Center for Theoretical & Computational Nanoscience

243
Implicit time integration for multiscale molecular dynamics using transcendental Pade approximants

Implicit time integration for multiscale molecular dynamics using transcendental Pade approximants

Andrew AbiMansour and Peter J. Ortoleva, “Implicit time integration for multiscale molecular dynamics using transcendental Pade approximants”, Journal of Chemical Theory and Compuation, Just Accepted (2016)

242
ProtoMD: A prototyping toolkit for multiscale molecular dynamics

ProtoMD: A prototyping toolkit for multiscale molecular dynamics

Endre Somogyi, Andrew Abi Mansour, Peter J. Ortoleva, “ProtoMD: A prototyping toolkit for multiscale molecular dynamics”, Computer Physics Communications, In Press (2016)

241
Autonomous Oscillation in Supramolecular Assemblies: Role of Free Energy Landscape and Fluctuations

Autonomous Oscillation in Supramolecular Assemblies: Role of Free Energy Landscape and Fluctuations

Yuriy V. Sereda, Peter J. Ortoleva, “Autonomous Oscillation in Supramolecular Assemblies: Role of Free Energy Landscape and Fluctuations”, Physica A 437 (2015), 442-456.

240
Prospective on Multiscale Simulation of Virus-like Particles: Application to Computer-aided Vaccine Design

Prospective on Multiscale Simulation of Virus-like Particles: Application to Computer-aided Vaccine Design

Andrew AbiMansour, Yuriy V. Sereda, Jing Yang, Peter J. Ortoleva, “Prospective on Multiscale Simulation of Virus-like Particles: Application to Computer-aided Vaccine Design”, Vaccine (2015)

239
Broad Spectrum Assessment of the Epitope Fluctuation-Immunogenicity Hypothesis

Broad Spectrum Assessment of the Epitope Fluctuation-Immunogenicity Hypothesis

Jason S. Grosch, Jing Yang, Alice Shen, Yuriy V. Sereda, Peter J. Ortoleva, “Broad Spectrum Assessment of the Epitope Fluctuation-Immunogenicity Hypothesis”, Vaccine (2015), DOI: 10.1016/j.vaccine.2015.06.111

238
Early Stage P22 Viral Capsid Self-Assembly Mediated by Scaffolding Protein: Atom-Resolved Model and Molecular Dynamics Simulation

Early Stage P22 Viral Capsid Self-Assembly Mediated by Scaffolding Protein: Atom-Resolved Model and Molecular Dynamics Simulation

Jiajin Jiang, Jing Yang, Yuriy V. Sereda, Peter J. Ortoleva, “Early Stage P22 Viral Capsid Self-Assembly Mediated by Scaffolding Protein: Atom-Resolved Model and Molecular Dynamics Simulation”, J. of Physical Chemistry B (2015), DOI: 10.1021/acs.jpcb.5b00303.

237
A multiscale variational approach to the kinetics of viscous classical liquids: The coarse-grained mean field approximation

A multiscale variational approach to the kinetics of viscous classical liquids: The coarse-grained mean field approximation

Y. V. Sereda, P. J. Ortoleva. “A multiscale variational approach to the kinetics of viscous classical liquids: The coarse-grained mean field approximation”. The Journal of Chemical Physics (2014). 140(134104). doi: 10.1063/1.4869860.

236
Multiscale Factorization Method for Simulating Mesoscopic Systems with Atomic Precision

Multiscale Factorization Method for Simulating Mesoscopic Systems with Atomic Precision

A. Abi Mansour, P. J. Ortoleva. “Multiscale Factorization Method for Simulating Mesoscopic Systems with Atomic Precision”. Journal of Chemical Theory and Computation, (2014).

235
Quasiequivalence of multiscale coevolution and ensemble MD simulations: A deomnstration with lactoferrin

Quasiequivalence of multiscale coevolution and ensemble MD simulations: A deomnstration with lactoferrin

Jing Yang, Abhishek Singharoy, Yuriy V. Sereda, Peter J. Ortoleva, “Quasiequivalence of multiscale coevolution and ensemble MD simulations: A deomnstration with lactoferrin”, Chemical Physics Letters, 616-617 (2014), 154-160.

234
Energy Transfer Between a Nanosystem and its Host Fluid: A Multiscale Factorication Approach

Energy Transfer Between a Nanosystem and its Host Fluid: A Multiscale Factorication Approach

Yuriy V. Sereda, John-Michael Espinosa-Duran and Peter J. Ortoleva, “Energy Transfer Between a Nanosystem and its Host Fluid: A Multiscale Factorication Approach”, J. of Chemiscal Physics 140 (2014) #7, 07412.

233
Variational methods for time-dependent classical many-particle systems

Variational methods for time-dependent classical many-particle systems

Yuriy V. Sereda, Peter J. Ortoleva, “Variational methods for time-dependent classical many-particle systems”, Physica A 392 (2013) #4, 628-638

232
Epitope Fluctuation in the Human Papillomavirus Are Under Dynamic Allosteric Control:A Computational Evaluation of a New Vaccine Design Strategy

Epitope Fluctuation in the Human Papillomavirus Are Under Dynamic Allosteric Control:A Computational Evaluation of a New Vaccine Design Strategy

A. Singharoy, A. Polavarapu, H. Joshi, M. Baik, and P. Ortoleva. “Epitope Fluctuation in the Human Papillomavirus Are Under Dynamic Allosteric Control:A Computational Evaluation of a New Vaccine Design Strategy”. Journal of the American Chemical Society. 2013. 135(40) 18458-18468.. doi: 10.1021/ja407489r

231
Epitope Engineering and Molecular Metrics of Immunogenicity: A Computational Approach to VLP-based Vaccine Design

Epitope Engineering and Molecular Metrics of Immunogenicity: A Computational Approach to VLP-based Vaccine Design

H. Joshi, K. Lewis, A. Singharoy, P. Ortoleva. “Epitope Engineering and Molecular Metrics of Immunogenicity: A Computational Approach to VLP-based Vaccine Design”. Vaccine. 31(42): 4841-4847. http://www.sciencedirect.com/science/article/pii/S0264410X13010669

230
Quasiperiodic Oscillation and Possible Second Law Violation in a Nanosystem

Quasiperiodic Oscillation and Possible Second Law Violation in a Nanosystem

R. Quick, A. Singharoy, P. Ortoleva, Quasiperiodic Oscillation and Possible Second Law Violation in a Nanosystem, Chemical Physics Letters, 571 (2013), 61-65. http://www.sciencedirect.com/science/article/pii/S0009261413004466

229
Variational methods for time-dependent classical many-particle systems

Variational methods for time-dependent classical many-particle systems

Yuriy V. Sereda, Peter J. Ortoleva, “Variational methods for time-dependent classical many-particle systems”, Physica A 392 (2013) #4, 628-638.

228
Multiscale Macromolecular Simulation: Role of Evolving Ensembles. Journal of Chemical Information and Modeling

Multiscale Macromolecular Simulation: Role of Evolving Ensembles. Journal of Chemical Information and Modeling

A. Singharoy, H. Joshi, P. Ortoleva. Multiscale Macromolecular Simulation: Role of Evolving Ensembles. Journal of Chemical Information and Modeling. 2012. 52(10) 2638-49. doi: 10.1021/ci3002952

227
Hierarchical Order Parameters for Macromolecular Assembly Simulations. 1. Construction and Dynamical Properties of Order Parameters

Hierarchical Order Parameters for Macromolecular Assembly Simulations. 1. Construction and Dynamical Properties of Order Parameters

Abhishek Singharoy, Yuriy Sereda, and Peter J. Ortoleva, “Hierarchical Order Parameters for Macromolecular Assembly Simulations. 1. Construction and Dynamical Properties of Order Parameters”, J. of Chemical Theory and Computation 8 (2012) #4, 1379-1392. PMCID: PMC3361912 doi:10.1021/ct200574x

226
Nanosystem Self-Assembly Pathways Discovered via All-Atom Multiscale Analysis

Nanosystem Self-Assembly Pathways Discovered via All-Atom Multiscale Analysis

Pankavich, S. and Ortoleva, P, Nanosystem Self-Assembly Pathways Discovered via All-Atom Multiscale Analysis. Journal of Physical Chemistry. (2012) 116 (29), (2012) p. 8355-8362. doi:10.1021/jp210407e.

225
Discovering Free Energy Basins for Macromolecular Systems via Guided Multiscale Simulation

Discovering Free Energy Basins for Macromolecular Systems via Guided Multiscale Simulation

Sereda, Y., Singharoy, A., Jarrold, M., and Ortoleva, P., Discovering Free Energy Basins for Macromolecular Systems via Guided Multiscale Simulation. Journal of Physical Chemistry, (2012). vol. 116 (29). p. 8534-44.

224
Space Warping Order Parameters and Symmetry: Application to Multiscale Simulation of BionanoSystems

Space Warping Order Parameters and Symmetry: Application to Multiscale Simulation of BionanoSystems

Singharoy, A., Joshi, H., Ortoleva, P. and Miao, Y., Space Warping Order Parameters and Symmetry: Application to Multiscale Simulation of BionanoSystems. Journal of Physical Chemistry B , vol. 116 (29), (2012)  p. 8423-34. doi:10.1021/jp2119247

223
A molecular dynamics study of loop fluctuation in human papillomavirus type 16 virus-like particles: A possible indicator of immunogenicity

A molecular dynamics study of loop fluctuation in human papillomavirus type 16 virus-like particles: A possible indicator of immunogenicity

Joshi H, S. Cheluvaraja, E. Somogyi, DR Brown, P Ortoleva, A molecular dynamics study of loop fluctuation in human papillomavirus type 16 virus-like particles: A possible indicator of immunogenicity. Vaccine. 2011 Nov 28;29(51):9423-30. doi:10.1016/j.vaccine.2011.10.039

222
Multiscale simulation of microbe structure and dynamics

Multiscale simulation of microbe structure and dynamics

Joshi, H., Singharoy, A., Sereda, Y., Cheluvaraja, S., and P. Ortoleva, Multiscale simulation of microbe structure and dynamics (2011). Prog. Biophys Mol. Biol. 107: 200-217. doi:10.1016/j.pbiomolbio.2011.07.006

221
Electrometabolomic Modeling of Microbes: Applications in Fuel Cells and Environment Analysis

Electrometabolomic Modeling of Microbes: Applications in Fuel Cells and Environment Analysis

Fontus, M. and P. Ortoleva, Electrometabolomic Modeling of Microbes: Applications in Fuel Cells and Environment Analysis. Journal of Biotech Research, 2011. 3:37-50.

220
Scaling Behavior of Quantum Nanosystems: Emergence of Quasi-particles, Collective Modes, and Mixed Exchange Symmetry States

Scaling Behavior of Quantum Nanosystems: Emergence of Quasi-particles, Collective Modes, and Mixed Exchange Symmetry States

Shreif, Z. and P. Ortoleva, Scaling Behavior of Quantum Nanosystems: Emergence of Quasi-particles, Collective Modes, and Mixed Exchange Symmetry States. Journal of Chemical Physics, 2011. 134, 104106 (2011) doi:10.10631/1.3560450 (11 pages).

219
Multiscale Born-Oppenheimer Theory of Collective Electron-Nuclear Dynamics in Nanosystems

Multiscale Born-Oppenheimer Theory of Collective Electron-Nuclear Dynamics in Nanosystems

Shreif, Z. and P. Ortoleva, Multiscale Born-Oppenheimer Theory of Collective Electron-Nuclear Dynamics in Nanosystems. Journal of Theoretical and Computational Chemistry, 2011. 10 (5), 605-614; doi: 10.1142/S0219633611006669.

