Atmospheric neutrino oscillation analysis with subleading effects in Super-Kamiokande I, II, and III

We present a search for nonzero θ13 and deviations of sin2θ23 from 0.5 in the oscillations of atmospheric neutrino data from Super-Kamiokande I, II, and III. No distortions of the neutrino flux consistent with nonzero θ13 are found and both neutrino mass hierarchy hypotheses are in agreement with the data. The data are best fit at Δm2=2.1×10-3eV2, sin2θ13=0.0, and sin2θ23=0.5. In the normal (inverted) hierarchy θ13 and Δm2 are constrained at the one-dimensional 90% C.L. to sin2θ13<0.04(0.09) and 1.9(1.7)×10 -3<Δm2<2.6(2.7)×10-3eV2. The atmospheric mixing angle is within 0.407≤sin2θ23≤0.583 at 90% C.L. © 2010 The American Physical Society.

A von Bertalanffy Based Model for the Estimation of Oyster (Crassostrea virginica) Growth on Restored Oyster Reefs in Chesapeake Bay

A model to estimate the mean monthly growth of Crassostrea virginica oysters in Chesapeake Bay was developed. This model is based on the classic von Bertalanffy growth function, however the growth constant is changed every monthly timestep in response to short term changes in temperature and salinity. Using a dynamically varying growth constant allows the model to capture seasonal oscillations in growth, and growth responses to changing environmental conditions that previous applications of the von Bertalanffy model do not capture. This model is further expanded to include an estimation of Perkinsus marinus impacts on growth rates as well as estimations of ecosystem services provided by a restored oyster bar over time. The model was validated by comparing growth estimates from the model to oyster shell height observations from a variety of restoration sites in the upper Chesapeake Bay. Without using the P. marinus impact on growth, the model consistently overestimates mean oyster growth. However, when P. marinus effects are included in the model, the model estimates match the observed mean shell height closely for at least the first 3 years of growth. The estimates of ecosystem services suggested by this model imply that even with high levels of mortality on an oyster reef, the ecosystem services provided by that reef can still be maintained by growth for several years. Because larger oyster filter more water than smaller ones, larger oysters contribute more to the filtration and nutrient removal ecosystem services of the reef. Therefore a reef with an abundance of larger oysters will provide better filtration and nutrient removal. This implies that if an oyster restoration project is trying to improve water quality through oyster filtration, it is important to maintain the larger older oysters on the reef.

Transcription factors MYOCD, SRF, Mesp1 and SMARCD3 enhance the cardio-inducing effect of GATA4, TBX5, and MEF2C during direct cellular reprogramming.

Transient overexpression of defined combinations of master regulator genes can effectively induce cellular reprogramming: the acquisition of an alternative predicted phenotype from a differentiated cell lineage. This can be of particular importance in cardiac regenerative medicine wherein the heart lacks the capacity to heal itself, but simultaneously contains a large pool of fibroblasts. In this study we determined the cardio-inducing capacity of ten transcription factors to actuate cellular reprogramming of mouse embryonic fibroblasts into cardiomyocyte-like cells. Overexpression of transcription factors MYOCD and SRF alone or in conjunction with Mesp1 and SMARCD3 enhanced the basal but necessary cardio-inducing effect of the previously reported GATA4, TBX5, and MEF2C. In particular, combinations of five or seven transcription factors enhanced the activation of cardiac reporter vectors, and induced an upregulation of cardiac-specific genes. Global gene expression analysis also demonstrated a significantly greater cardio-inducing effect when the transcription factors MYOCD and SRF were used. Detection of cross-striated cells was highly dependent on the cell culture conditions and was enhanced by the addition of valproic acid and JAK inhibitor. Although we detected Ca(2+) transient oscillations in the reprogrammed cells, we did not detect significant changes in resting membrane potential or spontaneously contracting cells. This study further elucidates the cardio-inducing effect of the transcriptional networks involved in cardiac cellular reprogramming, contributing to the ongoing rational design of a robust protocol required for cardiac regenerative therapies.

Calcium dependent CAMTA1 in adult stem cell commitment to a myocardial lineage.

