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Algorithms & Applications Group
Publications

  This page lists publications by the Parasol Algorithms & Applications Group. The papers are (roughly) classified by topic area - in a few cases a paper appears more than once in the list. Please note that the copyrights of the papers with full citations have been signed over to the publishers.


MOTION PLANNING: TECHNIQUES AND APPLICATIONS

Studying learning techniques in different phases of PRM construction, Chinwe Ekenna, Diane Uwacu, Shawna Thomas, Nancy Amato, In Machine Learning in Planning and Control of Robot Motion Workshop (IROS-MLPC), Hamburg, Germany, Oct 2015.
Proceedings(pdf, abstract)

Improved Roadmap Connection via Local Learning for Sampling Based Planners, Chinwe Ekenna, Diane Uwacu, Shawna Thomas, Nancy Amato, In Proc. IEEE Int. Conf. Intel. Rob. Syst. (IROS), pp. 3227-3234, Hamburg, Germany, Oct 2015.
Proceedings(pdf, abstract)

A General Region-Based Framework for Collaborative Planning, Jory Denny, Read Sandstrom, Nancy M. Amato, In Proc. Inter. Symp. on Robotics Research (ISRR), Genova, Italy, Sep 2015.
Proceedings(ps, pdf, abstract)

Reachable Volume RRT, Troy McMahon, Shawna L. Thomas, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 2977-2984, Seattle, Washington, May 2015.
Proceedings(ps, pdf, abstract)

Sampling Based Motion Planning with Reachable Volumes: Application to Manipulators and Closed Chain Systems, Troy McMahon, Shawna L. Thomas, Nancy M. Amato, In Proc. IEEE Int. Conf. Intel. Rob. Syst. (IROS), Sep 2014.
Proceedings(pdf, abstract)

The Anatomy of a Distributed Motion Planning Roadmap, Sam Ade Jacobs, Nancy M. Amato, In Proc. IEEE Int. Conf. Intel. Rob. Syst. (IROS), Chicago, IL, USA, Sep 2014.
Proceedings(pdf, abstract)

A Region-Based Strategy for Collaborative Roadmap Construction, Jory Denny, Read Sandstrom, Nicole Julian, Nancy M. Amato, In Proc. Int. Wkshp. on Alg. Found. of Rob. (WAFR), pp. to appear, Istanbul, Turkey, Aug 2014.
Proceedings(ps, pdf, abstract)

MARRT: Medial Axis Biased Rapidly-Exploring Random Trees, Jory Denny, Evan Greco, Shawna L. Thomas, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 90 - 97, Hong Kong, China, Jun 2014.
Proceedings(ps, pdf, abstract)

Spark PRM: Using RRTs Within PRMs to EfÔ¨Āciently Explore Narrow Passages, Kensen Shi, Jory Denny, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 4659 - 4666, Hong Kong, China, Jun 2014.
Proceedings(ps, pdf, abstract)

UMAPRM: Uniformly Sampling the Medial Axis, Hsin-Yi (Cindy) Yeh, Jory Denny, Aaron Lindsey, Shawna L. Thomas, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 5798 - 5803, Hong Kong, China, Jun 2014.
Proceedings(ps, pdf, abstract)

Reciprocally-Rotating Velocity Obstacles, Andrew Giese, Daniel Latypov, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. to appear, Hong Kong, China, Jun 2014.
Proceedings(ps, pdf, abstract)

Robust Online Belief Space Planning in Changing Environments: Application to Physical Mobile Robots, Ali-akbar Agha-mohammadi, Saurav Agarwal, Aditya Mahadevan, Suman Chakravorty, Daniel Tomkins, Jory Denny, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 149 - 156, Hong Kong, China, May 2014. Also, Technical Report, TR13-007, Parasol Laboratory, Department of Computer Science, Texas A&M University, Jul 2013.
Proceedings(pdf, abstract) Technical Report(pdf, abstract)

Using Load Balancing to Scalably Parallelize Sampling-Based Motion Planning Algorithms, Adam Fidel, Sam Ade Jacobs, Shishir Sharma, Nancy M. Amato, Lawrence Rauchwerger, In Proc. Int. Par. and Dist. Proc. Symp. (IPDPS), Phoenix, Arizona, USA, May 2014.
Proceedings(pdf, abstract)

Sampling-Based Motion Planning with Reachable Volumes: Theoretical Foundations, Troy McMahon, Shawna L. Thomas, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), Hong Kong, China, May 2014.
Proceedings(pdf, abstract)

Adaptive Neighbor Connection using Node Characterization, Chinwe Ekenna, Shawna Thomas, Nancy Amato, Technical Report, TR14-005, Apr 2014.
Technical Report(pdf)

Sampling Based Motion Planning with Reachable Volumes, Troy McMahon, Shawna L. Thomas, Nancy M. Amato, Technical Report, TR14-003, Parasol Laboratory, Department of Computer Science, Texas A&M University, Feb 2014.
Technical Report(pdf, abstract)

Blind RRT: A Probabilistically Complete Distributed RRT, Cesar Rodriguez, Jory Denny, Sam Jacobs, Shawna L. Thomas, Nancy M. Amato, In Proc. IEEE Int. Conf. Intel. Rob. Syst. (IROS), pp. 1758 - 1765, Tokyo, Japan, Nov 2013.
Proceedings(ps, pdf, abstract)

Adapting RRT Growth for Heterogeneous Environments, Jory Denny, Marco A. Morales A., Samuel Rodriguez, Nancy M. Amato, In Proc. IEEE Int. Conf. Intel. Rob. Syst. (IROS), pp. 1772 - 1778, Tokyo, Japan, Nov 2013.
Proceedings(ps, pdf, abstract)

Adaptive Neighbor Connection for PRMs: A Natural Fit for Heterogeneous Environments and Parallelism, Chinwe Ekenna, Sam Ade Jacobs, Shawna Thomas, Nancy M. Amato, In Proc. IEEE Int. Conf. Intel. Rob. Syst. (IROS), Tokyo, Japan, Nov 2013.
Proceedings(pdf, abstract)

Rigidity Analysis for Protein Motion and Folding Core Identification, Shawna Thomas, Lydia Tapia, Chinwe Ekenna, Hsin-Yi (Cindy) Yeh, Nancy M. Amato, In Proc. of 2013 AAAI Wkshp. on Art. Int. and Robot. Meth. in Comp. Bio., Bellevue, WA, Jul 2013.
Proceedings(pdf, abstract)

Graph-based Stochastic Control with Constraints: A Unified Approach with Perfect and Imperfect Measurements, Ali-akbar Agha-mohammadi, Suman Chakravorty, Nancy M. Amato, In American Control Conference, Washington, DC, Jun 2013.
Proceedings(pdf, abstract)

FIRM: Sampling-based Feedback Motion Planning Under Motion Uncertainty and Imperfect Measurements, Ali-akbar Agha-mohammadi, Suman Chakravorty, Nancy M. Amato, International Journal of Robotics Research, To appear, 2013.
Journal(pdf, abstract)

Online Replanning in Belief Space for Dynamical Systems: Towards Handling Discrete Changes of Goal Location, Ali-akbar Agha-mohammadi, Suman Chakravorty, Nancy M. Amato, In IEEE ICRA 2013 Workshop on Combining Task and Motion Planning, Karlsruhe, Germany, May 2013.
Proceedings(pdf, abstract)

Lazy Toggle PRM: A Single-Query Approach to Motion Planning, Jory Denny, Kensen Shi, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 2407 - 2414, Karlsruhe, Germany, May 2013.
Proceedings(ps, pdf, abstract)

A Scalable Distributed RRT for Motion Planning, Sam Ade Jacobs, Nicholas Stradford, Cesar Rodriguez, Shawna Thomas, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 5088-5095, Karlsruhe, Germany, May 2013.
Proceedings(ps, pdf, abstract)

Improving Roadmap Quality through Connected Component Expansion, Juan Burgos, Jory Denny, Nancy M. Amato, Technical Report, TR13-003, Texas A&M University, Apr 2013.
Technical Report(ps, pdf, abstract)

Load Balancing Techniques for Scalable Parallelization of Sampling-Based Motion Planning Algorithms, Adam Fidel, Sam Ade Jacobs, Shishir Sharma, Lawrence Rauchwerger, Nancy M. Amato, Technical Report, TR13-002 , Parasol Laboratory, Department of Computer Science, Texas A&M University, Mar 2013.
Technical Report(pdf, abstract)

Environmental Effect on Egress Simulation, Samuel Rodriguez, Andrew Giese, Nancy M. Amato, Saeid Zarrinmehr, Firas Al-Douri, Mark Clayton, In Proc. of the 5th Intern. Conf. on Motion in Games (MIG), 2012, in Lecture Notes in Computer Science (LNCS), pp. to appear, Rennes, Brittany, France, Nov 2012.
Proceedings(ps, pdf, abstract)

Local Randomization in Neighbor Selection Improves PRM Roadmap Quality, Troy McMahon, Sam Ade Jacobs, Bryan Boyd, Lydia Tapia, Nancy M. Amato, In Proc. IEEE Int. Conf. Intel. Rob. Syst. (IROS), Vilamoura, Algarve [Portugal], Oct 2012.
Proceedings(ps, pdf, abstract)

A Multi-Directional Rapidly Exploring Random Graph (mRRG) for Protein Folding, Shuvra Nath, Shawna Thomas, Chinwe Ekenna, Nancy M. Amato, In ACM Conference on Bioinformatics, Computational Biology and Biomedicine, pp. 44-51, Orlando, FL, USA, Oct 2012.
Proceedings(ps, pdf, abstract)

Sampling-based Nonholonomic Motion Planning in Belief Space via Dynamic Feedback Linearization-based FIRM, Ali-akbar Agha-mohammadi, Suman Chakravorty, Nancy M. Amato, In Proc. IEEE Int. Conf. Intel. Rob. Syst. (IROS), Vilamoura, Portugal, Oct 2012. Also, Technical Report, TR12-004, Parasol Laboratory, Department of Computer Science, Texas A&M University, Mar 2012.
Proceedings(pdf, abstract) Technical Report(pdf, abstract)