218
Simulating Microbial Systems: Addressing Model uncertainty/incompleteness via Multiscaling and Entropy methods

Simulating Microbial Systems: Addressing Model uncertainty/incompleteness via Multiscaling and Entropy methods

Singharoy, A., et al., eds. Simulating Microbial Systems: Addressing Model uncertainty/incompleteness via Multiscaling and Entropy methods Microbial Systems Biology: Methods and Protocols, ed. A. Navid. 2010, Springer Science: New York.

217
Electrophysiological-Metabolic Modeling of Microbes: Applications in Fuel Cells and Environment Analysis

Electrophysiological-Metabolic Modeling of Microbes: Applications in Fuel Cells and Environment Analysis

Fontus, F. and P. Ortoleva, Electrophysiological-Metabolic Modeling of Microbes: Applications in Fuel Cells and Environment Analysis. Microbial Systems Biology: Methods and Protocols, ed. A. Navid. 2010, Springer Science: New York.

216
Order Parameters for Macromolecules: Application to Multiscale simulations

Order Parameters for Macromolecules: Application to Multiscale simulations

Singharoy, A., S. Cheluvaraja, and P. Ortoleva, Order Parameters for Macromolecules: Application to Multiscale simulations. J. Chem. Phys, 2011. 134, 044104; doi: 10.1063/1.3524532.

215
Viral Structural Transition Mechanisms Revealed by Multiscale Molecular Dynamics/Order Parameter eXtrapolation Simulation

Viral Structural Transition Mechanisms Revealed by Multiscale Molecular Dynamics/Order Parameter eXtrapolation Simulation

Miao, Y., and P. Ortoleva, Viral Structural Transition Mechanisms Revealed by Multiscale Molecular Dynamics/Order Parameter eXtrapolation Simulation. Biopolymers, 2010. 93(1): p.61-73.

214
Multiscaling for systems with a broad continuum of characteristic lengths and times: Structural transitions in nanocomposites.

Multiscaling for systems with a broad continuum of characteristic lengths and times: Structural transitions in nanocomposites.

Pankavich, S. and P. Ortoleva. Journal of Mathematical Physics. Vol. 51, Issue 6. “Multiscaling for systems with a broad continuum of characteristic lengths and times: Structural transitions in nanocomposites.” J. Math. Phys. 51, 063303 (2010); doi:10.1063/1.3420578

213
All-Atom Multiscale Simulation of Cowpea Chlorotic Mottle Virus Capsid Swelling

All-Atom Multiscale Simulation of Cowpea Chlorotic Mottle Virus Capsid Swelling

Miao, Y., J.E. Johnson, and P. Ortoleva, All-Atom Multiscale Simulation of Cowpea Chlorotic Mottle Virus Capsid Swelling. J. Phys. Chem B, 2010. 114(34) 11181-11195; doi: 10.1021/jp102314e

212
Multiscale analytic continuation approach to nanosystem simulation: Applications to virus electrostatics

Multiscale analytic continuation approach to nanosystem simulation: Applications to virus electrostatics

A. Singharoy, A. Yesnik, P. Ortoleva. 2010. Multiscale analytic continuation approach to nanosystem simulation: Applications to virus electrostatics. Journal of Chemical Physics 132 (17) 174112.

211
Scaling Behavior of Electronic Excitations in Assemblies of Molecules with Degenerate Ground States

Scaling Behavior of Electronic Excitations in Assemblies of Molecules with Degenerate Ground States

H-J Fan, C. Perkins, and P. J. Ortoleva. 2010. Scaling Behavior of Electronic Excitations in Assemblies of Molecules with Degenerate Ground States. Journal of Physical Chemistry A 114, (5) 2213-2220. doi:10.1021/jp908441s

210
Alternative splicing regulatory network reconstruction from exon array data

Alternative splicing regulatory network reconstruction from exon array data

K. Qu, A.M. Yesnik, and P.J. Ortoleva. Alternative splicing regulatory network reconstruction from exon array data. J. Theoret. Biol. 2010 Apr 21;263®:471-80. Epub 2010 Jan 5.

209
Thermal nanostructure: An Order Parameter/Multiscale Ensemble Approach

Thermal nanostructure: An Order Parameter/Multiscale Ensemble Approach

Cheluvaraja and P. Ortoleva, Thermal nanostructure: An Order Parameter/Multiscale Ensemble Approach. Journal of Chemical Physics, 2010. 132: p. 075102

208
Modeling biogeochemical dynamics in porous media: practical considerations of pore scale variability, reaction networks, and microbial population dynamics in a sandy aquifer

Modeling biogeochemical dynamics in porous media: practical considerations of pore scale variability, reaction networks, and microbial population dynamics in a sandy aquifer

King, E.L., K. Tuncay, P. Ortoleva, and C. Meile. 2009. Modeling biogeochemical dynamics in porous media: practical considerations of pore scale variability, reaction networks, and microbial population dynamics in a sandy aquifer. Journal of Contaminant Hydrology 112, 130-140.

207
Liquid-Crystal Transitions: A First-principles Multiscale Approach

Liquid-Crystal Transitions: A First-principles Multiscale Approach

Shreif, Z., Pankavich, S. & Ortoleva, P. (2009). Liquid-Crystal Transitions: A First-principles Multiscale Approach. Physical Review E, 80 (3), 031703.

206
Self-Assembly of Nanocomponents into Composite Structures: Derivation and Simulation of a Langevin Model

Self-Assembly of Nanocomponents into Composite Structures: Derivation and Simulation of a Langevin Model

S. Pankavich, Z. Shreif, Y. Miao, and P.J. Ortoleva. 2009. Self-Assembly of Nanocomponents into Composite Structures: Derivation and Simulation of a Langevin Model.  J. Chem. Physics 130, 194115 (2009).

205
Computer-Aided Design of Nanocapsules for Therapeutic Delivery

Computer-Aided Design of Nanocapsules for Therapeutic Delivery

Z. Shreif, and P.J. Ortoleva.  Computer-Aided Design of Nanocapsules for Therapeutic Delivery. Comp. Math. Methods in Med. 10 (1): 49-70 (2009).

204
In Silico Geobacter sulferreducens Metabolism and Its Representation in Reactive Transport Models

In Silico Geobacter sulferreducens Metabolism and Its Representation in Reactive Transport Models

E. L. King, K. Tuncay,  P. J. Ortoleva, and C. Meile.  In Silico Geobacter sulferreducens Metabolism and Its Representation in Reactive Transport Models. Applied and Environmental Microbiology 75(1): 83-92 (2009).

203
Deriving Principles of Microbiology by Multiscaling Laws of Molecular Physics: Applications in Nanomedicine and Energy

Deriving Principles of Microbiology by Multiscaling Laws of Molecular Physics: Applications in Nanomedicine and Energy

P. J. Ortoleva, P. Adhangale, S. Cheluvaraja, J. Fan, A. Roy, and Z. Shreif. Deriving Principles of Microbiology by Multiscaling Laws of Molecular Physics: Applications in Nanomedicine and Energy. IEEE Eng Med Biol Mag.; 28 (2): 70-79 (2009)

202
Crystal growth and the fast reaction paradox: Implication for habit and compositional zoning

Crystal growth and the fast reaction paradox: Implication for habit and compositional zoning

P. J. Ortoleva. Crystal growth and the fast reaction paradox: Implication for habit and compositional zoning.  American Mineralogist. 94: 172-175 (2009).

201
Enveloped Viruses Understood Via Multiscale Simulation: Computer-Aided Vaccine Design

Enveloped Viruses Understood Via Multiscale Simulation: Computer-Aided Vaccine Design

Z. Shreif, P. Adhangale, S. Cheluvaraja, R. Perera, R. Kuhn, and P. J. Ortoleva. Enveloped Viruses Understood Via Multiscale Simulation: Computer-Aided Vaccine Design. Series: Lecture Notes in Computational Science and Engineering, Vol 15 (1-3): 363-380,Yip, Sidney;Diaz de la Rubia, Tomas, (Eds), Springer Netherlands (2008).

200
Multiscale Approach to Nanocapsule Design

Multiscale Approach to Nanocapsule Design

Z. Shreif, P. J. Ortoleva. Multiscale Approach to Nanocapsule Design. Technical Proceedings of the 2008 NSTI Nanotechnology Conference and Trade Show. 3: 741-744 (2008).

199
Multiscale Theory of Finite Size Bose Systems: Implications for Collective and Single-Particle Excitations

Multiscale Theory of Finite Size Bose Systems: Implications for Collective and Single-Particle Excitations

S. Pankavich, Z. Shreif, Y. Chen, and P. J. Ortoleva. Multiscale Theory of Finite Size Bose Systems: Implications for Collective and Single-Particle Excitations. Phys. Rev. A. 79 (1): 013628 (2008).

198
Multiscale Derivation of an Augmented Smoluchowski Equation

Multiscale Derivation of an Augmented Smoluchowski Equation

Z. Z. Shreif  and P. J. Ortoleva. Multiscale Derivation of an Augmented Smoluchowski Equation. Physica A. 388 (5): 593-600. (Published online Nov 2008) (2009).

197
Multiscaling for Classical Nanosystems: Derivation of the Smoluchowski and Fokker-Planck Equations

Multiscaling for Classical Nanosystems: Derivation of the Smoluchowski and Fokker-Planck Equations

S. Pankavich, Z. Shreif, and P. J. Ortoleva. Multiscaling for Classical Nanosystems: Derivation of the Smoluchowski and Fokker-Planck Equations. Physica A. 387(16-17): 4053-4069 (2008).

196
Stochastic dynamics of bionanosystems:  Multi-scale analysis and specialized ensembles

Stochastic dynamics of bionanosystems: Multi-scale analysis and specialized ensembles

S. Pankavich, Y. Miao, Z. Shreif, and P. J. Ortoleva. Stochastic dynamics of bionanosystems:  Multi-scale analysis and specialized ensembles. J. Chem. Phys. 128: 234908 (2008).

195
Molecular Dynamics/Order Parameter EXtrapolation (MD/OPX) for Bionanosystem Simulations

Molecular Dynamics/Order Parameter EXtrapolation (MD/OPX) for Bionanosystem Simulations

Y. Miao, and P. J. Ortoleva. Molecular Dynamics/Order Parameter EXtrapolation (MD/OPX) for Bionanosystem Simulations. J. Comp. Chem. 30 (3): 423-437 (2008).

194
Multiscale Theory of Collective and Single-Particle Modes in Quantum Nanosystem

Multiscale Theory of Collective and Single-Particle Modes in Quantum Nanosystem

P. J. Ortoleva and S. S. Iyengar. Multiscale Theory of Collective and Single-Particle Modes in Quantum Nanosystem. J. Chem. Phys. 128: 164716 (2008).

193
Poisson-Boltzmann Theory of Bionanosystems

Poisson-Boltzmann Theory of Bionanosystems

A. Sayyed-Ahmad, Y. Miao, and P. J. Ortoleva. Poisson-Boltzmann Theory of Bionanosystems. Commun. Comp. Phys., 3, pp. 1100-1116. (Published Online 28 Feb 2008) (2008).

192
Curvilinear All-Atom Multiscale (CAM) Theory of Macromolecular Dynamics

Curvilinear All-Atom Multiscale (CAM) Theory of Macromolecular Dynamics

Z. Shreif, and P. J. Ortoleva. Curvilinear All-Atom Multiscale (CAM) Theory of Macromolecular Dynamics. J. Stat. Phys.  130: 669-685. (Published online 10 Nov. 2007) (2008).

191
Understanding Stem Cell Differentiation through Self-Organization Theory

Understanding Stem Cell Differentiation through Self-Organization Theory

K. K. Qu, and P. J. Ortoleva. Understanding Stem Cell Differentiation through Self-Organization Theory. J. Theoret. Bio. 250: 606-620 (2008)

190
Chromosome Segregation in E. coli Division: A Free Energy-Driven String Model

Chromosome Segregation in E. coli Division: A Free Energy-Driven String Model

J. Fan, K. Tuncay and P. J. Ortoleva.  Chromosome Segregation in E. coli Division: A Free Energy-Driven String Model. J. Comp. Bio. and Chem . 31:257-264 (2007).

