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Gaurav Arya

Title(s)Associate Professor, Nanoengineering
SchoolAcademic Aff
Phone858-822-5542
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    Collapse Research 
    Collapse Research Activities and Funding
    Linking Kinetics, Subunit Coordination & Structure of a Viral DNA Packaging Motor
    NIH/NIGMS R01GM118817Jul 1, 2016 - Jun 30, 2020
    Role: Principal Investigator

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    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. 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. J Mol Biol. 2019 Aug 29. PMID: 31473160.
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    2. Meluzzi D, Arya G. Computational Approaches for Inferring 3D Conformations of Chromatin from Chromosome Conformation Capture Data. Methods. 2019 Aug 27. PMID: 31470090.
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    3. Lee BH, Arya G. Orientational phase behavior of polymer-grafted nanocubes. Nanoscale. 2019 Aug 16. PMID: 31417994.
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    4. Tang TY, Zhou Y, Arya G. Interfacial Assembly of Tunable Anisotropic Nanoparticle Architectures. ACS Nano. 2019 Apr 23; 13(4):4111-4123. PMID: 30883090.
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    5. 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. Phys Rev Lett. 2019 Mar 15; 122(10):107802. PMID: 30932658.
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    6. 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 Res. 2018 Dec 12. PMID: 30541105.
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    7. Marras AE, Shi Z, Lindell MG, Patton RA, Huang CM, Zhou L, Su HJ, Arya G, Castro CE. Cation-Activated Avidity for Rapid Reconfiguration of DNA Nanodevices. ACS Nano. 2018 09 25; 12(9):9484-9494. PMID: 30169013.
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    8. Hsu SW, Rodarte AL, Som M, Arya G, Tao AR. Colloidal Plasmonic Nanocomposites: From Fabrication to Optical Function. Chem Rev. 2018 03 28; 118(6):3100-3120. PMID: 29419286.
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    9. 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 HP1a. Nat Commun. 2018 01 16; 9(1):235. PMID: 29339721.
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    10. Shi Z, Castro CE, Arya G. Conformational Dynamics of Mechanically Compliant DNA Nanostructures from Coarse-Grained Molecular Dynamics Simulations. ACS Nano. 2017 05 23; 11(5):4617-4630. PMID: 28423273.
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    11. Nam GM, Arya G. Free-energy landscape of mono- and dinucleosomes: Enhanced rotational flexibility of interconnected nucleosomes. Phys Rev E. 2016 Mar; 93(3):032406. PMID: 27078389.
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    12. Murthy CR, Gao B, Tao AR, Arya G. Dynamics of nanoparticle assembly from disjointed images of nanoparticle-polymer composites. Phys Rev E. 2016 Feb; 93(2):022501. PMID: 26986370.
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    13. 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. J Biomol Struct Dyn. 2016 May; 34(5):919-34. PMID: 26196228.
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    14. Zaretski AV, Root SE, Savchenko A, Molokanova E, Printz AD, Jibril L, Arya G, Mercola M, Lipomi DJ. Metallic Nanoislands on Graphene as Highly Sensitive Transducers of Mechanical, Biological, and Optical Signals. Nano Lett. 2016 Feb 10; 16(2):1375-80. PMID: 26765039.
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    15. Gurunatha KL, Marvi S, Arya G, Tao AR. Computationally Guided Assembly of Oriented Nanocubes by Modulating Grafted Polymer-Surface Interactions. Nano Lett. 2015 Nov 11; 15(11):7377-82. PMID: 26457977.
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    16. Meluzzi D, Arya G. Quantification of DNA cleavage specificity in Hi-C experiments. Nucleic Acids Res. 2016 Jan 08; 44(1):e4. PMID: 26264668.
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    17. Singh VV, Kaufmann K, Orozco J, Li J, Galarnyk M, Arya G, Wang J. Micromotor-based on-off fluorescence detection of sarin and soman simulants. Chem Commun (Camb). 2015 Jun 30; 51(56):11190-3. PMID: 26072740.
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    18. Takahashi T, Vo Ngo BC, Xiao L, Arya G, Heller MJ. Molecular mechanical properties of short-sequence peptide enzyme mimics. J Biomol Struct Dyn. 2016; 34(3):463-74. PMID: 25921736.
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    19. Murthy CR, Gao B, Tao AR, Arya G. Automated quantitative image analysis of nanoparticle assembly. Nanoscale. 2015 Jun 07; 7(21):9793-805. PMID: 25963444.
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    20. Kabra H, Hwang Y, Lim HL, Kar M, Arya G, Varghese S. Biomimetic Material-Assisted Delivery of Human Embryonic Stem Cell Derivatives for Enhanced In Vivo Survival and Engraftment. ACS Biomater Sci Eng. 2015 Jan 12; 1(1):7-12. PMID: 26280019.
