Mark Moll  | publications

@Article{	  moll2008workshop-on-self-reconfigurable-modular-robots,
  author	= {Mark Moll and Daniela Rus},
  doi		= {10.1177/0278364908089348},
  journal	= {Intl.\ J.\ of Robotics Research},
  month		= {March/April},
  number	= {3/4},
  pages		= {277-278},
  title		= {Special Issue on Self-Reconfiguring Modular Robots (Guest
		  Editorial)},
  volume	= {27},
  year		= {2008}
}

@Article{	  yim2007modular-self-reconfigurable-robot-systems,
  abstract	= {The field of modular self-reconfigurable robotic systems
		  addresses the design, fabrication, motion planning, and
		  control of autonomous kinematic machines with variable
		  morphology. Beyond conventional actuation, sensing, and
		  control typically found in fixed-morphology robots,
		  self-reconfigurable robots are also able to deliberately
		  change their own shape by rearranging the connectivity of
		  their parts in order to adapt to new circumstances, perform
		  new tasks, or recover from damage. Over the last two
		  decades, this field has advanced from proof-of-concept
		  systems to elaborate physical implementations and
		  simulations. The goal of this article is to outline some of
		  this progress and identify key challenges and opportunities
		  that lay ahead.},
  author	= {Mark Yim and Wei-Min Shen and Benham Salemi and Daniela
		  Rus and Mark Moll and Hod Lipson and Eric Klavins},
  doi		= {10.1109/MRA.2007.339623},
  journal	= {{IEEE} Robotics \& Automation Magazine},
  month		= mar,
  number	= {1},
  pages		= {43--52},
  title		= {Modular Self-reconfigurable Robot Systems: Challenges and
		  Opportunities for the Future},
  volume	= {14},
  year		= {2007}
}

@Article{	  das2006low-dimensional-free-energy-landscapes,
  abstract	= {The definition of reaction coordinates for the
		  characterization of a protein-folding reaction has long
		  been a controversial issue, even for the ``simple'' case in
		  which one single free-energy barrier separates the folded
		  and unfolded ensemble. We propose a general approach to
		  this problem to obtain a few collective coordinates by
		  using nonlinear dimensionality reduction. We validate the
		  usefulness of this method by characterizing the folding
		  landscape associated with a coarse-grained protein model of
		  src homology 3 as sampled by molecular dynamics
		  simulations. The folding free-energy landscape projected on
		  the few relevant coordinates emerging from the
		  dimensionality reduction can correctly identify the
		  transition-state ensemble of the reaction. The first
		  embedding dimension efficiently captures the evolution of
		  the folding process along the main folding route. These
		  results clearly show that the proposed method can
		  efficiently find a low-dimensional representation of a
		  complex process such as protein folding.},
  author	= {Payel Das and Mark Moll and Hernan Stamati and Lydia E.
		  Kavraki and Cecilia Clementi},
  doi		= {10.1073/pnas.0603553103},
  journal	= {Proc.\ Natl.\ Acad.\ of Science USA},
  keywords	= {reaction coordinate, transition state, manifold,
		  embedding, ISOMAP, ScIMAP},
  month		= jun,
  number	= {26},
  pages		= {9885--9890},
  title		= {Low-dimensional, free-energy landscapes of protein-folding
		  reactions by nonlinear dimensionality reduction},
  volume	= {103},
  year		= {2006}
}

@Article{	  moll2006path-planning-for-deformable-linear,
  abstract	= {We present a new approach to path planning for deformable
		  linear (one-dimensional) objects such as flexible wires. We
		  introduce a method for efficiently computing stable
		  configurations of a wire subject to manipulation
		  constraints. These configurations correspond to
		  minimal-energy curves. By restricting the planner to
		  minimal-energy curves, the execution of a path becomes
		  easier. Our curve representation is adaptive in the sense
		  that the number of parameters automatically varies with the
		  complexity of the underlying curve. We introduce a planner
		  that computes paths from one minimal-energy curve to
		  another such that all intermediate curves are also
		  minimal-energy curves. This planner can be used as a
		  powerful local planner in a sampling-based roadmap method.
		  This makes it possible to compute a roadmap of the entire
		  ``shape space,'' which is not possible with previous
		  approaches. Using a simplified model for obstacles, we can
		  find minimal-energy curves of fixed length that pass
		  through specified tangents at given control points. Our
		  work has applications in cable routing, and motion planning
		  for surgical suturing and snake-like robots.},
  author	= {Mark Moll and Lydia E. Kavraki},
  doi		= {10.1109/TRO.2006.878933},
  journal	= {{IEEE} Trans.\ on Robotics},
  month		= aug,
  number	= {4},
  pages		= {625--636},
  title		= {Path Planning for Deformable Linear Objects},
  volume	= {22},
  year		= {2006}
}

