Nanophotonic trapping for precise manipulation of biomolecular arrays

Optical torque calculations and measurements for DNA torsional studies

The angular optical trap (AOT) is a powerful instrument for measuring the torsional and rotational properties of a biological molecule. Thus far, AOT studies of DNA torsional mechanics have been carried out using a high numerical aperture oil-immersion objective, which permits strong trapping but inevitably introduces spherical aberrations due to the glass-aqueous interface. However, the impact of these aberrations on torque measurements is not fully understood experimentally, partly due to a lack of theoretical guidance. Here, we present a numerical platform based on the finite element method to calculate forces and torques on a trapped quartz cylinder. We have also developed a new experimental method to accurately determine the shift in the trapping position due to the spherical aberrations by using a DNA molecule as a distance ruler. We found that the calculated and measured focal shift ratios are in good agreement. We further determined how the angular trap stiffness depends on the trap height and the cylinder displacement from the trap center and found full agreement between predictions and measurements. As a further verification of the methodology, we showed that DNA torsional properties, which are intrinsic to DNA, could be determined robustly under different trap heights and cylinder displacements. Thus, this work has laid both a theoretical and experimental framework that can be readily extended to investigate the trapping forces and torques exerted on particles with arbitrary shapes and optical properties.

Light Controlled Nanobiohybrids for Modulating Chiral Alcohol Synthesis

The modulation of whole-cell activity presents a considerable challenge in biocatalysis. Conventional approaches to whole-cell catalysis, while having their strengths, often rely on complex and deliberate enzyme designs, which could result in difficulties in activity modulation and prolonged response times. Additionally, the activity of intracellular enzymes in whole-cell catalysis is influenced by temperature. To address these limitations, we introduced a relationally designed nanobiohybrid system that utilized light to modulate whole-cell catalysis for chiral alcohol production. By incorporating platinum nanoparticles onto Rhodotorula sp. cell surfaces, the nanobiohybrid capitalized on the photothermal properties of the nanoparticles to regulate the overall cell activity. When exposed to light, the Pt nanoparticles generate heat through the photothermal effect, consequently leading to an increase in the catalytic activity of the whole cells. This innovative approach facilitates control over whole-cell production and provides an efficient method for regulating biocatalytic processes. The findings of this study demonstrate the significant potential of switchable control strategies in biomanufacturing across a wide range of industries.

Particle trapping with optical nanofibers: a review [Invited]

Optical trapping has proven to be an efficient method to control particles, including biological cells, single biological macromolecules, colloidal microparticles, and nanoparticles. Multiple types of particles have been successfully trapped, leading to various applications of optical tweezers ranging from biomedical through physics to material sciences. However, precise manipulation of particles with complex composition or of sizes down to nanometer-scales can be difficult with conventional optical tweezers, and an alternative manipulation tool is desirable. Optical nanofibers, that is, fibers with a waist diameter smaller than the propagating wavelength of light, are ideal candidates for optical manipulation due to their large evanescent field that extends beyond the fiber surface. They have the added advantages of being easily connected to a fibered experimental setup, being simple to fabricate, and providing strong electric field confinement and intense magnitude of evanescent fields at the nanofiber's surface. Many different particles have been trapped, rotated, transported, and assembled with such a system. This article reviews particle trapping using optical nanofibers and highlights some challenges and future potentials of this developing topic.

Nature of Optical Thermodynamic Pressure Exerted in Highly Multimoded Nonlinear Systems

The theory of optical thermodynamics provides a comprehensive framework that enables a self-consistent description of the intricate dynamics of nonlinear multimoded photonic systems. This theory, among others, predicts a pressurelike intensive quantity (p[over ^]) that is conjugate to the system's total number of modes (M)-its corresponding extensive variable. Yet at this point, the nature of this intensive quantity is still nebulous. In this Letter, we elucidate the physical origin of the optical thermodynamic pressure and demonstrate its dual essence. In this context, we rigorously derive an expression that splits p[over ^] into two distinct components, a term that is explicitly tied to the electrodynamic radiation pressure and a second entropic part that is responsible for the entropy change. We utilize this result to establish a formalism that simplifies the quantification of radiation pressure under nonlinear equilibrium conditions, thus eliminating the need for a tedious evaluation of the Maxwell stress tensor. Our theoretical analysis is corroborated by numerical simulations carried out in highly multimoded nonlinear optical structures. These results may provide a novel way in predicting and controlling radiation pressure processes in a variety of nonlinear electromagnetic settings.

Development of Single Molecule Techniques for Sensing and Manipulation of CRISPR and Polymerase Enzymes

Clustered regularly interspaced short palindromic repeats (CRISPR) and polymerases are powerful enzymes and their diverse applications in genomics, proteomics, and transcriptomics have revolutionized the biotechnology industry today. CRISPR has been widely adopted for genomic editing applications and Polymerases can efficiently amplify genomic transcripts via polymerase chain reaction (PCR). Further investigations into these enzymes can reveal specific details about their mechanisms that greatly expand their use. Single-molecule techniques are an effective way to probe enzymatic mechanisms because they may resolve intermediary conformations and states with greater detail than ensemble or bulk biosensing techniques. This review discusses various techniques for sensing and manipulation of single biomolecules that can help facilitate and expedite these discoveries. Each platform is categorized as optical, mechanical, or electronic. The methods, operating principles, outputs, and utility of each technique are briefly introduced, followed by a discussion of their applications to monitor and control CRISPR and Polymerases at the single molecule level, and closing with a brief overview of their limitations and future prospects.

Optical force exerted on the two dimensional transition-metal dichalcogenide coated dielectric particle by Gaussian beam

Two-dimensional transition-metal dichalcogenide (TMDC) exhibits a series of distinctive optical and electrical characteristics, which make it has a good application prospect in the field of optical manipulation. Based on the Mie theory, we investigate the radiation force exerted on the TMDC wrapped dielectric particle by Gaussian wave. Theoretical calculations show that the optical force spectra exhibit two resonant peaks in the visible region, which are generated by the interband exciton transitions in TMDC. Magnitude and morphology of the excitonic peaks could be modulated effectively by tuning the number of coated TMDC layers. Furthermore, the excitonic peaks transform significantly with particle size due to the variation of coupling strength between the dielectric particle and TMDC coating. The investigation provides potential applications in optical manipulations and light-matter interactions.

