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PRIMER Scanning probe microscopy Ke Bian 1, Christoph Gerber2, Andreas J. Heinrich 3,4 , Daniel J. Müller 5 , Simon Scheuring 6,7 and Ying Jiang 1,8,9,10 ✉ Abstract | Scanning probe microscopy (SPM), a key invention in nanoscience, has by now been extended to a wide spectrum of basic and applied fields. Its application to basic science led to a paradigm shift in the understanding and perception of matter at its nanoscopic and even atomic levels. SPM uses a sharp tip to physically raster-scan samples and locally collect information from the surface. Various signals can be directly detected by SPM in real space with atomic or nanoscale resolution, which provides insights into the structural, electronic, vibrational, optical, magnetic, (bio)chemical and mechanical properties. This Primer introduces the key aspects and general features of SPM and SPM set-up and variations, with particular focus on scanning tunnelling microscopy and atomic force microscopy. We outline how to conduct SPM experiments, as well as data analysis of SPM imaging, spectroscopy and manipulation. Recent applications of SPM to physics, chemistry, materials science and biology are then highlighted, with representative examples. We outline issues with reproducibility, and standards on open data are discussed. This Primer also raises awareness of the ongoing challenges and possible ways to overcome these difficulties, followed by an outlook of future possible directions. Tunnelling current Visualizing atoms on a solid surface has been a long- changed researchers’ perception and understanding The current created from standing dream for researchers, and was finally fulfilled of matter at atomic or molecular levels. It doubtlessly electrons tunnelling through a by the invention of scanning tunnelling microscopy opened up new possibilities and avenues in physics, finite barrier that is forbidden (STM) in 1981 by Rohrer, Binnig and Gerber at IBM chemistry, materials science, biology and medicine, in the classic regime. Zürich1. STM uses an atomically sharp biased metal tip and stimulates increasing numbers of students and Raster-scanning to collect tiny currents from the metal surface, based researchers around the world. A rectangular pattern of image on the quantum mechanical effect termed tunnelling SPM would not be possible without the piezoelectric capture and reconstruction. (Fig. 1a). Owing to the highly localized nature of the effect, that is, the deformation of materials as the result tunnelling current, atomically resolved images could be of applying an electric field. The effect enables scanning Tip–sample junction The tunnelling junction obtained by raster-scanning the tip over the surface while with picometre precision by simply applying voltages between the tip and the using a feedback loop to keep the tunnelling current con- to piezo elements. The core of the SPM is the scanner, sample where electrons stant. Soon after the invention of STM, Binnig et al. were which allows stably approaching the tip to the surface tunnel through a finite barrier able to map the tip–sample interaction by atomic forces from a macroscopic distance to the nanometre scale. An in between. instead of the tunnelling current, which led to the birth atomically sharp tip is another key component of SPM Piezoelectric effect of atomic force microscopy (AFM)2 (Fig. 1b). AFM is able ultimately determining the lateral resolution. In addi- The effect showing a finite to image almost any type of surface, unlike STM that tion, vibrational isolation and high-gain, low-noise sig- induced voltage on both sides requires conducting or semiconducting samples. AFM nal amplifiers are also critical for achieving a sufficiently of a material when a specific and STM take advantage of different feedback signals to high signal to noise ratio to ensure atomically resolved pressure is applied on it. maintain the tip–sample interaction, but the basic prin- images by SPM. ciple of operation is similar in both techniques and rem- This Primer starts by introducing the technical aspects iniscent of a record player, where a tip senses the surface of SPM (Experimentation) and the general features of topography of the sample via physical raster-scanning. SPM data (Results). The applications of SPM to physics, A large family of scanning probe microscopy (SPM) chemistry, materials science and biology are then high- methods have emerged as variations of STM and AFM, lighted with some representative examples (Applications). by integrating nanosensors on the tip or coupling vari- Afterwards, we discuss issues with reproducibility and ous electromagnetic waves with the tip–sample junction. field standards on open data (Reproducibility and data The measurable physical quantities range from the elec- deposition). We also point out the limitations of SPM and ✉e-mail: yjiang@pku.edu.cn tric current, force and capacitance to photons, magnetic/ possible ways to overcome those difficulties (Limitations https://doi.org/10.1038/ electric field, strain and temperature. The emergence and optimizations). Finally, some possible future s43586-021-00033-2 of SPM in the then-fledgling field of nanotechnology directions of SPM are envisaged (Outlook). NATURE REvIEWS | METHoDS PRimERS | Article citation ID: (2021) 1:36 1 0123456789();:
Primer Author addresses tunnelling current. Vibrational noise, such as shaking of the laboratory floor and/or the vacuum chambers, must 1 International Center for Quantum Materials, School of Physics, Peking University, be reduced. The STM system must be built with a rigid Beijing, P. R. China. scanner head that minimizes changes to the tip–sample 2 Swiss Nanoscience Institute (SNI), Institute of Physics, University of Basel, Basel, distance, as some external shaking of the scanner head Switzerland. is unavoidable. Therefore, the equipment should be kept 3 Center for Quantum Nanoscience, Institute for Basic Science (IBS), Seoul, Republic of Korea. on a very quiet laboratory floor, usually the basement 4 Department of Physics, Ewha Womans University, Seoul, Republic of Korea. of the building. The lowest vibration levels are achieved 5 Department of Biosystems Science and Engineering, Eidgenössische Technische in custom facilities built using heavy (100 ton) concrete Hochschule (ETH) Zürich, Basel, Switzerland. blocks floating on special air springs, for example, at the 6 Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA. Precision Laboratory of the Max Planck Institute for 7 Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA. Solid State Research4. A custom building with a heavy 8 Collaborative Innovation Center of Quantum Matter, Beijing, P. R. China. concrete floor that is isolated from other buildings 9 Interdisciplinary Institute of Light-Element Quantum Materials and Research Center can also provide low vibration levels. However, even a for Light-Element Advanced Materials, Peking University, Beijing, P. R. China. well-built general laboratory building can have low lev- 10 CAS Center for Excellence in Topological Quantum Computation, University of Chinese els of vibration below 10 Hz (the IBM Almaden labora- Academy of Sciences, Beijing, P. R. China. tory), despite the increased floor-level vibrations above 10 Hz (Fig. 2c). Experimentation Quiet laboratory space must be complemented In this section, we introduce the basics of STM and AFM with a rigid STM scanner design with high mechani- experimental set-ups, including the key components to