Sensitivity of AMPA receptor channel to calcium oscillations: A computational study

We used a computational model of biochemical pathways that are involved in the phosphorylation/dephosphorylation of AMPA receptor to study the receptor responses to calcium oscillations. In the model, the biochemical pathways are assumed to be located immediately under the postsynaptic membrane and we included three states of AMPA receptor: dephosphorylated, and phosphorylated in one or in two sites. To characterize the effects of calcium oscillations on the AMPA receptor, we exposed the model to stimuli with three varying parameters, namely frequency, number of pulses and calcium spike duration. Our model showed sensitivity to all of these three parameters. © 2002 Elsevier Science B.V. All rights reserved.

Simulation of computational grids scheduling politics

Computational grids allow users to share resources of distributed machines, even if those machines belong to different corporations. The scheduling of applications must be performed aiming at performance goals, and focusing on choose which processes can have access to specif resources, and which resources. In this article we discuss aspects of scheduling of application in grid computing environment. We also present a tool for scheduling simulation along with test scenarios and results.

Methodology analysis of a computational tool used in electronic circuit design

This paper considers the importance of using a top-down methodology and suitable CAD tools in the development of electronic circuits. The paper presents an evaluation of the methodology used in a computational tool created to support the synthesis of digital to analog converter models by translating between different tools used in a wide variety of applications. This tool is named MS 2SV and works directly with the following two commercial tools: MATLAB/Simulink and SystemVision. Model translation of an electronic circuit is achieved by translating a mixed-signal block diagram developed in Simulink into a lower level of abstraction in VHDL-AMS and the simulation project support structure in SystemVision. The method validation was performed by analyzing the power spectral of the signal obtained by the discrete Fourier transform of a digital to analog converter simulation model. © 2011 IEEE.

Fractional order and dynamic simulation of a system involving an elastic wide plate

Numerous researchers have studied about nonlinear dynamics in several areas of science and engineering. However, in most cases, these concepts have been explored mainly from the standpoint of analytical and computational methods involving integer order calculus (IOC). In this paper we have examined the dynamic behavior of an elastic wide plate induced by two electromagnets of a point of view of the fractional order calculus (FOC). The primary focus of this study is on to help gain a better understanding of nonlinear dynamic in fractional order systems. © 2011 American Institute of Physics.

Entropy effect in quantum computing and information: an open-source environment simulation

The technologies are rapidly developing, but some of them present in the computers, as for instance their processing capacity, are reaching their physical limits. It is up to quantum computation offer solutions to these limitations and issues that may arise. In the field of information security, encryption is of paramount importance, being then the development of quantum methods instead of the classics, given the computational power offered by quantum computing. In the quantum world, the physical states are interrelated, thus occurring phenomenon called entanglement. This study presents both a theoretical essay on the merits of quantum mechanics, computing, information, cryptography and quantum entropy, and some simulations, implementing in C language the effects of entropy of entanglement of photons in a data transmission, using Von Neumann entropy and Tsallis entropy.

Computational tools for comparing asymmetric GARCH models via Bayes factors

In this paper we use Markov chain Monte Carlo (MCMC) methods in order to estimate and compare GARCH models from a Bayesian perspective. We allow for possibly heavy tailed and asymmetric distributions in the error term. We use a general method proposed in the literature to introduce skewness into a continuous unimodal and symmetric distribution. For each model we compute an approximation to the marginal likelihood, based on the MCMC output. From these approximations we compute Bayes factors and posterior model probabilities. (C) 2012 IMACS. Published by Elsevier B.V. All rights reserved.

Analysis of energy dissipation in stirred suspension polymerisation reactors using computational fluid dynamics

This work evaluates the spatial distribution of normalised rates of droplet breakage and droplet coalescence in liquidliquid dispersions maintained in agitated tanks at operation conditions normally used to perform suspension polymerisation reactions. Particularly, simulations are performed with multiphase computational fluid dynamics (CFD) models to represent the flow field in liquidliquid styrene suspension polymerisation reactors for the first time. CFD tools are used first to compute the spatial distribution of the turbulent energy dissipation rates (e) inside the reaction vessel; afterwards, normalised rates of droplet breakage and particle coalescence are computed as functions of e. Surprisingly, multiphase simulations showed that the rates of energy dissipation can be very high near the free vortex surfaces, which has been completely neglected in previous works. The obtained results indicate the existence of extremely large energy dissipation gradients inside the vessel, so that particle breakage occurs primarily in very small regions that surround the impeller and the free vortex surface, while particle coalescence takes place in the liquid bulk. As a consequence, particle breakage should be regarded as an independent source term or a boundary phenomenon. Based on the obtained results, it can be very difficult to justify the use of isotropic assumptions to formulate particle population balances in similar systems, even when multiple compartment models are used to describe the fluid dynamic behaviour of the agitated vessel. (C) 2011 Canadian Society for Chemical Engineering