UOBPRM: A Uniformly Distributed Obstacle-Based PRM, Cindy (Hsin-Yi) Yeh, Shawna Thomas, David Eppstein, Nancy M. Amato, In Proc. IEEE Int. Conf. Intel. Rob. Syst. (IROS), pp. 2655-2662, Vilamoura, Algarve, Portugal, Oct 2012.
Proceedings(ps, pdf, ppt, abstract)

Toggle PRM: A Coordinated Mapping of C-free and C-obstacle in Arbitrary Dimension, Jory Denny, Nancy M. Amato, In Proc. Int. Wkshp. on Alg. Found. of Rob. (WAFR), pp. 297-312, Boston, MA, USA, Jun 2012.
Proceedings(ps, pdf, abstract)

A Scalable Method for Parallelizing Sampling-Based Motion Planning Algorithms, Sam Ade Jacobs, Kasra Manavi, Juan Burgos, Jory Denny, Shawna Thomas, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 2529-2536, St. Paul, Minnesota, USA, May 2012.
Proceedings(ps, pdf, abstract)

A Sampling-Based Approach to Probabilistic Pursuit Evasion, Aditya Mahadevan, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 3192 - 3199, St. Paul, Minnesota, USA, May 2012.
Proceedings(pdf, abstract)

The Toggle Local Planner for Sampling-Based Motion Planning, Jory Denny, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 1779-1786, St. Paul, Minnesota, USA, May 2012.
Proceedings(ps, pdf, abstract)

On the Probabilistic Completeness of the Sampling-based Feedback Motion Planners in Belief Space, Ali-akbar Agha-mohammadi, Suman Chakravorty, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), Saint Paul, Minnesota, May 2012. Also, Technical Report, TR11-006, Parasol Laboratory, Department of Computer Science, Texas A&M University, Nov 2011.
Proceedings(pdf, abstract) Technical Report(pdf, abstract)

Periodic-Feedback Motion Planning in Belief Space for Nonholonomic and/or Nonstoppable Robots, Ali-akbar Agha-mohammadi, Suman Chakravorty, Nancy M. Amato, Technical Report, TR12-003, Parasol Laboratory, Department of Computer Science, Texas A&M University, Feb 2012.
Technical Report(pdf, abstract)

Roadmap-Based Techniques for Modeling Group Behaviors in Multi-Agent Systems, Samuel Rodriguez, Ph.D. Thesis, Department of Computer Science and Engineering, Texas A&M University, Jan 2012.
Ph.D. Thesis(ps, pdf, abstract)

Sampling-based Feedback Motion Planning Under Motion Uncertainty and Imperfect Measurements, Ali-akbar Agha-mohammadi, Suman Chakravorty, Nancy M. Amato, Technical Report, TR11-007, Parasol Laboratory, Department of Computer Science, Texas A&M University, Dec 2011.
Technical Report(pdf, abstract)

From Days to Seconds: Scalable Parallel Algorithms for Motion Planning, Sam Ade Jacobs, Nancy M. Amato, In ACM Student Research Compet, Conf. on High Performance Computing Networking, Storage and Analysis Companion Proceedings, Seattle, Washington, USA, Nov 2011.
Proceedings(pdf, abstract)

Roadmap-Based Level Clearing of Buildings, Samuel Rodriguez, Nancy M. Amato, In Proc. of the 4th Intern. Conf. on Motion in Games (MIG), 2011, in Lecture Notes in Computer Science (LNCS), pp. 340-352, Edinburgh, UK, Oct 2011.
Proceedings(ps, pdf, abstract)

Toggle PRM: Simultaneous Mapping of C-free and C-obstacle - A Study in 2D -, Jory Denny, Nancy M. Amato, In Proc. IEEE Int. Conf. Intel. Rob. Syst. (IROS), pp. 2632 - 2639, San Francisco, California, U.S.A., Sep 2011.
Proceedings(ps, pdf, abstract)

FIRM: Feedback Controller-Based Information-State Roadmap -- A Framework for Motion Planning Under Uncertainty --, Ali-akbar Agha-mohammadi, Suman Chakravorty, Nancy M. Amato, In Proc. IEEE Int. Conf. Intel. Rob. Syst. (IROS), San Francisco, CA, Sep 2011.
Proceedings(pdf, abstract)

Roadmap-Based Pursuit-Evasion in 3D Structures, Samuel Rodriguez, Jory Denny, Aditya Mahadevan, Jeremy (Cong-Trung) Vu, Juan Burgos, Takis Zourntos, Nancy M. Amato, In Proc. of 24th Intern. Conf. on Computer Animation and Social Agents (CASA), 2011, in Transactions on Edutainment, pp. to appear, May 2011.
Proceedings(ps, pdf, abstract)

Toward Realistic Pursuit-Evasion Using a Roadmap-Based Approach, Samuel Rodriguez, Jory Denny, Juan Burgos, Aditya Mahadevan, Kasra Manavi, Luke Murray, Anton Kodochygov, Takis Zourntos, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 1738-1745, May 2011.
Proceedings(ps, pdf, abstract)

Utilizing Roadmaps in Evacuation Planning, Samuel Rodriguez, Nancy M. Amato, In Proc. of 24th Intern. Conf. on Computer Animation and Social Agents (CASA), 2011, in Intern. J. of Virtual Reality (IJVR), pp. 67-73, May 2011.
Proceedings(ps, pdf, abstract)

FIRM: Feedback Controller-Based Information-State Roadmap, A Framework for Motion Planning Under Uncertainty, Ali-akbar Agha-mohammadi, Suman Chakravorty, Nancy Amato, Technical Report, TR11-001, Parasol Laboratory, Department of Computer Science, Texas A&M University, Jan 2011.
Technical Report(pdf, abstract)

Toward Simulating Realistic Pursuit-Evasion Using a Roadmap-Based Approach, Samuel Rodriguez, Jory Denny, Takis Zourntos, Nancy M. Amato, In Proc. of the 3rd Intern. Conf. on Motion in Games (MIG), 2010, in Lecture Notes in Computer Science (LNCS), pp. 82-93, Nov 2010.
Proceedings(ps, pdf, abstract)

Region Identification Methods for Efficient and Automated Motion Planning, Jory Denny, Anshul Agrawal, Evan Greco, Lydia Tapia, Nancy M. Amato, Technical Report, TR10-002, Parasol Laboratory, Department of Computer Science, Texas A&M University, College Station, Texas, U.S.A., Sep 2010.
Technical Report(ps, pdf, abstract)

Reachable Distance Space: Efficient Sampling-Based Planning for Spatially Constrained Systems, Xinyu Tang, Shawna Thomas, Philip Coleman, Nancy M. Amato, International Journal of Robotics Research, 29(7):916-934, Jun 2010.
Journal(pdf, abstract)

A Motion Planning Approach to Studying Molecular Motions, Lydia Tapia, Shawna Thomas, Nancy M. Amato, Communications in Information and Systems, 10(1):53-68, 2010.
Journal(pdf, abstract)

Behavior-Based Evacuation Planning, Sam Rodriguez, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 350-355, Anchorage, AK, May 2010.
Proceedings(ps, pdf, abstract)

Rigidity Analysis for Modeling Protein Motion, Shawna Thomas, Ph.D. Thesis, Department of Computer Science and Engineering, Texas A&M University, May 2010.
Ph.D. Thesis(ps, pdf, abstract)

Intelligent Motion Planning and Analysis with Probabilistic Roadmap Methods for the Study of Complex and High-Dimensional Motions, Lydia Tapia, Ph.D. Thesis, Parasol Laboratory, Department of Computer Science, Texas A&M University, College Station, Texas, Dec 2009.
Ph.D. Thesis(pdf, abstract)

An Unsupervised Adaptive Strategy for Constructing Probabilistic Roadmaps, Lydia Tapia, Shawna Thomas, Bryan Boyd, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 4037-4044, Kobe, Japan, May 2009.
Proceedings(pdf, abstract)

Planning with Reachable Distances, Xinyu Tang, Shawna Thomas, Nancy M. Amato, In Proc. Int. Wkshp. on Alg. Found. of Rob. (WAFR), Guanajuato, Mexico, Dec 2008.
Proceedings(ps, pdf, abstract)

Simulating RNA Folding Kinetics on Approximated Energy Landscapes, Xinyu Tang, Shawna Thomas, Lydia Tapia, David P. Giedroc, Nancy M. Amato, Journal of Molecular Biology, 3811(4):1055-1067, Sep 2008.
Journal(pdf, abstract)

Structural Improvement Filtering Strategy for PRM, Roger Pearce, Marco Morales, Nancy M. Amato, In Proc. Int. Conf. on Robotics: Science and Systems, pp. 167-174, Zurich, Switzerland, Jun 2008.
Proceedings(pdf, abstract)

Techniques for Modeling and Analyzing RNA and Protein Folding Energy Landscapes, Xinyu Tang, Ph.D. Thesis, Department of Computer Science and Engineering, Texas A&M University, Dec 2007.
Ph.D. Thesis(ps, pdf, abstract)

Metrics for Sampling-Based Motion Planning, Marco Morales, Ph.D. Thesis, Parasol Laboratory, Department of Computer Science, Texas A&M University, College Station, Texas, Dec 2007.
Ph.D. Thesis(pdf, abstract)

A Framework for Planning Motion in Environments with Moving Obstacles, Sam Rodriguez, Jyh-Ming Lien, Nancy M. Amato, In Proc. IEEE Int. Conf. Intel. Rob. Syst. (IROS), pp. 3309-3314, Oct 2007.
Proceedings(ps, pdf, abstract)

