Distributed Individual-Based Environmental Simulation

This paper describes the development and construction of a distributed model allowing the simulation of a large population. Particular attention will be paid to allowing the modelling of an individual's behaviour, communication and interaction with a shared environment. Individual based modelling is not a new concept, nor is the idea of distributed simulations, the system detailed here offers a means of combining these two paradigms into one large-scale modelling environment. A key concept in this system is that each individual being modelled is implemented as a separate process. This atomisation of the model allows the simulation a greater flexibility, individuals can be rapidly developed and the simulation can be spread over a wide number of machines of varying architectures. In an attempt to produce a flexible, extensible, individual based model of a large number of individual subjects the client-server paradigm has been employed. Combining the individual-based modelling techniques with a client-server network architecture has been found to be quite straightforward with the added bonus of having communication between individuals included for free. The idea of considering the problem as one of interaction between an individual and the environment means that the problems normally associated with distributed simulations, those of continuity of world-views for different clients and of communication between clients, are easily solved. Although this system has been developed originally to allow simulations of the Mountain Gorilla (Gorilla Gorilla Beringe) population, the modelling methods employed have meant that almost any entity can be simulated with very little change to the basic simulation processes

Parametrizable cameras for 3D computational steering

We present a method for the definition of multiple views in 3D interfaces for computational steering. The method uses the concept of a point-based parametrizable camera object. This concept enables a user to create and configure multiple views on his custom 3D interface in an intuitive graphical manner. Each view can be coupled to objects present in the interface, parametrized to (simulation) data, or adjusted through direct manipulation or user defined camera controls. Although our focus is on 3D interfaces for computational steering, we think that the concept is valuable for many other 3D graphics applications as well

Visual support for the understanding of simulation processes

Current visualization systems are typically based on the concept of interactive post-processing. This decoupling of data visualiza-tion from the process of data generation offers a flexible applica-tion of visualization tools. It can also lead, however, to information loss in the visualization. Therefore, a combination of the visual-ization of the data generating process with the visualization of the produced data offers significant support for the understanding of the abstract data sets as well as the underlying process. Due to the application-specific characteristics of data generating processes, the task requires tailored visualization concepts. In this work, we focus on the application field of simulating biochemical reaction networks as discrete-event systems. These stochastic processes generate multi-run and multivariate time-series, which are analyzed and compared on three different process levels: model, experiment, and the level of multi-run simulation data, each associated with a broad range of analysis goals. To meet these challenging characteristics, we present visualization concepts specifically tailored to all three process levels. The fundament of all three visualization concepts is a compact view that relates the multi-run simulation data to the characteristics of the model structure and the experiment. The view provides the visualization at the experi-ment level. The visualization at the model level coordinates mul-tiple instances of this view for the comparison of experiments. At the level of multi-run simulation data, the views gives an overview on the data, which can be analyzed in detail in time-series views suited for the analysis goals. Although we derive our visualization concepts for one concrete simulation process, our general concept of tailoring the visualization concepts to process levels is generally applicable for the visualization of simulation processes

Experiences on Using TRAKLA2 to Teach Spatial Data Algorithms

AbstractThis paper reports on the results of a two year project in which visual algorithm simulation exercises were developed for a spatial data algorithms course. The success of the project is studied from several point of views, i.e., from developer's, teachers's, and student's perspective. The amount of work, learning outcomes, and feasibility of the system has been estimated based on the data gathered during the project. The results are encouraging, which motivates to extend the concept also for other courses in the future

Syntactic approach to electric mobility in metropolitian areas: NE 1 district core, segment map

