Publications



Molecular Dynamics

56. Long Timestep Molecular Dynamics on the Graphical Processing Unit

James C. Sweet, Ronald J. Nowling, Trevor Cickovski, Christopher R. Sweet, Vijay S. Pande, and Jesús A. Izaguirre

J Chem Theory Comput (2013), http://dx.doi.org/10.1021/ct400331r

55. Modeling conformational ensembles of slow functional motions in Pin1-WW

Faruck Morcos, Santanu Chatterjee, Christopher L. McClendon, Paul R. Brenner, Roberto Lopez-Rendon, John Zintsmaster, Maria Ercsey-Ravasz, Chris R. Sweet, Matthew P. Jacobson, Jeffrey W. Peng, and Jesús A. Izaguirre

PLoS Comput Biol 6(12): e1001015. (2010) doi:10.1371/journal.pcbi.1001015

54. Inferring protein-protein interactions from multiple protein domain combinations

Kanaan SP, Huang C, Wuchty S, Chen DZ, Izaguirre JA

Methods Mol Biol. (2009) 541:43-59

PLoS Comput Biol 6(12): e1001015. (2010) doi:10.1371/journal.pcbi.1001015

53. MDLab: A Molecular Dynamics Simulation Prototyping Environment

Cickovski T, Chatterjee S, Wenger J, Sweet CR, Izaguirre JA

J Comput Chem (2010) 31:1345-1356

51. Belief Propagation Estimation of Protein and Domain Interactions using the Sum-Product Algorithm

Faruck Morcos, Marcin Sikora, Mark Alber, Dale Kaiser, and Jesús A. Izaguirre

IEEE T. Inform. Theory, Special Issue on Neuroscience and Molecular Biology (2010) 56:742-755

46. A separable shadow hybrid Monte Carlo method

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

J. Chem. Phys. (2009) 131, 174106

28. Multiscale dynamics of macromolecules using Normal Mode Langevin

Jesús A. Izaguirre, Chris R. Sweet, and Vijay S. Pande

Pac Symp Biocomput. (2010) 15:240-51

27. Estimation of Protein and Domain Interactions in the Switching Motility System of Myxococcus xanthus

Faruck Morcos, Marcin Sikora, Mark Alber, Dale Kaiser, and Jesús A. Izaguirre

Pac Symp Biocomput. (2010) 15:157-65

26. Determination of Specificity Residues in Two Component Systems using Graphlets

Faruck Morcos, Charles Lamanna, Nitesh V. Chawla, and Jesús A. Izaguirre, Proc.

International Conference on Bioinformatics & Computational Biology BIOCOMP '09

25. Adaptive dimensionality reduction of stochastic differential equations for protein dynamics

Jesús A. Izaguirre and Christopher R. Sweet, Proc.

Second International Workshop on Model Reduction in Reacting Flows, April 2009, Notre Dame, IN

49. Biomolecular committor probability calculation enabled by processing in network storage

Paul Brenner, Justin M. Wozniak, Douglas Thain, Aaron Striegel, Jeff W. Peng, and Jesús A. Izaguirre

Parallel Computing, 34:652-660, 2008

48. Normal Mode Partitioning of Langevin Dynamics for Biomolecules

C.R. Sweet, P. Petrone, V.S. Pande, J.A. Izaguirre

J. Chem. Phys. 128: 145101, 2008

S48. Supplementary Information for Normal Mode Partitioning of Langevin Dynamics for Biomolecules

47. Accelerating the Replica Exchange Method Through an Efficient All-Pairs Exchange

P. Brenner, C. R. Sweet, D. VonHandorf, J. A. Izaguirre

J. Chem. Phys. 126(7):074103, 2007

22. MDL, A Domain-Specific Language for Molecular Dynamics

T. Cickovski, C. Sweet, and J. A. Izaguirre, Proc.

40th Annual Simulation Symposium, March 2007, Norfolk, VA

20. Backward error analysis of multiscale symplectic integrators and propagators

C. R. Sweet and J. A. Izaguirre, Proc.

Third International Conference Multiscale Materials Modeling MMM2006, Freiburg, Germany, September 2006