Kinetics Analysis Methods For Approximate Folding Landscapes, Lydia Tapia, Xinyu Tang, Shawna Thomas, Nancy M. Amato, In Int. Conf. on Int. Sys. for Mol. Bio. (ISMB)/European Conf. on Comp. Bio.(ECCB), Vienna, Austria, Jul 2007. Also, Bioinformatics, 23(13):i539-i548, Jul 2007.
Journal(pdf, abstract)

Biasing Samplers to Improve Motion Planning Performance, Shawna Thomas, Marco Morales, Xinyu Tang, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 1625-1630, Rome, Italy, Apr 2007.
Proceedings(ps, pdf, abstract)

Planning with Reachable Distances: Fast Enforcement of Closure Constraints, Xinyu Tang, Shawna Thomas, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 2694-2699, Rome, Italy, Apr 2007.
Proceedings(ps, pdf, abstract)

Tools for Simulating and Analyzing RNA Folding Kinetics, Xinyu Tang, Shawna Thomas, Lydia Tapia, Nancy M. Amato, In Proc. Int. Conf. Comput. Molecular Biology (RECOMB), pp. 268-282, San Francisco, CA, Apr 2007.
Proceedings(ps, pdf, abstract)

Approximate Convex Decomposition and Its Applications, Jyh-Ming Lien, Ph.D. Thesis, Department of Computer Science and Engineering, Texas A&M University, Dec 2006.
Ph.D. Thesis(pdf, abstract)

RESAMPL: A Region-Sensitive Adaptive Motion Planner, Samuel Rodriguez, Shawna Thomas, Roger Pearce, Nancy M. Amato, In Proc. Int. Wkshp. on Alg. Found. of Rob. (WAFR), pp. 285-300, New York City, NY, Jul 2006.
Proceedings(ps, pdf, abstract)

Incremental Map Generation (IMG), Dawen Xie, Marco Morales, Roger Pearce, Shawna Thomas, Jyh-Ming Lien, Nancy M. Amato, In Proc. Int. Wkshp. on Alg. Found. of Rob. (WAFR), New York City, NY, Jul 2006. Also, Technical Report, TR06-005, Department of Computer Science and Engineering, Texas A&M University, Mar 2006.
Proceedings(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

Simultaneous Shape Decomposition and Skeletonization, Jyh-Ming Lien, John Keyser, Nancy M. Amato, In Proc. ACM Solid and Physical Modeling Symp. (SPM), pp. 219-228, Cardiff, Wales, UK, Jun 2006.
Proceedings(pdf, abstract)

VIZMO++: a Visualization, Authoring, and Educational Tool for Motion Planning, Aimée Vargas E., Jyh-Ming Lien, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 727-732, Orlando, Florida, To appear, May 2006. Also, Technical Report, TR05-014, Parasol Laboratory, Department of Computer Science, Texas A&M University, Sep 2005.
Proceedings(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

Planning Motion in Completely Deformable Environments, Samuel Rodriguez, Jyh-Ming Lien, N. M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 2466-2471, Orlando, FL, May 2006.
Proceedings(ps, pdf, abstract)

An Obstacle-Based Rapidly-Exploring Random Tree, Samuel Rodriguez, Xinyu Tang, Jyh-Ming Lien, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 895-900, Orlando, FL, May 2006. Also, Technical Report, TR05-009, Parasol Laboratory, Department of Computer Science, Texas A&M University, Sep 2005.
Proceedings(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

Visualization Tools for Moving Objects, Aimée Vargas E., Masters Thesis, Parasol Laboratory, Department of Computer Science, Texas A&M University, Dec 2005.
Masters Thesis(ps, pdf, abstract)

Protein Folding by Motion Planning, Shawna Thomas, Guang Song, Nancy M. Amato, Physical Biology, 2:S148-S155, Nov 2005.
Journal(ps, pdf, abstract)

Metrics for Comparing C-space Roadmaps, Marco A. Morales A., Roger Pearce, Aimée Vargas E., Nancy M. Amato, Technical Report, TR05-012, Parasol Laboratory, Department of Computer Science, Texas A&M University, College Station, Texas, U.S.A., Sep 2005.
Technical Report(ps, pdf, abstract)

Iterative Relaxation of Constraints: A Framework for Improving Automated Motion Planning, O. Burchan Bayazit, Dawen Xie, Nancy M. Amato, In Proc. IEEE Int. Conf. Intel. Rob. Syst. (IROS), pp. 586 - 593, Edmonton, Alberta, Canada, Aug 2005.
Proceedings(ps, pdf, abstract)

Using Motion Planning to Study RNA Folding Kinetics, Xinyu Tang, Bonnie Kirkpatrick, Shawna Thomas, Guang Song, Nancy M. Amato, Journal of Computational Biology, 12(6):862-881, Jul 2005. Also, In Proc. Int. Conf. Comput. Molecular Biology (RECOMB), pp. 252-261, San Diego, CA, Mar 2004.
Journal(ps, pdf, abstract) Proceedings(ps, pdf, abstract)

C-Space Subdivision and Integration in Feature-Sensitive Motion Planning, Marco A. Morales A., Lydia Tapia, Roger Pearce, Samuel Rodriguez, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 3114-3119, Barcelona, Spain, May 2005. Also, Technical Report, TR04-004, Parasol Laboratory, Department of Computer Science, Texas A&M University, College Station, Texas, U.S.A., Sep 2004.
Proceedings(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

Swarming Behavior Using Probabilistic Roadmap Techniques, O. Burchan Bayazit, Jyh-Ming Lien, Nancy M. Amato, Lecture Notes in Computer Science, 3342/2005:112-125, Jan 2005.
Journal(ps, pdf, abstract)

A Machine Learning Approach for Feature-Sensitive Motion Planning, Marco Morales, Lydia Tapia, Roger Pearce, Samuel Rodriguez, Nancy M. Amato, In Proc. Int. Wkshp. on Alg. Found. of Rob. (WAFR), pp. 361-376, Utrecht/Zeist, The Netherlands, Jul 2004. Also, Technical Report, TR04-001, Parasol Laboratory, Department of Computer Science, Texas A&M University, College Station, Texas, U.S.A., Feb 2004.
Proceedings(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

Enveloping multi-pocket obstacles with Hexagonal Metamorphic Robots, Jennifer E. Walter, Mary E. Brooks, David F. Little, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 2204-2209, New Orleans, LA, Apr 2004.
Proceedings(pdf)

Shepherding Behaviors, Jyh-Ming Lien, O. Burchan Bayazit, Ross T. Sowell, Samuel Rodriguez, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 4159-4164, New Orleans, Apr 2004. Also, Technical Report, TR03-006, Parasol Laboratory, Department of Computer Science, Texas A&M University, Nov 2003.
Proceedings(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

Filling an Obstacle Pocket with Hexagonal Metamorphic Robots, Jennifer E. Walter, Mary E. Brooks, Nancy M. Amato, In Proc. Conf. on Intelligent Autonomous Systems, pp. 703-711, Amsterdam, The Netherlands, Mar 2004.


A Motion Planning Approach to Folding: From Paper Craft to Protein Folding, Guang Song, Nancy M. Amato, IEEE Transactions on Robotics and Automation, 20(1):60-71, Feb 2004. Also, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 948-953, Seoul, Korea, May 2001. Also, Technical Report, TR00-017, Department of Computer Science and Engineering, Texas A&M University, Jul 2000.
Journal(ps, pdf, abstract) Proceedings(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

A General Framework for PRM Motion Planning, Guang Song, Shawna Thomas, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 4445-4450, Taipei, Taiwan, Sep 2003.
Proceedings(ps, pdf, abstract)

A General Framework for Sampling on the Medial Axis of the Free Space, Jyh-Ming Lien, Shawna L. Thomas, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 4439-4444, Taipei, Taiwan, Sep 2003.
Proceedings(ps, pdf, abstract)

Extracting Optimal Paths from Roadmaps for Motion Planning, Jinsuck Kim, Roger A. Pearce, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 2424-2429, vol 2, Sep 2003.
Proceedings(ps, pdf, abstract)

Enveloping Obstacles with Hexagonal Metamorphic Robots, Jennifer E. Walter, Elizabeth M. Tsai, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 741-748, Taipei, Taiwan, Sep 2003.
Proceedings(ps, pdf, abstract)

Feature-Based Localization using Scannable Visibility Sectors, Jinsuck Kim, Roger A. Pearce, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 2854-2859, vol 2, Sep 2003.
Proceedings(ps, pdf, abstract)

Improving the Connectivitiy of PRM Roadmaps, Marco Morales, Samuel Rodriguez, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 4427-4432, Taipei, Taiwan, Sep 2003.
Proceedings(ps, abstract)

Algorithms for Filling Obstacle Pockets with Hexagonal Metamorphic Robots, Mary E. Brooks, Technical Report, TR03-002, Parasol Laboratory, Department of Computer Science, Texas A&M University, Aug 2003.
Technical Report(ps, pdf)

Neuron PRM: A Framework for Constructing Cortical Networks, Jyh-Ming Lien, Marco Morales, Nancy M. Amato, Neurocomputing, 52-54(28):191-197, Jun 2003. Also, Technical Report, TR01-002, Parasol Laboratory, Department of Computer Science, Texas A&M University, Oct 2001.
Journal(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of Known Native Structures, Nancy M. Amato, Ken Dill, Guang Song, Journal of Computational Biology, 10(3-4):239-255, Jun 2003. Also, In Proc. Int. Conf. Comput. Molecular Biology (RECOMB), pp. 2-11, Apr 2002.
Journal(ps, pdf, abstract) Proceedings(pdf, abstract)

Solving Motion Planning Problems by Iterative Relaxation of Constraints, Osman BurÁhan Bayazit, Ph.D. Thesis, Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, U.S.A., May 2003.
Ph.D. Thesis(ps, pdf, abstract)