cal resonance frequencies (Fig. 2b), which makes the achieve high spatial resolution, the working principle microscope resistant against low-frequency shaking. and a guide to conduct SPM experiments. We also intro- In practice, the lowest frequencies of the STM scan head duce some representative SPM variations based on STM are found at 1–5 kHz; such a scan head is good at reject- and AFM, which can map out various physical quanti- ing low-frequency vibrational noise from the building ties besides current and force. The sensing mechanism, but it is important to limit higher-frequency mechanical advantages and applications of those SPM variations are noise sources, which can be effectively reduced by soft briefly discussed. springs combined with eddy current damping (Fig. 2a). In practice, a properly built scanner head in a low-noise Scanning tunnelling microscopy laboratory can reduce tip–sample shaking well below STM has at its heart a very simple idea: a metal needle 1 pm, which limits the fluctuation of the detected tunnel that is sharpened to a single atom is approached very current within several per cent. close to a surface while a biased voltage between the tip It is seemingly an impossible task to move the STM and the surface is applied. When the tip–sample distance tip by atomic-scale dimensions without adding noise, reaches the atomic-scale range, some electrons will jump but this has been made possible with the use of piezo- between the tip and the sample, known as the tunnel- electric materials such as lead zirconate or lead titanate ling current. The tunnelling current is sensitive to the ceramics1. A typical piezoelectric material used in STM tip–sample distance; it has exponential dependence on will change its size by about 1 nm when a voltage of 1 V the tip–sample distance. For example, in a clean vacuum is applied across its sides1. Hence, stable high-voltage tunnel junction, the tunnelling current decreases by a sources can hold the tip stable to better than 1 pm while factor of ten when the tip–sample distance increases by allowing a maximum scan range around 1 μm. However, 0.1 nm (the typical tip–sample distance is in the range as for STM systems under ultra-high vacuum (UHV) 0.3–1 nm). This effect gives STM its atomic-scale lateral conditions, it is necessary to change samples without spatial resolution as the majority of the tunnelling current opening the vacuum chamber. The tip must be moved at stems from only the last atom of the tip apex3 (Fig. 1a). least 1 mm away from the sample before the sample can The STM tip is usually attached to piezoelectric con- be extracted. Although piezoelectric materials are good trol elements that allow the tip to be moved with atomic- at atomic-scale length changes, they cannot provide scale precision (Fig. 2a,b). In almost all STM systems, the such large displacements; instead, this task is achieved tip and the sample should be replaced with new ones by the coarse approach mechanism with a type of piezo in a convenient manner without violently changing the motor, which is the kernel component of the STM scan- STM configuration. Generally, STMs are very sensitive ner head (Fig. 2b). The action of such a motor can be to noise, which includes electronic noise and vibra- easily visualized: the tip is held on a body — often made tional noise from the laboratory environment. Here, we from a ceramic — which is mounted on piezoelectric Biased voltage focus on controlling some of these noise sources, from materials. When the piezo materials move slowly, The DC voltage applied to the large to atomic scale. The scanner head of the micro- the ceramic body will follow. However, when the piezo tunnelling junction, either on the sample or on the tip. scope, or the STM body, has macroscopic dimensions materials move rapidly (>100 nm in 10 µs), the body will typically in the range of a few centimetres. By contrast, hold still owing to its inertia. Each step gives a motion in Eddy current the tip–sample distance is often smaller than 1 nm. the range of 100 nm. This process can then be repeated Loops of electrical current Ideally, the tip–sample distance is kept stable at approx- many thousands of times to arrive at a macroscopic induced within a conductor by changing the magnetic field imately 1 pm. As the tunnelling current is sensitive to motion. Such a stick–slip motion5,6 is reliable in provid- through this conductor based the tip–sample distance (and, hence, to fluctuations in ing coarse motion in the range of a few millimetres, but on Faraday’s law of induction. this distance), mechanical shaking causes noise in the is among the most difficult parts of STM design as it is 2 | Article citation ID: (2021) 1:36 www.nature.com/nrmp 0123456789();:
Primer Mechanical resonance challenging to provide a rigid enough movable motor Atomic force microscopy frequency with mechanical resonance frequency larger than several As STM can only probe conductive surfaces relying on The frequency at which a kilohertz. The well-known types of motor for the coarse the tunnelling current, AFM was conceived to extend mechanical system vibrates approach include the louse type7, beetle type5, Pan type6 atomic resolution to non-conducting surfaces2. The with greater amplitude than it does at other frequencies, and various single-tube types. advantage of AFM is that it can be employed in a vacuum, generally determined by the There is no way to sharpen the tip to a single atom, an ambient atmosphere and a liquid, and from high to stiffness and mass of this and so in situ protocols have been developed for this ultra-low temperatures. AFM shares many basic features mechanical system. task. Most often, we start with either a cut platinum/ and key components with STM, such as the vibrational iridium wire or with an etched tungsten wire8. A cut wire isolation, scanning process, coarse-approaching mech- Quantum corrals The barriers constructed by has the advantage of fewer oxide films on its surface, anism and tip treatments. However, as AFM detects individually positioning the iron whereas an etched tip has a much better macroscopic local force instead of the tunnelling current, there are adatom through the scanning shape. The platinum/iridium tip can be produced by some differences in the signal acquisition and the feed- tunnelling microscopy tip. mechanical cutting or electrochemical etching, whereas back loop (Fig. 1b). In AFM, a tip is mounted at the end Local force the tungsten tip can only be made by etching owing to of a flexible cantilever, which deflects linearly with the The local interaction between tungsten’s brittleness. For most STM measurements, the force applied. Contact mode AFM measures tiny deflec- the atoms on the tip apex overall shape of the tip does not matter as the tunnel- tions of the scanning cantilever and uses a force-feedback and the surface within a ling only occurs from the atom or cluster of atoms at the circuit to move the sample or tip held by a piezoelec- volume of several cubic very end of the tip. However, for some applications — tric element in the z direction (maintaining a constant nanometres. most notably optical experiments — the macroscopic tip–sample distance) to keep the deflection, and thus the Dynamical AFM shape can have a pronounced effect on the plasmonic applied force, constant. Plotting the z-direction position A type of atomic force enhancement of Raman scattering and fluorescence9. (height) of the scanned surface pixel by pixel provides the microscopy (AFM) where