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 |
0.508 |
|
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 |
0.52 |
|
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 |
0.522 |
|
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 |
0.534 |
|
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 |
0.551 |
|
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