Low cost and massively parallel force spectroscopy with fluid loading on a chip

Current approaches for single molecule force spectroscopy are typically constrained by low throughput and high instrumentation cost. Herein, a low-cost, high throughput technique is demonstrated using microfluidics for multiplexed mechanical manipulation of up to ~4000 individual molecules via molecular fluid loading on-a-chip (FLO-Chip). The FLO-Chip consists of serially connected microchannels with varying width, allowing for simultaneous testing at multiple loading rates. Molecular force measurements are demonstrated by dissociating Biotin-Streptavidin and Digoxigenin-AntiDigoxigenin interactions along with unzipping of double stranded DNA of varying sequence under different dynamic loading rates and solution conditions. Rupture force results under varying loading rates and solution conditions are in good agreement with prior studies, verifying a versatile approach for single molecule biophysics and molecular mechanobiology. FLO-Chip enables straightforward, rapid, low-cost, and portable mechanical testing of single molecules that can be implemented on a wide range of microscopes to broaden access and may enable new applications of molecular force spectroscopy.

Controllable transportation of microparticles along structured waveguides by the plasmonic spin-hall effect

With the nanoscale integration advantage of near field photonics, controllable manipulation and transportation of micro-objects have possessed plentiful applications in the fields of physics, biology and material sciences. However, multifunctional optical manipulation like controllable transportation and synchronous routing by nano-devices are limited and rarely reported. Here we propose a new type of Y-shaped waveguide optical conveyor belt, which can transport and route particles along the structured waveguide based on the plasmonic spin-hall effect. The routing of micro-particles in different branches is determined by the optical force components difference at the center of the Y junction along the two branches of the waveguide. The influence of light source and structural parameters on the optical forces and transportation capability are numerically studied. The results illustrate that the proposed structured waveguide optical conveyor belt can transport the microparticles controllably in different branches of the waveguide. Due to the selective transportation ability of microparticles by the 2D waveguide, our work shows great application potential in the region of on-chip optical manipulation.

Resonator nanophotonic standing-wave array trap for single-molecule manipulation and measurement

Nanophotonic tweezers represent emerging platforms with significant potential for parallel manipulation and measurements of single biological molecules on-chip. However, trapping force generation represents a substantial obstacle for their broader utility. Here, we present a resonator nanophotonic standing-wave array trap (resonator-nSWAT) that demonstrates significant force enhancement. This platform integrates a critically-coupled resonator design to the nSWAT and incorporates a novel trap reset scheme. The nSWAT can now perform standard single-molecule experiments, including stretching DNA molecules to measure their force-extension relations, unzipping DNA molecules, and disrupting and mapping protein-DNA interactions. These experiments have realized trapping forces on the order of 20 pN while demonstrating base-pair resolution with measurements performed on multiple molecules in parallel. Thus, the resonator-nSWAT platform now meets the benchmarks of a table-top precision optical trapping instrument in terms of force generation and resolution. This represents the first demonstration of a nanophotonic platform for such single-molecule experiments.

Applications of nanophotonic tweezers have been limited by the low trapping force. Here, the authors present enhanced force generation in a nanophotonic standing-wave array trap by integrating a critically-coupled resonator design and demonstrate common single-molecule experiments.

The Rise of the OM-LoC: Opto-Microfluidic Enabled Lab-on-Chip

The integration of optical circuits with microfluidic lab-on-chip (LoC) devices has resulted in a new era of potential in terms of both sample manipulation and detection at the micro-scale. On-chip optical components increase both control and analytical capabilities while reducing reliance on expensive laboratory photonic equipment that has limited microfluidic development. Notably, in-situ LoC devices for bio-chemical applications such as diagnostics and environmental monitoring could provide great value as low-cost, portable and highly sensitive systems. Multiple challenges remain however due to the complexity involved with combining photonics with micro-fabricated systems. Here, we aim to highlight the progress that optical on-chip systems have made in recent years regarding the main LoC applications: (1) sample manipulation and (2) detection. At the same time, we aim to address the constraints that limit industrial scaling of this technology. Through evaluating various fabrication methods, material choices and novel approaches of optic and fluidic integration, we aim to illustrate how optic-enabled LoC approaches are providing new possibilities for both sample analysis and manipulation.

Massively Parallelized Molecular Force Manipulation with On-Demand Thermal and Optical Control

In single-molecule force spectroscopy (SMFS), a tethered molecule is stretched using a specialized instrument to study how macromolecules extend under force. One problem in SMFS is the serial and slow nature of the measurements, performed one molecule at a time. To address this long-standing challenge, we report on the origami polymer force clamp (OPFC) which enables parallelized manipulation of the mechanical forces experienced by molecules without the need for dedicated SMFS instruments or surface tethering. The OPFC positions target molecules between a rigid nanoscale DNA origami beam and a responsive polymer particle that shrinks on demand. As a proof-of-concept, we record the steady state and time-resolved mechanical unfolding dynamics of DNA hairpins using the fluorescence signal from ensembles of molecules and confirm our conclusion using modeling.

Unsupervised selection of optimal single-molecule time series idealization criterion

Single-molecule (SM) approaches have provided valuable mechanistic information on many biophysical systems. As technological advances lead to ever-larger data sets, tools for rapid analysis and identification of molecules exhibiting the behavior of interest are increasingly important. In many cases the underlying mechanism is unknown, making unsupervised techniques desirable. The divisive segmentation and clustering (DISC) algorithm is one such unsupervised method that idealizes noisy SM time series much faster than computationally intensive approaches without sacrificing accuracy. However, DISC relies on a user-selected objective criterion (OC) to guide its estimation of the ideal time series. Here, we explore how different OCs affect DISC’s performance for data typical of SM fluorescence imaging experiments. We find that OCs differing in their penalty for model complexity each optimize DISC’s performance for time series with different properties such as signal/noise and number of sample points. Using a machine learning approach, we generate a decision boundary that allows unsupervised selection of OCs based on the input time series to maximize performance for different types of data. This is particularly relevant for SM fluorescence data sets, which often have signal/noise near the derived decision boundary and include time series of nonuniform length because of stochastic bleaching. Our approach, AutoDISC, allows unsupervised per-molecule optimization of DISC, which will substantially assist in the rapid analysis of high-throughput SM data sets with noisy samples and nonuniform time windows.

