Publications

Pfeifer, W. G., Huang, C.-M., Poirier, M. G., Arya, G., & Castro, C. E. (2023). Versatile computer-aided design of free-form DNA nanostructures and assemblies. Science Advances, 9(30), eadi0697. https://doi.org/10.1126/sciadv.adi0697

DeLuca, M., Ye, T., Poirier, M., Ke, Y., Castro, C., & Arya, G. (2023). Mechanism of DNA origami folding elucidated by mesoscopic simulations. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2023.06.20.545758

Wang, Y., Sensale, S., Pedrozo, M., Huang, C.-M., Poirier, M. G., Arya, G., & Castro, C. E. (2023). Steric Communication between Dynamic Components on DNA Nanodevices. Acs Nano, 17(9), 8271–8280. https://doi.org/10.1021/acsnano.2c12455

DeLuca, M., Pfeifer, W. G., Randoing, B., Huang, C.-M., Poirier, M. G., Castro, C. E., & Arya, G. (2023). Thermally reversible pattern formation in arrays of molecular rotors. Nanoscale, 15(18), 8356–8365. https://doi.org/10.1039/d2nr05813h

Zhou, Y., Bore, S., Tao, A., Paesani, F., & Arya, G. (2023). Many-body Potential for Simulating the Self-Assembly of Polymer-Grafted Nanoparticles in a Polymer Matrix. American Chemical Society (ACS). https://doi.org/10.26434/chemrxiv-2023-8s90g

DeLuca, M., Sensale, S., Lin, P.-A., & Arya, G. (2023). Prediction and Control in DNA Nanotechnology. Acs Applied Bio Materials. https://doi.org/10.1021/acsabm.2c01045

Pfeifer, W., Huang, C.-M., Poirier, M., Arya, G., & Castro, C. (2023). Versatile Computer Aided Design of Freeform DNA Nanostructures and Assemblies. bioRxiv. https://doi.org/10.1101/2023.03.30.535006

Zhou, Y., & Arya, G. (2022). Discovery of two-dimensional binary nanoparticle superlattices using global Monte Carlo optimization. Nature Communications, 13(1), 7976. https://doi.org/10.1038/s41467-022-35690-8

Barcus, K., Lin, P.-A., Zhou, Y., Arya, G., & Cohen, S. M. (2022). Influence of Polymer Characteristics on the Self-Assembly of Polymer-Grafted Metal-Organic Framework Particles. Acs Nano, 16(11), 18168–18177. https://doi.org/10.1021/acsnano.2c05175

Zhou, C., Yang, D., Sensale, S., Sharma, P., Wang, D., Yu, L., … Wang, P. (2022). A bistable and reconfigurable molecular system with encodable bonds. Science Advances, 8(46), eade3003. https://doi.org/10.1126/sciadv.ade3003

Pajak, J., & Arya, G. (2022). Molecular dynamics of DNA translocation by FtsK. Nucleic Acids Research, 50(15), 8459–8470. https://doi.org/10.1093/nar/gkac668

Simões, V., Cizubu, B. K., Harley, L., Zhou, Y., Pajak, J., Snyder, N. A., … Silva, G. M. (2022). Redox-sensitive E2 Rad6 controls cellular response to oxidative stress via K63-linked ubiquitination of ribosomes. Cell Rep, 39(8), 110860. https://doi.org/10.1016/j.celrep.2022.110860

Zhou, Y., Tang, T.-Y., Lee, B.-J., & Arya, G. (2022). Tunable Orientation and Assembly of Polymer-Grafted Nanocubes at Fluid-Fluid Interfaces. Acs Nano, 16(5), 7457–7470. https://doi.org/10.1021/acsnano.1c10416

Sensale, S., Sharma, P., & Arya, G. (2022). Binding kinetics of harmonically confined random walkers. Physical Review. E, 105(4–1), 044136. https://doi.org/10.1103/physreve.105.044136

Lee, B.-J., & Arya, G. (2022). Assembly mechanism of surface-functionalized nanocubes. Nanoscale, 14(10), 3917–3928. https://doi.org/10.1039/d1nr07995f

Tang, Q., Sensale, S., Bond, C., Qiao, A., Hugelier, S., Arab, A., … Lakadamyali, M. (2022). Detyrosination enrichment on microtubule subsets is established by the interplay between a stochastically-acting enzyme and microtubule stability. bioRxiv. https://doi.org/10.1101/2022.09.29.510213

Yang, Y., Lu, Q., Huang, C.-M., Qian, H., Zhang, Y., Deshpande, S., … Zauscher, S. (2021). Programmable Site-Specific Functionalization of DNA Origami with Polynucleotide Brushes. Angewandte Chemie (International Ed. in English), 60(43), 23241–23247. https://doi.org/10.1002/anie.202107829

Lee, B.-J., Kotov, N. A., & Arya, G. (2021). Reconfigurable Chirality of DNA-Bridged Nanorod Dimers. Acs Nano, 15(8), 13547–13558. https://doi.org/10.1021/acsnano.1c04326

Wang, J., Ding, J., Delaire, O., & Arya, G. (2021). Atomistic Mechanisms Underlying Non-Arrhenius Ion Transport in Superionic Conductor AgCrSe₂. Acs Applied Energy Materials, 4(7), 7157–7167. https://doi.org/10.1021/acsaem.1c01237

Kumar, V., Ko, U. H., Zhou, Y., Hoque, J., Arya, G., & Varghese, S. (2021). Microengineered Materials with Self‐Healing Features for Soft Robotics. Advanced Intelligent Systems, 3(7). https://doi.org/10.1002/aisy.202100005

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