41. Parallel Multigrid Summation for the N-body Problem

Jesús A. Izaguirre, Scott S. Hampton, and Thierry Matthey

Journal of Parallel and Distributed Computing, 65:949-962, 2005

40. MDSimAid: Automatic Parameter Optimization in Fast Electrostatic Algorithms

Michael S. Crocker, Scott S. Hampton, Thierry Matthey, and Jesús A. Izaguirre

Journal of Computational Chemistry, Vol. 26, pp. 1021-1031, 2005

38. Shadow Hybrid Monte Carlo: An Efficient Propagator in Phase Space of Macromolecules

Jesús A. Izaguirre and Scott S. Hampton

Journal of Computational Physics, Vol. 200, No. 2, pp. 581-604, 2004

37. ProtoMol, an Object-Oriented Framework for Prototyping Novel Algorithms for Molecular Dynamics

Thierry Matthey, Trevor Cickovski, Scott Hampton, Alice Ko, Qun Ma, Matthew Nyerges, Troy Raeder, Thomas Slabach and Jesús A. Izaguirre

ACM Transactions on Mathematical Software, Vol. 20, No. 3, pp. 237-265, 2004

12. Improved Sampling for Biological Molecules Using Shadow Hybrid Monte Carlo

Scott S. Hampton and Jesús A. Izaguirre

M. Bubak, G. D. von Albada, and P. M. A. Sloot, J. J. Dongarra, editors

4th International Conference on Computational Science, Kraków, Poland, Volu me 3037 of Lecture Notes in Computer Science, pp. 268-274. Springer-Verlag, New York, 2004

35. Targeted mollified impulse - a multiscale stochastic integrator for long molecular dynamics simulations

Q. Ma and J. A. Izaguirre

Multiscale Modeling and Simulation, Vol. 2, No. 1, pp. 1-21, 2003

34. Verlet-I/r-RESPA is limited by nonlinear instability

Qun Ma, Jesús A. Izaguirre and Robert D. Skeel

SIAM Journal on Scientific Computing, Vol. 24, No. 6, pp. 1951-1973, May 6, 2003

10. ProtoMol: A Molecular Dynamics Research Framework for Algorithmic Development

Thierry Matthey, Alice N. Ko and Jesús A. Izaguirre

Springer Verlag LNCS 2659, Computational Science- ICCS 2003, International conference Melbourne, Australia and St. Petersburg, Russia, June 2003, Part III, pp 50-59

9. Long time step molecular dynamics using targeted Langevin stabilization

Qun Ma and Jesús A. Izaguirre

Proceedings of the ACM Symposium on Applied Computing SAC 03, pp. 178-182, 2003

8. Nonlinear instability in multiple time stepping molecular dynamics

Qun Ma, Jesús A. Izaguirre and Robert D. Skeel

Proceedings of the ACM Symposium on Applied Computing SAC 03, pp. 167-171, 2003

33. An Impulse Integrator for Langevin Dynamics

R.D. Skeel and J.A. Izaguirre

Molecular Physics, Vol. 100, No. 24, 3885-3891, 2002

7. Overcoming instabilities in Verlet-I/r-RESPA with the mollified impulse method

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

Computational Methods for Macromolecules: Challenges and Applications, Proceedings of the 3rd International Workshop on Algorithms for Macromolecular Modeling, New York, Oct. 12-14, 2000

Lecture Notes in Computational Science and Engineering (LNCSE), Vol. 24, pp . 146-174. Springer Verlag, Berlin, 2002. Editors: T. Schlick and H. H. Gan

32. Langevin Stabilization of Molecular Dynamics

Jesús A. Izaguirre, Justin M. Wozniak, Daniel P. Catarello, and Robert D. Skeel

J. Chem. Phys., 114(5):2090-2098, Feb. 1 2001

6. Petaflop Computing for Protein Folding

Shannon K. Kuntz, Richard C. Murphy, Michael T. Niemier, Jesús A. Izaguirre and Peter M. Kogge, Proc.