The toxicity of SiO2 NPs on cell proliferation and cellular uptake of human lung fibroblastic cell line during the variation of calcination temperature and its modeling by artificial neural network

Less attention had been paid to cell toxicity of the various synthesis methods of nanoparticles, this study investigated the effect of the calcination temperature(CT) on the crystallization of SiO2 nanoparticles(NPs), cell proliferation(CP), and cellular uptake(CU) in MRC-5. In this study, parameters were adjusted as CT(70-1000 °C), calcination time(2, 12, and 24 h), and catalyst feed rate(0.01, 0.05, and 0.1 mL.min1). CP was determined by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide(MTT) test after a 24-h exposure. The CU was achieved using ICP-MS. Results were analyzed using MATLAB2018. Results revealed that the size of synthesized particles was lower than 50 nm and, the XRD peak varied from 21 to 30° during the increase in CT. FTIR spectra confirmed the existence of Si-O and Si-Cl bonds. The maximum level of crystallization was at 1000 °C. CP decreased with the rise in the concentration of NPs(p < 0.05), as well as an increase in feed rate. A positive relationship between increased crystallization and decreased CP(R = 0.78) was seen, while such a trend was not observed in calcination time. The suggested structure in this study was 4:10:1 with Rall = 0.97, Rtest = 0.97, RMSE = 0.25, and MSE = 0.003. Furthermore, the CU rate increased with the rise in CT and calcination time. The maximum and minimum CU levels were related to NPs calcinated in 1000 °C-24 h and 350 °C-2 h, respectively. As a consequence, the most toxicity of SiO2 NPs was related to the crystalline NP. Therefore, the increase in CT and the calcination time were significant factors affecting on crystallization of SiO2 NPs, CP of lung cell, as well as CU of SiO2.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s40201-021-00663-4.

Field-Portable Microplastic Sensing in Aqueous Environments: A Perspective on Emerging Techniques

Microplastics (MPs) have been found in aqueous environments ranging from rural ponds and lakes to the deep ocean. Despite the ubiquity of MPs, our ability to characterize MPs in the environment is limited by the lack of technologies for rapidly and accurately identifying and quantifying MPs. Although standards exist for MP sample collection and preparation, methods of MP analysis vary considerably and produce data with a broad range of data content and quality. The need for extensive analysis-specific sample preparation in current technology approaches has hindered the emergence of a single technique which can operate on aqueous samples in the field, rather than on dried laboratory preparations. In this perspective, we consider MP measurement technologies with a focus on both their eventual field-deployability and their respective data products (e.g., MP particle count, size, and/or polymer type). We present preliminary demonstrations of several prospective MP measurement techniques, with an eye towards developing a solution or solutions that can transition from the laboratory to the field. Specifically, experimental results are presented from multiple prototype systems that measure various physical properties of MPs: pyrolysis-differential mobility spectroscopy, short-wave infrared imaging, aqueous Nile Red labeling and counting, acoustophoresis, ultrasound, impedance spectroscopy, and dielectrophoresis.

Highly-Parallel Microfluidics-Based Force Spectroscopy on Single Cytoskeletal Motors

Cytoskeletal motors transform chemical energy into mechanical work to drive essential cellular functions. Optical trapping experiments have provided crucial insights into the operation of these molecular machines under load. However, the throughput of such force spectroscopy experiments is typically limited to one measurement at a time. Here, a highly-parallel, microfluidics-based method that allows for rapid collection of force-dependent motility parameters of cytoskeletal motors with two orders of magnitude improvement in throughput compared to currently available methods is introduced. Tunable hydrodynamic forces to stepping kinesin-1 motors via DNA-tethered beads and utilize a large field of view to simultaneously track the velocities, run lengths, and interaction times of hundreds of individual kinesin-1 molecules under varying resisting and assisting loads are applied. Importantly, the 16 µm long DNA tethers between the motors and the beads significantly reduces the vertical component of the applied force pulling the motors away from the microtubule. The approach is readily applicable to other molecular systems and constitutes a new methodology for parallelized single-molecule force studies on cytoskeletal motors.

Plasmonic Optical Tweezers for Particle Manipulation: Principles, Methods, and Applications

Inspired by the idea of combining conventional optical tweezers with plasmonic nanostructures, a technique named plasmonic optical tweezers (POT) has been widely explored from fundamental principles to applications. With the ability to break the diffraction barrier and enhance the localized electromagnetic field, POT techniques are especially effective for high spatial-resolution manipulation of nanoscale or even subnanoscale objects, from small bioparticles to atoms. In addition, POT can be easily integrated with other techniques such as lab-on-chip devices, which results in a very promising alternative technique for high-throughput single-bioparticle sensing or imaging. Despite its label-free, high-precision, and high-spatial-resolution nature, it also suffers from some limitations. One of the main obstacles is that the plasmonic nanostructures are located over the surfaces of a substrate, which makes the manipulation of bioparticles turn from a three-dimensional problem to a nearly two-dimensional problem. Meanwhile, the operation zone is limited to a predefined area. Therefore, the target objects must be delivered to the operation zone near the plasmonic structures. This review summarizes the state-of-the-art target delivery methods for the POT-based particle manipulating technique, along with its applications in single-bioparticle analysis/imaging, high-throughput bioparticle purifying, and single-atom manipulation. Future developmental perspectives of POT techniques are also discussed.

