Understanding the Role of M13 Bacteriophage Thin Films on a Metallic Nanostructure through a Standard and Dynamic Model.

The dynamic and surface manipulation of the M13 bacteriophage via the meeting application demands the creation of a pathway to design efficient applications with high selectivity and responsivity rates. Here, we report the role of the M13 bacteriophage thin film layer that is deposited on an optical nanostructure involving gold nanoparticles/SiO2/Si, as well as its influence on optical and geometrical properties. The thickness of the M13 bacteriophage layer was controlled by varying either the concentration or humidity exposure levels, and optical studies were conducted. We designed a standard and dynamic model based upon three-dimensional finite-difference time-domain (3D FDTD) simulations that distinguished the respective necessity of each model under variable conditions. As seen in the experiments, the origin of respective peak wavelength positions was addressed in detail with the help of simulations. The importance of the dynamic model was noted when humidity-based experiments were conducted. Upon introducing varied humidity levels, the dynamic model predicted changes in plasmonic properties as a function of changes in NP positioning, gap size, and effective index (this approach agreed with the experiments and simulated results). We believe that this work will provide fundamental insight into understanding and interpreting the geometrical and optical properties of the nanostructures that involve the M13 bacteriophage. By combining such significant plasmonic properties with the numerous benefits of M13 bacteriophage (like low-cost fabrication, multi-wavelength optical characteristics devised from a single structure, reproducibility, reversible characteristics, and surface modification to suit application requirements), it is possible to develop highly efficient integrated plasmonic biomaterial-based sensor nanostructures.

Three-Dimensional Plasmonic Nanocluster-Driven Light-Matter Interaction for Photoluminescence Enhancement and Picomolar-Level Biosensing.

Plasmonic nanoparticle clusters promise to support unique engineered electromagnetic responses at optical frequencies, realizing a new concept of devices for nanophotonic applications. However, the technological challenges associated with the fabrication of three-dimensional nanoparticle clusters with programmed compositions remain unresolved. Here, we present a novel strategy for realizing heterogeneous structures that enable efficient near-field coupling between the plasmonic modes of gold nanoparticles and various other nanomaterials via a simple three-dimensional coassembly process. Quantum dots embedded in the plasmonic structures display ∼56 meV of a blue shift in the emission spectrum. The decay enhancement factor increases as the total contribution of radiative and nonradiative plasmonic modes increases. Furthermore, we demonstrate an ultracompact diagnostic platform to detect M13 viruses and their mutations from femtoliter volume, sub-100 pM analytes. This platform could pave the way toward an effective diagnosis of diverse pathogens, which is in high demand for handling pandemic situations.

Engineering Efficient Self-Assembled Plasmonic Nanostructures by Configuring Metallic Nanoparticle's Morphology.

We reveal the significance of plasmonic nanoparticle's (NP) shape and its surface morphology en route to an efficient self-assembled plasmonic nanoparticle cluster. A simplified model is simulated in the form of free-space dimer and trimer nanostructures (NPs in the shape of a sphere, cube, and disk). A ~200% to ~125% rise in near-field strength (gap mode enhancement) is observed for spherical NPs in comparison with cubical NPs (from 2 nm to 8 nm gap sizes). Full-width three-quarter maximum reveals better broad-spectral optical performance in a range of ~100 nm (dimer) and ~170 nm (trimer) from spherical NPs as compared to a cube (~60 nm for dimer and trimer). These excellent properties for sphere-based nanostructures are merited from its dipole mode characteristics.

Experimental and numerical evaluation of a genetically engineered M13 bacteriophage with high sensitivity and selectivity for 2,4,6-trinitrotoluene.

Selective and sensitive detection of desired targets is very critical in sensor design. Here, we report a genetically engineered M13 bacteriophage-based sensor system evaluated by quantum mechanics (QM) calculations. Phage display is a facile way to develop the desired peptide sequences, but the resulting sequences can be imperfect peptides for binding of target molecules. A TNT binding peptide (WHW) carrying phage was self-assembled to fabricate thin films and tested for the sensitive and selective surface plasmon resonance-based detection of TNT molecules at the 500 femtomole level. SPR studies performed with the WHW peptide and control peptides (WAW, WHA, AHW) were well-matched with those of the QM calculations. Our combined method between phage engineering and QM calculation will significantly enhance our ability to design selective and sensitive sensors.

Design for an efficient single photon source based on a single quantum dot embedded in a parabolic solid immersion lens.

