New space warping method for the simulation of large-scale macromolecular conformational changes. - Khuloud Jaqaman; Peter J. Ortoleva (J. Comput. Chem., 2002)

Simulating cellular dynamics through a coupled transcription, translation, metabolic model. - Elizabeth L. Weitzke; Peter J. Ortoleva (Comput. Biol. Chem., 2003)

Efficient solution technique for solving the Poisson-Boltzmann equation. - Abdallah Sayyed-Ahmad; Kagan Tuncay; Peter J. Ortoleva (J. Comput. Chem., 2004)

Parallel implementation of a velocity-stress staggered-grid finite-difference method for 2-D poroelastic wave propagation. - Dong-Hoon Sheen; Kagan Tuncay; Chang-Eob Baag; Peter J. Ortoleva (Comput. Geosci., 2006)

Transcriptional regulatory network discovery via multiple method integration: application to e. coli K12. - Jingjun Sun; Kagan Tuncay; Alaa Abi-Haidar; Lisa Ensman; Frank Stanley; Michael Trelinski; Peter J. Ortoleva (Algorithms Mol. Biol., 2007)

Transcriptional regulatory network refinement and quantification through kinetic modeling, gene expression microarray data and information theory. - Abdallah Sayyed-Ahmad; Kagan Tuncay; Peter J. Ortoleva (BMC Bioinform., 2007)

Chromosome segregation in Escherichia coli division: A free energy-driven string model. - Jianmiao Fan; Kagan Tuncay; Peter J. Ortoleva (Comput. Biol. Chem., 2007)

Transcriptional Regulatory Networks via Gene Ontology and Expression Data. - Kagan Tuncay; Lisa Ensman; Jingjun Sun; Alaa Abi-Haidar; Frank Stanley; Michael Trelinski; Peter J. Ortoleva (Silico Biol., 2007)

Molecular dynamics/order parameter extrapolation for bionanosystem simulations. - Yinglong Miao; Peter J. Ortoleva (J. Comput. Chem., 2009)

Multiscale Macromolecular Simulation: Role of Evolving Ensembles. - Abhishek Singharoy; Harshad Joshi; Peter J. Ortoleva (J. Chem. Inf. Model., 2012)

A Review of Two Multiscale Methods for the Simulation of Macromolecular Assemblies: Multiscale Perturbation and Multiscale Factorization. - Stephen Pankavich; Peter J. Ortoleva (Comput., 2015)

ProtoMD: A prototyping toolkit for multiscale molecular dynamics. - Endre T. Somogyi; Andrew Abi Mansour; Peter J. Ortoleva (Comput. Phys. Commun., 2016)