Meluzzi, D., & Arya, G. (2016). Quantification of DNA cleavage specificity in Hi-C experiments. Nucleic Acids Research, 44(1), e4.

Takahashi, T., Vo Ngo, B. C., Xiao, L., Arya, G., & Heller, M. J. (2016). Molecular mechanical properties of short-sequence peptide enzyme mimics. Journal of Biomolecular Structure & Dynamics, 34(3), 463–474.


Gurunatha, K. L., Marvi, S., Arya, G., & Tao, A. R. (2015). Computationally Guided Assembly of Oriented Nanocubes by Modulating Grafted Polymer-Surface Interactions. Nano Letters, 15(11), 7377–7382.

Singh, V. V., Kaufmann, K., Orozco, J., Li, J., Galarnyk, M., Arya, G., & Wang, J. (2015). Micromotor-based on-off fluorescence detection of sarin and soman simulants. Chemical Communications, 51(56), 11190–11193.

Oswald, J., Arya, G., Cui, Z., & Brinson, L. C. (2015). Molecular Dynamics (MD) and Coarse Grain Simulation of High Strain-Rate Elastomeric Polymers (HSREP): Molecular and Coarse-Grained Methods for Microstructure-Property Relations in HSREP. In R. Barsoum (Ed.), Elastomeric Polymers with High Rate Sensitivity Applications in Blast, Shockwave, and Penetration Mechanics. William Andrew.

Murthy, C. R., Gao, B., Tao, A. R., & Arya, G. (2015). Automated quantitative image analysis of nanoparticle assembly. Nanoscale, 7(21), 9793–9805.

Hattemer, G. D., & Arya, G. (2015). Viscoelastic properties of polymer-grafted nanoparticle composites from molecular dynamics simulations. Macromolecules, 48(4), 1240–1255.

Meluzzi, D., & Arya, G. (2015). Efficient estimation of contact probabilities from inter-bead distance distributions in simulated polymer chains. Journal of Physics. Condensed Matter : An Institute of Physics Journal, 27(6), 064120.

Kabra, H., Hwang, Y., Lim, H. L., Kar, M., Arya, G., & Varghese, S. (2015). Biomimetic Material-Assisted Delivery of Human Embryonic Stem Cell Derivatives for Enhanced In Vivo Survival and Engraftment. Acs Biomater Sci Eng, 1(1), 7–12.


Migliori, A. D., Smith, D. E., & Arya, G. (2014). Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor. Journal of Molecular Biology, 426(24), 4002–4017.

Nam, G.-M., & Arya, G. (2014). Torsional behavior of chromatin is modulated by rotational phasing of nucleosomes. Nucleic Acids Research, 42(15), 9691–9699.

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

Agrawal, V., Arya, G., & Oswald, J. (2014). Simultaneous iterative boltzmann inversion for coarse-graining of polyurea. Macromolecules, 47(10), 3378–3389.


Walker, S. I., Callahan, B. J., Arya, G., Barry, J. D., Bhattacharya, T., Grigoryev, S., … Rosenberg, S. M. (2013). Evolutionary dynamics and information hierarchies in biological systems. Annals of the New York Academy of Sciences, 1305, 1–17.

Meluzzi, D., & Arya, G. (2013). Recovering ensembles of chromatin conformations from contact probabilities. Nucleic Acids Research, 41(1), 63–75.


Dobrovolskaia, I. V., & Arya, G. (2012). Dynamics of Forced Nucleosome Unraveling and Role of Nonuniform Histone-DNA Interactions. Biophysical Journal, 103(5), 989–998.

Iyer, B. V. S., & Arya, G. (2012). Lattice animal model of chromosome organization. Physical Review E  Statistical, Nonlinear, and Soft Matter Physics, 86(1).

Gao, B., Arya, G., & Tao, A. R. (2012). Self-orienting nanocubes for the assembly of plasmonic nanojunctions. Nature Nanotechnology, 7(7), 433–437.

Arman, B., Reddy, A. S., & Arya, G. (2012). Viscoelastic properties and shock response of coarse-grained models of multiblock versus diblock copolymers: Insights into dissipative properties of polyurea. Macromolecules, 45(7), 3247–3255.

Phadke, A., Zhang, C., Arman, B., Hsu, C.-C., Mashelkar, R. A., Lele, A. K., … Varghese, S. (2012). Rapid self-healing hydrogels. Proc Natl Acad Sci U S A, 109(12), 4383–4388.

Meluzzi, D., Olson, K. E., Dolan, G. F., Arya, G., & Müller, U. F. (2012). Computational prediction of efficient splice sites for trans-splicing ribozymes. Rna (New York, N.Y.), 18(3), 590–602.


Ayala, R., Zhang, C., Yang, D., Hwang, Y., Aung, A., Shroff, S. S., … Varghese, S. (2011). Engineering the cell-material interface for controlling stem cell adhesion, migration, and differentiation. Biomaterials, 32(15), 3700–3711.

Iyer, B. V., Kenward, M., & Arya, G. (2011). Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations. Bmc Biophysics, 4, 8.

Maitra, A., & Arya, G. (2011). Influence of pulling handles and device stiffness in single-molecule force spectroscopy. Physical Chemistry Chemical Physics : Pccp, 13(5), 1836–1842.

Yang, D., & Arya, G. (2011). Structure and binding of the H4 histone tail and the effects of lysine 16 acetylation. Physical Chemistry Chemical Physics : Pccp, 13(7), 2911–2921.