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Sample records for fluorophores long-wavelength single-molecule

  1. Bright photoactivatable fluorophores for single-molecule imaging.

    Science.gov (United States)

    Grimm, Jonathan B; English, Brian P; Choi, Heejun; Muthusamy, Anand K; Mehl, Brian P; Dong, Peng; Brown, Timothy A; Lippincott-Schwartz, Jennifer; Liu, Zhe; Lionnet, Timothée; Lavis, Luke D

    2016-12-01

    Small-molecule fluorophores are important tools for advanced imaging experiments. We previously reported a general method to improve small, cell-permeable fluorophores which resulted in the azetidine-containing 'Janelia Fluor' (JF) dyes. Here, we refine and extend the utility of these dyes by synthesizing photoactivatable derivatives that are compatible with live-cell labeling strategies. Once activated, these derived compounds retain the superior brightness and photostability of the JF dyes, enabling improved single-particle tracking and facile localization microscopy experiments.

  2. Colloidal lenses allow high-temperature single-molecule imaging and improve fluorophore photostability

    Science.gov (United States)

    Schwartz, Jerrod J.; Stavrakis, Stavros; Quake, Stephen R.

    2010-02-01

    Although single-molecule fluorescence spectroscopy was first demonstrated at near-absolute zero temperatures (1.8 K), the field has since advanced to include room-temperature observations, largely owing to the use of objective lenses with high numerical aperture, brighter fluorophores and more sensitive detectors. This has opened the door for many chemical and biological systems to be studied at native temperatures at the single-molecule level both in vitro and in vivo. However, it is difficult to study systems and phenomena at temperatures above 37 °C, because the index-matching fluids used with high-numerical-aperture objective lenses can conduct heat from the sample to the lens, and sustained exposure to high temperatures can cause the lens to fail. Here, we report that TiO2 colloids with diameters of 2 µm and a high refractive index can act as lenses that are capable of single-molecule imaging at 70 °C when placed in immediate proximity to an emitting molecule. The optical system is completed by a low-numerical-aperture optic that can have a long working distance and an air interface, which allows the sample to be independently heated. Colloidal lenses were used for parallel imaging of surface-immobilized single fluorophores and for real-time single-molecule measurements of mesophilic and thermophilic enzymes at 70 °C. Fluorophores in close proximity to TiO2 also showed a 40% increase in photostability due to a reduction of the excited-state lifetime.

  3. Investigation of photobleaching and saturation of single molecules by fluorophore recrossing events

    Energy Technology Data Exchange (ETDEWEB)

    Burrows, Sean M.; Reif, Randall D. [Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061 (United States); Pappas, Dimitri [Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061 (United States)], E-mail: d.pappas@ttu.edu

    2007-08-15

    A method for investigation of photobleaching and saturation of single molecules by fluorophore recrossing events in a laser beam is described. The diffraction-limited probe volumes encountered in single-molecule detection (SMD) produce high excitation irradiance, which can decrease available signal. The single molecules of several dyes were detected and the data was used to extract interpeak times above a defined threshold value. The interpeak times revealed the number of fluorophore recrossing events. The number of molecules detected that were within 2 ms of each other represented a molecular recrossing for this work. Calcein, fluorescein and R-phycoerythrin were analyzed and the saturation irradiance and photobleaching effects were determined as a function of irradiance. This approach is simple and it serves as a method of optimizing experimental conditions for single-molecule detection.

  4. Single Molecule Study of Photoconversion and Spectral Heterogeneities of Fluorophores

    DEFF Research Database (Denmark)

    Liao, Zhiyu

    of conformational changes and dynamics. The photophysical properties of organic dyes directly determine the quality of the experiments. So the better understanding of the photophysical properties of organic dyes, the better we are able to design the experiments and interpret the data, especially in single molecule...... important criteria for a good fluorophore. Improving the photostability of organic dyes by designing the structure is always a difficult task for organic chemists. It requires a comprehensive understanding of the mechanism of the photobleaching behavior of fluorophores. It is the aim of this work...... to understand the mechanisms of photobleaching behaviors of organic dyes, terrylene diimide (TDI) and amino-trioxatriangulenium dye (A3-TOTA+). Photobleaching is usually seen as permanent loss of fluorescence. In this work, we show that organic fluorophores can be converted into another chemical compound after...

  5. DNA origami-based shape IDs for single-molecule nanomechanical genotyping

    Science.gov (United States)

    Zhang, Honglu; Chao, Jie; Pan, Dun; Liu, Huajie; Qiang, Yu; Liu, Ke; Cui, Chengjun; Chen, Jianhua; Huang, Qing; Hu, Jun; Wang, Lianhui; Huang, Wei; Shi, Yongyong; Fan, Chunhai

    2017-04-01

    Variations on DNA sequences profoundly affect how we develop diseases and respond to pathogens and drugs. Atomic force microscopy (AFM) provides a nanomechanical imaging approach for genetic analysis with nanometre resolution. However, unlike fluorescence imaging that has wavelength-specific fluorophores, the lack of shape-specific labels largely hampers widespread applications of AFM imaging. Here we report the development of a set of differentially shaped, highly hybridizable self-assembled DNA origami nanostructures serving as shape IDs for magnified nanomechanical imaging of single-nucleotide polymorphisms. Using these origami shape IDs, we directly genotype single molecules of human genomic DNA with an ultrahigh resolution of ~10 nm and the multiplexing ability. Further, we determine three types of disease-associated, long-range haplotypes in samples from the Han Chinese population. Single-molecule analysis allows robust haplotyping even for samples with low labelling efficiency. We expect this generic shape ID-based nanomechanical approach to hold great potential in genetic analysis at the single-molecule level.

  6. Differentiation of ocular fundus fluorophores by fluorescence lifetime imaging using multiple excitation and emission wavelengths

    Science.gov (United States)

    Hammer, M.; Schweitzer, D.; Schenke, S.; Becker, W.; Bergmann, A.

    2006-10-01

    Ocular fundus autofluorescence imaging has been introduced into clinical diagnostics recently. It is in use for the observation of the age pigment lipofuscin, a precursor of age - related macular degeneration (AMD). But other fluorophores may be of interest too: The redox pair FAD - FADH II provides information on the retinal energy metabolism, advanced glycation end products (AGE) indicate protein glycation associated with pathologic processes in diabetes as well as AMD, and alterations in the fluorescence of collagen and elastin in connective tissue give us the opportunity to observe fibrosis by fluorescence imaging. This, however, needs techniques able to differentiate particular fluorophores despite limited permissible ocular exposure as well as excitation wavelength (limited by the transmission of the human ocular lens to >400 nm). We present an ophthalmic laser scanning system (SLO), equipped with picosecond laser diodes (FWHM 100 ps, 446 nm or 468 nm respectively) and time correlated single photon counting (TCSPC) in two emission bands (500 - 560 nm and 560 - 700 nm). The decays were fitted by a bi-exponential model. Fluorescence spectra were measured by a fluorescence spectrometer fluorolog. Upon excitation at 446 nm, the fluorescence of AGE, FAD, and lipofuscin were found to peak at 503 nm, 525 nm, and 600 nm respectively. Accordingly, the statistical distribution of the fluorescence decay times was found to depend on the different excitation wavelengths and emission bands used. The use of multiple excitation and emission wavelengths in conjunction with fluorescence lifetime imaging allows us to discriminate between intrinsic fluorophores of the ocular fundus. Taken together with our knowledge on the anatomical structure of the fundus, these findings suggest an association of the short, middle and long fluorescence decay time to the retinal pigment epithelium, the retina, and connective tissue respectively.

  7. Single-Molecule Plasmon Sensing: Current Status and Future Prospects.

    Science.gov (United States)

    Taylor, Adam B; Zijlstra, Peter

    2017-08-25

    Single-molecule detection has long relied on fluorescent labeling with high quantum-yield fluorophores. Plasmon-enhanced detection circumvents the need for labeling by allowing direct optical detection of weakly emitting and completely nonfluorescent species. This review focuses on recent advances in single molecule detection using plasmonic metal nanostructures as a sensing platform, particularly using a single particle-single molecule approach. In the past decade two mechanisms for plasmon-enhanced single-molecule detection have been demonstrated: (1) by plasmonically enhancing the emission of weakly fluorescent biomolecules, or (2) by monitoring shifts of the plasmon resonance induced by single-molecule interactions. We begin with a motivation regarding the importance of single molecule detection, and advantages plasmonic detection offers. We describe both detection mechanisms and discuss challenges and potential solutions. We finalize by highlighting the exciting possibilities in analytical chemistry and medical diagnostics.

  8. Single-Molecule Detection in Nanogap-Embedded Plasmonic Gratings

    Directory of Open Access Journals (Sweden)

    Biyan Chen

    2015-07-01

    Full Text Available We introduce nanogap-embedded silver plasmonic gratings for single-molecule (SM visualization using an epifluorescence microscope. This silver plasmonic platform was fabricated by a cost-effective nano-imprint lithography technique, using an HD DVD template. DNA/ RNA duplex molecules tagged with Cy3/Cy5 fluorophores were immobilized on SiO 2 -capped silver gratings. Light was coupled to the gratings at particular wavelengths and incident angles to form surface plasmons. The SM fluorescence intensity of the fluorophores at the nanogaps showed approximately a 100-fold mean enhancement with respect to the fluorophores observed on quartz slides using an epifluorescence microscope. This high level of enhancement was due to the concentration of surface plasmons at the nanogaps. When nanogaps imaged with epifluorescence mode were compared to quartz imaged using total internal reflection fluorescence (TIRF microscopy, more than a 30-fold mean enhancement was obtained. Due to the SM fluorescence enhancement of plasmonic gratings and the correspondingly high emission intensity, the required laser power can be reduced, resulting in a prolonged detection time prior to photobleaching. This simple platform was able to perform SM studies with a low-cost epifluorescence apparatus, instead of the more expensive TIRF or confocal microscopes, which would enable SM analysis to take place in most scientific laboratories.

  9. Improved Dye Stability in Single-Molecule Fluorescence Experiments

    Science.gov (United States)

    EcheverrÍa Aitken, Colin; Marshall, R. Andrew; Pugi, Joseph D.

    Complex biological systems challenge existing single-molecule methods. In particular, dye stability limits observation time in singlemolecule fluorescence applications. Current approaches to improving dye performance involve the addition of enzymatic oxygen scavenging systems and small molecule additives. We present an enzymatic oxygen scavenging system that improves dye stability in single-molecule experiments. Compared to the currently-employed glucose-oxidase/catalase system, the protocatechuate-3,4-dioxygenase system achieves lower dissolved oxygen concentration and stabilizes single Cy3, Cy5, and Alexa488 fluorophores. Moreover, this system possesses none of the limitations associated with the glucose oxidase/catalase system. We also tested the effects of small molecule additives in this system. Biological reducing agents significantly destabilize the Cy5 fluorophore as a function of reducing potential. In contrast, anti-oxidants stabilize the Cy3 and Alexa488 fluorophores. We recommend use of the protocatechuate-3,4,-dioxygenase system with antioxidant additives, and in the absence of biological reducing agents. This system should have wide application to single-molecule fluorescence experiments.

  10. Optical detection of two-color-fluorophore barcode for nanopore DNA sensing

    Science.gov (United States)

    Zhang, M.; Sychugov, I.; Schmidt, T.; Linnros, J.

    2015-06-01

    A simple schematic on parallel optical detection of two-fluorophore barcode for single-molecule nanopore sensing is presented. The chosen two fluorophores, ATTO-532 and DY-521-XL, emitting in well-separated spectrum range can be excited at the same wavelength. A beam splitter was employed to separate signals from the two fluorophores and guide them to the same CCD camera. Based on a conventional microscope, sources of background in the nanopore sensing system, including membranes, compounds in buffer solution, and a detection cell was characterized. By photoluminescence excitation measurements, it turned out that silicon membrane has a negligible photoluminescence under the examined excitation from 440 nm to 560 nm, in comparison with a silicon nitrite membrane. Further, background signals from the detection cell were suppressed. Brownian motion of 450 bps DNA labelled with single ATTO-532 or DY-521-XL was successfully recorded by our optical system.

  11. Single-step generation of fluorophore-encapsulated gold nanoparticle core-shell materials

    International Nuclear Information System (INIS)

    Sardar, R; Shem, P M; Pecchia-Bekkum, C; Bjorge, N S; Shumaker-Parry, J S

    2010-01-01

    We report a simple route to produce fluorophore-encapsulated gold nanoparticles (AuNPs) in a single step under aqueous conditions using the fluorophore 1-pyrenemethylamine (PMA). Different amounts of PMA were used and the resulting core-shell gold nanoparticles were analyzed using UV-visible absorption spectroscopy, fluorescence spectroscopy, and transmission and scanning electron microscopy. Electron microscopy analysis shows nanoparticles consisting of a gold nanoparticle core which is encapsulated with a lower contrast shell. In the UV-visible spectra, we observed a significant red shift (37 nm) of the localized surface plasmon resonance (LSPR) absorption maximum (λ max ) compared to citrate-stabilized AuNPs of a similar size. We attribute the prominent LSPR wavelength shift for PMA-AuNP conjugates to the increase in the local dielectric environment near the gold nanoparticles due to the shell formation. This simple, aqueous-based synthesis is a new approach to the production of fluorophore-encapsulated AuNPs that could be applicable in biological sensing systems and photonic device fabrication.

  12. Single-molecule three-color FRET with both negligible spectral overlap and long observation time.

    Directory of Open Access Journals (Sweden)

    Sanghwa Lee

    Full Text Available Full understanding of complex biological interactions frequently requires multi-color detection capability in doing single-molecule fluorescence resonance energy transfer (FRET experiments. Existing single-molecule three-color FRET techniques, however, suffer from severe photobleaching of Alexa 488, or its alternative dyes, and have been limitedly used for kinetics studies. In this work, we developed a single-molecule three-color FRET technique based on the Cy3-Cy5-Cy7 dye trio, thus providing enhanced observation time and improved data quality. Because the absorption spectra of three fluorophores are well separated, real-time monitoring of three FRET efficiencies was possible by incorporating the alternating laser excitation (ALEX technique both in confocal microscopy and in total-internal-reflection fluorescence (TIRF microscopy.

  13. Cell biochemistry studied by single-molecule imaging.

    Science.gov (United States)

    Mashanov, G I; Nenasheva, T A; Peckham, M; Molloy, J E

    2006-11-01

    Over the last decade, there have been remarkable developments in live-cell imaging. We can now readily observe individual protein molecules within living cells and this should contribute to a systems level understanding of biological pathways. Direct observation of single fluorophores enables several types of molecular information to be gathered. Temporal and spatial trajectories enable diffusion constants and binding kinetics to be deduced, while analyses of fluorescence lifetime, intensity, polarization or spectra give chemical and conformational information about molecules in their cellular context. By recording the spatial trajectories of pairs of interacting molecules, formation of larger molecular complexes can be studied. In the future, multicolour and multiparameter imaging of single molecules in live cells will be a powerful analytical tool for systems biology. Here, we discuss measurements of single-molecule mobility and residency at the plasma membrane of live cells. Analysis of diffusional paths at the plasma membrane gives information about its physical properties and measurement of temporal trajectories enables rates of binding and dissociation to be derived. Meanwhile, close scrutiny of individual fluorophore trajectories enables ideas about molecular dimerization and oligomerization related to function to be tested directly.

  14. Single-base resolution and long-coverage sequencing based on single-molecule nanomanipulation

    International Nuclear Information System (INIS)

    An Hongjie; Huang Jiehuan; Lue Ming; Li Xueling; Lue Junhong; Li Haikuo; Zhang Yi; Li Minqian; Hu Jun

    2007-01-01

    We show new approaches towards a novel single-molecule sequencing strategy which consists of high-resolution positioning isolation of overlapping DNA fragments with atomic force microscopy (AFM), subsequent single-molecule PCR amplification and conventional Sanger sequencing. In this study, a DNA labelling technique was used to guarantee the accuracy in positioning the target DNA. Single-molecule multiplex PCR was carried out to test the contamination. The results showed that the two overlapping DNA fragments isolated by AFM could be successfully sequenced with high quality and perfect contiguity, indicating that single-base resolution and long-coverage sequencing have been achieved simultaneously

  15. Versatile single-molecule multi-color excitation and detection fluorescence setup for studying biomolecular dynamics

    KAUST Repository

    Sobhy, M. A.

    2011-11-07

    Single-molecule fluorescence imaging is at the forefront of tools applied to study biomolecular dynamics both in vitro and in vivo. The ability of the single-molecule fluorescence microscope to conduct simultaneous multi-color excitation and detection is a key experimental feature that is under continuous development. In this paper, we describe in detail the design and the construction of a sophisticated and versatile multi-color excitation and emission fluorescence instrument for studying biomolecular dynamics at the single-molecule level. The setup is novel, economical and compact, where two inverted microscopes share a laser combiner module with six individual laser sources that extend from 400 to 640 nm. Nonetheless, each microscope can independently and in a flexible manner select the combinations, sequences, and intensities of the excitation wavelengths. This high flexibility is achieved by the replacement of conventional mechanical shutters with acousto-optic tunable filter (AOTF). The use of AOTF provides major advancement by controlling the intensities, duration, and selection of up to eight different wavelengths with microsecond alternation time in a transparent and easy manner for the end user. To our knowledge this is the first time AOTF is applied to wide-field total internal reflection fluorescence (TIRF) microscopy even though it has been commonly used in multi-wavelength confocal microscopy. The laser outputs from the combiner module are coupled to the microscopes by two sets of four single-mode optic fibers in order to allow for the optimization of the TIRF angle for each wavelength independently. The emission is split into two or four spectral channels to allow for the simultaneous detection of up to four different fluorophores of wide selection and using many possible excitation and photoactivation schemes. We demonstrate the performance of this new setup by conducting two-color alternating excitation single-molecule fluorescence resonance energy

  16. Strong plasmonic enhancement of single molecule photostability in silver dimer optical antennas

    Directory of Open Access Journals (Sweden)

    Kaminska Izabela

    2018-02-01

    Full Text Available Photobleaching is an effect terminating the photon output of fluorophores, limiting the duration of fluorescence-based experiments. Plasmonic nanoparticles (NPs can increase the overall fluorophore photostability through an enhancement of the radiative rate. In this work, we use the DNA origami technique to arrange a single fluorophore in the 12-nm gap of a silver NP dimer and study the number of emitted photons at the single molecule level. Our findings yielded a 30× enhancement in the average number of photons emitted before photobleaching. Numerical simulations are employed to rationalize our results. They reveal the effect of silver oxidation on decreasing the radiative rate enhancement.

  17. Probing Enzyme-Surface Interactions via Protein Engineering and Single-Molecule Techniques

    Science.gov (United States)

    2017-06-26

    SECURITY CLASSIFICATION OF: The overall objective of this research was to exploit protein engineering and fluorescence single-molecule methods to...enhance our understanding of the interaction of proteins and surfaces. Given this objective, the specific aims of this research were to: 1) exploit the...incorporation of unnatural amino acids in proteins to introduce single-molecule probes (i.e., fluorophores for fluorescence resonance energy transfer

  18. A general approach to break the concentration barrier in single-molecule imaging

    KAUST Repository

    Loveland, Anna B.

    2012-09-09

    Single-molecule fluorescence imaging is often incompatible with physiological protein concentrations, as fluorescence background overwhelms an individual molecule\\'s signal. We solve this problem with a new imaging approach called PhADE (PhotoActivation, Diffusion and Excitation). A protein of interest is fused to a photoactivatable protein (mKikGR) and introduced to its surface-immobilized substrate. After photoactivation of mKikGR near the surface, rapid diffusion of the unbound mKikGR fusion out of the detection volume eliminates background fluorescence, whereupon the bound molecules are imaged. We labeled the eukaryotic DNA replication protein flap endonuclease 1 with mKikGR and added it to replication-competent Xenopus laevis egg extracts. PhADE imaging of high concentrations of the fusion construct revealed its dynamics and micrometer-scale movements on individual, replicating DNA molecules. Because PhADE imaging is in principle compatible with any photoactivatable fluorophore, it should have broad applicability in revealing single-molecule dynamics and stoichiometry of macromolecular protein complexes at previously inaccessible fluorophore concentrations. © 2012 Nature America, Inc. All rights reserved.

  19. Structure-guided approach to site-specific fluorophore labeling of the lac repressor LacI.

    Directory of Open Access Journals (Sweden)

    Kalle Kipper

    Full Text Available The lactose operon repressor protein LacI has long served as a paradigm of the bacterial transcription factors. However, the mechanisms whereby LacI rapidly locates its cognate binding site on the bacterial chromosome are still elusive. Single-molecule fluorescence imaging approaches are well suited for the study of these mechanisms but rely on a functionally compatible fluorescence labeling of LacI. Particularly attractive for protein fluorescence labeling are synthetic fluorophores due to their small size and favorable photophysical characteristics. Synthetic fluorophores are often conjugated to natively occurring cysteine residues using maleimide chemistry. For a site-specific and functionally compatible labeling with maleimide fluorophores, the target protein often needs to be redesigned to remove unwanted native cysteines and to introduce cysteines at locations better suited for fluorophore attachment. Biochemical screens can then be employed to probe for the functional activity of the redesigned protein both before and after dye labeling. Here, we report a mutagenesis-based redesign of LacI to enable a functionally compatible labeling with maleimide fluorophores. To provide an easily accessible labeling site in LacI, we introduced a single cysteine residue at position 28 in the DNA-binding headpiece of LacI and replaced two native cysteines with alanines where derivatization with bulky substituents is known to compromise the protein's activity. We find that the redesigned LacI retains a robust activity in vitro and in vivo, provided that the third native cysteine at position 281 is retained in LacI. In a total internal reflection microscopy assay, we observed individual Cy3-labeled LacI molecules bound to immobilized DNA harboring the cognate O1 operator sequence, indicating that the dye-labeled LacI is functionally active. We have thus been able to generate a functional fluorescently labeled LacI that can be used to unravel mechanistic

  20. Optical indicators based on environment sensitive fluorophors

    Energy Technology Data Exchange (ETDEWEB)

    Shakhsher, Z.M.; Seitz, W.R. (Univ. of New Hampshire, Durham, NC (USA))

    1990-01-01

    The authors are interested in the development of optical indicators based on environment sensitive fluorophors. The fluorophor is immobilized on a solid substrate. Interaction with analyte modifies the fluorophor environment, leading to a shift in the distribution of emission wavelengths. Because the indicator is based on spectral shift, it is possible to relate analyte concentration to a ratio of intensities at two different wavelengths. This parameter is insensitive to instrumental drift and slow loss of indicator. Two indicator systems have been investigated. Both involve dansyl derivation, i.e., derivatives of 5-dimethylamino-1-naphthalene sulfonic acid.

  1. Single-molecule imaging reveals topological isomer-dependent diffusion by 4-armed star and dicyclic 8-shaped polymers

    KAUST Repository

    Habuchi, Satoshi; Fujiwara, Susumu; Yamamoto, Takuya; Tezuka, Yasuyuki

    2015-01-01

    Diffusion dynamics of topological isomers of polymer molecules was investigated at the single-molecule level in a melt state by employing the fluorophore-incorporated 4-armed star and the corresponding doubly-cyclized, 8-shaped poly(THF) chains

  2. Single Fluorescent Molecules as Nano-Illuminators for Biological Structure and Function

    Science.gov (United States)

    Moerner, W. E.

    2011-03-01

    Since the first optical detection and spectroscopy of a single molecule in a solid (Phys. Rev. Lett. {62}, 2535 (1989)), much has been learned about the ability of single molecules to probe local nanoenvironments and individual behavior in biological and nonbiological materials in the absence of ensemble averaging that can obscure heterogeneity. Because each single fluorophore acts a light source roughly 1 nm in size, microscopic imaging of individual fluorophores leads naturally to superlocalization, or determination of the position of the molecule with precision beyond the optical diffraction limit, simply by digitization of the point-spread function from the single emitter. For example, the shape of single filaments in a living cell can be extracted simply by allowing a single molecule to move through the filament (PNAS {103}, 10929 (2006)). The addition of photoinduced control of single-molecule emission allows imaging beyond the diffraction limit (super-resolution) and a new array of acronyms (PALM, STORM, F-PALM etc.) and advances have appeared. We have used the native blinking and switching of a common yellow-emitting variant of green fluorescent protein (EYFP) reported more than a decade ago (Nature {388}, 355 (1997)) to achieve sub-40 nm super-resolution imaging of several protein structures in the bacterium Caulobacter crescentus: the quasi-helix of the actin-like protein MreB (Nat. Meth. {5}, 947 (2008)), the cellular distribution of the DNA binding protein HU (submitted), and the recently discovered division spindle composed of ParA filaments (Nat. Cell Biol. {12}, 791 (2010)). Even with these advances, better emitters would provide more photons and improved resolution, and a new photoactivatable small-molecule emitter has recently been synthesized and targeted to specific structures in living cells to provide super-resolution images (JACS {132}, 15099 (2010)). Finally, a new optical method for extracting three-dimensional position information based on

  3. Single Molecule Fluorescence: from Physical Fascination to Biological Relevance

    OpenAIRE

    Segers-Nolten, Gezina M.J.

    2003-01-01

    Confocal fluorescence microscopy is particularly well-known from the beautiful images that have been obtained with this technique from cells. Several cellular components could be nicely visualized simultaneously by staining them with different fluorophores. Not only for ensemble applications but also in single molecule research confocal fluorescence microscopy became a popular technique. In this thesis the possibilities are shown to study a complicated biological process, which is Nucleotide ...

  4. DNA-psoralen interaction: a single molecule experiment.

    Science.gov (United States)

    Rocha, M S; Viana, N B; Mesquita, O N

    2004-11-15

    By attaching one end of a single lambda-DNA molecule to a microscope coverslip and the other end to a polystyrene microsphere trapped by an optical tweezers, we can study the entropic elasticity of the lambda-DNA by measuring force versus extension as we stretch the molecule. This powerful method permits single molecule studies. We are particularly interested in the effects of the photosensitive drug psoralen on the elasticity of the DNA molecule. We have illuminated the sample with different light sources, studying how the different wavelengths affect the psoralen-DNA linkage. To do this, we measure the persistence length of individual DNA-psoralen complexes.

  5. Maximum likelihood-based analysis of photon arrival trajectories in single-molecule FRET

    Energy Technology Data Exchange (ETDEWEB)

    Waligorska, Marta [Adam Mickiewicz University, Faculty of Chemistry, Grunwaldzka 6, 60-780 Poznan (Poland); Molski, Andrzej, E-mail: amolski@amu.edu.pl [Adam Mickiewicz University, Faculty of Chemistry, Grunwaldzka 6, 60-780 Poznan (Poland)

    2012-07-25

    Highlights: Black-Right-Pointing-Pointer We study model selection and parameter recovery from single-molecule FRET experiments. Black-Right-Pointing-Pointer We examine the maximum likelihood-based analysis of two-color photon trajectories. Black-Right-Pointing-Pointer The number of observed photons determines the performance of the method. Black-Right-Pointing-Pointer For long trajectories, one can extract mean dwell times that are comparable to inter-photon times. -- Abstract: When two fluorophores (donor and acceptor) are attached to an immobilized biomolecule, anti-correlated fluctuations of the donor and acceptor fluorescence caused by Foerster resonance energy transfer (FRET) report on the conformational kinetics of the molecule. Here we assess the maximum likelihood-based analysis of donor and acceptor photon arrival trajectories as a method for extracting the conformational kinetics. Using computer generated data we quantify the accuracy and precision of parameter estimates and the efficiency of the Akaike information criterion (AIC) and the Bayesian information criterion (BIC) in selecting the true kinetic model. We find that the number of observed photons is the key parameter determining parameter estimation and model selection. For long trajectories, one can extract mean dwell times that are comparable to inter-photon times.

  6. 48-spot single-molecule FRET setup with periodic acceptor excitation

    Science.gov (United States)

    Ingargiola, Antonino; Segal, Maya; Gulinatti, Angelo; Rech, Ivan; Labanca, Ivan; Maccagnani, Piera; Ghioni, Massimo; Weiss, Shimon; Michalet, Xavier

    2018-03-01

    Single-molecule Förster resonance energy transfer (smFRET) allows measuring distances between donor and acceptor fluorophores on the 3-10 nm range. Solution-based smFRET allows measurement of binding-unbinding events or conformational changes of dye-labeled biomolecules without ensemble averaging and free from surface perturbations. When employing dual (or multi) laser excitation, smFRET allows resolving the number of fluorescent labels on each molecule, greatly enhancing the ability to study heterogeneous samples. A major drawback to solution-based smFRET is the low throughput, which renders repetitive measurements expensive and hinders the ability to study kinetic phenomena in real-time. Here we demonstrate a high-throughput smFRET system that multiplexes acquisition by using 48 excitation spots and two 48-pixel single-photon avalanche diode array detectors. The system employs two excitation lasers allowing separation of species with one or two active fluorophores. The performance of the system is demonstrated on a set of doubly labeled double-stranded DNA oligonucleotides with different distances between donor and acceptor dyes along the DNA duplex. We show that the acquisition time for accurate subpopulation identification is reduced from several minutes to seconds, opening the way to high-throughput screening applications and real-time kinetics studies of enzymatic reactions such as DNA transcription by bacterial RNA polymerase.

  7. A novel single fluorophore-labeled double-stranded oligonucleotide probe for fluorescence-enhanced nucleic acid detection based on the inherent quenching ability of deoxyguanosine bases and competitive strand-displacement reaction.

    Science.gov (United States)

    Zhang, Yingwei; Tian, Jingqi; Li, Hailong; Wang, Lei; Sun, Xuping

    2012-01-01

    We develop a novel single fluorophore-labeled double-stranded oligonucleotide (OND) probe for rapid, nanostructure-free, fluorescence-enhanced nucleic acid detection for the first time. We further demonstrate such probe is able to well discriminate single-base mutation in nucleic acid. The design takes advantage of an inherent quenching ability of guanine bases. The short strand of the probe is designed with an end-labeled fluorophore that is placed adjacent to two guanines as the quencher located on the long opposite strand, resulting in great quenching of dye fluorescence. In the presence of a target complementary to the long strand of the probe, a competitive strand-displacement reaction occurs and the long strand forms a more stable duplex with the target, resulting in the two strands of the probe being separated from each other. As a consequence of this displacement, the fluorophore and the quencher are no longer in close proximity and dye fluorescence increases, signaling the presence of target.

  8. Imaging Live Cells at the Nanometer-Scale with Single-Molecule Microscopy: Obstacles and Achievements in Experiment Optimization for Microbiology

    Science.gov (United States)

    Haas, Beth L.; Matson, Jyl S.; DiRita, Victor J.; Biteen, Julie S.

    2015-01-01

    Single-molecule fluorescence microscopy enables biological investigations inside living cells to achieve millisecond- and nanometer-scale resolution. Although single-molecule-based methods are becoming increasingly accessible to non-experts, optimizing new single-molecule experiments can be challenging, in particular when super-resolution imaging and tracking are applied to live cells. In this review, we summarize common obstacles to live-cell single-molecule microscopy and describe the methods we have developed and applied to overcome these challenges in live bacteria. We examine the choice of fluorophore and labeling scheme, approaches to achieving single-molecule levels of fluorescence, considerations for maintaining cell viability, and strategies for detecting single-molecule signals in the presence of noise and sample drift. We also discuss methods for analyzing single-molecule trajectories and the challenges presented by the finite size of a bacterial cell and the curvature of the bacterial membrane. PMID:25123183

  9. In Planta Single-Molecule Pull-Down Reveals Tetrameric Stoichiometry of HD-ZIPIII:LITTLE ZIPPER Complexes.

    Science.gov (United States)

    Husbands, Aman Y; Aggarwal, Vasudha; Ha, Taekjip; Timmermans, Marja C P

    2016-08-01

    Deciphering complex biological processes markedly benefits from approaches that directly assess the underlying biomolecular interactions. Most commonly used approaches to monitor protein-protein interactions typically provide nonquantitative readouts that lack statistical power and do not yield information on the heterogeneity or stoichiometry of protein complexes. Single-molecule pull-down (SiMPull) uses single-molecule fluorescence detection to mitigate these disadvantages and can quantitatively interrogate interactions between proteins and other compounds, such as nucleic acids, small molecule ligands, and lipids. Here, we establish SiMPull in plants using the HOMEODOMAIN LEUCINE ZIPPER III (HD-ZIPIII) and LITTLE ZIPPER (ZPR) interaction as proof-of-principle. Colocalization analysis of fluorophore-tagged HD-ZIPIII and ZPR proteins provides strong statistical evidence of complex formation. In addition, we use SiMPull to directly quantify YFP and mCherry maturation probabilities, showing these differ substantially from values obtained in mammalian systems. Leveraging these probabilities, in conjunction with fluorophore photobleaching assays on over 2000 individual complexes, we determined HD-ZIPIII:ZPR stoichiometry. Intriguingly, these complexes appear as heterotetramers, comprising two HD-ZIPIII and two ZPR molecules, rather than heterodimers as described in the current model. This surprising result raises new questions about the regulation of these key developmental factors and is illustrative of the unique contribution SiMPull is poised to make to in planta protein interaction studies. © 2016 American Society of Plant Biologists. All rights reserved.

  10. Single-wavelength functional photoacoustic microscopy in biological tissue.

    Science.gov (United States)

    Danielli, Amos; Favazza, Christopher P; Maslov, Konstantin; Wang, Lihong V

    2011-03-01

    Recently, we developed a reflection-mode relaxation photoacoustic microscope, based on saturation intensity, to measure picosecond relaxation times using a nanosecond laser. Here, using the different relaxation times of oxygenated and deoxygenated hemoglobin molecules, both possessing extremely low fluorescence quantum yields, the oxygen saturation was quantified in vivo with single-wavelength photoacoustic microscopy. All previous functional photoacoustic microscopy measurements required imaging with multiple-laser-wavelength measurements to quantify oxygen saturation. Eliminating the need for multiwavelength measurements removes the influence of spectral properties on oxygenation calculations and improves the portability and cost-effectiveness of functional or molecular photoacoustic microscopy.

  11. Single-wavelength functional photoacoustic microscopy in biological tissue

    OpenAIRE

    Danielli, Amos; Favazza, Christopher P.; Maslov, Konstantin; Wang, Lihong V.

    2011-01-01

    Recently, we developed a reflection-mode relaxation photoacoustic microscope, based on saturation intensity, to measure picosecond relaxation times using a nanosecond laser. Here, using the different relaxation times of oxygenated and deoxygenated hemoglobin molecules, both possessing extremely low fluorescence quantum yields, the oxygen saturation was quantified in vivo with single-wavelength photoacoustic microscopy. All previous functional photoacoustic microscopy measurements required ima...

  12. A laser scanner for imaging fluorophore labeled molecules in electrophoretic gels

    Energy Technology Data Exchange (ETDEWEB)

    Fisk, D.J.; Sutherland, J.C. [Brookhaven National Lab., Upton, NY (United States). Biology Dept.

    1995-08-01

    A laser scanner for imaging electrophoretic gels was constructed and tested. The scanner incorporates a green helium-neon (HeNe) laser (543.5nm wavelength) and can achieve a spatial resolution of 19{micro}m. The instrument can function in two modes : snap-shot and finish-line. In snapshot mode, all samples are electrophoresed for the same time and the gel is scanned after completion of electrophoresis, while in finish-line mode, fluorophore labeled samples are electrophoresed for a constant distance and the image is formed as the samples pass under the detector. The resolving power of the finish-line mode of imaging is found to be greater than that of the snapshot mode of imaging. This laser scanner is also compared with a Charge Coupled Device (CCD) camera and in terms of resolving power is found to be superior. Sensitivity of the instrument is presented in terms of the minimum amount of DNA that can be detected verses its molecular length.

  13. Single-molecule spectromicroscopy: a route towards sub-wavelength refractometry.

    Science.gov (United States)

    Anikushina, T A; Gladush, M G; Gorshelev, A A; Naumov, A V

    2015-01-01

    We suggest a novel approach for spatially resolved probing of local fluctuations of the refractive index n in solids by means of single-molecule (SM) spectroscopy. It is based on the dependence T1(n) of the effective radiative lifetime T1 of dye centres in solids on n due to the local-field effects. Detection of SM zero-phonon lines at low temperatures gives the values of the SM natural spectral linewidth (which is inversely proportional to T1) and makes it possible to reveal the distribution of the local n values in solids. Here we demonstrate this possibility on the example of amorphous polyethylene and polycrystalline naphthalene doped with terrylene. In particular, we show that the obtained distributions of lifetime limited spectral linewidths of terrylene molecules embedded into these matrices are due to the spatial fluctuations of the refractive index local values.

  14. Labeling proteins inside living cells using external fluorophores for microscopy.

    Science.gov (United States)

    Teng, Kai Wen; Ishitsuka, Yuji; Ren, Pin; Youn, Yeoan; Deng, Xiang; Ge, Pinghua; Lee, Sang Hak; Belmont, Andrew S; Selvin, Paul R

    2016-12-09

    Site-specific fluorescent labeling of proteins inside live mammalian cells has been achieved by employing Streptolysin O, a bacterial enzyme which forms temporary pores in the membrane and allows delivery of virtually any fluorescent probes, ranging from labeled IgG's to small ligands, with high efficiency (>85% of cells). The whole process, including recovery, takes 30 min, and the cell is ready to be imaged immediately. A variety of cell viability tests were performed after treatment with SLO to ensure that the cells have intact membranes, are able to divide, respond normally to signaling molecules, and maintains healthy organelle morphology. When combined with Oxyrase, a cell-friendly photostabilizer, a ~20x improvement in fluorescence photostability is achieved. By adding in glutathione, fluorophores are made to blink, enabling super-resolution fluorescence with 20-30 nm resolution over a long time (~30 min) under continuous illumination. Example applications in conventional and super-resolution imaging of native and transfected cells include p65 signal transduction activation, single molecule tracking of kinesin, and specific labeling of a series of nuclear and cytoplasmic protein complexes.

  15. Single Mode Fiber Optic Transceiver Using Short Wavelength Active Devices In Long Wavelength Fiber

    Science.gov (United States)

    Gillham, Frederick J.; Campbell, Daniel R.; Corke, Michael; Stowe, David W.

    1990-01-01

    Presently, single mode optical fiber technology is being utilized in systems to supply telephone service to the subscriber. However, in an attempt to be competitive with copper based systems, there are many development programs underway to determine the most cost effective solution while still providing a service that will either satisfy or be upgradeable to satisfy the demands of the consumer for the next 10 to 20 years. One such approach is to combine low cost laser transmitters and silicon receivers, which have been developed for the "compact disc" industry, with fiber that operates in the single mode regime at 1300 nm. In this paper, an optical transceiver will be presented, consisting of a compact disc laser, a silicon detector and a single mode coupler at 1300 nm. A possible system layout is presented which operates at 780 nm bi-directionally for POTS and upgradeable to 1300 nm for video services. There are several important design criteria that have to be considered in the development of such a system which will be addressed. These include: 1. Optimization of coupled power from laser to fiber while maintaining stable launched conditions over a wide range of environmental conditions. 2. Consideration of the multimode operation of the 1300 nm single mode fiber while operating in the 780 nm wavelength region. 3. Development of a low cost pseudo-wavelength division multiplexer for 1300 nm single mode/780 nm multimode operation and a low cost dual mode 50/50, 780 nm splitter using 1300 nm fiber. Details will be given of the design criteria and solution in terms of optimized design. Results of the performance of several prototype devices will be given with indications of the merits of this approach and where further development effort should be applied.

  16. Circumvention of fluorophore photobleaching in fluorescence fluctuation experiments: a beam scanning approach.

    Science.gov (United States)

    Satsoura, Dmitri; Leber, Brian; Andrews, David W; Fradin, Cécile

    2007-04-23

    Photobleaching is a fluorophore-damaging process that commonly afflicts single-molecule fluorescence studies. It becomes an especially severe problem in fluorescence fluctuation experiments when studying slowly diffusing particles. One way to circumvent this problem is to use beam scanning to decrease the residence time of the fluorophores in the excitation volume. We report a systematic study of the effects of circular beam scanning on the photobleaching of fluorescent particles as observed in single-photon excitation fluorescence fluctuation experiments. We start by deriving a simple expression relating the average detected fluorescence to the photobleaching cross section of the fluorophores. We then perform numerical calculations of the spatial distribution of fluorescent particles in order to understand under which conditions beam scanning can prevent the formation of a photobleaching hole. To support these predictions, we show experimental results obtained for large unilamellar vesicles containing a small amount of the fluorescent lipophilic tracer DiD. We establish the required scanning radius and frequency range in order to obtain sufficient reduction of the photobleaching effect for that system. From the detected increase in fluorescence upon increase in scanning speed, we estimate the photobleaching cross section of DiD.

  17. Single molecule localization imaging of telomeres and centromeres using fluorescence in situ hybridization and semiconductor quantum dots.

    Science.gov (United States)

    Wang, Le; Zong, Shenfei; Wang, Zhuyuan; Lu, Ju; Chen, Chen; Zhang, Ruohu; Cui, Yiping

    2018-07-13

    Single molecule localization microscopy (SMLM) is a powerful tool for imaging biological targets at the nanoscale. In this report, we present SMLM imaging of telomeres and centromeres using fluorescence in situ hybridization (FISH). The FISH probes were fabricated by decorating CdSSe/ZnS quantum dots (QDs) with telomere or centromere complementary DNA strands. SMLM imaging experiments using commercially available peptide nucleic acid (PNA) probes labeled with organic fluorophores were also conducted to demonstrate the advantages of using QDs FISH probes. Compared with the PNA probes, the QDs probes have the following merits. First, the fluorescence blinking of QDs can be realized in aqueous solution or PBS buffer without thiol, which is a key buffer component for organic fluorophores' blinking. Second, fluorescence blinking of the QDs probe needs only one excitation light (i.e. 405 nm). While fluorescence blinking of the organic fluorophores usually requires two illumination lights, that is, the activation light (i.e. 405 nm) and the imaging light. Third, the high quantum yield, multiple switching times and a good optical stability make the QDs more suitable for long-term imaging. The localization precision achieved in telomeres and centromeres imaging experiments is about 30 nm, which is far beyond the diffraction limit. SMLM has enabled new insights into telomeres or centromeres on the molecular level, and it is even possible to determine the length of telomere and become a potential technique for telomere-related investigation.

  18. Coherent interaction of single molecules and plasmonic nanowires

    Science.gov (United States)

    Gerhardt, Ilja; Grotz, Bernhard; Siyushev, Petr; Wrachtrup, Jörg

    2017-09-01

    Quantum plasmonics opens the option to integrate complex quantum optical circuitry onto chip scale devices. In the past, often external light sources were used and nonclassical light was coupled in and out of plasmonic structures, such as hole arrays or waveguide structures. Another option to launch single plasmonic excitations is the coupling of single emitters in the direct proximity of, e.g., a silver or gold nanostructure. Here, we present our attempts to integrate the research of single emitters with wet-chemically grown silver nanowires. The emitters of choice are single organic dye molecules under cryogenic conditions, which are known to act as high-brightness and extremely narrow-band single photon sources. Another advantage is their high optical nonlinearity, such that they might mediate photon-photon interactions on the nanoscale. We report on the coupling of a single molecule fluorescence emission through the wire over the length of several wavelengths. The transmission of coherently emitted photons is proven by an extinction type experiment. As for influencing the spectral properties of a single emitter, we are able to show a remote change of the line-width of a single terrylene molecule, which is in close proximity to the nanowire.

  19. A green-light-emitting, spontaneously blinking fluorophore based on intramolecular spirocyclization for dual-colour super-resolution imaging.

    Science.gov (United States)

    Uno, Shin-Nosuke; Kamiya, Mako; Morozumi, Akihiko; Urano, Yasuteru

    2017-12-19

    We have developed the first green-light-emitting, spontaneously blinking fluorophore (SBF), HEtetTFER. In combination with our near-infrared-light-emitting SBF (HMSiR), HEtetTFER allows dual-colour single-molecule localization microscopy (SMLM) in buffer solution without any additive and without photoactivation.

  20. Single-molecule imaging reveals topological isomer-dependent diffusion by 4-armed star and dicyclic 8-shaped polymers

    KAUST Repository

    Habuchi, Satoshi

    2015-04-21

    Diffusion dynamics of topological isomers of polymer molecules was investigated at the single-molecule level in a melt state by employing the fluorophore-incorporated 4-armed star and the corresponding doubly-cyclized, 8-shaped poly(THF) chains. While the single-molecule fluorescence imaging experiment revealed that the diffusion of the 4-armed star polymer was described by a single Gaussian distribution, the diffusion of the 8-shaped polymer exhibited a double Gaussian distribution behaviour. We reasoned that the two 8-shaped polymeric isomers have distinct diffusion modes in the melt state, although ensemble-averaged experimental methods cannot detect differences in overall conformational state of the isomers. The single-molecule experiments suggested that one of the 8-shaped polymeric isomer, having the horizontally oriented form, causes an efficient threading with the linear matrix chains which leads to the slower diffusion compared with the corresponding 4-armed star polymer, while the other 8-shaped polymeric isomer, having the vertically oriented form, displayed faster diffusion by the suppression of effective threading with the linear matrix chains due to its contracted chain conformation.

  1. Förster resonance energy transfer: Role of diffusion of fluorophore orientation and separation in observed shifts of FRET efficiency.

    Directory of Open Access Journals (Sweden)

    Bram Wallace

    Full Text Available Förster resonance energy transfer (FRET is a widely used single-molecule technique for measuring nanoscale distances from changes in the non-radiative transfer of energy between donor and acceptor fluorophores. For macromolecules and complexes this observed transfer efficiency is used to infer changes in molecular conformation under differing experimental conditions. However, sometimes shifts are observed in the FRET efficiency even when there is strong experimental evidence that the molecular conformational state is unchanged. We investigate ways in which such discrepancies can arise from kinetic effects. We show that significant shifts can arise from the interplay between excitation kinetics, orientation diffusion of fluorophores, separation diffusion of fluorophores, and non-emitting quenching.

  2. Compact quantum dots for single-molecule imaging.

    Science.gov (United States)

    Smith, Andrew M; Nie, Shuming

    2012-10-09

    Single-molecule imaging is an important tool for understanding the mechanisms of biomolecular function and for visualizing the spatial and temporal heterogeneity of molecular behaviors that underlie cellular biology (1-4). To image an individual molecule of interest, it is typically conjugated to a fluorescent tag (dye, protein, bead, or quantum dot) and observed with epifluorescence or total internal reflection fluorescence (TIRF) microscopy. While dyes and fluorescent proteins have been the mainstay of fluorescence imaging for decades, their fluorescence is unstable under high photon fluxes necessary to observe individual molecules, yielding only a few seconds of observation before complete loss of signal. Latex beads and dye-labeled beads provide improved signal stability but at the expense of drastically larger hydrodynamic size, which can deleteriously alter the diffusion and behavior of the molecule under study. Quantum dots (QDs) offer a balance between these two problematic regimes. These nanoparticles are composed of semiconductor materials and can be engineered with a hydrodynamically compact size with exceptional resistance to photodegradation (5). Thus in recent years QDs have been instrumental in enabling long-term observation of complex macromolecular behavior on the single molecule level. However these particles have still been found to exhibit impaired diffusion in crowded molecular environments such as the cellular cytoplasm and the neuronal synaptic cleft, where their sizes are still too large (4,6,7). Recently we have engineered the cores and surface coatings of QDs for minimized hydrodynamic size, while balancing offsets to colloidal stability, photostability, brightness, and nonspecific binding that have hindered the utility of compact QDs in the past (8,9). The goal of this article is to demonstrate the synthesis, modification, and characterization of these optimized nanocrystals, composed of an alloyed HgxCd1-xSe core coated with an

  3. Spectroscopic characterization of Venus at the single molecule level.

    Science.gov (United States)

    David, Charlotte C; Dedecker, Peter; De Cremer, Gert; Verstraeten, Natalie; Kint, Cyrielle; Michiels, Jan; Hofkens, Johan

    2012-02-01

    Venus is a recently developed, fast maturating, yellow fluorescent protein that has been used as a probe for in vivo applications. In the present work the photophysical characteristics of Venus were analyzed spectroscopically at the bulk and single molecule level. Through time-resolved single molecule measurements we found that single molecules of Venus display pronounced fluctuations in fluorescence emission, with clear fluorescence on- and off-times. These fluorescence intermittencies were found to occupy a broad range of time scales, ranging from milliseconds to several seconds. Such long off-times can complicate the analysis of single molecule counting experiments or single-molecule FRET experiments. This journal is © The Royal Society of Chemistry and Owner Societies 2012

  4. Long wavelength approximation of transport processes in a single-band crystal

    International Nuclear Information System (INIS)

    Ferrari, Loris

    2014-01-01

    The single band, long wavelength approximation (SBA–LWA) is currently used in textbooks as a quasi-free-particle picture of the motion in a quantum crystal. The resulting transport process might thereby look a trivial issue. In contrast, we shall show that the SBA–LWA hides some controversial aspects that should be clarified at the level of an advanced course of condensed matter physics, and refer to the incompleteness of the SBA representation. In particular, it will be shown that the single-band velocity v 1B , expressed in terms of the projectors on the Bloch states, cannot be a transport velocity in a full sense, since the resulting current violates the continuity equation. The drawback manifests itself as a ‘lost’ current J lost , which provides a non conventional estimate of the limits of accuracy of SBA–LWA. The vanishing of J lost corresponds to the effective mass approximation in which the dispersion relation can be reduced to a quadratic form in the (pseudo) momentum components. In practice, the quantity transported by v 1B is not the bare mass, but the effective mass, until this notion does make sense. Recalling that the non-quadratic expression of the relativistic kinetic energy leads to a difference between the rest and moving mass, the notion of the lost current is finally used as a non-conventional approach to relativistic quantum mechanics, with special reference to Dirac’s theory. (paper)

  5. Extending Single-Molecule Microscopy Using Optical Fourier Processing

    Science.gov (United States)

    2015-01-01

    This article surveys the recent application of optical Fourier processing to the long-established but still expanding field of single-molecule imaging and microscopy. A variety of single-molecule studies can benefit from the additional image information that can be obtained by modulating the Fourier, or pupil, plane of a widefield microscope. After briefly reviewing several current applications, we present a comprehensive and computationally efficient theoretical model for simulating single-molecule fluorescence as it propagates through an imaging system. Furthermore, we describe how phase/amplitude-modulating optics inserted in the imaging pathway may be modeled, especially at the Fourier plane. Finally, we discuss selected recent applications of Fourier processing methods to measure the orientation, depth, and rotational mobility of single fluorescent molecules. PMID:24745862

  6. SISGR: Room Temperature Single-Molecule Detection and Imaging by Stimulated Emission Microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Xiaoliang Sunney [Harvard Univ., Cambridge, MA (United States). Dept. of Chemistry and Chemical Biology

    2017-03-13

    specificity than absorption and fluorescence. Current sensitivity limit of SRS microscopy has not yet reached single molecule detection. We proposed to capitalize on our state-of-the-art SRS microscopy and develop near-resonance enhanced SRS for single molecule detection of carotenoids and heme proteins. The specific aims we pursued are: (1) building the next SRS generation microscope that utilizes near resonance enhancement to allow detection and imaging of single molecules with undetectable fluorescence, such as -carotene. (2) using near-resonance SRS as a contrast mechanism to study dye-sensitize semiconductor interface, elucidating the heterogeneous electron ejection kinetics with high spatial and temporal resolution. (3) studying the binding and unbinding of oxygen in single hemoglobin molecules in order to gain molecular level understanding of the long-standing issue of cooperativity. The new methods developed in the fund period of this grant have advanced the detection sensitivity in many aspects. Near-resonance SRS improved the signal by using shorter wavelengths for SRS microscopy. Frequency modulation and multi-color SRS target the reduction of background to improve the chemical specificity of SRS while maintaining the high imaging speed. Time-domain coherent Raman scattering microscopy targets to reduce the noise floor of coherent Raman microscopy. These methods have already demonstrated first-of-a-kind new applications in biology and medical research. However, we are still one order of magnitude away from single molecule limit. It is important to continue to improve the laser specification and develop new imaging methods to finally achieve label-free single molecule microscopy.

  7. Choice of Illumination System & Fluorophore for Multiplex Immunofluorescence on FFPE Tissue Sections.

    Directory of Open Access Journals (Sweden)

    Sandrine Prost

    Full Text Available The recent availability of novel dyes and alternative light sources to facilitate complex tissue immunofluorescence studies such as multiplex labelling has not been matched by reports critically evaluating the considerations and relative benefits of these new tools, particularly in combination. Product information is often limited to wavelengths used for older fluorophores (FITC, TRITC & corresponding Alexa dyes family. Consequently, novel agents such as Quantum dots are not widely appreciated or used, despite highly favourable properties including extremely bright emission, stability and potentially reduced tissue autofluorescence at the excitation wavelength. Using spectral analysis, we report here a detailed critical appraisal and comparative evaluation of different light sources and fluorophores in multiplex immunofluorescence of clinical biopsy sections. The comparison includes mercury light, metal halide and 3 different LED-based systems, using 7 Qdots (525, 565, 585, 605, 625, 705, Cy3 and Cy5. We discuss the considerations relevant to achieving the best combination of light source and fluorophore for accurate multiplex fluorescence quantitation. We highlight practical limitations and confounders to quantitation with filter-based approaches.

  8. A Single Molecule Investigation of the Photostability of Quantum Dots

    DEFF Research Database (Denmark)

    Christensen, Eva Arnspang; Kulatunga, Pasad; Lagerholm, B. Christoffer

    2012-01-01

    Quantum dots (QDs) are very attractive probes for multi-color fluorescence applications. We report here however that single QDs that are subject to continuous blue excitation from a 100W mercury arc lamp will undergo a continuous blue-switching of the emission wavelength eventually reaching a per...... is especially detrimental for multi-color single molecule applications, as we regularly observe spectral blue-shifts of 50 nm, or more even after only ten seconds of illumination....

  9. Strong reduction of spectral heterogeneity in gold bipyramids for single-particle and single-molecule plasmon sensing.

    Science.gov (United States)

    Peters, S M E; Verheijen, M A; Prins, M W J; Zijlstra, P

    2016-01-15

    Single metal nanoparticles are attractive biomolecular sensors. Binding of analyte to a functional particle results in a plasmon shift that can be conveniently monitored in a far-field optical microscope. Heterogeneities in spectral properties of individual particles in an ensemble affect the reliability of a single-particle plasmon sensor, especially when plasmon shifts are monitored in real-time using a fixed irradiation wavelength. We compare the spectral heterogeneity of different plasmon sensor geometries (gold nanospheres, nanorods, and bipyramids) and correlate this to their size and aspect-ratio dispersion. We show that gold bipyramids exhibit a strongly reduced heterogeneity in aspect ratio and plasmon wavelength compared to commonly used gold nanorods. We show that this translates into a significantly improved homogeneity of the response to molecular binding without compromising single-molecule sensitivity.

  10. Long-wavelength photonic integrated circuits and avalanche photodetectors

    Science.gov (United States)

    Tsou, Yi-Jen D.; Zaytsev, Sergey; Pauchard, Alexandre; Hummel, Steve; Lo, Yu-Hwa

    2001-10-01

    Fast-growing internet traffic volume require high data communication bandwidth over longer distances. Access network bottlenecks put pressure on short-range (SR) telecommunication systems. To effectively address these datacom and telecom market needs, low-cost, high-speed laser modules at 1310 to 1550 nm wavelengths and avalanche photodetectors are required. The great success of GaAs 850nm VCSEls for Gb/s Ethernet has motivated efforts to extend VCSEL technology to longer wavelengths in the 1310 and 1550 nm regimes. However, the technological challenges associated with materials for long wavelength VCSELs are tremendous. Even with recent advances in this area, it is believed that significant additional development is necessary before long wavelength VCSELs that meet commercial specifications will be widely available. In addition, the more stringent OC192 and OC768 specifications for single-mode fiber (SMF) datacom may require more than just a long wavelength laser diode, VCSEL or not, to address numerous cost and performance issues. We believe that photonic integrated circuits (PICs), which compactly integrate surface-emitting lasers with additional active and passive optical components with extended functionality, will provide the best solutions to today's problems. Photonic integrated circuits have been investigated for more than a decade. However, they have produced limited commercial impact to date primarily because the highly complicated fabrication processes produce significant yield and device performance issues. In this presentation, we will discuss a new technology platform of InP-based PICs compatible with surface-emitting laser technology, as well as a high data rate externally modulated laser module. Avalanche photodetectors (APDs) are the key component in the receiver to achieve high data rate over long transmission distance because of their high sensitivity and large gain- bandwidth product. We have used wafer fusion technology to achieve In

  11. Problems of fluorescent imaging and its solution using nanofluorophores. Part I: Advantages of fluorescent nanoparticles over conventional organic fluorophores

    International Nuclear Information System (INIS)

    Zhelev, Z.; Hadjidekov, G.; Zlateva, G.; Spasov, L.; Bakalova, R.

    2011-01-01

    The application of fluorescence in deep-tissue imaging is rapidly expanding in fast several years. The progress in fluorescent molecular probes and fluorescent imaging techniques gives an opportunity to detect single cells and even molecules in live organisms. The highly sensitive and high-speed fluorescent molecular sensors and detection devices allow the application of fluorescence in functional imaging. With development of novel bright fluorophores based on nano-technologies and fluorescence scanners with high spatial and temporal resolution, the fluorescent imaging has a potential to become an alternative of the other non-invasive imaging techniques as magnetic resonance imaging, positron-emission tomography, X-ray, computing tomography. This review outlines the current status and future trends of fluorescent nanoparticles - quantum dots (QDs), as a new generation of fluorophores in experimental and pre-clinical fluorescent imaging diagnostic. Part 1 focuses on the advantages of quantum dots over conventional organic fluorophores and defines the major requirements to the 'perfect' fluorophore for fluorescent deep-tissue imaging diagnostic. The analysis is based on the limitations of fluorescent imaging in vivo and overcome by using quantum dots

  12. Synthesis of Cyclic Polymers and Characterization of Their Diffusive Motion in the Melt State at the Single Molecule Level

    KAUST Repository

    Habuchi, Satoshi

    2016-09-26

    We demonstrate a method for the synthesis of cyclic polymers and a protocol for characterizing their diffusive motion in a melt state at the single molecule level. An electrostatic self-assembly and covalent fixation (ESA-CF) process is used for the synthesis of the cyclic poly(tetrahydrofuran) (poly(THF)). The diffusive motion of individual cyclic polymer chains in a melt state is visualized using single molecule fluorescence imaging by incorporating a fluorophore unit in the cyclic chains. The diffusive motion of the chains is quantitatively characterized by means of a combination of mean-squared displacement (MSD) analysis and a cumulative distribution function (CDF) analysis. The cyclic polymer exhibits multiple-mode diffusion which is distinct from its linear counterpart. The results demonstrate that the diffusional heterogeneity of polymers that is often hidden behind ensemble averaging can be revealed by the efficient synthesis of the cyclic polymers using the ESA-CF process and the quantitative analysis of the diffusive motion at the single molecule level using the MSD and CDF analyses.

  13. Photoinduced electron transfer between anionic fluorophores and methyl viologen in homogeneous and microheterogeneous media

    International Nuclear Information System (INIS)

    Burai, Tarak Nath; Panda, Debashis; Iyer, E Siva Subramaniam; Datta, Anindya

    2012-01-01

    The rate and extent of photoinduced electron transfer change significantly as a result of confinement in nanovolumes. Study of such processes is an active area of research in physical chemistry. The effect is most interesting when the molecules that participate in PET are charged. In the present article, the modulation of PET has been studied for two anionic fluorophores: Lucifer Yellow CH and chlorin p 6 with Methylviologen dication. PET, manifested in the quenching of fluorescence of the fluorophores, has been modulated by incorporating the molecules in organized assemblies like micelles, reverse micelles and supramolecular hosts. The dynamics of the process has been monitored in the femtosecond to nanosecond timescale. The modulation of the electron transfer has been found to be occurring mainly due to the disruption of contact ion pairs formed between the fluorophores and the quencher. - Highlights: ► Modulation of PET of biologically active fluorophores and Methyl viologen. ► Static and Dynamic Quenching present. ► PET enhanced upon encapsulation, studied through Fluorescence upconversion experiments. ► Rotational anisotropy has significant contribution in quenching.

  14. Single molecules and nanotechnology

    CERN Document Server

    Vogel, Horst

    2007-01-01

    This book focuses on recent advances in the rapidly evolving field of single molecule research. These advances are of importance for the investigation of biopolymers and cellular biochemical reactions, and are essential to the development of quantitative biology. Written by leading experts in the field, the articles cover a broad range of topics, including: quantum photonics of organic dyes and inorganic nanoparticles their use in detecting properties of single molecules the monitoring of single molecule (enzymatic) reactions single protein (un)folding in nanometer-sized confined volumes the dynamics of molecular interactions in biological cells The book is written for advanced students and scientists who wish to survey the concepts, techniques and results of single molecule research and assess them for their own scientific activities.

  15. Two-photon interference at telecom wavelengths for time-bin-encoded single photons from quantum-dot spin qubits.

    Science.gov (United States)

    Yu, Leo; Natarajan, Chandra M; Horikiri, Tomoyuki; Langrock, Carsten; Pelc, Jason S; Tanner, Michael G; Abe, Eisuke; Maier, Sebastian; Schneider, Christian; Höfling, Sven; Kamp, Martin; Hadfield, Robert H; Fejer, Martin M; Yamamoto, Yoshihisa

    2015-11-24

    Practical quantum communication between remote quantum memories rely on single photons at telecom wavelengths. Although spin-photon entanglement has been demonstrated in atomic and solid-state qubit systems, the produced single photons at short wavelengths and with polarization encoding are not suitable for long-distance communication, because they suffer from high propagation loss and depolarization in optical fibres. Establishing entanglement between remote quantum nodes would further require the photons generated from separate nodes to be indistinguishable. Here, we report the observation of correlations between a quantum-dot spin and a telecom single photon across a 2-km fibre channel based on time-bin encoding and background-free frequency downconversion. The downconverted photon at telecom wavelengths exhibits two-photon interference with another photon from an independent source, achieving a mean wavepacket overlap of greater than 0.89 despite their original wavelength mismatch (900 and 911 nm). The quantum-networking operations that we demonstrate will enable practical communication between solid-state spin qubits across long distances.

  16. Single Molecule Electronics and Devices

    Science.gov (United States)

    Tsutsui, Makusu; Taniguchi, Masateru

    2012-01-01

    The manufacture of integrated circuits with single-molecule building blocks is a goal of molecular electronics. While research in the past has been limited to bulk experiments on self-assembled monolayers, advances in technology have now enabled us to fabricate single-molecule junctions. This has led to significant progress in understanding electron transport in molecular systems at the single-molecule level and the concomitant emergence of new device concepts. Here, we review recent developments in this field. We summarize the methods currently used to form metal-molecule-metal structures and some single-molecule techniques essential for characterizing molecular junctions such as inelastic electron tunnelling spectroscopy. We then highlight several important achievements, including demonstration of single-molecule diodes, transistors, and switches that make use of electrical, photo, and mechanical stimulation to control the electron transport. We also discuss intriguing issues to be addressed further in the future such as heat and thermoelectric transport in an individual molecule. PMID:22969345

  17. Photoinduced electron transfer between anionic fluorophores and methyl viologen in homogeneous and microheterogeneous media

    Energy Technology Data Exchange (ETDEWEB)

    Burai, Tarak Nath; Panda, Debashis; Iyer, E Siva Subramaniam [Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076 (India); Datta, Anindya, E-mail: anindya@chem.iitb.ac.in [Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076 (India)

    2012-11-15

    The rate and extent of photoinduced electron transfer change significantly as a result of confinement in nanovolumes. Study of such processes is an active area of research in physical chemistry. The effect is most interesting when the molecules that participate in PET are charged. In the present article, the modulation of PET has been studied for two anionic fluorophores: Lucifer Yellow CH and chlorin p{sub 6} with Methylviologen dication. PET, manifested in the quenching of fluorescence of the fluorophores, has been modulated by incorporating the molecules in organized assemblies like micelles, reverse micelles and supramolecular hosts. The dynamics of the process has been monitored in the femtosecond to nanosecond timescale. The modulation of the electron transfer has been found to be occurring mainly due to the disruption of contact ion pairs formed between the fluorophores and the quencher. - Highlights: Black-Right-Pointing-Pointer Modulation of PET of biologically active fluorophores and Methyl viologen. Black-Right-Pointing-Pointer Static and Dynamic Quenching present. Black-Right-Pointing-Pointer PET enhanced upon encapsulation, studied through Fluorescence upconversion experiments. Black-Right-Pointing-Pointer Rotational anisotropy has significant contribution in quenching.

  18. Single Molecule Kinetics of ENTH Binding to Lipid Membranes

    Energy Technology Data Exchange (ETDEWEB)

    Rozovsky, Sharon [Univ. of Delaware, Newark, DE (United States); Forstner, Martin B. [Syracuse Univ., NY (United States); Sondermann, Holger [Cornell Univ., Ithaca, NY (United States); Groves, Jay T. [Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2012-04-03

    Transient recruitment of proteins to membranes is a fundamental mechanism by which the cell exerts spatial and temporal control over proteins’ localization and interactions. Thus, the specificity and the kinetics of peripheral proteins’ membrane residence are an attribute of their function. In this article, we describe the membrane interactions of the interfacial epsin N-terminal homology (ENTH) domain with its target lipid phosphatidylinositol (4,5)-bisphosphate (PtdIns(4,5)P2). The direct visualization and quantification of interactions of single ENTH molecules with supported lipid bilayers is achieved using total internal reflection fluorescence microscopy (TIRFM) with a time resolution of 13 ms. This enables the recording of the kinetic behavior of ENTH interacting with membranes with physiologically relevant concentrations of PtdIns(4,5)P2 despite the low effective binding affinity. Subsequent single fluorophore tracking permits us to build up distributions of residence times and to measure ENTH dissociation rates as a function of membrane composition. In addition, due to the high time resolution, we are able to resolve details of the motion of ENTH associated with a simple, homogeneous membrane. In this case ENTH’s diffusive transport appears to be the result of at least three different diffusion processes.

  19. Long-range charge transport in single G-quadruplex DNA molecules

    DEFF Research Database (Denmark)

    Livshits, Gideon I.; Stern, Avigail; Rotem, Dvir

    2014-01-01

    DNA and DNA-based polymers are of interest in molecular electronics because of their versatile and programmable structures. However, transport measurements have produced a range of seemingly contradictory results due to differences in the measured molecules and experimental set-ups, and transport......DNA and DNA-based polymers are of interest in molecular electronics because of their versatile and programmable structures. However, transport measurements have produced a range of seemingly contradictory results due to differences in the measured molecules and experimental set......-ups, and transporting significant current through individual DNA-based molecules remains a considerable challenge. Here, we report reproducible charge transport in guanine-quadruplex (G4) DNA molecules adsorbed on a mica substrate. Currents ranging from tens of picoamperes to more than 100 pA were measured in the G4......-DNA over distances ranging from tens of nanometres to more than 100 nm. Our experimental results, combined with theoretical modelling, suggest that transport occurs via a thermally activated long-range hopping between multi-tetrad segments of DNA. These results could re-ignite interest in DNA...

  20. Single Molecule Analysis Research Tool (SMART: an integrated approach for analyzing single molecule data.

    Directory of Open Access Journals (Sweden)

    Max Greenfeld

    Full Text Available Single molecule studies have expanded rapidly over the past decade and have the ability to provide an unprecedented level of understanding of biological systems. A common challenge upon introduction of novel, data-rich approaches is the management, processing, and analysis of the complex data sets that are generated. We provide a standardized approach for analyzing these data in the freely available software package SMART: Single Molecule Analysis Research Tool. SMART provides a format for organizing and easily accessing single molecule data, a general hidden Markov modeling algorithm for fitting an array of possible models specified by the user, a standardized data structure and graphical user interfaces to streamline the analysis and visualization of data. This approach guides experimental design, facilitating acquisition of the maximal information from single molecule experiments. SMART also provides a standardized format to allow dissemination of single molecule data and transparency in the analysis of reported data.

  1. Single-molecule dynamics in nanofabricated traps

    Science.gov (United States)

    Cohen, Adam

    2009-03-01

    The Anti-Brownian Electrokinetic trap (ABEL trap) provides a means to immobilize a single fluorescent molecule in solution, without surface attachment chemistry. The ABEL trap works by tracking the Brownian motion of a single molecule, and applying feedback electric fields to induce an electrokinetic motion that approximately cancels the Brownian motion. We present a new design for the ABEL trap that allows smaller molecules to be trapped and more information to be extracted from the dynamics of a single molecule than was previously possible. In particular, we present strategies for extracting dynamically fluctuating mobilities and diffusion coefficients, as a means to probe dynamic changes in molecular charge and shape. If one trapped molecule is good, many trapped molecules are better. An array of single molecules in solution, each immobilized without surface attachment chemistry, provides an ideal test-bed for single-molecule analyses of intramolecular dynamics and intermolecular interactions. We present a technology for creating such an array, using a fused silica plate with nanofabricated dimples and a removable cover for sealing single molecules within the dimples. With this device one can watch the shape fluctuations of single molecules of DNA or study cooperative interactions in weakly associating protein complexes.