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    21. Meluzzi D, Arya G. Efficient estimation of contact probabilities from inter-bead distance distributions in simulated polymer chains. J Phys Condens Matter. 2015 Feb 18; 27(6):064120. PMID: 25563926.
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    22. Migliori AD, Smith DE, Arya G. Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor. J Mol Biol. 2014 Dec 12; 426(24):4002-4017. PMID: 25311860.
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    23. Nam GM, Arya G. Torsional behavior of chromatin is modulated by rotational phasing of nucleosomes. Nucleic Acids Res. 2014 Sep; 42(15):9691-9. PMID: 25100871.
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    24. 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. Nat Commun. 2014 Jun 17; 5:4173. PMID: 24937091.
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    25. Ahmad A, Arya G, Bansal N, Saxena AK. Stray notes on two phthirapteran species occurring on Indian grey Horn Bill, Tockus birostris Scopoli (Coraciformes: Bucerotidae). J Parasit Dis. 2015 Dec; 39(4):761-5. PMID: 26688647.
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    26. 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. Ann N Y Acad Sci. 2013 Dec; 1305:1-17. PMID: 23691975.
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    27. Kumar V, Hasan SS, Saxena AK, Arya G, Ahmed Z. Population levels of Phthiraptera on greylag goose, Anser anser (L.). Turkiye Parazitol Derg. 2013; 37(4):273-6. PMID: 24412869.
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    28. Meluzzi D, Arya G. Recovering ensembles of chromatin conformations from contact probabilities. Nucleic Acids Res. 2013 Jan 07; 41(1):63-75. PMID: 23143266.
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    29. Bansal N, Ahmad A, Arya G, Khan V, Saxena AK. Menacanthus palmai, a new species of chewing louse (Menoponidae: Amblycera: Phthiraptera) from the Coturnix coromandelica. J Parasit Dis. 2013 Oct; 37(2):276-80. PMID: 24431583.
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    30. Dobrovolskaia IV, Arya G. Dynamics of forced nucleosome unraveling and role of nonuniform histone-DNA interactions. Biophys J. 2012 Sep 05; 103(5):989-98. PMID: 23009848.
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    31. Iyer BV, Arya G. Lattice animal model of chromosome organization. Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Jul; 86(1 Pt 1):011911. PMID: 23005456.
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    32. Gao B, Arya G, Tao AR. Self-orienting nanocubes for the assembly of plasmonic nanojunctions. Nat Nanotechnol. 2012 Jun 10; 7(7):433-7. PMID: 22683842.
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    33. Majumdar U, Arya G, Singh S, Pillai A, Nair PP. Oro-dental findings in Bardet-Biedl syndrome. BMJ Case Rep. 2012 Apr 23; 2012. PMID: 22604765.
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    34. Phadke A, Zhang C, Arman B, Hsu CC, Mashelkar RA, Lele AK, Tauber MJ, Arya G, Varghese S. Rapid self-healing hydrogels. Proc Natl Acad Sci U S A. 2012 Mar 20; 109(12):4383-8. PMID: 22392977.
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    35. Meluzzi D, Olson KE, Dolan GF, Arya G, Müller UF. Computational prediction of efficient splice sites for trans-splicing ribozymes. RNA. 2012 Mar; 18(3):590-602. PMID: 22274956.
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    36. Saxena AK, Arya G, Bansal N. Egg laying site and oviposition pattern of two Phthirapteran species parasitizing red whiskered Bulbul (Pycnonotus jocosus). Turkiye Parazitol Derg. 2012; 36(3):166-8. PMID: 23169161.
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    37. Kalter HD, Mohan P, Mishra A, Gaonkar N, Biswas AB, Balakrishnan S, Arya G, Babille M. Maternal death inquiry and response in India--the impact of contextual factors on defining an optimal model to help meet critical maternal health policy objectives. Health Res Policy Syst. 2011 Nov 30; 9:41. PMID: 22128848.
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    38. Ahmad A, Arya G, Saxena R, Bansal N, Saxena AK. Prevalence of Myrsidea salimalii (Amblycera: Phthiraptera) on striated babblers (Turdoides earlei) (Timaliidae: Passeriformes: Aves). J Parasit Dis. 2011 Oct; 35(2):207-9. PMID: 23024506.
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    39. Ayala R, Zhang C, Yang D, Hwang Y, Aung A, Shroff SS, Arce FT, Lal R, Arya G, Varghese S. Engineering the cell-material interface for controlling stem cell adhesion, migration, and differentiation. Biomaterials. 2011 May; 32(15):3700-11. PMID: 21396708.
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    40. Iyer BV, Kenward M, Arya G. Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations. BMC Biophys. 2011 Apr 15; 4:8. PMID: 21595865.
