* corresponding author, # equal contributions, † undergraduate author
2024
125. V. Liao, T. Myers, A. Jayaraman*, A computational method for rapid analysis polymer structure and inverse design strategy (RAPSIDY) Soft Matter (2024) 20, 8246
124. S. Park# , T. Myers#, V. Liao, A. Jayaraman*, Self-Consistent Field Theory and Coarse-Grained Molecular Dynamics Simulations of Pentablock Copolymer Melt Phase Behavior Molecular Systems Design and Engineering (in press)
123. A. Paruchuri, Y. Wang, X. Gu, A. Jayaraman*, Machine Learning for Analyzing Atomic Force Microscopy (AFM) Images Generated from Polymer Blends, published in arXiv (2024) code on github
122. S. Kronenberger, N. Gupta, B. Gould, C. Peterson, A. Jayaraman*, Random field reconstruction of three-phase polymer structures with anisotropy from 2D-small-angle scattering data , Soft Matter (in press)
121. J. J. Madinya, S. Kronenberger, B. Gould , C. Peterson, A. Jayaraman*, Connecting features of ionomer scattering profiles to the real-space structural features of hydrophilic ionomer domains Macromolecules (2024), 57, 16, 8223–8239
120. S. Lu, A. Jayaraman*, Machine Learning for Analyses and Automation of Structural Characterization of Polymer Materials, invited review article for Progress in Polymer Science (2024) 153, 101828
119. S. V. R. Akepati, N. Gupta, A. Jayaraman*, Computational Reverse Engineering Analysis of Scattering Experiments Method for Interpretation of 2D Small-Angle Scattering Profiles (CREASE-2D) JACS Au (2024) 4, 4, 1570–1582
118. Z. Wu, A. Collins, A. Jayaraman*, Understanding self-assembly and molecular packing in methylcellulose aqueous solutions using multiscale modeling and simulation, Biomacromolecules, (2024), 25, 3, 1682–1695
2023
117. S. Lu, A. Jayaraman*, Pair-Variational Autoencoders (PairVAE) for Linking and Cross-Reconstruction of Characterization Data from Complementary Structural Characterization Techniques JACS Au (2023) 3, 9, 2510-2521
116. J. Ju, A. Jayaraman, R. Hayward*, Temperature-Sensitive Micro- and Macro-phase Separation of Hydrogen-Bonded Polystyrene-Polydimethylsiloxane Blends Macromolecules (2023) 56, 13, 4991–5000
115. N. Gupta, A. Jayaraman*, Computational Approach for Structure Generation of Anisotropic Particles (CASGAP) with Targeted Distributions of Particle Design and Orientational Order, Nanoscale (accepted)
114. Z. Wu, J. Wu, Q. Michaudel*, A. Jayaraman*, Investigating the hydrogen bond-induced self-assembly of polysulfamides using molecular simulations and experiments, Macromolecules (2023) 56, 13, 5033–5049
113. P. Taylor#, S. Kronenberger#, A. Kloxin, A. Jayaraman*, Effects of Solvent Conditions on the Self-Assembly of Heterotrimeric Collagen-Like Peptide (CLP) Triple Helices: A Coarse-Grained Simulation Study Soft Matter (2023),19, 4939-4953
112. Y. Ma, C. M. Heil, G. Nagy, W. Heller, Y. An, A. Jayaraman, B. Bharti*, Synergistic role of temperature and salinity in aggregation of nonionic surfactant coated silica nanoparticles, Langmuir 2023 39, 16, 5917–5928
111. C. M. Heil, Y. Ma, B. Bharti, A. Jayaraman*, Computational Reverse-Engineering Analysis for Scattering Experiments for Form Factor and Structure Factor Determination (‘P(q) and S(q) CREASE’) JACS Au 2023, 3, 3, 889–904
110. C. M. Heil , A. Patil , B. Vanthournout , S. Singla , M. Bleuel , J-J. Song , Z. Hu , N. Gianneschi , M. Shawkey , S. Sinha , A. Dhinojwala*, A. Jayaraman*, Mechanism of Structural Colors in Binary Mixtures of Colloidal Nanoparticle-based Supraballs Science Advances 2023, Vol 9, Issue 21
2022
109. Z. Wu, A. Jayaraman*, Machine learning enhanced computational reverse-engineering analysis for scattering experiments (CREASE) for analyzing fibrillar structures in polymer solutions, Macromolecules 2022, 55, 24, 11076–11091
108. C. M. Heil, A. Jayaraman*, Polymer solution structure and dynamics within pores in hexagonally close-packed nanoparticles, Soft Matter 2022,18, 8175-8187
107. S. Lu, B. Montz, T. Emrick, A. Jayaraman*, Self-supervised machine learning model for analysis of nanowire morphologies from transmission electron microscopy images Digital Discovery 2022, 1, 816 – 833
106. A. Kulshreshtha, A. Jayaraman*, Phase Behavior and Morphology of Blends containing Associating Polymers: Insights from Liquid State Theory and Molecular Simulations, Macromolecules 2022, 55, 20, 9297–9311
105. A. Patil#, C. M. Heil#, B. Vanthournout, S. Singla, Z. Hu, J. Ilavsky, N. C. Gianneschi, M. D. Shawkey, S. K. Sinha, A. Jayaraman,* and Ali Dhinojwala,* Modeling structural colors from disordered one-component supraballs using combined experimental and simulation techniques ACS Materials Letters 2022, 4, 9, 1848–1854
104. U. Kapoor, A. Jayaraman*, Impact of Polydopamine Nanoparticle Surface Pattern and Roughness on Interactions with Poly (ethylene glycol) in Aqueous Solution: A Multiscale Modeling and Simulation Study, J. Phys. Chem. B. 2022, 126, 33, 6301–6313
103. C. M. Heil, A. Patil, A. Dhinojwala, A. Jayaraman*, Computational Reverse-Engineering Analysis for Scattering Experiments (CREASE) with Machine Learning Enhancement to Determine Structure of Nanoparticle Mixtures and Solutions, ACS Central Science 2022, 8, 7, 996–1007
