Nanometer Precision Research Articles

Biophysics of high density nanometer regions extracted from super-resolution single particle trajectories: application to voltage-gated calcium channels and phospholipids

The cellular membrane is very heterogenous and enriched with high-density regions forming microdomains, as revealed by single particle tracking experiments. However the organization of these regions remain unexplained. We determine here the biophysical properties of these regions, when described as a basin of attraction. We develop two methods to recover the dynamics and local potential wells (field of force and boundary). The first method is based on the local density of points distribution of trajectories, which differs inside and outside the wells. The second method focuses on recovering the drift field that is convergent inside wells and uses the transient field to determine the boundary. Finally, we apply these two methods to the distribution of trajectories recorded from voltage gated calcium channels and phospholipid anchored GFP in the cell membrane of hippocampal neurons and obtain the size and energy of high-density regions with a nanometer precision.

Reactivity mapping of nanoscale defect chemistry under electrochemical reaction conditions

Electrocatalysts often show increased conversion at nanoscale chemical or topographic surface inhomogeneities, resulting in spatially heterogeneous reactivity. Identifying reacting species locally with nanometer precision during chemical conversion is one of the biggest quests in electrochemical surface science to advance (electro)catalysis and related fields. Here, we demonstrate that electrochemical tip-enhanced Raman spectroscopy can be used for combined topography and reactivity imaging of electro-active surface sites under reaction conditions. We map the electrochemical oxidation of Au nanodefects, a showcase energy conversion and corrosion reaction, with a chemical spatial sensitivity of about 10 nm. The results indicate the reversible, concurrent formation of spatially separated Au2O3 and Au2O species at defect-terrace and protrusion sites on the defect, respectively. Active-site chemical nano-imaging under realistic working conditions is expected to be pivotal in a broad range of disciplines where quasi-atomistic reactivity understanding could enable strategic engineering of active sites to rationally tune (electro)chemical device properties.

Atmospheric Pressure Plasma Processing of an Optical Sinusoidal Grid.

Sinusoidal grid with nanometric precision is adopted as a surface encoder to measure multiple degree-of-freedom motions. This paper proposes the atmospheric pressure plasma processing (APPP) technique to fabricate an optical sinusoidal grid surface. The characteristics of removal function and surface generation mechanism are firstly presented. Both simulation and experiment validate the effectiveness of APPP to fabricate a sinusoidal grid surface with nanometric precision. Post mechanical polishing experiments show that APPP features can be well maintained while the surface roughness is greatly reduced to meet the optical requirement.

Designer DNA architecture offers precise and multivalent spatial pattern-recognition for viral sensing and inhibition.

DNA, when folded into nanostructures with a specific shape, is capable of spacing and arranging binding sites into a complex geometric pattern with nanometre precision. Here we demonstrate a designer DNA nanostructure that can act as a template to display multiple binding motifs with precise spatial pattern-recognition properties, and that this approach can confer exceptional sensing and potent viral inhibitory capabilities. A star-shaped DNA architecture, carrying five molecular beacon-like motifs, was constructed to display ten dengue envelope protein domain III (ED3)-targeting aptamers into a two-dimensional pattern precisely matching the spatial arrangement of ED3 clusters on the dengue (DENV) viral surface. The resulting multivalent interactions provide high DENV-binding avidity. We show that this structure is a potent viral inhibitor and that it can act as a sensor by including a fluorescent output to report binding. Our molecular-platform design strategy could be adapted to detect and combat other disease-causing pathogens by generating the requisite ligand patterns on customized DNA nanoarchitectures.

Sample drift estimation method based on speckle patterns formed by backscattered laser light.

Single molecule localization microscopy (SMLM) has been established to acquire images with unprecedented resolution down to several nanometers. A typical time scale for image acquisition is several minutes to hours. Yet it is difficult to avoid completely sample drift for long time measurements. To estimate drift, we present a method based on the evaluation of speckle patterns formed by backscattered laser light from the cells using a single molecule localization microscope setup. A z-stack of unique speckle patterns is recorded prior to the measurements as a three-dimensional position reference. During the experiment, images of scattered laser light were acquired, and correlated individually with each of the images of the speckle reference stack to estimate x, y and z drift. Our method shows highly comparable results with a fiducial marker approach, achieving a precision of several nanometers. This method allows for high precision three dimensional drift correction of microscope systems without any additional sample preparation.

