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Sensors (Basel, Switzerland) Jan 2020Displacement measuring sensors play an essential role in all aspects of dimensional metrology. They can be used for direct displacement measurements but more often they... (Review)
Review
Displacement measuring sensors play an essential role in all aspects of dimensional metrology. They can be used for direct displacement measurements but more often they are part of a measurement system, such as an atomic force microscope, roughness tester or a coordinate measuring machine (CMM). In order to achieve traceable measurements that can be related to the meter, these sensors must be calibrated against a reference standard that is more noise- and error-free than the sensor under test. A description of the various methods to achieve the ultimate traceability, repeatability and accuracy of such a calibration system is the main part of this paper. Various interferometric methods will be reviewed including several methods that use directly a primary standard as a reference: either an iodine-stabilized laser or a frequency comb. It is shown that various methods exist to quantify or mitigate the periodic errors that are inherent to interferometric methods. Also it is shown that knowledge of this periodicity may lead to a separation of periodic and non-periodic non-linearity errors of both the calibration instrument as the sensor under test. This review is limited to small-range sensors, typically with a range <100 μm. It is concluded that today's technology enables sound and traceable sensor calibration up to the sub-nano and even picometer level of uncertainties.
PubMed: 31973080
DOI: 10.3390/s20030584 -
International Journal of Molecular... Feb 2022Membrane proteins change their conformations in response to chemical and physical stimuli and transmit extracellular signals inside cells. Several approaches have been... (Review)
Review
Membrane proteins change their conformations in response to chemical and physical stimuli and transmit extracellular signals inside cells. Several approaches have been developed for solving the structures of proteins. However, few techniques can monitor real-time protein dynamics. The diffracted X-ray tracking method (DXT) is an X-ray-based single-molecule technique that monitors the internal motion of biomolecules in an aqueous solution. DXT analyzes trajectories of Laue spots generated from the attached gold nanocrystals with a two-dimensional axis by tilting () and twisting (). Furthermore, high-intensity X-rays from synchrotron radiation facilities enable measurements with microsecond-timescale and picometer-spatial-scale intramolecular information. The technique has been applied to various membrane proteins due to its superior spatiotemporal resolution. In this review, we introduce basic principles of DXT, reviewing its recent and extended applications to membrane proteins and living cells, respectively.
Topics: Gold; Membrane Proteins; Motion; Nanotechnology; X-Ray Diffraction; X-Rays
PubMed: 35216461
DOI: 10.3390/ijms23042343 -
Nucleic Acids Research Oct 2022Helicases are essential for nearly all nucleic acid processes across the tree of life, yet detailed understanding of how they couple ATP hydrolysis to translocation and...
Helicases are essential for nearly all nucleic acid processes across the tree of life, yet detailed understanding of how they couple ATP hydrolysis to translocation and unwinding remains incomplete because their small (∼300 picometer), fast (∼1 ms) steps are difficult to resolve. Here, we use Nanopore Tweezers to observe single Escherichia coli RecQ helicases as they translocate on and unwind DNA at ultrahigh spatiotemporal resolution. Nanopore Tweezers simultaneously resolve individual steps of RecQ along the DNA and conformational changes of the helicase associated with stepping. Our data reveal the mechanochemical coupling between physical domain motions and chemical reactions that together produce directed motion of the helicase along DNA. Nanopore Tweezers measurements are performed under either assisting or opposing force applied directly on RecQ, shedding light on how RecQ responds to such forces in vivo. Determining the rates of translocation and physical conformational changes under a wide range of assisting and opposing forces reveals the underlying dynamic energy landscape that drives RecQ motion. We show that RecQ has a highly asymmetric energy landscape that enables RecQ to maintain velocity when encountering molecular roadblocks such as bound proteins and DNA secondary structures. This energy landscape also provides a mechanistic basis making RecQ an 'active helicase,' capable of unwinding dsDNA as fast as it translocates on ssDNA. Such an energy landscape may be a general strategy for molecular motors to maintain consistent velocity despite opposing loads or roadblocks.
Topics: Adenosine Triphosphate; DNA, Single-Stranded; Escherichia coli; Nanopores; Nucleic Acids; RecQ Helicases
PubMed: 36165957
DOI: 10.1093/nar/gkac837 -
ACS Nano Jun 2020Light absorption and emission have their origins in fast atomic-scale phenomena. To characterize these basic steps (.., in photosynthesis, luminescence, and quantum...
