Nanobiosensors: optofluidic, electrical and mechanical approaches to biomolecular detection at the nanoscale

Electrical Nanobiosensors for Nucleic Acid Based Diagnostics

Recent advances in nanotechnologies have promoted the iterative updating of nucleic acid sensors. Among various sensing technologies, the electrical nanobiosensor is regarded as one of the most promising prospects to achieve rapid, precise, and point-of-care nucleic acid based diagnostics. In this Perspective, we introduce recent progresses in electrical nanobiosensors for nucleic acid detection. First, the strategies for improving detection performance are summarized, including chemical amplification and electrical amplification. Then, the detection mechanism of electrical nanobiosensors, such as electrochemical biosensors, field-effect transistors, and photoelectric enhanced biosensors, is illustrated. At the same time, their applications in cancer screening, pathogen detection, gene sequencing, and genetic disease diagnosis are introduced. Finally, challenges and future prospects in clinical application are discussed.

Reflective FT-NIR and SERS studies of HER-II breast cancer biomarker using plasmonic-active nanostructured thin film immobilized oriented antibody

We describe the fabrication of plasmonic-active nanostructured thin film substrate as a label-free surface-enhanced Raman scattering (SERS)-based biosensor immobilized covalently with monoclonal HER-II antibody (mAb) to detect overexpressed HER-II as a biomarker in breast cancer serum (BCS). Oriented conjugation of mAb via hydrazone linkage to provide higher mAb accessibility was characterized by UV-vis and reflective Fourier transform near-infrared (FT-NIR) spectroscopic techniques. The interaction of BCS with mAb was studied by FT-NIR and nonresonant SERS at 637 nm. The results showed detection of glycoprotein content at different laser powers including a rise in amino acid and glycan content with varying results at higher power. With nonresonant SERS we observed nonlinear behavior of peak intensity. Analysis of variance was implemented to determine the effect of laser power which was found not to be a contributing factor. However, at the nanoscale, factors including the heating effect and aggregation of molecules can contribute to the nonlinearity of peak intensity.

Large-scale nano-biosensing technologies

Nanoscale technologies have brought significant advancements to modern diagnostics, enabling unprecedented bio-chemical sensitivities that are key to disease monitoring. At the same time, miniaturized biosensors and their integration across large areas enabled tessellating these into high-density biosensing panels, a key capability for the development of high throughput monitoring: multiple patients as well as multiple analytes per patient. This review provides a critical overview of various nanoscale biosensing technologies and their ability to unlock high testing throughput without compromising detection resilience. We report on the challenges and opportunities each technology presents along this direction and present a detailed analysis on the prospects of both commercially available and emerging biosensing technologies.

Rigorous coupled-wave analysis of a multi-layered plasmonic integrated refractive index sensor

We apply the rigorous coupled-wave analysis (RCWA) to the design of a multi-layer plasmonic refractive index sensor based on metallic nanohole arrays integrated with a Ge-on-Si photodetector. RCWA simulations benefit from modularity, frequency-domain computation, and a relatively simple computational setup. These features make the application of RCWA particularly interesting in the case of the simulation and optimization of multi-layered devices in conjunction with plasmonic nanostructures, where other methods can be computationally too expensive for multi-parameter optimization. Our application example serves as a demonstration that RCWA can be utilized as a low-cost, efficient method for device engineering.

Host-Pathogen Adhesion as the Basis of Innovative Diagnostics for Emerging Pathogens

Infectious diseases are an existential health threat, potentiated by emerging and re-emerging viruses and increasing bacterial antibiotic resistance. Targeted treatment of infectious diseases requires precision diagnostics, especially in cases where broad-range therapeutics such as antibiotics fail. There is thus an increasing need for new approaches to develop sensitive and specific in vitro diagnostic (IVD) tests. Basic science and translational research are needed to identify key microbial molecules as diagnostic targets, to identify relevant host counterparts, and to use this knowledge in developing or improving IVD. In this regard, an overlooked feature is the capacity of pathogens to adhere specifically to host cells and tissues. The molecular entities relevant for pathogen–surface interaction are the so-called adhesins. Adhesins vary from protein compounds to (poly-)saccharides or lipid structures that interact with eukaryotic host cell matrix molecules and receptors. Such interactions co-define the specificity and sensitivity of a diagnostic test. Currently, adhesin-receptor binding is typically used in the pre-analytical phase of IVD tests, focusing on pathogen enrichment. Further exploration of adhesin–ligand interaction, supported by present high-throughput “omics” technologies, might stimulate a new generation of broadly applicable pathogen detection and characterization tools. This review describes recent results of novel structure-defining technologies allowing for detailed molecular analysis of adhesins, their receptors and complexes. Since the host ligands evolve slowly, the corresponding adhesin interaction is under selective pressure to maintain a constant receptor binding domain. IVD should exploit such conserved binding sites and, in particular, use the human ligand to enrich the pathogen. We provide an inventory of methods based on adhesion factors and pathogen attachment mechanisms, which can also be of relevance to currently emerging pathogens, including SARS-CoV-2, the causative agent of COVID-19.

