JA Izaguirre

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Justin M WozniakComputer Scientist, Argonne National LaboratoryVerified email at anl.gov
Douglas ThainProfessor, University of Notre DameVerified email at nd.edu
James A GlazierIndiana UniversityVerified email at indiana.edu
Stuart A. NewmanNew York Medical CollegeVerified email at nymc.edu
Faruck MorcosUniversity of Texas at Dallas - Dept. Biological SciencesVerified email at utdallas.edu
Aaron StriegelProfessor, Department of Computer Science and Engineering, University of Notre DameVerified email at nd.edu
H. George. E. HentschelProfessor of Physics, Emory UniversityVerified email at physics.emory.edu
Tilmann GlimmProfessor of Mathematics, Western Washington UniversityVerified email at wwu.edu
Vijay PandeAndreessen Horowitz, Stanford UniversityVerified email at stanford.edu
Eric DarveStanfordVerified email at stanford.edu
Troy RaederTwo SigmaVerified email at twosigma.com
Kedar ArasAssistant Professor, Department of Physiology & Biophysics, Jacobs School of Medicine SUNY BuffaloVerified email at buffalo.edu
Maria Ercsey-RavaszResearcher, Babeș-Bolyai UniversityVerified email at ubbcluj.ro
Matthew JacobsonUCSFVerified email at ucsf.edu
Roberto López-RendónUniversidad Autónoma del Estado de MéxicoVerified email at uaemex.mx
Danny Z ChenProfessor of Computer Science & Engineering, University of Notre DameVerified email at nd.edu
Sebastian ReichUniversity of PotsdamVerified email at uni-potsdam.de
Christopher McClendonSenior Principal Scientist, PfizerVerified email at pfizer.com
Roeland MerksProfessor of Mathematical Biology, Mathematical Institute and Institute of Biology, LeidenVerified email at math.leidenuniv.nl
Nan ChenComputational Scientist at University of Texas, M.D. Anderson Cancer CenterVerified email at mdanderson.org

JA Izaguirre

Notre Dame

Verified email at nd.edu

Computational molecular biophysics protein folding molecular dynamics numerical methods parallel computing


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Langevin stabilization of molecular dynamics JA Izaguirre, DP Catarello, JM Wozniak, RD Skeel The Journal of chemical physics 114 (5), 2090-2098, 2001	1126	2001
CompuCell, a multi-model framework for simulation of morphogenesis JA Izaguirre, R Chaturvedi, C Huang, T Cickovski, J Coffland, G Thomas, ... Bioinformatics 20 (7), 1129-1137, 2004	290	2004
Longer time steps for molecular dynamics JA Izaguirre, S Reich, RD Skeel The Journal of chemical physics 110 (20), 9853-9864, 1999	248	1999
An impulse integrator for Langevin dynamics RD Skeel, JA Izaguirre Molecular Physics 100 (24), 3885-3891, 2002	185	2002
A framework for three-dimensional simulation of morphogenesis TM Cickovski, C Huang, R Chaturvedi, T Glimm, HGE Hentschel, ... IEEE/ACM Transactions on Computational Biology and Bioinformatics 2 (4), 273-288, 2005	168	2005
On multiscale approaches to three-dimensional modelling of morphogenesis R Chaturvedi, C Huang, B Kazmierczak, T Schneider, JA Izaguirre, ... Journal of the Royal Society interface 2 (3), 237-253, 2005	158	2005
A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis N Chen, JA Glazier, JA Izaguirre, MS Alber Computer physics communications 176 (11-12), 670-681, 2007	143	2007
ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics T Matthey, T Cickovski, S Hampton, A Ko, Q Ma, M Nyerges, T Raeder, ... ACM Transactions on Mathematical Software (TOMS) 30 (3), 237-265, 2004	137	2004
Shadow hybrid Monte Carlo: an efficient propagator in phase space of macromolecules JA Izaguirre, SS Hampton Journal of Computational Physics 200 (2), 581-604, 2004	126	2004
Work queue+ python: A framework for scalable scientific ensemble applications P Bui, D Rajan, B Abdul-Wahid, J Izaguirre, D Thain Workshop on python for high performance and scientific computing at sc11, 2011	120	2011
Verlet-I/r-RESPA/Impulse is limited by nonlinear instabilities Q Ma, JA Izaguirre, RD Skeel SIAM Journal on Scientific Computing 24 (6), 1951-1973, 2003	118	2003
Predicting protein-protein interactions from protein domains using a set cover approach C Huang, F Morcos, SP Kanaan, S Wuchty, DZ Chen, JA Izaguirre IEEE/ACM Transactions on Computational Biology and Bioinformatics 4 (1), 78-87, 2007	94	2007
Modeling conformational ensembles of slow functional motions in Pin1-WW F Morcos, S Chatterjee, CL McClendon, PR Brenner, R López-Rendón, ... PLoS computational biology 6 (12), e1001015, 2010	89	2010
From genes to organisms via the cell: a problem-solving environment for multicellular development T Cickovski, K Aras, M Swat, RMH Merks, T Glimm, HGE Hentschel, ... Computing in science & engineering 9 (4), 50-60, 2007	77	2007
Converting a high performance application to an elastic cloud application D Rajan, A Canino, JA Izaguirre, D Thain 2011 IEEE Third International Conference on Cloud Computing Technology and …, 2011	73	2011
Multiscale dynamics of macromolecules using normal mode Langevin JA Izaguirre, CR Sweet, VS Pande Biocomputing 2010, 240-251, 2010	69	2010
Accelerating the replica exchange method through an efficient all-pairs exchange P Brenner, CR Sweet, D VonHandorf, JA Izaguirre The Journal of chemical physics 126 (7), 2007	68	2007
BioCoRE: a collaboratory for structural biology M Bhandarkar, G Budescu, WF Humphrey, JA Izaguirre, S Izrailev, ... Simulation Series 31, 242-251, 1999	62	1999
Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry T Dixon, D MacPherson, B Mostofian, T Dauzhenka, S Lotz, D McGee, ... Nature communications 13 (1), 5884, 2022	56	2022
Parallel multigrid summation for the N-body problem JA Izaguirre, SS Hampton, T Matthey Journal of Parallel and Distributed Computing 65 (8), 949-962, 2005	56	2005

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