@Article{	  moll-erdmann2002:manip-pose-distr,
  abstract	= {For assembly tasks parts often have to be oriented before
		  they can be put in an assembly. The results presented in
		  this paper are a component of the automated design of parts
		  orienting devices. The focus is on orienting parts with
		  minimal sensing and manipulation. We present a new approach
		  to parts orienting through the manipulation of pose
		  distributions. Through dynamic simulation we can determine
		  the pose distribution for an object being dropped from an
		  arbitrary height on an arbitrary surface. By varying the
		  drop height and the shape of the support surface we can
		  find the initial conditions that will result in a pose
		  distribution with minimal entropy. We are trying to
		  uniquely orient a part with high probability just by
		  varying the initial conditions. We will derive a condition
		  on the pose and velocity of a simple planar object in
		  contact with a sloped surface that will allow us to quickly
		  determine the final resting configuration of the object.
		  This condition can then be used to quickly compute the pose
		  distribution. We also present simulation and experimental
		  results that show how dynamic simulation can be used to
		  find optimal shapes and drop heights for a given part.},
  author	= {Mark Moll and Michael A. Erdmann},
  doi		= {10.1177/027836402320556449},
  journal	= {Intl.\ J.\ of Robotics Research},
  keywords	= {pose distributions, parts orienting, dynamic simulation},
  month		= mar,
  number	= {3},
  pages		= {277--292},
  title		= {Manipulation of Pose Distributions},
  volume	= {21},
  year		= {2002}
}

@Article{	  moll+2002:align-parts-micro-assem,
  abstract	= {Orienting parts that measure only a few micrometers in
		  diameter introduces several challenges that need not be
		  considered at the macro-scale. First, there are several
		  kinds of sticking effects due to Van der Waals forces and
		  static electricity which complicate hand-off motions and
		  release of a part. Second, the degrees of freedom of
		  micro-manipulators are limited. This paper proposes a pair
		  of manipulation primitives and a complete algorithm that
		  addresses these challenges. We will show that a sequence of
		  these two manipulation primitives can uniquely orient any
		  asymmetric part while maintaining contact without sensing.
		  This allows us to apply the same plan to many (identical)
		  parts simultaneously. For asymmetric parts we can find a
		  plan of length O(n) in O(n) time that orients the part,
		  where n is the number of vertices.},
  author	= {Mark Moll and Ken Goldberg and Michael A. Erdmann and Ron
		  Fearing},
  doi		= {10.1108/01445150210416673},
  journal	= {Assembly Automation},
  keywords	= {micromanipulation, parts orienting, parts feeding,
		  rolling},
  month		= feb,
  number	= {1},
  pages		= {46--54},
  title		= {Aligning Parts for Micro Assemblies},
  volume	= {22},
  year		= {2002}
}

@Article{	  moll-miikkulainen1997:conver-zone-episod-memor,
  abstract	= {Human episodic memory provides a seemingly unlimited
		  storage for everyday experiences, and a retrieval system
		  that allows us to access the experiences with partial
		  activation of their components. The system is believed to
		  consist of a fast, temporary storage in the hippocampus,
		  and a slow, long-term storage within the neocortex. This
		  paper presents a neural network model of the hippocampal
		  episodic memory inspired by Damasio's idea of Convergence
		  Zones. The model consists of a layer of perceptual feature
		  maps and a binding layer. A perceptual feature pattern is
		  coarse coded in the binding layer, and stored on the
		  weights between layers. A partial activation of the stored
		  features activates the binding pattern, which in turn
		  reactivates the entire stored pattern. For many
		  configurations of the model, a theoretical lower bound for
		  the memory capacity can be derived, and it can be an order
		  of magnitude or higher than the number of all units in the
		  model, and several orders of magnitude higher than the
		  number of binding-layer units. Computational simulations
		  further indicate that the average capacity is an order of
		  magnitude larger than the theoretical lower bound, and
		  making the connectivity between layers sparser causes an
		  even further increase in capacity. Simulations also show
		  that if more descriptive binding patterns are used, the
		  errors tend to be more plausible (patterns are confused
		  with other similar patterns), with a slight cost in
		  capacity. The convergence-zone episodic memory therefore
		  accounts for the immediate storage and associative
		  retrieval capability and large capacity of the hippocampal
		  memory, and shows why the memory encoding areas can be much
		  smaller than the perceptual maps, consist of rather coarse
		  computational units, and be only sparsely connected to the
		  perceptual maps.},
  author	= {Mark Moll and Risto Miikkulainen},
  doi		= {10.1016/S0893-6080(97)00016-6},
  journal	= {Neural Networks},
  number	= {6},
  pages		= {1017--1036},
  title		= {Convergence-Zone Episodic Memory: Analysis and
		  Simulations},
  volume	= {10},
  year		= {1997}
}

@InCollection{	  moll2007roadmap-methods-for-protein-folding,
  abstract	= {Protein folding refers to the process whereby a protein
		  assumes its intricate three-dimensional shape. Different
		  aspects of this problem have attracted much attention in
		  the last decade. Both experimental and computational
		  methods have been used to study protein folding and there
		  has been considerable progress This chapter reviews a class
		  of methods for studying protein folding called roadmap
		  methods. These methods are relatively new and are still
		  under active development. Roadmap methods are computational
		  methods that have been developed to understand the process
		  or the mechanism by which a protein folds or unfolds. It is
		  typically assumed that the folded state is already known.
		  Note that this is not a comprehensive survey of all
		  existing computational protein folding methods. In
		  particular, it does not cover Molecular Dynamics (MD)
		  methods, Monte Carlo methods (MC), the use of coarse grain
		  models in simulations and many others. },
  author	= {Mark Moll and David Schwarz and Lydia E. Kavraki},
  booktitle	= {Protein Structure Prediction: Methods and Protocols},
  edition	= {Second},
  editor	= {Mohammed Zaki and Chris Bystroff},
  month		= oct,
  publisher	= {Humana Press},
  series	= {Methods In Molecular Biology},
  title		= {Roadmap Methods for Protein Folding},
  url		= {http://www.springer.com/humana+press/biochemistry/book/978-1-58829-752-5?detailsPage=toc}
		  ,
  year		= {2007}
}

