Reshaping Covalent Nanowires by Exploiting an Unexpected Plasticity Mediated by Deformation Twinning.

Nanowires (NWs) are among the most studied nanostructures as they have numerous promising applications thanks to their various unique properties. Furthermore, the properties of NWs can be tailored during synthesis by introducing structural defects such as nano-twins, periodic polytypes, and kinks, i.e., abrupt changes in their axial direction. Here, this work reports for the first time the postsynthesis formation of such defects, achieved by exploiting a peculiar plasticity that may occur in nanosized covalent materials. Specifically, in this work the authors found that single-crystal CuO NWs can form double kinks when subjected to external mechanical loading. Both the microscopy and atomistic modeling suggest that deformation-induced twinning along the ( 1 ¯ 10 ) $( {\bar{1}10} )$ plane is the mechanism behind this effect. In a single case the authors are able to unkink a NW back to its initial straight profile, indicating the possibility of reversible plasticity in CuO NWs, which is supported by the atomistic simulations. The phenomenon reported here provides novel insights into the mechanisms of plastic deformation in covalent NWs and offers potential avenues for developing techniques to customize the shape of NWs postsynthesis and introduce new functionalities.

Cryptic Extensibility in von Willebrand Factor Revealed by Molecular Nanodissection.

Von Willebrand factor (VWF) is a multimer with a variable number of protomers, each of which is a head-to-head dimer of two multi-domain monomers. VWF responds to shear through the unfolding and extension of distinct domains, thereby mediating platelet adhesion and aggregation to the injured blood vessel wall. VWF's C1-6 segment uncoils and then the A2 domain unfolds and extends in a hierarchical and sequential manner. However, it is unclear whether there is any reservoir of further extensibility. Here, we explored the presence of cryptic extensibility in VWF by nanodissecting individual, pre-stretched multimers with atomic force microscopy (AFM). The AFM cantilever tip was pressed into the surface and moved in a direction perpendicular to the VWF axis. It was possible to pull out protein loops from VWF, which resulted in a mean contour length gain of 217 nm. In some cases, the loop became cleaved, and a gap was present along the contour. Frequently, small nodules appeared in the loops, indicating that parts of the nanodissected VWF segment remained folded. After analyzing the nodal structure, we conclude that the cryptic extensibility lies within the C1-6 and A1-3 regions. Cryptic extensibility may play a role in maintaining VWF's functionality in extreme shear conditions.

Experimental extraction of Young's modulus of MCF-7 tissue using atomic force microscopy and the spherical contact models.

The study of mechanical properties of tissues can be considered as biomarkers for early detection of cancer and help in new treatments. In this study, the Young's modulus of MCF-7 breast cancer tissue was extracted using atomic force microscopy (AFM) by measuring the interaction force of the sample and performing a simulation. The force-indentation depth diagram was plotted by averaging the experimental results. In this paper, the modulus of elasticity of breast cancer tissue has been extracted with complex models such as DMT, MD, BCP, and SUN. By comparing the experimental and theoretical results and by changing the amount of hypothetical Young's modulus in the spherical contact models, the Young's modulus of the cancer tissue is considered to be between 300 and 400 Pa. The geometry of the cell was also assumed to be spherical according to the images obtained by atomic force microscopy.

Shape memory effect nanotools for nano-creation: examples of nanowire-based devices with charge density waves.

Nanotweezers based on the shape memory effect have been developed and tested. In combination with a commercial nanomanipulator, they allow 3D nanoscale operation controlled in a scanning electron microscope. Here we apply the tweezers for the fabrication of nanostructures based on whiskers of NbS3, a quasi one-dimensional compound with room-temperature charge density wave (CDW). The nanowhiskers were separated without damage from the growth batch, an entangled array, and safely transferred to a substrate with a preliminary deposited Au film. The contacts were fabricated with Pt sputtering on top of the whisker and the film. The high degree of synchronization of the sliding CDW under a RF field with a frequency up to 600 MHz confirms the high quality of the contacts and of the sample structure after the manipulations. The proposed technique paves the way to novel type micro- and nanostructures fabrication and their various applications.