189
Coexistence of Twisted and Untwisted Crystals: An Impurity/Structural Order Model with Implications for Agate Patterns

Coexistence of Twisted and Untwisted Crystals: An Impurity/Structural Order Model with Implications for Agate Patterns

J. Comer, and P. J. Ortoleva. Coexistence of Twisted and Untwisted Crystals: An Impurity/Structural Order Model with Implications for Agate Patterns. American Mineralogist. 92 (11-12): 1952-1957 (2007).

188
Cancer Onset and Progression: A Genome-Wide, Nonlinear Dynamical Systems Perspective on Onconetworks

Cancer Onset and Progression: A Genome-Wide, Nonlinear Dynamical Systems Perspective on Onconetworks

K. Qu, A.E. Abi Haidar,  J. Fan, D. Basu, G. Lin, L. Ensman, M. Jolly, P. J. Ortoleva. Cancer Onset and Progression: A Genome-Wide, Nonlinear Dynamical Systems Perspective on Onconetworks. Journal of Theoretical Biology. May 21;246(2):234-44 (2007).

187
Transcriptional Regulatory Network Discovery via Multiple Method Integration: Application to E.coli K12

Transcriptional Regulatory Network Discovery via Multiple Method Integration: Application to E.coli K12

J. Sun, K. Tuncay, A.A. Haidar, L. Ensman, F. Stanley, M. Trelinkski, and P. J. Ortoleva. 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 (2007).

186
Transcriptional Regulatory Network Refinement and Quantification through Kinetic Modeling, Gene Expression Microarray Data and Information Theory

Transcriptional Regulatory Network Refinement and Quantification through Kinetic Modeling, Gene Expression Microarray Data and Information Theory

A. Sayyed-Ahmad,  K. Tuncay and P. J. Ortoleva. 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 (2007).

185
Transcriptional regulatory networks via gene ontology and expression data

Transcriptional regulatory networks via gene ontology and expression data

K. Tuncay, L. Ensman, A.A. Sun, J. Haidar, F. Stanley, M. Trelinski, and P.J. Ortoleva. Transcriptional regulatory networks via gene ontology and expression data. In Silico Biology, 7, 003 (2006).

184
Parallel implementation of a velocity-stress staggered-grid finite-difference method for 2-D poroelastic wave propagation

Parallel implementation of a velocity-stress staggered-grid finite-difference method for 2-D poroelastic wave propagation

D-H. Sheen, K. Tuncay, C-E. Bang, and P. J. Ortoleva. Parallel implementation of a velocity-stress staggered-grid finite-difference method for 2-D poroelastic wave propagation. Computers & Geosciences, Vol. 32, iss. 8, p. 1182-1191 (2006).

183
Time domain Gauss-Newton seismic waveform inversion in elastic media

Time domain Gauss-Newton seismic waveform inversion in elastic media

D-H. Sheen, K. Tuncay, C-E. Bang, and P. J. Ortoleva. Time domain Gauss-Newton seismic waveform inversion in elastic media. Geophysical Journal International, Vol 167, 1373-1384 (2006).K. Tuncay, G. Ozkan, P. J. Ortoleva. Interplay of gouge, fluid pressure and porosity in fault zone. Journal of Geochemical Exploration. 2003. 79: 91-195.

182
Viral structural transitions: An all-atom multiscale theory

Viral structural transitions: An all-atom multiscale theory

Y. Miao, and P. J. Ortoleva. Viral structural transitions: An all-atom multiscale theory. J. Chem. Phys. 125, 214901 (2006b).

181
All-atom multiscaling and new ensembles for dynamical nanoparticles

All-atom multiscaling and new ensembles for dynamical nanoparticles

Y. Miao, and P. J. Ortoleva. All-atom multiscaling and new ensembles for dynamical nanoparticles. J. Chem. Phys. Vol. 125: 044901 (8 pages) ( 2006a).

180
Involatile nanodroplets:  An asymptotic analysis

Involatile nanodroplets: An asymptotic analysis

L. Jarymowycz, and P. J. Ortoleva. Involatile nanodroplets:  An asymptotic analysis. J. Chem. Phys. Vol. 124: 234705 (4 pages) (2006).

179
Nanoparticle Dynamics: A Multiscale Analysis of the Liouville Equation

Nanoparticle Dynamics: A Multiscale Analysis of the Liouville Equation

P. J. Ortoleva. Nanoparticle Dynamics: A Multiscale Analysis of the Liouville Equation. J. Phys. Chem. B, 109, 21258-21266 (2005).

178
Simulated complex dynamics of glycolysis in the protozoan parasite

Simulated complex dynamics of glycolysis in the protozoan parasite

A. Navid, and P. J. Ortoleva. Simulated complex dynamics of glycolysis in the protozoan parasite Trypanosoma brucei. J. Theor. Biol. 228(4), 449-458 (2004).

177
Efficient Solution Technique for Solving Poisson-Boltzmann Equation

Efficient Solution Technique for Solving Poisson-Boltzmann Equation

A. Sayyed-Ahmad, K. Tuncay and P.J.  Ortoleva. Efficient Solution Technique for Solving Poisson-Boltzmann Equation, J. Comp. Chem. 25: 1068-1074 (2004).

176
Classical density functional theory of orientation order at interfaces: Application to water

Classical density functional theory of orientation order at interfaces: Application to water

K. Jaqaman, K. Tuncay and P. J. Ortoleva. Classical density functional theory of orientation order at interfaces: Application to water, J. Chem. Phys. Vol. 120 (2): 926-938 (2004).

175
Quantitative basin modeling: present state and developments toward predictability

Quantitative basin modeling: present state and developments toward predictability

K. Tuncay, and P. J. Ortoleva. Quantitative basin modeling: present state and developments toward predictability, Geofluids, Volume 4, Number 1, 23-39 (2004).

174
Karyote physico-chemical genome, proteome, metabolome cell modeling system

Karyote physico-chemical genome, proteome, metabolome cell modeling system

P. J. Ortoleva, Y. Brun, E. Berry, J. Fan, M. Fontus, A. Navid, A. Sayyed-Ahmad, Z. Shreif, F. Stanley, K. Tuncay, E. Weitzke and L-S. Wu. Karyote physico-chemical genome, proteome, metabolome cell modeling system, OMICS: J. Integrative Biol. Vol. 7, 169-183 (2003).

173
3-D coupled basin RTM modeling: Applications to fracture, fault and salt tectonic regimes

3-D coupled basin RTM modeling: Applications to fracture, fault and salt tectonic regimes

K. Tuncay, A. Park and P.J. Ortoleva. 3-D coupled basin RTM modeling: Applications to fracture, fault and salt tectonic regimes. Multidimensional basin modeling, edited by R. Marzi and S. Duppenbecker, AAPG Discovery Series, No 7, 217-242 (2003).

172
WRIS.TEQ: multi-mineralic water-rock interaction, mass-transfer and textural dynamics simulator

WRIS.TEQ: multi-mineralic water-rock interaction, mass-transfer and textural dynamics simulator

A. J. Park, and P. J. Ortoleva. WRIS.TEQ: multi-mineralic water-rock interaction, mass-transfer and textural dynamics simulator. Computers and Geosciences, Vol. 29(3), 277-290 (2003).

171
Simulating Cellular Dynamics Through a Coupled Transcription, Translation, Metabolic Model

Simulating Cellular Dynamics Through a Coupled Transcription, Translation, Metabolic Model

E. L. Weitzke, and P. J. Ortoleva. Simulating Cellular Dynamics Through a Coupled Transcription, Translation, Metabolic Model, Comp. Bio. Chem. 27:4-5, 469-481 (2003).

170
3-D fracture network dynamics in reservoirs, faults and salt tectonic systems

3-D fracture network dynamics in reservoirs, faults and salt tectonic systems

K. Tuncay, A. Park, D. Payne and P. J. Ortoleva. 3-D fracture network dynamics in reservoirs, faults and salt tectonic systems. Fracture and In-Situ Characterization of Hydrocarbon Reservoir, edited by M. Ameen, The Geological Society, London, UK, Special Publications, 209, 155-175 (2003).

169
Interplay of gouge, fluid pressure and porosity in fault zone

Interplay of gouge, fluid pressure and porosity in fault zone

K. Tuncay, G. Ozkan, and P. J. Ortoleva.  Interplay of gouge, fluid pressure and porosity in fault zone. J. Geochemical Exploration, Vol. 79, 191-195 (2003).

168
Estimating tectonic parameters for sedimentary basin evolution: Integration of basin modeling and reflection seismology

Estimating tectonic parameters for sedimentary basin evolution: Integration of basin modeling and reflection seismology

K. Tandon, K. Tuncay, J. Comer, K. Hubbard, and P. J. Ortoleva.  Estimating tectonic parameters for sedimentary basin evolution: Integration of basin modeling and reflection seismology, Geophys. J .Intl. 156 (1), 129-139 (2003).

167
Toward automated cell model development through information theory

Toward automated cell model development through information theory

A. Sayyed-Ahmad, K. Tuncay and P. J. Ortoleva. Toward automated cell model development through information theory. J. Phys. Chem. A, 107 (49); 10554-10565 (2003).

166
Probability functionals, homogenization and comprehensive reservoir simulators

Probability functionals, homogenization and comprehensive reservoir simulators

K. Tuncay, K. and P. J. Ortoleva.  Probability functionals, homogenization and comprehensive reservoir simulators. Resource Recovery, Confinement, and Remediation of Environmental Hazards, Institute of Mathematics and its Applications. Editors: John Chadam, Al Cunningham, Richard E. Ewing, Peter Ortoleva, and Mary Fanett Wheeler. Springer-Verlag, New York. Vol. 131:161-178 (2002).

165
Comprehensive modeling of fault dynamics during the seismic cycle

Comprehensive modeling of fault dynamics during the seismic cycle

K. Tuncay, F. Renard and P. J. Ortoleva.  Comprehensive modeling of fault dynamics during the seismic cycle. Poromechanics II, Edited by J. L.Auriault, C. Geindreau, P. Royer, J. F. Bloch, C. Boutin, J. Lewandowska, A.A. Balkema. 947-952 (2002).

164
Pits, outgrowths, and inclusions as coated grain kinetic instabilities

Pits, outgrowths, and inclusions as coated grain kinetic instabilities

K. Tuncay, J. Puckett, Z. Al-Shaeib and P. J. Ortoleva. Pits, outgrowths, and inclusions as coated grain kinetic instabilities. Geochimica et Cosmochimica Acta, Vol. 66, No. 22, 3901-3912 (2002).

163
Fractures, faults, and the nonlinear RTM dynamics of sedimentary basins

Fractures, faults, and the nonlinear RTM dynamics of sedimentary basins

K. Tuncay, A. Park and P. J. Ortoleva. Fractures, faults, and the nonlinear RTM dynamics of sedimentary basins. Resource Recovery, Confinement, and Remediation of Environmental Hazards, Institute of Mathematics and its Applications. Editors: John Chadam, Al Cunningham, Richard E. Ewing, Peter Ortoleva, and Mary Fanett Wheeler. Springer-Verlag, New York.  Vol. 131:131-160 (2002).

162
New space warping method for the simulation of large-scale macromolecular conformational changes

New space warping method for the simulation of large-scale macromolecular conformational changes

K. Jaqaman, and P. J. Ortoleva. New space warping method for the simulation of large-scale macromolecular conformational changes. J. Comp. Chem. 23: 484-491 (2002).

161
Terrestrial sequestration of CO2: An assessment of research needs

Terrestrial sequestration of CO2: An assessment of research needs

W. G. Wawersik, J. Rudnicki, P. Dove, J. Harris, J. Logan, L. Pyrak-Nolte, F.M. Orr, Jr., P. J. Ortoleva, F. Richter, N. Warpinski, J. Wilson, T. Wong. Terrestrial sequestration of CO2: An assessment of research needs, Advances in Geophysics, 43, 97-177 (2001).

