* corresponding author, # equal contributions, ^ undergraduate author

Group Research


90. A. M. Hilderbrand, P. A. Taylor1, F. Stanzione, M. LaRue, C. Guo, A. Jayaraman*, A. M. Kloxin*,Combining simulations and experiments for the molecular engineering of multifunctional collagen mimetic peptide-based materials, Soft Matter accepted (2020)

89.W. Cao,... N. Gianneschi*,Unraveling the Structure and Function of Melanin through Synthesis, J. Am. Chem. Soc. accepted (2020)

88. S. M. Maguire, N. M. Krook, A. Kulshreshtha, C.R. Bilchak, R. Brosnan, A.M. Pana, P. Rannou, M. Maréchal, K.Ohno, A. Jayaraman*, R. J. Composto*, Interfacial Compatibilization in Ternary Polymer Nanocomposites: Comparing Theory and Experiments Macromolecules accepted (2020)

87. M. Wessels#, A. Jayaraman*,Computational Reverse Engineering Analysis of Scattering Experiments (CREASE) on Amphiphilic Block Polymer Solutions: Cylindrical and Fibrillar Assembly Macromolecules accepted (2020)

86. U. Kapoor#, A. Kulshreshtha#, A. Jayaraman*,Development of Coarse-Grained Models for Poly(4-vinylphenol) and Poly(2-vinylpyridine): Polymer Chemistries with Hydrogen Bonding Polymers (2020) in press

85. J.L. Young, Y. Song, M. Wessels, A. Jayaraman, K. Wooley, D. Pochan*, Hierarchical Self-assembly of Poly(D-glucose carbonate) Amphiphilic Block Copolymers in Mixed Solvents, Macromolecules (2020) 53, 19, 8581-8591

84. P. A. Taylor, H. Huang, K. Kiick*, A. Jayaraman*,Placement of Tyrosine Residues Tunes the LCST-like Transition of ELP-CLP conjugates: Experiments and Simulations Molecular Systems Design and Engineering (2020) 5, 1239-1254

83. Z. Wu, D. Beltran-Villegas, A. Jayaraman*,Development of a new coarse-grained model to simulate assembly of cellulose chains due to hydrogen bonding Journal of Chem. Theory and Computation (2020) 16, 7, 4599–4614

82. P. Taylor, A. Jayaraman*,Molecular modeling and simulations of peptide-polymer conjugates. Annu. Rev. Chem. Biomol. Eng (2020) 11, 257-276

81. A. Jayaraman*, Modeling and simulation of macromolecules with hydrogen bonds: Challenges, successes and opportunities, an invited viewpoint in ACS Macro Letters (2020) 9, 656–665

80. T. E. Gartner III, C. M. Heil, A. Jayaraman*, Surface composition and ordering of binary nanoparticle mixtures in spherical confinement, Molecular Systems Design and Engineering (2020) 5, 864-875

79. U. Kapoor, A. Jayaraman*, Self-Assembly of Allomelanin Dimers and the Impact of Poly(ethylene glycol) on the Assembly: A Molecular Dynamics Simulation Study, Journal of Physical Chemistry B (2020) 124 (13), 2702-2714

78. A. Kulshreshtha, A. Jayaraman*,Dispersion and Aggregation of Polymer Grafted Particles in Polymer Nanocomposites Driven by the Hardness and Size of the Grafted Layer Tuned by Attractive Graft-Matrix Interactions Macromolecules (2020) 53, 4, 1302-1313

77. M. Wessels, A. Jayaraman*, Self-assembly of amphiphilic polymers of varying architectures near attractive surfaces, Soft Matter (2020) 16, 623-633


76. H. Kuang, T. E. Gartner, M. Dorneles de Mello, J. Guo, X. Zuo, M. Tsapatsis, A. Jayaraman and E. Kokkoli*, ssDNA-amphiphile architecture used to control dimensions of DNA nanotubes, Nanoscale (2019) 11, 19850-19861

75. D. Beltran-Villegas, M. Wessels, J.Y. Lee, Y.Song, K. Wooley*, D. Pochan*, A. Jayaraman*, Computational Reverse-Engineering Analysis for Scattering Experiments (CREASE) on Amphiphilic Block Polymer Solutions J. Am. Chem. Soc. , (2019) 141, 37, 14916-14930

74. M. Xiao#, Z. Hu#, T. E. Gartner III,# X. Yang, W. Li, A. Jayaraman*, N. C. Gianneschi*, M. D. Shawkey*, A. Dhinojwala*, Experimental and theoretical evidence for molecular forces driving surface segregation in photonic colloidal assemblies , Science Advances, (2019) Vol. 5, no. 9, eaax1254