Lower temperatures are desirable for STM because sample topography. An important development for AFM an oscillator (for example, cantilever, tuning fork) works of improved stability compared with room tempera- was the optical lever system18, which reflects a laser beam at its resonance frequency, ture, as well as higher energy resolution owing to the on the backside of the cantilever to efficiently magnify the detecting interactions between smaller thermal broadening of the electrons in both tiny cantilever deflections resulting from the interactions the tip and the sample the tip and the sample. Eigler introduced a machine of the tip and the sample (Fig. 3a), thus largely enhanc- through the changes of with a stable design operating at about 5 K reaching ing the signal to noise ratio during data acquisition. An frequency, amplitude and energy compensation of this a tip–sample distance noise below 1 pm, which was important development towards enabling biological AFM oscillator. used to build quantum corrals10 and move individual was the invention of a liquid cell in which the cantilever atoms11,12. Eventually, lower operating temperatures — and the sample are immersed in physiological solution19. down to 10 mK (ref. 13 ) — were achieved; such Dynamical AFM uses oscillating cantilevers20. Concomi ultra-low-temperature STM is also functional under tant amplitude modulation modes (for example, ‘inter- high magnetic fields up to 30 T (ref.14). On the other mittent contact’, ‘tapping’ or ‘oscillating’ mode) use extreme, STM has been used to image the growth of feedback controls to oscillate the cantilever at resonant materials in situ at temperatures up to several hundred frequency and constant amplitude21 (Fig. 3b). Other oscil- degrees Celsius15. STM has also been used to study cata- lating modes apply frequency (frequency modulation) or lytic processes under near-ambient pressures16. Whereas phase (phase modulation) for feedback control (Fig. 3b). operation of STM in air is often complicated owing to Such dynamic modes control the tip–sample interaction the presence of water films on the surfaces of samples, more gently compared with static AFM modes so that STM can work in a more stable manner at a solid–liquid interaction forces are minimized. interface, where both the potential stability and the Frequency modulation AFM (FM-AFM) is used chemical composition inside the aqueous environments for UHV and low-temperature physics22, as well as for are well controlled17. biological applications23. FM-AFM is usually more a b Sharp metal tip Cantilever I V e– Force Sample Fig. 1 | Basic set-up for scanning probe microscopy. Scanning tunnelling microscopy (STM) and atomic force microscopy (AFM) both use a tip to scan the sample. Both techniques use different feedback signals to maintain constant tip–sample interaction, but their basic principle of operation and image acquisition mechanisms are similar. a | STM collects the tunnelling current between the tip apex and the sample when a bias voltage is applied. b | AFM detects local forces and corresponding mechanical parameters through a spring-like cantilever. NATURE REvIEWS | METHoDS PRimERS | Article citation ID: (2021) 1:36 3 0123456789();:
Primer a Phase f2 – f1 f2 + f1 V0(f2,t) shifter ~ φ V Vibration Constant current isolation z V0(f2,t,φ) f V(f1,t) Constant height STS DC output Coarse Multiplier Low-pass filter motor Time 3D High voltage PID scanner Preamplifier output Bias x y z Tunnelling Raster-scan Summator current Magnet Controller Damping Data Analogue input Modulator b c 10–5 10–6 1/3 octave spectral density RMS velocity (m s–1) Tip Coarse motor 10–7 Sample 10–8 10–9 10–10 1 10 100 Frequency (Hz) IBM Almaden QNS floor IBM ETH Zurich QNS block MPI Stuttgart Fig. 2 | Scanning tunnelling microscopy set-up. a | Scanning tunnelling microscopy (STM) set-up consisting of a coarse motor, three-dimensional (3D) scanner, vibration isolation device, damping device, preamplifier and controller unit. The frame shields the external electric noise. The proportional integral differential unit (PID) is used for controlling the tip–sample distance in constant current operational mode. Inset: schematic showing lock-in for scanning tunnelling spectroscopy (STS) measurements. The basic electric circuit demonstrates both the process of modulations and its corresponding demodulations, where V is the modulated signal and V0 is the reference. b | Photograph of STM scan head with tip, sample on sample holder and slip–stick walker, all mounted on a metal base plate. c | Vibration levels in various STM laboratories from around the world between 1 and 200 Hz. y axis represents the velocity scaled in a fashion typical for architectural comparisons. The lowest vibration levels are dependent on floating concrete blocks (IBM ETH Zurich, MPI Stuttgart, QNS block), high-quality basement levels of laboratory buildings (QNS floor) and regular basement-level laboratory floors (IBM Almaden). RMS, root mean square. Part c reprinted with permission from ref.4, Royal Society of Chemistry. precise than amplitude modulation AFM, as the time It is more challenging to obtain high-resolution images and frequency can be measured with higher accuracy in AFM systems, as forces have multiple long-range and than amplitude changes. However, force detection by short-range components and the force–distance rela- amplitude modulation AFM is simpler and faster, and tion between tip and sample can be more complicated Temporal resolution the amplitude changes with the tip–sample distance in than the current–distance relation in STM26,27. Presently, The duration of time for acquisition or capture of a a nearly monotonic manner. Time-lapse AFM imaging subatomic details such as orbitals or chemical bonds can single event in measurements. can monitor cellular machines at work at the nanoscale be observed by probing short-range forces with chem- level24. When using a small cantilever with a high res- ically functionalized tips in high vacuum. Meanwhile, Functionalized tips onant frequency, time-lapse AFM can work at much researchers developed a plethora of new AFM-based Modified tips with a single molecule or specific clusters in faster speeds, which allows observation of machinery approaches to probe chemical, magnetic and friction order to make the tip adapted at a temporal resolution of ~100 ms (ref.25); this set-up is forces, and to introduce different spectroscopies such as for specific applications. known as high-speed AFM. force spectroscopy with sub-piconewton sensitivity28,29 4 | Article citation ID: (2021) 1:36 www.nature.com/nrmp 0123456789();:
Primer Quality factor or single-molecule and single-cell force spectroscopy in corresponding image will be measured at constant cur- The dimensionless factor biology30–32. Now, we approach the time at which AFM rent in STM or constant force in AFM. On the other describing the dissipation imaging simultaneously quantifies and structurally maps hand, when the feedback is not used, the tip height is and damping of the mechanical the various physical, chemical and biological properties kept constant, resulting in the constant-height imag- oscillator during a single oscillating cycle. of non-living and living objects24,33,34 (Fig. 3c). ing mode. Under the constant-current/force mode, Progress in instrumentation has been key to recent the tip–sample distance is determined by the preset Thermal drift AFM developments. After the quartz tuning fork was current/force and typically higher resolution is obtained The steady and monotonic first used as the force sensors for non-contact AFM35, at smaller tip–sample distance, simultaneously with changes of the specific one example of prominent progress is the development higher risk of tip damage. By contrast, constant-height location or parameter with time resulting from the of the qPlus sensor, with one prong fixed to enhance imaging only works for flat surfaces, and the results are changed temperature. the quality factor up to ~100,000 at small amplitude more straightforward to interpret owing to the absence (
