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Ph.D Theses

Leveraging novel information sources for protein structure prediction

Michael Bohlke-Schneider, December 2015

Three-dimensional protein structures are an invaluable stepping stone towards the understanding of cellular processes. Not surprisingly, state-of-the-art structure prediction methods heavily rely on information. This thesis aims to leverage new information sources: Physicochemical information encoded in predicted structure models and experimental data from high-density cross-linking / mass spectrometry (CLMS) experiments. We demonstrate that these information sources allow improved structure prediction and the reconstruction of human serum albumin domain structures from experimental data collected in its native environment, human blood serum.



Multimodal human computer interaction in virtual realities based on an exoskeleton

Ingo Kossyk, August 2012

The key features of this system are a high degree of immersion into the computer generated virtual environment and a large working volume. The high degree of immersion will be achieved by multimodal human-exoskeleton interaction based on haptic effects, audio and three- dimensional visualization. The large working volume will be achieved by a lightweight wearable construction that can be carried on the back of the user.



Efcient Motion Planning for Intuitive Task Execution in Modular Manipulation Systems

Markus Rickert, Mai 2011

Computationally efficient motion planning mus avoid exhaustive exploration of high-dimensional configuration spaces by leveraging the structure present in real-world planning problems. We argue that this can be accomplished most effectively by carefully balancing exploration and exploitation.

Exploration seeks to understand configuration space,
irrespective of the planning problem, and exploitation acts to
solve the problem, given the available information obtained
by exploration. We present an exploring/exploiting tree (EET)
planner that balances its exploration and exploitation behavior.

The planner acquires workspace information and subsequently
uses this information for exploitation in configuration space. If
exploitation fails in difficult regions the planner gradually shifts
to its behavior towards exploration.



Interactive Perception of Articulated Objects for Autonomous Manipulation

Dov Katz, 2011

This thesis develops robotic skills for manipulating novel articulated objects. The degrees of freedom of an articulated object describe the relationship among its rigid bodies, and are often relevant to the object's intended function. Examples of everyday articulated objects include scissors, pliers, doors, door handles, books, and drawers. Autonomous manipulation of articulated objects is therefore a prerequisite for many robotic applications in our everyday environments.



Adaptive Balancing of Exploitation with Exploration to Improve Protein Structure Prediction

TJ Brunette, 2011

The most significant impediment for protein structure prediction is the inadequacy of conformation space search. Conformation space is too large and the energy landscape too rugged for existing search methods to consistently find near-optimal minima.


Exploiting Structure: A Guided Approach to Sampling-Based Robot Motion Planning

Brendan Burns, 2007

Robots already impact the way we understand our world and live our lives. However, their impact and use is limited by the skills they possess. Currently deployed autonomous robots lack the manipulation skills possessed by humans. To achieve general autonomy and applicability in the real world, robots must possess such skills.


Diploma / Master Theses

Predicting protein contacts by combining information from sequence and physicochemistry

Kolja Stahl, February 2016

In this thesis we present a new contact predictor that combines evolutionary, sequence-based and physicochemical information. The contact predictor uses a new and refined feature set with drastically reduced dimensionality.


Force-Controlled Action Primitives for Interactive Perception

Georg Flick, Oct 2015

Advisors: Roberto Martín-Martín, Sebastian Höfer and Oliver Brock

Interactive Perception exploits the robot capabilities to interact with the environment to reveal hidden properties, like the kinematic structures of articulated objects. However, when the robot faces a new environment, it needs to decide on how to interact to maximize the information gain based on sensor data, and use compliant controllers that allow the articulation to guide the motion...



Increasing the Stiffness of a Pneumatic Actuator with Granular and Layer Jamming

Vincent Wall, May 2014

The ability to selectively stiffen otherwise compliant soft actuators increases their versatility and dexterity. The thesis investigates granular jamming and layer jamming as two possible methods to achieve stiffening with PneuFlex actuators, a type of soft continuum actuator. It details five designs of jamming compartments that can be attached to an actuator. The strength of the most effective prototype based on layer jamming is also validated in the context of pushing buttons.



