Gaurav Arya
Professor in the Thomas Lord Department of Mechanical Engineering and Materials Science
My research laboratory uses physics-based computational tools to provide fundamental, molecular-level understanding of a diverse range of biological and soft-material systems, with the aim of discovering new phenomena and developing new technologies. The methods we use or develop are largely based on statistical mechanics, molecular modeling and simulations, stochastic dynamics, coarse-graining, bioinformatics, machine learning, and polymer/colloidal physics. Our current research interests fall within four main themes: genome organization and regulation; polymer-nanoparticle composites; viral-DNA-packaging; and DNA nanotechnology. Please visit our website for more details about each of these research projects.
Current Research Interests
Current Appointments & Affiliations
- Professor in the Thomas Lord Department of Mechanical Engineering and Materials Science, Pratt School of Engineering, Duke University 2021
- Associate Professor of Biomedical Engineering, Biomedical Engineering, Pratt School of Engineering 2018
Contact Information
- 144 Hudson Hall, Box 90300, Duke University, Durham, NC 27708
- 3383 Fitzpatrick Center (Ciemas), Duke University, Durham, NC 27708
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gaurav.arya@duke.edu
(919) 660-5435
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Arya Lab
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Google Scholar
- Background
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Education, Training, & Certifications
- Assistant Research Scientist, New York University 2005 - 2007
- Postdoc, Princeton University 2003 - 2005
- Ph.D., University of Notre Dame 2003
- B.Tech., Indian Institute of Technology (India) 1998
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Previous Appointments & Affiliations
- Associate Professor of Mechanical Engineering and Materials Science, Pratt School of Engineering, Duke University 2017 - 2021
- Associate Professor of Chemistry, Chemistry, Trinity College of Arts & Sciences 2018 - 2021
- Recognition
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In the News
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JUN 4, 2021 Pratt School of Engineering -
JUN 3, 2021 -
MAR 25, 2021 Pratt School of Engineering -
FEB 26, 2021 Pratt School of Engineering -
NOV 19, 2020 Pratt School of Engineering -
SEP 21, 2020 -
SEP 9, 2019 Pratt School of Engineering -
MAR 26, 2019 Pratt School of Engineering -
NOV 17, 2016
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- Expertise
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Subject Headings
- Research
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Selected Grants
- UC San Diego MRSEC: an NSF Materials Research Science and Engineering Center awarded by University of California - San Diego 2020 - 2026
- NRT-HDR: Harnessing AI for Autonomous Material Design awarded by National Science Foundation 2020 - 2025
- EFRI CEE: DNA origami tools to engineer chromatin structure and function in live cells awarded by Ohio State University 2019 - 2023
- DMREF: Collaborative Research: DNA-based sensing, communicating, and phase-separating materials awarded by National Science Foundation 2019 - 2023
- The DNA Packaging Motor of Bacteriophage Phi29 awarded by University of Minnesota 2021 - 2022
- Conformationally-Steered Hierarchical Self-Assembly at Solid Surfaces awarded by Department of Energy 2020 - 2022
- Linking Kinetics, Subunit Coordination, and Structure of a Viral DNA Packaging Motor awarded by University of California - San Diego 2017 - 2021
- Publications & Artistic Works
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Selected Publications
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Academic Articles
