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    Gaurav Arya

    TitleAssociate Professor
    SchoolUniversity of California, San Diego
    Address9500 Gilman Drive #0448
    CA La Jolla 92093
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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

      Collapse Bibliographic 
      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. Shi Z, Castro CE, Arya G. Conformational Dynamics of Mechanically Compliant DNA Nanostructures from Coarse-Grained Molecular Dynamics Simulations. ACS Nano. 2017 May 23; 11(5):4617-4630. PMID: 28423273.
        View in: PubMed
      2. 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.
        View in: PubMed
      3. 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.
        View in: PubMed
      4. 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.
        View in: PubMed
      5. 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; PMCID: PMC4751512.
      6. 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.
        View in: PubMed
      7. Meluzzi D, Arya G. Quantification of DNA cleavage specificity in Hi-C experiments. Nucleic Acids Res. 2016 Jan 08; 44(1):e4. PMID: 26264668; PMCID: PMC4705682.
      8. 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.
        View in: PubMed
      9. 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.
        View in: PubMed
      10. 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.
        View in: PubMed
      11. 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.
        View in: PubMed
      12. 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.
        View in: PubMed
      13. 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):4002-17. PMID: 25311860; PMCID: PMC4376518.
      14. 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; PMCID: PMC4150795.
      15. 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; PMCID: PMC4157569.
      16. 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; PMCID: PMC4675591 [Available on 12/01/16].
      17. 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.
        View in: PubMed
      18. 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.
        View in: PubMed
      19. Meluzzi D, Arya G. Recovering ensembles of chromatin conformations from contact probabilities. Nucleic Acids Res. 2013 Jan 07; 41(1):63-75. PMID: 23143266; PMCID: PMC3592477.
      20. 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; PMCID: PMC3793084.
      21. 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; PMCID: PMC3433614.
      22. 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.
        View in: PubMed
      23. 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.
        View in: PubMed
      24. 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; PMCID: PMC3339191.
      25. 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; PMCID: PMC3311386.
      26. 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; PMCID: PMC3285945.
      27. 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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      28. 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; PMCID: PMC3292953.
      29. 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; PMCID: PMC3235380.
      30. 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.
        View in: PubMed
      31. 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; PMCID: PMC3102647.
      32. 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.
        View in: PubMed
      33. 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; PMCID: PMC3281440.
      34. 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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      35. Dobrovolskaia IV, Kenward M, Arya G. Twist propagation in dinucleosome arrays. Biophys J. 2010 Nov 17; 99(10):3355-64. PMID: 21081084; PMCID: PMC2980718.
      36. 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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      37. 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; PMCID: PMC4136807.
      38. 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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      39. 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.
        View in: PubMed
      40. 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.
        View in: PubMed
      41. 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; PMCID: PMC3016757.
      42. Meluzzi D, Smith DE, Arya G. Biophysics of knotting. Annu Rev Biophys. 2010; 39:349-66. PMID: 20192771.
        View in: PubMed
      43. 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.
        View in: PubMed
      44. 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; PMCID: PMC2726360.
      45. 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; PMCID: PMC2693032.
      46. 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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      47. 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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      48. 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; PMCID: PMC1637566.
      49. 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; PMCID: PMC1479056.
      50. 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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      51. 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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      52. 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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      53. 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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