Point-of-Care Diagnostics: Molecularly Imprinted Polymers and Nanomaterials for Enhanced Biosensor Selectivity and Transduction

Significant healthcare disparities resulting from personal wealth, circumstances of birth, education level, and more are internationally prevalent. As such, advances in biomedical science overwhelmingly benefit a minority of the global population. Point-of-Care Testing (POCT) can contribute to societal equilibrium by making medical diagnostics affordable, convenient, and fast. Unfortunately, conventional POCT appears stagnant in terms of achieving significant advances. This is attributed to the high cost and instability associated with conventional biorecognition: primarily antibodies, but nucleic acids, cells, enzymes, and aptamers have also been used. Instead, state-of-the-art biosensor researchers are increasingly leveraging molecularly imprinted polymers (MIPs) for their high selectivity, excellent stability, and amenability to a variety of physical and chemical manipulations. Besides the elimination of conventional bioreceptors, the incorporation of nanomaterials has further improved the sensitivity of biosensors. Herein, modern nanobiosensors employing MIPs for selectivity and nanomaterials for improved transduction are systematically reviewed. First, a brief synopsis of fabrication and wide-spread challenges with selectivity demonstration are presented. Afterward, the discussion turns to an analysis of relevant case studies published in the last five years. The analysis is given through two lenses: MIP-based biosensors employing specific nanomaterials and those adopting particular transduction strategies. Finally, conclusions are presented along with a look to the future through recommendations for advancing the field. It is hoped that this work will accelerate successful efforts in the field, orient new researchers, and contribute to equitable health care for all.

Bacterial Sensing and Biofilm Monitoring for Infection Diagnostics

Recent insights into the rapidly emerging field of bacterial sensing and biofilm monitoring for infection diagnostics are discussed as well as recent key developments and emerging technologies in the field. Electrochemical sensing of bacteria and bacterial biofilm via synthetic, natural, and engineered recognition, as well as direct redox-sensing approaches via algorithm-based optical sensing, and tailor-made optotracing technology are discussed. These technologies are highlighted to answer the very critical question: "how can fast and accurate bacterial sensing and biofilm monitoring be achieved? Following on from that: "how can these different sensing concepts be translated for use in infection diagnostics? A central obstacle to this transformation is the absence of direct and fast analysis methods that provide high-throughput results and bio-interfaces that can control and regulate the means of communication between biological and electronic systems. Here, the overall progress made to date in building such translational efforts at the level of an individual bacterial cell to a bacterial community is discussed.

UV-Laser Interference Lithography for Local Functionalization of Plasmonic Nanostructures with Responsive Hydrogel

A novel approach to local functionalization of plasmonic hotspots at gold nanoparticles with biofunctional moieties is reported. It relies on photocrosslinking and attachment of a responsive hydrogel binding matrix by the use of a UV interference field. A thermoresponsive poly(N-isopropylacrylamide)-based (pNIPAAm) hydrogel with photocrosslinkable benzophenone groups and carboxylic groups for its postmodification was employed. UV-laser interference lithography with a phase mask configuration allowed for the generation of a high-contrast interference field that was used for the recording of periodic arrays of pNIPAAm-based hydrogel features with the size as small as 170 nm. These hydrogel arrays were overlaid and attached on the top of periodic arrays of gold nanoparticles, exhibiting a diameter of 130 nm and employed as a three-dimensional binding matrix in a plasmonic biosensor. Such a hybrid material was postmodified with ligand biomolecules and utilized for plasmon-enhanced fluorescence readout of an immunoassay. Additional enhancement of the fluorescence sensor signal by the collapse of the responsive hydrogel binding matrix that compacts the target analyte at the plasmonic hotspot is demonstrated.

Biofluidic Random Laser Cytometer for Biophysical Phenotyping of Cell Suspensions

Phenotypic profiling of single floating cells in liquid biopsies is the key to the era of precision medicine. A random laser in biofluids is a promising tool for the label-free characterization of the biophysical properties as a result of the high brightness and sharp peaks of the lasing spectra, yet previous reports were limited to the random laser in solid tissues with dense scattering. In this report, a random laser cytometer is demonstrated in an optofluidic device filled with gain medium and human breast normal/cancerous cells. The multiple lightscattering event induced by the microscale human cells promotes random lasing and influences the lasing properties in term of laser modes, spectral wavelengths, and lasing thresholds. A sensing strategy based on analyzing the lasing properties is developed to determine both the whole cell and the subcellular biophysical properties, and the malignant alterations of the cell suspensions are successfully detected. Our results provide a new approach to designing a label-free biophysical cytometer based on optofluidic random laser devices, which is advantageous for further research in the field of random laser bioapplication.

