Publications

Pajak, J., Dill, E., Reyes-Aldrete, E., White, M. A., Kelch, B. A., Jardine, P. J., … Morais, M. C. (2021). Atomistic basis of force generation, translocation, and coordination in a viral genome packaging motor. Nucleic Acids Research, 49(11), 6474–6488. https://doi.org/10.1093/nar/gkab372

Woodson, M., Pajak, J., Mahler, B. P., Zhao, W., Zhang, W., Arya, G., … Morais, M. C. (2021). A viral genome packaging motor transitions between cyclic and helical symmetry to translocate dsDNA. Science Advances, 7(19), eabc1955. https://doi.org/10.1126/sciadv.abc1955

Pajak, J., Atz, R., Hilbert, B. J., Morais, M. C., Kelch, B. A., Jardine, P. J., & Arya, G. (2021). Viral packaging ATPases utilize a glutamate switch to couple ATPase activity and DNA translocation. Proceedings of the National Academy of Sciences of the United States of America, 118(17), e2024928118. https://doi.org/10.1073/pnas.2024928118

Pajak, J., Arya, G., & Smith, D. (n.d.). Biophysics of DNA Packaging. In M. Feiss (Ed.), Encyclopedia of Virology, 4th Edition. Elsevier. https://doi.org/10.1016/B978-0-12-809633-8.20966-7

Wang, D., Yu, L., Huang, C.-M., Arya, G., Chang, S., & Ke, Y. (2021). Programmable Transformations of DNA Origami Made of Small Modular Dynamic Units. Journal of the American Chemical Society, 143(5), 2256–2263. https://doi.org/10.1021/jacs.0c10576

Lee, B.-J., & Arya, G. (2020). Analytical van der Waals interaction potential for faceted nanoparticles. Nanoscale Horizons, 5(12), 1628–1642. https://doi.org/10.1039/d0nh00526f

Meluzzi, D., & Arya, G. (2020). Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data. Methods (San Diego, Calif.), 181–182, 24–34. https://doi.org/10.1016/j.ymeth.2019.08.008

Ding, J., Niedziela, J. L., Bansal, D., Wang, J., He, X., May, A. F., … Delaire, O. (2020). Anharmonic lattice dynamics and superionic transition in AgCrSe ₂. Proceedings of the National Academy of Sciences, 117(8), 3930–3937. https://doi.org/10.1073/pnas.1913916117

Deluca, M., Shi, Z., Castro, C. E., & Arya, G. (2020). Dynamic DNA nanotechnology: Toward functional nanoscale devices. Nanoscale Horizons, 5(2), 182–201. https://doi.org/10.1039/c9nh00529c

Wang, J., Lee, B.-J., & Arya, G. (2020). Kinetically assembled binary nanoparticle networks. Nanoscale, 12(8), 5091–5102. https://doi.org/10.1039/c9nr09900j

Shi, Z., & Arya, G. (2020). Free energy landscape of salt-actuated reconfigurable DNA nanodevices. Nucleic Acids Research, 48(2), 548–560. https://doi.org/10.1093/nar/gkz1137

delToro, D., Ortiz, D., Ordyan, M., Pajak, J., Sippy, J., Catala, A., … Feiss, M. (2019). Functional Dissection of a Viral DNA Packaging Machine's Walker B Motif. Journal of Molecular Biology, 431(22), 4455–4474. https://doi.org/10.1016/j.jmb.2019.08.012

Lee, B.-J., & Arya, G. (2019). Orientational phase behavior of polymer-grafted nanocubes. Nanoscale, 11(34), 15939–15957. https://doi.org/10.1039/c9nr04859f

Tang, T.-Y., Zhou, Y., & Arya, G. (2019). Interfacial Assembly of Tunable Anisotropic Nanoparticle Architectures. ACS Nano, 13(4), 4111–4123. https://doi.org/10.1021/acsnano.8b08733

Song, J.-J., Bhattacharya, R., Kim, H., Chang, J., Tang, T.-Y., Guo, H., … Sinha, S. K. (2019). One-Dimensional Anomalous Diffusion of Gold Nanoparticles in a Polymer Melt. Physical Review Letters, 122(10), 107802. https://doi.org/10.1103/physrevlett.122.107802

Ortiz, D., delToro, D., Ordyan, M., Pajak, J., Sippy, J., Catala, A., … Catalano, C. E. (2019). Evidence that a catalytic glutamate and an 'Arginine Toggle' act in concert to mediate ATP hydrolysis and mechanochemical coupling in a viral DNA packaging motor. Nucleic Acids Research, 47(3), 1404–1415. https://doi.org/10.1093/nar/gky1217

Villanueva, J. T., Huang, Q., Fischer, N. O., Arya, G., & Sirbuly, D. J. (2018). Nanofiber-Based Total Internal Reflection Microscopy for Characterizing Colloidal Systems at the Microscale. Journal of Physical Chemistry C, 122(38), 22114–22124. https://doi.org/10.1021/acs.jpcc.8b03167

Marras, A. E., Shi, Z., Lindell, M. G., Patton, R. A., Huang, C.-M., Zhou, L., … Castro, C. E. (2018). Cation-Activated Avidity for Rapid Reconfiguration of DNA Nanodevices. ACS Nano, 12(9), 9484–9494. https://doi.org/10.1021/acsnano.8b04817

Hsu, S.-W., Rodarte, A. L., Som, M., Arya, G., & Tao, A. R. (2018). Colloidal Plasmonic Nanocomposites: From Fabrication to Optical Function. Chemical Reviews, 118(6), 3100–3120. https://doi.org/10.1021/acs.chemrev.7b00364

Kilic, S., Felekyan, S., Doroshenko, O., Boichenko, I., Dimura, M., Vardanyan, H., … Fierz, B. (2018). Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α. Nature Communications, 9(1), 235. https://doi.org/10.1038/s41467-017-02619-5

Shi, Z., Castro, C. E., & Arya, G. (2017). Conformational Dynamics of Mechanically Compliant DNA Nanostructures from Coarse-Grained Molecular Dynamics Simulations. ACS Nano, 11(5), 4617–4630. https://doi.org/10.1021/acsnano.7b00242

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