Journal articles:

42. Baokun Song, Jin Hou, Haonan Wang, Siraj Sidhik, Jinshui Miao, Honggang Gu, Huiqin Zhang, Shiyuan Liu, Zahra Fakhraai, Jacky Even, Jean-Christophe Blancon, Aditya D. Mohite, Deep Jariwala. “Determination of Dielectric Functions and Exciton Oscillator Strength of Two-Dimensional Hybrid Perovskites.” Under revisions, (2020)

41. Baokun Song, Fang Liu, Haonan Wang, Jinshui Miao, Yueli Chen, Pawan Kumar, Huiqin Zhang, Xiwen Liu, Honggang Gu, Eric A. Stach, Xuelei Liang, Shiyuan Liu, Zahra Fakhraai, and Deep Jariwala. “Giant Gate-Tunability of Complex Refractive Index in Semiconducting Carbon Nanotubes.” ACS Photonics, (2020)

40. Aixi Zhang, Yi Jin, Tianyi Liu, Richard B. Stephens, and Zahra Fakhraai. “Polyamorphism of vapor-deposited amorphous selenium in response to light.” Proceedings of the National Academy of Sciences,  (2020).

39. Sunghee Lee, Connor N. Woods, Omar Ibrahim, Sung Wook Kim, Seung Beom Pyun, Eun Chul Cho, Zahra Fakhraai, and So-Jung Park. “Distinct Optical Magnetism in Gold and Silver Probed by Dynamic Metamolecules.” J. Phys. Chem. C, 124, 37, 20436–20444 (2020).

Abstract Image

38. Connor R. Bilchak, Shivajee Govind, Guillermo Contreas, Boris Rasin, Shawn M. Maguire, Russell J. Composto, and Zahra Fakhraai. “Kinetic Monitoring of Block Copolymer Self-Assembly Using In Situ Spectroscopic Ellipsometry.ACS Macro Letters9, 8, 1095-1101 (2020).Abstract Image


37. Yi-Chih Lin, Hiroaki Komatsu, Jianqiang Ma, Paul H. Axelsen, and Zahra Fakhraai. “Identifying Polymorphs of Amyloid-β (1-40) Fibrils Using High-Resolution Atomic Force Microscopy.” The Journal of Physical Chemistry B, 123,10376-10383 (2019).

36. Haonan Wang, Yiwei Qiang, Ahmad Arabi Shamsabadi, Pratnik Mazumder, Kevin T. Turner, Daeyeon Lee, and Zahra Fakhraai. “Thermal Degradation of Polystyrene under Extreme Nanoconfinement.” ACS Macro Letters8, 11, 1413-1418 (2019).

35. Yi-Chih Lin, Murray Skolnick, and Zahra Fakhraai. “A Novel Method to Measure the Effective Change of the Interfacial Energy Due to Kinetic Self-Assembly of Amyloid Fibrils.” The Journal of Physical Chemistry B, 123, 32, 6990-6996 (2019).

Abstract Image

34. Devika Sil, Christopher Lane, Ethan Glor, Kyle D. Gilroy, Safiya Sylla, Bernardo Barbiellini, Robert Markiewicz, Maryam Hajfathalian, Svetlana Neretina, Arun Bansil, Zahra Fakhraai and Eric Borguet. “Synthesis and Properties of Au Hydride.” ChemistrySelect 4.14, 4287-4292 (2019).

33. Subarna Samanta, Georgia Huang, Gui Gao, Yue Zhang, Aixi Zhang, Sarah Wolf, Connor Woods, Yi Jin, Patrick J Walsh, and Zahra Fakhraai, “Exploring the Importance of Surface Diffusion in Stability of Vapor-Deposited Organic Glasses“, The Journal of Physical Chemistry B, 123, 18, 4108-4117 (2019).

Abstract Image

32. Alex R. Moore, Georgia Huang, Sarah Wolf, Patrick J. Walsh, Zahra Fakhraai, and Robert A. Riggleman, “Effects of Microstructure Formation on the Stability of Vapor Deposited Glasses“, Proceedings of the National Academy of Sciences (2019): 201821761. (arXiv:1810.06419)

31. Yue Zhang, Connor N. Woods, Mauricio Alvarez, Yi Jin, Robert A. Riggleman, and Zahra Fakhraai, ” Effect of Substrate Interactions on the Glass Transition and Length-scale of Correlated Dynamics in Ultra-thin Molecular Glass Films“, J. Phys. Chem149, 184902 (2018).

30. Yang Zhang, Chen Li, Zahra Fakhraai, Basem Moosa, Peng Yang, and Niveen M. Khashab, “Synthesis of Spiked Plasmonic Nanorods with an Interior Nanogap for Quantitative Surface-Enhanced Raman Scattering Analysis“, ACS Omega3(10), 14399-14405 (2018). 

