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
- NOV 17, 2016
  
  Gaurav Arya: Modeling Soft Matter with Hard Calculations
Expertise
Subject Headings
Research
Selected Grants
- Linking Kinetics, Subunit Coordination, and Structure of a Viral DNA Packaging Motor awarded by University of California - San Diego 2017 - 2020
Publications & Artistic Works
Selected Publications
- Academic Articles
  - Ortiz, D, delToro, D, Ordyan, M, Pajak, J, Sippy, J, Catala, A, Oh, C-S, Vu, A, Arya, G, Feiss, M, Smith, DE, and 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 (December 12, 2018). Full Text
  - Villanueva, JT, Huang, Q, Fischer, NO, Arya, G, and Sirbuly, DJ. "Nanofiber-Based Total Internal Reflection Microscopy for Characterizing Colloidal Systems at the Microscale." The Journal of Physical Chemistry C 122, no. 38 (September 27, 2018): 22114-22124. Full Text
  - Marras, AE, Shi, Z, Lindell, MG, Patton, RA, Huang, C-M, Zhou, L, Su, H-J, Arya, G, and Castro, CE. "Cation-Activated Avidity for Rapid Reconfiguration of DNA Nanodevices." Acs Nano 12, no. 9 (September 4, 2018): 9484-9494. Full Text
  - Hsu, S-W, Rodarte, AL, Som, M, Arya, G, and Tao, AR. "Colloidal Plasmonic Nanocomposites: From Fabrication to Optical Function." Chemical Reviews 118, no. 6 (March 2018): 3100-3120. Full Text
  - Kilic, S, Felekyan, S, Doroshenko, O, Boichenko, I, Dimura, M, Vardanyan, H, Bryan, LC, Arya, G, Seidel, CAM, and Fierz, B. "Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α." Nature Communications 9, no. 1 (January 16, 2018): 235-null. Full Text
  - Shi, Z, Castro, CE, and Arya, G. "Conformational Dynamics of Mechanically Compliant DNA Nanostructures from Coarse-Grained Molecular Dynamics Simulations." Acs Nano 11, no. 5 (May 2017): 4617-4630. Full Text
  - Tang, T-Y, and Arya, G. "Anisotropic Three-Particle Interactions between Spherical Polymer-Grafted Nanoparticles in a Polymer Matrix." Macromolecules 50, no. 3 (February 14, 2017): 1167-1183. Full Text
  - Arya, G. "Models for recovering the energy landscape of conformational transitions from single-molecule pulling experiments." Molecular Simulation 42, no. 13 (September 2016): 1102-1115. Full Text
  - Hamed, MY, and 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 34, no. 5 (May 2016): 919-934. Full Text
  - Root, SE, Savagatrup, S, Pais, CJ, Arya, G, and Lipomi, DJ. "Predicting the Mechanical Properties of Organic Semiconductors Using Coarse-Grained Molecular Dynamics Simulations." Macromolecules 49, no. 7 (April 12, 2016): 2886-2894. Full Text
  - Zaretski, AV, Root, SE, Savchenko, A, Molokanova, E, Printz, AD, Jibril, L, Arya, G, Mercola, M, and Lipomi, DJ. "Metallic Nanoislands on Graphene as Highly Sensitive Transducers of Mechanical, Biological, and Optical Signals." Nano Letters 16, no. 2 (February 2016): 1375-1380. Full Text Open Access Copy
  - Meluzzi, D, and Arya, G. "Quantification of DNA cleavage specificity in Hi-C experiments." Nucleic Acids Research 44, no. 1 (January 2016): e4-null. Full Text Open Access Copy
  - Takahashi, T, Vo Ngo, BC, Xiao, L, Arya, G, and Heller, MJ. "Molecular mechanical properties of short-sequence peptide enzyme mimics." Journal of Biomolecular Structure & Dynamics 34, no. 3 (January 2016): 463-474. Full Text
  - Gurunatha, KL, Marvi, S, Arya, G, and Tao, AR. "Computationally Guided Assembly of Oriented Nanocubes by Modulating Grafted Polymer–Surface Interactions." Nano Letters 15, no. 11 (November 11, 2015): 7377-7382. Full Text
