Simulation modelling and visualisation: toolkits for building artificial worlds

Simulations users at all levels make heavy use of compute resources to drive computational simulations for greatly varying applications areas of research using different simulation paradigms. Simulations are implemented in many software forms, ranging from highly standardised and general models that run in proprietary software packages to ad hoc hand-crafted simulations codes for very specific applications. Visualisation of the workings or results of a simulation is another highly valuable capability for simulation developers and practitioners. There are many different software libraries and methods available for creating a visualisation layer for simulations, and it is often a difficult and time-consuming process to assemble a toolkit of these libraries and other resources that best suits a particular simulation model. We present here a break-down of the main simulation paradigms, and discuss differing toolkits and approaches that different researchers have taken to tackle coupled simulation and visualisation in each paradigm

Three-dimensional lattice-Boltzmann simulations of critical spinodal decomposition in binary immiscible fluids

We use a modified Shan-Chen, noiseless lattice-BGK model for binary immiscible, incompressible, athermal fluids in three dimensions to simulate the coarsening of domains following a deep quench below the spinodal point from a symmetric and homogeneous mixture into a two-phase configuration. We find the average domain size growing with time as $t^\gamma$, where $\gamma$ increases in the range $0.545 < \gamma < 0.717$, consistent with a crossover between diffusive $t^{1/3}$ and hydrodynamic viscous, $t^{1.0}$, behaviour. We find good collapse onto a single scaling function, yet the domain growth exponents differ from others' works' for similar values of the unique characteristic length and time that can be constructed out of the fluid's parameters. This rebuts claims of universality for the dynamical scaling hypothesis. At early times, we also find a crossover from $q^2$ to $q^4$ in the scaled structure function, which disappears when the dynamical scaling reasonably improves at later times. This excludes noise as the cause for a $q^2$ behaviour, as proposed by others. We also observe exponential temporal growth of the structure function during the initial stages of the dynamics and for wavenumbers less than a threshold value.Comment: 45 pages, 18 figures. Accepted for publication in Physical Review

A mesoscopic lattice model for morphology formation in ternary mixtures with evaporation

We develop a mesoscopic lattice model to study the morphology formation in interacting ternary mixtures with the evaporation of one component. As concrete potential application of our model, we wish to capture morphologies as they are typically arising during the fabrication of organic solar cells. In this context, we consider an evaporating solvent into which two other components are dissolved, as a model for a 2-component coating solution that is drying on a substrate. We propose a 3-spins dynamics to describe the evolution of the three interacting species. As main tool, we use a Monte Carlo Metropolis-based algorithm, with the possibility of varying the system's temperature, mixture composition, interaction strengths, and evaporation kinetics. The main novelty is the structure of the mesoscopic model – a bi-dimensional lattice with periodic boundary conditions, divided into square cells to encode a mesoscopic range interaction among the units. We investigate the effect of the model parameters on the structure of the resulting morphologies. Finally, we compare the results obtained with the mesoscopic model with corresponding ones based on an analogous lattice model with a short range interaction among the units, i.e. when the mesoscopic length scale coincides with the microscopic length scale of the lattice

Sociohydrodynamics: data-driven modelling of social behavior

Living systems display complex behaviors driven not only by physical forces, but also decision-making guided by information processing and molded by cultural and/or biological evolution. Hydrodynamic theories hold promise for simplified, universal descriptions of these collective behaviors. However, incorporating the individual preferences of decision-making organisms into a hydrodynamic theory is an open problem. Here, we develop a data-driven pipeline that links micromotives to macrobehavior by augmenting hydrodynamics with utility functions that describe individual preferences in microeconomics. We show how to systematically validate the hypotheses underlying this construction from data using statistical tools based on neural networks. We illustrate this pipeline on the case study of human residential dynamics in the United States, for which census and sociological data is available, and show how trends in sociological surveys can be related to trends seen in racial segregation. In particular, we highlight that a history-dependence in the segregation-integration transition can arise even when agents have no memory. Beyond residential segregation, our work paves the way for systematic investigations of social-driven motility in real space from micro-organisms to humans, as well as fitness-mediated motion in more abstract genomic spaces

Process heat flow model for temperature and hardness prediction during friction taper stud welding of AISI 4140

