Gaurav Arya - Publications

Engineering Sciences (Engineering Physics) University of California, San Diego, La Jolla, CA 
General Engineering, General Biophysics

60 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Nam GM, Arya G. Free-energy landscape of mono- and dinucleosomes: Enhanced rotational flexibility of interconnected nucleosomes. Physical Review. E. 93: 032406. PMID 27078389 DOI: 10.1103/PhysRevE.93.032406  1
2016 Murthy CR, Gao B, Tao AR, Arya G. Dynamics of nanoparticle assembly from disjointed images of nanoparticle-polymer composites. Physical Review. E. 93: 022501. PMID 26986370 DOI: 10.1103/PhysRevE.93.022501  1
2016 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 Letters. PMID 26765039 DOI: 10.1021/acs.nanolett.5b04821  1
2016 Meluzzi D, Arya G. Quantification of DNA cleavage specificity in Hi-C experiments. Nucleic Acids Research. 44: e4. PMID 26264668 DOI: 10.1093/nar/gkv820  1
2016 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. Journal of Biomolecular Structure & Dynamics. 1-16. PMID 26196228 DOI: 10.1080/07391102.2015.1068224  1
2016 Arya G. Models for recovering the energy landscape of conformational transitions from single-molecule pulling experiments Molecular Simulation. 42: 1102-1115. DOI: 10.1080/08927022.2015.1123257  1
2016 Root SE, Savagatrup S, Pais CJ, Arya G, Lipomi DJ. Predicting the Mechanical Properties of Organic Semiconductors Using Coarse-Grained Molecular Dynamics Simulations Macromolecules. 49: 2886-2894. DOI: 10.1021/acs.macromol.6b00204  1
2015 Gurunatha KL, Marvi S, Arya G, Tao AR. Computationally Guided Assembly of Oriented Nanocubes by Modulating Grafted Polymer-Surface Interactions. Nano Letters. PMID 26457977 DOI: 10.1021/acs.nanolett.5b02748  1
2015 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 Biomaterials Science & Engineering. 1: 7-12. PMID 26280019 DOI: 10.1021/ab500021a  1
2015 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. Chemical Communications (Cambridge, England). 51: 11190-3. PMID 26072740 DOI: 10.1039/c5cc04120a  1
2015 Murthy CR, Gao B, Tao AR, Arya G. Automated quantitative image analysis of nanoparticle assembly. Nanoscale. 7: 9793-805. PMID 25963444 DOI: 10.1039/c5nr00809c  1
2015 Meluzzi D, 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: 064120. PMID 25563926 DOI: 10.1088/0953-8984/27/6/064120  1
2015 Takahashi T, Vo Ngo BC, Xiao L, Arya G, Heller MJ. Molecular mechanical properties of short-sequence peptide enzyme mimics Journal of Biomolecular Structure and Dynamics. DOI: 10.1080/07391102.2015.1039586  1
2015 Hattemer GD, Arya G. Viscoelastic properties of polymer-grafted nanoparticle composites from molecular dynamics simulations Macromolecules. 48: 1240-1255. DOI: 10.1021/ma502086c  1
2015 Oswald J, Arya G, Cui Z, Brinson LC. 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 Elastomeric Polymers With High Rate Sensitivity: Applications in Blast, Shockwave, and Penetration Mechanics. 216-232. DOI: 10.1016/B978-0-323-35400-4.00005-2  1
2014 Migliori AD, Smith DE, Arya G. Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor. Journal of Molecular Biology. 426: 4002-17. PMID 25311860 DOI: 10.1016/j.jmb.2014.09.023  1
2014 Nam GM, Arya G. Torsional behavior of chromatin is modulated by rotational phasing of nucleosomes. Nucleic Acids Research. 42: 9691-9. PMID 25100871 DOI: 10.1093/nar/gku694  1
2014 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. Nature Communications. 5: 4173. PMID 24937091 DOI: 10.1038/ncomms5173  1
2014 Agrawal V, Arya G, Oswald J. Simultaneous iterative boltzmann inversion for coarse-graining of polyurea Macromolecules. 47: 3378-3389. DOI: 10.1021/ma500320n  1
2013 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. Annals of the New York Academy of Sciences. 1305: 1-17. PMID 23691975 DOI: 10.1111/nyas.12140  1
2013 Meluzzi D, Arya G. Recovering ensembles of chromatin conformations from contact probabilities. Nucleic Acids Research. 41: 63-75. PMID 23143266 DOI: 10.1093/nar/gks1029  1