Atomic force microscope as a nano- and micrometer scale biological manipulator: A short review.

The amazing capacity of atomic force microscope to let us touch the molecular and cellular level samples with a sharp probe stimulated its application to bio-medical field among others. In addition to topographical imaging of the sample surface, a direct mechanical manipulation has attracted innovative minds to develop new methodologies aiming at direct handling of proteins, DNA/RNA, and cells. Measurement of their mechanical properties brought about a vivid picture of their physical nature. Direct handling of individual molecules and cells prompted development of nano-medical applications. This short review summarized recent application of AFM for measurement of mechanical properties of biological samples and attempts to perform direct manipulations of nano-medicine.

Discrimination of Protein Amino Acid or Its Protonated State at Single-Residue Resolution by Graphene Nanopores.

The function of a protein is determined by the composition of amino acids and is essential to proteomics. However, protein sequencing remains challenging due to the protein's irregular charge state and its high-order structure. Here, a proof of principle study on the capability of protein sequencing by graphene nanopores integrated with atomic force microscopy is performed using molecular dynamics simulations. It is found that nanopores can discriminate a protein sequence and even its protonation state at single-residue resolution. Both the pulling forces and current blockades induced by the permeation of protein residues are found to be highly correlated with the type of amino acids, which makes the residues identifiable. It is also found that aside from the dimension, both the conformation and charge state of the residue can significantly influence the force and current signal during its permeation through the nanopore. In particular, due to the electro-osmotic flow effect, the blockade current for the double-protonated histidine is slightly smaller than that for single-protonated histidine, which makes it possible for discrimination of different protonation states of amino acids. The results reported here present a novel protein sequencing scheme using graphene nanopores combined with nanomanipulation technology.

Sorting Metal Nanoparticles with Dynamic and Tunable Optical Driven Forces.

Precise sorting of colloidal nanoparticles is a challenging yet necessary task for size-specific applications of nanoparticles in nanophotonics and biochemistry. Here we present a new strategy for all-optical sorting of metal nanoparticles with dynamic and tunable optical driven forces generated by phase gradients of light. Size-dependent optical forces arising from the phase gradients of optical line traps can drive nanoparticles of different sizes with different velocities in solution, leading to their separation along the line traps. By using a sequential combination of optical lines to create differential trapping potentials, we realize precise sorting of silver and gold nanoparticles in the diameter range of 70-150 nm with a resolution down to 10 nm. Separation of the nanoparticles agrees with the analysis of optical forces acting on them and with simulations of their kinetic motions. The results provide new insights into all-optical nanoparticle manipulation and separation and reveal that there is still room to sort smaller nanoparticle with nanometer precision using dynamic phase-gradient forces.

Direct manipulation of metallic nanosheets by shear force microscopy.

Micro/nanomanipulation is a rapidly growing technology and holds promising applications in various fields, including photonic/electronic devices, chemical/biosensors etc. In this work, we present that shear force microscopy (ShFM) can be exploited to manipulate metallic nanosheets besides imaging. The manipulation is realized via controlling the shear force sensor probe position and shear force magnitude based on our homemade ShFM system under an optical microscopy for in situ observation. The main feature of the ShFM system is usage of a piezoelectric bimorph sensor, which has the ability of self-excitation and detection. Moreover, the shear force magnitude as a function of the spring constant of the sensor and setpoint is obtained, which indicates that operation modes can be switched between imaging and manipulation through designing the spring constant before experiment and changing the setpoint during manipulation process, respectively. We believe that this alternative manipulation technique could be used to assemble other nanostructures with different shapes, sizes and compositions for new properties and wider applications.

Visual Servoing-Based Nanorobotic System for Automated Electrical Characterization of Nanotubes inside SEM.