Primer Young’s modulus (d2I/dV2), such as inelastic electron tunnelling spectros The SPM tip is not only a perfect probe for surface A mechanical property that copy (IETS) (Fig. 4A). To obtain dI/dV and d2I/dV2 spec- characterization but also acts as a nanoscale hand quantifies the relationship tra, a small voltage modulation is added to the bias, and for manipulating single atoms or molecules11,41,42. Precise between tensile stress and the first-order and second-order components of I–V manipulation is usually achieved through voltage pulses axial strain, which reflects the tensile stiffness of a curves are extracted by lock-in amplifiers (Fig. 2a). In or forces when the tip is positioned directly above the solid material. AFM-based force spectroscopy, the tip is approached target sites. During such a process, the injected electrons and withdrawn from a sample surface while record- can excite the vibrational modes of atoms or molecules ing a force–distance curve (Fig. 4B). The force–distance and lead to diffusion, desorption and selective bond curves allow analysis of repulsive and adhesive interac- breaking or formation42–44. For vertical manipulation, tions between the tip and the sample, as well as sample an adsorbed molecule is picked up by an STM tip by deformation and elasticity40 (Box 1). AFM can combine injecting electrons into the surface, transferred above a imaging with force spectroscopy to simultaneously target site and then released from the tip by applying map mechanical, chemical and biological properties. a reversed bias voltage, leading to the formation of a new Therefore, the AFM record for each pixel of the result- complex42 (Fig. 4C). For the lateral manipulation, the tip ing AFM topography represents a force–distance curve, is brought close to the atom or molecule on the sur- from which multiple parameters such as Young’s modulus face, such that the tip–sample interaction force is large and energy dissipation, pressures and tension can be enough to pull or push the atom or molecule moving extracted (Fig. 3c). over the diffusion barrier41,45 (Fig. 4D). A B Ca [110] F [001] Tip Elastic tunnelling e– O hω Fe eV C Inelastic tunnelling Ag z Cb Tip Sample I Elastic Inelastic Pauli repulsion Attractive Cc –E0 E0 V Short-range chemical force Repulsive Long-range electrostatic/ Total interaction van der Waals interaction dI/dV e– D –E0 E0 V Tip path Cd d2I/dV2 Force Substrate –E0 E0 V Fig. 4 | Schematics of scanning probe spectroscopy and manipulations. the attractive force and repulsive force versus tip distance, respectively. A | Schematic revealing inelastic tunnelling (red) and elastic tunnelling C | Schematic showing formation of a single bond through scanning (blue). Vibrational excitation indicated by wavy lines, which leads to an tunnelling microscopy. A single molecule can be detached (part a), increase in conductance. Graphs show an I–V curve and corresponding translated (part b) and attached onto another adatom through precise dI/dV and d2I/dV2 spectra where extra tunnelling conductance caused manipulation of the scanning tunnelling microscopy (STM) tip (parts c,d). by inelastic tunnelling appears at ±E0. Dashed lines reflect the elastic and D | Schematic showing the process of laterally pulling an adatom inelastic tunnelling channels, whereas solid lines show the actual data. through the STM tip. Jump height (green arrow), lateral distance between B | Schematic showing typical force–distance curves. Both short-range the tip apex and the manipulated adatom (red arrow), and tip height (green region, Pauli repulsion; blue region, short-range chemical force) (blue arrow) during manipulation are indicated. Part C adapted with and long-range (orange region, long-range electrostatic or van der Waals permission from ref. 42, AAAS. Part D adapted with permission from interaction) components are indicated. Black and grey curves represent ref.41, APS. 6 | Article citation ID: (2021) 1:36 www.nature.com/nrmp 0123456789();:
Primer Tip preparation and functionalization Box 1 | Single-molecule force spectroscopy Atomically sharp tips are the key to achieving high res- olution in SPM. They are usually produced by mechan- The uniqueness of directly probing physical interactions ical cutting or milling, electrochemical etching or more between the atomic force microscopy (AFM) tip and complicated nanofabrication such as focused ion beam the biological sample has been exploited to develop single- molecule force spectroscopy. This technique measures systems46. However, the tip apex obtained by those meth- the bonds of single receptor–ligand pairs. In the early ods is not sharp enough for atomically resolved imaging. days of single-molecule force spectroscopy, the AFM To obtain an ideal tip terminated with a single atom or a tip (or a bead glued to the tip) was functionalized with small cluster of atoms, the tip needs to be treated (which ligands and the surface of the support, such as a bead includes both sharpening and functionalization) during on top of the substrate, with receptors30,288. If the tip scanning by poking the tip into the surface and grasping and sample are brought into sufficient proximity, the a small cluster of atoms. In STM experiments, the appli- ligand and receptor can bind. The AFM tip is then cation of high voltages up to 10 V can be used for tip withdrawn, and the force required to separate the treatment, at a tip–sample distance of ~1 nm to induce specific bond is measured. This unbinding force describes field emission47. The atoms at the very end of the tip the mechanical strength of the receptor–ligand bond. Typically, such experiments are repeated several determine the spatial resolution of SPM, not the overall thousand times to characterize a sufficient number radius of curvature at the apex. In order to obtain high of successful binding and unbinding events. The use of chemical resolution besides topography, one can also short cantilevers in high-speed AFM set-ups extends evaporate noble metal films such as gold and silver onto the accessible dynamic range in force spectroscopy the conventional silicon AFM tip; this type of tip has experiments to measure molecular dynamics been extensively used for nanoscale chemical analysis simulations319, whereas low-noise AFMs reach force under ambient conditions48,49. sensitivity comparable with that of optical tweezers320. For SPM experiments performed in UHV and low- temperature conditions, the most controllable and pre- chemical and biological interactions40. One approach to cise way to get a well-defined sharp tip is functionalizing study these interactions is to functionalize the AFM tip. the tip apex by picking up a single atom or molecule on the surface50,51. Under such conditions, SPM with Variations of SPM a CO-functionalized tip can image molecular orbitals52, By integrating microsensors on the tip or coupling the owing to the p-wave orbitals of the CO molecule. The electromagnetic