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«Augmented Chemical Reactions – Research on 3D Selection and Confirmation Methods Patrick Julian Ludwig Maier Institut für Informatik der ...»

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Institut für Informatik

der Technischen Universität


Augmented Chemical Reactions –

Research on 3D Selection and

Confirmation Methods

Patrick Julian Ludwig Maier

Institut für Informatik

der Technischen Universität


Fachgebiet Augmented Reality

Augmented Chemical Reactions –

Research on 3D Selection and

Confirmation Methods

Patrick Julian Ludwig Maier

Vollständiger Abdruck der von der Fakultät für Informatik der Technischen Universität

München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigten Dissertation.

Vorsitzender: Univ.-Prof. Dr.-Ing. Nils Thürey

Prüfer der Dissertation:

1. Univ.-Prof. Gudrun J. Klinker, Ph.D.

2. Prof. Arthur J. Olson, Ph.D., University of California / USA Die Dissertation wurde am 15.05.2014 bei der Technischen Universität München eingereicht und durch die Fakultät für Informatik am 13.08.2014 angenommen.

Abstract User interfaces are important components of a computer system with the user being in control. It is very difficult to build a user interface that fits the needs of a task and most important which is easy to use, understandable and effective. Thus, lots of work goes into research of new and better user interfaces. Whereas the 2D user interfaces of computers have already been there for a long time, 3D user interfaces are still quite new and most of them still lack some of the previous mentioned properties. In my thesis I have investigated and implemented new ways for communicating with the computer when being in a 3D virtual or augmented reality environment.

Evaluations on specific parts of a new user interface always bear the problem of being distorted by other factors surrounding the user interface. I therefore spent much effort on building a flexible system that has an easy to use interface itself which does not distort the results of the evaluations.

This thesis was based on a collaborating project between the Fachgebiet Molecular Catalysis (MolCat Laboratory) of the Chemistry Department and the Fachgebiet Augmented Reality (FAR) of the Computer Science Department here at the Technische Universität München. In this collaboration I built the application Augmented Chemical Reactions that lets the user visualize molecules as well as watch how molecules deform in their spatial structure while interacting with them. I have researched how a user can do Selection and Confirmation while at the same time controlling the pose of the virtual molecules in the 3D space.

An evaluation at a school showed that inspecting different molecules with a direct control of the pose, led to a better spatial understanding of the molecules than controlling the position and orientation of the molecules by using the mouse and keyboard.

Zusammenfassung Benutzerschnittstellen sind wichtige Komponenten eines Systems, in dem der Benutzer die Kontrolle hat. Es ist sehr schwierig eine Benutzerschnittstelle zu erstellen, welche den Bedürfnissen einer Aufgabe entspricht und – am wichtigsten – einfach zu bedienen, verständlich und effektiv ist. Dies ist der Grund, wieso viel Aufwand in die Erforschung von neuen und besseren Benutzerschnittstellen gesteckt wird. Während 2D Benutzerschnittstellen bereits lange Zeit existieren, sind 3D Benutzerschnittstellen noch relativ neu. Zudem fehlen den meisten von ihnen noch einige der zuvor genannten Eigenschaften. In meiner Arbeit habe ich neue Möglichkeiten erforscht, um mit dem Computer möglichst intuitiv in einer virtuellen oder augmentierten 3D Umgebung zu interagieren.

Studien zu bestimmten Elementen einer neuen Benutzerschnittstelle haben oftmals das Problem, dass die Ergebnisse durch externe Faktoren verfälscht werden, die nicht direkt das Design der Benutzerschnittstelle betreffen. Ich habe daher großes Augenmerk auf die Entwicklung eines flexiblen Systems gerichtet, welches eine einfach zu benutzende Schnittstelle bietet, um die Resultate meiner Evaluationen nicht zu verfälschen.

