Controlled Software Evaluation Methodology: Case Simulation and Cognitive User Analysis

Software for use with patient records is challenging to design and difficult to evaluate because of the tremendous variability of patient circumstances. A method was devised by the authors to overcome a number of difficulties. The method evaluates and compares objectively various software products for use in emergency departments and compares software to conventional methods like dictation and templated chart forms. The technique utilizes oral case simulation and video recording for analysis. The methodology and experiences of executing a study using this case simulation are discussed in this presentation.

Upconverter materials and upconversion solar-cell devices: simulation and characterization with broad solar spectrum illumination

Upconverter materials and upconverter solar devices were recently investigated with broad-band excitation revealing the great potential of upconversion to enhance the efficiency of solar cell at comparatively low solar concentration factors. In this work first attempts are made to simulate the behavior of the upconverter β-NaYF4 doped with Er3+ under broad-band excitation. An existing model was adapted to account for the lower absorption of broader excitation spectra. While the same trends as observed for the experiments were found in the simulation, the absolute values are fairly different. This makes an upconversion model that specifically considers the line shape function of the ground state absorption indispensable to achieve accurate simulations of upconverter materials and upconverter solar cell devices with broadband excitations, such as the solar radiation.

Experimenting and modeling: sharp distinctions, integration or just a mess?

At first sight, experimenting and modeling form two distinct modes of scientific inquiry. This spurs philosophical debates about how the distinction should be drawn (e.g. Morgan 2005, Winsberg 2009, Parker 2009). But much scientific practice casts serious doubts on the idea that the distinction makes much sense. There are two worries. First, the practices of modeling and experimenting are often intertwined in intricate ways because much modeling involves experimenting, and the interpretation of many experiments relies upon models. Second, there are borderline cases that seem to blur the distinction between experiment and model (if there is any). My talk tries to defend the philosophical project of distinguishing models from experiment and to advance the related philosophical debate. I begin with providing a minimalist framework of conceptualizing experimenting and modeling and their mutual relationships. The methods are conceptualized as different types of activities that are characterized by a primary goal, respectively. The minimalist framwork, which should be uncontroversial, suffices to accommodate the first worry. I address the second worry by suggesting several ways how to conceptualize the distinction in a more flexible way. I make a concrete suggestion of how the distinction may be drawn. I use examples from the history of science to argue my case. The talk concentrates and models and experiments, but I will comment on simulations too.

Resolving diffusion in clay minerals at different time scales: Combination of experimental and modeling approaches

Since no single experimental or modeling technique provides data that allow a description of transport processes in clays and clay minerals at all relevant scales, several complementary approaches have to be combined to understand and explain the interplay between transport relevant phenomena. In this paper molecular dynamics simulations (MD) were used to investigate the mobility of water in the interlayer of montmorillonite (Mt), and to estimate the influence of mineral surfaces and interlayer ions on the water diffusion. Random Walk (RW) simulations based on a simplified representation of pore space in Mt were used to estimate and understand the effect of the arrangement of Mt particles on the meso- to macroscopic diffusivity of water. These theoretical calculations were complemented with quasielastic neutron scattering (QENS) measurements of aqueous diffusion in Mt with two pseudo-layers of water performed at four significantly different energy resolutions (i.e. observation times). The size of the interlayer and the size of Mt particles are two characteristic dimensions which determine the time dependent behavior of water diffusion in Mt. MD simulations show that at very short time scales water dynamics has the characteristic features of an oscillatory motion in the cage formed by neighbors in the first coordination shell. At longer time scales, the interaction of water with the surface determines the water dynamics, and the effect of confinement on the overall water mobility within the interlayer becomes evident. At time scales corresponding to an average water displacement equivalent to the average size of Mt particles, the effects of tortuosity are observed in the meso- to macroscopic pore scale simulations. Consistent with the picture obtained in the simulations, the QENS data can be described using a (local) 3D diffusion at short observation times, whereas at sufficiently long observation times a 2D diffusive motion is clearly observed. The effects of tortuosity measured in macroscopic tracer diffusion experiments are in qualitative agreement with RW simulations. By using experimental data to calibrate molecular and mesoscopic theoretical models, a consistent description of water mobility in clay minerals from the molecular to the macroscopic scale can be achieved. In turn, simulations help in choosing optimal conditions for the experimental measurements and the data interpretation. (C) 2014 Elsevier B.V. All rights reserved.

