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#shared first authorship, *corresponding author
  1. Z. She, C. E. Castro, and G. Arya*, "Conformational Dynamics of Mechanically Compliant DNA Nanostructures from Coarse-Grained Molecular Dynamics Simulations, ACS Nano, in press (2017) [Supporting information].

  2. T.-Y. Tang and G. Arya*, "Anisotropic three-particle interactions between spherical polymer-grafted nanoparticles in a polymer matrix, Macromolecules, in press (2017) [Supporting information].

  3. S. E. Root, N. E. Jackson, S. Savagatrup, G. Arya*, D. J. Lipomi, "Modelling the morphology and thermomechanical behaviour of low-bandgap conjugated polymers and bulk heterojunction films," Energy & Environmental Science, in press (2017) [Supporting information].

  4. S. E. Root, S. Savagatrup, C. Pais, G. Arya*, D. J. Lipomi, "Predicting the mechanical properties of organic semiconductors using coarse-grained molecular dynamics simulations," Macromolecules, 49, 2886-94 (2016) [Supporting information].

  5. G.-M. Nam and G. Arya*, "Free energy landscape of mono and dinucleosomes: Enhanced rotational flexibility of interconnected nucleosomes," Physical Review E, 93, 032406 (2016).

  6. C. R. Murthy, B. Gao, A. R. Tao, and G. Arya*, "Dynamics of nanoparticle assembly from disjointed images of nanoparticle-polymer composites," Physical Review E, 93, 022501 (2016).

  7. A. Zaretski, S. E. Root, A. Savtchenko, E. Molokanova, A. Printz, L. Jibril, G. Arya, M. Mercola, D. Lipomi, "Metallic nanoislands on graphene as highly sensitive transducers of mechanical, biological, and optical signals," Nano Letters, 16, 1375-80 (2016) [Supporting information].

  8. G. Arya*, "Models for recovering the energy landscape of conformational transitions from single-molecule pulling experiments," Molecular Simulation, 42, 1102-15 (2016).
    Invited review article

  9. M. Y. Hamed and G. Arya, "Zinc finger protein binding to DNA: An energy perspective using molecular dynamics simulation and free energy calculations on mutants of both zinc finger domains and their specific DNA bases," Journal of Biomolecular Structure and Dynamics, 34, 919-34 (2016).

  10. T. Takahashi, B. C. Vo Ngo, L. Xiao, G. Arya, and M. J. Heller, "Molecular mechanical properties of short sequence peptide enzyme mimics," Journal of Biomolecular Structure and Dynamics, 34, 463-74 (2016).

  11. D. Meluzzi and G. Arya*, "Quantification of DNA cleavage specificity in Hi-C experiments," Nucleic Acids Research, 44, e4 (2016) [Supporting information].

  12. K. L. Gurunatha, S. Marvi, G. Arya, and A. R. Tao, "Computationally guided assembly of oriented nanocubes by modulating grafted polymer surface interactions ," Nano Letters, 15, 7377-82 (2015) [Supporting information].

  13. V. V. Singh, K. Kaufmann, J. Orozco, J. Li, M. Galarnyk, G. Arya and J. Wang, "Micromotor-based on-off fluorescence detection of sarin and soman simulants," Chemical Communications, 51, 11190-3 (2015) [Supporting information].

  14. C. R. Murthy, B. Gao, A. R. Tao, and G. Arya*, "Automated quantitative image analysis of nanoparticle assembly," Nanoscale, 7, 9793-805 (2015) [Supporting information].

  15. G. D. Hattemer and G. Arya*, "Viscoelastic properties of polymer-grafted nanoparticle composites from molecular dynamics simulations," Macromolecules, 48, 1240-55 (2015) [Supporting information].

  16. H. Kabra, Y. Hwang, H. L. Lim, M. Kar, G. Arya, and S. Varghese, "Biomimetic material-assisted delivery of human embryonic stem cell-derived cells for enhanced in vivo survival and engraftment," ACS Biomaterials Science & Engineering, 1, 7-12 (2015) [Supporting information].

  17. D. Meluzzi and G. Arya*, "Efficient estimation of contact probabilities from inter-bead distance distributions in simulated polymer chains," Journal of Physics: Condensed Matter, 27, 064120 (2015) (Invited Article).

  18. A. D. Migliori, D. E. Smith, and G. Arya*, "Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor," Journal of Molecular Biology, 426, 4002 (2014).

  19. G.-M. Nam and G. Arya*, "Torsional behavior of chromatin is modulated by rotational phasing of nucleosomes," Nucleic Acids Research, 42, 9691 (2014) [Supporting information].

  20. A. D. Migliori, N. Keller, T. I. Alam, M. Mahalingam, V. B. Rao, G. Arya*, and D. E. Smith, "Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor," Nature Communications, 5, 4173 (2014) [Supporting information].

