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Preprint: D.O. Byrne, S.M. Ribet, D. Kepaptsoglou, Q.M. Ramasse, C. Ophus, F.I. Allen, Fabrication and characterization of boron-terminated tetravacancies in monolayer hBN using STEM, EELS and electron ptychography (2025) arXiv:2504.14217

Preprint: D.O. Byrne, S.M. Ribet, K.C. Bustillo, C. Ophus, F.I. Allen, Neutral but Impactful: Gallium Cluster-Induced Nanopores from Beam-Blanked Gallium Ion Sources (2025) arXiv:2503.05199

59. D.O. Byrne, F.I. Allen, Atomic Engineering of Triangular Nanopores in Monolayer hBN for Membrane Applications: A Decoupled Seeding and Growth Approach, ACS Applied Nano Materials 8(9):4565 (2025) doi:10.1021/acsanm.4c06998

58. S. Mo, D.O. Byrne, F.I. Allen, Focused helium ion beam nanofabrication by near-surface swelling, Journal of Vacuum Science and Technology B 43(2):022803 (2025) doi:10.1116/6.0004100

57. M. Holz, M. Hofmann, F.I. Allen, C. Weigel, S. Strehle, Tip-Induced 3D Printing on the Nanoscale with Field Emission Scanning Probes, Small 21(5):2409035 (2025) doi:10.1002/smll.202409035

56. Z. Li, A.T. Hall, Y. Wang, Y. Li, D.O. Byrne, L.R. Scammell, R.R. Whitney, F.I. Allen, J. Cummings, A. Noy, Ion transport and ultra-efficient osmotic power generation in boron nitride nanotube porins, Science Advances 10(36):ado8081 (2024) doi:10.1126/sciadv.ado8081

55. D.O. Byrne, J. Ciston, F.I. Allen, Probing defectivity beneath the hydrocarbon blanket with TEM-EELS, Microscopy and Microanalysis 30(4):650 (2024) doi:10.1093/mam/ozae064

54. F.I. Allen, J.M. De Teresa, B. Onoa, Focused helium ion and electron beam induced deposition of organometallic tips for dynamic atomic force microscopy of biomolecules in liquid, ACS Applied Materials and Interfaces 16(4):4439 (2024) doi:10.1021/acsami.3c16407

53. K. Höflich, G. Hobler, F.I. Allen, T. Wirtz, G. Rius, L. McElwee-White, A.V. Krasheninnikov, M. Schmidt, I. Utke, N. Klingner, M. Osenberg, R. Córdoba, F. Djurabekova, I. Manke, P. Moll, M. Manoccio, J.M. De Teresa, L. Bischoff, J. Michler, O. De Castro, A. Delobbe, P. Dunne, O.V. Dobrovolskiy, N. Freese, A. Gölzhäuser, P. Mazarov, D. Kölle, W. Möller, F. Pérez- Murano, P. Philipp, F. Vollnhals, G. Hlawacek, Roadmap for focused ion beam technologies, Applied Physics Reviews 10(4):041311 (2023) doi:10.1063/5.0162597

52. F.I. Allen, P.T. Blanchard, R. Lake, D. Pappas, D. Xia, J.A. Notte, R. Zhang, A.M. Minor, N.A. Sanford, Fabrication of Specimens for Atom Probe Tomography Using a Combined Gallium and Neon Focused Ion Beam Milling Approach, Microscopy and Microanalysis 29(5):1628 (2023) doi:10.1093/micmic/ozad078

51. W. Redjem, A.J. Amsellem, F.I. Allen, G. Benndorf, J. Bin, S. Bulanov, E. Esarey, L.C. Feldman, J. Ferrer Fernandez, J. Garcia Lopez, L. Geulig, C.R. Geddes, H. Hijazi, Q. Ji, V. Ivanov, B. Kanté, A. Gonsalves, J. Meijer, K. Nakamura, A. Persaud, I. Pong, L. Obst-Huebl, P.A. Seidl, J. Simoni, C. Schroeder, S. Steinke, L.Z. Tan, R. Wunderlich, B. Wynne, T. Schenkel, Defect engineering of silicon with ion pulses from laser acceleration, Communications Materials 4(1):22 (2023) doi:10.1038/s43246-023-00349-4