In situ characterization of nanoscale strains in loaded whole joints via synchrotron X-ray tomography.

Imaging techniques for quantifying how the hierarchical structure of deforming joints changes are constrained by destructive sample treatments, sample-size restrictions and lengthy scan times. Here, we report the use of fast, low-dose pink-beam synchrotron X-ray tomography combined with mechanical loading at nanometric precision for the in situ imaging, at resolutions lower than 100 nm, of mechanical strain in intact untreated joints under physiologically realistic conditions. We show that, in young, aged, and osteoarthritic mice, hierarchical changes in tissue structure and mechanical behaviour can be simultaneously visualized, and that tissue structure at the cellular level correlates with whole-joint mechanical performance. We also used the tomographic approach to study the co-localization of tissue strains to specific chondrocyte lacunar organizations within intact loaded joints, and for the exploration of the role of calcified-cartilage stiffness on the biomechanics of healthy and pathological joints.

Optomechanical response with nanometer resolution in the self-mixing signal of a terahertz quantum cascade laser.

Owing to their intrinsic stability against optical feedback (OF), quantum cascade lasers (QCLs) represent a uniquely versatile source to further improve self-mixing interferometry at mid-infrared and terahertz (THz) frequencies. Here, we show the feasibility of detecting with nanometer precision, the deeply subwavelength ($ \lt \lambda /6000 $<λ/6000) mechanical vibrations of a suspended $ {{\rm Si}_3}{{\rm N}_4} $Si3N4 membrane used as the external element of a THz QCL feedback interferometer. Besides representing an extension of the applicability of vibrometric characterization at THz frequencies, our system can be exploited for the realization of optomechanical applications, such as dynamical switching between different OF regimes and a still-lacking THz master-slave configuration.

Design and synthesis of pleated DNA origami nanotubes with adjustable diameters.

DNA origami allows for the synthesis of nanoscale structures and machines with nanometre precision and high yields. Tubular DNA origami nanostructures are particularly useful because their geometry facilitates a variety of applications including nanoparticle encapsulation, the construction of artificial membrane pores and as structural scaffolds that can uniquely spatially arrange nanoparticles in circular, linear and helical arrays. Here we report a system of parametrization for the design of radially symmetric DNA origami nanotubes with adjustable diameter, length, crossover density, pleat angle and chirality. The system is implemented into a computational algorithm that provides a practical means to navigate the complex geometry of DNA origami nanotube design. We apply this in the design, synthesis and characterization of novel DNA origami nanotubes. These include structures with pleated walls where the same number of duplexes can form nanotubes with different diameters, and to vary the diameter within the same structure. We also construct nanotubes that can be reconfigured into different chiral shapes. Finally, we explore the effect of strain on the local and global geometry of DNA origami nanotubes and demonstrate how pleated walls can provide a strategy to rigidify nanotubes and to construct closely packed parallel duplexes.

English

Nanotechnology is the science of objects &lt;100 nm in size. Research into the development and application of nanomaterials takes a material science and engineering-based approach to nanotechnology. Nanomaterials often possess interesting optical, electronic and mechanical properties. The capacity to construct large, intricate structures with nanometer precision is rapidly increasing and consists several top-down reductive approaches and bottom-up additive approaches to satisfy its applicability in several fields of science. The physicochemical property of nano-functional materials and structural flexibility, promotes its vast application in chemistry and chemical engineering; physics and electronics; biochemistry and medical science, exploration and mining; computer science and engineering. A large pool of information was accessed via several reputable published books and articles, with the sole aim to contribute to the establishment of a stronger theoretical basis for the growing application of nanomaterials in several field of science. It has been established that nanomaterials and advancement in nanotechnology holds great potential in solving several global problems, and if properly harnessed with the right synergy between disciplines or fields in science, would increase the quality of life on Earth. &nbsp; Key words: Application, disciplines, nanotechnology, nanomaterials, properties, science.

