* corresponding author, # equal contributions, ^ undergraduate author


40. B. Lin, T. B. Martin, A. Jayaraman*,Decreasing Polymer Flexibility Improves Wetting and Dispersion of Polymer Grafted Particles in a Chemically Identical Polymer Matrix ACS Macroletters 3, 628-632 (2014)

39. T. B. Martin, A. Jayaraman*,Effect of Matrix Bidispersity on the Morphology of Polymer Grafted Nanoparticle filled Polymer Nanocomposites J. Polymer science B: Polymer Physics (accepted) part of special issue on "Hairy Particles"

38. H. Marsh#, E. Jankowski#, A. Jayaraman*,Controlling the morphology of model conjugated thiophene oligomers through alkyl side chain length, placement and interactionsMacromolecules 47(8) 2736-47 (2014)

37. R. Elder, A. Jayaraman*,Simulation Study of the Effects of Surface Chemistry and Temperature on the Conformations of ssDNA Oligomers near Hydrophilic and Hydrophobic Surfaces , J. Chem Phys 140, 155103 (2014)

36. C. Estridge, A. Jayaraman*,Assembly of diblock copolymer functionalized spherical nanoparticles as a function of copolymer composition , J Chem Phys 140 (14), 144905 (2014)

35. J. Roberts, R. Elder, A. Neumann, A. Jayaraman, S. Bryant*,Interaction of hyaluronan binding peptides with glycosaminoglycans in poly(ethylene glycol) hydrogels Biomacromolecules 15 (4), 1132-41 (2014) link to the article

34. V. Ganesan* and A. Jayaraman*, Theory and simulation studies of effective interactions, phase behavior and morphology in polymer nanocomposites Soft matter 10, 13-38 (2014) link to the article

33. A. Seifpour, S. Dahl, A. Jayaraman*, Molecular simulation studies of assembly of DNA grafted particles: Effect of bidispersity in DNA strand length.Molecular Simulations accepted and in press


32. T. Martin and A. Jayaraman*,Identifying the ideal characteristics of the grafted polymer chain length distribution for maximizing dispersion of polymer grafted nanoparticles in a polymer matrix Macromolecules 2013, 46 (22), pp 9144.9150 link to the article

31. R. Elder, A. Jayaraman*, Structure and Thermodynamics of ssDNA oligomers near Hydrophobic and Hydrophilic Surfaces: A molecular simulation study Soft Matter 2013, 9, 11521-11533 link to the article

30. R. Elder, A. Jayaraman*, Molecular simulations of polycation-DNA binding exploring the effect of peptide chemistry and sequence in nuclear localization sequence based polycations J Phys Chem B 117(40) 11988-11999 (2013) link to the article

29. E. Jankowski#, H. Marsh#, A. Jayaraman*, Computationally linking molecular features of conjugated polymers and fullerene derivatives to bulk heterojunction morphology Macromolecules 46 (14), pp 5775-5785 (2013) (#equal contributions) link to the article

28. T. Martin and A. Jayaraman*, Polydisperse homopolymer grafts stabilize dispersions of nanoparticles in a chemically identical homopolymer matrix: A computational studySoft Matter, special issue on Emerging Investigators in Soft Matter 9, 6876-6889, (2013) link to the article

27. A. Jayaraman*, Polymer grafted nanoparticles: Effect of Chemical and Physical Heterogeneity in Grafts on Particle Assembly and Dispersion, Highlight article in special issue in J. Polymer Science B: Poly Phys, 51, 12, pp524 (2013)link to the article

26. A. Seifpour, S. Dahl, B. Lin^, A. Jayaraman*, Molecular simulation studies of assembly of DNA-functionalized particles: Effect of DNA strand sequence and composition. Molecular Simulations 39 (9) 741-753

25. T. Martin, P. Dodd^, A. Jayaraman*, Polydispersity for tuning potential of mean force between polymer grafted nanoparticles in a polymer matrix Phys. Rev. Lett. 110,018301, 2013link to the article

24. T.Martin, C. McKinney^ and A. Jayaraman*,'Effect of blockiness in the grafted monomer sequences on assembly of copolymer grafted nanoparticles: A Monte Carlo simulation study'Soft Matter 9, 155-169 2013link to the article

23. H.Marsh and A. Jayaraman*,'Morphological Studies of Blends of Conjugated Polymers and Acceptor Molecules using Langevin Dynamics Simulations ' J. Polym Sci B: Polymer Physics 51, 64-77 2013link to the article


22. R. Elder and A. Jayaraman*,'Coarse-grained simulation studies of effects of polycation architecture on structure of the polycation and polycation-polyanion complexes' Macromolecules 45 (19), pp 8083-8096 (2012) link to the article

21. R. Elder and A. Jayaraman*,'Sequence-specific recognition of cancer drug-DNA adducts by HMGB1a repair protein' Biophys J. Volume 102, Issue 10, Pages 2331.2338 (2012)
link to the article

