Unlocking Molecular-Level Secrets
Journal Papers
41. Y. M. N. D. Y. Bandara, Shankar Dutt, Buddini I. Karawdeniya, Jugal Saharia, Patrick Kluth and, Antonio Tricoli “A Robust Parallel Computing Data Extraction Framework for Nanopore Experiments”, Small Methods, 2024.
40. Zain Ul Abideen, Waqas Arifeen and, Y. M. Nuwan. D. Y. Bandara. “Emerging Trends in Metal Oxide-based Electronic Noses for Healthcare Applications: A Review”, Nanoscale, 2024.
39. Y. M. Nuwan. D. Y. Bandara, Buddini I. Karawdeniya, Shankar Dutt, Patrick Kluth, and Antonio Tricoli. “Nanopore Fabrication Made Easy: A Portable, Affordable Microcontroller-Assisted Approach for Tailored Pore Formation via Controlled Breakdown”, Analytical Chemistry, 96, 5, 2124–2134, 2024.
38. Y. M. Nuwan D. Y. Bandara and Kevin J. Freedman. “Lithium Chloride Effects Field-Induced Protein Unfolding and the Transport Energetics Inside a Nanopipette”, Journal of The American Chemical Society, 146, 5, 3171–3185, 2024.
37. Jugal Saharia, Y. M. Nuwan D. Y. Bandara, Lokesh Saharan “Molybdenum Disulfide Solid-State Nanopores for Single-Molecule Biosensing”, ASME International Mechanical Engineering Congress and Exposition, 116801, 2024.
36. Shankar Dutt, Hancheng Shao, Buddini Karawdeniya, Y. M. Nuwan D. Y. Bandara, Elena Daskalaki, Hanna Suominen, Patrick Kluth. “High Accuracy Protein Identification: Fusion of Solid-State Nanopore Sensing and Machine Learning”, Small Methods, ,7, 2300676, 2023.
35. Jugal Saharia, Y. M. Nuwan D. Y. Bandara, Buddini I. Karawdeniya, Jason R. Dwyer and Min Jun Kim. “Over 1 million DNA and Protein events through ultra-stable chemically-tuned solid-state nanopores”, Small, 2300198, 2023.
34. Shankar Dutt, Buddini I. Karawdeniya, Y.M. Nuwan D.Y. Bandara, Nahid Afrin, and Patrick Kluth. “Ultra-Thin, High-Lifetime Silicon Nitride Membranes for Nanopore Sensing”, ACS Analytical Chemistry, 95(13), 5754-5763, 2023.
33. Matthew O'Donohue, Jugal Saharia, Nuwan Bandara, Georgios Alexandrakis, Min Jun Kim. “Use of a solid‐state nanopore for profiling the transferrin receptor protein and distinguishing between transferrin receptor and its ligand protein”, Electrophoresis, 44 (1-2), 349-359, 2023.
32. Y. M Nuwan D. Y Bandara and, Kevin J Freedman. “Enhanced Signal to Noise Ratio Enables High Bandwidth Nanopore Recordings and Molecular Weight Profiling of Proteins”, ACS Nano, 16 (9), 14111-14120, 2022.
31. Lauren S Lastra, Y. M Nuwan D. Y Bandara, Vinay Sharma and, Kevin J Freedman. “Protein and DNA Yield Current Enhancements, Slow Translocations, and an Enhanced Signal-to-Noise Ratio under a Salt Imbalance”, ACS sensors, 7(7), 1883-1893, 2022.
30. Buddini I. Karawdeniya, Adam M. Damry, Krishnan Murugappan, Shridhar Manjunath, Y. M Nuwan D. Y Bandara, Colin J. Jackson, Antonio Tricoli and, Dragomir Neshev “Surface Functionalization and Texturing of Optical Metasurfaces for Sensing Applications”, ACS Chemical Reviews, 122(19), 14990-15030, 2022.
29. Lauren S. Lastra, Y. M. Nuwan D. Y. Bandara, Michelle Nguyen, Nasim Farajpour, Kevin J. Freedman. “On the Origins of Conductive Pulse Sensing Inside a Nanopore”, Nature Communications, 13, 2186, 2022.
28. Y. M. Nuwan D. Y. Bandara, Nasim Farajpour and Kevin J. Freedman. “Nanopore Current Enhancements Lack Protein Charge Dependence and Elucidates Maximum Unfolding at Protein’s Isoelectric Point”, Journal of the American Chemical Society, 144, 7, 3063–3073, 2022.