The phenotype of somatic cells has recently been found to be reversible. Direct reprogramming of one cell type into another has been achieved with transduction and over expression of exogenous defined transcription factors emphasizing their role in specifying cell fate. To discover early and novel endogenous transcription factors that may have a role in adult-derived stem cell acquisition of a cardiomyocyte phenotype, mesenchymal stem cells from human and mouse bone marrow and rat liver were co-cultured with neonatal cardiomyocytes as an in vitro cardiogenic microenvironment. Cell-cell communications develop between the two cell types as early as 24 hrs in co-culture and are required for elaboration of a myocardial phenotype in the stem cells 8-16 days later. These intercellular communications are associated with novel Ca(2+) oscillations in the stem cells that are synchronous with the Ca(2+) transients in adjacent cardiomyocytes and are detected in the stem cells as early as 24-48 hrs in co-culture. Early and significant up-regulation of Ca(2+)-dependent effectors, CAMTA1 and RCAN1 ensues before a myocardial program is activated. CAMTA1 loss-of-function minimizes the activation of the cardiac gene program in the stem cells. While the expression of RCAN1 suggests involvement of the well-characterized calcineurin-NFAT pathway as a response to a Ca(2+) signal, the CAMTA1 up-regulated expression as a response to such a signal in the stem cells was unknown. Cell-cell communications between the stem cells and adjacent cardiomyocytes induce Ca(2+) signals that activate a myocardial gene program in the stem cells via a novel and early Ca(2+)-dependent intermediate, up-regulation of CAMTA1.

Role of DNA binding sites and slow unbinding kinetics in titration-based oscillators.

Genetic oscillators, such as circadian clocks, are constantly perturbed by molecular noise arising from the small number of molecules involved in gene regulation. One of the strongest sources of stochasticity is the binary noise that arises from the binding of a regulatory protein to a promoter in the chromosomal DNA. In this study, we focus on two minimal oscillators based on activator titration and repressor titration to understand the key parameters that are important for oscillations and for overcoming binary noise. We show that the rate of unbinding from the DNA, despite traditionally being considered a fast parameter, needs to be slow to broaden the space of oscillatory solutions. The addition of multiple, independent DNA binding sites further expands the oscillatory parameter space for the repressor-titration oscillator and lengthens the period of both oscillators. This effect is a combination of increased effective delay of the unbinding kinetics due to multiple binding sites and increased promoter ultrasensitivity that is specific for repression. We then use stochastic simulation to show that multiple binding sites increase the coherence of oscillations by mitigating the binary noise. Slow values of DNA unbinding rate are also effective in alleviating molecular noise due to the increased distance from the bifurcation point. Our work demonstrates how the number of DNA binding sites and slow unbinding kinetics, which are often omitted in biophysical models of gene circuits, can have a significant impact on the temporal and stochastic dynamics of genetic oscillators.

Role of Landau quantization on the neutron-drip transition in magnetar crusts

The role of a strong magnetic field on the neutron-drip transition in the crust of a magnetar is studied. The composition of the crust and the neutron-drip threshold are determined numerically for different magnetic field strengths using the experimental atomic mass measurements from the 2012 Atomic Mass Evaluation complemented with theoretical masses calculated from the Brussels-Montreal Hartree-Fock-Bogoliubov nuclear mass model HFB-24. The equilibrium nucleus at the neutron-drip point is found to be independent of the magnetic field strength. As demonstrated analytically, the neutron-drip density and pressure increase almost linearly with the magnetic field strength in the strongly quantizing regime for which electrons lie in the lowest Landau level. For weaker magnetic fields, the neutron-drip density exhibits typical quantum oscillations. In this case, the neutron-drip density can be either increased by about 14% or decreased by 25% depending on the magnetic field strength. These variations are shown to be almost universal, independently of the nuclear mass model employed. These results may have important implications for the physical interpretation of timing irregularities and quasiperiodic oscillations detected in soft gamma-ray repeaters and anomalous x-ray pulsars, as well as for the cooling of strongly magnetized neutron stars.

A multi-scale atomistic-continuum modelling of crack propagation in a two-dimensional macroscopic plate

A novel multi-scale seamless model of brittle-crack propagation is proposed and applied to the simulation of fracture growth in a two-dimensional Ag plate with macroscopic dimensions. The model represents the crack propagation at the macroscopic scale as the drift-diffusion motion of the crack tip alone. The diffusive motion is associated with the crack-tip coordinates in the position space, and reflects the oscillations observed in the crack velocity following its critical value. The model couples the crack dynamics at the macroscales and nanoscales via an intermediate mesoscale continuum. The finite-element method is employed to make the transition from the macroscale to the nanoscale by computing the continuum-based displacements of the atoms at the boundary of an atomic lattice embedded within the plate and surrounding the tip. Molecular dynamics (MD) simulation then drives the crack tip forward, producing the tip critical velocity and its diffusion constant. These are then used in the Ito stochastic calculus to make the reverse transition from the nanoscale back to the macroscale. The MD-level modelling is based on the use of a many-body potential. The model successfully reproduces the crack-velocity oscillations, roughening transitions of the crack surfaces, as well as the macroscopic crack trajectory. The implications for a 3-D modelling are discussed.