Light absorption and emission have their origins in fast atomic-scale phenomena. To characterize these basic steps (.., in photosynthesis, luminescence, and quantum optics), it is necessary to access picosecond temporal and picometer spatial scales simultaneously. In this Perspective, we describe how state-of-the-art picosecond photon correlation spectroscopy combined with luminescence induced at the atomic scale with a scanning tunneling microscope (STM) enables such studies. We outline recent STM-induced luminescence work on single-photon emitters and the dynamics of excitons, charges, molecules, and atoms as well as several prospective experiments concerning light-matter interactions at the nanoscale. We also describe future strategies for measuring and rationalizing ultrafast phenomena at the nanoscale.
PubMed: 32479059
DOI: 10.1021/acsnano.0c03704 -
Physical Chemistry Chemical Physics :... May 2008In this perspective we highlight developments and concepts in the field of 4D electron imaging. With spatial and temporal resolutions reaching the picometer and... (Review)
Review
In this perspective we highlight developments and concepts in the field of 4D electron imaging. With spatial and temporal resolutions reaching the picometer and femtosecond, respectively, the field is now embracing ultrafast electron diffraction, crystallography and microscopy. Here, we overview the principles involved in the direct visualization of structural dynamics with applications in chemistry, materials science and biology. The examples include the studies of complex isolated chemical reactions, phase transitions and cellular structures. We conclude with an outlook on the potential of the approach and with some questions that may define new frontiers of research.
Topics: Animals; Crystallography; Intestines; Microscopy, Electron; Microscopy, Electron, Transmission; Models, Chemical; Molecular Structure; Particle Size; Phase Transition; Time Factors
PubMed: 18473037
DOI: 10.1039/b801626g -
Light, Science & Applications Jun 2023Miniaturization of optical spectrometers is important to enable spectroscopic analysis to play a role in in situ, or even in vitro and in vivo characterization systems....
Miniaturization of optical spectrometers is important to enable spectroscopic analysis to play a role in in situ, or even in vitro and in vivo characterization systems. However, scaled-down spectrometers generally exhibit a strong trade-off between spectral resolution and operating bandwidth, and are often engineered to identify signature spectral peaks only for specific applications. In this paper, we propose and demonstrate a novel global sampling strategy with distributed filters for generating ultra-broadband pseudo-random spectral responses. The geometry of all-pass ring filters is tailored to ensure small self- and cross-correlation for effective information acquisition across the whole spectrum, which dramatically reduces the requirement on sampling channels. We employ the power of reconfigurable photonics in spectrum shaping by embedding the engineered distributed filters. Using a moderate mesh of MZIs, we create 256 diverse spectral responses on a single chip and demonstrate a resolution of 20 pm for single spectral lines and 30 pm for dual spectral lines over a broad bandwidth of 115 nm, to the best of our knowledge achieving a new record of bandwidth-to-resolution ratio. Rigorous simulations reveal that this design will readily be able to achieve single-picometer-scale resolution. We further show that the reconfigurable photonics provides an extra degree of programmability, enabling user-defined features on resolution, computation complexity, and relative error. The use of SiN integration platform enables the spectrometer to exhibit excellent thermal stability of ±2.0 °C, effectively tackling the challenge of temperature variations at picometer-scale resolutions.
PubMed: 37357227
DOI: 10.1038/s41377-023-01195-2 -
Methods (San Diego, Calif.) Aug 2016Single-molecule picometer resolution nanopore tweezers (SPRNT) is a new tool for analyzing the motion of nucleic acids through molecular motors. With SPRNT, individual... (Review)
Review
Single-molecule picometer resolution nanopore tweezers (SPRNT) is a new tool for analyzing the motion of nucleic acids through molecular motors. With SPRNT, individual enzymatic motions along DNA as small as 40pm can be resolved on sub-millisecond time scales. Additionally, SPRNT reveals an enzyme's exact location with respect to a DNA strand's nucleotide sequence, enabling identification of sequence-specific behaviors. SPRNT is enabled by a mutant version of the biological nanopore formed by Mycobacterium smegmatis porin A (MspA). SPRNT is strongly rooted in nanopore sequencing and therefore requires a solid understanding of basic principles of nanopore sequencing. Furthermore, SPRNT shares tools developed for nanopore sequencing and extends them to analysis of single-molecule kinetics. As such, this review begins with a brief history of our work developing the nanopore MspA for nanopore sequencing. We then describe the underlying principles of SPRNT, how it works in detail, and propose some potential future uses. We close with a comparison of SPRNT to other techniques and we present the methods that will enable others to use SPRNT.