73. T. E. Gartner, III, F. M. Haque, A. M. Gomi, S. M. Grayson*, M. J. A. Hore* and A. Jayaraman*, Scaling Exponent and Effective Interactions in Linear and Cyclic Polymer Solutions: Theory, Simulations, and Experiments Macromolecules (2019) 52, 4579-4589

72. D. J. Beltran-Villegas, D. Intriago†, K. Kim, N. Behaptu, J. D. Londono, A. Jayaraman*, Coarse-grained molecular dynamics simulations of α-1,3-glucan, Soft Matter, (2019) 15, 4669-4681

71. M. Wessels, A. Jayaraman*, Molecular dynamics simulation study of linear, bottlebrush, and star-like amphiphilic block polymer assembly in solution, Soft Matter, (2019) 15, 3987-3998

70. M. Dong#, M.G. Wessels#, J. Y.Lee, L. Su, H. Wang, R. A. Letteri, Y.Song, Y.N.Lin, Y. Chen, R Li, D. J. Pochan,* A. Jayaraman,* and K. L. Wooley*, Experiments and Simulations of Complex Sugar based Coil brush Block Polymer Nanoassemblies in Aqueous Solution, ACS Nano, (2019) 13, 5147-5162

69. A. Kulshreshtha, A. Jayaraman*, Impact of hydrogen bonding interactions on graft-matrix wetting and structure in polymer nanocomposites Macromolecules 52 (7), 2725-2735, (2019).

68. A. Prhashanna#, P. A. Taylor#, J. Qin#, K. L. Kiick*, A. Jayaraman*, Effect of peptide sequence on LCST-like transition of elastin-like peptides (ELP) and elastin-b-collagen-like peptide (ELP-CLP) conjugates: Simulations and experiments Biomacromolecules 20 (3), 1178, (2019) DOI: 10.1021/acs.biomac.8b01503

67. A. Prhashanna, A. Jayaraman*, Melting Thermodynamics of Oligonucleic Acids Conjugated with Relatively Solvophobic Linear Polymers: A Coarse-Grained Molecular Simulation Study, J. Polymer Science B. Polymer Physics

66. T. E. Gartner, III, A. Jayaraman*, Modeling and Simulations of Polymers: A Roadmap, invited perspective article to Macromolecules 2019, 52 (3), pp 755–786


65. I. Lyubimov , M. G. Wessels , A. Jayaraman*, Molecular dynamics simulation and PRISM theory study of assembly in solutions of amphiphilic bottlebrush block copolymers, Macromolecules 51 (19), 7586 (2018)

64. T. B. Martin*, T. Gartner, R. Jones, C. Synder*, A. Jayaraman* "pyPRISM: A Computational Tool for Liquid-State Theory Calculations of Macromolecular Materials" Macromolecules 51 (8), pp 2906–2922 (2018) Link to the code Link to the paper

63. D. J. Beltran-Villegas#, I. Lyubimov#, A. Jayaraman* " Molecular dynamics simulations and PRISM theory study of solutions of nanoparticles and triblock copolymers with solvophobic end blocks" Molecular Systems Design and Engineering 3, 453-472 (2018)

62. J. Condon, A. Jayaraman* "Development of Coarse-Grained Model of Collagen-like Peptide (CLP) for Studies of CLP Triple Helix Melting " J. Phys. Chem B 122 (6), pp 1929–1939 (2018)

61. D. J. Beltran-Villegas, A. Jayaraman* Assembly of amphiphilic block copolymers and nanoparticles in solution: Coarse-grained molecular simulation study J. Chem & Engg. Data 63 (7), pp 2351 (2018)

60. T. Gartner III., A. Jayaraman* Macromolecular ‘size’ and ‘hardness’ drives structure in solvent-swollen blends of linear, cyclic, and star polymers Soft Matter 2018, 14, pp 411 - 423


59. J. Condon, A. Jayaraman* "Effect of Oligonucleic Acid (ONA) Design on Assembly of ONA-Star Polymer Conjugates: A Coarse-Grained Molecular Simulation Study" Soft Matter 2017,13, 6770-6783 link to the article

58. I. Lyubimow, D. Beltran-Villegas, A. Jayaraman* "PRISM theory study of amphiphilic block copolymer solutions with varying copolymer sequence and composition" Macromolecules 2017,50 (18), pp 7419-7431 link to the article

57. K. Modica#^, T. B. Martin#, A. Jayaraman* ""Effect of Polymer Architecture on the Structure and Interactions of Polymer Grafted Particles: Theory and Simulations" Macromolecules 2017, 50 (12),4854 link to the article

