Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigation of optical clearing of gastric tissue immersed with hyperosmotic agents

In order to understand the role of water desorption and the mass transport process in the optical clearing effect on gastric tissues with the application of hyperosmotic agents, the porcine stomach tissues (pyloric mucosa) applied topically with glycerol and dimethyl sulfoxide (DMSO) are investigated with optical coherence tomography (OCT) and the near infrared reflectance spectroscopy. Three solutions of 80% and 50% glycerol, and 50% DMSO are studied, each of which shows significant improvement in light transmittance and, thus, reduction of the light scattering of tissue. It is found that, among the solutions investigated, 80% glycerol achieves the best clearing effect on improvement of both the light penetration and imaging contrast. More detailed microstructures of the mucosal layer can be observed for glycerol treatment, while these structures are not resolvable by the conventional OCT. Light transmittance is increased by approximately 23% and diffuse reflectance decreased by approximately 24% at 30 min after the topical application of 80% glycerol. 50% DMSO is more effective than 50% glycerol only at the beginning stage; thereafter the rate of optical clearing is slowed down with time. Although DMSO can enhance the light transmittance and thus reduce the scattering, it has a negligible effect on the imaging contrast improvement. The mass transport process of agent to tissue accounts for the different clearing effects for glycerol and DMSO, respectively. It is concluded that the optical clearing by the hyperosmotic agent is strongly correlated with the water desorption kinetics induced by agent and the agent mass transport process within tissue. In other words, the tissue dehydration induced by agent and the refractive index matching between the agent and the main scattering components within tissue facilitated by the agent mass transport are responsible for optical clearing effects.
Moyal implementation of flow equations—a non-perturbative approach to quantum many-body systems

We show how Wegner's flow equations can be reformulated as ordinary differential equations through the use of the Moyal bracket. In finite-dimensional Hilbert spaces the introduction of the Moyal bracket leads naturally to the identification of a small expansion parameter, namely the inverse of the dimensionality of the space. This expansion corresponds to a non-perturbative treatment of the coupling constant. In the case of infinite-dimensional spaces ℏ plays the role of the small parameter and the Moyal formulation then allows for a semi-classical treatment of the flow equation. We demonstrate these statements for the Lipkin and Dicke models as well as for the symmetric x4 and double-well potentials.
Route to chaos in porous-medium thermal convection

A pseudo-spectral numerical scheme is used to study two-dimensional, single-cell, time-dependent convection in a square cross-section of fluid saturated porous material heated from below. With increasing Rayleigh number R convection evolves from steady S to chaotic NP through the sequence of bifurcations S→P(1)→QP2→P(2)→NP, where P(1) and P(2) are simply periodic regimes and QP2 is a quasi-periodic state with two basic frequencies. The transitions (from onset of convection to chaos) occur at Rayleigh numbers of 4π2, 380–400, 500–520, 560–570, and 850–1000. In the first simply periodic regime the fundamental frequency f1 varies as $R^{\frac{7}{8}} $ and the average Nusselt number $\overline{Nu}$ is proportional to $R^{\frac{2}{3}}$; in P(2), f1 varies as $R^{\frac{3}{2}}$ and $\overline{Nu}\propto R^{\frac{11}{10}}$. Convection in QP2 exhibits hysteresis, i.e. if the QP2 state is reached from P(1) (P(2)) by increasing (decreasing) R then the frequency with the largest spectral power is the one consistent with the extrapolation of f1 according to $R^{\frac{7}{8}}(R^{\frac{3}{2}})$. The chaotic states are characterized by spectral peaks with at least 3 fundamental frequencies superimposed on a broadband background noise. The time dependence of these states arises from the random generation of tongue-like disturbances within the horizontal thermal boundary layers. Transition to the chaotic regime is accompanied by the growth of spectral components that destroy the centre-symmetry of convection in the other states. Over-truncation can lead to spurious transitions and bifurcation sequences; in general it produces overly complex flows.
A frequency extrapolation algorithm for FISC