Topics: Kinetics; Mycobacterium smegmatis; Nanopores; Nucleic Acids; Optical Tweezers; Porins; Single Molecule Imaging
PubMed: 27045943
DOI: 10.1016/j.ymeth.2016.03.026 -
ACS Nano Jan 2023Acquisition of dense, three-dimensional, force fields with intramolecular resolution via noncontact atomic force microscopy (NC-AFM) has yielded enormous progress in our...
Acquisition of dense, three-dimensional, force fields with intramolecular resolution via noncontact atomic force microscopy (NC-AFM) has yielded enormous progress in our ability to characterize molecular and two-dimensional materials at the atomic scale. To date, intramolecular force mapping has been performed exclusively at cryogenic temperatures, due to the stability afforded by low temperature operation, and as the carbon monoxide functionalization of the metallic scanning probe tip, normally required for submolecular resolution, is only stable at low temperature. In this paper we show that high-resolution, three-dimensional force mapping of a single organic molecule is possible even at room temperature. The physical limitations of room temperature operation are overcome using semiconducting materials to inhibit molecular diffusion and create robust tip apexes, while challenges due to thermal drift are overcome with atom tracking based feedforward correction. Three-dimensional force maps comparable in spatial and force resolution to those acquired at low temperature are demonstrated, permitting a quantitative analysis of the adsorption induced changes in the geometry of the molecule at the picometer level.
PubMed: 36603104
DOI: 10.1021/acsnano.2c09463 -
Optics Express Sep 2016Dual-comb spectroscopy holds the promise as real-time, high-resolution spectroscopy tools. However, in its conventional schemes, the stringent requirement on the...
Dual-comb spectroscopy holds the promise as real-time, high-resolution spectroscopy tools. However, in its conventional schemes, the stringent requirement on the coherence between two lasers requires sophisticated control systems. By replacing control electronics with an all-optical dual-comb lasing scheme, a simplified dual-comb spectroscopy scheme is demonstrated using one dual-wavelength, passively mode-locked fiber laser. Pulses with a intracavity-dispersion-determined repetition-frequency difference are shown to have good mutual coherence and stability. Capability to resolve the comb teeth and a picometer-wide optical spectral resolution are demonstrated using a simple data acquisition system. Energy-efficient, free-running fiber lasers with a small comb-tooth-spacing could enable low-cost dual-comb systems.
PubMed: 27661919
DOI: 10.1364/OE.24.021833 -
Scientific Reports May 2022White light interferometry is a well established technique with diverse precision applications, however, the conventional interferometers such as Michelson, Mach-Zehnder...
White light interferometry is a well established technique with diverse precision applications, however, the conventional interferometers such as Michelson, Mach-Zehnder or Linnik are large in size, demand tedious alignment for obtaining white light fringes, require noise-isolation techniques to achieve sub-nanometric stability and importantly, exhibit unbalanced dispersion causing uncertainty in absolute zero delay reference. Here, we demonstrate an ultrathin white light interferometer enabling picometer resolution by exploiting the wavefront division of a broadband incoherent light beam after transmission through a pair of micrometer thin identical glass plates. Spatial overlap between the two diffracted split wavefronts readily produce high-contrast and stable white light fringes, with unambiguous reference to absolute zero path-delay position. The colored fringes evolve when one of the ultrathin plates is rotated to tune the interferometer with picometric resolution over tens of μm range. Our theoretical analysis validates formation of fringes and highlights self-calibration of the interferometer for picoscale measurements. We demonstrate measurement of coherence length of several broadband incoherent sources as small as a few micrometer with picoscale resolution. Furthermore, we propose a versatile double-pass configuration using the ultrathin interferometer enabling a sample cavity for additional applications in probing dynamical properties of matter.
PubMed: 35606485
DOI: 10.1038/s41598-022-12620-8