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Simões, Vanessa, Blanche K. Cizubu, Lana Harley, Ye Zhou, Joshua Pajak, Nathan A. Snyder, Jonathan Bouvette, et al. “Redox-sensitive E2 Rad6 controls cellular response to oxidative stress via K63-linked ubiquitination of ribosomes.” Cell Reports 39, no. 8 (May 2022): 110860. https://doi.org/10.1016/j.celrep.2022.110860.Full Text
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Zhou, Yilong, Tsung-Yeh Tang, Brian Hyun-Jong Lee, and Gaurav Arya. “Tunable Orientation and Assembly of Polymer-Grafted Nanocubes at Fluid-Fluid Interfaces.” Acs Nano, April 22, 2022. https://doi.org/10.1021/acsnano.1c10416.Full Text
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Sensale, Sebastian, Pranav Sharma, and Gaurav Arya. “Binding kinetics of harmonically confined random walkers.” Physical Review. E 105, no. 4–1 (April 2022): 044136. https://doi.org/10.1103/physreve.105.044136.Full Text
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Lee, Brian Hyun-Jong, and Gaurav Arya. “Assembly mechanism of surface-functionalized nanocubes.” Nanoscale 14, no. 10 (March 10, 2022): 3917–28. https://doi.org/10.1039/d1nr07995f.Full Text
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Yang, Yunqi, Qinyi Lu, Chao-Min Huang, Hongji Qian, Yunlong Zhang, Sonal Deshpande, Gaurav Arya, Yonggang Ke, and Stefan Zauscher. “Programmable Site-Specific Functionalization of DNA Origami with Polynucleotide Brushes.” Angewandte Chemie (International Ed. in English) 60, no. 43 (October 2021): 23241–47. https://doi.org/10.1002/anie.202107829.Full Text
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Wang, Jiuling, Jingxuan Ding, Olivier Delaire, and Gaurav Arya. “Atomistic Mechanisms Underlying Non-Arrhenius Ion Transport in Superionic Conductor AgCrSe2.” Acs Applied Energy Materials 4, no. 7 (July 26, 2021): 7157–67. https://doi.org/10.1021/acsaem.1c01237.Full Text
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Lee, Brian Hyun-Jong, Nicholas A. Kotov, and Gaurav Arya. “Reconfigurable Chirality of DNA-Bridged Nanorod Dimers.” Acs Nano, July 22, 2021. https://doi.org/10.1021/acsnano.1c04326.Full Text
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Kumar, Vardhman, Ung Hyun Ko, Yilong Zhou, Jiaul Hoque, Gaurav Arya, and Shyni Varghese. “Microengineered Materials with Self‐Healing Features for Soft Robotics.” Advanced Intelligent Systems 3, no. 7 (July 2021): 2100005–2100005. https://doi.org/10.1002/aisy.202100005.Full Text
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Pajak, Joshua, Erik Dill, Emilio Reyes-Aldrete, Mark A. White, Brian A. Kelch, Paul J. Jardine, Gaurav Arya, and Marc C. Morais. “Atomistic basis of force generation, translocation, and coordination in a viral genome packaging motor.” Nucleic Acids Research 49, no. 11 (June 2021): 6474–88. https://doi.org/10.1093/nar/gkab372.Full Text
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Woodson, Michael, Joshua Pajak, Bryon P. Mahler, Wei Zhao, Wei Zhang, Gaurav Arya, Mark A. White, Paul J. Jardine, and Marc C. Morais. “A viral genome packaging motor transitions between cyclic and helical symmetry to translocate dsDNA.” Science Advances 7, no. 19 (May 7, 2021): eabc1955. https://doi.org/10.1126/sciadv.abc1955.Full Text
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Pajak, Joshua, Rockney Atz, Brendan J. Hilbert, Marc C. Morais, Brian A. Kelch, Paul J. Jardine, and Gaurav Arya. “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, no. 17 (April 2021): e2024928118. https://doi.org/10.1073/pnas.2024928118.Full Text
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Wang, Dongfang, Lei Yu, Chao-Min Huang, Gaurav Arya, Shuai Chang, and Yonggang Ke. “Programmable Transformations of DNA Origami Made of Small Modular Dynamic Units.” Journal of the American Chemical Society 143, no. 5 (February 2, 2021): 2256–63. https://doi.org/10.1021/jacs.0c10576.Full Text
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Lee, Brian Hyun-Jong, and Gaurav Arya. “Analytical van der Waals interaction potential for faceted nanoparticles.” Nanoscale Horizons 5, no. 12 (December 2020): 1628–42. https://doi.org/10.1039/d0nh00526f.Full Text
