scholarly journals Near-Field Spot for Localized Light-Excitation of a Single Fluorescent Molecule

2020 ◽  
Vol 10 (4) ◽  
pp. 364-374
Author(s):  
Muhammad Shemyal Nisar ◽  
Yujun Cui ◽  
Kaitong Dang ◽  
Liyong Jiang ◽  
Xiangwei Zhao
Keyword(s):  
Single Molecule ◽  
Degrees Of Freedom ◽  
Zero Mode ◽  
Near Field ◽  
3D Structure ◽  
Single Molecules ◽  
Evanescent Waves ◽  
Water Interface ◽  
Large Molecules ◽  
Light Excitation

Abstract Zero-mode waveguides have become important tools for the detection of single molecules. There are still, however, serious challenges because large molecules need to be packed into nano-holes. To circumvent this problem, we investigate and numerically simulate a novel planar sub-wavelength 3-dimension (3D) structure, which is named as near-field spot. It enables the detection of a single molecule in highly concentrated solutions. The near-field spot can produce evanescent waves at the dielectric/water interface, which exponentially decay as they travel away from the dielectric/water interface. These evanescent waves are keys for the detection of fluorescently tagged single molecules. A numerical simulation of the proposed device shows that the performance is comparable with a zero-mode waveguide. Additional degrees-of-freedom, however, can potentially supersede its performance.

scholarly journals High-Resolution Measurement of Molecular Internal Polarization Structure by Photoinduced Force Microscopy

2021 ◽  
Vol 11 (15) ◽  
pp. 6937
Author(s):  
Hidemasa Yamane ◽  
Nobuhiko Yokoshi ◽  
Hajime Ishihara
Keyword(s):  
High Resolution ◽  
Single Molecule ◽  
Near Field ◽  
Critical Role ◽  
Single Molecules ◽  
Atomic Scale ◽  
Metallic Surface ◽  
Metallic Surfaces ◽  
Force Microscopy

Near-field interactions between metallic surfaces and single molecules play an essential role in the application of metamaterials. To reveal the near-field around a photo-irradiated single molecule on the metallic surface, high-resolution photo-assisted scanning microscopy is required. In this study, we theoretically propose photoinduced force microscopy (PiFM) measurements of single molecules at the atomic resolution. For experimental demonstration, we performed a numerical calculation of PiFM images of various transition states, including optical forbidden transitions, and interpreted them in terms of the interaction between the molecular internal polarization structures and localized plasmon. We also clarified the critical role of atomic-scale structures on the tip surface for high-resolution PiFM measurements.

Coherently forming a single molecule in an optical trap

Science ◽  
2020 ◽  
Vol 370 (6514) ◽  
pp. 331-335 ◽  
Author(s):  
Xiaodong He ◽  
Kunpeng Wang ◽  
Jun Zhuang ◽  
Peng Xu ◽  
Xiang Gao ◽  
...  
Keyword(s):  
Single Molecule ◽  
Degrees Of Freedom ◽  
Optical Trap ◽  
Single Molecules ◽  
Precision Measurements ◽  
Weakly Bound ◽  
Full Control ◽  
Atomic Spins ◽  
Potential Applications ◽  
Complex Atom

Ultracold single molecules have wide-ranging potential applications, such as ultracold chemistry, precision measurements, quantum simulation, and quantum computation. However, given the difficulty of achieving full control of a complex atom-molecule system, the coherent formation of single molecules remains a challenge. Here, we report an alternative route to coherently bind two atoms into a weakly bound molecule at megahertz levels by coupling atomic spins to their two-body relative motion in a strongly focused laser with inherent polarization gradients. The coherent nature is demonstrated by long-lived atom-molecule Rabi oscillations. We further manipulate the motional levels of the molecules and measure the binding energy precisely. This work opens the door to full control of all degrees of freedom in atom-molecule systems.

