139 Publications (Page 2 of 6)
2013
Variational methods for time-dependent classical many-particle systems.
Sereda, Yuriy V and Ortoleva, Peter J
Physica A, vol. 392, (no. 4), pp. 628-638, February 15, 2013. | Journal Article
2012
Discovering free energy basins for macromolecular systems via guided multiscale simulation.
Sereda, Yuriy V⋅Sereda, Yuriy V⋅Singharoy, Abhishek B⋅Singharoy, Abhishek B⋅Jarrold, Martin F⋅Jarrold, Martin F⋅Ortoleva, Peter J and Ortoleva, Peter J
The journal of physical chemistry. B, vol. 116, (no. 29), pp. 8534-44, 2012/Jul/26. | Journal Article
 
Electrophysiological-metabolic modeling of microbes: applications in fuel cells and environment analysis.
Fontus, Max and Ortoleva, Peter J
Methods in molecular biology (Clifton, N.J.), vol. 881, pp. 411-31, 2012. | Journal Article
 
Hierarchical Order Parameters for Macromolecular Assembly Simulations I: Construction and Dynamical Properties of Order Parameters.
Singharoy, Abhishek⋅Singharoy, Abhishek⋅Sereda, Yuriy⋅Sereda, Yuriy⋅Ortoleva, Peter J and Ortoleva, Peter J
Journal of chemical theory and computation, vol. 8, (no. 4), pp. 1379-1392, April 10, 2012. | Journal Article
 
Macromolecular Systems Understood through Multiscale and Enhanced Sampling Techniques
Ortoleva, Peter J⋅Keyes, Tom and Tuckerman, Mark
The journal of physical chemistry. B, vol. 116, (no. 29), pp. 8336, 2012-Jul-26. | Journal Article
 
Multiscale macromolecular simulation: role of evolving ensembles.
Singharoy, A⋅Joshi, H and Ortoleva, Peter J
Journal of chemical information and modeling, vol. 52, (no. 10), pp. 2638-49, 2012/Oct/22. | Journal Article
 
Nanosystem self-assembly pathways discovered via all-atom multiscale analysis.
Pankavich, Stephen and Ortoleva, Peter J
The journal of physical chemistry. B, vol. 116, (no. 29), pp. 8355-62, 2012/Jul/26. | Journal Article
 
Simulating microbial systems: addressing model uncertainty/incompleteness via multiscale and entropy methods.
Singharoy, A⋅Joshi, H⋅Cheluvaraja, S⋅Miao, Yinglong⋅Brown, D and Ortoleva, Peter J
Methods in molecular biology (Clifton, N.J.), vol. 881, pp. 433-67, 2012. | Journal Article
 
Space warping order parameters and symmetry: application to multiscale simulation of macromolecular assemblies.
Singharoy, Abhishek⋅Joshi, Harshad⋅Miao, Yinglong and Ortoleva, Peter J
The journal of physical chemistry. B, vol. 116, (no. 29), pp. 8423-34, 2012/Jul/26. | Journal Article
2011
A molecular dynamics study of loop fluctuation in human papillomavirus type 16 virus-like particles: a possible indicator of immunogenicity.
Joshi, Harshad⋅Cheluvaraja, Srinath⋅Somogyi, Endre⋅Brown, Darron R and Ortoleva, Peter J
Vaccine, vol. 29, (no. 51), pp. 9423-30, 2011/Nov/28. | Journal Article
 
Electrometabolomic Modeling of Microbes: Applications in Fuel Cells and Environment Analysis
Fontus, Max⋅Fontus, Max⋅Ortoleva, Peter and Ortoleva, Peter
Journal of Biotech Research, vol. 3, pp. 37-50, 2011. | Journal Article
 