A Path Planning-based Study of Protein Folding With a Case Study of Hairpin Formation in Protein G and L, Guang Song, Shawna Thomas, Ken A. Dill, J. Martin Scholtz, Nancy M. Amato, In Proc. Pac. Symp. of Biocomputing (PSB), pp. 240-251, Lihue, HI, Jan 2003.
Proceedings(ps, pdf, abstract)

Better Group Behaviors using Rule-Based Roadmaps, O. Burchan Bayazit, Jyh-Ming Lien, Nancy M. Amato, In Proc. Int. Wkshp. on Alg. Found. of Rob. (WAFR), pp. 95-111, Nice, France, Dec 2002.
Proceedings(ps, pdf, abstract)

Using Motion Planning to Study Protein Folding Pathways, Guang Song, Nancy M. Amato, Journal of Computational Biology, 9(2):149-168, Nov 2002. Also, In Proc. Int. Conf. Comput. Molecular Biology (RECOMB), pp. 287-296, Apr 2001. Also, Technical Report, TR00-026, Parasol Laboratory, Department of Computer Science, Texas A&M University, Oct 2000.
Journal(ps, pdf, abstract) Proceedings(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

Concurrent Metamorphosis of Hexagonal Robot Chains into Simple Connected Configurations, Jennifer E. Walter, Jennifer L. Welch, Nancy M. Amato, IEEE Transactions on Robotics and Automation, 18(6):945-956, Nov 2002.
Journal(pdf, abstract)

Robust Geometric-Based Localization in Indoor Environments Using Sonar Sensors, Jinsuck Kim, Roger A. Pearce, Nancy M. Amato, In Proc. IEEE Int. Conf. Intel. Rob. Syst. (IROS), pp. 421-426, Oct 2002.
Proceedings(ps, pdf, abstract)

Roadmap-Based Flocking for Complex Environments, O. Burchan Bayazit, Jyh-Ming Lien, Nancy M. Amato, In Proc. Pacific Conf. on Computer Graphics and App. (PG), pp. 104-113, Beijing, China, Oct 2002. Also, Technical Report, TR02-003, Parasol Laboratory, Department of Computer Science, Texas A&M University, Apr 2002.
Proceedings(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

Probabilistic Roadmap Motion Planning for Deformable Objects, O. Burchan Bayazit, Jyh-Ming Lien, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 2126-2133, Washingon, D.C., May 2002. Also, Technical Report, TR01-003, Parasol Laboratory, Department of Computer Science, Texas A&M University, Oct 2001.
Proceedings(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

Choosing Good Paths for Fast Distributed Reconfiguration of Hexagonal Metamorphic Robots, Jennifer E. Walter, Elizabeth M. Tsai, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 102-109, Washington, D.C., May 2002.
Proceedings(ps, pdf, abstract)

Randomized Motion Planning for Car-like Robots with C-PRM, Guang Song, Nancy M. Amato, In Proc. IEEE Int. Conf. Intel. Rob. Syst. (IROS), pp. 37-42, Maui, Hawaii, Nov 2001. Also, Technical Report, TR01-002, Department of Computer Science and Engineering, Texas A&M University, Mar 2001.
Proceedings(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of Known Native Structures, Nancy M. Amato, Guang Song, Technical Report, TR01-001, Parasol Laboratory, Department of Computer Science, Texas A&M University, Oct 2001.
Technical Report(ps, pdf, abstract)

Multiple Robot Navigation and Localization Using Sonar Sensors in an Indoor Environment, Jinsuck Kim, Roger A. Pearce, Nancy M. Amato, Technical Report, TR01-004, Parasol Laboratory, Department of Computer Science, Texas A&M University, Oct 2001.
Technical Report(ps, pdf)

Enhancing Randomized Motion Planners: Exploring with Haptic Hints, O. Burchan Bayazit, Guang Song, Nancy M. Amato, Autonomous Robots, 10(2):163-174, 2001. Also, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 529-536, Apr 2000. Also, Technical Report, TR99-021, Parasol Laboratory, Department of Computer Science, Texas A&M University, Oct 1999.
Proceedings(pdf, abstract)

Disassembly Sequencing Using a Motion Planning Approach, Sujay Sundaram, Ian Remmler, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 1475-1480, May 2001. Also, Technical Report, TR00-027, Parasol Laboratory, Department of Computer Science, Texas A&M University, Jan 2000.
Proceedings(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

Probabilistic Roadmaps - Putting It All Together, Lucia K. Dale, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 1940-1947, Seoul, Korea, May 2001.
Proceedings(ps, pdf, abstract)

Ligand Binding with OBPRM and Haptic User Input, O. Burchan Bayazit, Guang Song, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 954-959, May 2001.
Proceedings(ps, pdf, abstract)

Customizing PRM Roadmaps at Query Time, Guang Song, Shawna Miller, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 1500-1505, Seoul, Korea, May 2001.
Proceedings(ps, pdf, abstract)

An Integrated Mobile Robot Path (Re)Planner and Localizer for Personal Robots, Jinsuck Kim, Nancy M. Amato, Sooyong Lee, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 3789-3794, May 2001. Also, Technical Report, TR00-028, Parasol Laboratory, Department of Computer Science, Texas A&M University, Nov 2000.
Proceedings(ps, pdf, abstract)

Hybrid Dynamic Simulation of Rigid-Body Contact with Coulomb Friction, Wookho Son, Jeffrey C. Trinkle, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 1376-1381, May 2001.
Proceedings(ps, pdf, abstract)

An Adaptive Framework for `Single Shot' Motion Planning: A Self-Tuning System for Rigid and Articulated Robots, Daniel Vallejo, Ian Remmler, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 21-26, Seoul, Korea, May 2001.
Proceedings(ps, pdf, abstract)

Optimization Techniques for Probabilistic Roadmaps, Lucia Kathryn Dale, Ph.D. Thesis, Department of Computer Science and Engineering, Texas A&M University, Dec 2000.
Ph.D. Thesis(ps, pdf, abstract)

Interactive Dynamic Simulation using Haptic Interaction, Wookho Son, Kyunghwan Kim, Nancy M. Amato, Jeffrey C. Trinkle, In Proc. IEEE Int. Conf. Intel. Rob. Syst. (IROS), pp. 145-150, Nov 2000.
Proceedings(ps, pdf, abstract)

An Adaptive Framework for `Single Shot' Motion Planning, Daniel R. Vallejo, Christopher Jones, Nancy M. Amato, In Proc. IEEE Int. Conf. Intel. Rob. Syst. (IROS), pp. 1722-1727, Kagawa University, Takamatsu, Japan, Nov 2000. Also, Technical Report, TR99-024, Department of Computer Science and Engineering, Texas A&M University, Oct 1999.
Proceedings(pdf, abstract)

Ligand Binding with OBPRM and Haptic User Input: Enhancing Automatic Motion Planning with Virtual Touch, O. Burchan Bayazit, Guang Song, Nancy M. Amato, Technical Report, TR00-025, Department of Computer Science and Engineering, Texas A&M University, Oct 2000.
Technical Report(ps, pdf, abstract)

Choosing Good Distance Metrics and Local Planners for Probabilistic Roadmap Methods, Nancy M. Amato, O. Burchan Bayazit, Lucia K. Dale, Christopher Jones, Daniel Vallejo, IEEE Transactions on Robotics and Automation, 16(4):442-447, Aug 2000. Also, Technical Report, TR98-010, Department of Computer Science and Engineering, Texas A&M University, May 1998.
Journal(pdf, abstract)

Distributed Reconfiguration of Metamorphic Robot Chains, Jennifer E. Walter, Jennifer L. Welch, Nancy M. Amato, In Proc. of ACM SIGACT-SIGOPS Symp. on Princ. of Dist. Comp. (PODC), pp. 171-180, Jul 2000.
Proceedings(ps, pdf)

Distributed Reconfiguration of Hexagonal Metamorphic Robots in Two Dimensions, Jennifer E. Walter, Jennifer L. Welch, Nancy M. Amato, In Proceedings of SPIE, pp. 441-453, Vol. 4196, 2000.
Proceedings(ps, pdf, abstract)

An Interactive Generalized Motion Simulator (GMS) in an Object-Oriented Framework, Wookho Son, Kyunghwan Kim, Nancy M. Amato, In Proc. of Computer Animation (CA), pp. 176-181, May 2000.
Proceedings(ps, pdf, abstract)

How does it fold? Searching for Folding Pathways using a Motion Planning Approach, Guang Song, Nancy Amato, Technical Report, 00-014, Department of Computer Science and Engineering, Texas A&M University, May 2000.
Technical Report(pdf, abstract)

A Kinematics-Based Probabilistic Roadmap Method for Closed Chain Systems, Li Han, Nancy M. Amato, In Proc. Int. Wkshp. on Alg. Found. of Rob. (WAFR), pp. 233-246, Hanover, NH, Mar 2000.
Proceedings(ps, pdf, abstract)

Localization based on Visibility Sectors using Range Sensors, Sooyong Lee, Nancy M. Amato, James Fellers, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 3505-3511, Jan 2000. Also, Technical Report, TR00-002, Department of Computer Science and Engineering, Texas A&M University, Jan 2000.
Proceedings(ps, pdf, abstract)

A Motion Planning Approach to Folding: From Paper Craft to Protein Structure Prediction, Guang Song, Nancy M. Amato, Technical Report, TR00-001, Department of Computer Science and Engineering, Texas A&M University, Jan 2000.
Technical Report(ps)

A Probabilistic Method for Rigid Body Motion Planning Using Sampling from the Medial Axis of the Free Space, Steven A. Wilmarth, Ph.D. Thesis, Department of Mathematics, Texas A&M University, Dec 1999.
Ph.D. Thesis(ps, pdf, abstract)

Providing Haptic 'Hints' to Automatic Motion Planners, O. Burchan Bayazit, Guang Song, Nancy M. Amato, In Phantom Users Group Work. (PUG), Oct 1999.
Proceedings(ps, pdf, abstract)

Motion Planning for a Rigid Body Using Random Networks on the Medial Axis of the Free Space, Steven A. Wilmarth, Nancy M. Amato, Peter F. Stiller, In Proc. ACM Symp. Comput. Geom., pp. 173-180, Miami Beach, FL, Jun 1999. Also, Technical Report, TR98-028, Department of Computer Science and Engineering, Texas A&M University, Dec 1998.
Proceedings(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

MAPRM: A Probabilistic Roadmap Planner with Sampling on the Medial Axis of the Free Space, Steven A. Wilmarth, Nancy M. Amato, Peter F. Stiller, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 1024-1031, Detroit, MI, May 1999. Also, Technical Report, TR98-0022, Department of Computer Science and Engineering, Texas A&M University, Nov 1998.
Proceedings(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

Probabilistic Roadmap Methods are Embarrassingly Parallel, Nancy M. Amato, Lucia K. Dale, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 688-694, Detroit, Michigan, USA, May 1999.
Proceedings(ps, pdf, abstract)

Providing Haptic 'Hints' to Automatic Motion Planners, Nancy M. Amato, O. Burchan Bayazit, Kyunghwan Kim, Wookho Son, Guang Song, Technical Report, TR98-026, Department of Computer Science and Engineering, Texas A&M University, Nov 1998.


