley & Sons, Ltd.
Bias due to missing exposure data using complete‐case analysis in the proportional hazards regression model
Authors: Demissie Serkalem , LaValley Michael P. , Horton Nicholas J. , Glynn Robert J. , Cupples L. Adrienne
Published: February 2003

We studied bias due to missing exposure data in the proportional hazards regression model when using complete‐case analysis (CCA). Eleven missing data scenarios were considered: one with missing completely at random (MCAR), four missing at random (MAR), and six non‐ignorable missingness scenarios, with a variety of hazard ratios, censoring fractions, missingness fractions and sample sizes. When missingness was MCAR or dependent only on the exposure, there was negligible bias (2–3 per cent) that was similar to the difference between the estimate in the full data set with no missing data and the true parameter. In contrast, substantial bias occurred when missingness was dependent on outcome or both outcome and exposure. For models with hazard ratio of 3.5, a sample size of 400, 20 per cent censoring and 40 per cent missing data, the relative bias for the hazard ratio ranged between 7 per cent and 64 per cent. We observed important differences in the direction and magnitude of biases under the various missing data mechanisms. For example, in scenarios where missingness was associated with longer or shorter follow‐up, the biases were notably different, although both mechanisms are MAR. The hazard ratio was underestimated (with larger bias) when missingness was associated with longer follow‐up and overestimated (with smaller bias) when associated with shorter follow‐up. If it is known that missingness is associated with a less frequently observed outcome or with both the outcome and exposure, CCA may result in an invalid inference and other methods for handling missing data should be considered. Copyright © 2003 John Wiley & Sons, Ltd.
A comparison of group sequential methods for binary longitudinal data
Authors: Spiessens Bart , Lesaffre Emmanuel , Verbeke Geert
Published: February 2003

Interim analyses are conducted to allow for early termination of the trial, for ethical as well as economical reasons. Here we consider interim analyses in repeated measurements studies where the measurements are binary. Two methods for analysing this kind of data are compared according to their operating characteristics. A subject‐specific approach based on the logistic random‐effects model is compared with the population‐averaged approach based on the generalized estimating equations. The comparison is illustrated with simulations using a randomized clinical trial for toenail fungal infection. Copyright © 2003 John Wiley & Sons, Ltd.
Maltodextrin‐binding proteins from diverse bacteria and archaea are potent solubility enhancers
Authors: Fox Jeffrey D. , Routzahn Karen M. , Bucher Matthew H. , Waugh David S.
Published: February 2003

Escherichia coli maltose‐binding protein (MBP) is frequently used as an affinity tag to facilitate the purification of recombinant proteins. An important additional attribute of MBP is its remarkable ability to enhance the solubility of its fusion partners. MBPs are present in a wide variety of microorganisms including both mesophilic and thermophilic bacteria and archaea. In the present study, we compared the ability of MBPs from six diverse microorganisms (E. coli, Pyrococcus furiosus, Thermococcus litoralis, Vibrio cholerae, Thermotoga maritima, and Yersinia pestis) to promote the solubility of eight different aggregation‐prone proteins in E. coli. In contrast to glutathione S‐transferase (GST), all of these MBPs proved to be effective solubility enhancers and some of them were even more potent solubilizing agents than E. coli MBP.
In bafilomycin A1‐resistant cells, bafilomycin A1 raised lysosomal pH and both prodigiosins and concanamycin A inhibited growth through apoptosis
Authors: Tanigaki Keiji , Sasaki Satoshi , Ohkuma Shoji
Published: February 2003

In bafilomycin A1‐resistant cells (Vero‐317 and MC‐3T3‐E1), bafilomycin A1 neither inhibited cell growth, induced cell death, nor activated caspase‐3. However, 100 nM bafilomycin A1 did raise the lysosomal pH similar to 10 mM NH4Cl. Prodigiosins, H+/Cl− symporters that raise the lysosomal pH, inhibited cell growth through apoptosis and caused the activation of caspase‐3. Concanamycin A also inhibited the growth of these cells through apoptosis. 10 mM NH4Cl inhibited the growth of these cells as well, but cytostatically. These results suggest that plecomacrolides inhibited cell growth apoptotically through specific site(s), in contrast to the cytostatic effect of 10 mM NH4Cl, besides raising the lysosomal pH.
Detection of novel truncated forms of human serum amyloid A protein in human plasma
Authors: Kiernan Urban A. , Tubbs Kemmons A. , Nedelkov Dobrin , Niederkofler Eric E. , Nelson Randall W.
Published: February 2003