56. J. Condon#, T. B. Martin#, A. Jayaraman* "Effect of Conjugation on Phase Transitions in Thermoresponsive Polymers: An Atomistic and Coarse-Grained Simulation Study" Soft Matter 2017, 13, 2907-2918 link to the article


55. T. B. Martin, A. Jayaraman* "Using Theory and Simulations to Calculate Effective Interactions in Polymer Nanocomposites with Polymer Grafted Nanoparticles" Macromolecules (2016), 49 (24), pp 9684

54. T. Gartner III,T. H. Epps III*, A. Jayaraman* "Leveraging Gibbs Ensemble Molecular Dynamics and Hybrid Monte Carlo/Molecular Dynamics for Efficient Study of Phase Equilibria Journal of Chemical Theory and Computation 2016, 12 (11), pp 5501 link to the article

53. A. Ghobadi, A. Jayaraman* Effects of Polymer Conjugation on Hybridization Thermodynamics of Oligonucleic Acids J.Phys Chem B. (2016) 120 (36), pp 9788 link to the article

52. F.Stanzione, A. Jayaraman* Hybrid Atomistic and Coarse-Grained Molecular Dynamics Simulations of Polyethylene glycol (PEG) in Explicit Water J. Phys Chem B. (2016) 120, 4160-4173 link to the article

51. T.B. Martin, A. Jayaraman*Tuning the Wetting-Dewetting and Dispersion-Aggregation Transitions in Polymer Nanocomposites using Composition of Graft and Matrix Polymers Materials Research Express Special Issue on Emerging Investigators in Materials Science, (2016), 3, 034001 link to the article

50. A. Ghobadi, A. Jayaraman* Effect of backbone chemistry on hybridization thermodynamics of oligonucleic acids: a coarse-grained molecular dynamics simulation study Soft matter (2016) 12, 2276-87 link to the article

49. A. Ghobadi, R. Letteri, S. Parelkar, Y. Zhao, D. Chan-Seng, T.Emrick, A.Jayaraman, Dispersing zwitterions into comb polymers for non-viral transfection: experiments and molecular simulation, Biomacromolecules (2016), 17(2),546-57 link to the article

48. H. S. Marsh, A. Jayaraman* Effect of side chain length on the morphology of blends of 2,5-bis(3-alkylthiophen-2-yl)thieno[3,2-b]thiophene (BTTT) oligomers and fullerene derivatives J. Poly Sci. B. Polymer Physics 2016,54,1, 89-97


47. F. Stanzione, A. Jayaraman* 'Computational design of oligopeptide containing poly(ethylene glycol) brushes for stimuli-responsive drug delivery' J. Phys Chem B. 2015, 119 (42), 13309-13320

46. T. B. Martin#, K. I. Mongocopai#, R. Ashkar, P. Butler, R. Krishnamoorti*, A. Jayaraman* 'Wetting-Dewetting and Dispersion-Aggregation Transitions are Distinct in Mixtures of Polymer Grafted Nanoparticles and a Chemically Dissimilar Polymer Matrix' J. Am. Chem. Soc. 2015, 137 (33), pp 10624–10631

45. R.M. Elder*, J. Pfaendtner, A. Jayaraman* 'Effect of hydrophobic and hydrophilic surfaces on double stranded DNA stability' Biomacromolecules (2015) 16 (6), pp 1862

44. H.S. Marsh, A.Jayaraman* 'Effect of additive length and chemistry on the morphology of blends of conjugated thiophenes and fullerene derivative acceptor molecules' J. Polymer Sciece B: Polymer Physics 2015 DOI: 10.1002/polb.23739

43. C. E. Estridge, A. Jayaraman* 'Diblock copolymer grafted particles as compatibilizers for immiscible homopolymer blends' ACS Macroletters (2015) 4 (2), pp 155 link to the article

42. C. E. Estridge, A. Jayaraman*,Effect of homopolymer matrix on diblock copolymer grafted nanoparticle conformation and potential of mean force: A molecular simulation study, J Polymer Science B: Polymer Physics 2015,53,76-88 link to the article Cover art


41. Lei Zhang, Feng Liu, Ying Diao, Hilary, S. Marsh, Nicholas S. Colella, Arthi Jayaraman, Thomas P. Russell, Stefan C. B. Mannsfeld*, and Alejandro L. Briseno* “The Good Host: Formation of Discrete 1-D Fullerene ‘Autobahnen’ in Well-Ordered BTTT Oligomers” J. Am. Chem. Soc. 136 (52), 18120 (2014) link to the article

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 for 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' 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 (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