Cellular dynamic simulator: an event driven molecular simulation environment for cellular physiology.

In this paper, we present the Cellular Dynamic Simulator (CDS) for simulating diffusion and chemical reactions within crowded molecular environments. CDS is based on a novel event driven algorithm specifically designed for precise calculation of the timing of collisions, reactions and other events for each individual molecule in the environment. Generic mesh based compartments allow the creation / importation of very simple or detailed cellular structures that exist in a 3D environment. Multiple levels of compartments and static obstacles can be used to create a dense environment to mimic cellular boundaries and the intracellular space. The CDS algorithm takes into account volume exclusion and molecular crowding that may impact signaling cascades in small sub-cellular compartments such as dendritic spines. With the CDS, we can simulate simple enzyme reactions; aggregation, channel transport, as well as highly complicated chemical reaction networks of both freely diffusing and membrane bound multi-protein complexes. Components of the CDS are generally defined such that the simulator can be applied to a wide range of environments in terms of scale and level of detail. Through an initialization GUI, a simple simulation environment can be created and populated within minutes yet is powerful enough to design complex 3D cellular architecture. The initialization tool allows visual confirmation of the environment construction prior to execution by the simulator. This paper describes the CDS algorithm, design implementation, and provides an overview of the types of features available and the utility of those features are highlighted in demonstrations.

Virtual simulator for mobile robots navigation systems

This paper presents the virtual environment implementation for project simulation and conception of supervision and control systems for mobile robots, that are capable to operate and adapting in different environments and conditions. This virtual system has as purpose to facilitate the development of embedded architecture systems, emphasizing the implementation of tools that allow the simulation of the kinematic conditions, dynamic and control, with real time monitoring of all important system points. For this, an open control architecture is proposal, integrating the two main techniques of robotic control implementation in the hardware level: systems microprocessors and reconfigurable hardware devices. The implemented simulator system is composed of a trajectory generating module, a kinematic and dynamic simulator module and of a analysis module of results and errors. All the kinematic and dynamic results shown during the simulation can be evaluated and visualized in graphs and tables formats, in the results analysis module, allowing an improvement in the system, minimizing the errors with the necessary adjustments optimization. For controller implementation in the embedded system, it uses the rapid prototyping, that is the technology that allows, in set with the virtual simulation environment, the development of a controller project for mobile robots. The validation and tests had been accomplish with nonholonomics mobile robots models with diferencial transmission. © 2008 IEEE.

Modellazione avanzata di un incendio in uno stabilimento industriale secondo i principi della fire safety engineering

Lo sviluppo di un incendio all’interno di depositi di liquidi infiammabili costituisce uno scenario particolarmente critico a causa della rilevanza delle conseguenze che ne possono scaturire. L’incendio causato dalla formazione di grandi pozze sviluppatesi a seguito di forature dei contenitori e il rapido coinvolgimento di tutto lo stoccaggio rappresentano uno scenario di incendio tipico di queste realtà. Si ha quindi la necessità di adottare provvedimenti atti a garantire specifici obiettivi di sicurezza tramite l’introduzione di misure antincendio. La prevenzione incendi, sino al 2007, era basata esclusivamente su norme di tipo prescrittivo, in base alle quali si definivano le misure di sicurezza secondo un criterio qualitativo. Successivamente l’ingegneria antincendio si è sempre più caratterizzata da approcci basati su analisi di tipo prestazionale, in grado di dimostrare il raggiungimento dell’obiettivo di sicurezza sulla base del comportamento reale d’incendio ottenuto mediante un’accurata simulazione del fuoco che ragionevolmente può prodursi nell'attività. La modellazione degli incendi è divenuta possibile grazie allo sviluppo di codici di fluidodinamica computazionale (CFD), in grado di descrivere accuratamente l’evoluzione delle fiamme. Il presente studio si inserisce proprio nell’ambito della modellazione CFD degli incendi, eseguita mediante il software Fire Dynamics Simulator (FDS). L’obiettivo dell’elaborato è studiare l’azione dell’impianto di spegnimento a schiuma sullo sviluppo di un incendio di pozza in un deposito di liquidi infiammabili, in termini di riduzione della potenza termica rilasciata dal fuoco, al fine di determinare le temperature massime raggiunte, in corrispondenza delle quali valutare il comportamento di resistenza strutturale degli edifici. Il presente lavoro è articolato in 6 capitoli. Dopo il Capitolo 1, avente carattere introduttivo, vengono richiamati nel Capitolo 2 i principali concetti della chimica e fisica degli incendi. Nel Capitolo 3 vengono esaminate le normative intese ad unificare l’approccio ingegneristico alla sicurezza antincendio. Il Capitolo 4 fornisce una dettagliata descrizione del software di calcolo, FDS - Fire Dynamics Simulator, adoperato per la modellazione dell’incendio. Nel Capitolo 5 si procede alla progettazione prestazionale che conduce alla determinazione della curva naturale d'incendio in presenza degli impianti di spegnimento automatici. Infine nel Capitolo 6 si riportano le considerazioni conclusive.

