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Items: 1 to 50 of 69

1.

The empirical relationship between nonstandard economic behaviors.

Dean M, Ortoleva P.

Proc Natl Acad Sci U S A. 2019 Aug 13;116(33):16262-16267. doi: 10.1073/pnas.1821353116. Epub 2019 Jul 26.

PMID:
31350346
2.

Amphiphile self-assembly dynamics at the solution-solid interface reveal asymmetry in head/tail desorption.

Castillo HD, Espinosa-Duran JM, Dobscha JR, Ashley DC, Debnath S, Hirsch BE, Schrecke SR, Baik MH, Ortoleva PJ, Raghavachari K, Flood AH, Tait SL.

Chem Commun (Camb). 2018 Sep 6;54(72):10076-10079. doi: 10.1039/c8cc04465a.

PMID:
30083691
3.

Multiscale Molecular Dynamics Approach to Energy Transfer in Nanomaterials.

Espinosa-Duran JM, Sereda YV, Abi-Mansour A, Ortoleva P.

J Chem Theory Comput. 2018 Feb 13;14(2):916-928. doi: 10.1021/acs.jctc.7b00702. Epub 2018 Feb 2.

PMID:
29191013
4.

Multiscale time-dependent density functional theory: Demonstration for plasmons.

Jiang J, Abi Mansour A, Ortoleva PJ.

J Chem Phys. 2017 Aug 7;147(5):054102. doi: 10.1063/1.4994896.

PMID:
28789546
5.

Exposure to and recall of violence reduce short-term memory and cognitive control.

Bogliacino F, Grimalda G, Ortoleva P, Ring P.

Proc Natl Acad Sci U S A. 2017 Aug 8;114(32):8505-8510. doi: 10.1073/pnas.1704651114. Epub 2017 Jul 24.

6.

Reverse Coarse-Graining for Equation-Free Modeling: Application to Multiscale Molecular Dynamics.

Abi Mansour A, Ortoleva PJ.

J Chem Theory Comput. 2016 Nov 8;12(11):5541-5548. Epub 2016 Oct 24.

PMID:
27631340
7.

Multiscale Modeling in the Clinic: Drug Design and Development.

Clancy CE, An G, Cannon WR, Liu Y, May EE, Ortoleva P, Popel AS, Sluka JP, Su J, Vicini P, Zhou X, Eckmann DM.

Ann Biomed Eng. 2016 Sep;44(9):2591-610. doi: 10.1007/s10439-016-1563-0. Epub 2016 Feb 17. Review.

8.

Implicit Time Integration for Multiscale Molecular Dynamics Using Transcendental Padé Approximants.

Abi Mansour A, Ortoleva PJ.

J Chem Theory Comput. 2016 Apr 12;12(4):1965-71. doi: 10.1021/acs.jctc.5b01232. Epub 2016 Mar 16.

PMID:
26845510
9.

Pathos & Ethos: Emotions and Willingness to Pay for Tobacco Products.

Bogliacino F, Codagnone C, Veltri GA, Chakravarti A, Ortoleva P, Gaskell G, Ivchenko A, Lupiáñez-Villanueva F, Mureddu F, Rudisill C.

PLoS One. 2015 Oct 20;10(10):e0139542. doi: 10.1371/journal.pone.0139542. eCollection 2015.

10.

Broad spectrum assessment of the epitope fluctuation--Immunogenicity hypothesis.

Grosch JS, Yang J, Shen A, Sereda YV, Ortoleva PJ.

Vaccine. 2015 Nov 4;33(44):5945-9. doi: 10.1016/j.vaccine.2015.06.111. Epub 2015 Jul 14.

PMID:
26187254
11.

Prospective on multiscale simulation of virus-like particles: Application to computer-aided vaccine design.

Abi Mansour A, Sereda YV, Yang J, Ortoleva PJ.

Vaccine. 2015 Nov 4;33(44):5890-6. doi: 10.1016/j.vaccine.2015.05.099. Epub 2015 Jun 11. Review.

PMID:
26073014
12.

Early stage P22 viral capsid self-assembly mediated by scaffolding protein: atom-resolved model and molecular dynamics simulation.

Jiang J, Yang J, Sereda YV, Ortoleva PJ.

J Phys Chem B. 2015 Apr 23;119(16):5156-62. doi: 10.1021/acs.jpcb.5b00303. Epub 2015 Apr 9.

PMID:
25815608
13.

Multiscale Factorization Method for Simulating Mesoscopic Systems with Atomic Precision.

Abi Mansour A, Ortoleva PJ.

J Chem Theory Comput. 2014 Feb 11;10(2):518-523. Epub 2014 Jan 9.

14.

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

Sereda YV, Ortoleva PJ.

J Chem Phys. 2014 Apr 7;140(13):134104. doi: 10.1063/1.4869860.

PMID:
24712777
15.

