WorldWideScience

Sample records for fluorophores long-wavelength single-molecule

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

    DEFF Research Database (Denmark)

    Liao, Zhiyu

    and mass spectrometry. Upon illumination, A3-TOTA+ degrades in a step-wise manner by de-ethylation on the periphery. The unusual red-shifted fluorescence from the photoproducts is not as intense as the original emission, but the photostability is improved. The acquired knowledge about photoconversion can...... stimulate new pathways in engineering and designing photoconvertible fluorophores, based on the reaction with oxygen or other chemicals. Besides, this results show that dyes that convert into other emissive species could give problems when interpreting single molecule FRET systems. The revealed mechanism...

  2. DNA visualization in single molecule studies carried out with optical tweezers: Covalent versus non-covalent attachment of fluorophores.

    Science.gov (United States)

    Suei, Sandy; Raudsepp, Allan; Kent, Lisa M; Keen, Stephen A J; Filichev, Vyacheslav V; Williams, Martin A K

    2015-10-16

    In this study, we investigated the use of the covalent attachment of fluorescent dyes to double-stranded DNA (dsDNA) stretched between particles using optical tweezers (OT) and compared the mechanical properties of the covalently-functionalized chain to that of unmodified DNA and to DNA bound to a previously uncharacterized groove-binder, SYBR-gold. Modified DNA species were obtained by covalently linking azide-functionalized organic fluorophores onto the backbone of DNA chains via the alkyne moieties of modified bases that were incorporated during PCR. These DNA molecules were then constructed into dumbbells by attaching polystyrene particles to the respective chain ends via biotin or digoxigenin handles that had been pre-attached to the PCR primers which formed the ends of the synthesized molecule. Using the optical tweezers, the DNA was stretched by separating the two optically trapped polystyrene particles. Displacements of the particles were measured in 3D using an interpolation-based normalized cross-correlation method and force-extension curves were calculated and fitted to the worm-like chain model to parameterize the mechanical properties of the DNA. Results showed that both the contour and persistence length of the covalently-modified dsDNAs were indistinguishable from that of the unmodified dsDNA, whereas SYBR-gold binding perturbed the contour length of the chain in a force-dependent manner. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. The Long Wavelength Array

    Science.gov (United States)

    Taylor, G. B.

    2006-08-01

    The Long Wavelength Array (LWA) will be a new, open, user-oriented astronomical instrument operating in the poorly explored window from 20-80 MHz at arcsecond level resolution and mJy level sensitivity. Key science drivers include (1) acceleration, propagation, and turbulence in the ISM, including the space-distribution and spectrum of Galactic cosmic rays, supernova remnants, and pulsars; (2) the high redshift universe, including the most distant radio galaxies and clusters - tools for understanding the earliest black holes and the cosmological evolution of Dark Matter and Dark Energy; (3) planetary, solar, and space science, including space weather prediction and extra-solar planet searches; and (4) the radio transient universe: including the known (e.g., SNe, GRBs) and the unknown. Because the LWA will explore one of the last and least investigated regions of the spectrum, the potential for new discoveries, including new classes of physical phenomena, is high, and there is a strong synergy with exciting new X-ray and Gamma-ray measurements, e.g. for cosmic ray acceleration, transients, and galaxy clusters. Operated by the University of New Mexico on behalf of the South West Consortium (SWC) the LWA will also provide a unique training ground for the next generation of radio astronomers. Students may also put skills learned on the LWA to work in computer science, electrical engineering, and the communications industry, among others. The development of the LWA will follow a phased build, which benefits from lessons learned at each phase. Four university-based Scientific Testing and Evaluation (ST&E) teams with different areas of concentration (1. High resolution imaging and particle acceleration; 2. Wide field imaging and large scale structures; 3. Ionosphere, and 4. RFI suppression and transient detection) will provide the feedback needed to assure that science objectives are met as the build develops. Currently in its first year of construction funding, the LWA

  4. 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.

  5. Towards the Long Wavelength Array

    Science.gov (United States)

    Kassim, N. E.; Erickson, W. C.

    2008-08-01

    Nearly three decades ago, the Very Large Array (VLA) opened the cm-wavelength radio sky to high-dynamic range imaging. By developing and exploiting new techniques to mitigate ionospheric phase fluctuations, the VLA 74 MHz system is providing the first sub-arcminute resolution view of the meter-wavelength radio universe. This technical innovation has inspired an emerging suite of much more powerful low-frequency instruments, including the Long Wavelength Array (LWA). The LWA, with its great collecting area (approaching one square kilometer at 20 MHz) and long baselines (up to 400 km), will surpass, by up to 2--3 orders of magnitude, the imaging power of any previous low-frequency interferometer. LWA science goals include Cosmic Evolution, the Acceleration of Relativistic Particles, Plasma Astrophysics, and Ionospheric & Space Weather Science. Because it will explore one of the last and most poorly investigated regions of the spectrum, the potential for unexpected new discoveries is high. For more on the LWA, see http://lwa.unm.edu. The LWA project is led by the University of New Mexico, and includes the Naval Research Laboratory, Applied Research Laboratories of U. Texas, Los Alamos National Laboratory, Virginia Tech, and U. Iowa, with cooperation from the National Radio Astronomy Observatory.

  6. 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.

  7. 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...

  8. State space approach to single molecule localization in fluorescence microscopy.

    Science.gov (United States)

    Vahid, Milad R; Chao, Jerry; Kim, Dongyoung; Ward, E Sally; Ober, Raimund J

    2017-03-01

    Single molecule super-resolution microscopy enables imaging at sub-diffraction-limit resolution by producing images of subsets of stochastically photoactivated fluorophores over a sequence of frames. In each frame of the sequence, the fluorophores are accurately localized, and the estimated locations are used to construct a high-resolution image of the cellular structures labeled by the fluorophores. Many methods have been developed for localizing fluorophores from the images. The majority of these methods comprise two separate steps: detection and estimation. In the detection step, fluorophores are identified. In the estimation step, the locations of the identified fluorophores are estimated through an iterative approach. Here, we propose a non-iterative state space-based localization method which combines the detection and estimation steps. We demonstrate that the estimated locations obtained from the proposed method can be used as initial conditions in an estimation routine to potentially obtain improved location estimates. The proposed method models the given image as the frequency response of a multi-order system obtained with a balanced state space realization algorithm based on the singular value decomposition of a Hankel matrix. The locations of the poles of the resulting system determine the peak locations in the frequency domain, and the locations of the most significant peaks correspond to the single molecule locations in the original image. The performance of the method is validated using both simulated and experimental data.

  9. Special Issue: Single Molecule Techniques

    Directory of Open Access Journals (Sweden)

    Hans H. Gorris

    2015-04-01

    Full Text Available Technological advances in the detection and manipulation of single molecules have enabled new insights into the function, structure and interactions of biomolecules. This Special Issue was launched to account for the rapid progress in the field of “Single Molecule Techniques”. Four original research articles and seven review articles provide an introduction, as well as an in-depth discussion, of technical developments that are indispensable for the characterization of individual biomolecules. Fluorescence microscopy takes center stage in this Special Issue because it is one of the most sensitive and flexible techniques, which has been adapted in many variations to the specific demands of single molecule analysis. Two additional articles are dedicated to single molecule detection based on atomic force microscopy.

  10. Optofluidic single molecule flow proteometry

    Science.gov (United States)

    Jing, Nan; Chou, Chao-Kai; Hung, Mien-Chie; Kameoka, Jun

    2009-02-01

    A microfluidic single molecule fluorescence-based detection scheme is developed to identify target protein direct from cell lysate by using polyclonal antibody. Relative concentration of target protein in solution is determined by twodimensional (2D) photon burst analysis. Compared to conventional ensemble measurement assays, this microfluidic single molecule approach combines the advantages of higher sensitivity, fast processing time, small sample consumption and high resolution quantitative analysis.

  11. Single Molecule Electronics and Devices

    Directory of Open Access Journals (Sweden)

    Makusu Tsutsui

    2012-05-01

    Full Text Available 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.

  12. Single-molecule magnet engineering

    DEFF Research Database (Denmark)

    Pedersen, Kasper Steen; Bendix, Jesper; Clérac, Rodolphe

    2014-01-01

    to delicately tune, for instance, the properties of molecules that behave as "magnets", the so-called single-molecule magnets (SMMs). Although many interesting SMMs have been prepared by a more or less serendipitous approach, the assembly of predesigned, isolatable molecular entities into higher nuclearity...... complexes constitutes an elegant and fascinating strategy. This Feature article focuses on the use of building blocks or modules (both terms being used indiscriminately) to direct the structure, and therefore also the magnetic properties, of metal ion complexes exhibiting SMM behaviour. This journal...

  13. Methodology for Quantitative Characterization of Fluorophore Photoswitching to Predict Superresolution Microscopy Image Quality

    Science.gov (United States)

    Bittel, Amy M.; Nickerson, Andrew; Saldivar, Isaac S.; Dolman, Nick J.; Nan, Xiaolin; Gibbs, Summer L.

    2016-07-01

    Single-molecule localization microscopy (SMLM) image quality and resolution strongly depend on the photoswitching properties of fluorophores used for sample labeling. Development of fluorophores with optimized photoswitching will considerably improve SMLM spatial and spectral resolution. Currently, evaluating fluorophore photoswitching requires protein-conjugation before assessment mandating specific fluorophore functionality, which is a major hurdle for systematic characterization. Herein, we validated polyvinyl alcohol (PVA) as a single-molecule environment to efficiently quantify the photoswitching properties of fluorophores and identified photoswitching properties predictive of quality SMLM images. We demonstrated that the same fluorophore photoswitching properties measured in PVA films and using antibody adsorption, a protein-conjugation environment analogous to labeled cells, were significantly correlated to microtubule width and continuity, surrogate measures of SMLM image quality. Defining PVA as a fluorophore photoswitching screening platform will facilitate SMLM fluorophore development and optimal image buffer assessment through facile and accurate photoswitching property characterization, which translates to SMLM fluorophore imaging performance.

  14. Inertial confinement fusion driven by long wavelength electromagnetic pulses

    Institute of Scientific and Technical Information of China (English)

    Baifei; Shen; Xueyan; Zhao; Longqing; Yi; Wei; Yu; Zhizhan; Xu

    2013-01-01

    A method for inertial confinement fusion driven by powerful long wavelength electromagnetic pulses(EMPs), such as CO2 laser pulses or high power microwave pulses, is proposed. Due to the high efficiency of generating such long wavelength electromagnetic pulses, this method is especially important for the future fusion electricity power. Special fuel targets are designed to overcome the shortcomings of the long wavelength electromagnetic pulses.

  15. Single Molecule Studies of Chromatin

    Energy Technology Data Exchange (ETDEWEB)

    Jeans, C; Thelen, M P; Noy, A

    2006-02-06

    In eukaryotic cells, DNA is packaged as chromatin, a highly ordered structure formed through the wrapping of the DNA around histone proteins, and further packed through interactions with a number of other proteins. In order for processes such as DNA replication, DNA repair, and transcription to occur, the structure of chromatin must be remodeled such that the necessary enzymes can access the DNA. A number of remodeling enzymes have been described, but our understanding of the remodeling process is hindered by a lack of knowledge of the fine structure of chromatin, and how this structure is modulated in the living cell. We have carried out single molecule experiments using atomic force microscopy (AFM) to study the packaging arrangements in chromatin from a variety of cell types. Comparison of the structures observed reveals differences which can be explained in terms of the cell type and its transcriptional activity. During the course of this project, sample preparation and AFM techniques were developed and optimized. Several opportunities for follow-up work are outlined which could provide further insight into the dynamic structural rearrangements of chromatin.

  16. 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.

  17. Single-molecule stochastic resonance

    CERN Document Server

    Hayashi, K; Manosas, M; Huguet, J M; Ritort, F; 10.1103/PhysRevX.2.031012

    2012-01-01

    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 noise. Here we carry out the first experimental study of SR in single DNA hairpins which exhibit cooperatively folding/unfolding transitions under the action of an applied oscillating mechanical force with optical tweezers. By varying the frequency of the force oscillation, we investigated the folding/unfolding kinetics of DNA hairpins in a periodically driven bistable free-energy potential. We measured 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 the signal-to-noise ratio (SNR) of the spectral density of measured fluctuations in molecular extension of the DNA hairpins is a good quantifier of the SR. The frequency dependence of the SNR exhibits a peak at a frequency value given by the resonance match...

  18. 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.

  19. Cosmological long-wavelength solutions and primordial black hole formation

    CERN Document Server

    Harada, Tomohiro; Nakama, Tomohiro; Koga, Yasutaka

    2015-01-01

    We construct cosmological long-wavelength solutions without symmetry in general gauge conditions compatible with the long-wavelength scheme. We then specify the relationship among the solutions in different time slicings. Nonspherical long-wavelength solutions are particularly important for primordial structure formation in the epoch of soft equations of state. Applying this framework to spherical symmetry, we show the equivalence between long-wavelength solutions in the constant mean curvature slicing and asymptotic quasi-homogeneous solutions in the comoving slicing. We derive the correspondence relation and compare the results of numerical simulations of primordial black hole (PBH) formation. In terms of $\\tilde{\\delta}_{c}$, the value which the averaged density perturbation at threshold in the comoving slicing would take at horizon entry in the first-order long-wavelength expansion, we find that the sharper the transition from the overdense region to the FRW universe is, the larger the $\\tilde{\\delta}_{c}...

  20. Making "Operations" inside a Single Molecule

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    @@ Free and delicate manipulation of single molecules has long been expected by scientists so as to realize specific functions. In the 1990s, the laboratory led by Prof. Wison Ho from the University of California was successful in inducing chemical reactions at the single molecule level with scanning tunneling microscopy (STM), revealing the extensive potentials of "single molecule operation." However, until recently, researchers have failed to utilize the reaction to give rise to special physical properties.

  1. Photophysics of Fluorescent Probes for Single-Molecule Biophysics and Super-Resolution Imaging

    Science.gov (United States)

    Ha, Taekjip; Tinnefeld, Philip

    2012-05-01

    Single-molecule fluorescence spectroscopy and super-resolution microscopy are important elements of the ongoing technical revolution to reveal biochemical and cellular processes in unprecedented clarity and precision. Demands placed on the photophysical properties of the fluorophores are stringent and drive the choice of appropriate probes. Such fluorophores are not simple light bulbs of a certain color and brightness but instead have their own “personalities” regarding spectroscopic parameters, redox properties, size, water solubility, photostability, and several other factors. Here, we review the photophysics of fluorescent probes, both organic fluorophores and fluorescent proteins, used in applications such as particle tracking, single-molecule FRET, stoichiometry determination, and super-resolution imaging. Of particular interest is the thiol-induced blinking of Cy5, a curse for single-molecule biophysical studies that was later overcome using Trolox through a reducing/oxidizing system but a boon for super-resolution imaging owing to the controllable photoswitching. Understanding photophysics is critical in the design and interpretation of single-molecule experiments.

  2. Single-molecule dynamics at variable temperatures

    NARCIS (Netherlands)

    Zondervan, Rob

    2006-01-01

    Single-molecule optics has evolved from a specialized variety of optical spectroscopy at low temperatures into a versatile tool to address questions in physics, chemistry, biology, and materials science. In this thesis, the potential of single-molecule (and ensemble) optical microscopy at variable t

  3. Single-Molecule Spectroscopy, Imaging, and Photocontrol: Foundations for Super-Resolution Microscopy (Nobel Lecture).

    Science.gov (United States)

    Moerner, W E William E

    2015-07-06

    The initial steps toward optical detection and spectroscopy of single molecules in condensed matter arose out of the study of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral signatures relating to the fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989 using frequency-modulation laser spectroscopy. In the early 90s, many fascinating physical effects were observed for individual molecules, and the imaging of single molecules as well as observations of spectral diffusion, optical switching and the ability to select different single molecules in the same focal volume simply by tuning the pumping laser frequency provided important forerunners of the later super-resolution microscopy with single molecules. In the room temperature regime, imaging of single copies of the green fluorescent protein also uncovered surprises, especially the blinking and photoinduced recovery of emitters, which stimulated further development of photoswitchable fluorescent protein labels. Because each single fluorophore acts a light source roughly 1 nm in size, microscopic observation and localization of individual fluorophores is a key ingredient to imaging beyond the optical diffraction limit. Combining this with active control of the number of emitting molecules in the pumped volume led to the super-resolution imaging of Eric Betzig and others, a new frontier for optical microscopy beyond the diffraction limit. The background leading up to these observations is described and current developments are summarized.

  4. Nobel Lecture: Single-molecule spectroscopy, imaging, and photocontrol: Foundations for super-resolution microscopy*

    Science.gov (United States)

    Moerner, W. E. William E.

    2015-10-01

    The initial steps toward optical detection and spectroscopy of single molecules in condensed matter arose out of the study of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral signatures relating to the fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989 using frequency-modulation laser spectroscopy. In the early 1990s, many fascinating physical effects were observed for individual molecules, and the imaging of single molecules as well as observations of spectral diffusion, optical switching and the ability to select different single molecules in the same focal volume simply by tuning the pumping laser frequency provided important forerunners of the later super-resolution microscopy with single molecules. In the room-temperature regime, imaging of single copies of the green fluorescent protein also uncovered surprises, especially the blinking and photoinduced recovery of emitters, which stimulated further development of photoswitchable fluorescent protein labels. Because each single fluorophore acts as a light source roughly 1 nm in size, microscopic observation and localization of individual fluorophores is a key ingredient to imaging beyond the optical diffraction limit. Combining this with active control of the number of emitting molecules in the pumped volume led to the super-resolution imaging of Eric Betzig and others, a new frontier for optical microscopy beyond the diffraction limit. The background leading up to these observations is described and selected current developments are summarized.

  5. Long wavelength infrared photodetector design based on electromagnetically induced transparency

    Science.gov (United States)

    Zyaei, M.; Saghai, H. Rasooli; Abbasian, K.; Rostami, A.

    2008-07-01

    A novel long-wavelength infrared (IR) photodetector based on Electromagnetically induced transparency (EIT) which is suitable for operation in about room temperature and THz range is proposed and analyzed in detail in this article. The main point in this paper for operation in room temperature is related to convert the incoming long-wavelength IR signal to short-wavelength or visible probe optical field through EIT phenomena. For realization of the idea, we used 4, 5- and 6-level atoms implemented by quantum wells or dots. In the proposed structure long-wavelength IR signal does not interact directly with electrons, but affects the absorption characteristics of short-wavelength or visible probe optical field. Therefore, the proposed structure reduces and cancels out the important thermionic dark current component. So, the proposed idea can operate as long wavelength photodetector.

  6. Long-wavelength 256x256 QWIP handheld camera

    Science.gov (United States)

    Gunapala, Sarath D.; Liu, J. K.; Sundaram, Mani; Bandara, Sumith V.; Shott, C. A.; Hoelter, T.; Maker, Paul D.; Muller, Richard E.

    1996-06-01

    In this paper, we discuss the development of very sensitive long wavelength infrared GaAs/AlxGa1-xAs quantum well infrared photodetectors (QWIPs), fabrication of random reflectors for efficient light coupling, and the demonstration of first hand-held long-wavelength 256 X 256 QWIP focal plane array camera. Excellent imagery, with a noise equivalent differential temperature of 25 mK has been achieved.

  7. Toward single-molecule microscopy on a smart phone.

    Science.gov (United States)

    Khatua, Saumyakanti; Orrit, Michel

    2013-10-22

    Thanks to fluorescence, single nano-objects down to individual fluorophores can now be imaged in optical microscopes. Fluorescence imaging is still restricted to laboratory facilities as it usually involves expensive and bulky instrumentation. A report by Wei et al. in this issue of ACS Nano, however, shows that a sensitive, cost-effective, and portable device can be developed to image individual nano-objects as small as large viruses. This work opens the fascinating prospects of single-molecule microscopy and spectroscopy on a smart phone. We speculate on the possible applications of such a portable imaging device and on the perspectives it may open in different fields of science and technology.

  8. The Single-Molecule Approach to Membrane Protein Stoichiometry.

    Science.gov (United States)

    Nichols, Michael G; Hallworth, Richard

    2016-01-01

    The advent of techniques for imaging solitary fluorescent molecules has made possible many new kinds of biological experiments. Here, we describe the application of single-molecule imaging to the problem of subunit stoichiometry in membrane proteins. A membrane protein of unknown stoichiometry, prestin, is coupled to the fluorescent enhanced green fluorescent protein (eGFP) and synthesized in the human embryonic kidney (HEK) cell line. We prepare adherent membrane fragments containing prestin-eGFP by osmotic lysis. The molecules are then exposed to continuous low-level excitation until their fluorescence reaches background levels. Their fluorescence decreases in discrete equal-amplitude steps, consistent with the photobleaching of single fluorophores. We count the number of steps required to photobleach each molecule. The molecular stoichiometry is then deduced using a binomial model.

  9. Common fluorescent proteins for single-molecule localization microscopy

    Science.gov (United States)

    Klementieva, Natalia V.; Bozhanova, Nina G.; Mishina, Natalie M.; Zagaynova, Elena V.; Lukyanov, Konstantin A.; Mishin, Alexander S.

    2015-07-01

    Super-resolution techniques for breaking the diffraction barrier are spread out over multiple studies nowadays. Single-molecule localization microscopy such as PALM, STORM, GSDIM, etc allow to get super-resolved images of cell ultrastructure by precise localization of individual fluorescent molecules via their temporal isolation. However, these methods are supposed the use of fluorescent dyes and proteins with special characteristics (photoactivation/photoconversion). At the same time, there is a need for retaining high photostability of fluorophores during long-term acquisition. Here, we first showed the potential of common red fluorescent protein for single-molecule localization microscopy based on spontaneous intrinsic blinking. Also, we assessed the effect of different imaging media on photobleaching of these fluorescent proteins. Monomeric orange and red fluorescent proteins were examined for stochastic switching from a dark state to a bright fluorescent state. We studied fusions with cytoskeletal proteins in NIH/3T3 and HeLa cells. Imaging was performed on the Nikon N-STORM system equipped with EMCCD camera. To define the optimal imaging conditions we tested several types of cell culture media and buffers. As a result, high-resolution images of cytoskeleton structure were obtained. Essentially, low-intensity light was sufficient to initiate the switching of tested red fluorescent protein reducing phototoxicity and provide long-term live-cell imaging.

  10. SINGLE MOLECULE ENZYMOLOGY FINDS ITS STRIDE.

    Science.gov (United States)

    Perkel, Jeffrey

    2015-10-01

    More techniques aimed at probing the nature of single molecules are being developed and advanced in biophysics labs. Jeffrey Perkel takes a look at the scientists leading the charge into the micro-world.

  11. Largely Enhanced Single-molecule Fluorescence in Plasmonic Nanogaps formed by Hybrid Silver Nanostructures

    Science.gov (United States)

    Zhang, Jian; Lakowicz, Joseph R.

    2013-01-01

    It has been suggested that narrow gaps between metallic nanostructures can be practical for producing large field enhancement. We design a hybrid silver nanostructure geometry in which fluorescent emitters are sandwiched between silver nanoparticles and silver island film (SIF). A desired number of polyelectrolyte layers are deposited on the SIF surface before the self-assembly of a second silver nanoparticle layer. Layer-by-layer configuration provides a well-defined dye position. It allows us to study the photophyical behaviors of fluorophores in the resulting gap at the single molecule level. The enhancement factor of a fluorophore located in the gap is much higher than those on silver surfaces alone and on glass. These effects may be used for increased detectability of single molecules bound to surfaces which contain metallic structures for either biophysical studies or high sensitivity assays. PMID:23373787

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

    Directory of Open Access Journals (Sweden)

    Beth L. Haas

    2014-08-01

    Full Text Available 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.

  13. 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.

  14. A state space based approach to localizing single molecules from multi-emitter images.

    Science.gov (United States)

    Vahid, Milad R; Chao, Jerry; Ward, E Sally; Ober, Raimund J

    2017-01-28

    Single molecule super-resolution microscopy is a powerful tool that enables imaging at sub-diffraction-limit resolution. In this technique, subsets of stochastically photoactivated fluorophores are imaged over a sequence of frames and accurately localized, and the estimated locations are used to construct a high-resolution image of the cellular structures labeled by the fluorophores. Available localization methods typically first determine the regions of the image that contain emitting fluorophores through a process referred to as detection. Then, the locations of the fluorophores are estimated accurately in an estimation step. We propose a novel localization method which combines the detection and estimation steps. The method models the given image as the frequency response of a multi-order system obtained with a balanced state space realization algorithm based on the singular value decomposition of a Hankel matrix, and determines the locations of intensity peaks in the image as the pole locations of the resulting system. The locations of the most significant peaks correspond to the locations of single molecules in the original image. Although the accuracy of the location estimates is reasonably good, we demonstrate that, by using the estimates as the initial conditions for a maximum likelihood estimator, refined estimates can be obtained that have a standard deviation close to the Cramér-Rao lower bound-based limit of accuracy. We validate our method using both simulated and experimental multi-emitter images.

  15. Single-Molecule Studies in Live Cells

    Science.gov (United States)

    Yu, Ji

    2016-05-01

    Live-cell single-molecule experiments are now widely used to study complex biological processes such as signal transduction, self-assembly, active trafficking, and gene regulation. These experiments' increased popularity results in part from rapid methodological developments that have significantly lowered the technical barriers to performing them. Another important advance is the development of novel statistical algorithms, which, by modeling the stochastic behaviors of single molecules, can be used to extract systemic parameters describing the in vivo biochemistry or super-resolution localization of biological molecules within their physiological environment. This review discusses recent advances in experimental and computational strategies for live-cell single-molecule studies, as well as a selected subset of biological studies that have utilized these new technologies.

  16. Theoretical study on single-molecule spectroscopy

    Institute of Scientific and Technical Information of China (English)

    SHAN Guang-cun; HUANG Wei

    2006-01-01

    The photon-by-photon approach for single molecule spectroscopy experiments utilizes the information carried by each detected photon and allows the measurements of conformational fluctuation with time resolution on a vast range of time scales,where each photon represents a data point.Here,we theoretically simulate the photon emission dynamics of a single molecule spectroscopy using the kinetic Monte Carlo algorithm to understand the underlying complex photon dynamic process of a single molecule.In addition,by following the molecular process in real time,the mechanism of complex biochemical reactions can be revealed.We hope that this theoretical study will serve as an introduction and a guideline into this exciting new field.

  17. 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

  18. 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. Fo...

  19. Cosmological long-wavelength solutions and primordial black hole formation

    Science.gov (United States)

    Harada, Tomohiro; Yoo, Chul-Moon; Nakama, Tomohiro; Koga, Yasutaka

    2015-04-01

    We construct cosmological long-wavelength solutions without symmetry in general gauge conditions which are compatible with the long-wavelength scheme. We then specify the relationship among the solutions in different time slicings. Nonspherical long-wavelength solutions are particularly important for primordial structure formation in the epoch of very soft equations of state. Applying this general framework to spherical symmetry, we show the equivalence between long-wavelength solutions in the constant mean curvature slicing with conformally flat spatial coordinates and asymptotic quasihomogeneous solutions in the comoving slicing with the comoving threading. We derive the correspondence relation between these two solutions and compare the results of numerical simulations of primordial black hole (PBH) formation in these two different approaches. To discuss the PBH formation, it is convenient and conventional to use δ˜c, the value which the averaged density perturbation at threshold in the comoving slicing would take at horizon entry in the lowest-order long-wavelength expansion. We numerically find that within (approximately) compensated models, the sharper the transition from the overdense region to the Friedmann-Robertson-Walker universe is, the larger the δ˜ c becomes. We suggest that, for the equation of state p =(Γ -1 )ρ , we can apply the analytic formulas for the minimum δ˜ c ,min≃[3 Γ /(3 Γ +2 )]sin2[π √{Γ -1 }/(3 Γ -2 )] and the maximum δ˜ c ,max≃3 Γ /(3 Γ +2 ) . As for the threshold peak value of the curvature variable ψ0 ,c , we find that the sharper the transition is, the smaller the ψ0 ,c becomes. We analytically explain this intriguing feature qualitatively with a compensated top-hat density model. Using simplified models, we also analytically deduce an environmental effect that ψ0 ,c can be significantly larger (smaller) if the underlying perturbation of much longer wavelength is positive (negative).

  20. Photophysical Behaviors of Single Fluorophores Localized on Zinc Oxide Nanostructures

    Science.gov (United States)

    Fu, Yi; Zhang, Jian; Lakowicz, Joseph R.

    2012-01-01

    Single-molecule fluorescence spectroscopy has now been widely used to investigate complex dynamic processes which would normally be obscured in an ensemble-averaged measurement. In this report we studied photophysical behaviors of single fluorophores in proximity to zinc oxide nanostructures by single-molecule fluorescence spectroscopy and time-correlated single-photon counting (TCSPC). Single fluorophores on ZnO surfaces showed enhanced fluorescence brightness to various extents compared with those on glass; the single-molecule time trajectories also illustrated pronounced fluctuations of emission intensities, with time periods distributed from milliseconds to seconds. We attribute fluorescence fluctuations to the interfacial electron transfer (ET) events. The fluorescence fluctuation dynamics were found to be inhomogeneous from molecule to molecule and from time to time, showing significant static and dynamic disorders in the interfacial electron transfer reaction processes. PMID:23109903

  1. Near-field single molecule spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Xie, X.S.; Dunn, R.C.

    1995-02-01

    The high spatial resolution and sensitivity of near-field fluorescence microscopy allows one to study spectroscopic and dynamical properties of individual molecules at room temperature. Time-resolved experiments which probe the dynamical behavior of single molecules are discussed. Ground rules for applying near-field spectroscopy and the effect of the aluminum coated near-field probe on spectroscopic measurements are presented.

  2. Nanoscience: Single-molecule instant replay

    Science.gov (United States)

    Camillone, Nicholas

    2016-11-01

    A nanoscale imaging method that uses ultrashort light pulses to initiate and follow the motion of a single molecule adsorbed on a solid surface opens a window onto the physical and chemical dynamics of molecules on surfaces. See Letter p.263

  3. Single-molecule Michaelis-Menten equations.

    Science.gov (United States)

    Kou, S C; Cherayil, Binny J; Min, Wei; English, Brian P; Xie, X Sunney

    2005-10-20

    This paper summarizes our present theoretical understanding of single-molecule kinetics associated with the Michaelis-Menten mechanism of enzymatic reactions. Single-molecule enzymatic turnover experiments typically measure the probability density f(t) of the stochastic waiting time t for individual turnovers. While f(t) can be reconciled with ensemble kinetics, it contains more information than the ensemble data; in particular, it provides crucial information on dynamic disorder, the apparent fluctuation of the catalytic rates due to the interconversion among the enzyme's conformers with different catalytic rate constants. In the presence of dynamic disorder, f(t) exhibits a highly stretched multiexponential decay at high substrate concentrations and a monoexponential decay at low substrate concentrations. We derive a single-molecule Michaelis-Menten equation for the reciprocal of the first moment of f(t), 1/, which shows a hyperbolic dependence on the substrate concentration [S], similar to the ensemble enzymatic velocity. We prove that this single-molecule Michaelis-Menten equation holds under many conditions, in particular when the intercoversion rates among different enzyme conformers are slower than the catalytic rate. However, unlike the conventional interpretation, the apparent catalytic rate constant and the apparent Michaelis constant in this single-molecule Michaelis-Menten equation are complicated functions of the catalytic rate constants of individual conformers. We also suggest that the randomness parameter r, defined as )2> / t2, can serve as an indicator for dynamic disorder in the catalytic step of the enzymatic reaction, as it becomes larger than unity at high substrate concentrations in the presence of dynamic disorder.

  4. Space-charge impedance calculations in long-wavelength approximation

    Science.gov (United States)

    Kurennoy, Sergey S.

    1999-12-01

    Space-charge impedance calculations for smooth vacuum chambers with an arbitrary cross-section and perfectly conducting walls are considered in the long-wavelength approximation, when ωb/(βγc)≪1, where b is a typical transverse size. For the SNS beam energies βγ⩽1.8, and the wavelengths are long when λ≫b. Within the long-wavelength approximation, the fields can be found by solving a 2-D electrostatic problem. Two examples are presented: the space-charge impedance of screening wires (RF-cage) and of a ceramic chamber with inner metal stripes. In addition, we explore the transverse space-charge impedance of a circular pipe with account of betatron oscillations in a wide frequency range.

  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. The symmetry of single-molecule conduction.

    Science.gov (United States)

    Solomon, Gemma C; Gagliardi, Alessio; Pecchia, Alessandro; Frauenheim, Thomas; Di Carlo, Aldo; Reimers, Jeffrey R; Hush, Noel S

    2006-11-14

    We introduce the conductance point group which defines the symmetry of single-molecule conduction within the nonequilibrium Green's function formalism. It is shown, either rigorously or to within a very good approximation, to correspond to a molecular-conductance point group defined purely in terms of the properties of the conducting molecule. This enables single-molecule conductivity to be described in terms of key qualitative chemical descriptors that are independent of the nature of the molecule-conductor interfaces. We apply this to demonstrate how symmetry controls the conduction through 1,4-benzenedithiol chemisorbed to gold electrodes as an example system, listing also the molecular-conductance point groups for a range of molecules commonly used in molecular electronics research.

  7. Diamond based single molecule magnetic resonance spectroscopy

    CERN Document Server

    Cai, J -M; Plenio, M B; Retzker, A

    2011-01-01

    The detection of a nuclear spin in an individual molecule represents a key challenge in physics and biology whose solution has been pursued for many years. The small magnetic moment of a single nucleus and the unavoidable environmental noise present the key obstacles for its realization. Here, we theoretically demonstrate that a single nitrogen-vacancy (NV) center in diamond can be used to construct a nano-scale single molecule spectrometer that is capable of detecting the position and spin state of a single nucleus and can determine the distance and alignment of a nuclear or electron spin pair. In combination with organic spin labels, this device will find applications in single molecule spectroscopy in chemistry and biology, such as in determining protein structure or monitoring macromolecular motions and can thus provide a tool to help unravelling the microscopic mechanisms underlying bio-molecular function.

  8. Single molecule transcription profiling with AFM

    Energy Technology Data Exchange (ETDEWEB)

    Reed, Jason [Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (United States); Mishra, Bud [Departments of Computer Science and Mathematics, Courant Institute of Mathematical Sciences, New York University, New York, NY 10012 (United States); Pittenger, Bede [Veeco Instruments, Santa Barbara, CA 93117 (United States); Magonov, Sergei [Veeco Instruments, Santa Barbara, CA 93117 (United States); Troke, Joshua [Department of Pathology and Center for Cell Control, an NIH Nanomedicine Development Center, UCLA, Los Angeles, CA 90095 (United States); Teitell, Michael A [Department of Pathology and Center for Cell Control, an NIH Nanomedicine Development Center, UCLA, Los Angeles, CA 90095 (United States); Gimzewski, James K [Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (United States)

    2007-01-31

    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.

  9. 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.

  10. Single Molecule Data Analysis: An Introduction

    CERN Document Server

    Tavakoli, Meysam; Li, Chun-Biu; Komatsuzaki, Tamiki; Pressé, Steve

    2016-01-01

    We review methods of data analysis for biophysical data with a special emphasis on single molecule applications. Our review is intended for anyone, from student to established researcher. For someone just getting started, we focus on exposing the logic, strength and limitations of each method and cite, as appropriate, the relevant literature for implementation details. We review traditional frequentist and Bayesian parametric approaches to data analysis and subsequently extend our discussion to recent non-parametric and information theoretic methods.

  11. Virtual-'light-sheet' single-molecule localisation microscopy enables quantitative optical sectioning for super-resolution imaging.

    Science.gov (United States)

    Palayret, Matthieu; Armes, Helen; Basu, Srinjan; Watson, Adam T; Herbert, Alex; Lando, David; Etheridge, Thomas J; Endesfelder, Ulrike; Heilemann, Mike; Laue, Ernest; Carr, Antony M; Klenerman, David; Lee, Steven F

    2015-01-01

    Single-molecule super-resolution microscopy allows imaging of fluorescently-tagged proteins in live cells with a precision well below that of the diffraction limit. Here, we demonstrate 3D sectioning with single-molecule super-resolution microscopy by making use of the fitting information that is usually discarded to reject fluorophores that emit from above or below a virtual-'light-sheet', a thin volume centred on the focal plane of the microscope. We describe an easy-to-use routine (implemented as an open-source ImageJ plug-in) to quickly analyse a calibration sample to define and use such a virtual light-sheet. In addition, the plug-in is easily usable on almost any existing 2D super-resolution instrumentation. This optical sectioning of super-resolution images is achieved by applying well-characterised width and amplitude thresholds to diffraction-limited spots that can be used to tune the thickness of the virtual light-sheet. This allows qualitative and quantitative imaging improvements: by rejecting out-of-focus fluorophores, the super-resolution image gains contrast and local features may be revealed; by retaining only fluorophores close to the focal plane, virtual-'light-sheet' single-molecule localisation microscopy improves the probability that all emitting fluorophores will be detected, fitted and quantitatively evaluated.

  12. Virtual-'light-sheet' single-molecule localisation microscopy enables quantitative optical sectioning for super-resolution imaging.

    Directory of Open Access Journals (Sweden)

    Matthieu Palayret

    Full Text Available Single-molecule super-resolution microscopy allows imaging of fluorescently-tagged proteins in live cells with a precision well below that of the diffraction limit. Here, we demonstrate 3D sectioning with single-molecule super-resolution microscopy by making use of the fitting information that is usually discarded to reject fluorophores that emit from above or below a virtual-'light-sheet', a thin volume centred on the focal plane of the microscope. We describe an easy-to-use routine (implemented as an open-source ImageJ plug-in to quickly analyse a calibration sample to define and use such a virtual light-sheet. In addition, the plug-in is easily usable on almost any existing 2D super-resolution instrumentation. This optical sectioning of super-resolution images is achieved by applying well-characterised width and amplitude thresholds to diffraction-limited spots that can be used to tune the thickness of the virtual light-sheet. This allows qualitative and quantitative imaging improvements: by rejecting out-of-focus fluorophores, the super-resolution image gains contrast and local features may be revealed; by retaining only fluorophores close to the focal plane, virtual-'light-sheet' single-molecule localisation microscopy improves the probability that all emitting fluorophores will be detected, fitted and quantitatively evaluated.

  13. Trapping and manipulating single molecules of DNA

    Science.gov (United States)

    Shon, Min Ju

    This thesis presents the development and application of nanoscale techniques to trap and manipulate biomolecules, with a focus on DNA. These methods combine single-molecule microscopy and nano- and micro-fabrication to study biophysical properties of DNA and proteins. The Dimple Machine is a lab-on-a-chip device that can isolate and confine a small number of molecules from a bulk solution. It traps molecules in nanofabricated chambers, or "dimples", and the trapped molecules are then studied on a fluorescence microscope at the single-molecule level. The sampling of bulk solution by dimples is representative, reproducible, and automated, enabling highthroughput single-molecule experiments. The device was applied to study hybridization of oligonucleotides, particularly in the context of reaction thermodynamics and kinetics in nanoconfinement. The DNA Pulley is a system to study protein binding and the local mechanical properties of DNA. A molecule of DNA is tethered to a surface on one end, and a superparamagnetic bead is attached to the other. A magnet pulls the DNA taut, and a silicon nitride knife with a nanoscale blade scans the DNA along its contour. Information on the local properties of the DNA is extracted by tracking the bead with nanometer precision in a white-light microscope. The system can detect proteins bound to DNA and localize their recognition sites, as shown with a model protein, EcoRI restriction enzyme. Progress on the measurements of nano-mechanical properties of DNA is included.

  14. High-sensitivity single-molecule fluorescence detection in theory and practice

    Energy Technology Data Exchange (ETDEWEB)

    Mathies, R.A.; Peck, K. (California Univ., Berkeley, CA (United States). Dept. of Chemistry); Stryer, L. (Stanford Univ., CA (United States). Dept. of Cell Biology)

    1989-01-01

    The number of emitted photons that can be obtained from a fluorophore increases with the incident light intensity and the duration of illumination. However, saturation of the absorption transition and photodestruction place natural limits on the ultimate signal-to-noise ratio that can be obtained. Equations have been derived to describe the fluorescence-to-background-noise ratio in the presence of saturating light intensities and photodestruction. The fluorescence lifetime and the photodestruction quantum yield are the key parameters that determine the optimum light intensity and exposure time. To test this theory we have performed single molecule detection of phycoerythrin (PE). The laser power was selected to give a mean time between absorptions approximately equal to the fluorescence decay rate. The transit time was selected to be nearly equal to the photodestruction time of {approximately}600 {mu}s. Under these conditions the photocount distribution function, the photocount autocorrelation function, and the concentration dependence clearly show that we are detecting bursts of fluorescence from individual fluorophores. A hard-wired version of this single-molecule detection system was used to measure the concentration of PE down to 10{sup {minus}15} M. This single-molecule counter is three orders-of-magnitude more sensitive than conventional fluorescence detection systems. The approach presented here should be useful in the optimization of fluorescence detected DNA sequencing gels. 17 refs., 4 figs.

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

    Energy Technology Data Exchange (ETDEWEB)

    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 {times} 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.

  16. Deep learning for single-molecule science.

    Science.gov (United States)

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

    2017-08-01

    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) offers an interesting, new avenues to address such challenges. In some applications, such as speech and image recognition, DL has been able to outperform conventional Machine Learning 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, may be used for base calling in DNA sequencing applications. We compare it with a Support Vector Machine as a more conventional ML method, and 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. © 2017 IOP Publishing Ltd.

  17. 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.

  18. Photoluminescence Study of Long Wavelength Superlattice Infrared Detectors

    Science.gov (United States)

    Hoglund, Linda; Khoshakhlagh, Arezou; Soibel, Alexander; Ting, David Z.; Hill, Cory J.; Keo, Sam; Gunapala, Sarath D.

    2011-01-01

    In this paper, the relation between the photoluminescence (PL) intensity and the PL peak wavelength was studied. A linear decrease of the PL intensity with increasing cut-off wavelength of long wavelength infrared CBIRDs was observed at 77 K and the trend remained unchanged in the temperature range 10 - 77 K. This relation between the PL intensity and the peak wavelength can be favorably used for comparison of the optical quality of samples with different PL peak wavelengths. A strong increase of the width of the PL spectrum in the studied temperature interval was observed, which was attributed to thermal broadening.

  19. Backward Raman amplification in the long-wavelength infrared

    Science.gov (United States)

    Johnson, L. A.; Gordon, D. F.; Palastro, J. P.; Hafizi, B.

    2017-03-01

    The wealth of work in backward Raman amplification in plasma has focused on the extreme intensity limit; however, backward Raman amplification may also provide an effective and practical mechanism for generating intense, broad bandwidth, long-wavelength infrared radiation (LWIR). An electromagnetic simulation coupled with a relativistic cold fluid plasma model is used to demonstrate the generation of picosecond pulses at a wavelength of 10 μm with terawatt powers through backward Raman amplification. The effects of collisional damping, Landau damping, pump depletion, and wave breaking are examined, as well as the resulting design considerations for an LWIR Raman amplifier.

  20. Quantifying and optimizing single-molecule switching nanoscopy at high speeds.

    Directory of Open Access Journals (Sweden)

    Yu Lin

    Full Text Available Single-molecule switching nanoscopy overcomes the diffraction limit of light by stochastically switching single fluorescent molecules on and off, and then localizing their positions individually. Recent advances in this technique have greatly accelerated the data acquisition speed and improved the temporal resolution of super-resolution imaging. However, it has not been quantified whether this speed increase comes at the cost of compromised image quality. The spatial and temporal resolution depends on many factors, among which laser intensity and camera speed are the two most critical parameters. Here we quantitatively compare the image quality achieved when imaging Alexa Fluor 647-immunolabeled microtubules over an extended range of laser intensities and camera speeds using three criteria - localization precision, density of localized molecules, and resolution of reconstructed images based on Fourier Ring Correlation. We found that, with optimized parameters, single-molecule switching nanoscopy at high speeds can achieve the same image quality as imaging at conventional speeds in a 5-25 times shorter time period. Furthermore, we measured the photoswitching kinetics of Alexa Fluor 647 from single-molecule experiments, and, based on this kinetic data, we developed algorithms to simulate single-molecule switching nanoscopy images. We used this software tool to demonstrate how laser intensity and camera speed affect the density of active fluorophores and influence the achievable resolution. Our study provides guidelines for choosing appropriate laser intensities for imaging Alexa Fluor 647 at different speeds and a quantification protocol for future evaluations of other probes and imaging parameters.

  1. Peering into Cells One Molecule at a Time: Single-molecule and plasmon-enhanced fluorescence super-resolution imaging

    Science.gov (United States)

    Biteen, Julie

    2013-03-01

    Single-molecule fluorescence brings the resolution of optical microscopy down to the nanometer scale, allowing us to unlock the mysteries of how biomolecules work together to achieve the complexity that is a cell. This high-resolution, non-destructive method for examining subcellular events has opened up an exciting new frontier: the study of macromolecular localization and dynamics in living cells. We have developed methods for single-molecule investigations of live bacterial cells, and have used these techniques to investigate thee important prokaryotic systems: membrane-bound transcription activation in Vibrio cholerae, carbohydrate catabolism in Bacteroides thetaiotaomicron, and DNA mismatch repair in Bacillus subtilis. Each system presents unique challenges, and we will discuss the important methods developed for each system. Furthermore, we use the plasmon modes of bio-compatible metal nanoparticles to enhance the emissivity of single-molecule fluorophores. The resolution of single-molecule imaging in cells is generally limited to 20-40 nm, far worse than the 1.5-nm localization accuracies which have been attained in vitro. We use plasmonics to improve the brightness and stability of single-molecule probes, and in particular fluorescent proteins, which are widely used for bio-imaging. We find that gold-coupled fluorophores demonstrate brighter, longer-lived emission, yielding an overall enhancement in total photons detected. Ultimately, this results in increased localization accuracy for single-molecule imaging. Furthermore, since fluorescence intensity is proportional to local electromagnetic field intensity, these changes in decay intensity and rate serve as a nm-scale read-out of the field intensity. Our work indicates that plasmonic substrates are uniquely advantageous for super-resolution imaging, and that plasmon-enhanced imaging is a promising technique for improving live cell single-molecule microscopy.

  2. Single molecule and single cell epigenomics.

    Science.gov (United States)

    Hyun, Byung-Ryool; McElwee, John L; Soloway, Paul D

    2015-01-15

    Dynamically regulated changes in chromatin states are vital for normal development and can produce disease when they go awry. Accordingly, much effort has been devoted to characterizing these states under normal and pathological conditions. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the most widely used method to characterize where in the genome transcription factors, modified histones, modified nucleotides and chromatin binding proteins are found; bisulfite sequencing (BS-seq) and its variants are commonly used to characterize the locations of DNA modifications. Though very powerful, these methods are not without limitations. Notably, they are best at characterizing one chromatin feature at a time, yet chromatin features arise and function in combination. Investigators commonly superimpose separate ChIP-seq or BS-seq datasets, and then infer where chromatin features are found together. While these inferences might be correct, they can be misleading when the chromatin source has distinct cell types, or when a given cell type exhibits any cell to cell variation in chromatin state. These ambiguities can be eliminated by robust methods that directly characterize the existence and genomic locations of combinations of chromatin features in very small inputs of cells or ideally, single cells. Here we review single molecule epigenomic methods under development to overcome these limitations, the technical challenges associated with single molecule methods and their potential application to single cells. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. Linear response to long wavelength fluctuations using curvature simulations

    CERN Document Server

    Baldauf, Tobias; Senatore, Leonardo; Zaldarriaga, Matias

    2015-01-01

    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, most probably more precise, 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 naive derivation assuming a universal mass function by 18%. This has implications for measurements of the amplitude of local non-Gaussianity using scale dependent bias. We also analyze the halo power spectrum...

  4. Synthesis of single-molecule nanocars.

    Science.gov (United States)

    Vives, Guillaume; Tour, James M

    2009-03-17

    The drive to miniaturize devices has led to a variety of molecular machines inspired by macroscopic counterparts such as molecular motors, switches, shuttles, turnstiles, barrows, elevators, and nanovehicles. Such nanomachines are designed for controlled mechanical motion and the transport of nanocargo. As researchers miniaturize devices, they can consider two complementary approaches: (1) the "top-down" approach, which reduces the size of macroscopic objects to reach an equivalent microscopic entity using photolithography and related techniques and (2) the "bottom-up" approach, which builds functional microscopic or nanoscopic entities from molecular building blocks. The top-down approach, extensively used by the semiconductor industry, is nearing its scaling limits. On the other hand, the bottom-up approach takes advantage of the self-assembly of smaller molecules into larger networks by exploiting typically weak molecular interactions. But self-assembly alone will not permit complex assembly. Using nanomachines, we hope to eventually consider complex, enzyme-like directed assembly. With that ultimate goal, we are currently exploring the control of nanomachines that would provide a basis for the future bottom-up construction of complex systems. This Account describes the synthesis of a class of molecular machines that resemble macroscopic vehicles. We designed these so-called nanocars for study at the single-molecule level by scanning probe microscopy (SPM). The vehicles have a chassis connected to wheel-terminated axles and convert energy inputs such as heat, electric fields, or light into controlled motion on a surface, ultimately leading to transport of nanocargo. At first, we used C(60) fullerenes as wheels, which allowed the demonstration of a directional rolling mechanism of a nanocar on a gold surface by STM. However, because of the low solubility of the fullerene nanocars and the incompatibility of fullerenes with photochemical processes, we developed new

  5. 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

  6. Effective long wavelength scalar dynamics in de Sitter

    CERN Document Server

    Moss, Ian

    2016-01-01

    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 $k/a \\sim H$ 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 $\\Delta t \\gg H^{-1}$, this results in the well-known Starobinsky stochastic evolution. Our approach allows for the computation of quantum UV corrections, generating an effective potential on which the stochastic dynamics takes place, as well as the description of dynamics on spatial and temporal scales comparable to $H^{-1}$ and above. We further elaborate on the use of a Wigner function to evaluate the non-perturbative expectation values of field correlators and the stress-energy tensor of $\\phi$ within the stochastic formalism.

  7. 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.

  8. The role of molecular dipole orientation in single-molecule fluorescence microscopy and implications for super-resolution imaging.

    Science.gov (United States)

    Backlund, Mikael P; Lew, Matthew D; Backer, Adam S; Sahl, Steffen J; Moerner, W E

    2014-03-17

    Numerous methods for determining the orientation of single-molecule transition dipole moments from microscopic images of the molecular fluorescence have been developed in recent years. At the same time, techniques that rely on nanometer-level accuracy in the determination of molecular position, such as single-molecule super-resolution imaging, have proven immensely successful in their ability to access unprecedented levels of detail and resolution previously hidden by the optical diffraction limit. However, the level of accuracy in the determination of position is threatened by insufficient treatment of molecular orientation. Here we review a number of methods for measuring molecular orientation using fluorescence microscopy, focusing on approaches that are most compatible with position estimation and single-molecule super-resolution imaging. We highlight recent methods based on quadrated pupil imaging and on double-helix point spread function microscopy and apply them to the study of fluorophore mobility on immunolabeled microtubules.

  9. Single Molecule Sensitive FRET in Attoliter Droplets

    CERN Document Server

    Milas, Peker; Gamari, Ben D; Goldner, Lori S

    2013-01-01

    Single molecular-pair fluorescence resonance energy transfer (spFRET) has become an cross-disciplinary tool for understanding molecular folding and interactions. While providing detailed information about the individual members of a molecular ensemble, this technique is always limited by fluorophore brightness and stability. In the case of diffusing molecules, the experiment is further limited by the number of photons that can be collected during the time it takes for a molecule to diffuse across the detection volume. To maximize the number of photons it is common to either increase the detection volume at the expense of increased background, or increase the diffusion time by adding glycerol or sucrose to increase viscosity. Here we demonstrate that FRET from attoliter volume (100 nm radius) aqueous droplets in perfluorinated oil has significantly higher signal-to-noise and a much wider dynamic range than FRET from molecules diffusing in solution. However, our measurements also reveal a droplet environment th...

  10. Limits of single-molecule super-resolution microscopy in thin polymer films

    Science.gov (United States)

    Wang, Muzhou; Davanco, Marcelo; Marr, James M.; Liddle, J. Alexander; Gilman, Jeffrey W.

