Direct calculation of interfacial tensions from computer simulation: Results for freely jointed tangent hard sphere chains

We develop a methodology for the calculation of surface free energies based on the probability distribution of a wandering interface. Using a simple extension of the NpT sampling, we allow the interface area to randomly probe the available space and evaluate the surface free energy from histogram analysis and the corresponding average. The method is suitable for studying systems with either continuous or discontinuous potentials, as it does not require explicit evaluation of the virial. The proposed algorithm is compared with known results for the surface tension of Lennard--Jones and Square Well fluid, as well as for the interface tension of a bead--spring polymer model and good agreement is found. We also calculate interfacial tensions of freely jointed tangent hard sphere chains on athermal walls for a wide range of chain lengths and densities. The results are compared with three different theoretical approaches, Scaled Particle Theory, the Yu and Wu density functional theory and an analytical approximation based on the latter approach. Whereas SPT only yields qualitative results, the last two approaches are found to yield very good agreement with simulations.Comment: 20 pages, 6 figures, Phys. Rev. E in press

In Vitro Recombination of Non-Homologous Genes Can Result in Gene Fusions that Confer a Switching Phenotype to Cells

Regulation of protein activity is central to the complexity of life. The ability to regulate protein activity through exogenously added molecules has biotechnological/biomedical applications and offers tools for basic science. Such regulation can be achieved by establishing a means to modulate the specific activity of the protein (i.e. allostery). An alternative strategy for intracellular regulation of protein activity is to control the amount of protein through effects on its production, accumulation, and degradation. We have previously demonstrated that the non-homologous recombination of the genes encoding maltose binding protein (MBP) and TEM1 β-lactamase (BLA) can result in fusion proteins in which β-lactamase enzyme activity is allosterically regulated by maltose. Here, through use of a two-tiered genetic selection scheme, we demonstrate that such recombination can result in genes that confer maltose-dependent resistance to β-lactam even though they do not encode allosteric enzymes. These ‘phenotypic switch’ genes encode fusion proteins whose accumulation is a result of a specific interaction with maltose. Phenotypic switches represent an important class of proteins for basic science and biotechnological applications in vivo

A Revised Design for Microarray Experiments to Account for Experimental Noise and Uncertainty of Probe Response

Background Although microarrays are analysis tools in biomedical research, they are known to yield noisy output that usually requires experimental confirmation. To tackle this problem, many studies have developed rules for optimizing probe design and devised complex statistical tools to analyze the output. However, less emphasis has been placed on systematically identifying the noise component as part of the experimental procedure. One source of noise is the variance in probe binding, which can be assessed by replicating array probes. The second source is poor probe performance, which can be assessed by calibrating the array based on a dilution series of target molecules. Using model experiments for copy number variation and gene expression measurements, we investigate here a revised design for microarray experiments that addresses both of these sources of variance. Results Two custom arrays were used to evaluate the revised design: one based on 25 mer probes from an Affymetrix design and the other based on 60 mer probes from an Agilent design. To assess experimental variance in probe binding, all probes were replicated ten times. To assess probe performance, the probes were calibrated using a dilution series of target molecules and the signal response was fitted to an adsorption model. We found that significant variance of the signal could be controlled by averaging across probes and removing probes that are nonresponsive or poorly responsive in the calibration experiment. Taking this into account, one can obtain a more reliable signal with the added option of obtaining absolute rather than relative measurements. Conclusion The assessment of technical variance within the experiments, combined with the calibration of probes allows to remove poorly responding probes and yields more reliable signals for the remaining ones. Once an array is properly calibrated, absolute quantification of signals becomes straight forward, alleviating the need for normalization and reference hybridizations

