Distance software: design and analysis of distance sampling surveys for estimating population size

1. Distance sampling is a widely used technique for estimating the size or density of biological populations. Many distance sampling designs and most analyses use the software Distance. 2. We briefly review distance sampling and its assumptions, outline the history, structure and capabilities of Distance, and provide hints on its use. 3. Good survey design is a crucial prerequisite for obtaining reliable results. Distance has a survey design engine, with a built-in geographic information system, that allows properties of different proposed designs to be examined via simulation, and survey plans to be generated. 4. A first step in analysis of distance sampling data is modeling the probability of detection. Distance contains three increasingly sophisticated analysis engines for this: conventional distance sampling, which models detection probability as a function of distance from the transect and assumes all objects at zero distance are detected; multiple-covariate distance sampling, which allows covariates in addition to distance; and mark–recapture distance sampling, which relaxes the assumption of certain detection at zero distance. 5. All three engines allow estimation of density or abundance, stratified if required, with associated measures of precision calculated either analytically or via the bootstrap. 6. Advanced analysis topics covered include the use of multipliers to allow analysis of indirect surveys (such as dung or nest surveys), the density surface modeling analysis engine for spatial and habitat-modeling, and information about accessing the analysis engines directly from other software. 7. Synthesis and applications. Distance sampling is a key method for producing abundance and density estimates in challenging field conditions. The theory underlying the methods continues to expand to cope with realistic estimation situations. In step with theoretical developments, state-of- the-art software that implements these methods is described that makes the methods accessible to practicing ecologists.

Aplicação do software Autodesk™ inventor na elaboração do projeto de um redutor de velocidades

Through a current and practical approach, this work aims to demonstrate how a speed reducer would behave in a real situation, but using a digital environment. Therefore, first, it was made the modeling of each component of the reducer, driven by gears. Completed the modeling of the components, it was possible to realize the connection between them and thus characterize the work as a speed reducer; and using properly sized and shaped reducer, we could finally demonstrate the operation of the same, the very Autodesk Inventor ™ 2014 environment

Avaliação do software Autodesk Revit 2016 para quantificação por meio da modelagem da informação da construção

The building budgeting quickly and accurately is a challenge faced by the companies in the sector. The cost estimation process is performed from the quantity takeoff and this process of quantification, historically, through the analysis of the project, scope of work and project information contained in 2D design, text files and spreadsheets. This method, in many cases, present itself flawed, influencing the making management decisions, once it is closely coupled to time and cost management. In this scenario, this work intends to make a critical analysis of conventional process of quantity takeoff, from the quantification through 2D designs, and with the use of the software Autodesk Revit 2016, which uses the concepts of building information modeling for automated quantity takeoff of 3D model construction. It is noted that the 3D modeling process should be aligned with the goals of budgeting. The use of BIM technology programs provides several benefits compared to traditional quantity takeoff process, representing gains in productivity, transparency and assertiveness

An in-depth analysis of the HIV-1/AIDS dynamics by comprehensive mathematical modeling

This work presents major results from a novel dynamic model intended to deterministically represent the complex relation between HIV-1 and the human immune system. The novel structure of the model extends previous work by representing different host anatomic compartments under a more in-depth cellular and molecular immunological phenomenology. Recently identified mechanisms related to HIV-1 infection as well as other well known relevant mechanisms typically ignored in mathematical models of HIV-1 pathogenesis and immunology, such as cell-cell transmission, are also addressed. (C) 2011 Elsevier Ltd. All rights reserved.

