Label-free DNA quantification using isothermal amplification on an exposed core optical fiber microfluidic platform.

Isothermal amplification technology has triggered a surge in research due to its compatibility with small and portable equipment, simplicity, and high efficiency, especially in light of the COVID-19 pandemic where reliable widescale testing is critical to outbreak management. In this paper, a label-free isothermal deoxyribonucleic acid (DNA) amplification method based on refractive index (RI) quantification is proposed and demonstrated for the first time by combining optical fiber sensing, microfluidics, and isothermal amplification. A highly RI-sensitive Mach-Zehnder (MZ) interference is formed by splicing a short length of an exposed-core fiber between two lengths of a single-mode fiber while the microfluidic liquid channel on the exposed side of the ECF is filled with target DNA and the amplification solution. Real-time quantitative measurement of the target DNA is then realized by monitoring the change in RI of the solution during the isothermal DNA amplification process. The experimental results show that the platform successfully realizes real-time label-free monitoring of isothermal amplification of 0.16 aM DNA samples. This method is a breakthrough for applications in the fields of DNA detection and quantification where simple operation, rapid detection, portability, small size, high selectivity, and high sensitivity are required.

Machine learning for sensing with a multimode exposed core fiber specklegram sensor.

Fiber specklegram sensors (FSSs) traditionally use statistical methods to analyze specklegrams obtained from fibers for sensing purposes, but can suffer from limitations such as vulnerability to noise and lack of dynamic range. In this paper we demonstrate that deep learning improves the analysis of specklegrams for sensing, which we show here for both air temperature and water immersion length measurements. Two deep neural networks (DNNs); a convolutional neural network and a multi-layer perceptron network, are used and compared to a traditional correlation technique on data obtained from a multimode fiber exposed-core fiber. The ability for the DNNs to be trained against a random noise source such as specklegram translations is also demonstrated.

Temperature compensated fiber optic magnetic sensor based on the combination interference principle.

In this paper, a highly sensitive temperature compensated fiber optic magnetic field sensor by Sagnac and Mach-Zehnder combination interference (SMZI) is proposed and verified. The sensing structure relies on microstructured exposed core fiber (ECF) filled with ethanol and magnetic fluid (MF). The refractive index of MF and ethanol is affected by the magnetic field and temperature (MFT). SMZI is based on the multimode and birefringence characteristics of ECF. The measurement principle is that the spectra of Sagnac interference and Mach-Zehnder interference have respective sensitivities to the MFT. The magnetic sensitivity can reach 1.17 nm/mT, and the temperature sensitivity is up to -1.93 nm/°C. At the same time, the sensor has good repeatability and low detection limits of 0.41 mT and 0.25°C, respectively. It not only solves the cross-influence of temperature but also makes the spectral analysis more intuitive. The sensor has a broad development prospect in the application of MFT detection.

In Situ Temperature-Compensated DNA Hybridization Detection Using a Dual-Channel Optical Fiber Sensor.

A multifunction, high-sensitivity, and temperature-compensated optical fiber DNA hybridization sensor combining surface plasmon resonance (SPR) and Mach-Zehnder interference (MZI) has been designed and implemented. We demonstrate, for the first time to our knowledge, the dual-parameter measurement of temperature and refractive index (RI) by simultaneously using SPR and MZI in a simple single-mode fiber (SMF)-no-core fiber (NCF)-SMF structure. The experimental results show RI sensitivities of 930 and 1899 nm/RIU and temperature sensitivities of 0.4 and -1.4 nm/°C for the MZI and SPR, respectively. We demonstrate a sensitivity matrix used to simultaneously detect both parameters, solving the problem of temperature interference of RI variation-based biosensors. In addition, the sensor can also distinguish biological binding events by detecting the localized RI changes at the fiber's surface. We realize label-free sensing of DNA hybridization detection by immobilizing probe DNA (pDNA) onto the fiber as the probe to capture complementary DNA (cDNA). The experimental results show that the sensor can qualitatively detect cDNA after temperature compensation, and the limit of detection (LOD) of the sensor reaches 80 nM. The proposed sensor has advantages of high sensitivity, real time, low cost, temperature compensation, and low detection limit and is suitable for in situ monitoring, high-precision sensing of DNA molecules, and other related fields, such as gene diagnosis, kinship judgment, environmental monitoring, and so on.