    Structural characterization by super-resolution microscopy has become increasingly widespread, particularly in the biological community. The technique is powerful because it can produce real-space images with resolutions of tens of nanometers, while sample preparation is relatively non-invasive. Previous studies have applied these techniques to important scientific problems in the life sciences, but relatively little work has explored the attainable limit of resolution using samples of known structure. In this work, we apply photo-activated localization microscopy (PALM) to polymer films that have been nanopatterned using electron-beam lithography. Trace amounts of a rhodamine spiroamide dye are dispersed into nanostructured poly(methyl methacrylate), and UV-induced switching of the fluorophores enables nanoscale localization of single molecules to generate a final composite super-resolution image. Features as small as 50 nm are clearly resolvable. To determine the ultimate resolution limit, we investigate sources of error in the system, particularly from systematic mislocalizations due to the effect of fluorophore orientation on the single-molecule point-spread function.

  11. 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.

  12. Grafting single molecule magnets on gold nanoparticles.

    Science.gov (United States)

    Perfetti, Mauro; Pineider, Francesco; Poggini, Lorenzo; Otero, Edwige; Mannini, Matteo; Sorace, Lorenzo; Sangregorio, Claudio; Cornia, Andrea; Sessoli, Roberta

    2014-01-29

    The chemical synthesis and characterization of the first hybrid material composed by gold nanoparticles and single molecule magnets (SMMs) are described. Gold nanoparticles are functionalized via ligand exchange using a tetrairon(III) SMM containing two 1,2-dithiolane end groups. The grafting is evidenced by the shift of the plasmon resonance peak recorded with a UV-vis spectrometer, by the suppression of nuclear magnetic resonance signals, by X-ray photoemission spectroscopy peaks, and by transmission electron microscopy images. The latter evidence the formation of aggregates of nanoparticles as a consequence of the cross-linking ability of Fe4 through the two 1,2-dithiolane rings located on opposite sides of the metal core. The presence of intact Fe4 molecules is directly proven by synchrotron-based X-ray absorption spectroscopy and X-ray magnetic circular dichroism spectroscopy, while a detailed magnetic characterization, obtained using electron paramagnetic resonance and alternating-current susceptibility, confirms the persistence of SMM behavior in this new hybrid nanostructure. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Irving Langmuir Prize Talk: Single-Molecule Fluorescence Imaging: Nanoscale Emitters with Photoinduced Switching Enable Superresolution.

    Science.gov (United States)

    Moerner, W. E.

    2009-03-01

    In the two decades 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. The early years concentrated on high-resolution spectroscopy in solids, which provided observations of lifetime-limited spectra, optical saturation, spectral diffusion, optical switching, vibrational spectra, and magnetic resonance of a single molecular spin. In the mid-1990's, much of the field moved to room temperature, where a wide variety of biophysical effects were subsequently explored, but it is worth noting that several features from the low-temperature studies have analogs at high temperature. For example, in our first studies of yellow-emitting variants of green fluorescent protein (EYFP) in the water-filled pores of a gel (Nature 388, 355 (1997)), optically induced switching of the emission was observed, a room-temperature analog of the earlier low-temperature behavior. 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. Recent work has allowed measurement of the shape of single filaments in a living cell simply by allowing a single molecule to move through the filament (PNAS 103, 10929 (2006)). The additional use of photoinduced control of single-molecule emission allows imaging beyond the diffraction limit (superresolution) by several novel approaches proposed by different researchers. For example, using photoswitchable EYFP, a novel protein superstructure can now be directly imaged in a living bacterial cell at

  14. 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.

  15. Rational design of fluorophores for in vivo applications.

    Science.gov (United States)

    Ptaszek, Marcin

    2013-01-01

    Several classes of small organic molecules exhibit properties that make them suitable for fluorescence in vivo imaging. The most promising candidates are cyanines, squaraines, boron dipyrromethenes, porphyrin derivatives, hydroporphyrins, and phthalocyanines. The recent designing and synthetic efforts have been dedicated to improving their optical properties (shift the absorption and emission maxima toward longer wavelengths and increase the brightness) as well as increasing their stability and water solubility. The most notable advances include development of encapsulated cyanine dyes with increased stability and water solubility, squaraine rotaxanes with increased stability, long-wavelength-absorbing boron dipyrromethenes, long-wavelength-absorbing porphyrin and hydroporphyrin derivatives, and water-soluble phthalocyanines. Recent advances in luminescence and bioluminescence have made self-illuminating fluorophores available for in vivo applications. Development of new types of hydroporphyrin energy-transfer dyads gives the promise for further advances in in vivo multicolor imaging.

  16. Tether enabled spacecraft systems for ultra long wavelength radio astronomy

    Science.gov (United States)

    Gemmer, Thomas; Yoder, Christopher D.; Reedy, Jacob; Mazzoleni, Andre P.

    2017-09-01

    This paper describes a proposed CubeSat mission to perform unique experiments involving interferometry and tether dynamics. A 3U CubeSat is to be placed in orbit where it will separate into three 1U CubeSats connected by a total of 100 m of tether. The separation between the three units will allow for the demonstration of high resolution radio interferometry. The increased resolution will provide access to the Ultra-Long Wavelength (ULW) scale of the electromagnetic spectrum, which is largely unexplored. During and after completion of the primary experiment, the CubeSat will be able to gather data on tethered dynamics of a space vehicle. Maneuvers to be performed and studied include direct testing of tether deployment and tethered formation flying. Tether deployment is a vital area where more data is needed as this is the phase where many tethered missions have experienced complications and failures. There are a large number of complex dynamical responses predicted by the theory associated with the deployment of an orbiting tethered system. Therefore, it is imperative to conduct an experiment that provides data on what dynamic responses actually occur.

  17. Long wavelength undulations dominate dynamics in large surfactant membrane patches

    Science.gov (United States)

    Lipfert, Frederik; Holderer, Olaf; Frielinghaus, Henrich; Appavou, Marie-Sousai; Do, Changwoo; Ohl, Michael; Richter, Dieter

    2015-01-01

    By exposing microemulsions to small (80 nm diameter) and large (500 nm) disk shaped clay particles we were able to show the presence of long wavelength undulations that only occur for large membrane patches. A combination of small angle neutron scattering (SANS) and neutron spin echo (NSE) experiments have been applied to study microemulsions. These, consisting of D2O, d-decane and the surfactant C10E4, were used in connection with Laponite (small) and Nanofil (large) clay. To our knowledge our experiments show for the first time that the clay platelets induce lamellar ordering adjacent to the clay discs in the otherwise bicontinuous microemulsion. This is due to the fact that in purely structural investigations, radial averaging smears out the signature of the lamellar phase. For thermodynamically fluctuating membranes near interfaces the theory of Seifert predicts a cross-over of the dispersion relationship from k2 to a k3-dependence. With the correlation length of the membrane patches being confined by the dimension of the clay platelets we were able to show that this in fact takes place but is only present for the larger Nanofil particles.

  18. Commissioning the First Station of the Long Wavelength Array

    Science.gov (United States)

    Dowell, Jayce; LWA Collaboration

    2012-01-01

    The Long Wavelength Array (LWA, http://lwa.unm.edu/) is a low frequency array operating between 10 and 88 MHz being constructed in New Mexico, USA. The first station of the LWA, LWA-1, consists of 256 dual polarization dipoles that can be sampled independently or combined together into four electronically steerable beams. A second station, LWA-2, is also being constructed and currently consists of 20 dual polarization dipoles. I will discuss the current status of commissioning the instrument and show early results from both stations. I will also provide an overview of the LWA Software Library (LSL, http://fornax.phys.unm.edu/lwa/trac/wiki) that is being developed. LSL is a general purpose Python module that runs on Linux and Mac OSX platforms. The library provides a variety of visualization and analysis tools for the various LWA data products. Some of the tasks which users can accomplish within the LSL framework include working with LWA data in the time or frequency domain, identifying RFI, forming images, and applying incoherent de-dispersion to pulsar data. LSL also provides facilities for converting the LWA data products into forms readable by other popular analysis packages.

  19. Long-wavelength infrared hyperspectral data "mining" at Cuprite, NV

    Science.gov (United States)

    Sundberg, Robert; Adler-Golden, Steven; Conforti, Patrick

    2015-09-01

    In recent years long-wavelength infrared (LWIR) hyperspectral imagery has significantly improved in quality and become much more widely available, sparking interest in a variety of applications involving remote sensing of surface composition. This in turn has motivated the development and study of LWIR-focused algorithms for atmospheric retrieval, temperature-emissivity separation (TES) and material detection and identification. In this paper we evaluate some LWIR algorithms for atmospheric retrieval, TES, endmember-finding and rare material detection for their utility in characterizing mineral composition in SEBASS hyperspectral imagery taken near Cuprite, NV. Atmospheric correction results using the In-Scene Atmospheric Correction (ISAC) method are compared with those from the first-principles, MODTRAN©-based FLAASH-IR method. Covariance-whitened endmember-finding methods are observed to be sensitive to image artifacts. However, with clean data and all-natural terrain they can automatically locate and distinguish many minor mineral components, with especially high sensitivity to varieties of calcite. Not surprisingly, the major scene materials, including silicates, are best located using unwhitened techniques. Minerals that we identified in the data include calcite, quartz, alunite and (tentatively) kaolinite.

  20. The First Station of the Long Wavelength Array

    CERN Document Server

    Henning, Patricia; Taylor, Gregory B; Craig, Joseph; Pihlström, Ylva; Rickard, Lee J; Clarke, Tracy E; Kassim, Namir E; Cohen, Aaron

    2010-01-01

    The Long Wavelength Array (LWA) will be a new multi-purpose radio telescope operating in the frequency range 10-88 MHz. Upon completion, LWA will consist of 53 phased array "stations" distributed over a region about 400 km in diameter in the state of New Mexico. Each station will consist of 256 pairs of dipole-type antennas whose signals are formed into beams, with outputs transported to a central location for high-resolution aperture synthesis imaging. The resulting image sensitivity is estimated to be a few mJy (5 sigma, 8 MHz, 2 polarizations, 1 hr, zenith) in 20-80 MHz; with resolution and field of view of (8", 8 deg) and (2",2 deg) at 20 MHz and 80 MHz, respectively. All 256 dipole antennas are in place for the first station of the LWA (called LWA-1), and commissioning activities are well underway. The station is located near the core of the EVLA, and is expected to be fully operational in early 2011.

  1. 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.

  2. 'Single molecule': theory and experiments, an introduction.

    Science.gov (United States)

    Riveline, Daniel

    2013-01-01

    At scales below micrometers, Brownian motion dictates most of the behaviors. The simple observation of a colloid is striking: a permanent and random motion is seen, whereas inertial forces play a negligible role. This Physics, where velocity is proportional to force, has opened new horizons in biology. The random feature is challenged in living systems where some proteins--molecular motors--have a directed motion whereas their passive behaviors of colloid should lead to a Brownian motion. Individual proteins, polymers of living matter such as DNA, RNA, actin or microtubules, molecular motors, all these objects can be viewed as chains of colloids. They are submitted to shocks from molecules of the solvent. Shapes taken by these biopolymers or dynamics imposed by motors can be measured and modeled from single molecules to their collective effects. Thanks to the development of experimental methods such as optical tweezers, Atomic Force Microscope (AFM), micropipettes, and quantitative fluorescence (such as Förster Resonance Energy Transfer, FRET), it is possible to manipulate these individual biomolecules in an unprecedented manner: experiments allow to probe the validity of models; and a new Physics has thereby emerged with original biological insights. Theories based on statistical mechanics are needed to explain behaviors of these systems. When force-extension curves of these molecules are extracted, the curves need to be fitted with models that predict the deformation of free objects or submitted to a force. When velocity of motors is altered, a quantitative analysis is required to explain the motions of individual molecules under external forces. This lecture will give some elements of introduction to the lectures of the session 'Nanophysics for Molecular Biology'.

  3. Single-molecule electronics: from chemical design to functional devices.

    Science.gov (United States)

    Sun, Lanlan; Diaz-Fernandez, Yuri A; Gschneidtner, Tina A; Westerlund, Fredrik; Lara-Avila, Samuel; Moth-Poulsen, Kasper

    2014-11-07

    The use of single molecules in electronics represents the next limit of miniaturisation of electronic devices, which would enable us to continue the trend of aggressive downscaling of silicon-based electronic devices. More significantly, the fabrication, understanding and control of fully functional circuits at the single-molecule level could also open up the possibility of using molecules as devices with novel, not-foreseen functionalities beyond complementary metal-oxide semiconductor technology (CMOS). This review aims at highlighting the chemical design and synthesis of single molecule devices as well as their electrical and structural characterization, including a historical overview and the developments during the last 5 years. We discuss experimental techniques for fabrication of single-molecule junctions, the potential application of single-molecule junctions as molecular switches, and general physical phenomena in single-molecule electronic devices.

  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 was ident......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. Prototype for Long Wavelength Array Sees First Light

    Science.gov (United States)

    2007-03-01

    Astronomers at the Naval Research Laboratory have produced the first images of the sky from a prototype of the Long Wavelength Array (LWA), a revolutionary new radio telescope to be constructed in southwestern New Mexico. The images show emissions from the center of our Galaxy, a supermassive black hole, and the remnant of a star that exploded in a supernova over 300 years ago. Not only a milestone in the development of the LWA, the images are also a first glimpse through a new window on the cosmos. "First light" is an astronomical term for the first image produced with a telescope. It is a key milestone for any telescope because it indicates that all of the individual components are working in unison as planned. Once completed, the LWA will provide an entirely novel view of the sky, in the radio frequency range of 20-80 MHz, currently one of the most poorly explored regions of the electromagnetic spectrum in astronomy. The LWA will be able to make sensitive high-resolution images, and scan the sky rapidly for new and transient sources of radio waves, which might represent the explosion of distant, massive stars, the emissions from planets outside of our own solar system or even previously unknown objects or phenomena. "The LWA will allow us to make the sharpest images ever possible using very long wavelength radio waves. This newly opened window on the universe will help us understand the acceleration of relativistic particles in a variety of extreme astrophysical environments including from the most distant supermassive black holes. But perhaps most exciting is the promise of new source classes waiting to be discovered," says Dr. Namir Kassim, an NRL astronomer in the Remote Sensing Division and LWA Project Scientist. Dr. Tracy Clarke, of Interferometrics, Inc. in Herndon, Virginia, another astronomer on the NRL team adds, "By detecting distant clusters of galaxies the LWA may also provide new insights on the cosmological evolution of the mysterious dark matter

  6. 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

  7. Formulation of long-wavelength indocyanine green nanocarriers.

    Science.gov (United States)

    Pansare, Vikram J; Faenza, William J; Lu, Hoang; Adamson, Douglas H; Prud'homme, Robert K

    2017-09-01

    Indocyanine green (ICG), a Food and Drug Administration (FDA)-approved fluorophore with excitation and emission wavelengths inside the "optical imaging window," has been incorporated into nanocarriers (NCs) to achieve enhanced circulation time, targeting, and real-time tracking in vivo. While previous studies transferred ICG exogenously into NCs, here, a one-step rapid precipitation process [flash nanoprecipitation (FNP)] creates ICG-loaded NCs with tunable, narrow size distributions from 30 to 180 nm. A hydrophobic ion pair of ICG-tetraoctylammonium or tetradodecylammonium chloride is formed either in situ during FNP or preformed then introduced into the FNP feed stream. The NCs are formulated with cores comprising either vitamin E (VE) or polystyrene (PS). ICG core loadings of 30 wt. % for VE and 10 wt. % for PS are achieved. However, due to a combination of molecular aggregation and Förster quenching, maximum fluorescence (FL) occurs at 10 wt. % core loading. The FL-per-particle scales with core diameter to the third power, showing that FNP enables uniform volume encapsulation. By varying the ICG counter-ion ratio, encapsulation efficiencies above 80% are achieved even in the absence of ion pairing, which rises to 100% with 1∶1 ion pairing. Finally, while ICG ion pairs are shown to be stable in buffer, they partition out of NC cores in under 30 min in the presence of physiological albumin concentrations. (2017) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

  8. Single-Molecule FRET Study of DNA G-Quadruplex

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The DNA G-quadruplex formed by the human telomeric sequence is a potential target for novel anticancer drugs. We have investigated an intramolecular DNA G-quadruplex using single-molecule fluorescence resonance energy transfer and shown that individual folded quadruplexes can be identified. The mean proximity ratio measured at the single-molecule level was consistent with ensemble measurement.

  9. Single-molecule approaches to characterizing kinetics of biomolecular interactions

    NARCIS (Netherlands)

    van Oijen, Antoine M.

    2011-01-01

    Single-molecule fluorescence techniques have emerged as powerful tools to study biological processes at the molecular level. This review describes the application of these methods to the characterization of the kinetics of interaction between biomolocules. A large number of single-molecule assays ha

  10. 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....

  11. 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...

  12. Micropolarizing device for long wavelength infrared polarization imaging.

    Energy Technology Data Exchange (ETDEWEB)

    Wendt, Joel Robert; Carter, Tony Ray; Samora, Sally; Cruz-Cabrera, Alvaro Augusto; Vawter, Gregory Allen; Kemme, Shanalyn A.; Alford, Charles Fred; Boye, Robert R.; Smith, Jody Lynn

    2006-11-01

    The goal of this project is to fabricate a four-state pixelated subwavelength optical device that enables mid-wave infrared (MWIR) or long-wave infrared (LWIR) snapshot polarimetric imaging. The polarization information can help to classify imaged materials and identify objects of interest for numerous remote sensing and military applications. While traditional, sequential polarimetric imaging produces scenes with polarization information through a series of assembled images, snapshot polarimetric imaging collects the spatial distribution of all four Stokes parameters simultaneously. In this way any noise due to scene movement from one frame to the next is eliminated. We fabricated several arrays of subwavelength components for MWIR polarization imaging applications. Each pixel unit of the array consists of four elements. These elements are micropolarizers with three or four different polarizing axis orientations. The fourth element sometimes has a micro birefringent waveplate on the top of one of the micropolarizers. The linear micropolarizers were fabricated by patterning nano-scale metallic grids on a transparent substrate. A large area birefringent waveplate was fabricated by deeply etching a subwavelength structure into a dielectric substrate. The principle of making linear micropolarizers for long wavelengths is based upon strong anisotropic absorption of light in the nano-metallic grid structures. The nano-metallic grid structures are patterned with different orientations; therefore, the micropolarizers have different polarization axes. The birefringent waveplate is a deeply etched dielectric one-dimensional subwavelength grating; therefore two orthogonally polarized waves have different phase delays. Finally, in this project, we investigated the near field and diffractive effects of the subwavelength element apertures upon detection. The fabricated pixelated polarizers had a measured extinction ratios larger than 100:1 for pixel sizes in the order of 15

  13. Analyzing single-molecule time series via nonparametric Bayesian inference.

    Science.gov (United States)

    Hines, Keegan E; Bankston, John R; Aldrich, Richard W

    2015-02-03

    The ability to measure the properties of proteins at the single-molecule level offers an unparalleled glimpse into biological systems at the molecular scale. The interpretation of single-molecule time series has often been rooted in statistical mechanics and the theory of Markov processes. While existing analysis methods have been useful, they are not without significant limitations including problems of model selection and parameter nonidentifiability. To address these challenges, we introduce the use of nonparametric Bayesian inference for the analysis of single-molecule time series. These methods provide a flexible way to extract structure from data instead of assuming models beforehand. We demonstrate these methods with applications to several diverse settings in single-molecule biophysics. This approach provides a well-constrained and rigorously grounded method for determining the number of biophysical states underlying single-molecule data. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  14. Single Molecule Localization Microscopy of Mammalian Cell Nuclei on the Nanoscale

    Science.gov (United States)

    Szczurek, Aleksander; Xing, Jun; Birk, Udo J.; Cremer, Christoph

    2016-01-01

    Nuclear texture analysis is a well-established method of cellular pathology. It is hampered, however, by the limits of conventional light microscopy (ca. 200 nm). These limits have been overcome by a variety of super-resolution approaches. An especially promising approach to chromatin texture analysis is single molecule localization microscopy (SMLM) as it provides the highest resolution using fluorescent based methods. At the present state of the art, using fixed whole cell samples and standard DNA dyes, a structural resolution of chromatin in the 50–100 nm range is obtained using SMLM. We highlight how the combination of localization microscopy with standard fluorophores opens the avenue to a plethora of studies including the spatial distribution of DNA and associated proteins in eukaryotic cell nuclei with the potential to elucidate the functional organization of chromatin. These views are based on our experience as well as on recently published research in this field. PMID:27446198

  15. Structural dynamics of potassium-channel gating revealed by single-molecule FRET.

    Science.gov (United States)

    Wang, Shizhen; Vafabakhsh, Reza; Borschel, William F; Ha, Taekjip; Nichols, Colin G

    2016-01-01

    Crystallography has provided invaluable insights regarding ion-channel selectivity and gating, but to advance understanding to a new level, dynamic views of channel structures within membranes are essential. We labeled tetrameric KirBac1.1 potassium channels with single donor and acceptor fluorophores at different sites and then examined structural dynamics within lipid membranes by single-molecule fluorescence resonance energy transfer (FRET). We found that the extracellular region is structurally rigid in both closed and open states, whereas the N-terminal slide helix undergoes marked conformational fluctuations. The cytoplasmic C-terminal domain fluctuates between two major structural states, both of which become less dynamic and move away from the pore axis and away from the membrane in closed channels. Our results reveal mobile and rigid conformations of functionally relevant KirBac1.1 channel motifs, implying similar dynamics for similar motifs in eukaryotic Kir channels and in cation channels in general.

  16. Structural dynamics of potassium channel gating revealed by single molecule FRET

    Science.gov (United States)

    Borschel, William F.; Ha, Taekjip; Nichols, Colin G.

    2016-01-01

    Crystallography has provided invaluable insights to ion channel selectivity and gating, but to advance understanding to a new level, dynamic views of channel structures within membranes are essential. We labeled tetrameric KirBac1.1 potassium channels with single donor and acceptor fluorophores at different sites, and examined structural dynamics within lipid membranes by single molecule FRET. We found that the extracellular region is structurally rigid in both closed and open states, whereas the N-terminal slide helix undergoes marked conformational fluctuations. The cytoplasmic C-terminal domain fluctuates between two major structural states both of which become less dynamic and move away from the pore axis and away from the membrane in closed channels. Our results reveal mobile and rigid conformations of functionally relevant KirBac1.1 channel motifs, implying similar dynamics for similar motifs in eukaryotic Kir channels and for cation channels in general. PMID:26641713

  17. An optical nanofiber-based interface for single molecules

    CERN Document Server

    Skoff, Sarah M; Schauffert, Hardy; Rauschenbeutel, Arno

    2016-01-01

    Optical interfaces for quantum emitters are a prerequisite for implementing quantum networks. Here, we couple single molecules to the guided modes of an optical nanofiber. The molecules are embedded within a crystal that provides photostability and due to its inhomogeneous environment, a means to spectrally address single molecules. Single molecules are excited and detected solely via the nanofiber interface without the requirement of additional optical access. In this way, we realize a fully fiber-integrated system that is scalable and may become a versatile constituent for quantum hybrid systems.

  18. Stochastic single-molecule dynamics of synaptic membrane protein domains

    CERN Document Server

    Kahraman, Osman; Haselwandter, Christoph A

    2016-01-01

    Motivated by single-molecule experiments on synaptic membrane protein domains, we use a stochastic lattice model to study protein reaction and diffusion processes in crowded membranes. We find that the stochastic reaction-diffusion dynamics of synaptic proteins provide a simple physical mechanism for collective fluctuations in synaptic domains, the molecular turnover observed at synaptic domains, key features of the single-molecule trajectories observed for synaptic proteins, and spatially inhomogeneous protein lifetimes at the cell membrane. Our results suggest that central aspects of the single-molecule and collective dynamics observed for membrane protein domains can be understood in terms of stochastic reaction-diffusion processes at the cell membrane.

  19. 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.

  20. Direct Characterization of Amyloidogenic Oligomers by Single-Molecule Fluorescence

    National Research Council Canada - National Science Library

    Angel Orte; Neil R. Birkett; Richard W. Clarke; Glyn L. Devlin; Christopher M. Dobson; David Klenerman

    2008-01-01

    .... We describe here the application of a two-color single-molecule fluorescence technique to examine the assembly of oligomeric species formed during the aggregation of the SH3 domain of PI3 kinase...

  1. Single Molecule Scanning of DNA Radiation Oxidative Damage Project

    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;...

  2. Single Molecule Spectroscopy in Chemistry, Physics and Biology Nobel Symposium

    CERN Document Server

    Gräslund, Astrid; Widengren, Jerker

    2010-01-01

    Written by the leading experts in the field, this book describes the development and current state-of-the-art in single molecule spectroscopy. The application of this technique, which started 1989, in physics, chemistry and biosciences is displayed.

  3. Massively parallel single-molecule manipulation using centrifugal force

    CERN Document Server

    Halvorsen, Ken

    2009-01-01

    Precise manipulation of single molecules has already led to remarkable insights in physics, chemistry, biology and medicine. However, widespread adoption of single-molecule techniques has been impeded by equipment cost and the laborious nature of making measurements one molecule at a time. We have solved these issues with a new approach: massively parallel single-molecule force measurements using centrifugal force. This approach is realized in a novel instrument that we call the Centrifuge Force Microscope (CFM), 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. Additionally, we verify the force accuracy of the instrument by measuring the well-est...

  4. Single Molecule Imaging in Living Cell with Optical Method

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Significance, difficult, international developing actuality and our completed works for single molecules imaging in living cell with optical method are described respectively. Additionally we give out some suggestions for the technology development further.

  5. 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.

  6. Single-molecule emulsion PCR in microfluidic droplets.

    Science.gov (United States)

    Zhu, Zhi; Jenkins, Gareth; Zhang, Wenhua; Zhang, Mingxia; Guan, Zhichao; Yang, Chaoyong James

    2012-06-01

    The application of microfluidic droplet PCR for single-molecule amplification and analysis has recently been extensively studied. Microfluidic droplet technology has the advantages of compartmentalizing reactions into discrete volumes, performing highly parallel reactions in monodisperse droplets, reducing cross-contamination between droplets, eliminating PCR bias and nonspecific amplification, as well as enabling fast amplification with rapid thermocycling. Here, we have reviewed the important technical breakthroughs of microfluidic droplet PCR in the past five years and their applications to single-molecule amplification and analysis, such as high-throughput screening, next generation DNA sequencing, and quantitative detection of rare mutations. Although the utilization of microfluidic droplet single-molecule PCR is still in the early stages, its great potential has already been demonstrated and will provide novel solutions to today's biomedical engineering challenges in single-molecule amplification and analysis.

  7. Probing molecular choreography through single-molecule biochemistry.

    Science.gov (United States)

    van Oijen, Antoine M; Dixon, Nicholas E

    2015-12-01

    Single-molecule approaches are having a dramatic impact on views of how proteins work. The ability to observe molecular properties at the single-molecule level allows characterization of subpopulations and acquisition of detailed kinetic information that would otherwise be hidden in the averaging over an ensemble of molecules. In this Perspective, we discuss how such approaches have successfully been applied to in vitro-reconstituted systems of increasing complexity.

  8. Long-wavelength chlorophylls in photosystem I of cyanobacteria: origin, localization, and functions.

    Science.gov (United States)

    Karapetyan, N V; Bolychevtseva, Yu V; Yurina, N P; Terekhova, I V; Shubin, V V; Brecht, M

    2014-03-01

    The structural organization of photosystem I (PSI) complexes in cyanobacteria and the origin of the PSI antenna long-wavelength chlorophylls and their role in energy migration, charge separation, and dissipation of excess absorbed energy are discussed. The PSI complex in cyanobacterial membranes is organized preferentially as a trimer with the core antenna enriched with long-wavelength chlorophylls. The contents of long-wavelength chlorophylls and their spectral characteristics in PSI trimers and monomers are species-specific. Chlorophyll aggregates in PSI antenna are potential candidates for the role of the long-wavelength chlorophylls. The red-most chlorophylls in PSI trimers of the cyanobacteria Arthrospira platensis and Thermosynechococcus elongatus can be formed as a result of interaction of pigments peripherally localized on different monomeric complexes within the PSI trimers. Long-wavelength chlorophylls affect weakly energy equilibration within the heterogeneous PSI antenna, but they significantly delay energy trapping by P700. When the reaction center is open, energy absorbed by long-wavelength chlorophylls migrates to P700 at physiological temperatures, causing its oxidation. When the PSI reaction center is closed, the P700 cation radical or P700 triplet state (depending on the P700 redox state and the PSI acceptor side cofactors) efficiently quench the fluorescence of the long-wavelength chlorophylls of PSI and thus protect the complex against photodestruction.

  9. Uncovering hierarchical data structure in single molecule transport

    Science.gov (United States)

    Wu, Ben H.; Ivie, Jeffrey A.; Johnson, Tyler K.; Monti, Oliver L. A.

    2017-03-01

    Interpretation of single molecule transport data is complicated by the fact that all such data are inherently highly stochastic in nature. Features are often broad, seemingly unstructured and distributed over more than an order of magnitude. However, the distribution contains information necessary for capturing the full variety of processes relevant in nanoscale transport, and a better understanding of its hierarchical structure is needed to gain deeper insight into the physics and chemistry of single molecule electronics. Here, we describe a novel data analysis approach based on hierarchical clustering to aid in the interpretation of single molecule conductance-displacement histograms. The primary purpose of statistically partitioning transport data is to provide avenues for unbiased hypothesis generation in single molecule break junction experiments by revealing otherwise potentially hidden aspects in the conductance data. Our approach is generalizable to the analysis of a wide variety of other single molecule experiments in molecular electronics, as well as in single molecule fluorescence spectroscopy, force microscopy, and ion-channel conductance measurements.

  10. Modulation sensing of fluorophores in tissue: a new approach to drug compliance monitoring

    Science.gov (United States)

    Abugo, Omoefe O.; Gryczynski, Zygmunt; Lakowicz, Joseph R.

    1999-10-01

    We describe a method to detect the presence of fluorophores in scattering media, including intralipid suspensions and chicken muscle covered with skin. The fluorophores were rhodamine 800 (Rb800) and indocyanine green (IcG), both of which can be excited at long wavelengths where there is minimal absorption by tissues. These fluorophores were dissolved in intralipid or in chicken muscle under skin. A method to approximate the fluorophore concentration in such samples was developed using a long lifetime reference fluorophores in a polymer film placed immediately on the illuminated surface of the sample. Because of the long lifetime of the reference film, the modulation of its emission at low frequencies near 2 MHz is near zero. Since the lifetime of Rh800 and IcG are below 2 ns the modulation of the combined emission is a measure of the intensity of the fluorophore (Rh800 or IcG) relative to the long lifetime reference. Using this method we were able to measure the concentration-dependent intensities of Rh800 and IcG in an intralipid suspension. Additionally, micromolar concentrations of these probes could be detected in chicken muscles, even when the muscle was covered with a layer of chicken skin. The presence of an India ink absorber in the intralipid had only a moderate effect on the modulation values. We suggest the use of this transdermal detection of long-wavelength fluorophores as a noninvasive method to monitor patient compliance when taking medicines used for treatment of chronic diseases such as AIDS or tuberculosis.

  11. PREFACE: Nanoelectronics, sensors and single molecule biophysics Nanoelectronics, sensors and single molecule biophysics

    Science.gov (United States)

    Tao, Nongjian

    2012-04-01

    This special section of Journal of Physics: Condensed Matter (JPCM) is dedicated to Professor Stuart M Lindsay on the occasion of his 60th birthday and in recognition of his outstanding contributions to multiple research areas, including light scattering spectroscopy, scanning probe microscopy, biophysics, solid-liquid interfaces and molecular and nanoelectronics. It contains a collection of 14 papers in some of these areas, including a feature article by Lindsay. Each paper was subject to the normal rigorous review process of JPCM. In Lindsay's paper, he discusses the next generations of hybrid chemical-CMOS devices for low cost and personalized medical diagnosis. The discussion leads to several papers on nanotechnology for biomedical applications. Kawaguchi et al report on the detection of single pollen allergen particles using electrode embedded microchannels. Stern et al describe a structural study of three-dimensional DNA-nanoparticle assemblies. Hihath et al measure the conductance of methylated DNA, and discuss the possibility of electrical detection DNA methylation. Portillo et al study the electrostatic effects on the aggregation of prion proteins and peptides with atomic force microscopy. In an effort to understand the interactions between nanostructures and cells, Lamprecht et al report on the mapping of the intracellular distribution of carbon nanotubes with a confocal Raman imaging technique, and Wang et al focus on the intracellular delivery of gold nanoparticles using fluorescence microscopy. Park and Kristic provide theoretical analysis of micro- and nano-traps and their biological applications. This section also features several papers on the fundamentals of electron transport in single atomic wires and molecular junctions. The papers by Xu et al and by Wandlowksi et al describe new methods to measure conductance and forces in single molecule junctions and metallic atomic wires. Scullion et al report on the conductance of molecules with similar

  12. Long-Wavelength 256 x 256 QWIP Hand-Held Camera

    Science.gov (United States)

    Gunapala, S. D.; Liu, J. K.; Sundaram, M.; Bandara, S. V.; Shott, C. A.; Hoelter, T.; Maker, P. D.; Muller, R. E.

    1996-01-01

    In this paper, we discuss the development of very sensitive long wavelength infrared (LWIR) GaAs/Al(x)Ga(l-x)As quantum well infrared photodetectors (QWIPs), fabrication of random reflectors for efficient light coupling, and the demonstration of the first hand-held long-wavelength 256 x 256 QWIP focal plane array camera. Excellent imagery, with a noise equivalent differential temperature (NE Delta T) of 25 mK has been achieved.

  13. Quantitative study of single molecule location estimation techniques.

    Science.gov (United States)

    Abraham, Anish V; Ram, Sripad; Chao, Jerry; Ward, E S; Ober, Raimund J

    2009-12-21

    Estimating the location of single molecules from microscopy images is a key step in many quantitative single molecule data analysis techniques. Different algorithms have been advocated for the fitting of single molecule data, particularly the nonlinear least squares and maximum likelihood estimators. Comparisons were carried out to assess the performance of these two algorithms in different scenarios. Our results show that both estimators, on average, are able to recover the true location of the single molecule in all scenarios we examined. However, in the absence of modeling inaccuracies and low noise levels, the maximum likelihood estimator is more accurate than the nonlinear least squares estimator, as measured by the standard deviations of its estimates, and attains the best possible accuracy achievable for the sets of imaging and experimental conditions that were tested. Although neither algorithm is consistently superior to the other in the presence of modeling inaccuracies or misspecifications, the maximum likelihood algorithm emerges as a robust estimator producing results with consistent accuracy across various model mismatches and misspecifications. At high noise levels, relative to the signal from the point source, neither algorithm has a clear accuracy advantage over the other. Comparisons were also carried out for two localization accuracy measures derived previously. Software packages with user-friendly graphical interfaces developed for single molecule location estimation (EstimationTool) and limit of the localization accuracy calculations (FandPLimitTool) are also discussed.

  14. Single-molecule manipulation experiments to explore friction and adhesion

    Science.gov (United States)

    Pawlak, R.; Kawai, S.; Meier, T.; Glatzel, T.; Baratoff, A.; Meyer, E.

    2017-03-01

    Friction forces, which arise when two bodies that are in contact are moved with respect to one another, are ubiquitous phenomena. Although various measurement tools have been developed to study these phenomena at all length scales, such investigations are highly challenging when tackling the scale of single molecules in motion on a surface. This work reviews the recent advances in single-molecule manipulation experiments performed at low temperature with the aim of understanding the fundamental frictional response of single molecules. Following the advent of ‘nanotribology’ in the field based on the atomic force microscopy technique, we will show the technical requirements to direct those studies at the single-molecule level. We will also discuss the experimental prerequisites needed to obtain and interpret the phenomena, such as the implementation of single-molecule manipulation techniques, the processing of the experimental data or their comparison with appropriate numerical models. Finally, we will report examples of the controlled vertical and lateral manipulation of long polymeric chains, graphene nanoribbons or single porphyrin molecules that systematically reveal friction-like characteristics while sliding over atomically clean surfaces.

  15. Single-molecule mechanochemical sensing using DNA origami nanostructures.

    Science.gov (United States)

    Koirala, Deepak; Shrestha, Prakash; Emura, Tomoko; Hidaka, Kumi; Mandal, Shankar; Endo, Masayuki; Sugiyama, Hiroshi; Mao, Hanbin

    2014-07-28

    While single-molecule sensing offers the ultimate detection limit, its throughput is often restricted as sensing events are carried out one at a time in most cases. 2D and 3D DNA origami nanostructures are used as expanded single-molecule platforms in a new mechanochemical sensing strategy. As a proof of concept, six sensing probes are incorporated in a 7-tile DNA origami nanoassembly, wherein binding of a target molecule to any of these probes leads to mechanochemical rearrangement of the origami nanostructure, which is monitored in real time by optical tweezers. Using these platforms, 10 pM platelet-derived growth factor (PDGF) are detected within 10 minutes, while demonstrating multiplex sensing of the PDGF and a target DNA in the same solution. By tapping into the rapid development of versatile DNA origami nanostructures, this mechanochemical platform is anticipated to offer a long sought solution for single-molecule sensing with improved throughput.

  16. 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.

  17. Probing the Conformations of Single Molecule via Photon Counting Statistics

    CERN Document Server

    Peng, Yonggang; Yang, Chuanlu; Zheng, Yujun

    2014-01-01

    We suggest an approach to detect the conformation of single molecule by using the photon counting statistics. The generalized Smoluchoswki equation is employed to describe the dynamical process of conformational change of single molecule. The resonant trajectories of the emission photon numbers $$ and the Mandel's $Q$ parameter, in the space of conformational coordinates $\\bm{\\mathcal{X}}$ and frequency $\\omega_L$ of external field ($\\bm{\\mathcal{X}}-\\omega_L$ space), can be used to rebuild the conformation of the single molecule. As an example, we consider Thioflavin T molecule. It demonstrates that the results of conformations extracted by employing the photon counting statistics is excellent agreement with the results of {\\it ab initio} computation.

  18. Single molecule detection using charge-coupled device array technology

    Energy Technology Data Exchange (ETDEWEB)

    Denton, M.B.

    1992-07-29

    A technique for the detection of single fluorescent chromophores in a flowing stream is under development. This capability is an integral facet of a rapid DNA sequencing scheme currently being developed by Los Alamos National Laboratory. In previous investigations, the detection sensitivity was limited by the background Raman emission from the water solvent. A detection scheme based on a novel mode of operating a Charge-Coupled Device (CCD) is being developed which should greatly enhance the discrimination between fluorescence from a single molecule and the background Raman scattering from the solvent. Register shifts between rows in the CCD are synchronized with the sample flow velocity so that fluorescence from a single molecule is collected in a single moving charge packet occupying an area approaching that of a single pixel while the background is spread evenly among a large number of pixels. Feasibility calculations indicate that single molecule detection should be achieved with an excellent signal-to-noise ratio.

  19. Extending single-molecule microscopy using optical Fourier processing.

    Science.gov (United States)

    Backer, Adam S; Moerner, W E

    2014-07-17

    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.

  20. Single Molecule Spectroscopy of Monomeric LHCII: Experiment and Theory

    CERN Document Server

    Malý, Pavel; van Grondelle, Rienk; Mančal, Tomáš

    2015-01-01

    We derive approximate equations of motion for excited state dynamics of a multilevel open quantum system weakly interacting with light to describe fluorescence detected single molecule spectra. Based on the Frenkel exciton theory, we construct a model for the chlorophyll part of the LHCII complex of higher plants and its interaction with previously proposed excitation quencher in the form of the lutein molecule Lut 1. The resulting description is valid over a broad range of timescales relevant for single molecule spectroscopy, i.e. from ps to minutes. Validity of these equations is demonstrated by comparing simulations of ensemble and single-molecule spectra of monomeric LHCII with experiments. Using a conformational change of the LHCII protein as a switching mechanism, the intensity and spectral time traces of individual LHCII complexes are simulated, and the experimental statistical distributions are reproduced. Based on our model, it is shown that with reasonable assumptions about its interaction with chlo...

  1. 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

  2. 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.

  3. 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.

  4. Single-molecule detection in electrochemical nanogap devices

    NARCIS (Netherlands)

    Kang, Shuo

    2014-01-01

    This thesis presents results obtained during a research project aimed at realizing electrochemical single-molecule detection in water. By virtue of being inherently electrical in nature, electrochemical sensors are particularly well suited for integration with microelectronics compared to sensors ba

  5. 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...

  6. Single-molecule choreography between telomere proteins and G quadruplexes.

    Science.gov (United States)

    Hopfner, Karl-Peter

    2014-06-10

    Telomeric DNA binds proteins to protect chromosome ends, but it also adopts G quadruplex (GQ) structures. Two new studies by Hwang and colleagues (in this issue of Structure) and Ray and colleagues (published elsewhere) use single molecule imaging to reveal how GQs affect the binding of different telomere associated proteins. The data suggest that GQs play important roles in regulating accessibility of telomeres.

  7. Visualizing DNA Replication at the Single-Molecule Level

    NARCIS (Netherlands)

    Tanner, Nathan A.

    2010-01-01

    Recent advances in single-molecule methodology have made it possible to study the dynamic behavior of individual enzymes and their interactions with other proteins in multiprotein complexes. Here, we describe newly developed methods to study the coordination of DNA unwinding, priming, and synthesis

  8. VISUALIZING DNA REPLICATION AT THE SINGLE-MOLECULE LEVEL

    NARCIS (Netherlands)

    Tanner, Nathan A.; van Oijen, Antoine M.; Walter, NG

    2010-01-01

    Recent advances in single-molecule methodology have made it possible to study the dynamic behavior of individual enzymes and their interactions with other proteins in multiprotein complexes. Here, we describe newly developed methods to study the coordination of DNA unwinding, priming, and synthesis

  9. 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

  10. Alternating-laser excitation : single-molecule FRET and beyond

    NARCIS (Netherlands)

    Hohlbein, Johannes; Craggs, Timothy D.; Cordes, Thorben

    2014-01-01

    The alternating-laser excitation (ALEX) scheme continues to expand the possibilities of fluorescence-based assays to study biological entities and interactions. Especially the combination of ALEX and single-molecule Forster Resonance Energy Transfer (smFRET) has been very successful as ALEX enables

  11. Photoemission of Mn6Cr single-molecule magnets

    Science.gov (United States)

    Heinzmann, U.; Merschjohann, F.; Helmstedt, A.; Gryzia, A.; Winter, A.; Steppeler, S.; Müller, N.; Brechling, A.; Sacher, M.; Richthofen, C.-G. Freiherr v.; Glaser, T.; Voss, S.; Fonin, M.; Rüdiger, U.

    2009-11-01

    We present the status of new experimental studies of X-ray absorption spectroscopy, magnetic circular dichroism in photoemission and spin-resolved photoelectron spectroscopy of Mn6Cr single-molecule magnet systems by use of circularly-polarized synchrotron radiation of the electron storage rings in Maxlab Lund, Sweden und BESSY, Berlin, Germany.

  12. 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 ...

  13. Large negative differential conductance in single-molecule break junctions

    NARCIS (Netherlands)

    Perrin, Mickael L.; Frisenda, Riccardo; Koole, Max; Seldenthuis, Johannes S.; Gil, Jose A. Celis; Valkenier, Hennie; Hummelen, Jan C.; Renaud, Nicolas; Grozema, Ferdinand C.; Thijssen, Joseph M.; Dulic, Diana; van der Zant, Herre S. J.

    2014-01-01

    Molecular electronics aims at exploiting the internal structure and electronic orbitals of molecules to construct functional building blocks(1). To date, however, the overwhelming majority of experimentally realized single-molecule junctions can be described as single quantum dots, where transport i

  14. Single Molecule Study of Cellulase Hydrolysis of Crystalline Cellulose

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Y.-S.; Luo, Y.; Baker, J. O.; Zeng, Y.; Himmel, M. E.; Smith, S.; Ding, S.-Y.

    2009-12-01

    This report seeks to elucidate the role of cellobiohydrolase-I (CBH I) in the hydrolysis of crystalline cellulose. A single-molecule approach uses various imaging techniques to investigate the surface structure of crystalline cellulose and changes made in the structure by CBH I.

  15. 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 g

  16. VISUALIZING DNA REPLICATION AT THE SINGLE-MOLECULE LEVEL

    NARCIS (Netherlands)

    Tanner, Nathan A.; van Oijen, Antoine M.; Walter, NG

    2010-01-01

    Recent advances in single-molecule methodology have made it possible to study the dynamic behavior of individual enzymes and their interactions with other proteins in multiprotein complexes. Here, we describe newly developed methods to study the coordination of DNA unwinding, priming, and synthesis

  17. Visualizing DNA Replication at the Single-Molecule Level

    NARCIS (Netherlands)

    Tanner, Nathan A.

    2010-01-01

    Recent advances in single-molecule methodology have made it possible to study the dynamic behavior of individual enzymes and their interactions with other proteins in multiprotein complexes. Here, we describe newly developed methods to study the coordination of DNA unwinding, priming, and synthesis

  18. 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.

  19. Time-Varying Triplet State Lifetimes of Single Molecules

    NARCIS (Netherlands)

    Veerman, J.A.; Garcia-Parajo, M.F.; Kuipers, L.; Hulst, van N.F.

    1999-01-01

    It is found that triplet state lifetimes and intersystem crossing yields of individual molecules embedded in a polymer host at room temperature are not constant in time. The range over which the triplet lifetime of a single molecule varies during long observation times shows a strong similarity with

  20. Assembling a single-molecule view on nucleosome dynamics

    NARCIS (Netherlands)

    Vlijm, R.

    2014-01-01

    The main focus of this thesis is a better understanding of the basic compaction mechanism of our DNA using multiple single-molecule techniques. The stretched-out length of our DNA is enormous compared with the dimensions of a cell. To make DNA fit within a cell it is systematically wrapped around pr

  1. Large negative differential conductance in single-molecule break junctions

    NARCIS (Netherlands)

    Perrin, Mickael L.; Frisenda, Riccardo; Koole, Max; Seldenthuis, Johannes S.; Gil, Jose A. Celis; Valkenier, Hennie; Hummelen, Jan C.; Renaud, Nicolas; Grozema, Ferdinand C.; Thijssen, Joseph M.; Dulic, Diana; van der Zant, Herre S. J.

    2014-01-01

    Molecular electronics aims at exploiting the internal structure and electronic orbitals of molecules to construct functional building blocks(1). To date, however, the overwhelming majority of experimentally realized single-molecule junctions can be described as single quantum dots, where transport i

  2. An RNA toolbox for single-molecule force spectroscopy studies

    NARCIS (Netherlands)

    Vilfan, I.D.; Kamping, W.; Van den Hout, M.; Candelli, A.; Hage, S.; Dekker, N.H.

    2007-01-01

    Precise, controllable single-molecule force spectroscopy studies of RNA and RNA-dependent processes have recently shed new light on the dynamics and pathways of RNA folding and RNAenzyme interactions. A crucial component of this research is the design and assembly of an appropriate RNA construct. Su

  3. The optics inside an automated single molecule array analyzer

    Science.gov (United States)

    McGuigan, William; Fournier, David R.; Watson, Gary W.; Walling, Les; Gigante, Bill; Duffy, David C.; Rissin, David M.; Kan, Cheuk W.; Meyer, Raymond E.; Piech, Tomasz; Fishburn, Matthew W.

    2014-02-01

    Quanterix and Stratec Biomedical have developed an instrument that enables the automated measurement of multiple proteins at concentration ~1000 times lower than existing immunoassays. The instrument is based on Quanterix's proprietary Single Molecule Array technology (Simoa™ ) that facilitates the detection and quantification of biomarkers previously difficult to measure, thus opening up new applications in life science research and in-vitro diagnostics. Simoa is based on trapping individual beads in arrays of femtoliter-sized wells that, when imaged with sufficient resolution, allows for counting of single molecules associated with each bead. When used to capture and detect proteins, this approach is known as digital ELISA (Enzyme-linked immunosorbent assay). The platform developed is a merger of many science and engineering disciplines. This paper concentrates on the optical technologies that have enabled the development of a fully-automated single molecule analyzer. At the core of the system is a custom, wide field-of-view, fluorescence microscope that images arrays of microwells containing single molecules bound to magnetic beads. A consumable disc containing 24 microstructure arrays was developed previously in collaboration with Sony DADC. The system cadence requirements, array dimensions, and requirement to detect single molecules presented significant optical challenges. Specifically, the wide field-of-view needed to image the entire array resulted in the need for a custom objective lens. Additionally, cost considerations for the system required a custom solution that leveraged the image processing capabilities. This paper will discuss the design considerations and resultant optical architecture that has enabled the development of an automated digital ELISA platform.

  4. The long wavelength emission of interstellar PAHs: characterizing the spinning dust emission

    CERN Document Server

    Ysard, Nathalie

    2009-01-01

    The emission of cold dust grains at long wavelengths will soon be observed by the Planck and Herschel satellites and provide new constraints on the nature of interstellar dust. The microwave anomalous emission, proposed to be due to spinning PAHs, should help to better define these species. Moreover, understanding the fluctuations of the anomalous emission over the sky is crucial for CMB studies. We focus on the long wavelength emission of interstellar PAHs in their rovibrational and rotational transitions. The PAH emission spectrum from the IR to the microwave range is presented and compared to anomalous emission observations. To model their long wavelength emission, we treat PAHs as isolated systems and follow consistently their IR and rotational emissions. We consider several interstellar phases and discuss how the anomalous emission may constrain their size distribution. Our model of PAH emission accounts for the mid-IR spectra of the diffuse interstellar medium and of the Orion Bar. For lambda<3mm the...

  5. Temperature reduction of solar cells in a concentrator photovoltaic system using a long wavelength cut filter

    Science.gov (United States)

    Ahmad, Nawwar; Ota, Yasuyuki; Nishioka, Kensuke

    2017-03-01

    We propose a Fresnel lens optical concentration system that can reduce the solar cell temperature. For the reduction of the solar cell temperature, we added a long-wavelength cut filter in order to utilize the part of the solar spectrum that is beneficial to a solar cell while reflecting the rest of the long-wavelength spectrum. A thermal simulation was conducted to estimate the actual cell temperature for optical systems with and without the long-wavelength cut filter, and the results showed a decrease of approximately 25.3 °C in the solar cell temperature using the filter. The lifetime of a solar cell can be extended by reducing its temperature, and the results showed an increase of 1.9 × 105 h in the lifetime of the solar cell.

  6. Long-Wavelength Rupturing Instability in Surface-Tension-Driven Benard Convection

    Science.gov (United States)

    Swift, J. B.; Hook, Stephen J. Van; Becerril, Ricardo; McCormick, W. D.; Swinney, H. L.; Schatz, Michael F.

    1999-01-01

    A liquid layer with a free upper surface and heated from below is subject to thermocapillary-induced convective instabilities. We use very thin liquid layers (0.01 cm) to significantly reduce buoyancy effects and simulate Marangoni convection in microgravity. We observe thermocapillary-driven convection in two qualitatively different modes, short-wavelength Benard hexagonal convection cells and a long-wavelength interfacial rupturing mode. We focus on the long-wavelength mode and present experimental observations and theoretical analyses of the long-wavelength instability. Depending on the depths and thermal conductivities of the liquid and the gas above it, the interface can rupture downwards and form a dry spot or rupture upwards and form a high spot. Linear stability theory gives good agreement to the experimental measurements of onset as long as sidewall effects are taken into account. Nonlinear theory correctly predicts the subcritical nature of the bifurcation and the selection between the dry spot and high spots.

  7. Effects of long-wavelength dissipation on beam-driven Langmuir turbulence

    Science.gov (United States)

    Robinson, P. A.; Newman, D. L.; Rubenchik, A. M.