Centrifuge Modeling of Sandy Slopes

Slope failure occurs in many areas throughout the world and it becomes an important problem when it interferes with human activity, in which disasters provoke loss of life and property damage. In this research we investigate the slope failure through the centrifuge modeling, where a reduced-scale model, N times smaller than the full-scale (prototype), is used whereas the acceleration is increased by N times (compared with the gravity acceleration) to preserve the stress and the strain behavior. The aims of this research “Centrifuge modeling of sandy slopes” are in extreme synthesis: 1) test the reliability of the centrifuge modeling as a tool to investigate the behavior of a sandy slope failure; 2) understand how the failure mechanism is affected by changing the slope angle and obtain useful information for the design. In order to achieve this scope we arranged the work as follows: Chapter one: centrifuge modeling of slope failure. In this chapter we provide a general view about the context in which we are working on. Basically we explain what is a slope failure, how it happens and which are the tools available to investigate this phenomenon. Afterwards we introduce the technology used to study this topic, that is the geotechnical centrifuge. Chapter two: testing apparatus. In the first section of this chapter we describe all the procedures and facilities used to perform a test in the centrifuge. Then we explain the characteristics of the soil (Nevada sand), like the dry unit weight, water content, relative density, and its strength parameters (c,φ), which have been calculated in laboratory through the triaxial test. Chapter three: centrifuge tests. In this part of the document are presented all the results from the tests done in centrifuge. When we talk about results we refer to the acceleration at failure for each model tested and its failure surface. In our case study we tested models with the same soil and geometric characteristics but different angles. The angles tested in this research were: 60°, 75° and 90°. Chapter four: slope stability analysis. We introduce the features and the concept of the software: ReSSA (2.0). This software allows us to calculate the theoretical failure surfaces of the prototypes. Then we show in this section the comparisons between the experimental failure surfaces of the prototype, traced in the laboratory, and the one calculated by the software. Chapter five: conclusion. The conclusion of the research presents the results obtained in relation to the two main aims, mentioned above.

Interactions between normative systems and software cognitive agents. A formalization in temporal modal defeasible logic and its implementation

Sustainable computer systems require some flexibility to adapt to environmental unpredictable changes. A solution lies in autonomous software agents which can adapt autonomously to their environments. Though autonomy allows agents to decide which behavior to adopt, a disadvantage is a lack of control, and as a side effect even untrustworthiness: we want to keep some control over such autonomous agents. How to control autonomous agents while respecting their autonomy? A solution is to regulate agents’ behavior by norms. The normative paradigm makes it possible to control autonomous agents while respecting their autonomy, limiting untrustworthiness and augmenting system compliance. It can also facilitate the design of the system, for example, by regulating the coordination among agents. However, an autonomous agent will follow norms or violate them in some conditions. What are the conditions in which a norm is binding upon an agent? While autonomy is regarded as the driving force behind the normative paradigm, cognitive agents provide a basis for modeling the bindingness of norms. In order to cope with the complexity of the modeling of cognitive agents and normative bindingness, we adopt an intentional stance. Since agents are embedded into a dynamic environment, things may not pass at the same instant. Accordingly, our cognitive model is extended to account for some temporal aspects. Special attention is given to the temporal peculiarities of the legal domain such as, among others, the time in force and the time in efficacy of provisions. Some types of normative modifications are also discussed in the framework. It is noteworthy that our temporal account of legal reasoning is integrated to our commonsense temporal account of cognition. As our intention is to build sustainable reasoning systems running unpredictable environment, we adopt a declarative representation of knowledge. A declarative representation of norms will make it easier to update their system representation, thus facilitating system maintenance; and to improve system transparency, thus easing system governance. Since agents are bounded and are embedded into unpredictable environments, and since conflicts may appear amongst mental states and norms, agent reasoning has to be defeasible, i.e. new pieces of information can invalidate formerly derivable conclusions. In this dissertation, our model is formalized into a non-monotonic logic, namely into a temporal modal defeasible logic, in order to account for the interactions between normative systems and software cognitive agents.

Characterization and modeling of the barrier properties in nanostructured systems