Simultaneous 3-D Surface Profiling of Multiple Targets by Repetition Rate Scanning of a Single Femtosecond Laser

We present an integrated scheme of 3-D surface profile measurements made at multiple sites concurrently by employing only a single fiber femtosecond laser as the common light source of low coherence scanning interferometry. This versatile use of an ultrashort mode-locked laser is enabled by linear scanning control of the pulse repetition rate on the source site, while diverse forms of unequal-path, non-symmetric measurements are taken with nanometer precision for different targets simply by delivering fr-scanned pulses through a fiber network. This proposed scheme has no restriction on the number of interferometer sites being integrated concurrently, allowing more diverse industrial applications of ultrashort lasers despite increased system cost and complexity.

Structure and Dynamics of Confined Liquids: Challenges and Perspectives for the X-ray Surface Forces Apparatus.

The molecular-scale structure and dynamics of confined liquids has increasingly gained relevance for applications in nanotechnology. Thus, a detailed knowledge of the structure of confined liquids on molecular length scales is of great interest for fundamental and applied sciences. To study confined structures under dynamic conditions, we constructed an in situ X-ray surface forces apparatus (X-SFA). This novel device can create a precisely controlled slit-pore confinement down to dimensions on the 10 nm scale by using a cylinder-on-flat geometry for the first time. Complementary structural information can be obtained by simultaneous force measurements and X-ray scattering experiments. The in-plane structure of liquids parallel to the slit pore and density profiles perpendicular to the confining interfaces are studied by X-ray scattering and reflectivity. The normal load between the opposing interfaces can be modulated to study the structural dynamics of confined liquids. The confinement gap distance is tracked simultaneously with nanometer precision by analyzing optical interference fringes of equal chromatic order. Relaxation processes can be studied by driving the system out of equilibrium by shear stress or compression/decompression cycles of the slit pore. The capability of the new device is demonstrated on the liquid crystal 4′-octyl-4-cyano-biphenyl (8CB) in its smectic A (SmA) mesophase. Its molecular-scale structure and orientation confined in 100 nm to 1.7 μm slit pores was studied under static and dynamic nonequilibrium conditions.

Production of Multicomponent Protein Templates for the Positioning and Stabilization of Enzymes.

Harnessing the ability of proteins to self-assemble into complex structures has enabled the creation of templates for applications in nanotechnology. Protein templates can be used to position functional molecules in regular patterns with nanometer precision over large surface areas. A difficult but successful approach to building customizable protein templates involves designing novel protein-protein interfaces to join protein building blocks into ordered arrangements. This approach was illustrated recently by engineering the protein interfaces of a molecular chaperone to produce filamentous templates composed of repeating subunits. In this chapter, we describe how these multicomponent protein templates can be produced recombinantly, assembled into filaments, and used as material templates. The templates enable the positioning and alignment of functional molecules at varying distances along the length of the filament, which can be demonstrated using a Förster resonance energy transfer (FRET) assay. In addition, we describe a method to quantify the chaperone ability of these filaments to stabilize and protect other proteins from thermal-induced aggregation-a useful property for bionanotechnology applications that involve molecular scaffolds for positioning and stabilizing enzymes.

Contactless optical trapping and manipulation of nanoparticles utilizing SIBA mechanism and EDL force.

On-chip optical tweezers based on evanescent fields overcome the diffraction limit of the free-space optical tweezers and can be a promising technique for developing lab-on-a-chip devices. While such trapping allows for low-cost and precise manipulation, it suffers from unavoidable contact with the device surface, which eliminates one of the major advantages of the optical trapping. Here, we use a 1D photonic crystal cavity to trap nanoparticles and propose a novel method to control and manipulate the particle distance from the cavity utilizing a self-induced back-action (SIBA) mechanism and electrical-double-layer (EDL) force. It is numerically shown that a 200 nm radius silica particle can be trapped near the cavity with a potential well deeper than 178kBT by 1 mW of input power without any contact with the surface and easily moved vertically with nanometer precision by wavelength detuning.