  2. Single-photon sources based on single molecules in solids

    International Nuclear Information System (INIS)

    Moerner, W E

    2004-01-01

    Single molecules in suitable host crystals have been demonstrated to be useful single-photon emitters both at liquid-helium temperatures and at room temperature. The low-temperature source achieved controllable emission of single photons from a single terrylene molecule in p-terphenyl by an adiabatic rapid passage technique. In contrast with almost all other single-molecule systems, terrylene single molecules show extremely high photostability under continuous, high-intensity irradiation. A room-temperature source utilizing this material has been demonstrated, in which fast pumping into vibrational sidebands of the electronically excited state achieved efficient inversion of the emissive level. This source yielded a single-photon emission probability p(1) of 0.86 at a detected count rate near 300 000 photons s -1 , with very small probability of emission of more than one photon. Thus, single molecules in solids can be considered as contenders for applications of single-photon sources such as quantum key distribution

  3. Single-molecule chemical reactions on DNA origami

    DEFF Research Database (Denmark)

    Voigt, Niels Vinther; Tørring, Thomas; Rotaru, Alexandru

    2010-01-01

    as templates for building materials with new functional properties. Relatively large nanocomponents such as nanoparticles and biomolecules can also be integrated into DNA nanostructures and imaged. Here, we show that chemical reactions with single molecules can be performed and imaged at a local position...... on a DNA origami scaffold by atomic force microscopy. The high yields and chemoselectivities of successive cleavage and bond-forming reactions observed in these experiments demonstrate the feasibility of post-assembly chemical modification of DNA nanostructures and their potential use as locally......DNA nanotechnology and particularly DNA origami, in which long, single-stranded DNA molecules are folded into predetermined shapes, can be used to form complex self-assembled nanostructures. Although DNA itself has limited chemical, optical or electronic functionality, DNA nanostructures can serve...

  4. Single-Molecule Spectroscopy

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 20; Issue 2. Single-Molecule Spectroscopy: Every Molecule is Different! Kankan Bhattacharyya. General Article Volume 20 Issue 2 February 2015 pp 151-164. Fulltext. Click here to view fulltext PDF. Permanent link:

  5. Preface: Special Topic on Single-Molecule Biophysics.

    Science.gov (United States)

    Makarov, Dmitrii E; Schuler, Benjamin

    2018-03-28

    Single-molecule measurements are now almost routinely used to study biological systems and processes. The scope of this special topic emphasizes the physics side of single-molecule observations, with the goal of highlighting new developments in physical techniques as well as conceptual insights that single-molecule measurements bring to biophysics. This issue also comprises recent advances in theoretical physical models of single-molecule phenomena, interpretation of single-molecule signals, and fundamental areas of statistical mechanics that are related to single-molecule observations. A particular goal is to illustrate the increasing synergy between theory, simulation, and experiment in single-molecule biophysics.

  6. Silicon photon-counting avalanche diodes for single-molecule fluorescence spectroscopy

    Science.gov (United States)

    Michalet, Xavier; Ingargiola, Antonino; Colyer, Ryan A.; Scalia, Giuseppe; Weiss, Shimon; Maccagnani, Piera; Gulinatti, Angelo; Rech, Ivan; Ghioni, Massimo

    2014-01-01

    Solution-based single-molecule fluorescence spectroscopy is a powerful experimental tool with applications in cell biology, biochemistry and biophysics. The basic feature of this technique is to excite and collect light from a very small volume and work in a low concentration regime resulting in rare burst-like events corresponding to the transit of a single molecule. Detecting photon bursts is a challenging task: the small number of emitted photons in each burst calls for high detector sensitivity. Bursts are very brief, requiring detectors with fast response time and capable of sustaining high count rates. Finally, many bursts need to be accumulated to achieve proper statistical accuracy, resulting in long measurement time unless parallelization strategies are implemented to speed up data acquisition. In this paper we will show that silicon single-photon avalanche diodes (SPADs) best meet the needs of single-molecule detection. We will review the key SPAD parameters and highlight the issues to be addressed in their design, fabrication and operation. After surveying the state-of-the-art SPAD technologies, we will describe our recent progress towards increasing the throughput of single-molecule fluorescence spectroscopy in solution using parallel arrays of SPADs. The potential of this approach is illustrated with single-molecule Förster resonance energy transfer measurements. PMID:25309114

  7. Multi-wavelength search for complex molecules in Titan's Atmosphere

    Science.gov (United States)

    Nixon, C. A.; Cordiner, M. A.; Greathouse, T. K.; Richter, M.; Kisiel, Z.; Irwin, P. G.; Teanby, N. A.; Kuan, Y. J.; Charnley, S. B.

    2017-12-01

    Titan's atmosphere is one of the most complex astrochemical environments known: the photochemistry of methane and nitrogen, induced by solar UV and Saturn magnetospheric electron impacts, creates a bonanza of organic molecules like no other place in the solar system. Cassini has unveiled the first glimpses of Titan's chemical wonderland, but many gaps remain. In particular, interpreting the mass spectra of Titan's upper atmosphere requires external knowledge, to disentangle the signature of molecules from their identical-mass brethren. Cassini infrared spectroscopy with CIRS has helped to some extent, but is also limited by low spectral resolution. Potentially to the rescue, comes high-resolution spectroscopy from the Earth at infrared and sub-millimeter wavelengths, where molecules exhibit vibrational and rotational transitions respectively. In this presentation, we describe the quest to make new, unique identifications of large molecules in Titan's atmosphere, focusing specifically on cyclic molecules including N-heterocycles. This molecular family is of high astrobiological significance, forming the basic ring structure for DNA nucleobases. We present the latest spectroscopic observations of Titan from ALMA and NASA's IRTF telescope, discussing present findings and directions for future work.

  8. Single-molecule study on polymer diffusion in a melt state: Effect of chain topology

    KAUST Repository

    Habuchi, Satoshi

    2013-08-06

    We report a new methodology for studying diffusion of individual polymer chains in a melt state, with special emphasis on the effect of chain topology. A perylene diimide fluorophore was incorporated into the linear and cyclic poly(THF)s, and real-time diffusion behavior of individual chains in a melt of linear poly(THF) was measured by means of a single-molecule fluorescence imaging technique. The combination of mean squared displacement (MSD) and cumulative distribution function (CDF) analysis demonstrated the broad distribution of diffusion coefficient of both the linear and cyclic polymer chains in the melt state. This indicates the presence of spatiotemporal heterogeneity of the polymer diffusion which occurs at much larger time and length scales than those expected from the current polymer physics theory. We further demonstrated that the cyclic chains showed marginally slower diffusion in comparison with the linear counterparts, to suggest the effective suppression of the translocation through the threading-entanglement with the linear matrix chains. This coincides with the higher activation energy for the diffusion of the cyclic chains than of the linear chains. These results suggest that the single-molecule imaging technique provides a powerful tool to analyze complicated polymer dynamics and contributes to the molecular level understanding of the chain interaction. © 2013 American Chemical Society.

  9. Single-molecule study on polymer diffusion in a melt state: Effect of chain topology

    KAUST Repository

    Habuchi, Satoshi; Fujiwara, Susumu; Yamamoto, Takuya; Vá cha, Martin; Tezuka, Yasuyuki

    2013-01-01

    We report a new methodology for studying diffusion of individual polymer chains in a melt state, with special emphasis on the effect of chain topology. A perylene diimide fluorophore was incorporated into the linear and cyclic poly(THF)s, and real-time diffusion behavior of individual chains in a melt of linear poly(THF) was measured by means of a single-molecule fluorescence imaging technique. The combination of mean squared displacement (MSD) and cumulative distribution function (CDF) analysis demonstrated the broad distribution of diffusion coefficient of both the linear and cyclic polymer chains in the melt state. This indicates the presence of spatiotemporal heterogeneity of the polymer diffusion which occurs at much larger time and length scales than those expected from the current polymer physics theory. We further demonstrated that the cyclic chains showed marginally slower diffusion in comparison with the linear counterparts, to suggest the effective suppression of the translocation through the threading-entanglement with the linear matrix chains. This coincides with the higher activation energy for the diffusion of the cyclic chains than of the linear chains. These results suggest that the single-molecule imaging technique provides a powerful tool to analyze complicated polymer dynamics and contributes to the molecular level understanding of the chain interaction. © 2013 American Chemical Society.

  10. Transition paths in single-molecule force spectroscopy.

    Science.gov (United States)

    Cossio, Pilar; Hummer, Gerhard; Szabo, Attila

    2018-03-28

    In a typical single-molecule force spectroscopy experiment, the ends of the molecule of interest are connected by long polymer linkers to a pair of mesoscopic beads trapped in the focus of two laser beams. At constant force load, the total extension, i.e., the end-to-end distance of the molecule plus linkers, is measured as a function of time. In the simplest systems, the measured extension fluctuates about two values characteristic of folded and unfolded states, with occasional transitions between them. We have recently shown that molecular (un)folding rates can be recovered from such trajectories, with a small linker correction, as long as the characteristic time of the bead fluctuations is shorter than the residence time in the unfolded (folded) state. Here, we show that accurate measurements of the molecular transition path times require an even faster apparatus response. Transition paths, the trajectory segments in which the molecule (un)folds, are properly resolved only if the beads fluctuate more rapidly than the end-to-end distance of the molecule. Therefore, over a wide regime, the measured rates may be meaningful but not the transition path times. Analytic expressions for the measured mean transition path times are obtained for systems diffusing anisotropically on a two-dimensional free energy surface. The transition path times depend on the properties both of the molecule and of the pulling device.

  11. Fluorescence Imaging In Vivo at Wavelengths beyond 1500 nm.

    Science.gov (United States)

    Diao, Shuo; Blackburn, Jeffrey L; Hong, Guosong; Antaris, Alexander L; Chang, Junlei; Wu, Justin Z; Zhang, Bo; Cheng, Kai; Kuo, Calvin J; Dai, Hongjie

    2015-12-01

    Compared to imaging in the visible and near-infrared regions below 900 nm, imaging in the second near-infrared window (NIR-II, 1000-1700 nm) is a promising method for deep-tissue high-resolution optical imaging in vivo mainly owing to the reduced scattering of photons traversing through biological tissues. Herein, semiconducting single-walled carbon nanotubes with large diameters were used for in vivo fluorescence imaging in the long-wavelength NIR region (1500-1700 nm, NIR-IIb). With this imaging agent, 3-4 μm wide capillary blood vessels at a depth of about 3 mm could be resolved. Meanwhile, the blood-flow speeds in multiple individual vessels could be mapped simultaneously. Furthermore, NIR-IIb tumor imaging of a live mouse was explored. NIR-IIb imaging can be generalized to a wide range of fluorophores emitting at up to 1700 nm for high-performance in vivo optical imaging. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Photon-counting single-molecule spectroscopy for studying conformational dynamics and macromolecular interactions

    Energy Technology Data Exchange (ETDEWEB)

    Laurence, Ted Alfred [Univ. of California, Berkeley, CA (United States)

    2002-01-01

    Single-molecule methods have the potential to provide information about conformational dynamics and molecular interactions that cannot be obtained by other methods. Removal of ensemble averaging provides several benefits, including the ability to detect heterogeneous populations and the ability to observe asynchronous reactions. Single-molecule diffusion methodologies using fluorescence resonance energy transfer (FRET) are developed to monitor conformational dynamics while minimizing perturbations introduced by interactions between molecules and surfaces. These methods are used to perform studies of the folding of Chymotrypsin Inhibitor 2, a small, single-domain protein, and of single-stranded DNA (ssDNA) homopolymers. Confocal microscopy is used in combination with sensitive detectors to detect bursts of photons from fluorescently labeled biomolecules as they diffuse through the focal volume. These bursts are analyzed to extract fluorescence resonance energy transfer (FRET) efficiency. Advances in data acquisition and analysis techniques that are providing a more complete picture of the accessible molecular information are discussed. Photon Arrival-time Interval Distribution (PAID) analysis is a new method for monitoring macromolecular interactions by fluorescence detection with simultaneous determination of coincidence, brightness, diffusion time, and occupancy (proportional to concentration) of fluorescently-labeled molecules undergoing diffusion in a confocal detection volume. This method is based on recording the time of arrival of all detected photons, and then plotting the two-dimensional histogram of photon pairs, where one axis is the time interval between each pair of photons 1 and 2, and the second axis is the number of other photons detected in the time interval between photons 1 and 2. PAID is related to Fluorescence Correlation Spectroscopy (FCS) by a collapse of this histogram onto the time interval axis. PAID extends auto- and cross-correlation FCS

  13. Photon-counting single-molecule spectroscopy for studying conformational dynamics and macromolecular interactions

    International Nuclear Information System (INIS)

    Laurence, Ted Alfred

    2002-01-01

    Single-molecule methods have the potential to provide information about conformational dynamics and molecular interactions that cannot be obtained by other methods. Removal of ensemble averaging provides several benefits, including the ability to detect heterogeneous populations and the ability to observe asynchronous reactions. Single-molecule diffusion methodologies using fluorescence resonance energy transfer (FRET) are developed to monitor conformational dynamics while minimizing perturbations introduced by interactions between molecules and surfaces. These methods are used to perform studies of the folding of Chymotrypsin Inhibitor 2, a small, single-domain protein, and of single-stranded DNA (ssDNA) homopolymers. Confocal microscopy is used in combination with sensitive detectors to detect bursts of photons from fluorescently labeled biomolecules as they diffuse through the focal volume. These bursts are analyzed to extract fluorescence resonance energy transfer (FRET) efficiency. Advances in data acquisition and analysis techniques that are providing a more complete picture of the accessible molecular information are discussed. Photon Arrival-time Interval Distribution (PAID) analysis is a new method for monitoring macromolecular interactions by fluorescence detection with simultaneous determination of coincidence, brightness, diffusion time, and occupancy (proportional to concentration) of fluorescently-labeled molecules undergoing diffusion in a confocal detection volume. This method is based on recording the time of arrival of all detected photons, and then plotting the two-dimensional histogram of photon pairs, where one axis is the time interval between each pair of photons 1 and 2, and the second axis is the number of other photons detected in the time interval between photons 1 and 2. PAID is related to Fluorescence Correlation Spectroscopy (FCS) by a collapse of this histogram onto the time interval axis. PAID extends auto- and cross-correlation FCS

  14. Single-Molecule Interfacial Electron Transfer

    Energy Technology Data Exchange (ETDEWEB)

    Lu, H. Peter [Bowling Green State Univ., Bowling Green, OH (United States). Dept. of Chemistry and Center for Photochemical Sciences

    2017-11-28

    This project is focused on the use of single-molecule high spatial and temporal resolved techniques to study molecular dynamics in condensed phase and at interfaces, especially, the complex reaction dynamics associated with electron and energy transfer rate processes. The complexity and inhomogeneity of the interfacial ET dynamics often present a major challenge for a molecular level comprehension of the intrinsically complex systems, which calls for both higher spatial and temporal resolutions at ultimate single-molecule and single-particle sensitivities. Combined single-molecule spectroscopy and electrochemical atomic force microscopy approaches are unique for heterogeneous and complex interfacial electron transfer systems because the static and dynamic inhomogeneities can be identified and characterized by studying one molecule at a specific nanoscale surface site at a time. The goal of our project is to integrate and apply these spectroscopic imaging and topographic scanning techniques to measure the energy flow and electron flow between molecules and substrate surfaces as a function of surface site geometry and molecular structure. We have been primarily focusing on studying interfacial electron transfer under ambient condition and electrolyte solution involving both single crystal and colloidal TiO2 and related substrates. The resulting molecular level understanding of the fundamental interfacial electron transfer processes will be important for developing efficient light harvesting systems and broadly applicable to problems in fundamental chemistry and physics. We have made significant advancement on deciphering the underlying mechanism of the complex and inhomogeneous interfacial electron transfer dynamics in dyesensitized TiO2 nanoparticle systems that strongly involves with and regulated by molecule-surface interactions. We have studied interfacial electron transfer on TiO2 nanoparticle surfaces by using ultrafast single-molecule

  15. Design of single-polarization wavelength splitter based on photonic crystal fiber.

    Science.gov (United States)

    Zhang, Shanshan; Zhang, Weigang; Geng, Pengcheng; Li, Xiaolan; Ruan, Juan

    2011-12-20

    A new single-polarization wavelength splitter based on the photonic crystal fiber (PCF) has been proposed. The full-vector finite-element method (FEM) is applied to analyze the single-polarization single-mode guiding properties. Splitting of two different wavelengths is realized by adjusting the structural parameters. The semi-vector three-dimensional beam propagation method is employed to confirm the wavelength splitting characteristics of the PCF. Numerical simulations show that the wavelengths of 1.3 μm and 1.55 μm are split for a fiber length of 10.7 mm with single-polarization guiding in each core. The crosstalk between the two cores is low over appreciable optical bandwidths.

  16. Combination of structured illumination and single molecule localization microscopy in one setup

    Science.gov (United States)

    Rossberger, Sabrina; Best, Gerrit; Baddeley, David; Heintzmann, Rainer; Birk, Udo; Dithmar, Stefan; Cremer, Christoph

    2013-09-01

    Understanding the positional and structural aspects of biological nanostructures simultaneously is as much a challenge as a desideratum. In recent years, highly accurate (20 nm) positional information of optically isolated targets down to the nanometer range has been obtained using single molecule localization microscopy (SMLM), while highly resolved (100 nm) spatial information has been achieved using structured illumination microscopy (SIM). In this paper, we present a high-resolution fluorescence microscope setup which combines the advantages of SMLM with SIM in order to provide high-precision localization and structural information in a single setup. Furthermore, the combination of the wide-field SIM image with the SMLM data allows us to identify artifacts produced during the visualization process of SMLM data, and potentially also during the reconstruction process of SIM images. We describe the SMLM-SIM combo and software, and apply the instrument in a first proof-of-principle to the same region of H3K293 cells to achieve SIM images with high structural resolution (in the 100 nm range) in overlay with the highly accurate position information of localized single fluorophores. Thus, with its robust control software, efficient switching between the SMLM and SIM mode, fully automated and user-friendly acquisition and evaluation software, the SMLM-SIM combo is superior over existing solutions.

  17. Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data.

    Science.gov (United States)

    Greenfeld, Max; van de Meent, Jan-Willem; Pavlichin, Dmitri S; Mabuchi, Hideo; Wiggins, Chris H; Gonzalez, Ruben L; Herschlag, Daniel

    2015-01-16

    Single-molecule techniques have emerged as incisive approaches for addressing a wide range of questions arising in contemporary biological research [Trends Biochem Sci 38:30-37, 2013; Nat Rev Genet 14:9-22, 2013; Curr Opin Struct Biol 2014, 28C:112-121; Annu Rev Biophys 43:19-39, 2014]. The analysis and interpretation of raw single-molecule data benefits greatly from the ongoing development of sophisticated statistical analysis tools that enable accurate inference at the low signal-to-noise ratios frequently associated with these measurements. While a number of groups have released analysis toolkits as open source software [J Phys Chem B 114:5386-5403, 2010; Biophys J 79:1915-1927, 2000; Biophys J 91:1941-1951, 2006; Biophys J 79:1928-1944, 2000; Biophys J 86:4015-4029, 2004; Biophys J 97:3196-3205, 2009; PLoS One 7:e30024, 2012; BMC Bioinformatics 288 11(8):S2, 2010; Biophys J 106:1327-1337, 2014; Proc Int Conf Mach Learn 28:361-369, 2013], it remains difficult to compare analysis for experiments performed in different labs due to a lack of standardization. Here we propose a standardized single-molecule dataset (SMD) file format. SMD is designed to accommodate a wide variety of computer programming languages, single-molecule techniques, and analysis strategies. To facilitate adoption of this format we have made two existing data analysis packages that are used for single-molecule analysis compatible with this format. Adoption of a common, standard data file format for sharing raw single-molecule data and analysis outcomes is a critical step for the emerging and powerful single-molecule field, which will benefit both sophisticated users and non-specialists by allowing standardized, transparent, and reproducible analysis practices.

  18. Proposal for probing energy transfer pathway by single-molecule pump-dump experiment

    OpenAIRE

    Tao, Ming-Jie; Ai, Qing; Deng, Fu-Guo; Cheng, Yuan-Chung

    2016-01-01

    The structure of Fenna-Matthews-Olson (FMO) light-harvesting complex has long been recognized as containing seven bacteriochlorophyll (BChl) molecules. Recently, an additional BChl molecule was discovered in the crystal structure of the FMO complex, which may serve as a link between baseplate and the remaining seven molecules. Here, we investigate excitation energy transfer (EET) process by simulating single-molecule pump-dump experiment in the eight-molecules complex. We adopt the coherent m...

  19. Spectrally Resolved and Functional Super-resolution Microscopy via Ultrahigh-Throughput Single-Molecule Spectroscopy.

    Science.gov (United States)

    Yan, Rui; Moon, Seonah; Kenny, Samuel J; Xu, Ke

    2018-03-20

    As an elegant integration of the spatial and temporal dimensions of single-molecule fluorescence, single-molecule localization microscopy (SMLM) overcomes the diffraction-limited resolution barrier of optical microscopy by localizing single molecules that stochastically switch between fluorescent and dark states over time. While this type of super-resolution microscopy (SRM) technique readily achieves remarkable spatial resolutions of ∼10 nm, it typically provides no spectral information. Meanwhile, current scanning-based single-location approaches for mapping the positions and spectra of single molecules are limited by low throughput and are difficult to apply to densely labeled (bio)samples. In this Account, we summarize the rationale, design, and results of our recent efforts toward the integration of the spectral dimension of single-molecule fluorescence with SMLM to achieve spectrally resolved SMLM (SR-SMLM) and functional SRM ( f-SRM). By developing a wide-field scheme for spectral measurement and implementing single-molecule fluorescence on-off switching typical of SMLM, we first showed that in densely labeled (bio)samples it is possible to record the fluorescence spectra and positions of millions of single molecules synchronously within minutes, giving rise to ultrahigh-throughput single-molecule spectroscopy and SR-SMLM. This allowed us to first show statistically that for many dyes, single molecules of the same species exhibit near identical emission in fixed cells. This narrow distribution of emission wavelengths, which contrasts markedly with previous results at solid surfaces, allowed us to unambiguously identify single molecules of spectrally similar dyes. Crosstalk-free, multiplexed SRM was thus achieved for four dyes that were merely 10 nm apart in emission spectrum, with the three-dimensional SRM images of all four dyes being automatically aligned within one image channel. The ability to incorporate single-molecule fluorescence measurement with

  20. Fluorescent Biosensors Based on Single-Molecule Counting.

    Science.gov (United States)

    Ma, Fei; Li, Ying; Tang, Bo; Zhang, Chun-Yang

    2016-09-20

    Biosensors for highly sensitive, selective, and rapid quantification of specific biomolecules make great contributions to biomedical research, especially molecular diagnostics. However, conventional methods for biomolecular assays often suffer from insufficient sensitivity and poor specificity. In some case (e.g., early disease diagnostics), the concentration of target biomolecules is too low to be detected by these routine approaches, and cumbersome procedures are needed to improve the detection sensitivity. Therefore, there is an urgent need for rapid and ultrasensitive analytical tools. In this respect, single-molecule fluorescence approaches may well satisfy the requirement and hold promising potential for the development of ultrasensitive biosensors. Encouragingly, owing to the advances in single-molecule microscopy and spectroscopy over past decades, the detection of single fluorescent molecule comes true, greatly boosting the development of highly sensitive biosensors. By in vitro/in vivo labeling of target biomolecules with proper fluorescent tags, the quantification of certain biomolecule at the single-molecule level is achieved. In comparison with conventional ensemble measurements, single-molecule detection-based analytical methods possess the advantages of ultrahigh sensitivity, good selectivity, rapid analysis time, and low sample consumption. Consequently, single-molecule detection may be potentially employed as an ideal analytical approach to quantify low-abundant biomolecules with rapidity and simplicity. In this Account, we will summarize our efforts for developing a series of ultrasensitive biosensors based on single-molecule counting. Single-molecule counting is a member of single-molecule detection technologies and may be used as a very simple and ultrasensitive method to quantify target molecules by simply counting the individual fluorescent bursts. In the fluorescent sensors, the signals of target biomolecules may be translated to the

  1. Single molecule localization imaging of exosomes using blinking silicon quantum dots

    Science.gov (United States)

    Zong, Shenfei; Zong, Junzhu; Chen, Chen; Jiang, Xiaoyue; Zhang, Yizhi; Wang, Zhuyuan; Cui, Yiping

    2018-02-01

    Discovering new fluorophores, which are suitable for single molecule localization microscopy (SMLM) is important for promoting the applications of SMLM in biological or material sciences. Here, we found that silicon quantum dots (Si QDs) possess a fluorescence blinking behavior, making them an excellent candidate for SMLM. The Si QDs are fabricated using a facile microwave-assisted method. Blinking of Si QDs is confirmed by single particle fluorescence measurement and the spatial resolution achieved is about 30 nm. To explore the potential application of Si QDs as the nanoprobes for SMLM imaging, cell derived exosomes are chosen as the object owing to their small size (50-100 nm in diameter). Since CD63 is commonly presented on the membrane of exosomes, CD63 aptamers are attached to the surface of Si QDs to form nanoprobes which can specifically recognize exosomes. SMLM imaging shows that Si QDs based nanoprobes can indeed realize super resolved optical imaging of exosomes. More importantly, blinking of Si QDs is observed in water or PBS buffer with no need for special imaging buffers. Besides, considering that silicon is highly biocompatible, Si QDs should have minimal cytotoxicity. These features make Si QDs quite suitable for SMLM applications especially for live cell imaging.

  2. Extracting Models in Single Molecule Experiments

    Science.gov (United States)

    Presse, Steve

    2013-03-01

    Single molecule experiments can now monitor the journey of a protein from its assembly near a ribosome to its proteolytic demise. Ideally all single molecule data should be self-explanatory. However data originating from single molecule experiments is particularly challenging to interpret on account of fluctuations and noise at such small scales. Realistically, basic understanding comes from models carefully extracted from the noisy data. Statistical mechanics, and maximum entropy in particular, provide a powerful framework for accomplishing this task in a principled fashion. Here I will discuss our work in extracting conformational memory from single molecule force spectroscopy experiments on large biomolecules. One clear advantage of this method is that we let the data tend towards the correct model, we do not fit the data. I will show that the dynamical model of the single molecule dynamics which emerges from this analysis is often more textured and complex than could otherwise come from fitting the data to a pre-conceived model.

  3. 4D super-resolution microscopy with conventional fluorophores and single wavelength excitation in optically thick cells and tissues.

    Directory of Open Access Journals (Sweden)

    David Baddeley

    Full Text Available BACKGROUND: Optical super-resolution imaging of fluorescently stained biological samples is rapidly becoming an important tool to investigate protein distribution at the molecular scale. It is therefore important to develop practical super-resolution methods that allow capturing the full three-dimensional nature of biological systems and also can visualize multiple protein species in the same sample. METHODOLOGY/PRINCIPAL FINDINGS: We show that the use of a combination of conventional near-infrared dyes, such as Alexa 647, Alexa 680 and Alexa 750, all excited with a 671 nm diode laser, enables 3D multi-colour super-resolution imaging of complex biological samples. Optically thick samples, including human tissue sections, cardiac rat myocytes and densely grown neuronal cultures were imaged with lateral resolutions of ∼15 nm (std. dev. while reducing marker cross-talk to <1%. Using astigmatism an axial resolution of ∼65 nm (std. dev. was routinely achieved. The number of marker species that can be distinguished depends on the mean photon number of single molecule events. With the typical photon yields from Alexa 680 of ∼2000 up to 5 markers may in principle be resolved with <2% crosstalk. CONCLUSIONS/SIGNIFICANCE: Our approach is based entirely on the use of conventional, commercially available markers and requires only a single laser. It provides a very straightforward way to investigate biological samples at the nanometre scale and should help establish practical 4D super-resolution microscopy as a routine research tool in many laboratories.

  4. A stable wavelength-tunable single frequency and single polarization linear cavity erbium-doped fiber laser

    International Nuclear Information System (INIS)

    Feng, T; Yan, F P; Li, Q; Peng, W J; Tan, S Y; Feng, S C; Wen, X D; Liu, P

    2013-01-01

    We report the configuration and operation of a wavelength-tunable single frequency and single polarization erbium-doped fiber laser (EDFL) with a stable and high optical signal to noise ratio (OSNR) laser output. A narrow-band fiber Bragg grating (NBFBG), a FBG-based Fabry–Perot (FP) filter, a polarization controller (PC) and an unpumped erbium-doped fiber (EDF) as a saturable absorber (SA) are employed to realize stable single frequency lasing operation. An all-fiber polarizer (AFP) is introduced to suppress mode hopping and ensure the single polarization mode operation. By adjusting the length of the NBFBG using a stress adjustment module (SAM), four stable single frequency and single polarization laser outputs at wavelengths of 1544.946, 1545.038, 1545.118 and 1545.182 nm are obtained. At room temperature, performance with an OSNR of larger than 60 dB, power fluctuation of less than 0.04 dB, wavelength variation of less than 0.01 nm for about 5 h measurement, and degree of polarization (DOP) of close to 100% has been experimentally demonstrated for the fiber laser operating at these four wavelengths. (paper)

  5. Electrochemically-gated single-molecule electrical devices

    International Nuclear Information System (INIS)

    Guo, Shaoyin; Artés, Juan Manuel; Díez-Pérez, Ismael

    2013-01-01

    In the last decade, single-molecule electrical contacts have emerged as a new experimental platform that allows exploring charge transport phenomena in individual molecular blocks. This novel tool has evolved into an essential element within the Molecular Electronics field to understand charge transport processes in hybrid (bio)molecule/electrode interfaces at the nanoscale, and prospect the implementation of active molecular components into functional nanoscale optoelectronic devices. Within this area, three-terminal single-molecule devices have been sought, provided that they are highly desired to achieve full functionality in logic electronic circuits. Despite the latest experimental developments offer consistent methods to bridge a molecule between two electrodes (source and drain in a transistor notation), placing a third electrode (gate) close to the single-molecule electrical contact is still technically challenging. In this vein, electrochemically-gated single-molecule devices have emerged as an experimentally affordable alternative to overcome these technical limitations. In this review, the operating principle of an electrochemically-gated single-molecule device is presented together with the latest experimental methodologies to built them and characterize their charge transport characteristics. Then, an up-to-date comprehensive overview of the most prominent examples will be given, emphasizing on the relationship between the molecular structure and the final device electrical behaviour

  6. In-vacuum long-wavelength macromolecular crystallography.

    Science.gov (United States)

    Wagner, Armin; Duman, Ramona; Henderson, Keith; Mykhaylyk, Vitaliy

    2016-03-01

    Structure solution based on the weak anomalous signal from native (protein and DNA) crystals is increasingly being attempted as part of synchrotron experiments. Maximizing the measurable anomalous signal by collecting diffraction data at longer wavelengths presents a series of technical challenges caused by the increased absorption of X-rays and larger diffraction angles. A new beamline at Diamond Light Source has been built specifically for collecting data at wavelengths beyond the capability of other synchrotron macromolecular crystallography beamlines. Here, the theoretical considerations in support of the long-wavelength beamline are outlined and the in-vacuum design of the endstation is discussed, as well as other hardware features aimed at enhancing the accuracy of the diffraction data. The first commissioning results, representing the first in-vacuum protein structure solution, demonstrate the promising potential of the beamline.

  7. 80-nm-tunable high-index-contrast subwavelength grating long-wavelength VCSEL: Proposal and numerical simulations

    DEFF Research Database (Denmark)

    Chung, Il-Sug; Mørk, Jesper; Sirbu, Alexei

    2010-01-01

    A widely-tunable single-mode long wavelength vertical-cavity surface-emitting laser structure employing a MEMStunable high-index-contrast subwavelength grating (HCG) is suggested and numerically investigated. A very large 80- nm linear tuning range was obtained as the HCG was actuated by -220 to ...

  8. Single-molecule fluorescence microscopy review: shedding new light on old problems.

    Science.gov (United States)

    Shashkova, Sviatlana; Leake, Mark C

    2017-08-31

    Fluorescence microscopy is an invaluable tool in the biosciences, a genuine workhorse technique offering exceptional contrast in conjunction with high specificity of labelling with relatively minimal perturbation to biological samples compared with many competing biophysical techniques. Improvements in detector and dye technologies coupled to advances in image analysis methods have fuelled recent development towards single-molecule fluorescence microscopy, which can utilize light microscopy tools to enable the faithful detection and analysis of single fluorescent molecules used as reporter tags in biological samples. For example, the discovery of GFP, initiating the so-called 'green revolution', has pushed experimental tools in the biosciences to a completely new level of functional imaging of living samples, culminating in single fluorescent protein molecule detection. Today, fluorescence microscopy is an indispensable tool in single-molecule investigations, providing a high signal-to-noise ratio for visualization while still retaining the key features in the physiological context of native biological systems. In this review, we discuss some of the recent discoveries in the life sciences which have been enabled using single-molecule fluorescence microscopy, paying particular attention to the so-called 'super-resolution' fluorescence microscopy techniques in live cells, which are at the cutting-edge of these methods. In particular, how these tools can reveal new insights into long-standing puzzles in biology: old problems, which have been impossible to tackle using other more traditional tools until the emergence of new single-molecule fluorescence microscopy techniques. © 2017 The Author(s).

  9. Long wavelength scintillators for fiber-optic applications

    International Nuclear Information System (INIS)

    Lyons, P.B.; Franks, L.; Lutz, S.; Flournoy, J.; Fullman, E.

    1980-01-01

    The use of fiber optics in plasma diagnostics has spurred the development of long wavelength scintillators with fast temporal characteristics. In this paper we describe several new liquid scintillator systems with fluorescent emissions maxima up to 730 nm. Subnanosecond scintillator FWHM response times have been obtained by the operation of liquid scintillators at elevated temperatures. Data on fiber system sensitivity versus fiber length and scintillator emission wavelength will be presented

  10. Assembly and diploid architecture of an individual human genome via single-molecule technologies.

    Science.gov (United States)

    Pendleton, Matthew; Sebra, Robert; Pang, Andy Wing Chun; Ummat, Ajay; Franzen, Oscar; Rausch, Tobias; Stütz, Adrian M; Stedman, William; Anantharaman, Thomas; Hastie, Alex; Dai, Heng; Fritz, Markus Hsi-Yang; Cao, Han; Cohain, Ariella; Deikus, Gintaras; Durrett, Russell E; Blanchard, Scott C; Altman, Roger; Chin, Chen-Shan; Guo, Yan; Paxinos, Ellen E; Korbel, Jan O; Darnell, Robert B; McCombie, W Richard; Kwok, Pui-Yan; Mason, Christopher E; Schadt, Eric E; Bashir, Ali

    2015-08-01

    We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality.

  11. Interfering Heralded Single Photons from Two Separate Silicon Nanowires Pumped at Different Wavelengths

    Directory of Open Access Journals (Sweden)

    Xiang Zhang

    2016-08-01

    Full Text Available Practical quantum photonic applications require on-demand single photon sources. As one possible solution, active temporal and wavelength multiplexing has been proposed to build an on-demand single photon source. In this scheme, heralded single photons are generated from different pump wavelengths in many temporal modes. However, the indistinguishability of these heralded single photons has not yet been experimentally confirmed. In this work, we achieve 88% ± 8% Hong–Ou–Mandel quantum interference visibility from heralded single photons generated from two separate silicon nanowires pumped at different wavelengths. This demonstrates that active temporal and wavelength multiplexing could generate indistinguishable heralded single photons.

  12. Nano-manipulation of single DNA molecules

    International Nuclear Information System (INIS)

    Hu Jun; Shanghai Jiaotong Univ., Shanghai; Lv Junhong; Wang Guohua; Wang Ying; Li Minqian; Zhang Yi; Li Bin; Li Haikuo; An Hongjie

    2004-01-01

    Nano-manipulation of single atoms and molecules is a critical technique in nanoscience and nanotechnology. This review paper will focus on the recent development of the manipulation of single DNA molecules based on atomic force microscopy (AFM). Precise manipulation has been realized including varied manipulating modes such as 'cutting', 'pushing', 'folding', 'kneading', 'picking up', 'dipping', etc. The cutting accuracy is dominated by the size of the AFM tip, which is usually 10 nm or less. Single DNA fragments can be cut and picked up and then amplified by single molecule PCR. Thus positioning isolation and sequencing can be performed. (authors)

  13. Synthesis of single-molecule nanocars.

    Science.gov (United States)

    Vives, Guillaume; Tour, James M

    2009-03-17

    p-carborane- and ruthenium-based wheels with greater solubility in organic solvents. Although fullerene wheels must be attached in the final synthetic step, p-carborane- and ruthenium-based wheels do not inhibit organometallic coupling reactions, which allows a more convergent synthesis of molecular machines. We also prepared functional nanotrucks for the transport of atoms and molecules, as well as self-assembling nanocars and nanotrains. Although engineering challenges such as movement over long distance and non-atomically flat surfaces remain, the greatest current research challenge is imaging. The detailed study of nanocars requires complementary single molecule imaging techniques such as STM, AFM, TEM, or single-molecule fluorescence microscopy. Further developments in engineering and synthesis could lead to enzyme-like manipulation and assembly of atoms and small molecules in nonbiological environments.

  14. Combination of structured illumination and single molecule localization microscopy in one setup

    International Nuclear Information System (INIS)

    Rossberger, Sabrina; Best, Gerrit; Birk, Udo; Cremer, Christoph; Baddeley, David; Heintzmann, Rainer; Dithmar, Stefan

    2013-01-01

    Understanding the positional and structural aspects of biological nanostructures simultaneously is as much a challenge as a desideratum. In recent years, highly accurate (20 nm) positional information of optically isolated targets down to the nanometer range has been obtained using single molecule localization microscopy (SMLM), while highly resolved (100 nm) spatial information has been achieved using structured illumination microscopy (SIM). In this paper, we present a high-resolution fluorescence microscope setup which combines the advantages of SMLM with SIM in order to provide high-precision localization and structural information in a single setup. Furthermore, the combination of the wide-field SIM image with the SMLM data allows us to identify artifacts produced during the visualization process of SMLM data, and potentially also during the reconstruction process of SIM images. We describe the SMLM–SIM combo and software, and apply the instrument in a first proof-of-principle to the same region of H3K293 cells to achieve SIM images with high structural resolution (in the 100 nm range) in overlay with the highly accurate position information of localized single fluorophores. Thus, with its robust control software, efficient switching between the SMLM and SIM mode, fully automated and user-friendly acquisition and evaluation software, the SMLM–SIM combo is superior over existing solutions. (special issue article)

  15. Synthesis and spectroscopic characterization of Y-shaped fluorophores with an imidazole core containing crown ether moieties

    Energy Technology Data Exchange (ETDEWEB)

    Doğru, Ümit; Öztürk Ürüt, Gülsiye, E-mail: gulsiye.ozturk@deu.edu.tr; Bayramin, Dilek

    2015-07-15

    In this study three new Y-shaped fluorophores, 4,5-(2,2'-diphenyl)vinyl-{2-[(1,4,7,10-tetraoxa-13-azacyclopentadecyl) phenyl]}-1H-imidazole (1a), 4,5-{[2,2'-bis(4-methoxyphenyl)vinyl]-[2-(1,4,7,10-tetraoxa-13- azacyclopentadecyl)-phenyl]}-1H-imidazole (1b) and 4,5-(2,2'-diphenyl)vinyl-{2-(1,4,7,10,13-benzopentaoxacyclopentadecyl)} -1H-imidazole (1c) were synthesized. 1,6-Diphenylhexa-1,5-diene-3,4-dione (2a) and 1,6-bis(4-methoxyphenyl)hexa-1,5-diene-3,4-dione (2b) were synthesized as preliminary fluorophores and then reacted with 4-formylbenzo-aza-15-crown-5 (3a) and 4-formylbenzo-15-crown-5 (3b) to obtain the three Y-shaped fluorophores 1a, 1b and 1c. 4-formylbenzo-aza-15-crown-5 and 4-formylbenzo-15-crown-5 intermediates were synthesized with Vilsmeier–Haack reaction. The photophysical properties such as maximum absorption wavelengths, maximum emission wavelengths, Stokes' shifts, singlet energies, fluorescence quantum yields and photostabilities of the compounds were investigated by measuring absorption and emission spectra in a series of solvents of varying polarities of toluene (TOL), dichloromethane (DCM), tetrahydrofuran (THF), ethyl acetate (EA), acetonitrile (ACN), and N,N-dimethylformamide (DMF). The three compounds 1a, 1b and 1c exhibited emission maxima in the 412–677 nm range. All the derivatives synthesized exhibited excellent photostability in all the solvents tested. - Highlights: • Three new Y-shaped fluorophores were synthesized for the first time. • Their absorption and emission properties were investigated. • All the derivatives synthesized exhibited excellent photostability.

  16. Synthesis and spectroscopic characterization of Y-shaped fluorophores with an imidazole core containing crown ether moieties

    International Nuclear Information System (INIS)

    Doğru, Ümit; Öztürk Ürüt, Gülsiye; Bayramin, Dilek

    2015-01-01

    In this study three new Y-shaped fluorophores, 4,5-(2,2'-diphenyl)vinyl-{2-[(1,4,7,10-tetraoxa-13-azacyclopentadecyl) phenyl]}-1H-imidazole (1a), 4,5-{[2,2'-bis(4-methoxyphenyl)vinyl]-[2-(1,4,7,10-tetraoxa-13- azacyclopentadecyl)-phenyl]}-1H-imidazole (1b) and 4,5-(2,2'-diphenyl)vinyl-{2-(1,4,7,10,13-benzopentaoxacyclopentadecyl)} -1H-imidazole (1c) were synthesized. 1,6-Diphenylhexa-1,5-diene-3,4-dione (2a) and 1,6-bis(4-methoxyphenyl)hexa-1,5-diene-3,4-dione (2b) were synthesized as preliminary fluorophores and then reacted with 4-formylbenzo-aza-15-crown-5 (3a) and 4-formylbenzo-15-crown-5 (3b) to obtain the three Y-shaped fluorophores 1a, 1b and 1c. 4-formylbenzo-aza-15-crown-5 and 4-formylbenzo-15-crown-5 intermediates were synthesized with Vilsmeier–Haack reaction. The photophysical properties such as maximum absorption wavelengths, maximum emission wavelengths, Stokes' shifts, singlet energies, fluorescence quantum yields and photostabilities of the compounds were investigated by measuring absorption and emission spectra in a series of solvents of varying polarities of toluene (TOL), dichloromethane (DCM), tetrahydrofuran (THF), ethyl acetate (EA), acetonitrile (ACN), and N,N-dimethylformamide (DMF). The three compounds 1a, 1b and 1c exhibited emission maxima in the 412–677 nm range. All the derivatives synthesized exhibited excellent photostability in all the solvents tested. - Highlights: • Three new Y-shaped fluorophores were synthesized for the first time. • Their absorption and emission properties were investigated. • All the derivatives synthesized exhibited excellent photostability

  17. Drift correction for single-molecule imaging by molecular constraint field, a distance minimum metric

    International Nuclear Information System (INIS)

    Han, Renmin; Wang, Liansan; Xu, Fan; Zhang, Yongdeng; Zhang, Mingshu; Liu, Zhiyong; Ren, Fei; Zhang, Fa

    2015-01-01

    The recent developments of far-field optical microscopy (single molecule imaging techniques) have overcome the diffraction barrier of light and improve image resolution by a factor of ten compared with conventional light microscopy. These techniques utilize the stochastic switching of probe molecules to overcome the diffraction limit and determine the precise localizations of molecules, which often requires a long image acquisition time. However, long acquisition times increase the risk of sample drift. In the case of high resolution microscopy, sample drift would decrease the image resolution. In this paper, we propose a novel metric based on the distance between molecules to solve the drift correction. The proposed metric directly uses the position information of molecules to estimate the frame drift. We also designed an algorithm to implement the metric for the general application of drift correction. There are two advantages of our method: First, because our method does not require space binning of positions of molecules but directly operates on the positions, it is more natural for single molecule imaging techniques. Second, our method can estimate drift with a small number of positions in each temporal bin, which may extend its potential application. The effectiveness of our method has been demonstrated by both simulated data and experiments on single molecular images

  18. Single molecule sequencing-guided scaffolding and correction of draft assemblies.

    Science.gov (United States)

    Zhu, Shenglong; Chen, Danny Z; Emrich, Scott J

    2017-12-06

    Although single molecule sequencing is still improving, the lengths of the generated sequences are inevitably an advantage in genome assembly. Prior work that utilizes long reads to conduct genome assembly has mostly focused on correcting sequencing errors and improving contiguity of de novo assemblies. We propose a disassembling-reassembling approach for both correcting structural errors in the draft assembly and scaffolding a target assembly based on error-corrected single molecule sequences. To achieve this goal, we formulate a maximum alternating path cover problem. We prove that this problem is NP-hard, and solve it by a 2-approximation algorithm. Our experimental results show that our approach can improve the structural correctness of target assemblies in the cost of some contiguity, even with smaller amounts of long reads. In addition, our reassembling process can also serve as a competitive scaffolder relative to well-established assembly benchmarks.

  19. Single Molecule Spectroscopy of Electron Transfer

    International Nuclear Information System (INIS)

    Holman, Michael; Zang, Ling; Liu, Ruchuan; Adams, David M.

    2009-01-01

    The objectives of this research are threefold: (1) to develop methods for the study electron transfer processes at the single molecule level, (2) to develop a series of modifiable and structurally well defined molecular and nanoparticle systems suitable for detailed single molecule/particle and bulk spectroscopic investigation, (3) to relate experiment to theory in order to elucidate the dependence of electron transfer processes on molecular and electronic structure, coupling and reorganization energies. We have begun the systematic development of single molecule spectroscopy (SMS) of electron transfer and summaries of recent studies are shown. There is a tremendous need for experiments designed to probe the discrete electronic and molecular dynamic fluctuations of single molecules near electrodes and at nanoparticle surfaces. Single molecule spectroscopy (SMS) has emerged as a powerful method to measure properties of individual molecules which would normally be obscured in ensemble-averaged measurement. Fluctuations in the fluorescence time trajectories contain detailed molecular level statistical and dynamical information of the system. The full distribution of a molecular property is revealed in the stochastic fluctuations, giving information about the range of possible behaviors that lead to the ensemble average. In the case of electron transfer, this level of understanding is particularly important to the field of molecular and nanoscale electronics: from a device-design standpoint, understanding and controlling this picture of the overall range of possible behaviors will likely prove to be as important as designing ia the ideal behavior of any given molecule.

  20. Fast recognition of single molecules based on single-event photon statistics

    International Nuclear Information System (INIS)

    Dong Shuangli; Huang Tao; Liu Yuan; Wang Jun; Zhang Guofeng; Xiao Liantuan; Jia Suotang

    2007-01-01

    Mandel's Q parameter, which is determined from single-event photon statistics, provides an alternative way to recognize single molecules with fluorescence detection, other than the second-order correlation function. It is shown that the Q parameter of an assumed ideal double-molecule fluorescence with the same average photon number as that of the sample fluorescence can act as the criterion for single-molecule recognition. The influence of signal-to-background ratio and the error estimates for photon statistics are also presented. We have applied this method to ascertain single Cy5 dye molecules within hundreds of milliseconds

  1. Long-Wavelength Phonon Scattering in Nonpolar Semiconductors

    DEFF Research Database (Denmark)

    Lawætz, Peter

    1969-01-01

    The long-wavelength acoustic- and optical-phonon scattering of carriers in nonpolar semiconductors is considered from a general point of view. The deformation-potential approximation is defined and it is shown that long-range electrostatic forces give a nontrivial correction to the scattering...... of the very-short-range nature of interactions in a covalent semiconductor....

  2. Long-Lived Feshbach Molecules in a Three-Dimensional Optical Lattice

    International Nuclear Information System (INIS)

    Thalhammer, G.; Winkler, K.; Lang, F.; Schmid, S.; Denschlag, J. Hecker; Grimm, R.

    2006-01-01

    We have created and trapped a pure sample of 87 Rb 2 Feshbach molecules in a three-dimensional optical lattice. Compared to previous experiments without a lattice, we find dramatic improvements such as long lifetimes of up to 700 ms and a near unit efficiency for converting tightly confined atom pairs into molecules. The lattice shields the trapped molecules from collisions and, thus, overcomes the problem of inelastic decay by vibrational quenching. Furthermore, we have developed an advanced purification scheme that removes residual atoms, resulting in a lattice in which individual sites are either empty or filled with a single molecule in the vibrational ground state of the lattice

  3. A Brief Introduction to Single-Molecule Fluorescence Methods.

    Science.gov (United States)

    van den Wildenberg, Siet M J L; Prevo, Bram; Peterman, Erwin J G

    2018-01-01

    One of the more popular single-molecule approaches in biological science is single-molecule fluorescence microscopy, which will be the subject of the following section of this volume. Fluorescence methods provide the sensitivity required to study biology on the single-molecule level, but they also allow access to useful measurable parameters on time and length scales relevant for the biomolecular world. Before several detailed experimental approaches will be addressed, we will first give a general overview of single-molecule fluorescence microscopy. We start with discussing the phenomenon of fluorescence in general and the history of single-molecule fluorescence microscopy. Next, we will review fluorescent probes in more detail and the equipment required to visualize them on the single-molecule level. We will end with a description of parameters measurable with such approaches, ranging from protein counting and tracking, single-molecule localization super-resolution microscopy, to distance measurements with Förster Resonance Energy Transfer and orientation measurements with fluorescence polarization.

  4. Nanomechanical DNA origami 'single-molecule beacons' directly imaged by atomic force microscopy

    Science.gov (United States)

    Kuzuya, Akinori; Sakai, Yusuke; Yamazaki, Takahiro; Xu, Yan; Komiyama, Makoto

    2011-01-01

    DNA origami involves the folding of long single-stranded DNA into designed structures with the aid of short staple strands; such structures may enable the development of useful nanomechanical DNA devices. Here we develop versatile sensing systems for a variety of chemical and biological targets at molecular resolution. We have designed functional nanomechanical DNA origami devices that can be used as 'single-molecule beacons', and function as pinching devices. Using 'DNA origami pliers' and 'DNA origami forceps', which consist of two levers ~170 nm long connected at a fulcrum, various single-molecule inorganic and organic targets ranging from metal ions to proteins can be visually detected using atomic force microscopy by a shape transition of the origami devices. Any detection mechanism suitable for the target of interest, pinching, zipping or unzipping, can be chosen and used orthogonally with differently shaped origami devices in the same mixture using a single platform. PMID:21863016

  5. Graphene oxide from silk cocoon: a novel magnetic fluorophore for multi-photon imaging.

    Science.gov (United States)

    Roy, Manas; Kusurkar, Tejas Sanjeev; Maurya, Sandeep Kumar; Meena, Sunil Kumar; Singh, Sushil Kumar; Sethy, Niroj; Bhargava, Kalpana; Sharma, Raj Kishore; Goswami, Debabrata; Sarkar, Sabyasachi; Das, Mainak

    2014-02-01

    In this work, we synthesized graphene oxide from silk cocoon embarking its new dimension as a magnetic fluorophore when compared with its present technical status, which at best is for extracting silk as a biomaterial for tissue engineering applications. We produced graphene oxide by pyrolysing the silk cocoon in an inert atmosphere. The collected raw carbon is oxidized by nitric acid that readily produces multilayer graphene oxide with nano carbon particulates. Structural properties of the graphene oxide were analyzed using scanning electron microscopy, transmission electron microscopy, Fourier transform infra-red spectroscopy, and Raman spectroscopy. The oxidized sample shows remarkable fluorescence, multi-photon imaging and magnetic properties. On increasing the excitation wavelength, the fluorescence emission intensity of the graphene oxide also increases and found maximum emission at 380 nm excitation wavelength. On studying the two photon absorption (TPA) property of aqueous graphene oxide using Z-scan technique, we found significant TPA activity at near infrared wavelength. In addition, the graphene oxide shows ferromagnetic behavior at room temperature. The observed fluorescence and magnetic property were attributed to the defects caused in the graphene oxide structure by introducing oxygen containing hydrophilic groups during the oxidation process. Previously silk cocoon has been used extensively in deriving silk-based tissue engineering materials and as gas filter. Here we show a novel application of silk cocoon by synthesizing graphene oxide based magnetic-fluorophore for bio-imaging applications.

  6. Single-Molecule Analysis of Pre-mRNA Splicing with Colocalization Single-Molecule Spectroscopy (CoSMoS).

    Science.gov (United States)

    Braun, Joerg E; Serebrov, Victor

    2017-01-01

    Recent development of single-molecule techniques to study pre-mRNA splicing has provided insights into the dynamic nature of the spliceosome. Colocalization single-molecule spectroscopy (CoSMoS) allows following spliceosome assembly in real time at single-molecule resolution in the full complexity of cellular extracts. A detailed protocol of CoSMoS has been published previously (Anderson and Hoskins, Methods Mol Biol 1126:217-241, 2014). Here, we provide an update on the technical advances since the first CoSMoS studies including slide surface treatment, data processing, and representation. We describe various labeling strategies to generate RNA reporters with multiple dyes (or other moieties) at specific locations.

  7. Surface Passivation for Single-molecule Protein Studies

    Science.gov (United States)

    Chandradoss, Stanley D.; Haagsma, Anna C.; Lee, Young Kwang; Hwang, Jae-Ho; Nam, Jwa-Min; Joo, Chirlmin

    2014-01-01

    Single-molecule fluorescence spectroscopy has proven to be instrumental in understanding a wide range of biological phenomena at the nanoscale. Important examples of what this technique can yield to biological sciences are the mechanistic insights on protein-protein and protein-nucleic acid interactions. When interactions of proteins are probed at the single-molecule level, the proteins or their substrates are often immobilized on a glass surface, which allows for a long-term observation. This immobilization scheme may introduce unwanted surface artifacts. Therefore, it is essential to passivate the glass surface to make it inert. Surface coating using polyethylene glycol (PEG) stands out for its high performance in preventing proteins from non-specifically interacting with a glass surface. However, the polymer coating procedure is difficult, due to the complication arising from a series of surface treatments and the stringent requirement that a surface needs to be free of any fluorescent molecules at the end of the procedure. Here, we provide a robust protocol with step-by-step instructions. It covers surface cleaning including piranha etching, surface functionalization with amine groups, and finally PEG coating. To obtain a high density of a PEG layer, we introduce a new strategy of treating the surface with PEG molecules over two rounds, which remarkably improves the quality of passivation. We provide representative results as well as practical advice for each critical step so that anyone can achieve the high quality surface passivation. PMID:24797261

  8. Narrow band wavelength selective filter using grating assisted single ring resonator

    Energy Technology Data Exchange (ETDEWEB)

    Prabhathan, P., E-mail: PPrabhathan@ntu.edu.sg; Murukeshan, V. M. [Centre for Optical and Laser Engineering (COLE), School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798 (Singapore)

    2014-09-15

    This paper illustrates a filter configuration which uses a single ring resonator of larger radius connected to a grating resonator at its drop port to achieve single wavelength selectivity and switching property with spectral features suitable for on-chip wavelength selection applications. The proposed configuration is expected to find applications in silicon photonics devices such as, on-chip external cavity lasers and multi analytic label-free biosensors. The grating resonator has been designed for a high Q-factor, high transmittivity, and minimum loss so that the wavelength selectivity of the device is improved. The proof-of-concept device has been demonstrated on a Silicon-on-Insulator (SOI) platform through electron beam lithography and Reactive Ion Etching (RIE) process. The transmission spectrum shows narrow band single wavelength selection and switching property with a high Free Spectral Range (FSR) ∼60 nm and side band rejection ratio >15 dB.

  9. A brief introduction to single-molecule fluorescence methods

    NARCIS (Netherlands)

    Wildenberg, S.M.J.L.; Prevo, B.; Peterman, E.J.G.; Peterman, EJG; Wuite, GJL

    2011-01-01

    One of the more popular single-molecule approaches in biological science is single-molecule fluorescence microscopy, which is the subject of the following section of this volume. Fluorescence methods provide the sensitivity required to study biology on the single-molecule level, but they also allow

  10. A brief introduction to single-molecule fluorescence methods

    NARCIS (Netherlands)

    van den Wildenberg, Siet M.J.L.; Prevo, Bram; Peterman, Erwin J.G.

    2018-01-01

    One of the more popular single-molecule approaches in biological science is single-molecule fluorescence microscopy, which will be the subject of the following section of this volume. Fluorescence methods provide the sensitivity required to study biology on the single-molecule level, but they also

  11. Direct single-molecule dynamic detection of chemical reactions.

    Science.gov (United States)

    Guan, Jianxin; Jia, Chuancheng; Li, Yanwei; Liu, Zitong; Wang, Jinying; Yang, Zhongyue; Gu, Chunhui; Su, Dingkai; Houk, Kendall N; Zhang, Deqing; Guo, Xuefeng

    2018-02-01

    Single-molecule detection can reveal time trajectories and reaction pathways of individual intermediates/transition states in chemical reactions and biological processes, which is of fundamental importance to elucidate their intrinsic mechanisms. We present a reliable, label-free single-molecule approach that allows us to directly explore the dynamic process of basic chemical reactions at the single-event level by using stable graphene-molecule single-molecule junctions. These junctions are constructed by covalently connecting a single molecule with a 9-fluorenone center to nanogapped graphene electrodes. For the first time, real-time single-molecule electrical measurements unambiguously show reproducible large-amplitude two-level fluctuations that are highly dependent on solvent environments in a nucleophilic addition reaction of hydroxylamine to a carbonyl group. Both theoretical simulations and ensemble experiments prove that this observation originates from the reversible transition between the reactant and a new intermediate state within a time scale of a few microseconds. These investigations open up a new route that is able to be immediately applied to probe fast single-molecule physics or biophysics with high time resolution, making an important contribution to broad fields beyond reaction chemistry.

  12. Ionoluminescence properties of polystyrene-hosted fluorophore films induced by helium ions of energy 50-350 keV

    Science.gov (United States)

    Chakraborty, Subha; Huang, Mengbing

    2017-10-01

    We report on measurements and analysis of ionoluminescence properties of pure polystyrene films and polystyrene films doped with four types of fluorophores in low kinetic energies (50-350 keV) of ion irradiation. We have developed a theoretical model to understand the experimentally observed ionoluminescence behaviors in terms of scintillation yield from individual ion tracks, photophysical energy transfer mechanisms, and irradiation-induced defects. A comparison of the model and experimental results suggests that singlet up-conversion resulting from triplet-triplet annihilation processes may be responsible for enhanced singlet emission of the fluorophores at high ion beam flux densities. Energy transfer from the polystyrene matrix to the fluorophore molecules has been identified as an effective pathway to increasing the fluorescence efficiency in the doped scintillator films.

  13. Single Molecule Nanoelectrochemistry in Electrical Junctions.

    Science.gov (United States)

    Nichols, Richard J; Higgins, Simon J

    2016-11-15

    It is now possible to reliably measure single molecule conductance in a wide variety of environments including organic liquids, ultrahigh vacuum, water, ionic liquids, and electrolytes. The most commonly used methods deploy scanning probe microscopes, mechanically formed break junctions, or lithographically formed nanogap contacts. Molecules are generally captured between a pair of facing electrodes, and the junction current response is measured as a function of bias voltage. Gating electrodes can also be added so that the electrostatic potential at the molecular bridge can be independently controlled by this third noncontacting electrode. This can also be achieved in an electrolytic environment using a four-electrode bipotentiostatic configuration, which allows independent electrode potential control of the two contacting electrodes. This is commonly realized using an electrochemical STM and enables single molecule electrical characterization as a function of electrode potential and redox state of the molecular bridge. This has emerged as a powerful tool in modern interfacial electrochemistry and nanoelectrochemistry for studying charge transport across single molecules as a function of electrode potential and the electrolytic environments. Such measurements are possible in electrolytes ranging from aqueous buffers to nonaqueous ionic liquids. In this Account, we illustrate a number of examples of single molecule electrical measurements under electrode potential control use a scanning tunneling microscope (STM) and demonstrate how these can help in the understanding of charge transport in single molecule junctions. Examples showing charge transport following phase coherent tunneling to incoherent charge hopping across redox active molecular bridges are shown. In the case of bipyridinium (or viologen) molecular wires, it is shown how electrochemical reduction leads to an increase of the single molecule conductance, which is controlled by the liquid electrochemical

  14. Challenges for single molecule electronic devices with nanographene and organic molecules. Do single molecules offer potential as elements of electronic devices in the next generation?

    Science.gov (United States)

    Enoki, Toshiaki; Kiguchi, Manabu

    2018-03-01

    Interest in utilizing organic molecules to fabricate electronic materials has existed ever since organic (molecular) semiconductors were first discovered in the 1950s. Since then, scientists have devoted serious effort to the creation of various molecule-based electronic systems, such as molecular metals and molecular superconductors. Single-molecule electronics and the associated basic science have emerged over the past two decades and provided hope for the development of highly integrated molecule-based electronic devices in the future (after the Si-based technology era has ended). Here, nanographenes (nano-sized graphene) with atomically precise structures are among the most promising molecules that can be utilized for electronic/spintronic devices. To manipulate single small molecules for an electronic device, a single molecular junction has been developed. It is a powerful tool that allows even small molecules to be utilized. External electric, magnetic, chemical, and mechanical perturbations can change the physical and chemical properties of molecules in a way that is different from bulk materials. Therefore, the various functionalities of molecules, along with changes induced by external perturbations, allows us to create electronic devices that we cannot create using current top-down Si-based technology. Future challenges that involve the incorporation of condensed matter physics, quantum chemistry calculations, organic synthetic chemistry, and electronic device engineering are expected to open a new era in single-molecule device electronic technology.

  15. Single-Molecule Electronics: Chemical and Analytical Perspectives.

    Science.gov (United States)

    Nichols, Richard J; Higgins, Simon J

    2015-01-01

    It is now possible to measure the electrical properties of single molecules using a variety of techniques including scanning probe microcopies and mechanically controlled break junctions. Such measurements can be made across a wide range of environments including ambient conditions, organic liquids, ionic liquids, aqueous solutions, electrolytes, and ultra high vacuum. This has given new insights into charge transport across molecule electrical junctions, and these experimental methods have been complemented with increasingly sophisticated theory. This article reviews progress in single-molecule electronics from a chemical perspective and discusses topics such as the molecule-surface coupling in electrical junctions, chemical control, and supramolecular interactions in junctions and gating charge transport. The article concludes with an outlook regarding chemical analysis based on single-molecule conductance.

  16. Single Molecule and Nanoparticle Imaging in Biophysical, Surface, and Photocatalysis Studies

    Energy Technology Data Exchange (ETDEWEB)

    Ha, Ji Won [Iowa State Univ., Ames, IA (United States)

    2013-01-01

    A differential interference contrast (DIC) polarization anisotropy is reported that was successfully used for rotational tracking of gold nanorods attached onto a kinesin-driven microtubule. A dual-wavelength detection of single gold nanorods rotating on a live cell membrane is described. Both transverse and longitudinal surface plasmon resonance (SPR) modes were used for tracking the rotational motions during a fast dynamic process under a DIC microscope. A novel method is presented to determine the full three-dimensional (3D) orientation of single plasmonic gold nanorods rotating on live cell membranes by combining DIC polarization anisotropy with an image pattern recognition technique. Polarization- and wavelength-sensitive DIC microscopy imaging of 2- m long gold nanowires as optical probes in biological studies is reported. A new method is demonstrated to track 3D orientation of single gold nanorods supported on a gold film without angular degeneracy. The idea is to use the interaction (or coupling) of gold nanorods with gold film, yielding characteristic scattering patterns such as a doughnut shape. Imaging of photocatalytic activity, polarity and selectivity on single Au-CdS hybrid nanocatalysts using a high-resolution superlocalization fluorescence imaging technique is described.

  17. Single-Molecule Rotational Switch on a Dangling Bond Dimer Bearing.

    Science.gov (United States)

    Godlewski, Szymon; Kawai, Hiroyo; Kolmer, Marek; Zuzak, Rafał; Echavarren, Antonio M; Joachim, Christian; Szymonski, Marek; Saeys, Mark

    2016-09-27

    One of the key challenges in the construction of atomic-scale circuits and molecular machines is to design molecular rotors and switches by controlling the linear or rotational movement of a molecule while preserving its intrinsic electronic properties. Here, we demonstrate both the continuous rotational switching and the controlled step-by-step single switching of a trinaphthylene molecule adsorbed on a dangling bond dimer created on a hydrogen-passivated Ge(001):H surface. The molecular switch is on-surface assembled when the covalent bonds between the molecule and the dangling bond dimer are controllably broken, and the molecule is attached to the dimer by long-range van der Waals interactions. In this configuration, the molecule retains its intrinsic electronic properties, as confirmed by combined scanning tunneling microscopy/spectroscopy (STM/STS) measurements, density functional theory calculations, and advanced STM image calculations. Continuous switching of the molecule is initiated by vibronic excitations when the electrons are tunneling through the lowest unoccupied molecular orbital state of the molecule. The switching path is a combination of a sliding and rotation motion over the dangling bond dimer pivot. By carefully selecting the STM conditions, control over discrete single switching events is also achieved. Combined with the ability to create dangling bond dimers with atomic precision, the controlled rotational molecular switch is expected to be a crucial building block for more complex surface atomic-scale devices.

  18. Single Molecule Biophysics Experiments and Theory

    CERN Document Server

    Komatsuzaki, Tamiki; Takahashi, Satoshi; Yang, Haw; Silbey, Robert J; Rice, Stuart A; Dinner, Aaron R

    2011-01-01

    Discover the experimental and theoretical developments in optical single-molecule spectroscopy that are changing the ways we think about molecules and atoms The Advances in Chemical Physics series provides the chemical physics field with a forum for critical, authoritative evaluations of advances in every area of the discipline. This latest volume explores the advent of optical single-molecule spectroscopy, and how atomic force microscopy has empowered novel experiments on individual biomolecules, opening up new frontiers in molecular and cell biology and leading to new theoretical approaches

  19. Single molecule detection, thermal fluctuation and life

    Science.gov (United States)

    YANAGIDA, Toshio; ISHII, Yoshiharu

    2017-01-01

    Single molecule detection has contributed to our understanding of the unique mechanisms of life. Unlike artificial man-made machines, biological molecular machines integrate thermal noises rather than avoid them. For example, single molecule detection has demonstrated that myosin motors undergo biased Brownian motion for stepwise movement and that single protein molecules spontaneously change their conformation, for switching to interactions with other proteins, in response to thermal fluctuation. Thus, molecular machines have flexibility and efficiency not seen in artificial machines. PMID:28190869

  20. On theory of single-molecule transistor

    International Nuclear Information System (INIS)

    Tran Tien Phuc

    2009-01-01

    The results of the study on single-molecule transistor are mainly investigated in this paper. The structure of constructed single-molecule transistor is similar to a conventional MOSFET. The conductive channel of the transistors is a single-molecule of halogenated benzene derivatives. The chemical simulation software CAChe was used to design and implement for the essential parameter of the molecules utilized as the conductive channel. The GUI of Matlab has been built to design its graphical interface, calculate and plot the output I-V characteristic curves for the transistor. The influence of temperature, length and width of the conductive channel, and gate voltage is considered. As a result, the simulated curves are similar to the traditional MOSFET's. The operating temperature range of the transistors is wider compared with silicon semiconductors. The supply voltage for transistors is only about 1 V. The size of transistors in this research is several nanometers.

  1. Molecular electronics: the single molecule switch and transistor

    NARCIS (Netherlands)

    Sotthewes, Kai; Geskin, Victor; Heimbuch, Rene; Kumar, Avijit; Zandvliet, Henricus J.W.

    2014-01-01

    In order to design and realize single-molecule devices it is essential to have a good understanding of the properties of an individual molecule. For electronic applications, the most important property of a molecule is its conductance. Here we show how a single octanethiol molecule can be connected

  2. In Vivo Imaging of Xenograft Tumors Using an Epidermal Growth Factor Receptor-Specific Affibody Molecule Labeled with a Near-infrared Fluorophore

    Directory of Open Access Journals (Sweden)

    Haibiao Gong

    2010-02-01

    Full Text Available Overexpression of epidermal growth factor receptor (EGFR is associated with many types of cancers. It is of great interest to noninvasively image the EGFR expression in vivo. In this study, we labeled an EGFR-specific Affibody molecule (Eaff with a near-infrared (NIR dye IRDye800CW maleimide and tested the binding of this labeled molecule (Eaff800 in cell culture and xenograft mouse tumor models. Unlike EGF, Eaff did not activate the EGFR signaling pathway. Results showed that Eaff800 was bound and taken up specifically by EGFR-overexpressing A431 cells. When Eaff800 was intravenously injected into nude mice bearing A431 xenograft tumors, the tumor could be identified 1 hour after injection and it became most prominent after 1 day. Images of dissected tissue sections demonstrated that the accumulation of Eaff800 was highest in the liver, followed by the tumor and kidney. Moreover, in combination with a human EGFR type 2 (HER2-specific probe Haff682, Eaff800 could be used to distinguish between EGFR- and HER2-overexpressing tumors. Interestingly, the organ distribution pattern and the clearance rate of Eaff800 were different from those of Haff682. In conclusion, Eaff molecule labeled with a NIR fluorophore is a promising molecular imaging agent for EGFR-overexpressing tumors.

