High throughput optical readout of dense arrays of nanomechanical systems for sensing applications

The Hypothesis of a "Living Pulse" in Cells

Motility is a great biosignature and its pattern is characteristic for specific microbes. However, motion does also occur within the cell by the myriads of ongoing processes within the cell and the exchange of gases and nutrients with the outside environment. Here, we propose that the sum of these processes in a microbial cell is equivalent to a pulse in complex organisms and suggest a first approach to measure the "living pulse" in microorganisms. We emphasize that if a "living pulse" can be shown to exist, it would have far-reaching applications, such as for finding life in extreme environments on Earth and in extraterrestrial locations, as well as making sure that life is not present where it should not be, such as during medical procedures and in the food processing industry.

Beyond biology: alternative uses of cantilever-based technologies

Micromechanical cantilever sensors are attracting a lot of attention because of the need for characterizing, detecting, and monitoring chemical and physical properties, as well as compounds at the nanoscale. The fields of application of micro-cantilever sensors span from biological and point-of-care, to military or industrial sectors. The purpose of this work focuses on thermal and mechanical characterization, environmental monitoring, and chemical detection, in order to provide a technical review of the most recent technical advances and applications, as well as the future prospective of micro-cantilever sensor research.

Nanotechnology for Targeted Detection and Removal of Bacteria: Opportunities and Challenges

The emergence of nanotechnology has created unprecedented hopes for addressing several unmet industrial and clinical issues, including the growing threat so-termed "antibiotic resistance" in medicine. Over the last decade, nanotechnologies have demonstrated promising applications in the identification, discrimination, and removal of a wide range of pathogens. Here, recent insights into the field of bacterial nanotechnology are examined that can substantially improve the fundamental understanding of nanoparticle and bacteria interactions. A wide range of developed nanotechnology-based approaches for bacterial detection and removal together with biofilm eradication are summarized. The challenging effects of nanotechnologies on beneficial bacteria in the human body and environment and the mechanisms of bacterial resistance to nanotherapeutics are also reviewed.

Role of plasmonics in detection of deadliest viruses: a review

Viruses have threatened animal and human lives since a long time ago all over the world. Some of these tiny particles have caused disastrous pandemics that killed a large number of people with subsequent economic downturns. In addition, the quarantine situation itself encounters the challenges like the deficiency in the online educational system, psychiatric problems and poor international relations. Although viruses have a rather simple protein structure, they have structural heterogeneity with a high tendency to mutation that impedes their study. On top of the breadth of such worldwide worrying issues, there are profound scientific gaps, and several unanswered questions, like lack of vaccines or antivirals to combat these pathogens. Various detection techniques like the nucleic acid test, immunoassay, and microscopy have been developed; however, there is a tradeoff between their advantages and disadvantages like safety in sample collecting, invasiveness, sensitivity, response time, etc. One of the highly resolved techniques that can provide early-stage detection with fast experiment duration is plasmonics. This optical technique has the capability to detect viral proteins and genomes at the early stage via highly sensitive interaction between the biological target and the plasmonic chip. The efficiency of this technique could be proved using commercialized techniques like reverse transcription polymerase chain reaction (RT-PCR) and enzyme-linked immunosorbent assay (ELISA) techniques. In this study, we aim to review the role of plasmonic technique in the detection of 11 deadliest viruses besides 2 common genital viruses for the human being. This is a rapidly moving topic of research, and a review article that encompasses the current findings may be useful for guiding strategies to deal with the pandemics. By investigating the potential aspects of this technique, we hope that this study could open new avenues toward the application of point-of-care techniques for virus detection at early stage that may inhibit the progressively hygienic threats.

Thermomechanical Response of a Representative Porin for Biomimetics

The thermomechanical response of Omp2a, a representative porin used for the fabrication of smart biomimetic nanomembranes, has been characterized using microcantilever technology and compared with standard proteins. For this purpose, thermally induced transitions involving the conversion of stable trimers to bigger aggregates, local reorganizations based on the strengthening or weakening of intermolecular interactions, and protein denaturation have been detected by the microcantilever resonance frequency and deflection as a function of the temperature. Measurements have been carried out on arrays of 8-microcantilevers functionalized with proteins (Omp2a, lysozyme and bovine serum albumin). To interpret the measured nanofeatures, the response of proteins to temperature has been also examined using other characterization techniques, including real time wide angle X-ray diffraction. Results not only demonstrate the complex behavior of porins, which exhibit multiple local thermal transitions before undergoing denaturation at temperatures higher than 105 °C, but also suggest a posttreatment to control the orientation of immobilized Omp2a molecules in functionalized biomimetic nanomembranes and, thus, increase their efficacy in ion transport.