Figure 1


29. Jyo Lyn Hor, Haonan Wang, Zahra Fakhraai, and Daeyeon Lee, “Effect of Physical Nanoconfinement on the Viscosity of Unentangled Polymers during Capillary Rise Infiltration.” Macromolecules51 (14), 5069–5078 (2018).

28. Haonan Wang, Jyo Lyn Hor, Yue Zhang, Tianyi Liu, Daeyeon Lee, and Zahra Fakhraai, “Dramatic Increase in Polymer Glass Transition Temperature under Extreme Nanoconfinement in Weakly-Interacting Nanoparticle Films.” ACS nano12 (6), 5580–5587 (2018).

27. Yi-Chih Lin, Chen Li, and Zahra Fakhraai, “Kinetics of Surface-Mediated Fibrillization of Amyloid-β (12-28) Peptides.Langmuir,  34 (15), 4665–4672(2018).

26. Chen Li, Sunghee Lee, Zhaoxia Qian, Connor Woods, So-Jung Park, and Zahra Fakhraai. “Controlling Magnetic Dipole Resonance in Raspberry-like Metamolecules.” The Journal of Physical Chemistry C, 122 (12), 6808–6817 (2018).

25. Jyo Lyn Hor, Haonan Wang, Zahra Fakhraai, and Daeyeon Lee. “Effect of Polymer-Nanoparticle Interactions on the Viscosity of Unentangled Polymers under Extreme Nanoconfinement during Capillary Rise Infiltration.” Soft Matter, 14, 2438-2446 (2018).

Graphical abstract: Effects of polymer–nanoparticle interactions on the viscosity of unentangled polymers under extreme nanoconfinement during capillary rise infiltration

24. Ferrie, John J., Conor M. Haney, Jimin Yoon, Buyan Pan, Yi-Chih Lin, Zahra Fakhraai, Elizabeth Rhoades, Abhinav Nath, and E. James Petersson. “Using a FRET Library with Multiple Probe Pairs To Drive Monte Carlo Simulations of α-Synuclein.” Biophysical Journal, 114, no. 1 (2018): 53-64.

23. E. D. Cubuk, R. J. S. Ivancic, S. S. Schoenholz, D. J. Strickland, A. Basu, Z. S. Davidson, J. Fontaine, J. L. Hor, Y.-R. Huang, Y. Jiang, N. C. Keim, K. D. Koshigan, J. A. Lefever, T. Liu, X.-G. Ma, D. J. Magagnosc, E. Morrow, C. P. Ortiz, J. M. Rieser, A. Shavit, T. Still, Y. Xu, Y. Zhang, K. N. Nordstrom, P. E. Arratia, R. W. Carpick, D. J. Durian, Z. Fakhraai, D. J. Jerolmack, Daeyeon Lee, Ju Li, R. Riggleman, K. T. Turner, A. G. Yodh, D. S. Gianola, Andrea J. Liu, “Structure-property relationships from universal signatures of plasticity in disordered solids”, Science, 358, 1033-1037 (2017).


22. Tianyi Liu, Annemarie L. Exarhos, Ethan C. Alguire, Feng Gao, Elmira Salami-Ranjbaran, Kevin Cheng, Tiezheng Jia, Joseph E. Subotnik, Patrick J. Walsh, James M. Kikkawa, and Zahra Fakhraai, “Birefringent Stable Glass with Predominantly Isotropic Molecular Orientation”Physical Review Letters, 119, 095502 (2017).

21. Ethan C. Glor, Gabriel V. Angrand, and Zahra Fakhraai, “Exploring the Broadening and the Existence of Two Glass Transitions Due to Competing  Interfacial Effects in Thin Supported Polymer Films”, The Journal of Chemical Physics, 146, 203330 (2017).

20. Yue Zhang and Zahra Fakhraai, “Decoupling of Surface Diffusion and Relaxation Dynamics of Molecular Glasses”Proceedings of the National Academy of Sciences, 117, 4915–4919 (2017).

19. Yi-Chih Lin, Milton H. Repollet-Pedrosa, John J. Ferrie, E. James Petersson, and Zahra Fakhraai, “Potential Artifacts in Sample Preparation Methods Used for Imaging Amyloid Oligomers and Protofibrils due to Surface-Mediated Fibril Formation”The Journal of Physical Chemistry B, 121, 2534–2542 (2017).

18. Ethan C. Glor, Robert C. Ferrier, Chen Li, Russell J. Composto, and Zahra Fakhraai. “Out-of-Plane Orientation Alignment and Reorientation Dynamics of Gold Nanorods in Polymer Nanocomposite Films.” Soft Matter 13, 2207-2215 (2017).

17. Y. Zhang, and Z. Fakhraai, “Invariant Fast Diffusion on the Surfaces of Ultrastable and Aged Molecular Glasses”, Phys. Rev. Lett., 118, 066101 (2017).

