Machine learning-based design of meta-plasmonic biosensors with negative index metamaterials.

In this work, we explore the performance of plasmonic biosensor designs that integrate metamaterials based on machine learning algorithms. The meta-plasmonic biosensors were designed for optimized detection of DNA with a layer of double negative metamaterial modeled by an effective medium. An iterative transfer matrix approach was employed to generate training and test sets of resonance characteristics in the parameter space for machine learning. As a machine learning-based prediction of optical characteristics of a meta-plasmonic biosensor, multilayer perceptron and autoencoder (AE) were used as an algorithm, while the clustering algorithm was constructed by dimensional reduction based on AE and t-Stochastic Neighbor Embedding (t-SNE) as well as k-means clustering. Use of meta-plasmonic structure with analysis based on machine learning has found that enhancement of detection sensitivity by more than 13 times over conventional detection should be achievable with excellent reflectance curves. Further enhancement may be attained by expanding the parameter space.

Inhibition of MEK1/2 and GSK3 (2i system) affects blastocyst quality and early differentiation of porcine parthenotes.

Inhibition of both MEK1/2 and glycogen synthase kinase-3 (GSK3; 2i system) facilitates the maintenance of naïve stemness for embryonic stem cells in various mammalian species. However, the effect of the inhibition of the 2i system on porcine early embryogenesis is unknown. We investigated the effect of the 2i system on early embryo development, expression of pluripotency-related genes, and epigenetic modifications. Inhibition of MEK1/2 (by PD0325901) and/or GSK3 (by CHIR99021) did not alter the developmental potential of porcine parthenogenetic embryos, but improved blastocyst quality, as judged by the blastocyst cell number, diameter, and reduction in the number of apoptotic cells. The expression levels of octamer-binding transcription factor 4 and SOX2, the primary transcription factors that maintain embryonic pluripotency, were significantly increased by 2i treatments. Epigenetic modification-related gene expression was altered upon 2i treatment. The collective results indicate that the 2i system in porcine embryos improved embryo developmental potential and blastocyst quality by regulating epigenetic modifications and pluripotency-related gene expression.

Molecular overlap with optical near-fields based on plasmonic nanolithography for ultrasensitive label-free detection by light-matter colocalization.

In this work, we investigate the detection sensitivity of surface plasmon resonance (SPR) biosensors by engineering spatial distribution of electromagnetic near-fields for colocalization with molecular distribution. The light-matter colocalization was based on plasmonic nanolithography, the concept of which was confirmed by detecting streptavidin biotin interactions on triangular nanoaperture arrays after the structure of the aperture arrays was optimized for colocalization efficiency. The colocalization was shown to amplify optical signature significantly and thereby to achieve detection on the order of 100 streptavidin molecules with a binding capacity below 1fg/mm2, an enhancement by more than three orders of magnitude over conventional SPR detection.

Three-Dimensional Superlocalization Imaging of Gliding Mycoplasma mobile by Extraordinary Light Transmission through Arrayed Nanoholes.

In this paper, we describe super-resolved sampling of live bacteria based on extraordinary optical transmission (EOT) of light. EOT is produced by surface plasmon confinement and coupling with nanostructures. Bacterial fluorescence is excited by the localized fields for subdiffraction-limited sampling. The concept was applied to elucidating bacterial dynamics of gliding Mycoplasma mobile (M. mobile). The results analyzed with multiple M. mobile bacteria show individual characters and reveal that M. mobile undergoes a significant axial variation at 94 nm. The sampling error of the method is estimated to be much smaller than 1/10 of the diffraction limit both in the lateral and depth axis. The method provides a powerful tool for investigation of biomolecular dynamics at subwavelength precision.

Surface plasmon-enhanced nanoscopy of intracellular cytoskeletal actin filaments using random nanodot arrays.

The feasibility of super-resolution microscopy has been investigated based on random localization of surface plasmon using blocked random nanodot arrays. The resolution is mainly determined by the size of localized fields in the range of 100-150 nm. The concept was validated by imaging FITC-conjugated phalloidin that binds to cellular actin filaments. The experimental results confirm improved resolution in reconstructed images. Effect of far-field registration on image reconstruction was also analyzed. Correlation between reconstructed images was maintained to be above 81% after registration. Nanodot arrays are synthesized by temperature-annealing without sophisticated lithography and thus can be mass-produced in an extremely large substrate. The results suggest a super-resolution imaging technique that can be accessible and available in large amounts.

A Protoberberine derivative HWY336 selectively inhibits MKK4 and MKK7 in mammalian cells: the importance of activation loop on selectivity.

