High Dynamic Range Nanowire Resonators.

Dynamic range quantifies the linear operation regime available in nanomechanical resonators. Nonlinearities dominate the response of flexural beams in the limit of very high aspect ratio and very small diameter, which leads to expectation of low dynamic range for nanowire resonators in general. However, the highest achievable dynamic range for nanowire resonators with practical dimensions remains to be determined. We report dynamic range measurements on singly clamped silicon nanowire resonators reaching remarkably high values of up to 90 dB obtained with a simple harmonic actuation scheme. We explain these measurements by a comprehensive theoretical examination of dynamic range in singly clamped flexural beams including the effect of tapering, a usual feature of semiconductor nanowires. Our analysis reveals the nanowire characteristics required for broad linear operation, and given the relationship between dynamic range and mass sensing performance, it also enables analytical determination of mass detection limits, reaching atomic-scale resolution for feasible nanowires.

Optical Transduction for Vertical Nanowire Resonators.

We describe an optical transduction mechanism to measure the flexural mode vibrations of vertically aligned nanowires on a flat substrate with high sensitivity, linearity, and ease of implementation. We demonstrate that the light reflected from the substrate when a laser beam strikes it parallel to the nanowires is modulated proportionally to their vibration, so that measuring such modulation provides a highly efficient resonance readout. This mechanism is applicable to single nanowires or arrays without specific requirements regarding their geometry or array pattern, and no fabrication process besides the nanowire generation is required. We show how to optimize the performance of this mechanism by characterizing the split flexural modes of vertical silicon nanowires in their full dynamic range and up to the fifth mode order. The presented transduction approach is relevant for any application of nanowire resonators, particularly for integrating nanomechanical sensing in functional substrates based on vertical nanowires for biological applications.

Top-down silicon microcantilever with coupled bottom-up silicon nanowire for enhanced mass resolution.

A stepped cantilever composed of a bottom-up silicon nanowire coupled to a top-down silicon microcantilever electrostatically actuated and with capacitive or optical readout is fabricated and analyzed, both theoretically and experimentally, for mass sensing applications. The mass sensitivity at the nanowire free end and the frequency resolution considering thermomechanical noise are computed for different nanowire dimensions. The results obtained show that the coupled structure presents a very good mass sensitivity thanks to the nanowire, where the mass depositions take place, while also presenting a very good frequency resolution due to the microcantilever, where the transduction is carried out. A two-fold improvement in mass sensitivity with respect to that of the microcantilever standalone is experimentally demonstrated, and at least an order-of-magnitude improvement is theoretically predicted, only changing the nanowire length. Very close frequency resolutions are experimentally measured and theoretically predicted for a standalone microcantilever and for a microcantilever-nanowire coupled system. Thus, an improvement in mass sensing resolution of the microcantilever-nanowire stepped cantilever is demonstrated with respect to that of the microcantilever standalone.

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.

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.

Optomechanics with silicon nanowires by harnessing confined electromagnetic modes.

The optomechanical coupling that emerges in an optical cavity in which one of the mirrors is a mechanical resonator has allowed sub-Kelvin cooling with the prospect of observing quantum phenomena and self-sustained oscillators with very high spectral purity. Both applications clearly benefit from the use of the smallest possible mechanical resonator. Unfortunately, the optomechanical coupling largely decays when the size of the mechanical system is below the light wavelength. Here, we propose to exploit the optical resonances associated to the light confinement in subwavelength structures to circumvent this limitation, efficiently extending optomechanics to nanoscale objects. We demonstrate this mechanism with suspended silicon nanowires. We are able to optically cool the mechanical vibration of the nanowires from room temperature to 30-40 K or to obtain regenerative mechanical oscillation with a frequency stability of about one part per million. The reported optomechanical phenomena can be exploited for developing cost-optimized mass sensors with sensitivities in the zeptogram range.

Nanomechanical Sensing for Mass Flow Control in Nanowire-Based Open Nanofluidic Systems.

Open nanofluidic systems, where liquids flow along the outer surface of nanoscale structures, provide otherwise unfeasible capabilities for extremely miniaturized liquid handling applications. A critical step toward fully functional applications is to obtain quantitative mass flow control. We demonstrate the application of nanomechanical sensing for this purpose by integrating voltage-driven liquid flow along nanowire open channels with mass detection based on flexural resonators. This approach is validated by assembling the nanowires with microcantilever resonators, enabling high-precision control of larger flows, and by using the nanowires as resonators themselves, allowing extremely small liquid volume handling. Both implementations are demonstrated by characterizing voltage-driven flow of ionic liquids along the surface of the nanowires. We find a voltage range where mass flow rate follows a nonlinear monotonic increase, establishing a steady flow regime for which we show mass flow control at rates from below 1 ag/s to above 100 fg/s and precise liquid handling down to the zeptoliter scale. The observed behavior of mass flow rate is consistent with a voltage-induced transition from static wetting to dynamic spreading as the mechanism underlying liquid transport along the nanowires.

Correlative confocal and scanning electron microscopy of cultured cells without using dedicated equipment.

