Axisymmetric thermoviscous and thermal expansion flows for microfluidics

Recent microfluidic experiments have explored the precise positioning of micron-sized particles in liquid environments via laser-induced thermoviscous flow. From micro-robotics to biology at the subcellular scale, this versatile technique has found a broad range of applications. Through the interplay between thermal expansion and thermal viscosity changes, the repeated scanning of the laser along a scan path results in fluid flow and hence net transport of particles, without physical channels. Building on previous work focusing on two-dimensional microfluidic settings, we present an analytical, theoretical model for the thermoviscous and thermal expansion flows and net transport induced by a translating heat spot in three-dimensional, unconfined fluid. We first numerically solve for the temperature field due to a translating heat source in the experimentally relevant limit. Then, in our flow model, the small, localised temperature increase causes local changes in the mass density, shear viscosity and bulk viscosity of the fluid. We derive analytically the instantaneous flow generated during one scan and compute the net transport of passive tracers due to a full scan, up to quadratic order in the thermal expansion and thermal shear viscosity coefficients. We further show that the flow and transport are independent of bulk viscosity. In the far field, while the leading-order instantaneous flow is typically a three-dimensional source or sink, the leading-order average velocity of tracers is instead a source dipole, whose strength depends on the relative magnitudes of the thermal expansion and thermal shear viscosity coefficients. Our quantitative results reveal the potential for future three-dimensional net transport and manipulation of particles at the microscale.

Electrostatic All-Passive Force Clamping of Charged Nanoparticles

In the past decades, many techniques have been explored for trapping microscopic and nanoscopic objects, but the investigation of nano-objects under arbitrary forces and conditions remains nontrivial. One fundamental case concerns the motion of a particle under a constant force, known as force clamping. Here, we employ metallic nanoribbons embedded in a glass substrate in a capacitor configuration to generate a constant electric field on a charged nanoparticle in a water-filled glass nanochannel. We estimate the force fields from Brownian trajectories over several micrometers and confirm the constant behavior of the forces both numerically and experimentally. Furthermore, we manipulate the diffusion and relaxation times of the nanoparticles by tuning the charge density on the electrode. Our highly compact and controllable setting allows for the trapping and force-clamping of charged nanoparticles in a solution, providing a platform for investigating nanoscopic diffusion phenomena.

Dynamically reconfigurable acoustofluidic metasurface for subwavelength particle manipulation and assembly

Particle manipulation plays a pivotal role in scientific and technological domains such as materials science, physics, and the life sciences. Here, we present a dynamically reconfigurable acoustofluidic metasurface that enables precise trapping and positioning of microscale particles in fluidic environments. By harnessing acoustic-structure interaction in a passive membrane resonator array, we generate localized standing acoustic waves that can be reconfigured in real-time. The resulting radiation force allows for subwavelength manipulation and patterning of particles on the metasurface at individual and collective scales, with actuation frequencies below 2 MHz. We further demonstrate the capabilities of the reconfigurable metasurface in trapping and enriching beads and biological cells flowing in microfluidic channels, showcasing its potential in high-throughput bioanalytical applications. Our versatile and biocompatible particle manipulation platform is suitable for applications ranging from the assembly of colloidal particles to enrichment of rare cells.

Optomagnetic Micromirror Arrays for Mapping Large Area Stiffness Distributions of Biomimetic Materials

A new device termed "Optomagnetic Micromirror Arrays" (OMA) is demonstrated capable of mapping the stiffness distribution of biomimetic materials across a 5.1 mm × 7.2 mm field of view with cellular resolution. The OMA device comprises an array of 50 000 magnetic micromirrors with optical grating structures embedded beneath an elastic PDMS film, with biomimetic materials affixed on top. Illumination of a broadband white light beam onto these micromirrors results in the reflection of microscale rainbow light rays on each micromirror. When a magnetic field is applied, it causes each micromirror to tilt differently depending on the local stiffness of the biomimetic materials. Through imaging these micromirrors with low N.A. optics, a specific narrow band of reflection light rays from each micromirror is captured. Changing a micromirror's tilt angle also alters the color spectrum it reflects back to the imaging system and the color of the micromirror image it represents. As a result, OMA can infer the local stiffness of the biomimetic materials through the color change detected on each micromirror. OMA offers the potential for high-throughput stiffness mapping at the tissue-level while maintaining spatial resolution at the cellular level.

Advancing membrane biology: single-molecule approaches meet model membrane systems

Model membrane systems have emerged as essential platforms for investigating membrane-associated processes in controlled environments, mimicking biological membranes without the complexity of cellular systems. However, integrating these model systems with single-molecule techniques remains challenging due to the fluidity of lipid membranes, including undulations and the lateral mobility of lipids and proteins. This mini-review explores the evolution of various model membranes ranging from black lipid membranes to nanodiscs and giant unilamellar vesicles as they adapt to accommodate electrophysiology, force spectroscopy, and fluorescence microscopy. We highlight recent advancements, including innovations in force spectroscopy and single-molecule imaging using free-standing lipid bilayers, and the development of membrane platforms with tunable composition and curvature for improving fluorescence-based studies of protein dynamics. These integrated approaches have provided deep insights into ion channel function, membrane fusion, protein mechanics, and protein dynamics. We highlight how the synergy between single-molecule techniques and model membranes enhances our understanding of complex cellular processes, paving the way for future discoveries in membrane biology and biophysics. [BMB Reports 2025; 58(1): 33-40].

A guide to building a low-cost centrifuge force microscope module for single-molecule force experiments

The ability to apply controlled forces to individual molecules or molecular complexes and observe their behaviors has led to many important discoveries in biology. Instruments capable of probing single-molecule forces typically cost >US$100,000, limiting the use of these techniques. The centrifuge force microscope (CFM) is a low-cost and easy-to-use instrument that enables high-throughput single-molecule studies. By combining the imaging capabilities of a microscope with the force application of a centrifuge, the CFM enables the simultaneous probing of hundreds to thousands of single-molecule interactions using tethered particles. Here we present a comprehensive set of instructions for building a CFM module that fits within a commercial benchtop centrifuge. The CFM module uses a 3D-printed housing, relies on off-the-shelf optical and electrical components, and can be built for less than US$1,000 in about 1 day. We also provide detailed instructions for setting up and running an experiment to measure force-dependent shearing of a short DNA duplex, as well as the software for CFM control and data analysis. The protocol is suitable for users with basic experience in analytical biochemistry and biophysics. The protocol enables the use of CFM-based experiments and may facilitate access to the single-molecule research field.