A two-dimensional numerical investigation of the oscillatory flow behaviour in rectangular fire compartments with a single horizontal ceiling vent

This paper presents a comparison of fire field model predictions with experiment for the case of a fire within a compartment which is vented (buoyancydriven) to the outside by a single horizontal ceiling vent. Unlike previous work, the mathematical model does not employ a mixing ratio to represent vent temperatures but allows the model to predict vent temperatures a priori. The experiment suggests that the flow through the vent produces oscillatory behaviour in vent temperatures with puffs of smoke emerging from the fire compartment. This type of flow is also predicted by the fire field model. While the numerical predictions are in good qualitative agreement with observations, they overpredict the amplitudes of the temperature oscillations within the vent and also the compartment temperatures. The discrepancies are thought to be due to three-dimensional effects not accounted for in this model as well as using standard ‘practices’ normally used by the community with regards to discretization and turbulence models. Furthermore, it is important to note that the use of the k–ε turbulence model in a transient mode, as is used here, may have a significant effect on the results. The numerical results also suggest that a linear relationship exists between the frequency of vent temperature oscillation (n) and the heat release rate (Q0) of the type n∝Q0.290, similar to that observed for compartments with two horizontal vents. This relationship is predicted to occur only for heat release rates below a critical value. Furthermore, the vent discharge coefficient is found to vary in an oscillatory fashion with a mean value of 0.58. Below the critical heat release rate the mean discharge coefficient is found to be insensitive to fire size.

Multiscale numerical modelling of crack propagation in two-dimensional metal plate

A novel multiscale model of brittle crack propagation in an Ag plate with macroscopic dimensions has been developed. The model represents crack propagation as stochastic drift-diffusion motion of the crack tip atom through the material, and couples the dynamics across three different length scales. It integrates the nanomechanics of bond rupture at the crack tip with the displacement and stress field equations of continuum based fracture theories. The finite element method is employed to obtain the continuum based displacement and stress fields over the macroscopic plate, and these are then used to drive the crack tip forward at the atomic level using the molecular dynamics simulation method based on many-body interatomic potentials. The linkage from the nanoscopic scale back to the macroscopic scale is established via the Ito stochastic calculus, the stochastic differential equation of which advances the tip to a new position on the macroscopic scale using the crack velocity and diffusion constant obtained on the nanoscale. Well known crack characteristics, such as the roughening transitions of the crack surfaces, crack velocity oscillations, as well as the macroscopic crack trajectories, are obtained.

Magneto-hydro-dynamic analysis of an electrolysis cell for aluminum production

An electrolytic cell for Aluminum production contains molten metal subject to high currents and magnetic flux density. The interaction between these two fields creates electromagnetic forces within the liquid metal and can generate oscillations of the fluid similar to the waves at the free surface of oceans and rivers. The study of this phenomenon requires the simulation of the current density field, of the magnetic flux density field and the solution of the equations of motion of the liquid mass. An attempt to analyze the dynamical behavior of this problem is made by coupling different codes, based on different numerical techniques, in a single tool. The simulations are presented and discussed.

AC & DC magnetic levitation and semi-levitation modelling

This work presents computation analysis of levitated liquid thermal and flow fields with free surface oscillations in AC and DC magnetic fields. The volume electromagnetic force distribution is continuously updated with the shape and position change. The oscillation frequency spectra are analysed for droplets levitation against gravity in AC and DC magnetic fields at various combinations. For larger volume liquid metal confinement and melting the semi-levitation induction skull melting process is simulated with the same numerical model. Applications are aimed at pure electromagnetic material processing techniques and the material properties measurements in uncontaminated conditions.