50. L. Jin, Y. Shi, F.I. Allen, L.-Q. Chen, J. Wu, Probing the critical nucleus size in the metal-insulator phase transition of VO2, Physical Review Letters 129:245701 (2022) doi:10.1103/PhysRevLett.129.245701

49. R.D. Kolasinski, C.S. Wong, A. Engel, J.A. Whaley, F.I. Allen, D.A. Buchenauer, Deciphering the influence of high-flux helium plasma exposure on tungsten nanostructure growth using real-time, in situ spectroscopic ellipsometry, Journal of Applied Physics 131(6):063303 (2022) doi:10.1063/5.0077458

48. M. Balooch, F.I. Allen, M.P. Popovic, and P. Hosemann, Mechanical and structural transformations of tungsten implanted with helium ions, Journal of Nuclear Materials 559:153436 (2022) doi:10.1016/j.jnucmat.2021.153436

47. F.I. Allen, A review of defect engineering, ion implantation, and nanofabrication using the helium ion microscope, Beilstein Journal of Nanotechnology 12:633 (2021) doi:10.3762/bjnano.12.52

46. F.I. Allen, T.C. Pekin, A. Persaud, S.J. Rozeveld, G.F. Meyers, J. Ciston, C. Ophus, and A.M. Minor, Fast Grain Mapping with Sub-Nanometer Resolution Using 4D-STEM with Grain Classification by Principal Component Analysis and Non-Negative Matrix Factorization, Microscopy and Microanalysis, 27(4):794 (2021) doi:10.1017/S1431927621011946

45. N.R. Velez, F.I. Allen, M.A. Jones, J. Donohue, W. Li, K. Pister, S. Govindjee, G.F. Meyers, and A.M. Minor, Nanomechanical testing of freestanding polymer films: in situ tensile testing and T𝑔 measurement, Journal of Materials Research 36:2456 (2021) doi:10.1557/s43578-021-00163-z

44. Y. Yang, S.Y. Wang, B. Xiang, S. Yin, T.C. Pekin, X. Li, R. Zhang, K. Yano, D. Hwang, M. Asta, C. Grigoropoulos, F.I. Allen, and A.M. Minor, Evaluating the effects of pillar shape and gallium ion beam damage on the mechanical properties of single crystal aluminum nanopillars, Journal of Materials Research 36:2515 (2021) doi:10.1557/s43578-021-00125-5

43. F.I. Allen, Branched High Aspect Ratio Nanostructures Fabricated by Focused Helium Ion Beam Induced Deposition of an Insulator, Micromachines 12(3):232 (2021) doi:10.3390/mi12030232

42. J. Liu, L. Jin, F.I. Allen, Y. Gao, P. Ci, F. Kang, and J. Wu, Selective Gas Permeation in Defect-Engineered Bilayer Graphene, Nano Letters 21(5):2183 (2021) doi:10.1021/acs.nanolett.0c04989

41. N.R. Velez, F.I. Allen, M.A. Jones, S. Govindjee, G.F. Meyers, and A.M. Minor, Extreme Ductility in Freestanding Polystyrene Thin Films, Macromolecules 53:8650 (2020) doi:10.1021/acs.macromol.0c01387

40. L. Jin, S.E. Zeltmann, H.S. Choe, H. Liu, F.I. Allen, A.M. Minor, and J. Wu, Disorder recovers the Wiedemann-Franz Law in metallic phase of VO2, Physical Review B 102:041120(R) (2020) doi:10.1103/PhysRevB.102.041120

39. R.C. Thayer, F.I. Allen, and N.H. Patel, Structural color in Junonia butterflies evolves by tuning scale lamina thickness, eLife 9:e52187 (2020) doi:10.7554/eLife.52187

38. F.I. Allen, P. Hosemann, and M. Balooch, Key mechanistic features of swelling and blistering of helium-ion-irradiated tungsten, Scripta Materialia 178:256 (2020) doi:10.1016/j.scriptamat.2019.11.039