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Meluzzi, Dario, and Gaurav Arya. “Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data.” Methods (San Diego, Calif.) 181–182 (October 2020): 24–34. https://doi.org/10.1016/j.ymeth.2019.08.008.Full Text
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Ding, Jingxuan, Jennifer L. Niedziela, Dipanshu Bansal, Jiuling Wang, Xing He, Andrew F. May, Georg Ehlers, et al. “Anharmonic lattice dynamics and superionic transition in AgCrSe 2.” Proceedings of the National Academy of Sciences 117, no. 8 (February 25, 2020): 3930–37. https://doi.org/10.1073/pnas.1913916117.Full Text Open Access Copy
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Deluca, M., Z. Shi, C. E. Castro, and G. Arya. “Dynamic DNA nanotechnology: Toward functional nanoscale devices.” Nanoscale Horizons 5, no. 2 (February 1, 2020): 182–201. https://doi.org/10.1039/c9nh00529c.Full Text
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Wang, Jiuling, Brian Hyun-Jong Lee, and Gaurav Arya. “Kinetically assembled binary nanoparticle networks.” Nanoscale 12, no. 8 (February 2020): 5091–5102. https://doi.org/10.1039/c9nr09900j.Full Text
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Shi, Ze, and Gaurav Arya. “Free energy landscape of salt-actuated reconfigurable DNA nanodevices.” Nucleic Acids Research 48, no. 2 (January 2020): 548–60. https://doi.org/10.1093/nar/gkz1137.Full Text
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delToro, Damian, David Ortiz, Mariam Ordyan, Joshua Pajak, Jean Sippy, Alexis Catala, Choon-Seok Oh, et al. “Functional Dissection of a Viral DNA Packaging Machine's Walker B Motif.” Journal of Molecular Biology 431, no. 22 (November 2019): 4455–74. https://doi.org/10.1016/j.jmb.2019.08.012.Full Text
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Lee, Brian Hyun-Jong, and Gaurav Arya. “Orientational phase behavior of polymer-grafted nanocubes.” Nanoscale 11, no. 34 (August 2019): 15939–57. https://doi.org/10.1039/c9nr04859f.Full Text
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Tang, Tsung-Yeh, Yilong Zhou, and Gaurav Arya. “Interfacial Assembly of Tunable Anisotropic Nanoparticle Architectures.” Acs Nano 13, no. 4 (April 2019): 4111–23. https://doi.org/10.1021/acsnano.8b08733.Full Text
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Song, Jing-Jin, Rupak Bhattacharya, Hyunki Kim, Jooyoung Chang, Tsung-Yeh Tang, Hongyu Guo, Sajal K. Ghosh, et al. “One-Dimensional Anomalous Diffusion of Gold Nanoparticles in a Polymer Melt.” Physical Review Letters 122, no. 10 (March 2019): 107802. https://doi.org/10.1103/physrevlett.122.107802.Full Text
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Ortiz, David, Damian delToro, Mariam Ordyan, Joshua Pajak, Jean Sippy, Alexis Catala, Choon-Seok Oh, 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 (February 2019): 1404–15. https://doi.org/10.1093/nar/gky1217.Full Text
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Villanueva, J. T., Q. Huang, N. O. Fischer, G. Arya, and D. J. Sirbuly. “Nanofiber-Based Total Internal Reflection Microscopy for Characterizing Colloidal Systems at the Microscale.” Journal of Physical Chemistry C 122, no. 38 (September 27, 2018): 22114–24. https://doi.org/10.1021/acs.jpcc.8b03167.Full Text
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Marras, Alexander E., Ze Shi, Michael G. Lindell, Randy A. Patton, Chao-Min Huang, Lifeng Zhou, Hai-Jun Su, Gaurav Arya, and Carlos E. Castro. “Cation-Activated Avidity for Rapid Reconfiguration of DNA Nanodevices.” Acs Nano 12, no. 9 (September 4, 2018): 9484–94. https://doi.org/10.1021/acsnano.8b04817.Full Text
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Hsu, Su-Wen, Andrea L. Rodarte, Madhura Som, Gaurav Arya, and Andrea R. Tao. “Colloidal Plasmonic Nanocomposites: From Fabrication to Optical Function.” Chemical Reviews 118, no. 6 (March 2018): 3100–3120. https://doi.org/10.1021/acs.chemrev.7b00364.Full Text