The maneuvering and electrical characterization of nanotubes inside a scanning electron microscope (SEM) has historically been time-consuming and laborious for operators. Before the development of automated nanomanipulation-enabled techniques for the performance of pick-and-place and characterization of nanoobjects, these functions were still incomplete and largely operated manually. In this paper, a dual-probe nanomanipulation system vision-based feedback was demonstrated to automatically perform 3D nanomanipulation tasks, to investigate the electrical characterization of nanotubes. The XY-position of Atomic Force Microscope (AFM) cantilevers and individual carbon nanotubes (CNTs) were precisely recognized via a series of image processing operations. A coarse-to-fine positioning strategy in the Z-direction was applied through the combination of the sharpness-based depth estimation method and the contact-detection method. The use of nanorobotic magnification-regulated speed aided in improving working efficiency and reliability. Additionally, we proposed automated alignment of manipulator axes by visual tracking the movement trajectory of the end effector. The experimental results indicate the system's capability for automated measurement electrical characterization of CNTs. Furthermore, the automated nanomanipulation system has the potential to be extended to other nanomanipulation tasks.

Simple calibration of TIR field depth using the supercoiling response of DNA.

The combination of single-molecule fluorescence and nanomanipulation techniques into a single experimental platform enables one to carry out correlative analysis of the composition and the activity of complex, multicomponent molecular systems. Here we describe implementation and calibration of such a combined system allowing simultaneous single-molecule force spectroscopy and fluorescence imaging of proteins acting on the DNA using magnetic trapping coupled with fluorescence excitation based on a Total Internal Reflection (TIR), or evanescent, field. We propose a simple and robust in situ method for calibration of the TIR field depth against the mechanical properties of nanomanipulated DNA, and which is made possible by the fact that the magnetic bead used to trap and nanomanipulate DNA and measure its conformation also exhibits autofluorescence in the TIR field. Indeed, the fact that the bead size is on the 1-micron scale does not preclude sensitive probing of an intensity field which decays exponentially on the 0.1micron-scale. We demonstrate the usefulness of this approach by mapping out TIR field depth as a function of the angle of incidence of the illuminating laser at the glass-water interface and showing that one recovers the expected theoretical relationship between field depth and angle of incidence.

Quantifying the atomic-level mechanics of single long physisorbed molecular chains.

Individual in situ polymerized fluorene chains 10-100 nm long linked by C-C bonds are pulled vertically from an Au(111) substrate by the tip of a low-temperature atomic force microscope. The conformation of the selected chains is imaged before and after manipulation using scanning tunneling microscopy. The measured force gradient shows strong and periodic variations that correspond to the step-by-step detachment of individual fluorene repeat units. These variations persist at constant intensity until the entire polymer is completely removed from the surface. Calculations based on an extended Frenkel-Kontorova model reproduce the periodicity and magnitude of these features and allow us to relate them to the detachment force and desorption energy of the repeat units. The adsorbed part of the polymer slides easily along the surface during the pulling process, leading to only small oscillations as a result of the high stiffness of the fluorenes and of their length mismatch with respect to the substrate surface structure. A significant lateral force also is caused by the sequential detachment of individual units. The gained insight into the molecule-surface interactions during sliding and pulling should aid the design of mechanoresponsive nanosystems and devices.

Near-Field, On-Chip Optical Brownian Ratchets.

Nanoparticles in aqueous solution are subject to collisions with solvent molecules, resulting in random, Brownian motion. By breaking the spatiotemporal symmetry of the system, the motion can be rectified. In nature, Brownian ratchets leverage thermal fluctuations to provide directional motion of proteins and enzymes. In man-made systems, Brownian ratchets have been used for nanoparticle sorting and manipulation. Implementations based on optical traps provide a high degree of tunability along with precise spatiotemporal control. Here, we demonstrate an optical Brownian ratchet based on the near-field traps of an asymmetrically patterned photonic crystal. The system yields over 25 times greater trap stiffness than conventional optical tweezers. Our technique opens up new possibilities for particle manipulation in a microfluidic, lab-on-chip environment.

Crystal Phase- and Orientation-Dependent Electrical Transport Properties of InAs Nanowires.