  3. Pulse patterning effect in optical pulse division multiplexing for flexible single wavelength multiple access optical network

    Science.gov (United States)

    Jung, Sun-Young; Kim, Chang-Hun; Han, Sang-Kook

    2018-05-01

    A demand for high spectral efficiency requires multiple access within a single wavelength, but the uplink signals are significantly degraded because of optical beat interference (OBI) in intensity modulation/direct detection system. An optical pulse division multiplexing (OPDM) technique was proposed that could effectively reduce the OBI via a simple method as long as near-orthogonality is satisfied, but the condition was strict, and thus, the number of multiplexing units was very limited. We propose pulse pattern enhanced OPDM (e-OPDM) to reduce the OBI and improve the flexibility in multiple access within a single wavelength. The performance of the e-OPDM and patterning effect are experimentally verified after 23-km single mode fiber transmission. By employing pulse patterning in OPDM, the tight requirement was relaxed by extending the optical delay dynamic range. This could support more number of access with reduced OBI, which could eventually enhance a multiple access function.

  4. Continuous throughput and long-term observation of single-molecule FRET without immobilization.

    Science.gov (United States)

    Tyagi, Swati; VanDelinder, Virginia; Banterle, Niccolò; Fuertes, Gustavo; Milles, Sigrid; Agez, Morgane; Lemke, Edward A

    2014-03-01

    We present an automated microfluidic platform that performs multisecond observation of single molecules with millisecond time resolution while bypassing the need for immobilization procedures. With this system, we confine biomolecules to a thin excitation field by reversibly collapsing microchannels to nanochannels. We demonstrate the power of our method by studying a variety of complex nucleic acid and protein systems, including DNA Holliday junctions, nucleosomes and human transglutaminase 2.

  5. Single-photon generator for optical telecommunication wavelength

    International Nuclear Information System (INIS)

    Usuki, T; Sakuma, Y; Hirose, S; Takemoto, K; Yokoyama, N; Miyazawa, T; Takatsu, M; Arakawa, Y

    2006-01-01

    We report on the generation of single-photon pulses from a single InAs/InP quantum dot in telecommunication bands (1.3-1.55 μm: higher transmittance through an optical fiber). First we prepared InAs quantum dots on InP (0 0 1) substrates in a low-pressure MOCVD by using a so-called InP 'double-cap' procedure. The quantum dots have well-controlled photo emission wavelength in the telecommunication bands. We also developed a single-photon emitter in which quantum dots were embedded. Numerical simulation designed the emitter to realize efficient injection of the emitted photons into a single-mode optical fiber. Using a Hanbury-Brown and Twiss technique has proved that the photons through the fiber were single photons

  6. Long-wavelength microinstabilities in toroidal plasmas

    International Nuclear Information System (INIS)

    Tang, W.W.; Rewoldt, G.

    1993-01-01

    Realistic kinetic toroidal eigenmode calculations have been carried out to support a proper assessment of the influence of long-wavelength microturbulence on transport in tokamak plasmas. In order to efficiently evaluate large-scale kinetic behavior extending over many rational surfaces, significant improvements have been made to a toroidal finite element code used to analyze the fully two-dimensional (r,θ) mode structures of trapped-ion and toroidal ion temperature gradient (ITG) instabilities. It is found that even at very long wavelengths, these eigenmodes exhibit a strong ballooning character with the associated radial structure relatively insensitive to ion Landau damping at the rational surfaces. In contrast to the long-accepted picture that the radial extent of trapped-ion instabilities is characterized by the ion-gyroradius-scale associated with strong localization between adjacent rational surfaces, present results demonstrate that under realistic conditions, the actual scale is governed by the large-scale variations in the equilibrium gradients. Applications to recent measurements of fluctuation properties in TFTR L-mode plasmas indicate that the theoretical trends appear consistent with spectral characteristics as well as rough heuristic estimates of the transport level. Benchmarking calculations in support of the development of a three-dimensional toroidal gyrokinetic code indicate reasonable agreement with respect to both the properties of the eigenfunctions and the magnitude of the eigenvalues during the linear phase of the simulations of toroidal ITG instabilities

  7. Energy transfer from a fluorescent hydrogel to a hosted fluorophore

    NARCIS (Netherlands)

    Montalti, Marco; Dolci, Luisa Stella; Prodi, Luca; Zaccheroni, Nelsi; Stuart, Marc C.A.; van Bommel, Kjeld C.; Friggeri, Arianna

    2006-01-01

    The fluorescent properties of a new 1,3,5-cyclohexyltricarboxamide-based low-molecular-weight hydrogelator (1) derivatized with one hydrophobic fluorophore and two hydrophilic substituents have been investigated. Gels of I are composed of long, nonbranched fibers of uniform diameter, as shown by

  8. Effective long wavelength scalar dynamics in de Sitter

    Energy Technology Data Exchange (ETDEWEB)

    Moss, Ian; Rigopoulos, Gerasimos, E-mail: ian.moss@newcastle.ac.uk, E-mail: gerasimos.rigopoulos@ncl.ac.uk [School of Mathematics and Statistics, Newcastle University, Herschel Building, Newcastle upon Tyne, NE1 7RU U.K. (United Kingdom)

    2017-05-01

    We discuss the effective infrared theory governing a light scalar's long wavelength dynamics in de Sitter spacetime. We show how the separation of scales around the physical curvature radius k / a ∼ H can be performed consistently with a window function and how short wavelengths can be integrated out in the Schwinger-Keldysh path integral formalism. At leading order, and for time scales Δ t >> H {sup −1}, this results in the well-known Starobinsky stochastic evolution. However, our approach allows for the computation of quantum UV corrections, generating an effective potential on which the stochastic dynamics takes place. The long wavelength stochastic dynamical equations are now second order in time, incorporating temporal scales Δ t ∼ H {sup −1} and resulting in a Kramers equation for the probability distribution—more precisely the Wigner function—in contrast to the more usual Fokker-Planck equation. This feature allows us to non-perturbatively evaluate, within the stochastic formalism, not only expectation values of field correlators, but also the stress-energy tensor of φ.

  9. Observing single molecule chemical reactions on metal nanoparticles.

    Energy Technology Data Exchange (ETDEWEB)

    Emory, S. R. (Steven R.); Ambrose, W. Patrick; Goodwin, P. M. (Peter M); Keller, Richard A.

    2001-01-01

    We report the study of the photodecomposition of single Rhodamine 6G (R6G) dye molecules adsorbed on silver nanoparticles. The nanoparticles were immobilized and spatially isolated on polylysine-derivatized glass coverslips, and confocal laser microspectroscopy was used to obtain surface-enhanced Raman scattering (SERS) spectra from individual R6G molecules. The photodecomposition of these molecules was observed with 150-ms temporal resolution. The photoproduct was identified as graphitic carbon based on the appearance of broad SERS vibrational bands at 1592 cm{sup -1} and 1340 cm{sup -1} observed in both bulk and averaged single-molecule photoproduct spectra. In contrast, when observed at the single-molecule level, the photoproduct yielded sharp SERS spectra. The inhomogeneous broadening of the bulk SERS spectra is due to a variety of photoproducts in different surface orientations and is a characteristic of ensemble-averaged measurements of disordered systems. These single-molecule studies indicate a photodecomposition pathway by which the R6G molecule desorbs from the metal surface, an excited-state photoreaction occurs, and the R6G photoproduct(s) readsorbs to the surface. A SERS spectrum is obtained when either the intact R6G or the R6G photoproduct(s) are adsorbed on a SERS-active site. This work further illustrates the power of single-molecule spectroscopy (SMS) to reveal unique behaviors of single molecules that are not discernable with bulk measurements.

  10. Single-Molecule Transport at a Rectifying GaAs Contact.

    Science.gov (United States)

    Vezzoli, Andrea; Brooke, Richard J; Ferri, Nicolò; Higgins, Simon J; Schwarzacher, Walther; Nichols, Richard J

    2017-02-08

    In most single- or few-molecule devices, the contact electrodes are simple ohmic resistors. Here we describe a new type of single-molecule device in which metal and semiconductor contact electrodes impart a function, namely, current rectification, which is then modified by a molecule bridging the gap. We study junctions with the structure Au STM tip/X/n-GaAs substrate, where "X" is either a simple alkanedithiol or a conjugated unit bearing thiol/methylthiol contacts, and we detect current jumps corresponding to the attachment and detachment of single molecules. From the magnitudes of the current jumps we can deduce values for the conductance decay constant with molecule length that agree well with values determined from Au/molecule/Au junctions. The ability to impart functionality to a single-molecule device through the properties of the contacts as well as through the properties of the molecule represents a significant extension of the single-molecule electronics "tool-box".

  11. Single molecule force spectroscopy: methods and applications in biology

    International Nuclear Information System (INIS)

    Shen Yi; Hu Jun

    2012-01-01

    Single molecule measurements have transformed our view of biomolecules. Owing to the ability of monitoring the activity of individual molecules, we now see them as uniquely structured, fluctuating molecules that stochastically transition between frequently many substrates, as two molecules do not follow precisely the same trajectory. Indeed, it is this discovery of critical yet short-lived substrates that were often missed in ensemble measurements that has perhaps contributed most to the better understanding of biomolecular functioning resulting from single molecule experiments. In this paper, we give a review on the three major techniques of single molecule force spectroscopy, and their applications especially in biology. The single molecular study of biotin-streptavidin interactions is introduced as a successful example. The problems and prospects of the single molecule force spectroscopy are discussed, too. (authors)

  12. Investigating single molecule adhesion by atomic force spectroscopy.

    Science.gov (United States)

    Stetter, Frank W S; Kienle, Sandra; Krysiak, Stefanie; Hugel, Thorsten

    2015-02-27

    Atomic force spectroscopy is an ideal tool to study molecules at surfaces and interfaces. An experimental protocol to couple a large variety of single molecules covalently onto an AFM tip is presented. At the same time the AFM tip is passivated to prevent unspecific interactions between the tip and the substrate, which is a prerequisite to study single molecules attached to the AFM tip. Analyses to determine the adhesion force, the adhesion length, and the free energy of these molecules on solid surfaces and bio-interfaces are shortly presented and external references for further reading are provided. Example molecules are the poly(amino acid) polytyrosine, the graft polymer PI-g-PS and the phospholipid POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine). These molecules are desorbed from different surfaces like CH3-SAMs, hydrogen terminated diamond and supported lipid bilayers under various solvent conditions. Finally, the advantages of force spectroscopic single molecule experiments are discussed including means to decide if truly a single molecule has been studied in the experiment.

  13. Single-molecule mechanics of protein-labelled DNA handles

    Directory of Open Access Journals (Sweden)

    Vivek S. Jadhav

    2016-01-01

    Full Text Available DNA handles are often used as spacers and linkers in single-molecule experiments to isolate and tether RNAs, proteins, enzymes and ribozymes, amongst other biomolecules, between surface-modified beads for nanomechanical investigations. Custom DNA handles with varying lengths and chemical end-modifications are readily and reliably synthesized en masse, enabling force spectroscopic measurements with well-defined and long-lasting mechanical characteristics under physiological conditions over a large range of applied forces. Although these chemically tagged DNA handles are widely used, their further individual modification with protein receptors is less common and would allow for additional flexibility in grabbing biomolecules for mechanical measurements. In-depth information on reliable protocols for the synthesis of these DNA–protein hybrids and on their mechanical characteristics under varying physiological conditions are lacking in literature. Here, optical tweezers are used to investigate different protein-labelled DNA handles in a microfluidic environment under different physiological conditions. Digoxigenin (DIG-dsDNA-biotin handles of varying sizes (1000, 3034 and 4056 bp were conjugated with streptavidin or neutravidin proteins. The DIG-modified ends of these hybrids were bound to surface-modified polystyrene (anti-DIG beads. Using different physiological buffers, optical force measurements showed consistent mechanical characteristics with long dissociation times. These protein-modified DNA hybrids were also interconnected in situ with other tethered biotinylated DNA molecules. Electron-multiplying CCD (EMCCD imaging control experiments revealed that quantum dot–streptavidin conjugates at the end of DNA handles remain freely accessible. The experiments presented here demonstrate that handles produced with our protein–DNA labelling procedure are excellent candidates for grasping single molecules exposing tags suitable for molecular

  14. Exogenous near-infrared fluorophores and their applications in cancer diagnosis: biological and clinical perspectives.

    Science.gov (United States)

    Zhang, Hua; Uselman, Ryan R; Yee, Douglas

    2011-05-01

    Near-infrared fluorescent (NIRF) imaging is a rapidly growing research field which has the potential to be an important imaging modality in cancer diagnosis. Various exogenous NIR fluorophores have been developed for the technique, including small molecule fluorophores and nanoparticles. NIRF imaging has been used in animal models for the detection of cancer overthe last twenty years and has in recent years been used in human clinical trials. This article describes the types and characteristics of exogenous fluorophores available for in vivo fluorescent cancer imaging. The article also discusses the progression of NIRF cancer imaging over recent years and its future challenges, from both a biological and clinical perspective. in The review also looks at its application for lymph node mapping, tumor targeting and characterization, and tumor margin definition for surgical guidance. NIRF imaging is not in routine clinical cancer practice; yet, the authors predict that techniques using NIR fluorophores for tumor margin definition and lymph node mapping will enter clinical practice in the near future. The authors also anticipate that NIRF imaging research will lead to the development of flurophores with 'high brightness' that will overcome the limited penetration of this modality and be better suited for non invasive tumor targeting.

  15. Computer systems for annotation of single molecule fragments

    Science.gov (United States)

    Schwartz, David Charles; Severin, Jessica

    2016-07-19

    There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

  16. Proposal for probing energy transfer pathway by single-molecule pump-dump experiment

    Science.gov (United States)

    Tao, Ming-Jie; Ai, Qing; Deng, Fu-Guo; Cheng, Yuan-Chung

    2016-06-01

    The structure of Fenna-Matthews-Olson (FMO) light-harvesting complex had long been recognized as containing seven bacteriochlorophyll (BChl) molecules. Recently, an additional BChl molecule was discovered in the crystal structure of the FMO complex, which may serve as a link between baseplate and the remaining seven molecules. Here, we investigate excitation energy transfer (EET) process by simulating single-molecule pump-dump experiment in the eight-molecules complex. We adopt the coherent modified Redfield theory and non-Markovian quantum jump method to simulate EET dynamics. This scheme provides a practical approach of detecting the realistic EET pathway in BChl complexes with currently available experimental technology. And it may assist optimizing design of artificial light-harvesting devices.

  17. Massively Parallel Single-Molecule Manipulation Using Centrifugal Force

    Science.gov (United States)

    Wong, Wesley; Halvorsen, Ken

    2011-03-01

    Precise manipulation of single molecules has led to remarkable insights in physics, chemistry, biology, and medicine. However, two issues that have impeded the widespread adoption of these techniques are equipment cost and the laborious nature of making measurements one molecule at a time. To meet these challenges, we have developed an approach that enables massively parallel single- molecule force measurements using centrifugal force. This approach is realized in the centrifuge force microscope, an instrument in which objects in an orbiting sample are subjected to a calibration-free, macroscopically uniform force- field while their micro-to-nanoscopic motions are observed. We demonstrate high- throughput single-molecule force spectroscopy with this technique by performing thousands of rupture experiments in parallel, characterizing force-dependent unbinding kinetics of an antibody-antigen pair in minutes rather than days. Currently, we are taking steps to integrate high-resolution detection, fluorescence, temperature control and a greater dynamic range in force. With significant benefits in efficiency, cost, simplicity, and versatility, single-molecule centrifugation has the potential to expand single-molecule experimentation to a wider range of researchers and experimental systems.

  18. Determination of soy proteins in food samples by dispersive solid-phase immunoextraction and dynamic long-wavelength fluorometry

    International Nuclear Information System (INIS)

    Molina-Delgado, María Ángeles; Aguilar-Caballos, María Paz; Gomez-Hens, Agustina

    2013-01-01

    We report on a method for the determination of soy proteins in food samples via dispersive solid-phase immunoextraction using gold-coated magnetic nanoparticles (NPs) as a support. Soy proteins were first extracted using anti-soy protein antibodies immobilized on the NPs, and then quantified by measuring the increase in fluorescence of the long-wavelength fluorophore cresyl violet in the presence of the anionic surfactant sodium dodecyl sulfate at neutral pH in a flow system. The method involves the use of two standard or sample aliquots. The fluorescence intensity of one aliquot is directly measured whereas that of the other aliquot is measured after immunoextraction. The difference between the peak heights of both aliquots serves as the analytical information that is directly proportional to the protein concentration. The limit of detection is 0.35 mg L −1 , the linear range is from 1 to 15 mg L −1 , and the relative standard deviation is < 5 %. Proteins such as bovine serum albumin and globulins do not interfere at the same concentration level. The method was applied to the analysis of soy-based beverages and gave recoveries in the range between 80.0 and 107.3 %. (author)

  19. Single molecule transcription profiling with AFM

    International Nuclear Information System (INIS)

    Reed, Jason; Mishra, Bud; Pittenger, Bede; Magonov, Sergei; Troke, Joshua; Teitell, Michael A; Gimzewski, James K

    2007-01-01

    Established techniques for global gene expression profiling, such as microarrays, face fundamental sensitivity constraints. Due to greatly increasing interest in examining minute samples from micro-dissected tissues, including single cells, unorthodox approaches, including molecular nanotechnologies, are being explored in this application. Here, we examine the use of single molecule, ordered restriction mapping, combined with AFM, to measure gene transcription levels from very low abundance samples. We frame the problem mathematically, using coding theory, and present an analysis of the critical error sources that may serve as a guide to designing future studies. We follow with experiments detailing the construction of high density, single molecule, ordered restriction maps from plasmids and from cDNA molecules, using two different enzymes, a result not previously reported. We discuss these results in the context of our calculations

  20. Portable Long-Wavelength Infrared Camera for Civilian Application

    Science.gov (United States)

    Gunapala, S. D.; Krabach, T. N.; Bandara, S. V.; Liu, J. K.

    1997-01-01

    In this paper, we discuss the performance of this portable long-wavelength infrared camera in quantum efficiency, NEAT, minimum resolvable temperature differnce (MRTD), uniformity, etc. and its application in science, medicine and defense.

  1. Optical probing of single fluorescent molecules and proteins

    NARCIS (Netherlands)

    Garcia Parajo, M.F.; Veerman, J.A.; Bouwhuis, R.; Bouwhuis, Rudo; van Hulst, N.F.; Vallée, R.A.L.

    2001-01-01

    Single-molecule detection and analysis of organic fluorescent molecules and proteins are presented, with emphasis o­n the underlying principles methodology and the application of single-molecule analysis at room temperature. This Minireview is mainly focused o­n the application of confocal and

  2. Construction of a single/multiple wavelength RZ optical pulse source at 40 GHz by use of wavelength conversion in a high-nonlinearity DSF-NOLM

    DEFF Research Database (Denmark)

    Yu, Jianjun; Yujun, Qian; Jeppesen, Palle

    2001-01-01

    A single or multiple wavelength RZ optical pulse source at 40 GHz is successfully obtained by using wavelength conversion in a nonlinear optical loop mirror consisting of high nonlinearity-dispersion shifted fiber.......A single or multiple wavelength RZ optical pulse source at 40 GHz is successfully obtained by using wavelength conversion in a nonlinear optical loop mirror consisting of high nonlinearity-dispersion shifted fiber....

  3. 3D single-molecule super-resolution microscopy with a tilted light sheet.

    Science.gov (United States)

    Gustavsson, Anna-Karin; Petrov, Petar N; Lee, Maurice Y; Shechtman, Yoav; Moerner, W E

    2018-01-09

    Tilted light sheet microscopy with 3D point spread functions (TILT3D) combines a novel, tilted light sheet illumination strategy with long axial range point spread functions (PSFs) for low-background, 3D super-localization of single molecules as well as 3D super-resolution imaging in thick cells. Because the axial positions of the single emitters are encoded in the shape of each single-molecule image rather than in the position or thickness of the light sheet, the light sheet need not be extremely thin. TILT3D is built upon a standard inverted microscope and has minimal custom parts. The result is simple and flexible 3D super-resolution imaging with tens of nm localization precision throughout thick mammalian cells. We validate TILT3D for 3D super-resolution imaging in mammalian cells by imaging mitochondria and the full nuclear lamina using the double-helix PSF for single-molecule detection and the recently developed tetrapod PSFs for fiducial bead tracking and live axial drift correction.

  4. Theoretical Investigations Regarding Single Molecules

    DEFF Research Database (Denmark)

    Pedersen, Kim Georg Lind

    Neoclassical Valence Bond Theory, Quantum Transport, Quantum Interference, Kondo Effect, and Electron Pumping. Trap a single organic molecule between two electrodes and apply a bias voltage across this "molecular junction". When electrons pass through the molecule, the different electron paths can...... interfere destructively or constructively. Destructive interference effects in electron transport could potentially improve thermo-electrics, organic logic circuits and energy harvesting. We have investigated destructive interference in off-resonant transport through organic molecules, and have found a set...

  5. Single Molecule Nano-Metronome

    OpenAIRE

    Buranachai, Chittanon; McKinney, Sean A.; Ha, Taekjip

    2006-01-01

    We constructed a DNA-based nano-mechanical device called the nano-metronome. Our device is made by introducing complementary single stranded overhangs at the two arms of the DNA four-way junction. The ticking rates of this stochastic metronome depend on ion concentrations and can be changed by a set of DNA-based switches to deactivate/reactivate the sticky end. Since the device displays clearly distinguishable responses even with a single basepair difference, it may lead to a single molecule ...

  6. Investigation on Single-Molecule Junctions Based on Current–Voltage Characteristics

    Directory of Open Access Journals (Sweden)

    Yuji Isshiki

    2018-02-01

    Full Text Available The relationship between the current through an electronic device and the voltage across its terminals is a current–voltage characteristic (I–V that determine basic device performance. Currently, I–V measurement on a single-molecule scale can be performed using break junction technique, where a single molecule junction can be prepared by trapping a single molecule into a nanogap between metal electrodes. The single-molecule I–Vs provide not only the device performance, but also reflect information on energy dispersion of the electronic state and the electron-molecular vibration coupling in the junction. This mini review focuses on recent representative studies on I–Vs of the single molecule junctions that cover investigation on the single-molecule diode property, the molecular vibration, and the electronic structure as a form of transmission probability, and electronic density of states, including the spin state of the single-molecule junctions. In addition, thermoelectronic measurements based on I–Vs and identification of the charged carriers (i.e., electrons or holes are presented. The analysis in the single-molecule I–Vs provides fundamental and essential information for a better understanding of the single-molecule science, and puts the single molecule junction to more practical use in molecular devices.

  7. Novel approaches for single molecule activation and detection

    CERN Document Server

    Benfenati, Fabio; Torre, Vincent

    2014-01-01

    How can we obtain tools able to process and exchange information at the molecular scale In order to do this, it is necessary to activate and detect single molecules under controlled conditions. This book focuses on the generation of biologically-inspired molecular devices. These devices are based on the developments of new photonic tools able to activate and stimulate single molecule machines. Additionally, new light sensitive molecules can be selectively activated by photonic tools. These technological innovations will provide a way to control activation of single light-sensitive molecules, a

  8. A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing.

    Science.gov (United States)

    Chen, Shi-Yi; Deng, Feilong; Jia, Xianbo; Li, Cao; Lai, Song-Jia

    2017-08-09

    It is widely acknowledged that transcriptional diversity largely contributes to biological regulation in eukaryotes. Since the advent of second-generation sequencing technologies, a large number of RNA sequencing studies have considerably improved our understanding of transcriptome complexity. However, it still remains a huge challenge for obtaining full-length transcripts because of difficulties in the short read-based assembly. In the present study we employ PacBio single-molecule long-read sequencing technology for whole-transcriptome profiling in rabbit (Oryctolagus cuniculus). We totally obtain 36,186 high-confidence transcripts from 14,474 genic loci, among which more than 23% of genic loci and 66% of isoforms have not been annotated yet within the current reference genome. Furthermore, about 17% of transcripts are computationally revealed to be non-coding RNAs. Up to 24,797 alternative splicing (AS) and 11,184 alternative polyadenylation (APA) events are detected within this de novo constructed transcriptome, respectively. The results provide a comprehensive set of reference transcripts and hence contribute to the improved annotation of rabbit genome.

  9. Single-Molecule Imaging with X-Ray Free-Electron Lasers: Dream or Reality?

    KAUST Repository

    Fratalocchi, Andrea

    2011-03-09

    X-ray free-electron lasers (XFEL) are revolutionary photon sources, whose ultrashort, brilliant pulses are expected to allow single-molecule diffraction experiments providing structural information on the atomic length scale of nonperiodic objects. This ultimate goal, however, is currently hampered by several challenging questions basically concerning sample damage, Coulomb explosion, and the role of nonlinearity. By employing an original ab initio approach, we address these issues showing that XFEL-based single-molecule imaging will be only possible with a few-hundred long attosecond pulses, due to significant radiation damage and the formation of preferred multisoliton clusters which reshape the overall electronic density of the molecular system at the femtosecond scale.

  10. Single-Molecule Imaging with X-Ray Free-Electron Lasers: Dream or Reality?

    KAUST Repository

    Fratalocchi, Andrea; Ruocco, G.

    2011-01-01

    X-ray free-electron lasers (XFEL) are revolutionary photon sources, whose ultrashort, brilliant pulses are expected to allow single-molecule diffraction experiments providing structural information on the atomic length scale of nonperiodic objects. This ultimate goal, however, is currently hampered by several challenging questions basically concerning sample damage, Coulomb explosion, and the role of nonlinearity. By employing an original ab initio approach, we address these issues showing that XFEL-based single-molecule imaging will be only possible with a few-hundred long attosecond pulses, due to significant radiation damage and the formation of preferred multisoliton clusters which reshape the overall electronic density of the molecular system at the femtosecond scale.

  11. Long-wavelength Radar Studies of the Lunar Maria

    Science.gov (United States)

    Campbell, Bruce A.; Hawke, B. Ray; Thompson, Thomas W.

    1995-01-01

    Radar measurements at 70 cm and 7.5 m wavelengths provide insight into the structure and chemical properties of the upper 5-100 m of the lunar regolith and crust. Past work has identified a number of anomalous regions and changes in echo strength, some attributed to differences in titanium content. There has been little opportunity, however, to compare calibrated long-wavelength backscatter among different units or to theoretical model results. We combine recent high-resolution (3-5 km) 70-cm radar data for the nearside with earlier calibrated full-disk observations to provide a reasonable estimate of the true lunar backscatter coefficient. These data are tested against models for quasi-specular scattering from the surface, echoes from a buried substrate, and Mie scattering from surface and buried rocks. We find that 70 cm echoes likely arise from Mie scattering by distributed rocks within the soil, consistent with earlier hypotheses. Returns from a buried substrate would provide a plausible fit to the observations only if the regolith depth were 3 m or less and varied little across the maria. Depolarized echoes are due to some combination of single and multiple scattering events, but it appears that single scattering alone could account for the observed echo power, based on comparisons with terrestrial rocky surfaces. Backscatter strength from the regolith is most strongly affected by the loss tangent, whose variation with mineral content is still poorly defined. We compared the backscatter values for the mare deposits to the oxide contents inferred from spectral ratio methods, and found that in general the unit boundaries evident in radar images closely follow those seen in color difference images. The 70-cm data are not well correlated with TiO2 values found using the Charette relationship nor with Fe abundances derived from Clementine observations. The lack of a relationship between radar echo and Fe content is reasonable given the distribution of iron among

  12. A high-yield, one-step synthesis of surfactant-free gold nanostars and numerical study for single-molecule SERS application

    Energy Technology Data Exchange (ETDEWEB)

    Chatterjee, S.; Ringane, A. B.; Arya, A.; Das, G. M.; Dantham, V. R., E-mail: dantham@iitp.ac.in; Laha, R. [Indian Institute of Technology Patna, Department of Physics (India); Hussian, S. [Indian Institute of Technology Patna, Department of Chemistry (India)

    2016-08-15

    We report a high-yield synthesis of star-shaped gold nanostructures in one step, using a new surfactant-free wet chemistry method. Compared to the existing reports, these nanostars were found to have longer and sharper spikes anchored uniformly on the surface of the spherical core, allowing at least a few hot spots irrespective of the incident light polarization. The average experimental values of core radius and spike length were found to be 88.5 and 72 nm, respectively. Using these values in numerical simulations, the local electric field enhancement (η) and localized surface plasmon resonance (LSPR) spectrum were obtained. Moreover, the single-molecule surface-enhanced Raman scattering (SERS) enhancement factor was found to vary from 10{sup 10} to 10{sup 13} depending on the excitation wavelengths. Our theoretical calculations suggest that these nanostructures can be used to fabricate efficient SERS-based biosensors for the detection of single molecules in real time and for predicting structural information of single molecules.

  13. Towards the coupling of single photons from dye molecules to a photonic waveguide

    Science.gov (United States)

    Polisseni, Claudio; Kho, Kiang Wei; Major, Kyle; Grandi, Samuele; Boisser, Sebastien; Hwang, Jaesuk; Clark, Alex; Hinds, Edward

    Single photons are very attractive for quantum information processing given their long coherence time and their ability to carry information in many degrees of freedom. A current challenge is the efficient generation of single photons in a photonic chip in order to scale up the complexity of quantum operations. We have proposed that a dibenzoterrylene (DBT) molecule inside an anthracene (AC) crystal could couple lifetime-limited indistinguishable single photons into a photonic waveguide if deposited in its vicinity. In this talk I describe the recent progress towards the realization of this proposal. A new method has been developed for evaporating AC and DBT to produce crystals that are wide and thin. The crystals are typically several microns across and have remarkably uniform thickness, which we control between 20 and 150 nm. The crystal growth is carried out in a glove bag in order to exclude oxygen, which improves the photostability of the DBT molecules by orders of magnitude. We image the fluorescence of single DBT molecules using confocal microscopy and analyse the polarization of this light to determine the alignment of the molecules. I will report on our efforts to control the alignement of the molecules by aligning the host matrix with the substrate.

  14. Lattice diffusion of a single molecule in solution

    Science.gov (United States)

    Ruggeri, Francesca; Krishnan, Madhavi

    2017-12-01

    The ability to trap a single molecule in an electrostatic potential well in solution has opened up new possibilities for the use of molecular electrical charge to study macromolecular conformation and dynamics at the level of the single entity. Here we study the diffusion of a single macromolecule in a two-dimensional lattice of electrostatic traps in solution. We report the ability to measure both the size and effective electrical charge of a macromolecule by observing single-molecule transport trajectories, typically a few seconds in length, using fluorescence microscopy. While, as shown previously, the time spent by the molecule in a trap is a strong function of its effective charge, we demonstrate here that the average travel time between traps in the landscape yields its hydrodynamic radius. Tailoring the pitch of the lattice thus yields two different experimentally measurable time scales that together uniquely determine both the size and charge of the molecule. Since no information is required on the location of the molecule between consecutive departure and arrival events at lattice sites, the technique is ideally suited to measurements on weakly emitting entities such as single molecules.

  15. Getting the best out of long-wavelength X-rays: de novo chlorine/sulfur SAD phasing of a structural protein from ATV

    DEFF Research Database (Denmark)

    Goulet, Adeline; Vestergaard, Gisle Alberg; Felisberto-Rodrigues, Catarina

    2010-01-01

    The structure of a 14 kDa structural protein from Acidianus two-tailed virus (ATV) was solved by single-wavelength anomalous diffraction (SAD) phasing using X-ray data collected at 2.0 A wavelength. Although the anomalous signal from methionine sulfurs was expected to suffice to solve the structu...... on intrinsic protein light atoms along with associated chloride ions from the solvent. In such cases, data collection at long wavelengths may be a time-efficient alternative to selenomethionine substitution and heavy-atom derivatization....

  16. Thermally induced charge current through long molecules

    Science.gov (United States)

    Zimbovskaya, Natalya A.; Nitzan, Abraham

    2018-01-01

    In this work, we theoretically study steady state thermoelectric transport through a single-molecule junction with a long chain-like bridge. Electron transmission through the system is computed using a tight-binding model for the bridge. We analyze dependences of thermocurrent on the bridge length in unbiased and biased systems operating within and beyond the linear response regime. It is shown that the length-dependent thermocurrent is controlled by the lineshape of electron transmission in the interval corresponding to the HOMO/LUMO transport channel. Also, it is demonstrated that electron interactions with molecular vibrations may significantly affect the length-dependent thermocurrent.

  17. Single Molecule Nano-Metronome

    Science.gov (United States)

    Buranachai, Chittanon; McKinney, Sean A.; Ha, Taekjip

    2008-01-01

    We constructed a DNA-based nano-mechanical device called the nano-metronome. Our device is made by introducing complementary single stranded overhangs at the two arms of the DNA four-way junction. The ticking rates of this stochastic metronome depend on ion concentrations and can be changed by a set of DNA-based switches to deactivate/reactivate the sticky end. Since the device displays clearly distinguishable responses even with a single basepair difference, it may lead to a single molecule sensor of minute sequence differences of a target DNA. PMID:16522050

  18. Controlling single-molecule junction conductance by molecular interactions

    Science.gov (United States)

    Kitaguchi, Y.; Habuka, S.; Okuyama, H.; Hatta, S.; Aruga, T.; Frederiksen, T.; Paulsson, M.; Ueba, H.

    2015-01-01

    For the rational design of single-molecular electronic devices, it is essential to understand environmental effects on the electronic properties of a working molecule. Here we investigate the impact of molecular interactions on the single-molecule conductance by accurately positioning individual molecules on the electrode. To achieve reproducible and precise conductivity measurements, we utilize relatively weak π-bonding between a phenoxy molecule and a STM-tip to form and cleave one contact to the molecule. The anchoring to the other electrode is kept stable using a chalcogen atom with strong bonding to a Cu(110) substrate. These non-destructive measurements permit us to investigate the variation in single-molecule conductance under different but controlled environmental conditions. Combined with density functional theory calculations, we clarify the role of the electrostatic field in the environmental effect that influences the molecular level alignment. PMID:26135251

  19. Long wavelength irregularities in the equatorial electrojet

    International Nuclear Information System (INIS)

    Kudeki, E.; Farley, D.T.; Fejer, B.G.

    1982-01-01

    We have used the radar interferometer technique at Jicamarca to study in detail irregularities with wavelengths of a few kilometers generated in the unstable equatorial electrojet plasma during strong type 1 conditions. In-situ rocket observations of the same instability process are discussed in a companion paper. These large scale primary waves travel essentially horizontally and have large amplitudes. The vertical electron drift velocities driven by the horizontal wave electric fields reach or exceed the ion-acoustic velocity even though the horizontal phase velocity of the wave is considerably smaller. A straightforward extension to the long wavelength regime of the usual linear theory of the electrojet instability explains this and several other observed features of these dominant primary waves

  20. Long-range protein electron transfer observed at the single-molecule level: In situ mapping of redox-gated tunneling resonance

    DEFF Research Database (Denmark)

    Chi, Qijin; Farver, O; Ulstrup, Jens

    2005-01-01

    on the redox potential. Maximum resonance appears around the equilibrium redox potential of azurin with an on/off current ratio of approximate to 9. Simulation analyses, based on a two-step interfacial ET model for the scanning tunneling microscopy redox process, were performed and provide quantitative......A biomimetic long-range electron transfer (ET) system consisting of the blue copper protein azurin, a tunneling barrier bridge, and a gold single-crystal electrode was designed on the basis of molecular wiring self-assembly principles. This system is sufficiently stable and sensitive in a quasi...... constants display tunneling features with distance-decay factors of 0.83 and 0.91 angstrom(-1) in H2O and D2O, respectively. Redox-gated tunneling resonance is observed in situ at the single-molecule level by using electrochemical scanning tunneling microscopy, exhibiting an asymmetric dependence...

  1. Azadioxatriangulenium: a long fluorescence lifetime fluorophore for large biomolecule binding assay

    International Nuclear Information System (INIS)

    Sørensen, Thomas Just; Thyrhaug, Erling; Szabelski, Mariusz; Gryczynski, Ignacy; Gryczynski, Zygmunt; Luchowski, Rafal; Laursen, Bo W

    2013-01-01

    Of the many optical bioassays available, sensing by fluorescence anisotropy has great advantages as it provides a sensitive, instrumentally simple, ratiometric method of detection. However, it is hampered by a severe limitation, as the emission lifetime of the label needs to be comparable to the correlation lifetime (tumbling time) of the biomolecule which is labelled. For proteins of moderate size this is on the order of 20–200 ns, which due to practical issues currently limits the choice of labels to the dansyl-type dyes and certain aromatic dyes. These have the significant drawback of UV/blue absorption and emission as well as an often significant solvent sensitivity. Here, we report the synthesis and characterization of a new fluorescent label for high molecular weight biomolecule assay based on the azadioxatriangulenium motif. The NHS ester of the long fluorescence lifetime, red-emitting fluorophore: azadioxatriangulenium (ADOTA-NHS) was conjugated to anti-rabbit Immunoglobulin G (antiIgG). The long fluorescence lifetime was exploited to determine the correlation time of the high molecular weight antibody and its complex with rabbit Immunoglobulin G (IgG) with steady-state fluorescence anisotropy and time-resolved methods: solution phase immuno-assay was performed following either steady-state or time-resolved fluorescence anisotropy. By performing a variable temperature experiment it was determined that the binding of the ligand resulted in an increase in correlation time of more than 75%, and an increase in the steady-state anisotropy of 18%. The results show that the triangulenium class of dyes can be used in anisotropy assay to detect binding events involving biomolecules of far larger size than what is possible with most other red-emitting organic dyes. (paper)

  2. Azadioxatriangulenium: a long fluorescence lifetime fluorophore for large biomolecule binding assay

    Science.gov (United States)

    Just Sørensen, Thomas; Thyrhaug, Erling; Szabelski, Mariusz; Luchowski, Rafal; Gryczynski, Ignacy; Gryczynski, Zygmunt; Laursen, Bo W.

    2013-06-01

    Of the many optical bioassays available, sensing by fluorescence anisotropy has great advantages as it provides a sensitive, instrumentally simple, ratiometric method of detection. However, it is hampered by a severe limitation, as the emission lifetime of the label needs to be comparable to the correlation lifetime (tumbling time) of the biomolecule which is labelled. For proteins of moderate size this is on the order of 20-200 ns, which due to practical issues currently limits the choice of labels to the dansyl-type dyes and certain aromatic dyes. These have the significant drawback of UV/blue absorption and emission as well as an often significant solvent sensitivity. Here, we report the synthesis and characterization of a new fluorescent label for high molecular weight biomolecule assay based on the azadioxatriangulenium motif. The NHS ester of the long fluorescence lifetime, red-emitting fluorophore: azadioxatriangulenium (ADOTA-NHS) was conjugated to anti-rabbit Immunoglobulin G (antiIgG). The long fluorescence lifetime was exploited to determine the correlation time of the high molecular weight antibody and its complex with rabbit Immunoglobulin G (IgG) with steady-state fluorescence anisotropy and time-resolved methods: solution phase immuno-assay was performed following either steady-state or time-resolved fluorescence anisotropy. By performing a variable temperature experiment it was determined that the binding of the ligand resulted in an increase in correlation time of more than 75%, and an increase in the steady-state anisotropy of 18%. The results show that the triangulenium class of dyes can be used in anisotropy assay to detect binding events involving biomolecules of far larger size than what is possible with most other red-emitting organic dyes.

  3. Highly charged cyanine fluorophores for trafficking scaffold degradation

    International Nuclear Information System (INIS)

    Owens, Eric A; Alyabyev, Sergey; Henary, Maged; Hyun, Hoon; Kim, Soon Hee; Lee, Jeong Heon; Park, GwangLi; Ashitate, Yoshitomo; Choi, Jungmun; Hong, Gloria H; Choi, Hak Soo; Lee, Sang Jin; Khang, Gilson

    2013-01-01

    Biodegradable scaffolds have been extensively used in the field of tissue engineering and regenerative medicine. However, noninvasive monitoring of in vivo scaffold degradation is still lacking. In order to develop a real-time trafficking technique, a series of meso-brominated near-infrared (NIR) fluorophores were synthesized and conjugated to biodegradable gelatin scaffolds. Since the pentamethine cyanine core is highly lipophilic, the side chain of each fluorophore was modified with either quaternary ammonium salts or sulfonate groups. The physicochemical properties such as lipophilicity and net charge of fluorophores played a key role in the fate of NIR-conjugated scaffolds in vivo after biodegradation. The positively charged fluorophore-conjugated scaffold fragments were found in salivary glands, lymph nodes, and most of the hepatobiliary excretion route. However, halogenated fluorophores intensively accumulated into lymph nodes and the liver. Interestingly, balanced-charged gelatin scaffolds were degraded into urine in a short period of time. These results demonstrate that the noninvasive optical imaging using NIR fluorophores can be useful for the translation of biodegradable scaffolds into the clinic. (paper)

  4. Linear response to long wavelength fluctuations using curvature simulations

    Energy Technology Data Exchange (ETDEWEB)

    Baldauf, Tobias; Zaldarriaga, Matias [School of Natural Sciences, Institute for Advanced Study, Princeton, NJ (United States); Seljak, Uroš [Physics Department, Astronomy Department and Lawrence Berkeley National Laboratory, University of California, Berkeley, CA (United States); Senatore, Leonardo, E-mail: baldauf@ias.edu, E-mail: useljak@berkeley.edu, E-mail: senatore@stanford.edu, E-mail: matiasz@ias.edu [Stanford Institute for Theoretical Physics, Stanford University, Stanford, CA (United States)

    2016-09-01

    We study the local response to long wavelength fluctuations in cosmological N -body simulations, focusing on the matter and halo power spectra, halo abundance and non-linear transformations of the density field. The long wavelength mode is implemented using an effective curved cosmology and a mapping of time and distances. The method provides an alternative, more direct, way to measure the isotropic halo biases. Limiting ourselves to the linear case, we find generally good agreement between the biases obtained from the curvature method and the traditional power spectrum method at the level of a few percent. We also study the response of halo counts to changes in the variance of the field and find that the slope of the relation between the responses to density and variance differs from the naïve derivation assuming a universal mass function by approximately 8–20%. This has implications for measurements of the amplitude of local non-Gaussianity using scale dependent bias. We also analyze the halo power spectrum and halo-dark matter cross-spectrum response to long wavelength fluctuations and derive second order halo bias from it, as well as the super-sample variance contribution to the galaxy power spectrum covariance matrix.

  5. Handbook of Single-Molecule Biophysics

    CERN Document Server

    Hinterdorfer, Peter

    2009-01-01

    The last decade has seen the development of a number of novel biophysical methods that allow the manipulation and study of individual biomolecules. The ability to monitor biological processes at this fundamental level of sensitivity has given rise to an improved understanding of the underlying molecular mechanisms. Through the removal of ensemble averaging, distributions and fluctuations of molecular properties can be characterized, transient intermediates identified, and catalytic mechanisms elucidated. By applying forces on biomolecules while monitoring their activity, important information can be obtained on how proteins couple function to structure. The Handbook of Single-Molecule Biophysics provides an introduction to these techniques and presents an extensive discussion of the new biological insights obtained from them. Coverage includes: Experimental techniques to monitor and manipulate individual biomolecules The use of single-molecule techniques in super-resolution and functional imaging Single-molec...

  6. Long-wavelength microinstabilities in toroidal plasmas

    International Nuclear Information System (INIS)

    Tang, W.M.; Rewoldt, G.

    1993-01-01

    Realistic kinetic toroidal eigenmode calculations have been carried out to support a proper assessment of the influence of long-wavelength microturbulence on transport in tokamak plasmas. In order to efficiently evaluate large-scale kinetic behavior extending over many rational surfaces, significant improvements have been made to a toroidal finite element code used to analyze the fully two-dimensional (r,θ) mode structures of trapped-ion and toroidal ion temperature gradient (ITG) instabilities. It is found that even at very long wavelengths, these eigenmodes exhibit a strong ballooning character with the associated radial structure relatively insensitive to ion Landau damping at the rational surfaces. In contrast to the long-accepted picture that the radial extent of trapped-ion instabilities is characterized by the ion-gyroradius-scale associated with strong localization between adjacent rational surfaces, present results demonstrate that under realistic conditions, the actual scale is governed by the large-scale variations in the equilibrium gradients. Applications to recent measurements of fluctuation properties in Tokamak Fusion Test Reactor (TFTR) [Plasma Phys. Controlled Nucl. Fusion Res. (International Atomic Energy Agency, Vienna, 1985), Vol. 1, p. 29] L-mode plasmas indicate that the theoretical trends appear consistent with spectral characteristics as well as rough heuristic estimates of the transport level. Benchmarking calculations in support of the development of a three-dimensional toroidal gyrokinetic code indicate reasonable agreement with respect to both the properties of the eigenfunctions and the magnitude of the eigenvalues during the linear phase of the simulations of toroidal ITG instabilities

  7. Zero-mode waveguide nanophotonic structures for single molecule characterization

    Science.gov (United States)

    Crouch, Garrison M.; Han, Donghoon; Bohn, Paul W.

    2018-05-01

    Single-molecule characterization has become a crucial research tool in the chemical and life sciences, but limitations, such as limited concentration range, inability to control molecular distributions in space, and intrinsic phenomena, such as photobleaching, present significant challenges. Recent developments in non-classical optics and nanophotonics offer promising routes to mitigating these restrictions, such that even low affinity (K D ~ mM) biomolecular interactions can be studied. Here we introduce and review specific nanophotonic devices used to support single molecule studies. Optical nanostructures, such as zero-mode waveguides (ZMWs), are usually fabricated in thin gold or aluminum films and serve to confine the observation volume of optical microspectroscopy to attoliter to zeptoliter volumes. These simple nanostructures allow individual molecules to be isolated for optical and electrochemical analysis, even when the molecules of interest are present at high concentration (µM–mM) in bulk solution. Arrays of ZMWs may be combined with optical probes such as single molecule fluorescence, single molecule fluorescence resonance energy transfer, and fluorescence correlation spectroscopy for distributed analysis of large numbers of single-molecule reactions or binding events in parallel. Furthermore, ZMWs may be used as multifunctional devices, for example by combining optical and electrochemical functions in a single discrete architecture to achieve electrochemical ZMWs. In this review, we will describe the optical properties, fabrication, and applications of ZMWs for single-molecule studies, as well as the integration of ZMWs into systems for chemical and biochemical analysis.

  8. Investigation of polyelectrolyte desorption by single molecule force spectroscopy

    International Nuclear Information System (INIS)

    Friedsam, C; Seitz, M; Gaub, H E

    2004-01-01

    Single molecule force spectroscopy has evolved into a powerful method for the investigation of intra- and intermolecular interactions at the level of individual molecules. Many examples, including the investigation of the dynamic properties of complex biological systems as well as the properties of covalent bonds or intermolecular transitions within individual polymers, are reported in the literature. The technique has recently been extended to the systematic investigation of desorption processes of individual polyelectrolyte molecules adsorbed on generic surfaces. The stable covalent attachment of polyelectrolyte molecules to the AFM-tip provides the possibility of performing long-term measurements with the same set of molecules and therefore allows the in situ observation of the impact of environmental changes on the adsorption behaviour of individual molecules. Different types of interactions, e.g. electrostatic or hydrophobic interactions, that determine the adsorption process could be identified and characterized. The experiments provided valuable details that help to understand the nature and the properties of non-covalent interactions, which is helpful with regard to biological systems as well as for technical applications. Apart from this, desorption experiments can be utilized to characterize the properties of surfaces or polymer coatings. Therefore they represent a versatile tool that can be further developed in terms of various aspects

  9. Thousand-fold enhancement of single-molecule fluorescence near a single gold nanorod

    NARCIS (Netherlands)

    Yuan, H.; Khatua, S.; Zijlstra, P.; Yorulmaz, M.; Orrit, M.

    2013-01-01

    Single molecules: Large enhancements of single-molecule fluorescence up to 1100 times by using synthesized gold nanorods are reported (see picture). This high enhancement is achieved by selecting a dye with its adsorption and emission close to the surface plasmon resonance of the gold nanorods

  10. A turn-on near-infrared fluorescent chemosensor for selective detection of lead ions based on a fluorophore-gold nanoparticle assembly.

    Science.gov (United States)

    Wang, Shaozhen; Sun, Junyong; Gao, Feng

    2015-06-21

    A turn-on fluorescent chemosensor of Pb(2+) in the near-infrared (NIR) region, which is based on the Pb(2+)-tuned restored fluorescence of a weakly fluorescent fluorophore-gold nanoparticle (AuNPs) assembly, has been reported. In this fluorophore-AuNP assembly, NIR fluorescent dye brilliant cresyl blue (BCB) molecules act as fluorophores and are used for signal transduction of fluorescence, while AuNPs act as quenchers to quench the nearby fluorescent BCB molecules via electron transfer. In the presence of Pb(2+), fluorescent BCB molecules detached from AuNPs and restored their fluorescence due to the formation of a chelating complex between Pb(2+) and glutathione confined on AuNPs. Under the optimal conditions, the present BCB-AuNP assembly is capable of detecting Pb(2+) with a concentration ranging from 7.5 × 10(-10) to 1 × 10(-8) mol L(-1) (0.16-2.1 ng mL(-1)) and a detection limit of 0.51 nM (0.11 ng mL(-1)). The present BCB-AuNP assembly can be used in aqueous media for the determination of Pb(2+) unlike common organic fluorescent reagents, and also shows advantages of NIR fluorescence spectrophotometry such as less interference, lower detection limit, and higher sensitivity. Moreover, the present method was successfully applied for the detection of Pb(2+) in water samples with satisfactory results.

  11. Hybrid integrated single-wavelength laser with silicon micro-ring reflector

    Science.gov (United States)

    Ren, Min; Pu, Jing; Krishnamurthy, Vivek; Xu, Zhengji; Lee, Chee-Wei; Li, Dongdong; Gonzaga, Leonard; Toh, Yeow T.; Tjiptoharsono, Febi; Wang, Qian

    2018-02-01

    A hybrid integrated single-wavelength laser with silicon micro-ring reflector is demonstrated theoretically and experimentally. It consists of a heterogeneously integrated III-V section for optical gain, an adiabatic taper for light coupling, and a silicon micro-ring reflector for both wavelength selection and light reflection. Heterogeneous integration processes for multiple III-V chips bonded to an 8-inch Si wafer have been developed, which is promising for massive production of hybrid lasers on Si. The III-V layer is introduced on top of a 220-nm thick SOI layer through low-temperature wafer-boning technology. The optical coupling efficiency of >85% between III-V and Si waveguide has been achieved. The silicon micro-ring reflector, as the key element of the hybrid laser, is studied, with its maximized reflectivity of 85.6% demonstrated experimentally. The compact single-wavelength laser enables fully monolithic integration on silicon wafer for optical communication and optical sensing application.

  12. Isolating long-wavelength fluctuation from structural relaxation in two-dimensional glass: cage-relative displacement

    Science.gov (United States)

    Shiba, Hayato; Keim, Peter; Kawasaki, Takeshi

    2018-03-01

    It has recently been revealed that long-wavelength fluctuation exists in two-dimensional (2D) glassy systems, having the same origin as that given by the Mermin-Wagner theorem for 2D crystalline solids. In this paper, we discuss how to characterise quantitatively the long-wavelength fluctuation in a molecular dynamics simulation of a lightly supercooled liquid. We employ the cage-relative mean-square displacement (MSD), defined on relative displacement to its cage, to quantitatively separate the long-wavelength fluctuation from the original MSD. For increasing system size the amplitude of acoustic long wavelength fluctuations not only increases but shifts to later times causing a crossover with structural relaxation of caging particles. We further analyse the dynamic correlation length using the cage-relative quantities. It grows as the structural relaxation becomes slower with decreasing temperature, uncovering an overestimation by the four-point correlation function due to the long-wavelength fluctuation. These findings motivate the usage of cage-relative MSD as a starting point for analysis of 2D glassy dynamics.

  13. Single Molecule Conductance of Oligothiophene Derivatives

    Science.gov (United States)

    Dell, Emma J.

    This thesis studies the electronic properties of small organic molecules based on the thiophene motif. If we are to build next-generation devices, advanced materials must be designed which possess requisite electronic functionality. Molecules present attractive candidates for these ad- vanced materials since nanoscale devices are particularly sought after. However, selecting a molecule that is suited to a certain electronic function remains a challenge, and characterization of electronic behavior is therefore critical. Single molecule conductance measurements are a powerful tool to determine properties on the nanoscale and, as such, can be used to investigate novel building blocks that may fulfill the design requirements of next-generation devices. Combining these conductance results with strategic chemical synthesis allows for the development of new families of molecules that show attractive properties for future electronic devices. Since thiophene rings are the fruitflies of organic semiconductors on the bulk scale, they present an intriguing starting point for building functional materials on the nanoscale, and therefore form the structural basis of all molecules studied herein. First, the single-molecule conductance of a family of bithiophene derivatives was measured. A broad distribution in the single-molecule conductance of bithiophene was found compared with that of a biphenyl. This increased breadth in the conductance distribution was shown to be explained by the difference in 5-fold symmetry of thiophene rings as compared to the 6-fold symmetry of benzene rings. The reduced symmetry of thiophene rings results in a restriction on the torsion angle space available to these molecules when bound between two metal electrodes in a junction, causing each molecular junction to sample a different set of conformers in the conductance measurements. By contrast, the rotations of biphenyl are essentially unimpeded by junction binding, allowing each molecular junction

  14. Single-strand DNA molecule translocation through nanoelectrode gaps

    International Nuclear Information System (INIS)

    Zhao Xiongce; Payne, Christina M; Cummings, Peter T; Lee, James W

    2007-01-01

    Molecular dynamics simulations were performed to investigate the translocation of single-strand DNA through nanoscale electrode gaps under the action of a constant driving force. The application behind this theoretical study is a proposal to use nanoelectrodes as a screening gap as part of a rapid genomic sequencing device. Preliminary results from a series of simulations using various gap widths and driving forces suggest that the narrowest electrode gap that a single-strand DNA can pass is ∼1.5 nm. The minimum force required to initiate the translocation within nanoseconds is ∼0.3 nN. Simulations using DNA segments of various lengths indicate that the minimum initiation force is insensitive to the length of DNA. However, the average threading velocity of DNA varies appreciably from short to long DNA segments. We attribute such variation to the different nature of drag force experienced by the short and long DNA segments in the environment. It is found that DNA molecules deform significantly to fit in the shape of the nanogap during the translocation

  15. Long wavelength limit of evolution of nonlinear cosmological perturbations

    International Nuclear Information System (INIS)

    Hamazaki, Takashi

    2008-01-01

    In the general matter composition where the multiple scalar fields and the multiple perfect fluids coexist, in the leading order of the gradient expansion, we construct all of the solutions of the nonlinear evolutions of the locally homogeneous universe. From the momentum constraint, we derive the constraints which the solution constants of the locally homogeneous universe must satisfy. We construct the gauge invariant perturbation variables in the arbitrarily higher order nonlinear cosmological perturbation theory around the spatially flat Friedmann-Robertson-Walker universe. We construct the nonlinear long wavelength limit formula representing the long wavelength limit of the evolution of the nonlinear gauge invariant perturbation variables in terms of perturbations of the evolutions of the locally homogeneous universe. By using the long wavelength limit formula, we investigate the evolution of nonlinear cosmological perturbations in the universe dominated by the multiple slow rolling scalar fields with an arbitrary potential. The τ function and the N potential introduced in this paper make it possible to write the evolution of the multiple slow rolling scalar fields with an arbitrary interaction potential and the arbitrarily higher order nonlinear Bardeen parameter at the end of the slow rolling phase analytically. It is shown that the nonlinear parameters such as f NL and g NL are suppressed by the slow rolling expansion parameters.

  16. Probing Intranuclear Environments at the Single-Molecule Level

    Science.gov (United States)

    Grünwald, David; Martin, Robert M.; Buschmann, Volker; Bazett-Jones, David P.; Leonhardt, Heinrich; Kubitscheck, Ulrich; Cardoso, M. Cristina

    2008-01-01

    Genome activity and nuclear metabolism clearly depend on accessibility, but it is not known whether and to what extent nuclear structures limit the mobility and access of individual molecules. We used fluorescently labeled streptavidin with a nuclear localization signal as an average-sized, inert protein to probe the nuclear environment. The protein was injected into the cytoplasm of mouse cells, and single molecules were tracked in the nucleus with high-speed fluorescence microscopy. We analyzed and compared the mobility of single streptavidin molecules in structurally and functionally distinct nuclear compartments of living cells. Our results indicated that all nuclear subcompartments were easily and similarly accessible for such an average-sized protein, and even condensed heterochromatin neither excluded single molecules nor impeded their passage. The only significant difference was a higher frequency of transient trappings in heterochromatin, which lasted only tens of milliseconds. The streptavidin molecules, however, did not accumulate in heterochromatin, suggesting comparatively less free volume. Interestingly, the nucleolus seemed to exclude streptavidin, as it did many other nuclear proteins, when visualized by conventional fluorescence microscopy. The tracking of single molecules, nonetheless, showed no evidence for repulsion at the border but relatively unimpeded passage through the nucleolus. These results clearly show that single-molecule tracking can provide novel insights into mobility of proteins in the nucleus that cannot be obtained by conventional fluorescence microscopy. Our results suggest that nuclear processes may not be regulated at the level of physical accessibility but rather by local concentration of reactants and availability of binding sites. PMID:18065482

  17. Vesicle Encapsulation Studies Reveal that Single Molecule Ribozyme Heterogeneities Are Intrinsic

    Science.gov (United States)

    Okumus, Burak; Wilson, Timothy J.; Lilley, David M. J.; Ha, Taekjip

    2004-01-01

    Single-molecule measurements have revealed that what were assumed to be identical molecules can differ significantly in their static and dynamic properties. One of the most striking examples is the hairpin ribozyme, which was shown to exhibit two to three orders of magnitude variation in folding kinetics between molecules. Although averaged behavior of single molecules matched the bulk solution data, it was not possible to exclude rigorously the possibility that the variations around the mean values arose from different ways of interacting with the surface environment. To test this, we minimized the molecules' interaction with the surface by encapsulating DNA or RNA molecules inside 100- to 200-nm diameter unilamellar vesicles, following the procedures described by Haran and coworkers. Vesicles were immobilized on a supported lipid bilayer via biotin-streptavidin linkages. We observed no direct binding of DNA or RNA on the supported bilayer even at concentrations exceeding 100 nM, indicating that these molecules do not bind stably on the membrane. Since the vesicle diameter is smaller than the resolution of optical microscopy, the lateral mobility of the molecules is severely constrained, allowing long observation periods. We used fluorescence correlation spectroscopy, nuclease digestion, and external buffer exchange to show that the molecules were indeed encapsulated within the vesicles. When contained within vesicles, the natural form of the hairpin ribozyme exhibited 50-fold variation in both folding and unfolding rates in 0.5 mM Mg2+, which is identical to what was observed from the molecules tethered directly on the surface. This strongly indicates that the observed heterogeneity in dynamic properties does not arise as an artifact of surface attachment, but is intrinsic to the nature of the molecules. PMID:15454471

  18. Single molecule image formation, reconstruction and processing: introduction.

    Science.gov (United States)

    Ashok, Amit; Piestun, Rafael; Stallinga, Sjoerd

    2016-07-01

    The ability to image at the single molecule scale has revolutionized research in molecular biology. This feature issue presents a collection of articles that provides new insights into the fundamental limits of single molecule imaging and reports novel techniques for image formation and analysis.

  19. Single-Molecule Photocurrent at a Metal-Molecule-Semiconductor Junction.

    Science.gov (United States)

    Vezzoli, Andrea; Brooke, Richard J; Higgins, Simon J; Schwarzacher, Walther; Nichols, Richard J

    2017-11-08

    We demonstrate here a new concept for a metal-molecule-semiconductor nanodevice employing Au and GaAs contacts that acts as a photodiode. Current-voltage traces for such junctions are recorded using a STM, and the "blinking" or "I(t)" method is used to record electrical behavior at the single-molecule level in the dark and under illumination, with both low and highly doped GaAs samples and with two different types of molecular bridge: nonconjugated pentanedithiol and the more conjugated 1,4-phenylene(dimethanethiol). Junctions with highly doped GaAs show poor rectification in the dark and a low photocurrent, while junctions with low doped GaAs show particularly high rectification ratios in the dark (>10 3 for a 1.5 V bias potential) and a high photocurrent in reverse bias. In low doped GaAs, the greater thickness of the depletion layer not only reduces the reverse bias leakage current, but also increases the volume that contributes to the photocurrent, an effect amplified by the point contact geometry of the junction. Furthermore, since photogenerated holes tunnel to the metal electrode assisted by the HOMO of the molecular bridge, the choice of the latter has a strong influence on both the steady state and transient metal-molecule-semiconductor photodiode response. The control of junction current via photogenerated charge carriers adds new functionality to single-molecule nanodevices.

  20. A new microcavity design for single molecule detection

    International Nuclear Information System (INIS)

    Steiner, M.; Schleifenbaum, F.; Stupperich, C.; Failla, A.V.; Hartschuh, A.; Meixner, A.J.

    2006-01-01

    We present a new microcavity design which allows for efficient detection of single molecules by measuring the molecular fluorescence emission coupled into a resonant cavity mode. The Fabry-Perot-type microresonator consists of two silver mirrors separated by a thin polymer film doped with dye molecules in ultralow concenctration. By slightly tilting one of the mirrors different cavity lengths can be selected within the same sample. Locally, on a μm scale, the microcavity still acts as a planar Fabry-Perot resonator. Using scanning confocal fluorescence microscopy, single emitters on resonance with a single mode of the microresonator can be spatially addressed. Our microcavity is demonstrated to be well-suited for investigating the coupling mechanism between single quantum emitters and single modes of the electromagnetic field. The microcavity layout could be integrated in a lab-on-a-microchip design for ultrasensitive microfluidic analytics and can be considered as an important improvement for single photon sources based on single molecules operating at room temperature

  1. Sensing single electrons with single molecules

    International Nuclear Information System (INIS)

    Plakhotnik, Taras

    2007-01-01

    We propose a new methodology for probing transport of just one electron, a process of great importance both in nature and in artificial devices. Our idea for locating a single electron is analogues to the conventional GPS where signals from several satellites are used to locate a macro object. Using fluorescent molecules as tiny sensors, it is possible to determine 3D displacement vector of an electron

  2. Molecular electronics with single molecules in solid-state devices

    DEFF Research Database (Denmark)

    Moth-Poulsen, Kasper; Bjørnholm, Thomas

    2009-01-01

    The ultimate aim of molecular electronics is to understand and master single-molecule devices. Based on the latest results on electron transport in single molecules in solid-state devices, we focus here on new insights into the influence of metal electrodes on the energy spectrum of the molecule...

  3. Single Molecule Detection in Living Biological Cells using Carbon Nanotube Optical Probes

    Science.gov (United States)

    Strano, Michael

    2009-03-01

    Nanoscale sensing elements offer promise for single molecule analyte detection in physically or biologically constrained environments. Molecular adsorption can be amplified via modulation of sharp singularities in the electronic density of states that arise from 1D quantum confinement [1]. Single-walled carbon nanotubes (SWNT), as single molecule optical sensors [2-3], offer unique advantages such as photostable near-infrared (n-IR) emission for prolonged detection through biological media, single-molecule sensitivity and, nearly orthogonal optical modes for signal transduction that can be used to identify distinct classes of analytes. Selective binding to the SWNT surface is difficult to engineer [4]. In this lecture, we will briefly review the immerging field of fluorescent diagnostics using band gap emission from SWNT. In recent work, we demonstrate that even a single pair of SWNT provides at least four optical modes that can be modulated to uniquely fingerprint chemical agents by the degree to which they alter either the emission band intensity or wavelength. We validate this identification method in vitro by demonstrating detection and identification of six genotoxic analytes, including chemotherapeutic drugs and reactive oxygen species (ROS), which are spectroscopically differentiated into four distinct classes. We also demonstrate single-molecule sensitivity in detecting hydrogen peroxide, one of the most common genotoxins and an important cellular signal. Finally, we employ our sensing and fingerprinting method of these analytes in real time within live 3T3 cells, demonstrating the first multiplexed optical detection from a nanoscale biosensor and the first label-free tool to optically discriminate between genotoxins. We will also discuss our recent efforts to fabricate biomedical sensors for real time detection of glucose and other important physiologically relevant analytes in-vivo. The response of embedded SWNT in a swellable hydrogel construct to

  4. Research Update: Molecular electronics: The single-molecule switch and transistor

    Directory of Open Access Journals (Sweden)

    Kai Sotthewes

    2014-01-01

    Full Text Available In order to design and realize single-molecule devices it is essential to have a good understanding of the properties of an individual molecule. For electronic applications, the most important property of a molecule is its conductance. Here we show how a single octanethiol molecule can be connected to macroscopic leads and how the transport properties of the molecule can be measured. Based on this knowledge we have realized two single-molecule devices: a molecular switch and a molecular transistor. The switch can be opened and closed at will by carefully adjusting the separation between the electrical contacts and the voltage drop across the contacts. This single-molecular switch operates in a broad temperature range from cryogenic temperatures all the way up to room temperature. Via mechanical gating, i.e., compressing or stretching of the octanethiol molecule, by varying the contact's interspace, we are able to systematically adjust the conductance of the electrode-octanethiol-electrode junction. This two-terminal single-molecule transistor is very robust, but the amplification factor is rather limited.

  5. Single molecule microscopy and spectroscopy: concluding remarks.

    Science.gov (United States)

    van Hulst, Niek F

    2015-01-01

    Chemistry is all about molecules: control, synthesis, interaction and reaction of molecules. All too easily on a blackboard, one draws molecules, their structures and dynamics, to create an insightful picture. The dream is to see these molecules in reality. This is exactly what "Single Molecule Detection" provides: a look at molecules in action at ambient conditions; a breakthrough technology in chemistry, physics and biology. Within the realms of the Royal Society of Chemistry, the Faraday Discussion on "Single Molecule Microscopy and Spectroscopy" was a very appropriate topic for presentation, deliberation and debate. Undoubtedly, the Faraday Discussions have a splendid reputation in stimulating scientific debates along the traditions set by Michael Faraday. Interestingly, back in the 1830's, Faraday himself pursued an experiment that led to the idea that atoms in a compound were joined by an electrical component. He placed two opposite electrodes in a solution of water containing a dissolved compound, and observed that one of the elements of the compound accumulated on one electrode, while the other was deposited on the opposite electrode. Although Faraday was deeply opposed to atomism, he had to recognize that electrical forces were responsible for the joining of atoms. Probably a direct view on the atoms or molecules in his experiment would have convinced him. As such, Michael Faraday might have liked the gathering at Burlington House in September 2015 (). Surely, with the questioning eyes of his bust on the 1st floor corridor, the non-believer Michael Faraday has incited each passer-by to enter into discussion and search for deeper answers at the level of single molecules. In these concluding remarks, highlights of the presented papers and discussions are summarized, complemented by a conclusion on future perspectives.

  6. Single-molecule force-conductance spectroscopy of hydrogen-bonded complexes

    Science.gov (United States)

    Pirrotta, Alessandro; De Vico, Luca; Solomon, Gemma C.; Franco, Ignacio

    2017-03-01

    The emerging ability to study physical properties at the single-molecule limit highlights the disparity between what is observable in an ensemble of molecules and the heterogeneous contributions of its constituent parts. A particularly convenient platform for single-molecule studies are molecular junctions where forces and voltages can be applied to individual molecules, giving access to a series of electromechanical observables that can form the basis of highly discriminating multidimensional single-molecule spectroscopies. Here, we computationally examine the ability of force and conductance to inform about molecular recognition events at the single-molecule limit. For this, we consider the force-conductance characteristics of a prototypical class of hydrogen bonded bimolecular complexes sandwiched between gold electrodes. The complexes consist of derivatives of a barbituric acid and a Hamilton receptor that can form up to six simultaneous hydrogen bonds. The simulations combine classical molecular dynamics of the mechanical deformation of the junction with non-equilibrium Green's function computations of the electronic transport. As shown, in these complexes hydrogen bonds mediate transport either by directly participating as a possible transport pathway or by stabilizing molecular conformations with enhanced conductance properties. Further, we observe that force-conductance correlations can be very sensitive to small changes in the chemical structure of the complexes and provide detailed information about the behavior of single molecules that cannot be gleaned from either measurement alone. In fact, there are regions during the elongation that are only mechanically active, others that are only conductance active, and regions where both force and conductance changes as the complex is mechanically manipulated. The implication is that force and conductance provide complementary information about the evolution of molecules in junctions that can be used to

  7. Semisynthetic protein nanoreactor for single-molecule chemistry

    OpenAIRE

    Lee, Joongoo; Bayley, Hagan

    2015-01-01

    The modulation of ionic current flowing through an individual protein pore provides information at the single-molecule level about chemical reactions occurring within the pore. However, chemistry investigated in this way has been largely confined to the reactions of thiolates, presented by the side chains of cysteine residues. The introduction of unnatural amino acids would provide a large variety of reactive side chains with which additional single-molecule chemistry could be investigated. H...