The low-resolution 3D-structure of porin, a channel-forming protein in E. coliouter membranes

1983 ◽  
Vol 41 ◽  
pp. 440-441
Author(s):  
A. Engel ◽  
D.L. Dorset ◽  
A. Massalski ◽  
J.P. Rosenbusch
Keyword(s):  
Crystal Packing ◽  
3D Structure ◽  
Gram Negative Bacteria ◽  
Protein Ratio ◽  
Crystal Forms ◽  
Large Molecules ◽  
Functional Studies ◽  
Voltage Dependent ◽  
Planar Membranes ◽  
Hexagonal Arrays

Porins represent a group of channel forming proteins that facilitate diffusion of small solutes across the outer membrane of Gram-negative bacteria, while excluding large molecules (>650 Da). Planar membranes reconstituted from purified matrix porin (OmpF protein) trimers and phospholipids have allowed quantitative functional studies of the voltage-dependent channels and revealed concerted activation of triplets. Under the same reconstitution conditions but using high protein concentrations porin aggregated to 2D lattices suitable for electron microscopy and image processing. Depending on the lipid-to- protein ratio three different crystal packing arrangements were observed: a large (a = 93 Å) and a small (a = 79 Å) hexagonal and a rectangular (a = 79 Å b = 139 Å) form with p3 symmetry for the hexagonal arrays. In all crystal forms distinct stain filled triplet indentations could be seen and were found to be morphologically identical within a resolution of (22 Å). It is tempting to correlate stain triplets with triple channels, but the proof of this hypothesis requires an analysis of the structure in 3 dimensions.

Design and Fabrication of Linear-shaped Zero Mode Waveguides for Single Molecule Observation of Kinesin and Fluorescent ATP

2017 ◽  
Vol 137 (6) ◽  
pp. 159-164
Author(s):  
Kazuya Fujimoto ◽  
Yuki Morita ◽  
Ryota Iino ◽  
Michio Tomishige ◽  
Hirofumi Shintaku ◽  
...  
Keyword(s):  
Single Molecule ◽  
Zero Mode

Mechanically-Tunable Quantum Interference in Ferrocene-Based Single-Molecule Junctions

2020 ◽  
Author(s):  
María Camarasa-Gómez ◽  
Daniel Hernangómez-Pérez ◽  
Michael S. Inkpen ◽  
Giacomo Lovat ◽  
E-Dean Fung ◽  
...  
Keyword(s):  
Single Molecule ◽  
Quantum Interference ◽  
Degrees Of Freedom ◽  
Building Blocks ◽  
Ferrocene Derivative ◽  
Single Molecule Junctions ◽  
Molecule Junction ◽  
Single Molecule Junction ◽  
The Impact ◽  
D Orbitals

Ferrocenes are ubiquitous organometallic building blocks that comprise a Fe atom sandwiched between two cyclopentadienyl (Cp) rings that rotate freely at room temperature. Of widespread interest in fundamental studies and real-world applications, they have also attracted<br>some interest as functional elements of molecular-scale devices. Here we investigate the impact of<br>the configurational degrees of freedom of a ferrocene derivative on its single-molecule junction<br>conductance. Measurements indicate that the conductance of the ferrocene derivative, which is<br>suppressed by two orders of magnitude as compared to a fully conjugated analog, can be modulated<br>by altering the junction configuration. Ab initio transport calculations show that the low conductance is a consequence of destructive quantum interference effects that arise from the hybridization of metal-based d-orbitals and the ligand-based π-system. By rotating the Cp rings, the hybridization, and thus the quantum interference, can be mechanically controlled, resulting in a conductance modulation that is seen experimentally.<br>

scholarly journals Optimal Relabeling of Water Molecules and Single-Molecule Entropy Estimation

Biophysica ◽  
2021 ◽  
Vol 1 (3) ◽  
pp. 279-296
Author(s):  
Federico Fogolari ◽  
Gennaro Esposito
Keyword(s):  
Single Molecule ◽  
Degrees Of Freedom ◽  
Water Molecules ◽  
Maximum Information ◽  
Nearest Neighbours ◽  
Biomolecular Simulations ◽  
Solvent Molecules ◽  
Solvation Entropy ◽  
Dynamics Simulations ◽  
Internal Degrees Of Freedom