waves with different wavelengths into CO tip also allows access to the short-range Pauli the tip–sample junctions, a large family of SPM methods repulsions, reflecting the variations of electron density have been developed since the invention of STM and in individual chemical bonds53. As the CO tip has a AFM. In this section, we introduce some representative quadrupole-like charge distribution, it is also sensitive variations of SPM, which can map out various physical to the high-order electrostatic force54. One drawback quantities besides current and force, such as magnetic/ of the CO tip is the lateral relaxation of the CO mole- electric field, photons, strain, temperature, and dielectric cule at the tip apex, which leads to distortion or even and physiological responses. The sensing mechanism, artefacts in the SPM images. Functionalizing the tip at advantages and applications of those SPM variations are the atomic level, for example replacing the C–O group briefly discussed in the following sections. with oxygen55 and chlorine56, yields a more rigid tip with smaller relaxation of the tip apex. However, the reso Time-resolved STM. Despite achieving high spatial reso- lution of those tips is usually poorer than for the CO tip, lution in real space, one of the most interesting questions as strong relaxation of the CO molecule is also crucial about SPM is the speed at which such a device could to obtain sharply resolved structural resolution when capture a signal in real time. High-speed image acqui- the tip–sample distance is within the region of Pauli sition could be achieved by video-rate STM15,61, which repulsion57. typically scans a frame within a millisecond timescale. For biological AFM imaging applications, tips Recently, with the pulsed voltages, fast spin dynamics are typically made of silicon or silicon nitride, which such as spin relaxation was investigated by electrical upon exposure to air and immersion into physiologi- pump-probe STM at the level of a single atom62. As the cal buffer will feature an oxide layer at their surface58. bandwidth of the preamplifier and other electronics of To achieve sharper tips with higher aspect ratio, elec- SPM is limited to megahertz, ultra-fast dynamics within tron beam deposition can be used, resulting in the picoseconds and femtoseconds should be captured by growth of an amorphous carbon-based apex, which is incorporating pump-probe techniques into STM, lead- subsequently rendered hydrophilic using plasma clean- ing to femtosecond laser STM63,64 and terahertz STM65,66. ing59. Carbon nanotubes have been grafted as a quasi Examples of various time-resolved STM techniques can one-dimensional (1D) object at the end of AFM tips to be found in Table 1. create a super-sharp, very high aspect ratio apex, but despite efforts these tips have so far had no significant Magnetic field-sensitive SPM. Magnetic field or spin- impact in the AFM field, likely because of nanotube sensitive SPM is very useful for characterizing local mag- CO-functionalized tip buckling60. Overall for biological imaging applications netic structures and spin states in real space (Table 2). Modification of the tip with a single CO molecule in order to in liquid, the tip–sample interaction forces range from The simplest method for detecting the local magnetic enhance the spatial resolution short range (≈1–10 nm) to long range (>10 nm) and field is by replacing the conventional non-magnetic of scanning probe microscopy. can be composed of a repertoire of different physical, probe with a magnetic probe, which is extensively used NATURE REvIEWS | METHoDS PRimERS | Article citation ID: (2021) 1:36 7 0123456789();:
Primer Table 1 | Time-resolved scanning probe microscopy techniques Name Detected signal Utility Resolution Disadvantages and Refs limitations Video-rate Tunnelling current Fast dynamics Atomic resolution Spatial resolution is poor 15,61 scanning tunnelling during chemical and millisecond owing to short integration microscopy reactions, surface temporal time; temporal resolution reconstruction resolution is limited by the resonance and material frequency of the scanner growth at elevated and the bandwidth of the temperatures electronics Electrical pump- Tunnelling current Fast electron spin Atomic resolution Time resolution is limited 62 probe scanning dynamics and nanosecond by the bandwidth of tunnelling temporal advanced electronics such microscopy resolution as the preamplifier and pulse generators Femtosecond laser Photo-induced Ultra-fast charge, Atomic resolution Laser-induced thermal 63,64 scanning tunnelling tunnelling current spin and phonon and femtosecond expansion of the tip can microscopy dynamics at the temporal lead to artificial signals atomic scale resolution Terahertz scanning Photo-induced Ultra-fast charge, Atomic resolution Introduction of 65,66 tunnelling tunnelling current spin and phonon and femtosecond terahertz light into microscopy dynamics at the temporal the ultra-high vacuum atomic scale resolution and low-temperature scanning tunnelling microscopy system is complicated; the temporal resolution is limited by the wavelength and width of the terahertz pulse in magnetic force microscopy67,68, magnetic exchange for use in aqueous environments. The self-assembly and force microscopy 69 and spin-polarized STM 70,71 . reactivity of supramolecular systems inside non-ionic Another avenue is grafting a micro-magnetic sensor organic liquids has been investigated by liquid-phase such as a superconducting quantum interference device STM85–87. Meanwhile, working at the solid–electrolyte (SQUID) or Hall probe on the tip, constructing scan- interfaces, electrochemical STM (EC-STM) is developed ning SQUID microscopy72,73 and scanning Hall probe with four electrodes including the tip, working elec- microscopy74. In addition, by incorporating microwaves trode, counter electrode and reference electrode, which into SPM to excite magnetic resonance, the magnetic are controlled by a bipotentiostat17,88. As EC-STM only sensitivity of SPM can be enhanced up to single electron works on conductive surfaces, liquid-phase non-contact or nuclear spin, such as electron spin resonance (ESR) AFM was developed for imaging the local structures on STM75–77, magnetic resonant force microscopy78 and insulator–liquid interfaces89,90. In order to characterize nitrogen vacancy-based SPM79. complex biological systems such as living cells in phys- iological buffers with high spatial resolution, scanning Electric field-sensitive SPM. To map out the surface ion conductance microscopy should be chosen91. In this potential or charge with high resolution, typically a system, the ion current flow from the tip to the refer- conductive SPM tip biased with variable voltage is ence electrodes in the solution is monitored and used for used (Table 3). One form of electric field-sensitive SPM feedback to control the tip–surface distance. Compared is scanning capacitance microscopy80, where the local with EC-STM and liquid-phase AFM mentioned above, capacitive coupling between the tip and the sample is scanning ion conductance microscopy provides the detected for deriving the local dielectric and electrical unique possibility of locally probing the ion transport properties. Another option for sensing local potential of biological systems by monitoring the ion current92. is the integration of a microelectric sensor such as a Similarly, AFM can scan a hollow microcantilever to single-electron transistor onto the tip81. For single charge