A frequency extrapolation algorithm for the fast multipole method (FMM)-based moment method code FISC (Fast Illinois Solver Code) is presented. Our approach is to parameterize the induced current on the target, which is available from the FISC solution based on a multipath excitation model. The ESPRIT super-resolution algorithm is applied to extract the time-of-arrival and amplitude parameters in the model. Once the frequency-dependent model of the induced current on the target is constructed, the induced current can be extrapolated to a broad band of frequencies and the multifrequency scattered field can be computed. The range profiles for a missile model are calculated in this manner to demonstrate the accuracy and performance of the algorithm.
High Order Time-Accurate Partitioned Simulation of Unsteady Conjugate Heat Transfer; Analysis and Application of Implicit Runge-Kutta Time Integration Schemes

Time-accurate simulations of the thermal interaction of flows and structures, also referred to as conjugate heat transfer (CHT), can be computationally expensive. Furthermore, given the multi-physics nature of many engineering problems, resolution of other coupled phenomena, in addition to CHT, may also be of interest. This thesis aimed at developing a flexible and efficient numerical procedure for solving unsteady (transient) conjugate heat transfer. High order time integration schemes are considered, in place of commonly used second order implicit schemes, to reduce the computational work of advancing the coupled problem in time. For flexibility, the partitioned method is adopted for solving the coupled problem. For strongly coupled problems, a strongly-coupled solution algorithm is presented where high order explicit first stage singly diagonally implicit Runge-Kutta (ESDIRK) schemes are used for time integration. For Dirichlet-Neumann conditions at the interface, stability and rate of convergence of subiterations at each stage are analyzed analytically. Based on the analysis, the domain with the higher effusivity is assigned the Neumann condition and the one with the lower effusivity the Dirichlet condition. Furthermore, the interface iterations converge with a rate approximately given by the ratio of thermal effusivities of the subdomains. For weakly coupled problems, an order preserving loosely coupled solution algorithm is presented in which a family of high order implicit-explicit (IMEX) Runge-Kutta schemes are used for time integration. The IMEX schemes consist of the ESDIRK schemes for advancing the solution in time within each subdomain, and equal order and number of stages explicit Runge-Kutta (ERK) schemes for explicit integration of part of the coupling terms. Based on a stability investigation, when the ratio of thermal effusivities of the subdomains is much smaller than unity, it is possible to take large Fourier numbers using the loosely coupled algorithm. Another topic studied in this thesis is the application of high order ESDIRK schemes to cell-centered collocated finite volume discretization of unsteady incompressible Navier-Stokes equations. In particular, a face-velocity interpolation procedure (Rhie-Chow) which preserves the temporal design order of the multi-stage ESDIRK schemes is introduced. The influence of iterative errors on temporal order is minimized by using an iterative time advancing algorithm.
Rapid calculations for boundary-layer transfer using wedge solutions and asymptotic expansions

Exact transfer calculations for boundary layers with longitudinal pressure gradients are very complicated, but in the literature several approximate methods are known for the rapid calculation of both the wall friction and the heat transfer. A ‘wedge method’ propounded by Meksyn turns out to be one of the most rapid methods, being no less accurate than other approximate methods. A way of refining this method is proposed. This paper also shows that asymptotic expansions provide convenient relations which are capable of expressing the Nusselt number explicitly in terms of the Prandtl number. It is shown that, together with the asymptotic expansions, Meksyn's method permits rapid calculation of local heat transfer numbers. Some examples of application are given for elliptical cylinders and spheres for several values of the Prandtl number.
Theoretical study of frequency chirping and extinction ratio of wavelength-converted optical signals by XGM and XPM using SOA's