Dynamic high-resolution computer simulation of electrophoretic enantiomer separations with neutral cyclodextrins as chiral selectors.

GENTRANS, a comprehensive one-dimensional dynamic simulator for electrophoretic separations and transport, was extended for handling electrokinetic chiral separations with a neutral ligand. The code can be employed to study the 1:1 interaction of monovalent weak and strong acids and bases with a single monovalent weak or strong acid or base additive, including a neutral cyclodextrin, under real experimental conditions. It is a tool to investigate the dynamics of chiral separations and to provide insight into the buffer systems used in chiral capillary zone electrophoresis (CZE) and chiral isotachophoresis. Analyte stacking across conductivity and buffer additive gradients, changes of additive concentration, buffer component concentration, pH, and conductivity across migrating sample zones and peaks, and the formation and migration of system peaks can thereby be investigated in a hitherto inaccessible way. For model systems with charged weak bases and neutral modified β-cyclodextrins at acidic pH, for which complexation constants, ionic mobilities, and mobilities of selector-analyte complexes have been determined by CZE, simulated and experimentally determined electropherograms and isotachopherograms are shown to be in good agreement. Simulation data reveal that CZE separations of cationic enantiomers performed in phosphate buffers at low pH occur behind a fast cationic migrating system peak that has a small impact on the buffer composition under which enantiomeric separation takes place.

Dynamic simulation of chemical processes

This thesis describes the design and implementation of an interactive dynamic simulator called DASPRII. The starting point of this research has been an existing dynamic simulation package, DASP. DASPII is written in standard FORTRAN 77 and is implemented on universally available IBM-PC or compatible machines. It provides a means for the analysis and design of chemical processes. Industrial interest in dynamic simulation has increased due to the recent increase in concern over plant operability, resiliency and safety. DASPII is an equation oriented simulation package which allows solution of dynamic and steady state equations. The steady state can be used to initialise the dynamic simulation. A robust non linear algebraic equation solver has been implemented for steady state solution. This has increased the general robustness of DASPII, compared to DASP. A graphical front end is used to generate the process flowsheet topology from a user constructed diagram of the process. A conversational interface is used to interrogate the user with the aid of a database, to complete the topological information. An original modelling strategy implemented in DASPII provides a simple mechanism for parameter switching which creates a more flexible simulation environment. The problem description generated is by a further conversational procedure using a data-base. The model format used allows the same model equations to be used for dynamic and steady state solution. All the useful features of DASPI are retained in DASPII. The program has been demonstrated and verified using a number of example problems, Significant improvements using the new NLAE solver have been shown. Topics requiring further research are described. The benefits of variable switching in models has been demonstrated with a literature problem.