16. Y. Lin, H. Komatsu, J. Ma, P. H. Axelsen and Z. Fakhraai, “Quantitative analysis of amyloid polymorphism using height histograms to correct for tip convolution effects in atomic force microscopy imaging”RSC Adv., 6, 114286 (2016) .


15. Y. Zhang, R. Potter, W, Zhang and Z. Fakhraai, “Using Tobacco Mosaic Virus to Probe Enhanced Surface Diffusion of Molecular Glasses”Soft Matter, 12, 9115-9120 (2016).


14. Y. Zhang, E. Glor, M. Li, T. Liu, K. Wahid, W. Zhang, R. Riggleman and Z. Fakhraai, “Long-range correlated dynamics in ultra-thin molecular glass films”J. Chem. Phys. 145, 114502 (2016)


13. E. Glor, and Z. Fakhraai, “Cooling Rate Dependent Ellipsometry Measurements to Determine the Dynamics of Thin Glassy Films”J. Vis. Exp., 107, e53499 (2016).

12. Z. Qian, C. Li, Z. Fakhraai and S.J. Park, “Unusual Weak Interparticle-Distance Dependence in Raman Enhancement from Nanoparticle Dimers”J. Phys. Chem. C.120, 1824–1830 (2016).


11. E. Glor, R. J. Composto and Z. Fakhraai, “Glass Transition Dynamics and Fragility of Ultrathin Miscible Polymer Blend Films”, Macromolecules48, 6682–6689 (2015).


10. T. Liu, K. Cheng, E. Salami, F. Gao, C. Li, X. Tong, Y. Lin, Y. Zhang, W. Zhang, L. Klinge, P. Walsh and Z. Fakhraai, “The effect of chemical structure on the stability of physical vapor deposited glasses of 1,3,5-triarylbenzene”J. Chem. Phys., 143, 084506 (2015).


9. T. Liu, K. Cheng, E. Salami, F. Gao, E. Glor, M. Li, S. Link, P. Walsh and Z. Fakhraai,“Synthesis and High-Throughput Characterization of Structural Analogues of Molecular Glassformers: 1,3,5-Trisarylbenzenes”, Soft Matter, 11, 7558-7566 (2015).


8. S. P. Hastings, Z. Qian, P. Swanglap, Y. Fang, N. Engheta, S.J. Park, S. Link, and Z. Fakhraai,“Modal interference in spicky nanoshells”, Optics Express, 23, 11290-11311 (2015).


7. Z. Qian, S.P. Hastings, C. Li, B. Edward, C.K. McGinn, N. Engheta, Z. Fakhraai and S.J. Park,“Raspberry-like Metamolecules Exhibiting Strong Magnetic Resonances”ACS Nano,  9,1263–1270 (2015). Featured in PennNews!


6. E. Glor, and Z. Fakhraai, “Facilitation of Interfacial Dynamics in Entangled Polymer Films“, J.Chem. Phys., 141, 194505 (2014).

5. Y. Lin, E.J. Peterson, and Z. Fakhraai, “Surface Effects Mediate Self-Assembly of Amyloid-β Peptides”, ACS Nano, 8, 10178–10186 (2014).


4. S. P. Hastings, P. Swanglap, Z. Qian, Y. Fang, S.J. Park, S. Link, N. Engheta, and Z. Fakhraai, “Quadrupole-Enhanced Raman Scattering“, ACS Nano, 8, 9025–9034 (2014).


3. B. Sanchez-Gaytan, Z. Qian, S. Hastings, M. Reca, Z. Fakhraai, and S. J. Park, “Controlling the Topography and Surface Plasmon Resonance of Gold Nanoshells by a Templated Surfactant-Assisted Seed Growth Method ”, J. Phys. Chem. C. 117, 8916-8923 (2013).


2. B. L. Sanchez-Gaytan, P. Zwanglap, T. J. Lamkin, Z. Fakhraai, S. Link, and S. J. Park,“Synthesis and Optical Properties of Spiky Gold Nanoshells”, J. Phys. Chem. C, 116, 10318-10324 (2012).


1. C. R. Daley, Z. Fakhraai, M. D. Ediger, and J. A. Forrest, “Comparing Surface and Bulk Flow of a Molecular Glass Former”, Soft Matter, 8, 2206-2212 (2012).



Proceedings, Book Chapters, and Other Publications

1. Z. Fakhraai, “Teaching STEM at the Time of Political Distress”University of Pennsylvania Almanac, Talk about Teaching and Learning, Vol 63, No 20, (2017).



Previous Publications

18. S. S. Dalal, Z. Fakhraai, and M. D. Ediger, “High-Throughput Ellipsometric Characterization of Vapor-Deposited Indomethacin Glasses”J. Phys. Chem. B. 117, 15415–15425 (2013).