  - Hattemer, GD, and Arya, G. "Viscoelastic Properties of Polymer-Grafted Nanoparticle Composites from Molecular Dynamics Simulations." Macromolecules 48, no. 4 (February 24, 2015): 1240-1255. Full Text
  - Meluzzi, D, and 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, no. 6 (February 2015): 064120-null. Full Text
  - Kabra, H, Hwang, Y, Lim, HL, Kar, M, Arya, G, and Varghese, S. "Biomimetic Material-Assisted Delivery of Human Embryonic Stem Cell Derivatives for Enhanced In Vivo Survival and Engraftment." Acs Biomaterials Science & Engineering 1, no. 1 (January 12, 2015): 7-12. Full Text
  - Migliori, AD, Smith, DE, and Arya, G. "Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor." Journal of Molecular Biology 426, no. 24 (December 2014): 4002-4017. Full Text
  - Nam, G-M, and Arya, G. "Torsional behavior of chromatin is modulated by rotational phasing of nucleosomes." Nucleic Acids Research 42, no. 15 (September 2014): 9691-9699. Full Text Open Access Copy
  - Migliori, AD, Keller, N, Alam, TI, Mahalingam, M, Rao, VB, Arya, G, and Smith, DE. "Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor." Nature Communications 5 (June 17, 2014): 4173-null. Full Text Open Access Copy
  - Agrawal, V, Arya, G, and Oswald, J. "Simultaneous Iterative Boltzmann Inversion for Coarse-Graining of Polyurea." Macromolecules 47, no. 10 (May 27, 2014): 3378-3389. Full Text
  - Walker, SI, Callahan, BJ, Arya, G, Barry, JD, Bhattacharya, T, Grigoryev, S, Pellegrini, M, Rippe, K, and Rosenberg, SM. "Evolutionary dynamics and information hierarchies in biological systems." Annals of the New York Academy of Sciences 1305, no. 1 (December 2013): 1-17. Full Text
  - Meluzzi, D, and Arya, G. "Recovering ensembles of chromatin conformations from contact probabilities." Nucleic Acids Research 41, no. 1 (January 2013): 63-75. Full Text Open Access Copy
  - Dobrovolskaia, IV, and Arya, G. "Dynamics of forced nucleosome unraveling and role of nonuniform histone-DNA interactions." Biophysical Journal 103, no. 5 (September 2012): 989-998. Full Text
  - Gao, B, Arya, G, and Tao, AR. "Self-orienting nanocubes for the assembly of plasmonic nanojunctions." Nature Nanotechnology 7, no. 7 (July 2012): 433-437. Full Text
  - Arman, B, Reddy, AS, and Arya, G. "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): 3247-3255. Full Text
  - Phadke, A, Zhang, C, Arman, B, Hsu, C-C, Mashelkar, RA, Lele, AK, Tauber, MJ, Arya, G, and Varghese, S. "Rapid self-healing hydrogels." Proceedings of the National Academy of Sciences of the United States of America 109, no. 12 (March 5, 2012): 4383-4388. Full Text
  - Meluzzi, D, Olson, KE, Dolan, GF, Arya, G, and Müller, UF. "Computational prediction of efficient splice sites for trans-splicing ribozymes." Rna (New York, N.Y.) 18, no. 3 (March 2012): 590-602. Full Text
  - Ayala, R, Zhang, C, Yang, D, Hwang, Y, Aung, A, Shroff, SS, Arce, FT, Lal, R, Arya, G, and Varghese, S. "Engineering the cell-material interface for controlling stem cell adhesion, migration, and differentiation." Biomaterials 32, no. 15 (May 2011): 3700-3711. Full Text
  - Maitra, A, and Arya, G. "Influence of pulling handles and device stiffness in single-molecule force spectroscopy." Physical Chemistry Chemical Physics : Pccp 13, no. 5 (February 2011): 1836-1842. Full Text
  - Yang, D, and Arya, G. "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): 2911-2921. Full Text
