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Gaurav Arya, Ph.D. - Publications

Affiliations: 
2007-2017 NanoEngineering University of California, San Diego, La Jolla, CA 
 2017- Mechanical Engineering and Materials Science Duke University, Durham, NC 
Area:
General Engineering, General Biophysics
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74 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Pajak J, Arya G. Molecular dynamics of DNA translocation by FtsK. Nucleic Acids Research. PMID 35947697 DOI: 10.1093/nar/gkac668  0.666
2022 Simões V, Cizubu BK, Harley L, Zhou Y, Pajak J, Snyder NA, Bouvette J, Borgnia MJ, Arya G, Bartesaghi A, Silva GM. Redox-sensitive E2 Rad6 controls cellular response to oxidative stress via K63-linked ubiquitination of ribosomes. Cell Reports. 39: 110860. PMID 35613580 DOI: 10.1016/j.celrep.2022.110860  0.57
2022 Zhou Y, Tang TY, Lee BH, Arya G. Tunable Orientation and Assembly of Polymer-Grafted Nanocubes at Fluid-Fluid Interfaces. Acs Nano. PMID 35452220 DOI: 10.1021/acsnano.1c10416  0.761
2022 Lee BH, Arya G. Assembly mechanism of surface-functionalized nanocubes. Nanoscale. 14: 3917-3928. PMID 35225318 DOI: 10.1039/d1nr07995f  0.494
2021 Lee BH, Kotov NA, Arya G. Reconfigurable Chirality of DNA-Bridged Nanorod Dimers. Acs Nano. PMID 34292699 DOI: 10.1021/acsnano.1c04326  0.519
2021 Pajak J, Dill E, Reyes-Aldrete E, White MA, Kelch BA, Jardine PJ, Arya G, Morais MC. Atomistic basis of force generation, translocation, and coordination in a viral genome packaging motor. Nucleic Acids Research. PMID 34050764 DOI: 10.1093/nar/gkab372  0.646
2021 Woodson M, Pajak J, Mahler BP, Zhao W, Zhang W, Arya G, White MA, Jardine PJ, Morais MC. A viral genome packaging motor transitions between cyclic and helical symmetry to translocate dsDNA. Science Advances. 7. PMID 33962953 DOI: 10.1126/sciadv.abc1955  0.623
2021 Pajak J, Atz R, Hilbert BJ, Morais MC, Kelch BA, Jardine PJ, Arya G. 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. PMID 33888587 DOI: 10.1073/pnas.2024928118  0.649
2020 Lee BH, Arya G. Analytical van der Waals interaction potential for faceted nanoparticles. Nanoscale Horizons. 5: 1628-1642. PMID 33185642 DOI: 10.1039/d0nh00526f  0.461
2020 Wang J, Lee BH, Arya G. Kinetically assembled binary nanoparticle networks. Nanoscale. PMID 32068755 DOI: 10.1039/C9Nr09900J  0.508
2020 Pajak J, Dill E, White MA, Jardine P, Morais MC, Arya G. Dynamic Interrogation of a Viral DNA Packaging Motor Complex Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.2842  0.345
2019 Shi Z, Arya G. Free energy landscape of salt-actuated reconfigurable DNA nanodevices. Nucleic Acids Research. PMID 31799631 DOI: 10.1093/Nar/Gkz1137  0.781
2019 delToro D, Ortiz D, Ordyan M, Pajak J, Sippy J, Catala A, Oh CS, Vu A, Arya G, Smith DE, Catalano CE, Feiss M. Functional Dissection of a Viral DNA Packaging Machine's Walker B Motif. Journal of Molecular Biology. PMID 31473160 DOI: 10.1016/J.Jmb.2019.08.012  0.667
2019 Meluzzi D, Arya G. Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data. Methods (San Diego, Calif.). PMID 31470090 DOI: 10.1016/J.Ymeth.2019.08.008  0.721
2019 Lee BH, Arya G. Orientational phase behavior of polymer-grafted nanocubes. Nanoscale. PMID 31417994 DOI: 10.1039/C9Nr04859F  0.531
2019 Song JJ, Bhattacharya R, Kim H, Chang J, Tang TY, Guo H, Ghosh SK, Yang Y, Jiang Z, Kim H, Russell TP, Arya G, Narayanan S, Sinha SK. One-Dimensional Anomalous Diffusion of Gold Nanoparticles in a Polymer Melt. Physical Review Letters. 122: 107802. PMID 30932658 DOI: 10.1103/Physrevlett.122.107802  0.761
2019 Tang TY, Zhou Y, Arya G. Interfacial Assembly of Tunable Anisotropic Nanoparticle Architectures. Acs Nano. PMID 30883090 DOI: 10.1021/Acsnano.8B08733  0.761
