Realistic Single Cell Modeling – from Experiment to Simulation

This tutorial gives a step by step explanation of how one uses experimental data to construct a biologically realistic multicompartmental model. Special emphasis is given on the many ways that this process can be imprecise. The tutorial is intended for both experimentalists who want to get into computer modeling and for computer scientists who use abstract neural network models but are curious about biological realistic modeling. The tutorial is not dependent on the use of a specific simulation engine, but rather covers the kind of data needed for constructing a model, how they are used, and potential pitfalls in the process.

Computer Simulation of Crowd Dynamics and Destructive Crowd Behavior

The social processes that lead to destructive behavior in celebratory crowds can be studied through an agent-based computer simulation. Riots are an increasingly common outcome of sports celebrations, and pose the potential for harm to participants, bystanders, property, and the reputation of the groups with whom participants are associated. Rioting cannot necessarily be attributed to the negative emotions of individuals, such as anger, rage, frustration and despair. For instance, the celebratory behavior (e.g., chanting, cheering, singing) during UConn’s “Spring Weekend” and after the 2004 NCAA Championships resulted in several small fires and overturned cars. Further, not every individual in the area of a riot engages in violence, and those who do, do not do so continuously. Instead, small groups carry out the majority of violent acts in relatively short-lived episodes. Agent-based computer simulations are an ideal method for modeling complex group-level social phenomena, such as celebratory gatherings and riots, which emerge from the interaction of relatively “simple” individuals. By making simple assumptions about individuals’ decision-making and behaviors and allowing actors to affect one another, behavioral patterns emerge that cannot be predicted by the characteristics of individuals. The computer simulation developed here models celebratory riot behavior by repeatedly evaluating a single algorithm for each individual, the inputs of which are affected by the characteristics of nearby actors. Specifically, the simulation assumes that (a) actors possess 1 of 5 distinct social identities (group memberships), (b) actors will congregate with actors who possess the same identity, (c) the degree of social cohesion generated in the social context determines the stability of relationships within groups, and (d) actors’ level of aggression is affected by the aggression of other group members. Not only does this simulation provide a systematic investigation of the effects of the initial distribution of aggression, social identification, and cohesiveness on riot outcomes, but also an analytic tool others may use to investigate, visualize and predict how various individual characteristics affect emergent crowd behavior.

Simulation of Freight Trains Equipped with Partially Filled Tank Containers and Related Resonance Phenomenon

To study the fluid motion-vehicle dynamics interaction, a model of four, liquid filled two-axle container freight wagons was set up. The railway vehicle has been modelled as a multi-body system (MBS). To include fluid sloshing, an equivalent mechanical model has been developed and incorporated. The influence of several factors has been studied in computer simulations, such as track defects, curve negotiation, train velocity, wheel wear, liquid and solid wagonload, and container baffles. SIMPACK has been used for MBS analysis, and ANSYS for liquid sloshing modelling and equivalent mechanical systems validation. Acceleration and braking manoeuvres of the freight train set the liquid cargo into motion. This longitudinal sloshing motion of the fluid cargo inside the tanks initiated a swinging motion of some components of the coupling gear. The coupling gear consists of UIC standard traction hooks and coupling screws that are located between buffers. One of the coupling screws is placed in the traction hook of the opposite wagon thus joining the two wagons, whereas the unused coupling screw rests on a hanger. Simulation results showed that, for certain combinations of type of liquid, filling level and container dimensions, the liquid cargo could provoke an undesirable, although not hazardous, release of the unused coupling screw from its hanger. The coupling screw's release was especially obtained when a period of acceleration was followed by an abrupt braking manoeuvre at 1 m/s2. It was shown that a resonance effect between the liquid's oscillation and the coupling screw's rotary motion could be the reason for the coupling screw's undesired release. Possible solutions to avoid the phenomenon are given.Acceleration and braking manoeuvres of the freight train set the liquid cargo into motion. This longitudinal sloshing motion of the fluid cargo inside the tanks initiated a swinging motion of some components of the coupling gear. The coupling gear consists of UIC standard traction hooks and coupling screws that are located between buffers. One of the coupling screws is placed in the traction hook of the opposite wagon thus joining the two wagons, whereas the unused coupling screw rests on a hanger. This paper reports on a study of the fluid motion-train vehicle dynamics interaction. In the study, a model of four, liquid-filled two-axle container freight wagons was developed. The railway vehicle has been modeled as a multi-body system (MBS). To include fluid sloshing, an equivalent mechanical model has been developed and incorporated. The influence of several factors has been studied in computer simulations, such as track defects, curve negotiation, train velocity, wheel wear, liquid and solid wagonload, and container baffles. A simulation program was used for MBS analysis, and a finite element analysis program was used for liquid sloshing modeling and equivalent mechanical systems validation. Acceleration and braking maneuvers of the freight train set the liquid cargo into motion. This longitudinal sloshing motion of the fluid cargo inside the tanks initiated a swinging motion of some components of the coupling gear. Simulation results showed that, for certain combinations of type of liquid, filling level and container dimensions, the liquid cargo could provoke an undesirable, although not hazardous, release of an unused coupling screw from its hanger. It was shown that a resonance effect between the liquid's oscillation and the coupling screw's rotary motion could be the reason for the coupling screw's undesired release. Solutions are suggested to avoid the resonance problem, and directions for future research are given.