Diese Doktorarbeit basiert auf einem Kooperationsprojekt zwischen dem Fachgebiet Molecular Catalysis (MolCat Laboratory) des Instituts für Chemie und dem Fachgebiet Augmented Reality (FAR) des Instituts für Informatik der Technischen Universität München. In dieser Kooperation habe ich das Programm Augmented Chemical Reactions entwickelt, mit dem Benutzer Moleküle visualisieren können. Weiterhin ist es möglich die Veränderung der räumlichen Struktur von Molekülen zu betrachten, während man mit ihnen interagiert. Ich habe untersucht, wie Benutzer etwas selektieren und bestätigen können, während sie zur selben Zeit die Position und Ausrichtung virtueller Moleküle im 3D Raum kontrollieren.

Eine Studie an einer Schule hat gezeigt, dass das Betrachten verschiedener Moleküle mit einer direkten Steuerung der Position und Orientierung zu einem besseren räumlichen Verständnis führte, als das Betrachten der Moleküle mit einer indirekten Steuerung mit Maus und Tastatur.

Acknowledgment Many thanks to numerous great people who supported me in my research as well as in this thesis.

At first I would like to thank Gudrun for having been such a great supervisor of my PhD thesis, as well as for the encouraging words, helpful advice and the comfortable working atmosphere in her lab.

Many thanks also to all of my colleagues Andi, Tayfur, Amal, Marcus, Christian, Manuel, Frieder, Yuta and Manfred of the „Fachgebiet Augmented Reality” who were great to work with.

I would also like to thank Professor Olson from the Molecular Graphics Lab and his colleagues, who gave me a wonderful three month stay abroad in San Diego.

Big thanks go to my parents Geralda and Winfried as well as to Robert and Alex who greatly supported me during this time.

Thank you all so much!


–  –  –

With the power of graphics cards and modern computers, three-dimensional (3D) environments become more and more popular. Virtual 3D environments are mostly known from 3D computer games or from animated films. But also research fields such as Virtual Reality (VR) and Augmented Reality (AR) are based on 3D environments that the user can interact with. To interact with such a three-dimensional environment there is the need of 3D user interfaces. The classical way is to use the well-established mouse and keyboard interfaces to interact with parts of the 3D environment. But as it is not really a natural user interface (NUI) it can become a bit cumbersome sometimes. NUIs which incorporate direct interactions with the environment can be learned and used faster but are not yet commonly available. There still exists a lot of potential to extend, improve and design new 3D user interfaces. Bowman et al. presented an overview of research on 3D user interfaces and its definition [12, 13]. The research on such 3D user interfaces (especially on selection and confirmation) is the main focus in this thesis. To test and evaluate such 3D user interfaces, I worked in the area of chemistry and developed the application Augmented Chemical Reactions (ACR).

Parts of this chapter have already been published in papers [54] and [56] presented at IJAS 2009 and ICCE 2009.

1.1 3D User Interfaces for Chemistry

Designing new molecules is a complex and time consuming task which requires a spatial understanding of the molecules. When scientists create a new molecule like a catalyst, they generally first create a model of the desired molecule in 2D which is then transferred to a 3D model in a computer. The 3D computer representation of the molecule is examined to determine whether the desired structure can be implemented and whether it provides the desired abilities or whether a redesign is necessary. When the design process has settled, the molecule is synthesized in the laboratory and tested for the desired attributes.

Especially the design, the development and the examination of the spatial 3D structure still bears several issues. Even if the structure of the molecule is represented in 3D, examining the molecule from different perspectives requires the designer to interact

1. Introduction

with conventional computer input devices. Such devices


3D motions to keys on a keyboard or to the 2D space of a computer mouse. This way a mapping from the keys or the two dimensions of freedom of the computer mouse to the six dimensions of freedom (three dimensions for the position and three dimensions for the orientation) of the molecules has to be made. This mapping bears a relatively high mental load and can slow down or distract the user from the real task.

A second issue lies in the changes of the energy distribution of the molecule during its development. The spatial structure changes every time a new atom, ligand or radical is added to the existing molecule structure. Without the help of a computer system that continuously calculates the new structure and properties of the molecules, it becomes hard to predict the change in the structure during assembly.

