Are We Sims? How Computer Simulations Represent and What this Means for the Simulation Argument

N. Bostrom’s simulation argument and two additional assumptions imply that we are likely to live in a computer simulation. The argument is based upon the following assumption about the workings of realistic brain simulations: The hardware of a computer on which a brain simulation is run bears a close analogy to the brain itself. To inquire whether this is so, I analyze how computer simulations trace processes in their targets. I describe simulations as fictional, mathematical, pictorial, and material models. Even though the computer hardware does provide a material model of the target, this does not suffice to underwrite the simulation argument because the ways in which parts of the computer hardware interact during simulations do not resemble the ways in which neurons interact in the brain. Further, there are computer simulations of all kinds of systems, and it would be unreasonable to infer that some computers display consciousness just because they simulate brains rather than, say, galaxies.

Uso de DES y RANS no estacionario para la simulación del flujo alrededor de una carena Wigley - Use of Unsteady RANS and DES to simulate flows around a Wigley Hull)

Computer Fluid Dynamics tools have already become a valuable instrument for Naval Architects during the ship design process, thanks to their accuracy and the available computer power. Unfortunately, the development of RANSE codes, generally used when viscous effects play a major role in the flow, has not reached a mature stage, being the accuracy of the turbulence models and the free surface representation the most important sources of uncertainty. Another level of uncertainty is added when the simulations are carried out for unsteady flows, as those generally studied in seakeeping and maneuvering analysis and URANS equations solvers are used. Present work shows the applicability and the benefits derived from the use of new approaches for the turbulence modeling (Detached Eddy Simulation) and the free surface representation (Level Set) on the URANS equations solver CFDSHIP-Iowa. Compared to URANS, DES is expected to predict much broader frequency contents and behave better in flows where boundary layer separation plays a major role. Level Set methods are able to capture very complex free surface geometries, including breaking and overturning waves. The performance of these improvements is tested in set of fairly complex flows, generated by a Wigley hull at pure drift motion, with drift angle ranging from 10 to 60 degrees and at several Froude numbers to study the impact of its variation. Quantitative verification and validation are performed with the obtained results to guarantee their accuracy. The results show the capability of the CFDSHIP-Iowa code to carry out time-accurate simulations of complex flows of extreme unsteady ship maneuvers. The Level Set method is able to capture very complex geometries of the free surface and the use of DES in unsteady simulations highly improves the results obtained. Vortical structures and instabilities as a function of the drift angle and Fr are qualitatively identified. Overall analysis of the flow pattern shows a strong correlation between the vortical structures and free surface wave pattern. Karman-like vortex shedding is identified and the scaled St agrees well with the universal St value. Tip vortices are identified and the associated helical instabilities are analyzed. St using the hull length decreases with the increase of the distance along the vortex core (x), which is similar to results from other simulations. However, St scaled using distance along the vortex cores shows strong oscillations compared to almost constants for those previous simulations. The difference may be caused by the effect of the free-surface, grid resolution, and interaction between the tip vortex and other vortical structures, which needs further investigations. This study is exploratory in the sense that finer grids are desirable and experimental data is lacking for large α, especially for the local flow. More recently, high performance computational capability of CFDSHIP-Iowa V4 has been improved such that large scale computations are possible. DES for DTMB 5415 with bilge keels at α = 20º were conducted using three grids with 10M, 48M and 250M points. DES analysis for flows around KVLCC2 at α = 30º is analyzed using a 13M grid and compared with the results of DES on the 1.6M grid by. Both studies are consistent with what was concluded on grid resolution herein since dominant frequencies for shear-layer, Karman-like, horse-shoe and helical instabilities only show marginal variation on grid refinement. The penalties of using coarse grids are smaller frequency amplitude and less resolved TKE. Therefore finer grids should be used to improve V&V for resolving most of the active turbulent scales for all different Fr and α, which hopefully can be compared with additional EFD data for large α when it becomes available.