Dynamic simulation of chemical plant

This thesis describes the design and implementation of a new dynamic simulator called DASP. It is a computer program package written in standard Fortran 77 for the dynamic analysis and simulation of chemical plants. Its main uses include the investigation of a plant's response to disturbances, the determination of the optimal ranges and sensitivities of controller settings and the simulation of the startup and shutdown of chemical plants. The design and structure of the program and a number of features incorporated into it combine to make DASP an effective tool for dynamic simulation. It is an equation-oriented dynamic simulator but the model equations describing the user's problem are generated from in-built model equation library. A combination of the structuring of the model subroutines, the concept of a unit module, and the use of the connection matrix of the problem given by the user have been exploited to achieve this objective. The Executive program has a structure similar to that of a CSSL-type simulator. DASP solves a system of differential equations coupled to nonlinear algebraic equations using an advanced mixed equation solver. The strategy used in formulating the model equations makes it possible to obtain the steady state solution of the problem using the same model equations. DASP can handle state and time events in an efficient way and this includes the modification of the flowsheet. DASP is highly portable and this has been demonstrated by running it on a number of computers with only trivial modifications. The program runs on a microcomputer with 640 kByte of memory. It is a semi-interactive program, with the bulk of all input data given in pre-prepared data files with communication with the user is via an interactive terminal. Using the features in-built in the package, the user can view or modify the values of any input data, variables and parameters in the model, and modify the structure of the flowsheet of the problem during a simulation session. The program has been demonstrated and verified using a number of example problems.

Measurement and Simulation of Suppression Effects in a Buoyant Turbulent Line Fire

An experimental and numerical study of turbulent fire suppression is presented. For this work, a novel and canonical facility has been developed, featuring a buoyant, turbulent, methane or propane-fueled diffusion flame suppressed via either nitrogen dilution of the oxidizer or application of a fine water mist. Flames are stabilized on a slot burner surrounded by a co-flowing oxidizer, which allows controlled delivery of either suppressant to achieve a range of conditions from complete combustion through partial and total flame quenching. A minimal supply of pure oxygen is optionally applied along the burner to provide a strengthened flame base that resists liftoff extinction and permits the study of substantially weakened turbulent flames. The carefully designed facility features well-characterized inlet and boundary conditions that are especially amenable to numerical simulation. Non-intrusive diagnostics provide detailed measurements of suppression behavior, yielding insight into the governing suppression processes, and aiding the development and validation of advanced suppression models. Diagnostics include oxidizer composition analysis to determine suppression potential, flame imaging to quantify visible flame structure, luminous and radiative emissions measurements to assess sooting propensity and heat losses, and species-based calorimetry to evaluate global heat release and combustion efficiency. The studied flames experience notable suppression effects, including transition in color from bright yellow to dim blue, expansion in flame height and structural intermittency, and reduction in radiative heat emissions. Still, measurements indicate that the combustion efficiency remains close to unity, and only near the extinction limit do the flames experience an abrupt transition from nearly complete combustion to total extinguishment. Measurements are compared with large eddy simulation results obtained using the Fire Dynamics Simulator, an open-source computational fluid dynamics software package. Comparisons of experimental and simulated results are used to evaluate the performance of available models in predicting fire suppression. Simulations in the present configuration highlight the issue of spurious reignition that is permitted by the classical eddy-dissipation concept for modeling turbulent combustion. To address this issue, simple treatments to prevent spurious reignition are developed and implemented. Simulations incorporating these treatments are shown to produce excellent agreement with the experimentally measured data, including the global combustion efficiency.

Desenfumagem em edifícios: parque de estacionamento coberto (retail - Oeiras parque)

