Development of computer application for determination of chemical diffusion properties in biological tissues

The main objective of this work was to develop an application capable of determining the diffusion times and diffusion coefficients of optical clearing agents and water inside a known type of muscle. Different types of chemical agents can also be used with the method implemented, such as medications or metabolic products. Since the diffusion times can be calculated, it is possible to describe the dehydration mechanism that occurs in the muscle. The calculation of the diffusion time of an optical clearing agent allows to characterize the refractive index matching mechanism of optical clearing. By using both the diffusion times and diffusion of water and clearing agents not only the optical clearing mechanisms are characterized, but also information about optical clearing effect duration and magnitude is obtained. Such information is crucial to plan a clinical intervention in cooperation with optical clearing. The experimental method and equations implemented in the developed application are described in throughout this document, demonstrating its effectiveness. The application was developed in MATLAB code, but the method was personalized so it better fits the application needs. This process significantly improved the processing efficiency, reduced the time to obtain he results, multiple validations prevents common errors and some extra functionalities were added such as saving application progress or export information in different formats. Tests were made using glucose measurements in muscle. Some of the data, for testing purposes, was also intentionally changed in order to obtain different simulations and results from the application. The entire project was validated by comparing the calculated results with the ones found in literature, which are also described in this document.

SIMULATIONS OF NEWTONIAN AND NON-NEWTONIAN FLOWS IN DEFORMABLE TUBES

Computational models for the investigation of flows in deformable tubes are developed and implemented in the open source computing environment OpenFOAM. Various simulations for Newtonian and non-Newtonian fluids under various flow conditions are carried out and analyzed. First, simulations are performed to investigate the flow of a shear-thinning, non-Newtonian fluid in a collapsed elastic tube and comparisons are made with experimental data. The fluid is modeled by means of the Bird-Carreau viscosity law. The computational domain of the deformed tube is constructed from data obtained via computer tomography imaging. Comparison of the computed velocity fields with the ultrasound Doppler velocity profile measurements show good agreement, as does the adjusted pressure drop along the tube's axis. Analysis of the shear rates show that the shear-thinning effect of the fluid becomes relevant in the cross-sections with the biggest deformation. The peristaltic motion is simulated by means of upper and lower rollers squeezing the fluid along a tube. Two frames of reference are considered. In the moving frame the computational domain is fixed and the coordinate system is moving with the roller speed, and in the fixed frame the roller is represented by a deforming mesh. Several two-dimensional simulations are carried out for Newtonian and non-Newtonian fluids. The effect of the shear-thinning behavior of the fluid on the transport efficiency is examined. In addition, the influence of the roller speed and the gap width between the rollers on the xxvii transport efficiency is discussed. Comparison with experimental data is also presented and different types of moving waves are implemented. In addition, the influence of the roller speed and the gap width between the rollers on the transport efficiency is discussed. Comparison with experimental data is also presented and different types of moving waves are implemented.

Development of a Computer-Based methodology for tolerance selection and optimization applied to the automotive sector

The design optimization of industrial products has always been an essential activity to improve product quality while reducing time-to-market and production costs. Although cost management is very complex and comprises all phases of the product life cycle, the control of geometrical and dimensional variations, known as Dimensional Management (DM), allows compliance with product and process requirements. Hence, the tolerance-cost optimization becomes the main practice to provide an effective application of Design for Tolerancing (DfT) and Design to Cost (DtC) approaches by enabling a connection between product tolerances and associated manufacturing costs. However, despite the growing interest in this topic, a profitable application in the industry of these techniques is hampered by their complexity: the definition of a systematic framework is the key element to improving design optimization, enhancing the concurrent use of Computer-Aided tools and Model-Based Definition (MBD) practices. The present doctorate research aims to define and develop an integrated methodology for product/process design optimization, to better exploit the new capabilities of advanced simulations and tools. By implementing predictive models and multi-disciplinary optimization, a Computer-Aided Integrated framework for tolerance-cost optimization has been proposed to allow the integration of DfT and DtC approaches and their direct application for the design of automotive components. Several case studies have been considered, with the final application of the integrated framework on a high-performance V12 engine assembly, to achieve both functional targets and cost reduction. From a scientific point of view, the proposed methodology provides an improvement for the tolerance-cost optimization of industrial components. The integration of theoretical approaches and Computer-Aided tools allows to analyse the influence of tolerances on both product performance and manufacturing costs. The case studies proved the suitability of the methodology for its application in the industrial field, providing the identification of further areas for improvement and refinement.