perform scanning ion conductance microscopy mea Hall probe A micron-sized device for detection, the tip should be brought as close as possible surements, which is also called fluid force microscopy, detecting the external to the sample, which requires a sharp metal tip instead to patch clamp or to manipulate living cells93,94. Examples magnetic field through of a microelectric sensor, such as in Kelvin probe force of liquid-phase SPM can be found in Table 4. the Hall effect. microscopy82. Piezoresponse force microscopy (PFM) is another important electric-field sensitive SPM83,84, Electrical transport-compatible SPM. In order to make Bipotentiostat An electronic system in which a modulated pressure is applied locally on SPM suitable for investigating local electron transport capable of controlling two the sample by the tip and its piezoelectric response is properties both on the surface and the interface of sam- potentiostats, which include monitored during scanning. ples such as 2D material-based novel electronic devices, two working electrodes, one various electrodes should be fabricated on the surface shared reference electrode and one shared counter Liquid-phase SPM. Although surface characterization in addition to the bias electrode, acting as source, drain electrode for electrochemical with atomic resolution is ever-present in UHV and and electric gates. Immediately after the appearance of measurements. low-temperature experiments, it remains challenging STM, scanning tunnelling potentiometry was invented 8 | Article citation ID: (2021) 1:36 www.nature.com/nrmp 0123456789();:
Primer Table 2 | Magnetic field-sensitive scanning probe microscopy techniques Name Detected signal Utility Resolution Disadvantages and Refs and limitations sensitivity Spin-polarized Spin-polarized Nanoscale Atomic High-energy resolution 70,71 scanning tunnelling tunnelling current spin texture resolution only works on microscopy or long-range with sensitivity conductive samples spin ordering of of single under low temperature magnetic materials electron spin and ultra-high vacuum Electron spin Spin-polarized Spin identification, Atomic The spin-polarized 75–77 resonance tunnelling current electron spin resolution tip is not only a probe scanning tunnelling resonance spectra/ with sensitivity but has an effect on microscopy imaging and of single the coherence of the quantum sensing electron spin target spin Magnetic force Dipolar magnetic Magnetic structures Spatial The magnetic tip 67,68 microscopy interaction of sample surfaces resolution of will disturb the several tens magnetic state of of nanometres the sample, and vice versa, complicating quantitative interpretation of the magnetic force microscopy measurement; atomic resolution cannot be achieved owing to the long-range magnetic forces between tip and sample Scanning Magnetic flux and Scanning Spatial Only works under low 72,73 superconducting superconducting magnetometry and resolution of temperature; spatial quantum current thermometry at low several tens resolution is limited interference device temperature of nanometres by the size of the microscopy and magnetic superconducting loop sensitivity up to single electron spin Nitrogen vacancy Fluorescence of the Scanning Spatial The quantum sensor 79 centre scanning nitrogen vacancy magnetometry of resolution of is buried underneath probe microscopy centre nanoscale magnetic ~10 nm and the diamond surface, textures at various magnetic which makes atomic temperatures; sensitivity resolution challenging; compatible up to single the shallower nitrogen with an ambient nuclear spin vacancy has poorer environment and quantum coherence, biological systems which decreases the signal to noise ratio and sensitivity Magnetic resonance Magnetic dipolar Nanoscale electron Resolution Only works under 78 force microscopy interaction and nuclear
Primer Table 3 | Electric field-sensitive scanning probe microscopy techniques Name Detected signal Utility Resolution and Disadvantages and Refs sensitivity limitations Scanning Tunnelling current Local electric field and Spatial resolution Only works under low 81 single-electron potential caused by of several tens of temperature; spatial transistor the local charges, nanometres and resolution is limited by microscopy especially the local electric field the size of the device electronic states of sensitivity up to strongly correlated 2 μV Hz–1/2 materials Scanning Capacitance Dielectric and Spatial resolution Spatial resolution 80 capacitance electrical properties of several is limited by the microscopy of semiconductors nanometres with long-range capacitance and buried capacitance coupling two-dimensional sensitivity of electron gas attofarad Kelvin probe Contact potential Local work function Nanoscale spatial Unsuitable for 82 force microscopy difference and electric dipole resolution with characterization of distribution of various sensitivity up to voltage-sensitive samples a single charge samples; spatial resolution is limited by the long-range electrostatic force Piezoresponse Piezoelectric Ferroelectric ordering, Spatial resolution Tip wear can modify the 83,84 force microscopy response of the piezo coefficient and with several tip–surface interaction, sample energy dissipation nanometres affecting imaging contrast; the acquired force signals may not always arise from piezo/ferro electricity phenomena for investigating the local distribution of potential and tip-enhanced Raman spectroscopy (TERS)9,48. Recently, inhomogeneous conductivity of metals and semiconduc- TERS has demonstrated its ability in identifying and tors95. Without the need for detecting the tunnelling cur- resolving chemical structures of single molecules with rent, scanning gate microscopy uses a conductive tip as the sub-nanometre resolution9. Benefiting from the local movable electric gate and is capable of revealing the local plasmon confined within the tunnelling junction, scan- gating effects on the transport currents from the source ning tunnelling microscope-induced luminescence was and drain96,97. As the electrodes for transport measure- also developed and applied for detecting the optical ments are usually fixed by nanofabrication, much more emission from the electronic and vibrational transition precise and flexible positioning of such electrodes was at the single-molecule level103. Apart from working within realized by multi-probe STM98,99 (Table 5). the range of visible light, it is also attractive for investi- gating the dielectric response of materials in the mega- Near-field SPM. To optically probe the structural, dielec- hertz to gigahertz regime, such as microwave impedance tric and chemical properties with visible sub-wavelength microscopy, where a sharp metallic tip extended from resolution, scanning near-field optical microscopy a high-frequency resonator was used as the antenna to (SNOM) was developed and has been widely used in the emit and collect microwave photons104,105. In contrast past decades100 (Table 6). SNOM makes use of the eva- to conventional near-field SPM, photo-induced force nescent components of the light highly confined near the microscopy106 directly detects the near-field signal surface, thus overcoming the diffraction limit of far-field based on photo-induced dipolar forces, which efficiently optics. Generally, a sharpened optical fibre with a metal suppress the overwhelming background signals. shield and a nanoscale aperture is used as the light source or detector for scanning. However, the spatial