  - Lim, HL, Chuang, JC, Tran, T, Aung, A, Arya, G, and Varghese, S. "Dynamic Electromechanical Hydrogel Matrices for Stem Cell Culture." Advanced Functional Materials 21, no. 1 (January 7, 2011): 55-63. Full Text
  - Iyer, BVS, Kenward, M, and Arya, G. "Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations." Bmc Biophysics 4, no. 1 (2011): 8-8. Full Text
  - Arya, G. "Chain Stiffness and Attachment-Dependent Attraction between Polyelectrolyte-Grafted Colloids." The Journal of Physical Chemistry B 114, no. 48 (December 9, 2010): 15886-15896. Full Text
  - Sangaj, N, Kyriakakis, P, Yang, D, Chang, C-W, Arya, G, and Varghese, S. "Heparin mimicking polymer promotes myogenic differentiation of muscle progenitor cells." Biomacromolecules 11, no. 12 (December 2010): 3294-3300. Full Text
  - Dobrovolskaia, IV, Kenward, M, and Arya, G. "Twist propagation in dinucleosome arrays." Biophysical Journal 99, no. 10 (November 2010): 3355-3364. Full Text
  - Arya, G, Maitra, A, and Grigoryev, SA. "A structural perspective on the where, how, why, and what of nucleosome positioning." Journal of Biomolecular Structure & Dynamics 27, no. 6 (June 2010): 803-820. (Review) Full Text
  - Meluzzi, D, Smith, DE, and Arya, G. "Biophysics of knotting." Annual Review of Biophysics 39 (January 2010): 349-366. (Review) Full Text
  - Arya, G. "Energetic and Entropic Forces Governing the Attraction between Polyelectrolyte-Grafted Colloids." The Journal of Physical Chemistry B 113, no. 48 (December 3, 2009): 15760-15770. Full Text
  - Grigoryev, SA, Arya, G, Correll, S, Woodcock, CL, and 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, no. 32 (August 2009): 13317-13322. Full Text
  - Arya, G, and 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, no. 16 (April 2009): 4045-4059. Full Text
  - Hehmeyer, OJ, Arya, G, Panagiotopoulos, AZ, and Szleifer, I. "Monte Carlo simulation and molecular theory of tethered polyelectrolytes." The Journal of Chemical Physics 126, no. 24 (June 2007): 244902-null. Full Text
  - Arya, G, and Schlick, T. "Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo." The Journal of Chemical Physics 126, no. 4 (January 2007): 044107-null. Full Text
  - Arya, G, and 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, no. 44 (October 23, 2006): 16236-16241. Full Text
  - Arya, G, Zhang, Q, and Schlick, T. "Flexible histone tails in a new mesoscopic oligonucleosome model." Biophysical Journal 91, no. 1 (July 2006): 133-150. Full Text
  - Arya, G, and Panagiotopoulos, AZ. "Impact of Branching on the Phase Behavior of Polymers." Macromolecules 38, no. 25 (December 2005): 10596-10604. Full Text
  - Arya, G, Rottler, J, Panagiotopoulos, AZ, Srolovitz, DJ, and Chaikin, PM. "Shear Ordering in Thin Films of Spherical Block Copolymer." Langmuir 21, no. 24 (November 2005): 11518-11527. Full Text
  - Arya, G, and Panagiotopoulos, AZ. "Log-rolling micelles in sheared amphiphilic thin films." Physical Review Letters 95, no. 18 (October 28, 2005): 188301-null. Full Text
  - Arya, G, and Panagiotopoulos, AZ. "Molecular modeling of shear-induced alignment of cylindrical micelles." Computer Physics Communications 169, no. 1-3 (July 2005): 262-266. Full Text
  - Hehmeyer, OJ, Arya, G, and Panagiotopoulos, AZ. "Phase Transitions of Confined Lattice Homopolymers†." The Journal of Physical Chemistry B 108, no. 21 (May 2004): 6809-6815. Full Text