    1992-01-01

    The effects of long-wavelength dissipation on beam-driven Langmuir turbulence are investigated using numerical simulations that include both weak and strong turbulence effects. Strong-turbulence wave collapses occur concurrently with weak-turbulence energy cascades if the long-wavelength damping is sufficiently small relative to the growth rate of the beam-unstable waves. Above a threshold damping level, only the weak-turbulence backscatter cascade is observed, and it becomes increasingly truncated as the damping increases, eventually consisting of only a single backscatter. A simple Lotka-Volterra model gives an excellent description of the periodic evolution observed in the weak-turbulence regime. Suppression of the usual backscatter cascade by long-wavelength damping enables intense beam-aligned density troughs to form, which trap and duct Langmuir waves.

  8. Electronic transport in benzodifuran single-molecule transistors

    Science.gov (United States)

    Xiang, An; Li, Hui; Chen, Songjie; Liu, Shi-Xia; Decurtins, Silvio; Bai, Meilin; Hou, Shimin; Liao, Jianhui

    2015-04-01

    Benzodifuran (BDF) single-molecule transistors have been fabricated in electromigration break junctions for electronic measurements. The inelastic electron tunneling spectrum validates that the BDF molecule is the pathway of charge transport. The gating effect is analyzed in the framework of a single-level tunneling model combined with transition voltage spectroscopy (TVS). The analysis reveals that the highest occupied molecular orbital (HOMO) of the thiol-terminated BDF molecule dominates the charge transport through Au-BDF-Au junctions. Moreover, the energy shift of the HOMO caused by the gate voltage is the main reason for conductance modulation. In contrast, the electronic coupling between the BDF molecule and the gold electrodes, which significantly affects the low-bias junction conductance, is only influenced slightly by the applied gate voltage. These findings will help in the design of future molecular electronic devices.Benzodifuran (BDF) single-molecule transistors have been fabricated in electromigration break junctions for electronic measurements. The inelastic electron tunneling spectrum validates that the BDF molecule is the pathway of charge transport. The gating effect is analyzed in the framework of a single-level tunneling model combined with transition voltage spectroscopy (TVS). The analysis reveals that the highest occupied molecular orbital (HOMO) of the thiol-terminated BDF molecule dominates the charge transport through Au-BDF-Au junctions. Moreover, the energy shift of the HOMO caused by the gate voltage is the main reason for conductance modulation. In contrast, the electronic coupling between the BDF molecule and the gold electrodes, which significantly affects the low-bias junction conductance, is only influenced slightly by the applied gate voltage. These findings will help in the design of future molecular electronic devices. Electronic supplementary information (ESI) available: The fabrication procedure for BDF single-molecule

  9. Single Molecule Junctions: Probing Contact Chemistry and Fundamental Circuit Laws

    Energy Technology Data Exchange (ETDEWEB)

    Hybertsen M. S.

    2013-04-11

    By exploiting selective link chemistry, formation of single molecule junctions with reproducible conductance has become established. Systematic studies reveal the structure-conductance relationships for diverse molecules. I will draw on experiments from my collaborators at Columbia University, atomic-scale calculations and theory to describe progress in two areas. First, I will describe a novel route to form single molecule junctions, based on SnMe3 terminated molecules, in which gold directly bonds to carbon in the molecule backbone resulting in near ideal contact resistance [1]. Second, comparison of the conductance of junctions formed with molecular species containing either one backbone or two backbones in parallel allows demonstration of the role of quantum interference in the conductance superposition law at the molecular scale [2].

  10. Coherent spectroscopy in the single molecule limit (Conference Presentation)

    Science.gov (United States)

    Potma, Eric O.; Crampton, Kevin; Fast, Alex; Alfonso García, Alba; Apkarian, Vartkess A.

    2016-10-01

    Surface enhanced Raman scattering (SERS) is a popular technique for detecting and analyzing molecules at very low concentrations. The sensitivity of SERS is high enough to detect single molecules. It has proven difficult, however, to perform similar measurements in the so-called nonlinear optical regime, a regime in which the molecule is responding to multiple light pulses. Nonetheless, recent experiments indicate that after careful optimization, it is possible to generate signals derived from nonlinear analogs of SERS. Such measurements make it possible to view molecular vibrations in real time, which amounts to the femto- to pico-second range. In this contribution, we discuss in detail under which conditions detectable surface-enhanced coherent Raman signals can be expected, provide experimental evidence of coherent Raman scattering of single molecules, and highlight the unique information that can be attained from such measurements.

  11. Directly measuring single molecule heterogeneity using force spectroscopy

    CERN Document Server

    Hinczewski, Michael; Thirumalai, D

    2016-01-01

    One of the most intriguing results of single molecule experiments on proteins and nucleic acids is the discovery of functional heterogeneity: the observation that complex cellular machines exhibit multiple, biologically active conformations. The structural differences between these conformations may be subtle, but each distinct state can be remarkably long-lived, with random interconversions between states occurring only at macroscopic timescales, fractions of a second or longer. Though we now have proof of functional heterogeneity in a handful of systems---enzymes, motors, adhesion complexes---identifying and measuring it remains a formidable challenge. Here we show that evidence of this phenomenon is more widespread than previously known, encoded in data collected from some of the most well-established single molecule techniques: AFM or optical tweezer pulling experiments. We present a theoretical procedure for analyzing distributions of rupture/unfolding forces recorded at different pulling speeds. This re...

  12. Single molecule insights on conformational selection and induced fit mechanism

    DEFF Research Database (Denmark)

    Hatzakis, Nikos

    2014-01-01

    Biomolecular interactions regulate a plethora of vital cellular processes, including signal transduction, metabolism, catalysis and gene regulation. Regulation is encoded in the molecular properties of the constituent proteins; distinct conformations correspond to different functional outcomes...... of unsynchronized molecules, often masking intrinsic dynamic behavior of proteins and biologically significant transient intermediates. Single molecule measurements are emerging as a powerful tool for characterizing protein function. They offer the direct observation and quantification of the activity, abundance...... and lifetime of multiple states and transient intermediates in the energy landscape, that are typically averaged out in non-synchronized ensemble measurements. Here we survey new insights from single molecule studies that advance our understanding of the molecular mechanisms underlying biomolecular recognition....

  13. Single molecule imaging with longer x-ray laser pulses

    CERN Document Server

    Martin, Andrew V; Caleman, Carl; Quiney, Harry M

    2015-01-01

    In serial femtosecond crystallography, x-ray laser pulses do not need to outrun all radiation damage processes because Bragg diffraction exceeds the damage-induced background scattering for longer pulses ($\\sim$ 50--100 fs). This is due to a "self-gating pulse" effect whereby damage terminates Bragg diffraction prior to the pulse completing its passage through the sample, as if that diffraction were produced by a shorter pulse of equal fluence. We show here that a similar gating effect applies to single molecule diffraction with respect to spatially uncorrelated damage processes like ionization and ion diffusion. The effect is clearly seen in calculations of the diffraction contrast, by calculating the diffraction of average structure separately to the diffraction from statistical fluctuations of the structure due to damage ("damage noise"). Our results suggest that sub-nanometer single molecule imaging with longer pulses, like those produced at currently operating facilities, should not yet be ruled out. The...

  14. Electronic Single Molecule Identification of Carbohydrate Isomers by Recognition Tunneling

    CERN Document Server

    Im, JongOne; Liu, Hao; Zhao, Yanan; Sen, Suman; Biswas, Sudipta; Ashcroft, Brian; Borges, Chad; Wang, Xu; Lindsay, Stuart; Zhang, Peiming

    2016-01-01

    Glycans play a central role as mediators in most biological processes, but their structures are complicated by isomerism. Epimers and anomers, regioisomers, and branched sequences contribute to a structural variability that dwarfs those of nucleic acids and proteins, challenging even the most sophisticated analytical tools, such as NMR and mass spectrometry. Here, we introduce an electron tunneling technique that is label-free and can identify carbohydrates at the single-molecule level, offering significant benefits over existing technology. It is capable of analyzing sub-picomole quantities of sample, counting the number of individual molecules in each subset in a population of coexisting isomers, and is quantitative over more than four orders of magnitude of concentration. It resolves epimers not well separated by ion-mobility and can be implemented on a silicon chip. It also provides a readout mechanism for direct single-molecule sequencing of linear oligosaccharides.

  15. Tetraanionic biphenyl lanthanide complexes as single-molecule magnets.

    Science.gov (United States)

    Huang, Wenliang; Le Roy, Jennifer J; Khan, Saeed I; Ungur, Liviu; Murugesu, Muralee; Diaconescu, Paula L

    2015-03-02

    Inverse sandwich biphenyl complexes [(NN(TBS))Ln]2(μ-biphenyl)[K(solvent)]2 [NN(TBS) = 1,1'-fc(NSi(t)BuMe2)2; Ln = Gd, Dy, Er; solvent = Et2O, toluene; 18-crown-6], containing a quadruply reduced biphenyl ligand, were synthesized and their magnetic properties measured. One of the dysprosium biphenyl complexes was found to exhibit antiferromagnetic coupling and single-molecule-magnet behavior with Ueff of 34 K under zero applied field. The solvent coordinated to potassium affected drastically the nature of the magnetic interaction, with the other dysprosium complex showing ferromagnetic coupling. Ab initio calculations were performed to understand the nature of magnetic coupling between the two lanthanide ions bridged by the anionic arene ligand and the origin of single-molecule-magnet behavior.

  16. Single Molecule Detection in Solution: Methods and Applications

    Science.gov (United States)

    Zander, Christoph; Enderlein, Jorg; Keller, Richard A.

    2002-07-01

    The detection of single molecules opens up new horizons in analytical chemistry, biology and medicine. This discipline, which belongs to the expanding field of nanoscience, has been rapidly emerging over the last ten years. This handbook provides a thorough overview of the field. It begins with basics of single molecule detection in solution, describes methods and devices (fluorescense correlation spectroscopy, surface enhanced Raman scattering, sensors, especially dyes, screening techniques, especially confocal laser scanning microscopy). In the second part, various applications in life sciences and medicine provide the latest research results. This modern handbook is a highly accessible reference for a broad community from advanced researchers, specialists and company professionals in physics, spectroscopy, biotechnology, analytical chemistry, and medicine. Written by leading authorities in the field, it is timely and fills a gap - up to now there exists no handbook concerning this theme.

  17. STM CONTROL OF CHEMICAL REACTIONS: Single-Molecule Synthesis

    Science.gov (United States)

    Hla, Saw-Wai; Rieder, Karl-Heinz

    2003-10-01

    The fascinating advances in single atom/molecule manipulation with a scanning tunneling microscope (STM) tip allow scientists to fabricate atomic-scale structures or to probe chemical and physical properties of matters at an atomic level. Owing to these advances, it has become possible for the basic chemical reaction steps, such as dissociation, diffusion, adsorption, readsorption, and bond-formation processes, to be performed by using the STM tip. Complete sequences of chemical reactions are able to induce at a single-molecule level. New molecules can be constructed from the basic molecular building blocks on a one-molecule-at-a-time basis by using a variety of STM manipulation schemes in a systematic step-by-step manner. These achievements open up entirely new opportunities in nanochemistry and nanochemical technology. In this review, various STM manipulation techniques useful in the single-molecule reaction process are reviewed, and their impact on the future of nanoscience and technology are discussed.

  18. Semisynthetic Nanoreactor for Reversible Single-Molecule Covalent Chemistry

    Science.gov (United States)

    2016-01-01

    Protein engineering has been used to remodel pores for applications in biotechnology. For example, the heptameric α-hemolysin pore (αHL) has been engineered to form a nanoreactor to study covalent chemistry at the single-molecule level. Previous work has been confined largely to the chemistry of cysteine side chains or, in one instance, to an irreversible reaction of an unnatural amino acid side chain bearing a terminal alkyne. Here, we present four different αHL pores obtained by coupling either two or three fragments by native chemical ligation (NCL). The synthetic αHL monomers were folded and incorporated into heptameric pores. The functionality of the pores was validated by hemolysis assays and by single-channel current recording. By using NCL to introduce a ketone amino acid, the nanoreactor approach was extended to an investigation of reversible covalent chemistry on an unnatural side chain at the single-molecule level. PMID:27537396

  19. Incoherent x-ray scattering in single molecule imaging

    CERN Document Server

    Slowik, Jan Malte; Dixit, Gopal; Jurek, Zoltan; Santra, Robin

    2014-01-01

    Imaging of the structure of single proteins or other biomolecules with atomic resolution would be enormously beneficial to structural biology. X-ray free-electron lasers generate highly intense and ultrashort x-ray pulses, providing a route towards imaging of single molecules with atomic resolution. The information on molecular structure is encoded in the coherent x-ray scattering signal. In contrast to crystallography there are no Bragg reflections in single molecule imaging, which means the coherent scattering is not enhanced. Consequently, a background signal from incoherent scattering deteriorates the quality of the coherent scattering signal. This background signal cannot be easily eliminated because the spectrum of incoherently scattered photons cannot be resolved by usual scattering detectors. We present an ab initio study of incoherent x-ray scattering from individual carbon atoms, including the electronic radiation damage caused by a highly intense x-ray pulse. We find that the coherent scattering pa...

  20. Minimizing detection errors in single molecule localization microscopy.

    Science.gov (United States)

    Křížek, Pavel; Raška, Ivan; Hagen, Guy M

    2011-02-14

    Fluorescence microscopy using single molecule imaging and localization (PALM, STORM, and similar approaches) has quickly been adopted as a convenient method for obtaining multicolor, 3D superresolution images of biological samples. Using an approach based on extensive Monte Carlo simulations, we examined the performance of various noise reducing filters required for the detection of candidate molecules. We determined a suitable noise reduction method and derived an optimal, nonlinear threshold which minimizes detection errors introduced by conventional algorithms. We also present a new technique for visualization of single molecule localization microscopy data based on adaptively jittered 2D histograms. We have used our new methods to image both Atto565-phalloidin labeled actin in fibroblast cells, and mCitrine-erbB3 expressed in A431 cells. The enhanced methods developed here were crucial in processing the data we obtained from these samples, as the overall signal to noise ratio was quite low.

  1. Single Molecule DNA Detection with an Atomic Vapor Notch Filter

    CERN Document Server

    Uhland, Denis; Widmann, Matthias; Lee, Sang-Yun; Wrachtrup, Jörg; Gerhardt, Ilja

    2015-01-01

    The detection of single molecules has facilitated many advances in life- and material-sciences. Commonly, it founds on the fluorescence detection of single molecules, which are for example attached to the structures under study. For fluorescence microscopy and sensing the crucial parameters are the collection and detection efficiency, such that photons can be discriminated with low background from a labeled sample. Here we show a scheme for filtering the excitation light in the optical detection of single stranded labeled DNA molecules. We use the narrow-band filtering properties of a hot atomic vapor to filter the excitation light from the emitted fluorescence of a single emitter. The choice of atomic sodium allows for the use of fluorescent dyes, which are common in life-science. This scheme enables efficient photon detection, and a statistical analysis proves an enhancement of the optical signal of more than 15% in a confocal and in a wide-field configuration.

  2. Dysprosium Acetylacetonato Single-Molecule Magnet Encapsulated in Carbon Nanotubes

    Directory of Open Access Journals (Sweden)

    Ryo Nakanishi

    2016-12-01

    Full Text Available Dy single-molecule magnets (SMMs, which have several potential uses in a variety of applications, such as quantum computing, were encapsulated in multi-walled carbon nanotubes (MWCNTs by using a capillary method. Encapsulation was confirmed by using transmission electron microscopy (TEM. In alternating current magnetic measurements, the magnetic susceptibilities of the Dy acetylacetonato complexes showed clear frequency dependence even inside the MWCNTs, meaning that this hybrid can be used as magnetic materials in devices.

  3. Enhancing Single Molecule Imaging in Optofluidics and Microfluidics

    OpenAIRE

    Vasdekis, Andreas E.; Laporte, Gregoire P.J.

    2011-01-01

    Microfluidics and optofluidics have revolutionized high-throughput analysis and chemical synthesis over the past decade. Single molecule imaging has witnessed similar growth, due to its capacity to reveal heterogeneities at high spatial and temporal resolutions. However, both resolution types are dependent on the signal to noise ratio (SNR) of the image. In this paper, we review how the SNR can be enhanced in optofluidics and microfluidics. Starting with optofluidics, we outline integrated ph...

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

    OpenAIRE

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

    2014-01-01

    In contrast with advances in massively parallel DNA sequencing1, high-throughput protein analyses2-4 are often limited by ensemble measurements, individual analyte purification and hence compromised quality and cost-effectiveness. Single-molecule (SM) protein detection achieved using optical methods5 is limited by the number of spectrally nonoverlapping chromophores. Here, we introduce a single molecular interaction-sequencing (SMI-Seq) technology for parallel protein interaction profiling le...

  5. Density Functional Theory with Dissipation: Transport through Single Molecules

    Energy Technology Data Exchange (ETDEWEB)

    Kieron Burke

    2012-04-30

    A huge amount of fundamental research was performed on this grant. Most of it focussed on fundamental issues of electronic structure calculations of transport through single molecules, using density functional theory. Achievements were: (1) First density functional theory with dissipation; (2) Pseudopotential plane wave calculations with master equation; (3) Weak bias limit; (4) Long-chain conductance; and (5) Self-interaction effects in tunneling.

  6. Quantum Chemical Characterization of Single Molecule Magnets Based on Uranium.

    Science.gov (United States)

    Spivak, Mariano; Vogiatzis, Konstantinos D; Cramer, Christopher J; Graaf, Coen de; Gagliardi, Laura

    2017-03-02

    Multiconfigurational electronic structure theory calculations including spin-orbit coupling effects were performed on four uranium-based single-molecule-magnets. Several quartet and doublet states were computed and the energy gaps between spin-orbit states were then used to determine magnetic susceptibility curves. Trends in experimental magnetic susceptibility curves were well reproduced by the calculations, and key factors affecting performance were identified.

  7. Predicting single-molecule conductance through machine learning

    Science.gov (United States)

    Lanzillo, Nicholas A.; Breneman, Curt M.

    2016-10-01

    We present a robust machine learning model that is trained on the experimentally determined electrical conductance values of approximately 120 single-molecule junctions used in scanning tunnelling microscope molecular break junction (STM-MBJ) experiments. Quantum mechanical, chemical, and topological descriptors are used to correlate each molecular structure with a conductance value, and the resulting machine-learning model can predict the corresponding value of conductance with correlation coefficients of r 2 = 0.95 for the training set and r 2 = 0.78 for a blind testing set. While neglecting entirely the effects of the metal contacts, this work demonstrates that single molecule conductance can be qualitatively correlated with a number of molecular descriptors through a suitably trained machine learning model. The dominant features in the machine learning model include those based on the electronic wavefunction, the geometry/topology of the molecule as well as the surface chemistry of the molecule. This model can be used to identify promising molecular structures for use in single-molecule electronic circuits and can guide synthesis and experiments in the future.

  8. Single Molecule Electrochemical Detection in Aqueous Solutions and Ionic Liquids.

    Science.gov (United States)

    Byers, Joshua C; Paulose Nadappuram, Binoy; Perry, David; McKelvey, Kim; Colburn, Alex W; Unwin, Patrick R

    2015-10-20

    Single molecule electrochemical detection (SMED) is an extremely challenging aspect of electroanalytical chemistry, requiring unconventional electrochemical cells and measurements. Here, SMED is reported using a "quad-probe" (four-channel probe) pipet cell, fabricated by depositing carbon pyrolytically into two diagonally opposite barrels of a laser-pulled quartz quadruple-barreled pipet and filling the open channels with electrolyte solution, and quasi-reference counter electrodes. A meniscus forms at the end of the probe covering the two working electrodes and is brought into contact with a substrate working electrode surface. In this way, a nanogap cell is produced whereby the two carbon electrodes in the pipet can be used to promote redox cycling of an individual molecule with the substrate. Anticorrelated currents generated at the substrate and tip electrodes, at particular distances (typically tens of nanometers), are consistent with the detection of single molecules. The low background noise realized in this droplet format opens up new opportunities in single molecule electrochemistry, including the use of ionic liquids, as well as aqueous solution, and the quantitative assessment and analysis of factors influencing redox cycling currents, due to a precisely known gap size.

  9. 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.

  10. The northern European geoid: a case study on long-wavelength geoid errors

    DEFF Research Database (Denmark)

    Omang, O.C.D.; Forsberg, René

    2002-01-01

    The long-wavelength geoid errors on large-scale geoid solutions, and the use of modified kernels to mitigate these effects, are studied. The geoid around the Nordic area, from Greenland to the Ural mountains, is considered. The effect of including additional gravity data around the Nordic/Baltic ...

  11. Power-scalable long-wavelength Yb-doped photonic bandgap fiber sources

    DEFF Research Database (Denmark)

    Olausson, Christina Bjarnal Thulin; Shirakawa, Akira; Maurayama, Hiroki

    2010-01-01

    Ytterbium-doped photonic-bandgap fiber sources operationg at the long-wavelength edge of the ytterbium gain band are being investigated for high power amplification. Artificial shaping of the gain spectrum by the characteristic distributed filtering effect of the photonic bandgap enables...

  12. Long wavelength plasmon damping in the two-dimensional electron gas

    Science.gov (United States)

    Bachlechner, Martina E.; Böhm, Helga M.; Schinner, Andreas

    1993-07-01

    The damping of the long wavelength plasmon in a homogeneos electron layer is determined by two-electron-hole excitations. Analytical and numerical results for the corresponding imaginary part of the dielectric function and the plasmon half width are presented for various densities and different manners of screening.

  13. Solar neutrino problem and gravitationally induced long-wavelength neutrino oscillation

    Science.gov (United States)

    Gago; Nunokawa; Zukanovich Funchal R

    2000-05-01

    We have reexamined the possibility of explaining the solar neutrino data through long-wavelength neutrino oscillations induced by a tiny breakdown of the weak equivalence principle of general relativity. We have found that such gravitationally induced oscillations can provide a viable solution to the solar neutrino problem.

  14. [Influence of wearing long wavelength filter glasses on refractive development of children's hyperopia].

    Science.gov (United States)

    Huang, J; Yu, Z Q; Chu, R Y; Qian, Y S; Xu, Y; Wang, X Q

    2017-01-11

    Objective: To investigate the effect of wearing long wavelength filter glasses on refractive development of children's hyperopia. Methods: Case control study. Seventeen 5-7 years' old children with high hyperopia from optometry clinic of Eye and ENT Hospital Affiliated to Fudan University were enrolled in this research. The experiment design was self-control between right and left eye, 3 children were lost during two years' period of observation, all the children's hyperopic refraction were more than +6.00 D, cycloplegic by 1% atropine. All the children were required to wear long wavelength filter glasses for 6 hours after waking up, the rest of the time with the conventional glasses. Refraction, axis and red/green match point were tested before the intervention and 3, 6, 12, 18, 24 months, after the intervention. Results: After two years' intervention, hyperopia decreased, eye axis increased, the best corrected visual acuity increased both in experimental eyes and control eyes, but there were no statistically significant difference between the two groups at each time point. All children were with normal color vision, compared to the long-wavelength light, the hyperopic eyes were more sensitive to middle-wavelength light, no significant difference was found between two groups, red/green match points were 42.802±1.216 and 42.889±1.560 respectively. After wearing long wavelength filter, red/green match point were significant decreased in the experimental group in 6 months and 12 months time points (6 months: 0.995±0. 543 vs. 0.104±0.143, t=3.04, P=0.005, 12 months: 1.096±0.392 vs. 0.17±0.248, t=2.725, P=0.008). The experiment eyes were more sensitive to long-wavelength light than the control eyes. But in later time, there was no significant difference between two groups. Conclusion: Wearing long wavelength filter glasses two years has no effect on refractive development on children with high hyperopia, but it can cause short-term chromatic adaptation, making

  15. Single-Molecule Approaches for the Characterization of Riboswitch Folding Mechanisms.

    Science.gov (United States)

    Boudreault, Julien; Perez-Gonzalez, D Cibran; Penedo, J Carlos; Lafontaine, Daniel A

    2015-01-01

    Riboswitches are highly structured RNA molecules that control genetic expression by altering their structure as a function of metabolite binding. Accumulating evidence suggests that riboswitch structures are highly dynamic and perform conformational exchange between structural states that are important for the outcome of genetic regulation. To understand how ligand binding influences the folding of riboswitches, it is important to monitor in real time the riboswitch folding pathway as a function of experimental conditions. Single-molecule FRET (sm-FRET) is unique among biophysical techniques to study riboswitch conformational changes as it allows to both monitor steady-state populations of riboswitch conformers and associated interconversion dynamics. Since FRET fluorophores can be attached to virtually any nucleotide position, FRET assays can be adapted to monitor specific conformational changes, thus enabling to deduce complex riboswitch folding pathways. Herein, we show how to employ sm-FRET to study the folding pathway of the S-adenosylmethionine (SAM) and how this can be used to understand very specific conformational changes that are at the heart of riboswitch regulation mechanism.

  16. 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.

  17. Integrating Optical Tweezers, DNA Tightropes, and Single-Molecule Fluorescence Imaging: Pitfalls and Traps.

    Science.gov (United States)

    Wang, J; Barnett, J T; Pollard, M R; Kad, N M

    2017-01-01

    Fluorescence imaging is one of the cornerstone techniques for understanding how single molecules search for their targets on DNA. By tagging individual proteins, it is possible to track their position with high accuracy. However, to understand how proteins search for targets, it is necessary to elongate the DNA to avoid protein localization ambiguities. Such structures known as "DNA tightropes" are tremendously powerful for imaging target location; however, they lack information about how force and load affect protein behavior. The use of optically trapped microstructures offers the means to apply and measure force effects. Here we describe a system that we recently developed to enable individual proteins to be directly manipulated on DNA tightropes. Proteins bound to DNA can be conjugated with Qdot fluorophores for visualization and also directly manipulated by an optically trapped, manufactured microstructure. Together this offers a new approach to understanding the physical environment of molecules, and the combination with DNA tightropes presents opportunities to study complex biological phenomena. © 2017 Elsevier Inc. All rights reserved.

  18. An Efficient Site-Specific Method for Irreversible Covalent Labeling of Proteins with a Fluorophore.

    Science.gov (United States)

    Liu, Jiaquan; Hanne, Jeungphill; Britton, Brooke M; Shoffner, Matthew; Albers, Aaron E; Bennett, Jared; Zatezalo, Rachel; Barfield, Robyn; Rabuka, David; Lee, Jong-Bong; Fishel, Richard

    2015-11-19

    Fluorophore labeling of proteins while preserving native functions is essential for bulk Förster resonance energy transfer (FRET) interaction and single molecule imaging analysis. Here we describe a versatile, efficient, specific, irreversible, gentle and low-cost method for labeling proteins with fluorophores that appears substantially more robust than a similar but chemically distinct procedure. The method employs the controlled enzymatic conversion of a central Cys to a reactive formylglycine (fGly) aldehyde within a six amino acid Formylglycine Generating Enzyme (FGE) recognition sequence in vitro. The fluorophore is then irreversibly linked to the fGly residue using a Hydrazinyl-Iso-Pictet-Spengler (HIPS) ligation reaction. We demonstrate the robust large-scale fluorophore labeling and purification of E.coli (Ec) mismatch repair (MMR) components. Fluorophore labeling did not alter the native functions of these MMR proteins in vitro or in singulo. Because the FGE recognition sequence is easily portable, FGE-HIPS fluorophore-labeling may be easily extended to other proteins.

  19. Optical Methods to Study Protein-DNA Interactions in Vitro and in Living Cells at the Single-Molecule Level

    Directory of Open Access Journals (Sweden)

    Gionata Belcastro

    2013-02-01

    Full Text Available The maintenance of intact genetic information, as well as the deployment of transcription for specific sets of genes, critically rely on a family of proteins interacting with DNA and recognizing specific sequences or features. The mechanisms by which these proteins search for target DNA are the subject of intense investigations employing a variety of methods in biology. A large interest in these processes stems from the faster-than-diffusion association rates, explained in current models by a combination of 3D and 1D diffusion. Here, we present a review of the single-molecule approaches at the forefront of the study of protein-DNA interaction dynamics and target search in vitro and in vivo. Flow stretch, optical and magnetic manipulation, single fluorophore detection and localization as well as combinations of different methods are described and the results obtained with these techniques are discussed in the framework of the current facilitated diffusion model.

  20. 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

  1. Single molecule energetics of F1-ATPase motor.

    Science.gov (United States)

    Muneyuki, Eiro; Watanabe-Nakayama, Takahiro; Suzuki, Tetsuya; Yoshida, Masasuke; Nishizaka, Takayuki; Noji, Hiroyuki

    2007-03-01

    Motor proteins are essential in life processes because they convert the free energy of ATP hydrolysis to mechanical work. However, the fundamental question on how they work when different amounts of free energy are released after ATP hydrolysis remains unanswered. To answer this question, it is essential to clarify how the stepping motion of a motor protein reflects the concentrations of ATP, ADP, and P(i) in its individual actions at a single molecule level. The F(1) portion of ATP synthase, also called F(1)-ATPase, is a rotary molecular motor in which the central gamma-subunit rotates against the alpha(3)beta(3) cylinder. The motor exhibits clear step motion at low ATP concentrations. The rotary action of this motor is processive and generates a high torque. These features are ideal for exploring the relationship between free energy input and mechanical work output, but there is a serious problem in that this motor is severely inhibited by ADP. In this study, we overcame this problem of ADP inhibition by introducing several mutations while retaining high enzymatic activity. Using a probe of attached beads, stepping rotation against viscous load was examined at a wide range of free energy values by changing the ADP concentration. The results showed that the apparent work of each individual step motion was not affected by the free energy of ATP hydrolysis, but the frequency of each individual step motion depended on the free energy. This is the first study that examined the stepping motion of a molecular motor at a single molecule level with simultaneous systematic control of DeltaG(ATP). The results imply that microscopically defined work at a single molecule level cannot be directly compared with macroscopically defined free energy input.

  2. 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.

  3. Electronic Single Molecule Measurements with the Scanning Tunneling Microscope

    Science.gov (United States)

    Im, Jong One

    Richard Feynman said "There's plenty of room at the bottom". This inspired the techniques to improve the single molecule measurements. Since the first single molecule study was in 1961, it has been developed in various field and evolved into powerful tools to understand chemical and biological property of molecules. This thesis demonstrates electronic single molecule measurement with Scanning Tunneling Microscopy (STM) and two of applications of STM; Break Junction (BJ) and Recognition Tunneling (RT). First, the two series of carotenoid molecules with four different substituents were investigated to show how substituents relate to the conductance and molecular structure. The measured conductance by STM-BJ shows that Nitrogen induces molecular twist of phenyl distal substituents and conductivity increasing rather than Carbon. Also, the conductivity is adjustable by replacing the sort of residues at phenyl substituents. Next, amino acids and peptides were identified through STM-RT. The distribution of the intuitive features (such as amplitude or width) are mostly overlapped and gives only a little bit higher separation probability than random separation. By generating some features in frequency and cepstrum domain, the classification accuracy was dramatically increased. Because of large data size and many features, supporting vector machine (machine learning algorithm for big data) was used to identify the analyte from a data pool of all analytes RT data. The STM-RT opens a possibility of molecular sequencing in single molecule level. Similarly, carbohydrates were studied by STM-RT. Carbohydrates are difficult to read the sequence, due to their huge number of possible isomeric configurations. This study shows that STM-RT can identify not only isomers of mono-saccharides and disaccharides, but also various mono-saccharides from a data pool of eleven analytes. In addition, the binding affinity between recognition molecule and analyte was investigated by comparing with

  4. Single molecule studies of RNA polymerase II transcription in vitro.

    Science.gov (United States)

    Horn, Abigail E; Goodrich, James A; Kugel, Jennifer F

    2014-01-01

    Eukaryotic mRNA transcription by RNA polymerase II (RNAP II) is the first step in gene expression and a key determinant of cellular regulation. Elucidating the mechanism by which RNAP II synthesizes RNA is therefore vital to determining how genes are controlled under diverse biological conditions. Significant advances in understanding RNAP II transcription have been achieved using classical biochemical and structural techniques; however, aspects of the transcription mechanism cannot be assessed using these approaches. The application of single-molecule techniques to study RNAP II transcription has provided new insight only obtainable by studying molecules in this complex system one at a time.

  5. 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....

  6. Theoretical investigation on single-molecule chiroptical spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Wakabayashi, M. [Tokyo Institute of Technology, School and Graduate School of Bioscience and Biotechnology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa (Japan); Yokojima, S. [Tokyo University of Pharmacy and Life Sciences, 1423-1 Horinouchi, Hachiouji-shi, Tokyo (Japan); Fukaminato, T. [Research Institute for Electronic Science, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020 (Japan); Ogata, K.; Nakamura, S. [Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan)

    2013-12-10

    Some experimental results of chiroptical response of single molecule have already reported. In those experiments, dissymmetry parameter, g was used as an indicator of the relative circular dichroism intensity. The parameter for individual molecules was measured. For the purpose of giving an interpretation or explanation to the experimental result, the dissymmetry parameter is formulated on the basis of Fermi’s golden rule. Subsequently, the value of individual molecules is evaluated as a function of the direction of light propagation to the orientationary fixed molecules. The ground and excited wavefunction of electrons in the molecule and transition moments needed are culculated using the density functional theory.

  7. Hybrid photodetector for single-molecule spectroscopy and microscopy.

    Science.gov (United States)

    Michalet, X; Cheng, Adrian; Antelman, Joshua; Suyama, Motohiro; Arisaka, Katsushi; Weiss, Shimon

    2008-02-15

    We report benchmark tests of a new single-photon counting detector based on a GaAsP photocathode and an electron-bombarded avalanche photodiode developed by Hamamatsu Photonics. We compare its performance with those of standard Geiger-mode avalanche photodiodes. We show its advantages for FCS due to the absence of after-pulsing and for fluorescence lifetime measurements due to its excellent time resolution. Its large sensitive area also greatly simplifies setup alignment. Its spectral sensitivity being similar to that of recently introduced CMOS SPADs, this new detector could become a valuable tool for single-molecule fluorescence measurements, as well as for many other applications.

  8. Single Molecule Studies on Dynamics in Liquid Crystals

    Directory of Open Access Journals (Sweden)

    Daniela Täuber

    2013-09-01

    Full Text Available Single molecule (SM methods are able to resolve structure related dynamics of guest molecules in liquid crystals (LC. Highly diluted small dye molecules on the one hand explore structure formation and LC dynamics, on the other hand they report about a distortion caused by the guest molecules. The anisotropic structure of LC materials is used to retrieve specific conformation related properties of larger guest molecules like conjugated polymers. This in particular sheds light on organization mechanisms within biological cells, where large molecules are found in nematic LC surroundings. This review gives a short overview related to the application of highly sensitive SM detection schemes in LC.

  9. 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......Enkephalin, an endogeneous substance in the human brain showing morphine-like biological functions, has been detected at the single molecule level based on the surface-enhanced Raman signal of the ring breathing mode of phenylalanine, which is one building block of the molecule. For enhancing...

  10. 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....... Consequently, the technique is sensitive to sequence variation without requiring enzymatic labeling or a restriction step. This technique may serve as the basis for a new mapping technology ideally suited for investigating the long-range structure of entire genomes extracted from single cells....

  11. Long-wavelength limit of gyrokinetics in a turbulent tokamak and its intrinsic ambipolarity

    CERN Document Server

    Calvo, Ivan

    2012-01-01

    Recently, the electrostatic gyrokinetic Hamiltonian and change of coordinates have been computed to order $\\epsilon^2$ in general magnetic geometry. Here $\\epsilon$ is the gyrokinetic expansion parameter, the gyroradius over the macroscopic scale length. Starting from these results, the long-wavelength limit of the gyrokinetic Fokker-Planck and quasineutrality equations is taken for tokamak geometry. Employing the set of equations derived in the present article, it is possible to calculate the long-wavelength components of the distribution functions and of the poloidal electric field to order $\\epsilon^2$. These higher-order pieces contain both neoclassical and turbulent contributions, and constitute one of the necessary ingredients (the other is given by the short-wavelength components up to second order) that will eventually enter a complete model for the radial transport of toroidal angular momentum in a tokamak in the low flow ordering. Finally, we provide an explicit and detailed proof that the system co...

  12. Long wavelength unstable modes in the far upstream of relativistic collisionless shocks

    CERN Document Server

    Rabinak, Itay; Waxman, Eli

    2010-01-01

    The growth rate of long wavelength kinetic instabilities arising due to the interaction of a collimated beam of relativistic particles and a cold unmagnetized plasma are calculated in the ultra relativistic limit. For sufficiently culminated beams, all long wave-length modes are shown to be Weibel-unstable, and a simple analytic expression for their growth rate is derived. For large transverse velocity spreads, these modes become stable. An analytic condition for stability is given. These analytic results, which generalize earlier ones given in the literature, are shown to be in agreement with numerical solutions of the dispersion equation and with the results of novel PIC simulations in which the electro-magnetic fields are restricted to a given k-mode. The results may describe the interaction of energetic cosmic rays, propagating into the far upstream of a relativistic collisionless shock, with a cold unmagnetized upstream. The long wavelength modes considered may be efficient in deflecting particles and co...

  13. Support of long-wavelength topography on Mercury inferred from MESSENGER measurements of gravity and topography

    Science.gov (United States)

    James, Peter B.; Zuber, Maria T.; Phillips, Roger J.; Solomon, Sean C.

    2015-02-01

    To explore the mechanisms of support of surface topography on Mercury, we have determined the admittances and correlations of topography and gravity in Mercury's northern hemisphere from measurements obtained by NASA's MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft. These admittances and correlations can be interpreted in the context of a number of theoretical scenarios, including flexural loading and dynamic flow. We find that long-wavelength (spherical harmonic degree l shallow crustal compensation and are weakly correlated with positive mass anomalies in the mantle. The center of the Caloris basin features some of the thinnest crust on the planet, and the basin is underlain by a large negative mass anomaly. We also explore models of dynamic flow in the presence of compositional stratification above the liquid core. If there is substantial compositional stratification in Mercury's solid outer shell, relaxation of perturbed compositional interfaces may be capable of creating and sustaining long-wavelength topography.

  14. Dual-Colored DNA Comb Polymers for Single Molecule Rheology

    Science.gov (United States)

    Mai, Danielle; Marciel, Amanda; Schroeder, Charles

    2014-03-01

    We report the synthesis and characterization of branched biopolymers for single molecule rheology. In our work, we utilize a hybrid enzymatic-synthetic approach to graft ``short'' DNA branches to ``long'' DNA backbones, thereby producing macromolecular DNA comb polymers. The branches and backbones are synthesized via polymerase chain reaction with chemically modified deoxyribonucleotides (dNTPs): ``short'' branches consist of Cy5-labeled dNTPs and a terminal azide group, and ``long'' backbones contain dibenzylcyclooctyne-modified (DBCO) dNTPs. In this way, we utilize strain-promoted, copper-free cycloaddition ``click'' reactions for facile grafting of azide-terminated branches at DBCO sites along backbones. Copper-free click reactions are bio-orthogonal and nearly quantitative when carried out under mild conditions. Moreover, comb polymers can be labeled with an intercalating dye (e.g., YOYO) for dual-color fluorescence imaging. We characterized these materials using gel electrophoresis, HPLC, and optical microscopy, with atomic force microscopy in progress. Overall, DNA combs are suitable for single molecule dynamics, and in this way, our work holds the potential to improve our understanding of topologically complex polymer melts and solutions.

  15. Single-molecule enzymology à la Michaelis-Menten.

    Science.gov (United States)

    Grima, Ramon; Walter, Nils G; Schnell, Santiago

    2014-01-01

    Over the past 100 years, deterministic rate equations have been successfully used to infer enzyme-catalysed reaction mechanisms and to estimate rate constants from reaction kinetics experiments conducted in vitro. In recent years, sophisticated experimental techniques have been developed that begin to allow the measurement of enzyme-catalysed and other biopolymer-mediated reactions inside single cells at the single-molecule level. Time-course data obtained using these methods are considerably noisy because molecule numbers within cells are typically quite small. As a consequence, the interpretation and analysis of single-cell data requires stochastic methods, rather than deterministic rate equations. Here, we concisely review both experimental and theoretical techniques that enable single-molecule analysis, with particular emphasis on the major developments in the field of theoretical stochastic enzyme kinetics, from its inception in the mid-20th century to its modern-day status. We discuss the differences between stochastic and deterministic rate equation models, how these depend on enzyme molecule numbers and substrate inflow into the reaction compartment, and how estimation of rate constants from single-cell data is possible using recently developed stochastic approaches. © 2013 FEBS.

  16. From single molecules to life: microscopy at the nanoscale.

    Science.gov (United States)

    Turkowyd, Bartosz; Virant, David; Endesfelder, Ulrike

    2016-10-01

    Super-resolution microscopy is the term commonly given to fluorescence microscopy techniques with resolutions that are not limited by the diffraction of light. Since their conception a little over a decade ago, these techniques have quickly become the method of choice for many biologists studying structures and processes of single cells at the nanoscale. In this review, we present the three main approaches used to tackle the diffraction barrier of ∼200 nm: stimulated-emission depletion (STED) microscopy, structured illumination microscopy (SIM), and single-molecule localization microscopy (SMLM). We first present a theoretical overview of the techniques and underlying physics, followed by a practical guide to all of the facets involved in designing a super-resolution experiment, including an approachable explanation of the photochemistry involved, labeling methods available, and sample preparation procedures. Finally, we highlight some of the most exciting recent applications of and developments in these techniques, and discuss the outlook for this field. Graphical Abstract Super-resolution microscopy techniques. Working principles of the common approaches stimulated-emission depletion (STED) microscopy, structured illumination microscopy (SIM), and single-molecule localization microscopy (SMLM).

  17. 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

    2014-04-24

    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.

  18. Studying the Nucleated Mammalian Cell Membrane by Single Molecule Approaches

    Science.gov (United States)

    Wang, Feng; Wu, Jiazhen; Gao, Jing; Liu, Shuheng; Jiang, Junguang; Jiang, Shibo; Wang, Hongda

    2014-01-01

    The cell membrane plays a key role in compartmentalization, nutrient transportation and signal transduction, while the pattern of protein distribution at both cytoplasmic and ectoplasmic sides of the cell membrane remains elusive. Using a combination of single-molecule techniques, including atomic force microscopy (AFM), single molecule force spectroscopy (SMFS) and stochastic optical reconstruction microscopy (STORM), to study the structure of nucleated cell membranes, we found that (1) proteins at the ectoplasmic side of the cell membrane form a dense protein layer (4 nm) on top of a lipid bilayer; (2) proteins aggregate to form islands evenly dispersed at the cytoplasmic side of the cell membrane with a height of about 10–12 nm; (3) cholesterol-enriched domains exist within the cell membrane; (4) carbohydrates stay in microdomains at the ectoplasmic side; and (5) exposed amino groups are asymmetrically distributed on both sides. Based on these observations, we proposed a Protein Layer-Lipid-Protein Island (PLLPI) model, to provide a better understanding of cell membrane structure, membrane trafficking and viral fusion mechanisms. PMID:24806512

  19. High contrast single molecule tracking in the pericellular coat

    Science.gov (United States)

    Scrimgeour, Jan; McLane, Louis T.; Curtis, Jennifer E.

    2014-03-01

    The pericellular coat is a robust, hydrated, polymer brush-like structure that can extend several micrometers into the extracellular space around living cells. By controlling access to the cell surface, acting as a filter and storage reservoir for proteins, and actively controlling tissue-immune system interactions, the cell coat performs many important functions at scales ranging from the single cell to whole tissues. The cell coat consists of a malleable backbone - the large polysaccharide hyaluronic acid (HA) - with its structure, material properties, and ultimately its bio-functionality tuned by a diverse set of HA binding proteins. These proteins add charge, cross-links and growth factor-like ligands to the coat To probe the dynamic behavior of this soft biomaterial we have used high contrast single molecule imaging, based on highly inclined laser illumination, to observe individual fluorescently labeled HA binding proteins within the cell coat. Our work focuses on the cell coat of living chondrocyte (cartilage) cells, and in particular the effect of the large, highly charged, protein aggrecan on the properties of the coat. Through single molecule imaging we observe that aggrecan is tightly tethered to HA, and plays an important role in cell coat extension and stiffening.

  20. Single molecule study of a processivity clamp sliding on DNA

    Energy Technology Data Exchange (ETDEWEB)

    Laurence, T A; Kwon, Y; Johnson, A; Hollars, C; O?Donnell, M; Camarero, J A; Barsky, D

    2007-07-05

    Using solution based single molecule spectroscopy, we study the motion of the polIII {beta}-subunit DNA sliding clamp ('{beta}-clamp') on DNA. Present in all cellular (and some viral) forms of life, DNA sliding clamps attach to polymerases and allow rapid, processive replication of DNA. In the absence of other proteins, the DNA sliding clamps are thought to 'freely slide' along the DNA; however, the abundance of positively charged residues along the inner surface may create favorable electrostatic contact with the highly negatively charged DNA. We have performed single-molecule measurements on a fluorescently labeled {beta}-clamp loaded onto freely diffusing plasmids annealed with fluorescently labeled primers of up to 90 bases. We find that the diffusion constant for 1D diffusion of the {beta}-clamp on DNA satisfies D {le} 10{sup -14} cm{sup 2}/s, much slower than the frictionless limit of D = 10{sup -10} cm{sup 2}/s. We find that the {beta} clamp remains at the 3-foot end in the presence of E. coli single-stranded binding protein (SSB), which would allow for a sliding clamp to wait for binding of the DNA polymerase. Replacement of SSB with Human RP-A eliminates this interaction; free movement of sliding clamp and poor binding of clamp loader to the junction allows sliding clamp to accumulate on DNA. This result implies that the clamp not only acts as a tether, but also a placeholder.

  1. Large negative differential conductance in single-molecule break junctions.

    Science.gov (United States)

    Perrin, Mickael L; Frisenda, Riccardo; Koole, Max; Seldenthuis, Johannes S; Gil, Jose A Celis; Valkenier, Hennie; Hummelen, Jan C; Renaud, Nicolas; Grozema, Ferdinand C; Thijssen, Joseph M; Dulić, Diana; van der Zant, Herre S J

    2014-10-01

    Molecular electronics aims at exploiting the internal structure and electronic orbitals of molecules to construct functional building blocks. To date, however, the overwhelming majority of experimentally realized single-molecule junctions can be described as single quantum dots, where transport is mainly determined by the alignment of the molecular orbital levels with respect to the Fermi energies of the electrodes and the electronic coupling with those electrodes. Particularly appealing exceptions include molecules in which two moieties are twisted with respect to each other and molecules in which quantum interference effects are possible. Here, we report the experimental observation of pronounced negative differential conductance in the current-voltage characteristics of a single molecule in break junctions. The molecule of interest consists of two conjugated arms, connected by a non-conjugated segment, resulting in two coupled sites. A voltage applied across the molecule pulls the energy of the sites apart, suppressing resonant transport through the molecule and causing the current to decrease. A generic theoretical model based on a two-site molecular orbital structure captures the experimental findings well, as confirmed by density functional theory with non-equilibrium Green's functions calculations that include the effect of the bias. Our results point towards a conductance mechanism mediated by the intrinsic molecular orbitals alignment of the molecule.

  2. Tunable magnetoresistance in an asymmetrically coupled single-molecule junction

    Science.gov (United States)

    Warner, Ben; El Hallak, Fadi; Prüser, Henning; Sharp, John; Persson, Mats; Fisher, Andrew J.; Hirjibehedin, Cyrus F.

    2015-03-01

    Phenomena that are highly sensitive to magnetic fields can be exploited in sensors and non-volatile memories. The scaling of such phenomena down to the single-molecule level may enable novel spintronic devices. Here, we report magnetoresistance in a single-molecule junction arising from negative differential resistance that shifts in a magnetic field at a rate two orders of magnitude larger than Zeeman shifts. This sensitivity to the magnetic field produces two voltage-tunable forms of magnetoresistance, which can be selected via the applied bias. The negative differential resistance is caused by transient charging of an iron phthalocyanine (FePc) molecule on a single layer of copper nitride (Cu2N) on a Cu(001) surface, and occurs at voltages corresponding to the alignment of sharp resonances in the filled and empty molecular states with the Cu(001) Fermi energy. An asymmetric voltage-divider effect enhances the apparent voltage shift of the negative differential resistance with magnetic field, which inherently is on the scale of the Zeeman energy. These results illustrate the impact that asymmetric coupling to metallic electrodes can have on transport through molecules, and highlight how this coupling can be used to develop molecular spintronic applications.

  3. Probing Protein Channel Dynamics At The Single Molecule Level.

    Science.gov (United States)

    Lee, M. Ann; Dunn, Robert C.

    1997-03-01

    It would be difficult to overstate the importance played by protein ion channels in cellular function. These macromolecular pores allow the passage of ions across the cellular membrane and play indispensable roles in all aspects of neurophysiology. While the patch-clamp technique continues to provide elegant descriptions of the kinetic processes involved in ion channel gating, the associated conformational changes remain a mystery. We are using the spectroscopic capabilities and single molecule fluorescence sensitivity of near-field scanning optical microscopy (NSOM) to probe these dynamics at the single channel level. Using a newly developed cantilevered NSOM probe capable of probing soft biological samples with single molecule fluorescence sensitivity, we have begun mapping the location of single NMDA receptors in intact rat cortical neurons with <100 nm spatial resolution. We will also present recent results exploring the conformational changes accompanying activation of nuclear pore channels located in the nuclear membrane of Xenopus oocytes. Our recent NSOM and AFM measurements on single nuclear pore complexes reveal large conformational changes taking place upon activation, providing rich, new molecular level details of channel function.

  4. Method for measuring thermal properties using a long-wavelength infrared thermal image

    Science.gov (United States)

    Walker, Charles L.; Costin, Laurence S.; Smith, Jody L.; Moya, Mary M.; Mercier, Jeffrey A.

    2007-01-30

    A method for estimating the thermal properties of surface materials using long-wavelength thermal imagery by exploiting the differential heating histories of ground points in the vicinity of shadows. The use of differential heating histories of different ground points of the same surface material allows the use of a single image acquisition step to provide the necessary variation in measured parameters for calculation of the thermal properties of surface materials.

  5. Long-wavelength optical coherence tomography at 1.7 µm for enhanced imaging depth

    OpenAIRE

    Sharma, Utkarsh; Chang, Ernest W.; Seok H Yun

    2008-01-01

    Multiple scattering in a sample presents a significant limitation to achieve meaningful structural information at deeper penetration depths in optical coherence tomography (OCT). Previous studies suggest that the spectral region around 1.7 µm may exhibit reduced scattering coefficients in biological tissues compared to the widely used wavelengths around 1.3 µm. To investigate this long-wavelength region, we developed a wavelength-swept laser at 1.7 µm wavelength and conducted OCT or optical f...

  6. Power-scalable long-wavelength Yb-doped photonic bandgap fiber sources

    DEFF Research Database (Denmark)

    Olausson, Christina Bjarnal Thulin; Shirakawa, Akira; Maurayama, Hiroki

    2010-01-01

    Ytterbium-doped photonic-bandgap fiber sources operationg at the long-wavelength edge of the ytterbium gain band are being investigated for high power amplification. Artificial shaping of the gain spectrum by the characteristic distributed filtering effect of the photonic bandgap enables...... spontaneous-emission-free power svaling. As high as 167 W power and 16 dB saturated gain at 1178 nm have been demonstrated...

  7. Magnetic iron oxide nanoparticles as long wavelength photoinitiators for free radical polymerization

    OpenAIRE

    2015-01-01

    Polymer Chemistry COMMUNICATION Cite this: Polym. Chem., 2015, 6, 1918 Received 1st December 2014, Accepted 7th January 2015 DOI: 10.1039/c4py01658k www.rsc.org/polymers Magnetic iron oxide nanoparticles as long wavelength photoinitiators for free radical polymerization† Sajjad Dadashi-Silab,a Yasemin Yar,b Havva Yagci Acarb and Yusuf Yagci*a,c Iron oxide nanoparticles (Fe3O4 NPs) capped with lauric acid agents were synthesized and their photocatalyti...

  8. Long Wavelength 256 X 256 Quantum Well Infrared Photodetector Portable Camera

    Science.gov (United States)

    Gunapala, S. D.; Liu, J. K.; Shott, C. A.; Hoelter, T.; Sundaram, M.; Park, J. S.; Laband, S.; James, J.

