Molecular Dynamics

63. Accelerated molecular dynamics simulations of the octopamine receptor using GPUs: discovery of an alternate agonist‐binding position

Kevin W Kastner, Jesús A Izaguirre

Proteins: Structure, Function and Bioinformatics (2016) doi:10.1002/prot.25091

62. A comparison of weighted ensemble and Markov state model methodologies

Haoyun Feng, Ronan Costaouec, Eric Darve, Jesús A Izaguirre

The Journal of chemical physics 142:21, 214113 (2015)http://dx.doi.org.proxy.library.nd.edu/10.1063/1.4921890

61. Evaluation of conformational changes in diabetes‐associated mutation in insulin a chain: A molecular dynamics study

Yong Hwan Kim, Kevin Kastner, Badi Abdul‐Wahid, Jesús A Izaguirre

Proteins: Structure, Function, and Bioinformatics 83:4, 662-669 (2015), doi:10.1002/prot.24759 

60. Greedy Algorithms for Fast Discovery of Macrostates from Molecular Dynamics Simulations

Haoyun Feng, Geoffrey Siwo, Jesus A Izaguirre, Douglas Thain, Badi Abdul-Wahid

Lecture Notes on Information Theory Vol 2:4 (2014), http://www.lnit.org/uploadfile/2015/0115/20150115023532805.pdf 

59. Characterization of the Anopheles gambiae octopamine receptor and discovery of potential agonists and antagonists using a combined computational-experimental approach

Kevin W Kastner, Douglas A Shoue, Guillermina L Estiu, Julia Wolford, Megan F Fuerst, Lowell D Markley, Jesús A Izaguirre, Mary Ann McDowell

Malaria journal 13(1) 1 (2014), http://malariajournal.biomedcentral.com/articles/10.1186/1475-2875-13-434 

58. AWE-WQ: Fast-forwarding molecular dynamics using the accelerated weighted ensemble

Badi’ Abdul-Wahid, Haoyun Feng, Dinesh Rajan, Ronan Costaouec, Eric Darve, Douglas Thain, Jesus A Izaguirre

Journal of chemical information and modeling 54 (10), 3033-3043 (2014)  http://dx.doi.org/10.1021/ci500321g

57. Analysis of the accelerated weighted ensemble methodology

R Costaouec, H Feng, J Izaguirre, E Darve

Discrete and Continuous Dynamical Systems, 171-181 (2013), http://aimsciences.org/journals/pdfs.jsp?paperID=9201

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 9 (8), 3267-3281 (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 [Supplementary info.]

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 [Supplementary info.]

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