Optomechanical devices for deep plasma cancer proteomics

Most of the cancer deaths could be avoided by early detection of the tumor when it is confined to its primary site and it has not metastasized. To this aim, one of the most promising strategies is the discovery and detection of protein biomarkers shed by the young tumor to the bloodstream. Proteomic technologies, mainly mass spectrometry and multiplexed immunoassays, have rapidly developed during last years with improved limits of detection and multiplexing capability. Unfortunately, these developments together major investments and large international efforts have not resulted into new useful protein biomarkers. Here, we analyze the potential and limitations of current proteomic technologies for detecting protein biomarkers released into circulation by the tumor. We find that these technologies can hardly probe the deepest region of the plasma proteome, at concentrations below the pg/mL level, where protein biomarkers for early cancer detection may exist. This clearly indicates the need of incorporating novel ultrasensitive techniques to the proteomic tool-box that can cover the inaccessible regions of the plasma proteome. We here propose biological detectors based on nanomechanical systems for discovery and detection of cancer protein biomarkers in plasma. We review the modes of operation of these devices, putting our focus on recent developments on nanomechanical sandwich immunoassays and nanomechanical spectrometry. The first technique enables reproducible immunodetection of proteins at concentrations well below the pg/mL level, with a limit of detection on the verge of 10 ag/mL. This technology can potentially detect low abundance tumor-associated proteins in plasma at the very early stages of the tumor. The second technique enables the identification of individual intact proteins by two physical coordinates, the mass and stiffness, instead of the mass-to-charge ratio of the protein constituents. This technology enormously simplifies the identification of proteins and it can provide useful information on interactions and posttranslational modifications, that otherwise is lost in mass spectrometry.

Microcantilever array instrument based on optical fiber and performance analysis

We developed a microcantilever array biosensor instrument based on optical readout from a microcantilever array in fluid environment. The microcantilever signals were read out sequentially by laser beams emitted from eight optical fibers. The optical fibers were coupled to lasers, while the other ends of the fibers were embedded in eight V-grooves with 250 μm pitch microfabricated from a Si wafer. Aspherical lens was used to keep the distance between lasers. A programmable logic controller was used to make the system work stably. To make sure that the output of lasers was stable, a temperature controller was set up for each laser. When the deflection signal was collected, lasers used here were set to be on for at least 400 ms in each scanning cycle to get high signal-to-noise ratio deflection curves. A test was performed by changing the temperature of the liquid cell holding a microcantilever array to verify the consistent response of the instrument to the cantilever deflections. The stability and conformance of the instrument were demonstrated by quantitative detection of mercury ions in aqueous solution and comparison detection of clenbuterol by setting test and reference cantilevers. This microcantilever array detection instrument can be applied to highly sensitive detection of chemical and biological molecules in fluid environment.

Ultrasensitive detection of HIV-1 p24 antigen by a hybrid nanomechanical-optoplasmonic platform with potential for detecting HIV-1 at first week after infection

Early detection of HIV infection is the best way to prevent spread of the disease and to improve the efficiency of the antiretroviral therapy. Nucleic acid amplification tests (NAAT) have become the gold-standard for detecting low-concentrations of the virus in blood. However, these methods are technically demanding and cost-prohibitive in developing countries. Immunoassays are more affordable and can be more easily adapted for point-of-care diagnosis. However, the sensitivity so far of these methods has been too low. We here report the development of a sandwich immunoassay that combines nanomechanical and optoplasmonic transduction methods for detecting the HIV-1 capsid antigen p24 in human serum. The immunoreactions take place on the surface of a compliant microcantilever where gold nanoparticles are used as both mechanical and plasmonic labels. The microcantilever acts as both a mechanical resonator and an optical cavity for the transduction of the mechanical and plasmonic signals. The limit of detection of the immunoassay is 10⁻¹⁷ g/mL that is equivalent to one virion in 10 mL of plasma. This is 5 orders of magnitude better than last generation of approved immunoassays and 2 orders of magnitude better than NAAT. This technology meets the demands to be produced en masse at low cost and the capability for miniaturization to be used at the point-of-care.