160
Failure, memory and cyclic fault movement

Failure, memory and cyclic fault movement

K. Tuncay, A. Khalil and P.J. Ortoleva. Failure, memory and cyclic fault movement. Bulletin of Seismological Society of America 91:538-552 (2001).

159
A model for lignin alteration part II: numerical model of natural gas generation and application to the Piceance Basin, Western Colorado

A model for lignin alteration part II: numerical model of natural gas generation and application to the Piceance Basin, Western Colorado

D. F. Payne, and P. J. Ortoleva. A model for lignin alteration part II: numerical model of natural gas generation and application to the Piceance Basin, Western Colorado. Organic Geochemistry, vol. 32/9: 1087-1101 (2001).

158
A model for lignin alteration, part I: A kinetic reaction-network model

A model for lignin alteration, part I: A kinetic reaction-network model

D. F. Payne, and P. J. Ortoleva. A model for lignin alteration, part I: A kinetic reaction-network model. Organic Geochemistry, vol. 32/9: 1073-1085 (2001).

157
Salt tectonics as a self-organizing process: a three dimensional reaction, transport and mechanics model

Salt tectonics as a self-organizing process: a three dimensional reaction, transport and mechanics model

K. Tuncay,  and P. J. Ortoleva. Salt tectonics as a self-organizing process: a three dimensional reaction, transport and mechanics model. J. Geophys. Research 106: 803-817 (2001).

156
Numerical modeling of reaction-induced cavities in porous rock

Numerical modeling of reaction-induced cavities in porous rock

A. Ormond, and P. J. Ortoleva.  Numerical modeling of reaction-induced cavities in porous rock. J. Geophys. Research 105, NO.B7: 16,737-16,747 (2000).

155
Sedimentary basin deformation: An incremental stress rheology approach

Sedimentary basin deformation: An incremental stress rheology approach

K. Tuncay, K., A. Park and P. J. Ortoleva.  Sedimentary basin deformation: An incremental stress rheology approach. Tectonophysics 323: 77-104 (2000a).

154
A forward model of three-dimensional fracture orientation and characteristics

A forward model of three-dimensional fracture orientation and characteristics

K. Tuncay,  A. Park and P. J. Ortoleva. A forward model of three-dimensional fracture orientation and characteristics. J. Geophys. Research 105, B7:16,719-16,735 (2000b).

153
A reaction-transport-mechanical approach to modeling the interrelationships between gas generation, overpressuring, and fracturing - Implications for the Upper Cretaceous natural gas reservoirs of the Piceance Basin, Colorado

A reaction-transport-mechanical approach to modeling the interrelationships between gas generation, overpressuring, and fracturing - Implications for the Upper Cretaceous natural gas reservoirs of the Piceance Basin, Colorado

D. Payne, K. Tuncay, A. Park, J.B. Comer and P. J. Ortoleva. A reaction-transport-mechanical approach to modeling the interrelationships between gas generation, overpressuring, and fracturing – Implications for the Upper Cretaceous natural gas reservoirs of the Piceance Basin, Colorado. AAPG Bulletin 84: 545-565 (2000).

152
A mesoscopic model of nucleation and Ostwald ripening/stepping: Application to the silica polymorph system

A mesoscopic model of nucleation and Ostwald ripening/stepping: Application to the silica polymorph system

G. Ozkan, G. and P. J. Ortoleva. 2000. A mesoscopic model of nucleation and Ostwald ripening/stepping: Application to the silica polymorph system. J. Chem. Phys. 112: 1051010525 (2000).

151
Evolution of gouge grain particle size distribution: A Markov model

Evolution of gouge grain particle size distribution: A Markov model

G. Ozkan, G. and P. J. Ortoleva. Evolution of gouge grain particle size distribution: A Markov model. Pure and Applied Geophysics 157: 449-468 (2000).

150
Self-organization during reactive fluid flow in a porous medium

Self-organization during reactive fluid flow in a porous medium

F. Renard, F., J.-P. Gratier, P. J. Ortoleva, E. Brosse and B. Bazin. Self-organization during reactive fluid flow in a porous medium. Geophys. Research Letters 25(3):385-388 (1998).

149
Glass transitions: A chemical kinetic/Landau theory

Glass transitions: A chemical kinetic/Landau theory

P. J. Ortoleva, P. Glass transitions: A chemical kinetic/Landau theory.  J. Phys. Chem. B101(41): 8324-8330 (1997).

148
Pressure solution in sandstones: Influence of clays and dependence on temperatures and stress

Pressure solution in sandstones: Influence of clays and dependence on temperatures and stress

F. Renard, P. J. Ortoleva and J.P. Gratier. Pressure solution in sandstones: Influence of clays and dependence on temperatures and stress. Tectonophysics 280:257-266 (1997).

147
Naturally fractured reservoirs and compartments: A predictive basin modeling approach

Naturally fractured reservoirs and compartments: A predictive basin modeling approach

P. J. Ortoleva, M. Maxwell, D. Payne and W. Sibo. Naturally fractured reservoirs and compartments: A predictive basin modeling approach. In Fractured reservoirs: Characterization and modeling, RMAG 1997 Guidebook, edited by Thomas E. Hoak, Alan L. Klawitter, and Peter K. Blomquist, 227-242. Denver: Rocky Mountain Association of Geologists (1997).

146
Reaction-transport simulation of matrix acidizing and optimal acidizing strategies

Reaction-transport simulation of matrix acidizing and optimal acidizing strategies

K. Bartko, Y. Chen, J. Fambrough, Y. Li, C. Montgomery and P. J. Ortoleva. Reaction-transport simulation of matrix acidizing and optimal acidizing strategies. SPE 37282 (1997).

145
A geochemical reaction-transport simulator for matrix acidizing analysis and design

A geochemical reaction-transport simulator for matrix acidizing analysis and design

X. Liu, A. Ormond, K. Bartko, Y. Li and P. J. Ortoleva. A geochemical reaction-transport simulator for matrix acidizing analysis and design. J. Petrol. Science Engin. 17(1-2):181-196 (1997).

144
Water films at grain-grain contacts: Debye-Hückel, osmotic model of stress, salinity, and mineralogy dependence

Water films at grain-grain contacts: Debye-Hückel, osmotic model of stress, salinity, and mineralogy dependence

F. Renard, and P. J. Ortoleva. Water films at grain-grain contacts: Debye-Hückel, osmotic model of stress, salinity, and mineralogy dependence. Geochimica et Cosmochimica Acta 61(10):1963-1970 (1997).

143
A coupled reaction and transport model for assessing the injection, migration and fate of waste fluids

A coupled reaction and transport model for assessing the injection, migration and fate of waste fluids

X. Liu, and P. J. Ortoleva. A coupled reaction and transport model for assessing the injection, migration and fate of waste fluids. SPE 36640 (1996).

142
Simulation of waste injection and migration with the fully coupled hydrologic, mineral, and pore fluid reaction code CIRF.A.

Simulation of waste injection and migration with the fully coupled hydrologic, mineral, and pore fluid reaction code CIRF.A.

P. J. Ortoleva, Y. Chen, X. Liu, A. Ormond and R. Larkin. Simulation of waste injection and migration with the fully coupled hydrologic, mineral, and pore fluid reaction code CIRF.A. In Deep injection disposal of hazardous and industrial waste: Scientific and engineering aspects, edited by John A. Apps and Chin-Fu Tsang, 627-636. New York: Academic… View Article

141
Self-organized zoning in crystals: Free boundaries, matched asymptotics and bifurcation

Self-organized zoning in crystals: Free boundaries, matched asymptotics and bifurcation

P. J. Ortoleva. Self-organized zoning in crystals: Free boundaries, matched asymptotics and bifurcation. In Pattern formation: Symmetry methods and applications, Fields Institute Communications Vol. 5, edited by John Chadam, Martin Golubitsky, William Langford, and Brian Wetton, 321-333. Providence, RI: Amer. Math. Soc (1996).

140
Genesis and dynamics of basin compartments and seals

Genesis and dynamics of basin compartments and seals

P. J. Ortoleva, Z. Al-Shaieb and J. Puckette. Genesis and dynamics of basin compartments and seals. Amer. J. Science 295(4):345-427 (1995).

139
Propagating and stationary patterns in reaction-transport systems: Generic mechanisms, spatial geometries and response to external fields

Propagating and stationary patterns in reaction-transport systems: Generic mechanisms, spatial geometries and response to external fields

P. J. Ortoleva, P. Foerster and J. Ross. Propagating and stationary patterns in reaction-transport systems: Generic mechanisms, spatial geometries and response to external fields. In Advances in porous media, Vol. 2, edited by M. Yavuz Corapcioglu, 107-149. New York: Elsevier (1994).

138
The banded character of pressure seals

The banded character of pressure seals

Z. Al-Shaieb, Z., J.O. Puckette, A.A. Abdalla, V. Tigert and P. J. Ortoleva. The banded character of pressure seals. In Basin compartments and seals, AAPG Memoir 61, edited by P.J. Ortoleva, 351-367. Tulsa, OK: AAPG (1994).

137
Basin compartmentation: Definitions and mechanisms

Basin compartmentation: Definitions and mechanisms

P. J. Ortoleva. Basin compartmentation: Definitions and mechanisms. In Basin compartments and seals, AAPG Memoir 61, edited by P.J. Ortoleva, 39-51. Tulsa, OK: AAPG (1994).

136
Numerical simulations of overpressured compartments in sedimentary basins

Numerical simulations of overpressured compartments in sedimentary basins

E. Sonnenthal, E. and P. J. Ortoleva. Numerical simulations of overpressured compartments in sedimentary basins. In Basin compartments and seals, AAPG Memoir 61, edited by P.J. Ortoleva, 403-416. Tulsa, OK: AAPG (1994).

135
Banded diagenetic pressure seals: Types, mechanisms, and homogenized basin dynamics

Banded diagenetic pressure seals: Types, mechanisms, and homogenized basin dynamics

C. Qin, C. and P.J. Ortoleva. Banded diagenetic pressure seals: Types, mechanisms, and homogenized basin dynamics. In Basin compartments and seals, AAPG Memoir 61, edited by P.J. Ortoleva, 385-400. Tulsa, OK: AAPG (1994).

134
Role of pressure-sensitive reactions in seal formation and healing: Application of the CIRF.A reaction-transport code

Role of pressure-sensitive reactions in seal formation and healing: Application of the CIRF.A reaction-transport code

Y. Chen, Y., W. Chen, A. Park and P. J. Ortoleva. Role of pressure-sensitive reactions in seal formation and healing: Application of the CIRF.A reaction-transport code. In Basin compartments and seals, AAPG Memoir 61, edited by P.J. Ortoleva, 417-427. Tulsa, OK: AAPG (1994).

133
Simulating the development of a three-dimensional basinwide overpressured compartment

Simulating the development of a three-dimensional basinwide overpressured compartment

M. Maxwell, M. and P. J. Ortoleva. Simulating the development of a three-dimensional basinwide overpressured compartment. In Basin compartments and seals, AAPG Memoir 61, edited by P.J. Ortoleva, 429-433. Tulsa, OK: AAPG (1994).

132
Agates, geodes, concretions and orbicules:  Self-organized zoning and morphology

Agates, geodes, concretions and orbicules: Self-organized zoning and morphology

P. J. Ortoleva, P., Y. Chen and W. Chen. Agates, geodes, concretions and orbicules:  Self-organized zoning and morphology. In Fractals and dynamic systems in geoscience, edited by Jörn H. Kruhl, 283-305. New York: Springer-Verlag (1994).

131
Nonlinear dynamical aspects of deep basin hydrology: Fluid compartment formation and episodic fluid release

Nonlinear dynamical aspects of deep basin hydrology: Fluid compartment formation and episodic fluid release

T. Dewers, T. and P. J. Ortoleva. Nonlinear dynamical aspects of deep basin hydrology: Fluid compartment formation and episodic fluid release. Amer. J. Science 294:713-755 (1994).