Serum amyloid A protein (SAA) is a human plasma protein that has been recognized as potential biomarker of multiple ailments including myocardial infarction, inflammatory disease and amyloiosis. Presented here is the application of a novel immunoassay technique, termed mass spectrometric immunoassay for the detection and identification of SAA present in human plasma. Results demonstrate the ability to readily detect known SAA isotypes, and to identify novel truncated forms of SAA, in the plasma of healthy individuals and those suffering from acute and chronic inflammation. The approach represents a rapid and sensitive means for the routine structural characterization of known SAA isotypes and the discovery of associated post‐translational modifications.
Nicotinamide adenine dinucleotide stimulates oligomerization, interaction with adenovirus E1A and an intrinsic dehydrogenase activity of CtBP
Authors: Balasubramanian P. , Zhao Ling-Jun , Chinnadurai G.
Published: February 2003

The C‐terminal region of adenovirus E1A interacts with the transcriptional corepressor, CtBP. The mechanism of transcriptional regulation by CtBP is not known. CtBP shares a significant homology with NAD+‐dependent D2‐hydroxy acid dehydrogenases. CtBP binds to NAD+ and NADH. Both forms of the dinucleotide stimulate oligomerization of native CtBP and enhance complex formation with E1A. CtBP also has a slow dehydrogenase activity. Interaction of CtBP with E1A reduces the dehydrogenase activity. Our results raise the possibility that the oxidation/reduction reactions of CtBP may regulate transcription. Thus, CtBP is a unique transcriptional regulator with an enzymatic activity similar to metabolic dehydrogenases. The levels of intracellular nicotinamide adenine dinucleotide may modulate transcriptional activity of CtBP.
Role of molecular chaperones in inclusion body formation
Authors: Carrió M.Mar , Villaverde Antonio
Published: February 2003

Protein misfolding and aggregation are linked to several degenerative diseases and are responsible for the formation of bacterial inclusion bodies. Roles of molecular chaperones in promoting protein deposition have been speculated but not proven in vivo. We have investigated the involvement of individual chaperones in inclusion body formation by producing the misfolding‐prone but partially soluble VP1LAC protein in chaperone null bacterial strains. Unexpectedly, the absence of a functional GroEL significantly reduced aggregation and favoured the incidence of the soluble protein form, from 4 to 35% of the total VP1LAC protein. On the other hand, no regular inclusion bodies were then formed but more abundant small aggregates up to 0.05 μm3. Contrarily, in a DnaK− background, the amount of inclusion body protein was 2.5‐fold higher than in the wild‐type strain and the average volume of the inclusion bodies increased from 0.25 to 0.38 μm3. Also in the absence of DnaK, the minor fraction of soluble protein appears as highly proteolytically stable, suggesting an inverse connection between proteolysis and aggregation managed by this chaperone. In summary, GroEL and DnaK appear as major antagonist controllers of inclusion body formation by promoting and preventing, respectively, the aggregation of misfolded polypeptides. GroEL might have, in addition, a key role in driving the protein transit from the soluble to the insoluble cell fraction and also in the opposite direction. Although chaperones ClpB, ClpA, IbpA and IbpB also participate in these processes, the impact of the respective null mutations on bacterial inclusion body formation is much more moderate.
Folding and catalysis by the hairpin ribozyme
Authors: Lilley David M.J
Published: February 2003

The hairpin ribozyme undergoes a site‐specific transesterification cleavage of the phosphodiester backbone. The natural form of the ribozyme is a four‐way helical junction, where two arms contain unpaired loops. This folds by pairwise coaxial stacking of helical arms, and a rotation into an antiparallel conformation in which there is close association between the loops. This probably generates the local conformation required to facilitate the trajectory into an in‐line SN2 transition state. Folding is induced by the cooperative binding of at least two divalent metal ions, which are probably distributed between the junction and the loop‐loop interface. The junction forms the structural scaffold on which the geometry of the ribozyme is built, and structural perturbation of the junction leads to impaired catalytic activity.
Editing of messenger RNA precursors and of tRNAs by adenosine to inosine conversion
Authors: Keller Walter , Wolf Jeannette , Gerber André
Published: February 2003