Development and application of a computer-based methodology for design for additive manufacturing of automotive components

The research project aims to improve the Design for Additive Manufacturing of metal components. Firstly, the scenario of Additive Manufacturing is depicted, describing its role in Industry 4.0 and in particular focusing on Metal Additive Manufacturing technologies and the Automotive sector applications. Secondly, the state of the art in Design for Additive Manufacturing is described, contextualizing the methodologies, and classifying guidelines, rules, and approaches. The key phases of product design and process design to achieve lightweight functional designs and reliable processes are deepened together with the Computer-Aided Technologies to support the approaches implementation. Therefore, a general Design for Additive Manufacturing workflow based on product and process optimization has been systematically defined. From the analysis of the state of the art, the use of a holistic approach has been considered fundamental and thus the use of integrated product-process design platforms has been evaluated as a key element for its development. Indeed, a computer-based methodology exploiting integrated tools and numerical simulations to drive the product and process optimization has been proposed. A validation of CAD platform-based approaches has been performed, as well as potentials offered by integrated tools have been evaluated. Concerning product optimization, systematic approaches to integrate topology optimization in the design have been proposed and validated through product optimization of an automotive case study. Concerning process optimization, the use of process simulation techniques to prevent manufacturing flaws related to the high thermal gradients of metal processes is developed, providing case studies to validate results compared to experimental data, and application to process optimization of an automotive case study. Finally, an example of the product and process design through the proposed simulation-driven integrated approach is provided to prove the method's suitability for effective redesigns of Additive Manufacturing based high-performance metal products. The results are then outlined, and further developments are discussed.

Modelling, simulations and monitoring for sustainable plant and animal production systems through precision technique

Protected crop production is a modern and innovative approach to cultivating plants in a controlled environment to optimize growth, yield, and quality. This method involves using structures such as greenhouses or tunnels to create a sheltered environment. These productive solutions are characterized by a careful regulation of variables like temperature, humidity, light, and ventilation, which collectively contribute to creating an optimal microclimate for plant growth. Heating, cooling, and ventilation systems are used to maintain optimal conditions for plant growth, regardless of external weather fluctuations. Protected crop production plays a crucial role in addressing challenges posed by climate variability, population growth, and food security. Similarly, animal husbandry involves providing adequate nutrition, housing, medical care and environmental conditions to ensure animal welfare. Then, sustainability is a critical consideration in all forms of agriculture, including protected crop and animal production. Sustainability in animal production refers to the practice of producing animal products in a way that minimizes negative impacts on the environment, promotes animal welfare, and ensures the long-term viability of the industry. Then, the research activities performed during the PhD can be inserted exactly in the field of Precision Agriculture and Livestock farming. Here the focus is on the computational fluid dynamic (CFD) approach and environmental assessment applied to improve yield, resource efficiency, environmental sustainability, and cost savings. It represents a significant shift from traditional farming methods to a more technology-driven, data-driven, and environmentally conscious approach to crop and animal production. On one side, CFD is powerful and precise techniques of computer modeling and simulation of airflows and thermo-hygrometric parameters, that has been applied to optimize the growth environment of crops and the efficiency of ventilation in pig barns. On the other side, the sustainability aspect has been investigated and researched in terms of Life Cycle Assessment analyses.

On The Consistency Of Monte Carlo Track Structure Dna Damage Simulations.