  - Arya, G, Chang, H-C, and Maginn, EJ. "Molecular Simulations of Knudsen Wall-slip: Effect of Wall Morphology." Molecular Simulation 29, no. 10-11 (October 2003): 697-709. Full Text
  - Kioupis, LI, Arya, G, and Maginn, EJ. "Pressure-enthalpy driven molecular dynamics for thermodynamic property calculation II: applications." Fluid Phase Equilibria 200, no. 1 (July 2002): 93-110. Full Text
  - Arya, G, Chang, H-C, and Maginn, EJ. "A critical comparison of equilibrium, non-equilibrium and boundary-driven molecular dynamics techniques for studying transport in microporous materials." The Journal of Chemical Physics 115, no. 17 (November 2001): 8112-8124. Full Text
  - Arya, G, Maginn, EJ, and Chang, H-C. "Effect of the Surface Energy Barrier on Sorbate Diffusion in AlPO4-5." The Journal of Physical Chemistry B 105, no. 14 (April 2001): 2725-2735. Full Text
  - Arya, G, Maginn, EJ, and Chang, H-C. "Efficient viscosity estimation from molecular dynamics simulation via momentum impulse relaxation." The Journal of Chemical Physics 113, no. 6 (August 8, 2000): 2079-2087. Full Text
  - Arya, G, Chang, H-C, and Maginn, EJ. "Knudsen Diffusivity of a Hard Sphere in a Rough Slit Pore(Published online)." Physical Review Letters 91, no. 2. Full Text
  - Arya, G, and Panagiotopoulos, AZ. "Monte Carlo study of shear-induced alignment of cylindrical micelles in thin films(Published online)." Physical Review E 70, no. 3. Full Text
  - Iyer, BVS, and Arya, G. "Lattice animal model of chromosome organization(Published online)." Physical Review E 86, no. 1. Full Text
  - Maitra, A, and Arya, G. "Model Accounting for the Effects of Pulling-Device Stiffness in the Analyses of Single-Molecule Force Measurements(Published online)." Physical Review Letters 104, no. 10. Full Text
  - Murthy, CR, Gao, B, Tao, AR, and Arya, G. "Automated quantitative image analysis of nanoparticle assembly(Published online)." Nanoscale 7, no. 21: 9793-9805. Full Text
  - Murthy, CR, Gao, B, Tao, AR, and Arya, G. "Dynamics of nanoparticle assembly from disjointed images of nanoparticle-polymer composites(Published online)." Physical Review E 93, no. 2. Full Text
  - Nam, G-M, and Arya, G. "Free-energy landscape of mono- and dinucleosomes: Enhanced rotational flexibility of interconnected nucleosomes(Published online)." Physical Review E 93, no. 3. Full Text
  - Root, SE, Jackson, NE, Savagatrup, S, Arya, G, and Lipomi, DJ. "Modelling the morphology and thermomechanical behaviour of low-bandgap conjugated polymers and bulk heterojunction films(Published online)." Energy & Environmental Science 10, no. 2: 558-569. Full Text
  - Singh, VV, Kaufmann, K, Orozco, J, Li, J, Galarnyk, M, Arya, G, and Wang, J. "Micromotor-based on–off fluorescence detection of sarin and soman simulants(Published online)." Chemical Communications 51, no. 56: 11190-11193. Full Text
- Book Sections
  - "Molecular Dynamics (MD) and Coarse Grain Simulation of High Strain-Rate Elastomeric Polymers (HSREP)." In Elastomeric Polymers with High Rate Sensitivity, 187-232.: Elsevier, 2015. Full Text
Teaching & Mentoring
Recent Courses
- ME 555: Advanced Topics in Mechanical Engineering 2019
- ME 490: Special Topics in Mechanical Engineering 2018

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Education, Training, & Certifications

In the News

Subject Headings

Selected Grants

Selected Publications

Academic Articles

Book Sections

Recent Courses