Energy transfer between a nanosystem and its host fluid: a multiscale factorization approach.

Sereda YV, Espinosa-Duran JM, Ortoleva PJ.

J Chem Phys. 2014 Feb 21;140(7):074102. doi: 10.1063/1.4864200.

PMID:
24559333
16.

Epitope fluctuations in the human papillomavirus are under dynamic allosteric control: a computational evaluation of a new vaccine design strategy.

Singharoy A, Polavarapu A, Joshi H, Baik MH, Ortoleva P.

J Am Chem Soc. 2013 Dec 11;135(49):18458-68. doi: 10.1021/ja407489r. Epub 2013 Nov 25.

PMID:
24199651
17.

Epitope engineering and molecular metrics of immunogenicity: a computational approach to VLP-based vaccine design.

Joshi H, Lewis K, Singharoy A, Ortoleva PJ.

Vaccine. 2013 Oct 1;31(42):4841-7. doi: 10.1016/j.vaccine.2013.07.075. Epub 2013 Aug 9.

PMID:
23933338
18.

Hierarchical Multiscale Modeling of Macromolecules and their Assemblies.

Ortoleva P, Singharoy A, Pankavich S.

Soft Matter. 2013 Apr 28;9(16):4319-4335.

19.

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

Sereda YV, Ortoleva PJ.

Physica A. 2013 Feb 15;392(4):628-638.

20.

Multiscale macromolecular simulation: role of evolving ensembles.

Singharoy A, Joshi H, Ortoleva PJ.

J Chem Inf Model. 2012 Oct 22;52(10):2638-49. doi: 10.1021/ci3002952. Epub 2012 Sep 28.

21.

Macromolecular systems understood through multiscale and enhanced sampling techniques.

Ortoleva PJ, Keyes T, Tuckerman M.

J Phys Chem B. 2012 Jul 26;116(29):8335-6. doi: 10.1021/jp304524b. No abstract available.

PMID:
22831487
22.

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

Singharoy A, Sereda Y, Ortoleva PJ.

J Chem Theory Comput. 2012 Apr 10;8(4):1379-1392. Epub 2012 Mar 13.

23.

Simulating microbial systems: addressing model uncertainty/incompleteness via multiscale and entropy methods.

Singharoy A, Joshi H, Cheluvaraja S, Miao Y, Brown D, Ortoleva P.

Methods Mol Biol. 2012;881:433-67. doi: 10.1007/978-1-61779-827-6_15.

PMID:
22639222
24.

Electrophysiological-metabolic modeling of microbes: applications in fuel cells and environment analysis.

Fontus M, Ortoleva P.

Methods Mol Biol. 2012;881:411-31. doi: 10.1007/978-1-61779-827-6_14.

PMID:
22639221
25.

Discovering free energy basins for macromolecular systems via guided multiscale simulation.

Sereda YV, Singharoy AB, Jarrold MF, Ortoleva PJ.

J Phys Chem B. 2012 Jul 26;116(29):8534-44. doi: 10.1021/jp2126174. Epub 2012 Mar 30.

26.

Nanosystem self-assembly pathways discovered via all-atom multiscale analysis.

Pankavich SD, Ortoleva PJ.

J Phys Chem B. 2012 Jul 26;116(29):8355-62. doi: 10.1021/jp210407e. Epub 2012 Mar 21.

27.

Space warping order parameters and symmetry: application to multiscale simulation of macromolecular assemblies.

Singharoy A, Joshi H, Miao Y, Ortoleva PJ.

J Phys Chem B. 2012 Jul 26;116(29):8423-34. doi: 10.1021/jp2119247. Epub 2012 Mar 9.

28.

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

Joshi H, Cheluvaraja S, Somogyi E, Brown DR, Ortoleva P.

Vaccine. 2011 Nov 28;29(51):9423-30. doi: 10.1016/j.vaccine.2011.10.039. Epub 2011 Oct 24.

PMID:
22027487
29.

Multiscale simulation of microbe structure and dynamics.

Joshi H, Singharoy A, Sereda YV, Cheluvaraja SC, Ortoleva PJ.

Prog Biophys Mol Biol. 2011 Oct;107(1):200-17. doi: 10.1016/j.pbiomolbio.2011.07.006. Epub 2011 Jul 23.

30.

Scaling behavior of quantum nanosystems: emergence of quasi-particles, collective modes, and mixed exchange symmetry states.

Shreif Z, Ortoleva P.

J Chem Phys. 2011 Mar 14;134(10):104106. doi: 10.1063/1.3560450.

PMID:
21405155
31.

Order parameters for macromolecules: application to multiscale simulation.

Singharoy A, Cheluvaraja S, Ortoleva P.

J Chem Phys. 2011 Jan 28;134(4):044104. doi: 10.1063/1.3524532.

32.

All-atom multiscale simulation of cowpea chlorotic mottle virus capsid swelling.