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Kilic, Sinan, Suren Felekyan, Olga Doroshenko, Iuliia Boichenko, Mykola Dimura, Hayk Vardanyan, Louise C. Bryan, Gaurav Arya, Claus A. M. Seidel, and Beat Fierz. “Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α.” Nature Communications 9, no. 1 (January 16, 2018): 235. https://doi.org/10.1038/s41467-017-02619-5.Full Text
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Shi, Ze, Carlos E. Castro, and Gaurav Arya. “Conformational Dynamics of Mechanically Compliant DNA Nanostructures from Coarse-Grained Molecular Dynamics Simulations.” Acs Nano 11, no. 5 (May 2017): 4617–30. https://doi.org/10.1021/acsnano.7b00242.Full Text
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Tang, T. Y., and G. Arya. “Anisotropic Three-Particle Interactions between Spherical Polymer-Grafted Nanoparticles in a Polymer Matrix.” Macromolecules 50, no. 3 (February 14, 2017): 1167–83. https://doi.org/10.1021/acs.macromol.6b01936.Full Text
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Root, Samuel E., Nicholas E. Jackson, Suchol Savagatrup, Gaurav Arya, and Darren J. Lipomi. “Modelling the morphology and thermomechanical behaviour of low-bandgap conjugated polymers and bulk heterojunction films.” Energy & Environmental Science 10, no. 2 (2017): 558–69. https://doi.org/10.1039/c6ee03456j.Full Text
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Arya, G. “Models for recovering the energy landscape of conformational transitions from single-molecule pulling experiments.” Molecular Simulation 42, no. 13 (September 1, 2016): 1102–15. https://doi.org/10.1080/08927022.2015.1123257.Full Text
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Hamed, Mazen Y., and Gaurav Arya. “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 34, no. 5 (May 2016): 919–34. https://doi.org/10.1080/07391102.2015.1068224.Full Text
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Root, S. E., S. Savagatrup, C. J. Pais, G. Arya, and D. J. Lipomi. “Predicting the Mechanical Properties of Organic Semiconductors Using Coarse-Grained Molecular Dynamics Simulations.” Macromolecules 49, no. 7 (April 26, 2016): 2886–94. https://doi.org/10.1021/acs.macromol.6b00204.Full Text
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Nam, G. M., and G. Arya. “Free-energy landscape of mono- and dinucleosomes: Enhanced rotational flexibility of interconnected nucleosomes.” Physical Review E 93, no. 3 (March 10, 2016). https://doi.org/10.1103/PhysRevE.93.032406.Full Text
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Murthy, C. R., B. Gao, A. R. Tao, and G. Arya. “Dynamics of nanoparticle assembly from disjointed images of nanoparticle-polymer composites.” Physical Review E 93, no. 2 (February 18, 2016). https://doi.org/10.1103/PhysRevE.93.022501.Full Text
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Zaretski, Aliaksandr V., Samuel E. Root, Alex Savchenko, Elena Molokanova, Adam D. Printz, Liban Jibril, Gaurav Arya, Mark Mercola, and Darren J. Lipomi. “Metallic Nanoislands on Graphene as Highly Sensitive Transducers of Mechanical, Biological, and Optical Signals.” Nano Letters 16, no. 2 (February 2016): 1375–80. https://doi.org/10.1021/acs.nanolett.5b04821.Full Text Open Access Copy
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Meluzzi, Dario, and Gaurav Arya. “Quantification of DNA cleavage specificity in Hi-C experiments.” Nucleic Acids Research 44, no. 1 (January 2016): e4. https://doi.org/10.1093/nar/gkv820.Full Text Open Access Copy
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Takahashi, Tsukasa, Bao C. Vo Ngo, Leyang Xiao, Gaurav Arya, and Michael J. Heller. “Molecular mechanical properties of short-sequence peptide enzyme mimics.” Journal of Biomolecular Structure & Dynamics 34, no. 3 (January 2016): 463–74. https://doi.org/10.1080/07391102.2015.1039586.Full Text