We have designed a single photon emitter based on a single quantum dot embedded within a single mode parabolic solid immersion lens (pSIL) and a capping low-index pSIL. Numerical simulations predicted that the emitter performance should exhibit a high photon collection efficiency with excellent far-field emission properties, broadband operation, and good tolerance in its geometric (spatial configuration) parameters. Good geometric tolerance in a single-mode pSIL without yielding significant losses in the photon collection efficiency is advantageous for device fabrication. The low-index top pSIL layer provided this structure with a high photon collection efficiency, even in the case of a small numerical aperture (NA). Photon collection efficiencies of 64% and 78% were expected for NA values of 0.41 and 0.5, respectively. In addition to the benefits listed above, our combined pSIL design provided excellent broadband performance in a 100 nm range.

Multichannel Hierarchical Analysis of Time-Resolved Hyperspectral Data for Advanced Colorimetric E-Nose.

The colorimetric sensor-based electronic nose has been demonstrated to discriminate specific gaseous molecules for various applications, including health or environmental monitoring. However, conventional colorimetric sensor systems rely on RGB sensors, which cannot capture the complete spectral response of the system. This limitation can degrade the performance of machine learning analysis, leading to inaccurate identification of chemicals with similar functional groups. Here, we propose a novel time-resolved hyperspectral (TRH) data set from colorimetric array sensors consisting of 1D spatial, 1D spectral, and 1D temporal axes, which enables hierarchical analysis of multichannel 2D spectrograms via a convolution neural network (CNN). We assessed the outstanding classification performance of the TRH data set compared to an RGB data set by conducting a relative humidity (RH) concentration classification. The time-dependent spectral response of the colorimetric sensor was measured and trained as a CNN model using TRH and RGB sensor systems at different RH levels. While the TRH model shows a high classification accuracy of 97.5% for the RH concentration, the RGB model yields 72.5% under identical conditions. Furthermore, we demonstrated the detection of various functional volatile gases with the TRH system by using experimental and simulation approaches. The results reveal distinct spectral features from the TRH system, corresponding to changes in the concentration of each substance.

Metal 3D nanoprinting with coupled fields.

Metallized arrays of three-dimensional (3D) nanoarchitectures offer new and exciting prospects in nanophotonics and nanoelectronics. Engineering these repeating nanoarchitectures, which have dimensions smaller than the wavelength of the light source, enables in-depth investigation of unprecedented light-matter interactions. Conventional metal nanomanufacturing relies largely on lithographic methods that are limited regarding the choice of materials and machine write time and are restricted to flat patterns and rigid structures. Herein, we present a 3D nanoprinter devised to fabricate flexible arrays of 3D metallic nanoarchitectures over areas up to 4 × 4 mm2 within 20 min. By suitably adjusting the electric and flow fields, metal lines as narrow as 14 nm were printed. We also demonstrate the key ability to print a wide variety of materials ranging from single metals, alloys to multimaterials. In addition, the optical properties of the as-printed 3D nanoarchitectures can be tailored by varying the material, geometry, feature size, and periodic arrangement. The custom-designed and custom-built 3D nanoprinter not only combines metal 3D printing with nanoscale precision but also decouples the materials from the printing process, thereby yielding opportunities to advance future nanophotonics and semiconductor devices.

An Accessible Integrated Nanoparticle in a Metallic Hole Structure for Efficient Plasmonic Applications.

Addressing the severe deterioration of gap mode properties in spherical-shaped nanoparticles (NPs) becomes necessary due to their utilization in a wide range of multi-disciplinary applications. In this work, we report an integrated plasmonic nanostructure based on a spherical-shaped nanoparticle (NP) in a metallic hole as an alternative to a NP-only structure. With the help of three-dimensional (3D) electromagnetic simulations, we reveal that when a NP is positioned on the top of a metallic hole, it can exhibit superior gap-mode-based local-field intensity enhancement. The integrated nanostructure displayed a ~22-times increase in near-field enhancement characteristics, similar to cube- or disk-shaped nanostructure's plasmonic properties. From an experimental perspective, the NP positioning on top of the metallic hole can be realized more easily, facilitating a simple fabrication meriting our design approach. In addition to the above advantages, a good geometrical tolerance (metallic hole-gap size error of ~20 nm) supported by gap mode characteristics enhances flexibility in fabrication. These combined advantages from an integrated plasmonic nanostructure can resolve spherical-shaped NP disadvantages as an individual nanostructure and enhance its utilization in multi-disciplinary applications.