Friction Taper Stud Welding (FTSW) is a relatively new solid state welding process, developed from the concepts of friction welding, which theoretically operates below the melting temperatures of the material being welded. During friction welding, heat is generated by conversion of mechanical energy into thermal energy at the interface of the work pieces, during rotation under pressure. Quality welds are dependant on the correct selection of welding process parameters, which are currently chosen empirically, and the FTSW evaluated by mechanical testing. This method is time consuming, uneconomical and could cause that optimised conditions are overlooked. A proposed solution would be to numerically model the process, but reference to successful computational modelling of the FTSW process is currently not available and data regarding the responses during the process are limited. The ultimate aim of the present study is to develop a finite element model to simulate the FTSW process using AISI 4140 medium carbon low alloy steel, delivering temperature profiles and hardness predictions through the Heat Affected Zone (HAZ) – using a combined experimental and numerical study. To achieve the objectives of this study a systematic approach was adopted and conducted in several phases. A weld matrix was configured with ranging weld input parameters to determine the affect of weld input parameters on real-time responses. To provide a relationship between these factors, welding was conducted using a portable friction taper stud welding platform linked to a control and data logging system for measuring the real time axial forces, spindle speed, material displacement, torque and temperature responses as a function of time. The input process parameters applied being motor speed, axial forces, displacement and forging time. The temperature distribution through the weld, by direct measurement, as a function of weld time and position is investigated. During the experimental welds temperature responses, as influenced by welding parameters, were recorded using embedded N-Type thermocouples at various locations in the near vicinity of the weld interface. The main hot spots during welding were identified to be close to the top surface just before weld completion and at the bottom centre surface of the plug weld at the interface line. All the welds showed similar trends and a maximum temperature of 1078°C at the bottom of the weld was reached for a rotational tool speed of 5160rpm, axial friction force of 15kN and displacement of 6.5mm, due to the heat generated by friction between the tool and weld coupon. The weld torque increase rapidly at the start of the weld and reached a peak value shortly after the start of the weld, while a peak temperature of 1366°C, for a rotational tool speed of 5160rpm, axial friction force of 10kN and displacement of 8mm was reached at the top edge of the plug weld. This position of anticipated peak temperature value is due to the heat transferred during the FTSW process together with the accumulation of expelled material forming on the surface of the weld coupon. Statistical methods were applied to obtain knowledge of the trends and relationship between weld input parameters for various weld responses, including energy input, temperature, friction time, torque and displacement rate. Although it was shown that no single parameter solely controls the temperature gradients in the weld, the dominant influence of the rotational speed at the bottom of the weld and that of the displacement, at the top of the weld, were evident. The peak temperatures during the weld are of interest as these temperatures, together with the subsequent cooling rates, determine the Vickers hardness, of the material, through the weld. Spindle speed was found to have the dominant effect on temperature in the bottom half of the weld with displacement having a contributive effect closer to the top of the weld. Friction force dominate the effect on friction time, displacement rate and total energy input with friction force and spindle speed having an equal effect on torque. The multiple regression analysis resulted in valid models with varied, but acceptable accuracy with the equation for friction time resulting in an R predict value of 93.34%. These models provided a clear insight to the influence of weld input parameters on the weld responses and the model for friction time was used as an input parameter to the FTS welding simulation. The accurate prediction of the interface temperature is fundamental for process optimisation which will allow for producing consistent, reliable plug welds. A fully coupled transient two-dimensional axi-symmetrical analysis of heat flow during the FTSW process of AISI 4140 steel and subsequent Vickers hardness profiles through the HAZ, making use of numeric simulation applied in the commercially available FEA software, COMSOL Multiphysics®, is developed and reported on. Process optimisation hinges on a better understanding of the heat distribution during welding, making a major contribution to the resultant hardness. The thermal-plastic flow coupling of the model is such that temperature values are resolved together with that of the velocity field. The simulation utilises a Computational Fluid Dynamics (CFD) two phase laminar flow and Heat Transfer physics, applied in an Eulerian mesh-based scheme. The viscosity of the fluid is based on a constitutive law of the flow stress using the Zener-Hollomon parameter with a flow model based on the Navier-Stokes’ equations to simulate the plastic deformation. Temperature dependant thermo-physical material properties and coefficient of friction are applied, and the application of viscous heating is controlled by a material state variable. The heat source model, required for material softening, is applied as two components, frictional and shear, with the heat source moving along the z-axis delivering sufficient energy to soften the metal, causing flow. The Navier-Stokes approach is applied with solid-state material transport during the weld based on laminar, viscous flow of a non-Newtonian fluid, dependant on temperature and strain rate. Numerically calculated values for temperature profiles and peak temperatures through to the weld as well as subsequent Vickers hardness profiles at points through the HAZ, obtained from the Finite Element model, were found to be in close agreement with values from trial welds. The largest variance was 19% for the peak temperature of weld E4W2, applying an axial friction force of 7.5kN, 6.5mm displacement and a tool rotational speed of 4080rpm – resulting in a friction time of 330 seconds. Predictions of hardness are found to be between 0% and 19% (mean 3%) of experimentally determined values with the biggest variance at the positions of peak temperatures due to the friction interfaces. The heat applied as a result of plastic deformation was found to be 5.4% of the total heat. The FTSW model predicts the temperatures at the friction interface, during the welding process, to be within the range, and frequently exceeding the solidus temperature of AISI 4140 steel. Results show that the models applied in the FTSW simulation show good agreement when compared to experimental values. The main contribution of this thesis, towards knowledge of the FTSW process, is: The relationships between weld input parameters and responses; Temperature dependant models of thermo-physical properties for AISI 4140 in the high temperature region (ranging from ambient to the solidus temperature); Successful application of the Navier-Stokes approach to simulate the plastic flow during FTSW and A numerical finite element model for the prediction of temperature gradients and hardness profiles through a FTSW

