{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,18]],"date-time":"2026-04-18T14:11:51Z","timestamp":1776521511368,"version":"3.51.2"},"reference-count":61,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2023,3,23]],"date-time":"2023-03-23T00:00:00Z","timestamp":1679529600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Research Institute of Rangsit University (RSU)","award":["KREF016601"],"award-info":[{"award-number":["KREF016601"]}]},{"DOI":"10.13039\/501100007120","name":"School of Engineering of King Mongkut\u2019s Institute of Technology Ladkrabang (KMITL)","doi-asserted-by":"publisher","award":["KREF016601"],"award-info":[{"award-number":["KREF016601"]}],"id":[{"id":"10.13039\/501100007120","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Sensors"],"abstract":"<jats:p>Surface plasmon resonance (SPR) has been utilized in various optical applications, including biosensors. The SPR-based sensor is a gold standard for protein kinetic measurement due to its ultrasensitivity on the plasmonic metal surface. However, a slight change in the surface morphology, such as roughness or pattern, can significantly impact its performance. This study proposes a theoretical framework to explain sensing mechanisms and quantify sensing performance parameters of angular surface plasmon resonance detection for binding kinetic sensing at different levels of surface roughness. The theoretical investigation utilized two models, a protein layer coating on a rough plasmonic surface with and without sidewall coatings. The two models enable us to separate and quantify the enhancement factors due to the localized surface plasmon polaritons at sharp edges of the rough surfaces and the increased surface area for protein binding due to roughness. The Gaussian random surface technique was employed to create rough metal surfaces. Reflectance spectra and quantitative performance parameters were simulated and quantified using rigorous coupled-wave analysis and Monte Carlo simulation. These parameters include sensitivity, plasmonic dip position, intensity contrast, full width at half maximum, plasmonic angle, and figure of merit. Roughness can significantly impact the intensity measurement of binding kinetics, positively or negatively, depending on the roughness levels. Due to the increased scattering loss, a tradeoff between sensitivity and increased roughness leads to a widened plasmonic reflectance dip. Some roughness profiles can give a negative and enhanced sensitivity without broadening the SPR spectra. We also discuss how the improved sensitivity of rough surfaces is predominantly due to the localized surface wave, not the increased density of the binding domain.<\/jats:p>","DOI":"10.3390\/s23073377","type":"journal-article","created":{"date-parts":[[2023,3,23]],"date-time":"2023-03-23T05:19:24Z","timestamp":1679548764000},"page":"3377","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Sensing Mechanisms of Rough Plasmonic Surfaces for Protein Binding of Surface Plasmon Resonance Detection"],"prefix":"10.3390","volume":"23","author":[{"given":"Treesukon","family":"Treebupachatsakul","sequence":"first","affiliation":[{"name":"Department of Biomedical Engineering, School of Engineering, King Mongkut\u2019s Institute of Technology Ladkrabang, Bangkok 10520, Thailand"}]},{"given":"Siratchakrit","family":"Shinnakerdchoke","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, School of Engineering, King Mongkut\u2019s Institute of Technology Ladkrabang, Bangkok 10520, Thailand"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9105-8627","authenticated-orcid":false,"given":"Suejit","family":"Pechprasarn","sequence":"additional","affiliation":[{"name":"College of Biomedical Engineering, Rangsit University, Pathum Thani 12000, Thailand"}]}],"member":"1968","published-online":{"date-parts":[[2023,3,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Brongersma, M.L., and Kik, P.G. (2007). Surface Plasmon Nanophotonics, Springer.","DOI":"10.1007\/978-1-4020-4333-8"},{"key":"ref_2","unstructured":"Somekh, M.G., and Pechprasarn, S. (2017). Handbook of Photonics for Biomedical Engineering, Springer."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/S0925-4005(98)00321-9","article-title":"Surface plasmon resonance sensors","volume":"54","author":"Homola","year":"1999","journal-title":"Sens. Actuators B Chem."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1021\/bc0600620","article-title":"Immobilization and clustering of structurally defined oligosaccharides for sugar chips: An improved method for surface plasmon resonance analysis of protein-carbohydrate interactions","volume":"17","author":"Suda","year":"2006","journal-title":"Bioconjug. Chem."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2303","DOI":"10.1007\/s00216-014-7647-5","article-title":"Surface plasmon resonance applications in clinical analysis","volume":"406","author":"Mariani","year":"2014","journal-title":"Anal. Bioanal. Chem."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"5455","DOI":"10.1007\/s00216-017-0810-z","article-title":"Label-free screening of foodborne Salmonella using surface plasmon resonance imaging","volume":"410","author":"Chen","year":"2018","journal-title":"Anal. Bioanal. Chem."