20. A. Jayaraman* and N. Nair,'Integrating PRISM theory and Monte Carlo simulations for studying polymer functionalized particles and polymer nanocomposites' in press to Molecular Simulations special issue on New Developments in Molecular Simulations, 38, 751-761 (2012)

19. P. Dodd^, A. Jayaraman*,'Monte Carlo Simulations of Polydisperse Polymers Grafted on Spherical Surfaces' J. Polymer Science B: Polymer Physics in press (2012)
link to the article

18. R. Elder and A. Jayaraman*,'Role of Conformational Dynamics of DNA with Cisplatin and Oxaliplatin Adducts in Various Sequence Contexts on Binding of HMGB1a Protein: a Molecular Dynamics Simulation Study 'Molecular Simulation 38, 793-808 (2012)
link to the article


17. R. Elder, T. Emrick, and A. Jayaraman*,'Understanding the effect of polylysine architecture on DNA binding using molecular dynamics simulations' Biomacromolecules 12 (11), pp 3870.3879 (2011)
link to the article

16. T.Martin^#, A.Seifpour# and A. Jayaraman*,'Assembly of copolymer functionalized nanoparticles: A Monte Carlo simulation study.' Soft Matter 7,5952-5964 (2011) (# equal contributions) link to the article

15. N. Nair, N. Wentzel and A. Jayaraman*,'Effects of bidispersity on grafted chain conformation and Potential of Mean Force between Functionalized Nanoparticles in a Homopolymer Matrix: Self-Consistent PRISM Theory-Monte Carlo Simulation Study'J. Chem Phys 134, 194906 (2011) link to the article


14. N. Nair and A. Jayaraman*,'Self-Consistent PRISM Theory-Monte Carlo Simulation Studies of Copolymer Grafted Nanoparticles in a Homopolymer Matrix'Macromolecules 43 (19), pp 8251.8263 (2010) link to the article

13. A. Seifpour, P. Spicer^, N. Nair, A. Jayaraman*,'Effect of monomer sequences on conformations of copolymers grafted on spherical nanoparticles: A Monte Carlo simulation study' J. Chem. Phys. 132, 164901 (2010). link to the article

12. L. M. Hall, A. Jayaraman and K. S. Schweizer*,'Molecular Theories of Polymer Nanocomposites' invited article Current Opionion in Solid State and Materials Science 14, 8, 38-48 (2010)


11. A. Jayaraman and K. S. Schweizer*,'Effective Interactions and Self-Assembly of Hybrid Polymer Grafted Nanoparticles in a Homopolymer Matrix' Macromolecules 42,8423-8434,(2009)

10. A. Jayaraman* and K. S. Schweizer, 'Liquid State Theory of the Structure and Phase Behavior of Polymer-Tethered Nanoparticles in Dense Suspensions, Melts and Nanocomposites ' (invited article) Molecular Simulation 35, 838-845 (2009)


9. A. Jayaraman and K. S. Schweizer*,'Effective interactions, structure and phase behavior of lightly tethered nanoparticles in polymer melt' Macromolecules 41(23) 9430-9438 (2008)

8. A. Jayaraman and K. S. Schweizer*, `Effect of number and placement of polymer tethers on the structure of concentrated solutions and melts of hybrid nanoparticles ' Langmuir 24(19) 11119-11130 (2008)

7. A. Jayaraman and K. S. Schweizer*, `Structure and assembly of dense solutions and melts of single tethered nanoparticles' J. Chem. Phys. 128 164904 (2008)
This also appears in Virtual Journal of Nanoscale Science & Technology


6. A. Jayaraman, C. K. Hall* and J. Genzer, `Computer simulation study of probe-target hybridization in model DNA microarrays: Effect of probe surface density and target concentration'J. Chem. Phys. 127, 144912 (2007)
This also appears in Virtual Journal of Biological Physics

5. A. Jayaraman, E. E. Santiso, C. K. Hall* and J. Genzer, 'Theoretical study of kinetics of zipping in biomimetic polymers' Phys. Rev. E 76, 011915 (2007)
This also appears in Virtual Journal of Biological Physics


4. A. Jayaraman, C. K. Hall* and J. Genzer, 'Computer Simulation Study of Molecular Recognition in Model DNA Microarrays' Biophys. J. 91, 2227 (2006)


3. A. Striolo, A. Jayaraman, C. K. Hall, and J. Genzer, 'Adsorption of comb copolymers on weakly-attractive solid surfaces' J.Chem. Phys., 123, 064710 (2005)
This also appears in Virtual Journal of Biological Physics

2. A. Jayaraman, C. K. Hall*, and J. Genzer, 'Computer simulation study of pattern transfer in AB diblock copolymer film adsorbed on a heterogeneous surface' J. Chem. Phys.,123 124702 (2005)

1. A. Jayaraman, C. K. Hall*, and J. Genzer, 'Designing Pattern-Recognition Surfaces for Selective Adsorption of Copolymer Sequences Using Lattice Monte Carlo Simulation' , Phys. Rev. Lett., 94, 078103 (2005)
This also appears in Virtual Journal of Biological Physics

* corresponding author