Image-based force inference by biomechanical simulation

During morphogenesis, cells precisely generate forces that drive cell shape changes and cellular motion. These forces predominantly arise from contractility of the actomyosin cortex, allowing for cortical tension, protrusion formation, and cell division. Image-based force inference can derive such forces from microscopy images, without complicated and time-consuming experimental set-ups. However, current methods do not account for common effects, such as physical confinement and local force generation. Here we propose a force-inference method based on a biophysical model of cell shape, and assess relative cellular surface tension, adhesive tension between cells, as well as cytokinesis and protrusion formation. We applied our method on fluorescent microscopy images of the early C. elegans embryo. Predictions for cell surface tension at the 7-cell stage were validated by measurements using cortical laser ablation. Our non-invasive method facilitates the accurate tracking of force generation, and offers many new perspectives for studying morphogenesis.

Accurate drift-invariant single-molecule force calibration using the Hadamard variance

Single-molecule force spectroscopy (SMFS) techniques play a pivotal role in unraveling the mechanics and conformational transitions of biological macromolecules under external forces. Among these techniques, multiplexed magnetic tweezers (MT) are particularly well suited to probe very small forces, ≤1 pN, critical for studying noncovalent interactions and regulatory conformational changes at the single-molecule level. However, to apply and measure such small forces, a reliable and accurate force-calibration procedure is crucial. Here, we introduce a new approach to calibrate MT based on thermal motion using the Hadamard variance (HV). To test our method, we perform bead-tether Brownian dynamics simulations that mimic our experimental system and compare the performance of the HV method against two established techniques: power spectral density (PSD) and Allan variance (AV) analyses. Our analysis includes an assessment of each method's ability to mitigate common sources of additive noise, such as white and pink noise, as well as drift, which often complicate experimental data analysis. We find that the HV method exhibits overall similar or higher precision and accuracy, yielding lower force estimation errors across a wide range of signal-to-noise ratios (SNRs) and drift speeds compared with the PSD and AV methods. Notably, the HV method remains robust against drift, maintaining consistent uncertainty levels across the entire studied SNR and drift speed spectrum. We also explore the HV method using experimental MT data, where we find overall smaller force estimation errors compared with PSD and AV approaches. Overall, the HV method offers a robust method for achieving sub-pN resolution and precision in multiplexed MT measurements. Its potential extends to other SMFS techniques, presenting exciting opportunities for advancing our understanding of mechanosensitivity and force generation in biological systems. To make our methods widely accessible to the research community, we provide a well-documented Python implementation of the HV method as an extension to the Tweezepy package.

Probing the Nanonewton Mitotic Cell Deformation Force by Ion-Resonance-Enhanced Photonics Force Microscopy

Mechanical forces are essential for regulating dynamic changes in cellular activities. A comprehensive understanding of these forces is imperative for unraveling fundamental mechanisms. Here, we develop a microprobe capable of facilitating the measurement of biological forces up to nanonewton levels in living cells. This probe is designed by coating the core of anatase titania particles with amorphous titania and silica shells and an upconversion nanoparticles (UCNPs) layer. Leveraging both antireflection and ion resonance effects from the shells, the optically trapped probe attains a maximum lateral optical trap stiffness of 14.24 pN μm-1 mW-1, surpassing the best reported value by a factor of 3. Employing this advanced probe in a photonic force microscope, we determine the elasticity modulus of mitotic HeLa cells as 1.27 ± 0.3 kPa. Nanonewton probes offer the potential to explore 3D cellular mechanics with unparalleled precision and spatial resolution, fostering a deeper understanding of the underlying biomechanical mechanisms.

Joint subarray acoustic tweezers enable controllable cell translation, rotation, and deformation

Contactless microscale tweezers are highly effective tools for manipulating, patterning, and assembling bioparticles. However, current tweezers are limited in their ability to comprehensively manipulate bioparticles, providing only partial control over the six fundamental motions (three translational and three rotational motions). This study presents a joint subarray acoustic tweezers platform that leverages acoustic radiation force and viscous torque to control the six fundamental motions of single bioparticles. This breakthrough is significant as our manipulation mechanism allows for controlling the three translational and three rotational motions of single cells, as well as enabling complex manipulation that combines controlled translational and rotational motions. Moreover, our tweezers can gradually increase the load on an acoustically trapped cell to achieve controllable cell deformation critical for characterizing cell mechanical properties. Furthermore, our platform allows for three-dimensional (3D) imaging of bioparticles without using complex confocal microscopy by rotating bioparticles with acoustic tweezers and taking images of each orientation using a standard microscope. With these capabilities, we anticipate the JSAT platform to play a pivotal role in various applications, including 3D imaging, tissue engineering, disease diagnostics, and drug testing.

Tunable Acoustic Tweezer System for Precise Three-Dimensional Particle Manipulation

This study introduces a tunable acoustic tweezer system designed for precise three-dimensional particle trapping and manipulation. The system utilizes a dual-liquid-layer acoustic lens, which enables the dynamic control of the focal length through the adjustable curvature of a latex membrane. This tunability is essential for generating the acoustic forces necessary for effective manipulation of particles, particularly along the direction of acoustic wave propagation (z-axis). Experiments conducted with spherical particles as small as 1.5 mm in diameter demonstrated the system's capability for stable trapping and manipulation. Performance was rigorously evaluated through both z-axis and 3D manipulation tests. In the z-axis experiments, the system achieved a manipulation range of 33.4-53.4 mm, with a root-mean-square error and standard deviation of 0.044 ± 0.045 mm, which highlights its precision. Further, the 3D manipulation experiments showed that particles could be accurately guided along complex paths, including multilayer rectangular and helical trajectories, with minimal deviation. A visual feedback-based particle navigation system significantly enhanced positional accuracy, reducing errors relative to open-loop control. These results confirm that the tunable acoustic tweezer system is a robust tool for applications requiring precise control of particles with diameter of 1.5 mm in three-dimensional environments. Considering its ability to dynamically adjust the focal point and maintain stable trapping, this system is well suited for tasks demanding high precision, such as targeted particle delivery and other applications involving advanced material manipulation.

