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K.-C. Lee, Ajay Gopinathan, J. M. Schwarz, "Modeling the formation of in vitro filopodia", arXiv:0909.2594v1 (2009), Submitted to Journal of Theoretical Biology
 
Justin Yamada; Joshua L Phillips; Samir Patel; Gabriel Goldfien; Alison Calestagne-Morelli; Hans Huang; Ryan Reza; Justin Acheson; Viswanathan Krishnan; Shawn Newsam; Ajay Gopinathan; Edmond Y Lau; Michael Colvin; Vladimir N Uversky; Michael F Rexach, “A Bimodal Distribution of Two Distinct Categories of Natively Unfolded Structures with Separate Functions in FG Nucleoporins”, Submitted to Cell 
 
Sarah A. Nowak, Buddhapriya Chakrabarti, Tom Chou, and Ajay Gopinathan, "Frequency-dependent Chemotactic Target Selection", Submitted to: PLoS Com. Bio., (2009)
 
David S. Dean and Ajay Gopinathan, "The Non-equilibrium Behavior of Pseudo-Casimir Forces", J. Stat. Mech. L08001 (2009)
 
Chi-Cheng Fu, Anthony Grimes, Maureen Long, Christopher G. L. Ferri, Brent D. Rich, Somnath Ghosh, Sayantani Ghosh, Luke P. Lee, Ajay Gopinathan, Michelle Khine, "Tunable Nanowrinkles on Shape Memory Polymer Sheets", Advanced Materials (Early view : DOI 10.1002/adma.200902294)
 
 Igor Goncharenko and Ajay Gopinathan, “Optimal Kinetics for Chaperonin Assisted Protein Folding”, IAENG Transactions on Engineering Technologies 2, p13 (2009)
 
 Igor Goncharenko and Ajay Gopinathan, “Optimal Yield Rates in Enzymatic Reactions with Undesirable Intermediate States”, Proceedings of the International Conference on Computational Biology (WCECS 2008), p24 (2008)
 
Mark L. Henle, Brian DiDonna, Christian D. Santangelo, and Ajay Gopinathan, “Diffusion and binding of finite-size particles in confined geometries”, Phys. Rev. E 78, 031118 (2008)
 
Ajay Gopinathan and Y.W. Kim, “Polymer Translocation in Crowded Environments” Phys. Rev. Lett., 99, 228106 (2007)

Ajay Gopinathan, J. Schwarz, K.C. Lee and A.J. Liu, “Branching, Capping, and Severing in Dynamic Actin Structures”,  Phys. Rev. Lett. 99, 058103 (2007)

Wanli Ma, Ajay Gopinathan and Alan. J. Heeger, “Nanostructure of the Interpenetrating Networks in Poly(3-hexylthiophene)/fullerene Bulk Heterojunction Materials: Implications for Charge Transport”, Advanced Materials, 19(21), 3656 (2007)

N. Gov, A. Gopinathan, “Dynamics of Membranes Driven by Actin Polymerization”,  Biophys .J , 90(2), 454 (2006)
 
Ajay Gopinathan, “ Kinetic Self-Assembly of Metals on Co-Polymer Templates”,  Phys. Rev. E, 71(4) 041601 (2005)

Ajay Gopinathan, D.G. Grier, “Statistically Locked-in Transport through Periodic Potential Arrays”, Phys. Rev. Lett., 92, 130602 (2004)

Ajay Gopinathan, T.A. Witten, “Defect Formation and Kinetics of Atomic Terrace Merging”, Phys. Rev. E., 70, 041603 (2004)

 Ajay Gopinathan, T.A. Witten  and  S.C. Venkataramani, “Trapping of Vibrational Energy in Crumpled Sheets”  Phys. Rev. E., 65, 036613 (2002)

Ajay Gopinathan, T. Zhou, S.N. Coppersmith, L.P. Kadanoff and D.G. Grier, “Weak Long Range Casimir Attraction in Colloidal Crystals” Europhys. Lett., 57 (3), 451 (2002)

Ajay Gopinathan “Scaling Exponent β for Coarsening in a 1D q-state Potts System” J. Phys. A. 31, 5499 (1998)