Simulation, Design and Analysis of Air-Breathing Combined-Cycle Engines for High Speed Propulsion

Desde la aparición del turborreactor, el motor aeróbico con turbomaquinaria ha demostrado unas prestaciones excepcionales en los regímenes subsónico y supersónico bajo. No obstante, la operación a velocidades superiores requiere sistemas más complejos y pesados, lo cual ha imposibilitado la ejecución de estos conceptos. Los recientes avances tecnológicos, especialmente en materiales ligeros, han restablecido el interés por los motores de ciclo combinado. La simulación numérica de estos nuevos conceptos es esencial para estimar las prestaciones de la planta propulsiva, así como para abordar las dificultades de integración entre célula y motor durante las primeras etapas de diseño. Al mismo tiempo, la evaluación de estos extraordinarios motores requiere una metodología de análisis distinta. La tesis doctoral versa sobre el diseño y el análisis de los mencionados conceptos propulsivos mediante el modelado numérico y la simulación dinámica con herramientas de vanguardia. Las distintas arquitecturas presentadas por los ciclos combinados basados en sendos turborreactor y motor cohete, así como los diversos sistemas comprendidos en cada uno de ellos, hacen necesario establecer una referencia común para su evaluación. Es más, la tendencia actual hacia aeronaves "más eléctricas" requiere una nueva métrica para juzgar la aptitud de un proceso de generación de empuje en el que coexisten diversas formas de energía. A este respecto, la combinación del Primer y Segundo Principios define, en un marco de referencia absoluto, la calidad de la trasferencia de energía entre los diferentes sistemas. Esta idea, que se ha estado empleando desde hace mucho tiempo en el análisis de plantas de potencia terrestres, ha sido extendida para relacionar la misión de la aeronave con la ineficiencia de cada proceso involucrado en la generación de empuje. La metodología se ilustra mediante el estudio del motor de ciclo combinado variable de una aeronave para el crucero a Mach 5. El diseño de un acelerador de ciclo combinado basado en el turborreactor sirve para subrayar la importancia de la integración del motor y la célula. El diseño está limitado por la trayectoria ascensional y el espacio disponible en la aeronave de crucero supersónico. Posteriormente se calculan las prestaciones instaladas de la planta propulsiva en función de la velocidad y la altitud de vuelo y los parámetros de control del motor: relación de compresión, relación aire/combustible y área de garganta. ABSTRACT Since the advent of the turbojet, the air-breathing engine with rotating machinery has demonstrated exceptional performance in the subsonic and low supersonic regimes. However, the operation at higher speeds requires further system complexity and weight, which so far has impeded the realization of these concepts. Recent technology developments, especially in lightweight materials, have restored the interest towards combined-cycle engines. The numerical simulation of these new concepts is essential at the early design stages to compute a first estimate of the engine performance in addition to addressing airframe-engine integration issues. In parallel, a different analysis methodology is required to evaluate these unconventional engines. The doctoral thesis concerns the design and analysis of the aforementioned engine concepts by means of numerical modeling and dynamic simulation with state-of-the-art tools. A common reference is needed to evaluate the different architectures of the turbine and the rocket-based combined-cycle engines as well as the various systems within each one of them. Furthermore, the actual trend towards more electric aircraft necessitates a common metric to judge the suitability of a thrust generation process where different forms of energy coexist. In line with this, the combination of the First and the Second Laws yields the quality of the energy being transferred between the systems on an absolute reference frame. This idea, which has been since long applied to the analysis of on-ground power plants, was extended here to relate the aircraft mission with the inefficiency of every process related to the thrust generation. The methodology is illustrated with the study of a variable- combined-cycle engine for a Mach 5 cruise aircraft. The design of a turbine-based combined-cycle booster serves to highlight the importance of the engine-airframe integration. The design is constrained by the ascent trajectory and the allocated space in the supersonic cruise aircraft. The installed performance of the propulsive plant is then computed as a function of the flight speed and altitude and the engine control parameters: pressure ratio, air-to-fuel ratio and throat area.