  21. V. Agarwal, G. Arya, and J. Oswald, "Simultaneous iterative Boltzmann inversion for coarse-graining of polyurea," Macromolecules, 47, 3378 (2014).

  22. S. I. Walker, B. J.Callahan, G. Arya, J. D. Barry, T. Bhattacharya, S. Grigoryev, M. Pellegrini, K. Rippe, and S. M. Rosenberg, "Evolutionary dynamics and information hierarchies in biological systems," Annals of the New York Academy of Sciences, 1305, 1 (2013).

  23. D. Meluzzi and G. Arya*, "Recovering ensembles of chromatin conformations from contact probabilities," Nucleic Acids Research, 41, 63 (2013) [Supporting information].

  24. I. V. Dobrovolskaia and G. Arya*, "Dynamics of forced nucleosome unraveling and role of nonuniform histone-DNA interactions," Biophysical Journal, 103, 989 (2012) [Supporting information].

  25. B. V. S. Iyer and G. Arya*, "Lattice animal model of chromosome organization," Physical Review E, 86, 011911 (2012).

  26. B. Gao, G. Arya, and A. R. Tao, "Self-orienting nanocubes for the assembly of plasmonic nanojunctions," Nature Nanotechnology, 7, 433 (2012) [Supporting information].
    Commentary in Nature Nanotechnology
    Featured on the UCSD Jacobs School of Engineering website

  27. B. Arman, S. Reddy, and G. Arya*, "Viscoelastic properties and shock response of coarse-grained models of multiblock versus diblock copolymers: Insights into dissipative properties of polyurea," Macromolecules, 45, 3247 (2012) [Supporting information].

  28. A. Phadke, C. Zhang, B. Arman, C.-C Hsu, R. A. Mashelkar, A. K. Lele, M. Tauber, G. Arya, and S. Varghese, "Rapid self-healing hydrogels," Proceedings of the National Academy of Sciences (USA), 109, 4383 (2012) [Supporting information].
    Featured on the UCSD Jacobs School of Engineering website
    Featured on Scientific American science podcasts
    Highlighted by PNAS
    Highlighted by Biopolymers journal
    Selected for the Virtual Journal of Biological Physics

  29. D. Meluzzi, K. E. Olson, G. F. Dolan, G. Arya*, and U. F. Muller, "Computational prediction of efficient splice sites for trans-splicing ribozymes," RNA, 18, 590 (2012) [Supporting information].

  30. B. V. S. Iyer, M. Kenward, and G. Arya*, "Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations," BMC Biophysics, 4, 8 (2011).
    Featured article on BMC Biophysics website
    Highly accessed article on BMC Biophysics website

  31. R. Ayala, C. Zhang, D. Yang, A. Aung, Y.-S. Hwang, S. S. Shroff, F. T. C Arce, R. Lal, G. Arya, and S. Varghese, "Engineering cell-material interface for controlling stem cell adhesion, migration, and differentiation," Biomaterials, 32, 3700 (2011) [Supporting information].
    Top 25 downloaded article in Biomaterials in 2011

  32. D. Yang and G. Arya*, "Structure and binding of the H4 histone tail and the effects of lysine 16 acetylation," Physical Chemistry Chemical Physics, 13, 2911 (2011) [Supporting information].

  33. A. Maitra and G. Arya*, "Influence of pulling handles and device stiffness in single-molecule force spectroscopy," Physical Chemistry Chemical Physics, 13, 1836 (2011).
    Selected for the themed issue on Single Molecule Optical Studies of Soft and Complex matter

  34. H. L. Lim, J. C. Chuang, T. Tran, A. Aung, G. Arya*, and S. Varghese, "Dynamic electromechanical hydrogel matrices for stem cell culture," Advanced Functional Materials, 21, 55 (2011) [Supporting information].
    Featured on the Materials Views website
    Featured on the UCSD Jacobs School of Engineering website
    Featured on Chemical Engineering Progress magazine

  35. N. Sangaj, P. Kyriakakis, D. Yang, C.-W. Chang, G. Arya, and S. Varghese, "Heparin mimicking polymer promotes myogenic differentiation of muscle progenitor cells," Biomacromolecules, 11, 3294 (2010).

  36. G. Arya*, "Chain stiffness and attachment dependent attraction between polyelectrolyte-grafted colloids," Journal of Physical Chemistry B, 114, 15886 (2010) [Supporting information].

  37. I. V. Dobrovolskaia#, M. Kenward#, and G. Arya*, "Twist propagation in dinucleosome arrays," Biophysical Journal, 99, 3355 (2010) [Supporting information].