10th SIAM Conference on Parallel Processing for Scientific Computing, March 2001

5. ProtoMol: A Molecular Dynamics Framework with Incremental Parallelization

Thierry Matthey and Jesús A. Izaguirre, Proc.

10th SIAM Conference on Parallel Processing for Scientific Computing, March 2001

4. Langevin Stabilization of Multiscale Mollified Molecular Dynamics

Jesús A. Izaguirre

A. Brandt, K. Binder, and J. Bernholc, editors

Multiscale Computational Methods in Chemistry and Physics, volume 177 of NATO Science Series: Series III Computer and Systems Sciences, pp. 34-47, IOS Press, Amsterdam, Jan 2001

31. Longer Time Steps for Molecular Dynamics

Jesús A. Izaguirre, Sebastian Reich and Robert D. Skeel

J. Chem. Phys., 110(20), pp. 9853-9864, 22 May 1999

3. BioCoRE: A collaboratory for structural biology

M. Bhandarkar, G. Budescu, W. F. Humphrey, J. A. Izaguirre, S. Izrailev, L. V. Kalé, D. Kosztin, F. Molnar, J. C. Phillips, and K. Schulten

Agostino G. Bruzzone, Adelinde Uchrmacher, and Ernest H. Page, editors

Proceedings of the SCS International Conference on Web-Based Modeling and S imulation, pages 242-251, San Francisco, California, 1999

2. The Five Femtosecond Time Step Barrier

Robert D. Skeel and Jesús A. Izaguirre

Computational Molecular Dynamics: Challenges, Methods, Ideas, Vol. 4 of Lecture Notes in Computational Science and Engineering, pp. 303-318, Springer-Verlag, Berlin, 1998


Analysis of Protein Networks

50. Cytoprophet: A Cytoscape plug-in for protein and domain interaction networks inference

Faruck Morcos, Charles Lamanna, Marcin Sikora, and Jesús Izaguirre

Bioinformatics, 19:2265-2266, 2008

43. Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach

Chengbang Huang, Faruck Morcos, Simon P. Kanaan, Stefan Wuchty, Danny Z. Chen, and Jesús A. Izaguirre

IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 4, pp. 1-10, 2007

24. Bayesian Inference of Protein and Domain Interactions Using the Sum-Product Algorithm

Marcin Sikora, Faruck Morcos, Daniel J. Costello, Jr., and Jesús A. Izaguirre, Proc.

2007 Information Theory and Applications Workshop, San Diego, Jan. 29 2007

19. Prediction of domain interactions in C. elegans

Faruck Morcos, Mike Boxem, Niels Klitgord, Marc Vidal, and Jesús A. Izaguirre. Proc.

Workshop Computational Biophysics to Systems Biology CBSB06, Forschungszentrum Jülich, Germany, June 2006


Computational Developmental Biology (Morphogenesis)

48. A Parallel Implementation of the Cellular Potts Model for Simulation of Cell-Based Morphogenesis

N. Chen, J. A. Glazier, J. A. Izaguirre, and M. S. Alber

Computer Physics Communications 176:670 (2007)

45. From Genes To Organisms Via The Cell: A Problem Solving Environment For Multicellular Development

T. Cickovski, K. Aras, M. Swat, R. M. H. Merks, T. Glimm, H. G. E.Hentschel, M. S. Alber, J. A. Glazier, S. A. Newman, J. A. Izaguirre

Accepted, Computing in Science and Engineering (2007)

42. A Framework for Three-Dimensional Simulation of Morphogenesis

T. Cickovski, C. Huang, R. Chaturvedi, T. Glimm, H.G.E. Hentschel, M. Alber, J. A. Glazier, S. A. Newman, and J. A. Izaguirre

IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 2, pp. 237-288, 2005

39. On Multiscale Approaches to Three-Dimensional Modeling of Morphogenesis

R. Chaturvedi, C. Huang, B. Kazmierczak, T. Schneider, J. A. Izaguirre, S. A. Newman, J. A. Glazier, and M. Alber

Journal of the Royal Society, Interface, Vol. 2, pp. 237-253, 2005

36. CompuCell, a multi-model framework for simulation of morphogenesis

Jesús A. Izaguirre, Rajiv Chaturvedi, Chengbang Huang, Trevor Cickovski, Joseph Coffland, Gilberto Thomas, Gabor Forgacs, Mark Alber, Stuart A. Newman, and James A. Glazier

Bioinformatics, Vol. 20, No. 7, pp. 1129-1137, 2004

13. A Hybrid Discrete-Continuum Model for 3-D Skeletogenesis of the Vertebrate Limb

R. Chaturvedi, C. Huang, J. A. Izaguirre, S. A. Newman, J. A. Glazier, and M. Alber

Peter M. A. Sloot, Bastien Chopard, and Alfons G. Hoekstra, editors

Cellular Automata: 6th International Conference on Cellular Automata for Research and Industry, ACRI 2004, Amsterdam, The Netherlands, October 25-28, 2004

Volume 3305 of Lecture Notes in Computer Science, pp. 543-552. Springer Verlag, Berlin Heidelberg, 2004

11. Multi-model simulations of chicken limb morphogenesis

Rajiv Chaturvedi, Jesús A. Izaguirre, Chengbang Huang, Trevor Cickovski, Patrick Virtue, Gilberto Thomas, Gabor Forgacs, Mark Alber, Stuart A. Newman, and James A. Glazier

>Springer Verlag LNCS 2659, Computational Science- ICCS 2003, International conference Melbourne, Australia and St. Petersburg, Russia, June 2003, Part III, pp 39-49


Grid Computing

 

Folding Proteins at 500 ns/hour using Work Queue

Badi' Abdul-Wahid, Li Yu, Dinesh Rajan, Haoyun Feng, Eric Darve, Douglas Thain, Jesus A. Izaguirre

8th IEEE International Conference on eScience (eScience 2012), October 2012

44. Making the Best of a Bad Situation: Prioritized Storage Management in GEMS

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

J. of Future Generation Computer Systems 24:10-16 (2008)

23. Biomolecular Path Sampling Enabled by Processing in Network Storage

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

The Sixth IEEE International Workshop on High-Performance Computational Biology HiCOMB 2007

21. Access Control for a Replica Management Database

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

Workshop on Storage Security and Survivability, October 2006

18. Biomolecular Sampling: Algorithms, Test Molecules, and Metrics

Scott Hampton, Paul Brenner, Aaron Wenger, Santanu Chatterjee, and Jesús A. Izaguirre

New Algorithms for Macromolecular Simulation, pp. 103-123

Volume 49 in Lecture Notes in Computational Science and Engineering (LNCSE), Springer Verlag, Berlin and New York, 2006

17. Applying feedback control to a replica management system

Justin Wozniak, Paul Brenner, Doug Thain, Aaron Striegel, and Jesús A. Izaguirre

Proceedings of 38th Southeastern Symposium on System Theory, Cookeville, TN, March 2006

16. Separating Abstractions from Resources in a Tactical Storage System

Thain, D., Klous, S., Wozniak, J., Brenner, P., Striegel, A. and Izaguirre, J.

Supercomputing, Seattle, WA, Nov. 12-18, 2005

15. Generosity and Gluttony in GEMS: Grid Enabled Molecular Simulations

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

14th IEEE International Symposium on High Performance Distributed Computing (HPDC-14), Research Triangle Park, NC, July 24-27, 2005

14. GIPSE: Streamlining the Management of Simulation on the Grid

J. M. Wozniak, A. Striegel, D. Salyers, and J. A. Izaguirre

38th Annual Simulation Symposium ANSS 05, San Diego, CA, USA, April 2-8, 2005

1. Evaluation of Parallel Domain Partitioning Algorithms

Jesús A. Izaguirre

Proceedings of the First National Computer Science Encounter, Workshop of Distributed and Parallel Systems, pp. 44-50, Querétaro, México, Sept. 11-13, 1997


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