@InCollection{	  moll-erdmann2003:recon-shape-motion-unknow,
  abstract	= {We present a method to simultaneously reconstruct the
		  shape and motion of an unknown smooth convex object. The
		  object is manipulated by planar palms covered with tactile
		  elements. The shape and dynamics of the object can be
		  expressed as a function of the sensor values and the motion
		  of the palms. We present a brief review of previous results
		  for the planar case. In this paper we show that the 3D case
		  is fundamentally different from the planar case, due to
		  increased tangent dimensionality. The main contribution of
		  this paper is a shape-dynamics analysis in 3D, and the
		  synthesis of shape approximation methods via reconstructed
		  contact point curves.},
  author	= {Mark Moll and Michael A. Erdmann},
  booktitle	= {Algorithmic Foundations of Robotics V},
  doi		= {10.1007/b80173},
  editor	= {Jean-Daniel Boissonnat and Joel Burdick and Ken Goldberg
		  and Seth Hutchinson},
  keywords	= {tactile sensing, shape reconstruction, nonprehensile
		  manipulation, contact kinematics},
  pages		= {293--310},
  publisher	= {Springer Verlag},
  title		= {Reconstructing the Shape and Motion of Unknown Objects
		  with Active Tactile Sensors},
  year		= {2003}
}

@InCollection{	  moll-erdmann2001:manip-pose-distr,
  abstract	= {For assembly tasks parts often have to be oriented before
		  they can be put in an assembly. The results presented in
		  this paper are a component of the automated design of parts
		  orienting devices. The focus is on orienting parts with
		  minimal sensing and manipulation. We present a new approach
		  to parts orienting through the manipulation of pose
		  distributions. Through dynamic simulation we can determine
		  the pose distribution for an object being dropped from an
		  arbitrary height on an arbitrary surface. By varying the
		  drop height and the shape of the support surface we can
		  find the initial conditions that will result in a pose
		  distribution with minimal entropy. We are trying to
		  uniquely orient a part with high probability just by
		  varying the initial conditions. We will derive a condition
		  on the pose and velocity of an object in contact with a
		  sloped surface that will allow us to quickly determine the
		  final resting configuration of the object. This condition
		  can then be used to quickly compute the pose distribution.
		  We also present simulation and experimental results that
		  show how dynamic simulation can be used to find optimal
		  shapes and drop heights for a given part.},
  author	= {Mark Moll and Michael A. Erdmann},
  booktitle	= {Algorithmic and Computational Robotics: New Directions},
  editor	= {Bruce R. Donald and Kevin M. Lynch and Daniela Rus},
  keywords	= {pose distributions, parts orienting, dynamic simulation},
  pages		= {127--141},
  publisher	= {A. K. Peters},
  title		= {Manipulation of Pose Distributions},
  url		= {http://www.akpeters.com/book.asp?bID=139},
  year		= {2001}
}

@InProceedings{	  fofanov2008a-statistical-model-to-correct-systematic,
  abstract	= {The identification of protein function is crucial to
		  understanding cellular processes and selecting novel
		  proteins as drug targets. However, experimental methods for
		  determining protein function can be expensive and
		  time-consuming. Protein partial structure comparison
		  methods seek to guide and accelerate the process of
		  function determination by matching characterized functional
		  site representations, motifs, to substructures within
		  uncharacterized proteins, matches. One common difficulty of
		  all protein structural comparison techniques is the
		  computational cost of obtaining a match. In an effort to
		  maintain practical efficiency, some algorithms employ
		  efficient geometric threshold-based searches to eliminate
		  biologically irrelevant matches. Thresholds refine and
		  accelerate the method by limiting the number of potential
		  matches that need to be considered. However, because
		  statistical models rely on the output of the geometric
		  matching method to accurately measure statistical
		  significance, geometric thresholds can also artificially
		  distort the basis of statistical models, making statistical
		  scores dependant on geometric thresholds and potentially
		  causing significant reductions in accuracy of the
		  functional annotation method. This paper proposes a
		  point-weight based correction approach to quantify and
		  model the dependence of statistical scores to account for
		  the systematic bias introduced by heuristics. Using a
		  benchmark dataset of 20 structural motifs, we show that the
		  point-weight correction procedure accurately models the
		  information lost during the geometric comparison phase,
		  removing systematic bias and greatly reducing
		  misclassification rates of functionally related proteins,
		  while maintaining specificity. },
  author	= {Viacheslav Y. Fofanov and Brian Y. Chen and Drew H. Bryant
		  and Mark Moll and Olivier Lichtarge and Lydia E. Kavraki
		  and Marek Kimmel},
  booktitle	= {{IEEE} Intl.\ Conf.\ on Bioinformatics and Biomedicine
		  (BIBM)},
  doi		= {10.1109/BIBMW.2008.4686202},
  pages		= {1--8},
  title		= {A Statistical Model to Correct Systematic Bias Introduced
		  by Algorithmic Thresholds in Protein Structural Comparison
		  Algorithms},
  year		= {2008}
}