    1996-01-01

    In this paper, we discuss the development of very sensitive long wavelength infrared (LWIR) GaAs/AlGal-xAs Quantum well infrared photodetectors (QWIPS), fabrication of random reflectors for efficient light coupling, and the demonstration of a LWIR 256 X 256 focal plane array imaging camera. Excellent imagery, with a noise equivalent differential temperature (NE-delta-T) of 25 mK has been achieved.

  9. Propagation of Long-Wavelength Nonlinear Slow Sausage Waves in Stratified Magnetic Flux Tubes

    Science.gov (United States)

    Barbulescu, M.; Erdélyi, R.

    2016-05-01

    The propagation of nonlinear, long-wavelength, slow sausage waves in an expanding magnetic flux tube, embedded in a non-magnetic stratified environment, is discussed. The governing equation for surface waves, which is akin to the Leibovich-Roberts equation, is derived using the method of multiple scales. The solitary wave solution of the equation is obtained numerically. The results obtained are illustrative of a solitary wave whose properties are highly dependent on the degree of stratification.

  10. Simulation of Ultra-Long Wavelength interferometer in the Earth orbit and on the lunar surface

    OpenAIRE

    Zhang, Mo; Huang, Maohai; Yan, Yihua

    2014-01-01

    We present simulations for interferometer arrays in Earth orbit and on the lunar surface to guide the design and optimization of space-based Ultra-Long Wavelength missions, such as those of China's Chang'E program. We choose parameters and present simulations using simulated data to identify inter-dependencies and constraints on science and engineering parameters. A regolith model is created for the lunar surface array simulation, the results show that the lunar regolith will have an undesira...

  11. Conformational plasticity and dynamics in the generic protein folding catalyst SlyD unraveled by single-molecule FRET.

    Science.gov (United States)

    Kahra, Dana; Kovermann, Michael; Löw, Christian; Hirschfeld, Verena; Haupt, Caroline; Balbach, Jochen; Hübner, Christian Gerhard

    2011-08-26

    The relation between conformational dynamics and chemistry in enzyme catalysis recently has received increasing attention. While, in the past, the mechanochemical coupling was mainly attributed to molecular motors, nowadays, it seems that this linkage is far more general. Single-molecule fluorescence methods are perfectly suited to directly evidence conformational flexibility and dynamics. By labeling the enzyme SlyD, a member of peptidyl-prolyl cis-trans isomerases of the FK506 binding protein type with an inserted chaperone domain, with donor and acceptor fluorophores for single-molecule fluorescence resonance energy transfer, we directly monitor conformational flexibility and conformational dynamics between the chaperone domain and the FK506 binding protein domain. We find a broad distribution of distances between the labels with two main maxima, which we attribute to an open conformation and to a closed conformation of the enzyme. Correlation analysis demonstrates that the conformations exchange on a rate in the 100 Hz range. With the aid from Monte Carlo simulations, we show that there must be conformational flexibility beyond the two main conformational states. Interestingly, neither the conformational distribution nor the dynamics is significantly altered upon binding of substrates or other known binding partners. Based on these experimental findings, we propose a model where the conformational dynamics is used to search the conformation enabling the chemical step, which also explains the remarkable substrate promiscuity connected with a high efficiency of this class of peptidyl-prolyl cis-trans isomerases.

  12. Prosress in long wavelength emission in fluorene-based electroluminescent blue materials

    Institute of Scientific and Technical Information of China (English)

    JIANG HongJi; WAN JunHua; HUANG Wei

    2008-01-01

    On account of the advantages of organic electroluminescent materials compared with their inorganic counterparts, the development of organic electroluminescent materials is one of the hot areas of the optoelectronic materials. Fluorene and its derivatives, which have an aromatic biphenyl structure with a wide energy gap in the backbones and high luminescent efficiency, have drawn much attention of material chemists and device physicists. However, one drawback of fluorene-based electroluminescent blue materials is that there is an occurrence of long wavelength emission after annealing the films in air or after operating organic light-emitting diodes for a long time. To clarify the origin of this long wavelength emission, the scientists at home and abroad have put forward all kinds of correlative explanations. Among the scientists, some thought it was caused by excimer-related species, while some others claimed that it was caused by the fluorenone of photooxdized fluorene. The corresponding solutions to this problem have also been proposed and the problem has been partially resolved in some degree. The present review summarizes and analyzes the progress made on the origin of long wavelength emission in fluorene-based electroluminescent blue materials at home and abroad in the past few years. Some issues to be addressed and hotspots to be further investigated are also presented and discussed.

  13. Peripheral detection and resolution with mid-/long-wavelength and short-wavelength sensitive cone systems.

    Science.gov (United States)

    Zhu, Hai-Feng; Zele, Andrew J; Suheimat, Marwan; Lambert, Andrew J; Atchison, David A

    2016-08-01

    This study compared neural resolution and detection limits of the human mid-/long-wavelength and short-wavelength cone systems with anatomical estimates of photoreceptor and retinal ganglion cell spacings and sizes. Detection and resolution limits were measured from central fixation out to 35° eccentricity across the horizontal visual field using a modified Lotmar interferometer. The mid-/long-wavelength cone system was studied using a green (550 nm) test stimulus to which S-cones have low sensitivity. To bias resolution and detection to the short-wavelength cone system, a blue (450 nm) test stimulus was presented against a bright yellow background that desensitized the M- and L-cones. Participants were three trichromatic males with normal visual functions. With green stimuli, resolution showed a steep central-peripheral gradient that was similar between participants, whereas the detection gradient was shallower and patterns were different between participants. Detection and resolution with blue stimuli were poorer than for green stimuli. The detection of blue stimuli was superior to resolution across the horizontal visual field and the patterns were different between participants. The mid-/long-wavelength cone system's resolution is limited by midget ganglion cell spacing and its detection is limited by the size of the M- and L-cone photoreceptors, consistent with previous observations. We found that no such simple relationships occur for the short-wavelength cone system between resolution and the bistratified ganglion cell spacing, nor between detection and the S-cone photoreceptor sizes.

  14. Attosecond streaking measurement of extreme ultraviolet pulses using a long-wavelength electric field

    Science.gov (United States)

    Saito, Nariyuki; Ishii, Nobuhisa; Kanai, Teruto; Watanabe, Shuntaro; Itatani, Jiro

    2016-01-01

    Long-wavelength lasers have great potential to become a new-generation drive laser for tabletop coherent light sources in the soft X-ray region. Because of the significantly low conversion efficiency from a long-wavelength light field to high-order harmonics, their pulse characterization has been carried out by measuring the carrier-envelope phase and/or spatial dependences of high harmonic spectra. However, these photon detection schemes, in general, have difficulty in obtaining information on the spectral phases, which is crucial to determine the temporal structures of high-order harmonics. Here, we report the first attosecond streaking measurement of high harmonics generated by few-cycle optical pulses at 1.7 μm from a BiB3O6–based optical parametric chirped-pulse amplifier. This is also the first demonstration of time-resolved photoelectron spectroscopy using high harmonics from a long-wavelength drive laser other than Ti:sapphire lasers, which paves the way towards ultrafast soft X-ray photoelectron spectroscopy. PMID:27752115

  15. Attosecond streaking measurement of extreme ultraviolet pulses using a long-wavelength electric field

    Science.gov (United States)

    Saito, Nariyuki; Ishii, Nobuhisa; Kanai, Teruto; Watanabe, Shuntaro; Itatani, Jiro

    2016-10-01

    Long-wavelength lasers have great potential to become a new-generation drive laser for tabletop coherent light sources in the soft X-ray region. Because of the significantly low conversion efficiency from a long-wavelength light field to high-order harmonics, their pulse characterization has been carried out by measuring the carrier-envelope phase and/or spatial dependences of high harmonic spectra. However, these photon detection schemes, in general, have difficulty in obtaining information on the spectral phases, which is crucial to determine the temporal structures of high-order harmonics. Here, we report the first attosecond streaking measurement of high harmonics generated by few-cycle optical pulses at 1.7 μm from a BiB3O6-based optical parametric chirped-pulse amplifier. This is also the first demonstration of time-resolved photoelectron spectroscopy using high harmonics from a long-wavelength drive laser other than Ti:sapphire lasers, which paves the way towards ultrafast soft X-ray photoelectron spectroscopy.

  16. FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET.

    Science.gov (United States)

    Ingargiola, Antonino; Lerner, Eitan; Chung, SangYoon; Weiss, Shimon; Michalet, Xavier

    2016-01-01

    Single-molecule Förster Resonance Energy Transfer (smFRET) allows probing intermolecular interactions and conformational changes in biomacromolecules, and represents an invaluable tool for studying cellular processes at the molecular scale. smFRET experiments can detect the distance between two fluorescent labels (donor and acceptor) in the 3-10 nm range. In the commonly employed confocal geometry, molecules are free to diffuse in solution. When a molecule traverses the excitation volume, it emits a burst of photons, which can be detected by single-photon avalanche diode (SPAD) detectors. The intensities of donor and acceptor fluorescence can then be related to the distance between the two fluorophores. While recent years have seen a growing number of contributions proposing improvements or new techniques in smFRET data analysis, rarely have those publications been accompanied by software implementation. In particular, despite the widespread application of smFRET, no complete software package for smFRET burst analysis is freely available to date. In this paper, we introduce FRETBursts, an open source software for analysis of freely-diffusing smFRET data. FRETBursts allows executing all the fundamental steps of smFRET bursts analysis using state-of-the-art as well as novel techniques, while providing an open, robust and well-documented implementation. Therefore, FRETBursts represents an ideal platform for comparison and development of new methods in burst analysis. We employ modern software engineering principles in order to minimize bugs and facilitate long-term maintainability. Furthermore, we place a strong focus on reproducibility by relying on Jupyter notebooks for FRETBursts execution. Notebooks are executable documents capturing all the steps of the analysis (including data files, input parameters, and results) and can be easily shared to replicate complete smFRET analyzes. Notebooks allow beginners to execute complex workflows and advanced users to

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

    Energy Technology Data Exchange (ETDEWEB)

    Laurence, Ted Alfred

    2002-07-30

    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

  18. 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

  19. Single-molecule chemical reactions on DNA origami

    DEFF Research Database (Denmark)

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

    2010-01-01

    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...... 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...

  20. Single molecule Michaelis-Menten equation beyond quasistatic disorder.

    Science.gov (United States)

    Xue, Xiaochuan; Liu, Fei; Ou-Yang, Zhong-Can

    2006-09-01

    The classic Michaelis-Menten equation describes the catalytic activities for ensembles of enzyme molecules very well. But recent single-molecule experiments showed that the waiting time distribution and other properties of single enzyme molecules were not consistent with the prediction based on the ensemble viewpoint. They have contributed to the slow conformational changes of a single enzyme in the catalytic processes. In this work, we study the general dynamics of single enzymes in the presence of dynamic disorder. We find that, within the time separation regimes, i.e., the slow reaction and nondiffusion limits, the Michaelis-Menten equation holds exactly. In particular, by employing the decoupling approximation we demonstrate analytically that the classic Michaelis-Menten equation is still an excellent approximation in the presence of general dynamic disorder.

  1. Non-linear irreversible thermodynamics of single-molecule experiments

    CERN Document Server

    Santamaria-Holek, I; Hidalgo-Soria, M; Perez-Madrid, A

    2015-01-01

    Irreversible thermodynamics of single-molecule experiments subject to external constraining forces of a mechanical nature is presented. Extending Onsager's formalism to the non-linear case of systems under non-equilibrium external constraints, we are able to calculate the entropy production and the general non-linear kinetic equations for the variables involved. In particular, we analyze the case of RNA stretching protocols obtaining critical oscillations between di?erent con?gurational states when forced by external means to remain in the unstable region of its free-energy landscape, as observed in experiments. We also calculate the entropy produced during these hopping events, and show how resonant phenomena in stretching experiments of single RNA macromolecules may arise. We also calculate the hopping rates using Kramer's approach obtaining a good comparison with experiments.

  2. Linear trinuclear cobalt(II) single molecule magnet.

    Science.gov (United States)

    Zhang, Yuan-Zhu; Brown, Andrew J; Meng, Yin-Shan; Sun, Hao-Ling; Gao, Song

    2015-02-14

    The introduction of NaBPh(4) into a methanolic solution of CoCl(2)·(6)H(2)O and 2-[(pyridine-2-ylimine)-methyl]phenol (Hpymp) afforded {[Co(II)(3)(pymp)(4)(MeOH)(2)][BPh(4)](2)}·(2)MeOH (1) with a centro-symmetrically linear trinuclear structure. Magnetic analysis of 1 exhibited significant intracluster ferromagnetic exchange (2.4 cm(-1)) and slow relaxation of magnetization in both zero and non-zero static fields below 5 K, giving the first [Co(II)(3)] single molecule magnet with an effective energy barrier of 17.2(3) cm(-1) under a 500 Oe dc field.

  3. Enhancing single molecule imaging in optofluidics and microfluidics.

    Science.gov (United States)

    Vasdekis, Andreas E; Laporte, Gregoire P J

    2011-01-01

    Microfluidics and optofluidics have revolutionized high-throughput analysis and chemical synthesis over the past decade. Single molecule imaging has witnessed similar growth, due to its capacity to reveal heterogeneities at high spatial and temporal resolutions. However, both resolution types are dependent on the signal to noise ratio (SNR) of the image. In this paper, we review how the SNR can be enhanced in optofluidics and microfluidics. Starting with optofluidics, we outline integrated photonic structures that increase the signal emitted by single chromophores and minimize the excitation volume. Turning then to microfluidics, we review the compatible functionalization strategies that reduce noise stemming from non-specific interactions and architectures that minimize bleaching and blinking.

  4. Enhancing Single Molecule Imaging in Optofluidics and Microfluidics

    Directory of Open Access Journals (Sweden)

    Andreas E. Vasdekis

    2011-08-01

    Full Text Available Microfluidics and optofluidics have revolutionized high-throughput analysis and chemical synthesis over the past decade. Single molecule imaging has witnessed similar growth, due to its capacity to reveal heterogeneities at high spatial and temporal resolutions. However, both resolution types are dependent on the signal to noise ratio (SNR of the image. In this paper, we review how the SNR can be enhanced in optofluidics and microfluidics. Starting with optofluidics, we outline integrated photonic structures that increase the signal emitted by single chromophores and minimize the excitation volume. Turning then to microfluidics, we review the compatible functionalization strategies that reduce noise stemming from non-specific interactions and architectures that minimize bleaching and blinking.

  5. Low-temperature phonoemissive tunneling rates in single molecule magnets

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Yun, E-mail: yl2192@gmail.com [University of Illinois, Department of Physics, 1110 W. Green St., Urbana, IL 61801 (United States); Garg, Anupam, E-mail: agarg@northwestern.edu [Northwestern University, Department of Physics and Astronomy, 2145 Sheridan Rd., Evanston, IL 60208 (United States)

    2016-03-15

    Tunneling between the two lowest energy levels of single molecule magnets with Ising type anisotropy, accompanied by the emission or absorption of phonons, is considered. Quantitatively accurate calculations of the rates for such tunneling are performed for a model Hamiltonian especially relevant to the best studied example, Fe{sub 8}. Two different methods are used: high-order perturbation theory in the spin–phonon interaction and the non-Ising-symmetric parts of the spin Hamiltonian, and a novel semiclassical approach based on spin-coherent-state-path-integral instantons. The methods are found to be in good quantitative agreement with other, and consistent with previous approaches to the problem. The implications of these results for magnetization of molecular solids of these molecules are discussed briefly.

  6. A Single-Molecule Hershey-Chase Experiment

    CERN Document Server

    Van Valen, David; Chen, Yi-Ju; Tuson, Hannah; Wiggins, Paul; Phillips, Rob

    2012-01-01

    Ever since Hershey and Chase used phages to establish DNA as the carrier of genetic information in 1952, the precise mechanisms of phage DNA translocation have been a mystery. While bulk measurements have set a time scale for in vivo DNA translocation during bacteriophage infection, measurements of DNA ejection by single bacteriophages have only been made in vitro. Here, we present direct visualization of single bacteriophages infecting individual Escherichia coli cells. For bacteriophage lambda, we establish a mean ejection time of roughly 5 minutes with significant cell-to-cell variability, including pausing events. In contrast, corresponding in vitro single-molecule ejections take only 10 seconds to reach completion and do not exhibit significant variability. Our data reveal that the velocity of ejection for two different genome lengths collapses onto a single curve. This suggests that in vivo ejections are controlled by the amount of DNA ejected, in contrast with in vitro DNA ejections, which are governed...

  7. Few-photon coherent nonlinear optics with a single molecule

    CERN Document Server

    Maser, Andreas; Utikal, Tobias; Götzinger, Stephan; Sandoghdar, Vahid

    2015-01-01

    The pioneering experiments of linear spectroscopy were performed using flames in the 1800s, but nonlinear optical measurements had to wait until lasers became available in the twentieth century. Because the nonlinear cross section of materials is very small, usually macroscopic bulk samples and pulsed lasers are used. Numerous efforts have explored coherent nonlinear signal generation from individual nanoparticles or small atomic ensembles with millions of atoms. Experiments on a single semiconductor quantum dot have also been reported, albeit with a very small yield. Here, we report on coherent nonlinear spectroscopy of a single molecule under continuous-wave single-pass illumination, where efficient photon-molecule coupling in a tight focus allows switching of a laser beam by less than a handful of pump photons nearly resonant with the sharp molecular transition. Aside from their fundamental importance, our results emphasize the potential of organic molecules for applications such as quantum information pro...

  8. 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...

  9. Synergizing superresolution optical fluctuation imaging with single molecule localization microscopy

    CERN Document Server

    Schidorsky, Shachar; Razvag, Yair; Golan, Yonatan; Weiss, Shimon; Sherman, Eilon

    2016-01-01

    Single molecule localization microscopy (SMLM) techniques enable imaging biological samples well beyond the diffraction limit of light, but they vary significantly in their spatial and temporal resolutions. High-order statistical analysis of temporal fluctuations as in superresolution optical fluctuation imaging (SOFI) also enable imaging beyond diffraction limit, but usually at a lower resolution as compared to SMLM. Since the same data format is acquired for both methods, their algorithms can be applied to the same data set, and thus may be combined synergistically to improve overall imaging performance. Here, we find that SOFI converges much faster than SMLM, provides additive information to SMLM, and can efficiently reject background. We then show how SOFI-assisted SMLM imaging can improve SMLM image reconstruction by rejecting common sources of background, especially under low signal-to-background conditions. The performance of our approach was evaluated using a realistic simulation of fluorescence imagi...

  10. Single-Molecule Electrochemical Gating in Ionic Liquids

    DEFF Research Database (Denmark)

    Kay, Nicola J.; Higgins, Simon J.; Jeppesen, Jan O.

    2012-01-01

    The single-molecular conductance of a redox active molecular bridge has been studied in an electrochemical single-molecule transistor configuration in a room-temperature ionic liquid (RTIL). The redox active pyrrolo-tetrathiafulvalene (pTTF) moiety was attached to gold contacts at both ends through...... −(CH2)6S– groups, and gating of the redox state was achieved with the electrochemical potential. The water-free, room-temperature, ionic liquid environment enabled both the monocationic and the previously inaccessible dicationic redox states of the pTTF moiety to be studied in the in situ scanning...... and decreases again as the second redox process is passed. This is described as an “off–on–off–on–off” conductance switching behavior. This molecular conductance vs electrochemical potential relation could be modeled well as a sequential two-step charge transfer process with full or partial vibrational...

  11. Spin thermoelectric effects in organic single-molecule devices

    Energy Technology Data Exchange (ETDEWEB)

    Wang, H.L.; Wang, M.X.; Qian, C.; Hong, X.K.; Zhang, D.B.; Liu, Y.S.; Yang, X.F., E-mail: xfyang@cslg.edu.cn

    2017-05-25

    Highlights: • A stronger spin thermoelectric performance in a polyacetylene device is observed. • For the antiferromagnetic (AFM) ordering, a transport gap is opened. Thus the thermoelectric effects are largely enhanced. - Abstract: The spin thermoelectric performance of a polyacetylene chain bridging two zigzag graphene nanoribbons (ZGNRs) is investigated based on first principles method. Two different edge spin arrangements in ZGNRs are considered. For ferromagnetic (FM) ordering, transmission eigenstates with different spin indices distributed below and above Fermi level are observed, leading directly to a strong spin thermoelectric effect in a wide temperature range. With the edge spins arranged in the antiferromagnetic (AFM) ordering, an obvious transport gap appears in the system, which greatly enhances the thermoelectric effects. The presence of a small spin splitting also induces a spin thermoelectric effect greater than the charge thermoelectric effect in certain temperature range. In general, the single-molecule junction exhibits the potential to be used for the design of perfect thermospin devices.

  12. Electronic transport in benzodifuran single-molecule transistors.

    Science.gov (United States)

    Xiang, An; Li, Hui; Chen, Songjie; Liu, Shi-Xia; Decurtins, Silvio; Bai, Meilin; Hou, Shimin; Liao, Jianhui

    2015-05-07

    Benzodifuran (BDF) single-molecule transistors have been fabricated in electromigration break junctions for electronic measurements. The inelastic electron tunneling spectrum validates that the BDF molecule is the pathway of charge transport. The gating effect is analyzed in the framework of a single-level tunneling model combined with transition voltage spectroscopy (TVS). The analysis reveals that the highest occupied molecular orbital (HOMO) of the thiol-terminated BDF molecule dominates the charge transport through Au-BDF-Au junctions. Moreover, the energy shift of the HOMO caused by the gate voltage is the main reason for conductance modulation. In contrast, the electronic coupling between the BDF molecule and the gold electrodes, which significantly affects the low-bias junction conductance, is only influenced slightly by the applied gate voltage. These findings will help in the design of future molecular electronic devices.

  13. Single-molecule optomechanics in “picocavities”

    Science.gov (United States)

    Benz, Felix; Schmidt, Mikolaj K.; Dreismann, Alexander; Chikkaraddy, Rohit; Zhang, Yao; Demetriadou, Angela; Carnegie, Cloudy; Ohadi, Hamid; de Nijs, Bart; Esteban, Ruben; Aizpurua, Javier; Baumberg, Jeremy J.

    2016-11-01

    Trapping light with noble metal nanostructures overcomes the diffraction limit and can confine light to volumes typically on the order of 30 cubic nanometers. We found that individual atomic features inside the gap of a plasmonic nanoassembly can localize light to volumes well below 1 cubic nanometer (“picocavities”), enabling optical experiments on the atomic scale. These atomic features are dynamically formed and disassembled by laser irradiation. Although unstable at room temperature, picocavities can be stabilized at cryogenic temperatures, allowing single atomic cavities to be probed for many minutes. Unlike traditional optomechanical resonators, such extreme optical confinement yields a factor of 106 enhancement of optomechanical coupling between the picocavity field and vibrations of individual molecular bonds. This work sets the basis for developing nanoscale nonlinear quantum optics on the single-molecule level.

  14. Tracking Electrons in Biological Macromolecules: From Ensemble to Single Molecule

    Directory of Open Access Journals (Sweden)

    Leandro C. Tabares

    2014-08-01

    Full Text Available Nature utilizes oxido-reductases to cater to the energy demands of most biochemical processes in respiratory species. Oxido-reductases are capable of meeting this challenge by utilizing redox active sites, often containing transition metal ions, which facilitate movement and relocation of electrons/protons to create a potential gradient that is used to energize redox reactions. There has been a consistent struggle by researchers to estimate the electron transfer rate constants in physiologically relevant processes. This review provides a brief background on the measurements of electron transfer rates in biological molecules, in particular Cu-containing enzymes, and highlights the recent advances in monitoring these electron transfer events at the single molecule level or better to say, at the individual event level.

  15. 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.)

  16. Exploring single-molecule dynamics with fluorescence nanoscopy

    Energy Technology Data Exchange (ETDEWEB)

    Ringemann, Christian; Harke, Ben; Von Middendorff, Claas; Medda, Rebecca; Leutenegger, Marcel; Schoenle, Andreas; W Hell, Stefan; Eggeling, Christian [Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen (Germany); Honigmann, Alf; Wagner, Richard [Biophysik, University Osnabrueck, FB Biologie/Chemie, Osnabrueck (Germany)], E-mail: ceggeli@gwdg.de

    2009-10-15

    The study of molecular dynamics at the single-molecule level with fluorescence correlation spectroscopy (FCS) and far-field optics has contributed greatly to the functional understanding of complex systems. Unfortunately, such studies are restricted to length scales of >200 nm because diffraction does not allow further reduction of the measurement volume. This sets an upper limit on the applicable concentration of fluorescently labeled molecules and even more importantly, averages out details of nanoscale dynamics. By combining FCS and fluorescence intensity distribution analysis (FIDA) with sub-diffraction-resolution stimulated emission depletion (STED) nanoscopy, we remove this restriction and obtain open measurement volumes of nanoscale dimensions which are tunable in size. As a consequence, single-molecule studies can now be extended to nanoscale dynamics and may be applied to much larger, often endogenous concentrations. In solution, low-brightness signal from axial out-of-focus volume shells was taken into account by using both FCS and FIDA in conjunction to analyze the data. In two-dimensional systems, such as lipid membranes, the background is greatly reduced and measurements feature excellent signal-to-noise ratios. Measurement foci of down to 30 nm in diameter directly reveal anomalous diffusion of lipids in the plasma membrane of living cells and allow for the determination of on/off rates of the binding of lipids to other membrane constituents. Such important insight into the prominent biological question of lipid membrane organization or 'lipid rafts' shows that combining fluctuation analysis with STED-engineered ultra-small measurement volumes is a viable and powerful new approach to probing molecular dynamics on the nanoscale.

  17. Structure and mechanics of proteins from single molecules to cells

    Science.gov (United States)

    Brown, Andre E.

    2009-07-01

    Physical factors drive evolution and play important roles in motility and attachment as well as in differentiation. As animal cells adhere to survive, they generate force and "feel" various mechanical features of their surroundings and respond to externally applied forces. This mechanosensitivity requires a substrate for cells to adhere to and a mechanism for cells to apply force, followed by a cellular response to the mechanical properties of the substrate. We have taken an outside-in approach to characterize several aspects of cellular mechanosensitivity. First, we used single molecule force spectroscopy to measure how fibrinogen, an extracellular matrix protein that forms the scaffold of blood clots, responds to applied force and found that it rapidly unfolds in 23 nm steps at forces around 100 pN. Second, we used tensile testing to measure the force-extension behavior of fibrin gels and found that they behave almost linearly to strains of over 100%, have extensibilities of 170 +/- 15%, and undergo a large volume decrease that corresponds to a large and negative peak in compressibility at low strain, which indicates a structural transition. Using electron microscopy and X-ray scattering we concluded that these properties are likely due to coiled-coil unfolding, as observed at the single molecule level in fibrinogen. Moving inside cells, we used total internal reflection fluorescence and atomic force microscopy to image self-assembled myosin filaments. These filaments of motor proteins that are responsible for cell and muscle contractility were found to be asymmetric, with an average of 32% more force generating heads on one half than the other. This could imply a force imbalance, so that rather than being simply contractile, myosin filaments may also be motile in cells.

  18. 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

  19. Single-molecule experiments in biological physics: methods and applications.

    Science.gov (United States)

    Ritort, F

    2006-08-16

    I review single-molecule experiments (SMEs) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SMEs it is possible to manipulate molecules one at a time and measure distributions describing molecular properties, characterize the kinetics of biomolecular reactions and detect molecular intermediates. SMEs provide additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SMEs it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level, emphasizing the importance of SMEs to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SMEs from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOTs), magnetic tweezers (MTs), biomembrane force probes (BFPs) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation) and proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SMEs to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.

  20. Improvements in discrimination of bulk and trace elements in long-wavelength double pulse LIBS

    Energy Technology Data Exchange (ETDEWEB)

    Freeman, J.R., E-mail: freeman.justinr@gmail.com; Diwakar, P.K., E-mail: pdiwakar@purdue.edu; Harilal, S.S., E-mail: hari@pnnl.gov; Hassanein, A., E-mail: hassanein@purdue.edu

    2014-12-01

    In this work we study the effectiveness of long-wavelength heating in double pulse (DP) LIBS, quantitatively comparing figures of merit with those from traditional single pulse (SP) LIBS. The first laser pulse serves as the source of sample ablation, creating an aerosol-like plume that is subsequently reheated by the second laser pulse. At power densities used, the long-wavelength CO{sub 2} laser pulse does not ablate any of the solid sample in the atmospheric conditions investigated, meaning plasma emission and enhanced signal can be entirely attributed to the reheated plume rather than increased sample ablation. The signal discrimination was improved significantly using long-wavelength DP-LIBS. For bulk elemental analysis, DP-LIBS provided maximum enhancements of about 14 and 15 times for S/N and S/B, respectively, compared to SP-LIBS using the same quantity of ablated sample. For trace elemental analysis, maximum enhancements of about 7 and 4 times for S/N and S/B, respectively, were observed. These improvements are attributed to effective coupling between the second heating pulse and expanding plume and more efficient excitation of plume species than from the single pulse alone. Most significant improvements were observed in the case of low prepulse energy and minimal sample ablation. While bulk elemental analysis observed improvements for all prepulse energies studied, trace element discrimination only significantly improved for the lowest prepulse energy studied. - Highlights: • Enhancement by improved coupling and excitation efficiency, not increased ablated mass • S/N enhancements of 14 and 7 times for bulk and trace elements, respectively • S/B enhancements of 15 and 4 times for bulk and trace elements, respectively • Max enhancement observed for smaller quantities of ablated sample • Significant conclusions for delicate, mass-limited samples.

  1. Unselective regrowth buried heterostructure long-wavelength superluminescent diode realized with MOVPE

    Energy Technology Data Exchange (ETDEWEB)

    Ding Ying [Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083 (China)]. E-mail: yingding@red.semi.ac.cn; Zhou Fan [Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083 (China); Chen Weixi [School of Physics, Peking University, Beijing 100871 (China); Wang Wei [Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083 (China)

    2007-01-15

    A novel unselective regrowth buried heterostructure (BH) long-wavelength superluminescent diode (SLD), which has a grade-strained bulk InGaAs active region, was developed by metalorganic vapor-phase epitaxy (MOVPE). The 3 dB emission spectrum bandwidth of the SLD is about 65 nm with the range from 1596 to 1661 nm at 90 mA and from 1585 to 1650 nm at 150 mA.An output power of 3.5 mW is obtained at 200 mA injection current under CW operation at room temperature.

  2. Hybrid Ytterbium-doped large-mode-area photonic crystal fiber amplifier for long wavelengths

    DEFF Research Database (Denmark)

    Petersen, Sidsel Rübner; Alkeskjold, Thomas T.; Poli, Federica

    2012-01-01

    A large-mode-area Ytterbium-doped photonic crystal fiber amplifier with build-in gain shaping is presented. The fiber cladding consists of a hexagonal lattice of air holes, where three rows are replaced with circular high-index inclusions. Seven missing air holes define the large-mode-area core....... Light confinement is achieved by combined index and bandgap guiding, which allows for single-mode operation and gain shaping through distributed spectral filtering of amplified spontaneous emission. The fiber properties are ideal for amplification in the long wavelength regime of the Ytterbium gain...

  3. The source of the Earth's long wavelength geoid anomalies: Implications for mantle and core dynamics

    Science.gov (United States)

    Hager, B. H.; Richards, M. A.; Oconnell, R. J.

    1985-01-01

    The long wavelength components of the Earth's gravity field result mainly from density contrasts associated with convection in the mantle. Direct interpretation of the geoid for mantle convection is complicated by the fact that convective flow results in dynamically maintained deformation of the surface of the Earth, the core mantle boundary (CMB), and any interior chemical boundaries which might exist. These boundary deformations effect the geoid opposite in sign and are comparable in magnitude to those of the interior density contrasts driving the flow. The total difference of two relatively large quantities.

  4. 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

  5. Tunneling spectroscopy of organic monolayers and single molecules.

    Science.gov (United States)

    Hipps, K W

    2012-01-01

    Basic concepts in tunneling spectroscopy applied to molecular systems are presented. Junctions of the form M-A-M, M-I-A-M, and M-I-A-I'-M, where A is an active molecular layer, are considered. Inelastic electron tunneling spectroscopy (IETS) is found to be readily applied to all the above device types. It can provide both vibrational and electron spectroscopic data about the molecules comprising the A layer. In IETS there are no strong selection rules (although there are preferences) so that transitions that are normally IR, Raman, or even photon-forbidden can be observed. In the electronic transition domain, spin and Laporte forbidden transitions may be observed. Both vibrational and electronic IETS can be acquired from single molecules. The negative aspect of this seemingly ideal spectroscopic method is the thermal line width of about 5 k(B)T. This limits the useful measurement of vibrational IETS to temperatures below about 10 K. In the case of most electronic transitions where the intrinsic linewidth is much broader, useful experiments above 100 K are possible. One further limitation of electronic IETS is that it is generally limited to transitions with energy less than about 20,000 cm(-1). IETS can be identified by peaks in d(2) I/dV (2) vs bias voltage plots that occur at the same position (but not necessarily same intensity) in either bias polarity.Elastic tunneling spectroscopy is discussed in the context of processes involving molecular ionization and electron affinity states, a technique we call orbital mediated tunneling spectroscopy, or OMTS. OMTS can be applied readily to M-I-A-M and M-I-A-I'-M systems, but application to M-A-M junctions is problematic. Spectra can be obtained from single molecules. Ionization state results correlate well with UPS spectra obtained from the same systems in the same environment. Both ionization and affinity levels measured by OMTS can usually be correlated with one electron oxidation and reduction potentials for the

  6. Developing DNA nanotechnology using single-molecule fluorescence.

    Science.gov (United States)

    Tsukanov, Roman; Tomov, Toma E; Liber, Miran; Berger, Yaron; Nir, Eyal

    2014-06-17

    CONSPECTUS: An important effort in the DNA nanotechnology field is focused on the rational design and manufacture of molecular structures and dynamic devices made of DNA. As is the case for other technologies that deal with manipulation of matter, rational development requires high quality and informative feedback on the building blocks and final products. For DNA nanotechnology such feedback is typically provided by gel electrophoresis, atomic force microscopy (AFM), and transmission electron microscopy (TEM). These analytical tools provide excellent structural information; however, usually they do not provide high-resolution dynamic information. For the development of DNA-made dynamic devices such as machines, motors, robots, and computers this constitutes a major problem. Bulk-fluorescence techniques are capable of providing dynamic information, but because only ensemble averaged information is obtained, the technique may not adequately describe the dynamics in the context of complex DNA devices. The single-molecule fluorescence (SMF) technique offers a unique combination of capabilities that make it an excellent tool for guiding the development of DNA-made devices. The technique has been increasingly used in DNA nanotechnology, especially for the analysis of structure, dynamics, integrity, and operation of DNA-made devices; however, its capabilities are not yet sufficiently familiar to the community. The purpose of this Account is to demonstrate how different SMF tools can be utilized for the development of DNA devices and for structural dynamic investigation of biomolecules in general and DNA molecules in particular. Single-molecule diffusion-based Förster resonance energy transfer and alternating laser excitation (sm-FRET/ALEX) and immobilization-based total internal reflection fluorescence (TIRF) techniques are briefly described and demonstrated. To illustrate the many applications of SMF to DNA nanotechnology, examples of SMF studies of DNA hairpins and

  7. The effects of slippage and diffraction in long wavelength operation of a free electron laser

    Science.gov (United States)

    Zhulin, V. I.; Haselhoff, E. H.; van Amersfoort, P. W.

    1995-01-01

    The Free-Electron Laser user facility FELIX produces picosecond optical pulses in the wavelength range of 5 110 μm. The proposed installation of a new undulator with a larger magnetic period would allow extension towards considerably longer wavelengths. This would result in the production of extremely short, far-infrared pulses, with a duration of a single optical period or even less. In order to investigate the pulse propagation for free-electron lasers operating in the long wavelength limit, a three-dimensional simulation code was developed. Using the FELIX parameters, with the addition of a long-period undulator, the effects of slippage, diffraction losses, changes in the filling factor, as well as the effects of the optical cavity geometry were studied for wavelengths up to 300 μm, with electron pulses in the ps regime. It is shown that slippage effects are less restrictive for long wavelength operation than the increasing losses due to optical beam diffraction.

  8. Increasing long-wavelength relief across the southeastern flank of the Sierra Nevada, California

    Science.gov (United States)

    Bennett, R. A.; Fay, N. P.; Hreinsdóttir, S.; Chase, C.; Zandt, G.

    2009-09-01

    A high degree of correlation between present-day relative rock uplift measured using continuous GPS geodesy and spatially averaged surface elevations suggests that long-wavelength topographic relief is presently increasing along the southeastern flank of the Sierra Nevada range and within an adjacent portion of the northern Basin and Range province. Current estimates for erosion rate are an order of magnitude smaller than the relative rates determined by geodesy. Thus, although the uplift serves to enhance long-wavelength relief, it cannot be explained entirely as an isostatic response to erosion. If uplift rates have been constant through time, the duration over which the uplift could have been active (Sierra are evolving with time. According to either hypothesis, vertical surface motions may have slowly accelerated since ~mid-Pliocene time. Several possible mechanisms for progressive reduction of EET may be attributable to thermo-mechanical disequilibrium that began with the removal of an ultramafic root from the Sierran batholith during late Miocene or early Pliocene time. Specific mechanisms for ongoing enhancement of loads are less obvious. Based on these results, we suggest that dense networks of long-running continuous GPS stations around the world currently represent an underutilized resource for studies of orogenesis and upper mantle processes.

  9. Steps, kinetic anisotropy, and long-wavelength instabilities in directional solidification.

    Science.gov (United States)

    Grimm, H P; Davis, S H; McFadden, G B

    1999-05-01

    We consider the effect of anisotropic interface kinetics on long-wavelength instabilities during the directional solidification of a binary alloy having a vicinal interface. Linear theory predicts that a planar solidification front is stabilized under the effect of anisotropy as long as the segregation coefficient is small enough, whereas a novel instability appears at high rates of solidification. Furthermore, the neutral stability curve, indicating the values of the principal control parameter (here the morphological number) for which the growth rate of a sinusoidal perturbation of a given wavelength changes its sign, is shown to have up to three branches, two of them combining to form an isola for certain values of the control parameters. We identify conditions for which linear stability theory predicts the instability of the planar interface to long-wavelength traveling waves. A number of distinguished limits provide evolution equations that describe the resulting dynamical behavior of the crystal-melt interface and generalize previous work by Sivashinsky, Brattkus, and Davis and Riley and Davis. Bifurcation analysis and numerical computations for the derived evolution equations show that the anisotropy is able to promote the tendency to supercritical bifurcation, and also leads to the development of strongly preferred interface orientations for finite-amplitude deformations.

  10. Progress in long wavelength emission in fluorene-based electroluminescent blue materials

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    On account of the advantages of organic electroluminescent materials compared with their inorganic counterparts,the development of organic electroluminescent materials is one of the hot areas of the optoelectronic materials.Fluorene and its derivatives,which have an aromatic biphenyl structure with a wide energy gap in the backbones and high luminescent efficiency,have drawn much attention of ma-terial chemists and device physicists.However,one drawback of fluorene-based electroluminescent blue materials is that there is an occurrence of long wavelength emission after annealing the films in air or after operating organic light-emitting diodes for a long time.To clarify the origin of this long wave-length emission,the scientists at home and abroad have put forward all kinds of correlative explana-tions.Among the scientists,some thought it was caused by excimer-related species,while some others claimed that it was caused by the fluorenone of photooxdized fluorene.The corresponding solutions to this problem have also been proposed and the problem has been partially resolved in some degree.The present review summarizes and analyzes the progress made on the origin of long wavelength emission in fluorene-based electroluminescent blue materials at home and abroad in the past few years.Some issues to be addressed and hotspots to be further investigated are also presented and discussed.

  11. Gene duplication and divergence of long wavelength-sensitive opsin genes in the guppy, Poecilia reticulata.

    Science.gov (United States)

    Watson, Corey T; Gray, Suzanne M; Hoffmann, Margarete; Lubieniecki, Krzysztof P; Joy, Jeffrey B; Sandkam, Ben A; Weigel, Detlef; Loew, Ellis; Dreyer, Christine; Davidson, William S; Breden, Felix

    2011-02-01

    Female preference for male orange coloration in the genus Poecilia suggests a role for duplicated long wavelength-sensitive (LWS) opsin genes in facilitating behaviors related to mate choice in these species. Previous work has shown that LWS gene duplication in this genus has resulted in expansion of long wavelength visual capacity as determined by microspectrophotometry (MSP). However, the relationship between LWS genomic repertoires and expression of LWS retinal cone classes within a given species is unclear. Our previous study in the related species, Xiphophorus helleri, was the first characterization of the complete LWS opsin genomic repertoire in conjunction with MSP expression data in the family Poeciliidae, and revealed the presence of four LWS loci and two distinct LWS cone classes. In this study we characterized the genomic organization of LWS opsin genes by BAC clone sequencing, and described the full range of cone cell types in the retina of the colorful Cumaná guppy, Poecilia reticulata. In contrast to X. helleri, MSP data from the Cumaná guppy revealed three LWS cone classes. Comparisons of LWS genomic organization described here for Cumaná to that of X. helleri indicate that gene divergence and not duplication was responsible for the evolution of a novel LWS haplotype in the Cumaná guppy. This lineage-specific divergence is likely responsible for a third additional retinal cone class not present in X. helleri, and may have facilitated the strong sexual selection driven by female preference for orange color patterns associated with the genus Poecilia.

  12. Destabilization of long-wavelength Love and Stoneley waves in slow sliding

    CERN Document Server

    Ranjith, K

    2008-01-01

    Love waves are dispersive interfacial waves that are a mode of response for anti-plane motions of an elastic layer bonded to an elastic half-space. Similarly, Stoneley waves are interfacial waves in bonded contact of dissimilar elastic half-spaces, when the displacements are in the plane of the solids. It is shown that in slow sliding, long wavelength Love and Stoneley waves are destabilized by friction. Friction is assumed to have a positive instantaneous logarithmic dependence on slip rate and a logarithmic rate weakening behavior at steady-state. Long wavelength instabilities occur generically in sliding with rate- and state-dependent friction, even when an interfacial wave does not exist. For slip at low rates, such instabilities are quasi-static in nature, i.e., the phase velocity is negligibly small in comparison to a shear wave speed. The existence of an interfacial wave in bonded contact permits an instability to propagate with a speed of the order of a shear wave speed even in slow sliding, indicatin...

  13. A single molecule investigation of the photostability of quantum dots.

    Directory of Open Access Journals (Sweden)

    Eva Christensen Arnspang

    Full Text Available Quantum dots (QDs are very attractive probes for multi-color fluorescence imaging in biological applications because of their immense brightness and reported extended photostability. We report here however that single QDs, suitable for biological applications, that are subject to continuous blue excitation from a conventional 100 W mercury arc lamp will undergo a continuous blue-switching of the emission wavelength eventually reaching a permanent dark, photobleached state. We further show that β-mercaptoethanol has a dual stabilizing effect on the fluorescence emission of QDs: 1 by increasing the frequency of time that a QD is in its fluorescent state, and 2 by decreasing the photobleaching rate. The observed QD color spectral switching 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. However, of significant importance for biological applications, we find that even small, biologically compatible, concentrations (25 µM of β-mercaptoethanol has a significant stabilizing effect on the emission color of QDs, but that greater amounts are required to completely abolish the spectral blue shifting or to minimize the emission intermittency of QDs.

  14. Computing magnetic anisotropy constants of single molecule magnets

    Indian Academy of Sciences (India)

    S Ramasesha; Shaon Sahoo; Rajamani Raghunathan; Diptiman Sen

    2009-09-01

    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 and spin symmetry adaptation and we illustrate this technique by solving the exchange Hamiltonian of the Cu6Fe8 system. Treating the anisotropy Hamiltonian as perturbation, we compute the and values for various eigenstates of the exchange Hamiltonian. Since, the dipolar contribution to the magnetic anisotropy is negligibly small, we calculate the molecular anisotropy from the single-ion anisotropies of the metal centers. We have studied the variation of and by rotating the single-ion anisotropies in the case of Mn12Ac and Fe8 SMMs in ground and few low-lying excited states of the exchange Hamiltonian. In both the systems, we find that the molecular anisotropy changes drastically when the single-ion anisotropies are rotated. While in Mn12Ac SMM values depend strongly on the spin of the eigenstate, it is almost independent of the spin of the eigenstate in Fe8 SMM. We also find that the value is almost insensitive to the orientation of the anisotropy of the core Mn(IV) ions. The dependence of on the energy gap between the ground and the excited states in both the systems has also been studied by using different sets of exchange constants.

  15. 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.

  16. Mapping Transcription Factors on Extended DNA: A Single Molecule Approach

    Science.gov (United States)

    Ebenstein, Yuval; Gassman, Natalie; Weiss, Shimon

    The ability to determine the precise loci and distribution of nucleic acid binding proteins is instrumental to our detailed understanding of cellular processes such as transcription, replication, and chromatin reorganization. Traditional molecular biology approaches and above all Chromatin immunoprecipitation (ChIP) based methods have provided a wealth of information regarding protein-DNA interactions. Nevertheless, existing techniques can only provide average properties of these interactions, since they are based on the accumulation of data from numerous protein-DNA complexes analyzed at the ensemble level. We propose a single molecule approach for direct visualization of DNA binding proteins bound specifically to their recognition sites along a long stretch of DNA such as genomic DNA. Fluorescent Quantum dots are used to tag proteins bound to DNA, and the complex is deposited on a glass substrate by extending the DNA to a linear form. The sample is then imaged optically to determine the precise location of the protein binding site. The method is demonstrated by detecting individual, Quantum dot tagged T7-RNA polymerase enzymes on the bacteriophage T7 genomic DNA and assessing the relative occupancy of the different promoters.

  17. A single-molecule view of gene regulation in cancer

    Science.gov (United States)

    Larson, Daniel

    2013-03-01

    Single-cell analysis has revealed that transcription is dynamic and stochastic, but tools are lacking that can determine the mechanism operating at a single gene. Here we utilize single-molecule observations of RNA in fixed and living cells to develop a single-cell model of steroid-receptor mediated gene activation. Steroid receptors coordinate a diverse range of responses in higher eukaryotes and are involved in a wide range of human diseases, including cancer. Steroid receptor response elements are present throughout the human genome and modulate chromatin remodeling and transcription in both a local and long-range fashion. As such, steroid receptor-mediated transcription is a paradigm of genetic control in the metazoan nucleus. Moreover, the ligand-dependent nature of these transcription factors makes them appealing targets for therapeutic intervention, necessitating a quantitative understanding of how receptors control output from target genes. We determine that steroids drive mRNA synthesis by frequency modulation of transcription. This digital behavior in single cells gives rise to the well-known analog dose response across the population. To test this model, we developed a light-activation technology to turn on a single gene and follow dynamic synthesis of RNA from the activated locus. The response delay is a measure of time required for chromatin remodeling at a single gene.

  18. DONOR-ACCEPTOR CONJUGATED COOLIGOMERS FOR SINGLE MOLECULE SOLAR CELLS

    Institute of Scientific and Technical Information of China (English)

    Jian-fei Qu; Jian Liu; Si-da Li; Zhi-yuan Xie; Yan-hou Geng

    2013-01-01

    Five novel donor-acceptor (D-A) conjugated cooligomers (F4B-hP,F5B-hP,F5B2[1,2]-hP,F5B2[1,3]-hP and F7B2[1,2]-hP) were synthesized.The absorption spectra of the cooligomers cover a wide range from 300 nm to 630 nm.The cooligomers could form films featured by alternating D-A lamellar nanostructures with the periods relative to the molecular lengths after thermal annealing or solvent vapor annealing.Single molecule solar cells were fabricated,and F5B-hP exhibited the best device performance.When the film of F5B-hP was thermally annealed,a power conversion efficiency (PCE) of 1.56% was realized.With solvent vapor annealing,the PCE could be further improved to 1.72% with a short-circuit current (Jsc) of 5.76 mA/cm2,an open-circuit voltage (VoC) of 0.87 V and a fill factor (FF) of 0.34.

  19. Chapter 15: Live-cell single-molecule force spectroscopy.

    Science.gov (United States)

    Dobrowsky, Terrence M; Panorchan, Porntula; Konstantopoulos, Konstantinos; Wirtz, Denis

    2008-01-01

    We describe a method to measure the kinetics and micromechanical properties of individual receptor-ligand bonds formed between two living cells. Using living cells rather than recombinant proteins ensures that the orientation, surface density, and posttranslational modifications of the probed receptors are physiological and that their regulated attachment to the cytoskeleton can occur. A cell is tethered to a flexible cantilever and brought into contact with cells adherent to a substratum before being pulled at a controlled retraction velocity. Measurements of bond rupture forces and associated bond loading rates over an extended range of retraction velocities allow us to compute precisely the tensile strength, reactive compliance, lifetime, and dissociation rate of individual intercellular receptor-ligand bonds. We also describe tests of specificity and Monte Carlo simulations, which ensure that measurements obtained by this method correspond to a single type of intercellular adhesion bond. We illustrate this live-cell single molecule force spectroscopy assay by characterizing homotypic bonds composed of vascular endothelial -cadherin pairs formed between living endothelial cells. This versatile assay could be used to establish the molecular principles that drive a wide range of important physiological processes involving receptor-mediated intercellular adhesion, such as the immunological synapse between a lymphocyte and an antigen-presenting cell and synaptic interactions between neuron cells, and pathological processes resulting in altered intercellular adhesion.

  20. 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.

  1. Single molecule analysis of Trypanosoma brucei DNA replication dynamics.

    Science.gov (United States)

    Calderano, Simone Guedes; Drosopoulos, William C; Quaresma, Marina Mônaco; Marques, Catarina A; Kosiyatrakul, Settapong; McCulloch, Richard; Schildkraut, Carl L; Elias, Maria Carolina

    2015-03-11

    Eukaryotic genome duplication relies on origins of replication, distributed over multiple chromosomes, to initiate DNA replication. A recent genome-wide analysis of Trypanosoma brucei, the etiological agent of sleeping sickness, localized its replication origins to the boundaries of multigenic transcription units. To better understand genomic replication in this organism, we examined replication by single molecule analysis of replicated DNA. We determined the average speed of replication forks of procyclic and bloodstream form cells and we found that T. brucei DNA replication rate is similar to rates seen in other eukaryotes. We also analyzed the replication dynamics of a central region of chromosome 1 in procyclic forms. We present evidence for replication terminating within the central part of the chromosome and thus emanating from both sides, suggesting a previously unmapped origin toward the 5' extremity of chromosome 1. Also, termination is not at a fixed location in chromosome 1, but is rather variable. Importantly, we found a replication origin located near an ORC1/CDC6 binding site that is detected after replicative stress induced by hydroxyurea treatment, suggesting it may be a dormant origin activated in response to replicative stress. Collectively, our findings support the existence of more replication origins in T. brucei than previously appreciated.

  2. Single molecule atomic force microscopy and force spectroscopy of chitosan.

    Science.gov (United States)

    Kocun, Marta; Grandbois, Michel; Cuccia, Louis A

    2011-02-01

    Atomic force microscopy (AFM) and AFM-based force spectroscopy was used to study the desorption of individual chitosan polymer chains from substrates with varying chemical composition. AFM images of chitosan adsorbed onto a flat mica substrate show elongated single strands or aggregated bundles. The aggregated state of the polymer is consistent with the high level of flexibility and mobility expected for a highly positively charged polymer strand. Conversely, the visualization of elongated strands indicated the presence of stabilizing interactions with the substrate. Surfaces with varying chemical composition (glass, self-assembled monolayer of mercaptoundecanoic acid/decanethiol and polytetrafluoroethylene (PTFE)) were probed with chitosan modified AFM tips and the corresponding desorption energies, calculated from plateau-like features, were attributed to the desorption of individual polymer strands. Desorption energies of 2.0±0.3×10(-20)J, 1.8±0.3×10(-20)J and 3.5±0.3×10(-20)J were obtained for glass, SAM of mercaptoundecanoic/dodecanethiol and PTFE, respectively. These single molecule level results can be used as a basis for investigating chitosan and chitosan-based materials for biomaterial applications.