Label-free biosensing using a microring resonator integrated with poly-(dimethylsiloxane) microfluidic channels

Microring resonators have shown promising potential for highly sensitive, label-free, real-time detection of biomolecules. Accurate quantitative detection of target molecules through use of photonic integrated circuits has been demonstrated for environmental monitoring and medical diagnostics. Here, we described the design, fabrication, and characterization of a highly sensitive, label-free microring optical resonator integrated with poly-(dimethylsiloxane) microfluidic channels, which consumes only 30 µl of sample solution. The resonance wavelength shifts resulting from the change in the effective refraction index can be measured in situ, and thus the binding events on the resonator surface, including antibody immobilization, blocking of the resonator surface, and the specific binding of antibody and antigen, can be recorded throughout the entire experimental process in real time. We measured the binding events for the detection of human immunoglobulin G. The system had a detection limit of 0.5 µg/ml, a value substantially (14 times) lower than that of a previously reported microring resonator. To verify the usefulness and adaptability of this technique, human epidermal growth factor receptor 2 was used for the detection. The microring optical resonator was able to monitor reactions between biological molecules in real time and thus can be used in quantitative detection and biological sensing with little sample consumption.

CMOS Enabled Microfluidic Systems for Healthcare Based Applications

With the increased global population, it is more important than ever to expand accessibility to affordable personalized healthcare. In this context, a seamless integration of microfluidic technology for bioanalysis and drug delivery and complementary metal oxide semiconductor (CMOS) technology enabled data-management circuitry is critical. Therefore, here, the fundamentals, integration aspects, and applications of CMOS-enabled microfluidic systems for affordable personalized healthcare systems are presented. Critical components, like sensors, actuators, and their fabrication and packaging, are discussed and reviewed in detail. With the emergence of the Internet-of-Things and the upcoming Internet-of-Everything for a people-process-data-device connected world, now is the time to take CMOS-enabled microfluidics technology to as many people as possible. There is enormous potential for microfluidic technologies in affordable healthcare for everyone, and CMOS technology will play a major role in making that happen.

Optofluidic refractive-index sensors employing bent waveguide structures for low-cost, rapid chemical and biomedical sensing

We propose and develop an intensity-detection-based refractive-index (RI) sensor for low-cost, rapid RI sensing. The sensor is composed of a polymer bent ridge waveguide (BRWG) structure on a low-cost glass substrate and is integrated with a microfluidic channel. Different-RI solutions flowing through the BRWG sensing region induce output optical power variations caused by optical bend losses, enabling simple and real-time RI detection. Additionally, the sensors are fabricated using rapid and cost-effective vacuum-less processes, attaining the low cost and high throughput required for mass production. A good RI solution of 5.31 10^-4 × RIU^-1 is achieved from the RI experiments. This study demonstrates mass-producible and compact RI sensors for rapid and sensitive chemical analysis and biomedical sensing.

Micro-optics for microfluidic analytical applications

This critical review summarizes the developments in the integration of micro-optical elements with microfluidic platforms for facilitating detection and automation of bio-analytical applications.

Tip‐mould microcontact printing for functionalisation of optical microring resonator

We present an approach to functionalise optical microring resonators as hybridisation platforms, using tip‐mould reactive microcontact printing process. Derived from reactive microcontact printing using an ad hoc mould of polydimethylsiloxane (PDMS), the method functionalises single microring resonator with a target‐specific capture agent. The authors report the functionalisation of silicon nitride (SiN) 200 μ m diameter microring resonator with single‐strand DNA and the hybridisation detection of 100 nM target analyte, while concurrently monitoring not‐functionalised microring as a control sensor. Results show that the functionalisation approach permits to address single microring resonators with mutual distance lower than 100 μ m with high precision, enabling a better integration of multiple spotting zones on the chip concerning traditional functionalisation procedures.

Multiple Schottky Barrier-Limited Field-Effect Transistors on a Single Silicon Nanowire with an Intrinsic Doping Gradient

In comparison to conventional (channel-limited) field-effect transistors (FETs), Schottky barrier-limited FETs possess some unique characteristics which make them attractive candidates for some electronic and sensing applications. Consequently, modulation of the nano Schottky barrier at a metal-semiconductor interface promises higher performance for chemical and biomolecular sensor applications when compared to conventional FETs with ohmic contacts. However, the fabrication and optimization of devices with a combination of ideal ohmic and Schottky contacts as the source and drain, respectively, present many challenges. We address this issue by utilizing Si nanowires (NWs) synthesized by a chemical vapor deposition process which yields a pronounced doping gradient along the length of the NWs. Devices with a series of metal contacts on a single Si NW are fabricated in a single lithography and metallization process. The graded doping profile of the NW is manifested in monotonic increases in the channel and junction resistances and variation of the nature of the contacts from ohmic to Schottky of increasing effective barrier height along the NW. Hence multiple single Schottky junction-limited FETs with extreme asymmetry and high reproducibility are obtained on an individual NW. A definitive correlation between increasing Schottky barrier height and enhanced gate modulation is revealed. Having access to systematically varying Schottky barrier contacts on the same NW device provides an ideal platform for identifying optimal device characteristics for sensing and electronic applications.