The double‐stranded RNA‐specific adenosine deaminases ADAR1 and ADAR2 convert adenosine (A) residues to inosine (I) in messenger RNA precursors (pre‐mRNA). Their main physiological substrates are pre‐mRNAs encoding subunits of ionotropic glutamate receptors or serotonin receptors in the brain. ADAR1 and ADAR2 have similar sequence features, including double‐stranded RNA binding domains (dsRBDs) and a deaminase domain. The tRNA‐specific adenosine deaminases Tad1p and Tad2p/Tad3p modify A 37 in tRNA‐Ala1 of eukaryotes and the first nucleotide of the anticodon (A 34) of several bacterial and eukaryotic tRNAs, respectively. Tad1p is related to ADAR1 and ADAR2 throughout its sequence but lacks dsRBDs. Tad1p could be the ancestor of ADAR1 and ADAR2. The deaminase domains of ADAR1, ADAR2 and Tad1p are very similar and resemble the active site domains of cytosine/cytidine deaminases.
The effect of maternal hypothermia on the fetal heart rate
Authors: Aboud E. , Neales K.
Published: February 2003

Fetal bradycardia is a recognized response to maternal hypothermia but has not previously been reported in conjunction with diabetes. A 30‐year‐old insulin‐dependent diabetic was admitted at 35 weeks gestation for control of her diabetes. She developed maternal hypothermia and hypoglycemia and the fetal heart rate fell to 100 beats per minute (b.p.m.). However, the fetal heart rate gradually returned to normal after rewarming the patient.
Customised gravidogram and fetal growth chart in a South African population
Authors: van Bogaert L.‐J.
Published: February 2003

Objective:To investigate whether gravidograms and fetal growth curves should be customized, i.e. tailor made for a specific ethnic group.Methods:a cross‐sectional study of 800 pregnant Xhosa women attending antenatal care in the Eastern Cape Province (South Africa). The data measured was used to compare the correlation between the symphysis–fundus height measurement (SFHM) and the sonographic estimate of gestational age (SEGA), as well as the intra‐uterine fetal growth curve with existing gravidograms and fetal growth charts.Results:There was a good correlation between the SFHM and the SEGA:r=0.91 (P<0.0001). The correlation between the SFHM and the sonographic estimate of fetal weight (SEFW) yielded a correlation coefficient (r) of 0.40 (P<0.0001). The correlation between the SEFW and SEGA resulted in ar=0.97 (P<0.0001). The customized gravidogram and fetal growth chart followed the general trend seen in their Caucasian equivalents.Conclusion: The comparison of our customized gravidogram and intra‐uterine fetal growth curve with similar charts established in Caucasians does not show any significant difference.
Analysis of the landmark protein Bud3 of Ashbya gossypii reveals a novel role in septum construction
Authors: Wendland Jürgen
Published: February 2003

Cell division in fungal cells requires the coordination of three different processes: determination of the site of division, actomyosin ring formation, and the concomitant contraction of this ring together with chitin deposition at septal sites. This report describes the isolation of the AgBUD3 homologue and the characterization of Bud3 protein function in Ashbya gossypii. Bud3 fused to green fluorescent protein was shown to localize transiently either as a single ring to multiple sites of future septation or as a double ring to newly established septa. Deletion of AgBUD3 leads to a striking change in actin ring localization involving the mislocalization of AgCyk1, which is required for actin ring assembly. Aberrant chitin accumulation occurs subsequently, generating delocalized septa. Thus, in A. gossypii, Bud3 acts as a landmark, tagging future septal sites, and is involved in the positioning of the contractile ring, whereas it does not direct lateral branching.
Information encoding in homoclinic chaotic systems
Authors: Mariño I. P. , Allaria E. , Meucci R. , Boccaletti S. , Arecchi F. T.
Published: February 2003

We present a simple method for real-time encoding of information in the interspike intervals of a homoclinic chaotic system. The method has been experimentally tested on a CO2 laser with feedback displaying Sil’nikov chaos and synchronized with an external pulsed signal. Information is encoded by the length of the temporal intervals between consecutive pulses of the external signal. This length is varied each time a new pulse is generated.
Analyzing communication schemes using methods from nonlinear filtering
Authors: Bröcker Jochen , Parlitz Ulrich
Published: February 2003

The perfomance of a class of communication systems is investigated in a probabilistic framework. We investigate the bit error probability of the optimal as well as approximately optimal receivers. In general the latter turn out to be unavoidable due to the computational complexity of the former.
Control and synchronization in switched arrival systems
Authors: Rem Bart , Armbruster Dieter
Published: February 2003