Advanced Numerical Simulation of Silicon-Based Solar Cells

Photovoltaic (PV) conversion is the direct production of electrical energy from sun without involving the emission of polluting substances. In order to be competitive with other energy sources, cost of the PV technology must be reduced ensuring adequate conversion efficiencies. These goals have motivated the interest of researchers in investigating advanced designs of crystalline silicon solar (c-Si) cells. Since lowering the cost of PV devices involves the reduction of the volume of semiconductor, an effective light trapping strategy aimed at increasing the photon absorption is required. Modeling of solar cells by electro-optical numerical simulation is helpful to predict the performance of future generations devices exhibiting advanced light-trapping schemes and to provide new and more specific guidelines to industry. The approaches to optical simulation commonly adopted for c-Si solar cells may lead to inaccurate results in case of thin film and nano-stuctured solar cells. On the other hand, rigorous solvers of Maxwell equations are really cpu- and memory-intensive. Recently, in optical simulation of solar cells, the RCWA method has gained relevance, providing a good trade-off between accuracy and computational resources requirement. This thesis is a contribution to the numerical simulation of advanced silicon solar cells by means of a state-of-the-art numerical 2-D/3-D device simulator, that has been successfully applied to the simulation of selective emitter and the rear point contact solar cells, for which the multi-dimensionality of the transport model is required in order to properly account for all physical competing mechanisms. In the second part of the thesis, the optical problems is discussed. Two novel and computationally efficient RCWA implementations for 2-D simulation domains as well as a third RCWA for 3-D structures based on an eigenvalues calculation approach have been presented. The proposed simulators have been validated in terms of accuracy, numerical convergence, computation time and correctness of results.

Cyclotron production of 11^C: experimental assessment of saturation yield and validation with Monte Carlo simulation

Nell'ambito della Fisica Medica, le simulazioni Monte Carlo sono uno strumento sempre più diffuso grazie alla potenza di calcolo dei moderni calcolatori, sia nell'ambito diagnostico sia in terapia. Attualmente sono disponibili numerosi pacchetti di simulazione Monte Carlo di carattere "general purpose", tra cui Geant4. Questo lavoro di tesi, svolto presso il Servizio di Fisica Sanitaria del Policlinico "S.Orsola-Malpighi", è basato sulla realizzazione, utilizzando Geant4, di un modello Monte Carlo del target del ciclotrone GE-PETtrace per la produzione di C-11. Nel modello sono stati simulati i principali elementi caratterizzanti il target ed il fascio di protoni accelerato dal ciclotrone. Per la validazione del modello sono stati valutati diversi parametri fisici, tra i quali il range medio dei protoni nell'azoto ad alta pressione e la posizione del picco di Bragg, confrontando i risultati con quelli forniti da SRIM. La resa a saturazione relativa alla produzione di C-11 è stata confrontata sia con i valori forniti dal database della IAEA sia con i dati sperimentali a nostra disposizione. Il modello è stato anche utilizzato per la stima di alcuni parametri di interesse, legati, in particolare, al deterioramento dell'efficienza del target nel corso del tempo. L'inclinazione del target, rispetto alla direzione del fascio di protoni accelerati, è influenzata dal peso del corpo del target stesso e dalla posizione in cui questo é fissato al ciclotrone. Per questo sono stati misurati sia il calo della resa della produzione di C-11, sia la percentuale di energia depositata dal fascio sulla superficie interna del target durante l'irraggiamento, al variare dell'angolo di inclinazione del target. Il modello che abbiamo sviluppato rappresenta, dunque, un importante strumento per la valutazione dei processi che avvengono durante l'irraggiamento, per la stima delle performance del target nel corso del tempo e per lo sviluppo di nuovi modelli di target.