Whispering gallery mode excitation using exposed-core fiber.

Whispering gallery modes (WGMs) in micro-resonators are of interest due to their high Q-factors. Ultra-thin fiber tapers are widely deployed to couple light into micro-resonators but achieving stable and practical coupling for out-of-lab use remains challenging. Here, a new WGM coupling scheme using an exposed-core silica fiber (ECF) is proposed, which overcomes the challenge of using fragile fiber tapers. Microspheres are deposited onto the exposed channel for excitation via the evanescent field of the fiber's guided modes. The outer jacket of the ECF partially encapsulates the microspheres, protecting them from external physical disturbance. By varying the mode launching conditions in this few-mode ECF, in combination with a Fano resonance effect, we demonstrate a high degree of tunability in the reflection spectrum. Furthermore, we show multi-particle WGM excitation, which could be controlled to occur either simultaneously or separately through controlling the ECF mode launching conditions. This work can bring value towards applications such as optical switches and modulators, multiplexed/distributed biosensing, and multi-point lasing, integrated in a single optical fiber device that avoids fiber post-processing.

Single-peak fiber Bragg gratings in suspended-core optical fibers.

Femtosecond laser inscribed fiber Bragg gratings in pure-silica suspended-core optical fibers have previously been demonstrated as a promising platform for high temperature sensing. However, the density of gratings that could be written on a single fiber was limited by undesired reflections associated with higher order modes in these high numerical aperture fibers. This resulted in a complex, broadband reflection spectrum with limited multiplexing capability. In this work we utilize modifications to the fine structure of the suspended core optical fibers to fine tune the relative confinement loss of the optical fiber modes, thus reducing the contribution from such higher order modes. The effects of these changes on mode propagation are modeled, giving a range of fibers with different confinement loss properties which can be tailored to the specific length scale of a desired application. We achieve single-peak reflections from individual fiber Bragg gratings, significantly improving performance for multipoint sensing and demonstrate this technique by writing 20 gratings onto a single fiber.

Multimode exposed core fiber specklegram sensor.

The inception of photonic crystal fibers (PCFs) allowed for unprecedented tailoring of waveguide properties for specialty sensing probes. Exposed core microstructured fibers (ECFs) represent a natural evolution of the PCF design for practical liquid and gas sensing. Until now, to the best of our knowledge, only single-mode or few-modes ECFs have been explored. In this Letter, we demonstrate a highly multimode ECF with a lateral access that extends throughout the whole length of the fiber. The ECF is operated as a fiber specklegram sensor for assessing properties of fluids and interrogated using a simple and low-cost setup. The probe exhibits a refractive index resolution and sensitivity of at least 4.6×10-4 refractive index units (RIUs) and -10.97RIU-1, respectively. A maximum temperature resolution up to 0.017°C with a -0.20∘C-1 temperature sensitivity over the 23°C-28°C range and a liquid level sensing resolution up to 0.12 mm with -0.015mm-1 sensitivity over the 0.0-50.0 mm bathed the length range in water.

All-fiber all-optical quantitative polymerase chain reaction (qPCR).

Quantitative polymerase chain reaction (qPCR), the real-time amplification and measurement of a targeted DNA molecule, has revolutionized the biological sciences and is routinely applied in areas such as medical diagnostics, forensics, and agriculture. Despite widescale use of qPCR technology in the lab, the availability of low-cost and high-speed portable systems remains one of the barriers to routine in-field implementation. Here we propose and demonstrate a potential solution using a photonics-based qPCR system. By using an all-optical approach, we achieve ultra-fast temperature response with real-time temperature feedback using nanoliter scale reaction volumes. The system uses a microcavity to act as a nanoliter scale reaction vessel with a laser-driven and optically monitored temperature cycling system for ultrafast thermal cycling and incorporates an all-fiber fluorescence excitation/detection system to achieve real-time, high sensitivity fluorescence monitoring of the qPCR process. Further, we demonstrate the potential of the system to operate as a label-free qPCR system through direct optical measurement of the sample refractive index. Due to advantages in portability and fabrication simplicity, we anticipate that this platform technology will offer a new strategy for fundamental techniques in biochemistry applications, such as point-of-care and remote diagnostics.

