Semi-automatic generation of three-dimensional visual algorithm simulations

Algorithms and data structures constitute the theoretical foundations of computer science and are an integral part of any classical computer science curriculum. Due to their high level of abstraction, the understanding of algorithms is of crucial concern to the vast majority of novice students. To facilitate the understanding and teaching of algorithms, a new research field termed "algorithm visualisation" evolved in the early 1980's. This field is concerned with innovating techniques and concepts for the development of effective algorithm visualisations for teaching, study, and research purposes. Due to the large number of requirements that high-quality algorithm visualisations need to meet, developing and deploying effective algorithm visualisations from scratch is often deemed to be an arduous, time-consuming task, which necessitates high-level skills in didactics, design, programming and evaluation. A substantial part of this thesis is devoted to the problems and solutions related to the automation of three-dimensional visual simulation of algorithms. The scientific contribution of the research presented in this work lies in addressing three concerns: - Identifying and investigating the issues related to the full automation of visual simulations. - Developing an automation-based approach to minimising the effort required for creating effective visual simulations. - Designing and implementing a rich environment for the visualisation of arbitrary algorithms and data structures in 3D. The presented research in this thesis is of considerable interest to (1) researchers anxious to facilitate the development process of algorithm visualisations, (2) educators concerned with adopting algorithm visualisations as a teaching aid and (3) students interested in developing their own algorithm animations.Als fundamentale abstrakte Konzepte der theoretischen Informatik sind Algorithmen und Datenstrukturen ein integraler Bestandteil jedes klassischen Kurrikulums eines Informatik-Studiums. Aufgrund ihrer abstrakten Eigenschaften stellt das Verstehen der Arbeitsweise von Algorithmen für viele Studierende eine große Herausforderung dar. Um das Lernen, Lehren und Erforschen von Algorithmen und Datenstrukturen zu vereinfachen, wurde Anfang der 80er Jahre ein Forschungsgebiet namens Algorithmenvisualisierung geschaffen. Als Teildisziplin der Softwarevisualisierung befasst sich dieses Forschungsfeld mit der dynamischen Visualisierung des abstrakten Verhaltens von Algorithmen und den diesen zugrundeliegenden Datenstrukturen. Algorithmenvisualisierung gilt als ein modernes e-Learning- und e-Teaching-Instrument, das Computergraphiktechniken einsetzt, um das Verstehen, Vermitteln und Erforschen von Algorithmen zu erleichtern. Ein Hauptziel dieser Dissertation besteht darin, Ansätze zur Automatisierung von dreidimensionalen visuellen Algorithmensimulationen zu entwickeln und zu implementieren. Eine visuelle Simulation eines Algorithmus ist eine interaktive Animation seines Verhaltens und der Zustandsänderungen seiner Daten, der eine Echtzeitsimulation des Algorithmus zugrunde liegt. Der wissenschaftliche Beitrag dieser Arbeit besteht darin, die bislang unerforschten Probleme der vollautomatischen Visualisierung von Algorithmen zu identifizieren und zu analysieren, mögliche Lösungswege und -ansätze zu entwickeln und diese in eine zu schaffende Algorithmenvisualisierungsumgebung zu implementieren. Desweiteren präsentiert die Arbeit einen Ansatz zur Minimierung des Aufwands für die Entwicklung von visuellen Simulationen paralleler Algorithmen und einen Ansatz zur passiven Animation von Algorithmen zu NP-vollständigen Problemen. ..

Exploration of Reaction Pathways and Chemical Transformation Networks

For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These approaches differ in their application range, the level of completeness of the exploration, as well as the amount of heuristics and human intervention required. Here, we describe and compare the different approaches based on these criteria. Future directions leveraging the strengths of chemical heuristics, human interaction, and physical rigor are discussed.Comment: 48 pages, 4 figure

Toward improved streamflow forecasts: Value of semidistributed modeling

The focus of this study is to assess the performance improvements of semidistributed applications of the U.S. National Weather Service Sacramento Soil Moisture Accounting model on a watershed using radar-based remotely sensed precipitation data. Specifically, performance comparisons are made within an automated multicriteria calibration framework to evaluate the benefit of "spatial distribution" of the model input (precipitation), structural components (soil moisture and streamflow routing computations), and surface characteristics (parameters). A comparison of these results is made with those obtained through manual calibration. Results indicate that for the study watershed, there are performance improvements associated with semidistributed model applications when the watershed is partitioned into three subwatersheds; however, no additional benefit is gained from increasing the number of subwatersheds from three to eight. Improvements in model performance are demonstrably related to the spatial distribution of the model input and streamflow routing. Surprisingly, there is no improvement associated with the distribution of the surface characteristics (model parameters)

Leveraging legacy codes to distributed problem solving environments: A web service approach

This paper describes techniques used to leverage high performance legacy codes as CORBA components to a distributed problem solving environment. It first briefly introduces the software architecture adopted by the environment. Then it presents a CORBA oriented wrapper generator (COWG) which can be used to automatically wrap high performance legacy codes as CORBA components. Two legacy codes have been wrapped with COWG. One is an MPI-based molecular dynamic simulation (MDS) code, the other is a finite element based computational fluid dynamics (CFD) code for simulating incompressible Navier-Stokes flows. Performance comparisons between runs of the MDS CORBA component and the original MDS legacy code on a cluster of workstations and on a parallel computer are also presented. Wrapped as CORBA components, these legacy codes can be reused in a distributed computing environment. The first case shows that high performance can be maintained with the wrapped MDS component. The second case shows that a Web user can submit a task to the wrapped CFD component through a Web page without knowing the exact implementation of the component. In this way, a user’s desktop computing environment can be extended to a high performance computing environment using a cluster of workstations or a parallel computer

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

Physics-based visual characterization of molecular interaction forces

Molecular simulations are used in many areas of biotechnology, such as drug design and enzyme engineering. Despite the development of automatic computational protocols, analysis of molecular interactions is still a major aspect where human comprehension and intuition are key to accelerate, analyze, and propose modifications to the molecule of interest. Most visualization algorithms help the users by providing an accurate depiction of the spatial arrangement: the atoms involved in inter-molecular contacts. There are few tools that provide visual information on the forces governing molecular docking. However, these tools, commonly restricted to close interaction between atoms, do not consider whole simulation paths, long-range distances and, importantly, do not provide visual cues for a quick and intuitive comprehension of the energy functions (modeling intermolecular interactions) involved. In this paper, we propose visualizations designed to enable the characterization of interaction forces by taking into account several relevant variables such as molecule-ligand distance and the energy function, which is essential to understand binding affinities. We put emphasis on mapping molecular docking paths obtained from Molecular Dynamics or Monte Carlo simulations, and provide time-dependent visualizations for different energy components and particle resolutions: atoms, groups or residues. The presented visualizations have the potential to support domain experts in a more efficient drug or enzyme design process.Peer ReviewedPostprint (author's final draft