},{"key":"ref_7","unstructured":"Douzi, B. (2017). Bacterial Protein Secretion Systems: Methods and Protocols, Humana Press."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/bs.apcsb.2017.07.003","article-title":"Analysis of protein interactions by surface plasmon resonance","volume":"110","author":"Drescher","year":"2018","journal-title":"Adv. Protein Chem. Struct. Biol."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Sangworasil, M., Pechprasarn, S., Learkthanakhachon, S., Ittipornnuson, K., Suvarnaphaet, P., and Albutt, N. (2016, January 7\u20139). Investigation on feasibility of using surface plasmons resonance (SPR) sensor for ultrasonic detection: A novel optical detection of ultrasonic waves. Proceedings of the 2016 9th Biomedical Engineering International Conference (BMEiCON), Laung Prabang, Laos.","DOI":"10.1109\/BMEiCON.2016.7859607"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"3453","DOI":"10.1364\/AO.57.003453","article-title":"Adjustable microscopic measurement of nanogap waveguide and plasmonic structures","volume":"57","author":"Shen","year":"2018","journal-title":"Appl. Opt."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Suvarnaphaet, P., and Pechprasarn, S. (2018). Enhancement of long-range surface plasmon excitation, dynamic range and figure of merit using a dielectric resonant cavity. Sensors, 18.","DOI":"10.3390\/s18092757"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Suvarnaphaet, P., and Pechprasarn, S. (2018). Quantitative cross-platform performance comparison between different detection mechanisms in surface plasmon sensors for voltage sensing. Sensors, 18.","DOI":"10.3390\/s18093136"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1021\/jm049359e","article-title":"Surface plasmon resonance thermodynamic and kinetic analysis as a strategic tool in drug design. Distinct ways for phosphopeptides to plug into Src-and Grb2 SH2 domains","volume":"48","author":"Dekker","year":"2005","journal-title":"J. Med. Chem."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1809","DOI":"10.4155\/fmc.11.128","article-title":"Emerging role of surface plasmon resonance in fragment-based drug discovery","volume":"3","author":"Navratilova","year":"2011","journal-title":"Future Med. Chem."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"10797","DOI":"10.1364\/OE.24.010797","article-title":"Single shot embedded surface plasmon microscopy with vortex illumination","volume":"24","author":"Chow","year":"2016","journal-title":"Opt. Express"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1155\/2003\/372913","article-title":"Surface plasmon resonance: Principles, methods and applications in biomedical sciences","volume":"17","author":"Englebienne","year":"2003","journal-title":"Spectroscopy"},{"key":"ref_17","first-page":"2135","article-title":"Radiative decay of non radiative surface plasmons excited by light","volume":"23","author":"Kretschmann","year":"1968","journal-title":"Z. Nat. A"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1364\/OL.33.000512","article-title":"Dual-mode surface-plasmon-resonance sensors using angular interrogation","volume":"33","author":"Guo","year":"2008","journal-title":"Opt. Lett."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"111717","DOI":"10.1016\/j.bios.2019.111717","article-title":"Wavelength-scanning surface plasmon resonance microscopy: A novel tool for real time sensing of cell-substrate interactions","volume":"145","author":"Zeng","year":"2019","journal-title":"Biosens. Bioelectron."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"5641","DOI":"10.1364\/OE.14.005641","article-title":"Comparison between sensitivities of phase and intensity detection in surface plasmon resonance","volume":"14","author":"Ran","year":"2006","journal-title":"Opt. Express"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"21191","DOI":"10.1364\/OE.17.021191","article-title":"Phase and amplitude sensitivities in surface plasmon resonance bio and chemical sensing","volume":"17","author":"Kabashin","year":"2009","journal-title":"Opt. Express"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1038\/173821b0","article-title":"Refractive index of concentrated protein solutions","volume":"173","author":"Barer","year":"1954","journal-title":"Nature"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"794","DOI":"10.1364\/JOSA.60.000794","article-title":"Surface-plasmon effect in the reflectance of a metal","volume":"60","author":"Crowell","year":"1970","journal-title":"JOSA"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1016\/S0022-3697(74)80005-3","article-title":"Effect of surface roughness on surface plasmon resonance absorption","volume":"35","author":"Braundmeier","year":"1974","journal-title":"J. Phys. Chem. Solids"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2137","DOI":"10.1103\/PhysRevB.21.2137","article-title":"Surface-plasmon dispersion relation in the presence of surface roughness","volume":"21","author":"Rahman","year":"1980","journal-title":"Phys. Rev. B"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"5503","DOI":"10.1088\/0953-8984\/10\/24\/025","article-title":"Effect of roughness on surface plasmon scattering in gold films","volume":"10","author":"Hoffmann","year":"1998","journal-title":"J. Phys. Condens. Matter"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1021\/ac010820+","article-title":"Theoretical understanding of an absorption-based surface plasmon resonance sensor based on Kretchmann\u2019s theory","volume":"74","author":"Kurihara","year":"2002","journal-title":"Anal. Chem."