Acousto-dielectric tweezers enable independent manipulation of multiple particles

Acoustic tweezers have gained substantial interest in biology, engineering, and materials science for their label-free, precise, contactless, and programmable manipulation of small objects. However, acoustic tweezers cannot independently manipulate multiple microparticles simultaneously. This study introduces acousto-dielectric tweezers capable of independently manipulating multiple microparticles and precise control over intercellular distances and cyclical cell pairing and separation for detailed cell-cell interaction analysis. Our acousto-dielectric tweezers leverage the competition between acoustic radiation forces, generated by standing surface acoustic waves (SAWs), and dielectrophoretic (DEP) forces, induced by gradient electric fields. Modulating these fields allows for the precise positioning of individual microparticles at points where acoustic radiation and DEP forces are in equilibrium. This mechanism enables the simultaneous movement of multiple microparticles along specified paths as well as cyclical cell pairing and separation. We anticipate our acousto-dielectric tweezers to have enormous potential in colloidal assembly, cell-cell interaction studies, disease diagnostics, and tissue engineering.

When Force Met Fluorescence: Single-Molecule Manipulation and Visualization of Protein-DNA Interactions

Myriad DNA-binding proteins undergo dynamic assembly, translocation, and conformational changes while on DNA or alter the physical configuration of the DNA substrate to control its metabolism. It is now possible to directly observe these activities-often central to the protein function-thanks to the advent of single-molecule fluorescence- and force-based techniques. In particular, the integration of fluorescence detection and force manipulation has unlocked multidimensional measurements of protein-DNA interactions and yielded unprecedented mechanistic insights into the biomolecular processes that orchestrate cellular life. In this review, we first introduce the different experimental geometries developed for single-molecule correlative force and fluorescence microscopy, with a focus on optical tweezers as the manipulation technique. We then describe the utility of these integrative platforms for imaging protein dynamics on DNA and chromatin, as well as their unique capabilities in generating complex DNA configurations and uncovering force-dependent protein behaviors. Finally, we give a perspective on the future directions of this emerging research field.

Nanoalignment by critical Casimir torques

The manipulation of microscopic objects requires precise and controllable forces and torques. Recent advances have led to the use of critical Casimir forces as a powerful tool, which can be finely tuned through the temperature of the environment and the chemical properties of the involved objects. For example, these forces have been used to self-organize ensembles of particles and to counteract stiction caused by Casimir-Liftshitz forces. However, until now, the potential of critical Casimir torques has been largely unexplored. Here, we demonstrate that critical Casimir torques can efficiently control the alignment of microscopic objects on nanopatterned substrates. We show experimentally and corroborate with theoretical calculations and Monte Carlo simulations that circular patterns on a substrate can stabilize the position and orientation of microscopic disks. By making the patterns elliptical, such microdisks can be subject to a torque which flips them upright while simultaneously allowing for more accurate control of the microdisk position. More complex patterns can selectively trap 2D-chiral particles and generate particle motion similar to non-equilibrium Brownian ratchets. These findings provide new opportunities for nanotechnological applications requiring precise positioning and orientation of microscopic objects.

Optical microscopic imaging, manipulation, and analysis methods for morphogenesis research

Morphogenesis is a developmental process of organisms being shaped through complex and cooperative cellular movements. To understand the interplay between genetic programs and the resulting multicellular morphogenesis, it is essential to characterize the morphologies and dynamics at the single-cell level and to understand how physical forces serve as both signaling components and driving forces of tissue deformations. In recent years, advances in microscopy techniques have led to improvements in imaging speed, resolution and depth. Concurrently, the development of various software packages has supported large-scale, analyses of challenging images at the single-cell resolution. While these tools have enhanced our ability to examine dynamics of cells and mechanical processes during morphogenesis, their effective integration requires specialized expertise. With this background, this review provides a practical overview of those techniques. First, we introduce microscopic techniques for multicellular imaging and image analysis software tools with a focus on cell segmentation and tracking. Second, we provide an overview of cutting-edge techniques for mechanical manipulation of cells and tissues. Finally, we introduce recent findings on morphogenetic mechanisms and mechanosensations that have been achieved by effectively combining microscopy, image analysis tools and mechanical manipulation techniques.

Single-Macromolecule Studies of Eukaryotic Genomic Maintenance

Genomes are self-organized and self-maintained as long, complex macromolecules of chromatin. The inherent heterogeneity, stochasticity, phase separation, and chromatin dynamics of genome operation make it challenging to study genomes using ensemble methods. Various single-molecule force-, fluorescent-, and sequencing-based techniques rooted in different disciplines have been developed to fill critical gaps in the capabilities of bulk measurements, each providing unique, otherwise inaccessible, insights into the structure and maintenance of the genome. Capable of capturing molecular-level details about the organization, conformational changes, and packaging of genetic material, as well as processive and stochastic movements of maintenance factors, a single-molecule toolbox provides an excellent opportunity for collaborative research to understand how genetic material functions in health and malfunctions in disease. In this review, we discuss novel insights brought to genomic sciences by single-molecule techniques and their potential to continue to revolutionize the field-one molecule at a time.

Robot-assisted chirality-tunable acoustic vortex tweezers for contactless, multifunctional, 4-DOF object manipulation

Robotic manipulation of small objects has shown great potential for engineering, biology, and chemistry research. However, existing robotic platforms have difficulty in achieving contactless, high-resolution, 4-degrees-of-freedom (4-DOF) manipulation of small objects, and noninvasive maneuvering of objects in regions shielded by tissue and bone barriers. Here, we present chirality-tunable acoustic vortex tweezers that can tune acoustic vortex chirality, transmit through biological barriers, trap single micro- to millimeter-sized objects, and control object rotation. Assisted by programmable robots, our acoustic systems further enable contactless, high-resolution translation of single objects. Our systems were demonstrated by tuning acoustic vortex chirality, controlling object rotation, and translating objects along arbitrary-shaped paths. Moreover, we used our systems to trap single objects in regions with tissue and skull barriers and translate an object inside a Y-shaped channel of a thick biomimetic phantom. In addition, we showed the function of ultrasound imaging-assisted acoustic manipulation by monitoring acoustic object manipulation via live ultrasound imaging.

