Publications

Found 90 results
[ Type(Asc)] Year
Journal Article
BVS Iyer, M Kenward, and G Arya. "Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations." Bmc Biophysics 4, no. 1 (2011): 8.
N Sangaj, P Kyriakakis, D Yang, C-W Chang, G Arya, and S Varghese. "Heparin mimicking polymer promotes myogenic differentiation of muscle progenitor cells." Biomacromolecules 11, no. 12 (2010): 3294-3300.
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.
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).
Z Shi, and G Arya. "Free energy landscape of salt-actuated reconfigurable DNA nanodevices." Nucleic Acids Research 48, no. 2 (2020): 548-560.
G Arya, Q Zhang, and T Schlick. "Flexible histone tails in a new mesoscopic oligonucleosome model." Biophysical Journal 91, no. 1 (2006): 133-150.
SI Walker, BJ Callahan, G Arya, JD Barry, T Bhattacharya, S Grigoryev, M Pellegrini, K Rippe, and SM Rosenberg. "Evolutionary dynamics and information hierarchies in biological systems." Annals of the New York Academy of Sciences 1305, no. 1 (2013): 1-17.
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.
SA Grigoryev, G Arya, S Correll, CL Woodcock, and T Schlick. "Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions." Proceedings of the National Academy of Sciences of the United States of America 106, no. 32 (2009): 13317-13322.
AD Migliori, N Keller, TI Alam, M Mahalingam, VB Rao, G Arya, and DE Smith. "Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor." Nature Communications 5 (2014).
R Ayala, C Zhang, D Yang, Y Hwang, A Aung, SS Shroff, FT Arce, R Lal, G Arya, and S Varghese. "Engineering the cell-material interface for controlling stem cell adhesion, migration, and differentiation." Biomaterials 32, no. 15 (2011): 3700-3711.
G Arya. "Energetic and Entropic Forces Governing the Attraction between Polyelectrolyte-Grafted Colloids." Journal of Physical Chemistry B 113, no. 48 (2009): 15760-15770.
G Arya, EJ Maginn, and H-C Chang. "Efficient viscosity estimation from molecular dynamics simulation via momentum impulse relaxation." The Journal of Chemical Physics 113, no. 6 (2000): 2079-2087.
G Arya, and T Schlick. "Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo." The Journal of Chemical Physics 126, no. 4 (2007): 044107.
D Meluzzi, and G Arya. "Efficient estimation of contact probabilities from inter-bead distance distributions in simulated polymer chains." Journal of Physics. Condensed Matter : an Institute of Physics Journal 27, no. 6 (2015): 064120.
G Arya, EJ Maginn, and H-C Chang. "Effect of the Surface Energy Barrier on Sorbate Diffusion in AlPO4-5." Journal of Physical Chemistry B 105, no. 14 (2001): 2725-2735.
CR Murthy, B Gao, AR Tao, and G Arya. "Dynamics of nanoparticle assembly from disjointed images of nanoparticle-polymer composites." Physical Review. E 93, no. 2 (2016).
I V. Dobrovolskaia, and G Arya. "Dynamics of forced nucleosome unraveling and role of nonuniform histone-DNA interactions." Biophysical Journal 103, no. 5 (2012): 989-998.
HL Lim, JC Chuang, T Tran, A Aung, G Arya, and S Varghese. "Dynamic Electromechanical Hydrogel Matrices for Stem Cell Culture." Advanced Functional Materials 21, no. 1 (2011): 55-63.
M DeLuca, Z Shi, CE Castro, and G Arya. "Dynamic DNA nanotechnology: toward functional nanoscale devices." Nanoscale Horizons 5, no. 2 (2020): 182-201.
G Arya, H-C Chang, and EJ Maginn. "A critical comparison of equilibrium, non-equilibrium and boundary-driven molecular dynamics techniques for studying transport in microporous materials." The Journal of Chemical Physics 115, no. 17 (2001): 8112-8124.
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.
KL Gurunatha, S Marvi, G Arya, and AR Tao. "Computationally Guided Assembly of Oriented Nanocubes by Modulating Grafted Polymer–Surface Interactions." Nano Letters 15, no. 11 (2015): 7377-7382.
D Meluzzi, KE Olson, GF Dolan, G Arya, and UF Muller. "Computational prediction of efficient splice sites for trans-splicing ribozymes." Rna (New York, N.Y.) 18, no. 3 (2012): 590-602.
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.

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