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Publications 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. Trelinkski, and P. Ortoleva. 2006. Transcriptional regulatory networks via gene ontology and expression data. In Silico Biology (in press). 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. Trelinkski, and P. Ortoleva. 2007. Transcriptional Regulatory Network Discovery via Multiple Method Integration: Application to E.coli K12, Algorithms in Molecular Biology (accepted). 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. (in press) Submitted Papers Comer, J. and P. Ortoleva. Coupled Strain/Impurity Theory of Twisted Crystals: Implications for Agates and Other Natural Occurrences. American Mineralogist. Shreif, Z. and P. Ortoleva (2007a). Curvilinear All-Atom Multiscale (CAM) Theory of Macromolecular Dynamics. Submitted to the J. Stat. Physics. |