El microclima urbano en los espacios abiertos : estudio de casos en Madrid

El microclima urbano juega un rol importante en el consumo energético de los edificios y en las sensaciones de confort en los espacios exteriores. La urgente necesidad de aumentar la eficiencia energética, reducir las emisiones de los contaminantes y paliar la evidente falta de sostenibilidad que afecta a las ciudades, ha puesto la atención en el urbanismo bioclimático como referente para una propuesta de cambio en la forma de diseñar y vivir la ciudad. Hasta ahora las investigaciones en temas de microclima y eficiencia energética se han concentrado principalmente en como orientar el diseño de nuevos desarrollo. Sin embargo los principales problemas de la insostenibilidad de las actuales conurbaciones son el resultado del modelo de crecimiento especulativo y altamente agotador de recursos que han caracterizado el boom inmobiliario de las últimas décadas. Vemos entonces, tanto en España como en el resto de los Países Europeos, la necesidad de reorientar el sector de la construcción hacía la rehabilitación del espacio construido, como una alternativa capaz de dar una solución más sostenible para el mercado inmobiliario. En este propósito de mejorar la calidad de las ciudades actuales, el espacio público juega un papel fundamental, sobre todo como lugar para el encuentro y la socialización entre los ciudadanos. La sensación térmica condiciona la percepción de un ambiente, así que el microclima puede ser determinante para el éxito o el fracaso de un espacio urbano. Se plantea entonces cómo principal objetivo de la investigación, la definición de estrategias para el diseño bioclimático de los entornos urbanos construidos, fundamentados en las componentes morfotipológica, climática y de los requerimientos de confort para los ciudadanos. Como ulterior elemento de novedad se decide estudiar la rehabilitación de los barrios de construcción de mediado del siglo XX, que en muchos casos constituyen bolsas de degrado en la extendida periferia de las ciudades modernas. La metodología empleada para la investigación se basa en la evaluación de las condiciones climáticas y de confort térmico de diferentes escenarios de proyecto, aplicados a tres casos de estudio situados en un barrio periurbano de la ciudad de Madrid. Para la determinación de los parámetros climáticos se han empleado valores obtenidos con un proceso de simulación computarizada, basados en los principios de fluidodinámica, termodinámica y del intercambio radioactivo en el espacio construido. A través de uso de programas de simulación podemos hacer una previsión de las condiciones microclimáticas de las situaciones actuales y de los efectos de la aplicación de medidas. La gran ventaja en el uso de sistemas de cálculo es que se pueden evaluar diferentes escenarios de proyecto y elegir entre ellos el que asegura mejores prestaciones ambientales. Los resultados obtenidos en los diferentes escenarios han sido comparados con los valores de confort del estado actual, utilizando como indicador de la sensación térmica el índice UTCI. El análisis comparativo ha permitido la realización de una tabla de resumen donde se muestra la evaluación de las diferentes soluciones de rehabilitación. Se ha podido así demostrar que no existe una solución constructiva eficaz para todas las aplicaciones, sino que cada situación debe ser estudiada individualmente, aplicando caso por caso las medidas más oportunas. Si bien los sistemas de simulación computarizada pueden suponer un importante apoyo para la fase de diseño, es responsabilidad del proyectista emplear las herramientas más adecuadas en cada fase y elegir las soluciones más oportunas para cumplir con los objetivos del proyecto. The urban microclimate plays an important role on buildings energy consumption and comfort sensation in exterior spaces. Nowadays, cities need to increase energy efficiency, reduce the pollutants emissions and mitigate the evident lack of sustainability. In reason of this, attention has focused on the bioclimatic urbanism as a reference of change proposal of the way to design and live the city. Hitherto, the researches on microclimate and energy efficiency have mainly concentrated on guiding the design of new constructions. However the main problems of unsustainability of existing conurbations are the result of the growth model highly speculative and responsible of resources depletion that have characterized the real estate boom of recent decades. In Spain and other European countries, become define the need to redirect the construction sector towards urban refurbishment. This alternative is a more sustainable development model and is able to provide a solution for the real estate sector. In order to improve the quality of today's cities, the public space plays a key role, especially in order to provide to citizens places for meeting and socializing. The thermal sensation affects the environment perception, so microclimate conditions can be decisive for the success or failure of urban space. For this reasons, the main objective of this work is focused on the definition of bioclimatic strategies for existing urban spaces, based on the morpho-typological components, climate and comfort requirements for citizens. As novelty element, the regeneration of neighborhoods built in middle of the twentieth century has been studied, because are the major extended in periphery of modern cities and, in many cases, they represent deprived areas. The research methodology is based on the evaluation of climatic conditions and thermal comfort of different project scenarios, applied to three case studies located in a suburban neighborhood of Madrid. The climatic parameters have been obtained by computer simulation process, based on fluid dynamics, thermodynamics and radioactive exchange in urban environment using numerical approach. The great advantage in the use of computing systems is the capacity for evaluate different project scenarios. The results in the different scenarios were compared with the comfort value obtained in the current state, using the UTCI index as indicator of thermal sensation. Finally, an abacus of the thermal comfort improvement obtained by different countermeasures has been performed. One of the major achievement of doctoral work is the demonstration of there are not any design solution suitable for different cases. Each situation should be analyzed and specific design measures should be proposed. Computer simulation systems can be a significant support and help the designer in the decision making phase. However, the election of the most suitable tools and the appropriate solutions for each case is designer responsibility.