Os parques de estacionamento surgiram da necessidade de disponibilização de espaço de parqueamento de veículos que fazem parte do quotidiano do Homem, no entanto devido ao facto de poderem ser confinados ou subterrâneos requerem a instalação de ventilação forçada (ventiladores axiais e ventiladores de impulso). Este trabalho tem como objectivo a análise, utilizando métodos de simulação numérica da ventilação forçada criada pelos ventiladores de impulso e pelos ventiladores axiais instalados num parque de estacionamento subterrâneo. Vão ser comparadas várias simulações com situações diferentes em termos de condições de fronteira, obstruções ao escoamento, etc., por forma a tirar conclusões sobre o comportamento do parque numa situação de emergência, ou seja, num incêndio. Este comportamento vai ter em conta a eficiência de evacuação dos gases libertados, as temperaturas no parque que permitem verificar onde estão localizados os gases mais quentes e os campos de velocidade do ar que permitem uma visualização do escoamento e até certo ponto a turbulência do mesmo. No final pretende-se concluir por meio de comparação com outros documentos consultados, a “confiabilidade” do software usado (FDS-Fire Dynamics Simulator) e adicionalmente tirar conclusões sobre o projecto do parque, nomeadamente sobre a necessidade de introdução de alterações.

Estudo do escoamento dos produtos da combustão no interior de uma conduta de evacuação de turbinas a gás utilizadas para propulsão naval

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Engenharia Mecânica

Anàlisi d’un incendi en una nau industrial a Gavà. Conclusions per a l’aplicació del (RSCIEI) en naus de tipus A en horitzontal

1. SINISTRE D’UNA NAU INDÚSTRIAL A GAVÀ 2. ANÀLISI DE SINISTRES DE PÒRTICS ENTRE MITGERES 3. CONTROL DE LA FALLADA DE LES ESTRUCTURES AMB MESURES PASSIVES 3.1 Definició del model simulats 3.2 Paràmetres de càlcul amb OZONE 3.3 Corbes d’incendi resultants del model de zones 1D 3.4 Control tèrmic de l’estructura amb sistemes de ventilació 3.5 Control tèrmic de l’estructura amb aïllament 3.6 Taula de resultats 3.7 Conclusions 1D 4. SIMULACIÓ DELS INCENDIS AMB FIRE DYNAMICS SIMULATOR

Analisi comparativa dei modelli per gli incendi di liquidi infiammabili

I depositi di liquidi infiammabili sono stabilimenti industriali in cui avvengono spesso incendi di grandi dimensioni a causa degli ingenti quantitativi di sostanze infiammabili detenute. Gli incendi tipici dei liquidi infiammabili sono gli incendi di pozza in caso di rilascio del liquido al suolo e gli incendi di serbatoio in caso di ignizione del liquido all’interno del serbatoio stesso. Tali incendi hanno la potenzialità di danneggiare le apparecchiature limitrofe, determinandone il cedimento e dunque l’incremento delle dimensioni dell’incendio e dell’area di danno; tale fenomeno è detto effetto domino. Per la modellazione degli incendi sono disponibili diversi strumenti, divisibili essenzialmente in due categorie: modelli semplici, ovvero basati su correlazioni semi-empiriche e modelli avanzati, costituiti dai codici CFD. L’obiettivo principale del presente lavoro di tesi è il confronto tra le diverse tipologie di strumenti disponibili per la modellazione degli incendi di liquidi infiammabili. In particolare sono stati confrontati tra loro il codice FDS (Fire Dynamics Simulator), il metodo del TNO ed il modello per gli incendi di pozza incorporato nel software ALOHA. Il codice FDS è un modello avanzato, mentre il metodo del TNO ed il modello implementato nel software ALOHA sono modelli semplici appartenenti alla famiglia dei Solid Flame Models. La prima parte del presente lavoro di tesi è dedicata all’analisi delle caratteristiche e delle problematiche di sicurezza dei depositi di liquidi infiammabili, con specifico riferimento all’analisi storica. Nella seconda parte invece i tre metodi sopra citati sono applicati ad un parco serbatoi di liquidi infiammabili ed è effettuato il confronto dei risultati, anche ai fini di una valutazione preliminare dell’effetto domino. La tesi è articolata in 6 capitoli. Dopo il Capitolo 1, avente carattere introduttivo, nel Capitolo 2 vengono richiamati i principali concetti riguardanti gli incendi e vengono analizzate le caratteristiche e le problematiche di sicurezza dei depositi di liquidi infiammabili. Il Capitolo 3 è dedicato alla discussione delle caratteristiche degli incendi di pozza, alla presentazione delle tipologie di strumenti a disposizione per la loro modellazione ed alla descrizione di dettaglio dei modelli utilizzati nel presente lavoro di tesi. Il Capitolo 4 contiene la presentazione del caso di studio. Nel Capitolo 5, che costituisce il cuore del lavoro, i modelli descritti sono applicati al caso di studio, con un’approfondita discussione dei risultati e una valutazione preliminare dell’effetto domino. Nel Capitolo 6 infine sono riportate alcune considerazioni conclusive.

