Journal articles:

54. Zhang, A.; Moore, A. R.; Zhao, H.; Govind, S.; Wolf, S. E.; Jin, Y.; Walsh, P.; Riggleman, R. A.; Fakhraai, Z. The Role of Intra-molecular Relaxations on the Structure and Stability of vapor-Deposited GlassesThe Journal of Chemical Physics 2022, 156(24), 244703. DOI: 10.1063/5.0087600

53.  Lee, S.; Ibrahim, O.; Fakhraai, Z.; Park, S.-J. Heterogeneity in Dynamic MetamoleculesThe Journal of Physical Chemistry C 2022, 126(15), 6668-6677. DOI:10.1021/acs.jpcc.2c01214

52. Sarah E. Wolf, S. F., Aixi Zhang, Haoqiang Zhao, Patrick J. Walsh, Kevin T. Turner, and Zahra Fakhraai, Role of Molecular Layering in the Enhanced Mechanical Properties of Stable Glasses. The Journal of Physical Chemistry Letters 2022, 13(15), 3360-3368. DOI: 10.1021/acs.jpclett.2c00232

51. Burel, C.; Ibrahim, O.; Marino, E.; Bharti, H.; Murray, C. B.; Donnio, B.; Fakhraai, Z.; Dreyfus, R., Tunable Plasmonic Microcapsules with Embedded Noble Metal Nanoparticles for Optical MicrosensingACS Applied Nano Materials 2022, 5 (2), 2828-2838. DOI: 10.1021/acsanm.1c04542

50. Wolf, S. E.; Liu, T.; Govind, S.; Zhao, H.; Huang, G.; Zhang, A.; Wu, Y.; Chin, J.; Cheng, K.; Salami-Ranjbaran, E., Design of a homologous series of molecular glassformersThe Journal of Chemical Physics 2021, 155 (22), 224503. DOI: 10.1063/5.0066410

49. Maguire, S. M.; Bilchak, C. R.; Corsi, J. S.; Welborn, S. S.; Tsaggaris, T.; Ford, J.; Detsi, E.; Fakhraai, Z.; Composto, R. J., Effect of Nanoscale Confinement on Polymer-Infiltrated Scaffold Metal CompositesACS Applied Materials & Interfaces 2021, 13 (37), 44893-44903. DOI: 10.1021/acsami.1c12491


48. Ibrahim, O.; Lee, S.; Kim, S. W.; Pyun, S. B.; Woods, C.; Cho, E. C.; Park, S.-J.; Fakhraai, Z., Optical Magnetic Multipolar Resonances in Large Dynamic MetamoleculesThe Journal of Physical Chemistry C 2021, 125 (30), 16605-16619. DOI: 10.1021/acs.jpcc.1c04538

47. Jin, Y.; Zhang, A.; Wolf, S. E.; Govind, S.; Moore, A. R.; Zhernenkov, M.; Freychet, G.; Shamsabadi, A. A.; Fakhraai, Z., Glasses denser than the supercooled liquidProceedings of the National Academy of Sciences 2021, 118 (31). DOI: 10.1073/pnas.2100738118

46. Venkatesh, R. B.; Manohar, N.; Qiang, Y.; Wang, H.; Tran, H. H.; Kim, B. Q.; Neuman, A.; Ren, T.; Fakhraai, Z.; Riggleman, R. A., Polymer-Infiltrated Nanoparticle Films Using Capillarity-Based Techniques: Toward Multifunctional Coatings and MembranesAnnual review of chemical and biomolecular engineering 2021, 12, 411-437. DOI: 10.1146/annurev-chembioeng-101220-093836

45. Hosseini Jebeli, S. A.; West, C. A.; Lee, S. A.; Goldwyn, H. J.; Bilchak, C. R.; Fakhraai, Z.; Willets, K. A.; Link, S.; Masiello, D. J., Wavelength-dependent photothermal imaging probes nanoscale temperature differences among subdiffraction coupled plasmonic nanorodsNano Letters 2021, 21 (12), 5386-5393. DOI:


44. Fulco, S.; Wolf, S.; Jakes, J. E.; Fakhraai, Z.; Turner, K. T., Effect of surface detection error due to elastic–plastic deformation on nanoindentation measurements of elastic modulus and hardnessJournal of Materials Research 2021, 36 (11), 2176-2188. DOI: 10.1557/s43578-021-00223-4

43.Wang, H.; Kearns, K. L.; Zhang, A.; Arabi Shamsabadi, A.; Jin, Y.; Bond, A.; Hurney, S. M.; Morillo, C.; Fakhraai, Z., Effect of Nanopore Geometry in the Conformation and Vibrational Dynamics of a Highly Confined Molecular GlassNano Letters 2021, 21 (4), 1778-1784. DOI: 10.1021/acs.nanolett.0c04744

42. Song, B.; Hou, J.; Wang, H.; Sidhik, S.; Miao, J.; Gu, H.; Zhang, H.; Liu, S.; Fakhraai, Z.; Even, J., Determination of dielectric functions and exciton oscillator strength of two-dimensional hybrid perovskitesACS Materials Letters 2020, 3 (1), 148-159. DOI: 10.1021/acsmaterialslett.0c00505

Determination of Dielectric...

41. Song, B.; Liu, F.; Wang, H.; Miao, J.; Chen, Y.; Kumar, P.; Zhang, H.; Liu, X.; Gu, H.; Stach, E. A., Giant gate-tunability of complex refractive index in semiconducting carbon nanotubesACS Photonics 2020, 7 (10), 2896-2905. DOI: 10.1021/acsphotonics.0c01220

40. Zhang, A.; Jin, Y.; Liu, T.; Stephens, R. B.; Fakhraai, Z., Polyamorphism of vapor-deposited amorphous selenium in response to lightProceedings of the National Academy of Sciences 2020, 117 (39), 24076-24081. DOI: 10.1073/pnas.2009852117

39. Lee, S.; Woods, C. N.; Ibrahim, O.; Kim, S. W.; Pyun, S. B.; Cho, E. C.; Fakhraai, Z.; Park, S.-J., Distinct Optical Magnetism in Gold and Silver Probed by Dynamic MetamoleculesThe Journal of Physical Chemistry C 2020, 124 (37), 20436-20444. DOI: 10.1021/acs.jpcc.0c05943

Abstract Image

38. Bilchak, C. R.; Govind, S.; Contreas, G.; Rasin, B.; Maguire, S. M.; Composto, R. J.; Fakhraai, Z., Kinetic Monitoring of Block Copolymer Self-Assembly Using In Situ Spectroscopic EllipsometryACS Macro Letters 2020, 9 (8), 1095-1101. DOI: 10.1021/acsmacrolett.0c00444

Abstract Image


37.  Lin, Y.-C.; Komatsu, H.; Ma, J.; Axelsen, P. H.; Fakhraai, Z., Identifying polymorphs of amyloid-β (1–40) fibrils using high-resolution atomic force microscopyThe Journal of Physical Chemistry B 2019, 123 (49), 10376-10383. DOI: 10.1021/acs.jpcb.9b07854

36. Wang, H.; Qiang, Y.; Shamsabadi, A. A.; Mazumder, P.; Turner, K. T.; Lee, D.; Fakhraai, Z., Thermal degradation of polystyrene under extreme nanoconfinementACS Macro Letters 2019, 8 (11), 1413-1418. DOI: 10.1021/acsmacrolett.9b00649

35.  Lin, Y.-C.; Skolnick, M.; Fakhraai, Z., A Novel Method to Measure the Effective Change of the Interfacial Energy due to Kinetic Self-Assembly of Amyloid FibrilsThe Journal of Physical Chemistry B 2019, 123 (32), 6990-6996. DOI:  10.1021/acs.jpcb.9b04717