OBPRM: An Obstacle-Based PRM for 3D Workspaces, Nancy M. Amato, O. Burchan Bayazit, Lucia K. Dale, Christopher Jones, Daniel Vallejo, In Proc. Int. Wkshp. on Alg. Found. of Rob. (WAFR), pp. 155-168, Houston, TX, Mar 1998.
Proceedings(pdf, abstract)

Equipping CAD/CAM Systems with Geometric Intelligence, Nancy M. Amato, ACM Computing Surveys, 28(4es)(17):Dec 1996.
Journal(abstract)

A Randomized Roadmap Method for Path and Manipulation Planning, Nancy M. Amato, Yan Wu, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 113-120, Minneapolis, MN, Apr 1996.
Proceedings(pdf, abstract)


COMPUTATIONAL BIOLOGY

Adaptive Local Learning in Sampling Based Motion Planning for Protein Folding, Chinwe Ekenna, Shawna Thomas, Nancy Amato, In The IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 61-68, Washington DC, USA, Nov 2015.
Proceedings(pdf, abstract)

Rigidity Analysis for Protein Motion and Folding Core Identification, Shawna Thomas, Lydia Tapia, Chinwe Ekenna, Hsin-Yi (Cindy) Yeh, Nancy M. Amato, In Proc. of 2013 AAAI Wkshp. on Art. Int. and Robot. Meth. in Comp. Bio., Bellevue, WA, Jul 2013.
Proceedings(pdf, abstract)

A Multi-Directional Rapidly Exploring Random Graph (mRRG) for Protein Folding, Shuvra Nath, Shawna Thomas, Chinwe Ekenna, Nancy M. Amato, In ACM Conference on Bioinformatics, Computational Biology and Biomedicine, pp. 44-51, Orlando, FL, USA, Oct 2012.
Proceedings(ps, pdf, abstract)

A Motion Planning Approach to Studying Molecular Motions, Lydia Tapia, Shawna Thomas, Nancy M. Amato, Communications in Information and Systems, 10(1):53-68, 2010.
Journal(pdf, abstract)

Rigidity Analysis for Modeling Protein Motion, Shawna Thomas, Ph.D. Thesis, Department of Computer Science and Engineering, Texas A&M University, May 2010.
Ph.D. Thesis(ps, pdf, abstract)

Intelligent Motion Planning and Analysis with Probabilistic Roadmap Methods for the Study of Complex and High-Dimensional Motions, Lydia Tapia, Ph.D. Thesis, Parasol Laboratory, Department of Computer Science, Texas A&M University, College Station, Texas, Dec 2009.
Ph.D. Thesis(pdf, abstract)

Using Dimensionality Reduction to Better Capture RNA and Protein Folding Motions, Lydia Tapia, Shawna Thomas, Nancy M. Amato, Technical Report, TR08-005, Parasol Laboratory, Department of Computer Science, Texas A&M University, College Station, Texas, U.S.A., Oct 2008.
Technical Report(ps, pdf, abstract)

Simulating RNA Folding Kinetics on Approximated Energy Landscapes, Xinyu Tang, Shawna Thomas, Lydia Tapia, David P. Giedroc, Nancy M. Amato, Journal of Molecular Biology, 3811(4):1055-1067, Sep 2008.
Journal(pdf, abstract)

Techniques for Modeling and Analyzing RNA and Protein Folding Energy Landscapes, Xinyu Tang, Ph.D. Thesis, Department of Computer Science and Engineering, Texas A&M University, Dec 2007.
Ph.D. Thesis(ps, pdf, abstract)

Kinetics Analysis Methods For Approximate Folding Landscapes, Lydia Tapia, Xinyu Tang, Shawna Thomas, Nancy M. Amato, In Int. Conf. on Int. Sys. for Mol. Bio. (ISMB)/European Conf. on Comp. Bio.(ECCB), Vienna, Austria, Jul 2007. Also, Bioinformatics, 23(13):i539-i548, Jul 2007.
Journal(pdf, abstract)

Simulating Protein Motions with Rigidity Analysis, Shawna Thomas, Xinyu Tang, Lydia Tapia, Nancy M. Amato, Journal of Computational Biology, 14(6):839-855, Jul 2007. Also, In Proc. Int. Conf. Comput. Molecular Biology (RECOMB), pp. 394-409, Apr 2006.
Journal(ps, pdf, abstract) Proceedings(ps, pdf, abstract)

Tools for Simulating and Analyzing RNA Folding Kinetics, Xinyu Tang, Shawna Thomas, Lydia Tapia, Nancy M. Amato, In Proc. Int. Conf. Comput. Molecular Biology (RECOMB), pp. 268-282, San Francisco, CA, Apr 2007.
Proceedings(ps, pdf, abstract)

Parallel Protein Folding with STAPL, Shawna Thomas, Gabriel Tanase, Lucia K. Dale, Jose M. Moreira, Lawrence Rauchwerger, Nancy M. Amato, Concurrency and Computation: Practice and Experience, 17(14):1643-1656, Dec 2005.
Journal(ps, pdf, abstract)

Protein Folding by Motion Planning, Shawna Thomas, Guang Song, Nancy M. Amato, Physical Biology, 2:S148-S155, Nov 2005.
Journal(ps, pdf, abstract)

Using Motion Planning to Study RNA Folding Kinetics, Xinyu Tang, Bonnie Kirkpatrick, Shawna Thomas, Guang Song, Nancy M. Amato, Journal of Computational Biology, 12(6):862-881, Jul 2005. Also, In Proc. Int. Conf. Comput. Molecular Biology (RECOMB), pp. 252-261, San Diego, CA, Mar 2004.
Journal(ps, pdf, abstract) Proceedings(ps, pdf, abstract)

Parallel Protein Folding with STAPL, Shawna Thomas, Nancy M. Amato, In Proc. IEEE Int. Wkshp. on High Performance Computational Biology, Santa Fe, NM, Apr 2004.
Proceedings(ps, pdf, abstract)

A Motion Planning Approach to Folding: From Paper Craft to Protein Folding, Guang Song, Nancy M. Amato, IEEE Transactions on Robotics and Automation, 20(1):60-71, Feb 2004. Also, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 948-953, Seoul, Korea, May 2001. Also, Technical Report, TR00-017, Department of Computer Science and Engineering, Texas A&M University, Jul 2000.
Journal(ps, pdf, abstract) Proceedings(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

A Motion Planning Approach to Protein Folding, Guang Song, Ph.D. Thesis, Parasol Laboratory, Department of Computer Science, Texas A&M University, Dec 2003.
Ph.D. Thesis(ps, abstract)

Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of Known Native Structures, Nancy M. Amato, Ken Dill, Guang Song, Journal of Computational Biology, 10(3-4):239-255, Jun 2003.
Journal(ps, pdf, abstract)

Neuron PRM: A Framework for Constructing Cortical Networks, Jyh-Ming Lien, Marco Morales, Nancy M. Amato, Neurocomputing, 52-54(28):191-197, Jun 2003. Also, Technical Report, TR01-002, Parasol Laboratory, Department of Computer Science, Texas A&M University, Oct 2001.
Journal(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

A Path Planning-based Study of Protein Folding With a Case Study of Hairpin Formation in Protein G and L, Guang Song, Shawna Thomas, Ken A. Dill, J. Martin Scholtz, Nancy M. Amato, In Proc. Pac. Symp. of Biocomputing (PSB), pp. 240-251, Lihue, HI, Jan 2003.
Proceedings(ps, pdf, abstract)

Using Motion Planning to Study Protein Folding Pathways, Guang Song, Nancy M. Amato, Journal of Computational Biology, 9(2):149-168, Nov 2002. Also, In Proc. Int. Conf. Comput. Molecular Biology (RECOMB), pp. 287-296, Apr 2001. Also, Technical Report, TR00-026, Parasol Laboratory, Department of Computer Science, Texas A&M University, Oct 2000.
Journal(ps, pdf, abstract) Proceedings(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of Known Native Structures, Nancy M. Amato, Guang Song, Technical Report, TR01-001, Parasol Laboratory, Department of Computer Science, Texas A&M University, Oct 2001.
Technical Report(ps, pdf, abstract)

Ligand Binding with OBPRM and Haptic User Input, O. Burchan Bayazit, Guang Song, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 954-959, May 2001.
Proceedings(ps, pdf, abstract)

Ligand Binding with OBPRM and Haptic User Input: Enhancing Automatic Motion Planning with Virtual Touch, O. Burchan Bayazit, Guang Song, Nancy M. Amato, Technical Report, TR00-025, Department of Computer Science and Engineering, Texas A&M University, Oct 2000.
Technical Report(ps, pdf, abstract)