@InProceedings{	  moll2008labelhash-a-flexible-and-extensible-method,
  address	= {Toronto, Canada},
  author	= {Mark Moll and Lydia E. Kavraki},
  booktitle	= {Automated Function Prediction / BioSapiens Meeting
		  (AFP-BioSapiens)},
  doi		= {10.1038/npre.2008.2199.1},
  note		= {Available from Nature Precedings},
  title		= {{LabelHash}: A Flexible and Extensible Method for Matching
		  Structural Motifs},
  year		= {2008}
}

@InProceedings{	  moll2008matching-of-structural-motifs,
  abstract	= {There is an increasing number of proteins with known
		  structure but unknown function. Determining their function
		  would have a significant impact on understanding diseases
		  and designing new therapeutics. However, experimental
		  protein function determination is expensive and very
		  time-consuming. Computational methods can facilitate
		  function determination by identifying proteins that have
		  high structural and chemical similarity. Our focus is on
		  methods that determine binding site similarity. Although
		  several such methods exist, it still remains a challenging
		  problem to quickly find all functionally-related matches
		  for structural motifs in large data sets with high
		  specificity. In this context, a structural motif is a set
		  of 3D points annotated with physicochemical information
		  that characterize a molecular function. We propose a new
		  method called LabelHash that creates hash tables of
		  $n$-tuples of residues for a set of targets. Using these
		  hash tables, we can quickly look up partial matches to a
		  motif and expand those matches to complete matches. We show
		  that by applying only very mild geometric constraints we
		  can find statistically significant matches with extremely
		  high specificity in very large data sets and for very
		  general structural motifs. We demonstrate that our method
		  requires a reasonable amount of storage when employing a
		  simple geometric filter and further improves on the
		  specificity of our previous work while maintaining very
		  high sensitivity. Our algorithm is evaluated on 20 homolog
		  classes and a non-redundant version of the Protein Data
		  Bank as our background data set. We use cluster analysis to
		  analyze why certain classes of homologs are more difficult
		  to classify than others. The LabelHash algorithm is
		  implemented on a web server at
		  http://kavrakilab.org/labelhash/.},
  author	= {Mark Moll and Lydia E. Kavraki},
  booktitle	= {The Seventh Annual International Conference on
		  Computational Systems Bioinformatics (CSB2008)},
  pages		= {157-168},
  title		= {Matching of Structural Motifs Using Hashing on Residue
		  Labels and Geometric Filtering for Protein Function
		  Prediction},
  url		= {http://csb2008.org/csb2008papers/077Moll.pdf},
  year		= {2008}
}

@InProceedings{	  chen2007representations-of-structural-motifs-for-protein,
  address	= {Vienna, Austria},
  author	= {Brian Y. Chen and Drew H. Bryant and Joseph H. Bylund and
		  Amanda E. Cruess and David M. Kristensen and Viacheslav Y.
		  Fofanov and Mark Moll and Marek Kimmel and Olivier
		  Lichtarge and Lydia E. Kavraki},
  booktitle	= {15th Annual Intl.\ Conf.\ on Intelligent Systems for
		  Molecular Biology (ISMB) \& 6th European Conf.\ on Comp.\
		  Bio.\ (ECCB)},
  note		= {Poster},
  title		= {Representations of Structural Motifs for Protein Function
		  Prediction},
  url		= {http://www.iscb.org/uploaded/css/E108Moll.pdf},
  year		= {2007}
}

@InProceedings{	  chen2007geometry-inspired-optimization-methods-for-structural,
  address	= {Vienna, Austria},
  author	= {Brian Y. Chen and Drew H. Bryant and Viacheslav Y. Fofanov
		  and David M. Kristensen and Mark Moll and Marek Kimmel and
		  Olivier Lichtarge and Lydia E. Kavraki},
  booktitle	= {Automated Function Prediction Meeting (AFP)},
  note		= {Poster},
  title		= {Geometry-inspired Optimization Methods for Structural
		  Motifs for Protein Function Prediction},
  url		= {http://compbio.iupui.edu/afp/2007/files/afp-biosap-2007-full-program.pdf}
		  ,
  year		= {2007}
}

@InProceedings{	  moll2006distributed-control-of-the-center-of-mass,
  abstract	= {We present a distributed controller for the center of mass
		  of a modular robot. This is useful for locomotion of a
		  modular robot over uneven and unknown terrain. By
		  controlling the center of mass, a robot can prevent itself
		  from falling over. We present a distributed and
		  decentralized algorithm that computes the mass properties
		  of the robot. Additionally, each module also computes the
		  mass properties of the modules that are directly or
		  indirectly connected to each of its connectors. With this
		  information, each module can independently steer the center
		  of mass towards a desired position by adjusting its joint
		  positions. We present simulation results that show the
		  feasibility of the approach.},
  address	= {Beijing, China},
  author	= {Mark Moll and Peter Will and Maks Krivokon and Wei-Min
		  Shen},
  booktitle	= {Proc.\ 2006 {IEEE/RSJ} Intl.\ Conf.\ on Intelligent Robots
		  and Systems},
  doi		= {10.1109/IROS.2006.282261},
  month		= oct,
  pages		= {4710--4715},
  title		= {Distributed Control of the Center of Mass of a Modular
		  Robot},
  year		= {2006}
}