Modelling and measurement in synthetic biology

Synthetic biology applies engineering principles to make progress in the study of complex biological phenomena. The aim is to develop understanding through the praxis of construction and design. The computational branch of this endeavour explicitly brings the tools of abstraction and modularity to bear. This thesis pursues two distinct lines of inquiry concerning the application of computational tools in the setting of synthetic biology. One thread traces a narrative through multi-paradigm computational simulations, interpretation of results, and quantification of biological order. The other develops computational infrastructure for describing, simulating and discovering, synthetic genetic circuits. The emergence of structure in biological organisms, morphogenesis, is critically important for understanding both normal and pathological development of tissues. Here, we focus on epithelial tissues because models of two dimensional cellular monolayers are computationally tractable. We use a vertex model that consists of a potential energy minimisation process interwoven with topological changes in the graph structure of the tissue. To make this interweaving precise, we define a language for propagators from which an unambiguous description of the simulation methodology can be constructed. The vertex model is then used to reproduce laboratory results of patterning in engineered mammalian cells. The assertion that the claim of reproduction is justified is based on a novel measure of structure on coloured graphs which we call path entropy. This measure is then extended to the setting of continuous regions and used to quantify the development of structure in house mouse (Mus musculus) embryos using three dimensional segmented anatomical models. While it is recognised that DNA can be considered a powerful computational environment, it is far from obvious how to program with nucleic acids. Using rule-based modelling of modular biological parts, we develop a method for discovering synthetic genetic programs that meet a specification provided by the user. This method rests on the concept of annotation as applied to rule-based programs. We begin with annotating rules and proceed to generating entire rule-based programs from annotations themselves. Building on those tools we describe an evolutionary algorithm for discovering genetic circuits from specifications provided in terms of probability distributions. This strategy provides a dual benefit: using stochastic simulation captures circuit behaviour at low copy numbers as well as complex properties such as oscillations, and using standard biological parts produces results that are implementable in the laboratory

Computer Science & Technology Series : XIX Argentine Congress of Computer Science. Selected papers

CACIC’13 was the nineteenth Congress in the CACIC series. It was organized by the Department of Computer Systems at the CAECE University in Mar del Plata. The Congress included 13 Workshops with 165 accepted papers, 5 Conferences, 3 invited tutorials, different meetings related with Computer Science Education (Professors, PhD students, Curricula) and an International School with 5 courses. CACIC 2013 was organized following the traditional Congress format, with 13 Workshops covering a diversity of dimensions of Computer Science Research. Each topic was supervised by a committee of 3-5 chairs of different Universities. The call for papers attracted a total of 247 submissions. An average of 2.5 review reports were collected for each paper, for a grand total of 676 review reports that involved about 210 different reviewers. A total of 165 full papers, involving 489 authors and 80 Universities, were accepted and 25 of them were selected for this book.Red de Universidades con Carreras en Informática (RedUNCI

2009 program of studies : nonlinear waves

The fiftieth year of the program was dedicated to Nonlinear Waves, a topic with many applications in geophysical fluid dynamics. The principal lectures were given jointly by Roger Grimshaw and Harvey Segur and between them they covered material drawn from fundamental theory, fluid experiments, asymptotics, and reaching all the way to detailed applications. These lectures set the scene for the rest of the summer, with subsequent daily lectures by staff and visitors on a wide range of topics in GFD. It was a challenge for the fellows and lecturers to provide a consistent set of lecture notes for such a wide-ranging lecture course, but not least due to the valiant efforts of Pascale Garaud, who coordinated the write-up and proof-read all the notes, we are very pleased with the final outcome contained in these pages. This year’s group of eleven international GFD fellows was as diverse as one could get in terms of gender, origin, and race, but all were unified in their desire to apply their fundamental knowledge of fluid dynamics to challenging problems in the real world. Their projects covered a huge range of physical topics and at the end of the summer each student presented his or her work in a one-hour lecture. As always, these projects are the heart of the research and education aspects of our summer study.Funding was provided by the National Science Foundation through Grant No. OCE-0824636 and the Office of Naval Research under Contract No. N00014-09-10844