2019 Pajak J, Arya G. Novel Regulatory Mechanisms Identified in Viral DNA Packaging Proteins using Molecular Dynamics Simulations Biophysical Journal. 116. DOI: 10.1016/J.Bpj.2018.11.1854  0.399
2018 Ortiz D, delToro D, Ordyan M, Pajak J, Sippy J, Catala A, Oh CS, Vu A, Arya G, Feiss M, Smith DE, Catalano CE. 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. PMID 30541105 DOI: 10.1093/Nar/Gky1217  0.67
2018 Marras AE, Shi Z, Lindell Iii MG, Patton RA, Huang CM, Zhou L, Su HJ, Arya G, Castro CE. Cation-Activated Avidity for Rapid Reconfiguration of DNA Nanodevices. Acs Nano. PMID 30169013 DOI: 10.1021/Acsnano.8B04817  0.778
2018 Kilic S, Felekyan S, Doroshenko O, Boichenko I, Dimura M, Vardanyan H, Bryan LC, Arya G, Seidel CAM, Fierz B. Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α. Nature Communications. 9: 235. PMID 29339721 DOI: 10.1038/S41467-017-02619-5  0.377
2017 Shi Z, Castro CE, Arya G. Conformational Dynamics of Mechanically-Compliant DNA Nanostructures from Coarse-Grained Molecular Dynamics Simulations. Acs Nano. PMID 28423273 DOI: 10.1021/Acsnano.7B00242  0.793
2017 Tang T, Arya G. Anisotropic Three-Particle Interactions between Spherical Polymer-Grafted Nanoparticles in a Polymer Matrix Macromolecules. 50: 1183. DOI: 10.1021/Acs.Macromol.6B01936  0.341
2016 Nam GM, Arya G. Free-energy landscape of mono- and dinucleosomes: Enhanced rotational flexibility of interconnected nucleosomes. Physical Review. E. 93: 032406. PMID 27078389 DOI: 10.1103/Physreve.93.032406  0.394
2016 Murthy CR, Gao B, Tao AR, Arya G. Dynamics of nanoparticle assembly from disjointed images of nanoparticle-polymer composites. Physical Review. E. 93: 022501. PMID 26986370 DOI: 10.1103/Physreve.93.022501  0.302
2016 Meluzzi D, Arya G. Quantification of DNA cleavage specificity in Hi-C experiments. Nucleic Acids Research. 44: e4. PMID 26264668 DOI: 10.1093/Nar/Gkv820  0.741
2016 Hamed MY, Arya G. 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. 1-16. PMID 26196228 DOI: 10.1080/07391102.2015.1068224  0.323
2016 Arya G. Models for recovering the energy landscape of conformational transitions from single-molecule pulling experiments Molecular Simulation. 42: 1102-1115. DOI: 10.1080/08927022.2015.1123257  0.33
2016 Root SE, Savagatrup S, Pais CJ, Arya G, Lipomi DJ. Predicting the Mechanical Properties of Organic Semiconductors Using Coarse-Grained Molecular Dynamics Simulations Macromolecules. 49: 2886-2894. DOI: 10.1021/Acs.Macromol.6B00204  0.314
2015 Gurunatha KL, Marvi S, Arya G, Tao AR. Computationally Guided Assembly of Oriented Nanocubes by Modulating Grafted Polymer-Surface Interactions. Nano Letters. PMID 26457977 DOI: 10.1021/Acs.Nanolett.5B02748  0.333
2015 Meluzzi D, Arya G. 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: 064120. PMID 25563926 DOI: 10.1088/0953-8984/27/6/064120  0.735
2015 Hattemer GD, Arya G. Viscoelastic properties of polymer-grafted nanoparticle composites from molecular dynamics simulations Macromolecules. 48: 1240-1255. DOI: 10.1021/Ma502086C  0.33
2014 Migliori AD, Smith DE, Arya G. Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor. Journal of Molecular Biology. 426: 4002-17. PMID 25311860 DOI: 10.1016/J.Jmb.2014.09.023  0.388
2014 Nam GM, Arya G. Torsional behavior of chromatin is modulated by rotational phasing of nucleosomes. Nucleic Acids Research. 42: 9691-9. PMID 25100871 DOI: 10.1093/Nar/Gku694  0.394
2014 Migliori AD, Keller N, Alam TI, Mahalingam M, Rao VB, Arya G, Smith DE. Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor. Nature Communications. 5: 4173. PMID 24937091 DOI: 10.1038/Ncomms5173  0.354
2014 Agrawal V, Arya G, Oswald J. Simultaneous iterative boltzmann inversion for coarse-graining of polyurea Macromolecules. 47: 3378-3389. DOI: 10.1021/Ma500320N  0.389
2014 Meluzzi D, Arya G. Recovering Chromatin Conformations from Contact Probabilities Biophysical Journal. 106. DOI: 10.1016/J.Bpj.2013.11.500  0.755