  3. Single Molecule Analysis of Serotonin Transporter Regulation Using Quantum Dots

    Science.gov (United States)

    Chang, Jerry; Tomlinson, Ian; Warnement, Michael; Ustione, Alessandro; Carneiro, Ana; Piston, David; Blakely, Randy; Rosenthal, Sandra

    2011-03-01

    For the first time, we implement a novel, single molecule approach to define the localization and mobility of the brain's major target of widely prescribed antidepressant medications, the serotonin transporter (SERT). SERT labeled with single quantum dot (Qdot) revealed unsuspected features of transporter mobility with cholesterol-enriched membrane microdomains (often referred to as ``lipid rafts'') and cytoskeleton network linked to transporter activation. We document two pools of surface SERT proteins defined by their lateral mobility, one that exhibits relatively free diffusion in the plasma membrane and a second that displays significantly restricted mobility and localizes to cholesterol-enriched microdomains. Diffusion model prediction and instantaneous velocity analysis indicated that stimuli that act through p38 MAPK-dependent signaling pathways to activate SERT trigger rapid SERT movements within membrane microdomains. Cytoskeleton disruption showed that SERT lateral mobility behaves a membrane raft-constrained, cytoskeleton-associated manner. Our results identify an unsuspected aspect of neurotransmitter transporter regulation that we propose reflects the dissociation of inhibitory, SERT-associated cytoskeletal anchors.

  4. A theoretical justification for single molecule peptide sequencing.

    Directory of Open Access Journals (Sweden)

    Jagannath Swaminathan

    2015-02-01

    Full Text Available The proteomes of cells, tissues, and organisms reflect active cellular processes and change continuously in response to intracellular and extracellular cues. Deep, quantitative profiling of the proteome, especially if combined with mRNA and metabolite measurements, should provide an unprecedented view of cell state, better revealing functions and interactions of cell components. Molecular diagnostics and biomarker discovery should benefit particularly from the accurate quantification of proteomes, since complex diseases like cancer change protein abundances and modifications. Currently, shotgun mass spectrometry is the primary technology for high-throughput protein identification and quantification; while powerful, it lacks high sensitivity and coverage. We draw parallels with next-generation DNA sequencing and propose a strategy, termed fluorosequencing, for sequencing peptides in a complex protein sample at the level of single molecules. In the proposed approach, millions of individual fluorescently labeled peptides are visualized in parallel, monitoring changing patterns of fluorescence intensity as N-terminal amino acids are sequentially removed, and using the resulting fluorescence signatures (fluorosequences to uniquely identify individual peptides. We introduce a theoretical foundation for fluorosequencing and, by using Monte Carlo computer simulations, we explore its feasibility, anticipate the most likely experimental errors, quantify their potential impact, and discuss the broad potential utility offered by a high-throughput peptide sequencing technology.

  5. Ferromagnetic manganese "cubes": from PSII to single-molecule magnets.

    Science.gov (United States)

    Inglis, Ross; Stoumpos, Constantinos C; Prescimone, Alessandro; Siczek, Milosz; Lis, Tadeusz; Wernsdorfer, Wolfgang; Brechin, Euan K; Milios, Constantinos J

    2010-05-28

    The reaction of Mn(O₂CMe)₂·2H₂O with Me-saoH₂ (Me-saoH₂ = 2-hydroxyphenylethanone oxime) in MeCN forms the complex [Mn(III)₄(Me-sao)₄(Me-saoH)₄] (1) in good yields. Replacing Me-saoH₂ with Naphth-saoH₂ (Naphth-saoH₂ = 2-hydroxy-1-napthaldoxime) in the presence of CH₃ONa forms the complex [Mn(III)₄(Naphth-sao)₄(Naphth-saoH)₄] (2) in low yields, while the reaction between Mn(ClO₄)₂·6H₂O, Et-saoH₂ (Et-saoH₂= 2-hydroxypropiophenone oxime) and NBu₄OH in MeCN gives the complex [Mn(III)₄(Et-sao)₄(Et-saoH)₄] (3) in moderate yields. All three tetrametallic cages exclusively contain Mn(III) centres arranged in a "cube"-like topology, in which the metal centres are connected by -N-O(oximate) groups. The magnetic properties of 1-3 are near identical, revealing the presence of only ferromagnetic interactions between the metal ions leading to high-spin ground states of S = 8. The complexes display frequency dependent out-of-phase signals in ac susceptibility studies and, in the case of 1 single-molecule magnetism has been observed by means of single-crystal hysteresis loop measurements.

  6. High-resolution optical tweezers for single-molecule manipulation.

    Science.gov (United States)

    Zhang, Xinming; Ma, Lu; Zhang, Yongli

    2013-09-01

    Forces hold everything together and determine its structure and dynamics. In particular, tiny forces of 1-100 piconewtons govern the structures and dynamics of biomacromolecules. These forces enable folding, assembly, conformational fluctuations, or directional movements of biomacromolecules over sub-nanometer to micron distances. Optical tweezers have become a revolutionary tool to probe the forces, structures, and dynamics associated with biomacromolecules at a single-molecule level with unprecedented resolution. In this review, we introduce the basic principles of optical tweezers and their latest applications in studies of protein folding and molecular motors. We describe the folding dynamics of two strong coiled coil proteins, the GCN4-derived protein pIL and the SNARE complex. Both complexes show multiple folding intermediates and pathways. ATP-dependent chromatin remodeling complexes translocate DNA to remodel chromatin structures. The detailed DNA translocation properties of such molecular motors have recently been characterized by optical tweezers, which are reviewed here. Finally, several future developments and applications of optical tweezers are discussed. These past and future applications demonstrate the unique advantages of high-resolution optical tweezers in quantitatively characterizing complex multi-scale dynamics of biomacromolecules.

  7. 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.

  8. Optical microcavity: sensing down to single molecules and atoms.

    Science.gov (United States)

    Yoshie, Tomoyuki; Tang, Lingling; Su, Shu-Yu

    2011-01-01

    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.

  9. Rapid sequencing of DNA based on single-molecule detection

    Science.gov (United States)

    Soper, Steven A.; Davis, Lloyd M.; Fairfield, Frederick R.; Hammond, Mark L.; Harger, Carol A.; Jett, James H.; Keller, Richard A.; Marrone, Babetta L.; Martin, John C.; Nutter, Harvey L.; Shera, E. Brooks; Simpson, Daniel J.

    1991-07-01

    Sequencing the human genome is a major undertaking considering the large number of nucleotides present in the genome and the slow methods currently available to perform the task. The authors have recently reported on a scheme to sequence DNA rapidly using a non-gel based technique. The concept is based upon the incorporation of fluorescently labeled nucleotides into a strand of DNA, isolation and manipulation of a labeled DNA fragment and the detection of single nucleotides using ultra-sensitive laser-induced fluorescence detection following their cleavage from the fragment. Detection of individual fluorophores in the liquid phase was accomplished with time-gated detection following pulsed-laser excitation. The photon bursts from individual rhodamine 6G (R6G) molecules travelling through a laser beam have been observed, as have bursts from single fluorescently modified nucleotides. Using two different biotinylated nucleotides as a model system for fluorescently labeled nucleotides, the authors have observed synthesis of the complementary copy of M13 bacteriophage. Work with fluorescently labeled nucleotides is underway. Individual molecules of DNA attached to a microbead have been observed and manipulated with an epifluorescence microscope.

  10. 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.

  11. Single-molecule magnet Mn12 on graphene

    Science.gov (United States)

    Li, Xiang-Guo; Fry, James N.; Cheng, Hai-Ping

    2014-09-01

    We study energetics, electronic and magnetic structures, and magnetic anisotropy barriers of a monolayer of single-molecule magnets (SMMs), [Mn12O12(COOR)16](H2O)4 (abbreviated as Mn12, with R=H, CH3, C6H5, and CHCl2), on a graphene surface using spin-polarized density-functional theory with generalized gradient corrections and the inclusion of van der Waals interactions. We find that Mn12 molecules with ligands -H, -CH3, and -C6H5 are physically adsorbed on graphene through weak van der Waals interactions, and a much stronger ionic interaction occurs using a -CHCl2 ligand. The strength of bonding is closely related to the charge transfer between the molecule and the graphene sheet and can be manipulated by strain in the graphene; specifically, tension enhances n doping of graphene, and compression encourages p doping. The magnetic anisotropy barrier is computed by including the spin-orbit interaction within density-functional theory. The barriers for the Mn12 molecules with ligands -H, -CH3 and -C6H5 on graphene surfaces remain unchanged (within 1K) from those of isolated molecules because of their weak interaction, and a much larger reduction (10K) is observed when using the -CHCl2 ligand on graphene due to a substantial structural deformation as a consequence of the much stronger interaction. Neither strain in graphene nor charge transfer affects the magnetic anisotropy barrier significantly. Finally, we discuss the effect of strong correlation in the high-spin state of a Mn12 SMM and the consequence of SMM-surface adsorption.

  12. Lab-on-a-chip technologies for single-molecule studies.

    Science.gov (United States)

    Zhao, Yanhui; Chen, Danqi; Yue, Hongjun; French, Jarrod B; Rufo, Joseph; Benkovic, Stephen J; Huang, Tony Jun

    2013-06-21

    Recent developments on various lab-on-a-chip techniques allow miniaturized and integrated devices to perform on-chip single-molecule studies. Fluidic-based platforms that utilize unique microscale fluidic behavior are capable of conducting single-molecule experiments with high sensitivities and throughputs, while biomolecular systems can be studied on-chip using techniques such as DNA curtains, magnetic tweezers, and solid-state nanopores. The advances of these on-chip single-molecule techniques lead to next-generation lab-on-a-chip devices, such as DNA transistors, and single-molecule real-time (SMRT) technology for rapid and low-cost whole genome DNA sequencing. In this Focus article, we will discuss some recent successes in the development of lab-on-a-chip techniques for single-molecule studies and expound our thoughts on the near future of on-chip single-molecule studies.

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

    OpenAIRE

    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 ...

  14. Single-molecule studies of the Im7 folding landscape.

    Science.gov (United States)

    Pugh, Sara D; Gell, Christopher; Smith, D Alastair; Radford, Sheena E; Brockwell, David J

    2010-04-23

    Under appropriate conditions, the four-helical Im7 (immunity protein 7) folds from an ensemble of unfolded conformers to a highly compact native state via an on-pathway intermediate. Here, we investigate the unfolded, intermediate, and native states populated during folding using diffusion single-pair fluorescence resonance energy transfer by measuring the efficiency of energy transfer (or proximity or P ratio) between pairs of fluorophores introduced into the side chains of cysteine residues placed in the center of helices 1 and 4, 1 and 3, or 2 and 4. We show that while the native states of each variant give rise to a single narrow distribution with high P values, the distributions of the intermediates trapped at equilibrium (denoted I(eqm)) are fitted by two Gaussian distributions. Modulation of the folding conditions from those that stabilize the intermediate to those that destabilize the intermediate enabled the distribution of lower P value to be assigned to the population of the unfolded ensemble in equilibrium with the intermediate state. The reduced stability of the I(eqm) variants allowed analysis of the effect of denaturant concentration on the compaction and breadth of the unfolded state ensemble to be quantified from 0 to 6 M urea. Significant compaction is observed as the concentration of urea is decreased in both the presence and absence of sodium sulfate, as previously reported for a variety of proteins. In the presence of Na(2)SO(4) in 0 M urea, the P value of the unfolded state ensemble approaches that of the native state. Concurrent with compaction, the ensemble displays increased peak width of P values, possibly reflecting a reduction in the rate of conformational exchange among iso-energetic unfolded, but compact conformations. The results provide new insights into the initial stages of folding of Im7 and suggest that the unfolded state is highly conformationally constrained at the outset of folding.

  15. Communication: One size fits all: Equilibrating chemically different polymer liquids through universal long-wavelength description

    Science.gov (United States)

    Zhang, Guojie; Stuehn, Torsten; Daoulas, Kostas Ch.; Kremer, Kurt

    2015-06-01

    Mesoscale behavior of polymers is frequently described by universal laws. This physical property motivates us to propose a new modeling concept, grouping polymers into classes with a common long-wavelength representation. In the same class, samples of different materials can be generated from this representation, encoded in a single library system. We focus on homopolymer melts, grouped according to the invariant degree of polymerization. They are described with a bead-spring model, varying chain stiffness and density to mimic chemical diversity. In a renormalization group-like fashion, library samples provide a universal blob-based description, hierarchically backmapped to create configurations of other class-members. Thus, large systems with experimentally relevant invariant degree of polymerizations (so far accessible only on very coarse-grained level) can be microscopically described. Equilibration is verified comparing conformations and melt structure with smaller scale conventional simulations.

  16. Observations of Rotating Radio Transients with the First Station of the Long Wavelength Array

    CERN Document Server

    Taylor, G B; McCrackan, M; McLaughlin, M A; Miller, R; Karako-Argaman, C; Dowell, J; Schinzel, F K

    2016-01-01

    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 MHz and 88 MHz. The RRATs observed here were first detected in higher frequency pulsar surveys. Of the 19 RRATs observed, 2 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 the higher frequency telescopes, and the result of scattering by the interstellar medium or a spectral turnover.

  17. Long-Wavelength X-Ray Diffraction and Its Applications in Macromolecular Crystallography.

    Science.gov (United States)

    Weiss, Manfred S

    2017-01-01

    For many years, diffraction experiments in macromolecular crystallography at X-ray wavelengths longer than that of Cu-K α (1.54 Å) have been largely underappreciated. Effects caused by increased X-ray absorption result in the fact that these experiments are more difficult than the standard diffraction experiments at short wavelengths. However, due to the also increased anomalous scattering of many biologically relevant atoms, important additional structural information can be obtained. This information, in turn, can be used for phase determination, for substructure identification, in molecular replacement approaches, as well as in structure refinement. This chapter reviews the possibilities and the difficulties associated with such experiments, and it provides a short description of two macromolecular crystallography synchrotron beam lines dedicated to long-wavelength X-ray diffraction experiments.

  18. Performance of PILATUS detector technology for long-wavelength macromolecular crystallography

    Science.gov (United States)

    Marchal, J.; Wagner, A.

    2011-05-01

    The long-wavelength MX beamline I23 currently under design at Diamond Light Source will be optimized in the X-ray energy range between 3 and 5 keV. At the moment no commercial off-the-shelf detector with high quantum efficiency and dynamic range is available to cover the large area required for diffraction experiments in this energy range. The hybrid pixel detector technology used in PILATUS detectors could overcome these limitations as the modular design could allow a large coverage in reciprocal space and high detection efficiency. Experiments were carried out on the Microfocus Spectroscopy beamline I18 at Diamond Light Source to test the performance of a 100K PILATUS module in the low-energy range from 2.3 to 3.7 keV.

  19. Long wavelength gravity anomalies over India: Crustal and lithospheric structures and its flexure

    Science.gov (United States)

    Tiwari, V. M.; Ravi Kumar, M.; Mishra, D. C.

    2013-07-01

    Long wavelength gravity anomalies over India were obtained from terrestrial gravity data through two independent methods: (i) wavelength filtering and (ii) removing crustal effects. The gravity fields due to the lithospheric mantle obtained from two methods were quite comparable. The long wavelength gravity anomalies were interpreted in terms of variations in the depth of the lithosphere-asthenosphere boundary (LAB) and the Moho with appropriate densities, that are constrained from seismic results at certain points. Modeling of the long wavelength gravity anomaly along a N-S profile (77°E) suggest that the thickness of the lithosphere for a density contrast of 0.05 g/cm3 with the asthenosphere is maximum of ˜190 km along the Himalayan front that reduces to ˜155 km under the southern part of the Ganga and the Vindhyan basins increasing to ˜175 km south of the Satpura Mobile belt, reducing to ˜155-140 km under the Eastern Dharwar craton (EDC) and from there consistently decreasing south wards to ˜120 km under the southernmost part of India, known as Southern Granulite Terrain (SGT). The crustal model clearly shows three distinct terrains of different bulk densities, and thicknesses, north of the SMB under the Ganga and the Vindhyan basins, and south of it the Eastern Dharwar Craton (EDC) and the Southern Granulite Terrain (SGT) of bulk densities 2.87, 2.90 and 2.96 g/cm3, respectively. It is confirmed from the exposed rock types as the SGT is composed of high bulk density lower crustal rocks and mafic/ultramafic intrusives while the EDC represent typical granite/gneisses rocks and the basement under the Vindhyan and Ganga basins towards the north are composed of Bundelkhand granite massif of the lower density. The crustal thickness along this profile varies from ˜37-38 km under the EDC, increasing to ˜40-45 km under the SGT and ˜40-42 km under the northern part of the Ganga basin with a bulge up to ˜36 km under its southern part. Reduced lithospheric and

  20. Long Wavelength Plasmonic Absorption Enhancement in Silicon Using Optical Lithography Compatible Core-Shell-Type Nanowires

    Directory of Open Access Journals (Sweden)

    Mohammed Shahriar Sabuktagin

    2014-01-01

    Full Text Available Plasmonic properties of rectangular core-shell type nanowires embedded in thin film silicon solar cell structure were characterized using FDTD simulations. Plasmon resonance of these nanowires showed tunability from  nm. However this absorption was significantly smaller than the Ohmic loss in the silver shell due to very low near-bandgap absorption properties of silicon. Prospect of improving enhanced absorption in silicon to Ohmic loss ratio by utilizing dual capability of these nanowires in boosting impurity photovoltaic effect and efficient extraction of the photogenerated carriers was discussed. Our results indicate that high volume fabrication capacity of optical lithography techniques can be utilized for plasmonic absorption enhancement in thin film silicon solar cells over the entire long wavelength range of solar radiation.

  1. Carrier field shock formation of long wavelength femtosecond pulses in dispersive media

    CERN Document Server

    Panagiotopoulos, Paris; Kolesik, Miroslav; Moloney, Jerome V

    2015-01-01

    We numerically demonstrate the formation of carrier field shocks in various dispersive media for a wide variety of input conditions using two different electric field propagation models. In addition, an investigation of the impact of numerous physical effects on carrier wave shock is performed. It is shown that in many cases a field shock is essentially unavoidable and therefore extremely important in the propagation of intense long wavelength pulses in weakly dispersive nonlinear media such as noble gases, air, and single-crystal diamond. The results presented here are expected to have a significant impact in the field of ultrashort nonlinear optics, attosecond pulse generation, and wavepacket synthesis where the use of mid-IR wavelengths is becoming increasingly more important.

  2. Convection-driven compaction as a possible origin of Enceladus's long wavelength topography

    Science.gov (United States)

    Besserer, J.; Nimmo, F.; Roberts, J. H.; Pappalardo, R. T.

    2013-05-01

    The long wavelength surface topography of Enceladus shows depressions about 1 km in depth and ˜102 km wide. One possible cause of this topography is spatially variable amounts of compaction of an initially porous ice shell, driven by spatial variations in heat flux. Here, we show that the heat flux variations associated with convection in the shell can quantitatively match the observed features. We develop a simple model of viscous compaction that includes the effect of porosity on thermal conductivity, and find that an initial shell porosity of at least 20-25% is required to develop the observed topography over ˜1 Ga. This mechanism produces topographic depressions, not rises, above convective upwellings, and does not generate detectable gravity anomalies. Unlike transient dynamic topography, it can potentially leave a permanent record of ancient convective processes in the shallow lithospheres of icy satellites.

  3. Characterisation of the RNA interference response against the long-wavelength receptor of the honeybee.

    Science.gov (United States)

    Leboulle, Gérard; Niggebrügge, Claudia; Roessler, Reinhard; Briscoe, Adriana D; Menzel, Randolf; Hempel de Ibarra, Natalie

    2013-10-01

    Targeted knock-down is the method of choice to advance the study of sensory and brain functions in the honeybee by using molecular techniques. Here we report the results of a first attempt to interfere with the function of a visual receptor, the long-wavelength-sensitive (L-) photoreceptor. RNA interference to inhibit this receptor led to a reduction of the respective mRNA and protein. The interference effect was limited in time and space, and its induction depended on the time of the day most probably because of natural daily variations in opsin levels. The inhibition did not effectively change the physiological properties of the retina. Possible constraints and implications of this method for the study of the bee's visual system are discussed. Overall this study underpins the usefulness and feasibility of RNA interference as manipulation tool in insect brain research.

  4. Simulation of Ultra-Long Wavelength interferometer in the Earth orbit and on the lunar surface

    CERN Document Server

    Zhang, Mo; Yan, Yihua

    2014-01-01

    We present simulations for interferometer arrays in Earth orbit and on the lunar surface to guide the design and optimization of space-based Ultra-Long Wavelength missions, such as those of China's Chang'E program. We choose parameters and present simulations using simulated data to identify inter-dependencies and constraints on science and engineering parameters. A regolith model is created for the lunar surface array simulation, the results show that the lunar regolith will have an undesirable effect on the observation. We estimate data transmission requirement, calculate sensitivities for both cases, and discuss the trade-off between brightness temperature sensitivity and angular resolution for the Earth orbit array case.

  5. Properties of new, long-wavelength, voltage-sensitive dyes in the heart.

    Science.gov (United States)

    Salama, G; Choi, B-R; Azour, G; Lavasani, M; Tumbev, V; Salzberg, B M; Patrick, M J; Ernst, L A; Waggoner, A S

    2005-11-01

    Membrane potential measurements using voltage-sensitive dyes (VSDs) have made important contributions to our understanding of electrophysiological properties of multi-cellular systems. Here, we report the development of long wavelength VSDs designed to record cardiac action potentials (APs) from deeper layers in the heart. The emission spectrum of styryl VSDs was red-shifted by incorporating a thienyl group in the polymethine bridge to lengthen and retain the rigidity of the chromophore. Seven dyes, Pittsburgh I to IV and VI to VIII (PGH I-VIII) were synthesized and characterized with respect to their spectral properties in organic solvents and heart muscles. PGH VSDs exhibited 2 absorption, 2 excitation and 2 voltage-sensitive emission peaks, with large Stokes shifts (> 100 nm). Hearts (rabbit, guinea pig and Rana pipiens) and neurohypophyses (CD-1 mice) were effectively stained by injecting a bolus (10-50 microl) of stock solution of VSD (2-5 mM) dissolved in in dimethylsulfoxide plus low molecular weight Pluronic (16% of L64). Other preparations were better stained with a bolus of VSD (2-5 mM) Tyrode's solution at pH 6.0. Action spectra measured with a fast CCD camera showed that PGH I exhibited an increase in fractional fluorescence, DeltaF/F = 17.5 % per AP at 720 nm with 550 nm excitation and DeltaF/F = - 6% per AP at 830 nm with 670 nm excitation. In frog hearts, PGH1 was stable with approximately 30% decrease in fluorescence and AP amplitude during 3 h of intermittent excitation or 1 h of continuous high intensity excitation (300 W Xe-Hg Arc lamp), which was attributed to a combination of dye wash out > photobleaching > dynamic damage > run down of the preparation. The long wavelengths, large Stokes shifts, high DeltaF/F and low baseline fluorescence make PGH dyes a valuable tool in optical mapping and for simultaneous mapping of APs and intracellular Ca(2+).

  6. Exploring the Last Electromagnetic Frontier with the Long Wavelength Array (LWA)

    Science.gov (United States)

    Kassim, Namir E.; Cohen, A. S.; Crane, P. C.; Gross, C. A.; Hicks, B. C.; Lane, W. M.; Lazio, J.; Polisensky, E. J.; Ray, P. S.; Weiler, K. W.; Clarke, T. E.; Schmitt, H. R.; Hartman, J. M.; Helmboldt, J. F.; Craig, J.; Gerstle, W.; Pihlstrom, Y.; Rickard, L. J.; Taylor, G. B.; Ellingson, S. W.; D'Addario, L. R.; Navarro, R.

    2009-05-01

    Several decades ago, instruments like the Very Large Array (VLA) first opened the GHz frequency sky to high dynamic range imaging. Today, a path-finding VLA 74 MHz system is providing the first sub-arcminute resolution view of the radio universe below 100 MHz, a technical innovation inspiring an emerging suite of large (> 100 km), much more powerful long-wavelength instruments including the Long Wavelength Array (LWA). Similar in philosophy to the VLA and also located in New Mexico, the LWA will be a versatile, user-oriented electronic array designed to open the 20--80 MHz frequency range to detailed exploration for the first time. The LWA's mJy sensitivity and near-arcsecond resolution will surpass, by 2--3 orders of magnitude, the imaging power of previous interferometers in its frequency range. LWA scientific frontiers include: (1) the high-z universe, including distant radio galaxies and clusters - tools for understanding the earliest black holes and the cosmological evolution of Dark Matter and Dark Energy, respectively; (2) acceleration, propagation, and turbulence in the ISM, including the space-distribution and spectrum of Galactic cosmic rays and supernova remnants; (3) planetary, solar, and space science, including space-weather prediction and extra-solar planet searches; and (4) the radio transient universe including GRBs, ultra-high energy cosmic rays, and new sources of unknown origin. Because the LWA will explore one of the most poorly investigated spectral regions the potential for new discoveries is high, and there is a strong synergy with exciting new X-ray and Gamma-ray measurements. The LWA will also provide an unparalleled measure of small-scale ionospheric structure, a pre-requisite for accurate calibration and imaging. This presentation focuses on LWA science, while a companion paper reviews the technical design subjected to Preliminary Design Review in March 2009. Basic research in radio astronomy at the Naval Research Laboratory is supported

  7. From nanofabrication to self-fabrication--tailored chemistry for control of single molecule electronic devices

    DEFF Research Database (Denmark)

    Moth-Poulsen, Kasper; Bjørnholm, Thomas

    2010-01-01

    as alternatives to the dominant top-down nanofabrication techniques. One example is solution-based self-assembly of a molecule enclosed by two gold nanorod electrodes. This article will discuss recent attempts to control the self-assembly process by the use of supramolecular chemistry and how to tailor......Single molecule electronics is a field of research focused on the use of single molecules as electronics components. During the past 15 years the field has concentrated on development of test beds for measurements on single molecules. Bottom-up approaches to single molecule devices are emerging...

  8. Calix[4]arene Based Single-Molecule Magnets

    Energy Technology Data Exchange (ETDEWEB)

    Karotsis, Georgios; Teat, Simon J.; Wernsdorfer, Wolfgang; Piligkos, Stergios; Dalgarno, Scott J.; Brechin, Euan K.

    2009-06-04

    Single-molecule magnets (SMMs) have been the subject of much interest in recent years because their molecular nature and inherent physical properties allow the crossover between classical and quantum physics to be observed. The macroscopic observation of quantum phenomena - tunneling between different spin states, quantum interference between tunnel paths - not only allows scientists to study quantum mechanical laws in great detail, but also provides model systems with which to investigate the possible implementation of spin-based solid state qubits and molecular spintronics. The isolation of small, simple SMMs is therefore an exciting prospect. To date almost all SMMs have been made via the self-assembly of 3d metal ions in the presence of bridging/chelating organic ligands. However, very recently an exciting new class of SMMs, based on 3d metal clusters (or single lanthanide ions) housed within polyoxometalates, has appeared. These types of molecule, in which the SMM is completely encapsulated within (or shrouded by) a 'protective' organic or inorganic sheath have much potential for design and manipulation: for example, for the removal of unwanted dipolar interactions, the introduction of redox activity, or to simply aid functionalization for surface grafting. Calix[4]arenes are cyclic (typically bowl-shaped) polyphenols that have been used extensively in the formation of versatile self-assembled supramolecular structures. Although many have been reported, p-{sup t}But-calix[4]arene and calix[4]arene (TBC4 and C4 respectively, Figure 1A) are frequently encountered due to (a) synthetic accessibility, and (b) vast potential for alteration at either the upper or lower rim of the macrocyclic framework. Within the field of supramolecular chemistry, TBC4 is well known for interesting polymorphic behavior and phase transformations within anti-parallel bi-layer arrays, while C4 often forms self-included trimers. The polyphenolic nature of calix[n]arenes (where

  9. Theoretical analysis of single molecule spectroscopy lineshapes of conjugated polymers

    Science.gov (United States)

    Devi, Murali

    Conjugated Polymers(CPs) exhibit a wide range of highly tunable optical properties. Quantitative and detailed understanding of the nature of excitons responsible for such a rich optical behavior has significant implications for better utilization of CPs for more efficient plastic solar cells and other novel optoelectronic devices. In general, samples of CPs are plagued with substantial inhomogeneous broadening due to various sources of disorder. Single molecule emission spectroscopy (SMES) offers a unique opportunity to investigate the energetics and dynamics of excitons and their interactions with phonon modes. The major subject of the present thesis is to analyze and understand room temperature SMES lineshapes for a particular CP, called poly(2,5-di-(2'-ethylhexyloxy)-1,4-phenylenevinylene) (DEH-PPV). A minimal quantum mechanical model of a two-level system coupled to a Brownian oscillator bath is utilized. The main objective is to identify the set of model parameters best fitting a SMES lineshape for each of about 200 samples of DEH-PPV, from which new insight into the nature of exciton-bath coupling can be gained. This project also entails developing a reliable computational methodology for quantum mechanical modeling of spectral lineshapes in general. Well-known optimization techniques such as gradient descent, genetic algorithms, and heuristic searches have been tested, employing an L2 measure between theoretical and experimental lineshapes for guiding the optimization. However, all of these tend to result in theoretical lineshapes qualitatively different from experimental ones. This is attributed to the ruggedness of the parameter space and inadequateness of the L2 measure. On the other hand, when the dynamic reduction of the original parameter space to a 2-parameter space through feature searching and visualization of the search space paths using directed acyclic graphs(DAGs), the qualitative nature of the fitting improved significantly. For a more

  10. Single molecule studies of DNA packaging by bacteriophages

    Science.gov (United States)

    Fuller, Derek Nathan

    The DNA packaging dynamics of bacteriophages φ29, gamma, and T4 were studied at the single molecule level using a dual trap optical tweezers. Also, a method for producing long DNA molecules by PCR for optical tweezers studies of protein DNA interactions is presented and thoroughly characterized. This DNA preparation technique provided DNA samples for the φ29 and T4 studies. In the studies of φ29, the role of charge was investigated by varying the ionic conditions of the packaging buffer. Ionic conditions in which the DNA charge was highly screened due to divalent and trivalent cations showed the lowest resistance to packaging of the DNA to high density. This confirmed the importance of counterions in shielding the DNA interstrand repulsion when packaged to high density. While the ionic nature of the packaging buffer had a strong effect on packaging velocities, there was no clear trend between the counterion-screened charge of the DNA and the maximum packaging velocity. The packaging studies of lambda and T4 served as systems for comparative studies with φ29. Each system showed similarities to the φ29 system and unique differences. Both the lambda and T4 packaging motors were capable of generating forces in excess of 50 pN and showed remarkably high processivity, similar to φ29. However, dynamic structural transitions were observed with lambda that are not observed with φ29. The packaging of the lambda genome showed capsid expansion at approximately 30 percent of the genome packaged and capsid rupture at 90 percent of the genome packaged in the absence of capsid stabilizing protein gpD. Unique to the T4 packaging motor, packaging dynamics showed a remarkable amount of variability in velocities. This variability was seen both within individual packaging phages and from one phage to the next. This is possibly due to different conformational states of the packaging machinery. Additionally, lambda and T4 had average packaging velocities under minimal load of 600

  11. Calix[4]arene Based Single-Molecule Magnets

    Energy Technology Data Exchange (ETDEWEB)

    Karotsis, Georgios; Teat, Simon J.; Wernsdorfer, Wolfgang; Piligkos, Stergios; Dalgarno, Scott J.; Brechin, Euan K.

    2009-06-04

    Single-molecule magnets (SMMs) have been the subject of much interest in recent years because their molecular nature and inherent physical properties allow the crossover between classical and quantum physics to be observed. The macroscopic observation of quantum phenomena - tunneling between different spin states, quantum interference between tunnel paths - not only allows scientists to study quantum mechanical laws in great detail, but also provides model systems with which to investigate the possible implementation of spin-based solid state qubits and molecular spintronics. The isolation of small, simple SMMs is therefore an exciting prospect. To date almost all SMMs have been made via the self-assembly of 3d metal ions in the presence of bridging/chelating organic ligands. However, very recently an exciting new class of SMMs, based on 3d metal clusters (or single lanthanide ions) housed within polyoxometalates, has appeared. These types of molecule, in which the SMM is completely encapsulated within (or shrouded by) a 'protective' organic or inorganic sheath have much potential for design and manipulation: for example, for the removal of unwanted dipolar interactions, the introduction of redox activity, or to simply aid functionalization for surface grafting. Calix[4]arenes are cyclic (typically bowl-shaped) polyphenols that have been used extensively in the formation of versatile self-assembled supramolecular structures. Although many have been reported, p-{sup t}But-calix[4]arene and calix[4]arene (TBC4 and C4 respectively, Figure 1A) are frequently encountered due to (a) synthetic accessibility, and (b) vast potential for alteration at either the upper or lower rim of the macrocyclic framework. Within the field of supramolecular chemistry, TBC4 is well known for interesting polymorphic behavior and phase transformations within anti-parallel bi-layer arrays, while C4 often forms self-included trimers. The polyphenolic nature of calix[n]arenes (where

  12. Localization microscopy: mapping cellular dynamics with single molecules.

    Science.gov (United States)

    Nelson, A J; Hess, S T

    2014-04-01

    Resolution describes the smallest details within a sample that can be recovered by a microscope lens system. For optical microscopes detecting visible light, diffraction limits the resolution to ∼200-250 nm. In contrast, localization measures the position of an isolated object using its image. Single fluorescent molecules can be localized with an uncertainty of a few tens of nanometres, and in some cases less than one nanometre. Superresolution fluorescence localization microscopy (SRFLM) images and localizes fluorescent molecules in a sample. By controlling the visibility of the fluorescent molecules with light, it is possible to cause a sparse subset of the tags to fluoresce and be spatially separated from each other. A movie is acquired with a camera, capturing images of many sets of visible fluorescent tags over a period of time. The movie is then analysed by a computer whereby all of the single molecules are independently measured, and their positions are recorded. When the coordinates of a sufficient number of molecules are collected, an image can be rendered by plotting the coordinates of the localized molecules. The spatial resolution of these rendered images can be better than 20 nm, roughly an order of magnitude better than the diffraction limited resolution. The invention of SRFLM has led to an explosion of related techniques. Through the use of specialized optics, the fluorescent signal can be split into multiple detection channels. These channels can capture additional information such as colour (emission wavelength), orientation and three-dimensional position of the detected molecules. Measurement of the colour of the detected fluorescence can allow researchers to distinguish multiple types of fluorescent tags and to study the interaction between multiple molecules of interest. Three-dimensional imaging and determination of molecular orientations offer insight into structural organization of the sample. SRFLM is compatible with living samples and

  13. Novel High-Activity Organic Piezoelectric Materials - From Single-Molecule Response to Energy Harvesting Films

    Science.gov (United States)

    2015-08-24

    Mirman, B.; Karapetian, E. “Relationship between Direct and Converse Piezoelectric Effect in a Nanoscale Electromechanical Contact,” Physical Review B...response of organic hydrogen-bonded crystals and single-molecule electromechanical response. Using the known piezoelectric response of crystalline 2...Using computational exploration of the electromechanical response other molecular scaffolds, we explored single-molecule ferroelectrics based on

  14. Direct Observation of Magnetic Anisotropy in an Individual Fe4 Single-Molecule Magnet

    NARCIS (Netherlands)

    Burzuri, E.; Zyazin, A.S.; Cornia, A.; Van der Zant, H.S.J.

    2012-01-01

    We study three-terminal charge transport through individual Fe4 single-molecule magnets. Magnetic anisotropy of the single molecule is directly observed by introducing a spectroscopic technique based on measuring the position of the degeneracy point as a function of gate voltage and applied magnetic

  15. 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

  16. Electrochemical detection of single molecules using abiotic nanopores having electrically tunable dimensions

    Science.gov (United States)

    Sansinena, Jose-Maria; Redondo, Antonio; Olazabal, Virginia; Hoffbauer, Mark A.; Akhadov, Elshan A.

    2009-12-29

    A barrier structure for use in an electrochemical stochastic membrane sensor for single molecule detection. The sensor is based upon inorganic nanopores having electrically tunable dimensions. The inorganic nanopores are formed from inorganic materials and an electrically conductive polymer. Methods of making the barrier structure and sensing single molecules using the barrier structure are also described.

  17. Injection molded nanofluidic chips: Fabrication method and functional tests using single-molecule DNA experiments

    DEFF Research Database (Denmark)

    Utko, Pawel; Persson, Karl Fredrik; Kristensen, Anders;

    2011-01-01

    We demonstrate that fabrication of nanofluidic systems can be greatly simplified by injection molding of polymers. We functionally test our devices by single-molecule DNA experiments in nanochannels.......We demonstrate that fabrication of nanofluidic systems can be greatly simplified by injection molding of polymers. We functionally test our devices by single-molecule DNA experiments in nanochannels....

  18. Direct Observation of Magnetic Anisotropy in an Individual Fe4 Single-Molecule Magnet

    NARCIS (Netherlands)

    Burzuri, E.; Zyazin, A.S.; Cornia, A.; Van der Zant, H.S.J.

    2012-01-01

    We study three-terminal charge transport through individual Fe4 single-molecule magnets. Magnetic anisotropy of the single molecule is directly observed by introducing a spectroscopic technique based on measuring the position of the degeneracy point as a function of gate voltage and applied magnetic

  19. Single molecules in soft matter : a study of biomolecular conformation, heterogeneity and plasmon enhanced fluorescence

    NARCIS (Netherlands)

    Yuan, Haifeng

    2013-01-01

    We study the dynamics of single molecules and individual gold nanorods in glycerol at variable temperatures. We demonstrate temperature-cycle microscopy on FRET-labeled polyproline and double-stranded DNA molecules to access micro-second dynamics of single molecules, and reveal the influences of dye

  20. 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

    2012-01-01

    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 d

  1. Electrochemical detection of single molecules using abiotic nanopores having electrically tunable dimensions

    Energy Technology Data Exchange (ETDEWEB)

    Sansinena, Jose-Maria; Redondo, Antonio; Olazabal, Virginia; Hoffbauer, Mark A.

    2017-09-12

    A barrier structure for use in an electrochemical stochastic membrane sensor for single molecule detection. The sensor is based upon inorganic nanopores having electrically tunable dimensions. The inorganic nanopores are formed from inorganic materials and an electrically conductive polymer. Methods of making the barrier structure and sensing single molecules using the barrier structure are also described.

  2. Electrochemical detection of single molecules using abiotic nanopores having electrically tunable dimensions

    Energy Technology Data Exchange (ETDEWEB)

    Sansinena, Jose-Maria; Redondo, Antonio; Olazabal, Virginia; Hoffbauer, Mark A.; Akhadov, Elshan A.

    2017-07-18

    A barrier structure for use in an electrochemical stochastic membrane sensor for single molecule detection. The sensor is based upon inorganic nanopores having electrically tunable dimensions. The inorganic nanopores are formed from inorganic materials and an electrically conductive polymer. Methods of making the barrier structure and sensing single molecules using the barrier structure are also described.

  3. Recent Advances in Biological Single-Molecule Applications of Optical Tweezers and Fluorescence Microscopy

    NARCIS (Netherlands)

    Hashemi Shabestari, M; Meijering, A E C; Roos, W H; Wuite, G J L; Peterman, E J G

    2017-01-01

    Over the past two decades, single-molecule techniques have evolved into robust tools to study many fundamental biological processes. The combination of optical tweezers with fluorescence microscopy and microfluidics provides a powerful single-molecule manipulation and visualization technique that

  4. Resolving Single-Molecule Assembled Patterns with Superresolution Blink-Microscopy

    NARCIS (Netherlands)

    Cordes, Thorben; Strackharn, Mathias; Stahl, Stefan W.; Summerer, Wolfram; Steinhauer, Christian; Forthmann, Carsten; Puchner, Elias M.; Vogelsang, Jan; Gaub, Hermann E.; Tinnefeld, Philip

    2010-01-01

    In this paper we experimentally combine a recently developed AFM-based molecule-by-molecule assembly (single-molecule cut-and-paste, SMCP) with subdiffraction resolution fluorescence imaging. Using “Blink-Microscopy”, which exploits the fluctuating emission of single molecules for the reconstruction

  5. An Organolanthanide Building Block Approach to Single-Molecule Magnets.

    Science.gov (United States)

    Harriman, Katie L M; Murugesu, Muralee

    2016-06-21

    Single-molecule magnets (SMMs) are highly sought after for their potential application in high-density information storage, spintronics, and quantum computing. SMMs exhibit slow relaxation of the magnetization of purely molecular origin, thus making them excellent candidates towards the aforementioned applications. In recent years, significant focus has been placed on the rare earth elements due to their large intrinsic magnetic anisotropy arising from the near degeneracy of the 4f orbitals. Traditionally, coordination chemistry has been utilized to fabricate lanthanide-based SMMs; however, heteroatomic donor atoms such as oxygen and nitrogen have limited orbital overlap with the shielded 4f orbitals. Thus, control over the anisotropic axis and induction of f-f interactions are limited, meaning that the performance of these systems can only extend so far. To this end, we have placed considerable attention on the development of novel SMMs whose donor atoms are conjugated hydrocarbons, thereby allowing us to perturb the crystal field of lanthanide ions through the use of an electronic π-cloud. This approach allows for fine tuning of the anisotropic axis of the molecule, allowing this method the potential to elicit SMMs capable of reaching much larger values for the two vital performance measurements of an SMM, the energy barrier to spin reversal (Ueff), and the blocking temperature of the magnetization (TB). In this Account, we describe our efforts to exploit the inherent anisotropy of the late 4f elements; namely, Dy(III) and Er(III), through the use of cyclooctatetraenyl (COT) metallocenes. With respect to the Er(III) derivatives, we have seen record breaking success, reaching blocking temperatures as high as 14 K with frozen solution magnetometry. These results represent the first example of such a high TB being observed for a system with only a single spin center, formally known as a single-ion magnet (SIM). Our continued interrelationship between theoretical

  6. 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

  7. Directional Raman scattering from single molecules in the feed gaps of optical antennas.

    Science.gov (United States)

    Wang, Dongxing; Zhu, Wenqi; Best, Michael D; Camden, Jon P; Crozier, Kenneth B

    2013-05-08

    Controlling light from single emitters is an overarching theme of nano-optics. Antennas are routinely used to modify the angular emission patterns of radio wave sources. "Optical antennas" translate these principles to visible and infrared wavelengths and have been recently used to modify fluorescence from single quantum dots and single molecules. Understanding the properties of single molecules, however, would be advanced were one able to observe their vibrational spectra through Raman scattering in a very reproducible manner but it is a hugely challenging task, as Raman scattering cross sections are very weak. Here we measure for the first time the highly directional emission patterns of Raman scattering from single molecules in the feed gaps of optical antennas fabricated on a chip. More than a thousand single molecule events are observed, revealing that an unprecedented near-unity fraction of optical antennas have single molecule sensitivity.

  8. An Optical Tweezers Platform for Single Molecule Force Spectroscopy in Organic Solvents.

    Science.gov (United States)

    Black, Jacob; Kamenetska, Maria; Ganim, Ziad

    2017-10-03

    Observation at the single molecule level has been a revolutionary tool for molecular biophysics and materials science, but single molecule studies of solution-phase chemistry are less widespread. In this work we develop an experimental platform for solution-phase single molecule force spectroscopy in organic solvents. This optical-tweezer-based platform was designed for broad chemical applicability and utilizes optically trapped core-shell microspheres, synthetic polymer tethers, and click chemistry linkages formed in situ. We have observed stable optical trapping of the core-shell microspheres in ten different solvents, and single molecule link formation in four different solvents. These experiments demonstrate how to use optical tweezers for single molecule force application in the study of solution-phase chemistry.

  9. Wavelet-based denoising of the Fourier metric in real-time wavefront correction for single molecule localization microscopy

    Science.gov (United States)

    Tehrani, Kayvan Forouhesh; Mortensen, Luke J.; Kner, Peter

    2016-03-01

    Wavefront sensorless schemes for correction of aberrations induced by biological specimens require a time invariant property of an image as a measure of fitness. Image intensity cannot be used as a metric for Single Molecule Localization (SML) microscopy because the intensity of blinking fluorophores follows exponential statistics. Therefore a robust intensity-independent metric is required. We previously reported a Fourier Metric (FM) that is relatively intensity independent. The Fourier metric has been successfully tested on two machine learning algorithms, a Genetic Algorithm and Particle Swarm Optimization, for wavefront correction about 50 μm deep inside the Central Nervous System (CNS) of Drosophila. However, since the spatial frequencies that need to be optimized fall into regions of the Optical Transfer Function (OTF) that are more susceptible to noise, adding a level of denoising can improve performance. Here we present wavelet-based approaches to lower the noise level and produce a more consistent metric. We compare performance of different wavelets such as Daubechies, Bi-Orthogonal, and reverse Bi-orthogonal of different degrees and orders for pre-processing of images.

  10. Monte-Carlo simulation of a high-resolution inverse geometry spectrometer on the SNS. Long Wavelength Target Station

    Energy Technology Data Exchange (ETDEWEB)

    Bordallo, H.N. [Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, IL (United States); Herwig, K.W. [Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, TN (United States)

    2001-03-01

    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)

  11. Reverse breakdown in long wavelength lateral collection Cd sub x Hg sub 1 sub minus x Te diodes

    Energy Technology Data Exchange (ETDEWEB)

    Elliott, C.T.; Gordon, N.T.; Hall, R.S. (Royal Signals, Malvern, Worcs WR14 3PS, (England) Radar Establishment, Malvern, Worcs WR14 3PS, England (GB)); Crimes, G. (Philips Components, Southampton, Hants S09 7BH, (England))

    1990-03-01

    Long wavelength diodes in Cd{sub {ital x}}Hg{sub 1{minus}{ital x}}Te show large deviations from ideality in their reverse characteristics. The excess currents are attributed in many published papers on band to band tunneling at high reverse bias and to trap assisted tunneling at low reverse bias. Measurements of photocurrent multiplication, current--voltage characteristics, and noise have been made on long wavelength loophole diodes to determine the breakdown mechanism. This has produced strong evidence that the reverse characteristics of good quality diodes of this type are limited by impact ionization. At higher biases, there is evidence of an additional breakdown mechanism, probably tunneling.

  12. Near-Field Fluorescence and Topography Characterization of a Single Nanometre Fluorophore by Apertureless Tip-Enhanced Scanning Near-Field Microscopy

    Institute of Scientific and Technical Information of China (English)

    WU Xiao-Bin; WANG Jia; XU Ji-Ying; WANG Rui; TIAN Qian; YU Jian-Yuan

    2007-01-01

    Tip-enhanced near-field fluorescence and topography characterization of a single nanometre fluorophore is conducted by using an apertureless scanning near-field microscopy system. A fluorophore with size 80nm is mapped with a spatial resolution of 10nm. The corresponding near-field fluorescence data shows significant signal enhancement due to the apertureless tip-enhanced effect. With the nanometre spatial resolution capability and nanometre local tip-enhanced effect, the apertureless tip-enhanced scanning near-field microscopy may be further used to characterize a single molecule by realizing the local near-field spectrum assignment corresponding to topography at nanometre scale.

  13. Improved long wavelength 14xx and 19xx nm InGaAsp/InP lasers

    Science.gov (United States)

    Tanbun-Ek, T.; Pathak, R.; Xu, Z.; Winhold, H.; Zhou, F.; Peters, M.; Schleuning, D.; Acklin, B.

    2016-03-01

    We report on our progress developing long wavelength high power laser diodes based on the InGaAsP/InP alloy system emitting in the range from 1400 to 2010 nm. Output power levels exceeding 50 Watts CW and 40% conversion efficiency were obtained at 1470 nm wavelength from 20% fill factor (FF) bars with 2 mm cavity length mounted on water cooled plates. Using these stackable plates we built a water cooled stack with 8 bars, successfully demonstrating 400 W at 1470 nm with good reliability. In all cases the maximum conversion efficiency was greater than 40% and the maximum power achievable was limited by thermal rollover. For lasers emitting in the range from 1930 to 2010 nm we achieved output power levels over 15 W and 20 % conversion efficiency from 20% FF bars with 2 mm cavity length on a conductively cooled platform. Life testing of the 1470 nm lasers bars over 14,000 hours under constant current mode has shown no significant degradation.

  14. Long wavelength perfect fluidity from short distance jet transport in quark-gluon plasmas

    CERN Document Server

    Xu, Jiechen; Gyulassy, Miklos

    2015-01-01

    We build a new phenomenological framework that bridges the long wavelength bulk viscous transport properties of the strongly-coupled quark-gluon plasma (sQGP) and short distance hard jet transport properties in the QGP. The full nonperturbative chromo-electric (E) and chromo-magnetic (M) structure of the near "perfect fluid" like sQGP in the critical transition region are integrated into a semi-Quark-Gluon-Monopole Plasma (sQGMP) model lattice-compatibly and implemented into the new CUJET3.0 jet quenching framework. All observables computed from CUJET3.0 are found to be consistent with available data at RHIC and LHC simultaneously. A quantitative connection between the shear viscosity and jet transport parameter is rigorously established within this framework. We deduce the $T=160-600$ MeV dependence of the QGP's $\\eta/s$: its near vanishing value in the near $T_c$ regime is determined by the composition of E and M charges, it increases as $T$ rises, and its high $T$ limit is fixed by color screening scales.

  15. 21 cm Fluctuations of the Cosmic Dawn with the Owens Valley Long Wavelength Array

    Science.gov (United States)

    Eastwood, Michael; Hallinan, Gregg; Owens Valley LWA Collaboration

    2016-01-01

    The Owens Valley Long Wavelength Array (OVRO LWA) is a 288-antenna interferometer covering 30 to 80 MHz located at the Owens Valley Radio Observatory (OVRO) near Big Pine, California. I am leading the effort to detect spatial fluctuations of the 21 cm transition from the cosmic dawn (z~20) with the OVRO LWA. These spatial fluctuations are primarily sourced by inhomogeneous X-ray heating from early star formation. The spectral hardness of early X-ray sources, stellar feedback mechanisms, and baryon streaming therefore all play a role in shaping the power spectrum. I will present the application of m-mode analysis (Shaw et al. 2014, Shaw et al. 2015) to OVRO LWA data to: 1. compress the data set, 2. create maps of the northern sky that can be fed back into the calibration pipeline, and 3. filter foreground emission. Finally I will present the current status and future prospects of the OVRO LWA for detecting the 21 cm power spectrum at z~20.

  16. First Light for the First Station of the Long Wavelength Array

    CERN Document Server

    Taylor, G B; Kassim, N E; Craig, J; Dowell, J; Wolfe, C N; Hartman, J; Bernardi, G; Clarke, T; Cohen, A; Dalal, N P; Erickson, W C; Hicks, B; Greenhill, L J; Jacoby, B; Lane, W; Lazio, J; Mitchell, D; Navarro, R; Ord, S M; Pihlstrom, Y; Polisensky, E; Ray, P S; Rickard, L J; Schinzel, F K; Schmitt, H; Sigman, E; Soriano, M; Stewart, K P; Stovall, K; Tremblay, S; Wang, D; Weiler, K W; White, S; Wood, D L

    2012-01-01

    The first station of the Long Wavelength Array (LWA1) was completed in April 2011 and is currently performing observations resulting from its first call for proposals in addition to a continuing program of commissioning and characterization observations. The instrument consists of 258 dual-polarization dipoles, which are digitized and combined into beams. Four independently-steerable dual-polarization beams are available, each with two "tunings" of 16 MHz bandwidth that can be independently tuned to any frequency between 10 MHz and 88 MHz. The system equivalent flux density for zenith pointing is ~3 kJy and is approximately independent of frequency; this corresponds to a sensitivity of ~5 Jy/beam (5sigma, 1 s); making it one of the most sensitive meter-wavelength radio telescopes. LWA1 also has two "transient buffer" modes which allow coherent recording from all dipoles simultaneously, providing instantaneous all-sky field of view. LWA1 provides versatile and unique new capabilities for Galactic science, puls...