Figure 1.1: AR-based visualization of a dynamic adaptation of a molecule structure to forces from atoms of other molecules.

–  –  –

To support this development process, I implemented a 3D visualization and interaction system which helps users to easily visualize chemical molecules as tangible balland-stick models on pre-defined markers. It also simulates the dynamic change of the spatial structure while reacting with other molecules or atoms and visualizes it in an intuitive way (see Fig. 1.1). The system incorporates the paradigm of Augmented Reality (AR) where users can manipulate virtual 3D objects in a simple and intuitive way by moving real 3D objects. With this natural user interface (NUI), users can interactively explore the influence of different molecular properties on a reaction, such as the change of the spatial structure of the molecules during their manipulation, the rigidity of the molecules as well as steric clashes, resulting, for example, in chiral biases.

A real-time simulation calculates the attracting and repulsive forces between the reactants of a molecule and can be steered by manipulating the associated tracked, physical objects („tangibles”) in the real 3D space. The motion of those tangible placeholders for reactants leads to a dynamic deformation in the structure of the possible molecule product.

With this method, scientists can examine design issues at the early stage of molecular design. The opportunity to also change the viewpoint on the molecule in a 3D interaction space concurrently by using the same tangible handlers, extends the capabilities of the system in comparison to conventional approaches that use mice or keyboards for navigation.

In such „hands-on” explorations and visualizations of chemical behaviors, 3D positioning and timing of user gestures are an essential part for the simulation results.

Users need to move molecules to the right place and keep them there while the next steps of a reaction take place. Depending on the number of molecules involved, this may require one or more hands or support structures to hold the tangibles – possibly even a team of researchers, analog to puppetry.

Even though the direct manipulation via tangibles can control some very important aspects of a chemical simulation, many more parameters exist – and even those that are under direct positional control may be susceptible to imprecise user gestures. For example, many bonds between two molecules may be theoretically possible (see Fig. 1.2).

If only one is to be selected, which one will it be? If it is selected based on the distance between the atoms involved (Fig. 1.1), this may require users to have a high level of dexterity and the ability to hold very still when non-trivial molecules are involved.

A number of solutions are possible to provide such system control commands, e.g.

to select a particular bond out of a list of bonding options, alongside with direct manipulation. I will present and discuss some of them in this thesis.

If one hand can be freed from direct tangible interaction with the molecules, it can be used to control the system via regular mouse or keyboard. It can also be used to interact with widgets that are embedded into the 3D environment [52, 80].

1. Introduction Figure 1.2: Expemplary display of all potential bonds between pairs of atoms on two molecules. The possible bonds are visualized as semi-transparent cylinders between the atoms of the two molecules.

However, if both hands are regularly involved in the direct manipulation of the molecules, system control gestures must be integrated more deeply. To this end, tangibles may be equipped with extra sensors or special buttons – requiring a specialized environmental setting. If no such scene modifications are acceptable, interactive (un)clutching metaphors must be provided that allow users to switch between gestures for direct manipulation (in the true sense of Augmented Reality) and gestures for system control while temporarily „freezing” the manipulated objects. Another alternative to (un)clutching metaphors is to integrate the gestures for system control in the direct manipulation task. Here it becomes very difficult to differentiate between the direct manipulation movements and the movements for the system control gestures.

One possible option is using gestures at very different speeds: slow motions for direct

1.1 3D User Interfaces for Chemistry

manipulation and fast (meta) motions or no movement (See section 5.2.2) for system control. Without (un)clutching metaphors it might still be possible to perform system control along with direct manipulation, but it reduces the options for suitable gestures.

Voice-based input or the use of foot pedals are further interactive options. Yet, it may be hard for users to describe a specific bond concisely with spoken words or with their feet.

To support the users with an easy and understandable user interface, I had to think of input techniques other than the classic keyboard and mouse based user interfaces.

The structure of the following chapters is as follows:

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