2004
Jaqaman, K., K. Tuncay and P. Ortoleva. 2004. Classical density functional theory of orientation order at interfaces: Application to water, J. Chem. Phys. Vol. 120 (2): 926-938.
Sayyed-Ahmad, A., K. Tuncay and P. Ortoleva. 2004. Efficient Solution Technique for Solving Poisson-Boltzmann Equation, J. Comp. Chem. 25: 1068-1074.
Navid, A. and P. Ortoleva. 2004. Simulated complex dynamics of glycolysis in the protozoan parasite Trypanosoma brucei. J. Theor. Biol. 228(4), 449-458.
2005
Ortoleva, P. Nanoparticle Dynamics: A Multiscale Analysis of the Liouville Equation. J. Phys. Chem. B, 109, 21258-21266.
2006
Jarymowycz, L. and P. Ortoleva. 2006. Involatile nanodroplets: An asymptotic analysis. J. Chem. Phys. Vol. 124: 234705 (4 pages).
Miao, Y. and P. Ortoleva. 2006a. All-atom multiscaling and new ensembles for dynamical nanoparticles. J. Chem. Phys. Vol. 125: 044901 (8 pages).
Miao, Y. and P. Ortoleva. 2006b. Viral structural transitions: An all-atom multiscale theory. J. Chem. Phys. 125, 214901.
Sheen, D-H., K. Tuncay, C-E. Bang, and P. Ortoleva. 2006. Time domain Gauss-Newton seismic waveform inversion in elastic media,Geophysical Journal International, Vol 167, 1373-1384.
Sheen, D-H., K. Tuncay, C-E. Bang, and P. Ortoleva. 2006. Parallel implementation of a velocity-stress staggered-grid finite-difference method for 2-D poroelastic wave propagation. Computers & Geosciences, v. 32, iss. 8, p. 1182-1191.
Tuncay, K., L. Ensman, A.A. Sun, J. Haidar, F. Stanley, M. Trelinski, and P. Ortoleva. 2006. Transcriptional regulatory networks via gene ontology and expression data. In Silico Biology, 7, 003.
2007
Sayyed-Ahmad, A., K. Tuncay and P. Ortoleva. 2007. Transcriptional Regulatory Network Refinement and Quantification Through Kinetic Modeling, Gene Expression Microarray Data and Information Theory. BMC Bioinformatics, 8:20, doi:10.1186/1471-2105-8-20.
Sun, J., K. Tuncay, A.A. Haidar, F. Stanley, M. Trelinski, and P. Ortoleva. 2007. Transcriptional Regulatory Network Discovery via Multiple Method Integration: Application to E.coli K12, Algorithms in Molecular Biology, 2:2, doi:10.1186/1748-7188-2-2.
Qu, K., A.E. Abi Haidar, J. Fan, D. Basu, G. Lin, L. Ensman, M. Jolly, P. Ortoleva. 2007. Cancer Onset and Progression: A Genome-Wide, Nonlinear Dynamical Systems Perspective on Onconetworks. Journal of Theoretical Biology. May 21;246(2): 234-244.
Qu, K. and P. Ortoleva. 2007. Understanding Stem Cell Differentiation Through Self-Organization Theory. Journal of Theoretical Biology. 250(4): 606-620.
Comer, J. and P. Ortoleva. 2007.Coexistence of twisted and untwisted crystals: An impurity/structural order model with implications for agate patterns. American Minerologist. 92:1952-1957.
Shreif, Z. and P. Ortoleva. 2007. Curvilinear All-Atom Multiscale (CAM) Theory of Macromolecular Dynamics.J. Stat. Physics., 130: 669-685. (Published online 10 Nov 2007).
J. Fan, K. Tuncay and P.J. Ortoleva. 2007. Chromosome Segregation in E. Coli Division: A Free Energy-Driven String Model. J. Comp. Bio. and Chem,31:257-264.
2008
P. Ortoleva, and S. Iyengar. 2008. Multiscale Theory of Collective and Single-Particle Modes in Quantum Nanosystems. J. Chem. Phys.128(16):164716.
Sayyed-Ahmad, A., Y. Miao, and P. Ortoleva. 2008. Poisson-Boltzmann Theory of Bionanosystems. Communications in Computational Physics,3,pp.1100-1116. (Published online 28 Feb 2008).
Shrief, Z. and P. Ortoleva. 2008. Computer-aided Design of Nanocapsules for Therapeutic Delivery. Computational and Mathematical Methods in Medicine 10(1): 49-70
Pankavich, S., Y. Miao, J. Ortoleva, Z. Shreif, and P. Ortoleva. 2008. Stochastic Dynamics of Bionanosystems: Multiscale Analysis and Specialized Ensembles. J. Chem. Phys.128,pp.234908
Miao, Y. and P. Ortoleva. 2008. Molecular Dynamics/Order Parameter eXtrapolation (MD/OPX) for Bionanosystem Simulations. J. Comp. Chem.30(3):423-437.
Pankavich, S., Z. Shreif, Y. Miao, P. Ortoleva. Self-Assembly of Nanocomponents into Composite Structures: Derivation and Simulation of Langevin Equations. J. Chem. Phys. (abstract)
Pankavich, S. and P. Ortoleva. Self-Assembly of Nanocomponents into Composite Structures: A Multiscale Stochastic Kinetic Theory (abstract)
P.J. Ortoleva. 2008. Crystal Growth and the fast reaction paradox: Implications for habit and compositional zoning. American Mineralogist 94:172-175.
S. Pankavich, Z. Shreif, and P.J. Ortoleva. 2008. Multiscaling for Classical Nanosystems: Derivation of the Smoluchowski and Kokker-Planck Equations. Physica A. 382(16-17): 4053-4069.
S. Pankavich, Z. Shreif, Y. Chen, and P.J. Ortoleva. 2008.Multiscale Theory of Finite Size Bose Systems: Implications for Collective and Single-Particle Excitaitions. Phys. Rev. A.79(1): 013628.
Z. Shreif, P.J. Ortoleva. 2008. Multiscale Approach to Nanocapsule Design.Technical Proceedings of the 2008 NSTI Nanotechnology Conference and Trade Show. 3: 741-744.
2009
Z. Shreif, P. Adhangale, S. Cheluvaraja, R. Perera, R. Kuhn, P. Ortoleva. Enveloped viruses understood via multiscale simulation: computer-aided vaccine design. Springer Science+Business Media B.V. 2008. Vol 15 (1-3): 363-380 Springer Netherlands.
S. Pankavich, Z. Shreif, Y. Miao, and P. Ortoleva. Self-assembly of nanocomponents into composite structures:Derivation and simulation of Langevin equations. The Journal of Chemical Physics 130, 194115 (2009).
Z. Shreif, P.J. Ortoleva. 2009. Multiscale Derivation of an Augmented Smoluchowski Equation. Physica A. 388 (5): 593-600.
E.L. King, K. Tuncay, P.J. Ortoleva. and C. Meile. 2009. Representations of microbial metabolism: An Analysis of model complexity based on Geobacter sulfurreducens. Applied and Envirnmental Microbiology 75: 29-38.