This protocol enables correlative light and electron microscopy (CLEM) imaging of cell surface features without using dedicated equipment. Cells are cultured and fixed on transparent substrates for confocal microscopy imaging. No conductive coating is employed in the scanning electron microscopy workflow, providing a clean cell surface observation, with fiducial markers assisting alignment of optical and topographical images. This protocol describes CLEM imaging for midbody remnants in MDCK cells but can also be applied to different cell types and surface features. For complete details on the use and execution of this protocol, please refer to Casares-Arias et al. (2020).

Effects of energy metabolism on the mechanical properties of breast cancer cells.

Tumorigenesis induces actin cortex remodeling, which makes cancerous cells softer. Cell deformability is largely determined by myosin-driven cortical tension and actin fiber architecture at the cell cortex. However, it is still unclear what the weight of each contribution is, and how these contributions change during cancer development. Moreover, little attention has been paid to the effect of energy metabolism on this phenomenon and its reprogramming in cancer. Here, we perform precise two-dimensional mechanical phenotyping based on power-law rheology to unveil the contributions of myosin II, actin fiber architecture and energy metabolism to the deformability of healthy (MCF-10A), noninvasive cancerous (MCF-7), and metastatic (MDA-MB-231) human breast epithelial cells. Contrary to the perception that the actin cortex is a passive structure that provides mechanical resistance to the cell, we find that this is only true when the actin cortex is activated by metabolic processes. The results show marked differences in the nature of the active processes that build up cell stiffness, namely that healthy cells use ATP-driven actin polymerization whereas metastatic cells use myosin II activity. Noninvasive cancerous cells exhibit an anomalous behavior, as their stiffness is not as affected by the lack of nutrients and ATP, suggesting that energy metabolism reprogramming is used to sustain active processes at the actin cortex.

Midbody Remnant Inheritance Is Regulated by the ESCRT Subunit CHMP4C.

The inheritance of the midbody remnant (MBR) breaks the symmetry of the two daughter cells, with functional consequences for lumen and primary cilium formation by polarized epithelial cells, and also for development and differentiation. However, despite its importance, neither the relationship between the plasma membrane and the inherited MBR nor the mechanism of MBR inheritance is well known. Here, the analysis by correlative light and ultra-high-resolution scanning electron microscopy reveals a membranous stalk that physically connects the MBR to the apical membrane of epithelial cells. The stalk, which derives from the uncleaved side of the midbody, concentrates the ESCRT machinery. The ESCRT CHMP4C subunit enables MBR inheritance, and its depletion dramatically reduces the percentage of ciliated cells. We demonstrate (1) that MBRs are physically connected to the plasma membrane, (2) how CHMP4C helps maintain the integrity of the connection, and (3) the functional importance of the connection.

Mechano-Optical Analysis of Single Cells with Transparent Microcapillary Resonators.

The study of biophysical properties of single cells is becoming increasingly relevant in cell biology and pathology. The measurement and tracking of magnitudes such as cell stiffness, morphology, and mass or refractive index have brought otherwise inaccessible knowledge about cell physiology, as well as innovative methods for high-throughput label-free cell classification. In this work, we present hollow resonator devices based on suspended glass microcapillaries for the simultaneous measurement of single-cell buoyant mass and reflectivity with a throughput of 300 cells/minute. In the experimental methodology presented here, both magnitudes are extracted from the devices' response to a single probe, a focused laser beam that enables simultaneous readout of changes in resonance frequency and reflected optical power of the devices as cells flow within them. Through its application to MCF-7 human breast adenocarcinoma cells and MCF-10A nontumorigenic cells, we demonstrate that this mechano-optical technique can successfully discriminate pathological from healthy cells of the same tissue type.

Nanomechanical properties of composite protein networks of erythroid membranes at lipid surfaces.

Erythrocyte membranes have been particularly useful as a model for studies of membrane structure and mechanics. Native erythroid membranes can be electroformed as giant unilamellar vesicles (eGUVs). In the presence of ATP, the erythroid membrane proteins of eGUVs rearrange into protein networks at the microscale. Here, we present a detailed nanomechanical study of individual protein microfilaments forming the protein networks of eGUVs when spread on supporting surfaces. Using Peak Force tapping Atomic Force Microscopy (PF-AFM) in liquid environment we have obtained the mechanical maps of the composite lipid-protein networks supported on solid surface. In the absence of ATP, the protein pool was characterized by a Young's Modulus Epool≈5-15MPa whereas the complex filaments were found softer after protein supramolecular rearrangement; Efil≈0.4MPa. The observed protein softening and reassembling could be relevant for understanding the mechanisms of cytoskeleton reorganization found in pathological erythrocytes or erythrocytes that are affected by biological agents.

Effect of Actin Organization on the Stiffness of Living Breast Cancer Cells Revealed by Peak-Force Modulation Atomic Force Microscopy.