Three-dimensional plasmonic nanoclusters driven by co-assembly of thermo-plasmonic nanoparticles and colloidal quantum dots.

Metallic nanoparticles that support localized surface plasmons have emerged as fundamental iconic building blocks for nanoscale photonics. Self-assembled clustering of plasmonic nanoparticles with controlled near-field interactions offers an interesting novel route to manipulate the electromagnetic fields at a subwavelength scale. Various bottom-up, self-assembly manners have been successfully devised to build plasmonic nanoparticle clusters displaying attractive optical properties. However, the incapability to configure on-demand architectures limits its practical reliability uses for scalable nanophotonic devices. Furthermore, a critical challenge has been addressing the accurate positioning of functional nanoparticles, including catalytic nanoparticles, dielectric nanoparticles, and quantum dots (QDs) in the clustered plasmonic hotspots. This work proposes a micropipette-based self-assembly method to fabricate three-dimensional architectures composed of colloidal clusters. The heterogeneous colloidal clusters comprising metallic nanoparticles and QDs are fabricated in one step by the micropipette-based self-assembly method. A plasmonic clustered pillar embedding QDs exhibited excellent photoluminescence characteristics compared to a collapsed pillar. The experimental and theoretical demonstration of the localized surface plasmon resonance and thermo-plasmonic properties of the colloidal clusters was performed.

Neural mechanism mimetic selective electronic nose based on programmed M13 bacteriophage.

The electronic nose is a reliable practical sensor device that mimics olfactory organs. Although numerous studies have demonstrated excellence in detecting various target substances with the help of ideal models, biomimetic approaches still suffer in practical realization because of the inability to mimic the signal processing performed by olfactory neural systems. Herein, we propose an electronic nose based on the programable surface chemistry of M13 bacteriophage, inspired by the neural mechanism of the mammalian olfactory system. The neural pattern separation (NPS) was devised to apply the pattern separation that operates in the memory and learning process of the brain to the electronic nose. We demonstrate an electronic nose in a portable device form, distinguishing polycyclic aromatic compounds (harmful in living environment) in an atomic-level resolution (97.5% selectivity rate) for the first time. Our results provide practical methodology and inspiration for the second-generation electronic nose development toward the performance of detection dogs (K9).

Programmable self-assembly of M13 bacteriophage for micro-color pattern with a tunable colorization.

Over the last decade, the M13 bacteriophage has been used widely in various applications, such as sensors, bio-templating, and solar cells. The M13 colorimetric sensor was developed to detect toxic gases to protect the environment, human health, and national security. Recent developments in phage-based colorimetric sensor technologies have focused on improving the sensing characteristics, such as the sensitivity and selectivity on a large scale. On the other hand, few studies have examined precisely controllable micro-patterning techniques in phage-based self-assembly. This paper developed a color patterning technique through self-assembly of the M13 bacteriophages. The phage was self-assembled into a nanostructure through precise temperature control at the meniscus interface. Furthermore, barcode color patterns could be fabricated using self-assembled M13 bacteriophage on micrometer scale areas by manipulating the grooves on the SiO2 surface. The color patterns exhibited color tunability based on the phage nano-bundles reactivity. Overall, the proposed color patterning technique is expected to be useful for preparing new color sensors and security patterns.

Optical bioelectronic nose of outstanding sensitivity and selectivity toward volatile organic compounds implemented with genetically engineered bacteriophage: Integrated study of multi-scale computational prediction and experimental validation.

Genetic engineering of a bacteriophage is a promising way to develop a highly functional biosensor. Almost countless configurational degree of freedom in the manipulation, considerable uncertainty and cost involved with the approach, however, have been huddles for the objective. In this paper, we demonstrate rapidly responding optical biosensor with high selectivity toward gaseous explosives with genetically engineered phages. The sensors are equipped with peptide sequences in phages optimally interacting with the volatile organic compounds (VOCs) in visible light regime. To overcome the conventional issues, we use extensive utilization of empirical calculations to construct a large database of 8000 tripeptides and screen the best for electronic nose sensing performance toward nine VOCs belonging to three chemical classes. First-principles density functional theory (DFT) calculations unveil underlying correlations between the chemical affinity and optical property change on an electronic band structure level. The computational outcomes are validated by in vitro experimental design and testing of multiarray sensors using genetically modified phage implemented with five selected tripeptide sequences and wild-type phages. The classification success rates estimated from hierarchical cluster analysis are shown to be very consistent with the calculations. Our optical biosensor demonstrates a 1 ppb level of sensing resolution for explosive VOCs, which is a substantial improvement over conventional biosensor. The systematic interplay of big data-based computational prediction and in situ experimental validation can provide smart design principles for unconventionally outstanding biosensors.

