Nanometer Distances Research Articles

Circular heat and momentum flux radiated by magneto-optical nanoparticles

In the present Letter we investigate the heat and momentum fluxes radiated by a hot magneto-optical nanoparticle in its surrounding under the action of an external magnetic field. We show that the flux lines circulate in a confined region at nanometric distance from the particle around the axis of magnetic field in a vortex-like configuration. Moreover we prove that the spatial orientation of these vortices (clockwise or counterclockwise) is associated to the contribution of optical resonances with topological charges m = +1 or m = -1 to the thermal emission. This work paves the way to a geometric description of heat and momentum transport in lattices of magneto-optical particles. Moreover it could have important applications in the field of energy storage as well as in thermal management at nanoscale.

Studying structure and function of membrane proteins with PELDOR/DEER spectroscopy - The crystallographers' perspective.

In 1985, the first X-ray structure of a membrane protein was determined. Today, more than 30 years later, many more structures have been solved. Nevertheless, studying the structure of membrane proteins remains a very challenging task. Due to their inherent conformational flexibility, having a single X-ray structure is usually only the first step towards truly understanding the function of these dynamic molecules. For this reason, additional methods are needed that can provide complementary information, especially about conformational flexibility. Pulsed electron-electron double resonance spectroscopy (PELDOR, also known as DEER) is such a method. It can be used to precisely measure nanometer distance distributions between intrinsic or artificially introduced spin-centers in macromolecules and thereby to probe the conformational state of the macromolecule. PELDOR can be applied in solution, in detergent, in lipid bilayers and even within cells. However, PELDOR is an advanced spectroscopy technique and requires specialised equipment and training. This chapter aims to be a starting point for crystallographers and other structural biologists who want to get a better understanding of PELDOR spectroscopy and its application. It gives an insight into the planning stages of the experiment (i.e., which spin labels are possible and where to place them), how a PELDOR experiment is conducted and how the results are interpreted. For this purpose, the substrate binding protein (SBP) from a Vibrio cholerae TRAP transporter is used as a step-by-step example. Further, the chapter gives examples of how PELDOR spectroscopy has previously been applied to overcome known limitations of X-ray crystallography in modern integrative structural biology approaches.

Plasmon-enhanced scattering and charge transfer in few-layer graphene interacting with buried printed 2D-pattern of silver nanoparticles

Hybrid structures combing silver nanoparticles and few-layer graphene have been synthetized by combining low-energy ion beam synthesis and stencil techniques. A single plane of metallic nanoparticles plays the role of an embedded plasmonic enhancer located in dedicated areas at a controlled nanometer distance from deposited graphene layers. Optical imaging, reflectance and Raman scattering mapping are used to measure the enhancement of electronic and vibrational properties of these layers. In particular electronic Raman scattering is shown as notably efficient to analyze the optical transfer of charge carriers between the systems and the presence of intrinsic and extrinsic defects.

Retardation effects in spectroscopic measurements of the Casimir-Polder interaction

Spectroscopy is a unique experimental tool for measuring the fundamental Casimir-Polder interaction between excited state atoms, or other polarisable quantum objects, and a macroscopic surface. Spectroscopic measurements probe atoms at nanometric distances away from the surface where QED retardation is usually negligeable and the atom-surface interaction is proportional to the inverse cube of the separation distance, otherwise known as the van der Waals regime. Here we focus on selective reflection, one of the main spectroscopic probes of Casimir-Polder interactions. We calculate for the first time selective reflection spectra using the full, distance dependent, Casimir-Polder energy shift and linewidth. We demonstrate that retardation can have significant effects, in particular for experiments with low lying energy states. We also show that the effective probing depth of selective reflection spectroscopy depends on the transition linewidth. Our analysis allows us to calculate selective reflection spectra with composite surfaces, such as metasurfaces, dielectric stacks, or even bi-dimensional materials.

A Christmas-Tree-Like Magnetic Field Sensor Based on Domain Wall Depinning in a Notched Nanowire

We propose a magnetic sensor with relatively high resolution that is based on domain wall (DW) pinning and depinning. In a nanowire patterned into a Christmas-tree-like geometry, asymmetric artificial notches serve as “bayonet locks”, which can pin a DW in one direction but allow it to pass in the other direction. The depinning field is linearly dependent on the inverse of the size of bayonet locks, and this dependence can be used to measure an external magnetic field. This concept is demonstrated with micromagnetic simulation, and the accuracy is experimentally estimated. At distances of nanometers, this type of sensor can be used to measure the magnetic fields of objects in biomedicine, such as cells labeled with immune-magnetic-nanoparticles.