17. S. S. Dalal, A. Sepúlveda, G. K. Pribil, Z. Fakhraai, and M. D. Ediger,  Density and birefringence of a highly stable α,α,β-trisnaphthylbenzene glass ”, J. Chem. Phys. 136, 204501 (2012).

16. M. Paulite, Z. Fakhraai, N. Gunari, A. Tanur, and G. C. Walker, “Imaging Secondary Structure of Individual Amyloid Fibrils of a β(2)-Microglobulin Fragment Using Near-Field Infrared Spectroscopy”, J. Am. Chem. Soc. 133, 7376- 7383 (2011).


15. Z. Fakhraai, T. Still, G. Fytas, and M. D. Ediger “Structural Variations of an Organic Glass-former”, J. Phys. Chem. Lett. 2, 423- 427 (2011).


14. Z.Fakhraai, D. Qi and J. A. Forrest, “Relation between Enhanced Surface Mobility and Tg Reduction in Thin Polymer films”, Abstract of Papers of the American Chemical Society, 242, 295-PMSE (2011).

13. V. H. Niri, B. K. Flatt, Z. Fakhraai, and J. A. Forrest “Simultaneous Monitoring of Electroformation of Phospholipid Vesicles by Quartz Crystal Microbalance and Optical Microscopy”, Chemistry and Physics of Lipids, 163, 36- 41 (2011).

12. L. Stebounova, M. Paulite, Z. Fakhraai, and G. C. Walker, “Biological Imaging Using Near-Field Scanning Microscopy”, Book Chapter in Comprehensive Nansocience and Nanotechnology by D. Andrews, G. Scholes, G. Wiederechts, Elsevier, 2011, ISBN: 978-0-12-374390-9.

11. R. Leal, C. T. Souza, M. R. da Silva, Z. Fakhraai, J. A. Forrest, and R. M. Papaleo “Relaxation of Surface Tracks of Polycarbonate Thin Films Induced by MeV Heavy-Ion Impacts”, Nuclear Instruments & Methods in Physics Research Section B – Beam Interactions with Materials and Atoms, 268, 3080- 3083(2010).

10. M. Paulit e, Z. Fakhraai, B. B. Akhremitchev, K. Mueller, and G. C. Walker, “Assembly, Tunning and Use of an Apertureless Near field Infrared Microscope for Protein Imaging”, Journal of Visualized Experiments, 33, e1581, (2009). (Video)

9. M. J. Kofke, D. H. Waldeck, Z. Fakhraai, S. Ip, and G. C. Walker, “The Effect of Periodicity on the Extraordinary Optical Transmission of Annular Aperture Arrays”, Appl. Phys. Lett. 94, 023104 (2009).

8. D. Qi, Z. Fakhraai, and J. A. Forrest, “Substrate and Chain Size Dependence of Near Surface Dynamics of Glassy Polymers”, Phys. Rev. Lett.101, 096101(2008).

7. K. Mueller, X. Yang, M. Paulite, Z. Fakhraai, N. Gunari, and G. C. Walker, “Chemical Imaging of the Surface of Self-Assembled Polystyrene-b-Poly(methyl methacrylate) Diblock Copolymer Films Using Apertureless Near-Field IR Microscopy”, Langmuir, 24, 6946- 6951 (2008).

6. Z. Fakhraai and J. A. Forrest, “Measuring the Surface Dynamics of Glassy Polymers”, Science, 319, 600- 604 (2008).

5. J. S. Sharp, J. A. Forrest, Z. Fakhraai, M. Khomenko, J. H. Teichroeb, K. Dalnoki-Veress, “Reply to Comment on “The Properties of Fee Polymer Surfaces and Their Effect upon the Glass Transition Temperature of Thin Polystyrene Films ” by S.A. Hutcheson and G.B. McKenna ”,Eur. Phys. J. E. 22, 287- 291 (2007).

4. Z. Fakhraai, and J. A. Forrest, “Probing Slow Dynamics in Supported Thin Polymer Films”,Phys. Rev. Lett. 95, 025701 (2005).

3. Z. Fakhraai, S. Valadkhan, J. A. Forrest, “Qualitative Discrepancy Between Different Measures of Dynamics in Thin Polymer Films ”, Eur. Phys. J. E. 18, 143- 148 (2005).

2. J. A. Forrest, and Z. Fakhraai, “Anomalous Long and Short Time Dynamics in Thin Films of Polystyrene ”, Abstract of Papers of the American Chemical Society, 229, 298-PMSE (2005).

1. Z. Fakhraai, J. S. Sharp, J. A. Forrest, “Effect of Sample Preparation on the Glass-Transition of Thin Polystyrene Films”, J. Poly. Sci. B – Poly. Phys. 42, 4503- 4507 (2004).