How does it fold? Searching for Folding Pathways using a Motion Planning Approach, Guang Song, Nancy Amato, Technical Report, 00-014, Department of Computer Science and Engineering, Texas A&M University, May 2000.
Technical Report(pdf, abstract)

A Motion Planning Approach to Folding: From Paper Craft to Protein Structure Prediction, Guang Song, Nancy M. Amato, Technical Report, TR00-001, Department of Computer Science and Engineering, Texas A&M University, Jan 2000.
Technical Report(ps)


HIGH-PERFORMANCE COMPUTING

MPMD Framework for Offloading Load Balance Computation, Olga Pearce, Todd Gamblin, Bronis de Supinski, Nancy Amato, In Proc. Int. Par. and Dist. Proc. Symp. (IPDPS), Chicago, IL, USA, May 2016.
Proceedings(pdf, abstract)

An Algorithmic Approach to Communication Reduction in Parallel Graph Algorithms, Harshvardhan, Adam Fidel, Nancy M. Amato, Lawrence Rauchwerger, In Proc. IEEE Int.Conf. on Parallel Architectures and Compilation Techniques (PACT), San Francisco, CA, Oct 2015.
Proceedings(pdf, abstract)

Asynchronous Nested Parallelism for Dynamic Applications in Distributed Memory, Adam Fidel, Ioannis Papadopoulos, Nathan Thomas, Dielli Hoxha, Nancy Amato, Lawrence Rauchwerger, In Wkshp. on Lang. and Comp. for Par. Comp. (LCPC), pp. 106-121, Chapel Hill, NC, Sep 2015.
Proceedings(pdf, abstract)

STAPL-RTS: An Application Driven Runtime System, Ioannis Papadopoulos, Nathan Thomas, Adam Fidel, Nancy M. Amato, Lawrence Rauchwerger, In Proc. ACM Int. Conf. Supercomputing (ICS), pp. 425-434 , Newport Beach, CA, USA, Jun 2015.
Proceedings(pdf, ppt, abstract)

Composing Algorithmic Skeletons to Express High-Performance Scientific Applications, Mani Zandifar, Mustafa Abdujabbar, Alireza Majidi, David Keyes, Nancy M. Amato, Lawrence Rauchwerger, In Proc. ACM Int. Conf. Supercomputing (ICS), pp. 415--424, Newport Beach, CA, USA, Jun 2015.
Proceedings(pdf, abstract)

A Hybrid Approach To Processing Big Data Graphs on Memory-Restricted Systems, Harshvardhan, Brandon West, Adam Fidel, Nancy M. Amato, Lawrence Rauchwerger, In Proc. Int. Par. and Dist. Proc. Symp. (IPDPS), pp. 799-808, Hyderabad, India, May 2015.
Proceedings(pdf, abstract)

A Hierarchical Approach to Reducing Communication in Parallel Graph Algorithms, Harshvardhan, Nancy M. Amato, Lawrence Rauchwerger, In Proc. ACM SIGPLAN Symp. Prin. Prac. Par. Prog. (PPOPP), pp. 285-286 (Poster), San Francisco, CA, USA, Jan 2015.
Proceedings(pdf, abstract)

Efficient, Reachability-based, Parallel Algorithms for Finding Strongly Connected Components, Daniel Tomkins, Timmie Smith, Nancy M. Amato, Lawrence Rauchwerger, Technical Report, TR15-002, Parasol Laboratory, Department of Computer Science, Texas A&M University, College Station, TX 77843-3112, Jan 2015.
Technical Report(pdf, abstract)

Faster Parallel Traversal of Scale Free Graphs at Extreme Scale with Vertex Delegates, Roger Pearce, Maya Gokhale, Nancy M. Amato, In Proc. Supercomputing (SC), New Orleans, LA, Nov 2014.
Proceedings(pdf, abstract)

The Anatomy of a Distributed Motion Planning Roadmap, Sam Ade Jacobs, Nancy M. Amato, In Proc. IEEE Int. Conf. Intel. Rob. Syst. (IROS), Chicago, IL, USA, Sep 2014.
Proceedings(pdf, abstract)

The STAPL Skeleton Framework, Mani Zandifar, Nathan Thomas, Nancy M. Amato, Lawrence Rauchwerger, In Wkshp. on Lang. and Comp. for Par. Comp. (LCPC), pp. 176--190, Hillsboro, OR, USA, Sep 2014.
Proceedings(pdf, abstract)

KLA: A New Algorithmic Paradigm for Parallel Graph Computations, Harshvardhan, Adam Fidel, Nancy M. Amato, Lawrence Rauchwerger, In Proc. IEEE Int.Conf. on Parallel Architectures and Compilation Techniques (PACT), pp. 27-38, Edmonton, AB, Canada, Aug 2014.
Proceedings(pdf, abstract)

Processing Big Data Graphs on Memory-Restricted Systems, Harshvardhan, Nancy M. Amato, Lawrence Rauchwerger, In Proc. IEEE Int.Conf. on Parallel Architectures and Compilation Techniques (PACT), pp. 517-518 (SRC Poster), Edmonton, AB, Canada, Aug 2014.
Proceedings(pdf, abstract)

From Petascale to the Pocket: Adaptively Scaling Parallel Programs for Mobile SoCs, Adam Fidel, Nancy M. Amato, Lawrence Rauchwerger, In Proc. IEEE Int.Conf. on Parallel Architectures and Compilation Techniques (PACT), SRC Poster, Aug 2014.
Proceedings(pdf)

Load Balancing N-Body Simulations with Highly Non-Uniform Density, Olga Pearce, Todd Gamblin, Bronis de Supinski, Nancy M. Amato, Tom Arsenlis, In Proc. ACM Int. Conf. Supercomputing (ICS), pp. 113-122 , Munchen, Germany, Jun 2014.
Proceedings(pdf, abstract)

Validation of Full-Domain Massively Parallel Transport Sweep Algorithms, W Hawkins, Marvin Adams, Michael Adams, Timmie Smith, Nancy Amato, Lawrence Rauchwerger, Teresa Bailey, Peter Brown, Adam Kunen, In Trans. Amer. Nucl. Soc., pp. 699-792, 2014.
Proceedings(pdf, abstract)

Using Load Balancing to Scalably Parallelize Sampling-Based Motion Planning Algorithms, Adam Fidel, Sam Ade Jacobs, Shishir Sharma, Nancy M. Amato, Lawrence Rauchwerger, In Proc. Int. Par. and Dist. Proc. Symp. (IPDPS), Phoenix, Arizona, USA, May 2014.
Proceedings(pdf, abstract)

Scaling Techniques for Massive Scale-Free Graphs in Distributed (External) Memory, Roger Pearce, Maya Gokhale, Nancy M. Amato, In Proc. Int. Par. and Dist. Proc. Symp. (IPDPS), May 2013.
Proceedings(pdf, abstract)

A Scalable Distributed RRT for Motion Planning, Sam Ade Jacobs, Nicholas Stradford, Cesar Rodriguez, Shawna Thomas, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 5088-5095, Karlsruhe, Germany, May 2013.
Proceedings(ps, pdf, abstract)

Provably Optimal Parallel Transport Sweeps on Regular Grids, W Hawkins, Timmie Smith, Michael Adams, Lawrence Rauchwerger, Nancy Amato, Marvin Adams, Teresa Bailey, Robert Falgout, In Proc. Int. Conf. on Math. Meth. and Supercomp. for Nuc. App., Idaho, May 2013.
Proceedings(pdf, abstract)

Load Balancing Techniques for Scalable Parallelization of Sampling-Based Motion Planning Algorithms, Adam Fidel, Sam Ade Jacobs, Shishir Sharma, Lawrence Rauchwerger, Nancy M. Amato, Technical Report, TR13-002 , Parasol Laboratory, Department of Computer Science, Texas A&M University, Mar 2013.
Technical Report(pdf, abstract)

Efficient Massively Parallel Transport Sweeps, W Hawkins, Timmie Smith, Michael Adams, Lawrence Rauchwerger, Nancy Amato, Marvin Adams, Trans. Amer. Nucl. Soc., 107(1):477-481, Nov 2012.
Journal(pdf)

The STAPL Parallel Graph Library, Harshvardhan, Adam Fidel, Nancy M. Amato, Lawrence Rauchwerger, In Wkshp. on Lang. and Comp. for Par. Comp. (LCPC), Tokyo, Japan, Sep 2012.
Proceedings(pdf, abstract)

Quantifying the Effectiveness of Load Balance Algorithms, Olga Pearce, Todd Gamblin, Bronis de Supinski, Martin Schulz, Nancy M. Amato, In Proc. ACM Int. Conf. Supercomputing (ICS), Jun 2012.
Proceedings(pdf, abstract)

A Scalable Method for Parallelizing Sampling-Based Motion Planning Algorithms, Sam Ade Jacobs, Kasra Manavi, Juan Burgos, Jory Denny, Shawna Thomas, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 2529-2536, St. Paul, Minnesota, USA, May 2012.
Proceedings(ps, pdf, abstract)

From Days to Seconds: Scalable Parallel Algorithms for Motion Planning, Sam Ade Jacobs, Nancy M. Amato, In ACM Student Research Compet, Conf. on High Performance Computing Networking, Storage and Analysis Companion Proceedings, Seattle, Washington, USA, Nov 2011.
Proceedings(pdf, abstract)

Radiative Effects in Radiative Shocks in Shock Tubes, R Drake, Forrest Doss, Ryan McClarren, Marvin Adams, Nancy Amato, Derek Bingham, C Chou, Carlos DiStefano, Krzysztof Fidkowski, Bruce Fryxell, Tamas Gombosi, Michael Grosskopf, James Holloway, Bart van der Holst, Channing Huntington, Smadar Karni, Christine Krauland, Carolyn Kuranz, Edward Larsen, Bram van Leer, Bani Mallick, D Marion, William Martin, Jim Morel, Eric Myra, Vijay Nair, Kenneth Powell, Lawrence Rauchwerger, Philip Roe, Erica Rutter, Igor Sokolov, Quentin Stout, Ben Torralva, Gabor Toth, Katsuyo Thornton, Anthony Visco, , 7(3):130-140, 2011.
Journal(pdf, abstract)