Optical tweezers in single-molecule biophysics

Optical tweezers have become the method of choice in single-molecule manipulation studies. In this Primer, we first review the physical principles of optical tweezers and the characteristics that make them a powerful tool to investigate single molecules. We then introduce the modifications of the method to extend the measurement of forces and displacements to torques and angles, and to develop optical tweezers with single-molecule fluorescence detection capabilities. We discuss force and torque calibration of these instruments, their various modes of operation and most common experimental geometries. We describe the type of data obtained in each experimental design and their analyses. This description is followed by a survey of applications of these methods to the studies of protein-nucleic acid interactions, protein/RNA folding and molecular motors. We also discuss data reproducibility, the factors that lead to the data variability among different laboratories and the need to develop field standards. We cover the current limitations of the methods and possible ways to optimize instrument operation, data extraction and analysis, before suggesting likely areas of future growth.

Coherently tunable metalens tweezers for optofluidic particle routing

Nanophotonic particle manipulation exploits unique light shaping capabilities of nanophotonic devices to trap, guide, rotate and propel particles in microfluidic channels. Recent introduction of metalens into microfluidics research demonstrates the new capability of using nanophotonics devices for far-field optical manipulation. In this work we demonstrate, via numerical simulation, the first tunable metalens tweezers that function under dual-beam illumination. The phase profile of the metalens is modulated by controlling the relative strength and phase of the two coherent incident light beams. As a result, the metalens creates a thin sheet of focus inside a microchannel. Changes to the illumination condition allow the focus to be swept across the microchannel, thereby producing a controllable and reconfigurable path for particle transport. Particle routing in a Y-branch junction, for both nano- and microparticles, is evaluated as an example functionality for the tunable metalens tweezers. This work shows that tunable far-field particle manipulation can be achieved using near-field nano-engineering and coherent control, opening a new way for the integration of nanophotonics and microfluidics.

Optical Tweezers Exploring Neuroscience

Over the past decade, optical tweezers (OT) have been increasingly used in neuroscience for studies of molecules and neuronal dynamics, as well as for the study of model organisms as a whole. Compared to other areas of biology, it has taken much longer for OT to become an established tool in neuroscience. This is, in part, due to the complexity of the brain and the inherent difficulties in trapping individual molecules or manipulating cells located deep within biological tissue. Recent advances in OT, as well as parallel developments in imaging and adaptive optics, have significantly extended the capabilities of OT. In this review, we describe how OT became an established tool in neuroscience and we elaborate on possible future directions for the field. Rather than covering all applications of OT to neurons or related proteins and molecules, we focus our discussions on studies that provide crucial information to neuroscience, such as neuron dynamics, growth, and communication, as these studies have revealed meaningful information and provide direction for the field into the future.

An optofluidic conveyor for particle transportation based on a fiber array and photothermal convection

In this paper, a thermal convection-based optofluidic conveyor has been introduced, which can flexibly capture and manipulate multiple 20-120 μm silica particles with utmost accuracy. Near the end face, a fiber-based light source can confine 100 μm silica particles within 100 microns. By switching the light source of the fiber array, centimeter-range transportation of 100 μm SiO2 particles has been successfully achieved, which was not possible in optical trapping devices as we know. Through the comparative experiment with silica, polystyrene, and zirconium dioxide particles, the presented conveyor system is proved to be independent of the particles' dielectric properties. Moreover, sorting of silica and polystyrene particles based on the difference of mass densities has also been achieved. Additionally, the components of this conveyor (fiber array) and chip parts (microfluidic chamber) are freely detachable. Here, instead of expensive laser systems, a non-coherent light source has been utilized, which eventually eliminates the use of optical lens assemblies. All these features lead to making the equipment extremely simple in structure and low in cost. Besides, this optofluidic conveyor can be applied to transmit and sort various objects such as blood/cancer cells and microorganisms.

Advances in Label-Free Detections for Nanofluidic Analytical Devices

Nanofluidics, a discipline of science and engineering of fluids confined to structures at the 1-1000 nm scale, has experienced significant growth over the past decade. Nanofluidics have offered fascinating platforms for chemical and biological analyses by exploiting the unique characteristics of liquids and molecules confined in nanospaces; however, the difficulty to detect molecules in extremely small spaces hampers the practical applications of nanofluidic devices. Laser-induced fluorescence microscopy with single-molecule sensitivity has been so far a major detection method in nanofluidics, but issues arising from labeling and photobleaching limit its application. Recently, numerous label-free detection methods have been developed to identify and determine the number of molecules, as well as provide chemical, conformational, and kinetic information of molecules. This review focuses on label-free detection techniques designed for nanofluidics; these techniques are divided into two groups: optical and electrical/electrochemical detection methods. In this review, we discuss on the developed nanofluidic device architectures, elucidate the mechanisms by which the utilization of nanofluidics in manipulating molecules and controlling light-matter interactions enhances the capabilities of biological and chemical analyses, and highlight new research directions in the field of detections in nanofluidics.

Recent advances in single-molecule fluorescence microscopy render structural biology dynamic

Single-molecule fluorescence microscopy has long been appreciated as a powerful tool to study the structural dynamics that enable biological function of macromolecules. Recent years have witnessed the development of more complex single-molecule fluorescence techniques as well as powerful combinations with structural approaches to obtain mechanistic insights into the workings of various molecular machines and protein complexes. In this review, we highlight these developments that together bring us one step closer to a dynamic understanding of biological processes in atomic details.

Next-Generation Optical Nanotweezers for Dynamic Manipulation: From Surface to Bulk

Optical traps based on strongly confined electromagnetic fields at metal-dielectric interfaces are far more efficient than conventional optical tweezers. Specifically, these near-field nanotweezers allow the trapping of smaller particles at lower optical intensities, which can impact diverse research fields ranging from soft condensed matter physics to materials science and biology. A major thrust in the past decade has been focused on extending the capabilities of plasmonically enhanced nanotweezers beyond diffusion-limited trapping on surfaces such as to achieve dynamic control in the bulk of fluidic environments. Here, we review the recent efforts in optical nanotweezers, especially those involving hybrid forcing schemes, covering both surface and bulk-based techniques. We summarize the important capabilities demonstrated with this promising approach, with niche applications in reconfigurable nanopatterning and on-chip assembly as well as in sorting and separating colloidal nanoparticles.