2013 Keller NA, Migliori AD, Arya G, Rao VB, Smith DE. Testing a structural model for viral DNA packaging motor function by optical tweezers measurements, site directed mutagenesis, and molecular dynamics calculations Proceedings of Spie - the International Society For Optical Engineering. 8810. DOI: 10.1117/12.2027158  1
2012 Dobrovolskaia IV, Arya G. Dynamics of forced nucleosome unraveling and role of nonuniform histone-DNA interactions. Biophysical Journal. 103: 989-98. PMID 23009848 DOI: 10.1016/j.bpj.2012.07.043  1
2012 Iyer BV, Arya G. Lattice animal model of chromosome organization. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 86: 011911. PMID 23005456 DOI: 10.1103/PhysRevE.86.011911  1
2012 Gao B, Arya G, Tao AR. Self-orienting nanocubes for the assembly of plasmonic nanojunctions. Nature Nanotechnology. 7: 433-7. PMID 22683842 DOI: 10.1038/nnano.2012.83  1
2012 Phadke A, Zhang C, Arman B, Hsu CC, Mashelkar RA, Lele AK, Tauber MJ, Arya G, Varghese S. Rapid self-healing hydrogels. Proceedings of the National Academy of Sciences of the United States of America. 109: 4383-8. PMID 22392977 DOI: 10.1073/pnas.1201122109  1
2012 Meluzzi D, Olson KE, Dolan GF, Arya G, Müller UF. Computational prediction of efficient splice sites for trans-splicing ribozymes. Rna (New York, N.Y.). 18: 590-602. PMID 22274956 DOI: 10.1261/rna.029884.111  1
2012 Migliori A, Arya G, Smith DE. Experimental and computational studies on the DNA translocation mechanism of the T4 viral packaging motor Proceedings of Spie - the International Society For Optical Engineering. 8458. DOI: 10.1117/12.930390  1
2012 Holzworth K, Williams G, Arman B, Guan Z, Arya G, Nemat-Nasser S. Polyurea with hybrid polymer grafted nanoparticles: A parametric study Asme International Mechanical Engineering Congress and Exposition, Proceedings (Imece). 8: 719-720. DOI: 10.1115/IMECE2012-88395  1
2012 Arman B, Reddy AS, Arya G. Viscoelastic properties and shock response of coarse-grained models of multiblock versus diblock copolymers: Insights into dissipative properties of polyurea Macromolecules. 45: 3247-3255. DOI: 10.1021/ma3001934  1
2011 Lim HL, Chuang JC, Tran T, Aung A, Arya G, Varghese S. Dynamic Electromechanical Hydrogel Matrices for Stem Cell Culture. Advanced Functional Materials. 21. PMID 24273479 DOI: 10.1002/adfm.201001519  1
2011 Iyer BV, Kenward M, Arya G. Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations. Bmc Biophysics. 4: 8. PMID 21595865 DOI: 10.1186/2046-1682-4-8  1
2011 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. 32: 3700-11. PMID 21396708 DOI: 10.1016/j.biomaterials.2011.02.004  1
2011 Yang D, Arya G. Structure and binding of the H4 histone tail and the effects of lysine 16 acetylation. Physical Chemistry Chemical Physics : Pccp. 13: 2911-21. PMID 21157623 DOI: 10.1039/c0cp01487g  1
2011 Maitra A, Arya G. Influence of pulling handles and device stiffness in single-molecule force spectroscopy. Physical Chemistry Chemical Physics : Pccp. 13: 1836-42. PMID 20938520 DOI: 10.1039/c0cp01528h  1
2010 Dobrovolskaia IV, Kenward M, Arya G. Twist propagation in dinucleosome arrays. Biophysical Journal. 99: 3355-64. PMID 21081084 DOI: 10.1016/j.bpj.2010.09.055  1
2010 Arya G. Chain stiffness and attachment-dependent attraction between polyelectrolyte-grafted colloids. The Journal of Physical Chemistry. B. 114: 15886-96. PMID 21069987 DOI: 10.1021/jp1029085  1
2010 Sangaj N, Kyriakakis P, Yang D, Chang CW, Arya G, Varghese S. Heparin mimicking polymer promotes myogenic differentiation of muscle progenitor cells. Biomacromolecules. 11: 3294-300. PMID 21058638 DOI: 10.1021/bm101041f  1
2010 Maitra A, Arya G. Model accounting for the effects of pulling-device stiffness in the analyses of single-molecule force measurements. Physical Review Letters. 104: 108301. PMID 20366455 DOI: 10.1103/PhysRevLett.104.108301  1