A chaotic model of a production flow called the switched arrival system is extended to include switching times and maintenance. The probability distribution of the chaotic return times is calculated. Scheduling maintenance, loss of production due to switching, and control of the chaotic dynamics is discussed. A coupling parameter to couple switched arrival systems serially, based on lost production, is identified. Simulations of three parallel and three serial levels were performed. Global synchronization of the switching frequencies between serial levels is achieved. An analytic model allows one to predict the self-balancing properties of the serial system.
Conditions for efficient chaos-based communication
Authors: Baptista Murilo S. , Macau Elbert E. , Grebogi Celso
Published: February 2003

We find the conditions for a chaotic system to transmit a general source of information efficiently. Transmission of information with very low probability of error is possible if the topological entropy of the transmitted wave signal is greater than or equal to the Shannon entropy of the source message minus the conditional entropy coming from the limitations of the channel (such as equivocation by the noise). This condition may not be always satisfied both due to dynamical constraints and due to the nonoptimal use of the dynamical partition. In both cases, we describe strategies to overcome these limitations.
Noise enhanced phase synchronization and coherence resonance in sets of chaotic oscillators with weak global coupling
Authors: Kiss István Z. , Zhai Yumei , Hudson John L. , Zhou Changsong , Kurths Jürgen
Published: February 2003

The effect of noise on phase synchronization in small sets and larger populations of weakly coupled chaotic oscillators is explored. Both independent and correlated noise are found to enhance phase synchronization of two coupled chaotic oscillators below the synchronization threshold; this is in contrast to the behavior of two coupled periodic oscillators. This constructive effect of noise results from the interplay between noise and the locking features of unstable periodic orbits. We show that in a population of nonidentical chaotic oscillators, correlated noise enhances synchronization in the weak coupling region. The interplay between noise and weak coupling induces a collective motion in which the coherence is maximal at an optimal noise intensity. Both the noise-enhanced phase synchronization and the coherence resonance numerically observed in coupled chaotic Rössler oscillators are verified experimentally with an array of chaotic electrochemical oscillators.
Control of localized structures in an optical feedback interferometer
Authors: Ramazza P. L. , Boccaletti S. , Bortolozzo U. , Arecchi F. T.
Published: February 2003

We report a detailed experimental investigation of the dependence of localized structures, observed in a nonlinear optical device, on several control parameters. A first step of the study consists in the determination of the region of existence of localized states as a function of the system variables. Subsequently, we show how different control parameters can be used to the aim of tuning several localized structures properties; among these, of particular relevance are the contrast and the amplitude and frequency of the oscillations appearing on the tails of the structures. A discussion of the relation between the localized states here studied and the one predicted by general model for pattern forming systems is also given.
Persistent clusters in lattices of coupled nonidentical chaotic systems
Authors: Belykh I. , Belykh V. , Nevidin K. , Hasler M.
Published: February 2003

Two-dimensional (2D) lattices of diffusively coupled chaotic oscillators are studied. In previous work, it was shown that various cluster synchronization regimes exist when the oscillators are identical. Here, analytical and numerical studies allow us to conclude that these cluster synchronization regimes persist when the chaotic oscillators have slightly different parameters. In the analytical approach, the stability of almost-perfect synchronization regimes is proved via the Lyapunov function method for a wide class of systems, and the synchronization error is estimated. Examples include a 2D lattice of nonidentical Lorenz systems with scalar diffusive coupling. In the numerical study, it is shown that in lattices of Lorenz and Rössler systems the cluster synchronization regimes are stable and robust against up to 10%–15% parameter mismatch and against small noise.
Chaotic synchronization and evolution of optical phase in a bidirectional solid-state ring laser
Authors: Kotomtseva L. A. , Kravtsov N. V. , Lariontsev E. G. , Chekina S. N.
Published: February 2003