The STAPL Parallel Container Framework, Gabriel Tanase, Antal Buss, Adam Fidel, Harshvardhan, Ioannis Papadopoulos, Olga Pearce, Timmie Smith, Nathan Thomas, Xiabing Xu, Nedhal Mourad, Jeremy Vu, Mauro Bianco, Nancy M. Amato, Lawrence Rauchwerger, In Proc. ACM SIGPLAN Symp. Prin. Prac. Par. Prog. (PPOPP), Feb 2011.
Proceedings(pdf, abstract)

Multithreaded Asynchronous Graph Traversal for In-Memory and Semi-External Memory, Roger Pearce, Maya Gokhale, Nancy M. Amato, In Proc. Supercomputing (SC), New Orleans, LA, Nov 2010.
Proceedings(pdf, abstract)

The STAPL pView, Antal Buss, Adam Fidel, Harshvardhan, Timmie Smith, Gabriel Tanase, Nathan Thomas, Xiabing Xu, Mauro Bianco, Nancy M. Amato, Lawrence Rauchwerger, Technical Report, TR10-001, Parasol Laboratory, Department of Computer Science, Texas A&M University, Jul 2010.
Technical Report(pdf, abstract)

STAPL: Standard Template Adaptive Parallel Library, Antal Buss, Harshvardhan, Ioannis Papadopoulos, Olga Tkachyshyn, Timmie Smith, Gabriel Tanase, Nathan Thomas, Xiabing Xu, Mauro Bianco, Nancy M. Amato, Lawrence Rauchwerger, In Haifa Experimental Systems Conference, Haifa, Israel, May 2010.
Proceedings(pdf, abstract)

The STAPL pList, Gabriel Tanase, Xiabing Xu, Antal Buss, Harshvardhan, Ioannis Papadopoulos, Olga Tkachyshyn, Timmie Smith, Nathan Thomas, Mauro Bianco, Nancy M. Amato, Lawrence Rauchwerger, In Wkshp. on Lang. and Comp. for Par. Comp. (LCPC), Newark, Delaware, Oct 2009.
Proceedings(pdf, abstract)

Design for Interoperability in STAPL : pMatrices and Linear Algebra Algorithms, Antal Buss, Timmie Smith, Gabriel Tanase, Nathan Thomas, Mauro Bianco, Nancy M. Amato, Lawrence Rauchwerger, In Wkshp. on Lang. and Comp. for Par. Comp. (LCPC), Jul 2008.
Proceedings(pdf, abstract)

Design for Interoperability in STAPL: pMatrices and Linear Algebra Algorithms, Antal Buss, Timmie Smith, Gabriel Tanase, Nathan Thomas, Mauro Bianco, Nancy M. Amato, Lawrence Rauchwerger, Lecture Notes in Computer Science, 5335/2008:304-315, 2008.
Journal(pdf, abstract)

Associative Parallel Containers In STAPL, Gabriel Tanase, Chidambareswaran (Chids) Raman, Mauro Bianco, Nancy M. Amato, Lawrence Rauchwerger, In Wkshp. on Lang. and Comp. for Par. Comp. (LCPC), Oct 2007.
Proceedings(pdf, abstract)

The STAPL pArray, Gabriel Tanase, Mauro Bianco, Nancy M. Amato, Lawrence Rauchwerger, In Proc. of Workshop MEDEA, pp. 81-88, Brasov, Romania, Sep 2007.
Proceedings(pdf, abstract)

SmartApps: Middleware for Adaptive Applications on Reconfigurable Platforms, Lawrence Rauchwerger, Nancy Amato, Operating System Reviews, 40(2):73-82, Apr 2006.
Journal(pdf, abstract)

Parallel Protein Folding with STAPL, Shawna Thomas, Gabriel Tanase, Lucia K. Dale, Jose M. Moreira, Lawrence Rauchwerger, Nancy M. Amato, Concurrency and Computation: Practice and Experience, 17(14):1643-1656, Dec 2005.
Journal(ps, pdf, abstract)

An Experimental Evaluation of the HP V-Class and SGI Origin 2000 Multiprocessors using Microbenchmarks and Scientific Applications, Ravi Iyer, Jack Perdue, Nancy M. Amato, Lawrence Rauchwerger, Laxmi Bhuyan, International Journal of Parallel Programming, 33(4):307-350, 2005.
Journal(ps, pdf, abstract)

A Framework for Adaptive Algorithm Selection in STAPL, Nathan Thomas, Gabriel Tanase, Olga Tkachyshyn, Jack Perdue, Nancy M. Amato, Lawrence Rauchwerger, In Proc. ACM SIGPLAN Symp. Prin. Prac. Par. Prog. (PPOPP), pp. 277-288, Chicago, Illinois, Jun 2005.
Proceedings(ps, pdf, abstract)

STAPL: An Adaptive, Generic Parallel C++ Library, Ping An, Alin Jula, Silvius Rus, Steven Saunders, Tim Smith, Gabriel Tanase, Nathan Thomas, Nancy Amato, Lawrence Rauchwerger, In Wkshp. on Lang. and Comp. for Par. Comp. (LCPC), pp. 193-208, Cumberland Falls, Kentucky, Aug 2001.
Proceedings(ps, pdf, abstract)

STAPL: A Standard Template Adaptive Parallel C++ Library, Ping An, Alin Jula, Silvius Rus, Steven Saunders, Tim Smith, Gabriel Tanase, Nathan Thomas, Nancy Amato, Lawrence Rauchwerger, In Int. Wkshp on Adv. Compiler Technology for High Perf. and Embedded Processors, pp. 10, Bucharest, Romania, Jul 2001.
Proceedings(ps, pdf, abstract)

SmartApps: An Application Centric Approach to High Performance Computing, Lawrence Rauchwerger, Nancy Amato, Josep Torrellas, In Wkshp. on Lang. and Comp. for Par. Comp. (LCPC), Yorktown Heights, New York, USA, Aug 2000.
Proceedings(ps, pdf, abstract)

A General Performance Model for Parallel Sweeps on Orthogonal Grids for Particle Transport Calculations, Mark M. Mathis, Nancy M. Amato, Marvin Adams, In Proc. ACM Int. Conf. Supercomputing (ICS), pp. 255-263, Santa Fe, NM, May 2000. Also, Technical Report, TR00-004, Parasol Laboratory, Department of Computer Science, Texas A&M University, Dec 1999.
Proceedings(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

Predicting Performance on SMPs. A Case Study: The SGI Power Challenge, Nancy M. Amato, Jack Perdue, Andrea Pietracaprina, Geppino Pucci, Mark Mathis, In Proc. Int. Par. and Dist. Proc. Symp. (IPDPS), pp. 729-737, Cancun, Mexico, May 2000. Also, Technical Report, TR99-020, Department of Computer Science and Engineering, Texas A&M University, Oct 1999.
Proceedings(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

Task Scheduling and Parallel Mesh-Sweeps in Transport Computations, Nancy M. Amato, Ping An, Technical Report, TR00-009, Department of Computer Science and Engineering, Texas A&M University, Jan 2000.
Technical Report(ps, pdf)

Comparing the Memory System Performance of the HP V-Class and SGI Origin 2000 Multiprocessors using Microbenchmarks and Scientific Applications, Ravi Iyer, Nancy M. Amato, Lawrence Rauchwerger, Laxmi Bhuyan, In Proc. ACM Int. Conf. Supercomputing (ICS), pp. 339-347, Rhodes, Greece, Jun 1999.
Proceedings(ps, pdf, abstract)

Comparing the Memory System Performance of the HP V-Class and SGI Origin 2000 Multiprocessors using Microbenchmarks and Scientific Applications, Ravi Iyer, Nancy M. Amato, Lawrence Rauchwerger, Laxmi Bhuyan, In Proc. ACM Int. Conf. Supercomputing (ICS), pp. 9, Rhodes, Greece, Jun 1999.
Proceedings(ps, pdf, abstract)

Probabilistic Roadmap Methods are Embarrassingly Parallel, Nancy M. Amato, Lucia K. Dale, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 688-694, Detroit, Michigan, USA, May 1999.
Proceedings(ps, pdf, abstract)

A Cost Model for Communication on a Symmetric MultiProcessor, Nancy M. Amato, Andrea Pietracaprina, Geppino Pucci, Lucia K. Dale, Jack Perdue, Technical Report, TR98-004, Department of Computer Science and Engineering, Texas A&M University, Presented at SPAA Revue, 1998., Jan 1998.
Technical Report(ps, pdf, abstract)

Hindsight Helps: Deterministic Task Scheduling with Backtracking, Yueh-O Wang, Nancy M. Amato, D. K. Friesen, In Workshop on Challenges for Parallel Processing, Aug 1997.
Proceedings(ps, pdf)

A Comparison of Parallel Sorting Algorithms on Different Architectures, Nancy M. Amato, Ravi Iyer, Sharad Sundaresan, Yan Wu, Technical Report, TR98-029, Department of Computer Science and Engineering, Texas A&M University, Jan 1996.
Technical Report(ps, pdf, abstract)

Run-Time Methods for Parallelizing Partially Parallel Loops, Lawrence Rauchwerger, Nancy M. Amato, David A. Padua, In Proc. ACM Int. Conf. Supercomputing (ICS), pp. 137-146, Barcelona, Spain, Aug 1995.
Proceedings(ps, pdf, abstract)

Improved Processor Bounds for Parallel Algorithms for Weighted Digraphs, Nancy M. Amato, Information Processing Letters, 45:147-152, 1993.
Journal(pdf, abstract)