Results resolution is limited by the aperture size of the optical SPM images are always acquired as a 2D matrix, whereas fibre, with a typical value of 30–50 nm. By contrast, aper- spectroscopic curves are saved in the form of arrays. tureless SNOM such as scattering-type SNOM101 uses a The main steps for data analysis include image inspec- metallic AFM tip as the near-field scatterer and works tion, noise analysis, filtering and image reconstruction. Scanning gate microscopy in a dynamical mode for suppressing the background For the curves of SPM spectra and the line profiles of A kind of scanning probe far-field signals, which improves the spatial resolution topographic images, a fitting procedure is usually nec- microscopy capable of up to 1 nm (ref.102). Furthermore, making use of a sharp essary for interpretation of the underlying quantities probing electrical transport noble tip and highly confined surface plasmon101, the and parameters. In this section, we showcase several at the nanoscale, where a conductive tip is used as the efficiency of Raman scattering in the tip–sample gap representative examples to discuss how to analyse SPM local gate capacitively coupled is enhanced several orders of magnitude as compared images and spectra. The popular software for processing to the sample. with conventional far-field Raman experiments, such as the SPM data are briefly introduced. 10 | Article citation ID: (2021) 1:36 www.nature.com/nrmp 0123456789();:
Primer Representative results biomolecules, the interaction force is detected and used SPM imaging provides pseudo-3D data. As a surface to describe the deformations of the sample33 (Fig. 5c). probing technique, it does not deliver information about On the other hand, upon withdrawing the tip, the force– the inside volume of the object under investigation but distance curve can be used to infer multi-mechanical provides an x–y grid of data points to each of which a sin- parameters such as adhesion, Young’s modulus, plas- gle z height is associated. SPM data are thus most often tic deformation and energy dissipation of the sample represented as an x–y 2D image, where a false-colour through fittings. scale represents the z height107 (Fig. 5a). Sometimes, SPM STS is suitable for investigating the local density data are represented as a 3D surface shown in perspec- of states of a sample. In Fig. 5d, a typical dI/dV curve tive (Fig. 5b) that is visually attractive but scientifically acquired on a single pentacene molecule shows prom- less precise because at least one of the in-plane axes is inent peaks at both the positive and negative biases, skewed, the z height sometimes increased and some which are attributed to the highest and lowest molecular structural features obstructed by the perspective view. orbitals (HOMO and LUMO, respectively)37. By fixing In the SPM field, unfortunately, no stringent standards the bias at the LUMO or HOMO and spatially mapping have been established regarding the representation of out the dI/dV intensity, the frontier orbitals of the sin- SPM data in publications, and sometimes filters are gle pentacene molecule can be directly visualized in real used to display images. Specifically, the application of space37 (Fig. 5f). Whereas the STM mode is only sensitive short-range median filters in the y dimension, which to the electronic states near the Fermi level, non-contact cancel lines from the fast scan axis (x dimension) of the AFM working under the frequency modulation mode image acquisition, is common. is able to probe the total electron density of the sample Force–distance curves are acquired by recording by entering into the region of short-range Pauli repul- the deflection signal of the AFM cantilever while con- sion108. In Fig. 5g, a CO-functionalized tip clearly resolves trolling the tip–sample distance. For example, when the chemical skeleton of the single pentacene molecule, the tip approaches the surface and interacts with the where the short-range Pauli repulsion dominates the Table 4 | Liquid-phase scanning probe microscopy techniques Name Detected signal Utility Resolution Disadvantages and Refs limitations Scanning ion Ion current Non-invasive imaging Spatial resolution Spatial resolution is 91,92 conductance of the tomography with several tens limited by the size of microscopy and investigation of nanometres the microchannel of the physiological properties of complex biological systems such as living cells in solutions Fluidic force Deflection of Single-cell Sub-micrometre Spatial resolution is 93,94 microscope the cantilever manipulation and limited by the size of controlled delivery the microchannel of bioactive agents Liquid-phase Tunnelling current Investigation of Atomic resolution Tip condition is not 85–87 scanning supramolecular well controllable tunnelling systems and their compared with microscope self-assembly, scanning tunnelling dynamics and reactivity microscopy in an ultra-high vacuum; only a conductive surface could be investigated Electrochemical Tunnelling current In situ detection Atomic resolution Tip condition is not 17,88 scanning of various easily controllable tunnelling electrochemical for electrochemical microscopy processes, such reactions; Faraday as formation of an currents interfere with electrochemical the tunnelling current double layer, metal corrosion and electrodeposition Liquid-phase Frequency shift In situ detection of Atomic resolution Three-dimensional 89,90 non-contact the structure of the force mapping for atomic force hydration layer and structural analyses on microscopy electrochemical solid–liquid interfaces double layer on a solid– is time consuming; only liquid interface with local liquid density can atomic resolution be probed NATURE REvIEWS | METHoDS PRimERS | Article citation ID: (2021) 1:36 11 0123456789();:
Primer Table 5 | Transport-compatible scanning probe microscopy techniques Name Detected signal Utility Resolution Disadvantages and Refs limitations Scanning Tunnelling current Imaging of the Atomic resolution Interpretation of the 95 tunnelling spatial distribution in principle signal is difficult because potentiometry of electrostatic distinguishing tomography potential from potentiometry is challenging Scanning gate Conductance Spatial mapping of Spatial resolution As the capacitive coupling 96,97 microscopy between source electron flows in of several tens of between tip and sample and drain two-dimensional nanometres is long range, the spatial electrodes materials and resolution is largely limited semiconducting by the sharpness of the tip materials apex and the tip–sample distance Four-probe Tunnelling current Local and in situ Atomic resolution Closest distance (10–20 nm) 98,99 scanning investigation of in principle between the probes is limited tunnelling in-plane electronic by the curvature radius of microscopy transport properties the tip apex; performance is generally poorer than that of conventional scanning tunnelling microscopy owing to the complex scanner design tip–molecular interaction108. The sharp lines arise from Here, we take the application of AFM in biology as the electron density build-up across the covalent bonds an example. When AFM is used for cellular imaging, between the carbon atoms. either proprietary software is used for analysis or images In some cases, inelastic electron tunnelling signals are exported in various file formats such as .tiff, .raw, may be superimposed on the large background of elas- .png, .sxm and .gwy to be analysed by laboratory-written