Gaurav Arya | Scholars@Duke

Gaurav Arya
Associate Professor 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

Molecular modeling, molecular simulations, statistical mechanics, coarse-graining, machine learning, polymer and colloidal physics, polymer-nanoparticle composites, chromatin biophysics, DNA nanotechnology, viral DNA packaging, single-molecule force spectroscopy, nanoscale transport

Current Appointments & Affiliations

Associate Professor of Mechanical Engineering and Materials Science, Pratt School of Engineering, Duke University 2017
Associate Professor of Chemistry, Chemistry, Trinity College of Arts & Sciences 2018
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
gaurav.arya@duke.edu (919) 660-5435
Arya Lab
Google Scholar

Background
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
Recognition
In the News
- MAR 27, 2019 Pratt School of Engineering
  
  To Engineer New Nanoparticle Spheres, Pratt Researchers Take a Vinaigrette Approach
- NOV 17, 2016
  
  Gaurav Arya: Modeling Soft Matter with Hard Calculations
Expertise
Subject Headings
Research
Selected Grants
- 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
- DMREF: Collaborative Research: DNA-based sensing, communicating, and phase-separating materials awarded by National Science Foundation 2019 - 2023
- Linking Kinetics, Subunit Coordination, and Structure of a Viral DNA Packaging Motor 2017 - 2020
- Linking Kinetics, Subunit Coordination, and Structure of a Viral DNA Packaging Motor 2017 - 2020
Publications & Artistic Works
Selected Publications
- Academic Articles
  - 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.
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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.), August 27, 2019. https://doi.org/10.1016/j.ymeth.2019.08.008.
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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.
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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.
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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.
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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.
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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.
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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.
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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). https://doi.org/10.1038/s41467-017-02619-5.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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). https://doi.org/10.1093/nar/gkv820.
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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.
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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 Derivatives for Enhanced in Vivo Survival and Engraftment.” Acs Biomaterials Science and Engineering 1, no. 1 (December 14, 2015): 7–12. https://doi.org/10.1021/ab500021a.
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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.
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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.
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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.
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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). https://doi.org/10.1088/0953-8984/27/6/064120.
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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 (January 1, 2015): 9793–9805. https://doi.org/10.1039/c5nr00809c.
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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.
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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.
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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). https://doi.org/10.1038/ncomms5173.
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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.
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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.
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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.
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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.
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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.
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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 (July 2012): 433–37. https://doi.org/10.1038/nnano.2012.83.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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). https://doi.org/10.1063/1.2747600.
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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). https://doi.org/10.1063/1.2428305.
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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.
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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.
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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.
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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.
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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). https://doi.org/10.1103/physrevlett.95.188301.
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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.
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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.
  - 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). https://doi.org/10.1103/PhysRevE.70.031501.
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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.
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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.
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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.
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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.
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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.
  - 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.
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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 (n.d.). https://doi.org/10.1103/physrevlett.122.107802.
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- Book Sections
  - 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, 216–32, 2015. https://doi.org/10.1016/B978-0-323-35400-4.00005-2.
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Teaching & Mentoring
Recent Courses
- ME 490: Special Topics in Mechanical Engineering 2019
- ME 555: Advanced Topics in Mechanical Engineering 2019

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Education, Training, & Certifications

In the News

Subject Headings

Selected Grants

Selected Publications

Academic Articles

Book Sections

Recent Courses