Investigation of colorimetric biosensor array based on programable surface chemistry of M13 bacteriophage towards artificial nose for volatile organic compound detection: From basic properties of the biosensor to practical application.

Various threats such as explosives, drugs, environmental hormones, and spoiled food manifest themselves with the presence of volatile organic compounds (VOCs) in our environment. In order to recognize and respond to these threats early, the demand for highly sensitive and selective electronic noses is increasing. The M13 bacteriophage-based optoelectronic nose is an excellent candidate to meet all these requirements. However, the phage-based electronic nose is still in its infancy, and strategies that include a systematic approach and development are still essential. Here, we have integrated theoretical and experimental approaches to analyze the correlation between the surface chemistry of genetically engineered phage and the phage-based optoelectronic nose properties. The reactivity of the genetically engineered phage color film to some VOCs were quantitatively analyzed, and the correlation with the binding affinity value calculated by Density-functional theory (DFT) was compared. This demonstrates that phage color films have controllable reactivity through a genetic engineering. We have selected phages that are advantageous in distinguishing each VOCs in this work through hierarchical cluster analysis (HCA). The reason for this difference was verified through the optimized geometry calculated by DFT. Through this, it was confirmed that the tryptophan-based and the Histidine-based of genetically engineered phage film are important in distinguishing the VOCs (Y-hexanolactone, 2-isopropyl-4-methylthiazole, ethanol, acetone, ethyl acetate, and acetaldehyde) used in this work to evaluate the peach freshness quality. This was applied to the design of a field-applied phage-based optoelectronic nose and verified by measuring the freshness of the actual fruit.

A DNA-derived phage nose using machine learning and artificial neural processing for diagnosing lung cancer.

There is a growing interest in electronic nose-based diagnostic systems that are fast and portable. However, existing technologies are suitable only for operation in the laboratory, making them difficult to apply in a rapid, non-face-to-face, and field-suitable manner. Here, we demonstrate a DNA-derived phage nose (D2pNose) as a portable respiratory disease diagnosis system requiring no pretreatment. D2pNose was produced based on phage colour films implanted with DNA sequences from mammalian olfactory receptor cells, and as a result, it possesses the comprehensive reactivity of these cells. The manipulated surface chemistry of the genetically engineered phages was verified through a correlation analysis between the calculated and the experimentally measured reactivity. Breaths from 31 healthy subjects and 31 lung cancer patients were collected and exposed to D2pNose without pretreatment. With the help of deep learning and neural pattern separation, D2pNose has achieved a diagnostic success rate of over 75% and a classification success rate of over 86% for lung cancer based on raw human breath. Based on these results, D2pNose can be expected to be directly applicable to other respiratory diseases.

A single bottom facet outperforms random multifacets in a nanoparticle-on-metallic-mirror system.

Highly efficient nanoparticle-on-metallic-mirror (NPOM) systems with a large gap size exhibiting good plasmonic enhancement are desirable for numerous practical applications. Careful, explicit design optimization strategies are required for preparing NPOMs and it is especially important in utilizing spherical nanoparticles. In this work, a new design blueprint for evaluating the role of random facets in spherical nanoparticles was investigated in detail to realize optimal NPOMs. We found that a precise single facet positioned at the nanoparticle's cavity outperformed multiple random facets due to the gap mode contribution. Differences and changes in the plasmonic modes were interpreted with the help of three-dimensional surface charge density mappings. A high-performance, single, bottom-faceted NPOM device with a large gap size (example 20 nm) was realized having 80-50% facet design, resulting in excellent gap mode enhancement. We succeeded in fabricating single bottom-faceted NPOMs (the non-facet region had a smooth spherical surface) with a large-scale unidirectionality (2 cm × 1.5 cm). Simulations and experimental characterizations of these components displayed excellent agreement. Our highly efficient NPOM design with a large gap size(s) enables interesting practical applications in the field of quantum emitters, energy devices, fuel generation and plasmon chemistry.

Hierarchical Cluster Analysis of Medical Chemicals Detected by a Bacteriophage-Based Colorimetric Sensor Array.