We study the correlation between cytoskeleton organization and stiffness of three epithelial breast cancer cells lines with different degrees of malignancy: MCF-10A (healthy), MCF-7 (tumorigenic/noninvasive), and MDA-MB-231 (tumorigenic/invasive). Peak-force modulation atomic force microscopy is used for high-resolution topography and stiffness imaging of actin filaments within living cells. In healthy cells, local stiffness is maximum where filamentous actin is organized as well-aligned stress fibers, resulting in apparent Young's modulus values up to 1 order of magnitude larger than those in regions where these structures are not observed, but these organized actin fibers are barely observed in tumorigenic cells. We further investigate cytoskeleton conformation in the three cell lines by immunofluorescence confocal microscopy. The combination of both techniques determines that actin stress fibers are present at apical regions of healthy cells, while in tumorigenic cells they appear only at basal regions, where they cannot contribute to stiffness as probed by atomic force microscopy. These results substantiate that actin stress fibers provide a dominant contribution to stiffness in healthy cells, while the elasticity of tumorigenic cells appears not predominantly determined by these structures. We also discuss the effects of the high-frequency indentations inherent to peak-force atomic force microscopy for the identification of mechanical cancer biomarkers. Whereas conventional low loading rate indentations (1 Hz) result in slightly differentiated average stiffness for each cell line, in high-frequency measurements (250 Hz) healthy cells are clearly discernible from both tumorigenic cells with an enhanced stiffness ratio; however, the two cancerous cell lines produced indistinguishable results.

High-sensitivity linear piezoresistive transduction for nanomechanical beam resonators.

Highly sensitive conversion of motion into readable electrical signals is a crucial and challenging issue for nanomechanical resonators. Efficient transduction is particularly difficult to realize in devices of low dimensionality, such as beam resonators based on carbon nanotubes or silicon nanowires, where mechanical vibrations combine very high frequencies with miniscule amplitudes. Here we describe an enhanced piezoresistive transduction mechanism based on the asymmetry of the beam shape at rest. We show that this mechanism enables highly sensitive linear detection of the vibration of low-resistivity silicon beams without the need of exceptionally large piezoresistive coefficients. The general application of this effect is demonstrated by detecting multiple-order modes of silicon nanowire resonators made by either top-down or bottom-up fabrication methods. These results reveal a promising approach for practical applications of the simplest mechanical resonators, facilitating its manufacturability by very large-scale integration technologies.

Silicon nanowires: where mechanics and optics meet at the nanoscale.

Mechanical transducers based on nanowires promise revolutionary advances in biological sensing and force microscopy/spectroscopy. A crucial step is the development of simple and non-invasive techniques able to detect displacements with subpicometer sensitivity per unit bandwidth. Here, we design suspended tapered silicon nanowires supporting a range of optical resonances that confine and efficiently scatter light in the visible range. Then, we develop an optical method for efficiently coupling the evanescent field to the regular interference pattern generated by an incoming laser beam and the reflected beam from the substrate underneath the nanowire. This optomechanical coupling is here applied to measure the displacement of 50 nm wide nanowires with sensitivity on the verge of 1 fm/Hz(1/2) at room temperature with a simple laser interferometry set-up. This method opens the door to the measurement of the Brownian motion of ultrashort nanowires for the detection of single biomolecular recognition events in liquids, and single molecule spectroscopy in vacuum.

Atomic force microscopy reveals two phases in single stranded DNA self-assembled monolayers.

We have investigated the structure of single-stranded (ss) DNA self-assembled monolayers (SAMs) on gold by combining peak force tapping, Kelvin probe and phase contrast atomic force microscopy (AFM) techniques. The adhesion, surface potential and phase shift signals show heterogeneities in the DNA film structure at two levels: microscale and nanoscale; which cannot be clearly discerned in the topography. Firstly, there is multilayer aggregation covering less than 5% of the surface. The DNA multilayers seem to be ordered phases and their existence suggests that DNA end-to-end interaction can play a role in the self-assembly process. Secondly, we find the formation of two phases in the DNA monolayer, which differ both in surface energy and surface potential. We relate the two domains to differences in the packing density and in the ssDNA conformation. The discovered heterogeneities in ssDNA SAMs provide a new scenario in our vision of these relevant films that have direct consequences on their biological, chemical and physical properties.

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.

Nanomechanical mass sensing and stiffness spectrometry based on two-dimensional vibrations of resonant nanowires.

One-dimensional nanomechanical resonators based on nanowires and nanotubes have emerged as promising candidates for mass sensors. When the resonator is clamped at one end and the atoms or molecules being measured land on the other end (which is free to vibrate), the resonance frequency of the device decreases by an amount that is proportional to the mass of the atoms or molecules. However, atoms and molecules can land at any position along the resonator, and many biomolecules have sizes that are comparable to the size of the resonator, so the relationship between the added mass and the frequency shift breaks down. Moreover, whereas resonators fabricated by top-down methods tend to vibrate in just one dimension because they are usually shaped like diving boards, perfectly axisymmetric one-dimensional nanoresonators can support flexural vibrations with the same amplitude and frequency in two dimensions. Here, we propose a new approach to mass sensing and stiffness spectroscopy based on the fact that the nanoresonator will enter a superposition state of two orthogonal vibrations with different frequencies when this symmetry is broken. Measuring these frequencies allows the mass, stiffness and azimuthal arrival direction of the adsorbate to be determined.