Ultrasensitive, Label Free, Chemiresistive Nanobiosensor Using Multiwalled Carbon Nanotubes Embedded Electrospun SU-8 Nanofibers

This paper reports the synthesis and fabrication of aligned electrospun nanofibers derived out of multiwalled carbon nanotubes (MWCNTs) embedded SU-8 photoresist, which are targeted towards ultrasensitive biosensor applications. The ultrasensitivity (detection in the range of fg/mL) and the specificity of these biosensors were achieved by complementing the inherent advantages of MWCNTs such as high surface to volume ratio and excellent electrical and transduction properties with the ease of surface functionalization of SU-8. The electrospinning process was optimized to precisely align nanofibers in between two electrodes of a copper microelectrode array. MWCNTs not only enhance the conductivity of SU-8 nanofibers but also act as transduction elements. In this paper, MWCNTs were embedded way beyond the percolation threshold and the optimum percentage loading of MWCNTs for maximizing the conductivity of nanofibers was figured out experimentally. As a proof of concept, the detection of myoglobin, an important biomarker for on-set of Acute Myocardial Infection (AMI) has been demonstrated by functionalizing the nanofibers with anti-myoglobin antibodies and carrying out detection using a chemiresistive method. This simple and robust device yielded a detection limit of 6 fg/mL.

SPR and SPR Imaging: Recent Trends in Developing Nanodevices for Detection and Real-Time Monitoring of Biomolecular Events

In this paper we review the underlying principles of the surface plasmon resonance (SPR) technique, particularly emphasizing its advantages along with its limitations regarding the ability to discriminate between the specific binding response and the interfering effects from biological samples. While SPR sensors were developed almost three decades, SPR detection is not yet able to reduce the time-consuming steps of the analysis, and is hardly amenable for miniaturized, portable platforms required in point-of-care (POC) testing. Recent advances in near-field optics have emerged, resulting in the development of SPR imaging (SPRi) as a powerful optical, label-free monitoring tool for multiplexed detection and monitoring of biomolecular events. The microarrays design of the SPRi chips incorporating various metallic nanostructures make these optofluidic devices more suitable for diagnosis and near-patient testing than the traditional SPR sensors. The latest developments indicate SPRi detection as being the most promising surface plasmon-based technique fulfilling the demands for implementation in lab-on-a-chip (LOC) technologies.

Sensitive and selective detection of prostate-specific antigen using a photonic crystal nanolaser

The detection of low-concentration biomarkers is expected to facilitate the early diagnosis of severe diseases, including malignant tumors. Using photonic crystal nanolaser sensors, we detected prostate-specific antigen (PSA) from a concentration of 1 fM, which is difficult to detect by conventional enzyme-linked immunosorbent assay. The signal intensity and stability were improved by using a surfactant (i.e., ethanolamine). Even when a contaminant such as bovine serum albumin was mixed into the PSA sample, thereby increasing the concentration of the contaminant ten billion times, it was still possible to maintain a high level of detection.

Reconfigurable liquid-core/liquid-cladding optical waveguides with dielectrophoresis-driven virtual microchannels on an electromicrofluidic platform

An electrically reconfigurable liquid-core/liquid-cladding (L(2)) optical waveguide with core liquid γ-butyrolactone (GBL, ncore = 1.4341, εcore = 39) and silicone oil (ncladding = 1.401, εcladding = 2.5) as cladding liquid is accomplished using dielectrophoresis (DEP) that attracts and deforms the core liquid with the greater permittivity to occupy the region of strong electric field provided by Teflon-coated ITO electrodes between parallel glass plates. Instead of continuously flowing core and cladding liquids along a physical microchannel, the DEP-formed L(2) optical waveguide guides light in a stationary virtual microchannel that requires liquids of limited volume without constant supply and creates stable liquid/liquid interfaces for efficient light guidance in a simply fabricated microfluidic device. We designed and examined (1) stationary and (2) moving L(2) optical waveguides on the parallel-plate electromicrofluidic platform. In the stationary L-shaped waveguide, light was guided in a GBL virtual microchannel core for a total of 27.85 mm via a 90° bend (radius 5 mm) before exiting from the light outlet of cross-sectional area 100 μm × 100 μm. For the stationary spiral waveguide, light was guided in a GBL core containing Rhodamine 6G (R6G, 1 mM) and through a series of 90° bends with decreasing radii from 5 mm to 2.5 mm. With the stationary straight waveguide, the propagation loss was measured to be 2.09 dB cm(-1) in GBL with R6G (0.01 mM). The moving L-shaped waveguide was implemented on a versatile electromicrofluidic platform on which electrowetting and DEP were employed to generate a precise GBL droplet and form a waveguide core. On sequentially applying appropriate voltage to one of three parallel L-shaped driving electrodes, the GBL waveguide core was shifted; the guided light was switched at a speed of up to 0.929 mm s(-1) (switching period 70 ms, switching rate 14.3 Hz) when an adequate electric signal (173.1 VRMS, 100 kHz) was applied.