Opto-thermoelectric speckle tweezers

Opto-thermoelectric tweezers present a new paradigm for optical trapping and manipulation of particles using low-power and simple optics. New real-life applications of opto-thermoelectric tweezers in areas such as biophysics, microfluidics, and nanomanufacturing will require them to have large-scale and high-throughput manipulation capabilities in complex environments. Here, we present opto-thermoelectric speckle tweezers, which use speckle field consisting of many randomly distributed thermal hotspots that arise from an optical speckle pattern to trap multiple particles over large areas. By further integrating the speckle tweezers with a microfluidic system, we experimentally demonstrate their application for size-based nanoparticle filtration. With their low-power operation, simplicity, and versatility, opto-thermoelectric speckle tweezers will broaden the applications of optical manipulation techniques.

Subwavelength optical trapping and transporting using a Bloch mode

Multi-functional optical manipulations, including optical trapping and transporting of subwavelength particles, are proposed using the Bloch modes in a dielectric photonic structure. We show that the Bloch modes in a periodic structure can generate a series of subwavelength trapping wells that are addressable by tuning the incident wavelength. This feature enables efficient optical trapping and transportation in a peristaltic way. Since we are using the guiding Bloch mode in a dielectric structure, rather than using plasmonic or dielectric resonant cavities, these operations are wide band and free from joule loss. The Bloch mode in a simple periodic dielectric structure provides a new platform for multi-functional optical operations and may find potential applications in nanophotonics and biomedicine.

Optical Trapping and Manipulating with a Silica Microring Resonator in a Self-Locked Scheme

Based on the gradient force of evanescent waves in silica waveguides and add-drop micro-ring resonators, the optical trapping and manipulation of micro size particles is demonstrated in a self-locked scheme that maintains the on-resonance system even if there is a change in the ambient temperature or environment. The proposed configuration allows the trapping of particles in the high Q resonator without the need for a precise wavelength adjustment of the input signal. On the one hand, a silicon dioxide waveguide having a lower refractive index and relatively larger dimensions facilitates the coupling of the laser with a single-mode fiber. Furthermore, the experimental design of the self-locked scheme reduces the sensitivity of the ring to the environment. This combination can trap the micro size particles with a high stability while manipulating them with high accuracy.

Nanoparticle trapping and routing on plasmonic nanorails in a microfluidic channel

Plasmonic nanostructures hold great promise for enabling advanced optical manipulation of nanoparticles in microfluidic channels, resulting from the generation of strong and controllable light focal points at the nanoscale. A primary remaining challenge in the current integration of plasmonics and microfluidics is to transport trapped nanoparticles along designated routes. Here we demonstrate through numerical simulation a plasmonic nanoparticle router that can trap and route a nanoparticle in a microfluidic channel with a continuous fluidic flow. The nanoparticle router contains a series of gold nanostrips on top of a continuous gold film. The nanostrips support both localised and propagating surface plasmons under light illumination, which underpin the trapping and routing functionalities. The nanoparticle guiding at a Y-branch junction is enabled by a small change of 50 nm in the wavelength of incident light.

Towards biological applications of nanophotonic tweezers

Optical trapping (synonymous with optical tweezers) has become a core biophysical technique widely used for interrogating fundamental biological processes on size scales ranging from the single-molecule to the cellular level. Recent advances in nanotechnology have led to the development of 'nanophotonic tweezers,' an exciting new class of 'on-chip' optical traps. Here, we describe how nanophotonic tweezers are making optical trap technology more broadly accessible and bringing unique biosensing and manipulation capabilities to biological applications of optical trapping.

Nanophotonic Array-Induced Dynamic Behavior for Label-Free Shape-Selective Bacteria Sieving

Current particle sorting methods such as microfluidics, acoustics, and optics focus on exploiting the differences in the mass, size, refractive index, or fluorescence staining. However, there exist formidable challenges for them to sort label-free submicron particles with similar volume and refractive index yet distinct shapes. In this work, we report an optofluidic nanophotonic sawtooth array (ONSA) that generates sawtooth-like light fields through light coupling, paving the physical foundation for shape-selective sieving. Submicron particles interact with the coupled hotspots which impose different optical torques on the particles according to their shapes. Unstained S. aureus and E. coli are used as a model system to demonstrate this shape-selective sorting mechanism based on the torque-induced body dynamics, which was previously unattainable by other particle sorting technologies. More than 95% of S. aureus is retained within ONSA, while more than 97% of E. coli is removed. This nanophotonic chip offers a paradigm shift in shape-selective sorting of submicron particles and expands the boundary of optofluidics-based particle manipulation.

Multi-parameter measurements of conformational dynamics in nucleic acids and nucleoprotein complexes

Biological macromolecules undergo dynamic conformational changes. Single-molecule methods can track such structural rearrangements in real time. However, while the structure of large macromolecules may change along many degrees of freedom, single-molecule techniques only monitor a limited number of these axes of motion. Advanced single-molecule methods are being developed to track multiple degrees of freedom in nucleic acids and nucleoprotein complexes at high resolution, to enable better manipulation and control of the system under investigation, and to collect measurements in massively parallel fashion. Combining complementary single-molecule methods within the same assay also provides unique measurement opportunities. Implementations of magnetic and optical tweezers combined with fluorescence and FRET have demonstrated results unattainable by either technique alone. Augmenting other advanced single-molecule methods with fluorescence detection will allow us to better capture the multidimensional dynamics of nucleic acids and nucleoprotein complexes central to biology.

Parallelized DNA tethered bead measurements to scrutinize DNA mechanical structure

Tethering beads to DNA offers a panel of single molecule techniques for the refined analysis of the conformational dynamics of DNA and the elucidation of the mechanisms of enzyme activity. Recent developments include the massive parallelization of these techniques achieved by the fabrication of dedicated nanoarrays by soft nanolithography. We focus here on two of these techniques: the Tethered Particle motion and Magnetic Tweezers allowing analysis of the behavior of individual DNA molecules in the absence of force and under the application of a force and/or a torque, respectively. We introduce the experimental protocols for the parallelization and discuss the benefits already gained, and to come, for these single molecule investigations.

