Publications

Meluzzi, D., & Arya, G. (2016). Quantification of DNA cleavage specificity in Hi-C experiments. Nucleic Acids Research, 44(1), e4. https://doi.org/10.1093/nar/gkv820

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. https://doi.org/10.1080/07391102.2015.1039586

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. https://doi.org/10.1021/acs.nanolett.5b02748

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. https://doi.org/10.1039/c5cc04120a

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. https://doi.org/10.1039/c5nr00809c

Hattemer, G. D., & Arya, G. (2015). Viscoelastic properties of polymer-grafted nanoparticle composites from molecular dynamics simulations. Macromolecules, 48(4), 1240–1255. https://doi.org/10.1021/ma502086c

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. https://doi.org/10.1088/0953-8984/27/6/064120

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. https://doi.org/10.1021/ab500021a

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. https://doi.org/10.1016/j.jmb.2014.09.023

Nam, G.-M., & Arya, G. (2014). Torsional behavior of chromatin is modulated by rotational phasing of nucleosomes. Nucleic Acids Research, 42(15), 9691–9699. https://doi.org/10.1093/nar/gku694

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. https://doi.org/10.1038/ncomms5173

Agrawal, V., Arya, G., & Oswald, J. (2014). Simultaneous iterative boltzmann inversion for coarse-graining of polyurea. Macromolecules, 47(10), 3378–3389. https://doi.org/10.1021/ma500320n

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. https://doi.org/10.1111/nyas.12140

Meluzzi, D., & Arya, G. (2013). Recovering ensembles of chromatin conformations from contact probabilities. Nucleic Acids Research, 41(1), 63–75. https://doi.org/10.1093/nar/gks1029

Dobrovolskaia, I. V., & Arya, G. (2012). Dynamics of Forced Nucleosome Unraveling and Role of Nonuniform Histone-DNA Interactions. Biophysical Journal, 103(5), 989–998. https://doi.org/10.1016/j.bpj.2012.07.043

Iyer, B. V. S., & Arya, G. (2012). Lattice animal model of chromosome organization. Physical Review E  Statistical, Nonlinear, and Soft Matter Physics, 86(1). https://doi.org/10.1103/PhysRevE.86.011911

Gao, B., Arya, G., & Tao, A. R. (2012). Self-orienting nanocubes for the assembly of plasmonic nanojunctions. Nature Nanotechnology, 7(7), 433–437. https://doi.org/10.1038/nnano.2012.83

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. https://doi.org/10.1021/ma3001934

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. https://doi.org/10.1073/pnas.1201122109

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. https://doi.org/10.1261/rna.029884.111

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. https://doi.org/10.1016/j.biomaterials.2011.02.004

Iyer, B. V., Kenward, M., & Arya, G. (2011). Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations. Bmc Biophysics, 4, 8. https://doi.org/10.1186/2046-1682-4-8

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. https://doi.org/10.1039/c0cp01528h

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. https://doi.org/10.1039/c0cp01487g