Computational simulations of latent heat thermal energy storage systems - with innovative and first-principles based simulation for the underlying unsteady melting (and solidification) processes

This thesis develops an effective modeling and simulation procedure for a specific thermal energy storage system commonly used and recommended for various applications (such as an auxiliary energy storage system for solar heating based Rankine cycle power plant). This thermal energy storage system transfers heat from a hot fluid (termed as heat transfer fluid - HTF) flowing in a tube to the surrounding phase change material (PCM). Through unsteady melting or freezing process, the PCM absorbs or releases thermal energy in the form of latent heat. Both scientific and engineering information is obtained by the proposed first-principle based modeling and simulation procedure. On the scientific side, the approach accurately tracks the moving melt-front (modeled as a sharp liquid-solid interface) and provides all necessary information about the time-varying heat-flow rates, temperature profiles, stored thermal energy, etc. On the engineering side, the proposed approach is unique in its ability to accurately solve – both individually and collectively – all the conjugate unsteady heat transfer problems for each of the components of the thermal storage system. This yields critical system level information on the various time-varying effectiveness and efficiency parameters for the thermal storage system.

Flow disturbances in stent-related coronary evaginations: a computational fluid-dynamic simulation study

Aims: Angiographic ectasias and aneurysms in stented segments have been associated with late stent thrombosis. Using optical coherence tomography (OCT), some stented segments show coronary evaginations reminiscent of ectasias. The purpose of this study was to explore, using computational fluid-dynamic (CFD) simulations, whether OCT-detected coronary evaginations can induce local changes in blood flow. Methods and results: OCT-detected evaginations are defined as outward bulges in the luminal vessel contour between struts, with the depth of the bulge exceeding the actual strut thickness. Evaginations can be characterised cross ectionally by depth and along the stented segment by total length. Assuming an ellipsoid shape, we modelled 3-D evaginations with different sizes by varying the depth from 0.2-1.0 mm, and the length from 1-9 mm. For the flow simulation we used average flow velocity data from non-diseased coronary arteries. The change in flow with varying evagination sizes was assessed using a particle tracing test where the particle transit time within the segment with evagination was compared with that of a control vessel. The presence of the evagination caused a delayed particle transit time which increased with the evagination size. The change in flow consisted locally of recirculation within the evagination, as well as flow deceleration due to a larger lumen - seen as a deflection of flow towards the evagination. Conclusions: CFD simulation of 3-D evaginations and blood flow suggests that evaginations affect flow locally, with a flow disturbance that increases with increasing evagination size.

Comparison of turbulence models for the computational fluid dynamics simulation of wind turbine wakes in the atmospheric boundary layer

An elliptic computational fluid dynamics wake model based on the actuator disk concept is used to simulate a wind turbine, approximated by a disk upon which a distribution of forces, defined as axial momentum sources, is applied on an incoming non-uniform shear flow. The rotor is supposed to be uniformly loaded with the exerted forces estimated as a function of the incident wind speed, thrust coefficient and rotor diameter. The model is assessed in terms of wind speed deficit and added turbulence intensity for different turbulence models and is validated from experimental measurements of the Sexbierum wind turbine experiment.