@InProceedings{	  salemi2006superbot,
  abstract	= {Self-reconfigurable robots are modular robots that can
		  autonomously change their shape and size to meet specific
		  operational demands. Recently, there has been a great
		  interest in using self-reconfigurable robots in
		  applications such as reconnaissance, rescue missions, and
		  space applications. Designing and controlling
		  self-reconfigurable robots is a difficult task. Hence, the
		  research has primarily been focused on developing systems
		  that can function in a controlled environment. This paper
		  presents a novel self-reconfigurable robotic system called
		  SuperBot, which addresses the challenges of building and
		  controlling deployable self-reconfigurable robots. Six
		  prototype modules have been built and preliminary
		  experimental results demonstrate that SuperBot is a
		  flexible and powerful system that can be used in
		  challenging real-world applications.},
  address	= {Beijing, China},
  author	= {Behnam Salemi and Mark Moll and Wei-Min Shen},
  booktitle	= {Proc.\ 2006 {IEEE/RSJ} Intl.\ Conf.\ on Intelligent Robots
		  and Systems},
  doi		= {10.1109/IROS.2006.281719},
  keywords	= {prl},
  month		= oct,
  pages		= {3636--3641},
  title		= {{SUPERBOT}: A Deployable, Multi-Functional, and Modular
		  Self-Reconfigurable Robotic System},
  year		= {2006}
}

@InProceedings{	  moll-kavraki2005:path-plann-variab-resol,
  abstract	= {We present a new approach to path planning for flexible
		  wires. We introduce a method for computing stable
		  configurations of a wire subject to manipulation
		  constraints. These configurations correspond to
		  minimal-energy curves. The representation is adaptive in
		  the sense that the number of parameters automatically
		  varies with the complexity of the underlying curve. We
		  introduce a planner that computes paths from one
		  minimal-energy curve to another such that all intermediate
		  curves are also minimal-energy curves. Using a simplified
		  model for obstacles, we can find minimal-energy curves of
		  fixed length that pass through specified tangents at given
		  control points. Our work has applications in motion
		  planning for surgical suturing and snake-like robots.},
  author	= {Mark Moll and Lydia E. Kavraki},
  booktitle	= {Proc.\ 2005 {IEEE} Intl.\ Conf.\ on Robotics and Automation},
  keywords	= {path planning, minimal-energy curves, subdivision},
  pages		= {2142--2147},
  title		= {Path Planning for Variable Resolution Minimal-Energy
		  Curves of Constant Length},
  url		= {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1570428}
		  ,
  year		= {2005}
}

@InProceedings{	  moll-kavraki2004:path-plann-minim-energ,
  abstract	= {In this paper we present a new path planning technique for
		  a flexible wire. We first introduce a new parametrization
		  designed to represent low-energy configurations. Based on
		  this parametrization we can find curves that satisfy
		  endpoint constraints. Next, we present three different
		  techniques for minimizing energy within the self-motion
		  manifold of the curve. We introduce a local planner to find
		  smooth minimal energy deformations for these curves that
		  can be used by a general path planning algorithm. Using a
		  simplified model for obstacles, we can find minimal energy
		  curves of fixed length that pass through specified tangents
		  at given control points. Finally, we show that the
		  parametrization introduced in this paper is a good
		  approximation of true minimal energy curves. Our work has
		  applications in surgical suturing and snake-like robots.},
  author	= {Mark Moll and Lydia E. Kavraki},
  booktitle	= {Proc.\ 2004 {IEEE} Intl.\ Conf.\ on Robotics and Automation},
  doi		= {10.1109/ROBOT.2004.1307489},
  keywords	= {path planning, curve parametrization, minimal energy
		  curves},
  pages		= {2826--2831},
  title		= {Path Planning for Minimal Energy Curves of Constant
		  Length},
  year		= {2004}
}

@InProceedings{	  moll-erdmann2002:dynam-shape-recon-using,
  abstract	= {We present new results on reconstruction of the shape and
		  motion of an unknown object using tactile sensors without
		  requiring object immobilization. A robot manipulates the
		  object with two flat palms covered with tactile sensors. We
		  model the full dynamics and prove local observability of
		  the shape, motion and center of mass of the object based on
		  the motion of the contact points as measured by the tactile
		  sensors.},
  author	= {Mark Moll and Michael A. Erdmann},
  booktitle	= {Proc.\ 2002 {IEEE} Intl.\ Conf.\ on Robotics and Automation},
  doi		= {10.1109/ROBOT.2002.1014777},
  keywords	= {shape reconstruction, tactile sensing, observability},
  pages		= {1636--1641},
  title		= {Dynamic Shape Reconstruction Using Tactile Sensors},
  year		= {2002}
}