Integrated sensitivity analysis, calibration, and uncertainty propagation analysis approaches for supporting hydrological modeling

The successful performance of a hydrological model is usually challenged by the quality of the sensitivity analysis, calibration and uncertainty analysis carried out in the modeling exercise and subsequent simulation results. This is especially important under changing climatic conditions where there are more uncertainties associated with climate models and downscaling processes that increase the complexities of the hydrological modeling system. In response to these challenges and to improve the performance of the hydrological models under changing climatic conditions, this research proposed five new methods for supporting hydrological modeling. First, a design of experiment aided sensitivity analysis and parameterization (DOE-SAP) method was proposed to investigate the significant parameters and provide more reliable sensitivity analysis for improving parameterization during hydrological modeling. The better calibration results along with the advanced sensitivity analysis for significant parameters and their interactions were achieved in the case study. Second, a comprehensive uncertainty evaluation scheme was developed to evaluate three uncertainty analysis methods, the sequential uncertainty fitting version 2 (SUFI-2), generalized likelihood uncertainty estimation (GLUE) and Parameter solution (ParaSol) methods. The results showed that the SUFI-2 performed better than the other two methods based on calibration and uncertainty analysis results. The proposed evaluation scheme demonstrated that it is capable of selecting the most suitable uncertainty method for case studies. Third, a novel sequential multi-criteria based calibration and uncertainty analysis (SMC-CUA) method was proposed to improve the efficiency of calibration and uncertainty analysis and control the phenomenon of equifinality. The results showed that the SMC-CUA method was able to provide better uncertainty analysis results with high computational efficiency compared to the SUFI-2 and GLUE methods and control parameter uncertainty and the equifinality effect without sacrificing simulation performance. Fourth, an innovative response based statistical evaluation method (RESEM) was proposed for estimating the uncertainty propagated effects and providing long-term prediction for hydrological responses under changing climatic conditions. By using RESEM, the uncertainty propagated from statistical downscaling to hydrological modeling can be evaluated. Fifth, an integrated simulation-based evaluation system for uncertainty propagation analysis (ISES-UPA) was proposed for investigating the effects and contributions of different uncertainty components to the total propagated uncertainty from statistical downscaling. Using ISES-UPA, the uncertainty from statistical downscaling, uncertainty from hydrological modeling, and the total uncertainty from two uncertainty sources can be compared and quantified. The feasibility of all the methods has been tested using hypothetical and real-world case studies. The proposed methods can also be integrated as a hydrological modeling system to better support hydrological studies under changing climatic conditions. The results from the proposed integrated hydrological modeling system can be used as scientific references for decision makers to reduce the potential risk of damages caused by extreme events for long-term water resource management and planning.