Small neutral Gd(iii) tags for distance measurements in proteins by double electron-electron resonance experiments.

Spin labels containing a Gd(iii) ion have become important for measuring nanometer distances in proteins by double electron-electron resonance (DEER) experiments at high EPR frequencies. The distance resolution and sensitivity of these measurements strongly depend on the Gd(iii) tag used. Here we report the performance of two Gd(iii) tags, propargyl-DO3A and C11 in DEER experiments carried out at W-band (95 GHz). Both tags are small, uncharged and devoid of bulky hydrophobic pendants. The propargyl-DO3A tag is designed for conjugation to the azide-group of an unnatural amino acid. The C11 tag is a new tag designed for attachment to a single cysteine residue. The tags delivered narrower distance distributions in the E. coli aspartate/glutamate binding protein and the Zika virus NS2B-NS3 protease than previously established Gd(iii) tags. The improved performance is consistent with the absence of specific hydrophobic or charge-charge interactions with the protein. In the case of the Zika virus NS2B-NS3 protease, unexpectedly broad Gd(iii)-Gd(iii) distance distributions observed with the previously published charged C9 tag, but not the C11 tag, illustrate the potential of tags to perturb a labile protein structure and the importance of different tags. The results obtained with the C11 tag demonstrate the closed conformation in the commonly used linked construct of the Zika virus NS2B-NS3 protease, both in the presence and absence of an inhibitor.

A periodic set of edge dislocations in an elastic semi-infinite solid with a planar boundary incorporating surface effects

The 2-D problem of interacting periodic set of edge dislocations and point forces with planar traction-free surface of semi-infinite elastic solid at the nanoscale is considered. Complex variable based technique and Gurtin-Murdoch model of surface elasticity, which leads to the hypersingular integral equation in surface stress, are used. The solution of this equation and explicit formulas for stress field (Green functions) are obtained in terms of Fourier series. The detailed numerical investigation of stress field induced by the dislocations at the nanometer distance from the surface and the force acting on each dislocation in classical and non-classical (with surface stress) solutions is presented. It is shown that formulas derived for the periodic set of dislocations can be applied to the analysis of the interaction of a single dislocation with the surface as well. The fundamental solutions obtained in the work can be used for applying the boundary integral equation method to an analysis of defects such as cracks and inhomogeneities, periodically distributed at the nanometer distance from the boundary.

A Versatile Method for the Distance-Dependent Structural Characterization of Interacting Soft Interfaces by Neutron Reflectometry.

Interactions between soft interfaces govern the behavior of emulsions and foams and crucially influence the functions of biological entities like membranes. To understand the character of these interactions, detailed insight into the interfaces' structural response in terms of molecular arrangements and conformations is often essential. This requires the realization of controlled interaction conditions and surface-sensitive techniques capable of resolving the structure of buried interfaces. Here, we present a new approach to determine the distance-dependent structure of interacting soft interfaces by neutron reflectometry. A solid/water interface and a water/oil interface are functionalized independently and initially macroscopically separated. They are then brought into contact and structurally characterized under interacting conditions. The nanometric distance between the two interfaces can be varied via the exertion of osmotic pressures. Our first experiments on lipid-anchored polymer brushes interacting across water with solid-grafted polyelectrolyte brushes and with bare silicon surfaces reveal qualitatively different interaction scenarios depending on the chemical composition of the two involved interfaces.

Ultrafast fluorescent decay induced by metal-mediated dipole–dipole interaction in two-dimensional molecular aggregates

Two-dimensional molecular aggregate (2DMA), a thin sheet of strongly interacting dipole molecules self-assembled at close distance on an ordered lattice, is a fascinating fluorescent material. It is distinctively different from the conventional (single or colloidal) dye molecules and quantum dots. In this paper, we verify that when a 2DMA is placed at a nanometric distance from a metallic substrate, the strong and coherent interaction between the dipoles inside the 2DMA dominates its fluorescent decay at a picosecond timescale. Our streak-camera lifetime measurement and interacting lattice-dipole calculation reveal that the metal-mediated dipole-dipole interaction shortens the fluorescent lifetime to about one-half and increases the energy dissipation rate by 10 times that expected from the noninteracting single-dipole picture. Our finding can enrich our understanding of nanoscale energy transfer in molecular excitonic systems and may designate a unique direction for developing fast and efficient optoelectronic devices.