@InProceedings{	  moll+2002:orien-micro-scale-parts,
  abstract	= {Orienting parts that measure only a few micrometers in
		  diameter introduces several challenges that need not be
		  considered at the macro-scale. First, there are several
		  kinds of sticking effects due to Van der Waals forces and
		  static electricity which complicate hand-off motions and
		  release of a part. Second, the degrees of freedom of
		  micro-manipulators are limited. This paper proposes a pair
		  of manipulation primitives and a complete algorithm that
		  addresses these challenges. We will show that a sequence of
		  these two manipulation primitives can uniquely orient any
		  asymmetric part while maintaining contact without sensing.
		  This allows us to apply the same plan to many (identical)
		  parts simultaneously. For asymmetric parts we can find a
		  plan of length O(n) in O(n) time that orients the part,
		  where n is the number of vertices.},
  author	= {Mark Moll and Ken Goldberg and Michael A. Erdmann and Ron
		  Fearing},
  booktitle	= {Proc.\ 2002 {IEEE} Intl.\ Conf.\ on Robotics and Automation},
  doi		= {10.1109/ROBOT.2002.1014823},
  keywords	= {micromanipulation, parts orienting, rolling},
  pages		= {1931--1936},
  title		= {Orienting Micro-Scale Parts with Squeeze and Roll
		  Primitives},
  year		= {2002}
}

@InProceedings{	  moll-erdmann2001:recon-shape-motion-using,
  abstract	= {We present a new method to reconstruct the shape of an
		  unknown object using tactile sensors without requiring
		  object immobilization. Instead, the robot manipulates the
		  object without prehension. The robot infers the shape,
		  motion and center of mass of the object based on the motion
		  of the contact points as measured by tactile sensors. Our
		  analysis is supported by simulation and experimental
		  results.},
  address	= {Maui, HI},
  author	= {Mark Moll and Michael A. Erdmann},
  booktitle	= {Proc.\ 2001 {IEEE/RSJ} Intl.\ Conf.\ on Intelligent Robots
		  and Systems},
  doi		= {10.1109/IROS.2001.976250},
  keywords	= {tactile sensing, shape reconstruction, contact
		  kinematics},
  month		= {October/November},
  pages		= {691--700},
  title		= {Reconstructing Shape from Motion Using Tactile Sensors},
  year		= {2001}
}

@InProceedings{	  moll-erdmann2000:uncer-reduc-using-dynam,
  abstract	= {For assembly tasks parts often have to be oriented before
		  they can be put in an assembly. The results presented in
		  this paper are a component of the automated design of parts
		  orienting devices. The focus is on orienting parts with
		  minimal sensing and manipulation. We present a new approach
		  to parts orienting through the manipulation of pose
		  distributions. Through dynamic simulation we can determine
		  the pose distribution for an object being dropped from an
		  arbitrary height on an arbitrary surface. By varying the
		  drop height and the shape of the support surface we can
		  find the initial conditions that will result in a pose
		  distribution with minimal entropy. We are trying to
		  uniquely orient a part with high probability just by
		  varying the initial conditions. We will derive a condition
		  on the pose and velocity of an object in contact with a
		  sloped surface that will allow us to quickly determine the
		  final resting configuration of the object. This condition
		  can then be used to quickly compute the pose distribution.
		  We also show simulation and experimental results that
		  confirm that our dynamic simulator can be used to find the
		  true pose distribution of an object.},
  address	= {San Francisco, California},
  author	= {Mark Moll and Michael A. Erdmann},
  booktitle	= {Proc.\ 2000 {IEEE} Intl.\ Conf.\ on Robotics and Automation},
  doi		= {10.1109/ROBOT.2000.845304},
  keywords	= {pose distributions, parts orienting, dynamic simulation},
  pages		= {3673--3680},
  title		= {Uncertainty Reduction Using Dynamics},
  year		= {2000}
}

@InProceedings{	  ter+1996:languag-engin-dialog-system,
  abstract	= {The analysis of natural language in the context of
		  keyboard-driven dialogue systems is the central issue
		  addressed in this paper. A module that corrects typing
		  errors, performs domain-specific morphological analysis is
		  developed. A parser for typed unification grammars has been
		  designed and implemented in C++; for description of the
		  lexicon and the grammar a suitable specification language
		  has been developed. It is argued that typed unification
		  grammars and especially the newly developed specification
		  language are convenient formalisms for describing natural
		  language use in dialogue systems. Finally we present a
		  dialogue manager that is based on a finite state automaton;
		  transitions in the automaton depend upon availability of
		  information in utterances of the user. In order to keep
		  track of the history of the dialogue, a context stack is
		  constructed during the dialogue. The manager is implemented
		  in Prolog. },
  address	= {Houston, TX},
  author	= {Ter Doest, Hugo and Mark Moll and Ren{\'e} Bos and Van de
		  Burgt, Stan and Anton Nijholt},
  booktitle	= {Computers in Engineering Symposium},
  pages		= {68--79},
  title		= {Language Engineering in Dialogue Systems},
  year		= {1996}
}