Co-simulation Methodologies for Hybrid and Electric Vehicle Dynamics

In recent decades, full electric and hybrid electric vehicles have emerged as an alternative to conventional cars due to a range of factors, including environmental and economic aspects. These vehicles are the result of considerable efforts to seek ways of reducing the use of fossil fuel for vehicle propulsion. Sophisticated technologies such as hybrid and electric powertrains require careful study and optimization. Mathematical models play a key role at this point. Currently, many advanced mathematical analysis tools, as well as computer applications have been built for vehicle simulation purposes. Given the great interest of hybrid and electric powertrains, along with the increasing importance of reliable computer-based models, the author decided to integrate both aspects in the research purpose of this work. Furthermore, this is one of the first final degree projects held at the ETSII (Higher Technical School of Industrial Engineers) that covers the study of hybrid and electric propulsion systems. The present project is based on MBS3D 2.0, a specialized software for the dynamic simulation of multibody systems developed at the UPM Institute of Automobile Research (INSIA). Automobiles are a clear example of complex multibody systems, which are present in nearly every field of engineering. The work presented here benefits from the availability of MBS3D software. This program has proven to be a very efficient tool, with a highly developed underlying mathematical formulation. On this basis, the focus of this project is the extension of MBS3D features in order to be able to perform dynamic simulations of hybrid and electric vehicle models. This requires the joint simulation of the mechanical model of the vehicle, together with the model of the hybrid or electric powertrain. These sub-models belong to completely different physical domains. In fact the powertrain consists of energy storage systems, electrical machines and power electronics, connected to purely mechanical components (wheels, suspension, transmission, clutch…). The challenge today is to create a global vehicle model that is valid for computer simulation. Therefore, the main goal of this project is to apply co-simulation methodologies to a comprehensive model of an electric vehicle, where sub-models from different areas of engineering are coupled. The created electric vehicle (EV) model consists of a separately excited DC electric motor, a Li-ion battery pack, a DC/DC chopper converter and a multibody vehicle model. Co-simulation techniques allow car designers to simulate complex vehicle architectures and behaviors, which are usually difficult to implement in a real environment due to safety and/or economic reasons. In addition, multi-domain computational models help to detect the effects of different driving patterns and parameters and improve the models in a fast and effective way. Automotive designers can greatly benefit from a multidisciplinary approach of new hybrid and electric vehicles. In this case, the global electric vehicle model includes an electrical subsystem and a mechanical subsystem. The electrical subsystem consists of three basic components: electric motor, battery pack and power converter. A modular representation is used for building the dynamic model of the vehicle drivetrain. This means that every component of the drivetrain (submodule) is modeled separately and has its own general dynamic model, with clearly defined inputs and outputs. Then, all the particular submodules are assembled according to the drivetrain configuration and, in this way, the power flow across the components is completely determined. Dynamic models of electrical components are often based on equivalent circuits, where Kirchhoff’s voltage and current laws are applied to draw the algebraic and differential equations. Here, Randles circuit is used for dynamic modeling of the battery and the electric motor is modeled through the analysis of the equivalent circuit of a separately excited DC motor, where the power converter is included. The mechanical subsystem is defined by MBS3D equations. These equations consider the position, velocity and acceleration of all the bodies comprising the vehicle multibody system. MBS3D 2.0 is entirely written in MATLAB and the structure of the program has been thoroughly studied and understood by the author. MBS3D software is adapted according to the requirements of the applied co-simulation method. Some of the core functions are modified, such as integrator and graphics, and several auxiliary functions are added in order to compute the mathematical model of the electrical components. By coupling and co-simulating both subsystems, it is possible to evaluate the dynamic interaction among all the components of the drivetrain. ‘Tight-coupling’ method is used to cosimulate the sub-models. This approach integrates all subsystems simultaneously and the results of the integration are exchanged by function-call. This means that the integration is done jointly for the mechanical and the electrical subsystem, under a single integrator and then, the speed of integration is determined by the slower subsystem. Simulations are then used to show the performance of the developed EV model. However, this project focuses more on the validation of the computational and mathematical tool for electric and hybrid vehicle simulation. For this purpose, a detailed study and comparison of different integrators within the MATLAB environment is done. Consequently, the main efforts are directed towards the implementation of co-simulation techniques in MBS3D software. In this regard, it is not intended to create an extremely precise EV model in terms of real vehicle performance, although an acceptable level of accuracy is achieved. The gap between the EV model and the real system is filled, in a way, by introducing the gas and brake pedals input, which reflects the actual driver behavior. This input is included directly in the differential equations of the model, and determines the amount of current provided to the electric motor. For a separately excited DC motor, the rotor current is proportional to the traction torque delivered to the car wheels. Therefore, as it occurs in the case of real vehicle models, the propulsion torque in the mathematical model is controlled through acceleration and brake pedal commands. The designed transmission system also includes a reduction gear that adapts the torque coming for the motor drive and transfers it. The main contribution of this project is, therefore, the implementation of a new calculation path for the wheel torques, based on performance characteristics and outputs of the electric powertrain model. Originally, the wheel traction and braking torques were input to MBS3D through a vector directly computed by the user in a MATLAB script. Now, they are calculated as a function of the motor current which, in turn, depends on the current provided by the battery pack across the DC/DC chopper converter. The motor and battery currents and voltages are the solutions of the electrical ODE (Ordinary Differential Equation) system coupled to the multibody system. Simultaneously, the outputs of MBS3D model are the position, velocity and acceleration of the vehicle at all times. The motor shaft speed is computed from the output vehicle speed considering the wheel radius, the gear reduction ratio and the transmission efficiency. This motor shaft speed, somehow available from MBS3D model, is then introduced in the differential equations corresponding to the electrical subsystem. In this way, MBS3D and the electrical powertrain model are interconnected and both subsystems exchange values resulting as expected with tight-coupling approach.When programming mathematical models of complex systems, code optimization is a key step in the process. A way to improve the overall performance of the integration, making use of C/C++ as an alternative programming language, is described and implemented. Although this entails a higher computational burden, it leads to important advantages regarding cosimulation speed and stability. In order to do this, it is necessary to integrate MATLAB with another integrated development environment (IDE), where C/C++ code can be generated and executed. In this project, C/C++ files are programmed in Microsoft Visual Studio and the interface between both IDEs is created by building C/C++ MEX file functions. These programs contain functions or subroutines that can be dynamically linked and executed from MATLAB. This process achieves reductions in simulation time up to two orders of magnitude. The tests performed with different integrators, also reveal the stiff character of the differential equations corresponding to the electrical subsystem, and allow the improvement of the cosimulation process. When varying the parameters of the integration and/or the initial conditions of the problem, the solutions of the system of equations show better dynamic response and stability, depending on the integrator used. Several integrators, with variable and non-variable step-size, and for stiff and non-stiff problems are applied to the coupled ODE system. Then, the results are analyzed, compared and discussed. From all the above, the project can be divided into four main parts: 1. Creation of the equation-based electric vehicle model; 2. Programming, simulation and adjustment of the electric vehicle model; 3. Application of co-simulation methodologies to MBS3D and the electric powertrain subsystem; and 4. Code optimization and study of different integrators. Additionally, in order to deeply understand the context of the project, the first chapters include an introduction to basic vehicle dynamics, current classification of hybrid and electric vehicles and an explanation of the involved technologies such as brake energy regeneration, electric and non-electric propulsion systems for EVs and HEVs (hybrid electric vehicles) and their control strategies. Later, the problem of dynamic modeling of hybrid and electric vehicles is discussed. The integrated development environment and the simulation tool are also briefly described. The core chapters include an explanation of the major co-simulation methodologies and how they have been programmed and applied to the electric powertrain model together with the multibody system dynamic model. Finally, the last chapters summarize the main results and conclusions of the project and propose further research topics. In conclusion, co-simulation methodologies are applicable within the integrated development environments MATLAB and Visual Studio, and the simulation tool MBS3D 2.0, where equation-based models of multidisciplinary subsystems, consisting of mechanical and electrical components, are coupled and integrated in a very efficient way.