CVP-АНАЛІЗ ЯК ЕФЕКТИВНИЙ ЗАСІБ ПЛАНУВАННЯ І ПРОГНОЗУВАННЯ ДІЯЛЬНОСТІ ПІДПРИЄМСТВ

In today’s economy, for the effective operation of the enterprise,important attention should be paid to management decisions andforecasting. For management of the enterprise the detailed informationconsidering technology and the organization of this enterprise is necessary.Very relevant and most effective analysis of the ratio of costs, volume and profit, that is, break-even analysis.In this article the methods of break-even point and margin analysis areinvestigated. The main goal of the article is to study theoretical and practical recommendations that will facilitate the application of this analysis in any situation.To achieve the results the break-even point analysis and marginanalysis indicators are used in the article. The methodology used in thiseconomic study is to make accurate calculation of indicators.In the course of the study it was found that the biggest problems in theapplication of CVP-analysis method arise in the distribution of fixed costs in the conditions of multiple products. Therefore at calculation of a break-even point of kinds of production two approaches have been applied forcomparison: traditional and administrative. They differ in the methodology of allocation of fixed costs, but show significant results of break-even production of certain products. Achievement of the critical point of production was not enough to predict the activity of the enterprise. It is necessary to know the amount of possible profit, the guarantees of its receipt and the amount of revenue to cover all costs to make profit.The results showed that CVP-analysis simplifies the cost/benefit ratioand assumes that it is based on linear relationships. Such an analysis willshow how efficient a single product is and in what quantities it must beproduced in order to achieve profit. The calculation of some indicatorsshowed that costs should be reduced and which should be increased.Thus, all generalizing indicators of CVP-analysis at the enterpriselevel have the full right to exist and use, especially since none of themcontradicts the classical theory of break-even at the level of a singleproduct.В условиях современной экономики, для эффективнойдеятельности предприятия, важное внимание следует уделятьуправленческим решениям и прогнозированию.В ходе исследования было выявлено, что наибольшие проблемыпри применении метода CVP-анализа возникают при распределениипостоянных затрат в условиях выпуска нескольких продуктов. Поэтому при расчете точки безубыточности видов продукции были применены для сравнения два подхода: традиционный и управленческий. Они отличаются методологии распределения постоянных расходов, но показывают существенные результаты безубыточного производства отдельных видов продукции. Достижения критической точки производства оказалось недостаточно для прогнозирования деятельности предприятия. Необходимо узнать величину возможной прибыли, гарантии его получения и сумму выручки для покрытия всех затрат, чтобы получить при этом прибыль.В умовах сучасної економіки, для ефективної діяльності підприємства, особливу увагу слід приділяти управлінським рішенням та прогнозуванню. В ході дослідження було виявлено, що найбільші проблеми при застосуванні методу CVP-аналізу виникають під час розподілу постійних витрат в умовах випуску декількох продуктів, тому при розрахунку точки беззбитковості видів продукції було застосовано для порівняння два підходи: традиційний та управлінський. Вони відрізняються методологією розподілу постійних витрат, але показують суттєві результати беззбиткового виробництва окремих видів продукції. Досягнення критичної точки виробництва виявилось недостатньо для прогнозування діяльності підприємства. Необхідно дізнатись величину можливого прибутку, гарантії його отримання та суму виручки для покриття всіх затрат, щоб отримати при цьому прибуток

School violence, school differences and school discourses

This article highlights one strand of a study which investigated the concept of the violenceresilient school. In six inner-city secondary schools, data on violent incidents in school and violent crime in the neighbourhood were gathered, and compared with school practices to minimise violence, accessed through interviews. Some degree of association between the patterns of behaviour and school practices was found: schools with a wider range of wellconnected practices seemed to have less difficult behaviour. Interviews also showed that the different schools had different organisational discourses for construing school violence, its possible causes and the possible solutions. Differences in practices are best understood in connection with differences in these discourses. Some of the features of school discourses are outlined, including their range, their core metaphor and their silences. We suggest that organisational discourse is an important concept in explaining school effects and school differences, and that improvement attempts could have clearer regard to this concept

Bayesian analysis in applications of hierarchical models: Issues and methods

In applications of hierarchical models (HMs), a potential weakness of empirical Bayes estimation approaches is that they do not to take into account uncertainty in the estimation of the variance components . One possible solution entails employing a fully Bayesian approach, which involves specifying a prior probability distribution for the variance components and then integrating over the variance components as well as other unknowns in the HM to obtain a marginal posterior distribution of interest (see, e.g., Draper, 1995

