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--------------------------------------------------------------------------------------- COMPUTATIONAL DEVELOPMENTAL
BIOLOGY (MORPHOGENESIS) DISSERTATIONS AND MISCELLANEOUS --------------------------------------------------------------------------------------- MOST CURRENT PUBLICATIONS (2009) J23. MDLab: A Molecular Dynamics Simulation Prototyping Environment. (PDF) Trevor Cickovski, Christopher R. Sweet, and Jesús A. Izaguirre. Submitted. 2009. J22. String Method with Collective Variables from Normal Modes: Application to Alanine Dipeptide. (PDF) Santanu Chatterjee, Christopher R. Sweet, and Jesús A. Izaguirre. Submitted. 2009. C26. Determination of Specificity Residues in Two Component Systems using Graphlets (PDF) Faruck Morcos, Charles Lamanna, Nitesh V. Chawla, and Jesús A. Izaguirre. Proc. 2009 International Conference on Bioinformatics & Computational Biology BIOCOMP’ 09 C25. 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. J16. A separable
shadow hybrid Monte Carlo method. (PDF) C. R. Sweet, S. S.
Hampton, R. D. Skeel, and J. A. Izaguirre, Accepted, J. Chem. Phys. (2009). J21. 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. Submitted. MOLECULAR
DYNAMICS J19. Biomolecular committor probability calculation enabled by processing in network storage. Paul Brenner, Justin M. Wozniak, Douglas Thain, Aaron Striegel, Jeff W. Peng, and Jesus A. Izaguirre. Parallel Computing, 34:652–660, 2008. J18. Normal Mode Partitioning of Langevin Dynamics for Biomolecules. (PDF) C.R. Sweet, P. Petrone, V.S. Pande, J.A. Izaguirre, J. Chem. Phys. 128:1, 2008. S18. Supplementary Information for Normal Mode Partitioning of Langevin Dynamics for Biomolecules.
(PDF) J17. 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. C22. 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. C20. 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. J11. Parallel Multigrid
Summation for the N-body Problem (PDF), Jesús A. Izaguirre, Scott S. Hampton, and J10. MDSimAid:
Automatic Parameter Optimization in Fast Electrostatic Algorithms (PDF), Michael S.
Crocker, Scott S. Hampton, J8. Shadow Hybrid J7. ProtoMol, an
Object-Oriented Framework for Prototyping Novel Algorithms for Molecular
Dynamics (PDF), C12. 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. J5. 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. J4. 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, C10. ProtoMol: A
Molecular Dynamics Research Framework for Algorithmic Development (PDF),
C9. 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. C8. 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. J3. An Impulse Integrator for Langevin
Dynamics (PS)
(PDF), R.D. Skeel
and J. C7. Overcoming instabilities in Verlet-I/r-RESPA with the mollified impulse method
(PS)(PDF), Jesús A. Izaguirre, J2. 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, C6. 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 C5. ProtoMol: A
Molecular Dynamics Framework with Incremental Parallelization (PS) (PDF), C4. Langevin
Stabilization of Multiscale Mollified Molecular
Dynamics (PS)
(PDF), Jesús J1. Longer Time Steps for Molecular Dynamics
(PDF), Jesús A. Izaguirre, Sebastian Reich and Robert D. Skeel),
J. Chem. Phys., 110(20), pp. 9853-9864, C3. 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, C2. The Five Femtosecond
Time Step Barrier (PS), Robert D. Skeel and Jesús J20. Cytoprophet: A Cytoscape plug-in for protein and domain interaction
networks inference. Faruck Morcos, Charles Lamanna, Marcin Sikora, and Jesus
Izaguirre. Bioinformatics,
19:2265–2266, 2008 J13. 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. C24. 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. C19. 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, COMPUTATIONAL DEVELOPMENTAL
BIOLOGY (MORPHOGENESIS) J18. 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). J15. 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). J12. 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. J9. 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. J6. CompuCell, a
multi-model framework for simulation of morphogenesis (PDF),
Jesús A. Izaguirre, C13. 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, C11. Multi-model simulations of chicken limb
morphogenesis (PDF),
Rajiv Chaturvedi, Jesús
A. Izaguirre, J14. 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). C23. 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. C21. 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. C18. Biomolecular
Sampling: Algorithms, Test Molecules, and Metrics (PDF). Scott
Hampton, Paul Brenner, Aaron Wenger, C17. Applying feedback control to a replica
management system. (PDF) C16. 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. C15. 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), C14. 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. C1. 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 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)
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, 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 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),
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), M2. Linearly scalable hybrid M1. A Tutorial on the Prototyping of Multiple
Time Stepping Integrators for Molecular Dynamics (PS) (PDF), Jesús A. Izaguirre, Last modified: 5/5/2009 |
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