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Gurunatha, K. L., S. Marvi, G. Arya, and A. R. Tao. “Computationally Guided Assembly of Oriented Nanocubes by Modulating Grafted Polymer-Surface Interactions.” Nano Letters 15, no. 11 (November 11, 2015): 7377–82. https://doi.org/10.1021/acs.nanolett.5b02748.Full Text
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Singh, V. V., K. Kaufmann, J. Orozco, J. Li, M. Galarnyk, G. Arya, and J. Wang. “Micromotor-based on-off fluorescence detection of sarin and soman simulants.” Chemical Communications 51, no. 56 (July 18, 2015): 11190–93. https://doi.org/10.1039/c5cc04120a.Full Text
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Murthy, C. R., B. Gao, A. R. Tao, and G. Arya. “Automated quantitative image analysis of nanoparticle assembly.” Nanoscale 7, no. 21 (June 7, 2015): 9793–9805. https://doi.org/10.1039/c5nr00809c.Full Text
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Hattemer, G. D., and G. Arya. “Viscoelastic properties of polymer-grafted nanoparticle composites from molecular dynamics simulations.” Macromolecules 48, no. 4 (February 24, 2015): 1240–55. https://doi.org/10.1021/ma502086c.Full Text
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Meluzzi, Dario, and Gaurav 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 (February 2015): 064120. https://doi.org/10.1088/0953-8984/27/6/064120.Full Text
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Kabra, H., Y. Hwang, H. L. Lim, M. Kar, G. Arya, and S. Varghese. “Biomimetic material-assisted delivery of human embryonic stem cell-derived cells for enhanced in vivo survival and engraftment.” Acs Biomaterials Science & Engineering 1 (2015): 7–12. https://doi.org/10.1021/ab500021a.Full Text Link to Item
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Migliori, Amy D., Douglas E. Smith, and Gaurav Arya. “Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor.” Journal of Molecular Biology 426, no. 24 (December 2014): 4002–17. https://doi.org/10.1016/j.jmb.2014.09.023.Full Text
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Nam, Gi-Moon, and Gaurav Arya. “Torsional behavior of chromatin is modulated by rotational phasing of nucleosomes.” Nucleic Acids Research 42, no. 15 (September 2014): 9691–99. https://doi.org/10.1093/nar/gku694.Full Text Open Access Copy
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Migliori, Amy D., Nicholas Keller, Tanfis I. Alam, Marthandan Mahalingam, Venigalla B. Rao, Gaurav Arya, and Douglas E. Smith. “Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor.” Nature Communications 5 (June 17, 2014): 4173. https://doi.org/10.1038/ncomms5173.Full Text Open Access Copy
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Agrawal, V., G. Arya, and J. Oswald. “Simultaneous iterative boltzmann inversion for coarse-graining of polyurea.” Macromolecules 47, no. 10 (May 27, 2014): 3378–89. https://doi.org/10.1021/ma500320n.Full Text
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Meluzzi, Dario, and Gaurav Arya. “Recovering ensembles of chromatin conformations from contact probabilities.” Nucleic Acids Research 41, no. 1 (January 2013): 63–75. https://doi.org/10.1093/nar/gks1029.Full Text Open Access Copy
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Walker, S. I., B. J. Callahan, G. Arya, J. D. Barry, T. Bhattacharya, S. Grigoryev, M. Pellegrini, K. Rippe, and S. M. Rosenberg. “Evolutionary dynamics and information hierarchies in biological systems.” Annals of the New York Academy of Sciences 1305, no. 1 (January 1, 2013): 1–17. https://doi.org/10.1111/nyas.12140.Full Text
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Dobrovolskaia, I. V., and G. Arya. “Dynamics of Forced Nucleosome Unraveling and Role of Nonuniform Histone-DNA Interactions.” Biophysical Journal 103, no. 5 (September 2012): 989–98. https://doi.org/10.1016/j.bpj.2012.07.043.Full Text
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Iyer, B. V. S., and G. Arya. “Lattice animal model of chromosome organization.” Physical Review E Statistical, Nonlinear, and Soft Matter Physics 86, no. 1 (July 12, 2012). https://doi.org/10.1103/PhysRevE.86.011911.Full Text