A General Performance Model for Parallel Sweeps on Orthogonal Grids for Particle Transport Calculations, Mark M. Mathis, Masters Thesis, Department of Computer Science and Engineering, Texas A&M University, Dec 2000.
Masters Thesis(ps, pdf, abstract)


GEOMETRIC COMPUTING

Distance-based aggregation, Mukulika Ghosh, Nancy M. Amato, Technical Report, TR14-006, Parasol Laboratory, Department of Computer Science, Texas A&M University, College Station, Texas, Apr 2014.
Technical Report(pdf, abstract)

Fast Approximate Convex Decomposition Using Relative Concavity, Mukulika Ghosh, Nancy M. Amato, Yanyan Lu, Jyh-Ming Lien, Computer Aided-Design, 45(2):494 - 504, 2013. Also, In Proc. ACM Solid and Physical Modeling Symp. (SPM), France, Oct 2012.
Journal(pdf, abstract) Proceedings(pdf, abstract)

Fast Approximate Convex Decomposition, Mukulika Ghosh, Masters Thesis, Department of Computer Science and Engineering, Texas A&M University, College Station, TX, USA, Aug 2012.
Masters Thesis(pdf)

Alpha decomposition of Polygons, Yanyan Lu, Jyh-Ming Lien, Mukulika Ghosh, Nancy M. Amato, Computers & Graphics, 36(5):466 - 476, 2012. Also, In Proc. of Shape Modeling International (SMI), College Station, TX, US, May 2012.
Journal(pdf, abstract) Proceedings(pdf, abstract)

Approximate Convex Decomposition of Polyhedra, Jyh-Ming Lien, Nancy M. Amato, Computer Aided Geometric Design, 25(7):503-522, Oct 2008. Also, In Proc. ACM Solid and Physical Modeling Symp. (SPM), pp. 121-131, New York, NY, USA, Jun 2007. Also, Technical Report, TR06-002, Parasol Laboratory, Department of Computer Science, Texas A&M University, Jan 2006. Also, Technical Report, TR05-001, Parasol Laboratory, Department of Computer Science, Texas A&M University, Jan 2005.
Journal(pdf, abstract) Proceedings(pdf, abstract) Technical Report(pdf, abstract) Technical Report(ps, pdf, abstract)

Approximate Convex Decomposition and Its Applications, Jyh-Ming Lien, Ph.D. Thesis, Department of Computer Science and Engineering, Texas A&M University, Dec 2006.
Ph.D. Thesis(pdf, abstract)

Simultaneous Shape Decomposition and Skeletonization, Jyh-Ming Lien, John Keyser, Nancy M. Amato, In Proc. ACM Solid and Physical Modeling Symp. (SPM), pp. 219-228, Cardiff, Wales, UK, Jun 2006.
Proceedings(pdf, abstract)

Approximate Convex Decomposition of Polygons, Jyh-Ming Lien, Nancy M. Amato, Computational Geometry: Theory & Applications, To appear:2005. Also, In Proc. ACM Symp. Comput. Geom., pp. 17-26, Brooklyn, New York, Jun 2004. Also, Technical Report, TR03-008, Parasol Laboratory, Department of Computer Science, Texas A&M University, Dec 2003. Also, Technical Report, TR03-008, Department of Computer Science and Engineering, Texas A&M University, Texas, Jun 2003.
Journal(ps, pdf, abstract) Proceedings(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

Approximate Convex Decomposition, Jyh-Ming Lien, Nancy M. Amato, In Proc. ACM Symp. Comput. Geom., pp. 457-458, Brooklyn, New York. Video Abstract, Jun 2004. Also, Technical Report, TR03-001, Department of Computer Science and Engineering, Texas A&M University, Jan 2003.
Proceedings(ps, pdf) Technical Report(ps, pdf, abstract)

A Randomized Algorithm for Triangulating a Simple Polygon in Linear Time, Nancy M. Amato, Michael T. Goodrich, Edgar A. Ramos, Discrete and Computational Geometry, 26(2):245‚Äď265, 2001.
Journal(pdf, abstract)

Linear-Time Triangulation of a Simple Polygon Made Easier Via Randomization, Nancy M. Amato, Michael T. Goodrich, Edgar Ramos, Discrete and Computational Geometry, 26:245-265, 2001. Also, In Proc. ACM Symp. Comput. Geom., pp. 201-212, Jun 2000.
Journal(ps, pdf, abstract) Proceedings(ps, pdf, abstract)

Computing the Arrangement of Curve Segments: Divide-and-Conquer Algorithms via Sampling, Nancy M. Amato, Michael T. Goodrich, Edgar A. Ramos, In Proc. ACM-SIAM Symp. Disc. Alg. (SODA), pp. 705-706, Jan 2000.
Proceedings(ps, pdf, abstract)

A Probabilistic Method for Rigid Body Motion Planning Using Sampling from the Medial Axis of the Free Space, Steven A. Wilmarth, Ph.D. Thesis, Department of Mathematics, Texas A&M University, Dec 1999.
Ph.D. Thesis(ps, pdf, abstract)

Motion Planning for a Rigid Body Using Random Networks on the Medial Axis of the Free Space, Steven A. Wilmarth, Nancy M. Amato, Peter F. Stiller, In Proc. ACM Symp. Comput. Geom., pp. 173-180, Miami Beach, FL, Jun 1999. Also, Technical Report, TR98-028, Department of Computer Science and Engineering, Texas A&M University, Dec 1998.
Proceedings(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

MAPRM: A Probabilistic Roadmap Planner with Sampling on the Medial Axis of the Free Space, Steven A. Wilmarth, Nancy M. Amato, Peter F. Stiller, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 1024-1031, Detroit, MI, May 1999. Also, Technical Report, TR98-0022, Department of Computer Science and Engineering, Texas A&M University, Nov 1998.
Proceedings(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

Equipping CAD/CAM Systems with Geometric Intelligence, Nancy M. Amato, ACM Computing Surveys, 28(4es)(17):Dec 1996.
Journal(abstract)

Strategic Directions in Computational Geometry, R. Tamassia (editor), P. K. Agarwal, N. M. Amato, D. Z. Chen, D. Dobkin, R. L. S. Drysdale, S. Fortune, M. T. Goodrich, J. Hershberger, J. O'Rourke, F. P. Preparata, J. -R. Sack, ACM Computing Surveys, 28(4):591-606, Dec 1996.
Journal(pdf, abstract)

On Computing Voronoi Diagrams by Divide-Prune-and-Conquer, Nancy M. Amato, Edgar A. Ramos, In Proc. ACM Symp. Comput. Geom., pp. 166-175, May 1996.
Proceedings(ps, pdf, abstract)

A Time-Optimal Parallel Algorithm for Three-Dimensional Convex Hulls, Nancy M. Amato, Franco P. Preparata, Algorithmica, 14(2):169-182, Aug 1995.
Journal(ps, pdf, abstract)

Finding a Closest Visible Vertex Pair Between Two Polygons, Nancy M. Amato, Algorithmica, 14(2):183-201, Aug 1995.
Journal(ps, pdf, abstract)

Computing Faces in Segment and Simplex Arrangements, Nancy M. Amato, Michael T. Goodrich, Edgar A. Ramos, In Proc. ACM Symp. Theory of Comp. (STOC), pp. 672-682, Las Vegas, Nevada, U.S.A., Jun 1995.
Proceedings(ps, pdf, abstract)

Determining the Separation of Simple Polygons, Nancy M. Amato, International Journal of Computational Geometry & Applications, 4(4):457-474, Dec 1994.
Journal(ps, pdf, abstract)

Parallel Algorithms for Convex Hulls and Proximity Problems, Nancy M. Amato, Ph.D. Thesis, Computer Science Department, University of Illinois, Dec 1994.
Ph.D. Thesis(abstract)

Parallel Algorithms for Higher-Dimensional Convex Hulls, Nancy M. Amato, Michael T. Goodrich, Edgar A. Ramos, In Proc. of the 35th IEEE Symposium on Foundations of Computer Science, pp. 683-694, Santa Fe, New Mexico, U.S.A., Nov 1994.
Proceedings(ps, pdf, abstract)

An Optimal Algorithm for Computing the Separation of Two Simple Polygons, Nancy M. Amato, In Proc. Wkshp. Alg. Data Str. (WADS), pp. 48-59, Jul 1993.
Proceedings(pdf, abstract)

An NC1 Parallel 3D Convex Hull Algorithm, Nancy M. Amato, Franco P. Preparata, In Proc. ACM Symp. Comput. Geom., pp. 289-297, San Diego, CA, May 1993.
Proceedings(pdf, abstract)

The Parallel 3D Convex-Hull Problem Revisited, Nancy M. Amato, Franco P. Preparata, International Journal of Computational Geometry & Applications, 2(2):163-174, Jun 1992.
Journal(pdf, abstract)


MISCELLANEOUS

Merging Physical Manipulatives and Digital Interface in Educational Software, Anna Zacchi, Nancy Amato, In World Conf. on Educ. Multimedia, Hypermedia and Telecom. (ED-MEDIA), Montreal, Canada, Jun 2000.
Proceedings(ps, pdf, abstract)

Checking Linked Data Structures, Nancy M. Amato, Michael C. Loui, In Proc. Int. Symp. on Fault-Tolerant Computing (FTCS), pp. 164-173, Austin, TX, Jun 1994.
Proceedings(ps, pdf, abstract)

Next Generation Geographic Modeling Framework Research at USACERL, Kurt Buehler, Jeffrey Wallace, Michael Shapiro, Nancy M. Amato, Unni Narayanan, GRASSClippings, 6(3):35-39, Dec 1992.


Reversing Trains: A Turn of the Century Sorting Problem, Nancy Amato, Manuel Blum, Sandra Irani, Ronitt Rubinfeld, Journal of Algorithms, 10(3):413-428, Sep 1989.
Journal(pdf, abstract)