2014 Nam G, Arya G. Torsional Behavior of Nucleosome Arrays Biophysical Journal. 106. DOI: 10.1016/J.Bpj.2013.11.454  0.407
2013 Walker SI, Callahan BJ, Arya G, Barry JD, Bhattacharya T, Grigoryev S, Pellegrini M, Rippe K, Rosenberg SM. Evolutionary dynamics and information hierarchies in biological systems. Annals of the New York Academy of Sciences. 1305: 1-17. PMID 23691975 DOI: 10.1111/Nyas.12140  0.327
2013 Meluzzi D, Arya G. Recovering ensembles of chromatin conformations from contact probabilities. Nucleic Acids Research. 41: 63-75. PMID 23143266 DOI: 10.1093/Nar/Gks1029  0.753
2013 Keller NA, Migliori AD, Arya G, Rao VB, Smith DE. Testing a structural model for viral DNA packaging motor function by optical tweezers measurements, site directed mutagenesis, and molecular dynamics calculations Proceedings of Spie - the International Society For Optical Engineering. 8810. DOI: 10.1117/12.2027158  0.396
2013 Meluzzi D, Arya G. 53 2D to 3D: interaction frequency maps to chromatin higher-order folded conformations Journal of Biomolecular Structure & Dynamics. 31: 33-33. DOI: 10.1080/07391102.2013.786487  0.743
2012 Dobrovolskaia IV, Arya G. Dynamics of forced nucleosome unraveling and role of nonuniform histone-DNA interactions. Biophysical Journal. 103: 989-98. PMID 23009848 DOI: 10.1016/J.Bpj.2012.07.043  0.792
2012 Iyer BV, Arya G. Lattice animal model of chromosome organization. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 86: 011911. PMID 23005456 DOI: 10.1103/Physreve.86.011911  0.31
2012 Gao B, Arya G, Tao AR. Self-orienting nanocubes for the assembly of plasmonic nanojunctions. Nature Nanotechnology. 7: 433-7. PMID 22683842 DOI: 10.1038/Nnano.2012.83  0.313
2012 Meluzzi D, Olson KE, Dolan GF, Arya G, Müller UF. Computational prediction of efficient splice sites for trans-splicing ribozymes. Rna (New York, N.Y.). 18: 590-602. PMID 22274956 DOI: 10.1261/Rna.029884.111  0.708
2012 Migliori A, Arya G, Smith DE. Experimental and computational studies on the DNA translocation mechanism of the T4 viral packaging motor Proceedings of Spie - the International Society For Optical Engineering. 8458. DOI: 10.1117/12.930390  0.367
2012 Arman B, Reddy AS, Arya G. Viscoelastic properties and shock response of coarse-grained models of multiblock versus diblock copolymers: Insights into dissipative properties of polyurea Macromolecules. 45: 3247-3255. DOI: 10.1021/Ma3001934  0.328
2012 Meluzzi D, Maitra A, Arya G. Extraction of Free Energy Parameters from Dynamic Single-Molecule Force-Extension Measurements Biophysical Journal. 102. DOI: 10.1016/J.Bpj.2011.11.942  0.741
2012 Arya G, Dobrovolskaia IV. Chromatin Structure and Dynamics in Response to External Forces and Torques Biophysical Journal. 102: 482a. DOI: 10.1016/J.Bpj.2011.11.2641  0.795
2011 Iyer BV, Kenward M, Arya G. Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations. Bmc Biophysics. 4: 8. PMID 21595865 DOI: 10.1186/2046-1682-4-8  0.332
2011 Yang D, Arya G. Structure and binding of the H4 histone tail and the effects of lysine 16 acetylation. Physical Chemistry Chemical Physics : Pccp. 13: 2911-21. PMID 21157623 DOI: 10.1039/C0Cp01487G  0.308
2010 Dobrovolskaia IV, Kenward M, Arya G. Twist propagation in dinucleosome arrays. Biophysical Journal. 99: 3355-64. PMID 21081084 DOI: 10.1016/J.Bpj.2010.09.055  0.784
2010 Arya G. Chain stiffness and attachment-dependent attraction between polyelectrolyte-grafted colloids. The Journal of Physical Chemistry. B. 114: 15886-96. PMID 21069987 DOI: 10.1021/Jp1029085  0.314
2010 Maitra A, Arya G. Model accounting for the effects of pulling-device stiffness in the analyses of single-molecule force measurements. Physical Review Letters. 104: 108301. PMID 20366455 DOI: 10.1103/Physrevlett.104.108301  0.314