The object of the present study is the process of gas transport in nano-sized materials, i.e. systems having structural elements of the order of nanometers. The aim of this work is to advance the understanding of the gas transport mechanism in such materials, for which traditional models are not often suitable, by providing a correct interpretation of the relationship between diffusive phenomena and structural features. This result would allow the development new materials with permeation properties tailored on the specific application, especially in packaging systems. The methods used to achieve this goal were a detailed experimental characterization and different simulation methods. The experimental campaign regarded the determination of oxygen permeability and diffusivity in different sets of organic-inorganic hybrid coatings prepared via sol-gel technique. The polymeric samples coated with these hybrid layers experienced a remarkable enhancement of the barrier properties, which was explained by the strong interconnection at the nano-scale between the organic moiety and silica domains. An analogous characterization was performed on microfibrillated cellulose films, which presented remarkable barrier effect toward oxygen when it is dry, while in the presence of water the performance significantly drops. The very low value of water diffusivity at low activities is also an interesting characteristic which deals with its structural properties. Two different approaches of simulation were then considered: the diffusion of oxygen through polymer-layered silicates was modeled on a continuum scale with a CFD software, while the properties of n-alkanthiolate self assembled monolayers on gold were analyzed from a molecular point of view by means of a molecular dynamics algorithm. Modeling transport properties in layered nanocomposites, resulting from the ordered dispersion of impermeable flakes in a 2-D matrix, allowed the calculation of the enhancement of barrier effect in relation with platelets structural parameters leading to derive a new expression. On this basis, randomly distributed systems were simulated and the results were analyzed to evaluate the different contributions to the overall effect. The study of more realistic three-dimensional geometries revealed a prefect correspondence with the 2-D approximation. A completely different approach was applied to simulate the effect of temperature on the oxygen transport through self assembled monolayers; the structural information obtained from equilibrium MD simulations showed that raising the temperature, makes the monolayer less ordered and consequently less crystalline. This disorder produces a decrease in the barrier free energy and it lowers the overall resistance to oxygen diffusion, making the monolayer more permeable to small molecules.

Parallel modeling of the electric field distribution in the brain

The term "Brain Imaging" identi�es a set of techniques to analyze the structure and/or functional behavior of the brain in normal and/or pathological situations. These techniques are largely used in the study of brain activity. In addition to clinical usage, analysis of brain activity is gaining popularity in others recent �fields, i.e. Brain Computer Interfaces (BCI) and the study of cognitive processes. In this context, usage of classical solutions (e.g. f MRI, PET-CT) could be unfeasible, due to their low temporal resolution, high cost and limited portability. For these reasons alternative low cost techniques are object of research, typically based on simple recording hardware and on intensive data elaboration process. Typical examples are ElectroEncephaloGraphy (EEG) and Electrical Impedance Tomography (EIT), where electric potential at the patient's scalp is recorded by high impedance electrodes. In EEG potentials are directly generated from neuronal activity, while in EIT by the injection of small currents at the scalp. To retrieve meaningful insights on brain activity from measurements, EIT and EEG relies on detailed knowledge of the underlying electrical properties of the body. This is obtained from numerical models of the electric �field distribution therein. The inhomogeneous and anisotropic electric properties of human tissues make accurate modeling and simulation very challenging, leading to a tradeo�ff between physical accuracy and technical feasibility, which currently severely limits the capabilities of these techniques. Moreover elaboration of data recorded requires usage of regularization techniques computationally intensive, which influences the application with heavy temporal constraints (such as BCI). This work focuses on the parallel implementation of a work-flow for EEG and EIT data processing. The resulting software is accelerated using multi-core GPUs, in order to provide solution in reasonable times and address requirements of real-time BCI systems, without over-simplifying the complexity and accuracy of the head models.

Towards model driven software development for Arduino platforms: a DSL and automatic code generation