Motion Planning in Dynamic Environments

with Probabilistic Connectivity Roadmaps


Peter Lehner, March 2014

We present an incremental method for motion generation in environments with unpredictably moving and initially unknown obstacles. The key to the method is its incremental nature: it locally augments and adapts global motion plans in response to changes in the environment, even if they significantly change the connectivity of the world.




Shifting the Boundary Between Planning and Control - Task-Consistent Motion Generation in Unstructured Environments


Nicolas Kuhnen, October 2012


In this thesis we present a motion generation approach that shifts the boundary between planning and control methods to generate task-consistent motion under uncertainty.



Using recurring spatially contiguous substructures in the Protein Database for protein structure prediction

Mahmoud Mabrouk, November 2012

In this work, we present a new approach for protein structure prediction using a novel source of information: Building Blocks. These are sequentially non-continuous, but structurally contiguous, structural motifs that are retrieved according to a given sequence. 


Aligning a Sequence to Non-contiguous Sequence Fragments

Stefan Dörr, 27. July 2012

Sequence alignment methods are frequently used in protein structure prediction to identify homologous protein structures. The existing methods make local and global alignments between sequentially contiguous protein sequences. However, in our ongoing protein structure prediction research, we have a unique sequence to sequence alignment problem. The potential sequence alignments need to be made between a target sequence and the sets of sequence fragments, where the sequence fragments may not be sequentially contiguous.



Grasping using Visual Feedback

Georg Bartels, März 2012

Interactively explore and grasp real-world objects using visual feedback.



3D Perception for Grasping

Stefan Schrandt, 07. June 2012

Allow Robots to grasp unknown objects while perceive the environment and the objects with a 3D sensors.



A Rendering Framework for Wearable Haptics in Large Virtual Environments

Jonas Dörr, April 2011

A novel wearable haptic interface based on an exoskelett was developed at RBO.



Using tree-based robot motion planning algorithms for protein loop closure

Florian Kamm, December 2010

A novel approach for the protein loop closure problem inspired from robot modeling is developed using the kinematic chain representation of the loop chain and a motion planning technique.



Simulating Physical Dynamics of Virtual Objects with a Wearable Haptic Interface

Lars Raschendörfer, September 2010

Haptic devices enhance the range of multi-modal interaction in virtual reality environments. With the wearable haptic device, developed at the RBO Lab, this interaction is not limited to a small workspace any longer. The wider range of motion allows for new application scenarios.



Evaluation of Three Sensor Technologies for Use in Soft Robot Fingers

Stefan Schirmeister, März 2016.

Sensing for soft continuum actuators as a necessary technology has emerged recently with the development of so called soft hands, which exploit the high deformability of soft structures and materials. Unfortunately, soft, stretchable sensors capable of withstanding a stretch of 100% are commercially not available. At the same time their tight integration into actuators is required to address the specific challenges of continuously deforming actuators. The thesis evaluates three potential sensor technologies for their suitability in soft hands. The thesis investigates their robustness, ease of use, long term stability and responsiveness with respect to the intended application in soft hands.


Bachelor Theses

Position-Based Servoing via Probabilistic Part-Based Object Models


Manuel Wöllhaf, January 2015

To extend the field of application of robots in unstructured environments it is necessary to develop new techniques of environment perception and interpretation. These methods must give machines the capability to generate sufficient information, which enables them to fulfill their tasks with the aid of their sensors. Therefore it is required to extract local and task dependent invariant structure out of the unstructured environment. more to: Position-Based Servoing via Probabilistic Part-Based Object Models

Three dimensional Joint Detection


Andreas Orthey, September 2012

Enable a robot to infer the type of joint between moving clusters of 3d features. This can further be used to build a kinematic structure of an observed object. more to: Three dimensional Joint Detection

Extended Visual Servoing for Manipulation


Sebastian Koch, February 2011

The interest in robots that are able to act in unstructured environments is increasing. more to: Extended Visual Servoing for Manipulation

A Practical Guide to Transformed Predictive State Representations


Niklas Gebauer, September 2015

Predictive state representations (PSRs) are gaining a lot of attention in the robotics community lately because, in theory, they promise a powerful model that might be learned directly from data. But the practical application of PSRs remains a difficult procedure. In this practical guide we aim to ease and encourage practical work with PSRs. more to: A Practical Guide to Transformed Predictive State Representations

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