Biosensors and nanobiosensors for therapeutic drug and response monitoring

Review of different biosensors and nanobiosensors increasingly used in therapeutic drug monitoring (TDM) for pharmaceutical drugs with dosage limitations or toxicity issues and for therapeutic response monitoring.

Democratization of Nanoscale Imaging and Sensing Tools Using Photonics

Providing means for researchers and citizen scientists in the developing world to perform advanced measurements with nanoscale precision can help to accelerate the rate of discovery and invention as well as improve higher education and the training of the next generation of scientists and engineers worldwide. Here, we review some of the recent progress toward making optical nanoscale measurement tools more cost-effective, field-portable, and accessible to a significantly larger group of researchers and educators. We divide our review into two main sections: label-based nanoscale imaging and sensing tools, which primarily involve fluorescent approaches, and label-free nanoscale measurement tools, which include light scattering sensors, interferometric methods, photonic crystal sensors, and plasmonic sensors. For each of these areas, we have primarily focused on approaches that have either demonstrated operation outside of a traditional laboratory setting, including for example integration with mobile phones, or exhibited the potential for such operation in the near future.

Homogeneous large-scale crystalline nanoparticle-covered substrate with high SERS performance

This article details the surface-enhanced Raman scattering (SERS) performance of plasmonic substrates fabricated by a physical metal evaporation technique that uses no precursor or intermediate coating. We outline a cost-effective nanofabrication protocol that uses common laboratory equipment to produce homogeneously covered crystalline nanoparticle substrates. Our fabrication yields a homogeneous SERS response over the whole surface. The platform is tested with methylene blue diluted at various concentrations to estimate the sensitivity, homogeneity, and reproducibility of the process. The capacity of the substrates is also confirmed with spectroscopic investigations of human microsomal cytochrome b5.

Molecular Dynamics Simulation Analysis of Anti-MUC1 Aptamer and Mucin 1 Peptide Binding

Aptasensors utilize aptamers as bioreceptors. Aptamers are highly efficient, have a high specificity and are reusable. Within the biosensor the aptamers are immobilized to maximize their access to target molecules. Knowledge of the orientation and location of the aptamer and peptide during binding could be gained through computational modeling. Experimentally, the aptamer (anti-MUC1 S2.2) has been identified as a bioreceptor for breast cancer biomarker mucin 1 (MUC1) protein. However, within this protein lie several peptide variants with the common sequence APDTRPAP that are targeted by the aptamer. Understanding orientation and location of the binding region for a peptide-aptamer complex is critical in their biosensor applicability. In this study, we investigate through computational modeling how this peptide sequence and its minor variants affect the peptide-aptamer complex binding. We use molecular dynamics simulations to study multiple peptide-aptamer systems consisting of MUC1 (APDTRPAP) and MUC1-G (APDTRPAPG) peptides with the anti-MUC1 aptamer under similar physiological conditions reported experimentally. Multiple simulations of the MUC1 peptide and aptamer reveal that the peptide interacts between 3' and 5' ends of the aptamer but does not fully bind. Multiple simulations of the MUC1-G peptide indicate consistent binding with the thymine loop of the aptamer, initiated by the arginine residue of the peptide. We find that the binding event induces structural changes in the aptamer by altering the number of hydrogen bonds within the aptamer and establishes a stable peptide-aptamer complex. In all MUC1-G cases the occurrence of binding was confirmed by systematically studying the distance distributions between peptide and aptamers. These results are found to corroborate well with experimental study reported in the literature that indicated a strong binding in the case of MUC1-G peptide and anti-MUC1 aptamer. Present MD simulations highlight the role of the arginine residue of MUC1-G peptide in initiating the binding. The addition of the glycine residue to the peptide, as in the case of MUC1-G, is shown to yield a stable binding. Our study clearly demonstrates the ability of MD simulations to obtain molecular insights for peptide-aptamer binding, and to provide details on the orientation and location of binding between the peptide-aptamer that can be instrumental in biosensor development.

