Dissertations and Miscellaneous

M17. Optimal implementation of the shadow hybrid Monte Carlo method

C. R. Sweet, S. S. Hampton, and J. A. Izaguirre

Technical Report TR-2006-09, University of Notre Dame, 2006

M16. On Being Close to the Data: Executing Code in a Replica Management System

J. M. Wozniak, P. Brenner, D. Thain, A. Striegel, J. A. Izaguirre

2006

M15. Multiscale Computational Methods for Morphogenesis and Algorithms for Protein-Protein Interaction Inference

Chengbang Huang

Ph.D. Dissertation, Dept. of Computer Science and Engineering, University of Notre Dame, July 2005

M14. Empirical Analysis of Design Patterns - A Case Study in CompuCell3D

Kedar Aras

Master's Thesis, Dept. of Computer Science & Eng., Univ. of Notre Dame, Oct. 2005

M13. Empirical Evaluation of Design Patterns in Scientific Application

Kedar Aras, Trevor Cickovski, and Jesús A. Izaguirre

Technical Report TR-2005-08, Dept. of Computer Science & Eng., Univ. of Notre Dame, 2005

M12. BIOLOGO: A Domain-Specific Language for Morphogenesis

T. Cickovski, R. Merks, and J. A. Izaguirre

In preparation, 2005

M10. BioLogo, a Domain-Specific Language for Morphogenesis

Trevor M. Cickovski

M.S. Thesis, Department of Computer Science and Engineering, University of Notre Dame, December 2004

M9. Design Patterns for Scientific Software

T. Cickovski, T. Matthey, and J. A. Izaguirre

Technical Report TR-2004-29, Department of Computer Science and Engineering, University of Notre Dame, 2004

M8. Polarizable Force Fields for Flexible Molecules

Asbjørn Holt

M.S. Thesis, NTNU and Lunds Univesitet, Norway, July 2004

M7. Improved Sampling of Configuration Space of Biomolecules using Shadow Hybrid Monte Carlo

Scott S. Hampton

M.S. Thesis, Department of Computer Science and Engineering, University of Notre Dame, August 2004

M6. GIPSE: A Toolset for Streamlining the Management Aspects of the Grid for Simulation-based Research

A. Striegel, M. Shorts, E. Stuntebeck, D. Salyers, J. A. Izaguirre

M6. MDSimAid: Automatic Optimization of Fast Electrostatics Algorithms for Molecular Simulations

Alice N. Ko and Jesús A. Izaguirre

International Conference on Computational Science ICCS 2003

M5. Novel Multiscale Algorithms for Molecular Dynamics

Qun Ma

Ph.D. Thesis, Department of Computer Science and Engineering, University of Notre Dame, June, 2003

M4. MDSimAid: An Automatic Recommender for Optimization of Fast Electrostatic Algorithms for Molecular Simulations

Alice N. Ko

M.S. Thesis, Department of Computer Science and Engineering, Notre Dame, IN, Dec. 2002

M3. Framework Design, Parallelization and Force Computation in Molecular Dynamics

Thierry Matthey

Ph.D. Thesis, Department of Informatics, University of Bergen, Norway, Sept. 2002

M2. Linearly scalable hybrid Monte Carlo method for conformational sampling of large biomolecules

Scott Hampton and Jesús A. Izaguirre

Preprint

M1. A Tutorial on the Prototyping of Multiple Time Stepping Integrators for Molecular Dynamics

Jesús A. Izaguirre, Thierry Matthey, Jeremiah Willcock, Branden Moore, Qun Ma, Thomas Slabach, and George Viamontes

2001