  8. Modulation and Control of Charge Transport Through Single-Molecule Junctions.

    Science.gov (United States)

    Wang, Kun; Xu, Bingqian

    2017-02-01

    The ability to modulate and control charge transport though single-molecule junction devices is crucial to achieving the ultimate goal of molecular electronics: constructing real-world-applicable electronic components from single molecules. This review aims to highlight the progress made in single-molecule electronics, emphasizing the development of molecular junction electronics in recent years. Among many techniques that attempt to wire a molecule to metallic electrodes, the single-molecule break junction (SMBJ) technique is one of the most reliable and tunable experimental platforms for achieving metal-molecule-metal configurations. It also provides great freedom to tune charge transport through the junction. Soon after the SMBJ technique was introduced, it was extensively used to measure the conductances of individual molecules; however, different conductances were obtained for the same molecule, and it proved difficult to interpret this wide distribution of experimental data. This phenomenon was later found to be mainly due to a lack of precise experimental control and advanced data analysis methods. In recent years, researchers have directed considerable effort into advancing the SMBJ technique by gaining a deeper physical understanding of charge transport through single molecules and thus enhancing its potential applicability in functional molecular-scale electronic devices, such as molecular diodes and molecular transistors. In parallel with that research, novel data analysis methods and approaches that enable the discovery of hidden yet important features in the data are being developed. This review discusses various aspects of molecular junction electronics, from the initial goal of molecular electronics, the development of experimental techniques for creating single-molecule junctions and determining single-molecule conductance, to the characterization of functional current-voltage features and the investigation of physical properties other than charge

  9. Single Molecules as Optical Probes for Structure and Dynamics

    Science.gov (United States)

    Orrit, Michel

    Single molecules and single nanoparticles are convenient links between the nanoscale world and the laboratory. We discuss the limits for their optical detection by three different methods: fluorescence, direct absorption, and photothermal detection. We briefly review some recent illustrations of qualitatively new information gathered from single-molecule signals: intermittency of the fluorescence intensity, acoustic vibrations of nanoparticles (1-100 GHz) or of extended defects in molecular crystals (0.1-1 MHz), and dynamical heterogeneity in glass-forming molecular liquids. We conclude with an outlook of future uses of single-molecule methods in physical chemistry, soft matter, and material science.

  10. Localization microscopy of DNA in situ using Vybrant{sup ®} DyeCycle™ Violet fluorescent probe: A new approach to study nuclear nanostructure at single molecule resolution

    Energy Technology Data Exchange (ETDEWEB)

    Żurek-Biesiada, Dominika [Laboratory of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków (Poland); Szczurek, Aleksander T. [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Prakash, Kirti [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Institute for Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg (Germany); Mohana, Giriram K. [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Lee, Hyun-Keun [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz (Germany); Roignant, Jean-Yves [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Birk, Udo J. [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz (Germany); Dobrucki, Jurek W., E-mail: jerzy.dobrucki@uj.edu.pl [Laboratory of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków (Poland); Cremer, Christoph, E-mail: c.cremer@imb-mainz.de [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Institute for Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg (Germany); Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz (Germany)

    2016-05-01

    Higher order chromatin structure is not only required to compact and spatially arrange long chromatids within a nucleus, but have also important functional roles, including control of gene expression and DNA processing. However, studies of chromatin nanostructures cannot be performed using conventional widefield and confocal microscopy because of the limited optical resolution. Various methods of superresolution microscopy have been described to overcome this difficulty, like structured illumination and single molecule localization microscopy. We report here that the standard DNA dye Vybrant{sup ®} DyeCycle™ Violet can be used to provide single molecule localization microscopy (SMLM) images of DNA in nuclei of fixed mammalian cells. This SMLM method enabled optical isolation and localization of large numbers of DNA-bound molecules, usually in excess of 10{sup 6} signals in one cell nucleus. The technique yielded high-quality images of nuclear DNA density, revealing subdiffraction chromatin structures of the size in the order of 100 nm; the interchromatin compartment was visualized at unprecedented optical resolution. The approach offers several advantages over previously described high resolution DNA imaging methods, including high specificity, an ability to record images using a single wavelength excitation, and a higher density of single molecule signals than reported in previous SMLM studies. The method is compatible with DNA/multicolor SMLM imaging which employs simple staining methods suited also for conventional optical microscopy. - Highlights: • Super-resolution imaging of nuclear DNA with Vybrant Violet and blue excitation. • 90nm resolution images of DNA structures in optically thick eukaryotic nuclei. • Enhanced resolution confirms the existence of DNA-free regions inside the nucleus. • Optimized imaging conditions enable multicolor super-resolution imaging.

  11. Single-Molecule Nanomagnets

    Science.gov (United States)

    Friedman, Jonathan R.; Sarachik, Myriam P.

    2010-04-01

    Single-molecule magnets straddle the classical and quantum mechanical worlds, displaying many fascinating phenomena. They may have important technological applications in information storage and quantum computation. We review the physical properties of two prototypical molecular nanomagnets, Mn12-acetate and Fe8: Each behaves as a rigid, spin-10 object and exhibits tunneling between up and down directions. As temperature is lowered, the spin-reversal process evolves from thermal activation to pure quantum tunneling. At low temperatures, magnetic avalanches occur in which the magnetization of an entire sample rapidly reverses. We discuss the important role that symmetry-breaking fields play in driving tunneling and in producing Berry-phase interference. Recent experimental advances indicate that quantum coherence can be maintained on timescales sufficient to allow a meaningful number of quantum computing operations to be performed. Efforts are under way to create monolayers and to address and manipulate individual molecules.

  12. Propagation of nonlinear ion acoustic wave with generation of long-wavelength waves

    International Nuclear Information System (INIS)

    Ohsawa, Yukiharu; Kamimura, Tetsuo

    1978-01-01

    The nonlinear propagation of the wave packet of an ion acoustic wave with wavenumber k 0 asymptotically equals k sub(De) (the electron Debye wavenumber) is investigated by computer simulations. From the wave packet of the ion acoustic wave, waves with long wavelengths are observed to be produced within a few periods for the amplitude oscillation of the original wave packet. These waves are generated in the region where the original wave packet exists. Their characteristic wavelength is of the order of the length of the wave packet, and their propagation velocity is almost equal to the ion acoustic speed. The long-wavelength waves thus produced strongly affect the nonlinear evolution of the original wave packet. (auth.)

  13. Quantum design rules for single molecule logic gates.

    Science.gov (United States)

    Renaud, N; Hliwa, M; Joachim, C

    2011-08-28

    Recent publications have demonstrated how to implement a NOR logic gate with a single molecule using its interaction with two surface atoms as logical inputs [W. Soe et al., ACS Nano, 2011, 5, 1436]. We demonstrate here how this NOR logic gate belongs to the general family of quantum logic gates where the Boolean truth table results from a full control of the quantum trajectory of the electron transfer process through the molecule by very local and classical inputs practiced on the molecule. A new molecule OR gate is proposed for the logical inputs to be also single metal atoms, one per logical input.

  14. Ordered array of CoPc-vacancies filled with single-molecule rotors

    Science.gov (United States)

    Xie, Zheng-Bo; Wang, Ya-Li; Tao, Min-Long; Sun, Kai; Tu, Yu-Bing; Yuan, Hong-Kuan; Wang, Jun-Zhong

    2018-05-01

    We report the highly ordered array of CoPc-vacancies and the single-molecule rotors inside the vacancies. When CoPc molecules are deposited on Cd(0001) at low-temperature, three types of molecular vacancies appeared randomly in the CoPc monolayer. Annealing the sample to higher temperature leads to the spontaneous phase separation and self-organized arrangement of the vacancies. Highly ordered arrays of two-molecule vacancies and single-molecule vacancies have been obtained. In particular, there is a rotating CoPc molecule inside each single-molecule vacancy, which constitutes the array of single-molecule rotors. These results provide a new routine to fabricate the nano-machines on a large scale.

  15. Single molecule transcription factor dynamics in the syncytial Drosophila embryo

    Science.gov (United States)

    Darzacq, Xavier

    During early development in the Drosophila embryo, cell fates are determined over the course of just 2 hours with exquisite spatio-temoral precision. One of the key regulators of this process is the transcription factor Bicoid which forms a concentration gradient across the long axis of the embryo. Although Bicoids' primary role is activation at the anterior, where concentrations are highest, it is also known to play a role in the posterior where there are only 100s of molecules per nucleus. Understanding how Bicoid can find its target at such low concentrations has remained intractable, largely due to the inability to perform single molecule imaging in the context of the developing embryo. Here we use lattice light sheet microscopy to overcome the technical barriers of sample thickness and auto-fluorescence to characterize the single molecule dynamics of Bicoid. We find that off-rates do not vary across the embryo and that instead the on-rates are modulated through the formation of clusters that enrich local concentration. This data is contrary to the current concentration dependent model of Bicoid function since local concentration within the nucleus is now a regulated parameter and suggests a previously unknown mechanism for regulation at extremely low concentrations.

  16. Supramolecular Systems and Chemical Reactions in Single-Molecule Break Junctions.

    Science.gov (United States)

    Li, Xiaohui; Hu, Duan; Tan, Zhibing; Bai, Jie; Xiao, Zongyuan; Yang, Yang; Shi, Jia; Hong, Wenjing

    2017-04-01

    The major challenges of molecular electronics are the understanding and manipulation of the electron transport through the single-molecule junction. With the single-molecule break junction techniques, including scanning tunneling microscope break junction technique and mechanically controllable break junction technique, the charge transport through various single-molecule and supramolecular junctions has been studied during the dynamic fabrication and continuous characterization of molecular junctions. This review starts from the charge transport characterization of supramolecular junctions through a variety of noncovalent interactions, such as hydrogen bond, π-π interaction, and electrostatic force. We further review the recent progress in constructing highly conductive molecular junctions via chemical reactions, the response of molecular junctions to external stimuli, as well as the application of break junction techniques in controlling and monitoring chemical reactions in situ. We suggest that beyond the measurement of single molecular conductance, the single-molecule break junction techniques provide a promising access to study molecular assembly and chemical reactions at the single-molecule scale.

  17. Electrochemical proton relay at the single-molecule level

    DEFF Research Database (Denmark)

    Kuznetsov, A. M.; Medvedev, I. G.; Ulstrup, Jens

    2009-01-01

    A scheme for the experimental study of single-proton transfer events, based on proton-coupled two-electron transfer between a proton donor and a proton acceptor molecule confined in the tunneling gap between two metal leads in electrolyte solution is suggested. Expressions for the electric current...... are derived and compared with formalism for electron tunneling through redox molecules. The scheme allows studying the kinetics of proton and hydrogen atom transfer as well as kinetic isotope effects at the single-molecule level under electrochemical potential control....

  18. Efficient production of long-lived ultracold Sr2 molecules

    Science.gov (United States)

    Ciamei, Alessio; Bayerle, Alex; Chen, Chun-Chia; Pasquiou, Benjamin; Schreck, Florian

    2017-07-01

    We associate Sr atom pairs on sites of a Mott insulator optically and coherently into weakly bound ground-state molecules, achieving an efficiency above 80%. This efficiency is 2.5 times higher than in our previous work [S. Stellmer, B. Pasquiou, R. Grimm, and F. Schreck, Phys. Rev. Lett. 109, 115302 (2012), 10.1103/PhysRevLett.109.115302] and obtained through two improvements. First, the lifetime of the molecules is increased beyond one minute by using an optical lattice wavelength that is further detuned from molecular transitions. Second, we compensate undesired dynamic light shifts that occur during the stimulated Raman adiabatic passage (STIRAP) used for molecule association. We also characterize and model STIRAP, providing insights into its limitations. Our work shows that significant molecule association efficiencies can be achieved even for atomic species or mixtures that lack Feshbach resonances suitable for magnetoassociation.

  19. The spontaneous formation of single-molecule junctions via terminal alkynes

    International Nuclear Information System (INIS)

    Pla-Vilanova, Pepita; Aragonès, Albert C; Sanz, Fausto; Darwish, Nadim; Diez-Perez, Ismael; Ciampi, Simone

    2015-01-01

    Herein, we report the spontaneous formation of single-molecule junctions via terminal alkyne contact groups. Self-assembled monolayers that form spontaneously from diluted solutions of 1, 4-diethynylbenzene (DEB) were used to build single-molecule contacts and assessed using the scanning tunneling microscopy-break junction technique (STM-BJ). The STM-BJ technique in both its dynamic and static approaches was used to characterize the lifetime (stability) and the conductivity of a single-DEB wire. It is demonstrated that single-molecule junctions form spontaneously with terminal alkynes and require no electrochemical control or chemical deprotonation. The alkyne anchoring group was compared against typical contact groups exploited in single-molecule studies, i.e. amine (benzenediamine) and thiol (benzendithiol) contact groups. The alkyne contact showed a conductance magnitude comparable to that observed with amine and thiol groups. The lifetime of the junctions formed from alkynes were only slightly less than that of thiols and greater than that observed for amines. These findings are important as (a) they extend the repertoire of chemical contacts used in single-molecule measurements to 1-alkynes, which are synthetically accessible and stable and (b) alkynes have a remarkable affinity toward silicon surfaces, hence opening the door for the study of single-molecule transport on a semiconducting electronic platform. (fast track communication)

  20. Characterization of nanostructures in the live cell plasma membrane utilizing advanced single molecule fluorescence techniques

    International Nuclear Information System (INIS)

    Brameshuber, M.

    2009-01-01

    lipid-lipid or protein-lipid interactions, protein-protein interactions play of mayor role for the regulation of cell metabolism and function. In this thesis I further characterized the interaction between human CD4, the major co-receptor in T cell activation, and human Lck, the protein tyrosine kinase essential for early T cell signaling using an ultra-sensitive fluorescence-based method. Interaction dynamics were studied in detail by performing photobleaching experiments and single molecule brightness analysis. This enabled a combined mobility and stoichiometry analysis of Lck-molecules interacting with the captured CD4 protein. In the last part of my thesis I present a single molecule fluorescence study using a variant of an oxidized phospholipid - which is known to induce apoptosis - to probe the structure of the cellular plasmamembrane. The cells were illuminated using a recently introduced technique which utilizes a highly inclined and laminated optical sheet (HILO) to reduce background signal arising from intracellular fluorophores or from cellular autofluorescence. Our data demonstrate the relevance of plasma membrane properties for uptake of oxidized phospholipids, and indicate a novel indirect mechanism for the control of endocytosis. (author) [de

  1. Central dogma at the single-molecule level in living cells.

    Science.gov (United States)

    Li, Gene-Wei; Xie, X Sunney

    2011-07-20

    Gene expression originates from individual DNA molecules within living cells. Like many single-molecule processes, gene expression and regulation are stochastic, that is, sporadic in time. This leads to heterogeneity in the messenger-RNA and protein copy numbers in a population of cells with identical genomes. With advanced single-cell fluorescence microscopy, it is now possible to quantify transcriptomes and proteomes with single-molecule sensitivity. Dynamic processes such as transcription-factor binding, transcription and translation can be monitored in real time, providing quantitative descriptions of the central dogma of molecular biology and the demonstration that a stochastic single-molecule event can determine the phenotype of a cell.

  2. MHz rate and efficient synchronous heralding of single photons at telecom wavelengths.

    Science.gov (United States)

    Pomarico, Enrico; Sanguinetti, Bruno; Guerreiro, Thiago; Thew, Rob; Zbinden, Hugo

    2012-10-08

    We report on the realization of a synchronous source of heralded single photons at telecom wavelengths with MHz heralding rates and high heralding efficiency. This source is based on the generation of photon pairs at 810 and 1550 nm via Spontaneous Parametric Down Conversion (SPDC) in a 1 cm periodically poled lithium niobate (PPLN) crystal pumped by a 532 nm pulsed laser. As high rates are fundamental for multi-photon experiments, we show that single telecom photons can be announced at 4.4 MHz rate with 45% heralding efficiency. When we focus only on the optimization of the coupling of the heralded photon, the heralding efficiency can be increased up to 80%. Furthermore, we experimentally observe that group velocity mismatch inside long crystals pumped in a pulsed mode affects the spectrum of the emitted photons and their fibre coupling efficiency. The length of the crystal in this source has been chosen as a trade off between high brightness and high coupling efficiency.

  3. Torque Measurement at the Single Molecule Level

    Science.gov (United States)

    Forth, Scott; Sheinin, Maxim Y.; Inman, James; Wang, Michelle D.

    2017-01-01

    Methods for exerting and measuring forces on single molecules have revolutionized the study of the physics of biology. However, it is often the case that biological processes involve rotation or torque generation, and these parameters have been more difficult to access experimentally. Recent advances in the single molecule field have led to the development of techniques which add the capability of torque measurement. By combining force, displacement, torque, and rotational data, a more comprehensive description of the mechanics of a biomolecule can be achieved. In this review, we highlight a number of biological processes for which torque plays a key mechanical role. We describe the various techniques that have been developed to directly probe the torque experienced by a single molecule, and detail a variety of measurements made to date using these new technologies. We conclude by discussing a number of open questions and propose systems of study which would be well suited for analysis with torsional measurement techniques. PMID:23541162

  4. Rotation of a single molecule within a supramolecular bearing

    DEFF Research Database (Denmark)

    Gimzewski, J.K.; Joachim, C.; Schlittler, R.R.

    1998-01-01

    Experimental visualization and verification of a single-molecule rotor operating within a supramolecular bearing is reported. Using a scanning tunneling microscope, single molecules were observed to exist in one of two spatially defined states Laterally separated by 0.26 nanometers. One...

  5. Molecular electronics with single molecules in solid-state devices.

    Science.gov (United States)

    Moth-Poulsen, Kasper; Bjørnholm, Thomas

    2009-09-01

    The ultimate aim of molecular electronics is to understand and master single-molecule devices. Based on the latest results on electron transport in single molecules in solid-state devices, we focus here on new insights into the influence of metal electrodes on the energy spectrum of the molecule, and on how the electron transport properties of the molecule depend on the strength of the electronic coupling between it and the electrodes. A variety of phenomena are observed depending on whether this coupling is weak, intermediate or strong.

  6. Single-molecule imaging and manipulation of biomolecular machines and systems.

    Science.gov (United States)

    Iino, Ryota; Iida, Tatsuya; Nakamura, Akihiko; Saita, Ei-Ichiro; You, Huijuan; Sako, Yasushi

    2018-02-01

    Biological molecular machines support various activities and behaviors of cells, such as energy production, signal transduction, growth, differentiation, and migration. We provide an overview of single-molecule imaging methods involving both small and large probes used to monitor the dynamic motions of molecular machines in vitro (purified proteins) and in living cells, and single-molecule manipulation methods used to measure the forces, mechanical properties and responses of biomolecules. We also introduce several examples of single-molecule analysis, focusing primarily on motor proteins and signal transduction systems. Single-molecule analysis is a powerful approach to unveil the operational mechanisms both of individual molecular machines and of systems consisting of many molecular machines. Quantitative, high-resolution single-molecule analyses of biomolecular systems at the various hierarchies of life will help to answer our fundamental question: "What is life?" This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Heterobifunctional crosslinkers for tethering single ligand molecules to scanning probes

    International Nuclear Information System (INIS)

    Riener, Christian K.; Kienberger, Ferry; Hahn, Christoph D.; Buchinger, Gerhard M.; Egwim, Innocent O.C.; Haselgruebler, Thomas; Ebner, Andreas; Romanin, Christoph; Klampfl, Christian; Lackner, Bernd; Prinz, Heino; Blaas, Dieter; Hinterdorfer, Peter; Gruber, Hermann J.

    2003-01-01

    Single molecule recognition force microscopy (SMRFM) is a versatile atomic force microscopy (AFM) method to probe specific interactions of cognitive molecules on the single molecule level. It allows insights to be gained into interaction potentials and kinetic barriers and is capable of mapping interaction sites with nm positional accuracy. These applications require a ligand to be attached to the AFM tip, preferably by a distensible poly(ethylene glycol) (PEG) chain between the measuring tip and the ligand molecule. The PEG chain greatly facilitates specific binding of the ligand to immobile receptor sites on the sample surface. The present study contributes to tip-PEG-ligand tethering in three ways: (i) a convenient synthetic route was found to prepare NH 2 -PEG-COOH which is the key intermediate for long heterobifunctional crosslinkers; (ii) a variety of heterobifunctional PEG derivatives for tip-PEG-ligand linking were prepared from NH 2 -PEG-COOH; (iii) in particular, a new PEG crosslinker with one thiol-reactive end and one terminal nitrilotriacetic acid (NTA) group was synthesized and successfully used to tether His 6 -tagged protein molecules to AFM tips via noncovalent NTA-Ni 2+ -His 6 bridges. The new crosslinker was applied to link a recombinant His 6 -tagged fragment of the very-low density lipoprotein receptor to the AFM tip whereupon specific docking to the capsid of human rhinovirus particles was observed by force microscopy. In a parallel study, the specific interaction of the small GTPase Ran with the nuclear import receptor importin β1 was studied in detail by SMRFM, using the new crosslinker to link His 6 -tagged Ran to the measuring tip [Nat. Struct. Biol. (2003), 10, 553-557

  8. A plasmonic biosensor with single-molecule sensitivity

    NARCIS (Netherlands)

    Zijlstra, P.; Paulo, P.M.R.; Yuan, H.; Khatua, S.; Yorulmaz, M.; Orrit, M.

    2013-01-01

    The plasmon resonance of a single metal nanoparticle induces an enhancement of the local electromagnetic field. We exploit this field enhancement to detect single molecules that are (1) poorly fluorescent or (2) completely non-fluorescent.

  9. Molecular electronics--resonant transport through single molecules.

    Science.gov (United States)

    Lörtscher, Emanuel; Riel, Heike

    2010-01-01

    The mechanically controllable break-junction technique (MCBJ) enables us to investigate charge transport through an individually contacted and addressed molecule in ultra-high vacuum (UHV) environment at variable temperature ranging from room temperature down to 4 K. Using a statistical measurement and analysis approach, we acquire current-voltage (I-V) characteristics during the repeated formation, manipulation, and breaking of a molecular junction. At low temperatures, voltages accessing the first molecular orbitals in resonance can be applied, providing spectroscopic information about the junction's energy landscape, in particular about the molecular level alignment in respect to the Fermi energy of the electrodes. Thereby, we can investigate the non-linear transport properties of various types of functional molecules and explore their potential use as functional building blocks for future nano-electronics. An example will be given by the reversible and controllable switching between two distinct conductive states of a single molecule. As a proof-of-principle for functional molecular devices, a single-molecule memory element will be demonstrated.

  10. Single Molecule Atomic Force Microscopy Studies of Photosensitized Singlet Oxygen Behavior on a DNA Origami Template

    DEFF Research Database (Denmark)

    Helmig, Sarah Wendelboe; Rotaru, Alexandru; Arian, Dumitru

    2010-01-01

    DNA origami, the folding of a long single-stranded DNA sequence (scaffold strand) by hundreds of short synthetic oligonucleotides (staple strands) into parallel aligned helices, is a highly efficient method to form advanced self-assembled DNA-architectures. Since molecules and various materials can...... be conjugated to each of the short staple strands, the origami method offers a unique possibility of arranging molecules and materials in well-defined positions on a structured surface. Here we combine the action of light with AFM and DNA nanostructures to study the production of singlet oxygen from a single...... photosensitizer molecule conjugated to a selected DNA origami staple strand on an origami structure. We demonstrate a distance-dependent oxidation of organic moieties incorporated in specific positions on DNA origami by singlet oxygen produced from a single photosensitizer located at the center of each origami....

  11. Directional rolling of positively charged nanoparticles along a flexibility gradient on long DNA molecules.

    Science.gov (United States)

    Park, Suehyun; Joo, Heesun; Kim, Jun Soo

    2018-01-31

    Directing the motion of molecules/colloids in any specific direction is of great interest in many applications of chemistry, physics, and biological sciences, where regulated positioning or transportation of materials is highly desired. Using Brownian dynamics simulations of coarse-grained models of a long, double-stranded DNA molecule and positively charged nanoparticles, we observed that the motion of a single nanoparticle bound to and wrapped by the DNA molecule can be directed along a gradient of DNA local flexibility. The flexibility gradient is constructed along a 0.8 kilobase-pair DNA molecule such that local persistence length decreases gradually from 50 nm to 40 nm, mimicking a gradual change in sequence-dependent flexibility. Nanoparticles roll over a long DNA molecule from less flexible regions towards more flexible ones as a result of the decreasing energetic cost of DNA bending and wrapping. In addition, the rolling becomes slightly accelerated as the positive charge of nanoparticles decreases due to a lower free energy barrier of DNA detachment from charged nanoparticle for processive rolling. This study suggests that the variation in DNA local flexibility can be utilized in constructing and manipulating supramolecular assemblies of DNA molecules and nanoparticles in structural DNA nanotechnology.

  12. Azadioxatriangulenium (ADOTA+): A long fluorescence lifetime fluorophore for large biomolecule binding assay

    Science.gov (United States)

    Sørensen, Thomas Just; Thyrhaug, Erling; Szabelski, Mariusz; Luchowski, Rafal; Gryczynski, Ignacy; Gryczynski, Zygmunt; Laursen, Bo W.

    2013-01-01

    Of the many optical bioassays available, sensing by fluorescence anisotropy have great advantages as it provides a sensitive, instrumentally simple, ratiometric method of detection. However, it is hampered by a severe limitation as the emission lifetime of the label needs to be comparable to the correlation lifetime (tumbling time) of the biomolecule which is labelled. For proteins of moderate size this is in the order of 20–200 ns, which due to practical issues currently limits the choice of labels to the dansyl-type dyes and certain aromatics dyes. These have the significant drawback of UV/blue absorption and emission as well as an often significant solvent sensitivity. Here, we report the synthesis and characterization of a new fluorescent label for high molecular weight biomolecules assay based on the azadioxatriangulenium motif. The NHS ester of the long fluorescence lifetime, red emitting fluorophore: azadioxatriangulenium (ADOTA-NHS) was conjugated to anti-rabbit Immunoglobulin G (antiIgG). The long fluorescence lifetime was exploited to determine the correlation time of the high molecular weight antibody and its complex with rabbit Immuniglobulin G (IgG) with steady-state fluorescence anisotropy and time-resolved methods: solution phase immuno-assay was performed following either steady-state or time-resolved fluorescence anisotropy. By performing a variable temperature experiment it was determined that the binding of the ligand resulted in an increase in correlation time by more than 75 %, and a change in the steady-state anisotropy increase of 18%. The results show that the triangulenium class of dyes can be used in anisotropy assay for detecting binding events involving biomolecules of far larger size than what is possible with the other red emitting organic dyes. PMID:24058730

  13. Wavelength and coherence effects on the growth mechanism of silicon nanopillars and their use in the modification of spontaneous lifetime emission of BODIPY dye molecules

    Energy Technology Data Exchange (ETDEWEB)

    Acikgoz, Sabriye [Bogazici University, Department of Physics, Istanbul (Turkey); Karamanoglu Mehmetbey University, Department of Material Science and Engineering, Karaman (Turkey); Bilen, Bukem; Saygili, Asli C.; Aktas, Gulen; Inci, Mehmet Naci [Bogazici University, Department of Physics, Istanbul (Turkey); Sanyal, Amitav [Bogazici University, Department of Chemistry, Istanbul (Turkey)

    2012-09-15

    Silicon nanopillars are grown by an electrochemical anodization of p-type silicon wafers at low current densities in a hydrofluoric acid solution. CW, white light, and various UV pulsed lasers are employed as illumination sources in sample preparation to study wavelength and coherence effects on the growth mechanism of the nanopillars. Coherence is observed to be the foundation of regularity in obtaining conical shapes. The pillar size is found to be almost linearly proportional to the employed illumination wavelength during their growth. BODIPY dye molecules are chemically attached to these silicon nanopillars and the radiative decay rates are investigated by means of a time-resolved fluorescence experiment. The decay rate of the dye molecules embedded in the vicinity of various size pillar tips is significantly affected due to different apex angles of the conical nature. It is demonstrated that the pillar size and the separation between pillars can be adjusted if one uses a coherent light source with an appropriate wavelength during the course of fabrication process. Since change in the decay rate is due to tips of the pillars only, separation of a few micrometers between pillar tips allows one to directly monitor a dye, which is embedded to the tip of a single nanopillar, via a confocal microscopic method for the spontaneous lifetime measurements, without having needed to any extra efforts for an in situ imaging process. It is observed that as the pillar size gets smaller, the inhibition in the spontaneous lifetime of BODIPY is more pronounced. In addition, a more regular pillar structure yields nonvarying decay rates of the dye molecules throughout the silicon sample. (orig.)

  14. Stereoelectronic Effect-Induced Conductance Switching in Aromatic Chain Single-Molecule Junctions.

    Science.gov (United States)

    Xin, Na; Wang, Jinying; Jia, Chuancheng; Liu, Zitong; Zhang, Xisha; Yu, Chenmin; Li, Mingliang; Wang, Shuopei; Gong, Yao; Sun, Hantao; Zhang, Guanxin; Liu, Zhirong; Zhang, Guangyu; Liao, Jianhui; Zhang, Deqing; Guo, Xuefeng

    2017-02-08

    Biphenyl, as the elementary unit of organic functional materials, has been widely used in electronic and optoelectronic devices. However, over decades little has been fundamentally understood regarding how the intramolecular conformation of biphenyl dynamically affects its transport properties at the single-molecule level. Here, we establish the stereoelectronic effect of biphenyl on its electrical conductance based on the platform of graphene-molecule single-molecule junctions, where a specifically designed hexaphenyl aromatic chain molecule is covalently sandwiched between nanogapped graphene point contacts to create stable single-molecule junctions. Both theoretical and temperature-dependent experimental results consistently demonstrate that phenyl twisting in the aromatic chain molecule produces different microstates with different degrees of conjugation, thus leading to stochastic switching between high- and low-conductance states. These investigations offer new molecular design insights into building functional single-molecule electrical devices.

  15. A single molecule DNA flow stretching microscope for undergraduates

    NARCIS (Netherlands)

    Williams, Kelly; Grafe, Brendan; Burke, Kathryn M.; Tanner, Nathan; van Oijen, Antoine M.; Loparo, Joseph; Price, Allen C.

    2011-01-01

    The design of a simple, safe, and inexpensive single molecule flow stretching instrument is presented. The instrument uses a low cost upright microscope coupled to a webcam for imaging single DNA molecules that are tethered in an easy to construct microfluidic flow cell. The system requires no

  16. Single particle tracking and single molecule energy transfer

    CERN Document Server

    Bräuchle, Christoph; Michaelis, Jens

    2009-01-01

    Closing a gap in the literature, this handbook gathers all the information on single particle tracking and single molecule energy transfer. It covers all aspects of this hot and modern topic, from detecting virus entry to membrane diffusion, and from protein folding using spFRET to coupled dye systems, as well recent achievements in the field. Throughout, the first-class editors and top international authors present content of the highest quality, making this a must-have for physical chemists, spectroscopists, molecular physicists and biochemists.

  17. Electrons, Photons, and Force: Quantitative Single-Molecule Measurements from Physics to Biology

    Science.gov (United States)

    2011-01-01

    Single-molecule measurement techniques have illuminated unprecedented details of chemical behavior, including observations of the motion of a single molecule on a surface, and even the vibration of a single bond within a molecule. Such measurements are critical to our understanding of entities ranging from single atoms to the most complex protein assemblies. We provide an overview of the strikingly diverse classes of measurements that can be used to quantify single-molecule properties, including those of single macromolecules and single molecular assemblies, and discuss the quantitative insights they provide. Examples are drawn from across the single-molecule literature, ranging from ultrahigh vacuum scanning tunneling microscopy studies of adsorbate diffusion on surfaces to fluorescence studies of protein conformational changes in solution. PMID:21338175

  18. Biological Nanopores: Confined Spaces for Electrochemical Single-Molecule Analysis.

    Science.gov (United States)

    Cao, Chan; Long, Yi-Tao

    2018-02-20

    Nanopore sensing is developing into a powerful single-molecule approach to investigate the features of biomolecules that are not accessible by studying ensemble systems. When a target molecule is transported through a nanopore, the ions occupying the pore are excluded, resulting in an electrical signal from the intermittent ionic blockade event. By statistical analysis of the amplitudes, duration, frequencies, and shapes of the blockade events, many properties of the target molecule can be obtained in real time at the single-molecule level, including its size, conformation, structure, charge, geometry, and interactions with other molecules. With the development of the use of α-hemolysin to characterize individual polynucleotides, nanopore technology has attracted a wide range of research interest in the fields of biology, physics, chemistry, and nanoscience. As a powerful single-molecule analytical method, nanopore technology has been applied for the detection of various biomolecules, including oligonucleotides, peptides, oligosaccharides, organic molecules, and disease-related proteins. In this Account, we highlight recent developments of biological nanopores in DNA-based sensing and in studying the conformational structures of DNA and RNA. Furthermore, we introduce the application of biological nanopores to investigate the conformations of peptides affected by charge, length, and dipole moment and to study disease-related proteins' structures and aggregation transitions influenced by an inhibitor, a promoter, or an applied voltage. To improve the sensing ability of biological nanopores and further extend their application to a wider range of molecular sensing, we focus on exploring novel biological nanopores, such as aerolysin and Stable Protein 1. Aerolysin exhibits an especially high sensitivity for the detection of single oligonucleotides both in current separation and duration. Finally, to facilitate the use of nanopore measurements and statistical analysis

  19. Microscopic single-crystal refractometry as a function of wavelength

    International Nuclear Information System (INIS)

    DeLoach, L.D.

    1994-01-01

    The refractive indices of crystal fragments 50--200 μm in size can be measured for light wavelengths between 365 and 1100 nm with a spindle-stage refractometer. Established methods from optical crystallograpy are used to orient a crystal on the microscope spindle stage and then to match its refractive index to an immersion fluid. The refractive index of the fluid for the wavelength of light and matching temperature is determined by comparison of a reference crystal on a second spindle axis with the fluid under the match conditions. Investigations of new nonlinear-optical crystals admirably demonstrate the advantages of measuring the refractive index to ± 0.0004 in small single crystals

  20. Long-Distance Single Photon Transmission from a Trapped Ion via Quantum Frequency Conversion

    Science.gov (United States)

    Walker, Thomas; Miyanishi, Koichiro; Ikuta, Rikizo; Takahashi, Hiroki; Vartabi Kashanian, Samir; Tsujimoto, Yoshiaki; Hayasaka, Kazuhiro; Yamamoto, Takashi; Imoto, Nobuyuki; Keller, Matthias

    2018-05-01

    Trapped atomic ions are ideal single photon emitters with long-lived internal states which can be entangled with emitted photons. Coupling the ion to an optical cavity enables the efficient emission of single photons into a single spatial mode and grants control over their temporal shape. These features are key for quantum information processing and quantum communication. However, the photons emitted by these systems are unsuitable for long-distance transmission due to their wavelengths. Here we report the transmission of single photons from a single 40Ca+ ion coupled to an optical cavity over a 10 km optical fiber via frequency conversion from 866 nm to the telecom C band at 1530 nm. We observe nonclassical photon statistics of the direct cavity emission, the converted photons, and the 10 km transmitted photons, as well as the preservation of the photons' temporal shape throughout. This telecommunication-ready system can be a key component for long-distance quantum communication as well as future cloud quantum computation.

  1. The dynamics of interacting nonlinearities governing long wavelength driftwave turbulence

    International Nuclear Information System (INIS)

    Newman, D.E.

    1993-09-01

    Because of the ubiquitous nature of turbulence and the vast array of different systems which have turbulent solutions, the study of turbulence is an area of active research. Much present day understanding of turbulence is rooted in the well established properties of homogeneous Navier-Stokes turbulence, which, due to its relative simplicity, allows for approximate analytic solutions. This work examines a group of turbulent systems with marked differences from Navier-Stokes turbulence, and attempts to quantify some of their properties. This group of systems represents a variety of drift wave fluctuations believed to be of fundamental importance in laboratory fusion devices. From extensive simulation of simple local fluid models of long wavelength drift wave turbulence in tokamaks, a reasonably complete picture of the basic properties of spectral transfer and saturation has emerged. These studies indicate that many conventional notions concerning directions of cascades, locality and isotropy of transfer, frequencies of fluctuations, and stationarity of saturation are not valid for moderate to long wavelengths. In particular, spectral energy transfer at long wavelengths is dominated by the E x B nonlinearity, which carries energy to short scale in a manner that is highly nonlocal and anisotropic. In marked contrast to the canonical self-similar cascade dynamics of Kolmogorov, energy is efficiently passed between modes separated by the entire spectrum range in a correlation time. At short wavelengths, transfer is dominated by the polarization drift nonlinearity. While the standard dual cascade applies in this subrange, it is found that finite spectrum size can produce cascades that are reverse directed and are nonconservative in enstrophy and energy similarity ranges. In regions where both nonlinearities are important, cross-coupling between the nolinearities gives rise to large no frequency shifts as well as changes in the spectral dynamics

  2. Studies of G-quadruplex DNA structures at the single molecule level

    DEFF Research Database (Denmark)

    Kragh, Sofie Louise

    2015-01-01

    Folding of G-quaduplex structures adopted by the human telomeric repeat is here studied by single molecule FRET microscopy. This method allows for the investigation of G-quadruplex structures and their conformational dynamic. Telomeres are located at the ends of our chromosomes and end in a single...... with human telomeric repeat adopt several different G-quadruplex conformations in the presence of K+ ions. G-quadruplexes inhibit telomerase activity and are therefore potential targets for anti-cancer drugs, which can be small molecule ligands capable of stabilizing G-quadruplex structures. Understanding...... range. FRET spectroscopy can be performed on an ensemble of molecules, or on the single molecule level. In single molecule FRET experiments it is possible to follow the behaviour in time for each molecule independently, allowing insight into both dynamically and statistically heterogeneous molecular...

  3. Automated imaging system for single molecules

    Science.gov (United States)

    Schwartz, David Charles; Runnheim, Rodney; Forrest, Daniel

    2012-09-18

    There is provided a high throughput automated single molecule image collection and processing system that requires minimal initial user input. The unique features embodied in the present disclosure allow automated collection and initial processing of optical images of single molecules and their assemblies. Correct focus may be automatically maintained while images are collected. Uneven illumination in fluorescence microscopy is accounted for, and an overall robust imaging operation is provided yielding individual images prepared for further processing in external systems. Embodiments described herein are useful in studies of any macromolecules such as DNA, RNA, peptides and proteins. The automated image collection and processing system and method of same may be implemented and deployed over a computer network, and may be ergonomically optimized to facilitate user interaction.

  4. Bolometric-Effect-Based Wavelength-Selective Photodetectors Using Sorted Single Chirality Carbon Nanotubes

    Science.gov (United States)

    Zhang, Suoming; Cai, Le; Wang, Tongyu; Shi, Rongmei; Miao, Jinshui; Wei, Li; Chen, Yuan; Sepúlveda, Nelson; Wang, Chuan

    2015-01-01

    This paper exploits the chirality-dependent optical properties of single-wall carbon nanotubes for applications in wavelength-selective photodetectors. We demonstrate that thin-film transistors made with networks of carbon nanotubes work effectively as light sensors under laser illumination. Such photoresponse was attributed to photothermal effect instead of photogenerated carriers and the conclusion is further supported by temperature measurements. Additionally, by using different types of carbon nanotubes, including a single chirality (9,8) nanotube, the devices exhibit wavelength-selective response, which coincides well with the absorption spectra of the corresponding carbon nanotubes. This is one of the first reports of controllable and wavelength-selective bolometric photoresponse in macroscale assemblies of chirality-sorted carbon nanotubes. The results presented here provide a viable route for achieving bolometric-effect-based photodetectors with programmable response spanning from visible to near-infrared by using carbon nanotubes with pre-selected chiralities. PMID:26643777

  5. Single-molecule force-conductance spectroscopy of hydrogen-bonded complexes

    DEFF Research Database (Denmark)

    Pirrotta, Alessandro; De Vico, Luca; Solomon, Gemma C.

    2017-01-01

    to inform about molecular recognition events at the single-molecule limit. For this, we consider the force-conductance characteristics of a prototypical class of hydrogen bonded bimolecular complexes sandwiched between gold electrodes. The complexes consist of derivatives of a barbituric acid and a Hamilton...... is mechanically manipulated. The implication is that force and conductance provide complementary information about the evolution of molecules in junctions that can be used to interrogate basic structure-transport relations at the single-molecule limit....

  6. Fast temporal fluctuations in single-molecule junctions.

    Science.gov (United States)

    Ochs, Roif; Secker, Daniel; Elbing, Mark; Mayor, Marcel; Weber, Heiko B

    2006-01-01

    The noise within the electrical current through single-molecule junctions is studied cryogenic temperature. The organic sample molecules were contacted with the mechanically controlled break-junction technique. The noise spectra refer to a where only few Lorentzian fluctuators occur in the conductance. The frequency dependence shows qualitative variations from sample to sample.

  7. High-quality asynchronous heralded single-photon source at telecom wavelength

    International Nuclear Information System (INIS)

    Fasel, Sylvain; Alibart, Olivier; Tanzilli, Sebastien; Baldi, Pascal; Beveratos, Alexios; Gisin, Nicolas; Zbinden, Hugo

    2004-01-01

    We report on the experimental realization and characterization of an asynchronous heralded single-photon source based on spontaneous parametric down-conversion. Photons at 1550 nm are heralded as being inside a single-mode fibre with more than 60% probability, and the multi-photon emission probability is reduced by a factor of up to more than 500 compared to Poissonian light sources. These figures of merit, together with the choice of telecom wavelength for the heralded photons, are compatible with practical applications needing very efficient and robust single-photon sources

  8. Monofunctional stealth nanoparticle for unbiased single molecule tracking inside living cells.

    Science.gov (United States)

    Lisse, Domenik; Richter, Christian P; Drees, Christoph; Birkholz, Oliver; You, Changjiang; Rampazzo, Enrico; Piehler, Jacob

    2014-01-01

    On the basis of a protein cage scaffold, we have systematically explored intracellular application of nanoparticles for single molecule studies and discovered that recognition by the autophagy machinery plays a key role for rapid metabolism in the cytosol. Intracellular stealth nanoparticles were achieved by heavy surface PEGylation. By combination with a generic approach for nanoparticle monofunctionalization, efficient labeling of intracellular proteins with high fidelity was accomplished, allowing unbiased long-term tracking of proteins in the outer mitochondrial membrane.

  9. Extracting rate coefficients from single-molecule photon trajectories and FRET efficiency histograms for a fast-folding protein.

    Science.gov (United States)

    Chung, Hoi Sung; Gopich, Irina V; McHale, Kevin; Cellmer, Troy; Louis, John M; Eaton, William A

    2011-04-28

    Recently developed statistical methods by Gopich and Szabo were used to extract folding and unfolding rate coefficients from single-molecule Förster resonance energy transfer (FRET) data for proteins with kinetics too fast to measure waiting time distributions. Two types of experiments and two different analyses were performed. In one experiment bursts of photons were collected from donor and acceptor fluorophores attached to a 73-residue protein, α(3)D, freely diffusing through the illuminated volume of a confocal microscope system. In the second, the protein was immobilized by linkage to a surface, and photons were collected until one of the fluorophores bleached. Folding and unfolding rate coefficients and mean FRET efficiencies for the folded and unfolded subpopulations were obtained from a photon by photon analysis of the trajectories using a maximum likelihood method. The ability of the method to describe the data in terms of a two-state model was checked by recoloring the photon trajectories with the extracted parameters and comparing the calculated FRET efficiency histograms with the measured histograms. The sum of the rate coefficients for the two-state model agreed to within 30% with the relaxation rate obtained from the decay of the donor-acceptor cross-correlation function, confirming the high accuracy of the method. Interestingly, apparently reliable rate coefficients could be extracted using the maximum likelihood method, even at low (rate coefficients and mean FRET efficiencies were also obtained in an approximate procedure by simply fitting the FRET efficiency histograms, calculated by binning the donor and acceptor photons, with a sum of three-Gaussian functions. The kinetics are exposed in these histograms by the growth of a FRET efficiency peak at values intermediate between the folded and unfolded peaks as the bin size increases, a phenomenon with similarities to NMR exchange broadening. When comparable populations of folded and unfolded

  10. Electrochemistry and bioelectrochemistry towards the single-molecule level: Theoretical notions and systems

    International Nuclear Information System (INIS)

    Zhang Jingdong; Chi Qijin; Albrecht, Tim; Kuznetsov, Alexander M.; Grubb, Mikala; Hansen, Allan G.; Wackerbarth, Hainer; Welinder, Anne C.; Ulstrup, Jens

    2005-01-01

    Surface structures controlled at the nanometer and single-molecule levels, with functions crucially determined by interfacial electron transfer (ET) are broadly reported in recent years, with different kinds of electrochemically controlled nanoscale/single molecule systems. One is the broad class of metallic and semiconductor-based nanoparticles, nano-arrays, nanotubes, and nanopits. Others are based on self-assembled molecular monolayers. The latter extend to bioelectrochemical systems with redox metalloproteins and DNA-based molecules as targets. We overview here some recent achievements in areas of interfacial electrochemical ET systems, mapped to the nanoscale and single-molecule levels. Focus is on both experimental and theoretical studies in our group. Systems addressed are organized monolayers of redox active transition metal complexes, and metalloproteins and metalloenzymes on single-crystal Au(1 1 1)-electrode surfaces. These systems have been investigated by voltammetry, spectroscopy, microcantilever technology, and scanning probe microscopy. A class of Os-complexes has shown suitable as targets for electrochemical in situ scanning tunnelling microscopy (STM), with close to single-molecule scanning tunnelling spectroscopic (STS) features. Mapping of redox metalloproteins from the three major classes, i.e. blue copper proteins, heme proteins, and iron-sulfur proteins, at the monolayer and single-molecule levels have also been achieved. In situ STM and spectroscopy of redox molecules and biomolecules have been supported by new theoretical frames, which extend established theory of interfacial electrochemical ET. The electrochemical nanoscale and single-molecule systems discussed are compared with other recent nanoscale and single-molecule systems with conspicuous device-like properties, particularly unimolecular rectifiers and single-molecule transistors. Both of these show analogies to electrochemical in situ STM features of redox molecules and

  11. Fluorophore-conjugated iron oxide nanoparticle labeling and analysis of engrafting human hematopoietic stem cells

    DEFF Research Database (Denmark)

    Maxwell, Dustin J; Bonde, Jesper; Hess, David A

    2008-01-01

    culture conditions to maintain viability without inducing terminal differentiation. In the current study, fluorescent molecules were covalently linked to dextran-coated iron oxide nanoparticles (Feridex) to characterize human HSC labeling to monitor the engraftment process. Conjugating fluorophores...... to the dextran coat for fluorescence-activated cell sorting purification eliminated spurious signals from nonsequestered nanoparticle contaminants. A short-term defined incubation strategy was developed that allowed efficient labeling of both quiescent and cycling HSC, with no discernable toxicity in vitro...

  12. Single-molecule electronics: Cooling individual vibrational modes by the tunneling current.

    Science.gov (United States)

    Lykkebo, Jacob; Romano, Giuseppe; Gagliardi, Alessio; Pecchia, Alessandro; Solomon, Gemma C

    2016-03-21

    Electronic devices composed of single molecules constitute the ultimate limit in the continued downscaling of electronic components. A key challenge for single-molecule electronics is to control the temperature of these junctions. Controlling heating and cooling effects in individual vibrational modes can, in principle, be utilized to increase stability of single-molecule junctions under bias, to pump energy into particular vibrational modes to perform current-induced reactions, or to increase the resolution in inelastic electron tunneling spectroscopy by controlling the life-times of phonons in a molecule by suppressing absorption and external dissipation processes. Under bias the current and the molecule exchange energy, which typically results in heating of the molecule. However, the opposite process is also possible, where energy is extracted from the molecule by the tunneling current. Designing a molecular "heat sink" where a particular vibrational mode funnels heat out of the molecule and into the leads would be very desirable. It is even possible to imagine how the vibrational energy of the other vibrational modes could be funneled into the "cooling mode," given the right molecular design. Previous efforts to understand heating and cooling mechanisms in single molecule junctions have primarily been concerned with small models, where it is unclear which molecular systems they correspond to. In this paper, our focus is on suppressing heating and obtaining current-induced cooling in certain vibrational modes. Strategies for cooling vibrational modes in single-molecule junctions are presented, together with atomistic calculations based on those strategies. Cooling and reduced heating are observed for two different cooling schemes in calculations of atomistic single-molecule junctions.

  13. Multiplexed single-molecule force spectroscopy using a centrifuge.

    Science.gov (United States)

    Yang, Darren; Ward, Andrew; Halvorsen, Ken; Wong, Wesley P

    2016-03-17

    We present a miniature centrifuge force microscope (CFM) that repurposes a benchtop centrifuge for high-throughput single-molecule experiments with high-resolution particle tracking, a large force range, temperature control and simple push-button operation. Incorporating DNA nanoswitches to enable repeated interrogation by force of single molecular pairs, we demonstrate increased throughput, reliability and the ability to characterize population heterogeneity. We perform spatiotemporally multiplexed experiments to collect 1,863 bond rupture statistics from 538 traceable molecular pairs in a single experiment, and show that 2 populations of DNA zippers can be distinguished using per-molecule statistics to reduce noise.

  14. Power-Law-Distributed Dark States are the Main Pathway for Photobleaching of Single Organic Molecules

    OpenAIRE

    Hoogenboom, J.P.; Hoogenboom, Jacob; van Dijk, E.M.H.P.; Hernando Campos, J.; van Hulst, N.F.; Garcia Parajo, M.F.

    2005-01-01

    We exploit the strong excitonic coupling in a superradiant trimer molecule to distinguish between long-lived collective dark states and photobleaching events. The population and depopulation kinetics of the dark states in a single molecule follow power-law statistics over 5 orders of magnitude in time. This result is consistent with the formation of a radical unit via electron tunneling to a time-varying distribution of trapping sites in the surrounding polymer matrix. We furthermore demonstr...

  15. Aligning of single and multiple wavelength chromatographic

    DEFF Research Database (Denmark)

    Nielsen, Niels-Peter Vest; Carstensen, Jens Michael; Smedsgaard, Jørn

    1998-01-01

    optimised warping (COW) using two input parameters which can be estimated from the observed peak width. COW is demonstrated on constructed single trace chromatograms and on single and multiple wavelength chromatograms obtained from HPLC diode detection analyses of fungal extractsA copy of the C program......The use of chemometric data processing is becoming an important part of modern chromatography. Most chemometric analyses are performed on reduced data sets using areas of selected peaks detected in the chromatograms, which means a loss of data and introduces the problem of extracting peak data from...... to utilise the entire data matrix or rely on peak detection, thus having the same limitations as the commonly used chemometric procedures. The method presented uses the entire chromatographic data matrices and does not require any preprocessing e.g., peak detection. It relies on piecewise linear correlation...

  16. Diode-side-pumped 131 W, 1319 nm single-wavelength cw Nd:YAG laser.

    Science.gov (United States)

    Haiyong, Zhu; Ge, Zhang; Chenghui, Huang; Yong, Wei; Lingxiong, Huang; Jing, Chen; Weidong, Chen; Zhenqiang, Chen

    2007-01-20

    A diode-side-pumped high-power 1319 nm single-wavelength Nd:YAG continuous wave (cw) laser is described. Through reasonable coating design of the cavity mirrors, the 1064 nm strongest line as well as the 1338 nm one have been successfully suppressed. The laser output powers corresponding to four groups of different output couplers operating at 1319 nm single wavelength have been compared. The output coupler with the transmission T=5.3% has the highest output power, and a 131 W cw output power was achieved at the pumping power of 555 W. The optical-optical conversion efficiency is 23.6%, and the slope efficiency is 46%. The output power is higher than the total output power of the dual-wavelength laser operating at 1319 nm and 1338 nm in the experiment.

  17. Isolated single-molecule magnets on native gold.

    Science.gov (United States)

    Zobbi, Laura; Mannini, Matteo; Pacchioni, Mirko; Chastanet, Guillaume; Bonacchi, Daniele; Zanardi, Chiara; Biagi, Roberto; Del Pennino, Umberto; Gatteschi, Dante; Cornia, Andrea; Sessoli, Roberta

    2005-03-28

    The incorporation of thioether groups in the structure of a Mn12 single-molecule magnet, [Mn12(O12)(L)16(H2O)4] with L = 4-(methylthio)benzoate, is a successful route to the deposition of well-separated clusters on native gold surfaces and to the addressing of individual molecules by scanning tunnelling microscopy.

  18. Homogeneous immunoassay for the cancer marker alpha-fetoprotein using single wavelength excitation fluorescence cross-correlation spectroscopy and CdSe/ZnS quantum dots and fluorescent dyes as labels

    International Nuclear Information System (INIS)

    Wang, Jinjie; Liu, Heng; Huang, Xiangyi; Ren, Jicun

    2016-01-01

    The article describes sensitive and selective homogeneous immunoassays for the liver cancer biomarker alpha-fetoprotein (AFP) in human serum by using single wavelength excitation fluorescence cross-correlation spectroscopy (SW-FCCS). Both competitive and sandwich immunoassay modes were applied, and AFP served as a model analyte. Fluorescent CdSe/ZnS quantum dots (with a 655 nm emission peak) and the fluorophore Alexa Fluor 488 (520 nm emission) were chosen to label the antibodies in the sandwich mode, and the antibody and the antigen in the competitive mode. Under optimized conditions, the sandwich assay has a linear dynamic range that covers the 20 pM to 5.0 nM concentration range. The competitive assay, in turn, extends from 180 pM to 15.0 nM. The respective detection limits are 20 pM and 180 pM. The method was successfully applied to directly determine AFP in (spiked) clinical samples, and results were in good agreement with data obtained via ELISAs. (author)

  19. Atomic-Scale Control of Electron Transport through Single Molecules

    DEFF Research Database (Denmark)

    Wang, Y. F.; Kroger, J.; Berndt, R.

    2010-01-01

    Tin-phthalocyanine molecules adsorbed on Ag(111) were contacted with the tip of a cryogenic scanning tunneling microscope. Orders-of-magnitude variations of the single-molecule junction conductance were achieved by controllably dehydrogenating the molecule and by modifying the atomic structure...

  20. Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments

    OpenAIRE

    Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

    2016-01-01

    We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long-term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode, photomultiplier tube, or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel n...

  1. Mapping absolute tissue endogenous fluorophore concentrations with chemometric wide-field fluorescence microscopy

    Science.gov (United States)

    Xu, Zhang; Reilley, Michael; Li, Run; Xu, Min

    2017-06-01

    We report chemometric wide-field fluorescence microscopy for imaging the spatial distribution and concentration of endogenous fluorophores in thin tissue sections. Nonnegative factorization aided by spatial diversity is used to learn both the spectral signature and the spatial distribution of endogenous fluorophores from microscopic fluorescence color images obtained under broadband excitation and detection. The absolute concentration map of individual fluorophores is derived by comparing the fluorescence from "pure" fluorophores under the identical imaging condition following the identification of the fluorescence species by its spectral signature. This method is then demonstrated by characterizing the concentration map of endogenous fluorophores (including tryptophan, elastin, nicotinamide adenine dinucleotide, and flavin adenine dinucleotide) for lung tissue specimens. The absolute concentrations of these fluorophores are all found to decrease significantly from normal, perilesional, to cancerous (squamous cell carcinoma) tissue. Discriminating tissue types using the absolute fluorophore concentration is found to be significantly more accurate than that achievable with the relative fluorescence strength. Quantification of fluorophores in terms of the absolute concentration map is also advantageous in eliminating the uncertainties due to system responses or measurement details, yielding more biologically relevant data, and simplifying the assessment of competing imaging approaches.

  2. Single-Molecule Analysis for RISC Assembly and Target Cleavage.

    Science.gov (United States)

    Sasaki, Hiroshi M; Tadakuma, Hisashi; Tomari, Yukihide

    2018-01-01

    RNA-induced silencing complex (RISC) is a small RNA-protein complex that mediates silencing of complementary target RNAs. Biochemistry has been successfully used to characterize the molecular mechanism of RISC assembly and function for nearly two decades. However, further dissection of intermediate states during the reactions has been warranted to fill in the gaps in our understanding of RNA silencing mechanisms. Single-molecule analysis with total internal reflection fluorescence (TIRF) microscopy is a powerful imaging-based approach to interrogate complex formation and dynamics at the individual molecule level with high sensitivity. Combining this technique with our recently established in vitro reconstitution system of fly Ago2-RISC, we have developed a single-molecule observation system for RISC assembly. In this chapter, we summarize the detailed protocol for single-molecule analysis of chaperone-assisted assembly of fly Ago2-RISC as well as its target cleavage reaction.

  3. Evaluation of the Kinetic Property of Single-Molecule Junctions by Tunneling Current Measurements.

    Science.gov (United States)

    Harashima, Takanori; Hasegawa, Yusuke; Kiguchi, Manabu; Nishino, Tomoaki

    2018-01-01

    We investigated the formation and breaking of single-molecule junctions of two kinds of dithiol molecules by time-resolved tunneling current measurements in a metal nanogap. The resulting current trajectory was statistically analyzed to determine the single-molecule conductance and, more importantly, to reveal the kinetic property of the single-molecular junction. These results suggested that combining a measurement of the single-molecule conductance and statistical analysis is a promising method to uncover the kinetic properties of the single-molecule junction.

  4. A Starting Point for Fluorescence-Based Single-Molecule Measurements in Biomolecular Research

    Directory of Open Access Journals (Sweden)

    Alexander Gust

    2014-09-01

    Full Text Available Single-molecule fluorescence techniques are ideally suited to provide information about the structure-function-dynamics relationship of a biomolecule as static and dynamic heterogeneity can be easily detected. However, what type of single-molecule fluorescence technique is suited for which kind of biological question and what are the obstacles on the way to a successful single-molecule microscopy experiment? In this review, we provide practical insights into fluorescence-based single-molecule experiments aiming for scientists who wish to take their experiments to the single-molecule level. We especially focus on fluorescence resonance energy transfer (FRET experiments as these are a widely employed tool for the investigation of biomolecular mechanisms. We will guide the reader through the most critical steps that determine the success and quality of diffusion-based confocal and immobilization-based total internal reflection fluorescence microscopy. We discuss the specific chemical and photophysical requirements that make fluorescent dyes suitable for single-molecule fluorescence experiments. Most importantly, we review recently emerged photoprotection systems as well as passivation and immobilization strategies that enable the observation of fluorescently labeled molecules under biocompatible conditions. Moreover, we discuss how the optical single-molecule toolkit has been extended in recent years to capture the physiological complexity of a cell making it even more relevant for biological research.

  5. Single-molecule study of full-length NaChBac by planar lipid bilayer recording.

    Directory of Open Access Journals (Sweden)

    Andrew Jo

    Full Text Available Planar lipid bilayer device, alternatively known as BLM, is a powerful tool to study functional properties of conducting membrane proteins such as ion channels and porins. In this work, we used BLM to study the prokaryotic voltage-gated sodium channel (Nav NaChBac in a well-defined membrane environment. Navs are an essential component for the generation and propagation of electric signals in excitable cells. The successes in the biochemical, biophysical and crystallographic studies on prokaryotic Navs in recent years has greatly promoted the understanding of the molecular mechanism that underlies these proteins and their eukaryotic counterparts. In this work, we investigated the single-molecule conductance and ionic selectivity behavior of NaChBac. Purified NaChBac protein was first reconstituted into lipid vesicles, which is subsequently incorporated into planar lipid bilayer by fusion. At single-molecule level, we were able to observe three distinct long-lived conductance sub-states of NaChBac. Change in the membrane potential switches on the channel mainly by increasing its opening probability. In addition, we found that individual NaChBac has similar permeability for Na+, K+, and Ca2+. The single-molecule behavior of the full-length protein is essentially highly stochastic. Our results show that planar lipid bilayer device can be used to study purified ion channels at single-molecule level in an artificial environment, and such studies can reveal new protein properties that are otherwise not observable in in vivo ensemble studies.

  6. Single molecules and single nanoparticles as windows to the nanoscale

    Science.gov (United States)

    Caldarola, Martín; Orrit, Michel

    2018-05-01

    Since the first optical detection of single molecules, they have been used as nanometersized optical sensors to explore the physical properties of materials and light-matter interaction at the nanoscale. Understanding nanoscale properties of materials is fundamental for the development of new technology that requires precise control of atoms and molecules when the quantum nature of matter cannot be ignored. In the following lines, we illustrate this journey into nanoscience with some experiments from our group.

  7. Long-wavelength phonons and the condensate in superfluid 4He

    International Nuclear Information System (INIS)

    Olinto, A.C.

    1987-08-01

    From Ward identities that take into account the condensate reservoir, the velocity of long-wavelength phonons is obtained as a function of the condensate fraction in the shielded potential approximation. The results are in good agreement with superfluid 4 He data. (Author) [pt

  8. Alternative types of molecule-decorated atomic chains in Au–CO–Au single-molecule junctions

    Directory of Open Access Journals (Sweden)

    Zoltán Balogh

    2015-06-01

    Full Text Available We investigate the formation and evolution of Au–CO single-molecule break junctions. The conductance histogram exhibits two distinct molecular configurations, which are further investigated by a combined statistical analysis. According to conditional histogram and correlation analysis these molecular configurations show strong anticorrelations with each other and with pure Au monoatomic junctions and atomic chains. We identify molecular precursor configurations with somewhat higher conductance, which are formed prior to single-molecule junctions. According to detailed length analysis two distinct types of molecule-affected chain-formation processes are observed, and we compare these results to former theoretical calculations considering bridge- and atop-type molecular configurations where the latter has reduced conductance due to destructive Fano interference.

  9. Quantum dots versus organic fluorophores in fluorescent deep-tissue imaging--merits and demerits.

    Science.gov (United States)

    Bakalova, Rumiana; Zhelev, Zhivko; Gadjeva, Veselina

    2008-12-01

    The use of fluorescence in deep-tissue imaging is rapidly expanding in last several years. The progress in fluorescent molecular probes and fluorescent imaging techniques gives an opportunity to detect single cells and even molecular targets in live organisms. The highly sensitive and high-speed fluorescent molecular sensors and detection devices allow the application of fluorescence in functional imaging. With the development of novel bright fluorophores based on nanotechnologies and 3D fluorescence scanners with high spatial and temporal resolution, the fluorescent imaging has a potential to become an alternative of the other non-invasive imaging techniques as magnetic resonance imaging, positron-emission tomography, X-ray, computing tomography. The fluorescent imaging has also a potential to give a real map of human anatomy and physiology. The current review outlines the advantages of fluorescent nanoparticles over conventional organic dyes in deep-tissue imaging in vivo and defines the major requirements to the "perfect fluorophore". The analysis proceeds from the basic principles of fluorescence and major characteristics of fluorophores, light-tissue interactions, and major limitations of fluorescent deep-tissue imaging. The article is addressed to a broad readership - from specialists in this field to university students.

  10. Subducted slabs and lateral viscosity variations: effects on the long-wavelength geoid

    Science.gov (United States)

    Tosi, Nicola; Čadek, Ondřej; Martinec, Zdeněk

    2009-11-01

    The characteristic broad local maxima exhibited by the long-wavelength geoid over subduction zones are investigated with a numerical model of mantle flow. In a spherical axisymmetric geometry, a synthetic model of buoyancy driven subduction is used to test the effects on the geoid caused by the depth of penetration of the lithosphere into the mantle, by the viscosity stratification and by lateral viscosity variations (LVV) in the lithosphere, upper and lower mantle. The presence of anomalous slab density in the lower mantle guarantees geoid amplitudes comparable with the observations, favouring the picture of slabs that penetrate the transition zone and sink into the deep mantle. The viscosity of the lower mantle controls the long-wavelength geoid to the first order, ensuring a clear positive signal when it is at least 30-times greater than the upper-mantle viscosity. The presence of LVV in the lithosphere, in the form of weak plate margins, helps to increase the contribution of the surface topography, causing a pronounced reduction of the geoid. Localized LVV associated with the cold slab play a secondary role if they are in the upper mantle. On the other hand, highly viscous slabs in the lower mantle exert a large influence on the geoid. They cause its amplitude to increase dramatically, way beyond the values typically observed over subduction zones. Long-wavelength flow becomes less vigorous as the slab viscosity increases. Deformation in the upper mantle becomes more localized and power is transferred to short wavelengths, causing the long-wavelength surface topography to diminish and the total geoid to increase. Slabs may be then weakened in the lower mantle or retain their high viscosity while other mechanisms act to lower the geoid. It is shown that a phase change from perovskite to post-perovskite above the core-mantle boundary can cause the geoid to reduce significantly, thereby helping to reconcile models and observations.

  11. Single-molecule analysis of DNA replication in Xenopus egg extracts

    NARCIS (Netherlands)

    Yardimci, Hasan; Loveland, Anna B.; van Oijen, Antoine M.; Walter, Johannes C.; Mechali, Marcel

    The recent advent in single-molecule imaging and manipulation methods has made a significant impact on the understanding of molecular mechanisms underlying many essential cellular processes. Single-molecule techniques such as electron microscopy and DNA fiber assays have been employed to study the

  12. Single Molecule Spectroscopy on Photosynthetic Pigment-Protein Complexes

    CERN Document Server

    Jelezko, F; Schuler, S; Thews, E; Tietz, C; Wechsler, A; Wrachtrup, J

    2001-01-01

    Single molecule spectroscopy was applied to unravel the energy transfer pathway in photosynthetic pigment-protein complexes. Detailed analysis of excitation and fluorescence emission spectra has been made for peripheral plant antenna LHC II and Photosystem I from cyanobacterium Synechococcus elongatus. Optical transitions of individual pigments were resolved under nonselective excitation of antenna chlorophylls. High-resolution fluorescence spectroscopy of individual plant antenna LHC II indicates that at low temperatures, the excitation energy is localized on the red-most Chl a pool absorbing at 680 nm. More than one pigment molecule is responsible for the fluorescence emission of the LHC II trimer. The spectral lines of single Chl a molecules absorbing at 675 nm are broadened because of the Foerster energy transfer towards the red-most pigments. Low-temperature spectroscopy on single PS I trimers indicates that two subgroups of pigments, which are present in the red antenna pool, differ by the strength of t...

  13. On very-large-scale motions (VLSMs) and long-wavelength patterns in turbine wakes

    Science.gov (United States)

    Önder, Asim; Meyers, Johan

    2017-11-01

    It is now widely accepted that very-large-scale motions (VLSMs) are a prominent feature of thermally-neutral atmospheric boundary layers (ABL). Up to date, the influence of these very long active motions on wind-energy harvesting is not sufficiently explored. This work is an effort in this direction. We perform large-eddy simulation of a turbine row operating under neutral conditions. The ABL data is produced separately in a very long domain of 240 δ . VLSMs are isolated from smaller-scale ABL and wake motions using a spectral cutoff at streamwise wavelength λx = 3.125 δ . Reynolds-averaging of low-pass filtered fields shows that the interaction of VLSMs and turbines produce very-long-wavelength motions in the wake region, which contain about 20 % of the Reynolds-shear stress, and 30 % of the streamwise kinetic energy. A conditional analysis of filtered fields further reveals that these long-wavelength wakes are produced by modification of very long velocity streaks in ABL. In particular, the turbine row acts as a sharp boundary between low and high velocity streaks, and accompanying roller structures remain relatively unaffected. This reorganization creates a two-way flux towards the wake region, which elucidates the side-way domination in turbulent transport. The authors acknowledg funding from ERC Grant No 306471.