Mass and stiffness spectrometry of nanoparticles and whole intact bacteria by multimode nanomechanical resonators

The identification of species is a fundamental problem in analytical chemistry and biology. Mass spectrometers identify species by their molecular mass with extremely high sensitivity (<10⁻²⁴ g). However, its application is usually limited to light analytes (<10⁻¹⁹ g). Here we demonstrate that by using nanomechanical resonators, heavier analytes can be identified by their mass and stiffness. The method is demonstrated with spherical gold nanoparticles and whole intact E. coli bacteria delivered by electrospray ionization to microcantilever resonators placed in low vacuum at 0.1 torr. We develop a theoretical procedure for obtaining the mass, position and stiffness of the analytes arriving the resonator from the adsorption-induced eigenfrequency jumps. These results demonstrate the enormous potential of this technology for identification of large biological complexes near their native conformation, a goal that is beyond the capabilities of conventional mass spectrometers.

Mass spectrometry can accurately identify species by molecular mass, but measuring large species can be difficult. Here the authors show that nanomechanical resonators can identify both the mass and stiffness of larger analytes, demonstrating it for gold nanoparticles and E. Coli bacteria.

Spatially Multiplexed Micro-Spectrophotometry in Bright Field Mode for Thin Film Characterization

Thickness characterization of thin films is of primary importance in a variety of nanotechnology applications, either in the semiconductor industry, quality control in nanofabrication processes or engineering of nanoelectromechanical systems (NEMS) because small thickness variability can strongly compromise the device performance. Here, we present an alternative optical method in bright field mode called Spatially Multiplexed Micro-Spectrophotometry that allows rapid and non-destructive characterization of thin films over areas of mm² and with 1 μm of lateral resolution. We demonstrate an accuracy of 0.1% in the thickness characterization through measurements performed on four microcantilevers that expand an area of 1.8 mm² in one minute of analysis time. The measured thickness variation in the range of few tens of nm translates into a mechanical variability that produces an error of up to 2% in the response of the studied devices when they are used to measure surface stress variations.

Note: A resonating reflector-based optical system for motion measurement in micro-cantilever arrays

A robust, compact optical measurement unit for motion measurement in micro-cantilever arrays enables development of portable micro-cantilever sensors. This paper reports on an optical beam deflection-based system to measure the deflection of micro-cantilevers in an array that employs a single laser source, a single detector, and a resonating reflector to scan the measurement laser across the array. A strategy is also proposed to extract the deflection of individual cantilevers from the acquired data. The proposed system and measurement strategy are experimentally evaluated and demonstrated to measure motion of multiple cantilevers in an array.

Hydration induced stress on DNA monolayers grafted on microcantilevers

Surface tethered single-stranded DNA films are relevant biorecognition layers for oligonucleotide sequence identification. Also, hydration induced effects on these films have proven useful for the nanomechanical detection of DNA hybridization. Here, we apply nanomechanical sensors and atomic force microscopy to characterize in air and upon varying relative humidity conditions the swelling and deswelling of grafted single stranded and double stranded DNA films. The combination of these techniques validates a two-step hybridization process, where complementary strands first bind to the surface tethered single stranded DNA probes and then slowly proceed to a fully zipped configuration. Our results also demonstrate that, despite the slow hybridization kinetics observed for grafted DNA onto microcantilever surfaces, ex situ sequence identification does not require hybridization times typically longer than 1 h, while quantification is a major challenge.