High Trap Stiffness Microcylinders for Nanophotonic Trapping

Nanophotonic waveguides have enabled on-chip optical trap arrays for high-throughput manipulation and measurements. However, the realization of the full potential of these devices requires trapping enhancement for applications that need large trapping force. Here, we demonstrate a solution via fabrication of high refractive index cylindrical trapping particles. Using two different fabrication processes, a cleaving method and a novel lift-off method, we produced cylindrical silicon nitride (Si₃N₄) particles and characterized their trapping properties using the recently developed nanophotonic standing-wave array trap (nSWAT) platform. Relative to conventionally used polystyrene microspheres, the fabricated Si₃N₄ microcylinders attain an approximately 3- to 6-fold trap stiffness enhancement. Furthermore, both fabrication processes permit tunable microcylinder geometry, and the lift-off method also results in ultrasmooth surface termination of the ends of the microcylinders. These combined features make the Si₃N₄ microcylinders uniquely suited for a broad range of high-throughput, high-force, nanophotonic waveguide-based optical trapping applications.

Tunable optofluidic sorting and manipulation on micro-ring resonators from a statistics perspective

Based on the optical trapping force of an evanescent wave at a micro-ring resonator alongside a waveguide, we propose a tunable optofluidic sorting unit for micro-nanoparticles by localized thermal phase tuning. With the tuning of field build-up factor of resonator, the depth of trapping potential well and the size of trapped particle are adjustable. Furthermore, by considering the Brownian motion of trapped particles from a statistics perspective, we verify the critical trapping threshold of a potential well, which is usually assumed to be 1k_BT. The threshold depends not only on the optical power and particle size, but also on the length of the coupling region. Compared with a wavelength tuning mechanism, localized thermal tuning enables large-scale integration of many independent tunable resonators. As a demonstration, we propose a set of operations with three resonators for nanoparticle manipulation, including sorting, storing, and mixing. Our proposed function units are of great importance for on-chip large-scale integration of optofluidic systems.

Broadband Generation of Photonic Spin-Controlled Arbitrary Accelerating Light Beams in the Visible

Bending light along arbitrary curvatures is a captivating and popular notion, triggering unprecedented endeavors in achieving diffraction-free propagation along a curved path in free-space. Much effort has been devoted to achieving this goal in homogeneous space, which solely relies on the transverse acceleration of beam centroid exerted by a beam generator. Here, based on an all-dielectric metasurface, we experimentally report a synthetic strategy of encoding and multiplexing acceleration features on a freely propagating light beam, synergized with photonic spin states of light. Independent switching between two arbitrary visible accelerating light beams with distinct acceleration directions and caustic trajectories is achieved. This proof-of-concept recipe demonstrates the strength of the designed metasurface chip: subwavelength pixel size, independent control over light beam curvature, broadband operation in the visible, and ultrathin scalable planar architecture. Our results open up the possibility of creating ultracompact, high-pixel density, and flat-profile nanophotonic platforms for efficient generation and dynamical control of structured light beams.

Tunable optical lattices in the near-field of a few-mode nanophotonic waveguide

Due to the action of the scattering force, particles that are optically trapped at the surface of a waveguide are propelled in the direction of the light propagation. In this work, we demonstrate an original approach for creating tunable periodic arrays of optical traps along a few-mode silicon nanophotonic waveguide. We show how the near-field optical forces at the surface of the waveguide are periodically modulated when two guided modes with different propagation constants are simultaneously excited. The phenomenon is used to achieve stable trapping of a large number of dielectric particles or bacteria along a single waveguide. By controlling the light coupling conditions and the laser wavelength, we investigate several techniques for manipulating the trapped particles. Especially, we demonstrate that the period of the optical lattice can be finely tuned by adjusting the laser wavelength. This effect can be used to control the trap positions, and thus transport the trapped particles in both directions along the waveguide.

Optical transport of fluorescent diamond particles inside a tapered capillary

Optical forces provide an efficient way to sort particles and biological materials according to their optical properties. However, both enhanced optical forces and a large interaction volume are needed in order to optically sort a large number of nanoparticles. We investigate the use of a tapered glass capillary as an optofluidic platform for optical manipulation and optical sorting applications. Tapered capillaries with micrometre and sub-micrometre sizes are fabricated. After filling the tapered capillary with a colloidal solution of red fluorescent diamond particles, a green laser light is coupled into the capillary. The tapered capillary acts both as a microfluidic channel and as an optical waveguide, making it possible for the light to interact with the particles inside the sample solution. Using an incident laser power of few tens of milliwatts, we achieve optical transportation of the brightest particles inside the tapered part of the capillary. Particle velocities as high as few tens of micrometres per second are measured.

Force Spectroscopy and Beyond: Innovations and Opportunities

Life operates at the intersection of chemistry and mechanics. Over the years, we have made remarkable progress in understanding life from a biochemical perspective and the mechanics of life at the single-molecule scale. Yet the full integration of physical and mechanical models into mainstream biology has been impeded by technical and conceptual barriers, including limitations in our ability to 1) easily measure and apply mechanical forces to biological systems, 2) scale these measurements from single-molecule characterization to more complex biomolecular systems, and 3) model and interpret biophysical data in a coherent way across length scales that span single molecules to cells to multicellular organisms. In this manuscript, through a look at historical and recent developments in force spectroscopy techniques and a discussion of a few exemplary open problems in cellular biomechanics, we aim to identify research opportunities that will help us reach our goal of a more complete and integrated understanding of the role of force and mechanics in biological systems.

Tunable size selectivity and nanoparticle immobilization on a photonic crystal optical trap

We harness residual thermal effects in a low-absorptivity system to manipulate parallel optical trapping of particles on the nanoscale. A photonic crystal is used to generate a 2D array of optical traps. We show that the size selectivity of the trap can be tuned by adding a non-ionic surfactant to the solution, altering the thermophoretic effect that delivers nanoparticles to trapping sites. We further show that particles can be permanently immobilized on the photonic crystal via photopolymerization of the trapping medium.