We present results on experimental and theoretical studies of chaos in a solid-state ring laser with periodic pump modulation. We show that the synchronized chaos in the counter-propagating waves is observed for the values of pump modulation frequency fp satisfying the inequality f1<fp<f2. The boundaries of this region, f1 and f2, depend on the pump-modulation depth. Inside the region of synchronized chaos we study not only dynamics of amplitudes of the counter-propagating waves but also the optical phases of them by mixing the fields of the counter-propagating waves and recording the intensity of the mixed signal. We demonstrate experimentally that in the regime of synchronized chaos the regular phase jumps appear during intervals between adjacent chaotic pulses. We improve the standard semi-classical model of a SSRL and consider an effect of spontaneous emission noise on the temporal evolution of intensities and phase dynamics in the regime of synchronized chaos. It is shown that at the parameters of the experimentally studied laser the noise strongly affects the temporal dependence of amplitudes of the counter-propagating waves.
Intensity coupling and synchronization of chaotic lasers
Authors: de S. Cavalcante Hugo L. D. , Rios Leite J. R.
Published: February 2003

The synchronization of chaotic lasers was studied considering the coupling scheme with the intensity of light pulses from one laser saturating the other one. The experimental synchronization of two single mode CO2 lasers with saturable absorber is reviewed. Numerical simulations are presented for diode lasers made chaotic by optical feedback. Optical intensity saturation coupling was introduced in Lang–Kobayashi equations. Parameters were chosen such that both lasers were uncorrelated and chaotic before coupling and partially synchronize after coupling. Correlation functions for the numerical solutions were used to characterize the properties of the synchronism. They show partial in-phase and antiphase synchronism for the pulse intensities, depending on the coupling mechanism. These synchronisms are independent of optical interferometric effects and so, relevant for communication applications.
Using nonisochronicity to control synchronization in ensembles of nonidentical oscillators
Authors: Montbrió Ernest , Blasius Bernd
Published: February 2003

We investigate the transition to synchronization in ensembles of coupled oscillators with quenched disorder. We find that small coupling is able to increase the frequency disorder and to induce a spread of oscillator frequencies. This new effect of anomalous desynchronization is studied with numerical and analytical means in a large class of systems including Rössler, Lotka–Volterra, Landau–Stuart, and Van-der-Pol oscillators. We show that anomalous effects arise due to an interplay between nonisochronicity and natural frequency of each oscillator and can either increase or inhibit synchronization in the ensemble. This provides a novel possibility to control the synchronization transition in nonidentical systems by suitably distributing the disorder among system parameters. We conjecture that our results are of relevance for biological systems.
Critical energies in random palindrome models
Authors: Carvalho Túlio O. , de Oliveira César R.
Published: February 2003

We investigate the occurrence of critical energies—where the Lyapunov exponent vanishes—in random Schrödinger operators when the potentials have some local order, which we call random palindrome models. We give necessary and sufficient conditions for the presence of such critical energies: the commutativity of finite word elliptic transfer matrices. Finally, we perform some numerical calculations of the Lyapunov exponents showing their behavior near the critical energies and the respective time evolution of an initially localized wave packet, obtaining the exponent ruling the algebraic growth of the second momentum. We also consider special random palindrome models with one-letter bounded gap property; the transport effects of such long range order are showed numerically.
Semidispersing billiards with an infinite cusp. II
Authors: Lenci Marco
Published: February 2003

In Lenci (2002) the following class of billiards was studied: For f:[0,+∞)→(0,+∞) convex, sufficiently smooth, and vanishing at infinity, let the billiard table be defined by Q, the planar domain delimited by the positive x semiaxis, the positive y semiaxis, and the graph of f. For a large class of f we proved that the billiard map was hyperbolic. Furthermore we gave an example of a family of f that makes this map ergodic. Here we extend the latter result to a much wider class of functions.
Leibnizian, Galilean and Newtonian structures of space–time
Authors: Bernal Antonio N. , Sánchez Miguel
Published: February 2003

The following three geometrical structures on a manifold are studied in detail: Leibnizian: a nonvanishing one-form Ω plus a Riemannian metric 〈⋅,⋅〉 on its annhilator vector bundle. In particular, the possible dimensions of the automorphism group of a Leibnizian G-structure are characterized. Galilean: Leibnizian structure endowed with an affine connection ∇ (gauge field) which parallelizes Ω and 〈⋅,⋅〉. For any fixed vector field of observers Z(Ω(Z)≡1), an explicit Koszul-type formula which reconstructs bijectively all the possible ∇’s from the gravitational G≔∇ZZ and vorticity ω≔12 rot Z fields (plus eventually the torsion) is provided. Newtonian: Galilean structure with 〈⋅,⋅〉 flat and a field of observers Z which is inertial (its flow preserves the Leibnizian structure and ω≡0). Classical concepts in Newtonian theory are revisited and discussed.
Three electrons in a harmonic oscillator potential: Pairs versus single particles
Authors: Taut M. , Pernal K. , Cioslowski J. , Staemmler V.
Published: February 2003