Quantum noise limited nanoparticle detection with exposed-core fiber.

Label-free biosensors are important tools for clinical diagnostics and for studying biology at the single molecule level. The development of optical label-free sensors has allowed extreme sensitivity but can expose the biological sample to photodamage. Moreover, the fragility and complexity of these sensors can be prohibitive to applications. To overcome these problems, we develop a quantum noise limited exposed-core fiber sensor providing robust platform for label-free biosensing with a natural path toward microfluidic integration. We demonstrate the detection of single nanoparticles down to 25 nm in radius with optical intensities beneath known biophysical damage thresholds.

Tunable multi-wavelength third-harmonic generation using exposed-core microstructured optical fiber.

We demonstrate that exposed-core microstructured optical fibers offer multiple degrees of freedom for tailoring third-harmonic generation through the core diameter, input polarization, and nanofilm deposition. Varying these parameters allows control of the phase-matching position between an infrared pump wavelength and the generated visible wavelengths. In this Letter, we show how increasing the core diameter over previous experiments (2.57 µm compared to 1.85 µm) allows the generation of multiple wavelengths, which can be further controlled by rotating the input pump polarization and the deposition of dielectric nanofilms. This can lead to highly tailorable light sources for applications such as spectroscopy or nonlinear microscopy.

Soft-glass imaging microstructured optical fibers.

We demonstrate the fabrication of multi-core (imaging) microstructured optical fiber via soft-glass preform extrusion through a 3D printed titanium die. The combination of extrusion through 3D printed dies and structured element (capillary) stacking allows for unprecedented control of the optical fiber geometry. We have exploited this to demonstrate a 100 pixel rectangular array imaging microstructured fiber. Due to the high refractive index of the glass used (n = 1.62), such a fiber can theoretically have a pixel pitch as small as 1.8 µm. This opens opportunities for ultra-small, high-resolution imaging fibers fabricated from diverse glass types.

Nanofilm-induced spectral tuning of third harmonic generation.

Intermodal third-harmonic generation using waveguides is an effective frequency conversion process due to the combination of long interaction lengths and strong modal confinement. Here we introduce the concept of tuning the third harmonic phase-matching condition via the use of dielectric nanofilms located on an open waveguide core. We experimentally demonstrate that tantalum oxide nanofilms coated onto the core of an exposed core fiber allow tuning the third harmonic wavelength over 30 nm, as confirmed by qualitative simulations. Due to its generic character, the presented tuning scheme can be applied to any form of exposed core waveguide and will find applications in fields including microscopy, biosensing, and quantum optics.

Direct core structuring of microstructured optical fibers using focused ion beam milling.

We demonstrate the use of focused ion beam milling to machine optical structures directly into the core of microstructured optical fibers. The particular fiber used was exposed-core microstructured optical fiber, which allowed direct access to the optically guiding core. Two different designs of Fabry-Perot cavity were fabricated and optically characterized. The first cavity was formed by completely removing a section of the fiber core, while the second cavity consisted of a shallow slot milled into the core, leaving the majority of the core intact. This work highlights the possibility of machining complex optical devices directly onto the core of microstructured optical fibers using focused ion beam milling for applications including environmental, chemical, and biological sensing.

Interferometric high temperature sensor using suspended-core optical fibers.

We propose and experimentally demonstrate, for the first time to our knowledge, high temperature fiber sensing using the multimode interference effect within a suspended-core microstructured optical fiber (SCF). Interference fringes were found to red-shift as the temperature increased and vice versa. Temperature sensing up to 1100°C was performed by measuring the wavelength shifts of the fringes after fast Fourier transform (FFT) filtering of the spectra. In addition, phase monitoring at the dominant spatial frequency in the Fourier spectrum was used as an interrogation method to monitor various temperature-change scenarios over a period of 80 hours. Our proposed high temperature fiber sensor is simple, cost-effective, and can operate at temperatures beyond 1000°C.