Investigating output accuracy for a discrete event simulation model and an agent based simulation model

In this paper, we investigate output accuracy for a Discrete Event Simulation (DES) model and Agent Based Simulation (ABS) model. The purpose of this investigation is to find out which of these simulation techniques is the best one for modelling human reactive behaviour in the retail sector. In order to study the output accuracy in both models, we have carried out a validation experiment in which we compared the results from our simulation models to the performance of a real system. Our experiment was carried out using a large UK department store as a case study. We had to determine an efficient implementation of management policy in the store’s fitting room using DES and ABS. Overall, we have found that both simulation models were a good representation of the real system when modelling human reactive behaviour.

Business process modeling : current issues and future challenges

Business process modeling has undoubtedly emerged as a popular and relevant practice in Information Systems. Despite being an actively researched field, anecdotal evidence and experiences suggest that the focus of the research community is not always well aligned with the needs of industry. The main aim of this paper is, accordingly, to explore the current issues and the future challenges in business process modeling, as perceived by three key stakeholder groups (academics, practitioners, and tool vendors). We present the results of a global Delphi study with these three groups of stakeholders, and discuss the findings and their implications for research and practice. Our findings suggest that the critical areas of concern are standardization of modeling approaches, identification of the value proposition of business process modeling, and model-driven process execution. These areas are also expected to persist as business process modeling roadblocks in the future.

Frontiers in Materials Science and Technology

This special issue aims to provide up-to-date knowledge and the latest scientific concepts and technological developments in the processing, characterization, testing, mechanics, modeling and applications of a broad range of advanced materials. The many contributors, from Denmark, Germany, UK, Iran, Saudi Arabia, Malaysia, Japan, the People’s Republic of China, Singapore, Taiwan, USA, New Zealand and Australia, present a wide range of topics including: nanomaterials, thin films and coatings, metals and alloys, composite materials, materials processing and characterization, biomaterials and biomechanics, and computational materials science and simulation. The work will therefore be of great interest to a broad spectrum of researchers and technologists.

On the usage of labels and icons in business process modeling

The value of business process models is dependent not only on the choice of graphical elements in the model, but also on their annotation with additional textual and graphical information. This research discusses the use of text and icons for labeling the graphical constructs in a process model. We use two established verb classification schemes to examine the choice of activity labels in process modeling practice. Based on our findings, we synthesize a set of twenty-five activity label categories. We propose a systematic approach for graphically representing these label categories through the use of graphical icons, such that the resulting process models are easier and more readily understandable by end users. Our findings contribute to an ongoing stream of research investigating the practice of process modeling and thereby contribute to the body of knowledge about conceptual modeling quality overall.

Building information modeling in the Australian architecture engineering and construction industry

Building Information Modeling (BIM) is a modern approach to the design, documentation, delivery, and life cycle management of buildings through the use of project information databases coupled with object-based parametric modeling. BIM has the potential to revolutionize the Architecture, Engineering and Construction (AEC) industry in terms of the positive impact it may have on information flows, working relationships between project participants from different disciplines and the resulting benefits it may achieve through improvements to conventional methods. This chapter reviews the development of BIM, the extent to which BIM has been implemented in Australia, and the factors which have affected the up-take of BIM. More specifically, the objectives of this chapter are to investigate the adoption of BIM in the Australian AEC industry and factors that contribute towards the uptake (or non uptake) of BIM. These objectives are met by a review of the related literature in the first instance, followed by the presentation of the results of a 2007 postal questionnaire survey and telephone interviews of a random sample of professionals in the Australian AEC industry. The responses suggest that less than 25 percent of the sample had been involved in BIM – rather less than might be expected from reading the literature. Also, of those who have been involved with BIM, there has been very little interdisciplinary collaboration. The main barriers impeding the implementation of BIM widely across the Australian AEC industry are also identified. These were found to be primarily a lack of BIM expertise, lack of awareness and resistance to change. The benefits experienced as a result of using BIM are also discussed. These include improved design consistency, better coordination, cost savings, higher quality work, greater productivity and increased speed of delivery. In terms of conclusion, some suggestions are made concerning the underlying practical reasons for the slow up-take of BIM and the successes for those early adopters. Prospects for future improvement are discussed and proposals are also made for a large scale worldwide comparative study covering industry-wide participants