Estimation of solvent entropy from equilibrium molecular dynamics simulations is a long-standing problem in statistical mechanics. In recent years, methods that estimate entropy using k-th nearest neighbours (kNN) have been applied to internal degrees of freedom in biomolecular simulations, and for the rigorous computation of positional-orientational entropy of one and two molecules. The mutual information expansion (MIE) and the maximum information spanning tree (MIST) methods were proposed and used to deal with a large number of non-independent degrees of freedom, providing estimates or bounds on the global entropy, thus complementing the kNN method. The application of the combination of such methods to solvent molecules appears problematic because of the indistinguishability of molecules and of their symmetric parts. All indistiguishable molecules span the same global conformational volume, making application of MIE and MIST methods difficult. Here, we address the problem of indistinguishability by relabeling water molecules in such a way that each water molecule spans only a local region throughout the simulation. Then, we work out approximations and show how to compute the single-molecule entropy for the system of relabeled molecules. The results suggest that relabeling water molecules is promising for computation of solvation entropy.

scholarly journals Three-dimensional total-internal reflection fluorescence nanoscopy with nanometric axial resolution by photometric localization of single molecules

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Alan M. Szalai ◽  
Bruno Siarry ◽  
Jerónimo Lukin ◽  
David J. Williamson ◽  
Nicolás Unsain ◽  
...  
Keyword(s):  
Single Molecule ◽  
Total Internal Reflection ◽  
Single Molecules ◽  
Fluorescence Microscope ◽  
Internal Reflection ◽  
Total Internal Reflection Fluorescence ◽  
Axial Position ◽  
Localization Microscopy ◽  
Localization Precision ◽  
Single Molecule Localization Microscopy

AbstractSingle-molecule localization microscopy enables far-field imaging with lateral resolution in the range of 10 to 20 nanometres, exploiting the fact that the centre position of a single-molecule’s image can be determined with much higher accuracy than the size of that image itself. However, attaining the same level of resolution in the axial (third) dimension remains challenging. Here, we present Supercritical Illumination Microscopy Photometric z-Localization with Enhanced Resolution (SIMPLER), a photometric method to decode the axial position of single molecules in a total internal reflection fluorescence microscope. SIMPLER requires no hardware modification whatsoever to a conventional total internal reflection fluorescence microscope and complements any 2D single-molecule localization microscopy method to deliver 3D images with nearly isotropic nanometric resolution. Performance examples include SIMPLER-direct stochastic optical reconstruction microscopy images of the nuclear pore complex with sub-20 nm axial localization precision and visualization of microtubule cross-sections through SIMPLER-DNA points accumulation for imaging in nanoscale topography with sub-10 nm axial localization precision.

UV laser-assisted multiple evanescent waves lithography for near-field nanopatterning

2009 ◽  
Vol 4 (4) ◽  
pp. 210-214 ◽  
Author(s):  
J.K. Chua ◽  
V.M. Murukeshan
Keyword(s):  
Near Field ◽  
Evanescent Waves ◽  
Uv Laser

Interfacial charge transfer events of BODIPY molecules: single molecule spectroelectrochemistry and substrate effects

2014 ◽  
Vol 16 (42) ◽  
pp. 23150-23156 ◽  
Author(s):  
Jia Liu ◽  
Caleb M. Hill ◽  
Shanlin Pan ◽  
Haiying Liu
Keyword(s):  
Charge Transfer ◽  
Single Molecule ◽  
Single Molecules ◽  
Transfer Mechanism ◽  
Substrate Effects ◽  
Interfacial Charge Transfer ◽  
Charge Transfer Mechanism ◽  
Nanostructured Substrates ◽  
Interfacial Charge

BODIPY dye single molecules on nanostructured substrates are studied with a single molecule spectroelectrochemistry technique to reveal the heterogeneous charge transfer mechanism.

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