(Invited) Towards Selective Etching with Nanometric Control Using Remote Plasma Source

The transition from planar Metal-Oxide-Semiconductor (MOS) transistor architecture to 3 Dimension (3D) Field Electron Transistor (FET) architecture has been necessary to pursue transistor scaling and overcome high power consumption of logic chip. Today, the Fin Field Electron Transistor (FinFET) structure is used in the most advanced (16-/14-nm generation) CMOS technologies.[1] To continue device scaling at least to the 5nm technology node, new 3D designs, such as GAA FEt are anticipated to be adopted in the future CMOS technology generations in order to provide for superior electrostatic integrity.[2] 3D MOS architectures bring their own set of challenges for etch applications. While planar devices relied more on anisotropic etching, 3D devices require more isotropic etch capabilities with high selectivity between different materials and a nanometric precision of the etching. This work proposes a new route to achieve selective etching using a prototype of reactor combining in the same chamber a remote plasma source (RPS) and a capacitively coupled plasma (CCP) source. The proposed approach relies on cycling a two-step process comprising a functionalization step and a selective removal step of the functionalized surface over the non-functionalized one. If isotropic selective etching is needed, the chemical and isotropic action of the radicals produced in the remote plasma is used to selectively functionalize the material surfaces. On the other side, if topographically-selective etching is needed, the horizontal surfaces are selectively functionalized over vertical surfaces by using implantation of ions produced by the CCP source. The subsequent removal step uses the high selective capability of remote plasma processes (cf. Figure 1). The cycling of those two steps allows the nanometric control of the etching. The concept is inspired by what is already done in the field of atomic layer deposition (ALD) to make selective deposition. [3] [4] The current trend in ALD is to chemically and locally bond a molecule directly to the surface in order to inhibit reactive sites and then prevent further reactions between the ALD precursor molecules. By selectively functionalizing the surface of the materials in presence, selective deposition can be obtained. In our case, it happens that remote plasma processes whose etching mechanisms rely on the action of chemical plasma neutrals are very sensitive to the chemistry of the substrate. By modifying the material surface state with a treatment, the etching can be delayed or even suppressed, converting a non-selective surface into one for which the etching process is area selective. The concept is validated in two case studies. First, it is developed to achieve the isotropic and selective removal of SiGe relative to Si layers in order to fabricate horizontal stacked-Si nanowires for Gate All Around devices. For this particular application, the two-step process is composed of an oxidation step using remote He/O2 remote plasma and an etching step using remote NH3/NF3/O2 remote plasma. It is shown that the Si oxidation during the first step delay or even suppress the Si etching in NH3/NF3/O2 plasma during the second step, allowing very high SiGe over Si selectivity (>60). Secondly, it is applied to the topographically-selective Nitride spacer etching. In this case, the horizontal nitride surfaces were functionalized by H2 ion implantation and the removal step used NH3/NF3/He remote plasma process. Indeed, while pristine SiN is not etched in NH3/NF3/He remote plasma, it is shown that the H implantation has a catalyzing effect on the etching, allowing the removal of horizontal SiN surface with almost infinite selectivity over vertical surface. This work shows that the concept that we propose is very promising for the development of highly area selective etching processes. This work was financially supported by the LabEx Minos ANR-10-LABX-55-01 and the French RENATECH network and technically supported by AMAT France and AMAT USA [1] S. Natarajan et al., “A 14 nm logic technology featuring 2nd-generation FinFET, air-gapped interconnects, self-aligned double patterning and a 0.0588 μm2 SRAM cell size,” in IEDM Tech. Dig., pp. 3.7.1–3.7.3 (2014). [2] P. Zheng, D. Connelly, F. Ding, and T.-J. King Liu, IEEE Trans. Elec. Dev., 62, NO. 12, 3945 (2015) [3] F. S. Minaye Hashemi, B. R. Birchansky, and S. F. Bent, “Selective Deposition of Dielectrics: Limits and Advantages of Alkanethiol Blocking Agents on Metal−Dielectric Patterns” Appl. Mater. Interfaces 2016, 8, 33264−33272 [4] W-H Kim, F. Sadat Minaye Hashemi, A. J. M. Mackus, J. Singh, Y. Kim, D Bobb-Semple, Y. Fan, T. Kaufman-Osborn, L. Godet, and S. F. Bent, A Process for Topographically Selective Deposition on 3D Nanostructures by Ion Implantation ACS Nano 2016, 10, 4451−4458 Figure 1