37. M. Holz, F.I. Allen, C. Reuter, A. Ahmad, M. Hofmann, A. Reum, Tsv. Ivanov, and I. W. Rangelow, Tip-based electron beam induced deposition using active cantilevers, Journal of Vacuum Science and Technology B 37(6):061812 (2019) doi:10.1116/1.5123287

36. H.S. Choe, R. Prabhakar, G. Wehmeyer, F.I. Allen, W. Lee, L. Jin, Y. Li, P. Yang, C. Qiu, C. Dames, M. Scott, A.M. Minor, J.-H. Bahk, and J. Wu, Ion write micro-thermotics: Programing thermal metamaterials at the microscale, Nano Letters 19:3830 (2019) doi:10.1021/acs.nanolett.9b00984

35. H.S. Choe, J. Li, W. Zheng, J. Lee, J. Suh, F.I. Allen, H. Liu, H.-J. Choi, W. Walukiewicz, H. Zheng, and J. Wu, Anomalously high electronic thermal conductivity and Lorenz ratio in Bi2Te3 nanoribbons far from the bipolar condition, Applied Physics Letters 114:152101 (2019) doi:10.1063/1.5092221

34. F.I. Allen, N.R. Velez, R.C. Thayer, N.H. Patel, M.A. Jones, G.F. Meyers, and A.M. Minor, Gallium, neon and helium focused ion beam milling of thin films demonstrated for polymeric materials: study of implantation artifacts, Nanoscale 11:1403 (2019) doi:10.1039/c8nr08224c

33. S. Ho, L. Chen, F.I. Allen, R. Hsi, A. Shimotake, S. Wiener, M. Kang, A.M. Minor, and M. Stoller, Architecture-guided fluid flow directs renal biomineralization, Scientific Reports 8:14157 (2018) doi:10.1038/s41598-018-30717-x

32. S. Saremi, R. Xu, F.I. Allen, J. Maher, J.C. Agar, R. Gao, P. Hosemann, and L.W. Martin, Local control of defects and switching properties in ferroelectric thin films, Physical Review Materials 8:084414 (2018) doi:10.1103/PhysRevMaterials.2.084414

31. E. Kim, Y. Lee, C. Ko, Y. Park, J. Yeo, Y. Chen, H.S. Choe, F.I. Allen, J. Rho, S. Tongay, J. Wu, K. Kim, and C.P. Grigoropoulos, Tuning the optical and electrical properties of MoS2 by selective Ag photo-reduction, Applied Physics Letters, 113:013105 (2018) doi:10.1063/1.5022705

30. B.S. Archanjo, T.L. Vasconcelos, B. Oliveira, C. Song, F.I. Allen, C.A. Achete, and P. Ercius, Plasmon 3D electron tomography and local electric-field enhancement of engineered plasmonic nano-antennas, ACS Photonics, 5:2834 (2018) doi:10.1021/acsphotonics.8b00125

29. G. Calafiore, A. Koshelev, T.P. Darlington, N.J. Borys, M. Melli, A. Polyakov, G. Cantarella, F.I. Allen, P. Lum, E. Wong, S. Sassolini, A. Weber-Bargioni, P.J. Schuck, S. Cabrini, and K. Munechika, Campanile near-field probes fabricated by nanoimprint lithography on the facet of an optical fiber, Scientific Reports, 7:1651 (2017) doi:10.1038/s41598-017-01871-5

28. R.H. Tunuguntla, X. Chen, A. Belliveau, F.I. Allen, and A. Noy, High-yeld synthesis and optical properties of carbon nanotube porins, Journal of Physical Chemistry C, 121:3117 (2017) doi:10.1021/acs.jpcc.6b11658

27. J.B. In, H.J. Kwon, J.H. Yoo, F.I. Allen, A.M. Minor, and C.P. Grigoropoulos, Laser welding of vertically aligned carbon nanotube arrays on polymer workpieces, Carbon, 115:688 (2017) doi:10.1016/j.carbon.2017.01.050

