Publications

Found 93 results
Type [ Year(Desc)]
2016
G-M Nam, and G Arya. "Free-energy landscape of mono- and dinucleosomes: Enhanced rotational flexibility of interconnected nucleosomes." Physical Review. E 93, no. 3 (2016).
AV Zaretski, SE Root, A Savchenko, E Molokanova, AD Printz, L Jibril, G Arya, M Mercola, and DJ Lipomi. "Metallic Nanoislands on Graphene as Highly Sensitive Transducers of Mechanical, Biological, and Optical Signals." Nano Letters 16, no. 2 (2016): 1375-1380.
G Arya. "Models for recovering the energy landscape of conformational transitions from single-molecule pulling experiments." Molecular Simulation 42, no. 13 (2016): 1102-1115.
T Takahashi, BC Vo Ngo, L Xiao, G Arya, and MJ Heller. "Molecular mechanical properties of short-sequence peptide enzyme mimics." Journal of Biomolecular Structure & Dynamics 34, no. 3 (2016): 463-474.
SE Root, S Savagatrup, CJ Pais, G Arya, and DJ Lipomi. "Predicting the Mechanical Properties of Organic Semiconductors Using Coarse-Grained Molecular Dynamics Simulations." Macromolecules 49, no. 7 (2016): 2886-2894.
D Meluzzi, and G Arya. "Quantification of DNA cleavage specificity in Hi-C experiments." Nucleic Acids Research 44, no. 1 (2016): e4.
MY Hamed, and G Arya. "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, no. 5 (2016): 919-934.
2017
T-Y Tang, and G Arya. "Anisotropic Three-Particle Interactions between Spherical Polymer-Grafted Nanoparticles in a Polymer Matrix." Macromolecules 50, no. 3 (2017): 1167-1183.
Z Shi, CE Castro, and G Arya. "Conformational Dynamics of Mechanically Compliant DNA Nanostructures from Coarse-Grained Molecular Dynamics Simulations." Acs Nano 11, no. 5 (2017): 4617-4630.
SE Root, NE Jackson, S Savagatrup, G Arya, and DJ Lipomi. "Modelling the morphology and thermomechanical behaviour of low-bandgap conjugated polymers and bulk heterojunction films." Energy Environ. Sci. 10, no. 2 (2017): 558-569.
2018
AE Marras, Z Shi, MG Lindell, RA Patton, C-M Huang, L Zhou, H-J Su, G Arya, and CE Castro. "Cation-Activated Avidity for Rapid Reconfiguration of DNA Nanodevices." Acs Nano 12, no. 9 (2018): 9484-9494.
S-W Hsu, AL Rodarte, M Som, G Arya, and AR Tao. "Colloidal Plasmonic Nanocomposites: From Fabrication to Optical Function." Chemical Reviews 118, no. 6 (2018): 3100-3120.
JT Villanueva, Q Huang, NO Fischer, G Arya, and DJ Sirbuly. "Nanofiber-Based Total Internal Reflection Microscopy for Characterizing Colloidal Systems at the Microscale." The Journal of Physical Chemistry C 122, no. 38 (2018): 22114-22124.
S Kilic, S Felekyan, O Doroshenko, I Boichenko, M Dimura, H Vardanyan, LC Bryan, G Arya, CAM Seidel, and B Fierz. "Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α." Nature Communications 9, no. 1 (2018).
2019
D Ortiz, D delToro, M Ordyan, J Pajak, J Sippy, A Catala, C-S Oh, A Vu, G Arya, M Feiss et al. "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, no. 3 (2019): 1404-1415.
D delToro, D Ortiz, M Ordyan, J Pajak, J Sippy, A Catala, C-S Oh, A Vu, G Arya, DE Smith et al. "Functional Dissection of a Viral DNA Packaging Machine's Walker B Motif." Journal of Molecular Biology 431, no. 22 (2019): 4455-4474.
T-Y Tang, Y Zhou, and G Arya. "Interfacial Assembly of Tunable Anisotropic Nanoparticle Architectures." ACS Nano 13, no. 4 (2019): 4111-4123.
J-J Song, R Bhattacharya, H Kim, J Chang, T-Y Tang, H Guo, SK Ghosh, Y Yang, Z Jiang, H Kim et al. "One-Dimensional Anomalous Diffusion of Gold Nanoparticles in a Polymer Melt." Physical Review Letters 122, no. 10 (2019).
BH-J Lee, and G Arya. "Orientational phase behavior of polymer-grafted nanocubes." Nanoscale 11, no. 34 (2019): 15939-15957.
2020
BH-J Lee, and G Arya. "Analytical van der Waals interaction potential for faceted nanoparticles." Nanoscale Horizons 5, no. 12 (2020): 1628-1642.
J Ding, JL Niedziela, D Bansal, J Wang, X He, AF May, G Ehlers, DL Abernathy, A Said, A Alatas et al. "Anharmonic lattice dynamics and superionic transition in AgCrSe2." Proceedings of the National Academy of Sciences of the United States of America 117, no. 8 (2020): 201913916.
D Meluzzi, and G Arya. "Computational Approaches for Inferring 3D Conformations of Chromatin from Chromosome Conformation Capture Data." Methods (San Diego, Calif.) 181-182 (2020): 24-34.
M DeLuca, Z Shi, CE Castro, and G Arya. "Dynamic DNA nanotechnology: toward functional nanoscale devices." Nanoscale Horizons 5, no. 2 (2020): 182-201.
Z Shi, and G Arya. "Free energy landscape of salt-actuated reconfigurable DNA nanodevices." Nucleic Acids Research 48, no. 2 (2020): 548-560.
J Wang, BH-J Lee, and G Arya. "Kinetically assembled binary nanoparticle networks." Nanoscale 12, no. 8 (2020): 5091-5102.

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