Sub-diffraction discrimination with polarization-resolved two-photon excited fluorescence microscopy

Imaging molecular structures separated by distances of a few nanometers still represents a complex challenge. Moreover, it is normally restricted to observations on thin (few micrometers) samples. In this work, we rotate the polarization of the excitation beam of two-photon excited fluorescence (TPEF) images to show that fluorescent structures at the molecular scale can be discriminated in a living organism. The polarization rotation generates a modulation of the signal intensity in each pixel of the TPEF images that carry information related to the fluorophore orientation. We analyze the signal modulation in every pixel of the polarization-resolved (PR) TPEF images through a Fourier analysis and generate images for the different Fourier components. Doing that, we show that two fluorophores oriented in different directions can be distinguished. Although by imaging the Fourier components the resolution of the optical system restricts the exact localization of two close molecules, discrimination is still possible even when the molecules are located at sub-diffraction distances. We propose a model that predicts this behavior, and demonstrate it experimentally in the neurons of a living Caenorhabditis elegans nematode, where we distinguish the walls of an axon with a diameter below the objective resolution. Since the technique is based in TPEF, the method can be extended to deep tissue imaging and has potential applications in single molecule detection, biological sensors, or super-resolution imaging techniques.

Self-assembled flat-faceted nanoparticles chains as a highly-tunable platform for plasmon-enhanced spectroscopy in the infrared.

Self-assembly fabrication methods can produce aggregates of metallic nanoparticles separated by nanometer distances which act as versatile platforms for field-enhanced spectroscopy due to the strong fields induced at the interparticle gaps. In this letter we show the advantages of using particles with large flat facets at the gap as the building elements of the aggregates. For this purpose, we analyze theoretically the plasmonic response of chains of metallic particles of increasing length. These chains may be a direct product of the chemical synthesis and can be seen as the key structural unit behind the plasmonic response of two and three dimensional self-assembled aggregates. The longitudinal chain plasmon that dominates the optical response redshifts following an exponential dependence on the number of particles in the chain for all facets studied, with a saturation wavelength and a characteristic decay length depending linearly on the diameter of the facet. According to our calculations, for small Au particles of 50 nm size separated by a 1 nanometer gap, the saturation wavelength for the largest facets considered correspond to a wavelength shift of ≈ 1200 nm with respect to the single particle resonance, compared to shifts of only ≈ 200 nm for the equivalent configuration of perfectly spherical particles. The corresponding decay lengths are 11.8 particles for the faceted nanoparticles and 3.5 particles for the spherical ones. Thus, large flat facets lead to an excellent tunability of the longitudinal chain plasmon, covering the whole biological window and beyond. Furthermore, the maximum near-field at the gap is only moderately weaker for faceted gaps than for spherical particles, while the region of strong local field enhancement extends over a considerably larger volume, allowing to accommodate more target molecules. Our results indicate that flat facets introduce significant advantages for spectroscopic and sensing applications using self-assembled aggregates.

Lipid-Mediated Clusters of Guest Molecules in Model Membranes and Their Dissolving in the Presence of Lipid Rafts

The clustering of molecules is an important feature of plasma membrane organization. It is challenging to develop methods for quantifying membrane heterogeneities because of their transient nature and small size. Here, we obtained evidence that transient membrane heterogeneities can be frozen at cryogenic temperatures which allows the application of solid-state experimental techniques sensitive to the nanoscale distance range. We employed the pulsed version of electron paramagnetic resonance (EPR) spectroscopy, the electron spin echo (ESE) technique, for spin-labeled molecules in multilamellar lipid bilayers. ESE decays were refined for pure contribution of spin-spin magnetic dipole-dipolar interaction between the labels; these interactions manifest themselves at a nanometer distance range. The bilayers were prepared from different types of saturated and unsaturated lipids and cholesterol (Chol); in all cases, a small amount of guest spin-labeled substances 5-doxyl-stearic-acid (5-DSA) or 3β-doxyl-5α-cholestane (DChl) was added. The local concentration found of 5-DSA and DChl molecules was remarkably higher than the mean concentration in the bilayer, evidencing the formation of lipid-mediated clusters of these molecules. To our knowledge, formation of nanoscale clusters of guest amphiphilic molecules in biological membranes is a new phenomenon suggested only recently. Two-dimensional 5-DSA molecular clusters were found, whereas flat DChl molecules were found to be clustered into stacked one-dimensional structures. These clusters disappear when the Chol content is varied between the boundaries known for lipid raft formation at room temperatures. The room temperature EPR evidenced entrapping of DChl molecules in the rafts.