  17. On Higher-order Corrections to Gyrokinetic Vlasov-Poisson Equations in the Long Wavelength Limit

    Energy Technology Data Exchange (ETDEWEB)

    W.W. Lee and R.A. Kolesnikov

    2009-02-17

    In this paper, we present a simple iterative procedure for obtaining the higher order E x B and dE/dt (polarization) drifts associated with the gyrokinetic Vlasov-Poisson equations in the long wavelength limit of k⊥ρi ~ o(ε) and k⊥L ~ o(1), where ρi is the ion gyroradius, L is the scale length of the background inhomogeneity and ε is a smallness parameter. It can be shown that these new higher order k⊥ρi terms, which are also related to the higher order perturbations of the electrostatic potential Φ, should have negligible effects on turbulent and neoclassical transport in tokamaks, regardless of the form of the background distribution and the amplitude of the perturbation. To address further the issue of a non-Maxwellian plasma, higher order finite Larmor radius terms in the gyrokinetic Poisson's equation have been studied and shown to be unimportant as well. On the other hand, the terms of o(k2⊥ρi2) ~ o(ε) and k⊥L ~ o(1) can indeed have impact on microturbulence, especially in the linear stage, such as those arising from the difference between the guiding center and the gyrocenter densities due to the presence of the background gradients. These results will be compared with a recent study questioning the validity of the commonly used gyrokinetic equations for long time simulations.

  18. The long wavelength view of GG Tau A: Rocks in the Ring World

    CERN Document Server

    Scaife, Anna M M

    2013-01-01

    We present the first detection of GG Tau A at centimeter-wavelengths, made with the Arcminute Microkelvin Imager Large Array (AMI-LA) at a frequency of 16 GHz ({\\lambda} = 1.8 cm). The source is detected at > 6 {\\sigma}_{rms} with an integrated flux density of S = 249+/-45 {\\mu}Jy. We use these new centimetre-wave data, in conjunction with additional measurements compiled from the literature, to investigate the long wavelength tail of the dust emission from this unusual proto-planetary system. We use an MCMC based method to determine maximum likelihood parameters for a simple parametric spectral model and consider the opacity and mass of the dust contributing to the microwave emission. We derive a dust mass of approximately 0.1 solar masses, constrain the dimensions of the emitting region and find that the opacity index at {\\lambda} > 7mm is less than unity, implying a contribution to the dust population from grains exceeding 4 cm in size. We suggest that this indicates coagulation within the GG Tau A system ...

  19. Comparison of scaling laws with PIC simulations for proton acceleration with long wavelength pulses

    Energy Technology Data Exchange (ETDEWEB)

    Turchetti, G., E-mail: turchetti@bo.infn.i [Dipartimento di Fisica Universita di Bologna, INFN Sezione di Bologna (Italy); Sgattoni, A.; Benedetti, C. [Dipartimento di Fisica Universita di Bologna, INFN Sezione di Bologna (Italy); Londrillo, P. [INFN Sezione di Bologna (Italy); Di Lucchio, L. [Dipartimento di Fisica Universita di Bologna, INFN Sezione di Bologna (Italy)

    2010-08-01

    We have performed a survey of proton acceleration induced by long wavelength pulses to explore their peak energy dependence on the pulse intensity, target thickness and density. The simulations carried out with the PIC code ALADYN for a circularly polarized pulse have been compared with the scaling laws for radiation pressure acceleration (RPA) in the thick target and thin target regimes known as hole boring (HB) and relativistic mirror (RM) respectively. Since the critical density scales as {lambda}{sup -2}, longer wavelength pulses allow to work with low density targets several microns thick and with moderate laser power. Under these conditions is possible to enter the RM region, where the key parameter is the ratio {alpha} between twice laser energy and the mirror rest energy; the corresponding acceleration efficiency is given by {alpha}/(1+{alpha}). For a fixed intensity the minimum thickness of the target, and consequently the highest acceleration, is determined by the threshold of self induced transparency. In this case the number of accelerated particles scales with {lambda} whereas the total energy does not depend on it. The agreement of PIC simulations with RPA and RM scalings, including the transition regions, suggests that these scalings can safely be used as the first step in the parametric scans also for large wavelength pulses such as CO{sub 2} lasers, to explore possible alternatives to short wavelength very high power Ti:Sa lasers for proton acceleration.

  20. 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

  1. Long wavelength perfect fluidity from short distance jet transport in quark-gluon plasmas

    Science.gov (United States)

    Xu, Jiechen; Liao, Jinfeng; Gyulassy, Miklos

    2016-12-01

    We build a new phenomenological framework that bridges the long wavelength bulk viscous transport properties of the strongly-coupled quark-gluon plasma (sQGP) and short distance hard jet transport properties in the QGP. The full nonperturbative chromo-electric (E) and chromo-magnetic (M) structure of the near "perfect fluid" like sQGP in the critical transition region are integrated into a semi-Quark-Gluon-Monopole Plasma (sQGMP) model lattice-compatibly and implemented into the new CUJET3.0 jet quenching framework. All observables computed from CUJET3.0 are found to be consistent with available data at RHIC and LHC simultaneously. A quantitative connection between the shear viscosity and jet transport parameter is rigorously established within this framework. We deduce the T = 160 - 600 MeV dependence of the QGP's η / s: its near vanishing value in the near Tc regime is determined by the composition of E and M charges, it increases as T rises, and its high T limit is fixed by color screening scales.

  2. Imaging at Both Ends of the Spectrum: the Long Wavelength Array and Fermi

    CERN Document Server

    Taylor, G B

    2012-01-01

    The Long Wavelength Array (LWA) will be a new multi-purpose radio telescope operating in the frequency range 10-88 MHz. Scientific programs include pulsars, supernova remnants, general transient searches, radio recombination lines, solar and Jupiter bursts, investigations into the "dark ages" using redshifted hydrogen, and ionospheric phenomena. Upon completion, LWA will consist of 53 phased array "stations" distributed across a region over 400 km in diameter. Each station consists of 256 pairs of dipole-type antennas whose signals are formed into beams, with outputs transported to a central location for high-resolution aperture synthesis imaging. The resulting image sensitivity is estimated to be a few mJy (5sigma, 8 MHz, 2 polarizations, 1 h, zenith) from 20-80 MHz; with angular resolution of a few arcseconds. Additional information is online at http://lwa.unm.edu. Partners in the LWA project include LANL, JPL, NRL, UNM, NMT, and Virginia Tech. The full LWA will be a powerful instrument for the study of par...

  3. Evaluation of the Effects of Long-Wavelength Perturbations in OMEGA 80-Gbar Cryogenic Implosions

    Science.gov (United States)

    McKenty, P. W.; Cao, D.; Collins, T. J. B.; Shvydky, A.; Anderson, K. S.

    2016-10-01

    The Laboratory for Laser Energetics, as part of the National Laser Direct Drive Program, has identified the goal of producing 100-Gbar neutron-averaged, hot-spot pressures (P*) by the year 2020. An intermediate goal of 80 Gbar is currently being pursued. This work first analyzes the behavior of P* as a function of the target convergence ratio. From this a critical converge ratio can be defined at which point the implosion achieves the P* = 80-Gbar goal. Further capsule convergence then maps out a target region in design space that details the acceptable degradation from 1-D performance an implosion could suffer while still achieving the 80-Gbar goal. Two-dimensional simulation results will be presented, indicating the maximum-allowed levels for long-wavelength perturbations (offset, power imbalance, and inner-surface ice roughness) while still completing this goal. This material is based upon work supported by the Department of Energy National Nuclear Security Administration under Award Number DENA0001944.

  4. Magnetic orientation of migratory robins, Erithacus rubecula, under long-wavelength light.

    Science.gov (United States)

    Wiltschko, Roswitha; Denzau, Susanne; Gehring, Dennis; Thalau, Peter; Wiltschko, Wolfgang

    2011-09-15

    The avian magnetic compass is an inclination compass that appears to be based on radical pair processes. It requires light from the short-wavelength range of the spectrum up to 565 nm green light; under longer wavelengths, birds are disoriented. When pre-exposed to longer wavelengths for 1 h, however, they show oriented behavior. This orientation is analyzed under 582 nm yellow light and 645 nm red light in the present study: while the birds in spring prefer northerly directions, they do not show southerly tendencies in autumn. Inversion of the vertical component does not have an effect whereas reversal of the horizontal component leads to a corresponding shift, indicating that a polar response to the magnetic field is involved. Oscillating magnetic fields in the MHz range do not affect the behavior but anesthesia of the upper beak causes disorientation. This indicates that the magnetic information is no longer provided by the radical pair mechanism in the eye but by the magnetite-based receptors in the skin of the beak. Exposure to long-wavelength light thus does not expand the spectral range in which the magnetic compass operates but instead causes a different mechanism to take over and control orientation.

  5. Long-wavelength, free-free spectral energy distributions from porous stellar winds

    Science.gov (United States)

    Ignace, R.

    2016-04-01

    The influence of macroclumps for free-free spectral energy distributions (SEDs) of ionized winds is considered. The goal is to emphasize distinctions between microclumping and macroclumping effects. Microclumping can alter SED slopes and flux levels if the volume filling factor of the clumps varies with radius; however, the modifications are independent of the clump geometry. To what extent does macroclumping alter SED slopes and flux levels? In addressing the question, two specific types of macroclump geometries are explored: shell fragments (pancake-shaped) and spherical clumps. Analytic and semi-analytic results are derived in the limiting case that clumps never obscure one another. Numerical calculations based on a porosity formalism is used when clumps do overlap. Under the assumptions of a constant expansion, isothermal, and fixed ionization wind, the fragment model leads to results that are essentially identical to the microclumping result. Mass-loss rate determinations are not affected by porosity effects for shell fragments. By contrast, spherical clumps can lead to a reduction in long-wavelength fluxes, but the reductions are only significant for extreme volume filling factors.

  6. Characteristics of long wavelength InGaN quantum well laser diodes

    Science.gov (United States)

    Kim, K. S.; Son, J. K.; Lee, S. N.; Sung, Y. J.; Paek, H. S.; Kim, H. K.; Kim, M. Y.; Ha, K. H.; Ryu, H. Y.; Nam, O. H.; Jang, T.; Park, Y. J.

    2008-03-01

    We demonstrated the long wavelength (485nm) lasing of InGaN laser diodes under continuous wave condition at room temperature over 10mW. Two InGaN laser structures were adapted with different indium composition for InGaN optical confinement layers (OCLs) below quantum wells. The blue shift of electroluminescence (EL) was reduced in InGaN laser diodes grown on 3% In concentration in InGaN OCL compared with 1.5% In concentration in InGaN OCL. The EL peak for laser diode with 3% In concentration in InGaN OCL occurs at longer wavelength for all current levels compared to the laser with 1.5% In concentration in InGaN OCL. In addition, the laterally nonuniform InGaN wells grown on 1.5% In concentration in InGaN OCL was verified by the cross-sectional view of InGaN active layer using high-resolution transmission electron microscopy.

  7. Probing Jovian Decametric Emission with the Long Wavelength Array Station 1

    CERN Document Server

    Clarke, T E; Skarda, Jinhie; Imai, Kazumasa; Imai, Masafumi; Reyes, Francisco; Thieman, Jim; Jaeger, Ted; Schmitt, Henrique; Dalal, Nagini Paravastu; Dowell, Jayce; Ellingson, S W; Hicks, Brian; Schinzel, Frank; Taylor, G B

    2014-01-01

    New observations of Jupiter's decametric radio emissions have been made with the Long Wavelength Array Station 1 (LWA1) which is capable of making high quality observations as low as 11 MHz. Full Stokes parameters were determined for bandwidths of 16 MHz. Here we present the first LWA1 results for the study of six Io-related events at temporal resolutions as fine as 0.25 ms. LWA1 data show excellent spectral detail in Jovian DAM such as simultaneous left hand circular (LHC) and right hand circular (RHC) polarized Io-related arcs and source envelopes, modulation lane features, S-bursts structures, narrow band N-events, and interactions between S-bursts and N-events. The sensitivity of the LWA1 combined with the low radio frequency interference environment allow us to trace the start of the LHC Io-C source region to much earlier CMLIII than typically found in the literature. We find the Io-C starts as early as CMLIII = 230 degrees at frequencies near 11 MHz. This early start of the Io-C emission may be valuable...

  8. Surveying the Dynamic Radio Sky with the Long Wavelength Demonstrator Array

    CERN Document Server

    Lazio, T J W; Lane, W M; Gross, C; Kassim, N E; Ray, P S; Wood, D; York, J A; Kerkhoff, A; Hicks, B; Polisensky, E; Stewart, K; 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 t...

  9. 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.

  10. A starting point for fluorescence-based single-molecule measurements in biomolecular research.

    Science.gov (United States)

    Gust, Alexander; Zander, Adrian; Gietl, Andreas; Holzmeister, Phil; Schulz, Sarah; Lalkens, Birka; Tinnefeld, Philip; Grohmann, Dina

    2014-09-30

    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.

  11. 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...

  12. Future challenges in single-molecule fluorescence and laser trap approaches to studies of molecular motors.

    Science.gov (United States)

    Elting, Mary Williard; Spudich, James A

    2012-12-11

    Single-molecule analysis is a powerful modern form of biochemistry, in which individual kinetic steps of a catalytic cycle of an enzyme can be explored in exquisite detail. Both single-molecule fluorescence and single-molecule force techniques have been widely used to characterize a number of protein systems. We focus here on molecular motors as a paradigm. We describe two areas where we expect to see exciting developments in the near future: first, characterizing the coupling of force production to chemical and mechanical changes in motors, and second, understanding how multiple motors work together in the environment of the cell.

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

    DEFF Research Database (Denmark)

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

    2017-01-01

    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...

  14. Hydrogel Droplet Microfluidics for High-Throughput Single Molecule/Cell Analysis.

    Science.gov (United States)

    Zhu, Zhi; Yang, Chaoyong James

    2017-01-17

    Heterogeneity among individual molecules and cells has posed significant challenges to traditional bulk assays, due to the assumption of average behavior, which would lose important biological information in heterogeneity and result in a misleading interpretation. Single molecule/cell analysis has become an important and emerging field in biological and biomedical research for insights into heterogeneity between large populations at high resolution. Compared with the ensemble bulk method, single molecule/cell analysis explores the information on time trajectories, conformational states, and interactions of individual molecules/cells, all key factors in the study of chemical and biological reaction pathways. Various powerful techniques have been developed for single molecule/cell analysis, including flow cytometry, atomic force microscopy, optical and magnetic tweezers, single-molecule fluorescence spectroscopy, and so forth. However, some of them have the low-throughput issue that has to analyze single molecules/cells one by one. Flow cytometry is a widely used high-throughput technique for single cell analysis but lacks the ability for intercellular interaction study and local environment control. Droplet microfluidics becomes attractive for single molecule/cell manipulation because single molecules/cells can be individually encased in monodisperse microdroplets, allowing high-throughput analysis and manipulation with precise control of the local environment. Moreover, hydrogels, cross-linked polymer networks that swell in the presence of water, have been introduced into droplet microfluidic systems as hydrogel droplet microfluidics. By replacing an aqueous phase with a monomer or polymer solution, hydrogel droplets can be generated on microfluidic chips for encapsulation of single molecules/cells according to the Poisson distribution. The sol-gel transition property endows the hydrogel droplets with new functionalities and diversified applications in single

  15. South American Weakly Electric Fish (Gymnotiformes) Are Long-Wavelength-Sensitive Cone Monochromats.

    Science.gov (United States)

    Liu, Da-Wei; Lu, Ying; Yan, Hong Young; Zakon, Harold H

    2016-01-01

    Losses of cone opsin genes are noted in animals that are nocturnal or rely on senses other than vision. We investigated the cone opsin repertoire of night-active South American weakly electric fish. We obtained opsin gene sequences from genomic DNA of 3 gymnotiforms (Eigenmannia virescens, Sternopygus macrurus, Apteronotus albifrons) and the assembled genome of the electric eel (Electrophorus electricus). We identified genes for long-wavelength-sensitive (LWS) and medium-wavelength-sensitive cone opsins (RH2) and rod opsins (RH1). Neither of the 2 short-wavelength-sensitive cone opsin genes were found and are presumed lost. The fact that Electrophorus has a complete repertoire of extraretinal opsin genes and conservation of synteny with the zebrafish (Danio rerio) for genes flanking the 2 short-wavelength-sensitive opsin genes supports the supposition of gene loss. With microspectrophotometry and electroretinograms we observed absorption spectra consistent with RH1 and LWS but not RH2 opsins in the retinal photoreceptors of E. virescens. This profile of opsin genes and their retinal expression is identical to the gymnotiform's sister group, the catfish, which are also nocturnally active and bear ampullary electroreceptors, suggesting that this pattern likely occurred in the common ancestor of gymnotiforms and catfish. Finally, we noted an unusual N-terminal motif lacking a conserved glycosylation consensus site in the RH2 opsin of gymnotiforms, a catfish and a characin (Astyanax mexicanus). Mutations at this site influence rhodopsin trafficking in mammalian photoreceptors and cause retinitis pigmentosa. We speculate that this unusual N terminus may be related to the absence of the RH2 opsin in the cones of gymnotiforms and catfish. © 2016 S. Karger AG, Basel.

  16. [Design and implementation of a long wavelength near infrared spectrometer based on MEMS scanning mirror].

    Science.gov (United States)

    Ye, Kun-Tao; Dong, Tai-Yuan; He, Wen-Xi; Li, Yu-Xiao; Cheng, Xian-Ming; Li, Guang-Yong; Li, Hao-Yu; Xu, Hao-Yu

    2014-10-01

    Long Wavelength Near InfraRed (LW-NIR) spectrometer has wide applications. Miniaturization and low-cost are two major goals of the development of LW-NIR spectrometer in the industrial or research community. Under the background that having a trend of spectrometer miniaturization and integration, method and main problems involved in miniaturization of LW-NIR spectrometer through MEMS scanning mirror, such as the design strategy of the light-splitting optical system, selection considerations of the MEMS scanning mirror, design method of the preamplifier circuit, etc, have been presented in detail. A prototype of miniaturized LW-NIR spectrometer, with the spectrum range of detection of 900-2,055 nm, is designed and implemented using MEMS scanning mirror, InGaAs single detector unit with high sensitivity. Littrow optical layout is used for its light-splitting optical system, and the spectral resolution is between 9.4-16 nm at 1,000-1,965 nm detection wavelength range. The prototype is successfully applied in LW-NIR spectrum measurement on pure water and ethanol aqueous solution, and a forecast analysis on ethanol aqueous solution concentration is also demonstrated. Through adopting MEMS scanning mirror into the spectrometer system, the complexity of the mechanical scanning fixtures and its controlling mechanism is greatly reduced therefore the size of the spectrometer is reduced. Furthermore, due to MEMS scanning mirror technology, LW-NIR spectrometer with single InGaAs detector is achieved, thus the cost reduction of the NIR spectrometer system is also realized because the expensive InGaAs arrays are avoided.

  17. New materials and new techniques for imaging of long wavelength IR radiation

    Science.gov (United States)

    Cross, L. E.

    1990-11-01

    Work on this program was directed towards the preliminary verification of the possibility of a completely new type of long wavelength infrared imaging system. This study proposed to explore the change in polarized reflectance from the pyro-optic surface, making use of the exceptional sensitivity of the newer ellipsometric techniques for reflectance studies. Cardinal advantages for the pyro-optic reflectance method are the following: (1) thermally sensitive film need only be thick enough to support the evanescent wave on reflection, so that pixel volume (mass) can be exceedingly small; (2) films can be mounted upon a critically dehydrated gel substrate which is transparent to visible light but affords near perfect thermal isolation; (3) there is no need for contacts to individual pixel elements as in the pyroelectric imagers; and (4) calculations show that for a film 0.1 micron meter thick, mounted on a silica gel substrate, the thermal efficiency is such that if the thermometric sensitivity of the film is sufficient to detect a temperature change of 1mK then for a system with f(1) optics this could correspond to a temperature difference in the object plane of 0.1K. The studies on this program were in two parts. The first objective was to verify the high values of temperature derivative of refractive index which has been reported in bismuth vanadate BiVO4, molybdenum MoS2, and antimony sulphur iodide SbSI. The second objective was to design and build a compact thermoelectric heater cooler which could be used to impart a known small AC temperature change to explore the detectivity limit for a pyro-optic application.

  18. Iii-V Semiconductor Electroabsorption Waveguide Modulators for Long Wavelength Fiber Communication.

    Science.gov (United States)

    Lin, Shyh-Chung

    Long wavelength fiber communication has particular advantages in high speed, long haul communication system applications due to the intrinsic low chromatic dispersion and low attenuation of silica fibers at 1.3 mu m and 1.55 μm wavelengths. However, its implementation has been hampered by the lack of a high speed laser light modulator which has a small frequency variation (chirp) of its optical carrier. This thesis concerns III-V semiconductor electroabsorption waveguide modulators with the intention of improving their chirping characteristics and high speed performance. Analytical work performed in the course of this thesis has led to the following conclusions concerning the design and construction of electroabsorption waveguide modulators (EWM) for laser light modulation. (i) In order to minimize frequency chirping, semiconducting materials chosen for EWM applications should have a direct, fundamental bandgap somewhat greater than that of the incident laser photon energy. (ii) High speed EWMs require some compromises in terms of material parameters as well as dimensional constraints intended to minimize parasitic coupling impedances while providing basic, optimized, modulator functions such as low insertion loss, high modulation index, low driving voltage, and minimum frequency chirping. Experimental research on EWMs performed in the course of this thesis using liquid phase, epitaxially grown, quaternary alloy In_ xGa _{1-x}As_ yP _{1-y} and a laser wavelength of 1.3 μm includes: (i) Design, construction, and performance evaluation of a low capacitance ridge EWM. (ii) Design, construction, and performance evaluation of a buried channel EWM with large on-off ratio and the monolithic integration, in cascade, of such EWMs in order to perform the functions of a high speed phase comparator.

  19. Charting the Last Electromagnetic Frontier with the Long Wavelength Array (LWA)

    Science.gov (United States)

    Kassim, N. E.; Clarke, T. E.; Cohen, A. S.; Crane, P. C.; Gaussiran, T. L.; Gross, C. A.; Henning, P. A.; Hicks, B. C.; Junor, W.; Lane, W. M.; Lazio, J.; Paravastu, N.; Pihlstrom, Y. M.; Polisensky, E. J.; Ray, P. S.; Stewart, K. P.; Taylor, G. B.; Weiler, K. W.

    2006-05-01

    Nearly three decades ago, the Very Large Array (VLA) first opened the 1-20 GHz radio sky to detailed study. Today, a path-finding VLA 74 MHz system is providing the first sub-arcminute resolution view of the radio universe below 100 MHz, a technical innovation that has inspired an emerging suite of much more powerful low-frequency instruments. Similar in philosophy to the VLA and also located in New Mexico, the Long Wavelength Array (LWA) will be a versatile, user-oriented electronic array poised to open the 20--80 MHz frequency range to detailed exploration for the first time. With a collecting area of one million square meters, the LWA will be a square kilometer telescope whose milli-Jansky sensitivity and near-arcsecond resolution will surpass, by 2--3 orders of magnitude, the imaging power of previous interferometers in its frequency range. LWA scientific frontiers include (1) the high-z universe, including distant radio galaxies and clusters - tools for understanding the earliest black holes and the cosmological evolution of Dark Matter and Dark Energy, respectively; (2) acceleration, propagation, and turbulence in the ISM, including the space-distribution and spectrum of Galactic cosmic rays and supernova remnants; (3) planetary, solar, and space science, including space-weather prediction and extra-solar planet searches; and (4) the radio transient universe including GRBs, ultra-high energy cosmic rays, and new sources of unknown origin. Because the LWA will explore one of the most poorly investigated spectral regions the potential for new discoveries is high, and there is a strong synergy with exciting new X-ray and Gamma-ray measurements, e.g. for cosmic ray acceleration, transients, and galaxy clusters. The LWA will also provide an unparalleled measure of small-scale ionospheric turbulence, a pre-requisite for accurate calibration and imaging. Basic research in radio astronomy at the Naval Research Laboratory is supported by the Office of Naval Research.

  20. Retention of duplicated long-wavelength opsins in mosquito lineages by positive selection and differential expression.

    Science.gov (United States)

    Giraldo-Calderón, Gloria I; Zanis, Michael J; Hill, Catherine A

    2017-03-21

    Opsins are light sensitive receptors associated with visual processes. Insects typically possess opsins that are stimulated by ultraviolet, short and long wavelength (LW) radiation. Six putative LW-sensitive opsins predicted in the yellow fever mosquito, Aedes aegypti and malaria mosquito, Anopheles gambiae, and eight in the southern house mosquito, Culex quinquefasciatus, suggest gene expansion in the Family Culicidae (mosquitoes) relative to other insects. Here we report the first detailed molecular and evolutionary analyses of LW opsins in three mosquito vectors, with a goal to understanding the molecular basis of opsin-mediated visual processes that could be exploited for mosquito control. Time of divergence estimates suggest that the mosquito LW opsins originated from 18 or 19 duplication events between 166.9/197.5 to 1.07/0.94 million years ago (MY) and that these likely occurred following the predicted divergence of the lineages Anophelinae and Culicinae 145-226 MY. Fitmodel analyses identified nine amino acid residues in the LW opsins that may be under positive selection. Of these, eight amino acids occur in the N and C termini and are shared among all three species, and one residue in TMIII was unique to culicine species. Alignment of 5' non-coding regions revealed potential Conserved Non-coding Sequences (CNS) and transcription factor binding sites (TFBS) in seven pairs of LW opsin paralogs. Our analyses suggest opsin gene duplication and residues possibly associated with spectral tuning of LW-sensitive photoreceptors. We explore two mechanisms - positive selection and differential expression mediated by regulatory units in CNS - that may have contributed to the retention of LW opsin genes in Culicinae and Anophelinae. We discuss the evolution of mosquito LW opsins in the context of major Earth events and possible adaptation of mosquitoes to LW-dominated photo environments, and implications for mosquito control strategies based on disrupting vision

  1. Probing Jovian decametric emission with the long wavelength array station 1

    Science.gov (United States)

    Clarke, T. E.; Higgins, C. A.; Skarda, Jinhie; Imai, Kazumasa; Imai, Masafumi; Reyes, Francisco; Thieman, Jim; Jaeger, Ted; Schmitt, Henrique; Dalal, Nagini Paravastu; Dowell, Jayce; Ellingson, S. W.; Hicks, Brian; Schinzel, Frank; Taylor, G. B.

    2014-12-01

    New observations of Jupiter's decametric radio emissions have been made with the Long Wavelength Array Station 1 (LWA1), which is capable of making high-quality observations as low as 11 MHz. Full Stokes parameters were determined for bandwidths of 16 MHz. Here we present the first LWA1 results for the study of six Io-related events at temporal resolutions as fine as 0.25 ms. LWA1 data show excellent spectral detail in Jovian DAM such as simultaneous left-hand circular (LHC) and right-hand circular (RHC) polarized Io-related arcs and source envelopes, modulation lane features, S-burst structures, narrow band N events, and interactions between S bursts and N events. The sensitivity of the LWA1 combined with the low-radio-frequency interference environment allow us to trace the start of the LHC Io-C source region to much earlier CMLIII than typically found in the literature. We find that the Io-C starts as early as CMLIII = 230° at frequencies near 11 MHz. This early start of the Io-C emission may be valuable for refining models of the emission mechanism. We also detect modulation lane structures that appear continuous across LHC and RHC emissions, suggesting that both polarizations may originate from the same hemisphere of Jupiter. We present a study of rare S bursts detected during an Io-D event and show that drift rates are consistent with those from other Io-related sources. Finally, S-N burst events are seen in high spectral and temporal resolution and our data strongly support the cospatial origins of these events.

  2. A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization

    Science.gov (United States)

    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 strategy to covalently link a synthetic organic fluorophore simultaneously to a photostabilizer and biomolecular target via unnatural amino acids. The modular approach uses commercially available starting materials and simple chemical transformations. The resulting photostabilizer-dye conjugates are based on rhodamines, carbopyronines and cyanines with excellent photophysical properties, that is, high photostability and minimal signal fluctuations. Their versatile use is demonstrated by single-step labelling of DNA, antibodies and proteins, as well as applications in single-molecule and super-resolution fluorescence microscopy. We are convinced that the presented scaffolding strategy and the improved characteristics of the conjugates in applications will trigger the broader use of intramolecular photostabilization and help to emerge this approach as a new gold standard.

  3. From the molecule to the mole: improving heterogeneous copper catalyzed click chemistry using single molecule spectroscopy.

    Science.gov (United States)

    Wang, Bowen; Durantini, Javier; Decan, Matthew R; Nie, Jun; Lanterna, Anabel E; Scaiano, Juan C

    2016-12-22

    Single molecule spectroscopy (SMS) inspired the optimization of a heterogeneous 'click' catalyst leading to enhanced yields of the Cu-catalyzed reaction of azides with terminal alkynes. Changes in SMS data after optimization confirm the improvements in catalyst performance.

  4. Single Molecule Photobleaching Probes the Exciton Wavefunction in a Multichromophoric System

    NARCIS (Netherlands)

    Hernando, J.; Hoogenboom, J.P.; Dijk, van E.M.H.P.; Garcia-Lopez, J.J.; Crego Calama, M.; Reinhoudt, D.N.; Hulst, van N.F.; Garcia-Parajo, M.F.

    2004-01-01

    The exciton wave function of a trichromophoric system is investigated by means of single molecule spectroscopy at room temperature. Individual trimers exhibit superradiance and loss of vibronic structure in emission spectrum, features proving exciton delocalization. We identify two distinct photodeg

  5. Variable-Temperature Tip-Enhanced Raman Spectroscopy of Single-Molecule Fluctuations and Dynamics.

    Science.gov (United States)

    Park, Kyoung-Duck; Muller, Eric A; Kravtsov, Vasily; Sass, Paul M; Dreyer, Jens; Atkin, Joanna M; Raschke, Markus B

    2016-01-13

    Structure, dynamics, and coupling involving single-molecules determine function in catalytic, electronic or biological systems. While vibrational spectroscopy provides insight into molecular structure, rapid fluctuations blur the molecular trajectory even in single-molecule spectroscopy, analogous to spatial averaging in measuring large ensembles. To gain insight into intramolecular coupling, substrate coupling, and dynamic processes, we use tip-enhanced Raman spectroscopy (TERS) at variable and cryogenic temperatures, to slow and control the motion of a single molecule. We resolve intrinsic line widths of individual normal modes, allowing detailed and quantitative investigation of the vibrational modes. From temperature dependent line narrowing and splitting, we quantify ultrafast vibrational dephasing, intramolecular coupling, and conformational heterogeneity. Through statistical correlation analysis of fluctuations of individual modes, we observe rotational motion and spectral fluctuations of the molecule. This work demonstrates single-molecule vibrational spectroscopy beyond chemical identification, opening the possibility for a complete picture of molecular motion ranging from femtoseconds to minutes.

  6. Single vesicle biochips for ultra-miniaturized nanoscale fluidics and single molecule bioscience

    DEFF Research Database (Denmark)

    Christensen, Andreas Lauge; Lohr, Christina; Christensen, Sune M.;

    2013-01-01

    , their fabrication via controlled self-assembly, and their characterization using fluorescence microscopy. We also highlight their applications in selected fields such as nanofluidics and single molecule bioscience. Despite their great potential for improved biocompatibility, extreme miniaturization and high...

  7. Shifting molecular localization by plasmonic coupling in a single-molecule mirage

    Science.gov (United States)

    Raab, Mario; Vietz, Carolin; Stefani, Fernando Daniel; Acuna, Guillermo Pedro; Tinnefeld, Philip

    2017-01-01

    Over the last decade, two fields have dominated the attention of sub-diffraction photonics research: plasmonics and fluorescence nanoscopy. Nanoscopy based on single-molecule localization offers a practical way to explore plasmonic interactions with nanometre resolution. However, this seemingly straightforward technique may retrieve false positional information. Here, we make use of the DNA origami technique to both control a nanometric separation between emitters and a gold nanoparticle, and as a platform for super-resolution imaging based on single-molecule localization. This enables a quantitative comparison between the position retrieved from single-molecule localization, the true position of the emitter and full-field simulations. We demonstrate that plasmonic coupling leads to shifted molecular localizations of up to 30 nm: a single-molecule mirage.

  8. Real-space observation of spin-split molecular orbitals of adsorbed single-molecule magnets

    National Research Council Canada - National Science Library

    Schwöbel, Jörg; Fu, Yingshuang; Brede, Jens; Dilullo, Andrew; Hoffmann, Germar; Klyatskaya, Svetlana; Ruben, Mario; Wiesendanger, Roland

    2012-01-01

    A key challenge in the field of molecular spintronics, and for the design of single-molecule magnet-based devices in particular, is the understanding and control of the molecular coupling at the electrode interfaces...

  9. Single-molecule detection at high concentrations with optical aperture nanoantennas

    Science.gov (United States)

    Alam, Md Shah; Karim, Farzia; Zhao, Chenglong

    2016-05-01

    Single-molecule detection has become an indispensable technology in life science, and medical research. In order to get meaningful information on many biological processes, single-molecule analysis is required in micro-molar concentrations. At such high concentrations, it is very challenging to isolate a single molecule with conventional diffraction-limited optics. Recently, optical aperture nanoantennas (OANs) have emerged as a powerful tool to enhance the single-molecule detection under a physiological environment. The OANs, which consist of nano-scale apertures on a metallic film, have the following unique properties: (1) nanoscale light confinement; (2) enhanced fluorescence emission; (3) tunable radiation pattern; (4) reduced background noise; and (5) massive parallel detection. This review presents the fundamentals, recent developments and future perspectives in this emerging field.

  10. Targeting neurotransmitter receptors with nanoparticles in vivo allows single-molecule tracking in acute brain slices

    Science.gov (United States)

    Varela, Juan A.; Dupuis, Julien P.; Etchepare, Laetitia; Espana, Agnès; Cognet, Laurent; Groc, Laurent

    2016-03-01

    Single-molecule imaging has changed the way we understand many biological mechanisms, particularly in neurobiology, by shedding light on intricate molecular events down to the nanoscale. However, current single-molecule studies in neuroscience have been limited to cultured neurons or organotypic slices, leaving as an open question the existence of fast receptor diffusion in intact brain tissue. Here, for the first time, we targeted dopamine receptors in vivo with functionalized quantum dots and were able to perform single-molecule tracking in acute rat brain slices. We propose a novel delocalized and non-inflammatory way of delivering nanoparticles (NPs) in vivo to the brain, which allowed us to label and track genetically engineered surface dopamine receptors in neocortical neurons, revealing inherent behaviour and receptor activity regulations. We thus propose a NP-based platform for single-molecule studies in the living brain, opening new avenues of research in physiological and pathological animal models.

  11. Giant Suppression of Photobleaching for Single Molecule Detection via the Purcell Effect

    Science.gov (United States)

    2013-11-18

    Giant Suppression of Photobleaching for Single Molecule Detection via the Purcell Effect Hu Cang,†,‡ Yongmin Liu,†,§,∥ Yuan Wang,† Xiaobo Yin,†,⊥ and...Information ABSTRACT: We report giant suppression of photobleaching and a prolonged lifespan of single fluorescent molecules via the Purcell effect in... Purcell effect to manipulate photochemical reactions at the subwavelength scale. KEYWORDS: Nano-optics, single-molecule fluorescence spectroscopy

  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. pyFRET: A Python Library for Single Molecule Fluorescence Data Analysis

    OpenAIRE

    Murphy, Rebecca R.; Jackson, Sophie E.; Klenerman, David

    2014-01-01

    Single molecule F\\"orster resonance energy transfer (smFRET) is a powerful experimental technique for studying the properties of individual biological molecules in solution. However, as adoption of smFRET techniques becomes more widespread, the lack of available software, whether open source or commercial, for data analysis, is becoming a significant issue. Here, we present pyFRET, an open source Python package for the analysis of data from single-molecule fluorescence experiments from freely...

  14. Photon counting imaging and centroiding with an electron-bombarded CCD using single molecule localisation software

    OpenAIRE

    Hirvonen, Liisa Maija; Barber, Matthew; Suhling, Klaus

    2016-01-01

    Photon event centroiding in photon counting imaging and single-molecule localisation in super-resolution fluorescence microscopy share many traits. Although photon event centroiding has traditionally been performed with simple single-iteration algorithms, we recently reported that iterative fitting algorithms originally developed for single-molecule localisation fluorescence microscopy work very well when applied to centroiding photon events imaged with an MCP-intensified CMOS camera. Here, w...

  15. Diversity of Chemical Mechanisms in Thioredoxin Catalysis Revealed by Single-Molecule Force Spectroscopy

    OpenAIRE

    2009-01-01

    Thioredoxins (Trxs) are oxidoreductase enzymes, present in all organisms, that catalyze the reduction of disulfide bonds in proteins. By applying a calibrated force to a substrate disulfide, the chemical mechanisms of Trx catalysis can be examined in detail at the single-molecule level. Here we use single-molecule force-clamp spectroscopy to explore the chemical evolution of Trx catalysis by probing the chemistry of eight different Trx enzymes. All Trxs show a characteristic Michaelis-Menten ...

  16. Modulation of homochiral Dy(III) complexes: single-molecule magnets with ferroelectric properties.

    Science.gov (United States)

    Li, Xi-Li; Chen, Chun-Lai; Gao, Yu-Liang; Liu, Cai-Ming; Feng, Xiang-Li; Gui, Yang-Hai; Fang, Shao-Ming

    2012-11-12

    Homochiral Dy(III) complexes: by changing the ligand-to-metal ratio, enantiomeric pairs of a Dy(III) complex of different nuclearity could be obtained. The mono- and dinuclear complexes exhibit characteristics of single-molecule magnets and different slow magnetic relaxation processes. In addition, the dinuclear complexes exhibit ferroelectric behavior, thus representing the first chiral polynuclear lanthanide-based single-molecule magnets with ferroelectric properties.

  17. Deciphering the Structure and Function of Nuclear Pores Using Single-Molecule Fluorescence Approaches.

    Science.gov (United States)

    Musser, Siegfried M; Grünwald, David

    2016-05-22

    Due to its central role in macromolecular trafficking and nucleocytoplasmic information transfer, the nuclear pore complex (NPC) has been studied in great detail using a wide spectrum of methods. Consequently, many aspects of its architecture, general function, and role in the life cycle of a cell are well understood. Over the last decade, fluorescence microscopy methods have enabled the real-time visualization of single molecules interacting with and transiting through the NPC, allowing novel questions to be examined with nanometer precision. While initial single-molecule studies focused primarily on import pathways using permeabilized cells, it has recently proven feasible to investigate the export of mRNAs in living cells. Single-molecule assays can address questions that are difficult or impossible to answer by other means, yet the complexity of nucleocytoplasmic transport requires that interpretation be based on a firm genetic, biochemical, and structural foundation. Moreover, conceptually simple single-molecule experiments remain technically challenging, particularly with regard to signal intensity, signal-to-noise ratio, and the analysis of noise, stochasticity, and precision. We discuss nuclear transport issues recently addressed by single-molecule microscopy, evaluate the limits of existing assays and data, and identify open questions for future studies. We expect that single-molecule fluorescence approaches will continue to be applied to outstanding nucleocytoplasmic transport questions, and that the approaches developed for NPC studies are extendable to additional complex systems and pathways within cells.

  18. Convection-driven compaction as the source of Enceladus' enigmatic long wavelength topography

    Science.gov (United States)

    Besserer, J.; Nimmo, F.; Pappalardo, R. T.

    2012-12-01

    The long wavelength topography of Enceladus shows depressions about 0.8-1.5 km in depth and 90-175 km wide [1,2]. One possible mechanism to cause this topography is spatial variations in heat flux, leading to variable amounts of compaction of an initially porous ice shell [1]. Here, we show that the heat flux variations associated with convection (e.g., [3]) can quantitatively match the observed features. We model the evolution of a 20-to-30 km thick conductive, initially porous stagnant lid. Heat conduction is modeled using a 1D-finite volume approach, in which thermal conductivity varies with porosity [4]. Porosity evolution due to viscous flow is modeled using the method of [5], with an Arrhenius law and appropriate rheological parameters for ice I, resulting in a feedback on the thermal evolution (e.g., [6]). The surface is kept at constant temperature and a constant (convective) heat flux is prescribed at the base of the conductive layer. Models are run during a period of 100 Myr and the resulting thermal and porosity equilibrium structures are compared, for a range of initial porosity and reference viscosity values. We vary the stagnant lid thickness from 20 to 30 km, as suggested by numerical models [3]. This variation in lid thickness results in an elevation difference of ~0.9 km for an initial porosity of 20 %. This result is not very sensitive to reference viscosity assumed but depends significantly on the initial porosity. For instance, a value of 10 % yields a topography variation of ~0.45 km, which becomes ~1.3 km for 30 % initial porosity. Evolution during a much longer period, e.g. 1 Gyr, results in a slight decrease of topography: ~1.2 km (initial porosity of 30 %) to ~0.41 km (initial porosity of 10 %). This mechanism provides a simple way to explain the wavelength and amplitude of the observed topographic features. Such a mechanism works best in low-gravity environments that are capable of sustaining thermal convection; Enceladus and (perhaps

  19. Long-wavelength fluorescence polarization immunoassay: determination of amikacin on solid surface and gliadins in solution.

    Science.gov (United States)

    Sánchez-Martínez, María Lourdes; Aguilar-Caballos, María Paz; Gómez-Hens, Agustina

    2007-10-01

    The versatility of the fluorescence polarization immunoassay (FPIA) is increased by using two long-wavelength labels, Nile Blue and a ruthenium(II) chelate. The first label has been used to study the potential of FPIA on a solid surface using dry reagent technology. The aminoglycoside antibiotic amikacin has been used as an analyte model, and the method has been applied to the analysis of serum samples. The second label has been used to show the practical application of FPIA to the determination of macromolecules, using gliadins as an analyte model, which have been determined in gluten-free food. Very low amounts of anti-amikacin antibodies and amikacin-Nile Blue tracer were immobilized onto nitrocellulose membranes, for the development of the amikacin method, and the consumption of reagents is lower than in conventional FPIA. Only the addition of the standard or sample extract at an adequate pH is required at the analysis time. The analyte displaces the tracer from the tracer-antibody immunocomplex, obtaining a decrease in the fluorescence polarization proportional to the analyte concentration. The gliadin-Ru(II) chelate tracer shows a relatively long lifetime, which allows the observation of differences in fluorescence polarization values between the tracer-antibody complex and the tracer alone. The dynamic range of the calibration graphs for both analytes is 0.5-10 microg mL-1 and the detection limits are 0.1 and 0.09 microg mL-1 for amikacin and gliadins, respectively. The study of the precision gave values of relative standard deviations lower than 5 and 1.5% for the amikacin and gliadin methods, respectively. Amikacin was determined in human serum samples using a previous deproteinization step with acetonitrile, obtaining recovery values in the range 83.4-122.8%. The gliadin method was applied to the analysis of gluten-free food samples by using a previous extraction step. The recovery study gave values between 94.3 and 105.0%.

  20. Space-based aperture array for ultra-long wavelength radio astronomy

    Science.gov (United States)

    Rajan, Raj Thilak; Boonstra, Albert-Jan; Bentum, Mark; Klein-Wolt, Marc; Belien, Frederik; Arts, Michel; Saks, Noah; van der Veen, Alle-Jan

    2016-02-01

    The past decade has seen the advent of various radio astronomy arrays, particularly for low-frequency observations below 100 MHz. These developments have been primarily driven by interesting and fundamental scientific questions, such as studying the dark ages and epoch of re-ionization, by detecting the highly red-shifted 21 cm line emission. However, Earth-based radio astronomy observations at frequencies below 30 MHz are severely restricted due to man-made interference, ionospheric distortion and almost complete non-transparency of the ionosphere below 10 MHz. Therefore, this narrow spectral band remains possibly the last unexplored frequency range in radio astronomy. A straightforward solution to study the universe at these frequencies is to deploy a space-based antenna array far away from Earths' ionosphere. In the past, such space-based radio astronomy studies were principally limited by technology and computing resources, however current processing and communication trends indicate otherwise. Furthermore, successful space-based missions which mapped the sky in this frequency regime, such as the lunar orbiter RAE-2, were restricted by very poor spatial resolution. Recently concluded studies, such as DARIS (Disturbuted Aperture Array for Radio Astronomy In Space) have shown the ready feasibility of a 9 satellite constellation using off the shelf components. The aim of this article is to discuss the current trends and technologies towards the feasibility of a space-based aperture array for astronomical observations in the Ultra-Long Wavelength (ULW) regime of greater than 10 m i.e., below 30 MHz. We briefly present the achievable science cases, and discuss the system design for selected scenarios such as extra-galactic surveys. An extensive discussion is presented on various sub-systems of the potential satellite array, such as radio astronomical antenna design, the on-board signal processing, communication architectures and joint space-time estimation of the

  1. Aircraft engine-mounted camera system for long wavelength infrared imaging of in-service thermal barrier coated turbine blades

    Science.gov (United States)

    Markham, James; Cosgrove, Joseph; Scire, James; Haldeman, Charles; Agoos, Ian

    2014-12-01

    This paper announces the implementation of a long wavelength infrared camera to obtain high-speed thermal images of an aircraft engine's in-service thermal barrier coated turbine blades. Long wavelength thermal images were captured of first-stage blades. The achieved temporal and spatial resolutions allowed for the identification of cooling-hole locations. The software and synchronization components of the system allowed for the selection of any blade on the turbine wheel, with tuning capability to image from leading edge to trailing edge. Its first application delivered calibrated thermal images as a function of turbine rotational speed at both steady state conditions and during engine transients. In advance of presenting these data for the purpose of understanding engine operation, this paper focuses on the components of the system, verification of high-speed synchronized operation, and the integration of the system with the commercial jet engine test bed.

  2. A precision fiber bragg grating interrogation system using long-wavelength vertical-cavity surface-emitting laser

    Science.gov (United States)

    Hu, Binxin; Jin, Guangxian; Liu, Tongyu; Wang, Jinyu

    2016-09-01

    This paper presents the development of a cost-effective precision fiber Bragg grating (FBG) interrogation system using long-wavelength vertical-cavity surface-emitting laser (VCSEL). Tuning properties of a long-wavelength VCSEL have been studied experimentally. An approximately quadratic dependence of its wavelength on the injection current has been observed. The overall design and key operations of this system including intensity normalization, peak detection, and quadratic curve fitting are introduced in detail. The results show that the system achieves an accuracy of 1.2 pm with a tuning range of 3 nm and a tuning rate of 1 kHz. It is demonstrated that this system is practical and effective by applied in the FBG transformer temperature monitoring.

  3. THEORETICAL DEPENDENCE OF LONG WAVELENGTH PHOTOEMISSION UPON THE SIZE OF Ag NANOPARTICLES EMBEDDED IN BaO SEMICONDUCTOR THIN FILM

    Institute of Scientific and Technical Information of China (English)

    杨海; 蔡武德; 许北雪; 吴锦雷

    2001-01-01

    The dependence of long wavelength photoemission upon the size of Ag nanoparticles embedded in a BaO semicon- ductor is predicted and discussed theoretically. The calculated results show that the increase in the diameter of the Ag nanoparticle, in the range from 1.5 to 37.0nm, leads to the emergence of a roughly Gaussian form of the photoemission spectra and the peaks become markedly narrower. The results also show that the increase in the diameter of the Agnanoparticle leads to the decrease of the long wavelength threshold. The incident light wavelength corresponding to the peak value of the photoemission gets bigger with the increase of the size of Ag nanoparticles, thus showing a redshift.

  4. Design of Synthesized DBRs for Long-Wavelength InP-Based Vertical-Cavity Surface-Emitting Lasers

    Institute of Scientific and Technical Information of China (English)

    HUANG Zhan-Chao; WU Hui-Zhen

    2004-01-01

    @@ We report applications of a metallic film and a phase matching layer (PML) to increase the reflectivity of the cavity mirror in a long-wavelength InP-based vertical-cavity surface-emitting laser (VCSEL). The synthesis of the InGaAsP/InP distributed-Bragg reflector (DBR) with an Au fllm and the InP PML leads to the decrease of periods of the DBR multilayer stacks from 33 to 20 while keeping the reflectivity of the structure over 99%.The reflectivity over the whole forbidden band is significantly increased and become flatter compared to the bare DBR. The use of smaller DBR periods in a long wavelength VCSEL makes the epitaxial growth well controllable,decrease of the heat resistance, and decrease of the in-series electrical resistance of the devices. This can improve the reliability of the VCSEL growth and possibly cut down the cost of VCSEL devices.

  5. 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

    Single-molecule spectroscopy has made considerable impact on many disciplines including chemistry, physics, and biology. To date, most single-molecule spectroscopy work is accomplished by detecting fluorescence. On the other hand, many naturally occurring chromophores, such as retinal, hemoglobin and cytochromes, do not have detectable fluorescence. There is an emerging need for single-molecule spectroscopy techniques that do not require fluorescence. In the last proposal period, we have successfully demonstrated stimulated emission microscopy, single molecule absorption, and stimulated Raman microscopy based on a high-frequency modulation transfer technique. These first-of-a- kind new spectroscopy/microscopy methods tremendously improved our ability to observe molecules that fluorescence weakly, even to the limit of single molecule detection for absorption measurement. All of these methods employ two laser beams: one (pump beam) excites a single molecule to a real or virtual excited state, and the other (probe beam) monitors the absorption/emission property of the single. We extract the intensity change of the probe beam with high sensitivity by implementing a high-frequency phase-sensitive detection scheme, which offers orders of magnitude improvement in detection sensitivity over direct absorption/emission measurement. However, single molecule detection based on fluorescence or absorption is fundamentally limited due to their broad spectral response. It is important to explore other avenues in single molecule detection and imaging which provides higher molecular specificity for studying a wide variety of heterogeneous chemical and biological systems. This proposal aimed to achieve single-molecule detection sensitivity with near resonance stimulated Raman scattering (SRS) microscopy. SRS microscopy was developed in our lab as a powerful technique for imaging heterogeneous samples based on their intrinsic vibrational contrasts, which provides much higher molecular

  6. 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

  7. Renormalization of Long Wavelength Spin Waves in the 2d Ferromagnet Rb2CrCl4

    DEFF Research Database (Denmark)

    Lindgård, Per-Anker; Als-Nielsen, Jens Aage; Hutchings, M. T.

    1980-01-01

    Rb2CrCl4 is a nearly 2d-ferromagnetic, optically transparent insulator isomorphous with K2CuF4. High resolution neutron scattering data for temperatures below Tc = 52.4 K of the low energy long wavelength spin waves are presented and a Hartree-Fock analysis yields Hamiltonian parameters and accou...... and accounts for the renormalization. No evidence of a Bose condensate is found. A spin canting angle θ ≈ 2° is predicted....

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

    Science.gov (United States)

    2016-11-29

    GRANT NUMBER FA9550-15-1-0272 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Dr . Jerome V. Moloney, Professor of Optical Sciences University of Arizona...afosr.reports.sgizmo.com/s3/> Subject: Final Report to Dr . Arje Nachman Contract/Grant Title: Long Wavelength Electromagnetic Light Bullets Generated by a 10.6...kilometer ranges. Our in- house ultrashort pulse simulation tool was used to provide basic research support for studying atmospheric propagation of a

  9. Multicolour single molecule imaging in cells with near infra-red dyes.

    Directory of Open Access Journals (Sweden)

    Christopher J Tynan

    Full Text Available BACKGROUND: The autofluorescence background of biological samples impedes the detection of single molecules when imaging. The most common method of reducing the background is to use evanescent field excitation, which is incompatible with imaging beyond the surface of biological samples. An alternative would be to use probes that can be excited in the near infra-red region of the spectrum, where autofluorescence is low. Such probes could also increase the number of labels that can be imaged in multicolour single molecule microscopes. Despite being widely used in ensemble imaging, there is a currently a shortage of information available for selecting appropriate commercial near infra-red dyes for single molecule work. It is therefore important to characterise available near infra-red dyes relevant to multicolour single molecule imaging. METHODOLOGY/PRINCIPAL FINDINGS: A range of commercially available near infra-red dyes compatible with multi-colour imaging was screened to find the brightest and most photostable candidates. Image series of immobilised samples of the brightest dyes (Alexa 700, IRDye 700DX, Alexa 790 and IRDye 800CW were analysed to obtain the mean intensity of single dye molecules, their photobleaching rates and long period blinking kinetics. Using the optimum dye pair, we have demonstrated for the first time widefield, multi-colour, near infra-red single molecule imaging using a supercontinuum light source in MCF-7 cells. CONCLUSIONS/SIGNIFICANCE: We have demonstrated that near infra-red dyes can be used to avoid autofluorescence background in samples where restricting the illumination volume of visible light fails or is inappropriate. We have also shown that supercontinuum sources are suited to single molecule multicolour imaging throughout the 470-1000 nm range. Our measurements of near infra-red dye properties will enable others to select optimal dyes for single molecule imaging.