Multi-level sorting of nanoparticles on multi-step optical waveguide splitter

We propose an optofluidic sorting method for nanoparticles with different size by using optical waveguide splitter, and moreover, multiple cascaded splitters with different threshold could act as multi-level sorting unit. For a directional coupler (DC) with a specific wavelength excitation, the power splitting ratio is related to the coupling length and the gap between parallel waveguides. The power splitting ratio further determines the trapping force and potential wells distribution of both output ports. Most importantly, the potential well distribution is dependent on the particle size. For larger particles, the potential wells of both waveguides are inclined to merge, which makes it easier to be attracted and transfers to the adjacent waveguide with deeper potential well. The critical size of sorting is corresponding to the case when the barrier between wells just disappears, or the second derivative of the potential distribution is exactly zero. Moreover, since the sorting threshold of nanoparticles is related to coupling length and gap, multiple cascaded splitters with length or gap gradually varied could act as a multi-level sorting unit. A four-level sorting unit with a critical particle size of 600nm, 700nm, and 800nm are demonstrated. By considering the Brownian motion of particles and using particle-tracking method, the random distribution of nanoparticles on parallel waveguides in the sorting process is statistically presented, which agreed well with its corresponding potential wells distribution analysis. This sorting method based on multi-step optical waveguide splitter offers a number of advantages including single wavelength excitation, low loss, low power performance and ease of fabrication. This design can realize the high-throughput and large-scale nanoparticle automatic sorting in integrated photonic circuits, which have great potential for a large scale lab-on-a-chip system.

Optical tweezing using tunable optical lattices along a few-mode silicon waveguide

Fourteen years ago, optical lattices and holographic tweezers were considered as a revolution, allowing for trapping and manipulating multiple particles at the same time using laser light. Since then, near-field optical forces have aroused tremendous interest as they enable efficient trapping of a wide range of objects, from living cells to atoms, in integrated devices. Yet, handling at will multiple objects using a guided light beam remains a challenging task for current on-chip optical trapping techniques. We demonstrate here on-chip optical trapping of dielectric microbeads and bacteria using one-dimensional optical lattices created by near-field mode beating along a few-mode silicon nanophotonic waveguide. This approach allows not only for trapping large numbers of particles in periodic trap arrays with various geometries, but also for manipulating them via diverse transport and repositioning techniques. Near-field mode-beating optical lattices may be readily implemented in lab-on-a-chip devices, addressing numerous scientific fields ranging from bio-analysis to nanoparticle processing.

Progress of Inertial Microfluidics in Principle and Application

Inertial microfluidics has become a popular topic in microfluidics research for its good performance in particle manipulation and its advantages of simple structure, high throughput, and freedom from an external field. Compared with traditional microfluidic devices, the flow field in inertial microfluidics is between Stokes state and turbulence, whereas the flow is still regarded as laminar. However, many mechanical effects induced by the inertial effect are difficult to observe in traditional microfluidics, making particle motion analysis in inertial microfluidics more complicated. In recent years, the inertial migration effect in straight and curved channels has been explored theoretically and experimentally to realize on-chip manipulation with extensive applications from the ordinary manipulation of particles to biochemical analysis. In this review, the latest theoretical achievements and force analyses of inertial microfluidics and its development process are introduced, and its applications in circulating tumor cells, exosomes, DNA, and other biological particles are summarized. Finally, the future development of inertial microfluidics is discussed. Owing to its special advantages in particle manipulation, inertial microfluidics will play a more important role in integrated biochips and biomolecule analysis.

Particle Manipulation by Optical Forces in Microfluidic Devices

Since the pioneering work of Ashkin and coworkers, back in 1970, optical manipulation gained an increasing interest among the scientific community. Indeed, the advantages and the possibilities of this technique are unsubtle, allowing for the manipulation of small particles with a broad spectrum of dimensions (nanometers to micrometers size), with no physical contact and without affecting the sample viability. Thus, optical manipulation rapidly found a large set of applications in different fields, such as cell biology, biophysics, and genetics. Moreover, large benefits followed the combination of optical manipulation and microfluidic channels, adding to optical manipulation the advantages of microfluidics, such as a continuous sample replacement and therefore high throughput and automatic sample processing. In this work, we will discuss the state of the art of these optofluidic devices, where optical manipulation is used in combination with microfluidic devices. We will distinguish on the optical method implemented and three main categories will be presented and explored: (i) a single highly focused beam used to manipulate the sample, (ii) one or more diverging beams imping on the sample, or (iii) evanescent wave based manipulation.

Quantifying Local Molecular Tension Using Intercalated DNA Fluorescence

The ability to measure mechanics and forces in biological nanostructures, such as DNA, proteins and cells, is of great importance as a means to analyze biomolecular systems. However, current force detection methods often require specialized instrumentation. Here, we present a novel and versatile method to quantify tension in molecular systems locally and in real time, using intercalated DNA fluorescence. This approach can report forces over a range of at least ∼0.5-65 pN with a resolution of 1-3 pN, using commercially available intercalating dyes and a general-purpose fluorescence microscope. We demonstrate that the method can be easily implemented to report double-stranded (ds)DNA tension in any single-molecule assay that is compatible with fluorescence microscopy. This is particularly useful for multiplexed techniques, where measuring applied force in parallel is technically challenging. Moreover, tension measurements based on local dye binding offer the unique opportunity to determine how an applied force is distributed locally within biomolecular structures. Exploiting this, we apply our method to quantify the position-dependent force profile along the length of flow-stretched DNA and reveal that stretched and entwined DNA molecules-mimicking catenated DNA structures in vivo-display transient DNA-DNA interactions. The method reported here has obvious and broad applications for the study of DNA and DNA-protein interactions. Additionally, we propose that it could be employed to measure forces in any system to which dsDNA can be tethered, for applications including protein unfolding, chromosome mechanics, cell motility, and DNA nanomachines.

Self-Induced Backaction Optical Pulling Force

We achieve long-range and continuous optical pulling in a periodic photonic crystal background, which supports a unique Bloch mode with the self-collimation effect. Most interestingly, the pulling force reported here is mainly contributed by the intensity gradient force originating from the self-induced backaction of the object to the self-collimation mode. This force is sharply distinguished from the widely held conception of optical tractor beams based on the scattering force. Also, this pulling force is insensitive to the angle of incidence and can pull multiple objects simultaneously.