  14. Single-Molecule Interfacial Electron Transfer

    Energy Technology Data Exchange (ETDEWEB)

    Ho, Wilson [Univ. of California, Irvine, CA (United States)

    2018-02-03

    Interfacial electron transfer (ET) plays an important role in many chemical and biological processes. Specifically, interfacial ET in TiO2-based systems is important to solar energy technology, catalysis, and environmental remediation technology. However, the microscopic mechanism of interfacial ET is not well understood with regard to atomic surface structure, molecular structure, bonding, orientation, and motion. In this project, we used two complementary methodologies; single-molecule fluorescence spectroscopy, and scanning-tunneling microscopy and spectroscopy (STM and STS) to address this scientific need. The goal of this project was to integrate these techniques and measure the molecular dependence of ET between adsorbed molecules and TiO2 semiconductor surfaces and the ET induced reactions such as the splitting of water. The scanning probe techniques, STM and STS, are capable of providing the highest spatial resolution but not easily time-resolved data. Single-molecule fluorescence spectroscopy is capable of good time resolution but requires further development to match the spatial resolution of the STM. The integrated approach involving Peter Lu at Bowling Green State University (BGSU) and Wilson Ho at the University of California, Irvine (UC Irvine) produced methods for time and spatially resolved chemical imaging of interfacial electron transfer dynamics and photocatalytic reactions. An integral aspect of the joint research was a significant exchange of graduate students to work at the two institutions. This project bridged complementary approaches to investigate a set of common problems by working with the same molecules on a variety of solid surfaces, but using appropriate techniques to probe under ambient (BGSU) and ultrahigh vacuum (UCI) conditions. The molecular level understanding of the fundamental interfacial electron transfer processes obtained in this joint project will be important for developing efficient light harvesting

  15. Long-wavelength instability of periodic flows and whistler waves in electron magnetohydrodynamics

    International Nuclear Information System (INIS)

    Lakhin, V.P.; Levchenko, V.D.

    2003-01-01

    Stability analysis of periodic flows and whistlers with respect to long-wavelength perturbations within the framework of dissipative electron magnetohydrodynamics (EMHD) based on two-scale asymptotic expansion technique is presented. Several types of flows are considered: two-dimensional Kolmogorov-like flow, helical flow, and anisotropic helical flow. It is shown hat the destabilizing effect on the long-wavelength perturbations is due to either the negative resistivity effect related to flow anisotropy or α-like effect to its micro helicity. The criteria of the corresponding instabilities are obtained. Numerical simulations of EMHD equations with the initial conditions corresponding to two types of periodic flows are presented. (author)

  16. Room temperature excitation spectroscopy of single quantum dots

    Directory of Open Access Journals (Sweden)

    Christian Blum

    2011-08-01

    Full Text Available We report a single molecule detection scheme to investigate excitation spectra of single emitters at room temperature. We demonstrate the potential of single emitter photoluminescence excitation spectroscopy by recording excitation spectra of single CdSe nanocrystals over a wide spectral range of 100 nm. The spectra exhibit emission intermittency, characteristic of single emitters. We observe large variations in the spectra close to the band edge, which represent the individual heterogeneity of the observed quantum dots. We also find specific excitation wavelengths for which the single quantum dots analyzed show an increased propensity for a transition to a long-lived dark state. We expect that the additional capability of recording excitation spectra at room temperature from single emitters will enable insights into the photophysics of emitters that so far have remained inaccessible.

  17. Single-molecule packaging initiation in real time by a viral DNA packaging machine from bacteriophage T4.

    Science.gov (United States)

    Vafabakhsh, Reza; Kondabagil, Kiran; Earnest, Tyler; Lee, Kyung Suk; Zhang, Zhihong; Dai, Li; Dahmen, Karin A; Rao, Venigalla B; Ha, Taekjip

    2014-10-21

    Viral DNA packaging motors are among the most powerful molecular motors known. A variety of structural, biochemical, and single-molecule biophysical approaches have been used to understand their mechanochemistry. However, packaging initiation has been difficult to analyze because of its transient and highly dynamic nature. Here, we developed a single-molecule fluorescence assay that allowed visualization of packaging initiation and reinitiation in real time and quantification of motor assembly and initiation kinetics. We observed that a single bacteriophage T4 packaging machine can package multiple DNA molecules in bursts of activity separated by long pauses, suggesting that it switches between active and quiescent states. Multiple initiation pathways were discovered including, unexpectedly, direct DNA binding to the capsid portal followed by recruitment of motor subunits. Rapid succession of ATP hydrolysis was essential for efficient initiation. These observations have implications for the evolution of icosahedral viruses and regulation of virus assembly.

  18. Synthesis and photophysical properties of a series of cyclopenta[b]naphthalene solvatochromic fluorophores.

    Science.gov (United States)

    Benedetti, Erica; Kocsis, Laura S; Brummond, Kay M

    2012-08-01

    The synthesis and photophysical properties of a series of naphthalene-containing solvatochromic fluorophores are described within. These novel fluorophores are prepared using a microwave-assisted dehydrogenative Diels-Alder reaction of styrene, followed by a palladium-catalyzed cross coupling reaction to install an electron donating amine group. The new fluorophores are structurally related to Prodan. Photophysical properties of the new fluorophores were studied and intriguing solvatochromic behavior was observed. For most of these fluorophores, high quantum yields (60-99%) were observed in methylene chloride in addition to large Stokes shifts (95-226 nm) in this same solvent. As the solvent polarity increased, so did the observed Stokes shift with one derivative displaying a Stokes shift of ~300 nm in ethanol. All fluorophore emission maxima, and nearly all absorption maxima were significantly red-shifted when compared to Prodan. Shifting the absorption and emission maxima of a fluorophore into the visible region increases its utility in biological applications. Moreover, the cyclopentane portion of the fluorophore structure provides an attachment point for biomolecules that will minimize disruptions of the photophysical properties.

  19. Metal-Controlled Magnetoresistance at Room Temperature in Single-Molecule Devices.

    Science.gov (United States)

    Aragonès, Albert C; Aravena, Daniel; Valverde-Muñoz, Francisco J; Real, José Antonio; Sanz, Fausto; Díez-Pérez, Ismael; Ruiz, Eliseo

    2017-04-26

    The appropriate choice of the transition metal complex and metal surface electronic structure opens the possibility to control the spin of the charge carriers through the resulting hybrid molecule/metal spinterface in a single-molecule electrical contact at room temperature. The single-molecule conductance of a Au/molecule/Ni junction can be switched by flipping the magnetization direction of the ferromagnetic electrode. The requirements of the molecule include not just the presence of unpaired electrons: the electronic configuration of the metal center has to provide occupied or empty orbitals that strongly interact with the junction metal electrodes and that are close in energy to their Fermi levels for one of the electronic spins only. The key ingredient for the metal surface is to provide an efficient spin texture induced by the spin-orbit coupling in the topological surface states that results in an efficient spin-dependent interaction with the orbitals of the molecule. The strong magnetoresistance effect found in this kind of single-molecule wire opens a new approach for the design of room-temperature nanoscale devices based on spin-polarized currents controlled at molecular level.

  20. Long Wavelength Electromagnetic Light Bullets Generated by a 10.6 micron CO2 Ultrashort Pulsed Source

    Science.gov (United States)

    2016-11-29

    AFRL-AFOSR-VA-TR-2016-0365 Long Wavelength Electromagnetic Light Bullets Generated by a 10.6 micron CO2 Ultrashort Pulsed Source Jerome Moloney...SUBTITLE "Long Wavelength Electromagnetic Light Bullets Generated by a 10.6 micron CO2 Ultrashort Pulsed Source 5a. CONTRACT NUMBER FA9550-15-1-0272 5b...Wavelength Electromagnetic Light Bullets Generated by a 10 µm CO2 Ultrashort Pulsed Source Grant/Contract Number AFOSR assigned control number. It must

  1. The Conformational Dynamics of Cas9 Governing DNA Cleavage Are Revealed by Single-Molecule FRET

    Directory of Open Access Journals (Sweden)

    Mengyi Yang

    2018-01-01

    Full Text Available Summary: Off-target binding and cleavage by Cas9 pose major challenges in its application. How the conformational dynamics of Cas9 govern its nuclease activity under on- and off-target conditions remains largely unknown. Here, using intra-molecular single-molecule fluorescence resonance energy transfer measurements, we revealed that Cas9 in apo, sgRNA-bound, and dsDNA/sgRNA-bound forms spontaneously transits among three major conformational states, mainly reflecting significant conformational mobility of the catalytic HNH domain. We also uncovered surprising long-range allosteric communication between the HNH domain and the RNA/DNA heteroduplex at the PAM-distal end to ensure correct positioning of the catalytic site, which demonstrated that a unique proofreading mechanism served as the last checkpoint before DNA cleavage. Several Cas9 residues were likely to mediate the allosteric communication and proofreading step. Modulating interactions between Cas9 and heteroduplex at the PAM-distal end by introducing mutations on these sites provides an alternative route to improve and optimize the CRISPR/Cas9 toolbox. : Yang et al. revealed significant conformational dynamics of Cas9 at global and local scales using single-molecule FRET. They uncovered surprising long-range allosteric communication between the HNH nuclease domain and the RNA/DNA heteroduplex at the PAM-distal end that serves as a proofreading checkpoint to govern the nuclease activity and specificity of Cas9. Keywords: CRISPR, Cas9, single-molecule, FRET, conformational dynamics, proofreading, off-target, allosteric communication, genome editing

  2. Single-Molecule Chemistry with Surface- and Tip-Enhanced Raman Spectroscopy.

    Science.gov (United States)

    Zrimsek, Alyssa B; Chiang, Naihao; Mattei, Michael; Zaleski, Stephanie; McAnally, Michael O; Chapman, Craig T; Henry, Anne-Isabelle; Schatz, George C; Van Duyne, Richard P

    2017-06-14

    Single-molecule (SM) surface-enhanced Raman spectroscopy (SERS) and tip-enhanced Raman spectroscopy (TERS) have emerged as analytical techniques for characterizing molecular systems in nanoscale environments. SERS and TERS use plasmonically enhanced Raman scattering to characterize the chemical information on single molecules. Additionally, TERS can image single molecules with subnanometer spatial resolution. In this review, we cover the development and history of SERS and TERS, including the concept of SERS hot spots and the plasmonic nanostructures necessary for SM detection, the past and current methodologies for verifying SMSERS, and investigations into understanding the signal heterogeneities observed with SMSERS. Moving on to TERS, we cover tip fabrication and the physical origins of the subnanometer spatial resolution. Then, we highlight recent advances of SMSERS and TERS in fields such as electrochemistry, catalysis, and SM electronics, which all benefit from the vibrational characterization of single molecules. SMSERS and TERS provide new insights on molecular behavior that would otherwise be obscured in an ensemble-averaged measurement.

  3. A New Theoretical Approach to Single-Molecule Fluorescence Optical Studies of RNA Dynamics

    International Nuclear Information System (INIS)

    Zhao Xinghai; Shan Guangcun; Bao Shuying

    2011-01-01

    Single-molecule fluorescence spectroscopy in condensed phases has many important chemical and biological applications. The single-molecule fluorescence measurements contain information about conformational dynamics on a vast range of time scales. Based on the data analysis protocols methodology proposed by X. Sunney Xie, the theoretical study here mainly focuses on the single-molecule studies of single RNA with interconversions among different conformational states, to with a single FRET pair attached. We obtain analytical expressions for fluorescence lifetime correlation functions that relate changes in fluorescence lifetime to the distance-dependent FRET mechanism within the context of the Smoluchowski diffusion model. The present work establishes useful guideline for the single-molecule studies of biomolecules to reveal the complicated folding dynamics of single RNA molecules at nanometer scale.

  4. Nonlinear and Nonsymmetric Single-Molecule Electronic Properties Towards Molecular Information Processing.

    Science.gov (United States)

    Tamaki, Takashi; Ogawa, Takuji

    2017-09-05

    This review highlights molecular design for nonlinear and nonsymmetric single-molecule electronic properties such as rectification, negative differential resistance, and switching, which are important components of future single-molecule information processing devices. Perspectives on integrated "molecular circuits" are also provided. Nonlinear and nonsymmetric single-molecule electronics can be designed by utilizing (1) asymmetric molecular cores, (2) asymmetric anchoring groups, (3) an asymmetric junction environment, and (4) asymmetric electrode materials. This review mainly focuses on the design of molecular cores.

  5. Estimating single molecule conductance from spontaneous evolution of a molecular contact

    Science.gov (United States)

    Gil, M.; Malinowski, T.; Iazykov, M.; Klein, H. R.

    2018-03-01

    We present an original method to estimate the conductivity of a single molecule anchored to nanometric-sized metallic electrodes, using a Mechanically Controlled Break Junction operated at room temperature in the liquid. We record the conductance through the metal/molecules/metal nanocontact while keeping the metallic electrodes at a fixed distance. Taking advantage of thermal diffusion and electromigration, we let the contact naturally explore the more stable configurations around a chosen conductance value. The conductance of a single molecule is estimated from a statistical analysis of raw conductance and conductance standard deviation data for molecular contacts containing up to 14 molecules. The single molecule conductance values are interpreted as time-averaged conductance of an ensemble of conformers at thermal equilibrium.

  6. Single-Molecule Light-Sheet Imaging of Suspended T Cells.

    Science.gov (United States)

    Ponjavic, Aleks; McColl, James; Carr, Alexander R; Santos, Ana Mafalda; Kulenkampff, Klara; Lippert, Anna; Davis, Simon J; Klenerman, David; Lee, Steven F

    2018-05-08

    Adaptive immune responses are initiated by triggering of the T cell receptor. Single-molecule imaging based on total internal reflection fluorescence microscopy at coverslip/basal cell interfaces is commonly used to study this process. These experiments have suggested, unexpectedly, that the diffusional behavior and organization of signaling proteins and receptors may be constrained before activation. However, it is unclear to what extent the molecular behavior and cell state is affected by the imaging conditions, i.e., by the presence of a supporting surface. In this study, we implemented single-molecule light-sheet microscopy, which enables single receptors to be directly visualized at any plane in a cell to study protein dynamics and organization in live, resting T cells. The light sheet enabled the acquisition of high-quality single-molecule fluorescence images that were comparable to those of total internal reflection fluorescence microscopy. By comparing the apical and basal surfaces of surface-contacting T cells using single-molecule light-sheet microscopy, we found that most coated-glass surfaces and supported lipid bilayers profoundly affected the diffusion of membrane proteins (T cell receptor and CD45) and that all the surfaces induced calcium influx to various degrees. Our results suggest that, when studying resting T cells, surfaces are best avoided, which we achieve here by suspending cells in agarose. Copyright © 2018. Published by Elsevier Inc.

  7. Graphical models for inferring single molecule dynamics

    Directory of Open Access Journals (Sweden)

    Gonzalez Ruben L

    2010-10-01

    Full Text Available Abstract Background The recent explosion of experimental techniques in single molecule biophysics has generated a variety of novel time series data requiring equally novel computational tools for analysis and inference. This article describes in general terms how graphical modeling may be used to learn from biophysical time series data using the variational Bayesian expectation maximization algorithm (VBEM. The discussion is illustrated by the example of single-molecule fluorescence resonance energy transfer (smFRET versus time data, where the smFRET time series is modeled as a hidden Markov model (HMM with Gaussian observables. A detailed description of smFRET is provided as well. Results The VBEM algorithm returns the model’s evidence and an approximating posterior parameter distribution given the data. The former provides a metric for model selection via maximum evidence (ME, and the latter a description of the model’s parameters learned from the data. ME/VBEM provide several advantages over the more commonly used approach of maximum likelihood (ML optimized by the expectation maximization (EM algorithm, the most important being a natural form of model selection and a well-posed (non-divergent optimization problem. Conclusions The results demonstrate the utility of graphical modeling for inference of dynamic processes in single molecule biophysics.

  8. Aperture Mask for Unambiguous Parity Determination in Long Wavelength Imagers

    Science.gov (United States)

    Bos, Brent

    2011-01-01

    A document discusses a new parity pupil mask design that allows users to unambiguously determine the image space coordinate system of all the James Webb Space Telescope (JWST) science instruments by using two out-of-focus images. This is an improvement over existing mask designs that could not completely eliminate the coordinate system parity ambiguity at a wavelength of 5.6 microns. To mitigate the problem of how the presence of diffraction artifacts can obscure the pupil mask detail, this innovation has been created with specifically designed edge features so that the image space coordinate system parity can be determined in the presence of diffraction, even at long wavelengths.

  9. Deep learning for single-molecule science

    Science.gov (United States)

    Albrecht, Tim; Slabaugh, Gregory; Alonso, Eduardo; Al-Arif, SM Masudur R.

    2017-10-01

    Exploring and making predictions based on single-molecule data can be challenging, not only due to the sheer size of the datasets, but also because a priori knowledge about the signal characteristics is typically limited and poor signal-to-noise ratio. For example, hypothesis-driven data exploration, informed by an expectation of the signal characteristics, can lead to interpretation bias or loss of information. Equally, even when the different data categories are known, e.g., the four bases in DNA sequencing, it is often difficult to know how to make best use of the available information content. The latest developments in machine learning (ML), so-called deep learning (DL) offer interesting, new avenues to address such challenges. In some applications, such as speech and image recognition, DL has been able to outperform conventional ML strategies and even human performance. However, to date DL has not been applied much in single-molecule science, presumably in part because relatively little is known about the ‘internal workings’ of such DL tools within single-molecule science as a field. In this Tutorial, we make an attempt to illustrate in a step-by-step guide how one of those, a convolutional neural network (CNN), may be used for base calling in DNA sequencing applications. We compare it with a SVM as a more conventional ML method, and discuss some of the strengths and weaknesses of the approach. In particular, a ‘deep’ neural network has many features of a ‘black box’, which has important implications on how we look at and interpret data.

  10. [Research on the temperature field detection method of hot forging based on long-wavelength infrared spectrum].

    Science.gov (United States)

    Zhang, Yu-Cun; Wei, Bin; Fu, Xian-Bin

    2014-02-01

    A temperature field detection method based on long-wavelength infrared spectrum for hot forging is proposed in the present paper. This method combines primary spectrum pyrometry and three-stage FP-cavity LCTF. By optimizing the solutions of three group nonlinear equations in the mathematical model of temperature detection, the errors are reduced, thus measuring results will be more objective and accurate. Then the system of three-stage FP-cavity LCTF was designed on the principle of crystal birefringence. The system realized rapid selection of any wavelength in a certain wavelength range. It makes the response of the temperature measuring system rapid and accurate. As a result, without the emissivity of hot forging, the method can acquire exact information of temperature field and effectively suppress the background light radiation around the hot forging and ambient light that impact the temperature detection accuracy. Finally, the results of MATLAB showed that the infrared spectroscopy through the three-stage FP-cavity LCTF could meet the requirements of design. And experiments verified the feasibility of temperature measuring method. Compared with traditional single-band thermal infrared imager, the accuracy of measuring result was improved.

  11. Vibrationally coupled electron transport through single-molecule junctions

    Energy Technology Data Exchange (ETDEWEB)

    Haertle, Rainer

    2012-04-26

    Single-molecule junctions are among the smallest electric circuits. They consist of a molecule that is bound to a left and a right electrode. With such a molecular nanocontact, the flow of electrical currents through a single molecule can be studied and controlled. Experiments on single-molecule junctions show that a single molecule carries electrical currents that can even be in the microampere regime. Thereby, a number of transport phenomena have been observed, such as, for example, diode- or transistor-like behavior, negative differential resistance and conductance switching. An objective of this field, which is commonly referred to as molecular electronics, is to relate these transport phenomena to the properties of the molecule in the contact. To this end, theoretical model calculations are employed, which facilitate an understanding of the underlying transport processes and mechanisms. Thereby, one has to take into account that molecules are flexible structures, which respond to a change of their charge state by a profound reorganization of their geometrical structure or may even dissociate. It is thus important to understand the interrelation between the vibrational degrees of freedom of a singlemolecule junction and the electrical current flowing through the contact. In this thesis, we investigate vibrational effects in electron transport through singlemolecule junctions. For these studies, we calculate and analyze transport characteristics of both generic and first-principles based model systems of a molecular contact. To this end, we employ a master equation and a nonequilibrium Green's function approach. Both methods are suitable to describe this nonequilibrium transport problem and treat the interactions of the tunneling electrons on the molecular bridge non-perturbatively. This is particularly important with respect to the vibrational degrees of freedom, which may strongly interact with the tunneling electrons. We show in detail that the resulting

  12. Dual Mode Fluorophore-Doped Nickel Nitrilotriacetic Acid-Modified Silica Nanoparticles Combine Histidine-Tagged Protein Purification with Site-Specific Fluorophore Labeling

    OpenAIRE

    Kim, Sung Hoon; Jeyakumar, M.; Katzenellenbogen, John A.

    2007-01-01

    We present the first example of a fluorophore-doped nickel chelate surface- modified silica nanoparticle that functions in a dual mode, combining histidine-tagged protein purification with site-specific fluorophore labeling. Tetramethylrhodamine (TMR)-doped silica nanoparticles, estimated to contain 700–900 TMRs per ca. 23-nm particle, were surface modified with nitrilotriacetic acid (NTA), producing TMR-SiO2-NTA-Ni+2. Silica-embedded TMR retains very high quantum yield, is resistant to quenc...

  13. Repurposing a Benchtop Centrifuge for High-Throughput Single-Molecule Force Spectroscopy.

    Science.gov (United States)

    Yang, Darren; Wong, Wesley P

    2018-01-01

    We present high-throughput single-molecule manipulation using a benchtop centrifuge, overcoming limitations common in other single-molecule approaches such as high cost, low throughput, technical difficulty, and strict infrastructure requirements. An inexpensive and compact Centrifuge Force Microscope (CFM) adapted to a commercial centrifuge enables use by nonspecialists, and integration with DNA nanoswitches facilitates both reliable measurements and repeated molecular interrogation. Here, we provide detailed protocols for constructing the CFM, creating DNA nanoswitch samples, and carrying out single-molecule force measurements.

  14. Hot-plasma decoupling condition for long-wavelength modes

    International Nuclear Information System (INIS)

    Berk, H.L.; Van Dam, J.W.; Spong, D.

    1982-10-01

    The stability of layer modes is analyzed for z-pinch and bumpy cylinder models. These modes are long wavelength across the layer and flute-like along the field line. The stability condition can be expressed in terms of the ratio of hot to core plasma density. It is shown that to achieve conditions close to the Nelson, Lee-Van Dam core beta limit, one needs a considerably smaller hot to core plasma density than is required to achieve stability at zero core beta

  15. Holography and coherent diffraction with low-energy electrons: A route towards structural biology at the single molecule level.

    Science.gov (United States)

    Latychevskaia, Tatiana; Longchamp, Jean-Nicolas; Escher, Conrad; Fink, Hans-Werner

    2015-12-01

    The current state of the art in structural biology is led by NMR, X-ray crystallography and TEM investigations. These powerful tools however all rely on averaging over a large ensemble of molecules. Here, we present an alternative concept aiming at structural analysis at the single molecule level. We show that by combining electron holography and coherent diffraction imaging estimations concerning the phase of the scattered wave become needless as the phase information is extracted from the data directly and unambiguously. Performed with low-energy electrons the resolution of this lens-less microscope is just limited by the De Broglie wavelength of the electron wave and the numerical aperture, given by detector geometry. In imaging freestanding graphene, a resolution of 2Å has been achieved revealing the 660.000 unit cells of the graphene sheet from a single data set. Once applied to individual biomolecules the method shall ultimately allow for non-destructive imaging and imports the potential to distinguish between different conformations of proteins with atomic resolution. Copyright © 2015. Published by Elsevier B.V.

  16. Real-time single-molecule imaging of quantum interference.

    Science.gov (United States)

    Juffmann, Thomas; Milic, Adriana; Müllneritsch, Michael; Asenbaum, Peter; Tsukernik, Alexander; Tüxen, Jens; Mayor, Marcel; Cheshnovsky, Ori; Arndt, Markus

    2012-03-25

    The observation of interference patterns in double-slit experiments with massive particles is generally regarded as the ultimate demonstration of the quantum nature of these objects. Such matter-wave interference has been observed for electrons, neutrons, atoms and molecules and, in contrast to classical physics, quantum interference can be observed when single particles arrive at the detector one by one. The build-up of such patterns in experiments with electrons has been described as the "most beautiful experiment in physics". Here, we show how a combination of nanofabrication and nano-imaging allows us to record the full two-dimensional build-up of quantum interference patterns in real time for phthalocyanine molecules and for derivatives of phthalocyanine molecules, which have masses of 514 AMU and 1,298 AMU respectively. A laser-controlled micro-evaporation source was used to produce a beam of molecules with the required intensity and coherence, and the gratings were machined in 10-nm-thick silicon nitride membranes to reduce the effect of van der Waals forces. Wide-field fluorescence microscopy detected the position of each molecule with an accuracy of 10 nm and revealed the build-up of a deterministic ensemble interference pattern from single molecules that arrived stochastically at the detector. In addition to providing this particularly clear demonstration of wave-particle duality, our approach could also be used to study larger molecules and explore the boundary between quantum and classical physics.

  17. Short wavelength FELs using the SLAC linac

    International Nuclear Information System (INIS)

    Winick, H.; Bane, K.; Boyce, R.

    1993-08-01

    Recent technological developments have opened the possibility to construct a device which we call a Linac Coherent Light Source (LCLS); a fourth generation light source, with brightness, coherence, and peak power far exceeding other sources. Operating on the principle of the free electron laser (FEL), the LCLS would extend the range of FEL operation to much aborter wavelength than the 240 mn that has so far been reached. We report the results of studies of the use of the SLAC linac to drive an LCLS at wavelengths from about 3-100 nm initially and possibly even shorter wavelengths in the future. Lasing would be achieved in a single pass of a low emittance, high peak current, high energy electron beam through a long undulator. Most present FELs use an optical cavity to build up the intensity of the light to achieve lasing action in a low gain oscillator configuration. By eliminating the optical cavity, which is difficult to make at short wavelengths, laser action can be extended to shorter wavelengths by Self-Amplified-Spontaneous-Emission (SASE), or by harmonic generation from a longer wavelength seed laser. Short wavelength, single pass lasers have been extensively studied at several laboratories and at recent workshops

  18. Photoinduced nuclear spin conversion of methyl groups of single molecules

    International Nuclear Information System (INIS)

    Sigl, A.

    2007-01-01

    A methyl group is an outstanding quantum system due to its special symmetry properties. The threefold rotation around one of its bond is isomorphic to the group of even permutations of the remaining protons, a property which imposes severe quantum restrictions on the system, for instance a strict correlation of rotational states with nuclear spin states. The resulting long lifetimes of the rotational tunneling states of the methyl group can be exploited for applying certain high resolution optical techniques, like hole burning or single molecule spectroscopy to optically switch the methyl group from one tunneling state to another therebye changing the nuclear spin of the protons. One goal of the thesis was to perform this switching in single methyl groups. To this end the methyl group was attached to a chromophoric system, in the present case terrylene, which is well suited for single molecule spectroscopy as well as for hole burning. Experiments were performed with the bare terrylene molecule in a hexadecane lattice which served as a reference system, with alphamethyl terrylene and betamethyl terrylene, both embedded in hexadecane, too. A single molecular probe is a highly sensitive detector for dynamic lattice instabilities. Already the bare terrylene probe showed a wealth of interesting local dynamic effects of the hexadecane lattice which could be well acounted for by the assumption of two nearly degenerate sites with rather different optical and thermal properties, all of which could be determined in a quantitative fashion. As to the methylated terrylene systems, the experiments verified that for betamethyl terrylene it is indeed possible to measure rotational tunneling events in single methyl groups. However, the spectral patterns obtained was much more complicated than expected pointing to the presence of three spectroscopically different methyl groups. In order to achieve a definite assignement, molecular mechanics simulations of the terrylene probes in the

  19. Development of new photon-counting detectors for single-molecule fluorescence microscopy

    Science.gov (United States)

    Michalet, X.; Colyer, R. A.; Scalia, G.; Ingargiola, A.; Lin, R.; Millaud, J. E.; Weiss, S.; Siegmund, Oswald H. W.; Tremsin, Anton S.; Vallerga, John V.; Cheng, A.; Levi, M.; Aharoni, D.; Arisaka, K.; Villa, F.; Guerrieri, F.; Panzeri, F.; Rech, I.; Gulinatti, A.; Zappa, F.; Ghioni, M.; Cova, S.

    2013-01-01

    Two optical configurations are commonly used in single-molecule fluorescence microscopy: point-like excitation and detection to study freely diffusing molecules, and wide field illumination and detection to study surface immobilized or slowly diffusing molecules. Both approaches have common features, but also differ in significant aspects. In particular, they use different detectors, which share some requirements but also have major technical differences. Currently, two types of detectors best fulfil the needs of each approach: single-photon-counting avalanche diodes (SPADs) for point-like detection, and electron-multiplying charge-coupled devices (EMCCDs) for wide field detection. However, there is room for improvements in both cases. The first configuration suffers from low throughput owing to the analysis of data from a single location. The second, on the other hand, is limited to relatively low frame rates and loses the benefit of single-photon-counting approaches. During the past few years, new developments in point-like and wide field detectors have started addressing some of these issues. Here, we describe our recent progresses towards increasing the throughput of single-molecule fluorescence spectroscopy in solution using parallel arrays of SPADs. We also discuss our development of large area photon-counting cameras achieving subnanosecond resolution for fluorescence lifetime imaging applications at the single-molecule level. PMID:23267185

  20. Molecular spintronics using single-molecule magnets

    Science.gov (United States)

    Bogani, Lapo; Wernsdorfer, Wolfgang

    2008-03-01

    A revolution in electronics is in view, with the contemporary evolution of the two novel disciplines of spintronics and molecular electronics. A fundamental link between these two fields can be established using molecular magnetic materials and, in particular, single-molecule magnets. Here, we review the first progress in the resulting field, molecular spintronics, which will enable the manipulation of spin and charges in electronic devices containing one or more molecules. We discuss the advantages over more conventional materials, and the potential applications in information storage and processing. We also outline current challenges in the field, and propose convenient schemes to overcome them.

  1. Modulation of intermolecular interactions in single-molecule magnets

    Science.gov (United States)

    Heroux, Katie Jeanne

    Polynuclear manganese clusters exhibiting interesting magnetic and quantum properties have been an area of intense research since the discovery of the first single-molecule magnet (SMM) in 1993. These molecules, below their blocking temperature, function as single-domain magnetic particles which exhibit classical macroscale magnetic properties as well as quantum mechanical phenomena such as quantum tunnelling of magnetization (QTM) and quantum phase interference. The union of classical and quantum behavior in these nanomaterials makes SMMs ideal candidates for high-density information storage and quantum computing. However, environmental coupling factors (nuclear spins, phonons, neighboring molecules) must be minimized if such applications are ever to be fully realized. The focus of this work is making small structural changes in well-known manganese SMMs in order to drastically enhance the overall magnetic and quantum properties of the system. Well-isolated molecules of high crystalline quality should lead to well-defined energetic and spectral properties as well. An advantage of SMMs over bulk magnetic materials is that they can be chemically altered from a "bottom-up" approach providing a synthetic tool for tuning magnetic properties. This systematic approach is utilized in the work presented herein by incorporating bulky ligands and/or counterions to "isolate" the magnetic core of [Mn4] dicubane SMMs. Reducing intermolecular interactions in the crystal lattice (neighboring molecules, solvate molecules, dipolar interactions) is an important step toward developing viable quantum computing devices. Detailed bulk magnetic studies as well as single crystal magnetization hysteresis and high-frequency EPR studies on these sterically-isolated complexes show enhanced, and sometimes even unexpected, quantum dynamics. The importance of intra- and intermolecular interactions remains a common theme throughout this work, extending to other SMMs of various topology including

  2. Towards single molecule biosensors using super-resolution fluorescence microscopy.

    Science.gov (United States)

    Lu, Xun; Nicovich, Philip R; Gaus, Katharina; Gooding, J Justin

    2017-07-15

    Conventional immunosensors require many binding events to give a single transducer output which represents the concentration of the analyte in the sample. Because of the requirements to selectively detect species in complex samples, immunosensing interfaces must allow immobilisation of antibodies while repelling nonspecific adsorption of other species. These requirements lead to quite sophisticated interfacial design, often with molecular level control, but we have no tools to characterise how well these interfaces work at the molecular level. The work reported herein is an initial feasibility study to show that antibody-antigen binding events can be monitored at the single molecule level using single molecule localisation microscopy (SMLM). The steps to achieve this first requires showing that indium tin oxide surfaces can be used for SMLM, then that these surfaces can be modified with self-assembled monolayers using organophosphonic acid derivatives, that the amount of antigens and antibodies on the surface can be controlled and monitored at the single molecule level and finally antibody binding to antigen modified surfaces can be monitored. The results show the amount of antibody that binds to an antigen modified surface is dependent on both the concentration of antigen on the surface and the concentration of antibody in solution. This study demonstrates the potential of SMLM for characterising biosensing interfaces and as the transducer in a massively parallel, wide field, single molecule detection scheme for quantitative analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Electrochemical Single-Molecule Transistors with Optimized Gate Coupling

    DEFF Research Database (Denmark)

    Osorio, Henrry M.; Catarelli, Samantha; Cea, Pilar

    2015-01-01

    Electrochemical gating at the single molecule level of viologen molecular bridges in ionic liquids is examined. Contrary to previous data recorded in aqueous electrolytes, a clear and sharp peak in the single molecule conductance versus electrochemical potential data is obtained in ionic liquids....... These data are rationalized in terms of a two-step electrochemical model for charge transport across the redox bridge. In this model the gate coupling in the ionic liquid is found to be fully effective with a modeled gate coupling parameter, ξ, of unity. This compares to a much lower gate coupling parameter...

  4. Effect of genomic long-range correlations on DNA persistence length: from theory to single molecule experiments.

    Science.gov (United States)

    Moukhtar, Julien; Faivre-Moskalenko, Cendrine; Milani, Pascale; Audit, Benjamin; Vaillant, Cedric; Fontaine, Emeline; Mongelard, Fabien; Lavorel, Guillaume; St-Jean, Philippe; Bouvet, Philippe; Argoul, Françoise; Arneodo, Alain

    2010-04-22

    Sequence dependency of DNA intrinsic bending properties has been emphasized as a possible key ingredient to in vivo chromatin organization. We use atomic force microscopy (AFM) in air and liquid to image intrinsically straight (synthetic), uncorrelated (hepatitis C RNA virus) and persistent long-range correlated (human) DNA fragments in various ionic conditions such that the molecules freely equilibrate on the mica surface before being captured in a particular conformation. 2D thermodynamic equilibrium is experimentally verified by a detailed statistical analysis of the Gaussian nature of the DNA bend angle fluctuations. We show that the worm-like chain (WLC) model, commonly used to describe the average conformation of long semiflexible polymers, reproduces remarkably well the persistence length estimates for the first two molecules as consistently obtained from (i) mean square end-to-end distance measurement and (ii) mean projection of the end-to-end vector on the initial orientation. Whatever the operating conditions (air or liquid, concentration of metal cations Mg(2+) and/or Ni(2+)), the persistence length found for the uncorrelated viral DNA underestimates the value obtained for the straight DNA. We show that this systematic difference is the signature of the presence of an uncorrelated structural intrinsic disorder in the hepatitis C virus (HCV) DNA fragment that superimposes on local curvatures induced by thermal fluctuations and that only the entropic disorder depends upon experimental conditions. In contrast, the WLC model fails to describe the human DNA conformations. We use a mean-field extension of the WLC model to account for the presence of long-range correlations (LRC) in the intrinsic curvature disorder of human genomic DNA: the stronger the LRC, the smaller the persistence length. The comparison of AFM imaging of human DNA with LRC DNA simulations confirms that the rather small mean square end-to-end distance observed, particularly for G

  5. Total Internal Reflection Fluorescence Microscopy Imaging-Guided Confocal Single-Molecule Fluorescence Spectroscopy

    OpenAIRE

    Zheng, Desheng; Kaldaras, Leonora; Lu, H. Peter

    2013-01-01

    We have developed an integrated spectroscopy system combining total internal reflection fluorescence microscopy imaging with confocal single-molecule fluorescence spectroscopy for two-dimensional interfaces. This spectroscopy approach is capable of both multiple molecules simultaneously sampling and in situ confocal fluorescence dynamics analyses of individual molecules of interest. We have demonstrated the calibration with fluorescent microspheres, and carried out single-molecule spectroscop...

  6. Anisotropic charge transport in large single crystals of π-conjugated organic molecules.

    Science.gov (United States)

    Hourani, Wael; Rahimi, Khosrow; Botiz, Ioan; Koch, Felix Peter Vinzenz; Reiter, Günter; Lienerth, Peter; Heiser, Thomas; Bubendorff, Jean-Luc; Simon, Laurent

    2014-05-07

    The electronic properties of organic semiconductors depend strongly on the nature of the molecules, their conjugation and conformation, their mutual distance and the orientation between adjacent molecules. Variations of intramolecular distances and conformation disturb the conjugation and perturb the delocalization of charges. As a result, the mobility considerably decreases compared to that of a covalently well-organized crystal. Here, we present electrical characterization of large single crystals made of the regioregular octamer of 3-hexyl-thiophene (3HT)8 using a conductive-atomic force microscope (C-AFM) in air. We find a large anisotropy in the conduction with charge mobility values depending on the crystallographic orientation of the single crystal. The smaller conduction is in the direction of π-π stacking (along the long axis of the single crystal) with a mobility value in the order of 10(-3) cm(2) V(-1) s(-1), and the larger one is along the molecular axis (in the direction normal to the single crystal surface) with a mobility value in the order of 0.5 cm(2) V(-1) s(-1). The measured current-voltage (I-V) curves showed that along the molecular axis, the current followed an exponential dependence corresponding to an injection mode. In the π-π stacking direction, the current exhibits a space charge limited current (SCLC) behavior, which allows us to estimate the charge carrier mobility.

  7. DNA analysis by single molecule stretching in nanofluidic biochips

    DEFF Research Database (Denmark)

    Abad, E.; Juarros, A.; Retolaza, A.

    2011-01-01

    Imprint Lithography (NIL) technology combined with a conventional anodic bonding of the silicon base and Pyrex cover. Using this chip, we have performed single molecule imaging on a bench-top fluorescent microscope system. Lambda phage DNA was used as a model sample to characterize the chip. Single molecules of λ-DNA......Stretching single DNA molecules by confinement in nanofluidic channels has attracted a great interest during the last few years as a DNA analysis tool. We have designed and fabricated a sealed micro/nanofluidic device for DNA stretching applications, based on the use of the high throughput Nano...... stained with the fluorescent dye YOYO-1 were stretched in the nanochannel array and the experimental results were analysed to determine the extension factor of the DNA in the chip and the geometrical average of the nanochannel inner diameter. The determination of the extension ratio of the chip provides...

  8. DNA-Based Single-Molecule Electronics: From Concept to Function

    Science.gov (United States)

    2018-01-01

    Beyond being the repository of genetic information, DNA is playing an increasingly important role as a building block for molecular electronics. Its inherent structural and molecular recognition properties render it a leading candidate for molecular electronics applications. The structural stability, diversity and programmability of DNA provide overwhelming freedom for the design and fabrication of molecular-scale devices. In the past two decades DNA has therefore attracted inordinate amounts of attention in molecular electronics. This review gives a brief survey of recent experimental progress in DNA-based single-molecule electronics with special focus on single-molecule conductance and I–V characteristics of individual DNA molecules. Existing challenges and exciting future opportunities are also discussed. PMID:29342091

  9. DNA-Based Single-Molecule Electronics: From Concept to Function.

    Science.gov (United States)

    Wang, Kun

    2018-01-17

    Beyond being the repository of genetic information, DNA is playing an increasingly important role as a building block for molecular electronics. Its inherent structural and molecular recognition properties render it a leading candidate for molecular electronics applications. The structural stability, diversity and programmability of DNA provide overwhelming freedom for the design and fabrication of molecular-scale devices. In the past two decades DNA has therefore attracted inordinate amounts of attention in molecular electronics. This review gives a brief survey of recent experimental progress in DNA-based single-molecule electronics with special focus on single-molecule conductance and I-V characteristics of individual DNA molecules. Existing challenges and exciting future opportunities are also discussed.

  10. Intramolecular didehydro-Diels-Alder reaction and its impact on the structure-function properties of environmentally sensitive fluorophores.

    Science.gov (United States)

    Brummond, Kay M; Kocsis, Laura S

    2015-08-18

    Reaction discovery plays a vital role in accessing new chemical entities and materials possessing important function.1 In this Account, we delineate our reaction discovery program regarding the [4 + 2] cycloaddition reaction of styrene-ynes. In particular, we highlight our studies that lead to the realization of the diverging reaction mechanisms of the intramolecular didehydro-Diels-Alder (IMDDA) reaction to afford dihydronaphthalene and naphthalene products. Formation of the former involves an intermolecular hydrogen atom abstraction and isomerization, whereas the latter is formed via an unexpected elimination of H2. Forming aromatic compounds by a unimolecular elimination of H2 offers an environmentally benign alternative to typical oxidation protocols. We also include in this Account ongoing work focused on expanding the scope of this reaction, mainly its application to the preparation of cyclopenta[b]naphthalenes. Finally, we showcase the synthetic utility of the IMDDA reaction by preparing novel environmentally sensitive fluorophores. The choice to follow this path was largely influenced by the impact this reaction could have on our understanding of the structure-function relationships of these molecular sensors by taking advantage of a de novo construction and functionalization of the aromatic portion of these compounds. We were also inspired by the fact that, despite the advances that have been made in the construction of small molecule fluorophores, access to rationally designed fluorescent probes or sensors possessing varied and tuned photophysical, spectral, and chemical properties are still needed. To this end, we report our studies to correlate fluorophore structure with photophysical property relationships for a series of solvatochromic PRODAN analogs and viscosity-sensitive cyanoacrylate analogs. The versatility of this de novo strategy for fluorophore synthesis was demonstrated by showing that a number of functional groups could be installed at

  11. DNA origami as biocompatible surface to match single-molecule and ensemble experiments

    Science.gov (United States)

    Gietl, Andreas; Holzmeister, Phil; Grohmann, Dina; Tinnefeld, Philip

    2012-01-01

    Single-molecule experiments on immobilized molecules allow unique insights into the dynamics of molecular machines and enzymes as well as their interactions. The immobilization, however, can invoke perturbation to the activity of biomolecules causing incongruities between single molecule and ensemble measurements. Here we introduce the recently developed DNA origami as a platform to transfer ensemble assays to the immobilized single molecule level without changing the nano-environment of the biomolecules. The idea is a stepwise transfer of common functional assays first to the surface of a DNA origami, which can be checked at the ensemble level, and then to the microscope glass slide for single-molecule inquiry using the DNA origami as a transfer platform. We studied the structural flexibility of a DNA Holliday junction and the TATA-binding protein (TBP)-induced bending of DNA both on freely diffusing molecules and attached to the origami structure by fluorescence resonance energy transfer. This resulted in highly congruent data sets demonstrating that the DNA origami does not influence the functionality of the biomolecule. Single-molecule data collected from surface-immobilized biomolecule-loaded DNA origami are in very good agreement with data from solution measurements supporting the fact that the DNA origami can be used as biocompatible surface in many fluorescence-based measurements. PMID:22523083

  12. Synthetic strategies for controlling inter- and intramolecular interactions: Applications in single-molecule fluorescence imaging, bioluminescence imaging, and palladium catalysis

    Science.gov (United States)

    Conley, Nicholas R.

    The field of synthetic organic chemistry has reached such maturity that, with sufficient effort and resources, the synthesis of virtually any small molecule which exhibits reasonable stability at room temperature can be realized. While representing a monumental achievement for the field, the ability to exert precise control over molecular structure is just a means to an end, and it is frequently the responsibility of the synthetic chemist to determine which molecules should actually be synthesized. For better or worse, there exists no competitive free market in academia for new molecules, and as a result, the decision of which compounds should be synthesized is seldom driven by the forces of supply and demand; rather, it is guided by the synthetic chemist's interest in an anticipated structure-function relationship or in the properties of a previously unstudied class of molecules. As a consequence, there exists a pervasive need for chemists with synthetic expertise in fields (e.g., molecular imaging) and subdisciplines of chemistry (e.g., physical chemistry) in which the identification of promising synthetic targets dramatically outpaces the synthetic output in that field or subdiscipline, and ample opportunities are available for synthetic chemists who choose to pursue such cross-disciplinary research. This thesis describes synthetic efforts that leverage these opportunities to realize applications in biological imaging and in palladium catalysis. In Part I, the synthesis and characterization of three novel luminophores and their imaging applications are discussed. The first is a molecular beacon that utilizes a fluorophorefluorophore pair which exhibits H-dimer quenching in the closed conformation. This probe offers several advantages over conventional fluorophore-quencher molecular beacons in the detection of oligonucleotides, both in bulk and at the single-molecule level. Secondly, a fluorescent, Cy3-Cy5 covalent heterodimer is reported, which on account of the

  13. Single-molecule conductivity of non-redox and redox molecules at pure and gold-mined Au(111)-electrode surfaces

    DEFF Research Database (Denmark)

    Zhang, Jingdong; Chi, Qijin; Ulstrup, Jens

    The structure, two-dimensional organization, and function of molecules immobilized on solid surfaces can be addressed in a degree of detail that has reached the level of the single-molecule. In this context redox molecules are “smart” molecules adding sophisticated electronic function. Redox meta...

  14. Synchronous optical packet switch architecture with tunable single and multi-channels wavelength converters

    Science.gov (United States)

    Hamza, Haitham S.; Adel, Reham

    2017-07-01

    In this paper, we propose a bufferless synchronous optical packet switch (OPS) architecture named the Limited-range wavelength conversion with Dynamic Pump-wavelength Selection (LDPS) architecture. LDPS is equipped with a dedicated limited-range wavelength converters (LRWCs, and a shared pool of parametric wavelength converters (PWCs) with dynamic pump-wavelength selection (DPS). The adoption of hybrid conversion types in the proposed architecture aims at improving the packet loss rate (PLR) compared to conventional architecture with single conversion types, while reducing (or at least maintaining) the conversion distance (d) of used wavelength converters. Packet contention in the proposed architecture is resolved using the first available algorithm (FAA) and the dynamic pump-wavelength selection algorithm (DPSA). The performance of the proposed architecture is compared to two well-known conventional architectures; namely, the LRWC architecture that uses dedicated LRWCS for each input wavelength, and the DPS architecture that uses a shared pool of dynamic pump-wavelength converters (PWCs). Simulation results show that, for the same value of d, the new architecture reduces the PLR compared to the LRWC architecture by up to 40 % and 99.7 % for traffic loads, 0.5 and 1; respectively. In addition, for d = 1 , the new architecture reduces the PLR compared to the DPS architecture by up to 10 % and 99.3 % for traffic loads, 0.5 and 1; respectively.

  15. Excitonic Behavior of Rhodamine Dimers: A Single-Molecule Study

    NARCIS (Netherlands)

    Hernando Campos, J.; van der Schaaf, Martijn; van Dijk, E.M.H.P.; Sauer, Markus; Garcia Parajo, M.F.; van Hulst, N.F.

    2003-01-01

    The optical behavior of a dimer of tetramethylrhodamine-5-isothiocyanate has been investigated by means of single-molecule measurements. Bulk absorption and fluorescence spectra show the existence of two populations of the dimer molecule that exhibit distinct excitonic interactions (strong and weak

  16. Nanogap Electrodes towards Solid State Single-Molecule Transistors.

    Science.gov (United States)

    Cui, Ajuan; Dong, Huanli; Hu, Wenping

    2015-12-01

    With the establishment of complementary metal-oxide-semiconductor (CMOS)-based integrated circuit technology, it has become more difficult to follow Moore's law to further downscale the size of electronic components. Devices based on various nanostructures were constructed to continue the trend in the minimization of electronics, and molecular devices are among the most promising candidates. Compared with other candidates, molecular devices show unique superiorities, and intensive studies on molecular devices have been carried out both experimentally and theoretically at the present time. Compared to two-terminal molecular devices, three-terminal devices, namely single-molecule transistors, show unique advantages both in fundamental research and application and are considered to be an essential part of integrated circuits based on molecular devices. However, it is very difficult to construct them using the traditional microfabrication techniques directly, thus new fabrication strategies are developed. This review aims to provide an exclusive way of manufacturing solid state gated nanogap electrodes, the foundation of constructing transistors of single or a few molecules. Such single-molecule transistors have the potential to be used to build integrated circuits. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Rational design of tetraphenylethylene-based luminescent down-shifting molecules: photophysical studies and photovoltaic applications in a CdTe solar cell from small to large units.

    Science.gov (United States)

    Li, Yilin; Li, Zhipeng; Ablekim, Tursunjan; Ren, Tianhui; Dong, Wen-Ji

    2014-12-21

    A rational design strategy of novel fluorophores for luminescent down-shifting (LDS) application was proposed and tested in this paper. Three new fluorophores (1a-c) with specific intramolecular charge transfer (ICT) and aggregation-induced emission (AIE) characteristics were synthesized as LDS molecules for increasing the output short circuit current density (Jsc) of a CdTe solar cell. Photophysical studies of their solution and solid states, and photovoltaic measurements of their PMMA solid films applied on a CdTe solar cell suggested that the specific spectroscopic properties and Jsc enhancement effects of these molecules were highly related to their chemical structures. The Jsc enhancement effects of these fluorophores were measured on both a CdTe small cell and a large panel. An increase in the output Jsc by as high as 5.69% for a small cell and 8.88% for a large panel was observed. Compared to a traditional LDS molecule, Y083, these fluorophores exhibited more superior capabilities of LDS.

  18. Long wavelength limit of the current convective instability

    International Nuclear Information System (INIS)

    Huba, J.D.

    1984-01-01

    A linear theory is presented of the current convective instability in the long wavelength limit, i.e., kL >ω) and inertial (ν/sub i/n>>ω) limits where ω is the wave frequency and ν/sub i/n is the ion-neutral collision frequency. It is shown that the growth rate scales as k in the collisional limit and as k/sup 2/3/ in the inertial limit. The analytical solutions are compared to exact numerical solutions, and very good agreement is found. Applications to the auroral ionosphere are discussed

  19. Voltage-Driven Conformational Switching with Distinct Raman Signature in a Single-Molecule Junction.

    Science.gov (United States)

    Bi, Hai; Palma, Carlos-Andres; Gong, Yuxiang; Hasch, Peter; Elbing, Mark; Mayor, Marcel; Reichert, Joachim; Barth, Johannes V

    2018-04-11

    Precisely controlling well-defined, stable single-molecule junctions represents a pillar of single-molecule electronics. Early attempts to establish computing with molecular switching arrays were partly challenged by limitations in the direct chemical characterization of metal-molecule-metal junctions. While cryogenic scanning probe studies have advanced the mechanistic understanding of current- and voltage-induced conformational switching, metal-molecule-metal conformations are still largely inferred from indirect evidence. Hence, the development of robust, chemically sensitive techniques is instrumental for advancement in the field. Here we probe the conformation of a two-state molecular switch with vibrational spectroscopy, while simultaneously operating it by means of the applied voltage. Our study emphasizes measurements of single-molecule Raman spectra in a room-temperature stable single-molecule switch presenting a signal modulation of nearly 2 orders of magnitude.

  20. Evaluation of the Electronic Structure of Single-Molecule Junctions Based on Current-Voltage and Thermopower Measurements: Application to C60 Single-Molecule Junction.

    Science.gov (United States)

    Komoto, Yuki; Isshiki, Yuji; Fujii, Shintaro; Nishino, Tomoaki; Kiguchi, Manabu

    2017-02-16

    The electronic structure of molecular junctions has a significant impact on their transport properties. Despite the decisive role of the electronic structure, a complete characterization of the electronic structure remains a challenge. This is because there is no straightforward way of measuring electron spectroscopy for an individual molecule trapped in a nanoscale gap between two metal electrodes. Herein, a comprehensive approach to obtain a detailed description of the electronic structure in single-molecule junctions based on the analysis of current-voltage (I-V) and thermoelectric characteristics is described. It is shown that the electronic structure of the prototypical C 60 single-molecule junction can be resolved by analyzing complementary results of the I-V and thermoelectric measurement. This combined approach confirmed that the C 60 single-molecule junction was highly conductive with molecular electronic conductances of 0.033 and 0.003 G 0 and a molecular Seebeck coefficient of -12 μV K -1 . In addition, we revealed that charge transport was mediated by a LUMO whose energy level was located 0.5≈0.6 eV above the Fermi level of the Au electrode. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Single molecule microscopy in 3D cell cultures and tissues.

    Science.gov (United States)

    Lauer, Florian M; Kaemmerer, Elke; Meckel, Tobias

    2014-12-15

    From the onset of the first microscopic visualization of single fluorescent molecules in living cells at the beginning of this century, to the present, almost routine application of single molecule microscopy, the method has well-proven its ability to contribute unmatched detailed insight into the heterogeneous and dynamic molecular world life is composed of. Except for investigations on bacteria and yeast, almost the entire story of success is based on studies on adherent mammalian 2D cell cultures. However, despite this continuous progress, the technique was not able to keep pace with the move of the cell biology community to adapt 3D cell culture models for basic research, regenerative medicine, or drug development and screening. In this review, we will summarize the progress, which only recently allowed for the application of single molecule microscopy to 3D cell systems and give an overview of the technical advances that led to it. While initially posing a challenge, we finally conclude that relevant 3D cell models will become an integral part of the on-going success of single molecule microscopy. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. A single molecule switch based on two Pd nanocrystals linked

    Indian Academy of Sciences (India)

    Conducting molecule; nanocrystals; scanning tunneling microscopy; negative differential resistance. Abstract. Tunneling spectroscopy measurements have been carried out on a single molecule device formed by two Pd ... Current Issue : Vol.

  3. Electron transfer dynamics of bistable single-molecule junctions

    DEFF Research Database (Denmark)

    Danilov, A.V; Kubatkin, S.; Kafanov, S. G.

    2006-01-01

    We present transport measurements of single-molecule junctions bridged by a molecule with three benzene rings connected by two double bonds and with thiol end-groups that allow chemical binding to gold electrodes. The I-V curves show switching behavior between two distinct states. By statistical ...... analysis of the switching events, we show that a 300 meV mode mediates the transition between the two states. We propose that breaking and reformation of a S-H bond in the contact zone between molecule and electrode explains the observed bistability....

  4. In vivo determination of optical properties and fluorophore characteristics of non-melanoma skin cancer

    Science.gov (United States)

    Rajaram, Narasimhan; Kovacic, Dianne; Migden, Michael F.; Reichenberg, Jason S.; Nguyen, Tri H.; Tunnell, James W.

    2009-02-01

    Diffuse optical spectroscopy (DOS) and laser-induced fluorescence (LIF) techniques have widely been used as noninvasive tools for early cancer detection in several organs including the cervix, oral cavity and gastrointestinal tract. Using a combined DOS/LIF approach, one can simultaneously measure the morphology and biochemical composition of tissue and use these features to diagnose malignancy. We report for the first time to our knowledge both the optical properties and native fluorophore characteristics of non-melanoma skin cancer in the UV-visible range. We collected in vivo diffuse reflectance and intrinsic fluorescence measurements from 44 skin lesions on 37 patients. The skin sites were further categorized into three groups of non-melanoma skin cancer according to histopathology: 1) pre-cancerous actinic keratosis 2) malignant squamous cell carcinoma (SCC) and 3) basal cell carcinoma (BCC). We used a custom-built probe-based clinical system that collects both white light reflectance and laser-induced fluorescence in the wavelength range of 350-700 nm. We extracted the blood volume fraction, oxygen saturation, blood vessel size, tissue microarchitecture and melanin content from diffuse reflectance measurements. In addition, we determined the native fluorophore contributions of NADH, collagen and FAD from laser-induced fluorescence for all groups. The scattering from tissue decreased with progression from clinically normal to precancerous actinic keratosis to malignant SCC. A similar trend was observed for clinically normal skin and malignant BCC. Statistically significant differences were observed in the collagen contributions, which were lower in malignant SCC and BCC as compared to normal skin. Our data demonstrates that the mean optical properties and fluorophore contributions of normal, benign and malignant nonmelanoma cancers are significantly different from each other and can potentially be used as biomarkers for the early detection of skin cancer.

  5. Quantum-Sequencing: Fast electronic single DNA molecule sequencing

    Science.gov (United States)

    Casamada Ribot, Josep; Chatterjee, Anushree; Nagpal, Prashant

    2014-03-01

    A major goal of third-generation sequencing technologies is to develop a fast, reliable, enzyme-free, high-throughput and cost-effective, single-molecule sequencing method. Here, we present the first demonstration of unique ``electronic fingerprint'' of all nucleotides (A, G, T, C), with single-molecule DNA sequencing, using Quantum-tunneling Sequencing (Q-Seq) at room temperature. We show that the electronic state of the nucleobases shift depending on the pH, with most distinct states identified at acidic pH. We also demonstrate identification of single nucleotide modifications (methylation here). Using these unique electronic fingerprints (or tunneling data), we report a partial sequence of beta lactamase (bla) gene, which encodes resistance to beta-lactam antibiotics, with over 95% success rate. These results highlight the potential of Q-Seq as a robust technique for next-generation sequencing.

  6. A tunable and switchable single-longitudinal-mode dual-wavelength fiber laser with a simple linear cavity.

    Science.gov (United States)

    He, Xiaoying; Fang, Xia; Liao, Changrui; Wang, D N; Sun, Junqiang

    2009-11-23

    A simple linear cavity erbium-doped fiber laser based on a Fabry-Perot filter which consists of a pair of fiber Bragg gratings is proposed for tunable and switchable single-longitudinal-mode dual-wavelength operation. The single-longitudinal-mode is obtained by the saturable absorption of an unpumed erbium-doped fiber together with a narrow-band fiber Bragg grating. Under the high pump power (>166 mW) condition, the stable dual-wavelength oscillation with uniform amplitude can be realized by carefully adjusting the polarization controller in the cavity. Wavelength selection and switching are achieved by tuning the narrow-band fiber Bragg grating in the system. The spacing of the dual-wavelength can be selected at 0.20 nm (approximately 25.62 GHz), 0.22 nm (approximately 28.19 GHz) and 0.54 nm (approximately 69.19 GHz).

  7. New Antifouling Platform Characterized by Single-Molecule Imaging

    Science.gov (United States)

    2015-01-01

    Antifouling surfaces have been widely studied for their importance in medical devices and industry. Antifouling surfaces mostly achieved by methoxy-poly(ethylene glycol) (mPEG) have shown biomolecular adsorption less than 1 ng/cm2 which was measured by surface analytical tools such as surface plasmon resonance (SPR) spectroscopy, quartz crystal microbalance (QCM), or optical waveguide lightmode (OWL) spectroscopy. Herein, we utilize a single-molecule imaging technique (i.e., an ultimate resolution) to study antifouling properties of functionalized surfaces. We found that about 600 immunoglobulin G (IgG) molecules are adsorbed. This result corresponds to ∼5 pg/cm2 adsorption, which is far below amount for the detection limit of the conventional tools. Furthermore, we developed a new antifouling platform that exhibits improved antifouling performance that shows only 78 IgG molecules adsorbed (∼0.5 pg/cm2). The antifouling platform consists of forming 1 nm TiO2 thin layer, on which peptidomimetic antifouling polymer (PMAP) is robustly anchored. The unprecedented antifouling performance can potentially revolutionize a variety of research fields such as single-molecule imaging, medical devices, biosensors, and others. PMID:24503420

  8. New antifouling platform characterized by single-molecule imaging.

    Science.gov (United States)

    Ryu, Ji Young; Song, In Taek; Lau, K H Aaron; Messersmith, Phillip B; Yoon, Tae-Young; Lee, Haeshin

    2014-03-12

    Antifouling surfaces have been widely studied for their importance in medical devices and industry. Antifouling surfaces mostly achieved by methoxy-poly(ethylene glycol) (mPEG) have shown biomolecular adsorption less than 1 ng/cm(2) which was measured by surface analytical tools such as surface plasmon resonance (SPR) spectroscopy, quartz crystal microbalance (QCM), or optical waveguide lightmode (OWL) spectroscopy. Herein, we utilize a single-molecule imaging technique (i.e., an ultimate resolution) to study antifouling properties of functionalized surfaces. We found that about 600 immunoglobulin G (IgG) molecules are adsorbed. This result corresponds to ∼5 pg/cm(2) adsorption, which is far below amount for the detection limit of the conventional tools. Furthermore, we developed a new antifouling platform that exhibits improved antifouling performance that shows only 78 IgG molecules adsorbed (∼0.5 pg/cm(2)). The antifouling platform consists of forming 1 nm TiO2 thin layer, on which peptidomimetic antifouling polymer (PMAP) is robustly anchored. The unprecedented antifouling performance can potentially revolutionize a variety of research fields such as single-molecule imaging, medical devices, biosensors, and others.

  9. Single molecule experiments challenge the strict wave-particle dualism of light.

    Science.gov (United States)

    Greulich, Karl Otto

    2010-01-21

    Single molecule techniques improve our understanding of the photon and light. If the single photon double slit experiment is performed at the "single photon limit" of a multi-atom light source, faint light pulses with more than one photon hamper the interpretation. Single molecules, quantum dots or defect centres in crystals should be used as light source. "Single photon detectors" do not meet their promise-only "photon number resolving single photon detectors" do so. Particularly, the accumulation time argument, the only safe basis for the postulate of a strictly particle like photon, has so far not yet been verified.

  10. Zero-phonon-line emission of single molecules for applications in quantum information processing

    Science.gov (United States)

    Kiraz, Alper; Ehrl, M.; Mustecaplioglu, O. E.; Hellerer, T.; Brauchle, C.; Zumbusch, A.

    2005-07-01

    A single photon source which generates transform limited single photons is highly desirable for applications in quantum optics. Transform limited emission guarantees the indistinguishability of the emitted single photons. This, in turn brings groundbreaking applications in linear optics quantum information processing within an experimental reach. Recently, self-assembled InAs quantum dots and trapped atoms have successfully been demonstrated as such sources for highly indistinguishable single photons. Here, we demonstrate that nearly transform limited zero-phonon-line (ZPL) emission from single molecules can be obtained by using vibronic excitation. Furthermore we report the results of coincidence detection experiments at the output of a Michelson-type interferometer. These experiments reveal Hong-Ou-Mandel correlations as a proof of the indistinguishability of the single photons emitted consecutively from a single molecule. Therefore, single molecules constitute an attractive alternative to single InAs quantum dots and trapped atoms for applications in linear optics quantum information processing. Experiments were performed with a home-built confocal microscope keeping the sample in a superfluid liquid Helium bath at 1.4K. We investigated terrylenediimide (TDI) molecules highly diluted in hexadecane (Shpol'skii matrix). A continuous wave single mode dye laser was used for excitation of vibronic transitions of individual molecules. From the integral fluorescence, the ZPL of single molecules was selected with a spectrally narrow interference filter. The ZPL emission was then sent to a scanning Fabry-Perot interferometer for linewidth measurements or a Michelson-type interferometer for coincidence detection.

  11. Detection of kinetic change points in piece-wise linear single molecule motion

    Science.gov (United States)

    Hill, Flynn R.; van Oijen, Antoine M.; Duderstadt, Karl E.

    2018-03-01

    Single-molecule approaches present a powerful way to obtain detailed kinetic information at the molecular level. However, the identification of small rate changes is often hindered by the considerable noise present in such single-molecule kinetic data. We present a general method to detect such kinetic change points in trajectories of motion of processive single molecules having Gaussian noise, with a minimum number of parameters and without the need of an assumed kinetic model beyond piece-wise linearity of motion. Kinetic change points are detected using a likelihood ratio test in which the probability of no change is compared to the probability of a change occurring, given the experimental noise. A predetermined confidence interval minimizes the occurrence of false detections. Applying the method recursively to all sub-regions of a single molecule trajectory ensures that all kinetic change points are located. The algorithm presented allows rigorous and quantitative determination of kinetic change points in noisy single molecule observations without the need for filtering or binning, which reduce temporal resolution and obscure dynamics. The statistical framework for the approach and implementation details are discussed. The detection power of the algorithm is assessed using simulations with both single kinetic changes and multiple kinetic changes that typically arise in observations of single-molecule DNA-replication reactions. Implementations of the algorithm are provided in ImageJ plugin format written in Java and in the Julia language for numeric computing, with accompanying Jupyter Notebooks to allow reproduction of the analysis presented here.

  12. Multiplex single-molecule interaction profiling of DNA-barcoded proteins.

    Science.gov (United States)

    Gu, Liangcai; Li, Chao; Aach, John; Hill, David E; Vidal, Marc; Church, George M

    2014-11-27

    In contrast with advances in massively parallel DNA sequencing, high-throughput protein analyses are often limited by ensemble measurements, individual analyte purification and hence compromised quality and cost-effectiveness. Single-molecule protein detection using optical methods is limited by the number of spectrally non-overlapping chromophores. Here we introduce a single-molecular-interaction sequencing (SMI-seq) technology for parallel protein interaction profiling leveraging single-molecule advantages. DNA barcodes are attached to proteins collectively via ribosome display or individually via enzymatic conjugation. Barcoded proteins are assayed en masse in aqueous solution and subsequently immobilized in a polyacrylamide thin film to construct a random single-molecule array, where barcoding DNAs are amplified into in situ polymerase colonies (polonies) and analysed by DNA sequencing. This method allows precise quantification of various proteins with a theoretical maximum array density of over one million polonies per square millimetre. Furthermore, protein interactions can be measured on the basis of the statistics of colocalized polonies arising from barcoding DNAs of interacting proteins. Two demanding applications, G-protein coupled receptor and antibody-binding profiling, are demonstrated. SMI-seq enables 'library versus library' screening in a one-pot assay, simultaneously interrogating molecular binding affinity and specificity.

  13. Photon antibunching in single-walled carbon nanotubes at telecommunication wavelengths and room temperature

    Energy Technology Data Exchange (ETDEWEB)

    Endo, Takumi, E-mail: endou@az.appi.keio.ac.jp; Ishi-Hayase, Junko; Maki, Hideyuki, E-mail: maki@appi.keio.ac.jp [Department of Applied Physics and Physico-Informatics, Keio University, Yokohama 223-8522 (Japan)

    2015-03-16

    We investigated the photoluminescence of individual air-suspended single-walled carbon nanotubes (SWNTs) from 6 to 300 K. Time-resolved and antibunching measurements over the telecommunication wavelength range were performed using a superconducting single-photon detector. We detected moderate temperature independent antibunching behavior over the whole temperature range studied. To investigate the exciton dynamics, which is responsible for the antibunching behavior, we measured excitation-power and temperature dependence of the photoluminescence spectra and lifetime decay curves. These measurements suggested an exciton confinement effect that is likely caused by high-dielectric amorphous carbon surrounding the SWNTs. These results indicate that SWNTs are good candidates for light sources in quantum communication technologies operating in the telecommunication wavelength range and at room temperature.

  14. Surface single-molecule dynamics controlled by entropy at low temperatures

    Science.gov (United States)

    Gehrig, J. C.; Penedo, M.; Parschau, M.; Schwenk, J.; Marioni, M. A.; Hudson, E. W.; Hug, H. J.

    2017-02-01

    Configuration transitions of individual molecules and atoms on surfaces are traditionally described using an Arrhenius equation with energy barrier and pre-exponential factor (attempt rate) parameters. Characteristic parameters can vary even for identical systems, and pre-exponential factors sometimes differ by orders of magnitude. Using low-temperature scanning tunnelling microscopy (STM) to measure an individual dibutyl sulfide molecule on Au(111), we show that the differences arise when the relative position of tip apex and molecule changes by a fraction of the molecule size. Altering the tip position on that scale modifies the transition's barrier and attempt rate in a highly correlated fashion, which results in a single-molecular enthalpy-entropy compensation. Conversely, appropriately positioning the STM tip allows selecting the operating point on the compensation line and modifying the transition rates. The results highlight the need to consider entropy in transition rates of single molecules, even at low temperatures.

  15. Single-Molecule Electronics with Cross- Conjugated Molecules: Quantum Interference, IETS and Non-Equilibrium "Temperatures"

    DEFF Research Database (Denmark)

    Jørgensen, Jacob Lykkebo

    Abstract The idea of using single-molecules as components in electronic devices is fas- cinating. For this idea to come into fruition, a number of technical and theo- retical challenges must be overcome. In this PhD thesis, the electron-phonon interaction is studied for a special class of molecules......, which is characterised by destructive quantum interference. The molecules are cross-conjugated, which means that the two parts of the molecules are conjugated to a third part, but not to each other. This gives rise to an anti-resonance in the trans- mission. In the low bias and low temperature regime......-conjugated molecules. We nd that the vibrational modes that would be expected to dominate, following the propensity, rules are very weak. Instead, other modes are found to be the dominant ones. We study this phenomenon for a number of cross-conjugated molecules, and link these ndings to the anti...

  16. Evidence for a single hydrogen molecule connected by an atomic chain

    DEFF Research Database (Denmark)

    Kiguchi, M.; Stadler, Robert; Bækgaard, Iben Sig Buur

    2007-01-01

    Stable, single-molecule conducting-bridge configurations are typically identified from peak structures in a conductance histogram. In previous work on Pt with H-2 at cryogenic temperatures it has been shown that a peak near 1G(0) identifies a single-molecule Pt-H-2-Pt bridge. The histogram shows...

  17. Single-Photon Source for Quantum Information Based on Single Dye Molecule Fluorescence in Liquid Crystal Host

    International Nuclear Information System (INIS)

    Lukishova, S.G.; Knox, R.P.; Freivald, P.; McNamara, A.; Boyd, R.W.; Stroud, Jr. C.R.; Schmid, A.W.; Marshall, K.L.