A molecular dynamics study of swift heavy ion irradiation of amorphous silica: the role of thermal effects

Irradiation with swift heavy ions (SHI), roughly defined as those having atomic masses larger than 15 and energies exceeding 1 MeV/amu, may lead to significant modification of the irradiated material in a nanometric region around the (straight) ion trajectory (latent tracks). In the case of amorphous silica, SHI irradiation originates nano-tracks of higher density than the virgin material (densification). As a result, the refractive index is increased with respect to that of the surroundings. Moreover, track overlapping leads to continuous amorphous layers that present a significant contrast with respect to the pristine substrate. We have recently demonstrated that SHI irradiation produces a large number of point defects, easily detectable by a number of experimental techniques (work presented in the parallel conference ICDIM). The mechanisms of energy transfer from SHI to the target material have their origin in the high electronic excitation induced in the solid. A number of phenomenological approaches have been employed to describe these mechanisms: coulomb explosion, thermal spike, non-radiative exciton decay, bond weakening. However, a detailed microscopic description is missing due to the difficulty of modeling the time evolution of the electronic excitation. In this work we have employed molecular dynamics (MD) calculations to determine whether the irradiation effects are related to the thermal phenomena described by MD (in the ps domain) or to electronic phenomena (sub-ps domain), e.g., exciton localization. We have carried out simulations of up to 100 ps with large boxes (30x30x8 nm3) using a home-modified version of MDCASK that allows us to define a central hot cylinder (ion track) from which heat flows to the surrounding cold bath (unirradiated sample). We observed that once the cylinder has cooled down, the Si and O coordination numbers are 4 and 2, respectively, as in virgin silica. On the other hand, the density of the (cold) cylinder increases with respect to that of silica and, furthermore, the silica network ring size decreases. Both effects are in agreement with the observed densification. In conclusion, purely thermal effects do not explain the generation of point defects upon irradiation, but they do account for the silica densification.

Simulating the remote handling of the blanket segments in DEMO fusion reactor with thermo-mechanical meshfree multibody dynamics

The present study shows a first approach to the simulation of the remote handling oper- ation which takes into account the thermal and flexible behavior of the blanket segments and its implications on the remote handling equipment, in order to validate and improve its design.

Numerical simulation of a synthetic jet with OpenFoam

Numerical simulations of flow surrounding a synthetic jet actuating device are presented. By modifying a dynamic mesh technique available in OpenFoam-a well-documented open-source solver for fluid dynamics, detailed computations of the sinusoidal motion of the synthetic jet diaphragm were possible. Numerical solutions were obtained by solving the two dimensional incompressible viscous N-S equations, with the use of a second order implicit time marching scheme and a central finite volume method for spatial discretization in both streamwise and crossflow directions. A systematic parametric study is reported here, in which the external Reynolds number, the diaphragm amplitude and frequency, and the slot dimensions are varied.