We develop a complete large-signal dynamic model of semiconductor optical amplifier (SOA)-based wavelength converters using cross-gain modulation (XGM) and cross-phase modulation (XPM). The large-signal dynamic model has been implemented using the modified transfer matrix method (TMM). This model takes into account longitudinal variations of carrier-induced refractive index, n-parameter, internal reflection, photon density, and amplified spontaneous emission noise at each small section. Therefore, we can accurately estimate frequency chirping, optical pulse patterns, and the extinction ratio as well as the dynamic characteristics of SOA's. Frequency chirping and the extinction ratio have been calculated for various parameters such as signal power and wavelength, CW power and wavelength, and facet reflectivity. Modulation bandwidth, defined by the 3-dB drop as the eye opening ratio (EOR) is investigated with current density, confinement factor, and cavity length.
Studying the Effectiveness of Online Homework for Different Skill Levels in a College Algebra Course

Abstract A comparison of the performance on the final exam for subpopulations of students in College Algebra was used to assess the effectiveness of online homework. Data was collected for two small groups of students, one with traditional paper homework and the other with online homework. The groups of students were further classified by incoming skill level measured by a departmental placement test. The data suggests that online homework was beneficial to the incoming higher-skilled group, whereas, the lower-skilled students did not benefit from online homework.
Class-uniformly resolvable designs

We investigate Class-Uniformly Resolvable Designs, which are resolvable designs in which each of the resolution classes has the same number of blocks of each size. We derive the fully general necessary conditions including a number of extremal bounds. We present two general constructions. We primarily consider the case of block sizes 2 and 3, where we find two infinite extremal families and finish two other infinite families by difference constructions. We present tables showing the current state of knowledge in the case of block size 2 and 3 for all orders up to 200. © 2001 John Wiley & Sons, Inc. J Combin Designs 8: 79–99, 2001
Numerical simulations of Rayleigh–Bénard convection for Prandtl numbers between 10−1 and 104 and Rayleigh numbers between 105 and 109

We summarize the results of an extensive campaign of direct numerical simulations of Rayleigh–Bénard convection at moderate and high Prandtl numbers (10−1 ≤ Pr ≤ 104) and moderate Rayleigh numbers (105 ≤ Ra ≤ 109). The computational domain is a cylindrical cell of aspect ratio Γ = 1/2, with the no-slip condition imposed on all boundaries. By scaling the numerical results, we find that the free-fall velocity should be multiplied by $1/\sqrt{{\it Pr}}$ in order to obtain a more appropriate representation of the large-scale velocity at high Pr. We investigate the Nusselt and the Reynolds number dependences on Ra and Pr, comparing the outcome with previous numerical and experimental results. Depending on Pr, we obtain different power laws of the Nusselt number with respect to Ra, ranging from Ra2/7 for Pr = 1 up to Ra0.31 for Pr = 103. The Nusselt number is independent of Pr. The Reynolds number scales as ${\it Re}\,{\sim}\,\sqrt{{\it Ra}}/{\it Pr}$, neglecting logarithmic corrections. We analyse the global and local features of viscous and thermal boundary layers and their scaling behaviours with respect to Ra and Pr, and with respect to the Reynolds and Péclet numbers. We find that the flow approaches a saturation state when Reynolds number decreases below the critical value, Res ≃ 40. The thermal-boundary-layer thickness increases slightly (instead of decreasing) when the Péclet number increases, because of the moderating influence of the viscous boundary layer. The simulated ranges of Ra and Pr contain steady, periodic and turbulent solutions. A rough estimate of the transition from the steady to the unsteady state is obtained by monitoring the time evolution of the system until it reaches stationary solutions. We find multiple solutions as long-term phenomena at Ra = 108 and Pr = 103, which, however, do not result in significantly different Nusselt numbers. One of these multiple solutions, even if stable over a long time interval, shows a break in the mid-plane symmetry of the temperature profile. We analyse the flow structures through the transitional phases by direct visualizations of the temperature and velocity fields. A wide variety of large-scale circulation and plume structures has been found. The single-roll circulation is characteristic only of the steady and periodic solutions. For other regimes at lower Pr, the mean flow generally consists of two opposite toroidal structures; at higher Pr, the flow is organized in the form of multi-jet structures, extending mostly in the vertical direction. At high Pr, plumes mainly detach from sheet-like structures. The signatures of different large-scale structures are generally well reflected in the data trends with respect to Ra, less in those with respect to Pr.
Carrier diffusion and depletion effects on multiwave mixing in semiconductor lasers