Revealing Assembly of a Pore-Forming Complex Using Single-Cell Kinetic Analysis and Modeling

Many biological processes depend on the sequential assembly of protein complexes. However, studying the kinetics of such processes by direct methods is often not feasible. As an important class of such protein complexes, pore-forming toxins start their journey as soluble monomeric proteins, and oligomerize into transmembrane complexes to eventually form pores in the target cell membrane. Here, we monitored pore formation kinetics for the well-characterized bacterial pore-forming toxin aerolysin in single cells in real time to determine the lag times leading to the formation of the first functional pores per cell. Probabilistic modeling of these lag times revealed that one slow and seven equally fast rate-limiting reactions best explain the overall pore formation kinetics. The model predicted that monomer activation is the rate-limiting step for the entire pore formation process. We hypothesized that this could be through release of a propeptide and indeed found that peptide removal abolished these steps. This study illustrates how stochasticity in the kinetics of a complex process can be exploited to identify rate-limiting mechanisms underlying multistep biomolecular assembly pathways.

Impact of Taylor-Aris diffusivity on analyte and system zone dispersion in CZE assessed by computer simulation and experimental validation.

Application of pressure-driven laminar flow has an impact on zone and boundary dispersion in open tubular CE. The GENTRANS dynamic simulator for electrophoresis was extended with Taylor-Aris diffusivity which accounts for dispersion due to the parabolic flow profile associated with pressure-driven flow. Effective diffusivity of analyte and system zones as functions of the capillary diameter and the amount of flow in comparison to molecular diffusion alone were studied for configurations with concomitant action of imposed hydrodynamic flow and electroosmosis. For selected examples under realistic experimental conditions, simulation data are compared with those monitored experimentally using modular CE setups featuring both capacitively coupled contactless conductivity and UV absorbance detection along a 50 μm id fused-silica capillary of 90 cm total length. The data presented indicate that inclusion of flow profile based Taylor-Aris diffusivity provides realistic simulation data for analyte and system peaks, particularly those monitored in CE with conductivity detection.

Collisional Formation and Modeling of Asteroid Families

In the last decade, thanks to the development of sophisticated numerical codes, major breakthroughs have been achieved in our understanding of the formation of asteroid families by catastrophic disruption of large parent bodies. In this review, we describe numerical simulations of asteroid collisions that reproduced the main properties of families, accounting for both the fragmentation of an asteroid at the time of impact and the subsequent gravitational interactions of the generated fragments. The simulations demonstrate that the catastrophic disruption of bodies larger than a few hundred meters in diameter leads to the formation of large aggregates due to gravitational reaccumulation of smaller fragments, which helps explain the presence of large members within asteroid families. Thus, for the first time, numerical simulations successfully reproduced the sizes and ejection velocities of members of representative families. Moreover, the simulations provide constraints on the family dynamical histories and on the possible internal structure of family members and their parent bodies.

Efficient numerical methods for global linear instability. Analysis and modeling of non-orthogonal swept attachment-line boundary layer flow