The three-dimensional Schrödinger equation for three electrons in a parabolic confinement potential (with strength measured by the frequency ω) can be decoupled into three pair problems, provided the expectation value of the center of mass vector R is small compared with the average distance between the electrons. This should be fulfilled at the strong correlation limit (small ω), where the electron system tends to crystallize. The remaining part of the Hamiltonian, which is not included in the independent pair model, is taken into account in perturbation theory. The complementary treatment of the weak correlation limit (large ω) considers noninteracting electrons as a zeroth-order approximation and includes the electron–electron interaction in perturbation theory. It turns out that both approaches match satisfactorily for intermediate ω. Our results are compared with those obtained with the Hartree–Fock, configuration interaction, multiconfigurational complete active space, and stochastic variational method approaches and the data from a Wigner crystal treatment in a harmonic approximation.
Quasi-homogeneous thermodynamics and black holes
Authors: Belgiorno F.
Published: February 2003

We propose a generalized thermodynamics in which quasi-homogeneity of the thermodynamic potentials plays a fundamental role. This thermodynamic formalism arises from a generalization of the approach presented in Ref. 1, and it is based on the requirement that quasi-homogeneity is a nontrivial symmetry for the Pfaffian form δQrev. It is shown that quasi-homogeneous thermodynamics fits the thermodynamic features of at least some self-gravitating systems. We analyze how quasi-homogeneous thermodynamics is suggested by black hole thermodynamics. Then, some existing results involving self-gravitating systems are also shortly discussed in the light of this thermodynamic framework. The consequences of the lack of extensivity are also recalled. We show that generalized Gibbs–Duhem equations arise as a consequence of quasi-homogeneity of the thermodynamic potentials. An heuristic link between this generalized thermodynamic formalism and the thermodynamic limit is also discussed.
The dynamical Yang–Baxter relation and the minimal representation of the elliptic quantum group
Authors: Fan Heng , Hou Boyu , Shi Kangjie , Yue Ruihong , Zhao Shaoyou
Published: February 2003

In this article, we give the general forms of the minimal L matrix (the elements of the L-matrix are c numbers) associated with the Boltzmann weights of the An−11 interaction-round-a-face (IRF) model and the minimal representation of the An−1 series elliptic quantum group given by Felder and Varchenko. The explicit dependence of elements of L-matrices on spectral parameter z are given. They are of five different forms [A(1-4) and B]. The algebra for the coefficients (which do not depend on z) are given. The algebra of form A is proved to be trivial, while that of form B obeys Yang–Baxter equation (YBE). We also give the PBW base and the centers for the algebra of form B.
Signatures of deterministic chaos in dyslipidemic erythrocytes under shear stress
Authors: Korol A. M. , Rasia R.
Published: February 2003

The erythrocytes deformation under shear stress, the viscoelastic properties and the effects observed on healthy donors and on dyslipidemic patients are investigated from the point of view of nonlinear dynamics. Finally it is suggested that the different results obtained could be useful with regard to pathophysiological disturbances and their treatment.
Monte Carlo simulation on the glass transition of free-standing atactic polypropylene thin films on a high coordination lattice
Authors: Xu Guoqiang , Mattice Wayne L.
Published: February 2003

A recently developed high coordination lattice based Monte Carlo method is applied to investigate the glass transition of free-standing atactic polypropylene thin films. In this method the short-range interactions are described by a rotational isomeric state model and the long-range interactions are obtained from a discretized form of a Lennard-Jones function. Simulations of five thin films of C150H302 with thickness of 20–100 Å at Tg are performed by a stepwise cooling from the melts to the glass states. The temperature dependence of the thickness of the thin films is obtained from the fitting of the density profile by a hyperbolic function. The glass transition temperatures of the thin films are evaluated from the change in thermal expansion coefficients at Tg. The Tg decreases as the films become thinner. For all but the thinnest film, 1/Tg is inversely proportional to the thickness of the film. The proportionality constant is within the range cited in experimental studies of other systems. The depression of the glass transition temperature arises mainly from the fast dynamics in the surface region.
The effects of added salt on the second virial coefficients of the complete proteome of E. coli
Authors: Sear Richard P.
Published: February 2003