130
Development of diagenetic differentiated structure through reaction-transport feedback

Development of diagenetic differentiated structure through reaction-transport feedback

P. J. Ortoleva. Development of diagenetic differentiated structure through reaction-transport feedback. In Diagenesis, IV, Developments in Sedimentology 51, edited by K. H. Wolf and G. V. Chilingarian, 79-94. New York: Elsevier (1994).

129
Formation of stylolites, marl/limestone alternations, and dissolution (clay) seams by unstable chemical compaction of argillaceous carbonates

Formation of stylolites, marl/limestone alternations, and dissolution (clay) seams by unstable chemical compaction of argillaceous carbonates

T. Dewers, T. and P. J. Ortoleva. Formation of stylolites, marl/limestone alternations, and dissolution (clay) seams by unstable chemical compaction of argillaceous carbonates. In Diagenesis, IV, Developments in Sedimentology 51, edited by K. H. Wolf and G. V. Chilingarian, 155-216. New York: Elsevier (1994).

128
Reactive flows in layered porous media II: The shape stability of the reaction interface

Reactive flows in layered porous media II: The shape stability of the reaction interface

J. Xin, A. Peirce, J. Chadam and P. J. Ortoleva. Reactive flows in layered porous media II: The shape stability of the reaction interface. SIAM J. Applied Math. 53(2):319-339 (1993).

127
Self-organization and nonlinear dynamics in sedimentary basins

Self-organization and nonlinear dynamics in sedimentary basins

P. J. Ortoleva. Self-organization and nonlinear dynamics in sedimentary basins. Philosophical Transactions of the Royal Society of London A344:171-179. [Reprinted with discussion in Quantifying sedimentary geochemical processes, 1994, edited by Max Coleman, Charles Curtis, and Grenville Turner, 171-179. New York: The Royal Society, Oxford University Press] (1993).

126
Optimizing matrix acidizing for near-borehole remediation using the CIRF reaction-transport simulator

Optimizing matrix acidizing for near-borehole remediation using the CIRF reaction-transport simulator

Y. Chen, J. Mu, W. Chen, D. Davis and P. J. Ortoleva. Optimizing matrix acidizing for near-borehole remediation using the CIRF reaction-transport simulator. SPE 26184:471-476 (1993).

125
Stability of reactive flows in porous media: Coupled porosity and viscosity changes

Stability of reactive flows in porous media: Coupled porosity and viscosity changes

J. Chadam, A.P. Peirce and P. J. Ortoleva. Stability of reactive flows in porous media: Coupled porosity and viscosity changes. In Free boundary problems in fluid flow with applications: Proceedings of the International Colloquium “Free Boundary Problems: Theory and Applications,” Pitman Research Notes in Mathematics Series 282, edited by John M. Chadam and Henning Rasmussen,… View Article

124
Development of complex reaction front morphologies through nonlinear fluid-rock interaction

Development of complex reaction front morphologies through nonlinear fluid-rock interaction

W. Chen, W. and P. J. Ortoleva. Development of complex reaction front morphologies through nonlinear fluid-rock interaction. In Free boundary problems in fluid flow with applications: Proceedings of the International Colloquium “Free Boundary Problems: Theory and Applications,” Pitman Research Notes in Mathematics Series 282, edited by John M. Chadam and Henning Rasmussen, 196-203. Harlow, Essex:… View Article

123
Free boundaries in geochemical systems

Free boundaries in geochemical systems

P. J. Ortoleva. Free boundaries in geochemical systems. In Emerging applications in free boundary problems: Proceedings of the International Colloquium “Free Boundary Problems: Theory and Applications,” Pitman Research Notes in Mathematics Series 280, edited by John M. Chadam and Henning Rasmussen, 29-63. Harlow, Essex: Longman Scientific and Technical (1993).

122
Periodic and aperiodic macroscopic patterning in two precipitate post-nucleation systems

Periodic and aperiodic macroscopic patterning in two precipitate post-nucleation systems

R. Sultan, R. and P.J. Ortoleva. Periodic and aperiodic macroscopic patterning in two precipitate post-nucleation systems. Physica D63:202-212 (1993).

121
Modeling diagenetic bedding, stylolites, concretions, and other mechanochemical structures

Modeling diagenetic bedding, stylolites, concretions, and other mechanochemical structures

P. J. Ortoleva, T. Dewers and B. Sauer. Modeling diagenetic bedding, stylolites, concretions, and other mechanochemical structures. In Carbonate microfabrics, edited by Richard Rezak and Dawn L. Lavoie, 291-300. New York: Springer-Verlag (1993).

120
Mechano-chemistry of compartmented basins

Mechano-chemistry of compartmented basins

E. L. Sonnenthal, J.M. Maxwell, C. Qin and P. J. Ortoleva. Mechano-chemistry of compartmented basins. In Water-rock interaction: Proceedings of the 7th International Symposium on Water-Rock Interaction, WRI-7, Park City, Utah, USA, 13-18 July 1992, Vol. 2: Moderate and high temperature environments, edited by Yousif K. Kharaka and Ann S. Maest, 1055-1058. Brookfield, VT: A…. View Article

119
CIRF: A general reaction-transport code: Mineralization fronts due to the infiltration of reactive fluids

CIRF: A general reaction-transport code: Mineralization fronts due to the infiltration of reactive fluids

J. L. Potdevin, W. Chen, A. Park, Y. Chen and P. J. Ortoleva. CIRF: A general reaction-transport code: Mineralization fronts due to the infiltration of reactive fluids. In Water-rock interaction: Proceedings of the 7th International Symposium on Water-Rock Interaction, WRI-7, Park City, Utah, USA, 13-18 July 1992, Vol. 2: Moderate and high temperature environments, edited… View Article

118
Non-linear dynamics in chemically compacting porous media

Non-linear dynamics in chemically compacting porous media

T. Dewers, T. and P. J. Ortoleva. Non-linear dynamics in chemically compacting porous media. In Modeling and analysis of diffusive and advective processes in geosciences, edited by W. E. Fitzgibbon and Mary Fanett Wheeler, 100-121. Philadelphia: Society for Industrial and Applied Mathematics (1992).

117
Development of complex reaction front morphologies through nonlinear fluid-rock interaction: Modeling, asymptotic and numerical studies

Development of complex reaction front morphologies through nonlinear fluid-rock interaction: Modeling, asymptotic and numerical studies

W. Chen, and P. J. Ortoleva. Development of complex reaction front morphologies through nonlinear fluid-rock interaction: Modeling, asymptotic and numerical studies. In Modeling and analysis of diffusive and advective processes in geosciences, edited by W. E. Fitzgibbon and Mary Fanett Wheeler, 52-70. Philadelphia: Society for Industrial and Applied Mathematics (1992).

116
A mathematical problem in geochemistry: The reaction-infiltration instability

A mathematical problem in geochemistry: The reaction-infiltration instability

J. Chadam, J. and P.J.  Ortoleva. A mathematical problem in geochemistry: The reaction-infiltration instability. Rocky Mountain J. Math. 21(2):631-643 (1991).

115
A plausible model for reversal of neoplastic transformations in plants based on multiple steady states

A plausible model for reversal of neoplastic transformations in plants based on multiple steady states

J-F. Hervagault,  P. J. Ortoleva and J. Ross. A plausible model for reversal of neoplastic transformations in plants based on multiple steady states. PNAS USA 88(23):10797-10800 (1991).

114
Influences of clay minerals on sandstone cementation and pressure solution

Influences of clay minerals on sandstone cementation and pressure solution

T. Dewers, and P. J. Ortoleva. Influences of clay minerals on sandstone cementation and pressure solution. Geology 19:1045-1048 (1991).

113
Geochemistry

Geochemistry

P. J. Ortoleva. Geochemistry. In McGraw-Hill Yearbook of Science and Technology 1992, 196-199. New York: McGraw-Hill (1991).

112
Stability of reactive flows in porous media: Coupled porosity and viscosity changes

Stability of reactive flows in porous media: Coupled porosity and viscosity changes

J. Chadam, A. Peirce and P. J. Ortoleva. Stability of reactive flows in porous media: Coupled porosity and viscosity changes. SIAM J. Applied Math. 51(3):684-692 (1991).

111
Reaction-infiltration instabilities

Reaction-infiltration instabilities

J. Chadam, and P. J. Ortoleva. Reaction-infiltration instabilities. In Free boundary problems: Theory and applications, Vol. 1, Pitman Research Notes in Mathematics 185, edited by K. H. Hoffmann and J. Sprekels, 395-404. Harlow, Essex: Longman Scientific and Technical (1990).

110
Morphological instabilities in physico-chemical systems

Morphological instabilities in physico-chemical systems

J. Chadam, and P. J. Ortoleva. Morphological instabilities in physico-chemical systems. Earth-Science Reviews 29:175-181 (1990).

109
Self-organization in far-from-equilibrium reactive porous media subject to reaction front fingering

Self-organization in far-from-equilibrium reactive porous media subject to reaction front fingering

P. J. Ortoleva, and W. Chen. Self-organization in far-from-equilibrium reactive porous media subject to reaction front fingering. In Patterns, defects and materials instabilities, edited by D. Walgraef and N. M. Ghoniem, 203-220. Boston: Kluwer Academic Publishers (1990).

108
Diagenesis through coupled processes: Modeling approach, self-organization, and implications for exploration

Diagenesis through coupled processes: Modeling approach, self-organization, and implications for exploration

W. Chen, A. Ghaith, A. Park and P. J. Ortoleva. Diagenesis through coupled processes: Modeling approach, self-organization, and implications for exploration. In Prediction of reservoir quality through chemical modeling, AAPG Memoir 49, edited by Indu D. Meshri and Peter J. Ortoleva, 103-130. Tulsa, OK: AAPG (1990).

107
Effects of fluid and rock compositions on diagenesis: A modeling investigation

Effects of fluid and rock compositions on diagenesis: A modeling investigation

C. H. Moore, and P. J. Ortoleva. Effects of fluid and rock compositions on diagenesis: A modeling investigation. In Prediction of reservoir quality through chemical modeling, AAPG Memoir 49, edited by Indu D. Meshri and Peter J. Ortoleva, 131-146. Tulsa, OK: AAPG (1990).

106
Interaction of reaction, mass transport, and rock deformation during diagenesis: Mathematical modeling of intergranular pressure solution, stylolites, and differential compaction/cementation

Interaction of reaction, mass transport, and rock deformation during diagenesis: Mathematical modeling of intergranular pressure solution, stylolites, and differential compaction/cementation

T. Dewers, and P. J. Ortoleva. Interaction of reaction, mass transport, and rock deformation during diagenesis: Mathematical modeling of intergranular pressure solution, stylolites, and differential compaction/cementation. In Prediction of reservoir quality through chemical modeling, AAPG Memoir 49, edited by Indu D. Meshri and Peter J. Ortoleva, 147-160. Tulsa, OK: AAPG (1990).

105
Oscillatory methane release from shale source rock

Oscillatory methane release from shale source rock

A. Ghaith, W. Chen and P. J. Ortoleva. 1990. Oscillatory methane release from shale source rock. Earth-Science Reviews 29:241-248 (1990).

104
Differentiated structures arising from mechano-chemical feedback in stressed rocks

Differentiated structures arising from mechano-chemical feedback in stressed rocks

T. Dewers, and P. J. Ortoleva. Differentiated structures arising from mechano-chemical feedback in stressed rocks. Earth-Science Reviews 29:283-298 (1990).

103
Role of attachment kinetic feedback in the oscillatory zoning of crystals grown from melts

Role of attachment kinetic feedback in the oscillatory zoning of crystals grown from melts

P. J. Ortoleva. Role of attachment kinetic feedback in the oscillatory zoning of crystals grown from melts. Earth-Science Reviews 29:3-8 (1990).