We report a systematic study on the correlation of the electrical transport properties with the crystal phase and orientation of single-crystal InAs nanowires (NWs) grown by molecular-beam epitaxy. A new method is developed to allow the same InAs NW to be used for both the electrical measurements and transmission electron microscopy characterization. We find both the crystal phase, wurtzite (WZ) or zinc-blende (ZB), and the orientation of the InAs NWs remarkably affect the electronic properties of the field-effect transistors based on these NWs, such as the threshold voltage (VT), ON-OFF ratio, subthreshold swing (SS) and effective barrier height at the off-state (ΦOFF). The SS increases while VT, ON-OFF ratio, and ΦOFF decrease one by one in the sequence of WZ ⟨0001⟩, ZB ⟨131⟩, ZB ⟨332⟩, ZB ⟨121⟩, and ZB ⟨011⟩. The WZ InAs NWs have obvious smaller field-effect mobility, conductivities, and electron concentration at VBG = 0 V than the ZB InAs NWs, while these parameters are not sensitive to the orientation of the ZB InAs NWs. We also find the diameter ranging from 12 to 33 nm shows much less effect than the crystal phase and orientation on the electrical transport properties of the InAs NWs. The good ohmic contact between InAs NWs and metal remains regardless of the variation of the crystal phase and orientation through temperature-dependent measurements. Our work deepens the understanding of the structure-dependent electrical transport properties of InAs NWs and provides a potential way to tailor the device properties by controlling the crystal phase and orientation of the NWs.

SOP-GPU: influence of solvent-induced hydrodynamic interactions on dynamic structural transitions in protein assemblies.

Hydrodynamic interactions (HI) are incorporated into Langevin dynamics of the Cα -based protein model using the Truncated Expansion approximation (TEA) to the Rotne-Prager-Yamakawa diffusion tensor. Computational performance of the obtained GPU realization demonstrates the model's capability for describing protein systems of varying complexity (10(2) -10(5) residues), including biological particles (filaments, virus shells). Comparison of numerical accuracy of the TEA versus exact description of HI reveals similar results for the kinetics and thermodynamics of protein unfolding. The HI speed up and couple biomolecular transitions through cross-communication among protein domains, which result in more collective displacements of structure elements governed by more deterministic (less variable) dynamics. The force-extension/deformation spectra from nanomanipulations in silico exhibit sharper force signals that match well the experimental profiles. Hence, biomolecular simulations without HI overestimate the role of tension/stress fluctuations. Our findings establish the importance of incorporating implicit water-mediated many-body effects into theoretical modeling of dynamic processes involving biomolecules. © 2016 Wiley Periodicals, Inc.

Aligned Immobilization of Proteins Using AC Electric Fields.

Protein molecules are aligned and immobilized from solution by AC electric fields. In a single-step experiment, the enhanced green fluorescent proteins are immobilized on the surface as well as at the edges of planar nanoelectrodes. Alignment is found to follow the molecules' geometrical shape with their longitudinal axes parallel to the electric field. Simultaneous dielectrophoretic attraction and AC electroosmotic flow are identified as the dominant forces causing protein movement and alignment. Molecular orientation is determined by fluorescence microscopy based on polarized excitation of the proteins' chromophores. The chromophores' orientation with respect to the whole molecule supports X-ray crystal data.

Strain Discontinuity, Avalanche, and Memory in Carbon Nanotube Serpentine Systems.

This work addresses the problem of how a nano-object adheres to a supporting media. The case of study are the serpentine-like structures of single-wall carbon nanotubes (SWNTs) grown on vicinal crystalline quartz. We develop in situ nanomanipulation and confocal Raman spectroscopy in such systems, and to explain the results, we propose a dynamical equation in which static friction is treated phenomenologically and implemented as cutoff for velocities, via Heaviside step function and an adhesion force tensor. We demonstrate that the strain profiles observed along the SWNTs are due to anisotropic adhesion, adhesion discontinuities, strain avalanches, and memory effects. The equation is general enough to make predictions for various one- and two-dimensional nanosystems adhered to a supporting media.

Resistive Switching of Individual, Chemically Synthesized TiO2 Nanoparticles.