tic tunnelling conductance during STS measurements. routines in the software packages mentioned above or in For example, the dI/dV curve taken on the bilayer MATLAB112. Analysis of data from the above-described NaCl(001) film grown on Au(111) demonstrates a broad hybrid imaging/nanomechanical mapping modes113 is peak (grey), which corresponds to the interfacial elec- often done in proprietary application mode software; tronic states109 (Fig. 5e). When the tip is positioned on the in this case, not only the data encoding but also the water molecule adsorbed on the surface, distinct kinks acquisition process is system-dependent. When AFM appear in addition to the interfacial electronic states is used for molecular imaging and analysis of protein (red). Such kinks are more clearly resolved as dips and structures and conformations, AFM users often borrow peaks in d2I/dV2 spectra, which are point-symmetrical methods from electron microscopy. The recent progress with respect to the zero bias. The energy positions of in electron microscopy to solve protein structures114 is those features reflect the energies of different vibrational directly associated with image analysis developments. modes of the single water molecule. To this end, there is a plethora of such programs for analysis of macromolecular structures, such as EMAN115, Visualization and analysis software IMAGIC 116, SPIDER 117 and RELION118. Given that The major problem of image visualization and image the contrast transfer function and the noise distribu- analysis originates from the fact that, so far, no com- tion of AFM are very different from those of electron mon SPM file format has been established. Each SPM microscopy, these programs must be adapted with care. company has a specific proprietary file format and SEMPER and MRC are most powerful to analyse 2D microscope-associated software for image data analysis. crystalline data58, and most other programs are adapted Among others, Gwyddion110, WSxM111 and ImageJ are to analyse single particles119. free and open source software. They are likely the most powerful SPM data visualization and analysis platforms, Analysis of biological data as they provide a large number of data processing func- When using AFM for the analysis of images of pro- tions. These include standard statistical characterization, teins, one particle is used for a cross-correlation data correction, filtering and grain marking functions. search of all other molecules in the image. Next, cross- Gwyddion and WSxM are compatible with most stand- correlation-based lateral and rotational alignment of ard file formats (such as .dat, .txt and .sxm) acquired the particles is performed. Particle selection based on from commercial SPM programs such as Nanonis, cross-correlation values can be performed to calculate Omicron and RHK. ImageJ has the advantage that it is an average of the most common particle structure120. widely used by the optical fluorescence microscopy com- During the averaging process, a standard deviation munity and, thus, features a large variety of functions map can be calculated that highlights the most flexi- that can be adapted for SPM data, and its capabilities are ble parts in the molecule121. From the stack of particle rapidly growing through contributions of analysis tools images that one has extracted using cross-correlation from a large scientific community. searches, one can statistically assess any parameter of 12 | Article citation ID: (2021) 1:36 www.nature.com/nrmp 0123456789();:
Primer interest characterizing the molecule, such as the height representations accompanied with statistical data, as is and volume distribution of the particles122, or molecular done in the electron microscopy field. symmetry123. For example, the complete perforin 2 rings shown in Fig. 5a can be distinguished from incomplete Applications arcs using cross-correlation-based selection and later- SPM has found a multitude of applications in the natural ally and rotationally aligned to calculate an ensemble sciences. In the following, we divide those applications average (Fig. 5a, insets). For the analysis of filamentous into physics, chemistry, materials science and biology, structures, such as DNA or filamentous proteins, auto- although they are often closely linked to each other and mated particle detection based on the height above the have strong overlap. background, followed by tracing of the filaments, allows direct extraction of the physical properties of the fila- Examples from physics ment, such as its persistence length124. Unfortunately, Surface science. The initial application for STM was in structural analysis using automated programs is not the field of surface science, where atomic-scale arrange- utilized enough in the AFM field, and it is still rather ment as well as the electronic properties of materials common to place arrows on image panels to high- needed investigation. The key initial experimental light features instead of calculating relevant molecular evidence for the power of STM in this regard was the Table 6 | Near-field scanning probe microscopy Name Detected signal Utility Resolution and Disadvantages and Refs sensitivity limitations Scanning near-field Emission of Local fluorescence Spatial resolution Spatial resolution 100 optical microscopy fluorescence or imaging of biological with tens of is largely limited adsorption of molecules and nanometres by the size of the excitation lights photoluminescent nanofibres used as spectroscopy of probes; near-field semiconductors signal is weak and easily disturbed by metallic coatings Scattering-type Elastic scattering Local dielectric Spatial resolution Requires cantilevers 101,102 scanning near-field of lights response from optical up to 1 nm and to work under optical microscopy light and plasmonic monolayer large amplitude to structures sensitivity eliminate far-field background, making the method insensitive to short-range tip– sample interactions Tip-enhanced Raman scattering Analysis and Single-molecule High spatial 9,48 of lights identification of sensitivity and resolution relies on Raman scattering the local chemical sub-nanometre the electromagnetic structure of spatial resolution coupling between small molecules, the tip and a biomolecules, plasmonic substrate, living cells and thus limiting the two-dimensional systems that can materials be studied Scanning tunnelling Photon emission Photon yield images Single-molecule High spatial 103 microscope-induced from sample and energy-resolved sensitivity and resolution relies on luminescence spectroscopic images sub-nanometre the electromagnetic spatial resolution coupling between the tip and a plasmonic substrate, thus limiting the systems that can be studied Microwave impedance Reflection or Local dielectric Spatial resolution Spatial resolution 104,105 microscopy transmission properties and of several tens of is limited by the parameters of conductivities; nanometres long wavelength of microwaves suitable for obtaining microwave photons information from a buried interface Photo-induced force Photo-induced Detection of both Spatial resolution Quantitative 106 microscopy dipolar topography and of sub-10 nm interpretation of interactions chemical signature on and monolayer the imaging contrast organic and inorganic sensitivity is difficult; only samples works with the narrow band of infrared lights NATURE REvIEWS | METHoDS PRimERS | Article citation ID: (2021) 1:36 13 0123456789();:
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