@InProceedings{	  op+1995:parsin-dialog-system-typed,
  abstract	= {The analysis of natural language in the context of
		  keyboard-driven dialogue systems is the central issue
		  addressed in this paper. A module that corrects typing
		  errors, performs domain-specific morphological analysis is
		  developed. A parser for typed unification grammars is
		  designed and implemented in C++; for description of the
		  lexicon and the grammer a specialised specification
		  language is developed. It is argued that typed unification
		  grammars and especially the newly developed specification
		  language are convenient formalisms for describing natural
		  language use in dialogue systems. Research on these issues
		  is carried out in the context of the Schisma project, a
		  research project in linguistic engineering; participants in
		  Schisma are KPN Research and the University of Twente.},
  address	= {Prague/Karlovy Vary, Czech Republic},
  author	= {Op den Akker, Rieks and Ter Doest, Hugo and Mark Moll and
		  Anton Nijholt},
  booktitle	= {Proceedings of the International Workshop on Parsing
		  Technologies},
  title		= {Parsing in Dialogue Systems using Typed Feature
		  Structures},
  year		= {1995}
}

@InProceedings{	  moll+1994:capac-conver-zone-episod,
  abstract	= {Human episodic memory provides a seemingly unlimited
		  storage for everyday experiences, and a retrieval system
		  that allows us to access the experiences with partial
		  activation of their components. This paper presents a
		  neural network model of episodic memory inspired by
		  Damasio's idea of Convergence Zones. The model consists of
		  a layer of perceptual feature maps and a binding layer. A
		  perceptual feature pattern is coarse coded in the binding
		  layer, and stored on the weights between layers. A partial
		  activation of the stored features activates the binding
		  pattern which in turn reactivates the entire stored
		  pattern. A worst-case analysis shows that with
		  realistic-size layers, the memory capacity of the model is
		  several times larger than the number of units in the model,
		  and could account for the large capacity of human episodic
		  memory.},
  address	= {Cambridge, MA},
  author	= {Mark Moll and Risto Miikkulainen and Jonathan Abbey},
  booktitle	= {Proc.\ 12th Natl. Conf.\ on Artificial Intelligence
		  (AAAI-94)},
  doi		= {10.1109/ICNN.1994.375017},
  pages		= {68--73},
  publisher	= {MIT Press},
  title		= {The Capacity of Convergence-Zone Episodic Memory},
  year		= {1994}
}

@InProceedings{	  shen2007multifunctional-and-reconfigurable-superbot-modules,
  author	= {Wei-Min Shen and Behnam Salemi and Mark Moll and Chi Ho
		  Chiu and Jacob Everist and Feili Hou and Nadeesha
		  Ranasinghe and Michael Rubenstein},
  booktitle	= {Proc.\ 2007 {IEEE/RSJ} Intl.\ Conf.\ on Intelligent Robots
		  and Systems},
  note		= {(video)}
		  ,
  title		= {Multifunctional Behaviors of Reconfigurable SuperBot
		  Modules},
  year		= {2007}
}

@TechReport{	  moll+2004:dockin-flexib-ligan,
  abstract	= {The activity of most drugs is regulated by the binding of
		  one molecule (the ligand) to a pocket of another, usually
		  larger, molecule, which is commonly a protein. This report
		  describes a new approach to creating low-energy structures
		  of flexible proteins to which ligands can be docked. The
		  flexibility of molecules is encoded with thousands of
		  parameters making the search for valid complexes a
		  formidable problem. Our method takes into account the
		  flexibility of the protein as this can be encoded by its
		  major modes of motion. The output of the program consists
		  of low-energy protein conformations that can then be docked
		  with a ligand using a traditional docking program. We
		  employ a robotics-based approach for exploring the
		  conformational space of the protein. Our long term goal is
		  to develop an efficient, accurate, and automated algorithm
		  that will be used to screen large databases of molecules
		  for novel therapeutics.},
  address	= {Houston, TX},
  author	= {Mark Moll and David Schwarz and Allison Heath and Lydia E.
		  Kavraki},
  institution	= {Rice University},
  number	= {04-443},
  title		= {On Flexible Docking Using Expansive Search},
  year		= {2004}
}

@PhDThesis{	  moll2002:shape-recon-using-activ,
  abstract	= {We present a new method to reconstruct the shape of an
		  unknown object using tactile sensors, without requiring
		  object immobilization. Instead, sensing and nonprehensile
		  manipulation occur simultaneously. The robot infers the
		  shape, motion and center of mass of the object based on the
		  motion of the contact points as measured by the tactile
		  sensors. This allows for a natural, continuous interaction
		  between manipulation and sensing. We analyze the planar
		  case first by assuming quasistatic dynamics, and present
		  simulation results and experimental results obtained using
		  this analysis. We extend this analysis to the full dynamics
		  and prove observability of the nonlinear system describing
		  the shape and motion of the object being manipulated. In
		  our simulations, a simple observer based on Newton's method
		  for root finding performs really well. Using the same
		  framework we can also describe the shape and dynamics of
		  three-dimensional objects. However, there are some
		  fundamental differences between the planar and
		  three-dimensional case, due to increased tangent
		  dimensionality. Also, perfect global shape reconstruction
		  is impossible in the 3D case, but it is almost trivial to
		  obtain upper and lower bounds on the shape. The 3D shape
		  reconstruction method has also been implemented and we
		  present some simulation results.},
  address	= {Pittsburgh, PA},
  author	= {Mark Moll},
  keywords	= {tactile sensing, shape reconstruction, nonprehensile
		  manipulation},
  month		= jul,
  school	= {Computer Science Department, Carnegie Mellon University},
  title		= {Shape Reconstruction Using Active Tactile Sensors},
  year		= {2002}
}