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Gao, Bo, Gaurav Arya, and Andrea R. Tao. “Self-orienting nanocubes for the assembly of plasmonic nanojunctions.” Nature Nanotechnology 7, no. 7 (June 10, 2012): 433–37. https://doi.org/10.1038/nnano.2012.83.Full Text
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Arman, B., A. S. Reddy, and G. Arya. “Viscoelastic properties and shock response of coarse-grained models of multiblock versus diblock copolymers: Insights into dissipative properties of polyurea.” Macromolecules 45, no. 7 (April 10, 2012): 3247–55. https://doi.org/10.1021/ma3001934.Full Text
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Phadke, Ameya, Chao Zhang, Bedri Arman, Cheng-Chih Hsu, Raghunath A. Mashelkar, Ashish K. Lele, Michael J. Tauber, Gaurav Arya, and Shyni Varghese. “Rapid self-healing hydrogels.” Proc Natl Acad Sci U S A 109, no. 12 (March 20, 2012): 4383–88. https://doi.org/10.1073/pnas.1201122109.Full Text Link to Item
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Meluzzi, Dario, Karen E. Olson, Gregory F. Dolan, Gaurav Arya, and Ulrich F. Müller. “Computational prediction of efficient splice sites for trans-splicing ribozymes.” Rna (New York, N.Y.) 18, no. 3 (March 2012): 590–602. https://doi.org/10.1261/rna.029884.111.Full Text
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Ayala, Ramses, Chao Zhang, Darren Yang, Yongsung Hwang, Aereas Aung, Sumeet S. Shroff, Fernando T. Arce, Ratnesh Lal, Gaurav Arya, and Shyni Varghese. “Engineering the cell-material interface for controlling stem cell adhesion, migration, and differentiation.” Biomaterials 32, no. 15 (May 2011): 3700–3711. https://doi.org/10.1016/j.biomaterials.2011.02.004.Full Text Link to Item
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Iyer, B. V. S., M. Kenward, and G. Arya. “Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations.” Bmc Biophysics 4, no. 1 (April 15, 2011). https://doi.org/10.1186/2046-1682-4-8.Full Text
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Maitra, Arijit, and Gaurav Arya. “Influence of pulling handles and device stiffness in single-molecule force spectroscopy.” Physical Chemistry Chemical Physics : Pccp 13, no. 5 (February 2011): 1836–42. https://doi.org/10.1039/c0cp01528h.Full Text
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Yang, Darren, and Gaurav Arya. “Structure and binding of the H4 histone tail and the effects of lysine 16 acetylation.” Physical Chemistry Chemical Physics : Pccp 13, no. 7 (February 2011): 2911–21. https://doi.org/10.1039/c0cp01487g.Full Text
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Lim, H. L., J. C. Chuang, T. Tran, A. Aung, G. Arya, and S. Varghese. “Dynamic electromechanical hydrogel matrices for stem cell culture.” Advanced Functional Materials 21, no. 1 (January 7, 2011): 55–63. https://doi.org/10.1002/adfm.201001519.Full Text
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Sangaj, Nivedita, Phillip Kyriakakis, Darren Yang, Chien-Wen Chang, Gaurav Arya, and Shyni Varghese. “Heparin mimicking polymer promotes myogenic differentiation of muscle progenitor cells.” Biomacromolecules 11, no. 12 (December 13, 2010): 3294–3300. https://doi.org/10.1021/bm101041f.Full Text Link to Item
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Arya, G. “Chain stiffness and attachment-dependent attraction between polyelectrolyte-grafted colloids.” Journal of Physical Chemistry B 114, no. 48 (December 9, 2010): 15886–96. https://doi.org/10.1021/jp1029085.Full Text
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Dobrovolskaia, Irina V., Martin Kenward, and Gaurav Arya. “Twist propagation in dinucleosome arrays.” Biophysical Journal 99, no. 10 (November 2010): 3355–64. https://doi.org/10.1016/j.bpj.2010.09.055.Full Text