26. F.I. Allen, E. Kim, N.C. Andresen, C.G. Grigoropoulos, and A.M. Minor, In situ TEM Raman spectroscopy and laser- based materials modification, Ultramicroscopy, 178:33 (2017) doi:10.1016/j.ultramic.2016.06.011

25. Z.J. Wang, F.I. Allen, Z.W.Shan, and P. Hosemann, Mechanical behavior of copper containing a gas-bubble superlattice, Acta Materialia, 121:78 (2016) doi:10.1016/j.actamat.2016.08.085

24. S. Ryu, E. Kim, F.I. Allen, D.J. Hwang, A.M. Minor, and C.P. Grigoropoulos, Incubation behavior of silicon nanowire growth investigated by laser-assisted rapid heating, Applied Physics Letters, 109:073106 (2016) doi:10.1063/1.4961374

23. A. Koshelev, G. Calafiore, C. Pina-Hernandez, F.I. Allen, S. Dhuey, S. Sassolini, E. Wong, P. Lum, K. Munechika, and S. Cabrini, High refractive index Fresnel lens on a fiber fabricated by nanoimprint lithography for immersion applications, Optics Letters, 41:3423 (2016) doi:10.1364/OL.41.003423

22. G. Calafiore, A. Koshelev, F.I. Allen, S. Dhuey, S. Sassolini, E. Wong, P. Lum, K. Munechika, and S. Cabrini, Nanoimprint of a 3D structure on an optical fiber for light wavefront manipulation, Nanotechnology, 27:375301 (2016) doi:10.1088/0957-4484/27/37/375301

21. T.C. Pekin, F.I. Allen, and A.M. Minor, Evaluation of neon focused ion beam milling for TEM sample preparation, Journal of Microscopy, 264:59 (2016) doi:10.1111/jmi.12416

20. R.H. Tunuguntla, F.I. Allen, K. Kim, A. Belliveau, and A. Noy, Ultrafast proton transport in sub-1-nm diameter carbon nanotube porins, Nature Nanotechnology, 11:639 (2016) doi:10.1038/nnano.2016.43

19. J. Hong, A. Hadjikhani, M. Stone, F.I. Allen, V. Safonov, P. Liang, J. Bokor, and S. Khizroev, The physics of spin-transfer torque switching in magnetic tunneling junctions in the sub-10-nm size range, IEEE Transactions on Magnetics, 52:1400504 (2016) doi:10.1109/TMAG.2016.2530622

18. C. Guo, F.I. Allen, Y. Lee, T.P. Le, C. Song, J. Ciston, A.M. Minor, and E.D. Gomez, Probing local electronic transitions in organic semiconductors through energy-loss spectrum imaging in the transmission electron microscope, Advanced Functional Materials, 25:6071 (2015) doi:10.1002/adfm.201502090

17. D. Paeng, D. Lee, J. Yeo, J.H. Yoo, F.I. Allen, E. Kim, H. So, H.K. Park, A.M. Minor, and C.P. Grigoropoulos, Laser-induced reductive sintering of nickel oxide nanoparticles under ambient conditions, Journal of Physical Chemistry C, 119:6363 (2015) doi:10.1021/jp512776p

16. F.I. Allen, L.R. Comolli, A. Kusoglu, M.A. Modestino, A.M. Minor, and A.Z. Weber, Morphology of hydrated as-cast Nafion revealed through cryo electron tomography, Macro Letters, 4:1 (2014) doi:10.1021/mz500606h

15. J. Geng, K. Kim, J. Zhang, A. Escalada, R. Tunuguntla, L.R. Comolli, F.I. Allen, A. V. Shnyrova, K.R. Cho, D. Munoz, Y.M. Wang, C.P. Grigoropoulos, C.M. Ajo-Franklin, and A. Noy, Stochastic transport through carbon nanotubes in lipid bilayers and live cell membranes, Nature, 514:612 (2014) doi:10.1038/nature13817

14. D. Lee, Y. Rho, F.I. Allen, A.M. Minor, S.H. Ko, and C.P. Grigoropoulos, Synthesis of hierarchical TiO2 nanowires with densely-packed and omnidirectional branches, Nanoscale, 5:11147 (2013) doi:10.1039/C3NR02584E