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    41. Lim HL, Chuang JC, Tran T, Aung A, Arya G, Varghese S. Dynamic Electromechanical Hydrogel Matrices for Stem Cell Culture. Adv Funct Mater. 2011 Jan 07; 21(1). PMID: 24273479.
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    42. Agarwal GP, Ahmad A, Rashmi A, Arya G, Bansal N, Saxena AK. Bio-ecology of the louse, Upupicola upupae, infesting the Common Hoopoe, Upupa epops. J Insect Sci. 2011; 11:46. PMID: 21861650.
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    43. Yang D, Arya G. Structure and binding of the H4 histone tail and the effects of lysine 16 acetylation. Phys Chem Chem Phys. 2011 Feb 21; 13(7):2911-21. PMID: 21157623.
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    44. Dobrovolskaia IV, Kenward M, Arya G. Twist propagation in dinucleosome arrays. Biophys J. 2010 Nov 17; 99(10):3355-64. PMID: 21081084.
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    45. Arya G. Chain stiffness and attachment-dependent attraction between polyelectrolyte-grafted colloids. J Phys Chem B. 2010 Dec 09; 114(48):15886-96. PMID: 21069987.
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    46. Sangaj N, Kyriakakis P, Yang D, Chang CW, Arya G, Varghese S. Heparin mimicking polymer promotes myogenic differentiation of muscle progenitor cells. Biomacromolecules. 2010 Dec 13; 11(12):3294-300. PMID: 21058638.
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    47. Maitra A, Arya G. Influence of pulling handles and device stiffness in single-molecule force spectroscopy. Phys Chem Chem Phys. 2011 Feb 07; 13(5):1836-42. PMID: 20938520.
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    48. Arya G, Maitra A, Grigoryev SA. A structural perspective on the where, how, why, and what of nucleosome positioning. J Biomol Struct Dyn. 2010 Jun; 27(6):803-20. PMID: 20232935.
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    49. Maitra A, Arya G. Model accounting for the effects of pulling-device stiffness in the analyses of single-molecule force measurements. Phys Rev Lett. 2010 Mar 12; 104(10):108301. PMID: 20366455.
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    50. Meluzzi D, Smith DE, Arya G. Biophysics of knotting. Annu Rev Biophys. 2010; 39:349-66. PMID: 20192771.
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    51. Ahmad A, Khan V, Badola S, Arya G, Bansal N, Saxena AK. Population characteristics and the nature of egg shells of two Phthirapteran species parasitizing Indian cattle egrets. J Insect Sci. 2010; 10:163. PMID: 21067416.
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    52. Arya G. Energetic and entropic forces governing the attraction between polyelectrolyte-grafted colloids. J Phys Chem B. 2009 Dec 03; 113(48):15760-70. PMID: 19842639.
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    53. Grigoryev SA, Arya G, Correll S, Woodcock CL, Schlick T. Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions. Proc Natl Acad Sci U S A. 2009 Aug 11; 106(32):13317-22. PMID: 19651606.
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    54. Arya G, Schlick T. A tale of tails: how histone tails mediate chromatin compaction in different salt and linker histone environments. J Phys Chem A. 2009 Apr 23; 113(16):4045-59. PMID: 19298048.
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    55. Hehmeyer OJ, Arya G, Panagiotopoulos AZ, Szleifer I. Monte Carlo simulation and molecular theory of tethered polyelectrolytes. J Chem Phys. 2007 Jun 28; 126(24):244902. PMID: 17614585.
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    56. Arya G, Schlick T. Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo. J Chem Phys. 2007 Jan 28; 126(4):044107. PMID: 17286462.
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    57. Arya G, Schlick T. Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model. Proc Natl Acad Sci U S A. 2006 Oct 31; 103(44):16236-41. PMID: 17060627.
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    58. Arya G, Zhang Q, Schlick T. Flexible histone tails in a new mesoscopic oligonucleosome model. Biophys J. 2006 Jul 01; 91(1):133-50. PMID: 16603492.
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    59. Arya G, Rottler J, Panagiotopoulos AZ, Srolovitz DJ, Chaikin PM. Shear ordering in thin films of spherical block copolymer. Langmuir. 2005 Nov 22; 21(24):11518-27. PMID: 16285835.
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    60. Arya G, Panagiotopoulos AZ. Log-rolling micelles in sheared amphiphilic thin films. Phys Rev Lett. 2005 Oct 28; 95(18):188301. PMID: 16383952.
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    61. Arya G, Panagiotopoulos AZ. Monte Carlo study of shear-induced alignment of cylindrical micelles in thin films. Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Sep; 70(3 Pt 1):031501. PMID: 15524524.
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    62. Arya G, Chang HC, Maginn EJ. Knudsen diffusivity of a hard sphere in a rough slit pore. Phys Rev Lett. 2003 Jul 11; 91(2):026102. PMID: 12906494.
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