Miao Y, Johnson JE, Ortoleva PJ.

J Phys Chem B. 2010 Sep 2;114(34):11181-95. doi: 10.1021/jp102314e.

33.
34.

Multiscale analytic continuation approach to nanosystem simulation: applications to virus electrostatics.

Singharoy A, Yesnik AM, Ortoleva P.

J Chem Phys. 2010 May 7;132(17):174112. doi: 10.1063/1.3424771.

35.

Thermal nanostructure: an order parameter multiscale ensemble approach.

Cheluvaraja S, Ortoleva P.

J Chem Phys. 2010 Feb 21;132(7):075102. doi: 10.1063/1.3316793.

36.

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

King EL, Tuncay K, Ortoleva P, Meile C.

J Contam Hydrol. 2010 Mar 1;112(1-4):130-40. doi: 10.1016/j.jconhyd.2009.12.002. Epub 2009 Dec 21.

PMID:
20097442
37.

Scaling behavior of electronic excitations in assemblies of molecules with degenerate ground states.

Fan HJ, Perkins C, Ortoleva PJ.

J Phys Chem A. 2010 Feb 11;114(5):2213-20. doi: 10.1021/jp908441s.

PMID:
20085246
38.

Alternative splicing regulatory network reconstruction from exon array data.

Qu K, Yesnik AM, Ortoleva PJ.

J Theor Biol. 2010 Apr 21;263(4):471-80. doi: 10.1016/j.jtbi.2009.12.025. Epub 2010 Jan 5.

PMID:
20043923
39.

Liquid-crystal transitions: a first-principles multiscale approach.

Shreif Z, Pankavich S, Ortoleva P.

Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Sep;80(3 Pt 1):031703. Epub 2009 Sep 10.

PMID:
19905127
40.

Viral structural transition mechanisms revealed by multiscale molecular dynamics/order parameter extrapolation simulation.

Miao Y, Ortoleva PJ.

Biopolymers. 2010 Jan;93(1):61-73. doi: 10.1002/bip.21299.

PMID:
19728362
41.

Self-assembly of nanocomponents into composite structures: derivation and simulation of Langevin equations.

Pankavich S, Shreif Z, Miao Y, Ortoleva P.

J Chem Phys. 2009 May 21;130(19):194115. doi: 10.1063/1.3134683.

PMID:
19466829
42.

Deriving principles of microbiology by multiscaling laws of molecular physics.

Ortoleva P, Adhangale P, Cheluvaraja S, Fontus M, Shreif Z.

IEEE Eng Med Biol Mag. 2009 Mar-Apr;28(2):70-9. doi: 10.1109/MEMB.2009.932389. Erratum in: IEEE Eng Med Biol Mag. 2009 May-Jun;28(3):65.

PMID:
19349253
43.

In silico Geobacter sulfurreducens metabolism and its representation in reactive transport models.

King EL, Tuncay K, Ortoleva P, Meile C.

Appl Environ Microbiol. 2009 Jan;75(1):83-92. doi: 10.1128/AEM.01799-08. Epub 2008 Nov 14.

44.

Molecular dynamics/order parameter extrapolation for bionanosystem simulations.

Miao Y, Ortoleva PJ.

J Comput Chem. 2009 Feb;30(3):423-37. doi: 10.1002/jcc.21071.

45.

Stochastic dynamics of bionanosystems: Multiscale analysis and specialized ensembles.

Pankavich S, Miao Y, Ortoleva J, Shreif Z, Ortoleva P.

J Chem Phys. 2008 Jun 21;128(23):234908. doi: 10.1063/1.2931572.

46.

Multiscale theory of collective and quasiparticle modes in quantum nanosystems.

Ortoleva P, Iyengar SS.

J Chem Phys. 2008 Apr 28;128(16):164716. doi: 10.1063/1.2877226.

PMID:
18447488
47.

Understanding stem cell differentiation through self-organization theory.

Qu K, Ortoleva P.

J Theor Biol. 2008 Feb 21;250(4):606-20. Epub 2007 Oct 23.

PMID:
18076908
48.

Transcriptional regulatory networks via gene ontology and expression data.

Tuncay K, Ensman L, Sun J, Haidar AA, Stanley F, Trelinski M, Ortoleva P.

In Silico Biol. 2007;7(1):21-34.

PMID:
17688426
49.

Chromosome segregation in Escherichia coli division: a free energy-driven string model.

Fan J, Tuncay K, Ortoleva PJ.

Comput Biol Chem. 2007 Aug;31(4):257-64. Epub 2007 May 22.

PMID:
17631415
50.

Transcriptional regulatory network discovery via multiple method integration: application to e. coli K12.

Sun J, Tuncay K, Haidar AA, Ensman L, Stanley F, Trelinski M, Ortoleva P.

Algorithms Mol Biol. 2007 Mar 30;2:2. doi: 10.1186/1748-7188-2-2.

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