Bacteria typically have a few thousand different proteins. The number of proteins with a given charge is a roughly Gaussian function of charge—centered near zero, and with a width around ten (in units of the charge on the proton). We have used the charges on E. coli’s proteins to estimate the changes in the second virial coefficients of all its proteins as the concentration of a 1:1 salt is increased. The second virial coefficient has dimensions of volume and we find that on average it decreases by about twice the average volume of a protein when the salt concentration is increased from 0.2 to 1 M. The standard deviation of the decrease is of the same order. The consequences of this for the complex mixture of proteins inside an E. coli cell, are briefly discussed.
Theoretical study of the UV-induced desorption of molecular oxygen from the reduced TiO2 (110) surface
Authors: de Lara-Castells M. P. , Krause Jeffrey L.
Published: February 2003

We investigate the UV-induced desorption of O2 from a reduced TiO2 rutile surface. The desorption mechanism considered is a direct, optical excitation of the adsorbate-substrate complex. The low-lying excited electronic states of the adsorbate-surface system and the transition dipole moments are calculated with a cluster model. We also estimate the effects of nonadiabatic coupling on the desorption yield. As a consequence of the localized nature of the adsorption process, ground state properties calculated with the cluster model agree well with previous results obtained with a slab model. To reduce the size of the calculation, we use optimal orbitals for each of the interacting electronic states, followed by transformation to biorthonormal orbital sets. Comparison with experimental photodesorption cross-section data shows excellent agreement for photon energies close to the vertical transition energy. At higher energies, we speculate that substrate-mediated electronic excitation mechanisms must be included in the model.
Dominant structural motifs of NO−⋅(H2O)n complexes: Infrared spectroscopic and ab initio studies
Authors: Myshakin Evgeniy M. , Jordan Kenneth D. , Robertson William H. , Weddle Gary H. , Johnson Mark A.
Published: February 2003

Argon predissociation spectroscopy is used together with ab initio electronic structure calculations to characterize the NO−⋅(H2O)n=1–3 clusters. In all cases, the water molecules bind to the ion through single ionic H bonds. Two isomeric forms are assigned for the n=1 species that differ according to whether the H bond occurs to the N or O atom of the core ion. While the spectra of the dihydrate indicate formation of an H-bonded water dimer subcluster consistent with all four predicted isomers, their calculated vibrational spectra are too similar to establish which of these forms is created in the ion source. Three classes of isomers are predicted for the NO−⋅(H2O)3 clusters, and in this case a comparison of the experimental and theoretical infrared spectra indicates the formation of a bridging arrangement in which two of the water molecules are attached to one atom and the third to the other atom of NO−. This distorted water trimer motif is intermediate between the symmetrical trimer found in the X−⋅(H2O)3 [X=Cl,Br,I] clusters and the open structure displayed by the O2−⋅(H2O)3 system. The structural differences between the complexes of water with O2− and NO− are discussed in the context of the relative proton affinities and the electronic structures of their ground states (i.e., ∑−3NO− versus ∏g2O2−). Spectra of the NO−⋅(H2O)4,5 clusters are also presented together with a qualitative discussion of the likely morphologies at play in these higher hydrates.
An initial value representation semiclassical approach for the study of molecular systems with geometric constraints
Authors: Harland Ben B. , Roy Pierre-Nicholas
Published: February 2003

We present an approach for the inclusion of geometric constraints in quantum dynamics calculations based on the semiclassical initial value representation. An important feature of the method is that a Cartesian coordinate system is used throughout, resulting in a general approach that does not require the definition of new coordinates. The Herman–Kluk [M. F. Herman and E. Kluk, Chem. Phys. 91, 27 (1984)] coherent state formulation is used. The required (constrained) classical trajectories are calculated using the standard techniques of molecular dynamics and initial conditions are sampled from a distribution that obeys the constraints. An approximate form of the Herman–Kluk prefactor is used and its evaluation requires the construction of a projected Hessian matrix. In its present form, the approach allows the calculation of energy levels from the Fourier transform of the autocorrelation function. The approach is tested on a model problem consisting of two particles in a harmonic trap and constrained to remain at a fixed distance from one another. The approach yields exact results for this simplified case when compared to the exact quantum mechanical formulation. The method is then applied to a real molecular system consisting of a water molecule with fixed OH bonds and yields accurate results when compared to exact quantum mechanical results. The accuracy of the method is comparable to that of the usual semiclassical implementation where the problem is written in a new set of coordinates. The approach can be extended to more complex cases in a straightforward manner.
Mass analyzed threshold ionization spectroscopy of N-methylaniline, N-ethylaniline, and N,N-dimethylaniline cations: Influence of N-alkyl substitution on the ionization energy and molecular vibration
Authors: Wu Rong Hu , Lin Jung Lee , Lin Jieli , Yang Shih Chang , Tzeng Wen Bih
Published: February 2003