102
Cellular and oscillatory self-induced methane migration

Cellular and oscillatory self-induced methane migration

A. Park, T. Dewers and P. J. Ortoleva. Cellular and oscillatory self-induced methane migration. Earth-Science Reviews 29:249-265 (1990).

101
A coupled reaction/transport/mechanical model for intergranular pressure solution, stylolites, and differential compaction and cementation in clean sandstones

A coupled reaction/transport/mechanical model for intergranular pressure solution, stylolites, and differential compaction and cementation in clean sandstones

T. Dewers, and P. J. Ortoleva. A coupled reaction/transport/mechanical model for intergranular pressure solution, stylolites, and differential compaction and cementation in clean sandstones. Geochimica et Cosmochimica Acta 54:1609-1625 (1990).

100
Reaction front fingering in carbonate-cemented sandstones

Reaction front fingering in carbonate-cemented sandstones

W. Chen, and P. J. Ortoleva. Reaction front fingering in carbonate-cemented sandstones. Earth-Science Reviews 29:183-198 (1990).

99
Static and propagating chemical spike structures and their electrical responses

Static and propagating chemical spike structures and their electrical responses

P. J. Ortoleva, and R. Sultan. Static and propagating chemical spike structures and their electrical responses. Chem. Phys. 148:47-55 (1990).

98
Geochemical self-organization III: A mechano-chemical model of metamorphic differentiation

Geochemical self-organization III: A mechano-chemical model of metamorphic differentiation

T. Dewers, and P. J. Ortoleva.  Geochemical self-organization III: A mechano-chemical model of metamorphic differentiation. Amer. J. Science 290:473-521 (1990).

97
Bifurcation of the Ostwald-Liesegang supersaturation-nucleation-depletion cycle

Bifurcation of the Ostwald-Liesegang supersaturation-nucleation-depletion cycle

R. Sultan, P. J. Ortoleva, F. DePasquale, and P. Tartaglia. Bifurcation of the Ostwald-Liesegang supersaturation-nucleation-depletion cycle. Earth-Science Reviews 29:163-173 (1990).

96
Force of crystallization during the growth of siliceous concretions

Force of crystallization during the growth of siliceous concretions

T. Dewers, and P. J. Ortoleva. Force of crystallization during the growth of siliceous concretions. Geology 18(3):204-207 (1990).

95
The electric field response of periodic chemical wave trains in folded slow manifold systems

The electric field response of periodic chemical wave trains in folded slow manifold systems

R. Sultan, and P. J. Ortoleva. The electric field response of periodic chemical wave trains in folded slow manifold systems. J. Chem. Phys. 92(2):1062-1068 (1990).

94
Nonequilibrium reaction-diffusion structures in rigid and visco-elastic media: Knots and unstable noninertial flows

Nonequilibrium reaction-diffusion structures in rigid and visco-elastic media: Knots and unstable noninertial flows

P. J. Ortoleva. Nonequilibrium reaction-diffusion structures in rigid and visco-elastic media: Knots and unstable noninertial flows. Math. Modeling Numerical Analysis 23(3):507-517 (1989).

93
Self-organization of mineralization patterns in metamorphic rocks through mechanochemical coupling

Self-organization of mineralization patterns in metamorphic rocks through mechanochemical coupling

T. Dewers, and P. J. Ortoleva. Self-organization of mineralization patterns in metamorphic rocks through mechanochemical coupling. J. Phys. Chem. 93:2842-2848 (1989).

92
Mechano-chemical coupling in stressed rocks

Mechano-chemical coupling in stressed rocks

T. Dewers, and P. J. Ortoleva. Mechano-chemical coupling in stressed rocks. Geochimica et Cosmochimica Acta 53:1243-1258 (1989).

91
Modeling acid stimulation of the Halfway Formation, Canada, using a geochemical computer model

Modeling acid stimulation of the Halfway Formation, Canada, using a geochemical computer model

H. K. Haskin, C.H. Moore and P. J. Ortoleva. Modeling acid stimulation of the Halfway Formation, Canada, using a geochemical computer model. SPE 18133:283-294 (1988).

90
The role of geochemical self-organization in the migration and trapping of hydrocarbons

The role of geochemical self-organization in the migration and trapping of hydrocarbons

T. Dewers, and P. J. Ortoleva. The role of geochemical self-organization in the migration and trapping of hydrocarbons. Applied Geochemistry 3:287-316 (1988).

89
A weakly nonlinear stability analysis of the reactive infiltration interface

A weakly nonlinear stability analysis of the reactive infiltration interface

J. Chadam, P. J. Ortoleva, and A. Sen. A weakly nonlinear stability analysis of the reactive infiltration interface. SIAM J. Applied Math. 48(6):1362-1378 (1988).

88
Existence and stability for spherical crystals growing in a supersaturated solution

Existence and stability for spherical crystals growing in a supersaturated solution

J. Chadam, S.D. Howison and P. J. Ortoleva. Existence and stability for spherical crystals growing in a supersaturated solution. IMA J. Applied Math. 39:1-15 (1987).

87
Geochemical self-organization II: The reactive-infiltration instability

Geochemical self-organization II: The reactive-infiltration instability

P. J. Ortoleva, J. Chadam, E. Merino, and A. Sen. Geochemical self-organization II: The reactive-infiltration instability. Amer. J. Science 287:1008-1040 (1987).

86
Geochemical self-organization I: Reaction-transport feedbacks and modeling approach

Geochemical self-organization I: Reaction-transport feedbacks and modeling approach

P. J. Ortoleva, E. Merino, C. Moore, and J. Chadam. Geochemical self-organization I: Reaction-transport feedbacks and modeling approach. Amer. J. Science 287:979-1007 (1987).

85
Chemical wave-electrical field interaction phenomena

Chemical wave-electrical field interaction phenomena

P. J. Ortoleva. Chemical wave-electrical field interaction phenomena. Physica D26:67-84 (1987).

84
Modeling geochemical self-organization

Modeling geochemical self-organization

P. J. Ortoleva. Modeling geochemical self-organization. In Irreversible phenomena and dynamical systems analysis in geosciences: Proceedings of the NATO Advanced Study Institute on Irreversible Phenomena and Dynamical Systems Analysis in Geosciences, Crete, Greece, July 14-24, 1985, NATO ASI series, Series C, Mathematical and Physical Sciences, Vol. 192, edited by C. Nicolis and G. Nicolis, 493-510…. View Article

83
Bifurcation problems arising in geochemistry

Bifurcation problems arising in geochemistry

J. Chadam, and P. J. Ortoleva. Bifurcation problems arising in geochemistry. In Oscillation, bifurcation, and chaos: Proceedings of the 1986 Annual Seminar held July 13-25, 1986, ed. by F. Atkinson, S. Langford and A. Mingarelli, 329-342. Providence, RI: Published by the American Mathematical Society for the Canadian Mathematical Society (1987).

82
Mineral zoning in sediment-hosted copper-iron sulfide deposits—A quantitative kinetic approach

Mineral zoning in sediment-hosted copper-iron sulfide deposits—A quantitative kinetic approach

E. Merino, C. Moore, P. J. Ortoleva, and E. Ripley. Mineral zoning in sediment-hosted copper-iron sulfide deposits—A quantitative kinetic approach. In Geology and metallogeny of copper deposits: Proceedings of the Copper Symposium, 27th International Geological Congress, Moscow, 1984, ed. by G. Friedrich, A. Genkin, A. Naldrett, J. Ridge, R. Sillitoe and F. Vokes, 559-571. New… View Article

81
Static reaction-diffusion structures in folded slow manifold systems

Static reaction-diffusion structures in folded slow manifold systems

R. Sultan, and P. J. Ortoleva. Static reaction-diffusion structures in folded slow manifold systems. J. Chem. Phys.  85(9):5068-5075 (1986).

80
Reactive infiltration instabilities

Reactive infiltration instabilities

J. Chadam, D. Hoff, E. Merino, P. J. Ortoleva, and A. Sen. Reactive infiltration instabilities. IMA J. Applied Math. 36:207-221(1986).

79
Rotating waves in reaction-diffusion systems with folded slow manifolds

Rotating waves in reaction-diffusion systems with folded slow manifolds

R. Sultan, and P. J. Ortoleva. Rotating waves in reaction-diffusion systems with folded slow manifolds. J. Chem. Phys.  84(12):6781-6789 (1986).

78
Redox front propagation and banding modalities

Redox front propagation and banding modalities

P. J. Ortoleva, G. Auchmuty, J. Chadam, J. Hettmer, E. Merino, C.H. Moore, and E. Ripley. 1986. Redox front propagation and banding modalities. Physica D19:334-354 (1986).

77
The structure and stability of propagating redox fronts

The structure and stability of propagating redox fronts

G. Auchmuty, J. Chadam, E. Merino, P. J. Ortoleva, and E. Ripley. The structure and stability of propagating redox fronts. SIAM J. Applied Math. 46(4):588-604 (1986).

76
Moving interfaces and their stability: Applications to chemical waves and solidification

Moving interfaces and their stability: Applications to chemical waves and solidification

J. Chadam, and P. J. Ortoleva. Moving interfaces and their stability: Applications to chemical waves and solidification. In Dynamics of nonlinear systems, edited by V. Hlavacek, 247-278. New York: Gordon and Breach (1986).

75
The structure and variety of chemical waves

The structure and variety of chemical waves

P. J. Ortoleva, and S.L. Schmidt. The structure and variety of chemical waves. In Oscillations and traveling waves in chemical systems, edited by Richard J. Field and Maria Burger, 333-418. New York: Wiley (1985).

74
Mineral zoning in sediment-hosted copper deposits

Mineral zoning in sediment-hosted copper deposits

E. Ripley, E. Merino, C. Moore and P. J. Ortoleva. Mineral zoning in sediment-hosted copper deposits. In Handbook of strata-bound and stratiform ore deposits, Part IV, Vol. 13: Regional studies and specific deposits, edited by K. H. Wolf, 237-260. New York: Elsevier (1985).

73
Existence, uniqueness and asymptotic behavior of solutions of the planar, supersaturated solidification, Cauchy-Stefan problem

Existence, uniqueness and asymptotic behavior of solutions of the planar, supersaturated solidification, Cauchy-Stefan problem

J. C. Baillon, M. Bertsch, J. Chadam, P. J. Ortoleva and L. A. Peletier. Existence, uniqueness and asymptotic behavior of solutions of the planar, supersaturated solidification, Cauchy-Stefan problem. In Nonlinear partial differential equations and their applications: Collège de France Seminar, Vol. III, Pitman Research Notes in Mathematics 109, edited by H. Brezis and J. L…. View Article

72
From nonlinear waves to spiral and speckle patterns: Nonequilibrium phenomena in geological and biological systems

From nonlinear waves to spiral and speckle patterns: Nonequilibrium phenomena in geological and biological systems

P. J. Ortoleva. From nonlinear waves to spiral and speckle patterns: Nonequilibrium phenomena in geological and biological systems. Physica 12D:305-320 [Reprinted in Fronts, interfaces and patterns: Proceedings of the Third Annual International Conference of the Center for Nonlinear Studies, Los Alamos, New Mexico 87545, USA, May 2-6, 1983, 1984, edited by Alan R. Bishop, Laurence… View Article

71
Macroscopic self organization at geological and other first order phase transitions

Macroscopic self organization at geological and other first order phase transitions

P. J. Ortoleva. Macroscopic self organization at geological and other first order phase transitions. In Non-equilibrium dynamics in chemical systems: Proceedings of the International Symposium, Bordeaux, France, September 3-7, 1984, edited by C. Vidal and A. Pacault, 94-98. New York: Springer-Verlag (1984).