Identical sequences, different behaviors: Protein diversity captured at the single-molecule level

The classical "one sequence, one structure, one function" paradigm has shaped much of our intuition of how proteins work inside the cell. Partially due to the insight provided by bulk biochemical assays, individual biomolecules are often assumed to behave as identical entities, and their characterization relies on ensemble averages that flatten any conformational diversity into a unique phenotype. While the emergence of single-molecule techniques opened the gates to interrogating individual molecules, technical shortcomings typically limit the duration of these measurements, which precludes a complete characterization of an individual protein and, hence, capturing the heterogeneity among molecular populations. Here, we introduce an ultrastable magnetic tweezers design, which enables us to measure the folding dynamics of a single protein during several uninterrupted days with high temporal and spatial resolution. Thanks to this instrumental development, we fully characterize the nanomechanics of two proteins with a very distinct force response, the talin R3IVVI domain and protein L. Days-long recordings on the same protein individual accumulate thousands of folding transitions with submicrosecond resolution, allowing us to reconstruct their free energy landscapes and describe how they evolve with force. By mapping the nanomechanical identity of many different protein individuals, we directly capture their molecular diversity as a quantifiable dispersion on their force response and folding kinetics. By significantly expanding the measurable timescales, our instrumental development offers a tool for profiling individual molecules, opening the gates to directly characterizing biomolecular heterogeneity.

Advances in Nanoarchitectonics: A Review of "Static" and "Dynamic" Particle Assembly Methods

Particle assembly is a promising technique to create functional materials and devices from nanoscale building blocks. However, the control of particle arrangement and orientation is challenging and requires careful design of the assembly methods and conditions. In this study, the static and dynamic methods of particle assembly are reviewed, focusing on their applications in biomaterial sciences. Static methods rely on the equilibrium interactions between particles and substrates, such as electrostatic, magnetic, or capillary forces. Dynamic methods can be associated with the application of external stimuli, such as electric fields, magnetic fields, light, or sound, to manipulate the particles in a non-equilibrium state. This study discusses the advantages and limitations of such methods as well as nanoarchitectonic principles that guide the formation of desired structures and functions. It also highlights some examples of biomaterials and devices that have been fabricated by particle assembly, such as biosensors, drug delivery systems, tissue engineering scaffolds, and artificial organs. It concludes by outlining the future challenges and opportunities of particle assembly for biomaterial sciences. This review stands as a crucial guide for scholars and professionals in the field, fostering further investigation and innovation. It also highlights the necessity for continuous research to refine these methodologies and devise more efficient techniques for nanomaterial synthesis. The potential ramifications on healthcare and technology are substantial, with implications for drug delivery systems, diagnostic tools, disease treatments, energy storage, environmental science, and electronics.

Magnetic tweezers characterization of the entropic elasticity of intrinsically disordered proteins and peptoids

Understanding the conformational behavior of biopolymers is essential to unlocking knowledge of their biophysical mechanisms and functional roles. Single-molecule force spectroscopy can provide a unique perspective on this by exploiting entropic elasticity to uncover key biopolymer structural parameters. A particularly powerful approach involves the use of magnetic tweezers, which can easily generate lower stretching forces (0.1-20 pN). For forces at the low end of this range, the elastic response of biopolymers is sensitive to excluded volume effects, and they can be described by Pincus blob elasticity model that allow robust extraction of the Flory polymer scaling exponent. Here, we detail protocols for the use of magnetic tweezers for force-extension measurements of intrinsically disordered proteins and peptoids. We also discuss procedures for fitting low-force elastic curves to the predictions of polymer physics models to extract key conformational parameters.

Horizontal magnetic tweezers and its applications in single molecule micromanipulation experiments

Magnetic tweezers (MTs) have become indispensable tools for gaining mechanistic insights into the behavior of DNA-processing enzymes and acquiring detailed, high-resolution data on the mechanical properties of DNA. Currently, MTs have two distinct designs: vertical and horizontal (or transverse) configurations. While the vertical design and its applications have been extensively documented, there is a noticeable gap in comprehensive information pertaining to the design details, experimental procedures, and types of studies conducted with horizontal MTs. This article aims to address this gap by providing a concise overview of the fundamental principles underlying transverse MTs. It will explore the multifaceted applications of this technique as an exceptional instrument for scrutinizing DNA and its interactions with DNA-binding proteins at the single-molecule level.

Single-molecule tethering methods for membrane proteins

Molecular tethering of a single membrane protein between the glass surface and a magnetic bead is essential for studying the structural dynamics of membrane proteins using magnetic tweezers. However, the force-induced bond breakage of the widely-used digoxigenin-antidigoxigenin tether complex has imposed limitations on its stable observation. In this chapter, we describe the procedures of constructing highly stable single-molecule tethering methods for membrane proteins. These methods are established using dibenzocyclooctyne click chemistry, traptavidin-biotin binding, SpyCatcher-SpyTag conjugation, and SnoopCatcher-SnoopTag conjugation. The molecular tethering approaches allow for more stable observation of structural transitions in membrane proteins under force.

Connecting the dots: key insights on ParB for chromosome segregation from single-molecule studies

Bacterial cells require DNA segregation machinery to properly distribute a genome to both daughter cells upon division. The most common system involved in chromosome and plasmid segregation in bacteria is the ParABS system. A core protein of this system - partition protein B (ParB) - regulates chromosome organization and chromosome segregation during the bacterial cell cycle. Over the past decades, research has greatly advanced our knowledge of the ParABS system. However, many intricate details of the mechanism of ParB proteins were only recently uncovered using in vitro single-molecule techniques. These approaches allowed the exploration of ParB proteins in precisely controlled environments, free from the complexities of the cellular milieu. This review covers the early developments of this field but emphasizes recent advances in our knowledge of the mechanistic understanding of ParB proteins as revealed by in vitro single-molecule methods. Furthermore, we provide an outlook on future endeavors in investigating ParB, ParB-like proteins, and their interaction partners.