Density functional formalism in the canonical ensemble

Density functional theory, when applied to systems with $T\neq 0$, is based on the grand canonical extension of the Hohenberg-Kohn-Sham theorem due to Mermin (HKSM theorem). While a straightforward canonical ensemble generalization fails, work in nanopore systems could certainly benefit from such extension. We show that, if the asymptotic behaviour of the canonical distribution functions is taken into account, the HKSM theorem can be extended to the canonical ensemble. We generate $N$-modified correlation and distribution functions hierarchies and prove that, if they are employed, either a modified external field or the density profiles can be indistinctly used as independent variables. We also write down the $N$% -modified free energy functional and prove that its minimum is reached when the equilibrium values of the new hierarchy are used. This completes the extension of the HKSM theorem.Comment: revtex, to be submitted to Phys. Rev. Let

Magnetism of small V clusters embedded in a Cu fcc matrix: an ab initio study

We present extensive first principles density functional theory (DFT) calculations dedicated to analyze the magnetic and electronic properties of small V$_{n}$ clusters (n=1,2,3,4,5,6) embedded in a Cu fcc matrix. We consider different cluster structures such as: i) a single V impurity, ii) several V$_{2}$ dimers having different interatomic distance and varying local atomic environment, iii) V$_{3}$ and iv) V$_{4}$ clusters for which we assume compact as well as 2- and 1-dimensional atomic configurations and finally, in the case of the v) V$_{5}$ and vi) V$_{6}$ structures we consider a square pyramid and a square bipyramid together with linear arrays, respectively. In all cases, the V atoms are embedded as substitutional impurities in the Cu network. In general, and as in the free standing case, we have found that the V clusters tend to form compact atomic arrays within the cooper matrix. Our calculated non spin-polarized density of states at the V sites shows a complex peaked structure around the Fermi level that strongly changes as a function of both the interatomic distance and local atomic environment, a result that anticipates a non trivial magnetic behavior. In fact, our DFT calculations reveal, in each one of our clusters systems, the existence of different magnetic solutions (ferromagnetic, ferrimagnetic, and antiferromagnetic) with very small energy differences among them, a result that could lead to the existence of complex finite-temperature magnetic properties. Finally, we compare our results with recent experimental measurements.Comment: 7 pages and 4 figure

Phosphorylation of Not4p Functions Parallel to BUR2 to Regulate Resistance to Cellular Stresses in Saccharomyces cerevisiae

Background The evolutionarily conserved Ccr4-Not and Bur1/2 kinase complexes are functionally related in Saccharomyces cerevisiae. In this study, we further explore the relationship between the subunits Not4p and Bur2p. Methodology/Principal Findings First, we investigated the presence of post-translational modifications on the Ccr4-Not complex. Using mass spectrometry analyses we identified several SP/TP phosphorylation sites on its Not4p, Not1p and Caf1p subunits. Secondly, the influence of Not4p phosphorylation on global H3K4 tri-methylation status was examined by immunoblotting. This histone mark is severely diminished in the absence of Not4p or of Bur2p, but did not require the five identified Not4p phosphorylation sites. Thirdly, we found that Not4p phosphorylation is not affected by the kinase-defective bur1-23 mutant. Finally, phenotypic analyses of the Not4p phosphomutant (not4S/T5A) and bur2Δ strains showed overlapping sensitivities to drugs that abolish cellular stress responses. The double-mutant not4S/T5A and bur2Δ strain even revealed enhanced phenotypes, indicating that phosphorylation of Not4p and BUR2 are active in parallel pathways for drug tolerance. Conclusions Not4p is a phospho-protein with five identified phosphorylation sites that are likely targets of a cyclin-dependent kinase(s) other than the Bur1/2p complex. Not4p phosphorylation on the five Not4 S/T sites is not required for global H3K4 tri-methylation. In contrast, Not4p phosphorylation is involved in tolerance to cellular stresses and acts in pathways parallel to BUR2 to affect stress responses in Saccharomyces cerevisiae