A detailed theoretical treatment has been undertaken of multiwave mixing in semiconductor lasers, taking into account the effects of pump/probe depletion, carrier diffusion, usual gain saturation, nonlinear gain compression, total power dependence of the coupling coefficients as well as the longitudinal dependence of the nonlinear interaction. It is shown that the effect of carrier diffusion can considerably enhance the probe and conjugate reflectivity for detuning frequency near the relaxation oscillation frequency of the pump laser. It is demonstrated, in particular that, for relatively high input probe power, the probe and conjugate reflectivity can be enhanced significantly near the relaxation oscillation frequency of the pump laser, compared to that for low input probe power. Furthermore, both the probe reflectivity and the conjugate reflectivity show asymmetric characteristics with respect to the zero pump/probe frequency detunings. The pump/probe depletion effect plays an important role in determining the optical output power when the input probe power is larger than /spl sim/0.1 /spl mu/W.
Planetary Magnetic Fields and Fluid Dynamos

The magnetic fields of the planets, including the Earth, are generated by dynamo action in their fluid cores. Numerical models of this process have been developed that solve the fundamental magnetohydrodynamic equations driven by convection in a rotating spherical shell. New results from these theoretical models are compared with observations of the geomagnetic field and magnetic data gathered from space missions. The mechanism by which a magnetic field is created is examined. The effects of rotation and magnetic field on the convection are of paramount importance in the simulations. A wide range of simulations with different convection models, varying boundary conditions, and parameter values have been performed over the past 10 years. The effects of these differences are assessed. Numerical considerations mean that all dynamo simulations use much enhanced values of the diffusivities. We consider to what extent this affects results and show how the asymptotic behavior at low diffusion is starting to be inferred using scaling laws. The results of specific models relating to individual planets are reviewed.
Linear Stability Analysis and Validation of a Unified Solution Method for Fluid-Structure-Interaction on Structural Dynamic Problems

In the conventional approach for fluid-structure interaction problems, the fluid and solid components are treated separately and information is exchanged across their interface. According to the conventional terminology, the current numerical methods can be grouped in two major categories: Partitioned methods and monolithic methods. Both methods use two separate sets of equations for fluid and solid. A unified solution method has been presented [1], which is different from these methods. The new method treats both fluid and solid as a single continuum, thus the whole computational domain is treated as one entity discretised on a single grid. Its behavior is described by a single set of equations, which are solved fully implicitly. In this paper, 2 time marching and one spatial discretisation scheme, widely used for fluids’ equations, are applied for the solution of the equations for solids. Using linear stability analysis, the accuracy and dissipation characteristics of the resulting difference equations are examined. The aforementioned schemes are applied to a transient structural problem (beam bending) and the results compare favorably with available analytic solutions and are consistent with the conclusions of the stability analysis. A parametric investigation using different meshes, time steps and beam sizes is also presented. For all cases examined the numerical solution was stable and robust and proved to be suitable for the next stage of application to full fluid-structure interaction problems.Copyright © 2005 by ASME
Comments on “Atmospheric Disturbance Caused by Human Modification of the Landscape”