La tesi ha lo scopo di esplorare la produzione di sistemi software per Embedded Systems mediante l'utilizzo di tecniche relative al mondo del Model Driven Software Development. La fase più importante dello sviluppo sarà la definizione di un Meta-Modello che caratterizza i concetti fondamentali relativi agli embedded systems. Tale modello cercherà di astrarre dalla particolare piattaforma utilizzata ed individuare quali astrazioni caratterizzano il mondo degli embedded systems in generale. Tale meta-modello sarà quindi di tipo platform-independent. Per la generazione automatica di codice è stata adottata una piattaforma di riferimento, cioè Arduino. Arduino è un sistema embedded che si sta sempre più affermando perché coniuga un buon livello di performance ed un prezzo relativamente basso. Tale piattaforma permette lo sviluppo di sistemi special purpose che utilizzano sensori ed attuatori di vario genere, facilmente connessi ai pin messi a disposizione. Il meta-modello definito è un'istanza del meta-metamodello MOF, definito formalmente dall'organizzazione OMG. Questo permette allo sviluppatore di pensare ad un sistema sotto forma di modello, istanza del meta-modello definito. Un meta-modello può essere considerato anche come la sintassi astratta di un linguaggio, quindi può essere definito da un insieme di regole EBNF. La tecnologia utilizzata per la definizione del meta-modello è stata Xtext: un framework che permette la scrittura di regole EBNF e che genera automaticamente il modello Ecore associato al meta-modello definito. Ecore è l'implementazione di EMOF in ambiente Eclipse. Xtext genera inoltre dei plugin che permettono di avere un editor guidato dalla sintassi, definita nel meta-modello. La generazione automatica di codice è stata realizzata usando il linguaggio Xtend2. Tale linguaggio permette di esplorare l'Abstract Syntax Tree generato dalla traduzione del modello in Ecore e di generare tutti i file di codice necessari. Il codice generato fornisce praticamente tutta la schematic part dell'applicazione, mentre lascia all'application designer lo sviluppo della business logic. Dopo la definizione del meta-modello di un sistema embedded, il livello di astrazione è stato spostato più in alto, andando verso la definizione della parte di meta-modello relativa all'interazione di un sistema embedded con altri sistemi. Ci si è quindi spostati verso un ottica di Sistema, inteso come insieme di sistemi concentrati che interagiscono. Tale difinizione viene fatta dal punto di vista del sistema concentrato di cui si sta definendo il modello. Nella tesi viene inoltre introdotto un caso di studio che, anche se abbastanza semplice, fornisce un esempio ed un tutorial allo sviluppo di applicazioni mediante l'uso del meta-modello. Ci permette inoltre di notare come il compito dell'application designer diventi piuttosto semplice ed immediato, sempre se basato su una buona analisi del problema. I risultati ottenuti sono stati di buona qualità ed il meta-modello viene tradotto in codice che funziona correttamente.

CFD modeling of two-phase boiling flows in the slug flow regime with an interface capturing technique

The objective of this thesis was to improve the commercial CFD software Ansys Fluent to obtain a tool able to perform accurate simulations of flow boiling in the slug flow regime. The achievement of a reliable numerical framework allows a better understanding of the bubble and flow dynamics induced by the evaporation and makes possible the prediction of the wall heat transfer trends. In order to save computational time, the flow is modeled with an axisymmetrical formulation. Vapor and liquid phases are treated as incompressible and in laminar flow. By means of a single fluid approach, the flow equations are written as for a single phase flow, but discontinuities at the interface and interfacial effects need to be accounted for and discretized properly. Ansys Fluent provides a Volume Of Fluid technique to advect the interface and to map the discontinuous fluid properties throughout the flow domain. The interfacial effects are dominant in the boiling slug flow and the accuracy of their estimation is fundamental for the reliability of the solver. Self-implemented functions, developed ad-hoc, are introduced within the numerical code to compute the surface tension force and the rates of mass and energy exchange at the interface related to the evaporation. Several validation benchmarks assess the better performances of the improved software. Various adiabatic configurations are simulated in order to test the capability of the numerical framework in modeling actual flows and the comparison with experimental results is very positive. The simulation of a single evaporating bubble underlines the dominant effect on the global heat transfer rate of the local transient heat convection in the liquid after the bubble transit. The simulation of multiple evaporating bubbles flowing in sequence shows that their mutual influence can strongly enhance the heat transfer coefficient, up to twice the single phase flow value.

Structure-Property Relationships and Charge Transport Modeling of Organic Molecular Materials