    2006-01-01

    This paper describes a new application for liquid crystals: quantum information technology. A deterministically polarized single-photon source that efficiently produces photons exhibiting antibunching is a pivotal hardware element in absolutely secure quantum communication. Planar-aligned nematic liquid crystal hosts deterministically align the single dye molecules which produce deterministically polarized single (antibunched) photons. In addition, 1-D photonic bandgap cholesteric liquid crystals will increase single-photon source efficiency. The experiments and challenges in the observation of deterministically polarized fluorescence from single dye molecules in planar-aligned glassy nematic-liquid-crystal oligomer as well as photon antibunching in glassy cholesteric oligomer are described for the first time

  18. Single Molecule Fluorescence: from Physical Fascination to Biological Relevance

    NARCIS (Netherlands)

    Segers-Nolten, Gezina M.J.

    2003-01-01

    Confocal fluorescence microscopy is particularly well-known from the beautiful images that have been obtained with this technique from cells. Several cellular components could be nicely visualized simultaneously by staining them with different fluorophores. Not only for ensemble applications but

  19. I19, the small-molecule single-crystal diffraction beamline at Diamond Light Source.

    Science.gov (United States)

    Nowell, Harriott; Barnett, Sarah A; Christensen, Kirsten E; Teat, Simon J; Allan, David R

    2012-05-01

    The dedicated small-molecule single-crystal X-ray diffraction beamline (I19) at Diamond Light Source has been operational and supporting users for over three years. I19 is a high-flux tunable-wavelength beamline and its key details are described in this article. Much of the work performed on the beamline involves structure determination from small and weakly diffracting crystals. Other experiments that have been supported to date include structural studies at high pressure, studies of metastable species, variable-temperature crystallography, studies involving gas exchange in porous materials and structural characterizations that require analysis of the diffuse scattering between Bragg reflections. A range of sample environments to facilitate crystallographic studies under non-ambient conditions are available as well as a number of options for automation. An indication of the scope of the science carried out on the beamline is provided by the range of highlights selected for this paper.

  20. Utilizing Biotinylated Proteins Expressed in Yeast to Visualize DNA–Protein Interactions at the Single-Molecule Level

    Directory of Open Access Journals (Sweden)

    Huijun Xue

    2017-10-01

    Full Text Available Much of our knowledge in conventional biochemistry has derived from bulk assays. However, many stochastic processes and transient intermediates are hidden when averaged over the ensemble. The powerful technique of single-molecule fluorescence microscopy has made great contributions to the understanding of life processes that are inaccessible when using traditional approaches. In single-molecule studies, quantum dots (Qdots have several unique advantages over other fluorescent probes, such as high brightness, extremely high photostability, and large Stokes shift, thus allowing long-time observation and improved signal-to-noise ratios. So far, however, there is no convenient way to label proteins purified from budding yeast with Qdots. Based on BirA–Avi and biotin–streptavidin systems, we have established a simple method to acquire a Qdot-labeled protein and visualize its interaction with DNA using total internal reflection fluorescence microscopy. For proof-of-concept, we chose replication protein A (RPA and origin recognition complex (ORC as the proteins of interest. Proteins were purified from budding yeast with high biotinylation efficiency and rapidly labeled with streptavidin-coated Qdots. Interactions between proteins and DNA were observed successfully at the single-molecule level.

  1. Upgrade of the MAGIC telescopes single wavelength micro power LIDAR system

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, Dominik [Max-Planck-Institut fuer Physik, Muenchen (Germany); Collaboration: MAGIC-Collaboration

    2016-07-01

    Since 2011 a single wavelength LIDAR system is operated alongside the observations of the MAGIC telescopes. It is used for real-time monitoring of the atmospheric transmission and for detecting cloud layers within the field of view of MAGIC. The system uses a pulsed Nd:YAG laser with 532 nm wavelength and a pulse energy of 5 μJ as transmitter. The receiver is mounted to a 60 cm spherical single mirror telescope with a F/D ratio of 2.5. To compensate for the low light intensities a sensitive detector with the capability of single photon detection as well as charge integration is needed. For this purpose, a hybrid photo diode with a peak quantum efficiency of 55% an a pulse width of 2.5ns is used in a custom designed detector. The analog signal is recorded by a computer mounted 8-bit FADC with 200 MS/s. A signal analysis algorithm converts the LIDAR return signal into a number of single photoelectron counts per range bin. The atmospheric transmission is calculated by fitting a Rayleigh back-scattering model with a sliding window. The resulting transmission profile is used to correct the MAGIC gamma ray data for adverse weather conditions. After five years of data taking the MAGIC LIDAR system is upgraded with a stronger laser and a new detector unit in order to extend the measurement range and to optimize the operation.

  2. 78 FR 18999 - Prospective Grant of Start-Up Exclusive License: Photosensitizing Antibody-Fluorophore Conjugates...

    Science.gov (United States)

    2013-03-28

    ...-Up Exclusive License: Photosensitizing Antibody-Fluorophore Conjugates for Photoimmunotherapy AGENCY...-205-2010/0-US-01), and entitled ``Photosensitizing Antibody- Fluorophore Conjugates,'' to Aspyrian... invention. The field of use may be limited to ``use of photosensitizing antibody-fluorophore conjugate by...

  3. A Single-Molecule Barcoding System using Nanoslits for DNA Analysis

    Science.gov (United States)

    Jo, Kyubong; Schramm, Timothy M.; Schwartz, David C.

    Single DNA molecule approaches are playing an increasingly central role in the analytical genomic sciences because single molecule techniques intrinsically provide individualized measurements of selected molecules, free from the constraints of bulk techniques, which blindly average noise and mask the presence of minor analyte components. Accordingly, a principal challenge that must be addressed by all single molecule approaches aimed at genome analysis is how to immobilize and manipulate DNA molecules for measurements that foster construction of large, biologically relevant data sets. For meeting this challenge, this chapter discusses an integrated approach for microfabricated and nanofabricated devices for the manipulation of elongated DNA molecules within nanoscale geometries. Ideally, large DNA coils stretch via nanoconfinement when channel dimensions are within tens of nanometers. Importantly, stretched, often immobilized, DNA molecules spanning hundreds of kilobase pairs are required by all analytical platforms working with large genomic substrates because imaging techniques acquire sequence information from molecules that normally exist in free solution as unrevealing random coils resembling floppy balls of yarn. However, nanoscale devices fabricated with sufficiently small dimensions fostering molecular stretching make these devices impractical because of the requirement of exotic fabrication technologies, costly materials, and poor operational efficiencies. In this chapter, such problems are addressed by discussion of a new approach to DNA presentation and analysis that establishes scaleable nanoconfinement conditions through reduction of ionic strength; stiffening DNA molecules thus enabling their arraying for analysis using easily fabricated devices that can also be mass produced. This new approach to DNA nanoconfinement is complemented by the development of a novel labeling scheme for reliable marking of individual molecules with fluorochrome labels

  4. Ghostly Glow Reveals a Hidden Class of Long-Wavelength Radio Emitters

    Science.gov (United States)

    2008-10-01

    (Washington, DC. 08)- A team of scientists, including astronomers from the Naval Research Laboratory (NRL), have detected long wavelength radio emission from a colliding, massive galaxy cluster which, surprisingly, is not detected at the shorter wavelengths typically seen in these objects. The discovery implies that existing radio telescopes have missed a large population of these colliding objects. It also provides an important confirmation of the theoretical prediction that colliding galaxy clusters accelerate electrons and other particles to very high energies through the process of turbulent waves. The team revealed their findings in the October 16, 2008 edition of Nature. This new population of objects is most easily detected at long wavelengths. Professor Greg Taylor of the University of New Mexico and scientific director of the Long Wavelength Array (LWA) points out, "This result is just the tip of the iceberg. When an emerging suite of much more powerful low frequency telescopes, including the LWA in New Mexico, turn their views to the cosmos, the sky will 'light up' with hundreds or even thousands of colliding galaxy clusters." NRL has played a key role in promoting the development of this generation of new instruments and is currently involved with the development of the LWA. NRL radio astronomer and LWA Project Scientist Namir Kassim says "Our discovery of a previously hidden class of low frequency cluster-radio sources is particularly important since the study of galaxy clusters was a primary motivation for development of the LWA." The discovery of the emission in the galaxy cluster Abell 521 (or A521 for short) was made using the Giant Metrewave Radiotelescope (GMRT) in India, and its long wavelength nature was confirmed by the National Science Foundation's (NRAO) Very Large Array (VLA) radio telescope in New Mexico. The attached image shows the radio emission at a wavelength of 125cm in red superimposed on a blue image made from data taken by the

  5. Single Molecule Experiments Challenge the Strict Wave-Particle Dualism of Light

    Directory of Open Access Journals (Sweden)

    Karl Otto Greulich

    2010-01-01

    Full Text Available Single molecule techniques improve our understanding of the photon and light. If the single photon double slit experiment is performed at the “single photon limit” of a multi-atom light source, faint light pulses with more than one photon hamper the interpretation. Single molecules, quantum dots or defect centres in crystals should be used as light source. “Single photon detectors” do not meet their promise―only “photon number resolving single photon detectors” do so. Particularly, the accumulation time argument, the only safe basis for the postulate of a strictly particle like photon, has so far not yet been verified.

  6. 12-Channel Peltier array temperature control unit for single molecule enzymology studies using capillary electrophoresis.

    Science.gov (United States)

    Craig, Douglas B; Reinfelds, Gundars; Henderson, Anna

    2014-08-01

    Capillary electrophoresis has been used to demonstrate that individual molecules of a given enzyme support different catalytic rates. In order to determine how rate varies with temperature, and determine activation energies for individual β-galactosidase molecules, a 12-channel Peltier array temperature control device was constructed where the temperature of each cell was separately controlled. This array was used to control the temperature of the central 30 cm of a 50 cm long capillary, producing a temperature gradient along its length. Continuous flow single β-galactosidase molecule assays were performed allowing measurement of the catalytic rates at different temperatures. Arrhenius plots were produced and the distribution of activation energies for individual β-galactosidase molecules was found to be 56 ± 10 kJ/mol with a range of 34-72 kJ/mol. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Site-Selection in Single-Molecule Junction for Highly Reproducible Molecular Electronics.

    Science.gov (United States)

    Kaneko, Satoshi; Murai, Daigo; Marqués-González, Santiago; Nakamura, Hisao; Komoto, Yuki; Fujii, Shintaro; Nishino, Tomoaki; Ikeda, Katsuyoshi; Tsukagoshi, Kazuhito; Kiguchi, Manabu

    2016-02-03

    Adsorption sites of molecules critically determine the electric/photonic properties and the stability of heterogeneous molecule-metal interfaces. Then, selectivity of adsorption site is essential for development of the fields including organic electronics, catalysis, and biology. However, due to current technical limitations, site-selectivity, i.e., precise determination of the molecular adsorption site, remains a major challenge because of difficulty in precise selection of meaningful one among the sites. We have succeeded the single site-selection at a single-molecule junction by performing newly developed hybrid technique: simultaneous characterization of surface enhanced Raman scattering (SERS) and current-voltage (I-V) measurements. The I-V response of 1,4-benzenedithiol junctions reveals the existence of three metastable states arising from different adsorption sites. Notably, correlated SERS measurements show selectivity toward one of the adsorption sites: "bridge sites". This site-selectivity represents an essential step toward the reliable integration of individual molecules on metallic surfaces. Furthermore, the hybrid spectro-electric technique reveals the dependence of the SERS intensity on the strength of the molecule-metal interaction, showing the interdependence between the optical and electronic properties in single-molecule junctions.

  8. Single molecule DNA detection with an atomic vapor notch filter

    Energy Technology Data Exchange (ETDEWEB)

    Uhland, Denis; Rendler, Torsten; Widmann, Matthias; Lee, Sang-Yun [University of Stuttgart and Stuttgart Research Center of Photonic Engineering (SCoPE) and IQST, 3rd Physics Institute, Stuttgart (Germany); Wrachtrup, Joerg; Gerhardt, Ilja [University of Stuttgart and Stuttgart Research Center of Photonic Engineering (SCoPE) and IQST, 3rd Physics Institute, Stuttgart (Germany); Max Planck Institute for Solid State Research, Stuttgart (Germany)

    2015-12-01

    The detection of single molecules has facilitated many advances in life- and material-science. Commonly the fluorescence of dye molecules is detected, which are attached to a non-fluorescent structure under study. For fluorescence microscopy one desires to maximize the detection efficiency together with an efficient suppression of undesired laser leakage. Here we present the use of the narrow-band filtering properties of hot atomic sodium vapor to selectively filter the excitation light from the red-shifted fluorescence of dye labeled single-stranded DNA molecules. A statistical analysis proves an enhancement in detection efficiency of more than 15% in a confocal and in a wide-field configuration. (orig.)

  9. Steady state and time resolved fluorescence studies of azadioxatriangulenium (ADOTA) fluorophore in silica and PVA thin films

    DEFF Research Database (Denmark)

    Chib, Rahul; Raut, Sangram; Shah, Sunil

    2015-01-01

    A cationic azadioxatriangulenium dye was entrapped in silica thin films obtained by the sol-gel process and in poly (vinyl) alcohol (PVA) thin films. Azadioxatriangulenium is a red emitting fluorophore with a long fluorescence lifetime of ∼20 ns. The fluorescent properties of azadioxatriangulenium...

  10. Single-Molecule Sensing with Nanopore Confinement: from Chemical Reactions to Biological Interactions.

    Science.gov (United States)

    Lin, Yao; Ying, Yi-Lun; Gao, Rui; Long, Yi-Tao

    2018-03-25

    The nanopore can generate an electrochemical confinement for single-molecule sensing which help understand the fundamental chemical principle in nanoscale dimensions. By observing the generated ionic current, individual bond-making and bond-breaking steps, single biomolecule dynamic conformational changes and electron transfer processes that occur within pore can be monitored with high temporal and current resolution. These single-molecule studies in nanopore confinement are revealing information about the fundamental chemical and biological processes that cannot be extracted from ensemble measurements. In this concept, we introduce and discuss the electrochemical confinement effects on single-molecule covalent reactions, conformational dynamics of individual molecules and host-guest interactions in protein nanopores. Then, we extend the concept of nanopore confinement effects to confine electrochemical redox reactions in solid-state nanopores for developing new sensing mechanisms. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Single-molecule diffusion and conformational dynamics by spatial integration of temporal fluctuations

    KAUST Repository

    Serag, Maged F.

    2014-10-06

    Single-molecule localization and tracking has been used to translate spatiotemporal information of individual molecules to map their diffusion behaviours. However, accurate analysis of diffusion behaviours and including other parameters, such as the conformation and size of molecules, remain as limitations to the method. Here, we report a method that addresses the limitations of existing single-molecular localization methods. The method is based on temporal tracking of the cumulative area occupied by molecules. These temporal fluctuations are tied to molecular size, rates of diffusion and conformational changes. By analysing fluorescent nanospheres and double-stranded DNA molecules of different lengths and topological forms, we demonstrate that our cumulative-area method surpasses the conventional single-molecule localization method in terms of the accuracy of determined diffusion coefficients. Furthermore, the cumulative-area method provides conformational relaxation times of structurally flexible chains along with diffusion coefficients, which together are relevant to work in a wide spectrum of scientific fields.

  12. Single-molecule diffusion and conformational dynamics by spatial integration of temporal fluctuations

    KAUST Repository

    Serag, Maged F.; Abadi, Maram; Habuchi, Satoshi

    2014-01-01

    Single-molecule localization and tracking has been used to translate spatiotemporal information of individual molecules to map their diffusion behaviours. However, accurate analysis of diffusion behaviours and including other parameters, such as the conformation and size of molecules, remain as limitations to the method. Here, we report a method that addresses the limitations of existing single-molecular localization methods. The method is based on temporal tracking of the cumulative area occupied by molecules. These temporal fluctuations are tied to molecular size, rates of diffusion and conformational changes. By analysing fluorescent nanospheres and double-stranded DNA molecules of different lengths and topological forms, we demonstrate that our cumulative-area method surpasses the conventional single-molecule localization method in terms of the accuracy of determined diffusion coefficients. Furthermore, the cumulative-area method provides conformational relaxation times of structurally flexible chains along with diffusion coefficients, which together are relevant to work in a wide spectrum of scientific fields.

  13. Reversible switching of fluorophore property based on intrinsic conformational transition of adenylate kinase during its catalytic cycle.

    Science.gov (United States)

    Fujii, Akira; Hirota, Shun; Matsuo, Takashi

    2013-07-17

    Adenylate kinase shows a conformational transition (OPEN and CLOSED forms) during substrate binding and product release to mediate the phosphoryl transfer between ADP and ATP/AMP. The protein motional characteristics will be useful to construct switching systems of fluorophore properties caused by the catalytic cycle of the enzyme. This paper demonstrates in situ reversible switching of a fluorophore property driven by the conformational transition of the enzyme. The pyrene-conjugated mutant adenylate kinase is able to switch the monomer/excimer emission property of pyrene on addition of ADP or P(1)P(5)-di(adenosine-5')pentaphosphate (Ap5A, a transition state analog). The observation under the dilute condition (~0.1 μM) indicates that the emission spectral change was caused by the motion of a protein molecule and not led by protein-protein interactions through π-π stacking of pyrene rings. The switching can be reversibly conducted by using hexokinase-coupling reaction. The fashion of the changes in emission intensities at various ligand concentrations is different between ADP, Mg(2+)-bound ADP, and Mg(2+)-bound Ap5A. The emission property switching is repeatable by a sequential addition of a substrate in a one-pot process. It is proposed that the property of a synthetic molecule on the enzyme surface is switchable in response to the catalytic cycle of adenylate kinase.

  14. Machine learning approach for single molecule localisation microscopy.

    Science.gov (United States)

    Colabrese, Silvia; Castello, Marco; Vicidomini, Giuseppe; Del Bue, Alessio

    2018-04-01

    Single molecule localisation (SML) microscopy is a fundamental tool for biological discoveries; it provides sub-diffraction spatial resolution images by detecting and localizing "all" the fluorescent molecules labeling the structure of interest. For this reason, the effective resolution of SML microscopy strictly depends on the algorithm used to detect and localize the single molecules from the series of microscopy frames. To adapt to the different imaging conditions that can occur in a SML experiment, all current localisation algorithms request, from the microscopy users, the choice of different parameters. This choice is not always easy and their wrong selection can lead to poor performance. Here we overcome this weakness with the use of machine learning. We propose a parameter-free pipeline for SML learning based on support vector machine (SVM). This strategy requires a short supervised training that consists in selecting by the user few fluorescent molecules (∼ 10-20) from the frames under analysis. The algorithm has been extensively tested on both synthetic and real acquisitions. Results are qualitatively and quantitatively consistent with the state of the art in SML microscopy and demonstrate that the introduction of machine learning can lead to a new class of algorithms competitive and conceived from the user point of view.

  15. Light-Induced Switching of Tunable Single-Molecule Junctions

    KAUST Repository

    Sendler, Torsten; Luka-Guth, Katharina; Wieser, Matthias; Lokamani; Wolf, Jannic Sebastian; Helm, Manfred; Gemming, Sibylle; Kerbusch, Jochen; Scheer, Elke; Huhn, Thomas; Erbe, Artur

    2015-01-01

    A major goal of molecular electronics is the development and implementation of devices such as single-molecular switches. Here, measurements are presented that show the controlled in situ switching of diarylethene molecules from their nonconductive to conductive state in contact to gold nanoelectrodes via controlled light irradiation. Both the conductance and the quantum yield for switching of these molecules are within a range making the molecules suitable for actual devices. The conductance of the molecular junctions in the opened and closed states is characterized and the molecular level E 0, which dominates the current transport in the closed state, and its level broadening Γ are identified. The obtained results show a clear light-induced ring forming isomerization of the single-molecule junctions. Electron withdrawing side-groups lead to a reduction of conductance, but do not influence the efficiency of the switching mechanism. Quantum chemical calculations of the light-induced switching processes correlate these observations with the fundamentally different low-lying electronic states of the opened and closed forms and their comparably small modification by electron-withdrawing substituents. This full characterization of a molecular switch operated in a molecular junction is an important step toward the development of real molecular electronics devices.

  16. Light-Induced Switching of Tunable Single-Molecule Junctions

    KAUST Repository

    Sendler, Torsten

    2015-04-16

    A major goal of molecular electronics is the development and implementation of devices such as single-molecular switches. Here, measurements are presented that show the controlled in situ switching of diarylethene molecules from their nonconductive to conductive state in contact to gold nanoelectrodes via controlled light irradiation. Both the conductance and the quantum yield for switching of these molecules are within a range making the molecules suitable for actual devices. The conductance of the molecular junctions in the opened and closed states is characterized and the molecular level E 0, which dominates the current transport in the closed state, and its level broadening Γ are identified. The obtained results show a clear light-induced ring forming isomerization of the single-molecule junctions. Electron withdrawing side-groups lead to a reduction of conductance, but do not influence the efficiency of the switching mechanism. Quantum chemical calculations of the light-induced switching processes correlate these observations with the fundamentally different low-lying electronic states of the opened and closed forms and their comparably small modification by electron-withdrawing substituents. This full characterization of a molecular switch operated in a molecular junction is an important step toward the development of real molecular electronics devices.

  17. A long-wavelength target station for the spallation neutron source

    International Nuclear Information System (INIS)

    Carpenter, J.M.; Mason, T.E.

    2005-01-01

    The Spallation Neutron Source (SNS), a major new user facility for studies of the structure and dynamics of materials, funded by the US Department of Energy (DOE), is under construction at Oak Ridge National Laboratory (ORNL). Details about the project are available in a recent paper and on the SNS Web site [MRS Bull. 28 (12) (2003) 923]. A Long-Wavelength Target Station (LWTS) [Technical Concepts for a Long-Wavelength Target Station for the Spallation Neutron Source, Argonne National Laboratory Report ANL-02/16, Oak Ridge National Laboratory Report ORNL/SNS-TM-2001/163, November 2002. See also www.pns.anl.gov/related/] will complement the High-Power Target Station (HPTS) facility of the SNS and will build upon the significant investment in the remainder of the installation by providing important new scientific opportunities. For areas of science using the optimized long-wavelength beam lines, the LWTS will at least double the overall scientific capability of the SNS and provide for up to an order of magnitude performance gain over the initial HPTS. The fully equipped SNS has the prospect to offer capabilities for neutron-scattering studies of the structure and dynamics of materials with sensitivity, resolution, dynamic range, and speed that are unparalleled in the world. Preliminary assessments of the performance of the several instruments treated in detail in the body of the paper bear out this expectation. The LWTS concept has been developed in close consultation with the scientific community through a series of workshops and conferences jointly sponsored by DOE's Office of Basic Energy Science and the National Science Foundation. We describe the principal features of the LWTS concept, and provide a preliminary summary of some neutron scattering instruments suited to exploit the unique features of the LWTS. It remains to develop concepts and designs for a full suite of instruments that exploit the capabilities of LWTS, a process that has begun in collaboration

  18. Linker-dependent Junction Formation Probability in Single-Molecule Junctions

    Energy Technology Data Exchange (ETDEWEB)

    Yoo, Pil Sun; Kim, Taekyeong [HankukUniversity of Foreign Studies, Yongin (Korea, Republic of)

    2015-01-15

    We compare the junction formation probabilities of single-molecule junctions with different linker molecules by using a scanning tunneling microscope-based break-junction technique. We found that the junction formation probability varies as SH > SMe > NH2 for the benzene backbone molecule with different types of anchoring groups, through quantitative statistical analysis. These results are attributed to different bonding forces according to the linker groups formed with Au atoms in the electrodes, which is consistent with previous works. Our work allows a better understanding of the contact chemistry in the metal.molecule junction for future molecular electronic devices.

  19. Structural and electronic properties of single molecules and organic layers on surfaces

    NARCIS (Netherlands)

    Sotthewes, Kai

    2016-01-01

    Single molecules and organic layers on well-defined solid surfaces have attracted tremendous attention owing to their interesting physical and chemical properties. The ultimate utility of single molecules or self-assembled monolayers (SAMs) for potential applications is critically dependent on the

  20. Electrochemistry and bioelectrochemistry towards the single-molecule level: Theoretical notions and systems

    DEFF Research Database (Denmark)

    Zhang, Jingdong; Chi, Qijin; Albrecht, Tim

    2005-01-01

    Surface structures controlled at the nanometer and single-molecule levels, with functions crucially determined by interfacial electron transfer (ET) are broadly reported in recent years, with different kinds of electrochemically controlled nanoscale/single molecule systems. One is the broad class...

  1. OBSERVATIONS OF ROTATING RADIO TRANSIENTS WITH THE FIRST STATION OF THE LONG WAVELENGTH ARRAY

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, G. B.; Stovall, K.; McCrackan, M.; Dowell, J.; Schinzel, F. K. [Department of Physics and Astronomy, University of New Mexico, Albuquerque NM, 87131 (United States); McLaughlin, M. A.; Miller, R. [Department of Physics and Astronomy, West Virginia University, Morgantown, WV 26506-6315 (United States); Karako-Argaman, C. [Department of Physics, McGill University, 3600 University Street, Montreal, QC H3A 2T8 (Canada)

    2016-11-10

    Rotating radio transients (RRATs) are a subclass of pulsars first identified in 2006 that are detected only in searches for single pulses and not through their time averaged emission. Here, we present the results of observations of 19 RRATs using the first station of the Long Wavelength Array (LWA1) at frequencies between 30 and 88 MHz. The RRATs observed here were first detected in higher frequency pulsar surveys. Of the 19 RRATs observed, two sources were detected and their dispersion measures, periods, pulse profiles, and flux densities are reported and compared to previous higher frequency measurements. We find a low detection rate (11%), which could be a combination of the lower sensitivity of LWA1 compared to higher frequency telescopes, and the result of scattering by the interstellar medium or a spectral turnover.

  2. Excitonic Coupling in Linear and Trefoil Trimer Perylenediimide Molecules Probed by Single-Molecule Spectroscopy

    KAUST Repository

    Yoo, Hyejin

    2012-10-25

    Perylenediimide (PDI) molecules are promising building blocks for photophysical studies of electronic interactions within multichromophore arrays. Such PDI arrays are important materials for fabrication of molecular nanodevices such as organic light-emitting diodes, organic semiconductors, and biosensors because of their high photostability, chemical and physical inertness, electron affinity, and high tinctorial strength over the entire visible spectrum. In this work, PDIs have been organized into linear (L3) and trefoil (T3) trimer molecules and investigated by single-molecule fluorescence microscopy to probe the relationship between molecular structures and interchromophoric electronic interactions. We found a broad distribution of coupling strengths in both L3 and T3 and hence strong/weak coupling between PDI units by monitoring spectral peak shifts in single-molecule fluorescence spectra upon sequential photobleaching of each constituent chromophore. In addition, we used a wide-field defocused imaging technique to resolve heterogeneities in molecular structures of L3 and T3 embedded in a PMMA polymer matrix. A systematic comparison between the two sets of experimental results allowed us to infer the correlation between intermolecular interactions and molecular structures. Our results show control of the PDI intermolecular interactions using suitable multichromophoric structures. © 2012 American Chemical Society.

  3. Excitonic Coupling in Linear and Trefoil Trimer Perylenediimide Molecules Probed by Single-Molecule Spectroscopy

    KAUST Repository

    Yoo, Hyejin; Furumaki, Shu; Yang, Jaesung; Lee, Ji-Eun; Chung, Heejae; Oba, Tatsuya; Kobayashi, Hiroyuki; Rybtchinski, Boris; Wilson, Thea M.; Wasielewski, Michael R.; Vacha, Martin; Kim, Dongho

    2012-01-01

    Perylenediimide (PDI) molecules are promising building blocks for photophysical studies of electronic interactions within multichromophore arrays. Such PDI arrays are important materials for fabrication of molecular nanodevices such as organic light-emitting diodes, organic semiconductors, and biosensors because of their high photostability, chemical and physical inertness, electron affinity, and high tinctorial strength over the entire visible spectrum. In this work, PDIs have been organized into linear (L3) and trefoil (T3) trimer molecules and investigated by single-molecule fluorescence microscopy to probe the relationship between molecular structures and interchromophoric electronic interactions. We found a broad distribution of coupling strengths in both L3 and T3 and hence strong/weak coupling between PDI units by monitoring spectral peak shifts in single-molecule fluorescence spectra upon sequential photobleaching of each constituent chromophore. In addition, we used a wide-field defocused imaging technique to resolve heterogeneities in molecular structures of L3 and T3 embedded in a PMMA polymer matrix. A systematic comparison between the two sets of experimental results allowed us to infer the correlation between intermolecular interactions and molecular structures. Our results show control of the PDI intermolecular interactions using suitable multichromophoric structures. © 2012 American Chemical Society.

  4. Chemical Principles and Interference in the Electrical Conductance of Single Molecules

    DEFF Research Database (Denmark)

    Borges, Anders Christian

    , the conductance of molecules can vary orders of magnitude and the concept of interference is believed to play a major role in this. This thesis investigates the links between single molecule conductance, chemistry and interference effects in short organic molecules. It is investigated to which extent...... the conductance can be understood in terms of separate contributions and when the effects of interference are important. Links between chemical principles and constructive- and destructive interference effects are demonstrated using a combination of simple models, atomistic calculations and Scanning......-Tunneling Microscope Break-Junction experiments (STM-BJ). It is demonstrated that these links can be used to design molecules exhibiting surprising interference effects and to interpret and predict the trends in the characteristic conductance of single molecules without resorting to numerical computational methods...

  5. Spectrally resolved single-molecule electrometry

    Science.gov (United States)

    Ruggeri, F.; Krishnan, M.

    2018-03-01

    Escape-time electrometry is a recently developed experimental technique that offers the ability to measure the effective electrical charge of a single biomolecule in solution with sub-elementary charge precision. The approach relies on measuring the average escape-time of a single charged macromolecule or molecular species transiently confined in an electrostatic fluidic trap. Comparing the experiments with the predictions of a mean-field model of molecular electrostatics, we have found that the measured effective charge even reports on molecular conformation, e.g., folded or disordered state, and non-uniform charge distribution in disordered proteins or polyelectrolytes. Here we demonstrate the ability to use the spectral dimension to distinguish minute differences in electrical charge between individual molecules or molecular species in a single simultaneous measurement, under identical experimental conditions. Using one spectral channel for referenced measurement, this kind of photophysical distinguishability essentially eliminates the need for accurate knowledge of key experimental parameters, otherwise obtained through intensive characterization of the experimental setup. As examples, we demonstrate the ability to detect small differences (˜5%) in the length of double-stranded DNA fragments as well as single amino acid exchange in an intrinsically disordered protein, prothymosin α.

  6. 2012 Gordon Research Conference, Single molecule approaches to biology, July 15-20 2012

    Energy Technology Data Exchange (ETDEWEB)

    Fernandez, Julio M. [Columbia Univ., New York, NY (United States)

    2012-04-20

    Single molecule techniques are rapidly occupying a central role in biological research at all levels. This transition was made possible by the availability and dissemination of robust techniques that use fluorescence and force probes to track the conformation of molecules one at a time, in vitro as well as in live cells. Single-molecule approaches have changed the way many biological problems are studied. These novel techniques provide previously unobtainable data on fundamental biochemical processes that are essential for all forms of life. The ability of single-molecule approaches to avoid ensemble averaging and to capture transient intermediates and heterogeneous behavior renders them particularly powerful in elucidating mechanisms of the molecular systems that underpin the functioning of living cells. Hence, our conference seeks to disseminate the implementation and use of single molecule techniques in the pursuit of new biological knowledge. Topics covered include: Molecular Motors on the Move; Origin And Fate Of Proteins; Physical Principles Of Life; Molecules and Super-resolution Microscopy; Nanoswitches In Action; Active Motion Or Random Diffusion?; Building Blocks Of Living Cells; From Molecular Mechanics To Physiology; Tug-of-war: Force Spectroscopy Of Single Proteins.

  7. Blinking effect and the use of quantum dots in single molecule spectroscopy

    International Nuclear Information System (INIS)

    Rombach-Riegraf, Verena; Oswald, Peter; Bienert, Roland; Petersen, Jan; Domingo, M.P.; Pardo, Julian; Gräber, P.; Galvez, E.M.

    2013-01-01

    Highlights: ► It is possible to eliminate the blinking effect of a water-soluble QD. ► We provide a direct method to study protein function and dynamics at the single level. ► QD, potent tool for single molecule studies of biochemical and biological processes. -- Abstract: Luminescent semiconductor nanocrystals (quantum dots, QD) have unique photo-physical properties: high photostability, brightness and narrow size-tunable fluorescence spectra. Due to their unique properties, QD-based single molecule studies have become increasingly more popular during the last years. However QDs show a strong blinking effect (random and intermittent light emission), which may limit their use in single molecule fluorescence studies. QD blinking has been widely studied and some hypotheses have been done to explain this effect. Here we summarise what is known about the blinking effect in QDs, how this phenomenon may affect single molecule studies and, on the other hand, how the “on”/“off” states can be exploited in diverse experimental settings. In addition, we present results showing that site-directed binding of QD to cysteine residues of proteins reduces the blinking effect. This option opens a new possibility of using QDs to study protein–protein interactions and dynamics by single molecule fluorescence without modifying the chemical composition of the solution or the QD surface.

  8. Blinking effect and the use of quantum dots in single molecule spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Rombach-Riegraf, Verena; Oswald, Peter; Bienert, Roland; Petersen, Jan [Albert-Ludwigs-Universitaet Freiburg, Institut fuer Physikalische Chemie, Albertstrasse 23a, 79104 Freiburg (Germany); Domingo, M.P. [Instituto de Carboquimica (CSIC), Miguel Luesma 4, 50018 Zaragoza (Spain); Pardo, Julian [Grupo Apoptosis, Inmunidad y Cancer, Departamento Bioquimica y Biologia Molecular y Celular, Fac. Ciencias, Universidad de Zaragoza, Zaragoza (Spain); Fundacion Aragon I-D (ARAID), Gobierno de Aragon, Zaragoza (Spain); Immune Effector Cells Group, Aragon Health Research Institute (IIS Aragon), Biomedical Research Centre of Aragon (CIBA) Fundacion Aragon I-D - ARAID, Gobierno de Aragon, Zaragoza (Spain); Graeber, P. [Albert-Ludwigs-Universitaet Freiburg, Institut fuer Physikalische Chemie, Albertstrasse 23a, 79104 Freiburg (Germany); Galvez, E.M., E-mail: eva@icb.csic.es [Instituto de Carboquimica (CSIC), Miguel Luesma 4, 50018 Zaragoza (Spain); Immune Effector Cells Group, Aragon Health Research Institute (IIS Aragon), Biomedical Research Centre of Aragon (CIBA) Fundacion Aragon I-D - ARAID, Gobierno de Aragon, Zaragoza (Spain)

    2013-01-04

    Highlights: Black-Right-Pointing-Pointer It is possible to eliminate the blinking effect of a water-soluble QD. Black-Right-Pointing-Pointer We provide a direct method to study protein function and dynamics at the single level. Black-Right-Pointing-Pointer QD, potent tool for single molecule studies of biochemical and biological processes. -- Abstract: Luminescent semiconductor nanocrystals (quantum dots, QD) have unique photo-physical properties: high photostability, brightness and narrow size-tunable fluorescence spectra. Due to their unique properties, QD-based single molecule studies have become increasingly more popular during the last years. However QDs show a strong blinking effect (random and intermittent light emission), which may limit their use in single molecule fluorescence studies. QD blinking has been widely studied and some hypotheses have been done to explain this effect. Here we summarise what is known about the blinking effect in QDs, how this phenomenon may affect single molecule studies and, on the other hand, how the 'on'/'off' states can be exploited in diverse experimental settings. In addition, we present results showing that site-directed binding of QD to cysteine residues of proteins reduces the blinking effect. This option opens a new possibility of using QDs to study protein-protein interactions and dynamics by single molecule fluorescence without modifying the chemical composition of the solution or the QD surface.

  9. Plasmonic tunnel junctions for single-molecule redox chemistry.

    Science.gov (United States)

    de Nijs, Bart; Benz, Felix; Barrow, Steven J; Sigle, Daniel O; Chikkaraddy, Rohit; Palma, Aniello; Carnegie, Cloudy; Kamp, Marlous; Sundararaman, Ravishankar; Narang, Prineha; Scherman, Oren A; Baumberg, Jeremy J

    2017-10-20

    Nanoparticles attached just above a flat metallic surface can trap optical fields in the nanoscale gap. This enables local spectroscopy of a few molecules within each coupled plasmonic hotspot, with near thousand-fold enhancement of the incident fields. As a result of non-radiative relaxation pathways, the plasmons in such sub-nanometre cavities generate hot charge carriers, which can catalyse chemical reactions or induce redox processes in molecules located within the plasmonic hotspots. Here, surface-enhanced Raman spectroscopy allows us to track these hot-electron-induced chemical reduction processes in a series of different aromatic molecules. We demonstrate that by increasing the tunnelling barrier height and the dephasing strength, a transition from coherent to hopping electron transport occurs, enabling observation of redox processes in real time at the single-molecule level.

  10. Exponential yield sensitivity to long-wavelength asymmetries in three-dimensional simulations of inertial confinement fusion capsule implosions

    Energy Technology Data Exchange (ETDEWEB)

    Haines, Brian M., E-mail: bmhaines@lanl.gov [Los Alamos National Laboratory, MS T087, Los Alamos, New Mexico 87545 (United States)

    2015-08-15

    In this paper, we perform a series of high-resolution 3D simulations of an OMEGA-type inertial confinement fusion (ICF) capsule implosion with varying levels of initial long-wavelength asymmetries in order to establish the physical energy loss mechanism for observed yield degradation due to long-wavelength asymmetries in symcap (gas-filled capsule) implosions. These simulations demonstrate that, as the magnitude of the initial asymmetries is increased, shell kinetic energy is increasingly retained in the shell instead of being converted to fuel internal energy. This is caused by the displacement of fuel mass away from and shell material into the center of the implosion due to complex vortical flows seeded by the long-wavelength asymmetries. These flows are not fully turbulent, but demonstrate mode coupling through non-linear instability development during shell stagnation and late-time shock interactions with the shell interface. We quantify this effect by defining a separation lengthscale between the fuel mass and internal energy and show that this is correlated with yield degradation. The yield degradation shows an exponential sensitivity to the RMS magnitude of the long-wavelength asymmetries. This strong dependence may explain the lack of repeatability frequently observed in OMEGA ICF experiments. In contrast to previously reported mechanisms for yield degradation due to turbulent instability growth, yield degradation is not correlated with mixing between shell and fuel material. Indeed, an integrated measure of mixing decreases with increasing initial asymmetry magnitude due to delayed shock interactions caused by growth of the long-wavelength asymmetries without a corresponding delay in disassembly.

  11. Viruses and Tetraspanins: Lessons from Single Molecule Approaches

    Science.gov (United States)

    Dahmane, Selma; Rubinstein, Eric; Milhiet, Pierre-Emmanuel

    2014-01-01

    Tetraspanins are four-span membrane proteins that are widely distributed in multi-cellular organisms and involved in several infectious diseases. They have the unique property to form a network of protein-protein interaction within the plasma membrane, due to the lateral associations with one another and with other membrane proteins. Tracking tetraspanins at the single molecule level using fluorescence microscopy has revealed the membrane behavior of the tetraspanins CD9 and CD81 in epithelial cell lines, providing a first dynamic view of this network. Single molecule tracking highlighted that these 2 proteins can freely diffuse within the plasma membrane but can also be trapped, permanently or transiently, in tetraspanin-enriched areas. More recently, a similar strategy has been used to investigate tetraspanin membrane behavior in the context of human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) infection. In this review we summarize the main results emphasizing the relationship in terms of membrane partitioning between tetraspanins, some of their partners such as Claudin-1 and EWI-2, and viral proteins during infection. These results will be analyzed in the context of other membrane microdomains, stressing the difference between raft and tetraspanin-enriched microdomains, but also in comparison with virus diffusion at the cell surface. New advanced single molecule techniques that could help to further explore tetraspanin assemblies will be also discussed. PMID:24800676

  12. Transport mirages in single-molecule devices

    Science.gov (United States)

    Gaudenzi, R.; Misiorny, M.; Burzurí, E.; Wegewijs, M. R.; van der Zant, H. S. J.

    2017-03-01

    Molecular systems can exhibit a complex, chemically tailorable inner structure which allows for targeting of specific mechanical, electronic, and optical properties. At the single-molecule level, two major complementary ways to explore these properties are molecular quantum-dot structures and scanning probes. This article outlines comprehensive principles of electron-transport spectroscopy relevant to both these approaches and presents a new, high-resolution experiment on a high-spin single-molecule junction exemplifying these principles. Such spectroscopy plays a key role in further advancing our understanding of molecular and atomic systems, in particular, the relaxation of their spin. In this joint experimental and theoretical analysis, particular focus is put on the crossover between the resonant regime [single-electron tunneling] and the off-resonant regime [inelastic electron (co)tunneling spectroscopy (IETS)]. We show that the interplay of these two processes leads to unexpected mirages of resonances not captured by either of the two pictures alone. Although this turns out to be important in a large fraction of the possible regimes of level positions and bias voltages, it has been given little attention in molecular transport studies. Combined with nonequilibrium IETS—four-electron pump-probe excitations—these mirages provide crucial information on the relaxation of spin excitations. Our encompassing physical picture is supported by a master-equation approach that goes beyond weak coupling. The present work encourages the development of a broader connection between the fields of molecular quantum-dot and scanning probe spectroscopy.

  13. Plasmonics and single-molecule detection in evaporated silver-island films

    Energy Technology Data Exchange (ETDEWEB)

    Moula, G.; Aroca, R.F. [Materials and Surface Science Group, University of Windsor, Ontario (Canada); Rodriguez-Oliveros, R.; Sanchez-Gil, J.A. [Instituto de Estructura de la Materia, Consejo Superior de Investigaciones Cientificas, Serrano 121, 28006 Madrid (Spain); Albella, P. [Centro de Fisica de Materiales (CSIC-UPV/EHU) and Donostia International Physics Center (DIPC), 20018 Donostia, San Sebastian (Spain)

    2012-11-15

    The plasmonic origin of surface-enhanced Raman scattering (SERS) leads to the concept of hotspots and plasmon coupling that can be realized in the interstitial regions, or on specially engineered, silver and gold nanostructures. It is also possible to achieve spatial locations of high local field or hotspots on silver-island films (SIF) allowing single-molecule detection (SMD). When a single monomolecular layer coating the SIFs contains dye molecules dispersed in it, single-molecule impurities, (with an average of one hundred dye molecules in 1 {mu}m{sup 2}, which is the field of view of the micro-Raman system), SMD is observed as a rare statistical event. Here, the SMD results for silver-island films are presented, with the same nominal mass thickness, but differing in the localized surface plasmon resonance that is a function of the temperature of substrate during deposition. A blue-shifted plasmon can be seen as a decrease in plasmon coupling for deposition at higher temperature. A simple two-particle model for localized plasmon resonance coupling calculations, including the shape and substrate effects seems to explain the trend of observations. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  14. Experimental demonstration of a single-molecule electric motor.

    Science.gov (United States)

    Tierney, Heather L; Murphy, Colin J; Jewell, April D; Baber, Ashleigh E; Iski, Erin V; Khodaverdian, Harout Y; McGuire, Allister F; Klebanov, Nikolai; Sykes, E Charles H

    2011-09-04

    For molecules to be used as components in molecular machines, methods that couple individual molecules to external energy sources and that selectively excite motion in a given direction are required. Significant progress has been made in the construction of molecular motors powered by light and by chemical reactions, but electrically driven motors have not yet been built, despite several theoretical proposals for such motors. Here we report that a butyl methyl sulphide molecule adsorbed on a copper surface can be operated as a single-molecule electric motor. Electrons from a scanning tunnelling microscope are used to drive the directional motion of the molecule in a two-terminal setup. Moreover, the temperature and electron flux can be adjusted to allow each rotational event to be monitored at the molecular scale in real time. The direction and rate of the rotation are related to the chiralities of both the molecule and the tip of the microscope (which serves as the electrode), illustrating the importance of the symmetry of the metal contacts in atomic-scale electrical devices.

  15. Tilted Light Sheet Microscopy with 3D Point Spread Functions for Single-Molecule Super-Resolution Imaging in Mammalian Cells.

    Science.gov (United States)

    Gustavsson, Anna-Karin; Petrov, Petar N; Lee, Maurice Y; Shechtman, Yoav; Moerner, W E

    2018-02-01

    To obtain a complete picture of subcellular nanostructures, cells must be imaged with high resolution in all three dimensions (3D). Here, we present tilted light sheet microscopy with 3D point spread functions (TILT3D), an imaging platform that combines a novel, tilted light sheet illumination strategy with engineered long axial range point spread functions (PSFs) for low-background, 3D super localization of single molecules as well as 3D super-resolution imaging in thick cells. TILT3D is built upon a standard inverted microscope and has minimal custom parts. The axial positions of the single molecules are encoded in the shape of the PSF rather than in the position or thickness of the light sheet, and the light sheet can therefore be formed using simple optics. The result is flexible and user-friendly 3D super-resolution imaging with tens of nm localization precision throughout thick mammalian cells. We validated TILT3D for 3D super-resolution imaging in mammalian cells by imaging mitochondria and the full nuclear lamina using the double-helix PSF for single-molecule detection and the recently developed Tetrapod PSF for fiducial bead tracking and live axial drift correction. We envision TILT3D to become an important tool not only for 3D super-resolution imaging, but also for live whole-cell single-particle and single-molecule tracking.

  16. Tilted light sheet microscopy with 3D point spread functions for single-molecule super-resolution imaging in mammalian cells

    Science.gov (United States)

    Gustavsson, Anna-Karin; Petrov, Petar N.; Lee, Maurice Y.; Shechtman, Yoav; Moerner, W. E.

    2018-02-01

    To obtain a complete picture of subcellular nanostructures, cells must be imaged with high resolution in all three dimensions (3D). Here, we present tilted light sheet microscopy with 3D point spread functions (TILT3D), an imaging platform that combines a novel, tilted light sheet illumination strategy with engineered long axial range point spread functions (PSFs) for low-background, 3D super localization of single molecules as well as 3D super-resolution imaging in thick cells. TILT3D is built upon a standard inverted microscope and has minimal custom parts. The axial positions of the single molecules are encoded in the shape of the PSF rather than in the position or thickness of the light sheet, and the light sheet can therefore be formed using simple optics. The result is flexible and user-friendly 3D super-resolution imaging with tens of nm localization precision throughout thick mammalian cells. We validated TILT3D for 3D superresolution imaging in mammalian cells by imaging mitochondria and the full nuclear lamina using the double-helix PSF for single-molecule detection and the recently developed Tetrapod PSF for fiducial bead tracking and live axial drift correction. We envision TILT3D to become an important tool not only for 3D super-resolution imaging, but also for live whole-cell single-particle and single-molecule tracking.

  17. Spin interactions in Graphene-Single Molecule Magnets Hybrids

    Science.gov (United States)

    Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Aña; Luis, Fernando; Rauschenbach, Stephan; Dressel, Martin; Kern, Klaus; Burghard, Marko; Bogani, Lapo

    2014-03-01

    Graphene is a potential component of novel spintronics devices owing to its long spin diffusion length. Besides its use as spin-transport channel, graphene can be employed for the detection and manipulation of molecular spins. This requires an appropriate coupling between the sheets and the single molecular magnets (SMM). Here, we present a comprehensive characterization of graphene-Fe4 SMM hybrids. The Fe4 clusters are anchored non-covalently to the graphene following a diffusion-limited assembly and can reorganize into random networks when subjected to slightly elevated temperature. Molecules anchored on graphene sheets show unaltered static magnetic properties, whilst the quantum dynamics is profoundly modulated. Interaction with Dirac fermions becomes the dominant spin-relaxation channel, with observable effects produced by graphene phonons and reduced dipolar interactions. Coupling to graphene drives the spins over Villain's threshold, allowing the first observation of strongly-perturbative tunneling processes. Preliminary spin-transport experiments at low-temperature are further presented.

  18. Ultra-high-density 3D DNA arrays within nanoporous biocompatible membranes for single-molecule-level detection and purification of circulating nucleic acids

    Science.gov (United States)

    Aramesh, M.; Shimoni, O.; Fox, K.; Karle, T. J.; Lohrmann, A.; Ostrikov, K.; Prawer, S.; Cervenka, J.

    2015-03-01

    alumina membrane. The few nanometer-thick, yet perfect and continuous DLC-coating confers the chemical stability and biocompatibility of the sensor, allowing its direct application in biological conditions. The selective detection is based on complementary hybridization of a fluorescently-tagged circulating cancer oncomarker (a 21-mer nucleic acid) with covalently immobilized DNA on the surface of the membrane. The captured DNAs are detected in the nanoporous structure of the sensor using confocal scanning laser microscopy. The flow-through membrane sensor demonstrates broad-range sensitivity, spanning from 1015 molecules per cm2 down to single molecules, which is several orders of magnitude improvement compared to the flat DNA microarrays. Our study suggests that these flow-through type nanoporous sensors represent a new powerful platform for large volume sampling and ultrasensitive detection of different chemical biomarkers. Electronic supplementary information (ESI) available: Time dependent fluorescence intensity measurements, photoluminescence decay on flat and nanoporous arrays, fluorophore time traces and photoluminescence of AAO and DLC-AAO. See DOI: 10.1039/c4nr07351g

  19. Single Molecule Raman Detection of Enkephalin on Silver Colloidal Particles

    DEFF Research Database (Denmark)

    Kneipp, Katrin; Kneipp, Holger; Abdali, Salim

    2004-01-01

    the Raman signal the enkephalin molecules have been attached to silver colloidal cluster structures. The experiments demonstrate that the SERS signal of the strongly enhanced ring breathing vibration of phenylalanine at 1000 cm-1 can be used as “intrinsic marker” for detecting a single enkephalin molecule...... and for monitoring its diffusion on the surface of the silver colloidal cluster without using a specific label molecule....

  20. Click strategies for single-molecule protein fluorescence.

    Science.gov (United States)

    Milles, Sigrid; Tyagi, Swati; Banterle, Niccolò; Koehler, Christine; VanDelinder, Virginia; Plass, Tilman; Neal, Adrian P; Lemke, Edward A

    2012-03-21

    Single-molecule methods have matured into central tools for studies in biology. Foerster resonance energy transfer (FRET) techniques, in particular, have been widely applied to study biomolecular structure and dynamics. The major bottleneck for a facile and general application of these studies arises from the need to label biological samples site-specifically with suitable fluorescent dyes. In this work, we present an optimized strategy combining click chemistry and the genetic encoding of unnatural amino acids (UAAs) to overcome this limitation for proteins. We performed a systematic study with a variety of clickable UAAs and explored their potential for high-resolution single-molecule FRET (smFRET). We determined all parameters that are essential for successful single-molecule studies, such as accessibility of the probes, expression yield of proteins, and quantitative labeling. Our multiparameter fluorescence analysis allowed us to gain new insights into the effects and photophysical properties of fluorescent dyes linked to various UAAs for smFRET measurements. This led us to determine that, from the extended tool set that we now present, genetically encoding propargyllysine has major advantages for state-of-the-art measurements compared to other UAAs. Using this optimized system, we present a biocompatible one-step dual-labeling strategy of the regulatory protein RanBP3 with full labeling position freedom. Our technique allowed us then to determine that the region encompassing two FxFG repeat sequences adopts a disordered but collapsed state. RanBP3 serves here as a prototypical protein that, due to its multiple cysteines, size, and partially disordered structure, is not readily accessible to any of the typical structure determination techniques such as smFRET, NMR, and X-ray crystallography.

  1. Single atom and-molecules chemisorption on solid surfaces

    International Nuclear Information System (INIS)

    Anda, E.V.; Ure, J.E.; Majlis, N.

    1981-01-01

    A simplified model for the microscopic interpretation of single atom and- molecules chemisorption on metallic surfaces is presented. An appropriated hamiltonian for this problem is resolved, through the Green's function formalism. (L.C.) [pt

  2. Long-wavelength fluctuations and the glass transition in two dimensions and three dimensions.

    Science.gov (United States)

    Vivek, Skanda; Kelleher, Colm P; Chaikin, Paul M; Weeks, Eric R

    2017-02-21

    Phase transitions significantly differ between 2D and 3D systems, but the influence of dimensionality on the glass transition is unresolved. We use microscopy to study colloidal systems as they approach their glass transitions at high concentrations and find differences between two dimensions and three dimensions. We find that, in two dimensions, particles can undergo large displacements without changing their position relative to their neighbors, in contrast with three dimensions. This is related to Mermin-Wagner long-wavelength fluctuations that influence phase transitions in two dimensions. However, when measuring particle motion only relative to their neighbors, two dimensions and three dimensions have similar behavior as the glass transition is approached, showing that the long-wavelength fluctuations do not cause a fundamental distinction between 2D and 3D glass transitions.

  3. Simple test system for single molecule recognition force microscopy

    International Nuclear Information System (INIS)

    Riener, Christian K.; Stroh, Cordula M.; Ebner, Andreas; Klampfl, Christian; Gall, Alex A.; Romanin, Christoph; Lyubchenko, Yuri L.; Hinterdorfer, Peter; Gruber, Hermann J.

    2003-01-01

    We have established an easy-to-use test system for detecting receptor-ligand interactions on the single molecule level using atomic force microscopy (AFM). For this, avidin-biotin, probably the best characterized receptor-ligand pair, was chosen. AFM sensors were prepared containing tethered biotin molecules at sufficiently low surface concentrations appropriate for single molecule studies. A biotin tether, consisting of a 6 nm poly(ethylene glycol) (PEG) chain and a functional succinimide group at the other end, was newly synthesized and covalently coupled to amine-functionalized AFM tips. In particular, PEG 800 diamine was glutarylated, the mono-adduct NH 2 -PEG-COOH was isolated by ion exchange chromatography and reacted with biotin succinimidylester to give biotin-PEG-COOH which was then activated as N-hydroxysuccinimide (NHS) ester to give the biotin-PEG-NHS conjugate which was coupled to the aminofunctionalized AFM tip. The motional freedom provided by PEG allows for free rotation of the biotin molecule on the AFM sensor and for specific binding to avidin which had been adsorbed to mica surfaces via electrostatic interactions. Specific avidin-biotin recognition events were discriminated from nonspecific tip-mica adhesion by their typical unbinding force (∼40 pN at 1.4 nN/s loading rate), unbinding length (<13 nm), the characteristic nonlinear force-distance relation of the PEG linker, and by specific block with excess of free d-biotin. The convenience of the test system allowed to evaluate, and compare, different methods and conditions of tip aminofunctionalization with respect to specific binding and nonspecific adhesion. It is concluded that this system is well suited as calibration or start-up kit for single molecule recognition force microscopy

  4. Fabrication of Low Noise Borosilicate Glass Nanopores for Single Molecule Sensing.

    Directory of Open Access Journals (Sweden)

    Jayesh A Bafna

    Full Text Available We show low-cost fabrication and characterization of borosilicate glass nanopores for single molecule sensing. Nanopores with diameters of ~100 nm were fabricated in borosilicate glass capillaries using laser assisted glass puller. We further achieve controlled reduction and nanometer-size control in pore diameter by sculpting them under constant electron beam exposure. We successfully fabricate pore diameters down to 6 nm. We next show electrical characterization and low-noise behavior of these borosilicate nanopores and compare their taper geometries. We show, for the first time, a comprehensive characterization of glass nanopore conductance across six-orders of magnitude (1M-1μM of salt conditions, highlighting the role of buffer conditions. Finally, we demonstrate single molecule sensing capabilities of these devices with real-time translocation experiments of individual λ-DNA molecules. We observe distinct current blockage signatures of linear as well as folded DNA molecules as they undergo voltage-driven translocation through the glass nanopores. We find increased signal to noise for single molecule detection for higher trans-nanopore driving voltages. We propose these nanopores will expand the realm of applications for nanopore platform.

  5. Precision analysis for standard deviation measurements of immobile single fluorescent molecule images.

    Science.gov (United States)

    DeSantis, Michael C; DeCenzo, Shawn H; Li, Je-Luen; Wang, Y M

    2010-03-29

    Standard deviation measurements of intensity profiles of stationary single fluorescent molecules are useful for studying axial localization, molecular orientation, and a fluorescence imaging system's spatial resolution. Here we report on the analysis of the precision of standard deviation measurements of intensity profiles of single fluorescent molecules imaged using an EMCCD camera.We have developed an analytical expression for the standard deviation measurement error of a single image which is a function of the total number of detected photons, the background photon noise, and the camera pixel size. The theoretical results agree well with the experimental, simulation, and numerical integration results. Using this expression, we show that single-molecule standard deviation measurements offer nanometer precision for a large range of experimental parameters.

  6. Applications of a single-molecule detection in early disease diagnosis and enzymatic reaction study

    Energy Technology Data Exchange (ETDEWEB)

    Li, Jiangwei [Iowa State Univ., Ames, IA (United States)

    2008-01-01

    polyclonal detector antibody. The capture antibody was covalently immobilized on modified glass slides. The detector antibody was conjugated with AF532 labeled secondary antibody prior to being used as probe for the antigen. Imaging was performed with a TIRF system. This technique is demonstrated for detecting HIV-1 p24 antigen down to 0.1 pg/mL with a dynamic range of over 4 orders of magnitude. A Langmuir isotherm fit the molecule count dependence on the target concentration. The results also showed that neither sensitivity nor dynamic range was affected by the biological matrix. SMISA is therefore a promising approach for the early diagnosis of virus-induced diseases. Single-molecule enzymatic kinetics and enantioselectivity were monitored in real time by using TIRF microscopy. AF532 labeled poly-L-lysine (PLL) or poly-D-lysine (PDL) was covalently immobilized on a dithiobis (succinimidyl undecanoate) self-assembled monolayer (DSU SAM). Chain shortening due to enzymatic hydrolysis resulted in the reduction of the individual fluorescence intensities. A broad distribution was obtained when 100 single-molecule half-lives were analyzed. However, the detailed hydrolysis process involved also a long-lived component and an induction period that varied significantly among molecules. Charge and steric heterogeneity at the surface are responsible for these features.

  7. Revealing the Raft Domain Organization in the Plasma Membrane by Single-Molecule Imaging of Fluorescent Ganglioside Analogs.

    Science.gov (United States)

    Suzuki, Kenichi G N; Ando, Hiromune; Komura, Naoko; Konishi, Miku; Imamura, Akihiro; Ishida, Hideharu; Kiso, Makoto; Fujiwara, Takahiro K; Kusumi, Akihiro

    2018-01-01

    Gangliosides have been implicated in a variety of physiological processes, particularly in the formation and function of raft domains in the plasma membrane. However, the scarcity of suitable fluorescent ganglioside analogs had long prevented us from determining exactly how gangliosides perform their functions in the live-cell plasma membrane. With the development of new fluorescent ganglioside analogs, as described by Komura et al. (2017), this barrier has been broken. We can now address the dynamic behaviors of gangliosides in the live-cell plasma membrane, using fluorescence microscopy, particularly by single-fluorescent molecule imaging and tracking. Single-molecule tracking of fluorescent GM1 and GM3 revealed that these molecules are transiently and dynamically recruited to monomers (monomer-associated rafts) and homodimer rafts of the raftophilic GPI-anchored protein CD59 in quiescent cells, with exponential residency times of 12 and 40ms, respectively, in a manner dependent on raft-lipid interactions. Upon CD59 stimulation, which induces CD59-cluster signaling rafts, the fluorescent GM1 and GM3 analogs were recruited to the signaling rafts, with a lifetime of 48ms. These results represent the first direct evidence that GPI-anchored receptors and gangliosides interact in a cholesterol-dependent manner. Furthermore, they show that gangliosides continually move in and out of rafts that contain CD59 in an extremely dynamic manner, with much higher frequency than expected previously. Such studies would not have been possible without fluorescent ganglioside probes, which exhibit native-like behavior and single-molecule tracking. In this chapter, we review the methods for single-molecule tracking of fluorescent ganglioside analogs and the results obtained by applying these methods. © 2018 Elsevier Inc. All rights reserved.

  8. Quantum interference effects at room temperature in OPV-based single-molecule junctions

    DEFF Research Database (Denmark)

    Arroyo, Carlos R.; Frisenda, Riccardo; Moth-Poulsen, Kasper

    2013-01-01

    Interference effects on charge transport through an individual molecule can lead to a notable modulation and suppression on its conductance. In this letter, we report the observation of quantum interference effects occurring at room temperature in single-molecule junctions based on oligo(3......)-phenylenevinylene (OPV3) derivatives, in which the central benzene ring is coupled to either para- or meta-positions. Using the break-junction technique, we find that the conductance for a single meta-OPV3 molecule wired between gold electrodes is one order of magnitude smaller than that of a para-OPV3 molecule...

  9. Single-molecule pull-down (SiMPull) for new-age biochemistry: methodology and biochemical applications of single-molecule pull-down (SiMPull) for probing biomolecular interactions in crude cell extracts.

    Science.gov (United States)

    Aggarwal, Vasudha; Ha, Taekjip

    2014-11-01

    Macromolecular interactions play a central role in many biological processes. Protein-protein interactions have mostly been studied by co-immunoprecipitation, which cannot provide quantitative information on all possible molecular connections present in the complex. We will review a new approach that allows cellular proteins and biomolecular complexes to be studied in real-time at the single-molecule level. This technique is called single-molecule pull-down (SiMPull), because it integrates principles of conventional immunoprecipitation with the powerful single-molecule fluorescence microscopy. SiMPull is used to count how many of each protein is present in the physiological complexes found in cytosol and membranes. Concurrently, it serves as a single-molecule biochemical tool to perform functional studies on the pulled-down proteins. In this review, we will focus on the detailed methodology of SiMPull, its salient features and a wide range of biological applications in comparison with other biosensing tools. © 2014 WILEY Periodicals, Inc.

  10. Nano- and micro-fabrication for single-molecule biological studies

    NARCIS (Netherlands)

    Huang, Z.

    2012-01-01

    Heterogeneity is a general feature in biological system. In order to avoid possible misleading effects of ensemble averaging, and to ensure a correct understanding of the biological system, it is very important to look into individuals, such as a single bio-molecule or a single cell, for details.

  11. Fluorescence blinking in MEH-PPV single molecules at low temperature

    International Nuclear Information System (INIS)

    Mirzov, O.; Cichos, F.; Borczyskowski, C. von; Scheblykin, I.

    2005-01-01

    Fluorescence intensity transients of single molecules of the conjugated polymer poly[2-methoxy,5-(2'-ethylhexyloxy)-p-phenylene-vinylene] (MEH-PPV) were studied at 15 K. Fluorescence blinking behavior was observed despite the expected low-temperature suppression of energy migration in such disordered molecular systems. Presence of the fluorescence blinking effect at 15 K indicates that the single molecules possess a collapsed conformation with characteristic size of not more than several nanometers, which corresponds to only a few exciton hops over a polymer chain

  12. Radio frequency scanning tunneling spectroscopy for single-molecule spin resonance.

    Science.gov (United States)

    Müllegger, Stefan; Tebi, Stefano; Das, Amal K; Schöfberger, Wolfgang; Faschinger, Felix; Koch, Reinhold

    2014-09-26

    We probe nuclear and electron spins in a single molecule even beyond the electromagnetic dipole selection rules, at readily accessible magnetic fields (few mT) and temperatures (5 K) by resonant radio-frequency current from a scanning tunneling microscope. We achieve subnanometer spatial resolution combined with single-spin sensitivity, representing a 10 orders of magnitude improvement compared to existing magnetic resonance techniques. We demonstrate the successful resonant spectroscopy of the complete manifold of nuclear and electronic magnetic transitions of up to ΔI(z)=±3 and ΔJ(z)=±12 of single quantum spins in a single molecule. Our method of resonant radio-frequency scanning tunneling spectroscopy offers, atom-by-atom, unprecedented analytical power and spin control with an impact on diverse fields of nanoscience and nanotechnology.

  13. Vertically integrated (Ga, In)N nanostructures for future single photon emitters operating in the telecommunication wavelength range

    International Nuclear Information System (INIS)

    Winden, A; Mikulics, M; Grützmacher, D; Hardtdegen, H

    2013-01-01

    Important technological steps are discussed and realized for future room-temperature operation of III-nitride single photon emitters. First, the growth technology of positioned single pyramidal InN nanostructures capped by Mg-doped GaN is presented. The optimization of their optical characteristics towards narrowband emission in the telecommunication wavelength range is demonstrated. In addition, a device concept and technology was developed so that the nanostructures became singularly addressable. It was found that the nanopyramids emit in the telecommunication wavelength range if their size is chosen appropriately. A p-GaN contacting layer was successfully produced as a cap to the InN pyramids and the top p-contact was achievable using an intrinsically conductive polymer PEDOT:PSS, allowing a 25% increase in light transmittance compared to standard Ni/Au contact technology. Single nanopyramids were successfully integrated into a high-frequency device layout. These decisive technology steps provide a promising route to electrically driven and room-temperature operating InN based single photon emitters in the telecommunication wavelength range. (paper)

  14. A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Hao; Suslov, Nikolai B.; Li, Nan-Sheng; Shelke, Sandip A.; Evans, Molly E.; Koldobskaya, Yelena; Rice, Phoebe A.; Piccirilli, Joseph A. [UC

    2014-08-21

    Spinach is an in vitro–selected RNA aptamer that binds a GFP-like ligand and activates its green fluorescence. Spinach is thus an RNA analog of GFP and has potentially widespread applications for in vivo labeling and imaging. We used antibody-assisted crystallography to determine the structures of Spinach both with and without bound fluorophore at 2.2-Å and 2.4-Å resolution, respectively. Spinach RNA has an elongated structure containing two helical domains separated by an internal bulge that folds into a G-quadruplex motif of unusual topology. The G-quadruplex motif and adjacent nucleotides comprise a partially preformed binding site for the fluorophore. The fluorophore binds in a planar conformation and makes extensive aromatic stacking and hydrogen bond interactions with the RNA. Our findings provide a foundation for structure-based engineering of new fluorophore-binding RNA aptamers.

  15. Single-molecule magnets on a polymeric thin film as magnetic quantum bits

    Science.gov (United States)

    Ruiz-Molina, Daniel; Gomez, Jordi; Mas-Torrent, Marta; Balana, Ana Isabel; Domingo, Nues; Tejada, Javier; Martinez, Maria Teresa; Rovira, Concepcio; Veciana, Jaume

    2003-04-01

    Single-molecule magnets (SMM) have a large-spin ground state with appreciable magnetic anisotropy, resulting in a barrier for the spin reversal As a consequence, interesting magnetic properties such as out-of-phase ac magnetic susceptibility signals and stepwise magnetization hysteresis loops are observed. In addition to resonant magnetization tunnelling, during the last few years several other interesting phenomena have also been reported. The origin of the slow magnetization relaxation rates as well as of other phenomena are due to individual molecules rather than to long-range ordering; as confirmed by magnetization relaxation and heat capacity studies. Therefore, SMM represent nanoscale magnetic particles of a sharply defined size that offer the potential access to the ultimate high-density information storage devices as well as for quantum computing applications. However, if a truly molecular computational device based on SMM is to be achieved, new systematic studies that allow us to find a proper way to address properly oriented individual molecules or molecular aggregates onto the surface of a thin film, where each molecule or molecular aggregate can be used as a bit of information, are highly required. Here we report a new soft, reliable and simple methodology to address individual Mn12 molecules onto a film surface, as revealed by Atomic Force Microscopy (AFM) and Magnetic Force Microscopy (MFM) images. Moreover, the advantageous properties of polymeric matrices, such as flexibility, transparency and low density, make this type of materials very interesting for potential applications.

  16. A 12 GHz wavelength spacing multi-wavelength laser source for wireless communication systems

    Science.gov (United States)

    Peng, P. C.; Shiu, R. K.; Bitew, M. A.; Chang, T. L.; Lai, C. H.; Junior, J. I.

    2017-08-01

    This paper presents a multi-wavelength laser source with 12 GHz wavelength spacing based on a single distributed feedback laser. A light wave generated from the distributed feedback laser is fed into a frequency shifter loop consisting of 50:50 coupler, dual-parallel Mach-Zehnder modulator, optical amplifier, optical filter, and polarization controller. The frequency of the input wavelength is shifted and then re-injected into the frequency shifter loop. By re-injecting the shifted wavelengths multiple times, we have generated 84 optical carriers with 12 GHz wavelength spacing and stable output power. For each channel, two wavelengths are modulated by a wireless data using the phase modulator and transmitted through a 25 km single mode fiber. In contrast to previously developed schemes, the proposed laser source does not incur DC bias drift problem. Moreover, it is a good candidate for radio-over-fiber systems to support multiple users using a single distributed feedback laser.