Efficient Small-Scale Conjugation of DNA to Primary Antibodies for Multiplexed Cellular Targeting.

The combination of the specificity of antibodies and the programmability of DNA nanotechnology has provided the scientific community with a powerful tool to label and unambiguously distinguish a large number of subcellular targets using fluorescence-based read-out methods. Whereas primary antibodies are commercially available for a large class of targets, a general stoichiometric site-selective DNA labeling strategy for this affinity reagent is lacking. Here we present a universal, site-selective conjugation method using a small photo-cross-linkable protein G adaptor that allows labeling of antibodies of different host species with a controlled number of short oligonucleotides (ODNs). Importantly, we illustrate that this conjugation method can be directly performed on commercially available primary antibodies on a small scale and without cross-reactivity towards bovine serum albumin. In addition, we present a general benchtop-compatible strategy to purify DNA-labeled antibodies without a loss of function. The application of protein G-ODN-labeled primary antibodies is demonstrated by employing three well-known methods for detecting subcellular targets using fluorescence read-out, including flow cytometry, DNA-PAINT, and dSTORM. This work thus establishes a general and efficient platform for the synthesis of a library of unique ODN–antibody conjugates, facilitating the broader use of DNA-based programmable tags for multiplexed labeling to identify subcellular features with nanometer precision and improving our understanding of cellular structure and function.

Correlated Cryo Super‐Resolution Light and Cryo‐Electron Microscopy on Mammalian Cells Expressing the Fluorescent Protein rsEGFP2

AbstractSuper‐resolution light microscopy (SRM) enables imaging of biomolecules within cells with nanometer precision. Cryo‐fixation by vitrification offers optimal structure preservation of biological specimens and permits sequential cryo electron microscopy (cryoEM) on the same sample, but is rarely used for SRM due to various technical challenges and the lack of fluorophores developed for vitrified conditions. Here, a protocol to perform correlated cryoSRM and cryoEM on intact mammalian cells using fluorescent proteins and commercially available equipment is described. After cell culture and sample preparation by plunge‐freezing, cryoSRM is performed using the reversibly photoswitchable fluorescent protein rsEGFP2. Next, a super‐resolved image is reconstructed to guide cryoEM imaging to the feature of interest. Finally, the cryoSRM and cryoEM images are correlated to combine information from both imaging modalities. Using this protocol, a localization precision of 30 nm for cryoSRM is routinely achieved. No impediments to successive cryoEM imaging are detected, and the protocol is compatible with a variety of cryoEM techniques. When the optical set‐up and analysis pipeline is established, the total duration of the protocol for experienced cryoEM users is 3 days, not including cell culture.

Valency-Controlled Molecular Spherical Nucleic Acids with Tunable Biosensing Performances.