Effects of antibacterial agents and drugs monitored by atomic force microscopy

Originally invented for topographic imaging, atomic force microscopy (AFM) has evolved into a multifunctional biological toolkit, enabling to measure structural and functional details of cells and molecules. Its versatility and the large scope of information it can yield make it an invaluable tool in any biologically oriented laboratory, where researchers need to perform characterizations of living samples as well as single molecules in quasi-physiological conditions and with nanoscale resolution. In the last 20 years, AFM has revolutionized the characterization of microbial cells by allowing a better understanding of their cell wall and of the mechanism of action of drugs and by becoming itself a powerful diagnostic tool to study bacteria. Indeed, AFM is much more than a high-resolution microscopy technique. It can reconstruct force maps that can be used to explore the nanomechanical properties of microorganisms and probe at the same time the morphological and mechanical modifications induced by external stimuli. Furthermore it can be used to map chemical species or specific receptors with nanometric resolution directly on the membranes of living organisms. In summary, AFM offers new capabilities and a more in-depth insight in the structure and mechanics of biological specimens with an unrivaled spatial and force resolution. Its application to the study of bacteria is extremely significant since it has already delivered important information on the metabolism of these small microorganisms and, through new and exciting technical developments, will shed more light on the real-time interaction of antimicrobial agents and bacteria.

Biosensors based on nanomechanical systems

The advances in micro- and nanofabrication technologies enable the preparation of increasingly smaller mechanical transducers capable of detecting the forces, motion, mechanical properties and masses that emerge in biomolecular interactions and fundamental biological processes. Thus, biosensors based on nanomechanical systems have gained considerable relevance in the last decade. This review provides insight into the mechanical phenomena that occur in suspended mechanical structures when either biological adsorption or interactions take place on their surface. This review guides the reader through the parameters that change as a consequence of biomolecular adsorption: mass, surface stress, effective Young's modulus and viscoelasticity. The mathematical background needed to correctly interpret the output signals from nanomechanical biosensors is also outlined here. Other practical issues reviewed are the immobilization of biomolecular receptors on the surface of nanomechanical systems and methods to attain that in large arrays of sensors. We then describe some relevant realizations of biosensor devices based on nanomechanical systems that harness some of the mechanical effects cited above. We finally discuss the intrinsic detection limits of the devices and the limitation that arises from non-specific adsorption.

Sensitive thermal transitions of nanoscale polymer samples using the bimetallic effect: application to ultra-thin polythiophene

A sensitive nanocalorimetric technology based on microcantilever sensors is presented. The technology, which combines very short response times with very small sample consumption, uses the bimetallic effect to detect thermal transitions. Specifically, abrupt variations in the Young's modulus and the thermal expansion coefficient produced by temperature changes have been employed to detect thermodynamic transitions. The technology has been used to determine the glass transition of poly(3-thiophene methyl acetate), a soluble semiconducting polymer with different nanotechnological applications. The glass transition temperature determined using microcantilevers coated with ultra-thin films of mass = 10(-13) g is 5.2 °C higher than that obtained using a conventional differential scanning calorimeter for bulk powder samples of mass = 5 × 10(-3) g. Atomistic molecular dynamics simulations on models that represent the bulk powder and the ultra-thin films have been carried out to provide understanding and rationalization of this feature. Simulations indicate that the film-air interface plays a crucial role in films with very small thickness, affecting both the organization of the molecular chains and the response of the molecules against the temperature.

Horizontally patterned Si nanowire growth for nanomechanical devices

We report a method to pattern horizontal vapor-liquid-solid growth of Si nanowires at vertical sidewalls of Si microstructures. The method allows one to produce either single nanowire structures or well-ordered nanowire arrays with predefined growth positions, thus enabling a practical development of nanomechanical devices that exploit the singular properties of Si nanowires. In particular, we demonstrate the fabrication of doubly clamped nanowire resonators and resonator arrays whose mechanical resonances can be measured by optical or electrical readout. We also show that the fabrication method enables the electrical readout of the resonant mode splitting of nanowire resonators in the VHF range, which allows the application of such an effect for enhanced nanomechanical sensing with nanowire resonators.

Tackling reproducibility in microcantilever biosensors: a statistical approach for sensitive and specific end-point detection of immunoreactions