  17. Current rectification in a single molecule diode: the role of electrode coupling.

    Science.gov (United States)

    Sherif, Siya; Rubio-Bollinger, Gabino; Pinilla-Cienfuegos, Elena; Coronado, Eugenio; Cuevas, Juan Carlos; Agraït, Nicolás

    2015-07-24

    We demonstrate large rectification ratios (> 100) in single-molecule junctions based on a metal-oxide cluster (polyoxometalate), using a scanning tunneling microscope (STM) both at ambient conditions and at low temperature. These rectification ratios are the largest ever observed in a single-molecule junction, and in addition these junctions sustain current densities larger than 10(5) A cm(-2). By following the variation of the I-V characteristics with tip-molecule separation we demonstrate unambiguously that rectification is due to asymmetric coupling to the electrodes of a molecule with an asymmetric level structure. This mechanism can be implemented in other type of molecular junctions using both organic and inorganic molecules and provides a simple strategy for the rational design of molecular diodes.

  18. White-light phosphorescence emission from a single molecule: application to OLED.

    Science.gov (United States)

    Bolink, Henk J; De Angelis, Filippo; Baranoff, Etienne; Klein, Cédric; Fantacci, Simona; Coronado, Eugenio; Sessolo, Michele; Kalyanasundaram, K; Grätzel, Michael; Nazeeruddin, Md K

    2009-08-21

    A simple mononuclear cyclometallated iridium(iii) complex exhibits white photo- and electro- luminescence in the wavelength range from 440 to 800 nm, which originates from a single emitting excited state of mixed character.

  19. Single molecule diffusion and the solution of the spherically symmetric residence time equation.

    Science.gov (United States)

    Agmon, Noam

    2011-06-16

    The residence time of a single dye molecule diffusing within a laser spot is propotional to the total number of photons emitted by it. With this application in mind, we solve the spherically symmetric "residence time equation" (RTE) to obtain the solution for the Laplace transform of the mean residence time (MRT) within a d-dimensional ball, as a function of the initial location of the particle and the observation time. The solutions for initial conditions of potential experimental interest, starting in the center, on the surface or uniformly within the ball, are explicitly presented. Special cases for dimensions 1, 2, and 3 are obtained, which can be Laplace inverted analytically for d = 1 and 3. In addition, the analytic short- and long-time asymptotic behaviors of the MRT are derived and compared with the exact solutions for d = 1, 2, and 3. As a demonstration of the simplification afforded by the RTE, the Appendix obtains the residence time distribution by solving the Feynman-Kac equation, from which the MRT is obtained by differentiation. Single-molecule diffusion experiments could be devised to test the results for the MRT presented in this work. © 2011 American Chemical Society

  20. Thermophoretic forces on DNA measured with a single-molecule spring balance

    DEFF Research Database (Denmark)

    Pedersen, Jonas Nyvold; Lüscher, Christopher James; Marie, Rodolphe

    2014-01-01

    We stretch a single DNA molecule with thermophoretic forces and measure these forces with a spring balance: the DNA molecule itself. It is an entropic spring which we calibrate, using as a benchmark its Brownian motion in the nanochannel that contains and prestretches it. This direct measurement ....... We find the Soret coefficient per unit length of DNA at various ionic strengths. It agrees, with novel precision, with results obtained in bulk for DNA too short to shield itself and with the thermodynamic model of thermophoresis.......We stretch a single DNA molecule with thermophoretic forces and measure these forces with a spring balance: the DNA molecule itself. It is an entropic spring which we calibrate, using as a benchmark its Brownian motion in the nanochannel that contains and prestretches it. This direct measurement...

  1. Experimental and Computational Characterization of Biological Liquid Crystals: A Review of Single-Molecule Bioassays

    Directory of Open Access Journals (Sweden)

    Sungsoo Na

    2009-09-01

    Full Text Available Quantitative understanding of the mechanical behavior of biological liquid crystals such as proteins is essential for gaining insight into their biological functions, since some proteins perform notable mechanical functions. Recently, single-molecule experiments have allowed not only the quantitative characterization of the mechanical behavior of proteins such as protein unfolding mechanics, but also the exploration of the free energy landscape for protein folding. In this work, we have reviewed the current state-of-art in single-molecule bioassays that enable quantitative studies on protein unfolding mechanics and/or various molecular interactions. Specifically, single-molecule pulling experiments based on atomic force microscopy (AFM have been overviewed. In addition, the computational simulations on single-molecule pulling experiments have been reviewed. We have also reviewed the AFM cantilever-based bioassay that provides insight into various molecular interactions. Our review highlights the AFM-based single-molecule bioassay for quantitative characterization of biological liquid crystals such as proteins.

  2. Ratiometric fluorescent sensing of pH values in living cells by dual-fluorophore-labeled i-motif nanoprobes.

    Science.gov (United States)

    Huang, Jin; Ying, Le; Yang, Xiaohai; Yang, Yanjing; Quan, Ke; Wang, He; Xie, Nuli; Ou, Min; Zhou, Qifeng; Wang, Kemin

    2015-09-01

    We designed a new ratiometric fluorescent nanoprobe for sensing pH values in living cells. Briefly, the nanoprobe consists of a gold nanoparticle (AuNP), short single-stranded oligonucleotides, and dual-fluorophore-labeled i-motif sequences. The short oligonucleotides are designed to bind with the i-motif sequences and immobilized on the AuNP surface via Au-S bond. At neutral pH, the dual fluorophores are separated, resulting in very low fluorescence resonance energy transfer (FRET) efficiency. At acidic pH, the i-motif strands fold into a quadruplex structure and leave the AuNP, bringing the dual fluorophores into close proximity, resulting in high FRET efficiency, which could be used as a signal for pH sensing. The nanoprobe possesses abilities of cellular transfection, enzymatic protection, fast response and quantitative pH detection. The in vitro and intracellular applications of the nanoprobe were demonstrated, which showed excellent response in the physiological pH range. Furthermore, our experimental results suggested that the nanoprobe showed excellent spatial and temporal resolution in living cells. We think that the ratiometric sensing strategy could potentially be applied to create a variety of new multicolor sensors for intracellular detection.

  3. Nonequilibrium Chemical Effects in Single-Molecule SERS Revealed by Ab Initio Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, Sean A.; Apra, Edoardo; Govind, Niranjan; Hess, Wayne P.; El-Khoury, Patrick Z.

    2017-02-03

    Recent developments in nanophotonics have paved the way for achieving significant advances in the realm of single molecule chemical detection, imaging, and dynamics. In particular, surface-enhanced Raman scattering (SERS) is a powerful analytical technique that is now routinely used to identify the chemical identity of single molecules. Understanding how nanoscale physical and chemical processes affect single molecule SERS spectra and selection rules is a challenging task, and is still actively debated. Herein, we explore underappreciated chemical phenomena in ultrasensitive SERS. We observe a fluctuating excited electronic state manifold, governed by the conformational dynamics of a molecule (4,4’-dimercaptostilbene, DMS) interacting with a metallic cluster (Ag20). This affects our simulated single molecule SERS spectra; the time trajectories of a molecule interacting with its unique local environment dictates the relative intensities of the observable Raman-active vibrational states. Ab initio molecular dynamics of a model Ag20-DMS system are used to illustrate both concepts in light of recent experimental results.

  4. Bright Single InAsP Quantum Dots at Telecom Wavelengths in Position-Controlled InP Nanowires: The Role of the Photonic Waveguide.

    Science.gov (United States)

    Haffouz, Sofiane; Zeuner, Katharina D; Dalacu, Dan; Poole, Philip J; Lapointe, Jean; Poitras, Daniel; Mnaymneh, Khaled; Wu, Xiaohua; Couillard, Martin; Korkusinski, Marek; Schöll, Eva; Jöns, Klaus D; Zwiller, Valery; Williams, Robin L

    2018-05-09

    We report on the site-selected growth of bright single InAsP quantum dots embedded within InP photonic nanowire waveguides emitting at telecom wavelengths. We demonstrate a dramatic dependence of the emission rate on both the emission wavelength and the nanowire diameter. With an appropriately designed waveguide, tailored to the emission wavelength of the dot, an increase in the count rate by nearly 2 orders of magnitude (0.4 to 35 kcps) is obtained for quantum dots emitting in the telecom O-band, showing high single-photon purity with multiphoton emission probabilities down to 2%. Using emission-wavelength-optimized waveguides, we demonstrate bright, narrow-line-width emission from single InAsP quantum dots with an unprecedented tuning range of 880 to 1550 nm. These results pave the way toward efficient single-photon sources at telecom wavelengths using deterministically grown InAsP/InP nanowire quantum dots.

  5. Enrichment of megabase-sized DNA molecules for single-molecule optical mapping and next-generation sequencing

    DEFF Research Database (Denmark)

    Łopacińska-Jørgensen, Joanna M; Pedersen, Jonas Nyvold; Bak, Mads

    2017-01-01

    Next-generation sequencing (NGS) has caused a revolution, yet left a gap: long-range genetic information from native, non-amplified DNA fragments is unavailable. It might be obtained by optical mapping of megabase-sized DNA molecules. Frequently only a specific genomic region is of interest, so......-megabase- to megabase-sized DNA molecules were recovered from the gel and analysed by denaturation-renaturation optical mapping. Size-selected molecules from the same gel were sequenced by NGS. The optically mapped molecules and the NGS reads showed enrichment from regions defined by NotI restriction sites. We...... demonstrate that the unannotated genome can be characterized in a locus-specific manner via molecules partially overlapping with the annotated genome. The method is a promising tool for investigation of structural variants in enriched human genomic regions for both research and diagnostic purposes. Our...

  6. A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization

    NARCIS (Netherlands)

    van der Velde, Jasper H M; Oelerich, Jens; Huang, Jingyi; Smit, Jochem H; Aminian Jazi, Atieh; Galiani, Silvia; Kolmakov, Kirill; Guoridis, Giorgos; Eggeling, Christian; Herrmann, Andreas; Roelfes, Gerard; Cordes, Thorben

    2016-01-01

    Intramolecular photostabilization via triple-state quenching was recently revived as a tool to impart synthetic organic fluorophores with 'self-healing' properties. To date, utilization of such fluorophore derivatives is rare due to their elaborate multi-step synthesis. Here we present a general

  7. Long-wavelength germanium photodetectors by ion implantation

    International Nuclear Information System (INIS)

    Wu, I.C.; Beeman, J.W.; Luke, P.N.; Hansen, W.L.; Haller, E.E.

    1990-11-01

    Extrinsic far-infrared photoconductivity in thin high-purity germanium wafers implanted with multiple-energy boron ions has been investigated. Initial results from Fourier transform spectrometer(FTS) measurements have demonstrated that photodetectors fabricated from this material have an extended long-wavelength threshold near 192μm. Due to the high-purity substrate, the ability to block the hopping conduction in the implanted IR-active layer yields dark currents of less than 100 electrons/sec at temperatures below 1.3 K under an operating bias of up to 70 mV. Optimum peak responsivity and noise equivalent power (NEP) for these sensitive detectors are 0.9 A/W and 5 x 10 -16 W/Hz 1/2 at 99 μm, respectively. The dependence of the performance of devices on the residual donor concentration in the implanted layer will be discussed. 12 refs., 4 figs

  8. Towards Controlled Single-Molecule Manipulation Using “Real-Time” Molecular Dynamics Simulation: A GPU Implementation

    Directory of Open Access Journals (Sweden)

    Dyon van Vreumingen

    2018-05-01

    Full Text Available Molecular electronics saw its birth with the idea to build electronic circuitry with single molecules as individual components. Even though commercial applications are still modest, it has served an important part in the study of fundamental physics at the scale of single atoms and molecules. It is now a routine procedure in many research groups around the world to connect a single molecule between two metallic leads. What is unknown is the nature of this coupling between the molecule and the leads. We have demonstrated recently (Tewari, 2018, Ph.D. Thesis our new setup based on a scanning tunneling microscope, which can be used to controllably manipulate single molecules and atomic chains. In this article, we will present the extension of our molecular dynamic simulator attached to this system for the manipulation of single molecules in real time using a graphics processing unit (GPU. This will not only aid in controlled lift-off of single molecules, but will also provide details about changes in the molecular conformations during the manipulation. This information could serve as important input for theoretical models and for bridging the gap between the theory and experiments.

  9. A Highly Specific Gold Nanoprobe for Live-Cell Single-Molecule Imaging

    Science.gov (United States)

    Leduc, Cécile; Si, Satyabrata; Gautier, Jérémie; Soto-Ribeiro, Martinho; Wehrle-Haller, Bernhard; Gautreau, Alexis; Giannone, Grégory; Cognet, Laurent; Lounis, Brahim

    2013-04-01

    Single molecule tracking in live cells is the ultimate tool to study subcellular protein dynamics, but it is often limited by the probe size and photostability. Due to these issues, long-term tracking of proteins in confined and crowded environments, such as intracellular spaces, remains challenging. We have developed a novel optical probe consisting of 5-nm gold nanoparticles functionalized with a small fragment of camelid antibodies that recognize widely used GFPs with a very high affinity, which we call GFP-nanobodies. These small gold nanoparticles can be detected and tracked using photothermal imaging for arbitrarily long periods of time. Surface and intracellular GFP-proteins were effectively labeled even in very crowded environments such as adhesion sites and cytoskeletal structures both in vitro and in live cell cultures. These nanobody-coated gold nanoparticles are probes with unparalleled capabilities; small size, perfect photostability, high specificity, and versatility afforded by combination with the vast existing library of GFP-tagged proteins.

  10. Single-Molecule Stochastic Resonance

    Directory of Open Access Journals (Sweden)

    K. Hayashi

    2012-08-01

    Full Text Available Stochastic resonance (SR is a well-known phenomenon in dynamical systems. It consists of the amplification and optimization of the response of a system assisted by stochastic (random or probabilistic noise. Here we carry out the first experimental study of SR in single DNA hairpins which exhibit cooperatively transitions from folded to unfolded configurations under the action of an oscillating mechanical force applied with optical tweezers. By varying the frequency of the force oscillation, we investigate the folding and unfolding kinetics of DNA hairpins in a periodically driven bistable free-energy potential. We measure several SR quantifiers under varied conditions of the experimental setup such as trap stiffness and length of the molecular handles used for single-molecule manipulation. We find that a good quantifier of the SR is the signal-to-noise ratio (SNR of the spectral density of measured fluctuations in molecular extension of the DNA hairpins. The frequency dependence of the SNR exhibits a peak at a frequency value given by the resonance-matching condition. Finally, we carry out experiments on short hairpins that show how SR might be useful for enhancing the detection of conformational molecular transitions of low SNR.

  11. Single Molecule Screening of Disease DNA Without Amplification

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Ji-Young [Iowa State Univ., Ames, IA (United States)

    2006-01-01

    The potential of single molecule detection as an analysis tool in biological and medical fields is well recognized today. This fast evolving technique will provide fundamental sensitivity to pick up individual pathogen molecules, and therefore contribute to a more accurate diagnosis and a better chance for a complete cure. Many studies are being carried out to successfully apply this technique in real screening fields. In this dissertation, several attempts are shown that have been made to test and refine the application of the single molecule technique as a clinical screening method. A basic applicability was tested with a 100% target content sample, using electrophoretic mobility and multiple colors as identification tools. Both electrophoretic and spectral information of individual molecule were collected within a second, while the molecule travels along the flow in a capillary. Insertion of a transmission grating made the recording of the whole spectrum of a dye-stained molecule possible without adding complicated instrumental components. Collecting two kinds of information simultaneously and combining them allowed more thorough identification, up to 98.8% accuracy. Probing mRNA molecules with fluorescently labeled cDNA via hybridization was also carried out. The spectral differences among target, probe, and hybrid were interpreted in terms of dispersion distances after transmission grating, and used for the identification of each molecule. The probes were designed to have the least background when they are free, but have strong fluorescence after hybridization via fluorescence resonance energy transfer. The mRNA-cDNA hybrids were further imaged in whole blood, plasma, and saliva, to test how far a crude preparation can be tolerated. Imaging was possible with up to 50% of clear bio-matrix contents, suggesting a simple lysis and dilution would be sufficient for imaging for some cells. Real pathogen DNA of human papillomavirus (HPV) type-I6 in human genomic DNA

  12. Fluorescence single-molecule counting assays for protein quantification using epi-fluorescence microscopy with quantum dots labeling

    International Nuclear Information System (INIS)

    Jiang Dafeng; Liu Chunxia; Wang Lei; Jiang Wei

    2010-01-01

    A single-molecule counting approach for quantifying the antibody affixed to a surface using quantum dots and epi-fluorescence microscopy is presented. Modifying the glass substrates with carboxyl groups provides a hydrophilic surface that reacts with amine groups of an antibody to allow covalent immobilization of the antibody. Nonspecific adsorption of single molecules on the modified surfaces was first investigated. Then, quantum dots were employed to form complexes with surface-immobilized antibody molecules and used as fluorescent probes for single-molecule imaging. Epi-fluorescence microscopy was chosen as the tool for single-molecule fluorescence detection here. The generated fluorescence signals were taken by an electron multiplying charge-coupled device and were found to be proportional to the sample concentrations. Under optimal conditions, a linear response range of 5.0 x 10 -14 -3.0 x 10 -12 mol L -1 was obtained between the number of single molecules and sample concentration via a single-molecule counting approach.

  13. Coupling single-molecule magnets to quantum circuits

    International Nuclear Information System (INIS)

    Jenkins, Mark; Martínez-Pérez, María José; Zueco, David; Luis, Fernando; Hümmer, Thomas; García-Ripoll, Juanjo

    2013-01-01

    In this work we study theoretically the coupling of single-molecule magnets (SMMs) to a variety of quantum circuits, including microwave resonators with and without constrictions and flux qubits. The main result of this study is that it is possible to achieve strong and ultrastrong coupling regimes between SMM crystals and the superconducting circuit, with strong hints that such a coupling could also be reached for individual molecules close to constrictions. Building on the resulting coupling strengths and the typical coherence times of these molecules (∼ μs), we conclude that SMMs can be used for coherent storage and manipulation of quantum information, either in the context of quantum computing or in quantum simulations. Throughout the work we also discuss in detail the family of molecules that are most suitable for such operations, based not only on the coupling strength, but also on the typical energy gaps and the simplicity with which they can be tuned and oriented. Finally, we also discuss practical advantages of SMMs, such as the possibility to fabricate the SMMs ensembles on the chip through the deposition of small droplets. (paper)

  14. Design of a TOF-SANS instrument for the proposed long wavelength target station at the spallation neutron source

    International Nuclear Information System (INIS)

    Thiyagarajan, P.; Littrell, K.; Seeger, P.A.

    2001-01-01

    We have designed a versatile high-throughput SANS instrument [Broad Range Intense Multipurpose SANS (BRIMS)] for the proposed Long Wavelength Target Station at the SNS by using acceptance diagrams and the Los Alamos NISP Monte Carlo simulation package. This instrument has been fully optimized to take advantage of the 10 Hz source frequency (broad wavelength bandwidth) and the cold neutron spectrum from a tall coupled solid methane moderator (12 cm x 20 cm). BRIMS has been designed to produce data in a Q range spanning from 0.0025 to 0.7 A -1 in a single measurement by simultaneously using neutrons with wavelengths ranging from 1 to 14.5 A in a time of flight mode. A supermirror guide and bender assembly is employed to separate and redirect the useful portion of the neutron spectrum with λ>1 A, by 2.3deg away from the direct beam containing high energy neutrons and γ rays. The effects of various collimation choices on count rate, resolution and Q min have been characterized using spherical particle and delta function scatterers. The overall performance of BRIMS has been compared with that of the best existing reactor-based SANS instrument D22 at ILL. (author)

  15. Conducting single-molecule magnet materials.

    Science.gov (United States)

    Cosquer, Goulven; Shen, Yongbing; Almeida, Manuel; Yamashita, Masahiro

    2018-05-11

    Multifunctional molecular materials exhibiting electrical conductivity and single-molecule magnet (SMM) behaviour are particularly attractive for electronic devices and related applications owing to the interaction between electronic conduction and magnetization of unimolecular units. The preparation of such materials remains a challenge that has been pursued by a bi-component approach of combination of SMM cationic (or anionic) units with conducting networks made of partially oxidized (or reduced) donor (or acceptor) molecules. The present status of the research concerning the preparation of molecular materials exhibiting SMM behaviour and electrical conductivity is reviewed, describing the few molecular compounds where both SMM properties and electrical conductivity have been observed. The evolution of this research field through the years is discussed. The first reported compounds are semiconductors in spite being able to present relatively high electrical conductivity, and the SMM behaviour is observed at low temperatures where the electrical conductivity of the materials is similar to that of an insulator. During the recent years, a breakthrough has been achieved with the coexistence of high electrical conductivity and SMM behaviour in a molecular compound at the same temperature range, but so far without evidence of a synergy between these properties. The combination of high electrical conductivity with SMM behaviour requires not only SMM units but also the regular and as far as possible uniform packing of partially oxidized molecules, which are able to provide a conducting network.

  16. Spin-Spin Cross Relaxation in Single-Molecule Magnets

    Science.gov (United States)

    Wernsdorfer, W.; Bhaduri, S.; Tiron, R.; Hendrickson, D. N.; Christou, G.

    2002-10-01

    The one-body tunnel picture of single-molecule magnets (SMMs) is not always sufficient to explain the measured tunnel transitions. An improvement to the picture is proposed by including also two-body tunnel transitions such as spin-spin cross relaxation (SSCR) which are mediated by dipolar and weak superexchange interactions between molecules. A Mn4 SMM is used as a model system. At certain external fields, SSCRs lead to additional quantum resonances which show up in hysteresis loop measurements as well-defined steps. A simple model is used to explain quantitatively all observed transitions.

  17. Entangled photons from single atoms and molecules

    Science.gov (United States)

    Nordén, Bengt

    2018-05-01

    The first two-photon entanglement experiment performed 50 years ago by Kocher and Commins (KC) provided isolated pairs of entangled photons from an atomic three-state fluorescence cascade. In view of questioning of Bell's theorem, data from these experiments are re-analyzed and shown sufficiently precise to confirm quantum mechanical and dismiss semi-classical theory without need for Bell's inequalities. Polarization photon correlation anisotropy (A) is useful: A is near unity as predicted quantum mechanically and well above the semi-classic range, 0 ⩽ A ⩽ 1 / 2 . Although yet to be found, one may envisage a three-state molecule emitting entangled photon pairs, in analogy with the KC atomic system. Antibunching in fluorescence from single molecules in matrix and entangled photons from quantum dots promise it be possible. Molecules can have advantages to parametric down-conversion as the latter photon distribution is Poissonian and unsuitable for producing isolated pairs of entangled photons. Analytical molecular applications of entangled light are also envisaged.

  18. Selective Activation of N,N'-Diacyl Rhodamine Pro-fluorophores Paired with Releasing Enzyme, Porcine Liver Esterase (PLE).

    Science.gov (United States)

    Abney, Kristopher K; Ramos-Hunter, Susan J; Romaine, Ian M; Godwin, J Shawn; Sulikowski, Gary A; Weaver, Charles David

    2018-04-21

    This study reports the synthesis and testing of a family of rhodamine pro-fluorophores and an enzyme capable of converting pro-fluorophores to Rhodamine 110. We prepared a library of simple N,N'-diacyl rhodamines and investigated Porcine Liver Esterase (PLE) as an enzyme to activate rhodamine-based pro-fluorophores. A PLE-expressing cell line generated an increase in fluorescence rapidly upon pro-fluorophore addition demonstrating the rhodamine pro-fluorophores are readily taken up and fluorescent upon PLE-mediated release. Rhodamine pro-fluorophore amides trifluoroacetamide (TFAm) and proponamide (PAm) appeared to be the best substrates using a cell-based assay using PLE expressing HEK293. Our pro-fluorophore series showed diffusion into live cells and resisted endogenous hydrolysis. The use of our engineered cell line containing the exogenous enzyme PLE demonstrated the rigorousness of amide masking when compared to cells not containing PLE. This simple and selective pro-fluorophore rhodamine pair with PLE offers the potential to be used in vitro and in vivo fluorescence based assays. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Visualizing Single-molecule DNA Replication with Fluorescence Microscopy

    NARCIS (Netherlands)

    Tanner, Nathan A.; Loparo, Joseph J.; Oijen, Antoine M. van

    2009-01-01

    We describe a simple fluorescence microscopy-based real-time method for observing DNA replication at the single-molecule level. A circular, forked DNA template is attached to a functionalized glass coverslip and replicated extensively after introduction of replication proteins and nucleotides. The

  20. Electric-Field Control of Interfering Transport Pathways in a Single-Molecule Anthraquinone Transistor

    NARCIS (Netherlands)

    Koole, Max; Thijssen, Jos M.; Valkenier, Hennie; Hummelen, Jan C.; van der Zant, Herre S. J.

    It is understood that molecular conjugation plays an important role in charge transport through single-molecule junctions. Here, we investigate electron transport through an anthraquinone based single-molecule three-terminal device. With the use of an electric-field induced by a gate electrode, the

  1. DNA Origami Directed Au Nanostar Dimers for Single-Molecule Surface-Enhanced Raman Scattering.

    Science.gov (United States)

    Tanwar, Swati; Haldar, Krishna Kanta; Sen, Tapasi

    2017-12-06

    We demonstrate the synthesis of Au nanostar dimers with tunable interparticle gap and controlled stoichiometry assembled on DNA origami. Au nanostars with uniform and sharp tips were immobilized on rectangular DNA origami dimerized structures to create nanoantennas containing monomeric and dimeric Au nanostars. Single Texas red (TR) dye was specifically attached in the junction of the dimerized origami to act as a Raman reporter molecule. The SERS enhancement factors of single TR dye molecules located in the conjunction region in dimer structures having interparticle gaps of 7 and 13 nm are 2 × 10 10 and 8 × 10 9 , respectively, which are strong enough for single analyte detection. The highly enhanced electromagnetic field generated by the plasmon coupling between sharp tips and cores of two Au nanostars in the wide conjunction region allows the accommodation and specific detection of large biomolecules. Such DNA-directed assembled nanoantennas with controlled interparticle separation distance and stoichiometry, and well-defined geometry, can be used as excellent substrates in single-molecule SERS spectroscopy and will have potential applications as a reproducible platform in single-molecule sensing.

  2. Waveguide-integrated single- and multi-photon detection at telecom wavelengths using superconducting nanowires

    International Nuclear Information System (INIS)

    Ferrari, Simone; Kahl, Oliver; Kovalyuk, Vadim; Goltsman, Gregory N.; Korneev, Alexander; Pernice, Wolfram H. P.

    2015-01-01

    We investigate single- and multi-photon detection regimes of superconducting nanowire detectors embedded in silicon nitride nanophotonic circuits. At near-infrared wavelengths, simultaneous detection of up to three photons is observed for 120 nm wide nanowires biased far from the critical current, while narrow nanowires below 100 nm provide efficient single photon detection. A theoretical model is proposed to determine the different detection regimes and to calculate the corresponding internal quantum efficiency. The predicted saturation of the internal quantum efficiency in the single photon regime agrees well with plateau behavior observed at high bias currents

  3. Waveguide-integrated single- and multi-photon detection at telecom wavelengths using superconducting nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Ferrari, Simone; Kahl, Oliver [Institute of Nanotechnology, Karlsruhe Institute of Technology, Karlsruhe 76132 (Germany); Kovalyuk, Vadim [Institute of Nanotechnology, Karlsruhe Institute of Technology, Karlsruhe 76132 (Germany); Department of Physics, Moscow State Pedagogical University, Moscow 119992 (Russian Federation); Goltsman, Gregory N. [Department of Physics, Moscow State Pedagogical University, Moscow 119992 (Russian Federation); National Research University Higher School of Economics, 20 Myasnitskaya Ulitsa, Moscow 101000 (Russian Federation); Korneev, Alexander [Department of Physics, Moscow State Pedagogical University, Moscow 119992 (Russian Federation); Moscow Institute of Physics and Technology (State University), Moscow 141700 (Russian Federation); Pernice, Wolfram H. P., E-mail: wolfram.pernice@kit.edu [Institute of Nanotechnology, Karlsruhe Institute of Technology, Karlsruhe 76132 (Germany); Department of Physics, University of Münster, 48149 Münster (Germany)

    2015-04-13

    We investigate single- and multi-photon detection regimes of superconducting nanowire detectors embedded in silicon nitride nanophotonic circuits. At near-infrared wavelengths, simultaneous detection of up to three photons is observed for 120 nm wide nanowires biased far from the critical current, while narrow nanowires below 100 nm provide efficient single photon detection. A theoretical model is proposed to determine the different detection regimes and to calculate the corresponding internal quantum efficiency. The predicted saturation of the internal quantum efficiency in the single photon regime agrees well with plateau behavior observed at high bias currents.

  4. Fluorophore-based sensor for oxygen radicals in processing plasmas

    International Nuclear Information System (INIS)

    Choudhury, Faraz A.; Shohet, J. Leon; Sabat, Grzegorz; Sussman, Michael R.; Nishi, Yoshio

    2015-01-01

    A high concentration of radicals is present in many processing plasmas, which affects the processing conditions and the properties of materials exposed to the plasma. Determining the types and concentrations of free radicals present in the plasma is critical in order to determine their effects on the materials being processed. Current methods for detecting free radicals in a plasma require multiple expensive and bulky instruments, complex setups, and often, modifications to the plasma reactor. This work presents a simple technique that detects reactive-oxygen radicals incident on a surface from a plasma. The measurements are made using a fluorophore dye that is commonly used in biological and cellular systems for assay labeling in liquids. Using fluorometric analysis, it was found that the fluorophore reacts with oxygen radicals incident from the plasma, which is indicated by degradation of its fluorescence. As plasma power was increased, the quenching of the fluorescence significantly increased. Both immobilized and nonimmobilized fluorophore dyes were used and the results indicate that both states function effectively under vacuum conditions. The reaction mechanism is very similar to that of the liquid dye

  5. Fluorophore-based sensor for oxygen radicals in processing plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Choudhury, Faraz A.; Shohet, J. Leon, E-mail: shohet@engr.wisc.edu [Plasma Processing and Technology Laboratory and Department of Electrical and Computer Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States); Sabat, Grzegorz; Sussman, Michael R. [Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States); Nishi, Yoshio [Department of Electrical Engineering, Stanford University, Stanford, California 94305 (United States)

    2015-11-15

    A high concentration of radicals is present in many processing plasmas, which affects the processing conditions and the properties of materials exposed to the plasma. Determining the types and concentrations of free radicals present in the plasma is critical in order to determine their effects on the materials being processed. Current methods for detecting free radicals in a plasma require multiple expensive and bulky instruments, complex setups, and often, modifications to the plasma reactor. This work presents a simple technique that detects reactive-oxygen radicals incident on a surface from a plasma. The measurements are made using a fluorophore dye that is commonly used in biological and cellular systems for assay labeling in liquids. Using fluorometric analysis, it was found that the fluorophore reacts with oxygen radicals incident from the plasma, which is indicated by degradation of its fluorescence. As plasma power was increased, the quenching of the fluorescence significantly increased. Both immobilized and nonimmobilized fluorophore dyes were used and the results indicate that both states function effectively under vacuum conditions. The reaction mechanism is very similar to that of the liquid dye.

  6. Single- and dual-wavelength laser pulses induced modification in 10×(Al/Ti)/Si multilayer system

    Energy Technology Data Exchange (ETDEWEB)

    Salatić, B. [University of Belgrade, Institute of Physics Belgrade, Pregrevica 118, 11080 Belgrade (Serbia); Petrović, S., E-mail: spetro@vinca.rs [University of Belgrade, Institute of Nuclear Science-Vinča, POB 522, 11001 Belgrade (Serbia); Peruško, D. [University of Belgrade, Institute of Nuclear Science-Vinča, POB 522, 11001 Belgrade (Serbia); Čekada, M.; Panjan, P. [Jožef Stefan Institute, Jamova 39, 1000 Ljubljana (Slovenia); Pantelić, D.; Jelenković, B. [University of Belgrade, Institute of Physics Belgrade, Pregrevica 118, 11080 Belgrade (Serbia)

    2016-01-01

    Graphical abstract: - Highlights: • Experimental and numerical study of laser-induced ablation and micro-sized crater formation. • Dual-wavelength pulses induce creation of wider and deeper craters due to synergies of two processes. • Sunflower-like structure formed by dual-wavelength pulses at low irradiance. • Numerical model of nanosecond pulsed laser ablation for complex (Al/Ti)/Si system has been developed. - Abstract: The surface morphology of the ablation craters created in the multilayer 10×(Al/Ti)/Si system by nanosecond laser pulses at single- and dual wavelength has been studied experimentally and numerically. A complex multilayer thin film including ten (Al/Ti) bilayers deposited by ion sputtering on Si(1 0 0) substrate to a total thickness of 260 nm were illuminated at different laser irradiance in the range 0.25–3.5 × 10{sup 9} W cm{sup −2}. Single pulse laser irradiation was done at normal incidence in air, with the single wavelength, either at 532 nm or 1064 nm or with both laser light simultaneously in the ratio of 1:10 for energy per pulse between second harmonic and 1064 nm. Most of the absorbed laser energy was rapidly transformed into heat, producing intensive modifications of composition and morphology on the sample surface. The results show an increase in surface roughness, formation of specific nanostructures, appearance of hydrodynamic features and ablation of surface material with crater formation. Applying a small fraction (10%) of the second harmonic in dual-wavelength pulses, a modification of the 10×(Al/Ti)/Si system by a single laser pulse was reflected in the formation of wider and/or deeper craters. Numerical calculations show that the main physical mechanism in ablation process is normal evaporation without phase explosion. The calculated and experimental results agree relatively well for the whole irradiance range, what makes the model applicable to complex Al/Ti multilayer systems.

  7. White-light phosphorescence emission from a single molecule: application to OLED

    OpenAIRE

    Bolink, Henk; De Angelis, Filippo; Baranoff, Etienne; Klein, Cedric; Fantacci, Simona; Coronado Miralles, Eugenio; Sessolo, Michele; Kalyanasundaram, K.; Grätzel, Michael; Nazeeruddin, Md. K.

    1999-01-01

    A simple mononuclear cyclometallated iridium(III) complex exhibits white photo- and electro- luminescence in the wavelength range from 440 to 800 nm, which originates from a single emitting excited state of mixed character. Bolink Henk, ; Coronado Miralles, Eugenio,

  8. Computing magnetic anisotropy constants of single molecule magnets

    Indian Academy of Sciences (India)

    We present here a theoretical approach to compute the molecular magnetic anisotropy parameters, and for single molecule magnets in any given spin eigenstate of exchange spin Hamiltonian. We first describe a hybrid constant -valence bond (VB) technique of solving spin Hamiltonians employing full spatial ...

  9. Single molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update

    Science.gov (United States)

    Widom, Julia R.; Dhakal, Soma; Heinicke, Laurie A.; Walter, Nils G.

    2015-01-01

    Toxicology is the highly interdisciplinary field studying the adverse effects of chemicals on living organisms. It requires sensitive tools to detect such effects. After their initial implementation during the 1990s, single-molecule fluorescence detection tools were quickly recognized for their potential to contribute greatly to many different areas of scientific inquiry. In the intervening time, technical advances in the field have generated ever-improving spatial and temporal resolution, and have enabled the application of single-molecule fluorescence to increasingly complex systems, such as live cells. In this review, we give an overview of the optical components necessary to implement the most common versions of single-molecule fluorescence detection. We then discuss current applications to enzymology and structural studies, systems biology, and nanotechnology, presenting the technical considerations that are unique to each area of study, along with noteworthy recent results. We also highlight future directions that have the potential to revolutionize these areas of study by further exploiting the capabilities of single-molecule fluorescence microscopy. PMID:25212907

  10. Ultrafast single-molecule photonics: Excited state dynamics in coherently coupled complexes

    International Nuclear Information System (INIS)

    Hernando, Jordi; Hoogenboom, Jacob; Dijk, Erik van; Garcia-Parajo, Maria; Hulst, Niek F. van

    2008-01-01

    We present a single-molecule study on femtosecond dynamics in multichromophoric systems, combining fs pump-probe, emission-spectra and fluorescence-lifetime analysis. The ultrafast fs approach gives direct information on the initial exciton dynamics after excitation. The lifetime data show superradiance, a direct measure for the extent of the coherent coupling and static disorder. The spectra finally reveal the role of exciton-phonon coupling. At the single-molecule level a wide range of exciton delocalization lengths and energy redistribution times is revealed

  11. Ultrafast single-molecule photonics: Excited state dynamics in coherently coupled complexes

    Energy Technology Data Exchange (ETDEWEB)

    Hernando, Jordi [Dept. de Quimica, Universitat Autonoma Barcelona, 08193 Cerdanyola del Valles (Spain); Hoogenboom, Jacob [ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels, Barcelona (Spain); Dijk, Erik van [Applied Optics Group, MESA Institute for Nanotechnology, University of Twente, 7500AE Enschede (Netherlands); Garcia-Parajo, Maria [IBEC-Institute of BioEngineering of Catalunya, 08028 Barcelona (Spain); ICREA-Institucio Catalana de Recerca i Estudis Avancats, 08015 Barcelona (Spain); Hulst, Niek F. van [ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels, Barcelona (Spain) and ICREA-Institucio Catalana de Recerca i Estudis Avancats, 08015 Barcelona (Spain)], E-mail: Niek.vanHulst@ICFO.es

    2008-05-15

    We present a single-molecule study on femtosecond dynamics in multichromophoric systems, combining fs pump-probe, emission-spectra and fluorescence-lifetime analysis. The ultrafast fs approach gives direct information on the initial exciton dynamics after excitation. The lifetime data show superradiance, a direct measure for the extent of the coherent coupling and static disorder. The spectra finally reveal the role of exciton-phonon coupling. At the single-molecule level a wide range of exciton delocalization lengths and energy redistribution times is revealed.

  12. SINGLE MOLECULE APPROACHES TO BIOLOGY, 2010 GORDON RESEARCH CONFERENCE, JUNE 27-JULY 2, 2010, ITALY

    Energy Technology Data Exchange (ETDEWEB)

    Professor William Moerner

    2010-07-09

    The 2010 Gordon Conference on Single-Molecule Approaches to Biology focuses on cutting-edge research in single-molecule science. Tremendous technical developments have made it possible to detect, identify, track, and manipulate single biomolecules in an ambient environment or even in a live cell. Single-molecule approaches have changed the way many biological problems are addressed, and new knowledge derived from these approaches continues to emerge. The ability of single-molecule approaches to avoid ensemble averaging and to capture transient intermediates and heterogeneous behavior renders them particularly powerful in elucidating mechanisms of biomolecular machines: what they do, how they work individually, how they work together, and finally, how they work inside live cells. The burgeoning use of single-molecule methods to elucidate biological problems is a highly multidisciplinary pursuit, involving both force- and fluorescence-based methods, the most up-to-date advances in microscopy, innovative biological and chemical approaches, and nanotechnology tools. This conference seeks to bring together top experts in molecular and cell biology with innovators in the measurement and manipulation of single molecules, and will provide opportunities for junior scientists and graduate students to present their work in poster format and to exchange ideas with leaders in the field. A number of excellent poster presenters will be selected for short oral talks. Topics as diverse as single-molecule sequencing, DNA/RNA/protein interactions, folding machines, cellular biophysics, synthetic biology and bioengineering, force spectroscopy, new method developments, superresolution imaging in cells, and novel probes for single-molecule imaging will be on the program. Additionally, the collegial atmosphere of this Conference, with programmed discussion sessions as well as opportunities for informal gatherings in the afternoons and evenings in the beauty of the Il Ciocco site in

  13. Extracting physics of life at the molecular level: A review of single-molecule data analyses.

    Science.gov (United States)

    Colomb, Warren; Sarkar, Susanta K

    2015-06-01

    Studying individual biomolecules at the single-molecule level has proved very insightful recently. Single-molecule experiments allow us to probe both the equilibrium and nonequilibrium properties as well as make quantitative connections with ensemble experiments and equilibrium thermodynamics. However, it is important to be careful about the analysis of single-molecule data because of the noise present and the lack of theoretical framework for processes far away from equilibrium. Biomolecular motion, whether it is free in solution, on a substrate, or under force, involves thermal fluctuations in varying degrees, which makes the motion noisy. In addition, the noise from the experimental setup makes it even more complex. The details of biologically relevant interactions, conformational dynamics, and activities are hidden in the noisy single-molecule data. As such, extracting biological insights from noisy data is still an active area of research. In this review, we will focus on analyzing both fluorescence-based and force-based single-molecule experiments and gaining biological insights at the single-molecule level. Inherently nonequilibrium nature of biological processes will be highlighted. Simulated trajectories of biomolecular diffusion will be used to compare and validate various analysis techniques. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Electron tunnelling through single azurin molecules can be on/off switched by voltage pulses

    Energy Technology Data Exchange (ETDEWEB)

    Baldacchini, Chiara [Biophysics and Nanoscience Centre, DEB-CNISM, Università della Tuscia, I-01100 Viterbo (Italy); Institute of Agro-Environmental and Forest Biology, CNR, I-05010 Porano (Italy); Kumar, Vivek; Bizzarri, Anna Rita; Cannistraro, Salvatore, E-mail: cannistr@unitus.it [Biophysics and Nanoscience Centre, DEB-CNISM, Università della Tuscia, I-01100 Viterbo (Italy)

    2015-05-04

    Redox metalloproteins are emerging as promising candidates for future bio-optoelectronic and nano-biomemory devices, and the control of their electron transfer properties through external signals is still a crucial task. Here, we show that a reversible on/off switching of the electron current tunnelling through a single protein can be achieved in azurin protein molecules adsorbed on gold surfaces, by applying appropriate voltage pulses through a scanning tunnelling microscope tip. The observed changes in the hybrid system tunnelling properties are discussed in terms of long-sustained charging of the protein milieu.

  15. Nonperturbative theory of single/multiphoton processes in atoms and molecules induced by intense laser fields

    International Nuclear Information System (INIS)

    Lau, A.M.F.

    1975-04-01

    A quantum nonperturbative theory is given for the problem of a general n discrete-level atomic/molecular system interacting with a strong single-mode/multimode radiation field. The atomic/molecular energy-level structures are modified due to interaction with the laser field. These energy level shifts are derived in the rigorous solution to the adiabatic eigenvalue problem of the charge--field system, involving a simple iterative procedure. The task of solution is simplified by recurrence relations between matrices connecting probability amplitudes of successive photon numbers. New formulae for calculating probability of single/multiphoton transitions between three resonant shifted levels and between some cases of two near-resonant shifted levels are derived. This general formalism can be applied to calculate transition probabilities of various atomic/molecular photo processes of interest. Numerical values are obtained for the inelastic cross section of the slow-collisional process Li + H and for dissociation cross section of LiH molecule. The transition probabilities of Na (3s → 5s by absorption of two photon of lambda = 0.60233μ -- 0.602396 μ) and of Li (2s → 3s by absorption of eight photons of lambda = 2.9406 μ -- 2.945 μ) irradiated by a strong pulse are calculated. Finally, a parametric study is carried out for the process where a molecular system is interacting with two intense radiation fields of different wavelengths. Owing to potential barrier shift due to the much more intense field, the molecular system penetrates into an otherwise inaccessible region in the potential level where it is allowed to radiate to a lower level by emitting photons at a second wavelength. (12 figures, 6 tables) (U.S.)

  16. Design and implementation of a dual-wavelength intrinsic fluorescence camera system

    Science.gov (United States)

    Ortega-Martinez, Antonio; Musacchia, Joseph J.; Gutierrez-Herrera, Enoch; Wang, Ying; Franco, Walfre

    2017-03-01

    Intrinsic UV fluorescence imaging is a technique that permits the observation of spatial differences in emitted fluorescence. It relies on the fluorescence produced by the innate fluorophores in the sample, and thus can be used for marker-less in-vivo assessment of tissue. It has been studied as a tool for the study of the skin, specifically for the classification of lesions, the delimitation of lesion borders and the study of wound healing, among others. In its most basic setup, a sample is excited with a narrow-band UV light source and the resulting fluorescence is imaged with a UV sensitive camera filtered to the emission wavelength of interest. By carefully selecting the excitation/emission pair, we can observe changes in fluorescence associated with physiological processes. One of the main drawbacks of this simple setup is the inability to observe more than a single excitation/emission pair at the same time, as some phenomena are better studied when two or more different pairs are studied simultaneously. In this work, we describe the design and the hardware and software implementation of a dual wavelength portable UV fluorescence imaging system. Its main components are an UV camera, a dual wavelength UV LED illuminator (295 and 345 nm) and two different emission filters (345 and 390 nm) that can be swapped by a mechanical filter wheel. The system is operated using a laptop computer and custom software that performs basic pre-processing to improve the image. The system was designed to allow us to image fluorescent peaks of tryptophan and collagen cross links in order to study wound healing progression.

  17. The Effect of a Fluorophore Photo-Physics on the Lipid Vesicle Diffusion Coefficient Studied by Fluorescence Correlation Spectroscopy.

    Science.gov (United States)

    Drabik, Dominik; Przybyło, Magda; Sikorski, Aleksander; Langner, Marek

    2016-03-01

    Fluorescence Correlation Spectroscopy (FCS) is a technique, which allows determination of the diffusion coefficient and concentration of fluorescent objects suspended in the solution. The measured parameter is the fluctuation of the fluorescence signal emitted by diffusing molecules. When 100 nm DOPC vesicles labeled with various fluorescent dyes (Fluorescein-PE, NBD-PE, Atto488 DOPE or βBodipy FL) were measured, different values of diffusion coefficients have been obtained. These diffusion coefficients were different from the expected values measured using the dynamic light scattering method (DLS). The FCS was initially developed for solutions containing small fluorescent molecules therefore the observed inconsistency may result from the nature of vesicle suspension itself. The duration of the fluorescence signal may depend on the following factors: the exposure time of the labeled object to the excitation beam, the photo-physical properties (e.g., stability) of a fluorophore, the theoretical model used for the calculations of the diffusion coefficient and optical properties of the vesicle suspension. The diffusion coefficients determined for differently labeled liposomes show that its dependence on vesicle size and quantity of fluorescent probed used for labeling was significant demonstrating that the fluorescence properties of the fluorophore itself (bleaching and/or blinking) were critical factors for a correct outcome of FCS experiment. The new, based on combined FCS and DLS measurements, method for the determination of the focal volume prove itself to be useful for the evaluation of a fluorescence dye with respect to its applicability for FCS experiment.

  18. Versatile single-molecule multi-color excitation and detection fluorescence setup for studying biomolecular dynamics

    KAUST Repository

    Sobhy, M. A.; Elshenawy, M. M.; Takahashi, Masateru; Whitman, B. H.; Walter, N. G.; Hamdan, S. M.

    2011-01-01

    Single-molecule fluorescence imaging is at the forefront of tools applied to study biomolecular dynamics both in vitro and in vivo. The ability of the single-molecule fluorescence microscope to conduct simultaneous multi-color excitation

  19. Long wavelength infrared radiation thermometry for non-contact temperature measurements in gas turbines

    Science.gov (United States)

    Manara, J.; Zipf, M.; Stark, T.; Arduini, M.; Ebert, H.-P.; Tutschke, A.; Hallam, A.; Hanspal, J.; Langley, M.; Hodge, D.; Hartmann, J.

    2017-01-01

    The objective of the EU project "Sensors Towards Advanced Monitoring and Control of Gas Turbine Engines (acronym STARGATE)" is the development of a suite of advanced sensors, instrumentation and related systems in order to contribute to the developing of the next generation of green and efficient gas turbine engines. One work package of the project deals with the design and development of a long wavelength infrared (LWIR) radiation thermometer for the non-contact measurement of the surface temperature of thermal barrier coatings (TBCs) during the operation of gas turbine engines. For opaque surfaces (e.g. metals or superalloys) radiation thermometers which are sensitive in the near or short wavelength infrared are used as state-of-the-art method for non-contact temperature measurements. But this is not suitable for oxide ceramic based TBCs (e.g. partially yttria stabilized zirconia) as oxide ceramics are semi-transparent in the near and short wavelength infrared spectral region. Fortunately the applied ceramic materials are non-transparent in the long wavelength infrared and additionally exhibit a high emittance in this wavelength region. Therefore, a LWIR pyrometer can be used for non-contact temperature measurements of the surfaces of TBCs as such pyrometers overcome the described limitation of existing techniques. For performing non-contact temperature measurements in gas turbines one has to know the infrared-optical properties of the applied TBCs as well as of the hot combustion gas in order to properly analyse the measurement data. For reaching a low uncertainty on the one hand the emittance of the TBC should be high (>0.9) in order to reduce reflections from the hot surrounding and on the other hand the absorbance of the hot combustion gas should be low (<0.1) in order to decrease the influence of the gas on the measured signal. This paper presents the results of the work performed by the authors with focus on the implementation of the LWIR pyrometer and the

  20. Single molecule conductance

    NARCIS (Netherlands)

    Willems, R.

    2008-01-01

    This thesis represents an excursion into the world of molecular electronics, i.e. the field of research trying to use individual (organic) molecules as electronic components; in this work various experimental methods have been explored to connect individual molecules to metallic contacts and

  1. Dual-mode fluorophore-doped nickel nitrilotriacetic acid-modified silica nanoparticles combine histidine-tagged protein purification with site-specific fluorophore labeling.

    Science.gov (United States)

    Kim, Sung Hoon; Jeyakumar, M; Katzenellenbogen, John A

    2007-10-31

    We present the first example of a fluorophore-doped nickel chelate surface-modified silica nanoparticle that functions in a dual mode, combining histidine-tagged protein purification with site-specific fluorophore labeling. Tetramethylrhodamine (TMR)-doped silica nanoparticles, estimated to contain 700-900 TMRs per ca. 23 nm particle, were surface modified with nitrilotriacetic acid (NTA), producing TMR-SiO2-NTA-Ni2+. Silica-embedded TMR retains very high quantum yield, is resistant to quenching by buffer components, and is modestly quenched and only to a certain depth (ca. 2 nm) by surface-attached Ni2+. When exposed to a bacterial lysate containing estrogen receptor alpha ligand binding domain (ERalpha) as a minor component, these beads showed very high specificity binding, enabling protein purification in one step. The capacity and specificity of these beads for binding a his-tagged protein were characterized by electrophoresis, radiometric counting, and MALDI-TOF MS. ERalpha, bound to TMR-SiO2-NTA-Ni++ beads in a site-specific manner, exhibited good activity for ligand binding and for ligand-induced binding to coactivators in solution FRET experiments and protein microarray fluorometric and FRET assays. This dual-mode type TMR-SiO2-NTA-Ni2+ system represents a powerful combination of one-step histidine-tagged protein purification and site-specific labeling with multiple fluorophore species.

  2. Measurement of the conductance properties of single organic molecules using gold nanoparticles

    Science.gov (United States)

    Gordin, Yoav

    In this work we describe the development and application of a new method for the electrical conductance measurement of single molecules. The issue of reliable theoretical modeling of molecular electronic transport is still very much in debate. The experimental methods used in the field are difficult to realize and interpret; most have very low yield, preventing proper statistical analysis and many have problems in the researchers' ability to characterize the system properly. We address this issue by using self assembly of gold nanoparticle-molecule-gold nanoparticle objects called dimers. This method allows fabrication of molecular junctions with greater ease; moreover it allows individual characterization of the various elements of the junction, removing much of the uncertainties that exist in this kind of measurements. We make use of home grown gold nanoparticles with a few tens of nanometer diameter to form the hybrid dimers. The dimers are large enough to connect between electrodes fabricated using electron beam lithography and to measure the electric properties of the molecule. We have invested significant effort in the characterization of the system, ensuring that the dimers are indeed bridged by the molecules, and that the chances that more than a single molecule exists in a dimer are negligibly small. We have made measurements on single gold nanoparticles, to characterize their properties separately from those of the molecule. These measurements have allowed us to observe single electron transistor (SET) behavior, resulting from the requirement that electrons charge the nanoparticle during transport. We have shown that the energy associated with this charging scales with nanoparticle size as expected. We have performed measurements on single organic molecules, showing that there is a very strong influence of molecular conjugation (the way electronic orbitals are spread along the molecular backbone) on its conductance. The molecules with broken conjugation

  3. A general approach to break the concentration barrier in single-molecule imaging

    KAUST Repository

    Loveland, Anna B.; Habuchi, Satoshi; Walter, Johannes C.; van Oijen, Antoine M.

    2012-01-01

    Single-molecule fluorescence imaging is often incompatible with physiological protein concentrations, as fluorescence background overwhelms an individual molecule's signal. We solve this problem with a new imaging approach called PhADE (Photo

  4. Single molecule SERS: Perspectives of analytical applications

    Czech Academy of Sciences Publication Activity Database

    Vlčková, B.; Pavel, I.; Sládková, M.; Šišková, K.; Šlouf, Miroslav

    834-836, - (2007), s. 42-47 ISSN 0022-2860. [European Congress on Molecular Spectroscopy /28./. Istanbul, 03.09.2006-08.09.2006] R&D Projects: GA ČR GA203/04/0688 Institutional research plan: CEZ:AV0Z40500505 Keywords : surface-enhanced Raman scattering (SERS) * surface-enhanced resonance Raman (SERRS) * single molecule SERS Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.486, year: 2007

  5. Statistical inference in single molecule measurements of protein adsorption

    Science.gov (United States)

    Armstrong, Megan J.; Tsitkov, Stanislav; Hess, Henry

    2018-02-01

    Significant effort has been invested into understanding the dynamics of protein adsorption on surfaces, in particular to predict protein behavior at the specialized surfaces of biomedical technologies like hydrogels, nanoparticles, and biosensors. Recently, the application of fluorescent single molecule imaging to this field has permitted the tracking of individual proteins and their stochastic contribution to the aggregate dynamics of adsorption. However, the interpretation of these results is complicated by (1) the finite time available to observe effectively infinite adsorption timescales and (2) the contribution of photobleaching kinetics to adsorption kinetics. Here, we perform a protein adsorption simulation to introduce specific survival analysis methods that overcome the first complication. Additionally, we collect single molecule residence time data from the adsorption of fibrinogen to glass and use survival analysis to distinguish photobleaching kinetics from protein adsorption kinetics.

  6. An all-electric single-molecule motor.

    Science.gov (United States)

    Seldenthuis, Johannes S; Prins, Ferry; Thijssen, Joseph M; van der Zant, Herre S J

    2010-11-23

    Many types of molecular motors have been proposed and synthesized in recent years, displaying different kinds of motion, and fueled by different driving forces such as light, heat, or chemical reactions. We propose a new type of molecular motor based on electric field actuation and electric current detection of the rotational motion of a molecular dipole embedded in a three-terminal single-molecule device. The key aspect of this all-electronic design is the conjugated backbone of the molecule, which simultaneously provides the potential landscape of the rotor orientation and a real-time measure of that orientation through the modulation of the conductivity. Using quantum chemistry calculations, we show that this approach provides full control over the speed and continuity of motion, thereby combining electrical and mechanical control at the molecular level over a wide range of temperatures. Moreover, chemistry can be used to change all key parameters of the device, enabling a variety of new experiments on molecular motors.

  7. Single-molecule conductance with nitrile and amino contacts with Ag or Cu electrodes

    International Nuclear Information System (INIS)

    Li, Dong-Fang; Mao, Jin-Chuan; Chen, De-Li; Chen, Fang; Ze-Wen, Hong; Zhou, Xiao-Yi; Wang, Ya-Hao; Zhou, Xiao-Shun; Niu, Zhen-Jiang; Maisonhaute, Emmanuel

    2015-01-01

    The single-molecule conductance of 1,4-dicyanobenzene (DCB), 1,4-benzenediamine (BDA) and 4,4'-biphenyldicarbonitrile (BPDC) with Ag and/or Cu electrodes is measured by electrochemical jump-to-contact STM-break junction. All single-molecule junctions present three sets of conductance values revealing different contact geometries. We observe that the single-molecule conductance of Ag-BDA-Ag junction is larger that of Ag-DCB-Ag junction, and DCB with Ag contacts are more conductive than that with Cu ones. This is related to a different electronic coupling between the molecules and the electrodes. Tunneling decay constants of 1.70 and 1.68 per phenyl group were found for Ag and Cu electrodes, respectively. The present study therefore shows that nitrile and amino groups can also be used as effective anchors for other metals than gold

  8. Electric-Field Control of Interfering Transport Pathways in a Single-Molecule Anthraquinone Transistor

    Science.gov (United States)

    Koole, Max; Thijssen, Jos M.; Valkenier, Hennie; Hummelen, Jan C.; Zant, Herre S. J. van der

    2015-08-01

    It is understood that molecular conjugation plays an important role in charge transport through single-molecule junctions. Here, we investigate electron transport through an anthraquinone based single-molecule three-terminal device. With the use of an electric-field induced by a gate electrode, the molecule is reduced resulting into a ten-fold increase in the off-resonant differential conductance. Theoretical calculations link the change in differential conductance to a reduction-induced change in conjugation, thereby lifting destructive interference of transport pathways.

  9. Memory effects in single-molecule spectroscopy

    International Nuclear Information System (INIS)

    Schmitt, Daniel T.; Schulz, Michael; Reineker, Peter

    2007-01-01

    From the time series of LH2 optical single-molecule fluorescence excitation spectra of Rhodospirillum molischianum the memory function of the Mori-Zwanzig equation for the optical intensity is derived numerically. We show that the time dependence of the excited states is determined by at least three different non-Markovian stochastic processes with decay constants for the Mori-Zwanzig kernel on the order of 1-5min -1 . We suggest that this decay stems from the conformational motion of the protein scaffold of LH2

  10. Comprehensive Wavelengths, Energy Levels, and Hyperfine Structure Parameters of Singly-Ionized Iron-Group Elements

    Science.gov (United States)

    Nave, Gillian

    We propose to measure wavelengths, energy levels, and hyperfine structure parameters of Ni II, Mn II, Sc II and other singly-ionized iron-group elements, covering the wavelength range 80 nm to 5500 nm. We shall use archival data from spectrometers at NIST and Kitt Peak National Observatory for spectra above 140 nm. Additional experimental observations will be taken if needed using Fourier transform spectrometers at NIST. Spectra will be taken using our normal incidence grating spectrograph to provide better sensitivity than the FT spectra and to extend the wavelength range down to 80 nm. We aim to produce a comprehensive description of the spectra of all singly-ionized iron- group elements. The wavelength uncertainty of the strong lines will be better than 1 part in 10^7. For most singly-ionized iron-group elements available laboratory data have uncertainties an order of magnitude larger than astronomical observations over wide spectra ranges. Some of these laboratory measurements date back to the 1960's. Since then, Fourier transform spectroscopy has made significant progress in improving the accuracy and quantity of data in the UV-vis-IR region, but high quality Fourier transform spectra are still needed for Mn II, Ni II and Sc II. Fourier transform spectroscopy has low sensitivity in the VUV region and is limited to wavelengths above 140 nm. Spectra measured with high-resolution grating spectrographs are needed in this region in order to obtain laboratory data of comparable quality to the STIS and COS spectrographs on the Hubble Space Telescope. Currently, such data exist only for Fe II and Cr II. Lines of Sc II, V II, and Mn II show hyperfine structure, but hyperfine structure parameters have been measured for relatively few lines of these elements. Significant errors can occur if hyperfine structure is neglected when abundances are determined from stellar spectra. Measurements of hyperfine structure parameters will be made using Fourier transform spectroscopy

  11. Small Molecule-Photoactive Yellow Protein Labeling Technology in Live Cell Imaging

    Directory of Open Access Journals (Sweden)

    Feng Gao

    2016-08-01

    Full Text Available Characterization of the chemical environment, movement, trafficking and interactions of proteins in live cells is essential to understanding their functions. Labeling protein with functional molecules is a widely used approach in protein research to elucidate the protein location and functions both in vitro and in live cells or in vivo. A peptide or a protein tag fused to the protein of interest and provides the opportunities for an attachment of small molecule probes or other fluorophore to image the dynamics of protein localization. Here we reviewed the recent development of no-wash small molecular probes for photoactive yellow protein (PYP-tag, by the means of utilizing a quenching mechanism based on the intramolecular interactions, or an environmental-sensitive fluorophore. Several fluorogenic probes have been developed, with fast labeling kinetics and cell permeability. This technology allows quick live-cell imaging of cell-surface and intracellular proteins without a wash-out procedure.

  12. Automation of a single-DNA molecule stretching device

    DEFF Research Database (Denmark)

    Sørensen, Kristian Tølbøl; Lopacinska, Joanna M.; Tommerup, Niels

    2015-01-01

    We automate the manipulation of genomic-length DNA in a nanofluidic device based on real-time analysis of fluorescence images. In our protocol, individual molecules are picked from a microchannel and stretched with pN forces using pressure driven flows. The millimeter-long DNA fragments free...

  13. Nanofluidic single-molecule sorting of DNA: a new concept in separation and analysis of biomolecules towards ultimate level performance

    International Nuclear Information System (INIS)

    Yamamoto, Takatoki; Fujii, Teruo

    2010-01-01

    Separation and separation-based analysis of biomolecules are fundamentally important techniques in the field of biotechnology. These techniques, however, depend on stochastic processes that intrinsically involve uncertainty, and thus it is not possible to achieve 100% separation accuracy. Theoretically, the ultimate resolution and sensitivity should be realized in a single-molecule system because of the deterministic nature of single-molecule manipulation. Here, we have proposed and experimentally demonstrated the concept of a 'single-molecule sorter' that detects and correctly identifies individual single molecules, realizing the ultimate level of resolution and sensitivity for any separation-based technology. The single-molecule sorter was created using a nanofluidic network consisting of a single inlet channel that branches off into multiple outlet channels. It includes two major functional elements, namely a single-molecule detection and identification element and a flow path switching element to accurately separate single molecules. With this system we have successfully demonstrated the world's first single-molecule sorting using DNA as a sample molecule. In the future, we hope to expand the application of such devices to comprehensive sorting of single-proteins from a single cell. We also believe that in addition to the single-molecule sorting method reported here, other types of single-molecule based processes will emerge and find use in a wide variety of applications.

  14. GaAsSb/InGaAs type-II quantum wells for long-wavelength lasers on GaAs substrates

    International Nuclear Information System (INIS)

    Klem, J. F.; Blum, O.; Kurtz, S. R.; Fritz, I. J.; Choquette, K. D.

    2000-01-01

    We have investigated the properties of GaAsSb/InGaAs type-II bilayer quantum-well structures grown by molecular-beam epitaxy for use in long-wavelength lasers on GaAs substrates. Structures with layer strains and thicknesses designed to be thermodynamically stable against dislocation formation exhibit room-temperature photoluminescence at wavelengths as long as 1.43 μm. The photoluminescence emission wavelength is significantly affected by growth temperature and the sequence of layer growth (InGaAs/GaAsSb versus GaAsSb/InGaAs), suggesting that Sb and/or In segregation results in nonideal interfaces under certain growth conditions. At low-injection currents, double-heterostructure lasers with GaAsSb/InGaAs bilayer quantum-well active regions display electroluminescence at wavelengths comparable to those obtained in photoluminescence, but at higher currents the electroluminescence shifts to shorter wavelengths. Lasers have been obtained with threshold current densities of 120 A/cm2 at 1.17 μm, and 2.1 kA/cm2 at 1.21 μm. (c) 2000 American Vacuum Society

  15. Enzymatic production of single-molecule FISH and RNA capture probes.

    Science.gov (United States)

    Gaspar, Imre; Wippich, Frank; Ephrussi, Anne

    2017-10-01

    Arrays of singly labeled short oligonucleotides that hybridize to a specific target revolutionized RNA biology, enabling quantitative, single-molecule microscopy analysis and high-efficiency RNA/RNP capture. Here, we describe a simple and efficient method that allows flexible functionalization of inexpensive DNA oligonucleotides by different fluorescent dyes or biotin using terminal deoxynucleotidyl transferase and custom-made functional group conjugated dideoxy-UTP. We show that (i) all steps of the oligonucleotide labeling-including conjugation, enzymatic synthesis, and product purification-can be performed in a standard biology laboratory, (ii) the process yields >90%, often >95% labeled product with minimal carryover of impurities, and (iii) the oligonucleotides can be labeled with different dyes or biotin, allowing single-molecule FISH, RNA affinity purification, and Northern blot analysis to be performed. © 2017 Gaspar et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  16. Long-wavelength photosensitivity in coral planula larvae.

    Science.gov (United States)

    Mason, Benjamin M; Cohen, Jonathan H

    2012-04-01

    Light influences the swimming behavior and settlement of the planktonic planula larvae of coral, but little is known regarding the photosensory biology of coral at this or any life-history stage. Here we used changes in the electrical activity of coral planula tissue upon light flashes to investigate the photosensitivity of the larvae. Recordings were made from five species: two whose larvae are brooded and contain algal symbionts (Porites astreoides and Agaricia agaricites), and three whose larvae are spawned and lack algal symbionts (Acropora cervicornis, Acropora palmata,and Montastrea faveolata). Photosensitivity originated from the coral larva rather than from, or in addition to, its algal symbionts as species with and without symbionts displayed similar tissue-level electrical responses to light. All species exhibited as much (or more) sensitivity to red stimuli as to blue/green stimuli, which is consistent with a role for long-wavelength visible light in the preference for substrata observed during settlement and in facilitating vertical positioning of larvae in the water column.

  17. SURVEYING THE DYNAMIC RADIO SKY WITH THE LONG WAVELENGTH DEMONSTRATOR ARRAY

    International Nuclear Information System (INIS)

    Lazio, T. Joseph W.; Clarke, Tracy E.; Lane, W. M.; Gross, C.; Kassim, N. E.; Hicks, B.; Polisensky, E.; Stewart, K.; Ray, P. S.; Wood, D.; York, J. A.; Kerkhoff, A.; Dalal, N. Paravastu; Cohen, A. S.; Erickson, W. C.

    2010-01-01

    This paper presents a search for radio transients at a frequency of 73.8 MHz (4 m wavelength) using the all-sky imaging capabilities of the Long Wavelength Demonstrator Array (LWDA). The LWDA was a 16-dipole phased array telescope, located on the site of the Very Large Array in New Mexico. The field of view of the individual dipoles was essentially the entire sky, and the number of dipoles was sufficiently small that a simple software correlator could be used to make all-sky images. From 2006 October to 2007 February, we conducted an all-sky transient search program, acquiring a total of 106 hr of data; the time sampling varied, being 5 minutes at the start of the program and improving to 2 minutes by the end of the program. We were able to detect solar flares, and in a special-purpose mode, radio reflections from ionized meteor trails during the 2006 Leonid meteor shower. We detected no transients originating outside of the solar system above a flux density limit of 500 Jy, equivalent to a limit of no more than about 10 -2 events yr -1 deg -2 , having a pulse energy density ∼>1.5 x 10 -20 J m -2 Hz -1 at 73.8 MHz for pulse widths of about 300 s. This event rate is comparable to that determined from previous all-sky transient searches, but at a lower frequency than most previous all-sky searches. We believe that the LWDA illustrates how an all-sky imaging mode could be a useful operational model for low-frequency instruments such as the Low Frequency Array, the Long Wavelength Array station, the low-frequency component of the Square Kilometre Array, and potentially the Lunar Radio Array.

  18. Single-molecule spectroscopy of amino acids and peptides by recognition tunnelling

    Science.gov (United States)

    Zhao, Yanan; Ashcroft, Brian; Zhang, Peiming; Liu, Hao; Sen, Suman; Song, Weisi; Im, Jongone; Gyarfas, Brett; Manna, Saikat; Biswas, Sovan; Borges, Chad; Lindsay, Stuart

    2014-06-01

    The human proteome has millions of protein variants due to alternative RNA splicing and post-translational modifications, and variants that are related to diseases are frequently present in minute concentrations. For DNA and RNA, low concentrations can be amplified using the polymerase chain reaction, but there is no such reaction for proteins. Therefore, the development of single-molecule protein sequencing is a critical step in the search for protein biomarkers. Here, we show that single amino acids can be identified by trapping the molecules between two electrodes that are coated with a layer of recognition molecules, then measuring the electron tunnelling current across the junction. A given molecule can bind in more than one way in the junction, and we therefore use a machine-learning algorithm to distinguish between the sets of electronic `fingerprints' associated with each binding motif. With this recognition tunnelling technique, we are able to identify D and L enantiomers, a methylated amino acid, isobaric isomers and short peptides. The results suggest that direct electronic sequencing of single proteins could be possible by sequentially measuring the products of processive exopeptidase digestion, or by using a molecular motor to pull proteins through a tunnel junction integrated with a nanopore.

  19. L-shaped benzimidazole fluorophores: synthesis, characterization and optical response to bases, acids and anions.

    Science.gov (United States)

    Lirag, Rio Carlo; Le, Ha T M; Miljanić, Ognjen Š

    2013-05-14

    Nine L-shaped benzimidazole fluorophores have been synthesized, computationally evaluated and spectroscopically characterized. These "half-cruciform" fluorophores respond to bases, acids and anions through changes in fluorescence that vary from moderate to dramatic.

