Publications

Found 93 results
[ Type(Asc)] Year
Journal Article
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.
GD Hattemer, and G Arya. "Viscoelastic Properties of Polymer-Grafted Nanoparticle Composites from Molecular Dynamics Simulations." Macromolecules 48, no. 4 (2015): 1240-1255.
B Arman, AS Reddy, and G Arya. "Viscoelastic Properties and Shock Response of Coarse-Grained Models of Multiblock versus Diblock Copolymers: Insights into Dissipative Properties of Polyurea." Macromolecules 45, no. 7 (2012): 3247-3255.
J Pajak, R Atz, BJ Hilbert, MC Morais, BA Kelch, PJ Jardine, and G Arya. "Viral packaging ATPases utilize a glutamate switch to couple ATPase activity and DNA translocation." Proc Natl Acad Sci U S A 118, no. 17 (2021).
M Woodson, J Pajak, BP Mahler, W Zhao, W Zhang, G Arya, MA White, PJ Jardine, and MC Morais. "A viral genome packaging motor transitions between cyclic and helical symmetry to translocate dsDNA." Science Advances 7, no. 19 (2021).
I V. Dobrovolskaia, M Kenward, and G Arya. "Twist propagation in dinucleosome arrays." Biophysical Journal 99, no. 10 (2010): 3355-3364.
Y Zhou, T-Y Tang, BH-J Lee, and G Arya. "Tunable Orientation and Assembly of Polymer-Grafted Nanocubes at Fluid–Fluid Interfaces." Acs Nano 16, no. 5 (2022): 7457-7470.
G-M Nam, and G Arya. "Torsional behavior of chromatin is modulated by rotational phasing of nucleosomes." Nucleic Acids Research 42, no. 15 (2014): 9691-9699.
M DeLuca, W Pfeifer, B Randoing, C-M Huang, M Poirier, C Castro, and G Arya. "Thermally Reversible Pattern Formation in Arrays of Molecular Rotors." (2022).
G Arya, and T Schlick. "A tale of tails: how histone tails mediate chromatin compaction in different salt and linker histone environments." The Journal of Physical Chemistry A 113, no. 16 (2009): 4045-4059.
D Yang, and G Arya. "Structure and binding of the H4 histone tail and the effects of lysine 16 acetylation." Physical Chemistry Chemical Physics : Pccp 13, no. 7 (2011): 2911-2921.
G Arya, A Maitra, and SA Grigoryev. "A structural perspective on the where, how, why, and what of nucleosome positioning." Journal of Biomolecular Structure & Dynamics 27, no. 6 (2010): 803-820.
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).
V Agrawal, G Arya, and J Oswald. "Simultaneous Iterative Boltzmann Inversion for Coarse-Graining of Polyurea." Macromolecules 47, no. 10 (2014): 3378-3389.
G Arya, J Rottler, AZ Panagiotopoulos, DJ Srolovitz, and PM Chaikin. "Shear Ordering in Thin Films of Spherical Block Copolymer." Langmuir : the Acs Journal of Surfaces and Colloids 21, no. 24 (2005): 11518-11527.
B Gao, G Arya, and AR Tao. "Self-orienting nanocubes for the assembly of plasmonic nanojunctions." Nature Nanotechnology 7, no. 7 (2012): 433-437.
G Arya, and T Schlick. "Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model." Proceedings of the National Academy of Sciences of the United States of America 103, no. 44 (2006): 16236-16241.
V Simões, BK Cizubu, L Harley, Y Zhou, J Pajak, NA Snyder, J Bouvette, MJ Borgnia, G Arya, A Bartesaghi et al. "Redox-sensitive E2 Rad6 controls cellular response to oxidative stress via K63-linked ubiquitination of ribosomes." Cell Reports 39, no. 8 (2022): 110860.
D Meluzzi, and G Arya. "Recovering ensembles of chromatin conformations from contact probabilities." Nucleic Acids Research 41, no. 1 (2013): 63-75.
BH-J Lee, NA Kotov, and G Arya. "Reconfigurable Chirality of DNA-Bridged Nanorod Dimers." Acs Nano 15, no. 8 (2021): 13547-13558.
A Phadke, C Zhang, B Arman, C-C Hsu, RA Mashelkar, AK Lele, MJ Tauber, G Arya, and S Varghese. "Rapid self-healing hydrogels." Proceedings of the National Academy of Sciences of the United States of America 109, no. 12 (2012): 4383-4388.
D Meluzzi, and G Arya. "Quantification of DNA cleavage specificity in Hi-C experiments." Nucleic Acids Research 44, no. 1 (2016): e4.
D Wang, L Yu, C-M Huang, G Arya, S Chang, and Y Ke. "Programmable Transformations of DNA Origami Made of Small Modular Dynamic Units." J Am Chem Soc 143, no. 5 (2021): 2256-2263.
Y Yang, Q Lu, C-M Huang, H Qian, Y Zhang, S Deshpande, G Arya, Y Ke, and S Zauscher. "Programmable site-specific functionalization of DNA origami with polynucleotide brushes." Angewandte Chemie International Edition 60, no. 43 (2021): 23241-23247.
LI Kioupis, G Arya, and EJ Maginn. "Pressure-enthalpy driven molecular dynamics for thermodynamic property calculation II: applications." Fluid Phase Equilibria 200, no. 1 (2002): 93-110.

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