Abstract Image

34. Sil, D.; Lane, C.; Glor, E.; Gilroy, K. D.; Sylla, S.; Barbiellini, B.; Markiewicz, R.; Hajfathalian, M.; Neretina, S.; Bansil, A., Synthesis and Properties of Au HydrideChemistrySelect 2019, 4 (14), 4287-4292. DOI: 10.1002/slct.201900925

33. Samanta, S.; Huang, G.; Gao, G.; Zhang, Y.; Zhang, A.; Wolf, S.; Woods, C. N.; Jin, Y.; Walsh, P. J.; Fakhraai, Z., Exploring the importance of surface diffusion in stability of vapor-deposited organic glassesThe Journal of Physical Chemistry B 2019, 123 (18), 4108-4117. DOI: 10.1021/acs.jpcb.9b01012

Abstract Image

32. Moore, A. R.; Huang, G.; Wolf, S.; Walsh, P. J.; Fakhraai, Z.; Riggleman, R. A., Effects of microstructure formation on the stability of vapor-deposited glassesProceedings of the National Academy of Sciences 2019, 116 (13), 5937-5942. DOI: 10.1073/pnas.1821761116

31. Zhang, Y.; Woods, C. N.; Alvarez, M.; Jin, Y.; Riggleman, R. A.; Fakhraai, Z., Effect of substrate interactions on the glass transition and length-scale of correlated dynamics in ultra-thin molecular glass filmsThe Journal of Chemical Physics 2018, 149 (18), 184902. DOI: 10.1063/1.5038174

30. Zhang, Y.; Li, C.; Fakhraai, Z.; Moosa, B.; Yang, P.; Khashab, N. M., Synthesis of spiked plasmonic nanorods with an interior nanogap for quantitative surface-enhanced Raman scattering analysisACS omega 2018, 3 (10), 14399-14405. DOI: 10.1021/acsomega.8b01153

Figure 1

29.  Hor, J. L.; Wang, H.; Fakhraai, Z.; Lee, D., Effect of physical nanoconfinement on the viscosity of unentangled polymers during capillary rise infiltrationMacromolecules 2018, 51 (14), 5069-5078. DOI: 10.1021/acs.macromol.8b00966

28. Wang, H.; Hor, J. L.; Zhang, Y.; Liu, T.; Lee, D.; Fakhraai, Z., Dramatic increase in polymer glass transition temperature under extreme nanoconfinement in weakly interacting nanoparticle filmsACS nano 2018, 12 (6), 5580-5587. DOI: 10.1021/acsnano.8b01341

27. Lin, Y.-C.; Li, C.; Fakhraai, Z., Kinetics of surface-mediated fibrillization of amyloid-β (12–28) peptidesLangmuir 2018, 34 (15), 4665-4672. DOI: 10.1021/acs.langmuir.7b02744

26. Li, C.; Lee, S.; Qian, Z.; Woods, C.; Park, S.-J.; Fakhraai, Z., Controlling magnetic dipole resonance in raspberry-like metamoleculesThe Journal of Physical Chemistry C 2018, 122 (12), 6808-6817. DOI: 10.1021/acs.jpcc.8b00439

25. Hor, J. L.; Wang, H.; Fakhraai, Z.; Lee, D., Effects of polymer–nanoparticle interactions on the viscosity of unentangled polymers under extreme nanoconfinement during capillary rise infiltrationSoft Matter 2018, 14 (13), 2438-2446. DOI: 10.1039/C7SM02465G

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

24. Ferrie, J. J.; Haney, C. M.; Yoon, J.; Pan, B.; Lin, Y.-C.; Fakhraai, Z.; Rhoades, E.; Nath, A.; Petersson, E. J., Using a FRET library with multiple probe pairs to drive Monte Carlo simulations of α-synucleinBiophysical journal 2018, 114 (1), 53-64. DOI: 10.1016/j.bpj.2017.11.006