In a recent article published in the February 2001 issue of the Bulletin of American Meteorological Society, Weaver and Avissar (hereafter WA) investigated the response of the atmosphere to landscape heterogeneity to assess the importance of mesoscale fluxes of sensible and latent heat arising from differences in land use in the southern Great Plains. To do so they used the RAMS mesoscale model and a surface flux data set derived from observations and the Simple Biosphere Model. They selected six days for analysis based on the criterion that the study region located at the Department of Energy's Atmospheric Radiation Measurement Program's Cloud and Radiation Testbed (CART) was not obscured by clouds with obvious non-local origins. WA noted that mesoscale fluxes of latent heat on those six days were large, especially near and above the top of the boundary layer. They argued that regions of strong vertical motion that they associated with mesoscale fluxes were closely correlated with regions of precipitation on one of the six days they studied and with cloudy regions on two other days. From these findings, WA concluded that landscape heterogeneity arising from human influences can''significantly affect local weather and climate. '' They further concluded that the inabilitymore » to predict mesoscale fluxes is a serious failing of general circulation models (GCMs) used to predict climate change and that further studies in parameterizing such fluxes for use in GCMs is therefore necessary. In this paper we offer a somewhat different interpretation and perspective on the findings of WA. « less
Direct Measurements of Energetic Neutral Hydrogen in the Interplanetary Medium

We present an analysis of hydrogen energetic neutral atoms (ENAs) measured by the ASPERA-3 instrument on board Mars Express. We focus on ENAs that have no Martian origin. The energy spectra of these ENAs are all very similar and can be fitted well by a two-component power law. The fluxes, integrated from 0.2 to 10 keV, vary between 5 × 103 and 105 cm-2 sr-1 s-1. We checked for possible sources for these ENAs, but we can rule out a planetary origin, a solar wind origin, contamination by UV from UV bright stars, and contamination by high-energy protons. With our present knowledge we conclude that the heliospheric termination shock is the most plausible source region.
Inflammatory Bowel Diseases and Gut Microbiota

Inflammatory bowel disease (IBD) is an inflammatory disease of the gastrointestinal tract, the incidence of which has rapidly increased worldwide, especially in developing and Western countries. Recent research has suggested that genetic factors, the environment, microbiota, and immune responses are involved in the pathogenesis; however, the underlying causes of IBD are unclear. Recently, gut microbiota dysbiosis, especially a decrease in the abundance and diversity of specific genera, has been suggested as a trigger for IBD-initiating events. Improving the gut microbiota and identifying the specific bacterial species in IBD are essential for understanding the pathogenesis and treatment of IBD and autoimmune diseases. Here, we review the different aspects of the role played by gut microbiota in the pathogenesis of IBD and provide a theoretical basis for modulating gut microbiota through probiotics, fecal microbiota transplantation, and microbial metabolites.
Development of the Upgraded Tangent Linear and Adjoint of the Weather Research and Forecasting (WRF) Model

The authors propose a new technique for parallelizations of tangent linear and adjoint codes, which were applied in the redevelopment for the Weather Research and Forecasting (WRF) model with its Advanced ResearchWRFdynamiccoreusingtheautomaticdifferentiation engine.Thetangentlinearandadjointcodes of the WRF model (WRFPLUS) now have the following improvements: A complete check interface ensures that developers write accurate tangent linear and adjoint codes with ease and efficiency. A new technique based on the nature of duality that existed among message passing interface communication routines was adopted to parallelize the WRFPLUS model. The registry in the WRF model was extended to automatically generate the tangent linear and adjoint codes of the required communication operations. This approach dramatically speeds up the software development cycle of the parallel tangent linear and adjoint codes and leads to improved parallel efficiency. Module interfaces were constructed for coupling tangent linear and adjoint codes of the WRF model with applications such as four-dimensional variational data assimilation, forecast sensitivity to observation, and others.
On the spectral gap of Kawasaki dynamics under a mixing condition revisited

We consider a conservative stochastic spin exchange dynamics which is reversible with respect to the canonical Gibbs measure of a lattice gas model. We assume that the corresponding grand canonical measure satisfies a suitable strong mixing condition. We give an alternative and quite natural, from the physical point of view, proof of the famous Lu–Yau result which states that the relaxation time in a box of side L scales like L2. We then show how to use such an estimate to prove a decay to equilibrium for local functions of the form 1/tα−e, where e is positive and arbitrarily small and α=12 for d=1, α=1 for d⩾2.