@TechReport{	  moll-erdmann2001:shape-recon-planar-dynam,
  abstract	= {We present a a new method to reconstruct the shape of an
		  unknown object using tactile sensors, without requiring
		  object immobilization. Instead, sensing and nonprehensile
		  manipulation occur simultaneously. The robot infers the
		  shape, motion and center of mass of the object based on the
		  motion of the contact points as measured by the tactile
		  sensors. We present analytic results and simulation results
		  assuming quasistatic dynamics. We prove that the shape and
		  motion are observable in both the quasistatic and the fully
		  dynamic case.},
  author	= {Mark Moll and Michael A. Erdmann},
  institution	= {Dept. of Computer Science, Carnegie Mellon University},
  keywords	= {tactile reconstruction, contact kinematics, nonlinear
		  observer theory, tactile sensing},
  number	= {CMU-CS-01-107},
  title		= {Shape Reconstruction in a Planar Dynamic Environment},
  year		= {2001}
}

@TechReport{	  moll1996:mappin-scien,
  address	= {Leiden, the Netherlands},
  author	= {Mark Moll},
  institution	= {Centre for Science and Technology Studies (CWTS)},
  month		= {August},
  note		= {Research report to the Netherlands Organization for
		  Scientific Research (NWO), Foundation for Economic and
		  Socio-Cultural Sciences (ESR)},
  number	= {96-06},
  title		= {Mapping Science: Methods and Tools for the Automatic
		  Creation of Semantic Maps of Large Corpora},
  type		= {Report CWTS},
  year		= {1996}
}

@TechReport{	  ter-doest1996language-engineering-in-dialogue-systems,
  abstract	= {The analysis of natural language in the context of
		  keyboard-driven dialogue systems is the central issue
		  addressed in this paper. A module that corrects typing
		  errors, performs domain-specific morphological analysis is
		  developed. A parser for typed unification grammars has been
		  designed and implemented in C++; for description of the
		  lexicon and the grammar a suitable specification language
		  has been developed. It is argued that typed unification
		  grammars and especially the newly developed specification
		  language are convenient formalisms for describing natural
		  language use in dialogue systems. Finally we present a
		  dialogue manager that is based on a finite state automaton;
		  transitions in the automaton depend upon availability of
		  information in utterances of the user. In order to keep
		  track of the history of the dialogue, a context stack is
		  constructed during the dialogue. The manager is implemented
		  in Prolog. },
  author	= {Ter Doest, Hugo and Mark Moll and Ren{\'e} Bos and Van de
		  Burgt, Stan and Anton Nijholt},
  institution	= {Department of Computer Science, University of Twente},
  month		= jan,
  number	= {96-2},
  title		= {Language Engineering in Dialogue Systems},
  type		= {Memoranda Informatica},
  year		= {1996}
}

@MastersThesis{	  moll1995:head-parsin-typed-featur,
  abstract	= {In this report a description will be given of how typed
		  feature structures can be specified. A specification
		  language will be presented for the specification of types,
		  words and grammar rules. An unification algorithm for typed
		  feature structures as well as an algorithm to compute the
		  least upper bound relation for a type lattice will be
		  given. Finally, a head-corner parsing schema for typed
		  feature structures will be presented.},
  author	= {Mark Moll},
  school	= {Department of Computer Science, University of Twente},
  title		= {Head-corner Parsing Using Typed Feature Structures},
  year		= {1995}
}

@TechReport{	  op+1995:parsin-dialog-system-typed-tr,
  abstract	= {The analysis of natural language in the context of
		  keyboard-driven dialogue systems is the central issue
		  addressed in this paper. A module that corrects typing
		  errors and performs domain-specific morphological analysis
		  has been developed. A parser for typed unification grammars
		  is designed and implemented in C++; for description of the
		  lexicon and the grammer a specialised specification
		  language has been developed. It is argued that typed
		  unification grammars and especially the newly developed
		  specification language are convenient formalisms for
		  describing natural language use in dialogue systems.
		  Research on these issues is carried out in the context of
		  the Schisma project, a research project of the Parlevink
		  group in linguistic engineering; participants in Schisma
		  are KPN Research and the University of Twente. The aims of
		  the Schisma project are twofold: both the accumulation of
		  knowledge in the field of computational linguistics and the
		  development of a natural language interfaced theatre
		  information and booking system is envisaged. The Schisma
		  project serves as a testbed for the development of the
		  various language analysis modules necessary for dialogue
		  systems.},
  author	= {Op den Akker, Rieks and Ter Doest, Hugo and Mark Moll and
		  Anton Nijholt},
  institution	= {Department of Computer Science, University of Twente},
  number	= {95-25},
  title		= {Parsing in Dialogue Systems using Typed Feature
		  Structures},
  type		= {Memoranda Informatica},
  url		= {http://eprints.eemcs.utwente.nl/9891/},
  year		= {1995}
}