Exploring the free energy landscape of proteins using magnetic tweezers

Proteins fold to their native states by searching through the free energy landscapes. As single-domain proteins are the basic building block of multiple-domain proteins or protein complexes composed of subunits, the free energy landscapes of single-domain proteins are of critical importance to understand the folding and unfolding processes of proteins. To explore the free energy landscapes of proteins over large conformational space, the stability of native structure is perturbed by biochemical or mechanical means, and the conformational transition process is measured. In single molecular manipulation experiments, stretching force is applied to proteins, and the folding and unfolding transitions are recorded by the extension time course. Due to the broad force range and long-time stability of magnetic tweezers, the free energy landscape over large conformational space can be obtained. In this article, we describe the magnetic tweezers instrument design, protein construct design and preparation, fluid chamber preparation, common-used measuring protocols including force-ramp and force-jump measurements, and data analysis methods to construct the free energy landscape. Single-domain cold shock protein is introduced as an example to build its free energy landscape by magnetic tweezers measurements.

Introduction to Optical Tweezers: Background, System Designs, and Applications

Optical tweezers are a means to manipulate objects with light. With the technique, microscopically small objects can be held and steered, allowing for accurate measurement of the forces applied to these objects. Optical tweezers can typically obtain a nanometer spatial resolution, a picoNewton force resolution, and a millisecond time resolution, which makes the technique well suited for the study of biological processes from the single-cell down to the single-molecule level. In this chapter, we aim to provide an introduction to the use of optical tweezers for single-molecule analyses. We start from the basic principles and methodology involved in optical trapping, force calibration, and force measurements. Next, we describe the components of an optical tweezers setup and their experimental relevance. Finally, we will provide an overview of the broad applications in context of biological research, with the emphasis on the measurement modes, experimental assays, and possible combinations with fluorescence microscopy techniques.

3D Motion Manipulation for Micro- and Nanomachines: Progress and Future Directions

In the past decade, micro- and nanomachines (MNMs) have made outstanding achievements in the fields of targeted drug delivery, tumor therapy, microsurgery, biological detection, and environmental monitoring and remediation. Researchers have made significant efforts to accelerate the rapid development of MNMs capable of moving through fluids by means of different energy sources (chemical reactions, ultrasound, light, electricity, magnetism, heat, or their combinations). However, the motion of MNMs is primarily investigated in confined two-dimensional (2D) horizontal setups. Furthermore, three-dimensional (3D) motion control remains challenging, especially for vertical movement and control, significantly limiting its potential applications in cargo transportation, environmental remediation, and biotherapy. Hence, an urgent need is to develop MNMs that can overcome self-gravity and controllably move in 3D spaces. This review delves into the latest progress made in MNMs with 3D motion capabilities under different manipulation approaches, discusses the underlying motion mechanisms, explores potential design concepts inspired by nature for controllable 3D motion in MNMs, and presents the available 3D observation and tracking systems.

Surface Functionalization, Nucleic Acid Tether Characterization, and Force Calibration for a Magnetic Tweezers Assay

Magnetic tweezers are a force spectroscopy single-molecule technique. They enable the mechanical manipulation of biomolecules via the means of a magnetic particle under an attractive force applied by a magnetic field source. The magnetic particle is tethered to the glass surface of a flow chamber by the biomolecule, and functionalization strategies have been developed to reduce the nonspecific interactions of either the magnetic particles or biomolecules with the surface. Here, we describe two complementary strategies to achieve a high tether density while reducing the interactions of both the magnetic particle and the biomolecule of interest with the glass surface. Using a large detector CMOS camera, the simultaneous observation of several hundreds of tethered magnetic beads is achievable, allowing high-throughput single-molecule measurements. We further describe here a simple procedure to perform the calibration in force of a magnetic tweezers assay.

An Introduction to Magnetic Tweezers

Magnetic tweezers are a single-molecule force and torque spectroscopy technique that enable the mechanical interrogation in vitro of biomolecules, such as nucleic acids and proteins. They use a magnetic field originating from either permanent magnets or electromagnets to attract a magnetic particle, thus stretching the tethering biomolecule. They nicely complement other force spectroscopy techniques such as optical tweezers and atomic force microscopy (AFM) as they operate as a very stable force clamp, enabling long-duration experiments over a very broad range of forces spanning from 10 fN to 1 nN, with 1-10 milliseconds time and sub-nanometer spatial resolution. Their simplicity, robustness, and versatility have made magnetic tweezers a key technique within the field of single-molecule biophysics, being broadly applied to study the mechanical properties of, e.g., nucleic acids, genome processing molecular motors, protein folding, and nucleoprotein filaments. Furthermore, magnetic tweezers allow for high-throughput single-molecule measurements by tracking hundreds of biomolecules simultaneously both in real-time and at high spatiotemporal resolution. Magnetic tweezers naturally combine with surface-based fluorescence spectroscopy techniques, such as total internal reflection fluorescence microscopy, enabling correlative fluorescence and force/torque spectroscopy on biomolecules. This chapter presents an introduction to magnetic tweezers including a description of the hardware, the theory behind force calibration, its spatiotemporal resolution, combining it with other techniques, and a (non-exhaustive) overview of biological applications.

Methods and Measures for Investigating Microscale Motility

Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks, and theoretical methods, we can begin to probe the complex lives of microscopic motile organisms and answer the intertwining biological and physical questions of how these diverse lifeforms navigate their surroundings. Herein, we summarize the main mechanisms of microscale motility and give an overview of different experimental, analytical, and mathematical methods used to study them across different scales encompassing the molecular-, individual-, to population-level. We identify transferable techniques, pressing challenges, and future directions in the field. This review can serve as a starting point for researchers who are interested in exploring and quantifying the movements of organisms in the microscale world.