23. Cubuk, E. D.; Ivancic, R.; Schoenholz, S. S.; Strickland, D.; Basu, A.; Davidson, Z.; Fontaine, J.; Hor, J. L.; Huang, Y.-R.; Jiang, Y., Structure-property relationships from universal signatures of plasticity in disordered solidsScience 2017, 358 (6366), 1033-1037. DOI: 10.1126/science.aai8830


22.  Liu, T.; Exarhos, A. L.; Alguire, E. C.; Gao, F.; Salami-Ranjbaran, E.; Cheng, K.; Jia, T.; Subotnik, J. E.; Walsh, P. J.; Kikkawa, J. M., Birefringent stable glass with predominantly isotropic molecular orientationPhysical Review Letters 2017, 119 (9), 095502. DOI: 10.1103/PhysRevLett.119.095502

21. Glor, E. C.; Angrand, G. V.; Fakhraai, Z., Exploring the broadening and the existence of two glass transitions due to competing interfacial effects in thin, supported polymer filmsThe Journal of Chemical Physics 2017, 146 (20), 203330. DOI: 10.1063/1.4979944

20. Zhang, Y.; Fakhraai, Z., Decoupling of surface diffusion and relaxation dynamics of molecular glassesProceedings of the National Academy of Sciences 2017, 114 (19), 4915-4919. DOI: 10.1073/pnas.1701400114

19. Lin, Y.-C.; Repollet-Pedrosa, M. H.; Ferrie, J. J.; Petersson, E. J.; Fakhraai, Z., Potential artifacts in sample preparation methods used for imaging amyloid oligomers and protofibrils due to surface-mediated fibril formationThe Journal of Physical Chemistry B 2017, 121 (12), 2534-2542. DOI: 10.1021/acs.jpcb.6b12560

18. Glor, E. C.; Ferrier, R. C.; Li, C.; Composto, R. J.; Fakhraai, Z., Out-of-plane orientation alignment and reorientation dynamics of gold nanorods in polymer nanocomposite filmsSoft Matter 2017, 13 (11), 2207-2215. DOI: 10.1039/C6SM02403C

17.  Zhang, Y.; Fakhraai, Z., Invariant fast diffusion on the surfaces of ultrastable and aged molecular glassesPhysical review letters 2017, 118 (6), 066101. DOI: 10.1103/PhysRevLett.118.066101

16. Lin, Y.-C.; Komatsu, H.; Ma, J.; Axelsen, P. H.; Fakhraai, Z., Quantitative analysis of amyloid polymorphism using height histograms to correct for tip convolution effects in atomic force microscopy imagingRSC advances 2016, 6 (115), 114286-114295. DOI: 10.1039/C6RA24031C


15.  Zhang, Y.; Potter, R.; Zhang, W.; Fakhraai, Z., Using tobacco mosaic virus to probe enhanced surface diffusion of molecular glassesSoft Matter 2016, 12 (44), 9115-9120. DOI: 10.1039/C6SM01566B


14. Zhang, Y.; Glor, E. C.; Li, M.; Liu, T.; Wahid, K.; Zhang, W.; Riggleman, R. A.; Fakhraai, Z., Long-range correlated dynamics in ultra-thin molecular glass filmsThe Journal of Chemical Physics 2016, 145 (11), 114502. DOI: 10.1063/1.4962734


13. Glor, E. C.; Fakhraai, Z., Cooling Rate Dependent Ellipsometry Measurements to Determine the Dynamics of Thin Glassy FilmsJoVE (Journal of Visualized Experiments) 2016, (107), e53499. DOI: 10.3791/53499

12. Qian, Z.; Li, C.; Fakhraai, Z.; Park, S.-J., Unusual weak interparticle distance dependence in Raman enhancement from nanoparticle dimersThe Journal of Physical Chemistry C 2016, 120 (3), 1824-1830. DOI: 10.1021/acs.jpcc.5b09396


11. Glor, E. C.; Composto, R. J.; Fakhraai, Z., Glass transition dynamics and fragility of ultrathin miscible polymer blend filmsMacromolecules 2015, 48 (18), 6682-6689. DOI: 10.1021/acs.macromol.5b00979