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Treebupachatsakul, T., Shinnakerdchoke, S., and Pechprasarn, S. (2021). Analysis of effects of surface roughness on sensing performance of surface plasmon resonance detection for refractive index sensing application. Sensors, 21.","DOI":"10.3390\/s21186164"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"5886","DOI":"10.1364\/AO.47.005886","article-title":"Effect of surface roughness on the extinction-based localized surface plasmon resonance biosensors","volume":"47","author":"Byun","year":"2008","journal-title":"Appl. Opt."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"3139","DOI":"10.1021\/nn100466p","article-title":"Enhanced surface plasmon resonance on a smooth silver film with a seed growth layer","volume":"4","author":"Liu","year":"2010","journal-title":"ACS Nano"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"670","DOI":"10.1002\/(SICI)1096-9918(199907)27:7<670::AID-SIA558>3.0.CO;2-1","article-title":"Surface roughness of sputter-deposited gold films: A combined x-ray technique and AFM study","volume":"27","author":"Schug","year":"1999","journal-title":"Surf. Interface Anal."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/s11671-015-0944-x","article-title":"Gold nanohole array with sub-1 nm roughness by annealing for sensitivity enhancement of extraordinary optical transmission biosensor","volume":"10","author":"Zhang","year":"2015","journal-title":"Nanoscale Res. Lett."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"465302","DOI":"10.1088\/1361-6528\/abae99","article-title":"Nanoaperture fabrication in ultra-smooth single-grain gold films with helium ion beam lithography","volume":"31","author":"Zhang","year":"2020","journal-title":"Nanotechnology"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2587","DOI":"10.1002\/adfm.201002303","article-title":"Ultrasmooth gold films via pulsed laser deposition","volume":"21","author":"Ng","year":"2011","journal-title":"Adv. Funct. Mater."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1007\/s11468-012-9432-7","article-title":"Optical fiber micro-taper with circular symmetric gold coating for sensor applications based on surface plasmon resonance","volume":"8","author":"Wieduwilt","year":"2013","journal-title":"Plasmonics"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1007\/s003390100935","article-title":"Fabrication of large-scale ultra-smooth metal surfaces by a replica technique","volume":"73","author":"Diebel","year":"2001","journal-title":"Appl. Phys. A"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"14171","DOI":"10.1021\/la5032027","article-title":"Ultrasmooth gold surfaces prepared by chemical mechanical polishing for applications in nanoscience","volume":"30","author":"Miller","year":"2014","journal-title":"Langmuir"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"5797","DOI":"10.1021\/am508681u","article-title":"Ultrathin, ultrasmooth gold layer on dielectrics without the use of additional metallic adhesion layers","volume":"7","author":"Leandro","year":"2015","journal-title":"ACS Appl. Mater. Interfaces"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"894","DOI":"10.1109\/PROC.1985.13220","article-title":"Analysis and applications of optical diffraction by gratings","volume":"73","author":"Gaylord","year":"1985","journal-title":"Proc. IEEE"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1068","DOI":"10.1364\/JOSAA.12.001068","article-title":"Formulation for stable and efficient implementation of the rigorous coupled-wave analysis of binary gratings","volume":"12","author":"Moharam","year":"1995","journal-title":"J. Opt. Soc. Am. A"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"16289","DOI":"10.1038\/s41598-021-95593-4","article-title":"Deep learning-based single-shot phase retrieval algorithm for surface plasmon resonance microscope based refractive index sensing application","volume":"11","author":"Thadson","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1194","DOI":"10.1364\/JOSAA.4.001194","article-title":"Experimental study of scattering from characterized random surfaces","volume":"4","author":"Mendez","year":"1987","journal-title":"JOSA A"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"4370","DOI":"10.1103\/PhysRevB.6.4370","article-title":"Optical constants of the noble metals","volume":"6","author":"Johnson","year":"1972","journal-title":"Phys. Rev. B"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"6807","DOI":"10.1021\/acs.analchem.7b01229","article-title":"Sensitive analysis of protein adsorption to colloidal gold by differential centrifugal sedimentation","volume":"89","author":"Davidson","year":"2017","journal-title":"Anal. Chem."