Capturing vehicular travel behavior is one of the most popular models that deal with relevant aspects of urban regions and communities. Since 1960s, it has been matured and evolved to cover all aspects of travel demand applications. Different theories are employed to predict the movement of trip makers' likewise metric method and the estimation of origin-destination matrixes, intervening opportunities method which counts more on probabilities, and finally the spatial configuration modeling. The latter is to apply topo-geometrical analysis to arrive at configurational measures that can optimally approximate movement patterns in the urban network. Space syntax is an alternative approach to estimate conventional vehicular travel demand without using O-D matrix trip data, which is difficult to be obtained. Space Syntax is an alternative approach to predict the vehicular movement in urban systems using the concept of accessibility measures (syntactic measures and maps) which reflects the complexity of routes from a road segment to all the others within the system. The syntactic approach is employed in this study to simulate a particular mobility system; electric vehicles (EVs) cluster. Simulating EVs'-systems is a subset of the conventional traffic modeling entire group. In particular, EV modeling environment set-up and configurations differ due to the special paradigms and behavioral characteristic aspects the system has. EV market is a niche market though it is expanding. This paper maps the current EV systems and focuses on one of which that needs prompt actions to be taken to have a mainstream supported and reliable market of EVs. Charging service is a thorny problem annoys the current users and hinders potential users to switch to low carbon emission vehicle purchase option. The study area located in the North East region of United Kingdom is investigated in detail. Spatial configuratioal analysis of the inner urban core of the metropolitan area, Newcastle-Gateshead, NE1 is undertaken. This paper presents a methodology to integrate configuratiomal modeling of NE1 to simulate the mobility mode within the context. Spatial analysis and segment maps have been generated via the use of Depthmap research software. Real information about users was collected from the service providers to employ some the simulation assumptions. A multi model simulation modeling is developed while incorporating configurational modeling to build the urban layer of an EV simulation environment. Space syntax analysis is conducted by using the open source application, Depthmap. Simulation is developed via a commercial tool, Anylogic. The paper views the necessary steps of forming and analyzing the urban system facilitating the integration of EV system to run the simulation

The Relation between Approximation in Distribution and Shadowing in Molecular Dynamics

Molecular dynamics refers to the computer simulation of a material at the atomic level. An open problem in numerical analysis is to explain the apparent reliability of molecular dynamics simulations. The difficulty is that individual trajectories computed in molecular dynamics are accurate for only short time intervals, whereas apparently reliable information can be extracted from very long-time simulations. It has been conjectured that long molecular dynamics trajectories have low-dimensional statistical features that accurately approximate those of the original system. Another conjecture is that numerical trajectories satisfy the shadowing property: that they are close over long time intervals to exact trajectories but with different initial conditions. We prove that these two views are actually equivalent to each other, after we suitably modify the concept of shadowing. A key ingredient of our result is a general theorem that allows us to take random elements of a metric space that are close in distribution and embed them in the same probability space so that they are close in a strong sense. This result is similar to the Strassen-Dudley Theorem except that a mapping is provided between the two random elements. Our results on shadowing are motivated by molecular dynamics but apply to the approximation of any dynamical system when initial conditions are selected according to a probability measure.Comment: 21 pages, final version accepted in SIAM Dyn Sy

Taming Graphical Modeling

Visual models help to understand complex systems. However, with the user interaction paradigms established today, activities such as creating, maintaining or browsing visual models can be very tedious. Valuable engineering time is wasted with archaic activities such as manual placement and routing of nodes and edges. This report presents an approach to enhance productivity by focusing on the pragmatics of model-based design. Our contribution is twofold: First, the concept of meta layout enables the synthesis of different diagrammatic views on graphical models. This modularly employs sophisticated layout algorithms, closing the gap between MDE and graph drawing theory. Second, a view management logic harnesses this auto layout to present customized views on models. These concepts have been implemented in the open source Kiel Integrated Environment for Layout Eclipse Rich Client (KIELER). Two applications---editing and simulation---illustrate how view management helps to increase developer productivity and tame model complexity

Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments

There is a gap between kinetic experiment and simulation in their views of the dynamics of complex biomolecular systems. Whereas experiments typically reveal only a few readily discernible exponential relaxations, simulations often indicate complex multistate behavior. Here, a theoretical framework is presented that reconciles these two approaches. The central concept is “dynamical fingerprints” which contain peaks at the time scales of the dynamical processes involved with amplitudes determined by the experimental observable. Fingerprints can be generated from both experimental and simulation data, and their comparison by matching peaks permits assignment of structural changes present in the simulation to experimentally observed relaxation processes. The approach is applied here to a test case interpreting single molecule fluorescence correlation spectroscopy experiments on a set of fluorescent peptides with molecular dynamics simulations. The peptides exhibit complex kinetics shown to be consistent with the apparent simplicity of the experimental data. Moreover, the fingerprint approach can be used to design new experiments with site-specific labels that optimally probe specific dynamical processes in the molecule under investigation

An embodied and grounded perspective on concepts

By the mainstream view in psychology and neuroscience, concepts are informational units, rather stable, and are represented in propositional format. In the view I will outline, instead, concepts correspond to patterns of activation of the perception, action and emotional systems which are typically activated when we interact with the entities they refer to. Starting from this embodied and grounded approach to concepts, I will focus on different research lines and present some experimental evidence concerning concepts of objects, concepts of actions, and abstract concepts. I will argue that, in order to account for abstract concepts, embodied and grounded theories should be extended

Perceptual simulation in conceptual tasks

No abstract available