10. Liu, T.; Cheng, K.; Salami-Ranjbaran, E.; Gao, F.; Li, C.; Tong, X.; Lin, Y.-C.; Zhang, Y.; Zhang, W.; Klinge, L., The effect of chemical structure on the stability of physical vapor deposited glasses of 1, 3, 5-triarylbenzeneThe Journal of Chemical Physics 2015, 143 (8), 084506. DOI: 10.1063/1.4928521


9. Liu, T.; Cheng, K.; Salami-Ranjbaran, E.; Gao, F.; Glor, E. C.; Li, M.; Walsh, P. J.; Fakhraai, Z., Synthesis and high-throughput characterization of structural analogues of molecular glassformers: 1, 3, 5-trisarylbenzenesSoft Matter 2015, 11 (38), 7558-7566. DOI: 10.1039/C5SM01044F


8.  Hastings, S. P.; Qian, Z.; Swanglap, P.; Fang, Y.; Engheta, N.; Park, S.-J.; Link, S.; Fakhraai, Z., Modal interference in spiky nanoshellsOptics Express 2015, 23 (9), 11290-11311. DOI: 10.1364/OE.23.011290


7. Qian, Z.; Hastings, S. P.; Li, C.; Edward, B.; McGinn, C. K.; Engheta, N.; Fakhraai, Z.; Park, S.-J., Raspberry-like metamolecules exhibiting strong magnetic resonancesACS nano 2015, 9 (2), 1263-1270. DOI: 10.1021/nn5050678 Featured in PennNews!


6. Glor, E. C.; Fakhraai, Z., Facilitation of interfacial dynamics in entangled polymer filmsThe Journal of chemical physics 2014, 141 (19), 194505. DOI: 10.1063/1.4901512

5.  Lin, Y.-C.; Petersson, E. J.; Fakhraai, Z., Surface effects mediate self-assembly of amyloid-β peptidesACS nano 2014, 8 (10), 10178-10186. DOI: 10.1021/nn5031669


4. Hastings, S. P.; Swanglap, P.; Qian, Z.; Fang, Y.; Park, S.-J.; Link, S.; Engheta, N.; Fakhraai, Z., Quadrupole-enhanced Raman scatteringACS nano 2014, 8 (9), 9025-9034. DOI: 10.1021/nn5022346


3. Sanchez-Gaytan, B. L.; Qian, Z.; Hastings, S. P.; Reca, M. L.; Fakhraai, Z.; Park, S.-J., Controlling the topography and surface plasmon resonance of gold nanoshells by a templated surfactant-assisted seed growth methodThe Journal of Physical Chemistry C 2013, 117 (17), 8916-8923. DOI: 10.1021/jp401189k


2. Sanchez-Gaytan, B. L.; Swanglap, P.; Lamkin, T. J.; Hickey, R. J.; Fakhraai, Z.; Link, S.; Park, S.-J., Spiky gold nanoshells: synthesis and enhanced scattering propertiesThe Journal of Physical Chemistry C 2012, 116 (18), 10318-10324. DOI: 10.1021/jp300009b


1. Daley, C.; Fakhraai, Z.; Ediger, M.; Forrest, J., Comparing surface and bulk flow of a molecular glass formerSoft Matter 2012, 8 (7), 2206-2212. DOI: 10.1039/c2sm06826e



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. Dalal, S. S.; Fakhraai, Z.; Ediger, M. D., High-throughput ellipsometric characterization of vapor-deposited indomethacin glassesThe Journal of Physical Chemistry B 2013, 117 (49), 15415-15425. DOI:10.1021/jp405005n |


17. Dalal, S. S.; Sepúlveda, A.; Pribil, G. K.; Fakhraai, Z.; Ediger, M., Density and birefringence of a highly stable α, α, β-trisnaphthylbenzene glassThe Journal of chemical physics 2012, 136 (20), 204501. DOI: 10.1063/1.4719532