Label-free, single molecule resonant cavity detection: a double-blind experimental study

Optical resonant cavity sensors are gaining increasing interest as a potential diagnostic method for a range of applications, including medical prognostics and environmental monitoring. However, the majority of detection demonstrations to date have involved identifying a “known” analyte, and the more rigorous double-blind experiment, in which the experimenter must identify unknown solutions, has yet to be performed. This scenario is more representative of a real-world situation. Therefore, before these devices can truly transition, it is necessary to demonstrate this level of robustness. By combining a recently developed surface chemistry with integrated silica optical sensors, we have performed a double-blind experiment to identify four unknown solutions. The four unknown solutions represented a subset or complete set of four known solutions; as such, there were 256 possible combinations. Based on the single molecule detection signal, we correctly identified all solutions. In addition, as part of this work, we developed noise reduction algorithms.

Computational modeling of peptide-aptamer binding

Evolution is the progressive process that holds each living creature in its grasp. From strands of DNA evolution shapes life with response to our ever-changing environment and time. It is the continued study of this most primitive process that has led to the advancement of modern biology. The success and failure in the reading, processing, replication, and expression of genetic code and its resulting biomolecules keep the delicate balance of life. Investigations into these fundamental processes continue to make headlines as science continues to explore smaller scale interactions with increasing complexity. New applications and advanced understanding of DNA, RNA, peptides, and proteins are pushing technology and science forward and together. Today the addition of computers and advances in science has led to the fields of computational biology and chemistry. Through these computational advances it is now possible not only to quantify the end results but also visualize, analyze, and fully understand mechanisms by gaining deeper insights. The biomolecular motion that exists governing the physical and chemical phenomena can now be analyzed with the advent of computational modeling. Ever-increasing computational power combined with efficient algorithms and components are further expanding the fidelity and scope of such modeling and simulations. This chapter discusses computational methods that apply biological processes, in particular computational modeling of peptide-aptamer binding.

In-fiber photo-immobilization of a bioactive surface

We demonstrate the first in-fiber light-induced bioactive biotin-functionalization via photobleaching fluorophore-conjugated biotin. Photobleaching the fluorophores generated free radicals that bind to the albumin-passivated inner surface of pure silica photonic crystal fiber. The subsequent attachment of dye-conjugated streptavidin to the bound biotin qualified the photo-immobilization process and demonstrated a potential for the construction of in-fiber macromolecular assemblies or multiplexes. Compared with other in-fiber bioactive coating methods, the proposed light-induced technique requires only a low-power light source, without the need for additional preactivation steps or toxic chemical reagents. This method, hence, enables a simple and compact implementation for potential biomedical applications.

Smartphone technology can be transformative to the deployment of lab-on-chip diagnostics

The rapid expansion of mobile technology is transforming the biomedical landscape. By 2016 there will be 260 M active smartphones in the US and millions of health accessories and software "apps" running off them. In parallel with this have come major technical achievements in lab-on-a-chip technology leading to incredible new biochemical sensors and molecular diagnostic devices. Despite these advancements, the uptake of lab-on-a-chip technologies at the consumer level has been somewhat limited. We believe that the widespread availability of smartphone technology and the capabilities they offer in terms of computation, communication, social networking, and imaging will be transformative to the deployment of lab-on-a-chip type technology both in the developed and developing world. In this paper we outline why we believe this is the case, the new business models that may emerge, and detail some specific application areas in which this synergy will have long term impact, namely: nutrition monitoring and disease diagnostics in limited resource settings.

Design low crosstalk ring-slot array structure for label-free multiplexed sensing

We theoretically demonstrate a low crosstalk ring-slot array structure used for label-free multiplexed sensing. The proposed sensors array is based on an array of three ring-slot and input/output line defect coupling waveguides. Each ring-slot cavity has slightly different cavity spacing and different resonant frequency. Results obtained using two dimensional finite-difference time-domain (2D-FDTD) simulation indicate that the resonant frequencies of each sensor unit in response to the refractive index variations are independent. The refractive index sensitivity is 134 ∼ 145.5 nm/RIU (refractive index unit) and the Q factors more than 10⁴ can be achieved. The calculated detect limit lower than 1.13 × 10⁻⁴ RIU is obtained. In addition, an extremely small crosstalk lower than −25.8 dB is achieved among the array of three ring-slot cavities. The results demonstrate that this multiplexed sensor array is a promising platform for integrated optical devices and enables highly parallel label-free detection.