Resistively switching devices are considered promising for next-generation nonvolatile random-access memories. Today, such memories are fabricated by means of "top-down approaches" applying thin films sandwiched between nanoscaled electrodes. In contrast, this work presents a "bottom-up approach" disclosing for the first time the resistive switching (RS) of individual TiO2 nanoparticles (NPs). The NPs, which have sizes of 80 and 350 nm, respectively, are obtained by wet chemical synthesis and thermally treated under oxidizing or vacuum conditions for crystallization, respectively. These NPs are deposited on a Pt/Ir bottom electrode and individual NPs are electrically characterized by means of a nanomanipulator system in situ, in a scanning electron microscope. While amorphous NPs and calcined NPs reveal no switching hysteresis, a very interesting behavior is found for the vacuum-annealed, crystalline TiO(2-x) NPs. These NPs reveal forming-free RS behavior, dominantly complementary switching (CS) and, to a small degree, bipolar switching (BS) characteristics. In contrast, similarly vacuum-annealed TiO2 thin films grown by atomic layer deposition show standard BS behavior under the same conditions. The interesting CS behavior of the TiO(2-x) NPs is attributed to the formation of a core-shell-like structure by re-oxidation of the reduced NPs as a unique feature.

Recent Progress on Man-Made Inorganic Nanomachines.

The successful development of nanoscale machinery, which can operate with high controllability, high precision, long lifetimes, and tunable driving powers, is pivotal for the realization of future intelligent nanorobots, nanofactories, and advanced biomedical devices. However, the development of nanomachines remains one of the most difficult research areas, largely due to the grand challenges in fabrication of devices with complex components and actuation with desired efficiency, precision, lifetime, and/or environmental friendliness. In this work, the cutting-edge efforts toward fabricating and actuating various types of nanomachines and their applications are reviewed, with a special focus on nanomotors made from inorganic nanoscale building blocks, which are introduced according to the employed actuation mechanism. The unique characteristics and obstacles for each type of nanomachine are discussed, and perspectives and challenges of this exciting field are presented.

Dielectrophoretic trapping of multilayer DNA origami nanostructures and DNA origami-induced local destruction of silicon dioxide.

DNA origami is a widely used method for fabrication of custom-shaped nanostructures. However, to utilize such structures, one needs to controllably position them on nanoscale. Here we demonstrate how different types of 3D scaffolded multilayer origamis can be accurately anchored to lithographically fabricated nanoelectrodes on a silicon dioxide substrate by DEP. Straight brick-like origami structures, constructed both in square (SQL) and honeycomb lattices, as well as curved "C"-shaped and angular "L"-shaped origamis were trapped with nanoscale precision and single-structure accuracy. We show that the positioning and immobilization of all these structures can be realized with or without thiol-linkers. In general, structural deformations of the origami during the DEP trapping are highly dependent on the shape and the construction of the structure. The SQL brick turned out to be the most robust structure under the high DEP forces, and accordingly, its single-structure trapping yield was also highest. In addition, the electrical conductivity of single immobilized plain brick-like structures was characterized. The electrical measurements revealed that the conductivity is negligible (insulating behavior). However, we observed that the trapping process of the SQL brick equipped with thiol-linkers tended to induce an etched "nanocanyon" in the silicon dioxide substrate. The nanocanyon was formed exactly between the electrodes, that is, at the location of the DEP-trapped origami. The results show that the demonstrated DEP-trapping technique can be readily exploited in assembling and arranging complex multilayered origami geometries. In addition, DNA origamis could be utilized in DEP-assisted deformation of the substrates onto which they are attached.

Optically controlled pore formation in self-sealing giant porphyrin vesicles.

Efforts to develop self-contained microreactors and artificial cells have been limited by difficulty in generating membranes that can be robustly and repeatedly manipulated to load and release cargo from phospholipid compartments. Here we describe a purely optical method to form pores in a membrane generated from porphyrin-phospholipid conjugates electro-assembled into microscale giant porphyrin vesicles and manipulated using confocal microscopy. The pores in the membrane resealed within a minute allowing for repeated pore formation with precise spatial and temporal control and optical gating to allow selective diffusion of biomolecules across the membrane. Temporal control of pore formation was illustrated by performing sequential DNA hybridization reactions. A biotin-avidin based strategy was developed to selectively attach enzymes to the interior of the vesicle, demonstrating spatial control and the potential of giant porphyrin vesicles as versatile microreactors.