Publications

 

 

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MOLECULAR DYNAMICS

ANALYSIS OF PROTEIN NETWORKS

COMPUTATIONAL DEVELOPMENTAL BIOLOGY (MORPHOGENESIS)

GRID COMPUTING

DISSERTATIONS AND MISCELLANEOUS

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MOST CURRENT PUBLICATIONS (2010/2009)

 

55. Modeling conformational ensembles of slow functional motions

in Pin1-WW. (HTML) (PDF) 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.  (PDF) Kanaan SP, Huang C, Wuchty S, Chen DZ, Izaguirre JA. Methods Mol Biol. (2009) 541:43-59.

53. MDLab: A Molecular Dynamics Simulation Prototyping Environment. (PDF) Cickovski T, Chatterjee S, Wenger J, Sweet CR, Izaguirre JA.  J Comput Chem (2010) 31:1345-1356.

52. String Method with Collective Variables from Normal Modes: Application to Alanine Dipeptide. (PDF) Santanu Chatterjee, Christopher R. Sweet, and Jesús A. Izaguirre. Submitted.

51. Belief Propagation Estimation of Protein and Domain Interactions using the Sum-Product Algorithm (PDF). 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. (PDF) 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 (PDF) 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 (PDF) 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 (PDF) 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 (PDF). Jesus A. Izaguirre and Christopher R. Sweet. Proc. Second International Workshop on Model Reduction in Reacting Flows, April 2009, Notre Dame, IN.

MOLECULAR DYNAMICS

49. Biomolecular committor probability calculation enabled by processing in network storage. (PDF) Paul Brenner, Justin M. Wozniak, Douglas Thain, Aaron Striegel, Jeff W. Peng, and Jesus A. Izaguirre. Parallel Computing, 34:652–660, 2008.

48. Normal Mode Partitioning of Langevin Dynamics for Biomolecules. (PDF) 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. (PDF)

47. Accelerating the Replica Exchange Method Through an Efficient All-Pairs Exchange. (PDF) 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 (PDF) 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 (PDF) 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 (PDF), 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 (PDF),  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 (PDF), 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 (PDF), 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 (PDF), Scott S. Hampton and Jesús A. Izaguirre, In M. Bubak, G. D. von Albada, and P. M. A. Sloot; J. J. Dongarra, editors, 4th International Conference on Computational Science, Kraków, Poland, volume 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 (PDF), 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 (PDF), 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 (PDF),  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 (PDF), 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 (PDF),  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 (PS) (PDF), 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 (PS)(PDF), 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, (PS) (PDF), 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 (PS) (PDF), 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 (PS) (PDF), 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 (PS) (PDF), Jesús A. Izaguirre, In 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 (PDF), 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. In Agostino G. Bruzzone, Adelinde Uchrmacher, and Ernest H. Page, editors, Proceedings of the SCS International Conference on Web-Based Modeling and Simulation, pages 242-251, San Francisco, California, 1999.

2. The Five Femtosecond Time Step Barrier (PS), Robert D. Skeel and Jesús A. Izaguirre, in 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. (PDF) Faruck Morcos, Charles Lamanna, Marcin Sikora, and Jesus Izaguirre. Bioinformatics, 19:2265–2266, 2008

43. Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach (PDF), 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 (PDF) 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 (PDF). 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. (PDF) 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 (PDF) 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 (PDF), 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 (PDF),  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 (PDF),  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 (PDF), R. Chaturvedi, C. Huang, J. A. Izaguirre, S. A. Newman, J. A. Glazier, and M. Alber. In 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 (PDF),  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

44. Making the Best of a Bad Situation: Prioritized Storage Management in GEMS (PDF) 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 (PDF) 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 (PDF) 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 (PDF). 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. (PDF) Justin Wozniak, Paul Brenner, Doug Thain, Aaron Striegel, and Jesus A. Izaguirre,  Proceedings of 38th Southeastern Symposium on System Theory, Cookeville, TN, March 2006.

16. Separating Abstractions from Resources in a Tactical Storage System (PDF) Thain, D.; Klous, S.; Wozniak, J.; Brenner, P.; Striegel, A. & Izaguirre, J.,  Supercomputing, Seattle, WA, Nov. 12-18, 2005.

15. Generosity and Gluttony in GEMS: Grid Enabled Molecular Simulations (PDF) 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 (PDF), 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 (PDF), Jesús A. Izaguirre, in 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. (PDF) 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. (PDF) 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, (PDF) 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 (PDF), 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 (PDF) 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 (PDF), T. Cickovski, R. Merks, and J. A. Izaguirre, in preparation, 2005.

M10. BioLogo, a Domain-Specific Language for Morphogenesis (PDF), Trevor M. Cickovski, M.S. Thesis, Department of Computer Science and Engineering, University of Notre Dame, December 2004.

M9. Design Patterns for Scientific Software (PDF), 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 (PDF), Asbjřrn Holt, M.S. Thesis, NTNU and Lunds Univesitet, Norway, July 2004.

M7. Improved Sampling of Configuration Space of Biomolecules using Shadow Hybrid Monte Carlo (PDF), 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 (PDF), A. Striegel, M. Shorts, E. Stuntebeck, D. Salyers, J. A. Izaguirre

M6. MDSimAid : Automatic Optimization of Fast Electrostatics Algorithms for Molecular Simulations (PDF), Alice N. Ko and Jesús A. Izaguirre, International Conference on Computational Science  ICCS 2003. 

M5. Novel Multiscale Algorithms for Molecular Dynamics (PDF), 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 (PDF), 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 (PDF), 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 (PDF), Scott Hampton and Jesús A. Izaguirre, preprint.

M1. A Tutorial on the Prototyping of Multiple Time Stepping Integrators for Molecular Dynamics (PS) (PDF), Jesús A. Izaguirre, Thierry Matthey, Jeremiah Willcock, Branden Moore, Qun Ma, Thomas Slabach, and George Viamontes, 2001.

Last modified: 3/8/2010