NURBS-Based Geometry Parameterization for Aerodynamic Shape Optimization

La motivación de esta tesis es el desarrollo de una herramienta de optimización automática para la mejora del rendimiento de formas aerodinámicas enfocado en la industria aeronáutica. Este trabajo cubre varios aspectos esenciales, desde el empleo de Non-Uniform Rational B-Splines (NURBS), al cálculo de gradientes utilizando la metodología del adjunto continuo, el uso de b-splines volumétricas como parámetros de diseño, el tratamiento de la malla en las intersecciones, y no menos importante, la adaptación de los algoritmos de la dinámica de fluidos computacional (CFD) en arquitecturas hardware de alto paralelismo, como las tarjetas gráficas, para acelerar el proceso de optimización. La metodología adjunta ha posibilitado que los métodos de optimización basados en gradientes sean una alternativa prometedora para la mejora de la eficiencia aerodinámica de los aviones. La formulación del adjunto permite calcular los gradientes de una función de coste, como la resistencia aerodinámica o la sustentación, independientemente del número de variables de diseño, a un coste computacional equivalente a una simulación CFD. Sin embargo, existen problemas prácticos que han imposibilitado su aplicación en la industria, que se pueden resumir en: integrabilidad, rendimiento computacional y robustez de la solución adjunta. Este trabajo aborda estas contrariedades y las analiza en casos prácticos. Como resumen, las contribuciones de esta tesis son: • El uso de NURBS como variables de diseño en un bucle de automático de optimización, aplicado a la mejora del rendimiento aerodinámico de alas en régimen transónico. • El desarrollo de algoritmos de inversión de punto, para calcular las coordenadas paramétricas de las coordenadas espaciales, para ligar los vértices de malla a las NURBS. • El uso y validación de la formulación adjunta para el calculo de los gradientes, a partir de las sensibilidades de la solución adjunta, comparado con diferencias finitas. • Se ofrece una estrategia para utilizar la geometría CAD, en forma de parches NURBS, para tratar las intersecciones, como el ala-fuselaje. • No existen muchas alternativas de librerías NURBS viables. En este trabajo se ha desarrollado una librería, DOMINO NURBS, y se ofrece a la comunidad como código libre y abierto. • También se ha implementado un código CFD en tarjeta gráfica, para realizar una valoración de cómo se puede adaptar un código sobre malla no estructurada a arquitecturas paralelas. • Finalmente, se propone una metodología, basada en la función de Green, como una forma eficiente de paralelizar simulaciones numéricas. Esta tesis ha sido apoyada por las actividades realizadas por el Área de Dinámica da Fluidos del Instituto Nacional de Técnica Aeroespacial (INTA), a través de numerosos proyectos de financiación nacional: DOMINO, SIMUMAT, y CORESFMULAERO. También ha estado en consonancia con las actividades realizadas por el departamento de Métodos y Herramientas de Airbus España y con el grupo Investigación y Tecnología Aeronáutica Europeo (GARTEUR), AG/52. ABSTRACT The motivation of this work is the development of an automatic optimization strategy for large scale shape optimization problems that arise in the aeronautics industry to improve the aerodynamic performance; covering several aspects from the use of Non-Uniform Rational B-Splines (NURBS), the calculation of the gradients with the continuous adjoint formulation, the development of volumetric b-splines parameterization, mesh adaptation and intersection handling, to the adaptation of Computational Fluid Dynamics (CFD) algorithms to take advantage of highly parallel architectures in order to speed up the optimization process. With the development of the adjoint formulation, gradient-based methods for aerodynamic optimization become a promising approach to improve the aerodynamic performance of aircraft designs. The adjoint methodology allows the evaluation the gradients to all design variables of a cost function, such as drag or lift, at the equivalent cost of more or less one CFD simulation. However, some practical problems have been delaying its full implementation to the industry, which can be summarized as: integrability, computer performance, and adjoint robustness. This work tackles some of these issues and analyse them in well-known test cases. As summary, the contributions comprises: • The employment of NURBS as design variables in an automatic optimization loop for the improvement of the aerodynamic performance of aircraft wings in transonic regimen. • The development of point inversion algorithms to calculate the NURBS parametric coordinates from the space coordinates, to link with the computational grid vertex. • The use and validation of the adjoint formulation to calculate the gradients from the surface sensitivities in an automatic optimization loop and evaluate its reliability, compared with finite differences. • This work proposes some algorithms that take advantage of the underlying CAD geometry description, in the form of NURBS patches, to handle intersections and mesh adaptations. • There are not many usable libraries for NURBS available. In this work an open source library DOMINO NURBS has been developed and is offered to the community as free, open source code. • The implementation of a transonic CFD solver from scratch in a graphic card, for an assessment of the implementability of conventional CFD solvers for unstructured grids to highly parallel architectures. • Finally, this research proposes the use of the Green's function as an efficient paralellization scheme of numerical solvers. The presented work has been supported by the activities carried out at the Fluid Dynamics branch of the National Institute for Aerospace Technology (INTA) through national founding research projects: DOMINO, SIMUMAT, and CORESIMULAERO; in line with the activities carried out by the Methods and Tools and Flight Physics department at Airbus and the Group for Aeronautical Research and Technology in Europe (GARTEUR) action group AG/52.