A computational model of coupled heat and moisture transfer with phase change in granular sugar during varying environmental conditions

As part of a comprehensive effort to predict the development of caking in granular materials, a mathematical model is introduced to model simultaneous heat and moisture transfer with phase change in porous media when undergoing temperature oscillations/cycling. The resulting model partial differential equations were solved using finite-volume procedures in the context of the PHYSICA framework and then applied to the analysis of sugar in storage. The influence of temperature on absorption/desorption and diffusion coefficients is coupled into the transport equations. The temperature profile, the depth of penetration of the temperature oscillation into the bulk solid, and the solids moisture content distribution were first calculated, and these proved to be in good agreement with experimental data. Then, the influence of temperature oscillation on absolute humidity, moisture concentration, and moisture migration for different parameters and boundary conditions was examined. As expected, the results show that moisture near boundary regions responds faster than farther away from them with surface temperature changes. The moisture absorption and desorption in materials occurs mainly near boundary regions (where interactions with the environment are more pronounced). Small amounts of solids moisture content, driven by both temperature and vapour concentration gradients, migrate between boundary and center with oscillating temperature.

Nonlinear MHD stability of aluminium reduction cells

An industrial electrolysis cell used to produce primary aluminium is sensitive to waves at the interface of liquid aluminium and electrolyte. The interface waves are similar to stratified sea layers [1], but the penetrating electric current and the associated magnetic field are intricately involved in the oscillation process, and the observed wave frequencies are shifted from the purely hydrodynamic ones [2]. The interface stability problem is of great practical importance because the electrolytic aluminium production is a major electrical energy consumer, and it is related to environmental pollution rate. The stability analysis was started in [3] and a short summary of the main developments is given in [2]. Important aspects of the multiple mode interaction have been introduced in [4], and a widely used linear friction law first applied in [5]. In [6] a systematic perturbation expansion is developed for the fluid dynamics and electric current problems permitting reduction of the three-dimensional problem to a two dimensional one. The procedure is more generally known as “shallow water approximation” which can be extended for the case of weakly non-linear and dispersive waves. The Boussinesq formulation permits to generalise the problem for non-unidirectionally propagating waves accounting for side walls and for a two fluid layer interface [1]. Attempts to extend the electrolytic cell wave modelling to the weakly nonlinear case have started in [7] where the basic equations are derived, including the nonlinearity and linear dispersion terms. An alternative approach for the nonlinear numerical simulation for an electrolysis cell wave evolution is attempted in [8 and references there], yet, omitting the dispersion terms and without a proper account for the dissipation, the model can predict unstable waves growth only. The present paper contains a generalisation of the previous non linear wave equations [7] by accounting for the turbulent horizontal circulation flows in the two fluid layers. The inclusion of the turbulence model is essential in order to explain the small amplitude self-sustained oscillations of the liquid metal surface observed in real cells, known as “MHD noise”. The fluid dynamic model is coupled to the extended electromagnetic simulation including not only the fluid layers, but the whole bus bar circuit and the ferromagnetic effects [9].

Time dependent electric, magnetic and hydrodynamic interaction in aluminium electrolysis cells

The waves in commercial cells for electrolytic aluminium production originate at the interface between the liquid aluminium and electrolyte, but their effect can spread into the surrounding busbar network as electric current perturbation, and the total magnetic field acquires a time dependent component. The presented model for the wave development accounts for the nonuniform electric current distribution at the cathode and the whole network of the surrounding busbars. The magnetic field is computed for the continuous current in the fluid zones, all busbars and the ferromagnetic construction elements. When the electric current and the associated magnetic field are computed according to the actual electrical circuit and updated for all times, the instability growth rate is significantly affected. The presented numerical model for the wave and electromagnetic interaction demonstrates how different physical coupling factors are affecting the wave development in the electrolysis cells. These small amplitude self-sustained interface oscillations are damped in the presence of intense turbulent viscosity created by the horizontal circulation velocity field. Additionally, the horizontal circulation vortices create a pressure gradient contributing to the deformation of the interface. Instructive examples for the 500 kA demonstration cell are presented.

Levitated liquid droplets in AC and DC magnetic field

Electromagnetic levitation of liquid metal droplets can be used to measure the properties of highly reactive liquid materials. Two independent numerical models, the commercial COMSOL and the spectral-collocation based free surface code SPHINX, have been applied to solve the transient electromagnetic, fluid flow and thermodynamic equations, which describe the levitated liquid motion and heating processes. The SPHINX model incorporates free surface deformation to accurately model the oscillations that result from the interaction between the electromagnetic and gravity forces, temperature dependent surface tension, magnetically controlled turbulent momentum transport. The models are adapted to incorporate periodic laser heating at the top of the droplet, which is used to measure the thermal conductivity of the material. Novel effects in the levitated droplet of magnetically damped turbulence and nonlinear growth of velocities in high DC magnetic field are analysed.