A protoberberine derivative library was used to search for selective inhibitors against kinases of the mitogen-activated protein kinase (MAPK) cascades in mammalian cells. Among kinases in mammalian MAPK pathways, we identified a compound (HWY336) that selectively inhibits kinase activity of mitogen-activated protein kinase kinase 4 and 7 (MKK4 and MKK7). The IC50 of HWY336 was 6 µM for MKK4 and 10 µM for MKK7 in vitro. HWY336 bound to both kinases reversibly via noncovalent interactions, and inhibited their activity by interfering with access of a protein substrate to its binding site. The binding affinity of HWY336 to MKK4 was measured by surface plasmon resonance to determine a dissociation constant (Kd) of 3.2 µM. When mammalian cells were treated with HWY336, MKK4 and MKK7 were selectively inhibited, resulting in inhibition of c-Jun NH2-terminal protein kinases in vivo. The structural model of HWY336 bound to either MKK4 or MKK7 predicted that HWY336 was docked to the activation loop, which is adjacent to the substrate binding site. This model suggested the importance of the activation loop of MKKs in HWY336 selectivity. We verified this model by mutating three critical residues within this loop of MKK4 to the corresponding residues in MKK3. The mutant MKK4 displayed similar kinase activity as wild-type kinase, but its activity was not inhibited by HWY336 compared to wild-type MKK4. We propose that the specific association of HWY336 to the activation loop of MKK4/MKK7 is responsible for its selective inhibition.

Effect of coupled graphene oxide on the sensitivity of surface plasmon resonance detection.

We investigated graphene-oxide-(GO-) coupled surface plasmon resonance (SPR) detection sensitivity for sandwiched antigen-antibody interaction between human and antihuman immunoglobulin G molecules. GO was prepared in a Langmuir-Blodgett solution on gold and dielectric surfaces. Theoretical and experimental data suggest that an increased dielectric spacer thickness reduces resonance shifts for GO-coupled SPR detection as dielectric properties of GO appear to prevail. In general, a metal-enhanced structure was shown to provide a larger resonance shift by plasmonic field enhancement. The far-field properties were described in terms of near-field overlap. The peak resonance shift that was obtained with GO-coupled SPR detection was enhanced to 113% of the resonance shift obtained by conventional thin-film-based SPR detection and may further be improved by GO stacking.

Self-aligned colocalization of 3D plasmonic nanogap arrays for ultra-sensitive surface plasmon resonance detection.

We report extremely sensitive plasmonic detection that was performed label-free based on the colocalization of target DNA molecules and electromagnetic hot spots excited at 3D nanogap arrays. The colocalization was self-aligned by oblique evaporation of a dielectric mask over the 3D nanopatterns, which creates nanogaps for spatially selective target binding. The feasibility was experimentally confirmed by measuring hybridization of 24-mer single-stranded DNA oligonucleotides on triangular and circular 3D nanogap arrays. We were able to achieve significantly amplified optical signatures that lead to sensitivity enhancement in terms of detectable binding capacity in reference to conventional thin film-based surface plasmon resonance detection on the order of 1 fg/mm(2).

Polarization-extinction-based detection of DNA hybridization in situ using a nanoparticle wire-grid polarizer.

Metallic wires can discriminate light polarization due to strong absorption of electric fields oscillating in parallel to wires. Here, we explore polarization-based biosensing of DNA hybridization in situ by employing metal target-conjugated nanoparticles to form a wire-grid polarizer (WGP) as complementary DNA strands hybridize. Experimental results using gold nanoparticles of 15 nm diameter to form a WGP of 400 nm period suggest that polarization extinction can detect DNA hybridization with a limit of detection in the range of 1 nM concentration. The sensitivity may be improved by more than an order of magnitude if larger nanoparticles are employed to define WGPs at a period between 400 and 500 nm.

Development and characterization of piezoelectrically actuated corner cube retroreflectors for applications in free-space optical sensor network.

In this paper, we report the development of an optical sensor network (OSN) based on piezoelectrically actuated corner cube retroreflectors (PA-CCRs). PA-CCRs were fabricated by microelectromechanical systems processes and assembled by aligning horizontally actuated mirrors and vertical side walls in a holder, which allows mass production. Fabricated PA-CCRs showed a tilting angle by more than 1.5 deg at 5 V bias voltage. A 3 dB cutoff frequency was measured to be in the range of 3.5 kHz. To show the feasilbility, an OSN was established based on fabricated PA-CCRs for on-off keying passive transmission links. The results demonstrated data transmission at a rate up to 5 kb/s.

Nanoscale localization sampling based on nanoantenna arrays for super-resolution imaging of fluorescent monomers on sliding microtubules.