25th anniversary article: label-free electrical biodetection using carbon nanostructures

Nanostructures are promising candidates for use as active materials for the detection of chemical and biological species, mainly due to the high surface-to-volume ratio and the unique physical properties arising at the nanoscale. Among the various nanostructures, materials comprised of sp(2) -carbon enjoy a unique position due to the possibility to readily prepare them in various dimensions ranging from 0D, through 1D to 2D. This review focuses on the use of 1D (carbon nanotubes) and 2D (graphene) carbon nanostructures for the detection of biologically relevant molecules. A key advantage is the possibility to perform the sensing operation without the use of any labels or complex reaction schemes. Along this spirit, various strategies reported for the label-free electrical detection of biomolecules using carbon nanostructures are discussed. With their promise for ultimate sensitivity and the capability to attain high selectivity through controlled chemical functionalization, carbon-based nanobiosensors are expected to open avenues to novel diagnostic tools as well as to obtain new fundamental insight into biomolecular interactions down to the single molecule level.

A magnetic nanobead-based bioassay provides sensitive detection of single- and biplex bacterial DNA using a portable AC susceptometer

Bioassays relying on magnetic read-out using probe-tagged magnetic nanobeads are potential platforms for low-cost biodiagnostic devices for pathogen detection. For optimal assay performance it is crucial to apply an easy, efficient and robust bead-probe conjugation protocol. In this paper, sensitive (1.5 pM) singleplex detection of bacterial DNA sequences is demonstrated in a portable AC susceptometer by a magnetic nanobead-based bioassay principle; the volume-amplified magnetic nanobead detection assay (VAM-NDA). Two bead sizes, 100 and 250 nm, are investigated along with a highly efficient, rapid, robust, and stable conjugation chemistry relying on the avidin–biotin interaction for bead-probe attachment. Avidin-biotin conjugation gives easy control of the number of detection probes per bead; thus allowing for systematic investigation of the impact of varying the detection probe surface coverage upon bead immobilization in rolling circle amplified DNA-coils. The existence of an optimal surface coverage is discussed. Biplex VAM-NDA detection is for the first time demonstrated in the susceptometer: Semi-quantitative results are obtained and it is concluded that the concentration of DNA-coils in the incubation volume is of crucial importance for target quantification. The present findings bring the development of commercial biodiagnostic devices relying on the VAM–NDA further towards implementation in point-of-care and outpatient settings.

Surface-enhanced molecular spectroscopy (SEMS) based on perfect-absorber metamaterials in the mid-infrared

Surface-enhanced infrared absorption spectroscopy has attracted increased attention for direct access to molecular vibrational fingerprints in the mid-infrared. Perfect-absorber metamaterials (PAMs) with multi-band spectral responses and significant enhancement of the local near-field intensity were developed to improve the intrinsic absorption cross sections of absorption spectrum to identify the vibrational spectra of biomolecules. To verify its performance, the proposed infrared PAM array was used to identify the molecular stretches of a Parylene C film. The resonant responses of the infrared PAMs were accurately tuned to the vibrational modes of the C = C target bonds. The vibrational stretches of the C = C moiety were observed and the auto-fluorescence mechanisms of the Parylene C film were monitored. The unique properties of the PAMs indicate that this approach is a promising strategy for surface-enhanced molecular absorption spectroscopy (SEMS) in the mid-infrared region and for the tracking of characteristic molecular vibrational modes.

Enabling systems biology approaches through microfabricated systems

With the experimental tools and knowledge that have accrued from a long history of reductionist biology, we can now start to put the pieces together and begin to understand how biological systems function as an integrated whole. Here, we describe how microfabricated tools have demonstrated promise in addressing experimental challenges in throughput, resolution, and sensitivity to support systems-based approaches to biological understanding.

Lectin-carbohydrate interactions on nanoporous gold monoliths

Monoliths of nanoporous gold (np-Au) were modified with self-assembled monolayers of octadecanethiol (C18-SH), 8-mercaptooctyl α-D-mannopyranoside (αMan-C8-SH), and 8-mercapto-3,6-dioxaoctanol (HO-PEG2-SH), and the loading was assessed using thermogravimetric analysis (TGA). Modification with mixed SAMs containing αMan-C8-SH (at a 0.20 mole fraction in the SAM forming solution) with either octanethiol or HO-PEG2-SH was also investigated. The np-Au monoliths modified with αMan-C8-SH bind the lectin Concanavalin A (Con A), and the additional mass due to bound protein was assessed using TGA analysis. A comparison of TGA traces measured before and after exposure of HO-PEG2-SH modified np-Au to Con A showed that the non-specific binding of Con A was minimal. In contrast, np-Au modified with octanethiol showed a significant mass loss due to non-specifically adsorbed Con A. A significant mass loss was also attributed to binding of Con A to bare np-Au monoliths. TGA revealed a mass loss due to the binding of Con A to np-Au monoliths modified with pure αMan-C8-SH. The use of mass losses determined by TGA to compare the binding of Con A to np-Au monoliths modified by mixed SAMs of αMan-C8-SH and either octanethiol or HO-PEG2-SH revealed that binding to mixed SAM modified surfaces is specific for the mixed SAMs with HO-PEG2-SH but shows a significant contribution from non-specific adsorption for the mixed SAMs with octanethiol. Minimal adsorption of immunoglobulin G (IgG) and peanut agglutinin (PNA) towards the mannoside modified np-Au monoliths was demonstrated. A greater mass loss was found for Con A bound onto the monolith than for either IgG or PNA, signifying that the mannose presenting SAMs in np-Au retain selectivity for Con A. TGA data also provide evidence that Con A bound to the αMan-C8-SH modified np-Au can be eluted by flowing a solution of methyl α-D-mannopyranoside through the structure. The presence of Con A proteins on the modified np-Au surface was also confirmed using atomic force microscopy (AFM). The results highlight the potential for application of carbohydrate modified np-Au monoliths to glycoscience and glycotechnology and demonstrate that they can be used for capture and release of carbohydrate binding proteins in significant quantities.