M13 bacteriophage-based colorimetric sensors, especially multi-array sensors, have been successfully demonstrated to be a powerful platform for detecting extremely small amounts of target molecules. Colorimetric sensors can be fabricated easily using self-assembly of genetically engineered M13 bacteriophage which incorporates peptide libraries on its surface. However, the ability to discriminate many types of target molecules is still required. In this work, we introduce a statistical method to efficiently analyze a huge amount of numerical results in order to classify various types of target molecules. To enhance the selectivity of M13 bacteriophage-based colorimetric sensors, a multi-array sensor system can be an appropriate platform. On this basis, a pattern-recognizing multi-array biosensor platform was fabricated by integrating three types of sensors in which genetically engineered M13 bacteriophages (wild-, RGD-, and EEEE-type) were utilized as a primary building block. This sensor system was used to analyze a pattern of color change caused by a reaction between the sensor array and external substances, followed by separating the specific target substances by means of hierarchical cluster analysis. The biosensor platform could detect drug contaminants such as hormone drugs (estrogen) and antibiotics. We expect that the proposed biosensor system could be used for the development of a first-analysis kit, which would be inexpensive and easy to supply and could be applied in monitoring the environment and health care.

Improvement of High Affinity and Selectivity on Biosensors Using Genetically Engineered Phage by Binding Isotherm Screening.

The genetically engineered M13 bacteriophage (M13 phage), developed via directed evolutionary screening process, can improve the sensitivity of sensors because of its selective binding to a target material. Herein, we propose a screening method to develop a selective and sensitive bioreporter for toxic material based on genetically engineered M13 phage. The paraquat (PQ)-binding M13 phage, developed by directed evolution, was used. The binding affinities of the PQ-binding M13 phage to PQ and similar molecules were analyzed using isothermal titration calorimetry (ITC). Based on the isotherms measured by ITC, binding affinities were calculated using the one-site binding model. The binding affinity was 5.161 × 10-7 for PQ, and 3.043 × 10-7 for diquat (DQ). The isotherm and raw ITC data show that the PQ-binding M13 phage does not selectively bind to difenzoquat (DIF). The phage biofilter experiment confirmed the ability of PQ-binding M13 bacteriophage to bind PQ. The surface-enhanced Raman scattering (SERS) platform based on the bioreporter, PQ-binding M13 phage, exhibited 3.7 times the signal intensity as compared with the wild-type-M13-phage-coated platform.

Distinguishable Plasmonic Nanoparticle and Gap Mode Properties in a Silver Nanoparticle on a Gold Film System Using Three-Dimensional FDTD Simulations.

We present a computational study of the near-field enhancement properties from a plasmonic nanomaterial based on a silver nanoparticle on a gold film. Our simulation studies show a clear distinguishability between nanoparticle mode and gap mode as a function of dielectric layer thickness. The observed nanoparticle mode is independent of dielectric layer thickness, and hence its related plasmonic properties can be investigated clearly by having a minimum of ~10-nm-thick dielectric layer on a metallic film. In case of the gap mode, the presence of minimal dielectric layer thickness is crucial (~≤4 nm), as deterioration starts rapidly thereafter. The proposed simple tunable gap-based particle on film design might open interesting studies in the field of plasmonics, extreme light confinement, sensing, and source enhancement of an emitter.

Self-Assembled Nanoporous Biofilms from Functionalized Nanofibrous M13 Bacteriophage.

Highly periodic and uniform nanostructures, based on a genetically engineered M13 bacteriophage, displayed unique properties at the nanoscale that have the potential for a variety of applications. In this work, we report a multilayer biofilm with self-assembled nanoporous surfaces involving a nanofiber-like genetically engineered 4E-type M13 bacteriophage, which was fabricated using a simple pulling method. The nanoporous surfaces were effectively formed by using the networking-like structural layers of the M13 bacteriophage during self-assembly. Therefore, an external template was not required. The actual M13 bacteriophage-based fabricated multilayered biofilm with porous nanostructures agreed well with experimental and simulation results. Pores formed in the final layer had a diameter of about 150⁻500 nm and a depth of about 15⁻30 nm. We outline a filter application for this multilayered biofilm that enables selected ions to be extracted from a sodium chloride solution. Here, we describe a simple, environmentally friendly, and inexpensive fabrication approach with large-scale production potential. The technique and the multi-layered biofilms produced may be applied to sensor, filter, plasmonics, and bio-mimetic fields.