  10. Quantification of the vascular endothelial growth factor with a bioluminescence resonance energy transfer (BRET) based single molecule biosensor.

    Science.gov (United States)

    Wimmer, T; Lorenz, B; Stieger, K

    2016-12-15

    Neovascular pathologies in the eye like age-related macular degeneration (AMD), the diabetic retinopathie (DR), retinopathie of prematurity (ROP) or the retinal vein occlusion (RVO) are caused through a hypoxia induced upregulation of the vascular endothelial growth factor (VEGF). So far a correlation of intraocular VEGF concentrations to the impact of the pathologies is limited because of invasive sampling. Therefore, a minimally invasive, repeatable quantification of VEGF levels in the eye is needed to correlate the stage of VEGF induced pathologies as well as the efficacy of anti-VEGF treatment. Here we describe the development of three variants of enhanced BRET2 (eBRET2) based, single molecule biosensors by fusing a Renilla luciferase mutant with enhanced light output (RLuc8) to the N-terminus and a suitable eBRET2 acceptor fluorophore (GFP2) to the C-terminus of a VEGF binding domain, directly fused or separated with two different peptide linkers for the quantification of VEGF in vitro. The VEGF binding domain consists of a single chain variable fragment (scFv) based on ranibizumab in which the light- and the heavy- F(ab) chains were connected with a peptide linker to generate one open reading frame (orf). All three variants generate measureable eBRET2 ratios by transferring energy from the luciferase donor to the GFP2 acceptor, whereas only the directly fused and the proline variant permit VEGF quantification. The directly fused biosensor variant allows the quantification of VEGF with higher sensitivity, compared to the widely used ELISA systems and a wide dynamic quantification range in vitro. Our system demonstrates not only an additional in vitro application on VEGF quantification but also a promising step towards an applicable biosensor in an implantable device able to quantify VEGF reliably after implantation in vivo.

  11. Long-wavelength Folding on Mercury: Lithospheric Boudinage in the Caloris Basin?

    Science.gov (United States)

    Klimczak, C.; Byrne, P. K.; Solomon, S. C.; Ernst, C. M.; Watters, T. R.; Murchie, S. L.; Preusker, F.; Oberst, J.

    2012-12-01

    Both laser altimetric and stereo photogrammetric datasets returned by the MESSENGER spacecraft in orbit about Mercury reveal impact craters whose floors show systematic tilts away from topographically high regions. Such tilted craters indicate that Mercury's lithosphere has been affected by large-scale folding that, when mapped, is manifest as several long-wavelength and low-amplitude rises and troughs, interpreted as anticlines and synclines, that cross the planet. Topographic profiles across the syn- and anticlines show that folding can be described as more or less harmonic with wavelengths of 800 to 1300 km and amplitudes of 1.5 to 3 km. These dimensions show that folding accommodated shortening strains of only ~0.002%. Several syn- and anticlines are found in the region in and around the Caloris basin, the largest recognized impact basin on the planet. The topography within the basin is characterized by two anticlines, each trending approximately east-west and having crests that rise more than 2 km above a low-lying region near the basin center. Fault displacement analysis of several radial graben and circumferential ridges, together with crater excavation depths of spectrally distinct materials, yields stratigraphic information on the uppermost smooth volcanic plains in the basin's interior, revealing a pinch-and-swell structure to these units. Specifically, the plains are thicker in the vicinity of the topographic highs and thinner at the topographic low. We used numerical simulations with the two-dimensional module of the finite-element modeling code ADELI to explore how folding of the lithosphere on Mercury and the pinching and swelling might have been accommodated for a range of assumed boundary conditions and properties of the lithosphere and mantle, informed by recent geophysical data returned by MESSENGER. We find that continuing lithospheric folding with periodic emplacement of volcanic plains units can account for the observed topography and

  12. Use of 8-methoxypsoralen and long-wavelength ultraviolet radiation for decontamination of platelet concentrates

    Science.gov (United States)

    Corash, Laurence; Lin, Lily; Wiesehahn, Gary; Cimino, George

    1992-06-01

    Transmission of viral diseases through blood products remains a problem in transfusion medicine. A number of methods have been developed to inactivate viral pathogens in plasma and plasma fractions, including: dry heating, wet heating, solvent-detergent treatment, and immunoaffinity purification. While some of these methods successfully inactivate pathogenic viruses, inactivation may be incomplete or result in damage to labile plasma proteins and cells. We have developed a photochemical decontamination system (PCD) for platelet concentrates (PC) utilizing treatment with long wavelength ultraviolet radiation (UVA, 320 - 400 nm) and 8-methoxypsoralen (8-MOP). This system is capable of inactivating 25 - 30 logs/hr of bacteria E. coli or S. aureus, 6 logs/hr of bacteriophage fd, 0.9 log/hr of bacteriophage R17 and 1.1 logs/hr of feline leukemia virus (FeLV) in PC. Immediately following 6 hrs of PCD treatment, platelet integrity and function of PCD treated and control PC were equivalent. After overnight storage PCD treated and control PC platelet properties were equal, but there was a slight reduction in TXB-2 production of PCD treated PC compared to controls. Following PCD treatment, PC were stored for 48 to 96 hrs. Platelet counts, morphology scores, extracellular LDH levels, aggregation response, dense body (db) content, and alpha granule ((alpha) g) content of PCD treated and control PC were comparable. We assessed the ability of the PCD technique to inactivate intracellular and extracellular virus, quantified the degree of DNA adduct formation in contaminating lymphocytes, and measured the inhibition of polymerase chain reaction (PCR) mediated amplification of intracellular DNA. High titers of cell-free murine cytomegalovirus added to human platelet concentrates (final concentration 106) were inactivated by PCD within 30 min. Cat renal fibroblasts infected at high levels with feline rhinotracheitis virus (FeRTV) were seeded into PC followed by PCD treatment with

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

    Science.gov (United States)

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

    2012-08-01

    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.

  14. 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.

  15. Single-molecule electrical contacts on silicon electrodes under ambient conditions

    Science.gov (United States)

    Aragonès, Albert C.; Darwish, Nadim; Ciampi, Simone; Sanz, Fausto; Gooding, J. Justin; Díez-Pérez, Ismael

    2017-04-01

    The ultimate goal in molecular electronics is to use individual molecules as the active electronic component of a real-world sturdy device. For this concept to become reality, it will require the field of single-molecule electronics to shift towards the semiconducting platform of the current microelectronics industry. Here, we report silicon-based single-molecule contacts that are mechanically and electrically stable under ambient conditions. The single-molecule contacts are prepared on silicon electrodes using the scanning tunnelling microscopy break-junction approach using a top metallic probe. The molecular wires show remarkable current-voltage reproducibility, as compared to an open silicon/nano-gap/metal junction, with current rectification ratios exceeding 4,000 when a low-doped silicon is used. The extension of the single-molecule junction approach to a silicon substrate contributes to the next level of miniaturization of electronic components and it is anticipated it will pave the way to a new class of robust single-molecule circuits.

  16. 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.

  17. 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.

  18. 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

    2017-08-05

    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.

  19. Next-Generation DNA Curtains for Single-Molecule Studies of Homologous Recombination.

    Science.gov (United States)

    Soniat, Michael M; Myler, Logan R; Schaub, Jeffrey M; Kim, Yoori; Gallardo, Ignacio F; Finkelstein, Ilya J

    2017-01-01

    Homologous recombination (HR) is a universally conserved DNA double-strand break repair pathway. Single-molecule fluorescence imaging approaches have revealed new mechanistic insights into nearly all aspects of HR. These methods are especially suited for studying protein complexes because multicolor fluorescent imaging can parse out subassemblies and transient intermediates that associate with the DNA substrates on the millisecond to hour timescales. However, acquiring single-molecule datasets remains challenging because most of these approaches are designed to measure one molecular reaction at a time. The DNA curtains platform facilitates high-throughput single-molecule imaging by organizing arrays of DNA molecules on the surface of a microfluidic flowcell. Here, we describe a second-generation UV lithography-based protocol for fabricating flowcells for DNA curtains. This protocol greatly reduces the challenges associated with assembling DNA curtains and paves the way for the rapid acquisition of large datasets from individual single-molecule experiments. Drawing on our recent studies of human HR, we also provide an overview of how DNA curtains can be used for observing facilitated protein diffusion, processive enzyme translocation, and nucleoprotein filament dynamics on single-stranded DNA. Together, these protocols and case studies form a comprehensive introduction for other researchers that may want to adapt DNA curtains for high-throughput single-molecule studies of DNA replication, transcription, and repair. © 2017 Elsevier Inc. All rights reserved.

  20. Single-molecule analysis of fluorescent carbon dots towards localization-based super-resolution microscopy

    Science.gov (United States)

    Verma, Navneet C.; Khan, Syamantak; Nandi, Chayan K.

    2016-12-01

    The advancement of high-resolution bioimaging has always been dependent on the discovery of bright and easily available fluorescent probes. Fluorescent carbon nanodots, an interesting class of relatively new nanomaterials, have emerged as a versatile alternative due to their superior optical properties, non-toxicity, cell penetrability and easy routes to synthesis. Although a plethora of reports is available on bioimaging using carbon dots, single-molecule-based super-resolution imaging is rare in the literature. In this study, we have systematically characterized the single-molecule fluorescence of three carbon dots and compared them with a standard fluorescent probe. Each of these carbon dots showed a long-lived dark state in the presence of an electron acceptor. The electron transfer mechanism was investigated in single-molecule as well as in ensemble experiments. The average on-off rate between the fluorescent bright and dark states, which is one of the important parameters for single-molecule localization-based super-resolution microscopy, was measured by changing the laser power. We report that the photon budget and on-off rate of these carbon dots were good enough to achieve single-molecule localization with a precision of ~35 nm.

  1. 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

  2. Dissecting contact mechanics from quantum interference in single-molecule junctions of stilbene derivatives.

    Science.gov (United States)

    Aradhya, Sriharsha V; Meisner, Jeffrey S; Krikorian, Markrete; Ahn, Seokhoon; Parameswaran, Radha; Steigerwald, Michael L; Nuckolls, Colin; Venkataraman, Latha

    2012-03-14

    Electronic factors in molecules such as quantum interference and cross-conjugation can lead to dramatic modulation and suppression of conductance in single-molecule junctions. Probing such effects at the single-molecule level requires simultaneous measurements of independent junction properties, as conductance alone cannot provide conclusive evidence of junction formation for molecules with low conductivity. Here, we compare the mechanics of the conducting para-terminated 4,4'-di(methylthio)stilbene and moderately conducting 1,2-bis(4-(methylthio)phenyl)ethane to that of insulating meta-terminated 3,3'-di(methylthio)stilbene single-molecule junctions. We simultaneously measure force and conductance across single-molecule junctions and use force signatures to obtain independent evidence of junction formation and rupture in the meta-linked cross-conjugated molecule even when no clear low-bias conductance is measured. By separately quantifying conductance and mechanics, we identify the formation of atypical 3,3'-di(methylthio)stilbene molecular junctions that are mechanically stable but electronically decoupled. While theoretical studies have envisaged many plausible systems where quantum interference might be observed, our experiments provide the first direct quantitative study of the interplay between contact mechanics and the distinctively quantum mechanical nature of electronic transport in single-molecule junctions.

  3. Capabilities for measuring the diffusivity of a single molecule by recycling it in a nanochannel

    Science.gov (United States)

    Wang, Bo; Davis, Lloyd

    2014-03-01

    Analysis of the fractions of fluorescently labeled molecules with different diffusivities within a microliter drop of solution is often used for high-throughput screening of molecular binding interactions in pharmaceutical drug discovery research. Assays frequently employ fluorescence correlation spectroscopy, an ensemble technique that is able to resolve fast diffusing small ligands from those bound to much larger biomolecules with considerably slower diffusion. Single-molecule measurements have the potential to resolve species with different diffusivities and to count the numbers of molecules of each species. Single-molecule recycling in a nanochannel, which entails detection of bursts of fluorescence photons from the repeated passage of a molecule through a focused laser beam as the flow along a nanochannel is periodically alternated, can be used to determine the diffusivity of a single molecule from the fluctuations in the intervals between successive detections. We discuss Monte Carlo studies to determine favorable experimental conditions for determining single-molecule diffusivities, together with a weighted-sliding-sum photon burst detection algorithm for flow-control and maximum-likelihood based analysis of recycle times. We also discuss incorporation of the algorithms into our experimental apparatus for single-molecule recycling, which uses a LabView real-time system for photon count analysis and flow control.

  4. A Preliminary Full Spectrum Magnetic Anomaly Database of the United States With Improved Long Wavelengths for Studying Continental Dynamics

    Science.gov (United States)

    Ravat, D.; Sabaka, T.; Elshayat, A.; Aref, A.; Elawadi, E.; Kucks, R.; Hill, P.; Phillips, J.; Finn, C.; Bouligand, C.; Blakely, R. J.

    2008-12-01

    Under an initiative started by Thomas G. Hildenbrand of the U. S. Geological Survey, we have improved the long-wavelength (50-2500 km) content of the regional magnetic anomaly compilation for the conterminous United States by utilizing a nearly homogeneous set of National Uranium Resource Evaluation (NURE) magnetic surveys flown from 1975 to 1981. The surveys were flown in quadrangles of 2° of longitude by 1° of latitude with E-W flight-lines spaced 4.8 to 9.6 km, N-S tie-lines variably spaced, and a nominal terrain clearance of 122 m. Many of the surveys used base-station magnetometers to remove external field variations. NURE surveys were originally processed with IGRF core-field models, which left behind non- uniform residual trends in the data and discontinuities at survey boundaries. In this study, in place of the IGRF/DGRF, we used a spatially and temporally continuous model of the magnetic field known as the Comprehensive Model (CM), which allowed us to avoid discontinuities at survey boundaries. The CM simultaneously models the core magnetic field and long-wavelength ionospheric and magnetospheric fields, along with their induced components in the earth. Because of the availability of base-stations for removing external fields, we removed only the core-derived geomagnetic field based on CM4 (spherical harmonic degree 13) for our compilation. The NURE data have short-wavelength (less than 30 km) noise due to cultural sources, base-station offsets, and residual external field effects. It is possible to reduce and even remove these defects by identifying and editing them and by applying leveling and micro-leveling. There are also many high resolution individual surveys over the U.S. which could be incorporated into the improved NURE database; however, this could take a few years. Therefore, we have created a preliminary full spectrum magnetic anomaly database by combining short-wavelength magnetic anomalies from the North American Magnetic Anomaly Map (NAMAM

  5. Single-molecule spectroscopy for plastic electronics: materials analysis from the bottom-up.

    Science.gov (United States)

    Lupton, John M

    2010-04-18

    pi-conjugated polymers find a range of applications in electronic devices. These materials are generally highly disordered in terms of chain length and chain conformation, besides being influenced by a variety of chemical and physical defects. Although this characteristic can be of benefit in certain device applications, disorder severely complicates materials analysis. Accurate analytical techniques are, however, crucial to optimising synthetic procedures and assessing overall material purity. Fortunately, single-molecule spectroscopic techniques have emerged as an unlikely but uniquely powerful approach to unraveling intrinsic material properties from the bottom up. Building on the success of such techniques in the life sciences, single-molecule spectroscopy is finding increasing applicability in materials science, effectively enabling the dissection of the bulk down to the level of the individual molecular constituent. This article reviews recent progress in single molecule spectroscopy of conjugated polymers as used in organic electronics.

  6. Measurement and understanding of single-molecule break junction rectification caused by asymmetric contacts.

    Science.gov (United States)

    Wang, Kun; Zhou, Jianfeng; Hamill, Joseph M; Xu, Bingqian

    2014-08-01

    The contact effects of single-molecule break junctions on rectification behaviors were experimentally explored by a systematic control of anchoring groups of 1,4-disubstituted benzene molecular junctions. Single-molecule conductance and I-V characteristic measurements reveal a strong correlation between rectifying effects and the asymmetry in contacts. Analysis using energy band models and I-V calculations suggested that the rectification behavior is mainly caused by asymmetric coupling strengths at the two contact interfaces. Fitting of the rectification ratio by a modified Simmons model we developed suggests asymmetry in potential drop across the asymmetric anchoring groups as the mechanism of rectifying I-V behavior. This study provides direct experimental evidence and sheds light on the mechanisms of rectification behavior induced simply by contact asymmetry, which serves as an aid to interpret future single-molecule electronic behavior involved with asymmetric contact conformation.

  7. Vibrationally dependent electron-electron interactions in resonant electron transport through single-molecule junctions

    Science.gov (United States)

    Erpenbeck, A.; Härtle, R.; Bockstedte, M.; Thoss, M.

    2016-03-01

    We investigate the role of electronic-vibrational coupling in resonant electron transport through single-molecule junctions, taking into account that the corresponding coupling strengths may depend on the charge and excitation state of the molecular bridge. Within an effective-model Hamiltonian approach for a molecule with multiple electronic states, this requires to extend the commonly used model and include vibrationally dependent electron-electron interaction. We use Born-Markov master equation methods and consider selected models to exemplify the effect of the additional interaction on the transport characteristics of a single-molecule junction. In particular, we show that it has a significant influence on local cooling and heating mechanisms, it may result in negative differential resistance, and it may cause pronounced asymmetries in the conductance map of a single-molecule junction.

  8. From single-molecule spectroscopy to super-resolution imaging of the neuron: a review

    Science.gov (United States)

    Laine, Romain F.; Kaminski Schierle, Gabriele S.; van de Linde, Sebastian; Kaminski, Clemens F.

    2016-06-01

    For more than 20 years, single-molecule spectroscopy has been providing invaluable insights into nature at the molecular level. The field has received a powerful boost with the development of the technique into super-resolution imaging methods, ca. 10 years ago, which overcome the limitations imposed by optical diffraction. Today, single molecule super-resolution imaging is routinely used in the study of macromolecular function and structure in the cell. Concomitantly, computational methods have been developed that provide information on numbers and positions of molecules at the nanometer-scale. In this overview, we outline the technical developments that have led to the emergence of localization microscopy techniques from single-molecule spectroscopy. We then provide a comprehensive review on the application of the technique in the field of neuroscience research.

  9. 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.

  10. 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

    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(111...... 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...

  11. Orbital-selective single molecule excitation and spectroscopy based on plasmon-exciton coupling

    CERN Document Server

    Imada, Hiroshi; Imai-Imada, Miyabi; Kawahara, Shota; Kimura, Kensuke; Kim, Yousoo

    2016-01-01

    The electronic excitation of molecules triggers diverse phenomena such as luminescence and photovoltaic effects, which are the bases of various energy-converting devices. Understanding and control of the excitations at the single-molecule level are long standing targets, however, they have been hampered by the limited spatial resolution in optical probing techniques. Here we investigate the electronic excitation of a single molecule with sub-molecular precision using a localised plasmon at the tip apex of a scanning tunnelling microscope (STM) as an excitation probe. Coherent energy transfer between the plasmon and molecular excitons is discovered when the plasmon is located in the proximity of isolated molecules, which is corroborated by a theoretical analysis. The polarised plasmonic field enables selective excitation of an electronic transition between anisotropic frontier molecular orbitals. Our findings have established the foundation of a novel single-molecule spectroscopy with STM, providing an integra...

  12. 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.

  13. Biophysical Insights from Temperature-Dependent Single-Molecule Förster Resonance Energy Transfer

    Science.gov (United States)

    Holmstrom, Erik D.; Nesbitt, David J.

    2016-05-01

    Single-molecule fluorescence microscopy techniques can be used in combination with micrometer length-scale temperature control and Förster resonance energy transfer (FRET) in order to gain detailed information about fundamental biophysical phenomena. In particular, this combination of techniques has helped foster the development of remarkable quantitative tools for studying both time- and temperature-dependent structural kinetics of biopolymers. Over the past decade, multiple research efforts have successfully incorporated precise spatial and temporal control of temperature into single-molecule FRET (smFRET)-based experiments, which have uncovered critical thermodynamic information on a wide range of biological systems such as conformational dynamics of nucleic acids. This review provides an overview of various temperature-dependent smFRET approaches from our laboratory and others, highlighting efforts in which such methods have been successfully applied to studies of single-molecule nucleic acid folding.

  14. Structure from Fleeting Illumination of Faint Spinning Objects in Flight with Application to Single Molecules

    CERN Document Server

    Fung, Russell; Saldin, Dilano K; Ourmazd, Abbas

    2008-01-01

    There are many instances when the structure of a weakly-scattering spinning object in flight must be determined to high resolution. Examples range from comets to nanoparticles and single molecules. The latter two instances are the subject of intense current interest. Substantial progress has recently been made in illuminating spinning single particles in flight with powerful X-ray bursts to determine their structure with the ultimate goal of determining the structure of single molecules. However, proposals to reconstruct the molecular structure from diffraction "snapshots" of unknown orientation require ~1000x more signal than available from next-generation sources. Using a new approach, we demonstrate the recovery of the structure of a weakly scattering macromolecule at the anticipated next-generation X-ray source intensities. Our work closes a critical gap in determining the structure of single molecules and nanoparticles by X-ray methods, and opens the way to reconstructing the structure of spinning, or ra...

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

    Science.gov (United States)

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

    2012-06-01

    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 duplication of genome in eukaryotes. Here, we describe a single-molecule assay that allows replication of DNA attached to the functionalized surface of a microfluidic flow cell in a soluble Xenopus leavis egg extract replication system and subsequent visualization of replication products via fluorescence microscopy. We also explain a method for detection of replication proteins, through fluorescently labeled antibodies, on partially replicated DNA immobilized at both ends to the surface.

  16. Single-Cell and Single-Molecule Analysis of Gene Expression Regulation

    Science.gov (United States)

    Vera, Maria; Biswas, Jeetayu; Senecal, Adrien

    2016-01-01

    Recent advancements in single-cell and single-molecule imaging technologies have resolved biological processes in time and space that are fundamental to understanding the regulation of gene expression. Observations of single-molecule events in their cellular context have revealed highly dynamic aspects of transcriptional and post-transcriptional control in eukaryotic cells. This approach can relate transcription with mRNA abundance and lifetimes. Another key aspect of single-cell analysis is the cell-to-cell variability among populations of cells. Definition of heterogeneity has revealed stochastic processes, determined characteristics of under-represented cell types or transitional states, and integrated cellular behaviors in the context of multicellular organisms. In this review, we discuss novel aspects of gene expression of eukaryotic cells and multicellular organisms revealed by the latest advances in single-cell and single-molecule imaging technology. PMID:27893965

  17. Single molecule detection using charge-coupled device array technology. Technical progress report

    Energy Technology Data Exchange (ETDEWEB)

    Denton, M.B.

    1992-07-29

    A technique for the detection of single fluorescent chromophores in a flowing stream is under development. This capability is an integral facet of a rapid DNA sequencing scheme currently being developed by Los Alamos National Laboratory. In previous investigations, the detection sensitivity was limited by the background Raman emission from the water solvent. A detection scheme based on a novel mode of operating a Charge-Coupled Device (CCD) is being developed which should greatly enhance the discrimination between fluorescence from a single molecule and the background Raman scattering from the solvent. Register shifts between rows in the CCD are synchronized with the sample flow velocity so that fluorescence from a single molecule is collected in a single moving charge packet occupying an area approaching that of a single pixel while the background is spread evenly among a large number of pixels. Feasibility calculations indicate that single molecule detection should be achieved with an excellent signal-to-noise ratio.

  18. Shedding light on protein folding, structural and functional dynamics by single molecule studies

    DEFF Research Database (Denmark)

    Bavishi, Krutika; Hatzakis, Nikos

    2014-01-01

    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...

  19. Single-Molecule Investigations of Morphology and Mass Transport Dynamics in Nanostructured Materials

    Science.gov (United States)

    Higgins, Daniel A.; Park, Seok Chan; Tran-Ba, Khanh-Hoa; Ito, Takashi

    2015-07-01

    Nanostructured materials such as mesoporous metal oxides and phase-separated block copolymers form the basis for new monolith, membrane, and thin film technologies having applications in energy storage, chemical catalysis, and separations. Mass transport plays an integral role in governing the application-specific performance characteristics of many such materials. The majority of methods employed in their characterization provide only ensemble data, often masking the nanoscale, molecular-level details of materials morphology and mass transport. Single-molecule fluorescence methods offer direct routes to probing these characteristics on a single-molecule/single-nanostructure basis. This article provides a review of single-molecule studies focused on measurements of anisotropic diffusion, adsorption, partitioning, and confinement in nanostructured materials. Experimental methods covered include confocal and wide-field fluorescence microscopy. The results obtained promise to deepen our understanding of mass transport mechanisms in nanostructures, thus aiding in the realization of advanced materials systems.

  20. Biophysical Insights from Temperature-Dependent Single-Molecule Förster Resonance Energy Transfer.

    Science.gov (United States)

    Holmstrom, Erik D; Nesbitt, David J

    2016-05-27

    Single-molecule fluorescence microscopy techniques can be used in combination with micrometer length-scale temperature control and Förster resonance energy transfer (FRET) in order to gain detailed information about fundamental biophysical phenomena. In particular, this combination of techniques has helped foster the development of remarkable quantitative tools for studying both time- and temperature-dependent structural kinetics of biopolymers. Over the past decade, multiple research efforts have successfully incorporated precise spatial and temporal control of temperature into single-molecule FRET (smFRET)-based experiments, which have uncovered critical thermodynamic information on a wide range of biological systems such as conformational dynamics of nucleic acids. This review provides an overview of various temperature-dependent smFRET approaches from our laboratory and others, highlighting efforts in which such methods have been successfully applied to studies of single-molecule nucleic acid folding.

  1. 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

  2. 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.

    2016-03-01

    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.

  3. Measuring long wavelength plasma density fluctuations by CO2 laser scattering (abstract)

    Science.gov (United States)

    Evans, D. E.

    1985-05-01

    Long wavelength density fluctuations can be observed by scattering even with a probe beam of much shorter wavelength provided the scattering angle is small enough. This paper is concerned with experiments in which the scattering angle is comparable with the probe beam divergence so the scattered and incident radiation never achieve spatial separation. Under these circumstances, the role of diffraction is preeminent and Fourier optics methods are used to describe the propagation of the beam, which is taken to be TEM00 mode Gaussian. Interaction between the probe beam and the plasma disturbance is described by refraction and no appeal is made to explicit scattering theory. Analysis of the effect of a monochromatic wave disturbance confined to a plane perpendicular to the probe beam (a plane grating in effect) reveals oscillations at the wave frequency induced on the probe with an intensity varying over the beam profile in a regular pattern symmetric about the beam axis. Detail of the pattern depends on the wavelength of the disturbance, its direction, and its axial position relative to a local beam waist. These oscillations are readily identified as due to radiation scattered by the plasma wave into diffraction orders, beating with the unperturbed part of the beam. Indeed, it can be shown1 that Fourier optics plus refraction produce almost the same result as conventional scattering theory,2 the small discrepancy being traceable to the neglect in the latter of incident beam wavefront curvature. The results of the two approaches coincide in the Fraunhofer limit. Computations of this sort have been confirmed by experiments using transducer-driven waves in air3 and by plasma experiments where the same regular patterns are observed from spontaneous plasma waves.4,5 Calculation suggests and experiments have demonstrated6 that additional information, such as the absolute direction of wave propagation, can be deduced from phase, measured with a multichannel detector array

  4. Understanding the physics of DNA using nanoscale single-molecule manipulation

    Science.gov (United States)

    Frey, Eric W.; Gooding, Ashton A.; Wijeratne, Sitara; Kiang, Ching-Hwa

    2012-10-01

    Processes for decoding the genetic information in cells, including transcription, replication, recombination and repair, involve the deformation of DNA from its equilibrium structures such as bending, stretching, twisting, and unzipping of the double helix. Single-molecule manipulation techniques have made it possible to control DNA conformation and simultaneously detect the induced changes, revealing a rich variety of mechanically-induced conformational changes and thermodynamic states. These single-molecule techniques helped us to reveal the physics of DNA and the processes involved in the passing on of the genetic code.

  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. 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.

  7. Controlled switching of single-molecule junctions by mechanical motion of a phenyl ring

    Directory of Open Access Journals (Sweden)

    Yuya Kitaguchi

    2015-10-01

    Full Text Available Mechanical methods for single-molecule control have potential for wide application in nanodevices and machines. Here we demonstrate the operation of a single-molecule switch made functional by the motion of a phenyl ring, analogous to the lever in a conventional toggle switch. The switch can be actuated by dual triggers, either by a voltage pulse or by displacement of the electrode, and electronic manipulation of the ring by chemical substitution enables rational control of the on-state conductance. Owing to its simple mechanics, structural robustness, and chemical accessibility, we propose that phenyl rings are promising components in mechanical molecular devices.

  8. Highlights from Faraday Discussion 184: Single-Molecule Microscopy and Spectroscopy, London, UK, September 2015.

    Science.gov (United States)

    Gellings, E; Faez, S; Piatkowski, L

    2016-02-07

    The 2015 Faraday Discussion on single-molecule microscopy and spectroscopy brought together leading scientists involved in various topics of single-molecule research. It attracted almost a hundred delegates from a broad spectrum of backgrounds and experience levels - from experimentalists to theoreticians, from biologists to materials scientists, from masters students to Nobel Prize Laureates. The meeting was merely a reflection of how big of an impact the ability to detect individual molecules has had on science over the past quarter of a century. In the following we give an overview of the topics covered during this meeting and briefly highlight the content of each presentation.

  9. Experimental observation of long-wavelength dispersive wave generation induced by self-defocusing nonlinearity in BBO crystal

    CERN Document Server

    Zhou, Binbin

    2015-01-01

    We experimentally observe long-wavelength dispersive waves generation in a BBO crystal. A soliton was formed in normal GVD regime of the crystal by a self-defocusing and negative nonlinearity through phase-mismatched quatradic interaction. Strong temporal pulse compression confirmed the formation of soliton during the pulse propagation inside the crystal. Significant dispersive wave radiation was measured in the anomalous GVD regime of the BBO crystal. With the pump wavelengths from 1.24 to 1.4 $\\mu$m, tunable dispersive waves are generated around 1.9 to 2.2 $\\mu$m. The observed dispersive wave generation is well understood by simulations.

  10. Blinking effect and the use of quantum dots in single molecule spectroscopy.

    Science.gov (United States)

    Rombach-Riegraf, Verena; Oswald, Peter; Bienert, Roland; Petersen, Jan; Domingo, M P; Pardo, Julian; Gräber, P; Galvez, E M

    2013-01-01

    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.

  11. Optical detection of electrokinetically manipulated single molecules in a nanofluidic chip

    NARCIS (Netherlands)

    Parikesit, G.O.F.; Kutchoukov, V.G.; Bossche, A.; Young, I,T.; Garini, Y.

    2005-01-01

    We report on the progress of a novel nanofluidic device for detecting and manipulating single molecules in solution. This paper discusses the development of an earlier proposed molecule separation method, where electrokinetic forces separate different molecules based on their masses and charges.

  12. 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.

  13. 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.

  14. Ninth international conference on hole burning, single molecule and related spectroscopies: science and applications (HBSM 2006)

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2006-07-01

    This conference was organized around 9 sessions: -) single molecule, -) quantum optics, -) hole-burning materials and mechanisms, -) single nano-particle spectroscopy, -) dephasing and spectral diffusion, -) microwave photonics, -) biological systems, -) rare earth doped materials, -) novel laser sources. This document gathers only the slides of the presentations.

  15. Frozen-solution magnetisation dynamics of hexanuclear oxime-based MnIII single-molecule magnets

    DEFF Research Database (Denmark)

    Inglis, R.; Bendix, J.; Brock-Nannestad, T.

    2010-01-01

    Frozen solution SQUID measurements of the hexanuclear Single-Molecule Magnets [Mn6O2(Et-sao)(6)(EtOH)(6)(Me(2)benz)(2)] (1) and [Mn6O2(Et-sao)(6)(EtOH)(4)(H2O)(2)(benz)(2)] (2) allow the molecular and solid state contributions to the magnetic properties to be quantified...

  16. Single-molecule diodes with high rectification ratios through environmental control.

    Science.gov (United States)

    Capozzi, Brian; Xia, Jianlong; Adak, Olgun; Dell, Emma J; Liu, Zhen-Fei; Taylor, Jeffrey C; Neaton, Jeffrey B; Campos, Luis M; Venkataraman, Latha

    2015-06-01

    Molecular electronics aims to miniaturize electronic devices by using subnanometre-scale active components. A single-molecule diode, a circuit element that directs current flow, was first proposed more than 40 years ago and consisted of an asymmetric molecule comprising a donor-bridge-acceptor architecture to mimic a semiconductor p-n junction. Several single-molecule diodes have since been realized in junctions featuring asymmetric molecular backbones, molecule-electrode linkers or electrode materials. Despite these advances, molecular diodes have had limited potential for applications due to their low conductance, low rectification ratios, extreme sensitivity to the junction structure and high operating voltages. Here, we demonstrate a powerful approach to induce current rectification in symmetric single-molecule junctions using two electrodes of the same metal, but breaking symmetry by exposing considerably different electrode areas to an ionic solution. This allows us to control the junction's electrostatic environment in an asymmetric fashion by simply changing the bias polarity. With this method, we reliably and reproducibly achieve rectification ratios in excess of 200 at voltages as low as 370 mV using a symmetric oligomer of thiophene-1,1-dioxide. By taking advantage of the changes in the junction environment induced by the presence of an ionic solution, this method provides a general route for tuning nonlinear nanoscale device phenomena, which could potentially be applied in systems beyond single-molecule junctions.

  17. Detailed analysis of complex single molecule FRET data with the software MASH

    Science.gov (United States)

    Hadzic, Mélodie C. A. S.; Kowerko, Danny; Börner, Richard; Zelger-Paulus, Susann; Sigel, Roland K. O.

    2016-04-01

    The processing and analysis of surface-immobilized single molecule FRET (Förster resonance energy transfer) data follows systematic steps (e.g. single molecule localization, clearance of different sources of noise, selection of the conformational and kinetic model, etc.) that require a solid knowledge in optics, photophysics, signal processing and statistics. The present proceeding aims at standardizing and facilitating procedures for single molecule detection by guiding the reader through an optimization protocol for a particular experimental data set. Relevant features were determined from single molecule movies (SMM) imaging Cy3- and Cy5-labeled Sc.ai5γ group II intron molecules synthetically recreated, to test the performances of four different detection algorithms. Up to 120 different parameterizations per method were routinely evaluated to finally establish an optimum detection procedure. The present protocol is adaptable to any movie displaying surface-immobilized molecules, and can be easily reproduced with our home-written software MASH (multifunctional analysis software for heterogeneous data) and script routines (both available in the download section of www.chem.uzh.ch/rna).

  18. Electron transfer behaviour of biological macromolecules towards the single-molecule level

    DEFF Research Database (Denmark)

    Zhang, Jingdong; Grubb, Mikala; Hansen, Allan Glargaard

    2003-01-01

    on Au(111) by chemisorption via exposed sulfur-containing residues. Voltammetric, interfacial capacitance, x-ray photoelectron spectroscopy and microcantilever sensor data, together with in situ STM with single-molecule resolution, all point to a coherent view of monolayer organization with protein...

  19. Spectral multitude and spectral dynamics reflect changing conjugation length in single molecules of oligophenylenevinylenes

    KAUST Repository

    Kobayashi, Hiroyuki

    2012-01-01

    Single-molecule study of phenylenevinylene oligomers revealed distinct spectral forms due to different conjugation lengths which are determined by torsional defects. Large spectral jumps between different spectral forms were ascribed to torsional flips of a single phenylene ring. These spectral changes reflect the dynamic nature of electron delocalization in oligophenylenevinylenes and enable estimation of the phenylene torsional barriers. © 2012 The Owner Societies.

  20. A versatile low-temperature setup for the electrical characterization of single-molecule junctions

    NARCIS (Netherlands)

    Martin, C.A.; Smit, R.H.M.; Van Egmond, R.; Van der Zant, H.S.J.; Van Ruitenbeek, J.M.

    2011-01-01

    We present a modular high-vacuum setup for the electrical characterization of single molecules down to liquid helium temperatures. The experimental design is based on microfabricated mechanically controllable break junctions, which offer control over the distance of two electrodes via the bending of

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

    NARCIS (Netherlands)

    Loveland, Anna B.; Habuchi, Satoshi; Walter, Johannes C.; Oijen, Antoine M. van

    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 (PhotoActivation, Diffusion and Excitation). A protein of intere

  2. Potential of protoporphyrin IX and metal derivatives for single molecule fluorescence studies

    Energy Technology Data Exchange (ETDEWEB)

    Hu Yi; Geissinger, Peter [Department of Chemistry and Biochemistry, Laboratory for Surface Studies, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, WI 53211 (United States); Woehl, Joerg C., E-mail: woehl@uwm.ed [Department of Chemistry and Biochemistry, Laboratory for Surface Studies, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, WI 53211 (United States)

    2011-03-15

    Metalloporphyrins are cofactors of a variety of proteins, and are often used as spectroscopic probes of the active site. Many high resolution techniques, such as single molecule spectroscopy, are based on fluorescence contrast and require the replacement of the native metalloporphyrin by a fluorescent analog. We have investigated the potential of several fluorescent analogs of heme, namely free-base protoporphyrin IX and its metal derivatives containing Zn, Sn, and Mg, for single molecule fluorescence studies by determining their room-temperature molecular absorption cross sections and fluorescence quantum yields. According to these data, free-base protoporphyrin IX and its Zn derivative, which have the highest fluorescence quantum yields, are the most suitable heme analogs for single molecule fluorescence studies. - Research highlights: Protoporphyrin IX and fluorescent metal derivatives for single molecule detection. Measurement of room temperature absorption cross sections for Q bands. Measurement of room temperature fluorescence quantum yields for Q bands. PPIX and Zn derivative have highest quantum yields for lowest-energy transition.

  3. Frontiers in Laser Cooling, Single-Molecule Biophysics, and Enrgy Science: A Talk by Carl Wieman

    Energy Technology Data Exchange (ETDEWEB)

    Wieman, Carl

    2008-08-30

    Carl Wieman presents a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

  4. Large Conductance Switching in a Single-Molecule Device through Room Temperature Spin-Dependent Transport.

    Science.gov (United States)

    Aragonès, Albert C; Aravena, Daniel; Cerdá, Jorge I; Acís-Castillo, Zulema; Li, Haipeng; Real, José Antonio; Sanz, Fausto; Hihath, Josh; Ruiz, Eliseo; Díez-Pérez, Ismael

    2016-01-13

    Controlling the spin of electrons in nanoscale electronic devices is one of the most promising topics aiming at developing devices with rapid and high density information storage capabilities. The interface magnetism or spinterface resulting from the interaction between a magnetic molecule and a metal surface, or vice versa, has become a key ingredient in creating nanoscale molecular devices with novel functionalities. Here, we present a single-molecule wire that displays large (>10000%) conductance switching by controlling the spin-dependent transport under ambient conditions (room temperature in a liquid cell). The molecular wire is built by trapping individual spin crossover Fe(II) complexes between one Au electrode and one ferromagnetic Ni electrode in an organic liquid medium. Large changes in the single-molecule conductance (>100-fold) are measured when the electrons flow from the Au electrode to either an α-up or a β-down spin-polarized Ni electrode. Our calculations show that the current flowing through such an interface appears to be strongly spin-polarized, thus resulting in the observed switching of the single-molecule wire conductance. The observation of such a high spin-dependent conductance switching in a single-molecule wire opens up a new door for the design and control of spin-polarized transport in nanoscale molecular devices at room temperature.

  5. The more the merrier: high-throughput single-molecule techniques.

    Science.gov (United States)

    Hill, Flynn R; Monachino, Enrico; van Oijen, Antoine M

    2017-06-15

    The single-molecule approach seeks to understand molecular mechanisms by observing biomolecular processes at the level of individual molecules. These methods have led to a developing understanding that for many processes, a diversity of behaviours will be observed, representing a multitude of pathways. This realisation necessitates that an adequate number of observations are recorded to fully characterise this diversity. The requirement for large numbers of observations to adequately sample distributions, subpopulations, and rare events presents a significant challenge for single-molecule techniques, which by their nature do not typically provide very high throughput. This review will discuss many developing techniques which address this issue by combining nanolithographic approaches, such as zero-mode waveguides and DNA curtains, with single-molecule fluorescence microscopy, and by drastically increasing throughput of force-based approaches such as magnetic tweezers and laminar-flow techniques. These methods not only allow the collection of large volumes of single-molecule data in single experiments, but have also made improvements to ease-of-use, accessibility, and automation of data analysis. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

  6. A new optical method for characterizing single molecule interactions based on dark field microscopy

    NARCIS (Netherlands)

    Dietrich, H.R.C.; Vermolen, B.J.; Rieger, B.; Young, I.T.; Garini, Y.

    2007-01-01

    Single-molecule techniques continue to gain in popularity in research disciplines such as the study of intermolecular interactions. These techniques provide information that otherwise would be lost by using bulk measurements that deal with a large number of molecules. We describe in this report the

  7. Single-Molecule Kinetics of λ Exonuclease Reveal Base Dependence and Dynamic Disorder

    NARCIS (Netherlands)

    Oijen, Antoine M. van; Blainey, Paul C.; Crampton, Donald J.; Richardson, Charles C.; Ellenberger, Tom; Xie, X. Sunney

    2003-01-01

    We used a multiplexed approach based on flow-stretched DNA to monitor the enzymatic digestion of λ-phage DNA by individual bacteriophage λ exonuclease molecules. Statistical analyses of multiple single-molecule trajectories observed simultaneously reveal that the catalytic rate is dependent on the l

  8. Single-molecule enzymatic analysis in a droplet-based microfluidic system

    NARCIS (Netherlands)

    Arayanarakool, R.; Shui, L.; Kengen, S.W.M.; Berg, van den A.; Eijkel, J.C.T.; Fujii, T.; Hibara, A.; Takeuchi, S.; Fukuba, T.

    2012-01-01

    The kinetic activity of individual enzyme molecules was determined in aqueous droplets generated in a nano- and microfluidic device. To avoid high background noise, the enzyme and substrate solution was confined into femtolitre carriers to achieve single-molecule encapsulation. The tiny droplets (f~

  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

    2014-11-01

    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.

  10. 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...

  11. Electrostatic melting in a single-molecule field-effect transistor with applications in genomic identification

    Science.gov (United States)

    Vernick, Sefi; Trocchia, Scott M.; Warren, Steven B.; Young, Erik F.; Bouilly, Delphine; Gonzalez, Ruben L.; Nuckolls, Colin; Shepard, Kenneth L.

    2017-05-01

    The study of biomolecular interactions at the single-molecule level holds great potential for both basic science and biotechnology applications. Single-molecule studies often rely on fluorescence-based reporting, with signal levels limited by photon emission from single optical reporters. The point-functionalized carbon nanotube transistor, known as the single-molecule field-effect transistor, is a bioelectronics alternative based on intrinsic molecular charge that offers significantly higher signal levels for detection. Such devices are effective for characterizing DNA hybridization kinetics and thermodynamics and enabling emerging applications in genomic identification. In this work, we show that hybridization kinetics can be directly controlled by electrostatic bias applied between the device and the surrounding electrolyte. We perform the first single-molecule experiments demonstrating the use of electrostatics to control molecular binding. Using bias as a proxy for temperature, we demonstrate the feasibility of detecting various concentrations of 20-nt target sequences from the Ebolavirus nucleoprotein gene in a constant-temperature environment.

  12. Advances in single-molecule magnet surface patterning through microcontact printing

    NARCIS (Netherlands)

    Mannini, Matteo; Bonacchi, D.; Bonacchi, Daniele; Zobbi, Laura; Piras, Federica M.; Speets, E.A.; Caneschi, Andrea; Cornia, Andrea; Magnani, Agnese; Ravoo, B.J.; Reinhoudt, David; Sessoli, Roberta; Gatteschi, Dante

    2005-01-01

    We present an implementation of strategies to deposit single-molecule magnets (SMMs) using microcontact printing (uCP). We describe different approaches of CP to print stripes of a sulfur-functionalized dodecamanganese(III,IV) cluster on gold surfaces. Comparison by atomic force microscopy profile

  13. Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy

    Science.gov (United States)

    Neuman, Keir C.; Nagy, Attila

    2012-01-01

    Single-molecule force spectroscopy has emerged as a powerful tool to investigate the forces and motions associated with biological molecules and enzymatic activity. The most common force spectroscopy techniques are optical tweezers, magnetic tweezers and atomic force microscopy. These techniques are described and illustrated with examples highlighting current capabilities and limitations. PMID:18511917

  14. Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy

    OpenAIRE

    Neuman, Keir C.; Nagy, Attila

    2008-01-01

    Single-molecule force spectroscopy has emerged as a powerful tool to investigate the forces and motions associated with biological molecules and enzymatic activity. The most common force spectroscopy techniques are optical tweezers, magnetic tweezers and atomic force microscopy. These techniques are described and illustrated with examples highlighting current capabilities and limitations.

  15. Real-time data acquisition incorporating high-speed software correlator for single-molecule spectroscopy.

    Science.gov (United States)

    Yang, L-L; Lee, H-Y; Wang, M-K; Lin, X-Y; Hsu, K-H; Chang, Y-R; Fann, W; White, J D

    2009-06-01

    Single-molecule spectroscopy and detection are powerful techniques for the study of single fluorescent particles and their interaction with their environment. We present a low-cost system for simultaneous real-time acquisition, storage of inter-photon arrival times and the calculation and display of the fluorescence time trace, autocorrelation function and distribution of delays histogram for single-molecule experiments. From a hardware perspective, in addition to a multi-core computer, only a standard low-cost counting board is required as processing is software-based. Software is written in a parallel programming environment with time crucial operations coded in ANSI-C. Crucial to system performance is a simple and efficient real-time autocorrelation algorithm (acf) optimized for the count rates (approximately 10(4) cps) encountered in single-molecule experiments. The algorithm's time complexity is independent of temporal resolution, which is maintained at all time delays. The system and algorithm's performance was validated by duplicating the signal from the photon detector and sending it to both the ordinary counter board and a commercial correlator simultaneously. The data acquisition system's robustness under typical single-molecule experimental conditions was tested by observing the diffusion of Rhodamine 6G molecules in deionized water.

  16. Theoretical Investigation of a Single Molecule Device:Geometrical Configurations and Electronic Properties

    Institute of Scientific and Technical Information of China (English)

    YUAN Zhe; SU Chang-Rong; ZHANG Shi-Zhong; LI Jia-Ming

    2004-01-01

    @@ Using the first-principle molecular dynamics simulations, we have studied the molecular geometrical configurations as well as the corresponding electronic structures of a single molecule device assembled by the mechanically controllable break junction technique with variations of the electrode distance. There are some very interesting features varying with the electrode distance.

  17. Probing the Conformational Landscape of DNA Polymerases Using Diffusion-Based Single-Molecule FRET

    NARCIS (Netherlands)

    Hohlbein, J.; Kapanidis, A.N.

    2016-01-01

    Monitoring conformational changes in DNA polymerases using single-molecule Förster resonance energy transfer (smFRET) has provided new tools for studying fidelity-related mechanisms that promote the rejection of incorrect nucleotides before DNA synthesis. In addition to the previously known open

  18. Step detection in single-molecule real time trajectories embedded in correlated noise.

    Directory of Open Access Journals (Sweden)

    Srikesh G Arunajadai

    Full Text Available Single-molecule real time trajectories are embedded in high noise. To extract kinetic or dynamic information of the molecules from these trajectories often requires idealization of the data in steps and dwells. One major premise behind the existing single-molecule data analysis algorithms is the gaussian 'white' noise, which displays no correlation in time and whose amplitude is independent on data sampling frequency. This so-called 'white' noise is widely assumed but its validity has not been critically evaluated. We show that correlated noise exists in single-molecule real time trajectories collected from optical tweezers. The assumption of white noise during analysis of these data can lead to serious over- or underestimation of the number of steps depending on the algorithms employed. We present a statistical method that quantitatively evaluates the structure of the underlying noise, takes the noise structure into account, and identifies steps and dwells in a single-molecule trajectory. Unlike existing data analysis algorithms, this method uses Generalized Least Squares (GLS to detect steps and dwells. Under the GLS framework, the optimal number of steps is chosen using model selection criteria such as Bayesian Information Criterion (BIC. Comparison with existing step detection algorithms showed that this GLS method can detect step locations with highest accuracy in the presence of correlated noise. Because this method is automated, and directly works with high bandwidth data without pre-filtering or assumption of gaussian noise, it may be broadly useful for analysis of single-molecule real time trajectories.

  19. Monte-Carlo simulations of a high-resolution backscattering spectrometer on the SNS - Long Wavelength Target Station

    Science.gov (United States)

    Bordallo, H. N.; Herwig, K. W.

    2001-03-01

    It is proposed to build an inverse geometry spectrometer to provide extremely high energy resolution (0.2 μeV FWHM, elastic) at the Long Wavelength Target Station (LWTS) at SNS. The design employs mica analyzers in close to backscattering geometry (final neutron wavelength of 20 ÅAnalytical calculations and Monte Carlo simulations (using the McStas package) have been used to optimize the layout of individual components and to estimate the instrument performance. This design requires a long initial guide section of 63 m from moderator to sample in order to achieve the timing resolution necessary for the desired δω. 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. Molecular biology, for example, often requires systematic studies of many similar molecules under slightly different conditions, requiring a large range of energy/timing resolutions for optimum study.

  20. Single molecule investigations of DNA looping using the tethered particle method and translocation by acto-myosin using polarized total internal reflection fluorescence microscopy

    Science.gov (United States)

    Beausang, John F.

    Single molecule biophysics aims to understand biological processes by studying them at the single molecule level in real time. The proteins and nucleic acids under investigation typically exist in an aqueous environment within ˜ ten degrees of room temperature. These seemingly benign conditions are actually quite chaotic at the nanoscale, where single bio-molecules perform their function. As a result, sensitive experiments and statistical analyses are required to separate the weak single molecule signal from its background. Protein-DNA interactions were investigated by monitoring DNA looping events in tethered particle experiments. A new analysis technique, called the Diffusive hidden Markov method, was developed to extract kinetic rate constants from experimental data without any filtering of the raw data; a common step that improves the signal to noise ratio, but at the expense of lower time resolution. In the second system, translocation of the molecular motor myosin along its actin filament track was studied using polarized total internal reflection (polTIRF) microscopy, a technique that determines the orientation and wobble of a single fluorophore attached to the bio-molecule of interest. The range of resolvable angles was increased 4-fold to include a hemisphere of possible orientations. As a result, the handedness of actin filament twirling as it translocated along a myosin-coated surface was determined to be left-handed. The maximum time resolution of a polTIRF setup was increased 50-fold, in part by recording the arrival times and polarization state of single photons using a modified time-correlated single photon counting device. A new analysis, the Multiple Intensity Change Point algorithm, was developed to detect changes in molecular orientation and wobble using the raw time-stamped data with no user-defined bins or thresholds. The analysis objectively identified changes in the orientation of a bifunctional-rhodamine labeled calmodulin that was attached

  1. A single molecule magnet to single molecule magnet transformation via a solvothermal process: Fe4Dy2 → Fe6Dy3.

    Science.gov (United States)

    Chen, Sihuai; Mereacre, Valeriu; Anson, Christopher E; Powell, Annie K

    2016-01-01

    Two series of heterometallic Fe(III)-Ln(III) compounds, [FeLn(μ3-OH)2(mdea)4(m-NO2C6H4COO)8]·3MeCN where Ln = Y (1) and Dy (2) and [FeLn(μ4-O)3(μ3-O)(mdea)5(m-NO2C6H4COO)9]·3MeCN where Ln = Y (3) and Dy (4), were synthesized. Compounds 1 and 2 were obtained under ambient conditions, whereas 3 and 4 were obtained via a solvothermal transformation process by heating 1 or 2 at 120 °C in MeCN. The magnetic properties of all four compounds have been measured and show that compounds 2 and 4 containing Dy(III) ions exhibit slow relaxation of magnetization characteristic of Single Molecule Magnetic (SMM) behaviour.