Recent insights into eukaryotic double-strand DNA break repair unveiled by single-molecule methods

Genome integrity and maintenance are essential for the viability of all organisms. A wide variety of DNA damage types have been described, but double-strand breaks (DSBs) stand out as one of the most toxic DNA lesions. Two major pathways account for the repair of DSBs: homologous recombination (HR) and non-homologous end joining (NHEJ). Both pathways involve complex DNA transactions catalyzed by proteins that sequentially or cooperatively work to repair the damage. Single-molecule methods allow visualization of these complex transactions and characterization of the protein:DNA intermediates of DNA repair, ultimately allowing a comprehensive breakdown of the mechanisms underlying each pathway. We review current understanding of the HR and NHEJ responses to DSBs in eukaryotic cells, with a particular emphasis on recent advances through the use of single-molecule techniques.

Profiling to Probing: Atomic force microscopy to characterize nano-engineered implants

Surface modification of implants in the nanoscale or implant nano-engineering has been recognized as a strategy for augmenting implant bioactivity and achieving long-term implant success. Characterizing and optimizing implant characteristics is crucial to achieving desirable effects post-implantation. Modified implant enables tailored, guided and accelerated tissue integration; however, our understanding is limited to multicellular (bulk) interactions. Finding the nanoscale forces experienced by a single cell on nano-engineered implants will aid in predicting implants' bioactivity and engineering the next generation of bioactive implants. Atomic force microscope (AFM) is a unique tool that enables surface characterization and understanding of the interactions between implant surface and biological tissues. The characterization of surface topography using AFM to gauge nano-engineered implants' characteristics (topographical, mechanical, chemical, electrical and magnetic) and bioactivity (adhesion of cells) is presented. A special focus of the review is to discuss the use of single-cell force spectroscopy (SCFS) employing AFM to investigate the minute forces involved with the adhesion of a single cell (resident tissue cell or bacterium) to the surface of nano-engineered implants. Finally, the research gaps and future perspectives relating to AFM-characterized current and emerging nano-engineered implants are discussed towards achieving desirable bioactivity performances. This review highlights the use of advanced AFM-based characterization of nano-engineered implant surfaces via profiling (investigating implant topography) or probing (using a single cell as a probe to study precise adhesive forces with the implant surface). STATEMENT OF SIGNIFICANCE: Nano-engineering is emerging as a surface modification platform for implants to augment their bioactivity and achieve favourable treatment outcomes. In this extensive review, we closely examine the use of Atomic Force Microscopy (AFM) to characterize the properties of nano-engineered implant surfaces (topography, mechanical, chemical, electrical and magnetic). Next, we discuss Single-Cell Force Spectroscopy (SCFS) via AFM towards precise force quantification encompassing a single cell's interaction with the implant surface. This interdisciplinary review will appeal to researchers from the broader scientific community interested in implants and cell adhesion to implants and provide an improved understanding of the surface characterization of nano-engineered implants.

Review of Ultrasonic Particle Manipulation Techniques: Applications and Research Advances

Ultrasonic particle manipulation technique is a non-contact label-free method for manipulating micro- and nano-scale particles using ultrasound, which has obvious advantages over traditional optical, magnetic, and electrical micro-manipulation techniques; it has gained extensive attention in micro-nano manipulation in recent years. This paper introduces the basic principles and manipulation methods of ultrasonic particle manipulation techniques, provides a detailed overview of the current mainstream acoustic field generation methods, and also highlights, in particular, the applicable scenarios for different numbers and arrangements of ultrasonic transducer devices. Ultrasonic transducer arrays have been used extensively in various particle manipulation applications, and many sound field reconstruction algorithms based on ultrasonic transducer arrays have been proposed one after another. In this paper, unlike most other previous reviews on ultrasonic particle manipulation, we analyze and summarize the current reconstruction algorithms for generating sound fields based on ultrasonic transducer arrays and compare these algorithms. Finally, we explore the applications of ultrasonic particle manipulation technology in engineering and biological fields and summarize and forecast the research progress of ultrasonic particle manipulation technology. We believe that this review will provide superior guidance for ultrasonic particle manipulation methods based on the study of micro and nano operations.

Single-Molecule Force Spectroscopy of Membrane Protein Folding

Single-molecule force spectroscopy is a unique method that can probe the structural changes of single proteins at a high spatiotemporal resolution while mechanically manipulating them over a wide force range. Here, we review the current understanding of membrane protein folding learned by using the force spectroscopy approach. Membrane protein folding in lipid bilayers is one of the most complex biological processes in which diverse lipid molecules and chaperone proteins are intricately involved. The approach of single protein forced unfolding in lipid bilayers has produced important findings and insights into membrane protein folding. This review provides an overview of the forced unfolding approach, including recent achievements and technical advances. Progress in the methods can reveal more interesting cases of membrane protein folding and clarify general mechanisms and principles.

Swirl-like Acoustofluidic Stirring Facilitates Microscale Reactions in Sessile Droplets

Sessile droplets play a crucial role in the microreactors of biochemical samples. Acoustofluidics provide a non-contact and label-free method for manipulating particles, cells, and chemical analytes in droplets. In the present study, we propose a micro-stirring application based on acoustic swirls in sessile droplets. The acoustic swirls are formed inside the droplets by asymmetric coupling of surface acoustic waves (SAWs). With the merits of the slanted design of the interdigital electrode, the excitation position of SAWs is selective by sweeping in wide frequency ranges, allowing for the droplet position to be customized within the aperture region. We verify the reasonable existence of acoustic swirls in sessile droplets by a combination of simulations and experiments. The different periphery of the droplet meeting with SAWs will produce acoustic streaming phenomena with different intensities. The experiments demonstrate that acoustic swirls formed after SAWs encountering droplet boundaries will be more obvious. The acoustic swirls have strong stirring abilities to rapidly dissolve the yeast cell powder granules. Therefore, acoustic swirls are expected to be an effective means for rapid stirring of biomolecules and chemicals, providing a new approach to micro-stirring in biomedicine and chemistry.