  20. Shedding Light on Protein Folding, Structural and Functional Dynamics by Single Molecule Studies

    Directory of Open Access Journals (Sweden)

    Krutika Bavishi

    2014-11-01

    Full Text Available The advent of advanced single molecule measurements unveiled a great wealth of dynamic information revolutionizing our understanding of protein dynamics and behavior in ways unattainable by conventional bulk assays. Equipped with the ability to record distribution of behaviors rather than the mean property of a population, single molecule measurements offer observation and quantification of the abundance, lifetime and function of multiple protein states. They also permit the direct observation of the transient and rarely populated intermediates in the energy landscape that are typically averaged out in non-synchronized ensemble measurements. Single molecule studies have thus provided novel insights about how the dynamic sampling of the free energy landscape dictates all aspects of protein behavior; from its folding to function. Here we will survey some of the state of the art contributions in deciphering mechanisms that underlie protein folding, structural and functional dynamics by single molecule fluorescence microscopy techniques. We will discuss a few selected examples highlighting the power of the emerging techniques and finally discuss the future improvements and directions.

  1. Switching behavior of double-decker single molecule magnets on a metal surface

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Yingshuang; Schwoebel, Joerg; Hoffmann, Germar; Brede, Jens; Wiesendanger, Roland [University of Hamburg, Hamburg (Germany); Dillulo, Andrew [Ohio University, Athens (United States); Klyatskaya, Svetlana [Karlsruhe Institute of Technology, Karlsruhe (Germany); Ruben, Mario [Karlsruhe Institute of Technology, Karlsruhe (Germany); Universite de Strasbourg, Strasbourg (France)

    2011-07-01

    Single molecule magnets (SMM) are most promising materials for spin based molecular electronics. Due to their large magnetic anisotropy stabilized by inside chemical bonds, SMM can potentially be used for information storage at the single molecule level. For applications, it is of importance to adsorb the SMM onto surfaces and to study their subsequent conformational, electronic and magnetic properties. We have investigated the adsorption behavior of Tb and Dy based double-decker SMM on an Ir(111) surface with low temperature scanning tunneling microscopy and spectroscopy. It is found that Tb double-decker molecules bind tightly to the Ir(111) surface. By resonantly injecting tunneling electrons into its LUMO or HOMO state, the Tb double-decker molecule can be switched from a four-lobed structure to an eight-lobed structure. After switching, energy positions of the HOMO and LUMO states both shift closer to the Fermi level. Dy double-decker molecules also exhibit the same switching properties on the Ir(111) surface. The switching behavior of the molecules is tentatively attributed to a conformational change of the double-decker molecular frame.

  2. Small-pixel long wavelength infrared focal plane arrays based on InAs/GaSb Type-II superlattice

    Science.gov (United States)

    Han, Xi; Jiang, Dongwei; Wang, Guowei; Hao, Hongyue; Sun, Yaoyao; Jiang, Zhi; Lv, Yuexi; Guo, Chunyan; Xu, Yingqiang; Niu, Zhichuan

    2018-03-01

    The paper reports a 640 × 512 long wavelength infrared focal plane arrays (FPAs) with 15 × 15 μm2 pixels pitch based on the type II InAs/GaSb superlattice. Material grown on a 3 in. GaSb substrate exhibits a 50% cutoff wavelength of 10.2 μm across the entire wafer. The peak quantum efficiency of the detector reaches 28% at 9.1 μm without anti-reflecting coating. Maximal resistance-area products of 8.95 Ω·cm2 at 77 K and 24.4 Ω·cm2 at 45 K are achieved in a single element device indicating that the generation-recombination and tunneling mechanisms dominate the device dark current, respectively. The peak Johnson Detectivity reaches 9.66 × 1011 cm Hz1/2/W at 9.1 μm with the bias voltage of 80 mV. In the whole zone, the operability and non-uniformity for the responsivity are 97.74% and 6.41% respectively. The average noise equivalent temperature difference of 31.9 mK at 77 K is achieved with an integration time of 0.5 ms, a 300 K background and f/2 optics.

  3. Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing

    Directory of Open Access Journals (Sweden)

    Yu-Chih Tsai

    2016-02-01

    Full Text Available Deep metagenomic shotgun sequencing has emerged as a powerful tool to interrogate composition and function of complex microbial communities. Computational approaches to assemble genome fragments have been demonstrated to be an effective tool for de novo reconstruction of genomes from these communities. However, the resultant “genomes” are typically fragmented and incomplete due to the limited ability of short-read sequence data to assemble complex or low-coverage regions. Here, we use single-molecule, real-time (SMRT sequencing to reconstruct a high-quality, closed genome of a previously uncharacterized Corynebacterium simulans and its companion bacteriophage from a skin metagenomic sample. Considerable improvement in assembly quality occurs in hybrid approaches incorporating short-read data, with even relatively small amounts of long-read data being sufficient to improve metagenome reconstruction. Using short-read data to evaluate strain variation of this C. simulans in its skin community at single-nucleotide resolution, we observed a dominant C. simulans strain with moderate allelic heterozygosity throughout the population. We demonstrate the utility of SMRT sequencing and hybrid approaches in metagenome quantitation, reconstruction, and annotation.

  4. Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing

    Science.gov (United States)

    Tsai, Yu-Chih; Deming, Clayton; Segre, Julia A.; Kong, Heidi H.; Korlach, Jonas

    2016-01-01

    ABSTRACT Deep metagenomic shotgun sequencing has emerged as a powerful tool to interrogate composition and function of complex microbial communities. Computational approaches to assemble genome fragments have been demonstrated to be an effective tool for de novo reconstruction of genomes from these communities. However, the resultant “genomes” are typically fragmented and incomplete due to the limited ability of short-read sequence data to assemble complex or low-coverage regions. Here, we use single-molecule, real-time (SMRT) sequencing to reconstruct a high-quality, closed genome of a previously uncharacterized Corynebacterium simulans and its companion bacteriophage from a skin metagenomic sample. Considerable improvement in assembly quality occurs in hybrid approaches incorporating short-read data, with even relatively small amounts of long-read data being sufficient to improve metagenome reconstruction. Using short-read data to evaluate strain variation of this C. simulans in its skin community at single-nucleotide resolution, we observed a dominant C. simulans strain with moderate allelic heterozygosity throughout the population. We demonstrate the utility of SMRT sequencing and hybrid approaches in metagenome quantitation, reconstruction, and annotation. PMID:26861018

  5. Dye molecules as single-photon sources and large optical nonlinearities on a chip

    International Nuclear Information System (INIS)

    Hwang, J; Hinds, E A

    2011-01-01

    We point out that individual organic dye molecules, deposited close to optical waveguides on a photonic chip, can act as single-photon sources. A thin silicon nitride strip waveguide is expected to collect 28% of the photons from a single dibenzoterrylene molecule. These molecules can also provide large, localized optical nonlinearities, which are enough to discriminate between one photon or two through a differential phase shift of 2 0 per photon. This new atom-photon interface may be used as a resource for processing quantum information.

  6. Optical Microcavity: Sensing down to Single Molecules and Atoms

    Directory of Open Access Journals (Sweden)

    Shu-Yu Su

    2011-02-01

    Full Text Available This review article discusses fundamentals of dielectric, low-loss, optical micro-resonator sensing, including figures of merit and a variety of microcavity designs, and future perspectives in microcavity-based optical sensing. Resonance frequency and quality (Q factor are altered as a means of detecting a small system perturbation, resulting in realization of optical sensing of a small amount of sample materials, down to even single molecules. Sensitivity, Q factor, minimum detectable index change, noises (in sensor system components and microcavity system including environments, microcavity size, and mode volume are essential parameters to be considered for optical sensing applications. Whispering gallery mode, photonic crystal, and slot-type microcavities typically provide compact, high-quality optical resonance modes for optical sensing applications. Surface Bloch modes induced on photonic crystals are shown to be a promising candidate thanks to large field overlap with a sample and ultra-high-Q resonances. Quantum optics effects based on microcavity quantum electrodynamics (QED would provide novel single-photo-level detection of even single atoms and molecules via detection of doublet vacuum Rabi splitting peaks in strong coupling.

  7. Revealing time bunching effect in single-molecule enzyme conformational dynamics.

    Science.gov (United States)

    Lu, H Peter

    2011-04-21

    In this perspective, we focus our discussion on how the single-molecule spectroscopy and statistical analysis are able to reveal enzyme hidden properties, taking the study of T4 lysozyme as an example. Protein conformational fluctuations and dynamics play a crucial role in biomolecular functions, such as in enzymatic reactions. Single-molecule spectroscopy is a powerful approach to analyze protein conformational dynamics under physiological conditions, providing dynamic perspectives on a molecular-level understanding of protein structure-function mechanisms. Using single-molecule fluorescence spectroscopy, we have probed T4 lysozyme conformational motions under the hydrolysis reaction of a polysaccharide of E. coli B cell walls by monitoring the fluorescence resonant energy transfer (FRET) between a donor-acceptor probe pair tethered to T4 lysozyme domains involving open-close hinge-bending motions. Based on the single-molecule spectroscopic results, molecular dynamics simulation, a random walk model analysis, and a novel 2D statistical correlation analysis, we have revealed a time bunching effect in protein conformational motion dynamics that is critical to enzymatic functions. Bunching effect implies that conformational motion times tend to bunch in a finite and narrow time window. We show that convoluted multiple Poisson rate processes give rise to the bunching effect in the enzymatic reaction dynamics. Evidently, the bunching effect is likely common in protein conformational dynamics involving in conformation-gated protein functions. In this perspective, we will also discuss a new approach of 2D regional correlation analysis capable of analyzing fluctuation dynamics of complex multiple correlated and anti-correlated fluctuations under a non-correlated noise background. Using this new method, we are able to map out any defined segments along the fluctuation trajectories and determine whether they are correlated, anti-correlated, or non-correlated; after which, a

  8. Crystal structure of core streptavidin determined from multi-wavelength anomalous diffraction of synchrotron radiation

    International Nuclear Information System (INIS)

    Hendrickson, W.A.; Paehler, A.; Smith, J.L.; Satow, Y.; Merritt, E.A.; Phizackerley, R.P.

    1989-01-01

    A three-dimensional crystal structure of the biotin-binding core of streptavidin has been determined at 3.1-angstrom resolution. The structure was analyzed from diffraction data measured at three wavelengths from a single crystal of the selenobiotinyl complex with streptavidin. Streptavidin is a tetramer with subunits arrayed in D 2 symmetry. Each protomer is an 8-stranded β-barrel with simple up-down topology. Biotin molecules are bound at one end of each barrel. This study demonstrates the effectiveness of multi-wavelength anomalous diffraction (MAD) procedures for macromolecular crystallography and provides a basis for detailed study of biotin-avidin interactions

  9. Flexible single molecule simulation of reaction-diffusion processes

    International Nuclear Information System (INIS)

    Hellander, Stefan; Loetstedt, Per

    2011-01-01

    An algorithm is developed for simulation of the motion and reactions of single molecules at a microscopic level. The molecules diffuse in a solvent and react with each other or a polymer and molecules can dissociate. Such simulations are of interest e.g. in molecular biology. The algorithm is similar to the Green's function reaction dynamics (GFRD) algorithm by van Zon and ten Wolde where longer time steps can be taken by computing the probability density functions (PDFs) and then sample from the distribution functions. Our computation of the PDFs is much less complicated than GFRD and more flexible. The solution of the partial differential equation for the PDF is split into two steps to simplify the calculations. The sampling is without splitting error in two of the coordinate directions for a pair of molecules and a molecule-polymer interaction and is approximate in the third direction. The PDF is obtained either from an analytical solution or a numerical discretization. The errors due to the operator splitting, the partitioning of the system, and the numerical approximations are analyzed. The method is applied to three different systems involving up to four reactions. Comparisons with other mesoscopic and macroscopic models show excellent agreement.

  10. Error-free 5.1 Tbit/s data generation on a single-wavelength channel using a 1.28 Tbaud symbol rate

    DEFF Research Database (Denmark)

    Mulvad, Hans Christian Hansen; Galili, Michael; Oxenløwe, Leif Katsuo

    2009-01-01

    We demonstrate a record bit rate of 5.1 Tbit/s on a single wavelength using a 1.28 Tbaud OTDM symbol rate, DQPSK data-modulation, and polarisation-multiplexing. Error-free performance (BER......We demonstrate a record bit rate of 5.1 Tbit/s on a single wavelength using a 1.28 Tbaud OTDM symbol rate, DQPSK data-modulation, and polarisation-multiplexing. Error-free performance (BER...

  11. Experimental techniques for single cell and single molecule biomechanics

    International Nuclear Information System (INIS)

    Lim, C.T.; Zhou, E.H.; Li, A.; Vedula, S.R.K.; Fu, H.X.

    2006-01-01

    Stresses and strains that act on the human body can arise either from external physical forces or internal physiological environmental conditions. These biophysical interactions can occur not only at the musculoskeletal but also cellular and molecular levels and can determine the health and function of the human body. Here, we seek to investigate the structure-property-function relationship of cells and biomolecules so as to understand their important physiological functions as well as establish possible connections to human diseases. With the recent advancements in cell and molecular biology, biophysics and nanotechnology, several innovative and state-of-the-art experimental techniques and equipment have been developed to probe the structural and mechanical properties of biostructures from the micro- down to picoscale. Some of these experimental techniques include the optical or laser trap method, micropipette aspiration, step-pressure technique, atomic force microscopy and molecular force spectroscopy. In this article, we will review the basic principles and usage of these techniques to conduct single cell and single molecule biomechanics research

  12. Fabrication and interfacing of nanochannel devices for single-molecule studies

    International Nuclear Information System (INIS)

    Hoang, H T; Berenschot, J W; De Boer, M J; Tas, N R; Haneveld, J; Elwenspoek, M C; Segers-Nolten, I M

    2009-01-01

    Nanochannel devices have been fabricated using standard micromachining techniques such as optical lithography, deposition and etching. 1D nanochannels with thin glass capping and through-wafer inlet/outlet ports were constructed. 2D nanochannels have been made transparent by oxidation of polysilicon channel wall for optical detection and these fragile channels were successfully connected to macro inlet ports. The interfacing from the macro world to the nanochannels was especially designed for optical observation of filling liquid inside nanochannels using an inverted microscope. Toward single-molecule studies, individual quantum dots were visualized in 150 nm height 1D nanochannels. The potential of 2D nanochannels for single-molecule studies was shown from a filling experiment with a fluorescent dye solution

  13. Lanthanide single molecule magnets

    CERN Document Server

    Tang, Jinkui

    2015-01-01

    This book begins by providing basic information on single-molecule magnets (SMMs), covering the magnetism of lanthanide, the characterization and relaxation dynamics of SMMs, and advanced means of studying lanthanide SMMs. It then systematically introduces lanthanide SMMs ranging from mononuclear and dinuclear to polynuclear complexes, classifying them and highlighting those SMMs with high barrier and blocking temperatures – an approach that provides some very valuable indicators for the structural features needed to optimize the contribution of an Ising type spin to a molecular magnet. The final chapter presents some of the newest developments in the lanthanide SMM field, such as the design of multifunctional and stimuli-responsive magnetic materials as well as the anchoring and organization of the SMMs on surfaces. In addition, the crystal structure and magnetic data are clearly presented with a wealth of illustrations in each chapter, helping newcomers and experts alike to better grasp ongoing trends and...

  14. Surveying the Dynamic Radio Sky with the Long Wavelength Demonstrator Array

    Science.gov (United States)

    2010-10-01

    radio wavelengths, there are well-known classes of transients, such as the Sun and ra- dio pulsars , as well as a long history of observ- ing transients...Rupen et al. 2002). Fur- ther, a series of observations and discoveries over the past decade have emphasized that the radio sky may be quite dynamic...Bailes 2010); intense giant pulses have been detected from the Crab pulsar (Hankins et al. 2003); and several as-yet unidentified radio transients have

  15. Can single molecule localization microscopy be used to map closely spaced RGD nanodomains?

    Directory of Open Access Journals (Sweden)

    Mahdie Mollazade

    Full Text Available Cells sense and respond to nanoscale variations in the distribution of ligands to adhesion receptors. This makes single molecule localization microscopy (SMLM an attractive tool to map the distribution of ligands on nanopatterned surfaces. We explore the use of SMLM spatial cluster analysis to detect nanodomains of the cell adhesion-stimulating tripeptide arginine-glycine-aspartic acid (RGD. These domains were formed by the phase separation of block copolymers with controllable spacing on the scale of tens of nanometers. We first determined the topology of the block copolymer with atomic force microscopy (AFM and then imaged the localization of individual RGD peptides with direct stochastic optical reconstruction microscopy (dSTORM. To compare the data, we analyzed the dSTORM data with DBSCAN (density-based spatial clustering application with noise. The ligand distribution and polymer topology are not necessary identical since peptides may attach to the polymer outside the nanodomains and/or coupling and detection of peptides within the nanodomains is incomplete. We therefore performed simulations to explore the extent to which nanodomains could be mapped with dSTORM. We found that successful detection of nanodomains by dSTORM was influenced by the inter-domain spacing and the localization precision of individual fluorophores, and less by non-specific absorption of ligands to the substratum. For example, under our imaging conditions, DBSCAN identification of nanodomains spaced further than 50 nm apart was largely independent of background localisations, while nanodomains spaced closer than 50 nm required a localization precision of ~11 nm to correctly estimate the modal nearest neighbor distance (NDD between nanodomains. We therefore conclude that SMLM is a promising technique to directly map the distribution and nanoscale organization of ligands and would benefit from an improved localization precision.

  16. Control of Single Molecule Fluorescence Dynamics by Stimulated Emission Depletion

    OpenAIRE

    Marsh, R. J.; Osborne, M. A.; Bain, A. J.

    2003-01-01

    The feasibility of manipulating the single molecule absorption-emission cycle using picosecond stimulated emission depletion (STED) is investigated using a stochastic computer simulation. In the simulation the molecule is subjected to repeated excitation and depletion events using time delayed pairs of excitation (PUMP) and depletion (DUMP) pulses derived from a high repetition rate pulsed laser system. The model is used to demonstrate that a significant and even substantial reduction in the ...

  17. Photobleaching correction in fluorescence microscopy images

    International Nuclear Information System (INIS)

    Vicente, Nathalie B; Diaz Zamboni, Javier E; Adur, Javier F; Paravani, Enrique V; Casco, Victor H

    2007-01-01

    Fluorophores are used to detect molecular expression by highly specific antigen-antibody reactions in fluorescence microscopy techniques. A portion of the fluorophore emits fluorescence when irradiated with electromagnetic waves of particular wavelengths, enabling its detection. Photobleaching irreversibly destroys fluorophores stimulated by radiation within the excitation spectrum, thus eliminating potentially useful information. Since this process may not be completely prevented, techniques have been developed to slow it down or to correct resulting alterations (mainly, the decrease in fluorescent signal). In the present work, the correction by photobleaching curve was studied using E-cadherin (a cell-cell adhesion molecule) expression in Bufo arenarum embryos. Significant improvements were observed when applying this simple, inexpensive and fast technique

  18. iSBatch: a batch-processing platform for data analysis and exploration of live-cell single-molecule microscopy images and other hierarchical datasets.

    Science.gov (United States)

    Caldas, Victor E A; Punter, Christiaan M; Ghodke, Harshad; Robinson, Andrew; van Oijen, Antoine M

    2015-10-01

    Recent technical advances have made it possible to visualize single molecules inside live cells. Microscopes with single-molecule sensitivity enable the imaging of low-abundance proteins, allowing for a quantitative characterization of molecular properties. Such data sets contain information on a wide spectrum of important molecular properties, with different aspects highlighted in different imaging strategies. The time-lapsed acquisition of images provides information on protein dynamics over long time scales, giving insight into expression dynamics and localization properties. Rapid burst imaging reveals properties of individual molecules in real-time, informing on their diffusion characteristics, binding dynamics and stoichiometries within complexes. This richness of information, however, adds significant complexity to analysis protocols. In general, large datasets of images must be collected and processed in order to produce statistically robust results and identify rare events. More importantly, as live-cell single-molecule measurements remain on the cutting edge of imaging, few protocols for analysis have been established and thus analysis strategies often need to be explored for each individual scenario. Existing analysis packages are geared towards either single-cell imaging data or in vitro single-molecule data and typically operate with highly specific algorithms developed for particular situations. Our tool, iSBatch, instead allows users to exploit the inherent flexibility of the popular open-source package ImageJ, providing a hierarchical framework in which existing plugins or custom macros may be executed over entire datasets or portions thereof. This strategy affords users freedom to explore new analysis protocols within large imaging datasets, while maintaining hierarchical relationships between experiments, samples, fields of view, cells, and individual molecules.

  19. Monte-Carlo simulation of a high-resolution inverse geometry spectrometer on the SNS. Long Wavelength Target Station

    International Nuclear Information System (INIS)

    Bordallo, H.N.; Herwig, K.W.

    2001-01-01

    Using the Monte-Carlo simulation program McStas, we present the design principles of the proposed high-resolution inverse geometry spectrometer on the SNS-Long Wavelength Target Station (LWTS). The LWTS will provide the high flux of long wavelength neutrons at the requisite pulse rate required by the spectrometer design. The resolution of this spectrometer lies between that routinely achieved by spin echo techniques and the design goal of the high power target station backscattering spectrometer. Covering this niche in energy resolution will allow systematic studies over the large dynamic range required by many disciplines, such as protein dynamics. (author)

  20. Tunable and switchable dual-wavelength single polarization narrow linewidth SLM erbium-doped fiber laser based on a PM-CMFBG filter.

    Science.gov (United States)

    Yin, Bin; Feng, Suchun; Liu, Zhibo; Bai, Yunlong; Jian, Shuisheng

    2014-09-22

    A tunable and switchable dual-wavelength single polarization narrow linewidth single-longitudinal-mode (SLM) erbium-doped fiber (EDF) ring laser based on polarization-maintaining chirped moiré fiber Bragg grating (PM-CMFBG) filter is proposed and demonstrated. For the first time as we know, the CMFBG inscribed on the PM fiber is applied for the wavelength-tunable and-switchable dual-wavelength laser. The PM-CMFBG filter with ultra-narrow transmission band (0.1 pm) and a uniform polarization-maintaining fiber Bragg grating (PM-FBG) are used to select the laser longitudinal mode. The stable single polarization SLM operation is guaranteed by the PM-CMFBG filter and polarization controller. A tuning range of about 0.25 nm with about 0.075 nm step is achieved by stretching the uniform PM-FBG. Meanwhile, the linewidth of the fiber laser for each wavelength is approximate 6.5 and 7.1 kHz with a 20 dB linewidth, which indicates the laser linewidth is approximate 325 Hz and 355 Hz FWHM.

  1. Single-molecule denaturation mapping of DNA in nanofluidic channels

    DEFF Research Database (Denmark)

    Reisner, Walter; Larsen, Niels Bent; Silahtaroglu, Asli

    2010-01-01

    Here we explore the potential power of denaturation mapping as a single-molecule technique. By partially denaturing YOYO (R)-1-labeled DNA in nanofluidic channels with a combination of formamide and local heating, we obtain a sequence-dependent "barcode" corresponding to a series of local dips...... and peaks in the intensity trace along the extended molecule. We demonstrate that this structure arises from the physics of local denaturation: statistical mechanical calculations of sequence-dependent melting probability can predict the barcode to be observed experimentally for a given sequence...

  2. Spatial and temporal superresolution concepts to study plasma membrane organization by single molecule fluorescence techniques

    International Nuclear Information System (INIS)

    Ruprecht, V.

    2010-01-01

    Fluorescence microscopy techniques are currently among the most important experimental tools to study cellular processes. Ultra-sensitive detection devices nowadays allow for measuring even individual farnesylacetate labeled target molecules with nanometer spatial accuracy and millisecond time resolution. The emergence of single molecule fluorescence techniques especially contributed to the field of membrane biology and provided basic knowledge on structural and dynamic features of the cellular plasma membrane. However, we are still confronted with a rather fragmentary understanding of the complex architecture and functional interrelations of membrane constituents. In this thesis new concepts in one- and dual-color single molecule fluorescence techniques are presented that allow for addressing organization principles and interaction dynamics in the live cell plasma membrane. Two complementary experimental strategies are described which differ in their detection principle: single molecule fluorescence imaging and fluorescence correlation spectroscopy. The presented methods are discussed in terms of their implementation, accuracy, quantitative and statistical data analysis, as well as live cell applications. State-of-the-art dual color single molecule imaging is introduced as the most direct experimental approach to study interaction dynamics between differently labeled target molecules. New analytical estimates for robust data analysis are presented that facilitate quantitative recording and identification of co localizations in dual color single molecule images. A novel dual color illumination scheme is further described that profoundly extends the current range and sensitivity of conventional dual color single molecule experiments. The method enables working at high surface densities of fluorescent molecules - a feature typically incommensurable with single molecule imaging - and is especially suited for the detection of rare interactions by tracking co localized

  3. Interference with a quantum dot single-photon source and a laser at telecom wavelength

    Energy Technology Data Exchange (ETDEWEB)

    Felle, M. [Toshiba Research Europe Limited, Cambridge Research Laboratory, 208 Cambridge Science Park, Milton Road, Cambridge CB4 0GZ (United Kingdom); Centre for Advanced Photonics and Electronics, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0FA (United Kingdom); Huwer, J., E-mail: jan.huwer@crl.toshiba.co.uk; Stevenson, R. M.; Skiba-Szymanska, J.; Ward, M. B.; Shields, A. J. [Toshiba Research Europe Limited, Cambridge Research Laboratory, 208 Cambridge Science Park, Milton Road, Cambridge CB4 0GZ (United Kingdom); Farrer, I.; Ritchie, D. A. [Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE (United Kingdom); Penty, R. V. [Centre for Advanced Photonics and Electronics, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0FA (United Kingdom)

    2015-09-28

    The interference of photons emitted by dissimilar sources is an essential requirement for a wide range of photonic quantum information applications. Many of these applications are in quantum communications and need to operate at standard telecommunication wavelengths to minimize the impact of photon losses and be compatible with existing infrastructure. Here, we demonstrate for the first time the quantum interference of telecom-wavelength photons from an InAs/GaAs quantum dot single-photon source and a laser; an important step towards such applications. The results are in good agreement with a theoretical model, indicating a high degree of indistinguishability for the interfering photons.

  4. Interference with a quantum dot single-photon source and a laser at telecom wavelength

    International Nuclear Information System (INIS)

    Felle, M.; Huwer, J.; Stevenson, R. M.; Skiba-Szymanska, J.; Ward, M. B.; Shields, A. J.; Farrer, I.; Ritchie, D. A.; Penty, R. V.

    2015-01-01

    The interference of photons emitted by dissimilar sources is an essential requirement for a wide range of photonic quantum information applications. Many of these applications are in quantum communications and need to operate at standard telecommunication wavelengths to minimize the impact of photon losses and be compatible with existing infrastructure. Here, we demonstrate for the first time the quantum interference of telecom-wavelength photons from an InAs/GaAs quantum dot single-photon source and a laser; an important step towards such applications. The results are in good agreement with a theoretical model, indicating a high degree of indistinguishability for the interfering photons

  5. Kondo effect in single-molecule magnet transistors

    Science.gov (United States)

    Gonzalez, Gabriel; Leuenberger, Michael; Mucciolo, Eduardo

    2009-03-01

    We present a careful and thorough microscopic derivation of the anisotropic Kondo Hamiltonian for single-molecule magnet (SMM) transistors. When the molecule is strongly coupled to metallic leads, we show that by applying a transverse magnetic field it is possible to topologically induce or quench the Kondo effect in the conductance of a SMM with either an integer or a half-integer spin S>1/2. This topological Kondo effect is due to the Berry-phase interference between multiple quantum tunneling paths of the spin. We calculate the renormalized Berry-phase oscillations of the two Kondo peaks as a function of a transverse magnetic field by means of the poor man's scaling approach. We illustrate our findings with the SMM Ni4, which we propose as a possible candidate for the experimental observation of the conductance oscillations.

  6. MCD spectroscopy of hexanuclear Mn(III) salicylaldoxime single-molecule magnets.

    Science.gov (United States)

    Bradley, Justin M; Thomson, Andrew J; Inglis, Ross; Milios, Constantinos J; Brechin, Euan K; Piligkos, Stergios

    2010-11-07

    The hexanuclear cages [Mn(6)O(2)(R-sao)(6)L(2)(EtOH)(x)(H(2)O)(y)] "Mn(6)" behave as single-molecule magnets (SMMs) below a characteristic blocking temperature. As with [Mn(12)O(12)(O(2)CR)(16)(H(2)O)(4)] "Mn(12)" the electronic absorption spectra are rather featureless, yielding little information on the electronic structure of the magnetic ions. Low temperature Magnetic Circular Dichroism (MCD) spectra afford greater resolution of the optical transitions and also probe the magnetic properties of the system. Both the ground state spin and blocking temperature of the Mn(6) cages are determined by subtle structural perturbations of a generic Mn(6)O(2) core. Absorbance and MCD spectra are reported for [Mn(6)O(2)(Et-sao)(6){O(2)CPh(Me)(2)}(2)(EtOH)(6)] (1), [Mn(6)O(2)(Et-sao)(6){O(2)CPh}(2)(EtOH)(4)(H(2)O)(2)] (2), [Mn(6)O(2)(sao)(6){O(2)CPh}(2)(EtOH)(4)]·EtOH (3) and the trinuclear precursor [Mn(3)O(Et-sao)(3)(MeOH)(3)](ClO(4)) (4) cast into polymer film. SMM behaviour has previously been observed using magnetic susceptibility measurements on powder and single-crystal samples. The ligand field environment of the magnetic ions is assumed to be similar in (1) and (2) and their different blocking temperatures are attributed to the magnitude of the effective exchange constant. The MCD spectra of (1) and (2), in which the ground state spin S = 12, show that the ligand field environments of the Mn ions are almost identical and that magnetic hysteresis persists for isolated molecules when crystal packing forces are removed. The subtle structural differences between (1) and (2) are manifested in the field dependence of the MCD response at different wavelengths that reflect changes in band polarisation. The MCD spectrum of (3) contains features not apparent in those of (1) and (2). These are attributed to 5-coordinate Mn(iii), which is unique to (3) among the compounds studied. (3) has ground state spin S = 4, a lower blocking temperature and consequently no observable

  7. Electron-vibron coupling effects on electron transport via a single-molecule magnet

    NARCIS (Netherlands)

    McCaskey, A.; Yamamoto, Y.; Warnock, M.; Burzuri, E.; Van der Zant, H.S.J.; Park, K.

    2015-01-01

    We investigate how the electron-vibron coupling influences electron transport via an anisotropic magnetic molecule, such as a single-molecule magnet (SMM) Fe4, by using a model Hamiltonian with parameter values obtained from density-functional theory (DFT). The magnetic anisotropy parameters,

  8. Lanthanide single molecule magnets

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Jinkui; Zhang, Peng [Chinese Academy of Sciences, Changchun (China). Changchun Inst. of Applied Chemistry

    2015-10-01

    This book begins by providing basic information on single-molecule magnets (SMMs), covering the magnetism of lanthanide, the characterization and relaxation dynamics of SMMs and advanced means of studying lanthanide SMMs. It then systematically introduces lanthanide SMMs ranging from mononuclear and dinuclear to polynuclear complexes, classifying them and highlighting those SMMs with high barrier and blocking temperatures - an approach that provides some very valuable indicators for the structural features needed to optimize the contribution of an Ising type spin to a molecular magnet. The final chapter presents some of the newest developments in the lanthanide SMM field, such as the design of multifunctional and stimuli-responsive magnetic materials as well as the anchoring and organization of the SMMs on surfaces. In addition, the crystal structure and magnetic data are clearly presented with a wealth of illustrations in each chapter, helping newcomers and experts alike to better grasp ongoing trends and explore new directions.

  9. Giant Magnetoresistance in Carbon Nanotubes with Single-Molecule Magnets TbPc2.

    Science.gov (United States)

    Krainov, Igor V; Klier, Janina; Dmitriev, Alexander P; Klyatskaya, Svetlana; Ruben, Mario; Wernsdorfer, Wolfgang; Gornyi, Igor V

    2017-07-25

    We present experimental results and a theoretical model for the gate-controlled spin-valve effect in carbon nanotubes with side-attached single-molecule magnets TbPc 2 (Terbium(III) bis-phthalocyanine). These structures show a giant magnetoresistance up to 1000% in experiments on single-wall nanotubes that are tunnel-coupled to the leads. The proposed theoretical model combines the spin-dependent Fano effect with Coulomb blockade and predicts a spin-spin interaction between the TbPc 2 molecules, mediated by conducting electrons via the charging effect. This gate-tuned interaction is responsible for the stable magnetic ordering of the inner spins of the molecules in the absence of magnetic field. In the case of antiferromagnetic arrangement, electrons with either spin experience the scattering by the molecules, which results in blocking the linear transport. In strong magnetic fields, the Zeeman energy exceeds the effective antiferromagnetic coupling and one species of electrons is not scattered by molecules, which leads to a much lower total resistance at the resonant values of gate voltage, and hence to a supramolecular spin-valve effect.

  10. Elastin-like Polypeptide Linkers for Single-Molecule Force Spectroscopy.

    Science.gov (United States)

    Ott, Wolfgang; Jobst, Markus A; Bauer, Magnus S; Durner, Ellis; Milles, Lukas F; Nash, Michael A; Gaub, Hermann E

    2017-06-27

    Single-molecule force spectroscopy (SMFS) is by now well established as a standard technique in biophysics and mechanobiology. In recent years, the technique has benefitted greatly from new approaches to bioconjugation of proteins to surfaces. Indeed, optimized immobilization strategies for biomolecules and refined purification schemes are being steadily adapted and improved, which in turn has enhanced data quality. In many previously reported SMFS studies, poly(ethylene glycol) (PEG) was used to anchor molecules of interest to surfaces and/or cantilever tips. The limitation, however, is that PEG exhibits a well-known trans-trans-gauche to all-trans transition, which results in marked deviation from standard polymer elasticity models such as the worm-like chain, particularly at elevated forces. As a result, the assignment of unfolding events to protein domains based on their corresponding amino acid chain lengths is significantly obscured. Here, we provide a solution to this problem by implementing unstructured elastin-like polypeptides as linkers to replace PEG. We investigate the suitability of tailored elastin-like polypeptides linkers and perform direct comparisons to PEG, focusing on attributes that are critical for single-molecule force experiments such as linker length, monodispersity, and bioorthogonal conjugation tags. Our results demonstrate that by avoiding the ambiguous elastic response of mixed PEG/peptide systems and instead building the molecular mechanical systems with only a single bond type with uniform elastic properties, we improve data quality and facilitate data analysis and interpretation in force spectroscopy experiments. The use of all-peptide linkers allows alternative approaches for precisely defining elastic properties of proteins linked to surfaces.

  11. Single-molecule detection of dihydroazulene photo-thermal reaction using break junction technique

    Science.gov (United States)

    Huang, Cancan; Jevric, Martyn; Borges, Anders; Olsen, Stine T.; Hamill, Joseph M.; Zheng, Jue-Ting; Yang, Yang; Rudnev, Alexander; Baghernejad, Masoud; Broekmann, Peter; Petersen, Anne Ugleholdt; Wandlowski, Thomas; Mikkelsen, Kurt V.; Solomon, Gemma C.; Brøndsted Nielsen, Mogens; Hong, Wenjing

    2017-05-01

    Charge transport by tunnelling is one of the most ubiquitous elementary processes in nature. Small structural changes in a molecular junction can lead to significant difference in the single-molecule electronic properties, offering a tremendous opportunity to examine a reaction on the single-molecule scale by monitoring the conductance changes. Here, we explore the potential of the single-molecule break junction technique in the detection of photo-thermal reaction processes of a photochromic dihydroazulene/vinylheptafulvene system. Statistical analysis of the break junction experiments provides a quantitative approach for probing the reaction kinetics and reversibility, including the occurrence of isomerization during the reaction. The product ratios observed when switching the system in the junction does not follow those observed in solution studies (both experiment and theory), suggesting that the junction environment was perturbing the process significantly. This study opens the possibility of using nano-structured environments like molecular junctions to tailor product ratios in chemical reactions.

  12. MULTI-WAVELENGTH RADIO CONTINUUM EMISSION STUDIES OF DUST-FREE RED GIANTS

    International Nuclear Information System (INIS)

    O'Gorman, Eamon; Harper, Graham M.; Brown, Alexander; Drake, Stephen; Richards, Anita M. S.

    2013-01-01

    Multi-wavelength centimeter continuum observations of non-dusty, non-pulsating K spectral-type red giants directly sample their chromospheres and wind acceleration zones. Such stars are feeble emitters at these wavelengths, however, and previous observations have provided only a small number of modest signal-to-noise measurements slowly accumulated over three decades. We present multi-wavelength Karl G. Jansky Very Large Array thermal continuum observations of the wind acceleration zones of two dust-free red giants, Arcturus (α Boo: K2 III) and Aldebaran (α Tau: K5 III). Importantly, most of our observations of each star were carried out over just a few days, so that we obtained a snapshot of the different stellar atmospheric layers sampled at different wavelengths, independent of any long-term variability. We report the first detections at several wavelengths for each star including a detection at 10 cm (3.0 GHz: S band) for both stars and a 20 cm (1.5 GHz: L band) detection for α Boo. This is the first time single (non-binary) luminosity class III red giants have been detected at these continuum wavelengths. Our long-wavelength data sample the outer layers of α Boo's atmosphere where its wind velocity is approaching (or possibly has reached) its terminal value and the ionization balance is becoming frozen-in. For α Tau, however, our long-wavelength data are still sampling its inner atmosphere, where the wind is still accelerating probably due to its lower mass-loss rate. We compare our data with published semi-empirical models based on ultraviolet data, and the marked deviations highlight the need for new atmospheric models to be developed. Spectral indices are used to discuss the possible properties of the stellar atmospheres, and we find evidence for a rapidly cooling wind in the case of α Boo. Finally, we develop a simple analytical wind model for α Boo based on our new long-wavelength flux measurements

  13. Multi-wavelength Radio Continuum Emission Studies of Dust-free Red Giants

    Science.gov (United States)

    O'Gorman, Eamon; Harper, Graham M.; Brown, Alexander; Dranke, Stephen; Richards, Anita M. S.

    2013-01-01

    Multi-wavelength centimeter continuum observations of non-dusty, non-pulsating K spectral-type red giants directly sample their chromospheres and wind acceleration zones. Such stars are feeble emitters at these wavelengths, however, and previous observations have provided only a small number of modest signal-to-noise measurements slowly accumulated over three decades. We present multi-wavelength Karl G. Jansky Very Large Array thermal continuum observations of the wind acceleration zones of two dust-free red giants, Arcturus (alpha Boo: K2 III) and Aldebaran (alpha Tau: K5 III). Importantly, most of our observations of each star were carried out over just a few days, so that we obtained a snapshot of the different stellar atmospheric layers sampled at different wavelengths, independent of any long-term variability. We report the first detections at several wavelengths for each star including a detection at 10 cm (3.0 GHz: S band) for both stars and a 20 cm (1.5 GHz: L band) detection for alpha Boo. This is the first time single (non-binary) luminosity class III red giants have been detected at these continuum wavelengths. Our long-wavelength data sample the outer layers of alpha Boo's atmosphere where its wind velocity is approaching (or possibly has reached) its terminal value and the ionization balance is becoming frozen-in. For alpha Tau, however, our long-wavelength data are still sampling its inner atmosphere, where the wind is still accelerating probably due to its lower mass-loss rate. We compare our data with published semi-empirical models based on ultraviolet data, and the marked deviations highlight the need for new atmospheric models to be developed. Spectral indices are used to discuss the possible properties of the stellar atmospheres, and we find evidence for a rapidly cooling wind in the case of alpha Boo. Finally, we develop a simple analytical wind model for alpha Boo based on our new long-wavelength flux measurements.

  14. MULTI-WAVELENGTH RADIO CONTINUUM EMISSION STUDIES OF DUST-FREE RED GIANTS

    Energy Technology Data Exchange (ETDEWEB)

    O' Gorman, Eamon; Harper, Graham M. [School of Physics, Trinity College Dublin, Dublin 2 (Ireland); Brown, Alexander [Center for Astrophysics and Space Astronomy, University of Colorado, 389 UCB, Boulder, CO 80309 (United States); Drake, Stephen [NASA Goddard Space Flight Center, Greenbelt, MD 20771 (United States); Richards, Anita M. S. [Jodrell Bank Centre for Astrophysics, School of Physics and Astronomy, University of Manchester, Manchester M13 9PL (United Kingdom)

    2013-10-01

    Multi-wavelength centimeter continuum observations of non-dusty, non-pulsating K spectral-type red giants directly sample their chromospheres and wind acceleration zones. Such stars are feeble emitters at these wavelengths, however, and previous observations have provided only a small number of modest signal-to-noise measurements slowly accumulated over three decades. We present multi-wavelength Karl G. Jansky Very Large Array thermal continuum observations of the wind acceleration zones of two dust-free red giants, Arcturus (α Boo: K2 III) and Aldebaran (α Tau: K5 III). Importantly, most of our observations of each star were carried out over just a few days, so that we obtained a snapshot of the different stellar atmospheric layers sampled at different wavelengths, independent of any long-term variability. We report the first detections at several wavelengths for each star including a detection at 10 cm (3.0 GHz: S band) for both stars and a 20 cm (1.5 GHz: L band) detection for α Boo. This is the first time single (non-binary) luminosity class III red giants have been detected at these continuum wavelengths. Our long-wavelength data sample the outer layers of α Boo's atmosphere where its wind velocity is approaching (or possibly has reached) its terminal value and the ionization balance is becoming frozen-in. For α Tau, however, our long-wavelength data are still sampling its inner atmosphere, where the wind is still accelerating probably due to its lower mass-loss rate. We compare our data with published semi-empirical models based on ultraviolet data, and the marked deviations highlight the need for new atmospheric models to be developed. Spectral indices are used to discuss the possible properties of the stellar atmospheres, and we find evidence for a rapidly cooling wind in the case of α Boo. Finally, we develop a simple analytical wind model for α Boo based on our new long-wavelength flux measurements.

  15. Single-cell multiple gene expression analysis based on single-molecule-detection microarray assay for multi-DNA determination

    Energy Technology Data Exchange (ETDEWEB)

    Li, Lu [School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China); Wang, Xianwei [School of Life Sciences, Shandong University, Jinan 250100 (China); Zhang, Xiaoli [School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China); Wang, Jinxing [School of Life Sciences, Shandong University, Jinan 250100 (China); Jin, Wenrui, E-mail: jwr@sdu.edu.cn [School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China)

    2015-01-07

    Highlights: • A single-molecule-detection (SMD) microarray for 10 samples is fabricated. • The based-SMD microarray assay (SMA) can determine 8 DNAs for each sample. • The limit of detection of SMA is as low as 1.3 × 10{sup −16} mol L{sup −1}. • The SMA can be applied in single-cell multiple gene expression analysis. - Abstract: We report a novel ultra-sensitive and high-selective single-molecule-detection microarray assay (SMA) for multiple DNA determination. In the SMA, a capture DNA (DNAc) microarray consisting of 10 subarrays with 9 spots for each subarray is fabricated on a silanized glass coverslip as the substrate. On the subarrays, the spot-to-spot spacing is 500 μm and each spot has a diameter of ∼300 μm. The sequence of the DNAcs on the 9 spots of a subarray is different, to determine 8 types of target DNAs (DNAts). Thus, 8 types of DNAts are captured to their complementary DNAcs at 8 spots of a subarray, respectively, and then labeled with quantum dots (QDs) attached to 8 types of detection DNAs (DNAds) with different sequences. The ninth spot is used to detect the blank value. In order to determine the same 8 types of DNAts in 10 samples, the 10 DNAc-modified subarrays on the microarray are identical. Fluorescence single-molecule images of the QD-labeled DNAts on each spot of the subarray are acquired using a home-made single-molecule microarray reader. The amounts of the DNAts are quantified by counting the bright dots from the QDs. For a microarray, 8 types of DNAts in 10 samples can be quantified in parallel. The limit of detection of the SMA for DNA determination is as low as 1.3 × 10{sup −16} mol L{sup −1}. The SMA for multi-DNA determination can also be applied in single-cell multiple gene expression analysis through quantification of complementary DNAs (cDNAs) corresponding to multiple messenger RNAs (mRNAs) in single cells. To do so, total RNA in single cells is extracted and reversely transcribed into their cDNAs. Three

  16. Single molecule dynamics at a mechanically controllable break junction in solution at room temperature.

    Science.gov (United States)

    Konishi, Tatsuya; Kiguchi, Manabu; Takase, Mai; Nagasawa, Fumika; Nabika, Hideki; Ikeda, Katsuyoshi; Uosaki, Kohei; Ueno, Kosei; Misawa, Hiroaki; Murakoshi, Kei

    2013-01-23

    The in situ observation of geometrical and electronic structural dynamics of a single molecule junction is critically important in order to further progress in molecular electronics. Observations of single molecular junctions are difficult, however, because of sensitivity limits. Here, we report surface-enhanced Raman scattering (SERS) of a single 4,4'-bipyridine molecule under conditions of in situ current flow in a nanogap, by using nano-fabricated, mechanically controllable break junction (MCBJ) electrodes. When adsorbed at room temperature on metal nanoelectrodes in solution to form a single molecule junction, statistical analysis showed that nontotally symmetric b(1) and b(2) modes of 4,4'-bipyridine were strongly enhanced relative to observations of the same modes in solid or aqueous solutions. Significant changes in SERS intensity, energy (wavenumber), and selectivity of Raman vibrational bands that are coincident with current fluctuations provide information on distinct states of electronic and geometrical structure of the single molecule junction, even under large thermal fluctuations occurring at room temperature. We observed the dynamics of 4,4'-bipyridine motion between vertical and tilting configurations in the Au nanogap via b(1) and b(2) mode switching. A slight increase in the tilting angle of the molecule was also observed by noting the increase in the energies of Raman modes and the decrease in conductance of the molecular junction.

  17. Characterizing single-molecule FRET dynamics with probability distribution analysis.

    Science.gov (United States)

    Santoso, Yusdi; Torella, Joseph P; Kapanidis, Achillefs N

    2010-07-12

    Probability distribution analysis (PDA) is a recently developed statistical tool for predicting the shapes of single-molecule fluorescence resonance energy transfer (smFRET) histograms, which allows the identification of single or multiple static molecular species within a single histogram. We used a generalized PDA method to predict the shapes of FRET histograms for molecules interconverting dynamically between multiple states. This method is tested on a series of model systems, including both static DNA fragments and dynamic DNA hairpins. By fitting the shape of this expected distribution to experimental data, the timescale of hairpin conformational fluctuations can be recovered, in good agreement with earlier published results obtained using different techniques. This method is also applied to studying the conformational fluctuations in the unliganded Klenow fragment (KF) of Escherichia coli DNA polymerase I, which allows both confirmation of the consistency of a simple, two-state kinetic model with the observed smFRET distribution of unliganded KF and extraction of a millisecond fluctuation timescale, in good agreement with rates reported elsewhere. We expect this method to be useful in extracting rates from processes exhibiting dynamic FRET, and in hypothesis-testing models of conformational dynamics against experimental data.

  18. Effect of the environment on the electrical conductance of the single benzene-1,4-diamine molecule junction

    Directory of Open Access Journals (Sweden)

    Shigeto Nakashima

    2011-11-01

    Full Text Available We investigated the effect of the environment on the electrical conductance of a single benzene-1,4-diamine (BDA molecule bridging Au electrodes, using the scanning tunneling microscope (STM. The conductance of the single BDA molecule junction decreased upon a change in the environment from tetraglyme, to mesitylene, to water, and finally to N2 gas, while the spread in the conductance value increased. The order of the conductance values of the single BDA molecule junction was explained by the strength of the interaction between the solvent molecules and the Au electrodes. The order of the spread in the conductance values was explained by the diversity in the coverage of the BDA molecule at metal electrodes and atomic and molecular motion of the single-molecule junction.

  19. Binding and Translocation of Termination Factor Rho Studied at the Single-Molecule Level

    Science.gov (United States)

    Koslover, Daniel J.; Fazal, Furqan M.; Mooney, Rachel A.; Landick, Robert; Block, Steven M.

    2012-01-01

    Rho termination factor is an essential hexameric helicase responsible for terminating 20–50% of all mRNA synthesis in E. coli. We used single- molecule force spectroscopy to investigate Rho-RNA binding interactions at the Rho- utilization (rut) site of the ? tR1 terminator. Our results are consistent with Rho complexes adopting two states, one that binds 57 ±2 nucleotides of RNA across all six of the Rho primary binding sites, and another that binds 85 ±2 nucleotides at the six primary sites plus a single secondary site situated at the center of the hexamer. The single-molecule data serve to establish that Rho translocates 5′-to-3′ towards RNA polymerase (RNAP) by a tethered-tracking mechanism, looping out the intervening RNA between the rut site and RNAP. These findings lead to a general model for Rho binding and translocation, and establish a novel experimental approach that should facilitate additional single- molecule studies of RNA-binding proteins. PMID:22885804

  20. A versatile optical microscope for time-dependent single-molecule and single-particle spectroscopy

    Science.gov (United States)

    Li, Hao; Yang, Haw

    2018-03-01

    This work reports the design and implementation of a multi-function optical microscope for time-dependent spectroscopy on single molecules and single nanoparticles. It integrates the now-routine single-object measurements into one standalone platform so that no reconfiguration is needed when switching between different types of sample or spectroscopy modes. The illumination modes include evanescent field through total internal reflection, dark-field illumination, and epi-excitation onto a diffraction-limited spot suitable for confocal detection. The detection modes include spectrally resolved line imaging, wide-field imaging with dual-color capability, and two-color single-element photon-counting detection. The switch between different spectroscopy and data acquisition modes is fully automated and executed through computer programming. The capability of this microscope is demonstrated through selected proof-of-principle experiments.

  1. A versatile optical microscope for time-dependent single-molecule and single-particle spectroscopy.

    Science.gov (United States)

    Li, Hao; Yang, Haw

    2018-03-28

    This work reports the design and implementation of a multi-function optical microscope for time-dependent spectroscopy on single molecules and single nanoparticles. It integrates the now-routine single-object measurements into one standalone platform so that no reconfiguration is needed when switching between different types of sample or spectroscopy modes. The illumination modes include evanescent field through total internal reflection, dark-field illumination, and epi-excitation onto a diffraction-limited spot suitable for confocal detection. The detection modes include spectrally resolved line imaging, wide-field imaging with dual-color capability, and two-color single-element photon-counting detection. The switch between different spectroscopy and data acquisition modes is fully automated and executed through computer programming. The capability of this microscope is demonstrated through selected proof-of-principle experiments.

  2. Modelling single shot damage thresholds of multilayer optics for high-intensity short-wavelength radiation sources

    NARCIS (Netherlands)

    Loch, R.A.; Sobierajski, R.; Louis, Eric; Bosgra, J.; Bosgra, J.; Bijkerk, Frederik

    2012-01-01

    The single shot damage thresholds of multilayer optics for highintensity short-wavelength radiation sources are theoretically investigated, using a model developed on the basis of experimental data obtained at the FLASH and LCLS free electron lasers. We compare the radiation hardness of commonly

  3. Single-Molecule Fluorescence Studies of Membrane Transporters Using Total Internal Reflection Microscopy.

    Science.gov (United States)

    Goudsmits, Joris M H; van Oijen, Antoine M; Slotboom, Dirk J

    2017-01-01

    Cells are delineated by a lipid bilayer that physically separates the inside from the outer environment. Most polar, charged, or large molecules require proteins to reduce the energetic barrier for passage across the membrane and to achieve transport rates that are relevant for life. Here, we describe techniques to visualize the functioning of membrane transport proteins with fluorescent probes at the single-molecule level. First, we explain how to produce membrane-reconstituted transporters with fluorescent labels. Next, we detail the construction of a microfluidic flow cell to image immobilized proteoliposomes on a total internal reflection fluorescence microscope. We conclude by describing the methods that are needed to analyze fluorescence movies and obtain useful single-molecule data. © 2017 Elsevier Inc. All rights reserved.

  4. Smart SERS Hot Spots: Single Molecules Can Be Positioned in a Plasmonic Nanojunction Using Host-Guest Chemistry.

    Science.gov (United States)

    Kim, Nam Hoon; Hwang, Wooseup; Baek, Kangkyun; Rohman, Md Rumum; Kim, Jeehong; Kim, Hyun Woo; Mun, Jungho; Lee, So Young; Yun, Gyeongwon; Murray, James; Ha, Ji Won; Rho, Junsuk; Moskovits, Martin; Kim, Kimoon

    2018-04-04

    Single-molecule surface-enhanced Raman spectroscopy (SERS) offers new opportunities for exploring the complex chemical and biological processes that cannot be easily probed using ensemble techniques. However, the ability to place the single molecule of interest reliably within a hot spot, to enable its analysis at the single-molecule level, remains challenging. Here we describe a novel strategy for locating and securing a single target analyte in a SERS hot spot at a plasmonic nanojunction. The "smart" hot spot was generated by employing a thiol-functionalized cucurbit[6]uril (CB[6]) as a molecular spacer linking a silver nanoparticle to a metal substrate. This approach also permits one to study molecules chemically reluctant to enter the hot spot, by conjugating them to a moiety, such as spermine, that has a high affinity for CB[6]. The hot spot can accommodate at most a few, and often only a single, analyte molecule. Bianalyte experiments revealed that one can reproducibly treat the SERS substrate such that 96% of the hot spots contain a single analyte molecule. Furthermore, by utilizing a series of molecules each consisting of spermine bound to perylene bisimide, a bright SERS molecule, with polymethylene linkers of varying lengths, the SERS intensity as a function of distance from the center of the hot spot could be measured. The SERS enhancement was found to decrease as 1 over the square of the distance from the center of the hot spot, and the single-molecule SERS cross sections were found to increase with AgNP diameter.

  5. Virology: The Next Generation from Digital PCR to Single Virion Genomics

    Energy Technology Data Exchange (ETDEWEB)

    White, Richard A.; Brazelton De Cardenas, Jessica N.; Hayden, Randall T.

    2015-10-01

    In the past 25 years, virology has had major technology breakthroughs stemming first from the introduction of nucleic acid amplification testing, but more recently from the use of next-generation sequencing, digital PCR, and the possibility of single virion genomics. These technologies have and will improve diagnosis and disease state monitoring in clinical settings, aid in environmental monitoring, and reveal the vast genetic potential of viruses. Using the principle of limiting dilution, digital PCR amplifies single molecules of DNA in highly partitioned endpoint reactions and reads each of those reactions as either positive or negative based on the presence or absence of target fluorophore. In this review, digital PCR will be highlighted along with current studies, advantages/disadvantages, and future perspectives with regard to digital PCR, viral load testing, and the possibility of single virion genomics.

  6. Short-wavelength soft-x-ray laser pumped in double-pulse single-beam non-normal incidence

    International Nuclear Information System (INIS)

    Zimmer, D.; Ros, D.; Guilbaud, O.; Habib, J.; Kazamias, S.; Zielbauer, B.; Bagnoud, V.; Ecker, B.; Aurand, B.; Kuehl, T.; Hochhaus, D. C.; Neumayer, P.

    2010-01-01

    We demonstrated a 7.36 nm Ni-like samarium soft-x-ray laser, pumped by 36 J of a neodymium:glass chirped-pulse amplification laser. Double-pulse single-beam non-normal-incidence pumping was applied for efficient soft-x-ray laser generation. In this case, the applied technique included a single-optic focusing geometry for large beam diameters, a single-pass grating compressor, traveling-wave tuning capability, and an optimized high-energy laser double pulse. This scheme has the potential for even shorter-wavelength soft-x-ray laser pumping.

  7. Enrichment of megabase-sized DNA molecules for single-molecule optical mapping and next-generation sequencing

    DEFF Research Database (Denmark)

    Łopacińska-Jørgensen, Joanna M; Pedersen, Jonas Nyvold; Bak, Mads

    2017-01-01

    Next-generation sequencing (NGS) has caused a revolution, yet left a gap: long-range genetic information from native, non-amplified DNA fragments is unavailable. It might be obtained by optical mapping of megabase-sized DNA molecules. Frequently only a specific genomic region is of interest, so...

  8. Influence of quantum dot labels on single molecule movement in the plasma membrane

    DEFF Research Database (Denmark)

    Clausen, Mathias P.; Lagerholm, B. Christoffer

    2011-01-01

    Single particle tracking results are very dependent on the probe that is used. In this study we have investigated the influence that functionalized quantum dots (QDs) have on the recorded movement in single molecule tracking experiments of plasma membrane species in live cells. Potential issues...... for simultaneous investigations of different plasma membrane species in order to discriminate the effect of the label from differences in movement of the target molecules....

  9. Simulation of the Chang'E-5 mission contribution in lunar long wavelength gravity field improvement

    Science.gov (United States)

    Yan, Jianguo; Yang, Xuan; Ping, Jinsong; Ye, Mao; Liu, Shanhong; Jin, Weitong; Li, Fei; Barriot, Jean-Pierre

    2018-06-01

    The precision of lunar gravity field estimation has improved by means of three to five orders of magnitude since the successful GRAIL lunar mission. There are still discrepancies however, in the low degree coefficients and long wavelength components of the solutions developed by two space research centers (JPL and GSFC). These discrepancies hint at the possibilities for improving the accuracy in the long wavelength part of the lunar gravity field. In the near future, China will launch the Chang'E-5 lunar mission. In this sample-return mission, there will be a chance to do KBRR measurements between an ascending module and an orbiting module. These two modules will fly around lunar at an inclination of ˜49 degrees, with an orbital height of 100 km and an inter-satellite distance of 200 km. In our research, we simulated the contribution of the KBRR tracking mode for different GRAIL orbital geometries. This analysis indicated possible deficiencies in the low degree coefficient solutions for the polar satellite-to-satellite tracking mode at various orbital heights. We also investigated the potential contributions of the KBRR to the Chang'E-5 mission goal of lunar gravity field recovery, especially in the long wavelength component. Potential improvements were assessed using various power spectrums of the lunar gravity field models. In addition, we also investigated possible improvements in solving lunar tidal Love number K2. These results may assist the implementation of the Chang'E-5 mission.

  10. Single Molecule Scanning of DNA Radiation Oxidative Damage, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — This proposal will develop an assay to map genomic DNA, at the single molecule level and in a nanodevice, for oxidative DNA damage arising from radiation exposure;...

  11. On the combination of molecular replacement and single-wavelength anomalous diffraction phasing for automated structure determination

    International Nuclear Information System (INIS)

    Panjikar, Santosh; Parthasarathy, Venkataraman; Lamzin, Victor S.; Weiss, Manfred S.; Tucker, Paul A.

    2009-01-01

    The combination of molecular replacement and single-wavelength anomalous diffraction improves the performance of automated structure determination with Auto-Rickshaw. A combination of molecular replacement and single-wavelength anomalous diffraction phasing has been incorporated into the automated structure-determination platform Auto-Rickshaw. The complete MRSAD procedure includes molecular replacement, model refinement, experimental phasing, phase improvement and automated model building. The improvement over the standard SAD or MR approaches is illustrated by ten test cases taken from the JCSG diffraction data-set database. Poor MR or SAD phases with phase errors larger than 70° can be improved using the described procedure and a large fraction of the model can be determined in a purely automatic manner from X-ray data extending to better than 2.6 Å resolution

  12. Rationale for single molecule detection by means of Raman spectroscopy

    International Nuclear Information System (INIS)

    Gaponenko, S.V.; Guzatov, D.V.

    2009-01-01

    A consistent quantum electrodynamical description is proposed of Raman scattering of light by a molecule in a medium with a modified photon density of states. Enhanced local density of states near a metal nanobody is shown to increase a scattering rate by several orders of magnitude, thus providing a rationale for experimental detection of single molecules by means of Raman spectroscopy. For an ellipsoidal particle 10 14 -fold enhancement of the Raman scattering cross-section is obtained. (authors)

  13. Autofluorescence Imaging With Near-Infrared Excitation:Normalization by Reflectance to Reduce Signal From Choroidal Fluorophores

    Science.gov (United States)

    Cideciyan, Artur V.; Swider, Malgorzata; Jacobson, Samuel G.

    2015-01-01

    Purpose. We previously developed reduced-illuminance autofluorescence imaging (RAFI) methods involving near-infrared (NIR) excitation to image melanin-based fluorophores and short-wavelength (SW) excitation to image lipofuscin-based flurophores. Here, we propose to normalize NIR-RAFI in order to increase the relative contribution of retinal pigment epithelium (RPE) fluorophores. Methods. Retinal imaging was performed with a standard protocol holding system parameters invariant in healthy subjects and in patients. Normalized NIR-RAFI was derived by dividing NIR-RAFI signal by NIR reflectance point-by-point after image registration. Results. Regions of RPE atrophy in Stargardt disease, AMD, retinitis pigmentosa, choroideremia, and Leber congenital amaurosis as defined by low signal on SW-RAFI could correspond to a wide range of signal on NIR-RAFI depending on the contribution from the choroidal component. Retinal pigment epithelium atrophy tended to always correspond to high signal on NIR reflectance. Normalizing NIR-RAFI reduced the choroidal component of the signal in regions of atrophy. Quantitative evaluation of RPE atrophy area showed no significant differences between SW-RAFI and normalized NIR-RAFI. Conclusions. Imaging of RPE atrophy using lipofuscin-based AF imaging has become the gold standard. However, this technique involves bright SW lights that are uncomfortable and may accelerate the rate of disease progression in vulnerable retinas. The NIR-RAFI method developed here is a melanin-based alternative that is not absorbed by opsins and bisretinoid moieties, and is comfortable to view. Further development of this method may result in a nonmydriatic and comfortable imaging method to quantify RPE atrophy extent and its expansion rate. PMID:26024124

  14. Future Directions for Transuranic Single Molecule Magnets

    Directory of Open Access Journals (Sweden)

    Nicola Magnani

    2018-02-01

    Full Text Available Single Molecule Magnets (SMMs based on transition metals and rare earths have been the object of considerable attention for the past 25 years. These systems exhibit slow relaxation of the magnetization, arising from a sizeable anisotropy barrier, and magnetic hysteresis of purely molecular origin below a given blocking temperature. Despite initial predictions that SMMs based on 5f-block elements could outperform most others, the results obtained so far have not met expectations. Exploiting the versatile chemistry of actinides and their favorable intrinsic magnetic properties proved, indeed, to be more difficult than assumed. However, the large majority of studies reported so far have been dedicated to uranium molecules, thus leaving the largest part of the 5f-block practically unexplored. Here, we present a short review of the progress achieved up to now and discuss some options for a possible way forward.

  15. Long-wavelength (red) light produces hyperopia in juvenile and adolescent tree shrews.

    Science.gov (United States)

    Gawne, Timothy J; Ward, Alexander H; Norton, Thomas T

    2017-11-01

    In infant tree shrews, exposure to narrow-band long-wavelength (red) light, that stimulates long-wavelength sensitive cones almost exclusively, slows axial elongation and produces hyperopia. We asked if red light produces hyperopia in juvenile and adolescent animals, ages when plus lenses are ineffective. Animals were raised in fluorescent colony lighting (100-300 lux) until they began 13days of red-light treatment at 11 (n=5, "infant"), 35 (n=5, "juvenile") or 95 (n=5, "adolescent") days of visual experience (DVE). LEDs provided 527-749 lux on the cage floor. To control for the higher red illuminance, a fluorescent control group (n=5) of juvenile (35 DVE) animals was exposed to ∼975 lux. Refractions were measured daily; ocular component dimensions at the start and end of treatment and end of recovery in colony lighting. These groups were compared with normals (n=7). In red light, the refractive state of both juvenile and adolescent animals became significantly (Prefractions (0.6±0.3D) were normal. In red-treated juveniles the vitreous chamber was significantly smaller than normal (Plight-induced slowed growth and hyperopia in juvenile and adolescent tree shrews demonstrates that the emmetropization mechanism is still capable of restraining eye growth at these ages. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. How to determine the handedness of single molecules using Coulomb explosion imaging

    International Nuclear Information System (INIS)

    Pitzer, Martin

    2017-01-01

    This tutorial is based on a doctoral thesis that was shortlisted for the 2016 AMOP dissertation prize of the German Physical Society (DPG). The principal achievement of the thesis was to use Coulomb explosion imaging (CEI) to determine the microscopic handedness (‘chirality’) of molecular structures on a single-molecule level. It thus shows how a technique developed in atomic physics can address a long-standing problem in chemistry. Owing to these disparate backgrounds, the tutorial has two facets: on the one hand, the history of molecular chirality and recent developments are very briefly reviewed. On the other hand, an account is given of different experimental approaches to CEI, on the physical processes in light-induced Coulomb explosion and—most importantly—on the aspects that are relevant when designing and performing such an experiment. As structural chirality occurs only in polyatomic molecules, special attention will be given to multiple ionization and multi-coincidence measurements. A short discussion of the results presented in earlier papers is given, followed by an outlook on experiments that are under way or can realistically be performed within the next years. (phd tutorial)

  17. Heralded wave packet manipulation and storage of a frequency-converted pair photon at telecom wavelength

    Science.gov (United States)

    Kroh, Tim; Ahlrichs, Andreas; Sprenger, Benjamin; Benson, Oliver

    2017-09-01

    Future quantum networks require a hybrid platform of dissimilar quantum systems. Within the platform, joint quantum states have to be mediated either by single photons, photon pairs or entangled photon pairs. The photon wavelength has to lie within the telecommunication band to enable long-distance fibre transmission. In addition, the temporal shape of the photons needs to be tailored to efficiently match the involved quantum systems. Altogether, this requires the efficient coherent wavelength-conversion of arbitrarily shaped single-photon wave packets. Here, we demonstrate the heralded temporal filtering of single photons as well as the synchronisation of state manipulation and detection as key elements in a typical experiment, besides of delaying a photon in a long fibre. All three are realised by utilising commercial telecommunication fibre-optical components which will permit the transition of quantum networks from the lab to real-world applications. The combination of these renders a temporally filtering single-photon storage in a fast switchable fibre loop possible.

  18. Sub-Poissonian statistics of quantum jumps in single molecule or atomic ion

    International Nuclear Information System (INIS)

    Osad'ko, I.S.; Gus'kov, D.N.

    2007-01-01

    A theory for statistics of quantum jumps in single molecule or ion driven by continues wave laser field is developed. These quantum jumps can relate to nonradiative singlet-triplet transitions in a molecule or to on → off jumps in a single ion with shelving processes. Distribution function w N (T) of quantum jumps in time interval T is found. Computer simulation of quantum jumps is realized. Statistical treatment of simulated jumps reveals sub-Poissonian statistics of quantum jumps. The theoretical distribution function w N (T) fits well the distribution of jumps found from simulated data. Experimental data on quantum jumps found in experiments with single Hg + ion are described by the function w N (T) well

  19. madSTORM: a superresolution technique for large-scale multiplexing at single-molecule accuracy

    Science.gov (United States)

    Yi, Jason; Manna, Asit; Barr, Valarie A.; Hong, Jennifer; Neuman, Keir C.; Samelson, Lawrence E.

    2016-01-01

    Investigation of heterogeneous cellular structures using single-molecule localization microscopy has been limited by poorly defined localization accuracy and inadequate multiplexing capacity. Using fluorescent nanodiamonds as fiducial markers, we define and achieve localization precision required for single-molecule accuracy in dSTORM images. Coupled with this advance, our new multiplexing strategy, madSTORM, allows accurate targeting of multiple molecules using sequential binding and elution of fluorescent antibodies. madSTORM is used on an activated T-cell to localize 25 epitopes, 14 of which are on components of the same multimolecular T-cell receptor complex. We obtain an average localization precision of 2.6 nm, alignment error of 2.0 nm, and molecules within structures. Probing the molecular topology of complex signaling cascades and other heterogeneous networks is feasible with madSTORM. PMID:27708141

  20. Development of Fluorophore-Labeled Thailanstatin Antibody-Drug Conjugates for Cellular Trafficking Studies.

    Science.gov (United States)

    Kulkarni, Chethana; Finley, James E; Bessire, Andrew J; Zhong, Xiaotian; Musto, Sylvia; Graziani, Edmund I

    2017-04-19

    As the antibody-drug conjugate (ADC) field grows increasingly important for cancer treatment, it is vital for researchers to establish a firm understanding of how ADCs function at the molecular level. To gain insight into ADC uptake, trafficking, and catabolism-processes that are critical to ADC efficacy and toxicity-imaging studies have been performed with fluorophore-labeled conjugates. However, such labels may alter the properties and behavior of the ADC under investigation. As an alternative approach, we present here the development of a "clickable" ADC bearing an azide-functionalized linker-payload (LP) poised for "click" reaction with alkyne fluorophores; the azide group represents a significantly smaller structural perturbation to the LP than most fluorophores. Notably, the clickable ADC shows excellent potency in target-expressing cells, whereas the fluorophore-labeled product ADC suffers from a significant loss of activity, underscoring the impact of the label itself on the payload. Live-cell confocal microscopy reveals robust uptake of the clickable ADC, which reacts selectively in situ with a derivatized fluorescent label. Time-course trafficking studies show greater and more rapid net internalization of the ADCs than the parent antibody. More generally, the application of chemical biology tools to the study of ADCs should improve our understanding of how ADCs are processed in biological systems.