Temperature sensing up to 1300°C using suspended-core microstructured optical fibers.

We demonstrate a new approach to high temperature sensing using femtosecond laser ablation gratings within silica suspended-core microstructured optical fibers. The simple geometry of the suspended-core fiber allows for femtosecond laser processing directly through the fiber cladding. Pure silica glass is used, allowing the sensor to be used up to temperatures as high as 1300°C while still allowing the fibre to be spliced to conventional fiber. The sensor can also be wavelength division multiplexed, with three sensors in a single fiber demonstrated.

Third harmonic generation in exposed-core microstructured optical fibers.

Inter-modal phase-matched third harmonic generation has been demonstrated in an exposed-core microstructured optical fiber. Our fiber, with a partially open core having a diameter of just 1.85 µm, shows efficient multi-peak third-harmonic generation between 500 nm and 530 nm, with a maximum visible-wavelength output of 0.96 µW. Mode images and simulations show strong agreement, confirming the phase-matching process and polarization dependence. We anticipate this work will lead to tailorable and tunable visible light sources by exploiting the open access to the optical fiber core, such as depositing thin-film coatings in order to shift the phase matching conditions.

Quantification of the fluorescence sensing performance of microstructured optical fibers compared to multi-mode fiber tips.

Microstructured optical fibers, particularly those with a suspended-core geometry, have frequently been argued as efficient evanescent-field fluorescence-based sensors. However, to date there has not been a systematic comparison between such fibers and the more common geometry of a multi-mode fiber tip sensor. In this paper we make a direct comparison between these two fiber sensor geometries both theoretically and experimentally. Our results confirm that suspended-core fibers provide a significant advantage in terms of total collected fluorescence signal compared to multi-mode fibers using an equivalent experimental configuration.

Simultaneous measurement of temperature and refractive index using focused ion beam milled Fabry-Perot cavities in optical fiber micro-tips.

Optical fiber micro-tips are promising devices for sensing applications in small volume and difficult to access locations, such as biological and biomedical settings. The tapered fiber tips are prepared by dynamic chemical etching, reducing the size from 125 µm to just a few µm. Focused ion beam milling is then used to create cavity structures on the tapered fiber tips. Two different Fabry-Perot micro-cavities have been prepared and characterized: a solid silica cavity created by milling two thin slots and a gap cavity. A third multi-cavity structure is fabricated by combining the concepts of solid silica cavity and gap cavity. This micro-tip structure is analyzed using a fast Fourier transform method to demultiplex the signals of each cavity. Simultaneous measurement of temperature and external refractive index is then demonstrated, presenting sensitivities of - 15.8 pm/K and -1316 nm/RIU, respectively.

Exposed core microstructured optical fiber Bragg gratings: refractive index sensing.

Bragg gratings have been written in exposed-core microstructured optical fibers for the first time using a femtosecond laser. Second and third order gratings have been written and both show strong reflectivity at 1550 nm, with bandwidths as narrow as 60 pm. Due to the penetration of the guided field outside the fiber the Bragg reflections are sensitive to the external refractive index. As different modes have different sensitivities to refractive index but the same temperature sensitivity the sensor can provide temperature-compensated refractive index measurements. Since these Bragg gratings have been formed by physical ablation, these devices can also be used for high temperature sensing, demonstrated here up to 800°C. The fibers have been spliced to single mode fiber for improved handling and integration with commercial interrogation units.

Fabrication, splicing, Bragg grating writing, and polyelectrolyte functionalization of exposed-core microstructured optical fibers.

Femtosecond laser written Bragg gratings have been written in exposed-core microstructured optical fibers with core diameters ranging from 2.7 µm to 12.5 µm and can be spliced to conventional single mode fiber. Writing a Bragg grating on an open core fiber allows for real-time refractive index based sensing, with a view to multiplexed biosensing. Smaller core fibers are shown both experimentally and theoretically to provide a higher sensitivity. A 7.5 µm core diameter fiber is shown to provide a good compromise between sensitivity and practicality and was used for monitoring the deposition of polyelectrolyte layers, an important first step in developing a biosensor.