13. O. Waldmann, A. Persaud, R. Kapadia, K. Takei, F.I. Allen, A. Javey, and T. Schenkel, Effects of palladium coating on field-emission properties of carbon nanofibers in a hydrogen plasma, Thin Solid Films, 534:488 (2013) doi:10.1016/j.tsf.2013.02.053

12. M.A. Modestino, D.K Paul, S. Dishari, S.A Petrina, F.I. Allen, M.A Hickner, K. Karan, R.A Segalman, and A.Z. Weber, Self-assembly and transport limitations in confined Nafion films, Macromolecules, 46:867 (2013) doi:10.1021/ma301999a

11. F.I. Allen, P. Ercius, M.A. Modestino, R.A. Segalman, N.P. Balsara, and A.M. Minor, Deciphering the three-dimensional morphology of block copolymer thin films by transmission electron microscopy, Micron, 44:442 (2013) doi:10.1016/j.micron.2012.09.010

10. M. Watanabe and F.I. Allen, The SmartEFTEM-SI method: Development of a new spectrum-imaging acquisition scheme for quantitative mapping by energy-filtering transmission electron microscopy, Ultramicroscopy, 113:106 (2012) doi:10.1016/j.ultramic.2011.10.014

9. F.I. Allen, M. Watanabe, Z. Lee, N.P. Balsara, and A.M. Minor, Chemical mapping of a block copolymer electrolyte by low-loss EFTEM spectrum-imaging and principal component analysis, Ultramicroscopy, 111:239 (2011) doi:10.1016/j.ultramic.2010.11.035

8. F.I. Allen, C. Biedermann, R. Radtke, S. Fritzsche, and G. Fussmann, Energy dependence of angular momentum capture states in charge exchange collisions between slow highly charged argon ions and argon neutrals, Physical Review A, 78:032705 (2008) doi:10.1103/PhysRevA.78.032705

7. F.I. Allen, C. Biedermann, R. Radtke, and G. Fussmann, Charge exchange of highly charged argon ions as a function of projectile energy, Journal of Physics: Conference Series, 58:181 (2007) doi:10.1088/1742-6596/58/1/038

6. C. Biedermann, R. Radtke, G. Fussmann, and F.I. Allen, Extreme ultraviolet spectroscopy of highly charged argon ions at the Berlin EBIT, Journal of Physics: Conference Series, 72:012004 (2007) doi:10.1088/1742-6596/72/1/012004

5. F.I. Allen, C. Biedermann, R. Radtke, and G. Fussmann, Extraction of highly charged ions from the Berlin EBIT for interactions with a gas target, Review of Scientific Instruments, 77:03B903 (2006) doi:10.1063/1.2162847

4. F.I. Allen, A. Persaud, S.J. Park, A. Minor, M. Sakurai, D.H. Schneider, and T. Schenkel, Transport of multiply and highly charged ions through nanoscale apertures in silicon nitride membranes, Nuclear Instruments and Methods in Physics Research B, 244:323 (2006) doi:0.1016/j.nimb.2005.10.029

3. A. Persaud, F.I. Allen, F. Gicquel, S.J. Park, J.A. Liddle, T. Schenkel, Tzv. Ivanov, K. Ivanova, I.W. Rangelow, and J. Bokor, Single ion implantation with scanning probe alignment, Journal of Vacuum Science and Technology B, 22:2992 (2004) doi:10.1116/1.1802891

2. S.J. Park, J.A. Liddle, A. Persaud, F.I. Allen, J. Bokor, and T. Schenkel, Formation of 15nm scale Coulomb blockade structures in silicon by electron beam lithography with a bilayer resist process, Journal of Vacuum Science and Technology B, 22:3115 (2004) doi:10.1116/1.1825012

1. A. Persaud, S.J. Park, J.A. Liddle, I.W. Rangelow, J. Bokor, R. Keller, F.I. Allen, D.H. Schneider, and T. Schenkel, Quantum computer development with single ion implantation, Quantum Information Processing, 3:233 (2004) doi:10.1007/s11128-004-3879-1

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