Publications

Tang, T. Y., & Arya, G. (2017). Anisotropic Three-Particle Interactions between Spherical Polymer-Grafted Nanoparticles in a Polymer Matrix. Macromolecules, 50(3), 1167–1183. https://doi.org/10.1021/acs.macromol.6b01936

Root, S. E., Jackson, N. E., Savagatrup, S., Arya, G., & Lipomi, D. J. (2017). Modelling the morphology and thermomechanical behaviour of low-bandgap conjugated polymers and bulk heterojunction films. Energy & Environmental Science, 10(2), 558–569. https://doi.org/10.1039/c6ee03456j

Arya, G. (2016). Models for recovering the energy landscape of conformational transitions from single-molecule pulling experiments. Molecular Simulation, 42(13), 1102–1115. https://doi.org/10.1080/08927022.2015.1123257

Hamed, M. Y., & Arya, G. (2016). 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 & Dynamics, 34(5), 919–934. https://doi.org/10.1080/07391102.2015.1068224

Root, S. E., Savagatrup, S., Pais, C. J., Arya, G., & Lipomi, D. J. (2016). Predicting the Mechanical Properties of Organic Semiconductors Using Coarse-Grained Molecular Dynamics Simulations. Macromolecules, 49(7), 2886–2894. https://doi.org/10.1021/acs.macromol.6b00204

Nam, G. M., & Arya, G. (2016). Free-energy landscape of mono- and dinucleosomes: Enhanced rotational flexibility of interconnected nucleosomes. Physical Review E, 93(3). https://doi.org/10.1103/PhysRevE.93.032406

Murthy, C. R., Gao, B., Tao, A. R., & Arya, G. (2016). Dynamics of nanoparticle assembly from disjointed images of nanoparticle-polymer composites. Physical Review E, 93(2). https://doi.org/10.1103/PhysRevE.93.022501

Zaretski, A. V., Root, S. E., Savchenko, A., Molokanova, E., Printz, A. D., Jibril, L., … Lipomi, D. J. (2016). Metallic Nanoislands on Graphene as Highly Sensitive Transducers of Mechanical, Biological, and Optical Signals. Nano Letters, 16(2), 1375–1380. https://doi.org/10.1021/acs.nanolett.5b04821

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