27. J. Saharia, Y. M. Nuwan D. Y. Bandara and M.J. Kim. “Investigating protein translocation in the presence of an electrolyte concentration gradient across a solid‐state nanopore”, Electrophoresis, 43(5-6), 785-792, 2022.
26. Y. M. Nuwan D. Y. Bandara, J. Saharia, B.I. Karawdeniya, P. Kluth and M.J. Kim. “Nanopore Data Analysis: Baseline Construction and Abrupt Change-based Multilevel Fitting”, Analytical Chemistry 93, 34, 11710-11718, 2021.
25. J Saharia, Y. M. Nuwan D. Y. Bandara, B.I Karawdeniya, C. Hammond, G. Alexandrakis and M.J Kim. “Modulation of electrophoresis, electroosmosis and diffusion for electrical transport of proteins through a solid-state nanopore”, RSC Advances, 11, 24398–24409, 2021.
24. B.I Karawdeniya, RB Chevalier, Y. M. Nuwan D. Y. Bandara, JR Dwyer. “Targeting improved reproducibility in surface-enhanced Raman spectroscopy with planar substrates using 3D printed alignment holders”, Review of Scientific Instruments 92 (4), 043102, 2021.
23. J.S Lee, J.P Oviedo, Y. M. Nuwan D. Y. Bandara, X. Peng, L. Xia, Q. Wang, K. Garcia, J. Wang, M.J. Kim, M. J. Kim. “Detection of nucleotides in hydrated ssDNA via 2D h‐BN nanopore with ionic‐liquid/salt–water interface”, Electrophoresis, 42(7-8), 991-1002, 2021.
22. J Saharia, Y. M. Nuwan D. Y. Bandara, B.I Karawdeniya, G Alexandrakis, MJ Kim; “Assessment of 1/f noise associated with nanopores fabricated through chemically‐tuned controlled dielectric breakdown“, Electrophoresis, 42(7-8), 899-909, 2021.
21. B.I. Karawdeniya, Y. M. Nuwan D. Y. Bandara, A.I Khan, W.T Chen, H. Vu, A. Morshed, J. Suh, P. Dutta, and M.J. Kim. “Adeno Associated Virus Characterization for Cargo Discrimination through Nanopore Responsiveness”, Nanoscale, 12 (46), 23721-23731, 2020.
20. J.T. Hagan, B.S. Sheetz, Y.M Nuwan D. Y Bandara, B.I. Karawdeniya, M.A. Morris, R.B. Chevalier, J.R Dwyer. “Chemically tailoring nanopores for single-molecule sensing and glycomics”, Analytical and Bioanalytical Chemistry, 412, 6639-6654, 2020.
19. Y.M. Nuwan D.Y. Bandara, J. Saharia, B.I. Karawdeniya, J.T Hagan, J.R. Dwyer and M.J. Kim. “Beyond nanopore sizing: improving solid-state single-molecule sensing performance, lifetime, and analyte scope for omics by targeting surface chemistry during fabrication”, Nanotechnology, 31 (33), 335707, 2020.
18. B. Sheetz, Y.M. Nuwan D.Y. Bandara, B. Rickson, M. Auten, and J.R. Dwyer. “Rapid, Spatially Selective Modification of Silicon Nitride Thin Films Under Ambient Conditions Using a Hand-Held Tesla-Coil Lighter”, ACS Applied Nano Materials, 3 (3), 2969-2977, 2020.
17. A. Morshed, B.I. Karawdeniya, Y. M. Nuwan D. Y. Bandara, M.J. Kim, P. Dutta. “Mechanical Characterization of Vesicles: A Review”, Electrophoresis, 41 (7-8), 449-470, 2020
16. (invited) J. Saharia, Y. M. Nuwan D. Y. Bandara, J.S. Lee1, Q. Wang, M. J. Kim, M.J Kim. “Fabrication of Hexagonal Boron Nitride based 2-D Nanopore Sensor for the Assessment of Electro-Chemical Responsiveness of Human Serum Transferrin Protein”, Electrophoresis, 41 (7-8), 630-637, 2020.
15. Y. M. Nuwan D. Y. Bandara, J. Tang, J. Saharia, L.W. Rogowski, C.W. Ahn, and M.J. Kim. “Characterization of Flagellar Filaments and Flagellin through Optical Microscopy and Label-Free Nanopore Responsiveness”, ACS Analytical Chemistry, 91 (21), 13665-13674, 2020.