Biosensors in the small scale: methods and technology trends

This study presents a review on biosensors with an emphasis on recent developments in the field. A brief history accompanied by a detailed description of the biosensor concepts is followed by rising trends observed in contemporary micro- and nanoscale biosensors. Performance metrics to quantify and compare different detection mechanisms are presented. A comprehensive analysis on various types and subtypes of biosensors are given. The fields of interest within the scope of this review are label-free electrical, mechanical and optical biosensors as well as other emerging and popular technologies. Especially, the latter half of the last decade is reviewed for the types, methods and results of the most prominently researched detection mechanisms. Tables are provided for comparison of various competing technologies in the literature. The conclusion part summarises the noteworthy advantages and disadvantages of all biosensors reviewed in this study. Furthermore, future directions that the micro- and nanoscale biosensing technologies are expected to take are provided along with the immediate outlook.

Label-free detection with high-Q microcavities: a review of biosensing mechanisms for integrated devices

Optical microcavities that confine light in high-Q resonance promise all of the capabilities required for a successful next-generation microsystem biodetection technology. Label-free detection down to single molecules as well as operation in aqueous environments can be integrated cost-effectively on microchips, together with other photonic components, as well as electronic ones. We provide a comprehensive review of the sensing mechanisms utilized in this emerging field, their physics, engineering and material science aspects, and their application to nanoparticle analysis and biomolecular detection. We survey the most recent developments such as the use of mode splitting for self-referenced measurements, plasmonic nanoantennas for signal enhancements, the use of optical force for nanoparticle manipulation as well as the design of active devices for ultra-sensitive detection. Furthermore, we provide an outlook on the exciting capabilities of functionalized high-Q microcavities in the life sciences.

Mass transport effects in suspended waveguide biosensors integrated in microfluidic channels

Label-free optical biosensors based on integrated photonic devices have demonstrated sensitive and selective detection of biological analytes. Integrating these sensor platforms into microfluidic devices reduces the required sample volume and enables rapid delivery of sample to the sensor surface, thereby improving response times. Conventionally, these devices are embedded in or adjacent to the substrate; therefore, the effective sensing area lies within the slow-flow region at the floor of the channel, reducing the efficiency of sample delivery. Recently, a suspended waveguide sensor was developed in which the device is elevated off of the substrate and the sensing region does not rest on the substrate. This geometry places the sensing region in the middle of the parabolic velocity profile, reduces the distance that a particle must travel by diffusion to be detected, and allows binding to both surfaces of the sensor. We use a finite element model to simulate advection, diffusion, and specific binding of interleukin 6, a signaling protein, to this waveguide-based biosensor at a range of elevations within a microfluidic channel. We compare the transient performance of these suspended waveguide sensors with that of traditional planar devices, studying both the detection threshold response time and the time to reach equilibrium. We also develop a theoretical framework for predicting the behavior of these suspended sensors. These simulation and theoretical results provide a roadmap for improving sensor performance and minimizing the amount of sample required to make measurements.

Optofluidic opportunities in global health, food, water and energy

Optofluidics is a rapidly advancing field that utilizes the integration of optics and microfluidics to provide a number of novel functionalities in microsystems. In this review, we discuss how this approach can potentially be applied to address some of the greatest challenges facing both the developing and developed world, including healthcare, food shortages, malnutrition, water purification, and energy. While medical diagnostics has received most of the attention to date, here we show that some other areas can also potentially benefit from optofluidic technology. Whenever possible we briefly describe how microsystems are currently used to address these problems and then explain why and how optofluidics can provide better solutions. The focus of the article is on the applications of optofluidic techniques in low-resource settings, but we also emphasize that some of these techniques, such as those related to food production, food safety assessment, nutrition monitoring, and energy production, could be very useful in well-developed areas as well.