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Arya, Gaurav, Arijit Maitra, and Sergei A. Grigoryev. “A structural perspective on the where, how, why, and what of nucleosome positioning.” Journal of Biomolecular Structure & Dynamics 27, no. 6 (June 2010): 803–20. https://doi.org/10.1080/07391102.2010.10508585.Full Text
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Maitra, A., and G. Arya. “Model accounting for the effects of pulling-device stiffness in the analyses of single-molecule force measurements.” Physical Review Letters 104, no. 10 (March 12, 2010). https://doi.org/10.1103/PhysRevLett.104.108301.Full Text
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Meluzzi, Dario, Douglas E. Smith, and Gaurav Arya. “Biophysics of knotting.” Annual Review of Biophysics 39 (January 2010): 349–66. https://doi.org/10.1146/annurev.biophys.093008.131412.Full Text
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Arya, G. “Energetic and entropic forces governing the attraction between polyelectrolyte-grafted colloids.” Journal of Physical Chemistry B 113, no. 48 (December 3, 2009): 15760–70. https://doi.org/10.1021/jp908007z.Full Text
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Grigoryev, Sergei A., Gaurav Arya, Sarah Correll, Christopher L. Woodcock, and Tamar 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 (August 2009): 13317–22. https://doi.org/10.1073/pnas.0903280106.Full Text
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Arya, Gaurav, and Tamar Schlick. “A tale of tails: how histone tails mediate chromatin compaction in different salt and linker histone environments.” The Journal of Physical Chemistry. A 113, no. 16 (April 2009): 4045–59. https://doi.org/10.1021/jp810375d.Full Text
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Hehmeyer, Owen J., Gaurav Arya, Athanassios Z. Panagiotopoulos, and Igal Szleifer. “Monte Carlo simulation and molecular theory of tethered polyelectrolytes.” The Journal of Chemical Physics 126, no. 24 (June 2007): 244902. https://doi.org/10.1063/1.2747600.Full Text
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Arya, Gaurav, and Tamar Schlick. “Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo.” The Journal of Chemical Physics 126, no. 4 (January 2007): 044107. https://doi.org/10.1063/1.2428305.Full Text
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Arya, Gaurav, and Tamar Schlick. “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, no. 44 (October 23, 2006): 16236–41. https://doi.org/10.1073/pnas.0604817103.Full Text
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Arya, Gaurav, Qing Zhang, and Tamar Schlick. “Flexible histone tails in a new mesoscopic oligonucleosome model.” Biophysical Journal 91, no. 1 (July 2006): 133–50. https://doi.org/10.1529/biophysj.106.083006.Full Text
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Arya, G., and A. Z. Panagiotopoulos. “Impact of branching on the phase behavior of polymers.” Macromolecules 38, no. 25 (December 13, 2005): 10596–604. https://doi.org/10.1021/ma0515376.Full Text
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Arya, G., J. Rottler, A. Z. Panagiotopoulos, D. J. Srolovitz, and P. M. Chaikin. “Shear ordering in thin films of spherical block copolymer.” Langmuir 21, no. 24 (November 22, 2005): 11518–27. https://doi.org/10.1021/la0516476.Full Text
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Arya, Gaurav, and Athanassios Z. Panagiotopoulos. “Log-rolling micelles in sheared amphiphilic thin films.” Physical Review Letters 95, no. 18 (October 28, 2005): 188301. https://doi.org/10.1103/physrevlett.95.188301.Full Text
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Arya, G., and A. Z. Panagiotopoulos. “Molecular modeling of shear-induced alignment of cylindrical micelles.” Computer Physics Communications 169, no. 1–3 (July 1, 2005): 262–66. https://doi.org/10.1016/j.cpc.2005.03.060.Full Text
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Hehmeyer, O. J., G. Arya, and A. Z. Panagiotopoulos. “Phase transitions of confined lattice homopolymers.” Journal of Physical Chemistry B 108, no. 21 (May 27, 2004): 6809–15. https://doi.org/10.1021/jp037599k.Full Text