14. Y.M. Nuwan D.Y. Bandara, B.I. Karawdeniya, J. Hegan, R.B. Chevalier and J.R. Dwyer. “Chemically Functionalizing Controlled Dielectric Breakdown Silicon Nitride Nanopores by Direct Photohydrosilylation”, ACS Applied Materials and Interfaces, 11 (33), 30411-30420, 2019.
13. J. Saharia*, Y. M. Nuwan D. Y. Bandara*, G. Goyal, J.S. Lee, B.I. Karawdeniya and M.J. Kim. *authors contributed equally, “Molecular-Level Profiling of Human Serum Transferrin Protein through Assessment of Nanopore-Based Electrical and Chemical Responsiveness”, ACS Nano, 13 (4), 4246-4254, 2019.
12. B.I. Karawdeniya, Y. M. Nuwan D. Y. Bandara, J.W. Nichols, R.B. Chevalier, J.T. Hagan and J.R. Dwyer. “Challenging Nanopores with Analyte Scope and Environment”, Journal of Analysis and Testing, 3 (1), 61-79, 2019.
11. J.S. Lee, J. Saharia, Y. M. Nuwan D. Y. Bandara, B.I. Karawdeniya, G. Goyal, A. Darvish, Q. Wang, M.J. Kim, and M.J. Kim. “Stiffness measurement of nanosized liposomes using solid‐state nanopore sensor with automated recapturing platform”, Electrophoresis, 40 (9), 1337-1344, 2019.
10. Y. M. Nuwan D. Y. Bandara, Buddini I Karawdeniya and Jason R Dwyer. “Push-Button Method to Create Nanopores Using a Tesla Coil Lighter”, ACS Omega, 4 (1), 226-230, 2019.
9. A. Darvish, J.S. Lee, J. Saharia, R.V.K. Sundaram, G. Goyal, Nuwan Bandara, C.W. Ahn, J. Kim, P. Dutta, I. Chaiken, M.J. Kim. “Mechanical Characterization of HIV-1 with a Solid State Nanopore Sensor”, Electrophoresis, 40 (5), 776-783, 2019.
8. B.I. Karawdeniya, Y.M. Nuwan D.Y. Bandara, J.W. Nichols, R. B. Chevalier and J.R. Dwyer. “Surveying Silicon Nitride Nanopores for Glycomics and Heparin Quality Assurance”,Nature Communications, 9 (1), 1-8, 2018.
8. S. Chaudhuri, M. Verderame, Y. M. Nuwan D. Y. Bandara, A.I. Fernando, T. L. Mako and M. Levine. “Synthetic β-cyclodextrin Dimers for Squaraine Binding: Effect of Host Architecture on Photophysical Properties, Aggregate Formation and Chemical Reactivity”, European Journal of Organic Chemistry, (17), 1964-1974, 2018.
6. B.I. Karawdeniya, Y.M. Nuwan D.Y. Bandara, J.C. Whelan and J.R. Dwyer. “General strategy to make an on-demand library of structurally and functionally diverse SERS substrates”, ACS Applied Nano Materials, 1 (2), 960-968, 2018.
5. Y.M. Nuwan D.Y. Bandara, B.I. Karawdeniya, J.W. Nichols and J.R.Dwyer. “Conductance-Based Profiling of Nanopores: Accommodating Fabrication Irregularities”, Electrophoresis, 39 (4), 626-634, 2018.
4. Y. M. Nuwan D. Y. Bandara, B.I. Karawdeniya, J.C. Whelan, L.D.S. Ginsberg and J.R. Dwyer. “Solution-Based Photo-Patterned Gold Film Formation on Silicon Nitride”, ACS Applied Materials and Interfaces, 8 (51), 34964-34969, 2016.
3. Y. M. Nuwan D. Y. Bandara, B.I. Karawdeniya and J.R. Dwyer. “Real-Time Profiling of Solid-State Nanopores During Solution-Phase Nanofabrication”, ACS Applied Materials and Interfaces, 8 (44), 30583-30589, 2016.
2. J.C. Whelan, B.I. Karawdeniya*, Y. M. Nuwan D.Y. Bandara*, B. Velleco, C.M. Masterson and J.R. Dwyer. *authors contributed equally. “Electroless Plating of Ultrathin Gold Films Directly onto Silicon Nitride Thin Films and Into Micropores”, ACS Applied Materials and Interfaces, 6 (14), 10952-10957, 2014.
1. (cover article) C.M. Frament, Nuwan Bandara and J.R. Dwyer. “Nanopore Surface Coating Delivers Nanopore Size and Shape Through Conductance-Based Sizing”, ACS Applied Materials and Interfaces, 5 (19), 9330-9337, 2013.