2010 Arya G, Maitra A, Grigoryev SA. A structural perspective on the where, how, why, and what of nucleosome positioning. Journal of Biomolecular Structure & Dynamics. 27: 803-20. PMID 20232935 DOI: 10.1080/07391102.2010.10508585  1
2010 Meluzzi D, Smith DE, Arya G. Biophysics of knotting. Annual Review of Biophysics. 39: 349-66. PMID 20192771 DOI: 10.1146/annurev.biophys.093008.131412  1
2009 Arya G. Energetic and entropic forces governing the attraction between polyelectrolyte-grafted colloids. The Journal of Physical Chemistry. B. 113: 15760-70. PMID 19842639 DOI: 10.1021/jp908007z  1
2009 Grigoryev SA, Arya G, Correll S, Woodcock CL, 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: 13317-22. PMID 19651606 DOI: 10.1073/pnas.0903280106  1
2009 Arya G, 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: 4045-59. PMID 19298048 DOI: 10.1021/jp810375d  1
2007 Hehmeyer OJ, Arya G, Panagiotopoulos AZ, Szleifer I. Monte Carlo simulation and molecular theory of tethered polyelectrolytes. The Journal of Chemical Physics. 126: 244902. PMID 17614585 DOI: 10.1063/1.2747600  1
2007 Arya G, Schlick T. Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo. The Journal of Chemical Physics. 126: 044107. PMID 17286462 DOI: 10.1063/1.2428305  1
2006 Arya G, 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: 16236-41. PMID 17060627 DOI: 10.1073/pnas.0604817103  1
2006 Arya G, Zhang Q, Schlick T. Flexible histone tails in a new mesoscopic oligonucleosome model. Biophysical Journal. 91: 133-50. PMID 16603492 DOI: 10.1529/biophysj.106.083006  1
2005 Arya G, Panagiotopoulos AZ. Log-rolling micelles in sheared amphiphilic thin films. Physical Review Letters. 95: 188301. PMID 16383952 DOI: 10.1103/PhysRevLett.95.188301  1
2005 Arya G, Rottler J, Panagiotopoulos AZ, Srolovitz DJ, Chaikin PM. Shear ordering in thin films of spherical block copolymer. Langmuir : the Acs Journal of Surfaces and Colloids. 21: 11518-27. PMID 16285835 DOI: 10.1021/la0516476  1
2005 Arya G, Panagiotopoulos AZ. Molecular modeling of shear-induced alignment of cylindrical micelles Computer Physics Communications. 169: 262-266. DOI: 10.1016/j.cpc.2005.03.060  1
2005 Hehmeyer OJ, Arya G, Panagiotopoulos AZ. Monte Carlo simulations and self-consistent mean field theory of polyelectrolyte brushes Aiche Annual Meeting, Conference Proceedings. 5057.  1
2004 Arya G, Panagiotopoulos AZ. Monte Carlo study of shear-induced alignment of cylindrical micelles in thin films. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 70: 031501. PMID 15524524 DOI: 10.1103/PhysRevE.70.031501  1
2004 Hehmeyer OJ, Arya G, Panagiotopoulos AZ. Phase transitions of confined lattice homopolymers Journal of Physical Chemistry B. 108: 6809-6815.  1
2003 Arya G, Chang HC, Maginn EJ. Knudsen diffusivity of a hard sphere in a rough slit pore. Physical Review Letters. 91: 026102. PMID 12906494 DOI: 10.1103/PhysRevLett.91.026102  1
2003 Arya G, Chang HC, Maginn EJ. Molecular simulations of knudsen wall-slip: Effect of wall morphology Molecular Simulation. 29: 697-709. DOI: 10.1080/0892702031000103257  1
2002 Kioupis LI, Arya G, Maginn EJ. Pressure-enthalpy driven molecular dynamics for thermodynamic property calculation II: Applications Fluid Phase Equilibria. 200: 93-110. DOI: 10.1016/S0378-3812(02)00015-8  1
2001 Arya G, Chang HC, Maginn EJ. A critical comparison of equilibrium, non-equilibrium and boundary-driven molecular dynamics techniques for studying transport in microporous materials Journal of Chemical Physics. 115: 8112-8124. DOI: 10.1063/1.1407002  1
2001 Arya G, Maginn EJ, Chang HC. Effect of the surface energy barrier on sorbate diffusion in A1PO4-5 Journal of Physical Chemistry B. 105: 2725-2735.  1
2000 Arya G, Maginn EJ, Chang HC. Efficient viscosity estimation from molecular dynamics simulation via momentum impulse relaxation Journal of Chemical Physics. 113: 2079-2087. DOI: 10.1063/1.482019  1
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