70
Modeling nonlinear wave propagation and pattern formation at geochemical first order phase transitions

Modeling nonlinear wave propagation and pattern formation at geochemical first order phase transitions

P. J. Ortoleva. Modeling nonlinear wave propagation and pattern formation at geochemical first order phase transitions. In Chemical instabilities: Applications in chemistry, engineering, geology, and materials science, edited by G. Nicolis and F. Baras, 329-340. Boston: D. Reidel (1984).

69
The self-organization of Liesegang bands and other precipitate patterns

The self-organization of Liesegang bands and other precipitate patterns

P. J. Ortoleva. The self-organization of Liesegang bands and other precipitate patterns. In Chemical instabilities: Applications in chemistry, engineering, geology, and materials science, edited by G. Nicolis and F. Baras, 289-297. Boston: D. Reidel (1984).

68
Existence, uniqueness and asymptotic behavior of solutions of the planar, supersaturated solidification, Cauchy-Stefan problem

Existence, uniqueness and asymptotic behavior of solutions of the planar, supersaturated solidification, Cauchy-Stefan problem

J. B. Baillon, M. Bertsch, J. Chadam, L. A. Peletier and P. J. Ortoleva. Existence, uniqueness and asymptotic behavior of solutions of the planar, supersaturated solidification, Cauchy-Stefan problem. In Nonlinear partial differential equations and their applications: College de France Seminar, Volume VI, edited by H. Brezis and J. L. Lions, 27-41. Boston: Pitman Advanced Pub…. View Article

67
Moving redox fronts and worm hole-cave cascades

Moving redox fronts and worm hole-cave cascades

G. Auchmuty, J. Chadam, E. Merino, P. J. Ortoleva, and E. Ripley. Moving redox fronts and worm hole-cave cascades. In Proceedings of the Symposium on Nonlinear Problems in Energy Engineering, April 26-28, 1983 at Argonne National Laboratory, Argonne, Illinois (cosponsored by Office of Basic Energy Sciences, U.S. Department of Energy, and Components Technology Division, Argonne… View Article

66
Generation of evenly-spaced pressure-solution seams during (late) diagenesis: A kinetic theory

Generation of evenly-spaced pressure-solution seams during (late) diagenesis: A kinetic theory

E. Merino, P. J. Ortoleva, and P. Strickholm. Generation of evenly-spaced pressure-solution seams during (late) diagenesis: A kinetic theory. Contributions to Mineralogy and Petrology 82:360-370 (1983).

65
The stabilizing effect of surface tension on the development of the free boundary in a planar, one-dimensional, Cauchy-Stefan problem

The stabilizing effect of surface tension on the development of the free boundary in a planar, one-dimensional, Cauchy-Stefan problem

J. Chadam, and P. J. Ortoleva. The stabilizing effect of surface tension on the development of the free boundary in a planar, one-dimensional, Cauchy-Stefan problem. IMA J. Applied Math. 30:57-66 (1983).

64
Periodic precipitation and coarsening waves: Applications of the competitive particle growth model

Periodic precipitation and coarsening waves: Applications of the competitive particle growth model

R. Feeney, S. L. Schmidt, P. Strickholm, J. Chadam and P. J. Ortoleva. Periodic precipitation and coarsening waves: Applications of the competitive particle growth model. J. Chem. Phys. 78(3):1293-1311(1983).

63
Kinetics of metamorphic layering in anisotropically stressed rocks

Kinetics of metamorphic layering in anisotropically stressed rocks

P. J. Ortoleva, E. Merino and P. Strickholm. Kinetics of metamorphic layering in anisotropically stressed rocks. Amer. J. Science 282:617-643 (1982).

62
Solute reaction mediated precipitate patterns in cross gradient free systems

Solute reaction mediated precipitate patterns in cross gradient free systems

P. J. Ortoleva. Solute reaction mediated precipitate patterns in cross gradient free systems. Zeitschrift fur Physik B (Condensed Matter) 49:149-156 (1982).

61
A study of instability to electrical symmetry breaking in unicellular systems

A study of instability to electrical symmetry breaking in unicellular systems

R. Larter, and P. J. Ortoleva.  A study of instability to electrical symmetry breaking in unicellular systems. J. Theor. Biol. 96:175-200 (1982).

60
Mechanisms of bio- and geo-pattern formation and chemical signal propagation

Mechanisms of bio- and geo-pattern formation and chemical signal propagation

P. J. Ortoleva, J. Chadam, M. El-Badewi, R. Feeney, D. Feinn, S. Haase, R. Larter, E. Merino, A. Strickholm and S. Schmidt.  Mechanisms of bio- and geo-pattern formation and chemical signal propagation. In Instabilities, bifurcations, and fluctuations in chemical systems, edited by L. E. Reichl and W. C. Schieve, 125-195. Austin: University of Texas Press… View Article

59
Developmental bioelectricity

Developmental bioelectricity

P. J. Ortoleva. Developmental bioelectricity. In Biological effects of nonionizing radiation, edited by Karl H. Illinger, 163-212. Washington, DC: Amer. Chem. Soc (1981).

58
Experiments on electrical field-BZ chemical wave interactions: Annihilation and the crescent wave

Experiments on electrical field-BZ chemical wave interactions: Annihilation and the crescent wave

R. Feeney, S. L. Schmidt and P. J. Ortoleva. Experiments on electrical field-BZ chemical wave interactions: Annihilation and the crescent wave. Physica D2:536-544 (1981).

57
Third body effects on reactions in liquids

Third body effects on reactions in liquids

S. Bose, M. Medina-Noyola and P. J. Ortoleva. Third body effects on reactions in liquids. J. Chem. Phys. 75(4):1762-1771(1981).

56
Electrical field effects on propagating BZ waves: Predictions of an Oregonator and new pulse supporting models

Electrical field effects on propagating BZ waves: Predictions of an Oregonator and new pulse supporting models

S. Schmidt, S. and P. J. Ortoleva. Electrical field effects on propagating BZ waves: Predictions of an Oregonator and new pulse supporting models. J. Chem. Phys. 74(8):4488-4500 (1981).

55
A theoretical basis for self-electrophoresis

A theoretical basis for self-electrophoresis

R. Larter, and P. J. Ortoleva. A theoretical basis for self-electrophoresis. J. Theor. Biol. 88:599-630 (1981).

54
Complicated pulse structure and chaotic fronts in multispecies self-induced transparency

Complicated pulse structure and chaotic fronts in multispecies self-induced transparency

S. L. Schmidt, and P. J. Ortoleva. Complicated pulse structure and chaotic fronts in multispecies self-induced transparency. Physical Review A 24(2):967-974 (1981).

53
On growth and form

On growth and form

J. Chadam, J. and P. J. Ortoleva. On growth and form. In Mathematical biology: A conference on theoretical aspects of molecular science, edited by T. A. Burton, 21-32. New York: Pergamon Press (1981).

52
Electrical phenomena in developing biological systems

Electrical phenomena in developing biological systems

P. J. Ortoleva. Electrical phenomena in developing biological systems. In Mathematical biology: A conference on theoretical aspects of molecular science, edited by T. A. Burton, 209-224. New York: Pergamon Press (1981).

51
Temporal development of fabric in uniaxially stressed polycrystalline media—A theory

Temporal development of fabric in uniaxially stressed polycrystalline media—A theory

E. Merino, E. and P. J. Ortoleva. Temporal development of fabric in uniaxially stressed polycrystalline media—A theory. Contributions to Mineralogy and Petrology 71:429-435 (1980).

50
Scaling and Ginsburg criteria for critical bifurcations in nonequilibrium reacting systems

Scaling and Ginsburg criteria for critical bifurcations in nonequilibrium reacting systems

A. Nitzan, and P. J. Ortoleva. Scaling and Ginsburg criteria for critical bifurcations in nonequilibrium reacting systems. Physical Review A21(5):1735-1755 (1980).

49
Dynamic Padé approximants for chemical center waves

Dynamic Padé approximants for chemical center waves

S. Bose, and P. J. Ortoleva. Dynamic Padé approximants for chemical center waves. J. Chem. Phys. 72(8):4258-4263 (1980).

48
Asymptotic solutions of the FKN chemical wave equation

Asymptotic solutions of the FKN chemical wave equation

S. Schmidt, and P. J.  Ortoleva. Asymptotic solutions of the FKN chemical wave equation. J. Chem. Phys. 72(4):2733-2736 (1980).

47
Symmetry breaking and far-from-equilibrium order

Symmetry breaking and far-from-equilibrium order

P. J. Ortoleva. Symmetry breaking and far-from-equilibrium order. I­­n Symmetries in science, edited by Bruno Gruber and Richard S. Millman, 279-295. New York: Plenum Press (1980).

46
Periodic zoning in plagioclase feldspars

Periodic zoning in plagioclase feldspars

C. S. Haase, J. Chadam, D. Feinn, and P. J. Ortoleva. Periodic zoning in plagioclase feldspars. Science 209:272-274 (1980).

45
Dynamic Padé approximants and behavior singularities in nonlinear physico-chemical systems

Dynamic Padé approximants and behavior singularities in nonlinear physico-chemical systems

P. J. Ortoleva. Dynamic Padé approximants and behavior singularities in nonlinear physico-chemical systems. In Bifurcation and nonlinear eigenvalue problems: Proceedings, Université de Paris XIII, Villetaneuse, France, October 2-4, 1978, Lecture Notes in Mathematics Vol. 782, edited by C. Bardos, J. M. Lasry, and M. Schatzman, 255-264. New York: Springer-Verlag (1980).

44
Multiple chemical waves induced by applied electric field

Multiple chemical waves induced by applied electric field

S. Schmidt, and P. J. Ortoleva. Multiple chemical waves induced by applied electric field. J. Chem. Phys. 71(2):1010-1015 (1979).

43
Electrical effects in nonlinear physico-chemical systems: Field chemical wave interaction and bio-self electrophoresis

Electrical effects in nonlinear physico-chemical systems: Field chemical wave interaction and bio-self electrophoresis

R. Larter,  S. Schmidt and P. J. Ortoleva. Electrical effects in nonlinear physico-chemical systems: Field chemical wave interaction and bio-self electrophoresis. In Pattern formation by dynamic systems and pattern recognition: Proceedings of the International Symposium on Synergetics at Schloss Elmau, Bavaria, edited by H. Haken, 144-154. New York: Springer-Verlag (1979).

42
Critical fluctuation universality in chemically oscillatory systems: A soluble master equation

Critical fluctuation universality in chemically oscillatory systems: A soluble master equation

M. DelleDonne, and P. J. Ortoleva.  Critical fluctuation universality in chemically oscillatory systems: A soluble master equation. J. Stat. Phys. 20(5):473-486 (1979).

41
A hard sphere model of chemical reaction in condensed media

A hard sphere model of chemical reaction in condensed media

S. Bose, and P. J. Ortoleva.  A hard sphere model of chemical reaction in condensed media. Physics Letters A69(5):367-369 (1979).

40
Reacting hard sphere dynamics: Liouville equation for condensed media

Reacting hard sphere dynamics: Liouville equation for condensed media

S. Bose, and P. J. Ortoleva. Reacting hard sphere dynamics: Liouville equation for condensed media. J. Chem. Phys.  70(6):3041-3056 (1979).

39
Reply to the comment on

Reply to the comment on "Oscillations and runaway states in a closed illuminated system" made by Richard M. Noyes

M. DelleDonne, and P. J. Ortoleva. Reply to the comment on “Oscillations and runaway states in a closed illuminated system” made by Richard M. Noyes. J. Chem. Phys.  70(2):1073 (1979).

38
The multifaceted family of the nonlinear: Waves and fields, center dynamics, catastrophes, rock bands and precipitation patterns

The multifaceted family of the nonlinear: Waves and fields, center dynamics, catastrophes, rock bands and precipitation patterns

P. J. Ortoleva. The multifaceted family of the nonlinear: Waves and fields, center dynamics, catastrophes, rock bands and precipitation patterns. In Synergetics: Far from equilibrium: Proceedings of the Conference Far from Equilibrium, Instabilities and Structures, Bordeaux, France, September 27-29, 1978, edited by A. Pacault and C. Vidal, 114-127. New York: Springer-Verlag (1979).