  2. Organization of DNA partners and strand exchange mechanisms during Flp site-specific recombination analyzed by difference topology, single molecule FRET and single molecule TPM.

    Science.gov (United States)

    Ma, Chien-Hui; Liu, Yen-Ting; Savva, Christos G; Rowley, Paul A; Cannon, Brian; Fan, Hsiu-Fang; Russell, Rick; Holzenburg, Andreas; Jayaram, Makkuni

    2014-02-20

    Flp site-specific recombination between two target sites (FRTs) harboring non-homology within the strand exchange region does not yield stable recombinant products. In negatively supercoiled plasmids containing head-to-tail sites, the reaction produces a series of knots with odd-numbered crossings. When the sites are in head-to-head orientation, the knot products contain even-numbered crossings. Both types of knots retain parental DNA configuration. By carrying out Flp recombination after first assembling the topologically well defined Tn3 resolvase synapse, it is possible to determine whether these knots arise by a processive or a dissociative mechanism. The nearly exclusive products from head-to-head and head-to-tail oriented "non-homologous" FRT partners are a 4-noded knot and a 5-noded knot, respectively. The corresponding products from a pair of native (homologous) FRT sites are a 3-noded knot and a 4-noded catenane, respectively. These results are consistent with non-homology-induced two rounds of dissociative recombination by Flp, the first to generate reciprocal recombinants containing non-complementary base pairs and the second to produce parental molecules with restored base pairing. Single molecule fluorescence resonance energy transfer (smFRET) analysis of geometrically restricted FRTs, together with single molecule tethered particle motion (smTPM) assays of unconstrained FRTs, suggests that the sites are preferentially synapsed in an anti-parallel fashion. This selectivity in synapse geometry occurs prior to the chemical steps of recombination, signifying early commitment to a productive reaction path. The cumulative topological, smFRET and smTPM results have implications for the relative orientation of DNA partners and the directionality of strand exchange during recombination mediated by tyrosine site-specific recombinases.

  3. 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...... populations and thus providing more information than traditional ensemble experiments. Using single molecule FRET microscopy different aspects of G-quadruplex folding were investigated. We have obtained direct insight into G-quadruplex structural polymorphism both in K+ and Na+ solutions. Polymorphism have...... previously only been investigated in K+. Here, we observe significant polymorphism also in Na+. By investigating the dynamics of these conformational changes and comparing these findings with other experiments for G-quadruplexes with known topology we are able to identify different conformations and folding...

  4. Evidence of disorder in biological molecules from single molecule pulling experiments

    CERN Document Server

    Hyeon, Changbong; Thirumalai, D

    2014-01-01

    Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an exactly solvable model in which the unfolding rate due to mechanical force depends parametrically on an auxiliary variable representing an entropy barrier arising from fluctuations in internal dynamics. When the rate of fluctuations, a measure of dynamical disorder, is comparable to or smaller than the rate of force-induced unbinding, we show that there are two experimentally observable consequences: non-exponential survival probability at constant force, and a heavy-tailed rupture force distribution at constant loading rate. By fitting our analytical expressions to data from single molecule pulling experiments on proteins and DNA, we quantify the extent of disorder. We show that only by analyzing data over a wide range of forces and loading rates can the role of disorder due...

  5. The origin of relative intensity fluctuations in single-molecule tip-enhanced Raman spectroscopy.

    Science.gov (United States)

    Sonntag, Matthew D; Chulhai, Dhabih; Seideman, Tamar; Jensen, Lasse; Van Duyne, Richard P

    2013-11-13

    An explanation of the relative intensity fluctuations observed in single-molecule Raman experiments is described utilizing both single-molecule tip-enhanced Raman spectroscopy and time-dependent density functional theory calculations. No correlation is observed in mode to mode intensity fluctuations indicating that the changes in mode intensities are completely independent. Theoretical calculations provide convincing evidence that the fluctuations are not the result of diffusion, orientation, or local electromagnetic field gradients but rather are the result of subtle variations of the excited-state lifetime, energy, and geometry of the molecule. These variations in the excited-state properties will provide information on adsorbate-adsorbate and adsorbate-substrate interactions and may allow for inversion of experimental results to obtain these excited-state properties.

  6. Detection of Single Molecules Illuminated by a Light-Emitting Diode

    CERN Document Server

    Gerhardt, Ilja; Lamas-Linares, Antia; Kurtsiefer, Christian

    2011-01-01

    Optical detection and spectroscopy of single molecules has become an indispensable tool in biological imaging and sensing. Its success is based on fluorescence of organic dye molecules under carefully engineered laser illumination. In this paper we demonstrate optical detection of single molecules on a wide-field microscope with an illumination based on a commercially available, green light-emitting diode. The results are directly compared with laser illumination in the same experimental configuration. The setup and the limiting factors, such as light transfer to the sample, spectral filtering and the resulting signal-to-noise ratio are discussed. A theoretical and an experimental approach to estimate these parameters are presented. The results can be adapted to other single emitter and illumination schemes.

  7. 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.

  8. Supramolecular Chemistry and Mechanochemistry of Macromolecules: Recent Advances by Single-Molecule Force Spectroscopy.

    Science.gov (United States)

    Cheng, Bo; Cui, Shuxun

    2015-01-01

    Atomic force spectroscopy (AFM)-based single-molecule force spectroscopy (SMFS) was invented in the 1990s. Since then, SMFS has been developed into a powerful tool to study the inter- and intra-molecular interactions of macromolecules. Using SMFS, a number of problems in the field of supramolecular chemistry and mechanochemistry have been studied at the single-molecule level, which are not accessible by traditional ensemble characterization methods. In this review, the principles of SMFS are introduced, followed by the discussion of several problems of contemporary interest at the interface of supramolecular chemistry and mechanochemistry of macromolecules, including single-chain elasticity of macromolecules, interactions between water and macromolecules, interactions between macromolecules and solid surface, and the interactions in supramolecular polymers.

  9. Super-resolution Analysis of TCR-Dependent Signaling: Single-Molecule Localization Microscopy.

    Science.gov (United States)

    Barr, Valarie A; Yi, Jason; Samelson, Lawrence E

    2017-01-01

    Single-molecule localization microscopy (SMLM) comprises methods that produce super-resolution images from molecular locations of single molecules. These techniques mathematically determine the center of a diffraction-limited spot produced by a fluorescent molecule, which represents the most likely location of the molecule. Only a small cohort of well-separated molecules is visualized in a single image, and then many images are obtained from a single sample. The localizations from all the images are combined to produce a super-resolution picture of the sample. Here we describe the application of two methods, photoactivation localization microscopy (PALM) and direct stochastic optical reconstruction microscopy (dSTORM), to the study of signaling microclusters in T cells.

  10. Direct Measurement of Single-Molecule DNA Hybridization Dynamics with Single-Base Resolution.

    Science.gov (United States)

    He, Gen; Li, Jie; Ci, Haina; Qi, Chuanmin; Guo, Xuefeng

    2016-07-25

    Herein, we report label-free detection of single-molecule DNA hybridization dynamics with single-base resolution. By using an electronic circuit based on point-decorated silicon nanowires as electrical probes, we directly record the folding/unfolding process of individual hairpin DNAs with sufficiently high signal-to-noise ratio and bandwidth. These measurements reveal two-level current oscillations with strong temperature dependence, enabling us to determine the thermodynamic and kinetic properties of hairpin DNA hybridization. More importantly, successive, stepwise increases and decreases in device conductance at low temperature on a microsecond timescale are successfully observed, indicating a base-by-base unfolding/folding process. The process demonstrates a kinetic zipper model for DNA hybridization/dehybridization at the single base-pair level. This measurement capability promises a label-free single-molecule approach to probe biomolecular interactions with fast dynamics.

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

    KAUST Repository

    Bayoumi, Maged Fouad

    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 Diodes with High On/Off Ratios Through Environmental Control

    Science.gov (United States)

    Capozzi, Brian; Xia, Jianlong; Dell, Emma; Adak, Olgun; Liu, Zhen-Fei; Neaton, Jeffrey; Campos, Luis; Venkataraman, Latha

    2015-03-01

    Single-Molecule diodes were first proposed with an asymmetric molecule comprising a donor-bridge-acceptor architecture to mimic a semiconductor p-n junction. Progress in molecular electronics has led to the realization of several single-molecule diodes; these have relied on asymmetric molecular backbones, asymmetric molecule-electrode linkers, or asymmetric electrode materials. Despite these advances, molecular diodes have had limited potential for functional applications due to several pitfalls, including low rectification ratios (``on''/``off'' current ratios environment instead of an asymmetric molecule, we reproducibly achieve high rectification ratios at low operating voltages for molecular junctions based on a family of symmetric small-gap molecules. This technique serves as an unconventional approach for developing functional molecular-scale devices and probing their charge transport characteristics. Furthermore, this technique should be applicable to other nanoscale devices, providing a general route for tuning device properties.

  13. Inelastic transport and low-bias rectification in a single-molecule diode.

    Science.gov (United States)

    Hihath, Joshua; Bruot, Christopher; Nakamura, Hisao; Asai, Yoshihiro; Díez-Pérez, Ismael; Lee, Youngu; Yu, Luping; Tao, Nongjian

    2011-10-25

    Designing, controlling, and understanding rectification behavior in molecular-scale devices has been a goal of the molecular electronics community for many years. Here we study the transport behavior of a single molecule diode, and its nonrectifying, symmetric counterpart at low temperatures, and at both low and high biases to help elucidate the electron-phonon interactions and transport mechanisms in the rectifying system. We find that the onset of current rectification occurs at low biases, indicating a significant change in the elastic transport pathway. However, the peaks in the inelastic electron tunneling (IET) spectrum are antisymmetric about zero bias and show no significant changes in energy or intensity in the forward or reverse bias directions, indicating that despite the change in the elastic transmission probability there is little impact on the inelastic pathway. These results agree with first principles calculations performed to evaluate the IETS, which also allow us to identify which modes are active in the single molecule junction.

  14. Single molecule detection of 4-dimethylaminoazobenzene by surface-enhanced Raman spectroscopy

    Science.gov (United States)

    Zhang, Z. L.; Yin, Y. F.; Jiang, J. W.; Mo, Y. J.

    2009-02-01

    4-Dimethylaminoazobenzene (DAB) is anticipated to be a human carcinogen based on sufficient evidence of carcinogenicity in experimental animals. The trace detection of DAB is of great significance in environmental protection and safe life of the people. To test the availability of DAB trace detection using surface-enhanced Raman scattering (SERS), the SERS spectra of DAB single molecules adsorbed on the silver particle aggregates in colloid were investigated. The phenomena of blinking, spectral diffusion, and intensity fluctuations of the vibrational lines in the SERS spectra were observed. Statistical analysis of spectral intensity fluctuations indicates a multimodal distribution of some specific Raman bands, which are consistent with the identification of single molecule detection. Our results demonstrated that SERS can be applied to the trace detection of DAB molecules and other azo dyes.

  15. Revealing −1 Programmed Ribosomal Frameshifting Mechanisms by Single-Molecule Techniques and Computational Methods

    Directory of Open Access Journals (Sweden)

    Kai-Chun Chang

    2012-01-01

    Full Text Available Programmed ribosomal frameshifting (PRF serves as an intrinsic translational regulation mechanism employed by some viruses to control the ratio between structural and enzymatic proteins. Most viral mRNAs which use PRF adapt an H-type pseudoknot to stimulate −1 PRF. The relationship between the thermodynamic stability and the frameshifting efficiency of pseudoknots has not been fully understood. Recently, single-molecule force spectroscopy has revealed that the frequency of −1 PRF correlates with the unwinding forces required for disrupting pseudoknots, and that some of the unwinding work dissipates irreversibly due to the torsional restraint of pseudoknots. Complementary to single-molecule techniques, computational modeling provides insights into global motions of the ribosome, whose structural transitions during frameshifting have not yet been elucidated in atomic detail. Taken together, recent advances in biophysical tools may help to develop antiviral therapies that target the ubiquitous −1 PRF mechanism among viruses.

  16. Single-molecule chemistry and physics explored by low-temperature scanning probe microscopy.

    Science.gov (United States)

    Swart, Ingmar; Gross, Leo; Liljeroth, Peter

    2011-08-28

    It is well known that scanning probe techniques such as scanning tunnelling microscopy (STM) and atomic force microscopy (AFM) routinely offer atomic scale information on the geometric and the electronic structure of solids. Recent developments in STM and especially in non-contact AFM have allowed imaging and spectroscopy of individual molecules on surfaces with unprecedented spatial resolution, which makes it possible to study chemistry and physics at the single molecule level. In this feature article, we first review the physical concepts underlying image contrast in STM and AFM. We then focus on the key experimental considerations and use selected examples to demonstrate the capabilities of modern day low-temperature scanning probe microscopy in providing chemical insight at the single molecule level.

  17. 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...... in labeling single molecules with QDs (and other particles e.g. gold particles) are induction of cross-linking of the target molecules, which can cause activation of signaling pathways or reduced mobility, and steric hindrance as a result of the probe size. Cross-linking can be a result of the multivalent...... 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....

  18. pyFRET: A Python Library for Single Molecule Fluorescence Data Analysis

    CERN Document Server

    Murphy, Rebecca R; Klenerman, David

    2014-01-01

    Single molecule F\\"orster resonance energy transfer (smFRET) is a powerful experimental technique for studying the properties of individual biological molecules in solution. However, as adoption of smFRET techniques becomes more widespread, the lack of available software, whether open source or commercial, for data analysis, is becoming a significant issue. Here, we present pyFRET, an open source Python package for the analysis of data from single-molecule fluorescence experiments from freely diffusing biomolecules. The package provides methods for the complete analysis of a smFRET dataset, from burst selection and denoising, through data visualisation and model fitting. We provide support for both continuous excitation and alternating laser excitation (ALEX) data analysis. pyFRET is available as a package downloadable from the Python Package Index (PyPI) under the open source three-clause BSD licence, together with links to extensive documentation and tutorials, including example usage and test data. Additio...

  19. Aptamer-based single-molecule imaging of insulin receptors in living cells

    Science.gov (United States)

    Chang, Minhyeok; Kwon, Mijin; Kim, Sooran; Yunn, Na-Oh; Kim, Daehyung; Ryu, Sung Ho; Lee, Jong-Bong

    2014-05-01

    We present a single-molecule imaging platform that quantitatively explores the spatiotemporal dynamics of individual insulin receptors in living cells. Modified DNA aptamers that specifically recognize insulin receptors (IRs) with a high affinity were selected through the SELEX process. Using quantum dot-labeled aptamers, we successfully imaged and analyzed the diffusive motions of individual IRs in the plasma membranes of a variety of cell lines (HIR, HEK293, HepG2). We further explored the cholesterol-dependent movement of IRs to address whether cholesterol depletion interferes with IRs and found that cholesterol depletion of the plasma membrane by methyl-β-cyclodextrin reduces the mobility of IRs. The aptamer-based single-molecule imaging of IRs will provide better understanding of insulin signal transduction through the dynamics study of IRs in the plasma membrane.

  20. Monitoring patterned enzymatic polymerization on DNA origami at single-molecule level

    Science.gov (United States)

    Okholm, A. H.; Aslan, H.; Besenbacher, F.; Dong, M.; Kjems, J.

    2015-06-01

    DNA origami has been used to orchestrate reactions with nano-precision using a variety of biomolecules. Here, the dynamics of albumin-assisted, localized single-molecule DNA polymerization by terminal deoxynucleotidyl transferase on a 2D DNA origami are monitored using AFM in liquid. Direct visualization of the surface activity revealed the mechanics of growth.DNA origami has been used to orchestrate reactions with nano-precision using a variety of biomolecules. Here, the dynamics of albumin-assisted, localized single-molecule DNA polymerization by terminal deoxynucleotidyl transferase on a 2D DNA origami are monitored using AFM in liquid. Direct visualization of the surface activity revealed the mechanics of growth. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr01945a

  1. 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...... in labeling single molecules with QDs (and other particles e.g. gold particles) are induction of cross-linking of the target molecules, which can cause activation of signaling pathways or reduced mobility, and steric hindrance as a result of the probe size. Cross-linking can be a result of the multivalent...... functionalization tag (e.g. streptavidin (sAv)) or the presence of multiple mono- or multivalent functionalization tags per QD. In this work, we have compared commercially available sAv-QDs of different sizes with custom prepared Co enzyme A (CoA)-QDs both targeting a GPI-anchored protein modified with either...

  2. Single molecule fluorescence fluctuations of the cyanine dyes linked covalently to DNA

    Institute of Scientific and Technical Information of China (English)

    AUMILER; Damir

    2009-01-01

    The intersystem crossing and isomerization dynamics of free-Cy3,Cy3-ssDNA,free-Cy5 and Cy5-ssDNA are obtained through simple analysis of rapid on/off blinking from single molecule fluorescence intensity time-traces and the fluorescence correlation spectroscopy(FCS).The on-and off-times observed in fluorescence time traces of single cyanine dyes are due to the formation of the triplet state and isomerization,where both the interaction with DNA and long central polymethine chain of cyanine dyes increase the barriers of isomerization,leading to long off-time.The results indicate that the single molecule fluorescence fluctuation together with the resulting second autocorrelation analysis are powerful methods for determining the triplet state and isomerization dynamics,which could be the simple techniques and complementary to other spectroscopic techniques,such as fluorescence decay measurement and laser flash photolysis to study the photophysical processes of complex molecules.

  3. Single-molecule fluorescence spectroscopy maps the folding landscape of a large protein.

    Science.gov (United States)

    Pirchi, Menahem; Ziv, Guy; Riven, Inbal; Cohen, Sharona Sedghani; Zohar, Nir; Barak, Yoav; Haran, Gilad

    2011-10-11

    Proteins attain their function only after folding into a highly organized three-dimensional structure. Much remains to be learned about the mechanisms of folding of large multidomain proteins, which may populate metastable intermediate states on their energy landscapes. Here we introduce a novel method, based on high-throughput single-molecule fluorescence experiments, which is specifically geared towards tracing the dynamics of folding in the presence of a plethora of intermediates. We employ this method to characterize the folding reaction of a three-domain protein, adenylate kinase. Using thousands of single-molecule trajectories and hidden Markov modelling, we identify six metastable states on adenylate kinase's folding landscape. Remarkably, the connectivity of the intermediates depends on denaturant concentration; at low concentration, multiple intersecting folding pathways co-exist. We anticipate that the methodology introduced here will find broad applicability in the study of folding of large proteins, and will provide a more realistic scenario of their conformational dynamics.

  4. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing.

    Science.gov (United States)

    Berlin, Konstantin; Koren, Sergey; Chin, Chen-Shan; Drake, James P; Landolin, Jane M; Phillippy, Adam M

    2015-06-01

    Long-read, single-molecule real-time (SMRT) sequencing is routinely used to finish microbial genomes, but available assembly methods have not scaled well to larger genomes. We introduce the MinHash Alignment Process (MHAP) for overlapping noisy, long reads using probabilistic, locality-sensitive hashing. Integrating MHAP with the Celera Assembler enabled reference-grade de novo assemblies of Saccharomyces cerevisiae, Arabidopsis thaliana, Drosophila melanogaster and a human hydatidiform mole cell line (CHM1) from SMRT sequencing. The resulting assemblies are highly continuous, include fully resolved chromosome arms and close persistent gaps in these reference genomes. Our assembly of D. melanogaster revealed previously unknown heterochromatic and telomeric transition sequences, and we assembled low-complexity sequences from CHM1 that fill gaps in the human GRCh38 reference. Using MHAP and the Celera Assembler, single-molecule sequencing can produce de novo near-complete eukaryotic assemblies that are 99.99% accurate when compared with available reference genomes.

  5. A Stochastic Single-Molecule Event Triggers Phenotype Switching of a Bacterial Cell

    Science.gov (United States)

    Xie, Sunney; Choi, Paul; Cai, Long

    2009-03-01

    By monitoring fluorescently labeled lactose permease with single-molecule sensitivity, we investigated the molecular mechanism of how an Escherichia coli cell with the lac operon switches from one phenotype to another. At intermediate inducer concentrations, a population of genetically identical cells exhibits two phenotypes: induced cells with highly fluorescent membranes and uninduced cells with a small number of membrane-bound permeases. We found that this basal-level expression results from partial dissociation of the tetrameric lactose repressor from one of its operators on looped DNA. In contrast, infrequent events of complete dissociation of the repressor from DNA result in large bursts of permease expression that trigger induction of the lac operon. Hence, a stochastic single-molecule event determines a cell's phenotype.

  6. A stochastic model for magnetic dynamics in single-molecule magnets

    Energy Technology Data Exchange (ETDEWEB)

    López-Ruiz, R., E-mail: rlruiz@ifi.unicamp.br [Instituto de Física Gleb Wataghin - Universidade Estadual de Campinas, 13083-859 Campinas (SP) (Brazil); Almeida, P.T. [Instituto de Física Gleb Wataghin - Universidade Estadual de Campinas, 13083-859 Campinas (SP) (Brazil); Vaz, M.G.F. [Instituto de Química, Universidade Federal Fluminense, 24020-150 Niterói (RJ) (Brazil); Novak, M.A. [Instituto de Física - Universidade Federal do Rio de Janeiro, 21941-972 Rio de Janeiro (RJ) (Brazil); Béron, F.; Pirota, K.R. [Instituto de Física Gleb Wataghin - Universidade Estadual de Campinas, 13083-859 Campinas (SP) (Brazil)

    2016-04-01

    Hysteresis and magnetic relaxation curves were performed on double well potential systems with quantum tunneling possibility via stochastic simulations. Simulation results are compared with experimental ones using the Mn{sub 12} single-molecule magnet, allowing us to introduce time dependence in the model. Despite being a simple simulation model, it adequately reproduces the phenomenology of a thermally activated quantum tunneling and can be extended to other systems with different parameters. Assuming competition between the reversal modes, thermal (over) and tunneling (across) the anisotropy barrier, a separation of classical and quantum contributions to relaxation time can be obtained. - Highlights: • Single-molecule magnets are modeled using a simple stochastic approach. • Simulation reproduces thermally-activated tunnelling magnetization reversal features. • The time is introduced in hysteresis and relaxation simulations. • We can separate the quantum and classical contributions to decay time.

  7. Photon counting imaging and centroiding with an electron-bombarded CCD using single molecule localisation software

    Science.gov (United States)

    Hirvonen, Liisa M.; Barber, Matthew J.; Suhling, Klaus

    2016-06-01

    Photon event centroiding in photon counting imaging and single-molecule localisation in super-resolution fluorescence microscopy share many traits. Although photon event centroiding has traditionally been performed with simple single-iteration algorithms, we recently reported that iterative fitting algorithms originally developed for single-molecule localisation fluorescence microscopy work very well when applied to centroiding photon events imaged with an MCP-intensified CMOS camera. Here, we have applied these algorithms for centroiding of photon events from an electron-bombarded CCD (EBCCD). We find that centroiding algorithms based on iterative fitting of the photon events yield excellent results and allow fitting of overlapping photon events, a feature not reported before and an important aspect to facilitate an increased count rate and shorter acquisition times.

  8. Diversity of Chemical Mechanisms in Thioredoxin Catalysis Revealed by Single-Molecule Force Spectroscopy

    Science.gov (United States)

    Perez-Jimenez, Raul; Li, Jingyuan; Kosuri, Pallav; Sanchez-Romero, Inmaculada; Wiita, Arun P.; Rodriguez-Larrea, David; Chueca, Ana; Holmgren, Arne; Miranda-Vizuete, Antonio; Becker, Katja; Cho, Seung-Hyun; Beckwith, Jon; Gelhaye, Eric; Jacquot, Jean P.; Gaucher, Eric; Sanchez-Ruiz, Jose M.; Berne, Bruce J.; Fernandez, Julio M.

    2009-01-01

    Thioredoxins are oxido-reductase enzymes present in all organisms, catalyzing the reduction of disulfide bonds in proteins. By applying a calibrated force to a substrate disulfide, the chemical mechanisms of Trx catalysis can be examined in detail at the single molecule level. Here we use single molecule force-clamp spectroscopy to explore the chemical evolution of Trx catalysis by probing the chemistry of eight different thioredoxin enzymes. While all Trxs show a characteristic Michaelis-Menten mechanism detected when the disulfide bond is stretched at low forces, two different chemical behaviors distinguish bacterial from eukaryotic-origin Trxs at high forces. Eukaryotic-origin Trxs reduce disulfide bonds through a single-electron transfer reaction (SET) whereas bacterial-origin Trxs exhibit both nucleophilic substitution (SN2) and SET reactions. A computational analysis of Trx structures identifies the evolution of the binding groove as an important factor controlling the chemistry of Trx catalysis. PMID:19597482

  9. 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

  10. Vibronic excitation of single molecules: a new technique for studying low-temperature dynamics.

    Science.gov (United States)

    Kiraz, Alper; Ehrl, Moritz; Hellriegel, Christian; Bräuchle, Christoph; Zumbusch, Andreas

    2005-05-01

    Herein, we present vibronic excitation and detection of purely electronic zero-phonon lines (ZPL) of single molecules as a new tool for investigating dynamics at cryogenic temperatures. Applications of this technique to study crystalline and amorphous matrix materials are presented. In the crystalline environment, spectrally stable ZPLs are observed at moderate excitation powers. By contrast, investigations at higher excitation intensities reveal the opening of local degrees of freedom and spectral jumps, which we interpret as the observation of elementary steps in the melting of a crystal. We compare these results to spectral single-molecule trajectories recorded in a polymer. The way in which much more complicated spectral features can be analysed is shown. Surprisingly, pronounced spectral shifts on a previously not accessible large energy scale are observed, which are hard to reconcile with the standard two-level model system used to describe low-temperature dynamics in disordered systems.

  11. Reconstructing multiple free energy pathways of DNA stretching from single molecule experiments.

    Science.gov (United States)

    Frey, Eric W; Li, Jingqiang; Wijeratne, Sithara S; Kiang, Ching-Hwa

    2015-04-23

    Free energy landscapes provide information on the dynamics of proteins and nucleic acid folding. It has been demonstrated that such landscapes can be reconstructed from single molecule force measurement data using Jarzynski's equality, which requires only stretching data. However, when the process is reversible, the Crooks fluctuation theorem combines both stretch and relaxation force data for the analysis and can offer more rapid convergence of free energy estimates of different states. Here we demonstrate that, similar to Jarzynski's equality, the Crooks fluctuation theorem can be used to reconstruct the full free energy landscapes. In addition, when the free energy landscapes exhibit multiple folding pathways, one can use Jarzynski's equality to reconstruct individual free energy pathways if the experimental data show distinct work distributions. We applied the method to reconstruct the overstretching transition of poly(dA) to demonstrate that the nonequilibrium work theorem combined with single molecule force measurements provides a clear picture of the free energy landscapes.

  12. Carbon nanotube nanoelectromechanical systems as magnetometers for single-molecule magnets.

    Science.gov (United States)

    Ganzhorn, Marc; Klyatskaya, Svetlana; Ruben, Mario; Wernsdorfer, Wolfgang

    2013-07-23

    Due to outstanding mechanical and electronic properties, carbon nanotube nanoelectromechanical systems (NEMS) were recently proposed as ultrasensitive magnetometers for single-molecule magnets (SMM). In this article, we describe a noninvasive grafting of a SMM on a carbon nanotube NEMS, which conserves both the mechanical properties of the carbon nanotube NEMS and the magnetic properties of the SMM. We will demonstrate that the nonlinearity of a carbon nanotube's mechanical motion can be used to probe the reversal of a molecular spin, associated with a bis(phthalocyaninato)terbium(III) single-molecule magnet, providing an experimental evidence for the detection of a single spin by a mechanical degree of freedom on a molecular level.

  13. High-Resolution Optical Tweezers Combined With Single-Molecule Confocal Microscopy.

    Science.gov (United States)

    Whitley, K D; Comstock, M J; Chemla, Y R

    2017-01-01

    We describe the design, construction, and application of an instrument combining dual-trap, high-resolution optical tweezers and a confocal microscope. This hybrid instrument allows nanomechanical manipulation and measurement simultaneously with single-molecule fluorescence detection. We present the general design principles that overcome the challenges of maximizing optical trap resolution while maintaining single-molecule fluorescence sensitivity, and provide details on the construction and alignment of the instrument. This powerful new tool is just beginning to be applied to biological problems. We present step-by-step instructions on an application of this technique that highlights the instrument's capabilities, detecting conformational dynamics in a nucleic acid-processing enzyme. © 2017 Elsevier Inc. All rights reserved.

  14. Single-Molecule Protein Folding Experiments Using High-Precision Optical Tweezers.

    Science.gov (United States)

    Jiao, Junyi; Rebane, Aleksander A; Ma, Lu; Zhang, Yongli

    2017-01-01

    How proteins fold from linear chains of amino acids to delicate three-dimensional structures remains a fundamental biological problem. Single-molecule manipulation based on high-resolution optical tweezers (OT) provides a powerful approach to study protein folding with unprecedented spatiotemporal resolution. In this method, a single protein or protein complex is tethered between two beads confined in optical traps and pulled. Protein unfolding induced by the mechanical force is counteracted by the spontaneous folding of the protein, reaching a dynamic equilibrium at a characteristic force and rate. The transition is monitored by the accompanying extension change of the protein and used to derive conformations and energies of folding intermediates and their associated transition kinetics. Here, we provide general strategies and detailed protocols to study folding of proteins and protein complexes using optical tweezers, including sample preparation, DNA-protein conjugation and methods of data analysis to extract folding energies and rates from the single-molecule measurements.

  15. Roles of vacuum tunnelling and contact mechanics in single-molecule thermopower

    Science.gov (United States)

    Tsutsui, Makusu; Yokota, Kazumichi; Morikawa, Takanori; Taniguchi, Masateru

    2017-01-01

    Molecular junction is a chemically-defined nanostructure whose discrete electronic states are expected to render enhanced thermoelectric figure of merit suitable for energy-harvesting applications. Here, we report on geometrical dependence of thermoelectricity in metal-molecule-metal structures. We performed simultaneous measurements of the electrical conductance and thermovoltage of aromatic molecules having different anchoring groups at room temperature in vacuum. We elucidated the mutual contributions of vacuum tunnelling on thermoelectricity in the short molecular bridges. We also found stretching-induced thermoelectric voltage enhancement in thiol-linked single-molecule bridges along with absence of the pulling effects in diamine counterparts, thereby suggested that the electromechanical effect would be a rather universal phenomenon in Au-S anchored molecular junctions that undergo substantial metal-molecule contact elongation upon stretching. The present results provide a novel concept for molecular design to achieve high thermopower with single-molecule junctions. PMID:28281684

  16. 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.

  17. Single-molecule magnet behavior with a single metal center enhanced through peripheral ligand modifications.

    Science.gov (United States)

    Jurca, Titel; Farghal, Ahmed; Lin, Po-Heng; Korobkov, Ilia; Murugesu, Muralee; Richeson, Darrin S

    2011-10-12

    Bis(imino)pyridine pincer ligands in conjunction with two isothiocyanate ligands have been used to prepare two mononuclear Co(II) complexes. Both complexes have a distorted square-pyramidal geometry with the Co(II) centers lying above the basal plane. This leads to significant spin-orbit coupling for the d(7) Co(II) ions and consequently to slow relaxation of the magnetization that is characteristic of Single-Molecule Magnet (SMM) behavior.

  18. A gate controlled conjugated single molecule diode: Its rectification could be reversed

    Science.gov (United States)

    Zhang, Qun

    2014-10-01

    A gate controlled Au/diphenyldipyrimidinyl/Au single molecule diode is simulated by a tight-binding Hamiltonian combined with Green's Function and transport methods. After calculating a number of electronic transport characteristics under various gate voltages, a clear modulation by gate is got and when the positive voltage is high enough, the rectification could be reversed. This is advisable for the designing and building future molecular logic devices and integrated circuits.

  19. All-electric-controlled spin current switching in single-molecule magnet-tunnel junctions

    Institute of Scientific and Technical Information of China (English)

    Zhang Zheng-Zhong; Shen Rui; Sheng Li; Wang Rui-Qiang; Wang Bai-Gen; Xing Ding-Yu

    2011-01-01

    A single-molecule magnet (SMM)coupled to two normal metallic electrodes can both switch spin-up and spindown electronic currents within two different windows of SMM gate voltage. Such spin current switching in the SMM tunnel junction arises from spin-selected single electron resonant tunneling via the lowest unoccupied molecular orbit of the SMM. Since it is not magnetically controlled but all-electrically controlled, the proposed spin current switching effect may have potential applications in future spintronics.

  20. Surface-enhanced Raman spectroscopy at single-molecule scale and its implications in biology

    OpenAIRE

    Wang, Yuling; Irudayaraj, Joseph

    2013-01-01

    Single-molecule (SM) spectroscopy has been an exciting area of research offering significant promise and hope in the field of sensor development to detect targets at ultra-low levels down to SM resolution. To the experts and developers in the field of surface-enhanced Raman spectroscopy (SERS), this has often been a challenge and a significant opportunity for exploration. Needless to say, the opportunities and excitement of this multidisciplinary area impacts span the fields of physics, chemi...

  1. Single molecule studies of molecular diffusion in cellular membranes: determining membrane structure.

    Science.gov (United States)

    Ritchie, Ken; Spector, Jeff

    Since the advent of single particle/molecule microscopies, researchers have applied these techniques to understanding the fluid membranes of cells. By observing diffusion of membrane proteins and lipids in live cell membranes of eukaryotic cells, it has been found that membranes contain a mosaic of fluid compartments. Such structure may be instrumental in understanding key characteristics of the membrane. Recent single molecule observations on prokaryotic cell membranes will also be discussed.

  2. A Single-Molecule Study on the Structural Damage of Ultraviolet Radiated DNA

    Directory of Open Access Journals (Sweden)

    Pu Chun Ke

    2008-04-01

    Full Text Available The structural damage of double-stranded DNA under UV radiation was examined using single-molecule fluorescence microscopy. Compared to undamaged DNA, the diffusion coefficient of λ-DNA was significantly increased with 12 min or 20 min of radiation but remained unchanged for 40 min of exposure possibly due to strand crosslinking. The structural damage of DNA was further examined using transmission electron microscopy which revealed kinks and sharp bends along the DNA backbone.

  3. Molecular-crowding effects on single-molecule RNA folding/unfolding thermodynamics and kinetics.

    Science.gov (United States)

    Dupuis, Nicholas F; Holmstrom, Erik D; Nesbitt, David J

    2014-06-10

    The effects of "molecular crowding" on elementary biochemical processes due to high solute concentrations are poorly understood and yet clearly essential to the folding of nucleic acids and proteins into correct, native structures. The present work presents, to our knowledge, first results on the single-molecule kinetics of solute molecular crowding, specifically focusing on GAAA tetraloop-receptor folding to isolate a single RNA tertiary interaction using time-correlated single-photon counting and confocal single-molecule FRET microscopy. The impact of crowding by high-molecular-weight polyethylene glycol on the RNA folding thermodynamics is dramatic, with up to ΔΔG° ∼ -2.5 kcal/mol changes in free energy and thus >60-fold increase in the folding equilibrium constant (Keq) for excluded volume fractions of 15%. Most importantly, time-correlated single-molecule methods permit crowding effects on the kinetics of RNA folding/unfolding to be explored for the first time (to our knowledge), which reveal that this large jump in Keq is dominated by a 35-fold increase in tetraloop-receptor folding rate, with only a modest decrease in the corresponding unfolding rate. This is further explored with temperature-dependent single-molecule RNA folding measurements, which identify that crowding effects are dominated by entropic rather than enthalpic contributions to the overall free energy change. Finally, a simple "hard-sphere" treatment of the solute excluded volume is invoked to model the observed kinetic trends, and which predict ΔΔG° ∼ -5 kcal/mol free-energy stabilization at excluded volume fractions of 30%.

  4. An Undecanuclear Ferrimagnetic Cu9Dy2 Single Molecule Magnet Achieved through Ligand Fine-Tuning.

    Science.gov (United States)

    Kühne, Irina A; Kostakis, George E; Anson, Christopher E; Powell, Annie K

    2016-05-02

    We describe the concept of increasing the nuclearity of a previously reported high-spin Cu5Gd2 core using a "fine-tuning" ligand approach. Thus, two Cu9Ln2 coordination clusters, with Ln = Dy (1) and Gd (2), were synthesized with the Gd compound having a ground spin state of (17)/2 and the Dy analogue showing single-molecule-magnet behavior in zero field.

  5. Single molecule localization microscopy of the distribution of chromatin using Hoechst and DAPI fluorescent probes

    OpenAIRE

    Szczurek, Aleksander T; PRAKASH, KIRTI; Lee, Hyun-Keun; Żurek-Biesiada, Dominika J; Best, Gerrit; Hagmann, Martin; Dobrucki, Jurek W; Cremer, Christoph; Birk, Udo

    2014-01-01

    Several approaches have been described to fluorescently label and image DNA and chromatin in situ on the single-molecule level. These superresolution microscopy techniques are based on detecting optically isolated, fluorescently tagged anti-histone antibodies, fluorescently labeled DNA precursor analogs, or fluorescent dyes bound to DNA. Presently they suffer from various drawbacks such as low labeling efficiency or interference with DNA structure. In this report, we demonstrate that DNA mino...

  6. Effect of disorder on ultrafast exciton dynamics probed by single molecule spectroscopy

    OpenAIRE

    Hernando Campos, Jordi; van Dijk, Erik M. H. P.; Hoogenboom, Jacob P.; García López, Juan José; Reinhoudt, David N.; Crego Calama, Mercedes; García Parajó, María F.; van Hulst, Niek F.

    2006-01-01

    We present a single-molecule study unraveling the effect of static disorder on the vibrational-assisted ultrafast exciton dynamics in multichromophoric systems. For every single complex, we probe the initial exciton relaxation process by an ultrafast pump-probe approach and the coupling to vibrational modes by emission spectra, while fluorescence lifetime analysis measures the amount of static disorder. Exploiting the wide range of disorder found from complex to complex, we demonstrate that s...

  7. A Heterotetranuclear [NiIIReIV3] single-molecule magnet.

    Science.gov (United States)

    Martínez-Lillo, José; Armentano, Donatella; De Munno, Giovanni; Wernsdorfer, Wolfgang; Julve, Miguel; Lloret, Francesc; Faus, Juan

    2006-11-01

    The reaction of [ReIVCl4(ox)]2- and fully solvated Ni2+ ions in a MeCN/i-PrOH mixture affords the heterotetranuclear complex (NBu4)4[Ni{ReCl4(ox)}3] where the rhenium precursor acts as a bidentate ligand toward the nicke(II) ion through the oxalate group. The mixed 3d-5d species exhibits intramolecular ferromagnetic coupling and it behaves like a single-molecule magnet.

  8. Real-Time analysis and visualization for single-molecule based super-resolution microscopy

    OpenAIRE

    Kechkar, Adel; Nair, Deepak; Heilemann, Mike; Choquet, Daniel; Sibarita, Jean-Baptiste

    2013-01-01

    Accurate multidimensional localization of isolated fluorescent emitters is a time consuming process in single-molecule based super-resolution microscopy. We demonstrate a functional method for real-time reconstruction with automatic feedback control, without compromising the localization accuracy. Compatible with high frame rates of EM-CCD cameras, it relies on a wavelet segmentation algorithm, together with a mix of CPU/GPU implementation. A combination with Gaussian fitting allows direct ac...

  9. Real-Time Analysis and Visualization for Single-Molecule Based Super-Resolution Microscopy

    OpenAIRE

    Kechkar, Adel; Nair, Deepak; Heilemann, Mike; Choquet, Daniel; Sibarita, Jean-Baptiste

    2013-01-01

    Accurate multidimensional localization of isolated fluorescent emitters is a time consuming process in single-molecule based super-resolution microscopy. We demonstrate a functional method for real-time reconstruction with automatic feedback control, without compromising the localization accuracy. Compatible with high frame rates of EM-CCD cameras, it relies on a wavelet segmentation algorithm, together with a mix of CPU/GPU implementation. A combination with Gaussian fitting allows direct ac...

  10. Retention of transcription initiation factor sigma(70) in transcription elongation: Single-molecule analysis

    OpenAIRE

    Kapanidis, A. N.; Margeat, E; Laurence, T A; Doose, S.; Ho, S O; Mukhopadhyay, J.; Kortkhonjia, E; Mekler, V; Ebright, R H; S. Weiss

    2005-01-01

    We report a single-molecule assay that defines, simultaneously, the translocational position of a protein complex relative to DNA and the subunit stoichiometry of the complex. We applied the assay to define translocational positions and sigma(70) contents of bacterial transcription elongation complexes in vitro. The results confirm ensemble results indicating that a large fraction, similar to 70%-90%, of early elongation complexes retain sigma(70) and that a determinant for sigma(70) recognit...

  11. Single-Molecule Enzymology Based On The Principle Of The Millikan Oil Drop Experiment

    OpenAIRE

    Leiske, Danielle L; Chow, Andrea; Dettloff, Roger; Farinas, Javier

    2013-01-01

    The ability to monitor the progress of single molecule enzyme reactions is often limited by the need to use fluorogenic substrates. A method based on the principle of the Millikan Oil Drop Experiment was developed to monitor the change in charge of substrates bound to a nanoparticle and offers a means of detecting single enzyme reactions without fluorescence detection. As a proof of principle of the ability to monitor reactions which result in a change in substrate charge, polymerization on a...

  12. Single molecule magnet behaviour in a rare trinuclear {Cr(III)Dy} methoxo-bridged complex.

    Science.gov (United States)

    Car, Pierre-Emmanuel; Favre, Annaïck; Caneschi, Andrea; Sessoli, Roberta

    2015-09-28

    The reaction of the chromium(iii) chloride tetrahydrofuran complex with the dipivaloylmethane ligand, the lanthanide alcoholic salt DyCl3·CH3OH and the 1,1,1-tris(hydroxymethyl)-ethane ligand resulted in the formation of a new trinuclear chromium-dysprosium complex. Magnetic investigations revealed that the new 3d-4f complex exhibits single molecule magnet behaviour.

  13. Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins.

    Science.gov (United States)

    Nettels, Daniel; Müller-Späth, Sonja; Küster, Frank; Hofmann, Hagen; Haenni, Dominik; Rüegger, Stefan; Reymond, Luc; Hoffmann, Armin; Kubelka, Jan; Heinz, Benjamin; Gast, Klaus; Best, Robert B; Schuler, Benjamin

    2009-12-01

    We used single-molecule FRET in combination with other biophysical methods and molecular simulations to investigate the effect of temperature on the dimensions of unfolded proteins. With single-molecule FRET, this question can be addressed even under near-native conditions, where most molecules are folded, allowing us to probe a wide range of denaturant concentrations and temperatures. We find a compaction of the unfolded state of a small cold shock protein with increasing temperature in both the presence and the absence of denaturant, with good agreement between the results from single-molecule FRET and dynamic light scattering. Although dissociation of denaturant from the polypeptide chain with increasing temperature accounts for part of the compaction, the results indicate an important role for additional temperature-dependent interactions within the unfolded chain. The observation of a collapse of a similar extent in the extremely hydrophilic, intrinsically disordered protein prothymosin alpha suggests that the hydrophobic effect is not the sole source of the underlying interactions. Circular dichroism spectroscopy and replica exchange molecular dynamics simulations in explicit water show changes in secondary structure content with increasing temperature and suggest a contribution of intramolecular hydrogen bonding to unfolded state collapse.

  14. Single-molecule fluorescence study of the inhibition of the oncogenic functionality of STAT3

    Science.gov (United States)

    Liu, Baoxu; Badali, Daniel; Fletcher, Steven; Avadisian, Miriam; Gunning, Patrick; Gradinaru, Claudiu

    2009-06-01

    Signal-Transducer-and-Activator-of-Transcription 3 (STAT3) protein plays an important role in the onset of cancers such as leukemia and lymphoma. In this study, we aim to test the effectiveness of a novel peptide drug designed to tether STAT3 to the phospholipid bilayer of the cell membrane and thus inhibit unwanted transcription. As a first step, STAT3 proteins were successfully labelled with tetramethylrhodamine (TMR), a fluorescent dye with suitable photostability for single molecule studies. The effectiveness of labelling was determined using fluorescence correlation spectroscopy in a custom built confocal microscope, from which diffusion times and hydrodynamic radii of individual proteins were determined. A newly developed fluorescein derivative label (F-NAc) has been designed to be incorporated into the structure of the peptide drug so that peptide-STAT3 interactions can be examined. This dye is spectrally characterized and is found to be well suited for its application to this project, as well as other single-molecule studies. The membrane localization via high-affinity cholesterol-bound small-molecule binding agents can be demonstrated by encapsulating TMR-labeled STAT3 and inhibitors within a vesicle model cell system. To this end, unilaminar lipid vesicles were examined for size and encapsulation ability. Preliminary results of the efficiency and stability of the STAT3 anchoring in lipid membranes obtained via quantitative confocal imaging and single-molecule spectroscopy using a custom-built multiparameter fluorescence microscope are reported here.

  15. Magnetic relaxations in a Tb-based single molecule magnet studied by quasielastic neutron scattering

    Energy Technology Data Exchange (ETDEWEB)

    Kofu, Maiko [Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581 (Japan); Kajiwara, Takashi [Faculty of Science, Nara Women’s University, Nara, Nara 630-8506 (Japan); Gardner, Jason S. [NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899-6102 (United States); Simeoni, Giovanna G. [Technische Universität München, Forschungsneutronenquelle Heinz Maier-Leibnitz FRM II, D-85747 Garching (Germany); Tyagi, Madhusudan; Faraone, Antonio [NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899-6102 (United States); Department of Materials Science, University of Maryland, College Park, MD 20742 (United States); Nakajima, Kenji; Ohira-Kawamura, Seiko [Neutron Science Section, J-PARC Center, Tokai, Ibaraki 319-1195 (Japan); Nakano, Motohiro [Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871 (Japan); Yamamuro, Osamu, E-mail: yamamuro@issp.u-tokyo.ac.jp [Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581 (Japan)

    2013-12-12

    Highlights: • We examined a Tb based single molecule magnet by ac susceptibility and QENS. • We found two distinct magnetic relaxations in a wide time range from 0.1 ms to 1 ps. • The slower relaxation corresponds to the thermally activated tunneling process. • The faster one couples with the motion of H atoms around the magnetic ions. • The two relaxations exhibit a crossover around 100 ns. - Abstract: By using ac magnetic susceptibility and quasielatic neutron scattering (QENS) techniques, we have investigated a magnetization relaxation phenomenon of a rare-earth based single molecule magnet, TbCuC{sub 19}H{sub 20}N{sub 3}O{sub 16}. We clearly identified and characterized two magnetic relaxations. The slower relaxation observed in the ac susceptibility is at the ms timescale around T=2 K and its activation energy is 16 K. On the other hand, the faster relaxation in the QENS measurements occurs on the timescale between ns and ps with activation energy of 174 K. The slower relaxation may occur through thermally activated tunneling among magnetic substates. We discuss two possible origins for the faster relaxation; one is a thermally activated tunneling between the higher excited states, the other is the magnetic relaxation coupled with the motion of ligands around the magnetic ions. This is the first clear observation of magnetic relaxation on the single molecule magnet revealed by QENS.

  16. Single-Molecule Counting of Point Mutations by Transient DNA Binding

    Science.gov (United States)

    Su, Xin; Li, Lidan; Wang, Shanshan; Hao, Dandan; Wang, Lei; Yu, Changyuan

    2017-03-01

    High-confidence detection of point mutations is important for disease diagnosis and clinical practice. Hybridization probes are extensively used, but are hindered by their poor single-nucleotide selectivity. Shortening the length of DNA hybridization probes weakens the stability of the probe-target duplex, leading to transient binding between complementary sequences. The kinetics of probe-target binding events are highly dependent on the number of complementary base pairs. Here, we present a single-molecule assay for point mutation detection based on transient DNA binding and use of total internal reflection fluorescence microscopy. Statistical analysis of single-molecule kinetics enabled us to effectively discriminate between wild type DNA sequences and single-nucleotide variants at the single-molecule level. A higher single-nucleotide discrimination is achieved than in our previous work by optimizing the assay conditions, which is guided by statistical modeling of kinetics with a gamma distribution. The KRAS c.34 A mutation can be clearly differentiated from the wild type sequence (KRAS c.34 G) at a relative abundance as low as 0.01% mutant to WT. To demonstrate the feasibility of this method for analysis of clinically relevant biological samples, we used this technology to detect mutations in single-stranded DNA generated from asymmetric RT-PCR of mRNA from two cancer cell lines.

  17. Single-molecule nucleic acid interactions monitored on a label-free microcavity biosensor platform

    Science.gov (United States)

    Baaske, Martin D.; Foreman, Matthew R.; Vollmer, Frank

    2014-11-01

    Biosensing relies on the detection of molecules and their specific interactions. It is therefore highly desirable to develop transducers exhibiting ultimate detection limits. Microcavities are an exemplary candidate technology for demonstrating such a capability in the optical domain and in a label-free fashion. Additional sensitivity gains, achievable by exploiting plasmon resonances, promise biosensing down to the single-molecule level. Here, we introduce a biosensing platform using optical microcavity-based sensors that exhibits single-molecule sensitivity and is selective to specific single binding events. Whispering gallery modes in glass microspheres are used to leverage plasmonic enhancements in gold nanorods for the specific detection of nucleic acid hybridization, down to single 8-mer oligonucleotides. Detection of single intercalating small molecules confirms the observation of single-molecule hybridization. Matched and mismatched strands are discriminated by their interaction kinetics. Our platform allows us to monitor specific molecular interactions transiently, hence mitigating the need for high binding affinity and avoiding permanent binding of target molecules to the receptors. Sensor lifetime is therefore increased, allowing interaction kinetics to be statistically analysed.

  18. Magnetic Relaxation Study on Single Crystals of Ni4 Single-Molecule Magnets

    Institute of Scientific and Technical Information of China (English)

    LI Yan-Rong; LIU Hai-Qing; LIU Ying; SU Shao-Kui; WANG Yun-Ping

    2009-01-01

    The ac susceptibility of single crystals of Nia single-molecule magnets is measured by a compensation measurement setup. The magnetic relaxation time calculated from the peak of the out-phase component of the susceptibility fits the Arrhenius law well and gives an effective spin-flipping energy barrier of Ueff = 7.2 K. This value is far below the classical activation energy barrier of U = 14 K, whereas it is close to the energy gap between the Sz = ±4 and Sz = ±3 doublets, which indicates that quantum tunneling between the Sz = 3 and Sz = -3 states plays a key role in the magnetic relaxation. Therefore the relaxation process combines thermal activation and quantum tunneling. Also we deduce that the blocking temperature of Ni4 single-molecule magnets is lower than 0.3 K by extrapolating the relaxation time plot, which ensures that this single-molecule magnet material enters a long-range magnetic ordered state instead of a spin glass state at 0.91 K.

  19. 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.

  20. Ensemble and single-molecule studies on fluorescence quenching in transition metal bipyridine-complexes.

    Directory of Open Access Journals (Sweden)

    Dominik Brox

    Full Text Available Beyond their use in analytical chemistry fluorescent probes continuously gain importance because of recent applications of single-molecule fluorescence spectroscopy to monitor elementary reaction steps. In this context, we characterized quenching of a fluorescent probe by different metal ions with fluorescence spectroscopy in the bulk and at the single-molecule level. We apply a quantitative model to explain deviations from existing standard models for fluorescence quenching. The model is based on a reversible transition from a bright to a dim state upon binding of the metal ion. We use the model to estimate the stability constants of complexes with different metal ions and the change of the relative quantum yield of different reporter dye labels. We found ensemble data to agree widely with results from single-molecule experiments. Our data indicates a mechanism involving close molecular contact of dye and quenching moiety which we also found in molecular dynamics simulations. We close the manuscript with a discussion of possible mechanisms based on Förster distances and electrochemical potentials which renders photo-induced electron transfer to be more likely than Förster resonance energy transfer.