Monte Carlo track structures (MCTS) simulations have been recognized as useful tools for radiobiological modeling. However, the authors noticed several issues regarding the consistency of reported data. Therefore, in this work, they analyze the impact of various user defined parameters on simulated direct DNA damage yields. In addition, they draw attention to discrepancies in published literature in DNA strand break (SB) yields and selected methodologies. The MCTS code Geant4-DNA was used to compare radial dose profiles in a nanometer-scale region of interest (ROI) for photon sources of varying sizes and energies. Then, electron tracks of 0.28 keV-220 keV were superimposed on a geometric DNA model composed of 2.7 × 10(6) nucleosomes, and SBs were simulated according to four definitions based on energy deposits or energy transfers in DNA strand targets compared to a threshold energy ETH. The SB frequencies and complexities in nucleosomes as a function of incident electron energies were obtained. SBs were classified into higher order clusters such as single and double strand breaks (SSBs and DSBs) based on inter-SB distances and on the number of affected strands. Comparisons of different nonuniform dose distributions lacking charged particle equilibrium may lead to erroneous conclusions regarding the effect of energy on relative biological effectiveness. The energy transfer-based SB definitions give similar SB yields as the one based on energy deposit when ETH ≈ 10.79 eV, but deviate significantly for higher ETH values. Between 30 and 40 nucleosomes/Gy show at least one SB in the ROI. The number of nucleosomes that present a complex damage pattern of more than 2 SBs and the degree of complexity of the damage in these nucleosomes diminish as the incident electron energy increases. DNA damage classification into SSB and DSB is highly dependent on the definitions of these higher order structures and their implementations. The authors' show that, for the four studied models, different yields are expected by up to 54% for SSBs and by up to 32% for DSBs, as a function of the incident electrons energy and of the models being compared. MCTS simulations allow to compare direct DNA damage types and complexities induced by ionizing radiation. However, simulation results depend to a large degree on user-defined parameters, definitions, and algorithms such as: DNA model, dose distribution, SB definition, and the DNA damage clustering algorithm. These interdependencies should be well controlled during the simulations and explicitly reported when comparing results to experiments or calculations.

Finite-element Analysis Of 3 Situations Of Trauma In The Human Edentulous Mandible.

Maxillofacial trauma resulting from falls in elderly patients is a major social and health care concern. Most of these traumatic events involve mandibular fractures. The aim of this study was to analyze stress distributions from traumatic loads applied on the symphyseal, parasymphyseal, and mandibular body regions in the elderly edentulous mandible using finite-element analysis (FEA). Computerized tomographic analysis of an edentulous macerated human mandible of a patient approximately 65 years old was performed. The bone structure was converted into a 3-dimensional stereolithographic model, which was used to construct the computer-aided design (CAD) geometry for FEA. The mechanical properties of cortical and cancellous bone were characterized as isotropic and elastic structures, respectively, in the CAD model. The condyles were constrained to prevent free movement in the x-, y-, and z-axes during simulation. This enabled the simulation to include the presence of masticatory muscles during trauma. Three different simulations were performed. Loads of 700 N were applied perpendicular to the surface of the cortical bone in the symphyseal, parasymphyseal, and mandibular body regions. The simulation results were evaluated according to equivalent von Mises stress distributions. Traumatic load at the symphyseal region generated low stress levels in the mental region and high stress levels in the mandibular neck. Traumatic load at the parasymphyseal region concentrated the resulting stress close to the mental foramen. Traumatic load in the mandibular body generated extensive stress in the mandibular body, angle, and ramus. FEA enabled precise mapping of the stress distribution in a human elderly edentulous mandible (neck and mandibular angle) in response to 3 different traumatic load conditions. This knowledge can help guide emergency responders as they evaluate patients after a traumatic event.

Modelo dinâmico de simulação e otimização da força normal de reação do solo para um mecanismo de corte basal

The physical model was based on the method of Newton-Euler. The model was developed by using the scientific computer program Mathematica®. Several simulations where tried varying the progress speeds (0.69; 1.12; 1.48; 1.82 and 2.12 m s-1); soil profiles (sinoidal, ascending and descending ramp) and height of the profile (0.025 and 0.05 m) to obtain the normal force of soil reaction. After the initial simulations, the mechanism was optimized using the scientific computer program Matlab® having as criterion (function-objective) the minimization of the normal force of reaction of the profile (FN). The project variables were the lengths of the bars (L1y, L2, l3 and L4), height of the operation (L7), the initial length of the spring (Lmo) and the elastic constant of the spring (k t). The lack of robustness of the mechanism in relation to the variable height of the operation was outlined by using a spring with low rigidity and large length. The results demonstrated that the mechanism optimized showed better flotation performance in relation to the initial mechanism.

