Stochastic E2F activation and reconciliation of phenomenological cell-cycle models.

The transition of the mammalian cell from quiescence to proliferation is a highly variable process. Over the last four decades, two lines of apparently contradictory, phenomenological models have been proposed to account for such temporal variability. These include various forms of the transition probability (TP) model and the growth control (GC) model, which lack mechanistic details. The GC model was further proposed as an alternative explanation for the concept of the restriction point, which we recently demonstrated as being controlled by a bistable Rb-E2F switch. Here, through a combination of modeling and experiments, we show that these different lines of models in essence reflect different aspects of stochastic dynamics in cell cycle entry. In particular, we show that the variable activation of E2F can be described by stochastic activation of the bistable Rb-E2F switch, which in turn may account for the temporal variability in cell cycle entry. Moreover, we show that temporal dynamics of E2F activation can be recast into the frameworks of both the TP model and the GC model via parameter mapping. This mapping suggests that the two lines of phenomenological models can be reconciled through the stochastic dynamics of the Rb-E2F switch. It also suggests a potential utility of the TP or GC models in defining concise, quantitative phenotypes of cell physiology. This may have implications in classifying cell types or states.

Different phenomenological theories and their abilities to describe the interdiffusion process in a binary system during multiphase growth

There are essentially two different phenomenological models available to describe the interdiffusion process in binary systems in the olid state. The first of these, which is used more frequently, is based on the theory of flux partitioning. The second model, developed much more recently, uses the theory of dissociation and reaction. Although the theory of flux partitioning has been widely used, we found that this theory does not account for the mobility of both species and therefore is not suitable for use in most interdiffusion systems. We have first modified this theory to take into account the mobility of both species and then further extended it to develop relations or the integrated diffusion coefficient and the ratio of diffusivities of the species. The versatility of these two different models is examined in the Co-Si system with respect to different end-member compositions. From our analysis, we found that the applicability of the theory of flux partitioning is rather limited but the theory of dissociation and reaction can be used in any binary system.

Advantages and Applications of Transforming Empirical Model Input Space with Dimensional Models

Model-based calibration of steady-state engine operation is commonly performed with highly parameterized empirical models that are accurate but not very robust, particularly when predicting highly nonlinear responses such as diesel smoke emissions. To address this problem, and to boost the accuracy of more robust non-parametric methods to the same level, GT-Power was used to transform the empirical model input space into multiple input spaces that simplified the input-output relationship and improved the accuracy and robustness of smoke predictions made by three commonly used empirical modeling methods: Multivariate Regression, Neural Networks and the k-Nearest Neighbor method. The availability of multiple input spaces allowed the development of two committee techniques: a 'Simple Committee' technique that used averaged predictions from a set of 10 pre-selected input spaces chosen by the training data and the "Minimum Variance Committee" technique where the input spaces for each prediction were chosen on the basis of disagreement between the three modeling methods. This latter technique equalized the performance of the three modeling methods. The successively increasing improvements resulting from the use of a single best transformed input space (Best Combination Technique), Simple Committee Technique and Minimum Variance Committee Technique were verified with hypothesis testing. The transformed input spaces were also shown to improve outlier detection and to improve k-Nearest Neighbor performance when predicting dynamic emissions with steady-state training data. An unexpected finding was that the benefits of input space transformation were unaffected by changes in the hardware or the calibration of the underlying GT-Power model.

Moisture Aided Degradation of Oil Impregnated Paper Insulation in Power Transformers

The presence of moisture in oil impregnated paper insulation (OIP) is detrimental to its long time performance. Until recently, it was thought insulation ageing was only a function of temperature and electrical stress. It has now been realized that moisture in all its forms causes rapid degradation of the electrical and mechanical properties with time. In this study, insulation paper samples were conditioned for desired level of moisture and were impregnated with premium quality transformer oil. The oil impregnated samples with 1 to 3 % moisture content were aged at 90 to 130 C. The indices for determining the extent of ageing considered in this work are degree of polymerization (DP), furan, carbon monoxide and carbon dioxide content. These quantities were monitored throughout the ageing experimental run. End-of-life (EOL) criterion used here is the reduction in the value of DP. Phenomenological models for estimating the service life of insulation are proposed and are validated against actual experimental data.

Inorganic glasses, glass-forming liquids and amorphizing solids

Greaves, George; Sen, S., (2007) 'Inorganic glasses, glass-forming liquids and amorphizing solids', Advances in Physics 56(1) pp.1-166 RAE2008

Morphology dependence of the dielectric properties of epitaxial BaTiO3 films and epitaxial BaTiO3/SrTiO3 multilayers

Epitaxial BaTiO3 films and epitaxial BaTiO3/SrTiO3 multilayers were grown by pulsed laser deposition on vicinal surfaces of (001)-oriented Nb-doped SrTiO3 (SrTiO3:Nb) single-crystal substrates. Atomic force microscopy was used to investigate the surface topography of the deposited films. The morphology of the films, of the BaTiO3/SrTiO3 interfaces, and of the column boundaries was investigated by cross-sectional high-resolution transmission electron microscopy. Measurements of the dielectric properties were performed by comparing BaTiO3 films and BaTiO3/SrTiO3 multilayers of different numbers of individual layers, but equal overall thickness. The dielectric loss saturates for a thickness above 300 nm and linearly decreases with decreasing film thickness below a thickness of 75 nm. At the same thickness of 75 nm, the thickness dependence of the dielectric constant also exhibits a change in the linear slope both for BaTiO3 films and BaTiO3/SrTiO3 multilayers. This behaviour is explained by the change observed in the grain morphology at a thickness of 75 nm. For the thickness dependence of the dielectric constant, two phenomenological models are considered, viz. a 'series-capacitor' model and a 'dead-layer' model.