Brownian dynamics simulations of protein folding: Access to milliseconds time scale and beyond

Protein folding occurs on a time scale ranging from milliseconds to minutes for a majority of proteins. Computer simulation of protein folding, from a random configuration to the native structure, is nontrivial owing to the large disparity between the simulation and folding time scales. As an effort to overcome this limitation, simple models with idealized protein subdomains, e.g., the diffusion–collision model of Karplus and Weaver, have gained some popularity. We present here new results for the folding of a four-helix bundle within the framework of the diffusion–collision model. Even with such simplifying assumptions, a direct application of standard Brownian dynamics methods would consume 10,000 processor-years on current supercomputers. We circumvent this difficulty by invoking a special Brownian dynamics simulation. The method features the calculation of the mean passage time of an event from the flux overpopulation method and the sampling of events that lead to productive collisions even if their probability is extremely small (because of large free-energy barriers that separate them from the higher probability events). Using these developments, we demonstrate that a coarse-grained model of the four-helix bundle can be simulated in several days on current supercomputers. Furthermore, such simulations yield folding times that are in the range of time scales observed in experiments.

Large vortex-like structure of dipole field in computer models of liquid water and dipole-bridge between biomolecules

We propose a framework to describe the cooperative orientational motions of water molecules in liquid water and around solute molecules in water solutions. From molecular dynamics (MD) simulation a new quantity “site-dipole field” is defined as the averaged orientation of water molecules that pass through each spatial position. In the site-dipole field of bulk water we found large vortex-like structures of more than 10 Å in size. Such coherent patterns persist more than 300 ps although the orientational memory of individual molecules is quickly lost. A 1-ns MD simulation of systems consisting of two amino acids shows that the fluctuations of site-dipole field of solvent are pinned around the amino acids, resulting in a stable dipole-bridge between side-chains of amino acids. The dipole-bridge is significantly formed even for the side-chain separation of 14 Å, which corresponds to five layers of water. The way that dipole-bridge forms sensitively depends on the side-chain orientations and thereby explains the specificity in the solvent-mediated interactions between biomolecules.

Simulation analysis of a network computer,

Bibliography: p. 43.

In-flight simulation, theory and application,

"To be presented to the Fluid Dynamics Panel of the Advisory Group for Aeronautical Research and Development of the North Atlantic Treaty Organization, 10 April through 17 April 1961."

Molecular dynamics simulation of the structural and dynamic properties of dioctadecyldimethyl ammoniums in organoclays

The structural and dynamic properties of dioctadecyldimethylammoniums (DODDMA) intercalated into 2:1 layered clays are investigated using isothermal-isobaric (NPT) molecular dynamics (MD) simulation. The simulated results are in reasonably good agreement with the available experimental measurements, such as X-ray diffraction (XRD), atom force microscopy (AFM), Fourier transform infrared (FTIR), and nuclear magnetic resonance (NMR) spectroscopies. The nitrogen atoms are found to be located mainly within two layers close to the clay surface whereas methylene groups form a pseudoquadrilayer structure. The results of tilt angle and order parameter show that interior two-bond segments of alkyl chains prefer an arrangement parallel to the clay surface, whereas the segments toward end groups adopt a random orientation. In addition, the alkyl chains within the layer structure lie almost parallel to the clay surface whereas those out of the layer structure are essentially perpendicular to the surface. The trans conformations are predominant in all cases although extensive gauche conformations are observed, which is in agreement with previous simulations on n-butane. Moreover, an odd-even effect in conformation distributions is observed mainly along the chains close to the head and tail groups. The diffusion constants of both nitrogen atoms and methylene groups in these nanoconfined alkyl chains increase with the temperature and methelene position toward the tail groups.