MULTISCALE BORN-OPPENHEIMER THEORY OF COLLECTIVE ELECTRON-NUCLEAR DYNAMICS IN NANOSYSTEMS
Shreif, Zeina and Ortoleva, Peter J
Journal of Theoretical & Computational Chemistry, vol. 10, (no. 5), pp. 605-614, 2011. | Journal Article
 
Multiscale simulation of microbe structure and dynamics.
Joshi, Harshad⋅Singharoy, Abhishek⋅Sereda, Yuriy V⋅Cheluvaraja, Srinath C and Ortoleva, Peter J
Progress in biophysics and molecular biology, vol. 107, (no. 1), pp. 200-17, 2011/Oct. | Journal Article
 
Order parameters for macromolecules: application to multiscale simulation.
Singharoy, A⋅Cheluvaraja, S and Ortoleva, Peter J
The Journal of chemical physics, vol. 134, (no. 4), pp. 044104, 2011/Jan/28. | Journal Article
 
Order Parameters for Multiscale Simulation of Bio-Nanosystems
Singharoy, Abhishek and Ortoleva, Peter
Biophysical Journal, vol. 100, (no. 3), pp. 402a, 2011. | Journal Article
 
Scaling behavior of quantum nanosystems: emergence of quasi-particles, collective modes, and mixed exchange symmetry states.
Shreif, Zeina and Ortoleva, Peter J
The Journal of chemical physics, vol. 134, (no. 10), pp. 104106, 2011/Mar/14. | Journal Article
 
Thermal, Chemical and Mechanical Stability of HPV L1 VLP Vaccines: A Multiscale All-Atom Simulation Study
Joshi, Harshad and Ortoleva, Peter
Biophysical Journal, vol. 100, (no. 3), pp. 196a, 2011. | Journal Article
2010
All-atom multiscale simulation of cowpea chlorotic mottle virus capsid swelling.
Miao, Yinglong⋅Miao, Yinglong⋅Johnson, John E⋅Johnson, John E⋅Ortoleva, Peter J and Ortoleva, Peter J
The journal of physical chemistry. B, vol. 114, (no. 34), pp. 11181-95, 2010/Sep/2. | Journal Article
 
Alternative splicing regulatory network reconstruction from exon array data.
Qu, Kun⋅Yesnik, Anastasia M and Ortoleva, Peter J
Journal of theoretical biology, vol. 263, (no. 4), pp. 471-80, 2010/Apr/21. | Journal Article
 
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⋅Tuncay, Kağan⋅Ortoleva, Peter J and Meile, Christof
Journal of contaminant hydrology, vol. 112, (no. 1-4), pp. 130-40, 2010/Mar/1. | Journal Article
 
Multiscale analytic continuation approach to nanosystem simulation: applications to virus electrostatics.
Singharoy, Abhishek⋅Yesnik, Anastasia M and Ortoleva, Peter J
The Journal of chemical physics, vol. 132, (no. 17), pp. 174112, 2010/May/7. | Journal Article
 
Multiscaling for systems with a broad continuum of characteristic lengths and times: Structural transitions in nanocomposites
Pankavich, Stephen and Ortoleva, P.
Journal of Mathematical Physics, vol. 51, (no. 6), Jun 2010. | Journal Article
 
Scaling behavior of electronic excitations in assemblies of molecules with degenerate ground states.
Fan, H-J⋅Perkins, C and Ortoleva, Peter J
The journal of physical chemistry. A, vol. 114, (no. 5), pp. 2213-20, 2010/Feb/11. | Journal Article
 
Thermal nanostructure: an order parameter multiscale ensemble approach.
Cheluvaraja, S and Ortoleva, Peter J
The Journal of chemical physics, vol. 132, (no. 7), pp. 075102, 2010/Feb/21. | Journal Article
 
Viral structural transition mechanisms revealed by multiscale molecular dynamics/order parameter extrapolation simulation
Miao, Yinglong and Ortoleva, Peter J
Biopolymers, vol. 93, (no. 1), pp. 61-73, 2010. | Journal Article