Spherical nucleic acids (SNAs) play critical roles in many fields, such as molecular diagnostics, disease therapeutics, and materials application. Due to the important role of DNA density on the properties of SNAs, the controlled synthesis of monodisperse SNAs with precise DNA density is an important approach for the structure-function relationship study and finite functions regulation of SNAs. In particular, the construction of monodisperse SNAs in a valency-tunable and site-specific manner is highly important; however, it is still challenging. Herein, on the basis of the high controllability, nanometer precision, and addressable modification ability of framework nucleic acid (FNA), we develop the concept of valency-controlled framework nucleic acid core-based molecular spherical nucleic acids (FNA-mSNAs) with tunable biosensing performances. The FNA-mSNAs consist of a valency-tunable FNA-based DNA nanocube as the core and a controlled, precise number of DNA strands per core. By simply alternating the binding site number for shell DNA strands on the DNA nanocube, homogeneous FNA-mSNAs with different valencies were easily designed, which enabled the molecular level study of the effect of valency on their properties, such as nuclease stability and cellular uptake. Furthermore, taking advantage of the addressable modification ability of FNA, the first heterogeneous molecular SNAs with tunable valency were demonstrated. Importantly, the valency of heterogeneous FNA-mSNAs was able to tune their biosensing performance, such as response dynamics, detection sensitivity, and response range. With these remarkable features, FNA-mSNAs provide new research methods for the development of functional SNAs at the molecular level for a wide range of biological applications.

Stepwise Optimized 3D Printing of Arbitrary 3D Structures at Millimeter Scale with High Precision Surface

Abstract3D printing based on additive manufacturing has attracted widespread attention in the fields of microbiology and microelectronics due to its advantages of waste reduction, arbitrary manufacturing, and rapid prototyping in potential applications. These techniques can create structures at the centimeter scale, however, there are some limitations in terms of resolution and geometric constraints. Here, a micro–nano 3D printing protocol based on additive manufacturing to achieve the 3D structure (3DS) not only possessing millimeter scale structural dimensions but also nanometer features are proposed. A theory is verified to assist the design and fabrication of the 3DS with millimeter scale and nanometer precision. The structures are predesigned and the scanning strategy is optimized before 3D printing to improve the manufacturing efficiency and precision. A customized 3DS with a height of 2.2 mm is obtained, which is a challenge for the conventional two‐photon polymerization fabrication. Furthermore, a 1.2 mm 3DS with inside scaffold and smooth surface is efficiently achieved within 2.7 h with a nanometer surface roughness by using the proposed stepwise optimized 3D printing process. This study offers a flexible and low‐cost technology to generate highly customizable, precisely controllable 3DS for potential applications in microelectronics and microdevices.

Ultrasound experiments on acoustical activity in chiral mechanical metamaterials

Optical activity requires chirality and is a paradigm for chirality. Here, we present experiments on its mechanical counterpart, acoustical activity. The notion “activity” refers the rotation of the linear polarization axis of a transversely polarized (optical or mechanical) wave. The rotation angle is proportional to the propagation distance and does not depend on the orientation of the incident linear polarization. This kind of reciprocal polarization rotation is distinct from nonreciprocal Faraday rotation, which requires broken time-inversion symmetry. In our experiments, we spatiotemporally resolve the motion of three-dimensional chiral microstructured polymer metamaterials, with nanometer precision and under time-harmonic excitation at ultrasound frequencies in the range from 20 to 180 kHz. We demonstrate polarization rotations as large as 22° per unit cell. These experiments pave the road for molding the polarization and direction of elastic waves in three dimensions by micropolar mechanical metamaterials.

All-optical trapping, relocation, and manipulation of nanoparticles using SOI ring resonators

Optical tweezers have opened new doors in microscale research such as single-cell handling and analysis. To develop this technique to nanoscale applications, a number of near-field techniques have been introduced, but they suffer from issues and limitations. Here, we propose simple schemes built by SOI-based optical ring resonators that have efficient trapping and precise transporting functionalities, which are applicable for optical manipulation of nanoparticles. The distribution of the optical intensity excited in a ring resonator and its resultant optical forces on the nanoparticles are calculated numerically. According to the calculations, a subwavelength polystyrene particle as small as 12&#x00A0;nm in radius can be trapped with a depth of 10&#x2009;&#x2009;kBT by an input power of 10&#x00A0;mW and conveyed to a specified location along the ring with nanometer precision. In addition, we show that the introduced schemes are capable of analyzing physical properties of biostructures such as the binding force of a DNA molecule.