Effect of Flow Rate and Ionic Strength on the Stabilities of YOYO-1 and YO-PRO-1 Intercalated in DNA Molecules

Single-molecule DNA studies have improved our understanding of the DNAs' structure and their interactions with other molecules. A variety of DNA labeling dyes are available for single-molecule studies, among which the bis-intercalating dye YOYO-1 and mono-intercalating dye YO-PRO-1 are widely used. They have an extraordinarily strong affinity toward DNA and are bright with a high quantum yield (>0.5) when bound to DNAs. However, it is still not clear how these dyes behave in DNA molecules under higher ionic strength and strong buffer flow. Here, we have studied the effect of ionic strength and flow rate of buffer on their binding in single DNA molecules. The larger the flow rate and the higher the ionic strength, the faster the intercalated dyes are washed away from the DNAs. In the buffer with 1 M ionic strength, YOYO-1 and YO-PRO-1 are mostly washed away from DNA within 2 min of moderate buffer flow.

Looking at Biomolecular Interactions through the Lens of Correlated Fluorescence Microscopy and Optical Tweezers

Understanding complex biological events at the molecular level paves the path to determine mechanistic processes across the timescale necessary for breakthrough discoveries. While various conventional biophysical methods provide some information for understanding biological systems, they often lack a complete picture of the molecular-level details of such dynamic processes. Studies at the single-molecule level have emerged to provide crucial missing links to understanding complex and dynamic pathways in biological systems, which are often superseded by bulk biophysical and biochemical studies. Latest developments in techniques combining single-molecule manipulation tools such as optical tweezers and visualization tools such as fluorescence or label-free microscopy have enabled the investigation of complex and dynamic biomolecular interactions at the single-molecule level. In this review, we present recent advances using correlated single-molecule manipulation and visualization-based approaches to obtain a more advanced understanding of the pathways for fundamental biological processes, and how this combination technique is facilitating research in the dynamic single-molecule (DSM), cell biology, and nanomaterials fields.

Noncontact Manipulation of Intracellular Structure Based on Focused Surface Acoustic Waves

Cell orientation is essential in many applications in biology, medicine, and chemistry, such as cellular injection, intracellular biopsy, and genetic screening. However, the manual cell orientation technique is a trial-and-error approach, which suffers from low efficiency and low accuracy. Although several techniques have improved these issues to a certain extent, they still face problems deforming or disrupting cell membranes, physical damage to the intracellular structure, and limited particle size. This study proposes a noncontact and noninvasive cell orientation method that rotates a cell using surface acoustic waves (SAWs). To realize the acoustic cell orientation process, we have fabricated a microdevice consisting of two pairs of focused interdigital transducers (FIDTs). Instead of rotating the entire cell, the proposed method rotates the intracellular structure, the cytoplasm, directly through the cell membrane by acoustic force. We have tested the rotational manipulation process on 30 zebrafish embryos. The system was able to orientate a cell to a target orientation with a one-time success rate of 93%. Furthermore, the postoperation survival rate was 100%. Our acoustic rotational manipulation technique is noninvasive and easy to use, which provides a starting point for cell-manipulation-essential tasks, such as single-cell analysis, organism studies, and drug discovery.

Few-shot deep learning for AFM force curve characterization of single-molecule interactions

Deep learning (DL)-based analytics has the scope to transform the field of atomic force microscopy (AFM) with regard to fast and bias-free measurement characterization. For example, AFM force-distance curves can help estimate important parameters of binding kinetics, such as the most probable rupture force, binding probability, association, and dissociation constants, as well as receptor density on live cells. Other than the ideal single-rupture event in the force-distance curves, there can be no-rupture, double-rupture, or multiple-rupture events. The current practice is to go through such datasets manually, which can be extremely tedious work for the experimentalists. We address this issue by adopting a few-shot learning approach to build sample-efficient DL models that demonstrate better performance than shallow ML models while matching the performance of moderately trained humans. We also release our AFM force curve dataset and annotations publicly as a benchmark for the research community.

Emerging Diamond Quantum Sensing in Bio-Membranes

Bio-membranes exhibit complex but unique mechanical properties as communicative regulators in various physiological and pathological processes. Exposed to a dynamic micro-environment, bio-membranes can be seen as an intricate and delicate system. The systematical modeling and detection of their local physical properties are often difficult to achieve, both quantitatively and precisely. The recent emerging diamonds hosting quantum defects (i.e., nitrogen-vacancy (NV) center) demonstrate intriguing optical and spin properties, together with their outstanding photostability and biocompatibility, rendering them ideal candidates for biological applications. Notably, the extraordinary spin-based sensing enable the measurements of localized nanoscale physical quantities such as magnetic fields, electrical fields, temperature, and strain. These nanoscale signals can be optically read out precisely by simple optical microscopy systems. Given these exclusive properties, NV-center-based quantum sensors can be widely applied in exploring bio-membrane-related features and the communicative chemical reaction processes. This review mainly focuses on NV-based quantum sensing in bio-membrane fields. The attempts of applying NV-based quantum sensors in bio-membranes to investigate diverse physical and chemical events such as membrane elasticity, phase change, nanoscale bio-physical signals, and free radical formation are fully overviewed. We also discuss the challenges and future directions of this novel technology to be utilized in bio-membranes.

Single-molecule fluorescence imaging techniques reveal molecular mechanisms underlying deoxyribonucleic acid damage repair

Advances in single-molecule techniques have uncovered numerous biological secrets that cannot be disclosed by traditional methods. Among a variety of single-molecule methods, single-molecule fluorescence imaging techniques enable real-time visualization of biomolecular interactions and have allowed the accumulation of convincing evidence. These techniques have been broadly utilized for studying DNA metabolic events such as replication, transcription, and DNA repair, which are fundamental biological reactions. In particular, DNA repair has received much attention because it maintains genomic integrity and is associated with diverse human diseases. In this review, we introduce representative single-molecule fluorescence imaging techniques and survey how each technique has been employed for investigating the detailed mechanisms underlying DNA repair pathways. In addition, we briefly show how live-cell imaging at the single-molecule level contributes to understanding DNA repair processes inside cells.