An Eulerian Immersed Boundary Method for flow simulations over stationary and moving rigid bodies

The fluid flow over bodies with complex geometry has been the subject of research of many scientists and widely explored experimentally and numerically. The present study proposes an Eulerian Immersed Boundary Method for flows simulations over stationary or moving rigid bodies. The proposed method allows the use of Cartesians Meshes. Here, two-dimensional simulations of fluid flow over stationary and oscillating circular cylinders were used for verification and validation. Four different cases were explored: the flow over a stationary cylinder, the flow over a cylinder oscillating in the flow direction, the flow over a cylinder oscillating in the normal flow direction, and a cylinder with angular oscillation. The time integration was carried out by a classical 4th order Runge-Kutta scheme, with a time step of the same order of distance between two consecutive points in x direction. High-order compact finite difference schemes were used to calculate spatial derivatives. The drag and lift coefficients, the lock-in phenomenon and vorticity contour plots were used for the verification and validation of the proposed method. The extension of the current method allowing the study of a body with different geometry and three-dimensional simulations is straightforward. The results obtained show a good agreement with both numerical and experimental results, encouraging the use of the proposed method.

Turbulence in collisionless plasmas: statistical analysis from numerical simulations with pressure anisotropy

In recent years, we have experienced increasing interest in the understanding of the physical properties of collisionless plasmas, mostly because of the large number of astrophysical environments (e. g. the intracluster medium (ICM)) containing magnetic fields that are strong enough to be coupled with the ionized gas and characterized by densities sufficiently low to prevent the pressure isotropization with respect to the magnetic line direction. Under these conditions, a new class of kinetic instabilities arises, such as firehose and mirror instabilities, which have been studied extensively in the literature. Their role in the turbulence evolution and cascade process in the presence of pressure anisotropy, however, is still unclear. In this work, we present the first statistical analysis of turbulence in collisionless plasmas using three-dimensional numerical simulations and solving double-isothermal magnetohydrodynamic equations with the Chew-Goldberger-Low laws closure (CGL-MHD). We study models with different initial conditions to account for the firehose and mirror instabilities and to obtain different turbulent regimes. We found that the CGL-MHD subsonic and supersonic turbulences show small differences compared to the MHD models in most cases. However, in the regimes of strong kinetic instabilities, the statistics, i.e. the probability distribution functions (PDFs) of density and velocity, are very different. In subsonic models, the instabilities cause an increase in the dispersion of density, while the dispersion of velocity is increased by a large factor in some cases. Moreover, the spectra of density and velocity show increased power at small scales explained by the high growth rate of the instabilities. Finally, we calculated the structure functions of velocity and density fluctuations in the local reference frame defined by the direction of magnetic lines. The results indicate that in some cases the instabilities significantly increase the anisotropy of fluctuations. These results, even though preliminary and restricted to very specific conditions, show that the physical properties of turbulence in collisionless plasmas, as those found in the ICM, may be very different from what has been largely believed.

Architecture for machining process and production monitoring based in open computer numerical control

This paper proposes an architecture for machining process and production monitoring to be applied in machine tools with open Computer numerical control (CNC). A brief description of the advantages of using open CNC for machining process and production monitoring is presented with an emphasis on the CNC architecture using a personal computer (PC)-based human-machine interface. The proposed architecture uses the CNC data and sensors to gather information about the machining process and production. It allows the development of different levels of monitoring systems with mininium investment, minimum need for sensor installation, and low intrusiveness to the process. Successful examples of the utilization of this architecture in a laboratory environment are briefly described. As a Conclusion, it is shown that a wide range of monitoring solutions can be implemented in production processes using the proposed architecture.