  38. A. Maitra and G. Arya*, "Model accounting for the effects of pulling-device stiffness in the analyses of single-molecule force measurements," Physical Review Letters 104, 108301 (2010) [Erratum].
    Selected for the Virtual Journal of Biological Physics

  39. G. Arya*, A. Maitra, and S. Grigoryev, "A structural perspective on the where, how, why, and what of nucleosome positioning," Journal of Biomolecular Structure and Dynamics, 27, 803 (2010).

  40. D. Meluzzi, D. E. Smith, and G. Arya*, "Biophysics of knotting," Annual Review of Biophysics 39, 349 (2010).

  41. G. Arya*, "Energetic and entropic forces governing the attraction between polyelectrolyte grafted colloids," Journal of Physical Chemistry B 113, 15760 (2009).

  42. S. Grigoryev#, G. Arya#, S. Correll, C. Woodcock, and T. Schlick, "Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions," Proceedings of the National Academy of Sciences (USA) 106, 13317 (2009) [Supporting information].
    Featured in Stanford University magazine "Biomedical Computation Review"
    UCSD Jacobs school of engineering website and magazine "Pulse"
    Selected for the Virtual Journal of Biological Physics

  43. G. Arya* and T. Schlick, "A tale of tails: how histone tails mediate chromatin compaction in different salt and linker histone environments," Journal of Physical Chemistry A 113, 4045 (2009) (Invited Article).

  44. O. J. Hehmeyer, G. Arya, A. Z. Panagiotopoulos, and I. Szleifer, "Monte Carlo simulation and molecular theory of tethered polyelectrolytes." Journal of Chemical Physics 126, 244902 (2007) [Supporting information].
    Selected for the Virtual Journal of Biological Physics

  45. G. Arya and T. Schlick, "Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo," Journal of Chemical Physics 126, 044107 (2007).
    Selected for the Virtual Journal of Biological Physics

  46. G. Arya and T. Schlick, "Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model." Proceedings of the National Academy of Sciences (USA) 103, 16236 (2006) [Supporting information].
    Selected for the Virtual Journal of Nanoscale Science and Technology,
    Selected for the Virtual Journal of Biological Physics

  47. G. Arya#, Q. Zhang#, and T. Schlick, "Flexible histone tails in a new mesoscopic oligonucleosome model," Biophysical Journal 91, 133 (2006).
    Article featured on the cover of the Biophysical journal

  48. G. Arya* and A. Z. Panagiotopoulos, "Impact of branching on the phase behavior of polymers," Macromolecules 38, 10596 (2005) [Correction].

  49. G. Arya*, J. Rottler, A. Z. Panagiotopoulos, D. J. Srolovitz, and P. M. Chaikin, "Shear ordering in thin films of spherical block copolymer," Langmuir 21, 11518 (2005).

  50. G. Arya* and A. Z. Panagiotopoulos, "Log-rolling micelles in sheared amphiphilic thin films," Physical Review Letters 95, no. 188301 (2005).
    Selected for the Virtual Journal of Nanoscale Science and Technology

  51. G. Arya and A. Z. Panagiotopoulos, "Molecular modeling of shear-induced alignment of cylindrical micelles," Computer Physics Communications 169, 262 (2005).

  52. G. Arya and A. Z. Panagiotopoulos, "Monte Carlo study of shear-induced alignment of cylindrical micelles in thin films," Physical Review E 70, 031501 (2004).
    Selected for the Virtual Journal of Nanoscale Science and Technology

  53. O. J. Hehmeyer, G. Arya, and A. Z. Panagiotopoulos, "Phase transitions of confined lattice homopolymers," Journal of Physical Chemistry B 108, 6809 (2004).

  54. G. Arya, H.-C. Chang and E. J. Maginn, "Molecular simulations of Knudsen wall-slip: effect of wall morphology," Molecular Simulation 29, 697 (2003).

  55. G. Arya, H.-C. Chang and E. J. Maginn, "Knudsen diffusivity of a hard sphere in a rough slit pore," Physical Review Letters 91, no. 026102 (2003).

  56. L. I. Kioupis, G. Arya, and E. J. Maginn, "Pressure-enthalpy driven molecular dynamics for thermodynamic property calculation II: applications," Fluid Phase Equilibria 200, 93 (2002).

  57. G. Arya, H.-C. Chang and E. J. Maginn, "A critical comparison of equilibrium, non-equilibrium and boundary-driven molecular dynamics techniques for studying transport in microporous materials," Journal of Chemical Physics 115, 8112 (2001).

  58. G. Arya, E. J. Maginn, and H.-C. Chang, "Effect of the surface energy barrier on sorbate diffusion in AlPO4-5," Journal of Physical Chemistry B 105, 2725 (2001).

  59. G. Arya, E. J. Maginn, and H.-C. Chang, "Efficient viscosity estimation from molecular dynamics simulation via momentum impulse relaxation," Journal of Chemical Physics 113, 2079 (2000).

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