The aim of this thesis is to study the mechanisms of instability that occur in swept wings when the angle of attack increases. For this, a simplified model for the a simplified model for the non-orthogonal swept leading edge boundary layer has been used as well as different numerical techniques in order to solve the linear stability problem that describes the behavior of perturbations superposed upon this base flow. Two different approaches, matrix-free and matrix forming methods, have been validated using direct numerical simulations with spectral resolution. In this way, flow instability in the non-orthogonal swept attachment-line boundary layer is addressed in a linear analysis framework via the solution of the pertinent global (Bi-Global) PDE-based eigenvalue problem. Subsequently, a simple extension of the extended G¨ortler-H¨ammerlin ODEbased polynomial model proposed by Theofilis, Fedorov, Obrist & Dallmann (2003) for orthogonal flow, which includes previous models as particular cases and recovers global instability analysis results, is presented for non-orthogonal flow. Direct numerical simulations have been used to verify the stability results and unravel the limits of validity of the basic flow model analyzed. The effect of the angle of attack, AoA, on the critical conditions of the non-orthogonal problem has been documented; an increase of the angle of attack, from AoA = 0 (orthogonal flow) up to values close to _/2 which make the assumptions under which the basic flow is derived questionable, is found to systematically destabilize the flow. The critical conditions of non-orthogonal flows at 0 _ AoA _ _/2 are shown to be recoverable from those of orthogonal flow, via a simple analytical transformation involving AoA. These results can help to understand the mechanisms of destabilization that occurs in the attachment line of wings at finite angles of attack. Studies taking into account variations of the pressure field in the basic flow or the extension to compressible flows are issues that remain open. El objetivo de esta tesis es estudiar los mecanismos de la inestabilidad que se producen en ciertos dispositivos aerodinámicos cuando se aumenta el ángulo de ataque. Para ello se ha utilizado un modelo simplificado del flujo de base, así como diferentes técnicas numéricas, con el fin de resolver el problema de estabilidad lineal asociado que describe el comportamiento de las perturbaciones. Estos métodos; sin y con formación de matriz, se han validado utilizando simulaciones numéricas directas con resolución espectral. De esta manera, la inestabilidad del flujo de capa límite laminar oblicuo entorno a la línea de estancamiento se aborda en un marco de análisis lineal por medio del método Bi-Global de resolución del problema de valores propios en derivadas parciales. Posteriormente se propone una extensión simple para el flujo no-ortogonal del modelo polinomial de ecuaciones diferenciales ordinarias, G¨ortler-H¨ammerlin extendido, propuesto por Theofilis et al. (2003) para el flujo ortogonal, que incluye los modelos previos como casos particulares y recupera los resultados del analisis global de estabilidad lineal. Se han realizado simulaciones directas con el fin de verificar los resultados del análisis de estabilidad así como para investigar los límites de validez del modelo de flujo base utilizado. En este trabajo se ha documentado el efecto del ángulo de ataque AoA en las condiciones críticas del problema no ortogonal obteniendo que el incremento del ángulo de ataque, de AoA = 0 (flujo ortogonal) hasta valores próximos a _/2, en el cual las hipótesis sobre las que se basa el flujo base dejan de ser válidas, tiende sistemáticamente a desestabilizar el flujo. Las condiciones críticas del caso no ortogonal 0 _ AoA _ _/2 pueden recuperarse a partir del caso ortogonal mediante el uso de una transformación analítica simple que implica el ángulo de ataque AoA. Estos resultados pueden ayudar a comprender los mecanismos de desestabilización que se producen en el borde de ataque de las alas de los aviones a ángulos de ataque finitos. Como tareas pendientes quedaría realizar estudios que tengan en cuenta variaciones del campo de presión en el flujo base así como la extensión de éste al caso de flujos compresibles.

Selectivity of diacylhydrazine insecticides to the predatory bug Orius laevigatus: In vivo and modeling/docking experiments

BACKGROUND: Knowledge of pesticide selectivity to natural enemies is necessary for a successful implementation of biological and chemical control methods in integrated pest management (IPM) programs. Diacylhydrazine (DAH)-based ecdysone agonists also known as molting-accelerating compounds (MACs) are considered a selective group of insecticides, and their compatibility with predatory Heteroptera, which are used as biological control agents, is known. However, their molecular mode of action has not been explored in beneficial insects such as Orius laevigatus (Fieber) (Hemiptera: Anthocoridae). RESULTS: In this project in vivo toxicity assays demonstrated that the DAH-based RH-5849, tebufenozide and methoxyfenozide have no toxic effect against O. laevigatus. The ligand-binding domain (LBD) of the ecdysone receptor (EcR) of O. laevigatus was sequenced and a homology protein model was constructed which confirmed a cavity structure with 12 ?-helixes, harboring the natural insect molting hormone 20-hydroxyecdysone. However, docking studies showed that a steric clash occurred for the DAH-based insecticides due to a restricted extent of the ligand-binding cavity of the EcR of O. laevigatus. CONCLUSIONS: The insect toxicity assays demonstrated that MACs are selective for O. laevigatus. The modeling/docking experiments are indications that these pesticides do not bind with the LBD-EcR of O. laevigatus and support that they show no biological effects in the predatory bug. These data help in explaining the compatible use of MACs together with predatory bugs in IPM programs. Keywords: Orius laevigatus, selectivity, diacylhydrazine insecticides, ecdysone receptor, homology modelling, docking studies.