Sculpting nanoparticle dynamics for single-bacteria-level screening and direct binding-efficiency measurement

Particle trapping and binding in optical potential wells provide a versatile platform for various biomedical applications. However, implementation systems to study multi-particle contact interactions in an optical lattice remain rare. By configuring an optofluidic lattice, we demonstrate the precise control of particle interactions and functions such as controlling aggregation and multi-hopping. The mean residence time of a single particle is found considerably reduced from 7 s, as predicted by Kramer’s theory, to 0.6 s, owing to the mechanical interactions among aggregated particles. The optofluidic lattice also enables single-bacteria-level screening of biological binding agents such as antibodies through particle-enabled bacteria hopping. The binding efficiency of antibodies could be determined directly, selectively, quantitatively and efficiently. This work enriches the fundamental mechanisms of particle kinetics and offers new possibilities for probing and utilising unprecedented biomolecule interactions at single-bacteria level.

Optical trapping is a versatile tool for biomedical applications. Here, the authors use an optofluidic lattice to achieve controllable multi-particle hopping and demonstrate single-bacteria-level screening and measurement of binding efficiency of biological binding agents through particle-enabled bacteria hopping.

Repurposing a Benchtop Centrifuge for High-Throughput Single-Molecule Force Spectroscopy

We present high-throughput single-molecule manipulation using a benchtop centrifuge, overcoming limitations common in other single-molecule approaches such as high cost, low throughput, technical difficulty, and strict infrastructure requirements. An inexpensive and compact Centrifuge Force Microscope (CFM) adapted to a commercial centrifuge enables use by nonspecialists, and integration with DNA nanoswitches facilitates both reliable measurements and repeated molecular interrogation. Here, we provide detailed protocols for constructing the CFM, creating DNA nanoswitch samples, and carrying out single-molecule force measurements.

Surface enhanced Raman scattering (SERS) based biomicrofluidics systems for trace protein analysis

In recent years, Surface Enhanced Raman Scattering (SERS) has been widely applied to many different areas, including chemical analysis, biomolecule detection, bioagent diagnostics, DNA sequence, and environmental monitor, due to its capabilities of unlabeled fingerprint identification, high sensitivity, and rapid detection. In biomicrofluidic systems, it is also very powerful to integrate SERS based devices with specified micro-fluid flow fields to further focusing/enhancing/multiplexing SERS signals through molecule registration, concentration/accumulation, and allocation. In this review, after a brief introduction of the mechanism of SERS detection on proteins, we will first focus on the effectiveness of different nanostructures for SERS enhancement and light-to-heat conversion in trace protein analysis. Various protein molecule accumulation schemes by either (bio-)chemical or physical ways, such as immuno, electrochemical, Tip-enhanced Raman spectroscopy, and magnetic, will then be reviewed for further SERS signal amplification. The analytical and repeatability/stability issues of SERS detection on proteins will also be brought up for possible solutions. Then, the comparison about various ways employing microfluidic systems to register, concentrate, and enhance the signals of SERS and reduce the background noise by active or passive means to manipulate SERS nanostructures and protein molecules will be elaborated. Finally, we will carry on the discussion on the challenges and opportunities by introducing SERS into biomicrofluidic systems and their potential solutions.

Optical forces in silicon subwavelength-grating waveguides

A theoretical analysis is given for the optical forces induced by the Bloch mode propagating along a silicon subwavelength-grating (SWG) waveguide for the first time. As a periodical structure, an SWG waveguide supports periodical light field distribution along the waveguide. This makes it possible to trap many nano-particles stably periodically, which is very different from the case with a conventional optical waveguide. The separation of the trapped nano-particles can be designed easily by modifying the grating period of an SWG waveguide. Furthermore, an SWG waveguide has larger working distance in the lateral direction to trap nano-particles around the waveguide than a conventional optical waveguide.

A multiplexed magnetic tweezer with precision particle tracking and bi-directional force control

Background

In the past two decades, methods have been developed to measure the mechanical properties of single biomolecules. One of these methods, Magnetic tweezers, is amenable to aquisition of data on many single molecules simultaneously, but to take full advantage of this "multiplexing" ability, it is necessary to simultaneously incorprorate many capabilities that ahve been only demonstrated separately.

Methods

Our custom built magnetic tweezer combines high multiplexing, precision bead tracking, and bi-directional force control into a flexible and stable platform for examining single molecule behavior. This was accomplished using electromagnets, which provide high temporal control of force while achieving force levels similar to permanent magnets via large paramagnetic beads.

Results

Here we describe the instrument and its ability to apply 2–260 pN of force on up to 120 beads simultaneously, with a maximum spatial precision of 12 nm using a variety of bead sizes and experimental techniques. We also demonstrate a novel method for increasing the precision of force estimations on heterogeneous paramagnetic beads using a combination of density separation and bi-directional force correlation which reduces the coefficient of variation of force from 27% to 6%. We then use the instrument to examine the force dependence of uncoiling and recoiling velocity of type 1 fimbriae from Eschericia coli (E. coli) bacteria, and see similar results to previous studies.

Conclusion

This platform provides a simple, effective, and flexible method for efficiently gathering single molecule force spectroscopy measurements.

Tailoring Optical Forces Behavior in Nano-optomechanical Devices Immersed in Fluid Media

Emerging nano-optofluidic devices have allowed a synergetic relation between photonic integrated circuits and microfluidics, allowing manipulation and transport at the realm of nanoscale science. Simultaneously, optical gradient forces have allowed highly precise control of mechanical motion in nano-optomechanical devices. In this report, we show that the repulsive optical forces of the antisymmetric eigenmodes in an optomechanical device, based on a slot-waveguide structure, increases as the refraction index of the fluid medium increases. This effect provides a feasible way to tailor the repulsive optical forces when these nano-optomechanical devices are immersed in dielectric liquids. Furthermore, the total control of the attractive and repulsive optical forces inside liquids may be applied to design novel nanophotonic devices, containing both microfluidic and nanomechanical functionalities, which may find useful applications in several areas, such as biomedical sensors, manipulators and sorters, amongst others.