16. Paulite, M.; Fakhraai, Z.; Li, I. T.; Gunari, N.; Tanur, A. E.; Walker, G. C., Imaging Secondary Structure of Individual Amyloid Fibrils of a β(2)-Microglobulin Fragment Using Near-Field Infrared Spectroscopy”, J. Am. Chem. Soc 2011. 133, 7376- 7383. DOI: 10.1021/ja109316p


15. Fakhraai, Z.; Still, T.; Fytas, G.; Ediger, M., Structural variations of an organic glassformer vapor-deposited onto a temperature gradient stageThe Journal of Physical Chemistry Letters 2011, 2 (5), 423-427. DOI:10.1021/jz101723d


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

13. Niri, V.; Flatt, B.; Fakhraai, Z.; Forrest, J., Simultaneous monitoring of electroformation of phospholipid vesicles by quartz crystal microbalance and optical microscopyChemistry and physics of lipids 2010, 163 (1), 36-41. DOI:10.1016/j.chemphyslip.2

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. Leal, R.; Souza, C.; Da Silva, M.; Fakhraai, Z.; Forrest, J.; Papaleo, R., Relaxation of surface tracks on polycarbonate thin films induced by MeV heavy-ion impactsNuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms 2010, 268 (19), 3080-3083. DOI:10.1016/j.nimb.20

10.  Paulite, M.; Fakhraai, Z.; Akhremitchev, B. B.; Mueller, K.; Walker, G. C., Assembly, tuning and use of an apertureless near field infrared microscope for protein imaging. JoVE (Journal of Visualized Experiments) 2009, (33), e1581. DOI: 10.3791/1581

9. Kofke, M. J.; Waldeck, D. H.; Fakhraai, Z.; Ip, S.; Walker, G. C., The effect of periodicity on the extraordinary optical transmission of annular aperture arraysApplied Physics Letters 2009, 94 (2), 023104. DOI: 10.1063/1.3067835

8. Qi, D.; Fakhraai, Z.; Forrest, J., Substrate and chain size dependence of near surface dynamics of glassy polymersPhysical review letters 2008, 101 (9), 096101. DOI: 10.1103/PhysRevLett.101.096101

7. Mueller, K.; Yang, X.; Paulite, M.; Fakhraai, Z.; Gunari, N.; Walker, G. C., Chemical imaging of the surface of self-assembled polystyrene-b-poly (methyl methacrylate) diblock copolymer films using apertureless near-field IR microscopyLangmuir 2008, 24 (13), 6946-6951. DOI: 10.1021/la703406d

6. Fakhraai, Z.; Forrest, J., Measuring the surface dynamics of glassy polymersScience 2008, 319 (5863), 600-604. DOI: 10.1126/science.1151205

5. Sharp, J.; Forrest, J.; Fakhraai, Z.; Khomenko, M.; Teichroeb, J.; Dalnoki-Veress, K., Reply to comment on “The properties of free polymer surfaces and their effect upon the glass transition temperature of thin polystyrene films” by SA Hutcheson and GB McKennaThe European Physical Journal E 2007, 22 (4), 287-291. DOI: 10.1140/epje/e2007-00035-8

4. Fakhraai, Z.; Forrest, J. A., Probing slow dynamics in supported thin polymer filmsPhysical review letters 2005, 95 (2), 025701. DOI: 10.1103/PhysRevLett.95.025701

3.  Fakhraai, Z.; Valadkhan, S.; Forrest, J., Qualitative discrepancy between different measures of dynamics in thin polymer films⋆The European Physical Journal E 2005, 18 (2), 143-148. DOI: 10.1140/epje/i2004-10158-1

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

1.  Fakhraai, Z.; Sharp, J.; Forrest, J., Effect of sample preparation on the glass‐transition of thin polystyrene films. Journal of Polymer Science Part B: Polymer Physics 2004, 42 (24), 4503-4507. DOI: 10.1002/polb.20281