},{"key":"ref_45","unstructured":"Saleem, M.R., and Ali, R. (2018). Emerging Waveguide Technology, IntechOpen."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1039\/C2AY25470K","article-title":"Resonant waveguide grating (RWG): Overcoming the problem of angular sensitivity by conical, broad-band illumination for fluorescence measurements","volume":"5","author":"Nuutinen","year":"2013","journal-title":"Anal. Methods"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.1364\/JOSAB.35.001059","article-title":"Surface passivation of silicon photonic devices with high surface-to-volume-ratio nanostructures","volume":"35","author":"Mayet","year":"2018","journal-title":"JOSA B"},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Zhang, C., Zhou, Y., Mi, L., Ma, J., Wu, X., and Fei, Y. (2021). High performance of a metal layer-assisted guided-mode resonance biosensor modulated by double-grating. Biosensors, 11.","DOI":"10.3390\/bios11070221"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1364\/OL.32.000509","article-title":"High-resolution surface-plasmon imaging in air and in water: V (z) curve and operating conditions","volume":"32","author":"Berguiga","year":"2007","journal-title":"Opt. Lett."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1364\/JOSA.71.000811","article-title":"Rigorous coupled-wave analysis of planar-grating diffraction","volume":"71","author":"Moharam","year":"1981","journal-title":"JOSA"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"181108","DOI":"10.1063\/1.3012365","article-title":"Experimental observation of narrow surface plasmon resonances in gold nanoparticle arrays","volume":"93","author":"Chu","year":"2008","journal-title":"Appl. Phys. Lett."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"7977","DOI":"10.1364\/AO.45.007977","article-title":"Surface-plasmon microscopy with a two-piece solid immersion lens: Bright and dark fields","volume":"45","author":"Zhang","year":"2006","journal-title":"Appl. Opt."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"2052","DOI":"10.1038\/s41598-022-06065-2","article-title":"Measurement precision enhancement of surface plasmon resonance based angular scanning detection using deep learning","volume":"12","author":"Thadson","year":"2022","journal-title":"Sci. Rep."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Meng, Q.-Q., Zhao, X., Lin, C.-Y., Chen, S.-J., Ding, Y.-C., and Chen, Z.-Y. (2017). Figure of merit enhancement of a surface plasmon resonance sensor using a low-refractive-index porous silica film. Sensors, 17.","DOI":"10.3390\/s17081846"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"1784","DOI":"10.1364\/BOE.451023","article-title":"Generalized figure of merit for plasmonic dip measurement-based surface plasmon resonance sensors","volume":"13","author":"Treebupachatsakul","year":"2022","journal-title":"Biomed. Opt. Express"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"042401","DOI":"10.3788\/COL201614.042401","article-title":"Influence of surface roughness on surface plasmon resonance phenomenon of gold film","volume":"14","author":"Yang","year":"2016","journal-title":"Chin. Opt. Lett."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"8376","DOI":"10.1364\/OE.454344","article-title":"Self-referenced refractive index sensor based on double-dips method with bimetal-dielectric and double-groove grating","volume":"30","author":"Zhao","year":"2022","journal-title":"Opt. Express"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1016\/j.optcom.2016.08.072","article-title":"Influence of metal roughness on SPR sensor performance","volume":"383","author":"Agarwal","year":"2017","journal-title":"Opt. Commun."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"8547","DOI":"10.1038\/s41598-018-26424-2","article-title":"Application of confocal surface wave microscope to self-calibrated attenuation coefficient measurement by Goos-H\u00e4nchen phase shift modulation","volume":"8","author":"Pechprasarn","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1021\/acs.accounts.1c00682","article-title":"Exploiting plasmonic hot spots in Au-based nanostructures for sensing and photocatalysis","volume":"55","author":"Wy","year":"2022","journal-title":"Acc. Chem. Res."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"10628","DOI":"10.1109\/JSEN.2021.3063136","article-title":"Analysis of open grating-based Fabry\u2013P\u00e9rot resonance structures with potential applications for ultrasensitive refractive index sensing","volume":"21","author":"Sasivimolkul","year":"2021","journal-title":"IEEE Sens. J."}],"container-title":["Sensors"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1424-8220\/23\/7\/3377\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T19:01:21Z","timestamp":1760122881000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1424-8220\/23\/7\/3377"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,3,23]]},"references-count":61,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2023,4]]}},"alternative-id":["s23073377"],"URL":"https:\/\/doi.org\/10.3390\/s23073377","relation":{},"ISSN":["1424-8220"],"issn-type":[{"value":"1424-8220","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,3,23]]}}}