Numerical simulation of magnetite segregation in a dense medium cyclone

Numerical simulations of turbulent driven flow in a dense medium cyclone with magnetite medium have been conducted using Fluent. The predicted air core shape and diameter were found to be close to the experimental results measured by gamma ray tomography. It is possible that the Large eddy simulation (LES) turbulence model with Mixture multi-phase model can be used to predict the air/slurry interface accurately although the LES may need a finer grid. Multi-phase simulations (air/water/medium) are showing appropriate medium segregation effects but are over-predicting the level of segregation compared to that measured by gamma-ray tomography in particular with over prediction of medium concentrations near the wall. Further, investigated the accurate prediction of axial segregation of magnetite using the LES turbulence model together with the multi-phase mixture model and viscosity corrections according to the feed particle loading factor. Addition of lift forces and viscosity correction improved the predictions especially near the wall. Predicted density profiles are very close to gamma ray tomography data showing a clear density drop near the wall. The effect of size distribution of the magnetite has been fully studied. It is interesting to note that the ultra-fine magnetite sizes (i.e. 2 and 7 mu m) are distributed uniformly throughout the cyclone. As the size of magnetite increases, more segregation of magnetite occurs close to the wall. The cut-density (d(50)) of the magnetite segregation is 32 gm, which is expected with superfine magnetite feed size distribution. At higher feed densities the agreement between the [Dungilson, 1999; Wood, J.C., 1990. A performance model for coal-washing dense medium cyclones, Ph.D. Thesis, JKMRC, University of Queensland] correlations and the CFD are reasonably good, but the overflow density is lower than the model predictions. It is believed that the excessive underflow volumetric flow rates are responsible for under prediction of the overflow density. (c) 2006 Elsevier Ltd. All rights reserved.

Effect of adsorption deformation on thermodynamic characteristics of a fluid in slit pores at sub-critical conditions

Solvation. pressure due to adsorption of fluids in porous materials is the cause of elastic deformation of an adsorbent, which is accessible to direct experimental measurements. Such a deformation contributes to the Helmholtz free energy of the whole adsorbent-adsorbate system due to accumulation of compression or tension energy by the solid. It means that in the general case the solid has to be considered as not solely a source of the external potential field for the fluid confined in the pore volume, but also as thermodynamically nonmert component of the solid-fluid system. We present analysis of nitrogen adsorption isotherms and heat of adsorption in slit graphitic pores accounting for the adsorption deformation by means of nonlocal density functional theory. (c) 2006 Elsevier Ltd. All rights reserved.

The effect of pH on PAMAM dendrimer-siRNA complexation:endosomal considerations as determined by molecular dynamics simulation

Intracellular degradation of genes, most notably within the endo-lysosomal compartment is considered a significant barrier to (non-viral) gene delivery in vivo. Previous reports based on in vitro studies claim that carriers possessing a mixture of primary, secondary and tertiary amines are able to buffer the acidic environment within the endosome, allowing for timely release of their contents, leading to higher transfection rates. In this report, we adopt an atomistic molecular dynamics (MD) simulation approach, comparing the complexation of 21-bp siRNA with low-generation polyamidoamine (PAMAM) dendrimers (G0 and G1) at both neutral and acidic pHs, the latter of which mimics the degradative environment within maturing 'late-endosomes'. Our simulations reveal that the time taken for the dendrimer-gene complex (dendriplex) to reach equilibrium is appreciably longer at low pH and this is accompanied by more compact packaging of the dendriplex, as compared to simulations performed at neutral pH. We also note larger absolute values of calculated binding free energies of the dendriplex at low pH, indicating a higher dendrimer-nucleic acid affinity in comparison with neutral pH. These novel simulations provide a more detailed understanding of low molecular-weight polymer-siRNA behavior, mimicking the endosomal environment and provide input of direct relevance to the "proton sponge theory", thereby advancing the rational design of non-viral gene delivery systems.