Sub-diffraction-limited imaging of fluorescent monomers on sliding microtubules in vitro by nanoscale localization sampling (NLS) is reported. NLS is based on periodic nanohole antenna arrays that create locally amplified electromagnetic hot spots through surface plasmon localization. The localized near-field hot spot temporally samples microtubular movement for enhanced spatial resolution. A fourfold improvement in spatial resolution compared to conventional wide-field microscopy is demonstrated. The resolution enhancement is achieved by imaging rhodamine-labeled microtubules that are sampled by the hot spots to provide sub-diffraction-limited images at 76 nm resolution in the direction of movement and 135 nm orthogonally. The intensity distribution produced by the NLS is measured to be broader than that of conventional imaging, which is consistent with the improvement of imaging resolution. Correlation studies between neighboring nanoantennas are also performed. This confirms the possibility of measuring microtubular transport dynamics. NLS can be useful for moving objects that have a high labeling density or for performing fluctuation spectroscopy in small volumes, and may allow "super-resolution on demand" by customizing nanoantenna structures for specific resolution needs.

Grating-based surface plasmon resonance detection of core-shell nanoparticle mediated DNA hybridization.

In this report, we have investigated enhanced surface plasmon resonance (SPR) detection of DNA hybridization using gold core - silica shell nanoparticles in localized plasmonic fields. The plasmonic fields were localized by periodic linear gratings. Experimental results measured for hybridization of 24-mer single-stranded DNA oligomers suggest that core-shell nanoparticles (CSNPs) on gratings of 400 nm period provide enhanced optical signatures by 36 times over conventional thin film-based SPR detection. CSNP-mediated DNA hybridization produced 3 times larger angular shift compared to gold nanoparticles of the same core size. We have also analyzed the effect of structural variation. The enhancement using CSNPs was associated with increased surface area and index contrast that is combined by improved plasmon coupling with localized fields on gratings. The combined approach for conjugated measurement of a biomolecular interaction on grating structures is expected to lower the limit of detection to the order of a few tens of fg/mm(2).

Colocalization of gold nanoparticle-conjugated DNA hybridization for enhanced surface plasmon detection using nanograting antennas.

We have investigated enhanced surface plasmon resonance detection through colocalization of gold nanoparticle (GNP)-conjugated target molecules and near-fields established by nanograting-based antennas. The target colocalization was implemented by angled dielectric thin-film deposition on the nanograting structure. The concept was tested by detecting DNA hybridization and shows that the colocalization produces an additional 60%-80% increase of resonance shifts. The colocalization involves a much smaller number of target molecules, so that the measured enhancement per molecule by the colocalization of GNP-conjugated DNA oligomers was estimated to be by more than 2 orders of magnitude relative to that of thin-film-based conventional detection.

Plasmonics-based spatially activated light microscopy for super-resolution imaging of molecular fluorescence.

In this Letter, we explore plasmonics-based spatially activated light microscopy (PSALM) for sub-diffraction-limited imaging of biomolecules. PSALM is based on the spatially switched activation of local amplified electromagnetic hot spots under multiple light incidence conditions. The hot spots are associated with surface plasmons that are excited and localized by surface nanostructures. The feasibility of the concept was demonstrated by imaging fluorescent nanobeads on a two-dimensional gold nanograting of a 100-nm-wide grating ridge, the size of which is the measure of the imaging resolution. The result confirms the performance of PSALM for imaging nanobeads at a resolution below the conventional diffraction limit.

Surface-enhanced localized surface plasmon resonance biosensing of avian influenza DNA hybridization using subwavelength metallic nanoarrays.

We demonstrated enhanced localized surface plasmon resonance (SPR) biosensing based on subwavelength gold nanoarrays built on a thin gold film. Arrays of nanogratings (1D) and nanoholes (2D) with a period of 200 nm were fabricated by electron-beam lithography and used for the detection of avian influenza DNA hybridization. Experimental results showed that both nanoarrays provided significant sensitivity improvement and, especially, 1D nanogratings exhibited higher SPR signal amplification compared with 2D nanohole arrays. The sensitivity enhancement is associated with changes in surface-limited reaction area and strong interactions between bound molecules and localized plasmon fields. Our approach is expected to improve both the sensitivity and sensing resolution and can be applicable to label-free detection of DNA without amplification by polymerase chain reaction.

Plasmon-enhanced total-internal-reflection fluorescence by momentum-mismatched surface nanostructures.

We investigate optimum plasmon-enhanced total-internal-reflection fluorescence imaging by metallic thin films and nanostructures. The enhancement is based on the mismatch between the conditions of plasmon resonance and maximal near-field intensity. We have calculated plasmon-associated near-field and far-field characteristics using rigorous coupled-wave analysis. Near-field intensity was experimentally measured with fluorescent beads on silver thin films, nanogratings, and nanoislands. The results for nanostructure-based plasmon excitation confirm that momentum mismatching when exciting plasmons can increase the consequent emission of fluorescence substantially. The improvement can be critical depending on the specific structure.