From the perspective of a new-generation opto-electronic technology based on organic semiconductors, a major objective is to achieve a deep and detailed knowledge of the structure-property relationships, in order to optimize the electronic, optical, and charge transport properties by tuning the chemical-physical characteristics of the compounds. The purpose of this dissertation is to contribute to such understanding, through suitable theoretical and computational studies. Precisely, the structural, electronic, optical, and charge transport characteristics of several promising organic materials recently synthesized are investigated by means of an integrated approach encompassing quantum-chemical calculations, molecular dynamics and kinetic Monte Carlo simulations. Particular care is addressed to the rationalization of optical and charge transport properties in terms of both intra- and intermolecular features. Moreover, a considerable part of this project involves the development of a home-made set of procedures and parts of software code required to assist the modeling of charge transport properties in the framework of the non-adiabatic hopping mechanism applied to organic crystalline materials. As a first part of my investigations, I mainly discuss the optical, electronic, and structural properties of several core-extended rylene derivatives, which can be regarded to as model compounds for graphene nanoribbons. Two families have been studied, consisting in bay-linked perylene bisimide oligomers and N-annulated rylenes. Beside rylene derivatives, my studies also concerned electronic and spectroscopic properties of tetracene diimides, quinoidal oligothiophenes, and oxygen doped picene. As an example of device application, I studied the structural characteristics governing the efficiency of resistive molecular memories based on a derivative of benzoquinone. Finally, as a second part of my investigations, I concentrate on the charge transport properties of perylene bisimides derivatives. Precisely, a comprehensive study of the structural and thermal effects on the charge transport of several core-twisted chlorinated and fluoro-alkylated perylene bisimide n-type semiconductors is presented.

Numerical optimization,modeling and system evaluation of a thermophotovoltaic hybrid panel

Photovoltaic (PV) solar panels generally produce electricity in the 6% to 16% efficiency range, the rest being dissipated in thermal losses. To recover this amount, hybrid photovoltaic thermal systems (PVT) have been devised. These are devices that simultaneously convert solar energy into electricity and heat. It is thus interesting to study the PVT system globally from different point of views in order to evaluate advantages and disadvantages of this technology and its possible uses. In particular in Chapter II, the development of the PVT absorber numerical optimization by a genetic algorithm has been carried out analyzing different internal channel profiles in order to find a right compromise between performance and technical and economical feasibility. Therefore in Chapter III ,thanks to a mobile structure built into the university lab, it has been compared experimentally electrical and thermal output power from PVT panels with separated photovoltaic and solar thermal productions. Collecting a lot of experimental data based on different seasonal conditions (ambient temperature,irradiation, wind...),the aim of this mobile structure has been to evaluate average both thermal and electrical increasing and decreasing efficiency values obtained respect to separate productions through the year. In Chapter IV , new PVT and solar thermal equation based models in steady state conditions have been developed by software Dymola that uses Modelica language. This permits ,in a simplified way respect to previous system modelling softwares, to model and evaluate different concepts about PVT panel regarding its structure before prototyping and measuring it. Chapter V concerns instead the definition of PVT boundary conditions into a HVAC system . This was made trough year simulations by software Polysun in order to finally assess the best solar assisted integrated structure thanks to F_save(solar saving energy)factor. Finally, Chapter VI presents the conclusion and the perspectives of this PhD work.

Modeling the spatial dynamics of economic models

The advances that have been characterizing spatial econometrics in recent years are mostly theoretical and have not found an extensive empirical application yet. In this work we aim at supplying a review of the main tools of spatial econometrics and to show an empirical application for one of the most recently introduced estimators. Despite the numerous alternatives that the econometric theory provides for the treatment of spatial (and spatiotemporal) data, empirical analyses are still limited by the lack of availability of the correspondent routines in statistical and econometric software. Spatiotemporal modeling represents one of the most recent developments in spatial econometric theory and the finite sample properties of the estimators that have been proposed are currently being tested in the literature. We provide a comparison between some estimators (a quasi-maximum likelihood, QML, estimator and some GMM-type estimators) for a fixed effects dynamic panel data model under certain conditions, by means of a Monte Carlo simulation analysis. We focus on different settings, which are characterized either by fully stable or quasi-unit root series. We also investigate the extent of the bias that is caused by a non-spatial estimation of a model when the data are characterized by different degrees of spatial dependence. Finally, we provide an empirical application of a QML estimator for a time-space dynamic model which includes a temporal, a spatial and a spatiotemporal lag of the dependent variable. This is done by choosing a relevant and prolific field of analysis, in which spatial econometrics has only found limited space so far, in order to explore the value-added of considering the spatial dimension of the data. In particular, we study the determinants of cropland value in Midwestern U.S.A. in the years 1971-2009, by taking the present value model (PVM) as the theoretical framework of analysis.