Translation of rod-like template sequences into homochiral assemblies of stacked helical oligomers.

At the molecular level, translation refers to the production of a new entity according to a template that has a different chemical composition. In this way, chemical information may be translated from one molecule into another. The process is useful to synthesise structures and thus functions that might be difficult to create otherwise and reaches exquisite levels of efficiency in biological systems as illustrated by protein expression from mRNA templates1,2 or by the assembly of the tobacco mosaic virus capsid protein according to the length of its RNA3. In synthetic systems, examples of template-directed syntheses are numerous4–6, but general and versatile schemes in which a non-natural sequence actually encodes the information necessary to produce a different sequence are few, and far from being optimised7–10. Here we show high-fidelity enzyme-free translation of long rod-like alkylcarbamate oligomers into well-defined sequences of stacked helical aromatic oligoamides. Features present in the rods, including the number and distance between carbamate functions and stereogenic centres, template the self-assembly of complementary stacks of helices each having a defined right (P) or left (M) handedness, length, and single or double helicity. This process enables the production of very large (> 20 kDa) abiotic artificial folded architectures (foldamers11) that may, for example, serve as scaffolds to organize appended functional features at positions in space defined with atomic precision across nanometric distances.

Giant heat transfer in the crossover regime between conduction and radiation

Heat is transferred by radiation between two well-separated bodies at temperatures of finite difference in vacuum. At large distances the heat transfer can be described by black body radiation, at shorter distances evanescent modes start to contribute, and at separations comparable to inter-atomic spacing the transition to heat conduction should take place. We report on quantitative measurements of the near-field mediated heat flux between a gold coated near-field scanning thermal microscope tip and a planar gold sample at nanometre distances of 0.2–7 nm. We find an extraordinary large heat flux which is more than five orders of magnitude larger than black body radiation and four orders of magnitude larger than the values predicted by conventional theory of fluctuational electrodynamics. Different theories of phonon tunnelling are not able to describe the observations in a satisfactory way. The findings demand modified or even new models of heat transfer across vacuum gaps at nanometre distances.

Multiscale modeling of nonlinear electric conductivity in graphene-reinforced nanocomposites taking into account tunnelling effect

Tunnelling effect is a possible mechanism to explain the apparent large electric conductivity and nonlinear electric behavior of graphene-reinforced nanocomposites with polymer matrix. In this work, a numerical modeling framework is proposed to evaluate the effective electric conductivity in polymer composites reinforced with graphene sheets, taking into account the electrical tunnelling effect, which allows conduction between graphene sheets at nanometric distances. We introduce a nonlinear Finite Element formulation and a numerical methodology to model the nonlocal and nonlinear effects introduced by the tunnelling effect conduction model within the polymer matrix between close graphene sheets. In addition, to avoid meshing the thickness of the graphene sheets and in view of their very high aspect ratio, a highly conducting surface model is employed. The computed effective conductivity is evaluated over representative volume elements containing arbitrary distributed graphene sheets. The results exhibit tendencies and percolation thresholds which are in qualitative agreement with the available experimental results.

Submolecular Electroluminescence Mapping of Organic Semiconductors.

The electroluminescence of organic films is the central aspect in organic light emitting diodes (OLEDs) and widely used in current display technology. However, its spatial variation on the molecular scale is essentially unexplored. Here, we address this issue by using scanning tunneling microscopy (STM) and present an in-depth study of the electroluminescence from thin C60 films (<10 monolayers) on Ag(111) and Au(111) surfaces. Similar to an OLED, the metal substrate and STM tip inject complementary charge carriers that may recombine within the molecular film; however, the atomically defined charge injection by the tip enables mapping of the local electroluminescence down to the submolecular scale. We show that the radiative recombination in solid C60 is restricted to various structural defects, whose emission characteristics can be addressed individually. The emission fine structure reveals a coupling to Jahn-Teller active vibrational modes of C60, which implies that its parity-forbidden lowest singlet transition becomes locally allowed at the emission centers. At lateral distances of a few nanometers, only a weak emission from tip-induced plasmons is detectable. Their excitation evidences the injection of both charge carrier types and confirms that they are unable to recombine radiatively at positions far from structural defects. Finally, we demonstrate that the molecular orbital pattern visible in electroluminescence maps enables an unambiguous discrimination between the intrinsic radiative recombination of electron-hole pairs in the organic film and the technique-related emission of tip-induced plasmons. This capability is essential to consolidate STM as a tool to explore the light generation from organic films on the nanoscale.