Variational Bayes and the reduced dependence approximation for the autologistic model on an irregular grid with applications

Discrete Markov random field models provide a natural framework for representing images or spatial datasets. They model the spatial association present while providing a convenient Markovian dependency structure and strong edge-preservation properties. However, parameter estimation for discrete Markov random field models is difficult due to the complex form of the associated normalizing constant for the likelihood function. For large lattices, the reduced dependence approximation to the normalizing constant is based on the concept of performing computationally efficient and feasible forward recursions on smaller sublattices which are then suitably combined to estimate the constant for the whole lattice. We present an efficient computational extension of the forward recursion approach for the autologistic model to lattices that have an irregularly shaped boundary and which may contain regions with no data; these lattices are typical in applications. Consequently, we also extend the reduced dependence approximation to these scenarios enabling us to implement a practical and efficient non-simulation based approach for spatial data analysis within the variational Bayesian framework. The methodology is illustrated through application to simulated data and example images. The supplemental materials include our C++ source code for computing the approximate normalizing constant and simulation studies.

Patterns of correlation between vehicle occupant seat pressure and anthropometry

Seat pressure is known as a major factor of seat comfort in vehicles. In passenger vehicles, there is lacking research into the seat comfort of rear seat occupants. As accurate seat pressure measurement requires significant effort, simulation of seat pressure is evolving as a preferred method. However, analytic methods are based on complex finite element modeling and therefore are time consuming and involve high investment. Based on accurate anthropometric measurements of 64 male subjects and outboard rear seat pressure measurements in three different passenger vehicles, this study investigates if a set of parameters derived from seat pressure mapping are sensitive enough to differentiate between different seats and whether they correlate with anthropometry in linear models. In addition to the pressure map analysis, H-Points were measured with a coordinate measurement system based on palpated body landmarks and the range of H-Point locations in the three seats is provided. It was found that for the cushion, cushion contact area and cushion front area/force could be modeled by subject anthropometry,while only seatback contact area could be modeled based on anthropometry for all three vehicles. Major differences were found between the vehicles for other parameters.

Preface to special issue on digital human modelling for vehicle design and manufacturing

The automotive industry has been the focus of digital human modeling (DHM) research and application for many years. In the highly competitive marketplace for personal transportation, the desire to improve the customer’s experience has driven extensive research in both the physical and cognitive interaction between the vehicle and its occupants. Human models provide vehicle designers with tools to view and analyze product interactions before the first prototypes are built, potentially improving the design while reducing cost and development time. The focus of DHM research and applications began with prediction and representation of static postures for purposes of driver workstation layout, including assessments of seat adjustment ranges and exterior vision. Now DHMs are used for seat design and assessment of driver reach and ingress/egress. DHMs and related simulation tools are expanding into the cognitive domain, with computational models of perception and motion, and into the dynamic domain with models of physical responses to ride and vibration. Moreover, DHMs are now widely used to analyze the ergonomics of vehicle assembly tasks. In this case, the analysis aims to determine whether workers can be expected to complete the tasks safely and with good quality. This preface provides a review of the literature to provide context for the nine new papers presented in this special issue.

A coupled SPH-DEM model for fluid and solid mechanics of apple parenchyma cells during drying

A coupled SPH-DEM based two-dimensional (2-D) micro-scale single cell model is developed to predict basic cell-level shrinkage effects of apple parenchyma cells during air drying. In this newly developed drying model, Smoothed Particle Hydrodynamics (SPH) is used to model the low Reynolds Number fluid motions of the cell protoplasm, and a Discrete Element Method (DEM) is employed to simulate the polymer-like cell wall. Simulations results reasonably agree with published experimental drying results on cellular shrinkage properties such as cellular area, diameter and perimeter. These preliminary results indicate that the model is effective for the modelling and simulation of apple parenchyma cells during air drying.