Equilibrium fluctuations of DNA plectonemes

Plectonemes are intertwined helically looped domains which form when a DNA molecule is supercoiled, i.e., over- or underwound. They are ubiquitous in cellular DNA, and their physical properties have attracted significant interest both from the experimental side and from the modeling side. In this paper, we investigate fluctuations of the end-point distance z of supercoiled linear DNA molecules subject to external stretching forces. Our analysis is based on a two-phase model, which describes the supercoiled DNA as composed of a stretched phase and a plectonemic phase. A variety of mechanisms are found to contribute to extension fluctuations, characterized by the variance 〈Δz^{2}〉. We find the dominant contribution to 〈Δz^{2}〉 to originate from phase-exchange fluctuations, the transient shrinking and expansion of plectonemes, which is accompanied by an exchange of molecular length between the two phases. We perform Monte Carlo simulations of the twistable wormlike chain and analyze the fluctuation of various quantities, the results of which are found to agree with the two-phase model predictions. Furthermore, we show that the extension and its variance at high forces are very well captured by the two-phase model, provided that one goes beyond quadratic approximations.

Frontiers in single cell analysis: multimodal technologies and their clinical perspectives

Single cell multimodal analysis is at the frontier of single cell research: it defines the roles and functions of distinct cell types through simultaneous analysis to provide unprecedented insight into cellular processes. Current single cell approaches are rapidly moving toward multimodal characterizations. It replaces one-dimensional single cell analysis, for example by allowing for simultaneous measurement of transcription and post-transcriptional regulation, epigenetic modifications and/or surface protein expression. By providing deeper insights into single cell processes, multimodal single cell analyses paves the way to new understandings in various cellular processes such as cell fate decisions, physiological heterogeneity or genotype-phenotype linkages. At the forefront of this, microfluidics is key for high-throughput single cell analysis. Here, we present an overview of the recent multimodal microfluidic platforms having a potential in biomedical research, with a specific focus on their potential clinical applications.

A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices

Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.

Efficient golden gate assembly of DNA constructs for single molecule force spectroscopy and imaging

Single-molecule techniques such as optical tweezers and fluorescence imaging are powerful tools for probing the biophysics of DNA and DNA-protein interactions. The application of these methods requires efficient approaches for creating designed DNA structures with labels for binding to a surface or microscopic beads. In this paper, we develop a simple and fast technique for making a diverse range of such DNA constructs by combining PCR amplicons and synthetic oligonucleotides using golden gate assembly rules. We demonstrate high yield fabrication of torsionally-constrained duplex DNA up to 10 kbp in length and a variety of DNA hairpin structures. We also show how tethering to a cross-linked antibody substrate significantly enhances measurement lifetime under high force. This rapid and adaptable fabrication method streamlines the assembly of DNA constructs for single molecule biophysics.

Programmable motion control and trajectory manipulation of microparticles through tri-directional symmetrical acoustic tweezers

Acoustic tweezers based on travelling surface acoustic waves (TSAWs) have the potential for contactless trajectory manipulation and motion-parameter regulation of microparticles in biological and microfluidic applications. Here, we present a novel design of a tri-directional symmetrical acoustic tweezers device that enables the precise manipulation of linear, clockwise, and anticlockwise trajectories of microparticles. By switching the excitation combinations of interdigital electrodes (IDTs), various shape patterns of acoustic pressure fields can be formed to capture and steer microparticles accurately according to pre-defined trajectories. Numerical simulations and experimental tests were conducted in this study. By adjusting the input electric signals and the fluid's viscosity, the device is able to manipulate microparticles of various forms as well as brine shrimp egg cells with the accurate modulation of motion parameters. The results show that the proposed programmable design possesses low-cost, compact, non-contact, and high biocompatibility benefits, with the capacity to accurately manage microparticles in a range of motion trajectories, independent of their physical and/or chemical characteristics. Thus, our design has strong potential applications in chemical composition analysis, drug delivery, and cell assembly.

Acoustically manipulating internal structure of disk-in-sphere endoskeletal droplets

Manipulation of micro/nano particles has been well studied and demonstrated by optical, electromagnetic, and acoustic approaches, or their combinations. Manipulation of internal structure of droplet/particle is rarely explored and remains challenging due to its complicated nature. Here we demonstrated the manipulation of internal structure of disk-in-sphere endoskeletal droplets using acoustic wave. We developed a model to investigate the physical mechanisms behind this interesting phenomenon. Theoretical analysis of the acoustic interactions indicated that these assembly dynamics arise from a balance of the primary and secondary radiation forces. Additionally, the disk orientation was found to change with acoustic driving frequency, which allowed on-demand, reversible adjustment of the disk orientations with respect to the substrate. This dynamic behavior leads to unique reversible arrangements of the endoskeletal droplets and their internal architecture, which may provide an avenue for directed assembly of novel hierarchical colloidal architectures and intracellular organelles or intra-organoid structures.

Endoskeletal droplets are a class of complex colloids containing a solid internal phase cast within a liquid emulsion droplet. Here, authors show acoustic manipulation of solid disks inside liquid droplets whose orientation can be externally controlled with the frequency.

High-resolution Single-molecule Magnetic Tweezers

Single-molecule magnetic tweezers deliver magnetic force and torque to single target molecules, permitting the study of dynamic changes in biomolecular structures and their interactions. Because the magnetic tweezer setups can generate magnetic fields that vary slowly over tens of millimeters-far larger than the nanometer scale of the single molecule events being observed-this technique can maintain essentially constant force levels during biochemical experiments while generating a biologically meaningful force on the order of 1-100 pN. When using bead-tether constructs to pull on single molecules, smaller magnetic beads and shorter submicrometer tethers improve dynamic response times and measurement precision. In addition, employing high-speed cameras, stronger light sources, and a graphics programming unit permits true high-resolution single-molecule magnetic tweezers that can track nanometer changes in target molecules on a millisecond or even submillisecond time scale. The unique force-clamping capacity of the magnetic tweezer technique provides a way to conduct measurements under near-equilibrium conditions and directly map the energy landscapes underlying various molecular phenomena. High-resolution single-molecule magnetic tweezers can thus be used to monitor crucial conformational changes in single-protein molecules, including those involved in mechanotransduction and protein folding. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.