37
Bifurcations and perturbed attractors in physicochemical systems

Bifurcations and perturbed attractors in physicochemical systems

P. J. Ortoleva. Bifurcations and perturbed attractors in physicochemical systems. In Bifurcation theory and applications in scientific disciplines, Annals of the New York Academy of Sciences, Vol. 316, edited by Okan Gurel and Otto E. Rössler, 350-356. New York: New York Academy of Sciences (1979).

36
Strange attractors in 3-variable reaction systems

Strange attractors in 3-variable reaction systems

E. Rössler, Otto, and P. J. Ortoleva. Strange attractors in 3-variable reaction systems. In Lecture notes in biomathematics, No. 21: Theoretical approaches to complex systems: Proceedings, Tubingen, June 11-12, 1977, edited by R. Heim and G. Palm, 67-73. New York: Springer-Verlag (1978).

35
Turbulent spatio-temporal dynamics in reacting-diffusing systems: Results for a soluble model

Turbulent spatio-temporal dynamics in reacting-diffusing systems: Results for a soluble model

P. J. Ortoleva, and M. DelleDonne. Turbulent spatio-temporal dynamics in reacting-diffusing systems: Results for a soluble model. Zeitschrift fur Naturforschung A33:588-596 (1978).

34
Kinetic instabilities in first order phase transitions

Kinetic instabilities in first order phase transitions

R. Lovett, P. J. Ortoleva, and J. Ross. Kinetic instabilities in first order phase transitions. J. Chem. Phys. 69(3):947-955 (1978).

33
Instability and far-from-equilibrium states of chemically reacting systems

Instability and far-from-equilibrium states of chemically reacting systems

P. Hanusse, J. Ross, and P. J. Ortoleva. Instability and far-from-equilibrium states of chemically reacting systems. In For Ilya Prigogine, Advances in Chemical Physics, Vol. 38, edited by Stuart A. Rice, 317-361. New York: Wiley (1978).

32
Selected topics from the theory of physico-chemical phenomena

Selected topics from the theory of physico-chemical phenomena

P. J. Ortoleva. Selected topics from the theory of physico-chemical phenomena. In Theoretical chemistry: Advances and perspectives, Vol. 4: Periodicities in chemistry and biology, edited by Henry Eyring and Douglas Henderson, 235-286. New York: Academic Press (1978).

31
Dynamic Padé approximants in the theory of periodic and chaotic chemical center waves

Dynamic Padé approximants in the theory of periodic and chaotic chemical center waves

P. J. Ortoleva. Dynamic Padé approximants in the theory of periodic and chaotic chemical center waves. J. Chem. Phys.  69(1):300-307 (1978).

30
Generalized nonlinear master equations for local fluctuations: Dimensionality expansions and augmented mean field theory

Generalized nonlinear master equations for local fluctuations: Dimensionality expansions and augmented mean field theory

M. DelleDonne, and P. J. Ortoleva. Generalized nonlinear master equations for local fluctuations: Dimensionality expansions and augmented mean field theory. J. Stat. Phys. 18(3):319-331(1978).

29
Spontaneous pattern formation in precipitating systems

Spontaneous pattern formation in precipitating systems

D. Feinn, P. J. Ortoleva, W. Scalf, S. Schmidt, and M. Wolff. Spontaneous pattern formation in precipitating systems. J. Chem. Phys.  69(1):27-39 (1978).

28
A new chemical wave equation for ionic systems

A new chemical wave equation for ionic systems

Schmidt, and P. J. Ortoleva.  A new chemical wave equation for ionic systems. J. Chem. Phys. 67(8):3771-3776 (1977).

27
Cooperative instability phenomena in arrays of catalytic sites

Cooperative instability phenomena in arrays of catalytic sites

E. K. Bimpong-Bota, A. Nitzan, P. J. Ortoleva, and J. Ross. Cooperative instability phenomena in arrays of catalytic sites. J. Chem. Phys. 66(8):3650-3658 (1977).

26
Catastrophe and propagation in chemical reactions

Catastrophe and propagation in chemical reactions

D. Feinn, and P. J. Ortoleva. 1977. Catastrophe and propagation in chemical reactions. J. Chem. Phys.  67(5):2119-2131(1977).

25
Oscillations and runaway states in a closed illuminated system

Oscillations and runaway states in a closed illuminated system

M. DelleDonne, and P. J. Ortoleva. Oscillations and runaway states in a closed illuminated system. J. Chem. Phys.  67(5):1861-1867 (1977).

24
Computer molecular dynamics studies of a chemical instability

Computer molecular dynamics studies of a chemical instability

P. J. Ortoleva, and S. Yip. Computer molecular dynamics studies of a chemical instability. J. Chem. Phys.  65(6):2045-2051 (1976).

23
Local phase and renormalized frequency in inhomogeneous chemioscillations

Local phase and renormalized frequency in inhomogeneous chemioscillations

P. J. Ortoleva. Local phase and renormalized frequency in inhomogeneous chemioscillations. J. Chem. Phys.  64(4):1395-1406 (1976).

22
Theory of propagation of discontinuities in kinetic systems with multiple time scales: Fronts, front multiplicity, and pulses

Theory of propagation of discontinuities in kinetic systems with multiple time scales: Fronts, front multiplicity, and pulses

P. J. Ortoleva,  and J. Ross. Theory of propagation of discontinuities in kinetic systems with multiple time scales: Fronts, front multiplicity, and pulses. J. Chem. Phys. 63(8):3398-3408 (1975).

21
Studies in dissipative phenomena with biological applications

Studies in dissipative phenomena with biological applications

P. J. Ortoleva, and J. Ross.  Studies in dissipative phenomena with biological applications. In Membranes, dissipative structures and evolution, Advances in Chemical Physics, Vol. 29, edited by G. Nicolis and R. Lefever, 49-61. New York: Wiley (1975).

20
Nucleation in systems with multiple stationary states

Nucleation in systems with multiple stationary states

A. Nitzan, P. J. Ortoleva, and J. Ross.  Nucleation in systems with multiple stationary states. In Physical chemistry of oscillatory phenomena, Faraday Symposia of The Chemical Society No. 9, 241-253. London: Faraday Division, Chemical Society (1975).

19
Threshold excitations, relaxation oscillations, and effect of noise in an enzyme reaction

Threshold excitations, relaxation oscillations, and effect of noise in an enzyme reaction

H.-S. Hahn, A. Nitzan, P. J.  Ortoleva, and J. Ross. Threshold excitations, relaxation oscillations, and effect of noise in an enzyme reaction. PNAS USA 71(10):4067-4071 (1974).

18
On a variety of wave phenomena in chemical reactions

On a variety of wave phenomena in chemical reactions

P. J. Ortoleva and J. Ross. On a variety of wave phenomena in chemical reactions. J. Chem. Phys. 60(12):5090-5107 (1974).

17
Symmetry breaking instabilities in illuminated systems

Symmetry breaking instabilities in illuminated systems

Nitzan, A., P.J. Ortoleva, and J. Ross. Symmetry breaking instabilities in illuminated systems. J. Chem. Phys.  60(8):3134-3143 (1974).

16
Far-from-equilibrium phenomena at local sites of reaction

Far-from-equilibrium phenomena at local sites of reaction

K. Bimpong-Bota, P. J. Ortoleva, and J. Ross.  Far-from-equilibrium phenomena at local sites of reaction. J. Chem. Phys. 60(8):3124-3133 (1974).

15
Fluctuations and transitions at chemical instabilities: The analogy to phase transitions

Fluctuations and transitions at chemical instabilities: The analogy to phase transitions

A. Nitzan, P. J. Ortoleva, J. Deutch, and J. Ross.  Fluctuations and transitions at chemical instabilities: The analogy to phase transitions. J. Chem. Phys. 61(3):1056-1074 (1974).

14
A chemical instability mechanism for asymmetric cell differentiation

A chemical instability mechanism for asymmetric cell differentiation

P. J. Ortoleva, and J. Ross. A chemical instability mechanism for asymmetric cell differentiation. Biophysical Chemistry 1:87-96 (1973).

13
A theory of asymmetric cell division (differentiation)

A theory of asymmetric cell division (differentiation)

P. J. Ortoleva, and J. Ross. A theory of asymmetric cell division (differentiation). Developmental Biology 34:F19-F23 (1973).

12
Phase waves in oscillatory chemical reactions

Phase waves in oscillatory chemical reactions

P. J. Ortoleva, and J. Ross. Phase waves in oscillatory chemical reactions. J. Chem.Phys. 58(12):5673-5680 (1973).

11
Chemical oscillations and multiple steady states due to variable boundary permeability

Chemical oscillations and multiple steady states due to variable boundary permeability

H. -S. Hahn, P. J. Ortoleva and J. Ross.  Chemical oscillations and multiple steady states due to variable boundary permeability. J. Theor. Biol.41:503-521 (1973).

10
Nonequilibrium relaxation methods: Acoustic effects in transient chemical reactions

Nonequilibrium relaxation methods: Acoustic effects in transient chemical reactions

R. Gilbert, P. J. Ortoleva and J. Ross. Nonequilibrium relaxation methods: Acoustic effects in transient chemical reactions. J. Chem. Phys. 58(9):3625-3633 (1973).

9
Light scattering from systems with chemical oscillations and dissipative structures

Light scattering from systems with chemical oscillations and dissipative structures

J. M. Deutch, S. Hudson, P. J. Ortoleva, and J. Ross. Light scattering from systems with chemical oscillations and dissipative structures. J. Chem. Phys. 57(10):4327-4332 (1972).

8
Interaction of sound with gas phase reactions

Interaction of sound with gas phase reactions

R. G. Gilbert, H-S Hahn, P. J. Ortoleva and J. Ross. Interaction of sound with gas phase reactions. J. Chem. Phys. 57(7):2672-2679 (1972).

7
Local structures in chemical reactions with heterogeneous catalysis

Local structures in chemical reactions with heterogeneous catalysis

P. J. Ortoleva and J. Ross. Local structures in chemical reactions with heterogeneous catalysis. J. Chem. Phys. 56(9):4397-4400 (1972).

6
Penetration of boundary perturbations in unstable chemical systems

Penetration of boundary perturbations in unstable chemical systems

P. J. Ortoleva, and J. Ross. Penetration of boundary perturbations in unstable chemical systems. J. Chem. Phys. 56(1):287-292 (1972).

5
Response of unstable chemical systems to external perturbations

Response of unstable chemical systems to external perturbations

P. J. Ortoleva, and J. Ross. Response of unstable chemical systems to external perturbations. J. Chem. Phys.  56(1):293-294 (1972).

4
Instabilities in coupled chemical reactions with pressure-dependent rate coefficients

Instabilities in coupled chemical reactions with pressure-dependent rate coefficients

P. J. Ortoleva, and J. Ross.  Instabilities in coupled chemical reactions with pressure-dependent rate coefficients. J. Chem. Phys. 55(9):4378-4390 (1971).

3
Collective and single-particle effects in autocorrelation functions for dense classical fluids

Collective and single-particle effects in autocorrelation functions for dense classical fluids

P. J. Ortoleva, and M. Nelkin. Collective and single-particle effects in autocorrelation functions for dense classical fluids. Physical Review A2(1):187-195 (1970).

2
Fluctuations of the single-particle distribution function in classical fluids

Fluctuations of the single-particle distribution function in classical fluids

P. J. Ortoleva, and M. Nelkin. Fluctuations of the single-particle distribution function in classical fluids. Physical Review 181(1):429-437 (1969).

1
Collective modes in liquids and neutron scattering

Collective modes in liquids and neutron scattering

M. Nelkin, and P. J. Ortoleva. Collective modes in liquids and neutron scattering. In Neutron inelastic scattering, Vol. 1, 535-544. Vienna: International Atomic Energy Agency (1968).