Synthesis of Chromen[4,3-b]pyrrolidines by Intramolecular 1,3-Dipolar Cycloadditions of Azomethine Ylides: An Experimental and Computational Assessment of the Origin of Stereocontrol

Azomethine ylides, generated from imine-derived O-cinnamyl or O-crotonyl salicylaldeyde and α-amino acids, undergo intramolecular 1,3-dipolar cycloaddition, leading to chromene[4,3-b]pyrrolidines. Two reaction conditions are used: (a) microwave-assisted heating (200 W, 185 °C) of a neat mixture of reagents, and (b) conventional heating (170 °C) in PEG-400 as solvent. In both cases, a mixture of two epimers at the α-position of the nitrogen atom in the pyrrolidine nucleus was formed through the less energetic endo-approach (B/C ring fusion). In many cases, the formation of the stereoisomer bearing a trans-arrangement into the B/C ring fusion was observed in high proportions. Comprehensive computational and kinetic simulation studies are detailed. An analysis of the stability of transient 1,3-dipoles, followed by an assessment of the intramolecular pathways and kinetics are also reported.

SimuMap: a computational system for spatial modelling

The paper presents a computational system based upon formal principles to run spatial models for environmental processes. The simulator is named SimuMap because it is typically used to simulate spatial processes over a mapped representation of terrain. A model is formally represented in SimuMap as a set of coupled sub-models. The paper considers the situation where spatial processes operate at different time levels, but are still integrated. An example of such a situation commonly occurs in watershed hydrology where overland flow and stream channel flow have very different flow rates but are highly related as they are subject to the same terrain runoff processes. SimuMap is able to run a network of sub-models that express different time-space derivatives for water flow processes. Sub-models may be coded generically with a map algebra programming language that uses a surface data model. To address the problem of differing time levels in simulation, the paper: (i) reviews general approaches for numerical solvers, (ii) considers the constraints that need to be enforced to use more adaptive time steps in discrete time specified simulations, and (iii) scaling transfer rates in equations that use different time bases for time-space derivatives. A multistep scheme is proposed for SimuMap. This is presented along with a description of its visual programming interface, its modelling formalisms and future plans. (C) 2003 Elsevier Ltd. All rights reserved.