2010 Arya G, Maitra A, Grigoryev SA. A structural perspective on the where, how, why, and what of nucleosome positioning. Journal of Biomolecular Structure & Dynamics. 27: 803-20. PMID 20232935 DOI: 10.1080/07391102.2010.10508585  0.382
2010 Meluzzi D, Smith DE, Arya G. Biophysics of knotting. Annual Review of Biophysics. 39: 349-66. PMID 20192771 DOI: 10.1146/Annurev.Biophys.093008.131412  0.738
2010 Arya G, Maitra A. Model for Harnessing the Device Stiffness in Dynamic Single-Molecule Force Spectroscopy Biophysical Journal. 98. DOI: 10.1016/J.Bpj.2009.12.983  0.317
2009 Arya G. Energetic and entropic forces governing the attraction between polyelectrolyte-grafted colloids. The Journal of Physical Chemistry. B. 113: 15760-70. PMID 19842639 DOI: 10.1021/Jp908007Z  0.335
2009 Grigoryev SA, Arya G, Correll S, Woodcock CL, Schlick T. Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions. Proceedings of the National Academy of Sciences of the United States of America. 106: 13317-22. PMID 19651606 DOI: 10.1073/Pnas.0903280106  0.368
2009 Arya G, Schlick T. A tale of tails: how histone tails mediate chromatin compaction in different salt and linker histone environments. The Journal of Physical Chemistry. A. 113: 4045-59. PMID 19298048 DOI: 10.1021/Jp810375D  0.357
2007 Hehmeyer OJ, Arya G, Panagiotopoulos AZ, Szleifer I. Monte Carlo simulation and molecular theory of tethered polyelectrolytes. The Journal of Chemical Physics. 126: 244902. PMID 17614585 DOI: 10.1063/1.2747600  0.329
2006 Arya G, Schlick T. 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: 16236-41. PMID 17060627 DOI: 10.1073/Pnas.0604817103  0.363
2006 Arya G, Zhang Q, Schlick T. Flexible histone tails in a new mesoscopic oligonucleosome model. Biophysical Journal. 91: 133-50. PMID 16603492 DOI: 10.1529/Biophysj.106.083006  0.373
2005 Arya G, Rottler J, Panagiotopoulos AZ, Srolovitz DJ, Chaikin PM. Shear ordering in thin films of spherical block copolymer. Langmuir : the Acs Journal of Surfaces and Colloids. 21: 11518-27. PMID 16285835 DOI: 10.1021/La0516476  0.335
2005 Arya G, Panagiotopoulos AZ. Impact of branching on the phase behavior of polymers Macromolecules. 38: 10596-10604. DOI: 10.1021/Ma0515376  0.309
2005 Arya G, Panagiotopoulos AZ. Molecular modeling of shear-induced alignment of cylindrical micelles Computer Physics Communications. 169: 262-266. DOI: 10.1016/J.Cpc.2005.03.060  0.336
2004 Arya G, Panagiotopoulos AZ. Monte Carlo study of shear-induced alignment of cylindrical micelles in thin films. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 70: 031501. PMID 15524524 DOI: 10.1103/Physreve.70.031501  0.327
2003 Arya G, Chang HC, Maginn EJ. Knudsen diffusivity of a hard sphere in a rough slit pore. Physical Review Letters. 91: 026102. PMID 12906494 DOI: 10.1103/Physrevlett.91.026102  0.507
2003 Arya G, Chang HC, Maginn EJ. Molecular simulations of knudsen wall-slip: Effect of wall morphology Molecular Simulation. 29: 697-709. DOI: 10.1080/0892702031000103257  0.519
2002 Kioupis LI, Arya G, Maginn EJ. Pressure-enthalpy driven molecular dynamics for thermodynamic property calculation II: Applications Fluid Phase Equilibria. 200: 93-110. DOI: 10.1016/S0378-3812(02)00015-8  0.742
2001 Arya G, Chang HC, Maginn EJ. A critical comparison of equilibrium, non-equilibrium and boundary-driven molecular dynamics techniques for studying transport in microporous materials Journal of Chemical Physics. 115: 8112-8124. DOI: 10.1063/1.1407002  0.521
2001 Arya G, Maginn EJ, Chang HC. Effect of the surface energy barrier on sorbate diffusion in A1PO4-5 Journal of Physical Chemistry B. 105: 2725-2735. DOI: 10.1021/Jp003350G  0.533
2000 Arya G, Maginn EJ, Chang HC. Efficient viscosity estimation from molecular dynamics simulation via momentum impulse relaxation Journal of Chemical Physics. 113: 2079-2087. DOI: 10.1063/1.482019  0.55
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