Intraply fracture of fiber-reinforced composites: microscopic mechanisms and modeling

The fracture behavior parallel to the fibers of an E-glass/epoxy unidirectional laminate was studied by means of three-point tests on notched beams. Selected tests were carried out within a scanning electron microscope to ascertain the damage and fracture micromechanisms upon loading. The mechanical behavior of the notched beam was simulated within the framework of the embedded cell model, in which the actual composite microstructure was resolved in front of the notch tip. In addition, matrix and interface properties were independently measured in situ using a nanoindentor. The numerical simulations very accurately predicted the macroscopic response of the composite as well as the damage development and crack growth in front of the notch tip, demonstrating the ability of the embedded cell approach to simulate the fracture behavior of heterogeneous materials. Finally, this methodology was exploited to ascertain the influence of matrix and interface properties on the intraply toughness.

Design and modeling of the multi-agent robotic system: SMART

This article presents the design, kinematic model and communication architecture for the multi-agent robotic system called SMART. The philosophy behind this kind of system requires the communication architecture to contemplate the concurrence of the whole system. The proposed architecture combines different communication technologies (TCP/IP and Bluetooth) under one protocol designed for the cooperation among agents and other elements of the system such as IP-Cameras, image processing library, path planner, user Interface, control block and data block. The high level control is modeled by Work-Flow Petri nets and implemented in C++ and C♯♯. Experimental results show the performance of the designed architecture.

Ionoluminescence on α-quartz: mechanisms and modeling

Ionoluminescence of α - quartz exhibits two dominant emission bands peaking at 1.9 eV. (NBOHCs) and 2.7 eV (STEs. The evolution of the red emission yield does not show a correlation with the concentrations of neither the NBOHC nor with that of other color centers. The blue emission yield closely follows the amorphization kinetics independently measured by RBS/C spectrometry. A simple theoretical model has been proposed; it assumes that the formation and recombination of STEs are the primary event and both, the light emissions and the lattice structural damage are a consequence this phenomenon. The model leads to several simple mathematical equations that can be used to simulate the IL yields and provide a reasonable fit to experimental kinetic data.

Emission inventories and modeling activities for the development of air quality plans in Madrid (Spain)

1. Introduction 2. Air Quality Modeling system 3. Emission Inventories 4. Applications and Results 5. Conclusions

Emission inventories and modeling requirements for the development of air quality plans. Application to Madrid (Spain)

Modeling is an essential tool for the development of atmospheric emission abatement measures and air quality plans. Most often these plans are related to urban environments with high emission density and population exposure. However, air quality modeling in urban areas is a rather challenging task. As environmental standards become more stringent (e.g. European Directive 2008/50/EC), more reliable and sophisticated modeling tools are needed to simulate measures and plans that may effectively tackle air quality exceedances, common in large urban areas across Europe, particularly for NO2. This also implies that emission inventories must satisfy a number of conditions such as consistency across the spatial scales involved in the analysis, consistency with the emission inventories used for regulatory purposes and versatility to match the requirements of different air quality and emission projection models. This study reports the modeling activities carried out in Madrid (Spain) highlighting the atmospheric emission inventory development and preparation as an illustrative example of the combination of models and data needed to develop a consistent air quality plan at urban level. These included a series of source apportionment studies to define contributions from the international, national, regional and local sources in order to understand to what extent local authorities can enforce meaningful abatement measures. Moreover, source apportionment studies were conducted in order to define contributions from different sectors and to understand the maximum feasible air quality improvement that can be achieved by reducing emissions from those sectors, thus targeting emission reduction policies to the most relevant activities. Finally, an emission scenario reflecting the effect of such policies was developed and the associated air quality was modeled.