Shape memory and elastoplastic materials: from constitutive and numerical to fatigue modeling

Shape memory materials (SMMs) represent an important class of smart materials that have the ability to return from a deformed state to their original shape. Thanks to such a property, SMMs are utilized in a wide range of innovative applications. The increasing number of applications and the consequent involvement of industrial players in the field have motivated researchers to formulate constitutive models able to catch the complex behavior of these materials and to develop robust computational tools for design purposes. Such a research field is still under progress, especially in the prediction of shape memory polymer (SMP) behavior and of important effects characterizing shape memory alloy (SMA) applications. Moreover, the frequent use of shape memory and metallic materials in biomedical devices, particularly in cardiovascular stents, implanted in the human body and experiencing millions of in-vivo cycles by the blood pressure, clearly indicates the need for a deeper understanding of fatigue/fracture failure in microsize components. The development of reliable stent designs against fatigue is still an open subject in scientific literature. Motivated by the described framework, the thesis focuses on several research issues involving the advanced constitutive, numerical and fatigue modeling of elastoplastic and shape memory materials. Starting from the constitutive modeling, the thesis proposes to develop refined phenomenological models for reliable SMA and SMP behavior descriptions. Then, concerning the numerical modeling, the thesis proposes to implement the models into numerical software by developing implicit/explicit time-integration algorithms, to guarantee robust computational tools for practical purposes. The described modeling activities are completed by experimental investigations on SMA actuator springs and polyethylene polymers. Finally, regarding the fatigue modeling, the thesis proposes the introduction of a general computational approach for the fatigue-life assessment of a classical stent design, in order to exploit computer-based simulations to prevent failures and modify design, without testing numerous devices.

Monitoring the extracellular matrix mineralization processes in biological scaffolds using bioreactors, x-ray μct technology and 3-d modeling methods (monitoraggio dei processi di mineralizzazione della matrice extracellulare in scaffolds biologici, utilizzando bioreattore, tecnologia μct a raggi x e metodi di modellizzazione 3d)

Al fine di migliorare le tecniche di coltura cellulare in vitro, sistemi a bioreattore sono sempre maggiormente utilizzati, e.g. ingegnerizzazione del tessuto osseo. Spinner Flasks, bioreattori rotanti e sistemi a perfusione di flusso sono oggi utilizzati e ogni sistema ha vantaggi e svantaggi. Questo lavoro descrive lo sviluppo di un semplice bioreattore a perfusione ed i risultati della metodologia di valutazione impiegata, basata su analisi μCT a raggi-X e tecniche di modellizzazione 3D. Un semplice bioreattore con generatore di flusso ad elica è stato progettato e costruito con l'obiettivo di migliorare la differenziazione di cellule staminali mesenchimali, provenienti da embrioni umani (HES-MP); le cellule sono state seminate su scaffold porosi di titanio che garantiscono una migliore adesione della matrice mineralizzata. Attraverso un microcontrollore e un'interfaccia grafica, il bioreattore genera tre tipi di flusso: in avanti (senso orario), indietro (senso antiorario) e una modalità a impulsi (avanti e indietro). Un semplice modello è stato realizzato per stimare la pressione generata dal flusso negli scaffolds (3•10-2 Pa). Sono stati comparati tre scaffolds in coltura statica e tre all’interno del bioreattore. Questi sono stati incubati per 21 giorni, fissati in paraformaldehyde (4% w/v) e sono stati soggetti ad acquisizione attraverso μCT a raggi-X. Le immagini ottenute sono state poi elaborate mediante un software di imaging 3D; è stato effettuato un sezionamento “virtuale” degli scaffolds, al fine di ottenere la distribuzione del gradiente dei valori di grigio di campioni estratti dalla superficie e dall’interno di essi. Tale distribuzione serve per distinguere le varie componenti presenti nelle immagini; in questo caso gli scaffolds dall’ipotetica matrice cellulare. I risultati mostrano che sia sulla superficie che internamente agli scaffolds, mantenuti nel bioreattore, è presente una maggiore densità dei gradienti dei valori di grigio ciò suggerisce un migliore deposito della matrice mineralizzata. Gli insegnamenti provenienti dalla realizzazione di questo bioreattore saranno utilizzati per progettare una nuova versione che renderà possibile l’analisi di più di 20 scaffolds contemporaneamente, permettendo un’ulteriore analisi della qualità della differenziazione usando metodologie molecolari ed istochimiche.