Atomistic-continuum modeling of ultrafast laser-induced melting of silicon targets

In this work, we present an atomistic-continuum model for simulations of ultrafast laser-induced melting processes in semiconductors on the example of silicon. The kinetics of transient non-equilibrium phase transition mechanisms is addressed with MD method on the atomic level, whereas the laser light absorption, strong generated electron-phonon nonequilibrium, fast heat conduction, and photo-excited free carrier diffusion are accounted for with a continuum TTM-like model (called nTTM). First, we independently consider the applications of nTTM and MD for the description of silicon, and then construct the combined MD-nTTM model. Its development and thorough testing is followed by a comprehensive computational study of fast nonequilibrium processes induced in silicon by an ultrashort laser irradiation. The new model allowed to investigate the effect of laser-induced pressure and temperature of the lattice on the melting kinetics. Two competing melting mechanisms, heterogeneous and homogeneous, were identified in our big-scale simulations. Apart from the classical heterogeneous melting mechanism, the nucleation of the liquid phase homogeneously inside the material significantly contributes to the melting process. The simulations showed, that due to the open diamond structure of the crystal, the laser-generated internal compressive stresses reduce the crystal stability against the homogeneous melting. Consequently, the latter can take a massive character within several picoseconds upon the laser heating. Due to the large negative volume of melting of silicon, the material contracts upon the phase transition, relaxes the compressive stresses, and the subsequent melting proceeds heterogeneously until the excess of thermal energy is consumed. A series of simulations for a range of absorbed fluences allowed us to find the threshold fluence value at which homogeneous liquid nucleation starts contributing to the classical heterogeneous propagation of the solid-liquid interface. A series of simulations for a range of the material thicknesses showed that the sample width we chosen in our simulations (800 nm) corresponds to a thick sample. Additionally, in order to support the main conclusions, the results were verified for a different interatomic potential. Possible improvements of the model to account for nonthermal effects are discussed and certain restrictions on the suitable interatomic potentials are found. As a first step towards the inclusion of these effects into MD-nTTM, we performed nanometer-scale MD simulations with a new interatomic potential, designed to reproduce ab initio calculations at the laser-induced electronic temperature of 18946 K. The simulations demonstrated that, similarly to thermal melting, nonthermal phase transition occurs through nucleation. A series of simulations showed that higher (lower) initial pressure reinforces (hinders) the creation and the growth of nonthermal liquid nuclei. For the example of Si, the laser melting kinetics of semiconductors was found to be noticeably different from that of metals with a face-centered cubic crystal structure. The results of this study, therefore, have important implications for interpretation of experimental data on the kinetics of melting process of semiconductors.

Transport in the middle atmosphere

An overview is provided of the current understanding of transport in the middle atmosphere. Over the past quarter century this subject has evolved from a basic recognition of the Brewer-Dobson circulation to a detailed appreciation of many key features of transport such as the stratospheric surf zone, mixing barriers and the dynamics of filamentation. Whilst the elegant theoretical framework for middle atmosphere transport that emerged roughly twenty years ago never fulfilled its promise, useful phenomenological models have been developed together with innovative diagnostic methods. These advances were made possible by the advent of plenty of satellite and aircraft observations of long-lived chemical species together with developments in data assimilation and numerical modeling, and have been driven in large measure by the problem of stratospheric ozone depletion. This review is primarily focused on the stratosphere, where both the interest and the knowledge are the greatest, but a few remarks are also made on the mesosphere.

Volatile isoprenoid emissions from plastid to planet

Approximately 1–2% of net primary production by land plants is re-emitted to the atmosphere as isoprene and monoterpenes. These emissions play major roles in atmospheric chemistry and air pollution–climate interactions. Phenomenological models have been developed to predict their emission rates, but limited understanding of the function and regulation of these emissions has led to large uncertainties in model projections of air quality and greenhouse gas concentrations. We synthesize recent advances in diverse fields, from cell physiology to atmospheric remote sensing, and use this information to propose a simple conceptual model of volatile isoprenoid emission based on regulation of metabolism in the chloroplast. This may provide a robust foundation for scaling up emissions from the cellular to the global scale.