102. P. A. Taylor, A. M. Kloxin*, A. Jayaraman*, Impact of collagen-like peptide (CLP) heterotrimeric triple helix design on helical thermal stability and hierarchical assembly: A coarse-grained molecular dynamics simulation study, Soft Matter 2022,18, 3177-3192
101. A. Kulshreshtha, R. Hayward, A. Jayaraman*, Impact of Composition and Placement of Hydrogen Bonding Groups along Polymer Chains on Blend Phase Behavior: Coarse-Grained Molecular Dynamics Simulation Study, Macromolecules 2022, 55, 7, 2675–2690
100. A. Patil #, C. M. Heil #, B. Vanthournout, M. Bleuel, S. Singla, Z. Hu,6 N. C. Gianneschi, M. D. Shawkey, S. K. Sinha, A. Jayaraman*, A. Dhinojwala*, Structural Color Production in Melanin-based Disordered Colloidal Nanoparticle Assemblies in Spherical Confinement, Advanced Optical Materials, 2022, 10, 5, 2102162
2021
99. S. Lu, A. Jayaraman*, Effect of nanorod physical roughness on the aggregation and percolation of nanorods in polymer nanocomposites, ACS Macro Letters (2021) 10 (11), 1416–1422
98. U. Kapoor#, A. Kulshreshtha#, A. Jayaraman*, Understanding the Effect of Heterogeneous Particle Functionalization on Graft-Matrix Wetting and Structure in Polymer Nanocomposites Containing Grafted Nanoparticles Using Multiscale Modeling and Simulation, ACS Applied Polymer Materials (2021) 3 (11), 5642–5655
97. Z. Ye, Z. Wu, A. Jayaraman*,Computational Reverse-Engineering Analysis for Scattering Experiments CREASE) on Vesicles Assembled from Amphiphilic Macromolecular Solutions, JACS Au (2021) 1 (11), 1925–1936
96. C. M. Heil, A. Jayaraman*, Computational reverse-engineering analysis for scattering experiments of assembled binary mixture of nanoparticles ACS Materials Au (2021) 1 (2), 140–156
95. M. G. Wessels, A. Jayaraman*, Machine Learning Enhanced Computational Reverse Engineering Analysis for Scattering Experiments (CREASE) to Determine Structures in Amphiphilic Polymer Solutions, ACS Polymers Au (2021) 1, 3, 153–164
94. X. Zhou, X. Gong, W. Cao, C. J. Forman, J. Okatawiec, L. d’Alba, H. Sun, M. P. Thompson, Z. Hu, U. Kapoor, N. C. McCallum, O. Farha, A. Jayaraman, M. D. Shawkey, and N. C. Gianneschi*, Anisotropic Synthetic Allomelanin Materials via Solid State Polymerization of Self-Assembled 1, 8-Dihydroxynaphthalene Dimers , Angewandte Chemie International Edition 60, 32, 17464-17471 (2021)
93. A. Jayaraman*, A. Kulshreshtha, P. Taylor, A. Prhashanna, Coarse-Grained Modeling and Simulations of Thermoresponsive Biopolymers and Polymer Nanocomposites with Specific and Directional Interactions, Foundations of Molecular Modeling and Simulations: Select Papers from FOMMS 2018; Spring Nature (2021)
92. S. Lu#, Z. Wu#, A. Jayaraman*, Molecular Modeling and Simulation of Polymer Nanocomposites with Nanorod Fillers J. Phys Chem B. (2021) 125, 9, 2435-2449
91. P. Cummings, C. McCabe, C. Iacovella, A. Ledeczi, E. Jankowski, A. Jayaraman, J. Palmer, E. Maginn, S. Glotzer, J. Anderson, I. Siepmann, J. Potoff, R. Matsumoto, J. Gilmer, R. DeFever, R. Singh, B. Crawford, Open-Source Molecular Modeling Software in Chemical Engineering Focusing on the Molecular Simulation Design Framework, AIChE Journal 67, 3, e17206 (2021)
90. A. M. Hilderbrand, P. A. Taylor, 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 (2021) 17, 1985-1998
89. W. Cao, X. Zhou, N. C. McCallum, Z. Hu, Q. Z. Ni, U. Kapoor, C. M. Heil, K. S. Cay, T. Zand, A. J. Mantanona, A. Jayaraman, A. Dhinojwala, D. D. Deheyn, M. D. Shawkey, M. D. Burkart, J. D. Rinehart, and N. C. Gianneschi*, Unraveling the Structure and Function of Melanin Through Synthesis, J. Am. Chem. Soc. (2021) 143, 7, 2622-2637
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 (2020) 54, 2, 797-811
87. M. Wessels, A. Jayaraman*, Computational Reverse Engineering Analysis of Scattering Experiments (CREASE) on Amphiphilic Block Polymer Solutions: Cylindrical and Fibrillar Assembly Macromolecules (2020) 54,2, 783-796
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) 12(11) 2764
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, K. Modica†, 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
2019
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 https://doi.org/10.1002/polb.24780
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
2018
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
2017
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
2016
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
2015
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. Mongocopa#, 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
2014
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
2013
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
2012
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
2011
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
2010
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)
2009
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)
2008
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
2007
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
2006
4. A. Jayaraman, C. K. Hall* and J. Genzer, ‘Computer Simulation Study of Molecular Recognition in Model DNA Microarrays’ Biophys. J. 91, 2227 (2006)
2005
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