Dynamical models for computer viruses propagation

Nowadays, digital computer systems and networks are the main engineering tools, being used in planning, design, operation, and control of all sizes of building, transportation, machinery, business, and life maintaining devices. Consequently, computer viruses became one of the most important sources of uncertainty, contributing to decrease the reliability of vital activities. A lot of antivirus programs have been developed, but they are limited to detecting and removing infections, based on previous knowledge of the virus code. In spite of having good adaptation capability, these programs work just as vaccines against diseases and are not able to prevent new infections based on the network state. Here, a trial on modeling computer viruses propagation dynamics relates it to other notable events occurring in the network permitting to establish preventive policies in the network management. Data from three different viruses are collected in the Internet and two different identification techniques, autoregressive and Fourier analyses, are applied showing that it is possible to forecast the dynamics of a new virus propagation by using the data collected from other viruses that formerly infected the network. Copyright (c) 2008 J. R. C. Piqueira and F. B. Cesar. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

PRECESSING JETS AND X-RAY BUBBLES FROM NGC 1275 (3C 84) IN THE PERSEUS GALAXY CLUSTER: A VIEW FROM THREE-DIMENSIONAL NUMERICAL SIMULATIONS

The Perseus galaxy cluster is known to present multiple and misaligned pairs of cavities seen in X-rays, as well as twisted kiloparsec-scale jets at radio wavelengths; both morphologies suggest that the active galactic nucleus (AGN) jet is subject to precession. In this work, we performed three-dimensional hydrodynamical simulations of the interaction between a precessing AGN jet and the warm intracluster medium plasma, whose dynamics are coupled to a Navarro-Frenk-White dark matter gravitational potential. The AGN jet inflates cavities that become buoyantly unstable and rise up out of the cluster core. We found that under certain circumstances precession can originate multiple pairs of bubbles. For the physical conditions in the Perseus cluster, multiple pairs of bubbles are obtained for a jet precession opening angle >40 degrees acting for at least three precession periods, reproducing both radio and X-ray maps well. Based on such conditions, assuming that the Bardeen-Peterson effect is dominant, we studied the evolution of the precession opening angle of this system. We were able to constrain the ratio between the accretion disk and the black hole angular momenta as 0.7-1.4. We were also able to constrain the present precession angle to 30 degrees-40 degrees, as well as the approximate age of the inflated bubbles to 100-150 Myr.

The merging cluster Abell 1758 revisited: multi-wavelength observations and numerical simulations

Context. Cluster properties can be more distinctly studied in pairs of clusters, where we expect the effects of interactions to be strong. Aims. We here discuss the properties of the double cluster Abell 1758 at a redshift z similar to 0.279. These clusters show strong evidence for merging. Methods. We analyse the optical properties of the North and South cluster of Abell 1758 based on deep imaging obtained with the Canada-France-Hawaii Telescope (CFHT) archive Megaprime/Megacam camera in the g' and r' bands, covering a total region of about 1.05 x 1.16 deg(2), or 16.1 x 17.6 Mpc(2). Our X-ray analysis is based on archive XMM-Newton images. Numerical simulations were performed using an N-body algorithm to treat the dark-matter component, a semi-analytical galaxy-formation model for the evolution of the galaxies and a grid-based hydrodynamic code with a parts per million (PPM) scheme for the dynamics of the intra-cluster medium. We computed galaxy luminosity functions (GLFs) and 2D temperature and metallicity maps of the X-ray gas, which we then compared to the results of our numerical simulations. Results. The GLFs of Abell 1758 North are well fit by Schechter functions in the g' and r' bands, but with a small excess of bright galaxies, particularly in the r' band; their faint-end slopes are similar in both bands. In contrast, the GLFs of Abell 1758 South are not well fit by Schechter functions: excesses of bright galaxies are seen in both bands; the faint-end of the GLF is not very well defined in g'. The GLF computed from our numerical simulations assuming a halo mass-luminosity relation agrees with those derived from the observations. From the X-ray analysis, the most striking features are structures in the metal distribution. We found two elongated regions of high metallicity in Abell 1758 North with two peaks towards the centre. In contrast, Abell 1758 South shows a deficit of metals in its central regions. Comparing observational results to those derived from numerical simulations, we could mimic the most prominent features present in the metallicity map and propose an explanation for the dynamical history of the cluster. We found in particular that in the metal-rich elongated regions of the North cluster, winds had been more efficient than ram-pressure stripping in transporting metal-enriched gas to the outskirts. Conclusions. We confirm the merging structure of the North and South clusters, both at optical and X-ray wavelengths.