In the last decade, microcantilever biosensors have shown enormous potential for highly sensitive label-free detection of nucleic acid and proteins. Despite the enormous advances, the promise of applications of this technology in the biomedical field has been frustrated because of its low reproducibility. Here we tackle the reproducibility issue in microcantilever biosensors and provide the guidelines to minimize the deviations in the biosensor response between different assays. We use as a model system the label-free end-point detection of horseradish peroxidase. We choose the end-point detection mode because of its suitability for implementation in the clinical field that requires simplicity and point-of-care capability. Our study comprises the analysis of 1012 cantilevers with different antibody surface densities, two blocking strategies based on polyethylene-glycol (PEG) and bovine serum albumin (BSA) and stringent controls. The study reveals that the performance of the assay critically depends on both antibody surface density and blocking strategies. We find that the optimal conditions involve antibody surface densities near but below saturation and blocking with PEG. We find that the surface stress induced by the antibody-antigen binding is significantly correlated with the surface stress generated during the antibody attachment and blocking steps. The statistical correlation is harnessed to identify immobilization failure or success, and thus enhancing the specificity and sensitivity of the assay. This procedure enables achieving rates of true positives and true negatives of 90% and 91% respectively. The detection limit is of 10 ng mL(-1) (250 pM) that is similar to the detection limit obtained in our enzyme-linked immunosorbent assay (ELISA) and at least two orders of magnitude smaller than that achieved with well-established label-free biosensors such as a quartz crystal microbalance (QCM) and surface plasmon resonance (SPR) sensor.

Quantification of the surface stress in microcantilever biosensors: revisiting Stoney's equation

Microcantilever biosensors in the static operation mode translate molecular recognition into a surface stress signal. Surface stress is derived from the nanomechanical cantilever bending by applying Stoney's equation, derived more than 100 years ago. This equation ignores the clamping effect on the cantilever deformation, which induces significant errors in the quantification of the biosensing response. This leads to discrepancies in the surface stress induced by biomolecular interactions in measurements with cantilevers with different sizes and geometries. So far, more accurate solutions have been precluded by the formidable complexity of the theoretical problem that involves solving the two-dimensional biharmonic equation. In this paper, we present an accurate and simple analytical expression to quantify the response of microcantilever biosensors. The equation exhibits an excellent agreement with finite element simulations and DNA immobilization experiments on gold-coated microcantilevers.

Challenges for nanomechanical sensors in biological detection

Nanomechanical biosensing relies on changes in the movement and deformation of micro- and nanoscale objects when they interact with biomolecules and other biological targets. This field of research has provided ever-increasing records in the sensitivity of label-free detection but it has not yet been established as a practical alternative for biological detection. We analyze here the latest advancements in the field, along with the challenges remaining for nanomechanical biosensors to become a commonly used tool in biology and biochemistry laboratories.

Imaging the surface stress and vibration modes of a microcantilever by laser beam deflection microscopy

There is a need for noninvasive techniques for simultaneous imaging of the stress and vibration mode shapes of nanomechanical systems in the fields of scanning probe microscopy, nanomechanical biological and chemical sensors and the semiconductor industry. Here we show a novel technique that combines a scanning laser, the beam deflection method and digital multifrequency excitation and analysis for simultaneous imaging of the static out-of-plane displacement and the shape of five vibration modes of nanomechanical systems. The out-of-plane resolution is at least 100 pm Hz⁻¹/² and the lateral resolution, which is determined by the laser spot size, is 1-1.5 μm. The capability of the technique is demonstrated by imaging the residual surface stress of a microcantilever together with the shape of the first 22 vibration modes. The vibration behavior is compared with rigorous finite element simulations. The technique is suitable for major improvements in the imaging of liquids, such as higher bandwidth and enhanced spatial resolution.

High-throughput characterization of stresses in thin film materials libraries using Si cantilever array wafers and digital holographic microscopy

We report the development of an advanced high-throughput stress characterization method for thin film materials libraries sputter-deposited on micro-machined cantilever arrays consisting of around 1500 cantilevers on 4-inch silicon-on-insulator wafers. A low-cost custom-designed digital holographic microscope (DHM) is employed to simultaneously monitor the thin film thickness, the surface topography and the curvature of each of the cantilevers before and after deposition. The variation in stress state across the thin film materials library is then calculated by Stoney's equation based on the obtained radii of curvature of the cantilevers and film thicknesses. DHM with nanometer-scale out-of-plane resolution allows stress measurements in a wide range, at least from several MPa to several GPa. By using an automatic x-y translation stage, the local stresses within a 4-inch materials library are mapped with high accuracy within 10 min. The speed of measurement is greatly improved compared with the prior laser scanning approach that needs more than an hour of measuring time. A high-throughput stress measurement of an as-deposited Fe-Pd-W materials library was evaluated for demonstration. The fast characterization method is expected to accelerate the development of (functional) thin films, e.g., (magnetic) shape memory materials, whose functionality is greatly stress dependent.