Publications

2024

Wang, Y., Zhou, Y., Yang, Q., Basak, R., Xie, Y., Le, D., … Tao, A. R. (2024). Self-assembly of nanocrystal checkerboard patterns via non-specific interactions. Nature Communications, 15(1), 3913. https://doi.org/10.1038/s41467-024-47572-2

DeLuca, M., Duke, D., Ye, T., Poirier, M., Ke, Y., Castro, C., & Arya, G. (2024). Mechanism of DNA origami folding elucidated by mesoscopic simulations. Nature Communications, 15(1), 3015. https://doi.org/10.1038/s41467-024-46998-y

Shi, C., Yang, D., Ma, X., Pan, L., Shao, Y., Arya, G., … Wang, P. (2024). A Programmable DNAzyme for the Sensitive Detection of Nucleic Acids. Angewandte Chemie (International Ed. in English), 63(12), e202320179. https://doi.org/10.1002/anie.202320179

DeLuca, M., Sensale, S., Lin, P.-A., & Arya, G. (2024). Prediction and Control in DNA Nanotechnology. ACS Applied Bio Materials, 7(2), 626–645. https://doi.org/10.1021/acsabm.2c01045

Wang, S., Lin, P.-A., DeLuca, M., Zauscher, S., Arya, G., & Ke, Y. (2024). Controlling Silicification on DNA Origami with Polynucleotide Brushes. Journal of the American Chemical Society, 146(1), 358–367. https://doi.org/10.1021/jacs.3c09310

Roozbahani, G., Colosi, P., Oravecz, A., Sorokina, E., Pfeifer, W., Shokri, S., … Castro, C. (2024). Piggybacking functionalized DNA nanostructures into live cell nuclei. bioRxiv. https://doi.org/10.1101/2023.12.30.573746

2023

Tang, Q., Sensale, S., Bond, C., Xing, J., Qiao, A., Hugelier, S., … Lakadamyali, M. (2023). Interplay between stochastic enzyme activity and microtubule stability drives detyrosination enrichment on microtubule subsets. Current Biology : CB, 33(23), 5169-5184.e8. https://doi.org/10.1016/j.cub.2023.10.068

Zhou, Y., Bore, S. L., Tao, A. R., Paesani, F., & Arya, G. (2023). Many-body potential for simulating the self-assembly of polymer-grafted nanoparticles in a polymer matrix. Npj Computational Materials, 9(1). https://doi.org/10.1038/s41524-023-01166-6

Yang, Y., Lu, Q., Chen, Y., DeLuca, M., Arya, G., Ke, Y., & Zauscher, S. (2023). Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures. Angewandte Chemie (International Ed. in English), 62(48), e202311727. https://doi.org/10.1002/anie.202311727

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

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

2022

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

2021

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