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

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

Computer simulations of sample preconcentration in carrier-free systems and isoelectric focusing in microchannels using simple ampholytes.

In this work, electrophoretic preconcentration of protein and peptide samples in microchannels was studied theoretically using the 1D dynamic simulator GENTRANS, and experimentally combined with MS. In all configurations studied, the sample was uniformly distributed throughout the channel before power application, and driving electrodes were used as microchannel ends. In the first part, previously obtained experimental results from carrier-free systems are compared to simulation results, and the effects of atmospheric carbon dioxide and impurities in the sample solution are examined. Simulation provided insight into the dynamics of the transport of all components under the applied electric field and revealed the formation of a pure water zone in the channel center. In the second part, the use of an IEF procedure with simple well defined amphoteric carrier components, i.e. amino acids, for concentration and fractionation of peptides was investigated. By performing simulations a qualitative description of the analyte behavior in this system was obtained. Neurotensin and [Glu1]-Fibrinopeptide B were separated by IEF in microchannels featuring a liquid lid for simple sample handling and placement of the driving electrodes. Component distributions in the channel were detected using MALDI- and nano-ESI-MS and data were in agreement with those obtained by simulation. Dynamic simulations are demonstrated to represent an effective tool to investigate the electrophoretic behavior of all components in the microchannel.

Multiagent realization of prediction-based diagnosis and loss prevention

A multiagent diagnostic system implemented in a Protege-JADE-JESS environment interfaced with a dynamic simulator and database services is described in this paper. The proposed system architecture enables the use of a combination of diagnostic methods from heterogeneous knowledge sources. The process ontology and the process agents are designed based on the structure of the process system, while the diagnostic agents implement the applied diagnostic methods. A specific completeness coordinator agent is implemented to coordinate the diagnostic agents based on different methods. The system is demonstrated on a case study for diagnosis of faults in a granulation process based on HAZOP and FMEA analysis.

Simulazione CFD di incendio in galleria: confronto tra modello e test in scala reale

Le tecniche di fluidodinamica computazionale vengono utilizzate in numerosi settori dell’ingegneria per risolvere in modo efficiente i problemi di flusso e di termodinamica nei fluidi. Uno di questi settori in cui si è diffuso l’utilizzo delle tecniche CFD (Computational Fluid Dynamics) è il settore dell’ingegneria antincendio. Tra i vari software di simulazione presenti, FDS (Fire Dynamics Simulator) è quello più diffuso nella comunità antincendio e utilizzato all’interno della presente analisi. L’elaborato introduce le basi dell’ingegneria antincendio spiegando le varie fasi attraverso il quale passa la metodologia prestazionale, passando poi ad approfondire le dinamiche d’incendio, in particolare nelle gallerie stradali e le tecniche di modellazione termo fluidodinamica degli incendi. L’analisi tratta il confronto tra delle prove d’incendio in scala reale effettuate all’interno di una galleria e le relative simulazioni fluidodinamiche realizzate al fine di verificare la corrispondenza tra la modellazione con software e l’effettiva evoluzione dell’incendio. Nell’analisi verranno confrontati diversi metodi di modellazione, evidenziando i vantaggi e i limiti incontrati nel corso delle simulazioni, confrontandoli al tempo stesso con i risultati ottenuti dai test in scala reale. I modelli ottenuti hanno permesso di estendere le simulazioni a focolari di potenza maggiore al fine di effettuare un’analisi delle prestazioni antincendio della galleria oggetto di studio.