Crescimento de filmes nanométricos monocristalinos de Fe/MgO(100) por "SPUTTERING" DC

The research behind this master dissertation started with the installation of a DC sputtering system, from its first stage, the adaptation of a refrigerating system, passing by the introduction of a heating system for the chamber using a thermal belt, until the deposition of a series of Fe/MgO(100) single crystal nanometric film samples. The deposition rates of some materials such as Fe, Py and Cu were investigated through an Atomic Force Microscope (AFM). For the single crystal samples, five of them have the same growth parameters and a thickness of 250Å, except for the temperature, which varies from fifty degrees from one to another, from 100ºC to 300ºC. Three other samples also have the same deposition parameters and a temperature of 300ºC, but with thickness of 62,5Å, 150Å, and 250Å. Magneto-optical Kerr Effect (MOKE) of the magnetic curves measurements and Ferromagnetic Resonance (FMR) were made to in order to study the influence of the temperature and thickness on the sample s magnetic properties. In the present dissertation we discuss such techniques, and the experimental results are interpreted using phenomenological models, by simulation, and discussed from a physical point of view, taking into account the system s free magnetic energy terms. The results show the growth of the cubic anisotropy field (Hac) as the sample s deposition temperature increases, presenting an asymptotic behavior, similar to the characteristic charging curve of a capacitor in a RC circuit. A similar behavior was also observed for the Hac due to the increase in the samples thicknesses. The 250˚A sample, growth at 300°C, presented a Hac field close to the Fe bulk value

Shear viscosity from thermal fluctuations in relativistic conformal fluid dynamics

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Measurement of the underlying event activity in pp collisions at √s = 0.9 and 7 TeV with the novel jet-area/median approach

The first measurement of the charged component of the underlying event using the novel jet-area/median approach is presented for proton-proton collisions at centre-of-mass energies of 0.9 and 7 TeV. The data were recorded in 2010 with the CMS experiment at the LHC. A new observable, sensitive to soft particle production, is introduced and investigated inclusively and as a function of the event scale defined by the transverse momentum of the leading jet. Various phenomenological models are compared to data, with and without corrections for detector effects. None of the examined models describe the data satisfactorily. © 2012 SISSA.

Síntese e caracterização de filmes finos de ferrita de bismuto dopados com cálcio visando aplicação em memórias de múltiplos estados

The increasing demand for electro-electronic devices, with high performance and multi-functional and the rapid advances of the nanotechnology require the development of new methods and techniques for the production and characterization of nanostructure materials and phenomenological models to describe/to predict some of its properties. The demand for multifunctionality requires, at least, new materials, that can integrate ferroelectric and magnetic properties of high technological interest. Inside of this context, multiferroics material can be considered suitable to integrate two or more physical properties of high technological interest. It can also provides new challenges in the processes of synthesis of new materials, and development of new devices with controlling and simulation of its physical properties and modeling. For this Calcium (Ca)-doped bismuth ferrite (BiFeO3) thin films prepared by using the polymeric precursor method (PPM) were characterized by X-ray diffraction (XRD), field emission gun scanning electron microscopy (FEG-SEM), transmission electron microscopy (TEM), polarization and piezoelectric measurements.In order to study the behavior and determine which are the most important parameters to achieve the optimal property to be applied to a multiferroic materials

Scalar field description of decaying-Lambda cosmologies

The conditions under which cosmologies driven by time-varying cosmological terms can be described by a scalar field coupled to a perfect fluid are discussed. An algorithm to reconstruct potentials dynamically and thermodynamically analogous to given phenomenological λ models is presented. As a working example, the deflationary cosmology which evolves from a pure de Sitter vacuum state to a slightly modified Friedmann-Robertson-Walker cosmology is considered. It is found that this is an example of nonsingular warm inflation with an asymptotic exponential potential. Differences with respect to other scalar field descriptions of decaying vacuum cosmologies are addressed and possible extensions are indicated.

Compulsive features in behavioural addictions: the case of pathological gambling

Aims To describe, in the context of DSM-V, how a focus on addiction and compulsion is emerging in the consideration of pathological gambling (PG). Methods A systematic literature review of evidence for the proposed re-classification of PG as an addiction. Results Findings include: (i) phenomenological models of addiction highlighting a motivational shift from impulsivity to compulsivity associated with a protracted withdrawal syndrome and blurring of the ego-syntonic/ego-dystonic dichotomy; (ii) common neurotransmitter (dopamine, serotonin) contributions to PG and substance use disorders (SUDs); (iii) neuroimaging support for shared neurocircuitries between behavioural and substance addictions and differences between obsessivecompulsive disorder (OCD), impulse control disorders (ICDs) and SUDs; (iv) genetic findings more closely related to endophenotypic constructs such as compulsivity and impulsivity than to psychiatric disorders; (v) psychological measures such as harm avoidance identifying a closer association between SUDs and PG than with OCD; (vi) community and pharmacotherapeutic trials data supporting a closer association between SUDs and PG than with OCD. Adapted behavioural therapies, such as exposure therapy, appear applicable to OCD, PG or SUDs, suggesting some commonalities across disorders. Conclusions PG shares more similarities with SUDs than with OCD. Similar to the investigation of impulsivity, studies of compulsivity hold promising insights concerning the course, differential diagnosis and treatment of PG, SUDs, and OCD.