We have applied two-color resonant two-photon mass analyzed threshold ionization spectroscopy to investigate some ionic properties of N-alkylanilines. The respective adiabatic ionization energies of N-methylaniline (NMA), N-ethylaniline (NEA), and N,N-dimethylaniline (DMA) are determined to be 59 822, 59 204, and 58 018 cm−1 with an uncertainty of about 5 cm−1. This indicates that the longer alkyl chain gives rise to a larger redshift in the IE due to a stronger interaction between the alkyl group and the nitrogen atom in the ionic state. Because the alkyl group gives rise to an increase in the electron density around the nitrogen atom of the neutral species, the IE of DMA is lower than that of NMA. In addition, the N-alkyl substitution also influences the frequency of the internal motion of the cations. However, the frequency variation is dependent upon the vibrational pattern and the extent of the coupling between the N-alkyl group and ring vibrations.
An arbitrary Lagrangian–Eulerian approach to solving the quantum hydrodynamic equations of motion: Equidistribution with “smart” springs
Authors: Trahan Corey J. , Wyatt Robert E.
Published: February 2003

Recently, the quantum trajectory method (QTM) has been utilized in solving several quantum mechanical wave packet scattering problems including barrier transmission and electronic nonadiabatic dynamics. By propagating the real-valued action and amplitude functions in the Lagrangian frame, only a fraction of the grid points needed for Eulerian fixed-grid methods are used while still obtaining accurate solutions. Difficulties arise, however, near wave function nodes and in regions of sharp oscillatory features, and because of this many quantum mechanical problems have not yet been amenable to solution with the QTM. This study proposes a hybrid of both the Lagrangian and Eulerian techniques in what is termed the arbitrary Lagrangian–Eulerian method (ALE). In the ALE method, an additional equation of motion governing the momentum of the grid points is coupled into the quantum hydrodynamic equations. These new “quasi-” Bohmian trajectories can be dynamically adapted to the emergent features of the time evolving hydrodynamic fields and are non-Lagrangian. In this study it is shown that the ALE method applied to an uphill ramp potential that was previously unsolvable by the current Lagrangian QTM not only yields stable transmission probabilities with accuracies comparable to that of a high resolution Eulerian method, but does so with a small number of grid points and for extremely long propagation times. To determine the grid point positions at each new time, an equidistribution method is used that is constructed similar to the stiffness matrix of a classical spring system in equilibrium. Each “smart” spring is dependent on a local function M(x) called the monitor function which can sense gradients or curvatures of the fields surrounding its position. To constrain grid points from having zero separation and possible overlap, a new system of equations is derived that includes a minimum separation parameter which prevents this from occurring.
A systematic study of spirals and spiral turbulence in a reaction-diffusion system
Authors: Guo Hongyu , Li Liang , Ouyang Qi , Liu Jian , She Zhensu
Published: February 2003

We report our experimental study on chemical patterns in a spatial open reactor using the Belousov–Zhabotinsky reaction. A phase diagram showing different regimes of spiral dynamics is presented. The focus of the study is on transitions leading to defect-mediated turbulence (spiral turbulence). Some new interesting phenomena are described, including a transition from one type of spiral turbulence to another type, and the re-entry from spiral turbulence into ordered spiral waves. We also try to characterize different states of turbulence using the hierarchical structure theory.
Zenithal bistability in a nematic liquid-crystal device with a monostable surface condition
Authors: Parry-Jones L. A. , Edwards E. G. , Elston S. J. , Brown C. V.
Published: February 2003

The ground-state director configurations in a grating-aligned, zenithally bistable nematic device are calculated in two dimensions using a Q tensor approach. The director profiles generated are well described by a one-dimensional variation of the director across the width of the device, with the distorted region near the grating replaced by an effective surface anchoring energy. This work shows that device bistability can in fact be achieved by using a monostable surface term in the one-dimensional model. This implies that is should be possible to construct a device showing zenithal bistability without the need for a micropatterned surface.