Near-Field Radiative Heat Transfer under Temperature Gradients and Conductive Transfer

Abstract We describe a recently developed formulation of coupled conductive and radiative heat transfer (RHT) between objects separated by nanometric, vacuum gaps. Our results rely on analytical formulas of RHT between planar slabs (based on the scattering-matrix method) as well as a general formulation of RHT between arbitrarily shaped bodies (based on the fluctuating–volume current method), which fully captures the existence of temperature inhomogeneities. In particular, the impact of RHT on conduction, and vice versa, is obtained via self-consistent solutions of the Fourier heat equation and Maxwell’s equations. We show that in materials with low thermal conductivities (e.g. zinc oxides and glasses), the interplay of conduction and RHT can strongly modify heat exchange, exemplified for instance by the presence of large temperature gradients and saturating flux rates at short (nanometric) distances. More generally, we show that the ability to tailor the temperature distribution of an object can modify the behaviour of RHT with respect to gap separations, e.g. qualitatively changing the asymptotic scaling at short separations from quadratic to linear or logarithmic. Our results could be relevant to the interpretation of both past and future experimental measurements of RHT at nanometric distances.

Selective turn-on and modulation of resonant energy transfer in single plasmonic hybrid nanostructures.

Förster resonant energy transfer (FRET) is a nonradiative process by which the energy of light absorbed by a donor molecule is transferred to an acceptor molecule over a distance of several nanometers. FRET plays a crucial role in photosynthesis and nature-inspired artificial light-harvesting systems that are being explored for use in energy conversion applications. Localized plasmons of metal nanoparticles can potentially lead to a significant increase of FRET efficiency and effective donor-acceptor distance. Here, we prepare hybrid nanostructures composed of a gold nanorod and donor and acceptor molecules covalently attached to its surface, and study them on the level of a single nanoparticle by simultaneous dark-field scattering, fluorescence imaging and spectroscopy. The single-particle approach enables selective excitation of the longitudinal plasmon of the gold nanorod by polarization of the excitation light. The emission intensity of the acceptor molecules can be controllably and reversibly modulated over a wide range by the polarization angle, thus enabling a selective turn-on of the FRET process and control over the emission color of the hybrid nanostructure. Numerical simulations show that the interactions of the donor and acceptor molecules with the plasmon lead to an increase of the energy transfer efficiency by a factor of ∼65. These findings represent the concept of a novel colour switching approach and could pave the way for innovative applications in optoelectronics and nanophotonics.

Fife organizes synaptic vesicles and calcium channels for high-probability neurotransmitter release.

The strength of synaptic connections varies significantly and is a key determinant of communication within neural circuits. Mechanistic insight into presynaptic factors that establish and modulate neurotransmitter release properties is crucial to understanding synapse strength, circuit function, and neural plasticity. We previously identified Drosophila Piccolo-RIM-related Fife, which regulates neurotransmission and motor behavior through an unknown mechanism. Here, we demonstrate that Fife localizes and interacts with RIM at the active zone cytomatrix to promote neurotransmitter release. Loss of Fife results in the severe disruption of active zone cytomatrix architecture and molecular organization. Through electron tomographic and electrophysiological studies, we find a decrease in the accumulation of release-ready synaptic vesicles and their release probability caused by impaired coupling to Ca2+ channels. Finally, we find that Fife is essential for the homeostatic modulation of neurotransmission. We propose that Fife organizes active zones to create synaptic vesicle release sites within nanometer distance of Ca2+ channel clusters for reliable and modifiable neurotransmitter release.

Versatile Trityl Spin Labels for Nanometer Distance Measurements on Biomolecules In Vitro and within Cells.

Structure determination of biomacromolecules under in-cell conditions is a relevant yet challenging task. Electron paramagnetic resonance (EPR) distance measurements in combination with site-directed spin labeling (SDSL) are a valuable tool in this endeavor but the usually used nitroxide spin labels are not well-suited for in-cell measurements. In contrast, triarylmethyl (trityl) radicals are highly persistent, exhibit a long relaxation time and a narrow spectral width. Here, the synthesis of a versatile collection of trityl spin labels and their application in in vitro and in-cell trityl-iron distance measurements on a cytochrome P450 protein are described. The trityl labels show similar labeling efficiencies and better signal-to-noise ratios (SNR) as compared to the popular methanethiosulfonate spin label (MTSSL) and enabled a successful in-cell measurement.