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Arya, G., and A. Z. Panagiotopoulos. “Monte Carlo study of shear-induced alignment of cylindrical micelles in thin films.” Physical Review E Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics 70, no. 3 (January 1, 2004): 9. https://doi.org/10.1103/PhysRevE.70.031501.Full Text
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Arya, G., H. C. Chang, and E. J. Maginn. “Knudsen diffusivity of a hard sphere in a rough slit pore.” Physical Review Letters 91, no. 2 (July 11, 2003): 026102/1-026102/4. https://doi.org/10.1103/PhysRevLett.91.026102.Full Text
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Arya, G., H. C. Chang, and E. J. Maginn. “Molecular simulations of knudsen wall-slip: Effect of wall morphology.” Molecular Simulation 29, no. 10–11 (January 1, 2003): 697–709. https://doi.org/10.1080/0892702031000103257.Full Text
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Kioupis, L. I., G. Arya, and E. J. Maginn. “Pressure-enthalpy driven molecular dynamics for thermodynamic property calculation II: Applications.” Fluid Phase Equilibria 200, no. 1 (July 15, 2002): 93–110. https://doi.org/10.1016/S0378-3812(02)00015-8.Full Text
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Arya, G., H. C. Chang, and E. J. Maginn. “A critical comparison of equilibrium, non-equilibrium and boundary-driven molecular dynamics techniques for studying transport in microporous materials.” Journal of Chemical Physics 115, no. 17 (November 1, 2001): 8112–24. https://doi.org/10.1063/1.1407002.Full Text
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Arya, G., E. J. Maginn, and H. C. Chang. “Effect of the surface energy barrier on sorbate diffusion in A1PO4-5.” Journal of Physical Chemistry B 105, no. 14 (April 12, 2001): 2725–35. https://doi.org/10.1021/jp003350g.Full Text
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Arya, G., E. J. Maginn, and H. C. Chang. “Efficient viscosity estimation from molecular dynamics simulation via momentum impulse relaxation.” Journal of Chemical Physics 113, no. 6 (August 8, 2000): 2079–87. https://doi.org/10.1063/1.482019.Full Text
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Pajak, Joshua, and Gaurav Arya. “Molecular Dynamics of DNA Translocation by FtsK,” n.d. https://doi.org/10.1101/2022.01.03.474797.Full Text
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Book Sections
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Oswald, J., G. Arya, Z. Cui, and L. C. Brinson. “Molecular Dynamics (MD) and Coarse Grain Simulation of High Strain-Rate Elastomeric Polymers (HSREP): Molecular and Coarse-Grained Methods for Microstructure-Property Relations in HSREP.” In Elastomeric Polymers with High Rate Sensitivity Applications in Blast, Shockwave, and Penetration Mechanics, edited by R. Barsoum. William Andrew, 2015.
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Pajak, Joshua, Gaurav Arya, and Douglas Smith. “Biophysics of DNA Packaging.” In Encyclopedia of Virology, 4th Edition, edited by Michael Feiss. Elsevier, n.d. https://doi.org/10.1016/B978-0-12-809633-8.20966-7.Full Text
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- Teaching & Mentoring
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Recent Courses
- BME 493: Projects in Biomedical Engineering (GE) 2022
- BME 494: Projects in Biomedical Engineering (GE) 2022
- EGR 201L: Mechanics of Solids 2022
- ME 555: Advanced Topics in Mechanical Engineering 2022
- ME 560S: Materials Science and Engineering Seminar 2022
- BME 493: Projects in Biomedical Engineering (GE) 2021
- EGR 201L: Mechanics of Solids 2021
- ME 490: Special Topics in Mechanical Engineering 2021
- ME 555: Advanced Topics in Mechanical Engineering 2021
- EGR 201L: Mechanics of Solids 2020
- ME 490: Special Topics in Mechanical Engineering 2020
- ME 555: Advanced Topics in Mechanical Engineering 2020
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