Sample records for single-molecule interfacial electron

  1. Single Molecule Electronics and Devices

    PubMed Central

    Tsutsui, Makusu; Taniguchi, Masateru

    2012-01-01

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

  2. Single Molecule Electron Paramagnetic Resonance

    NASA Astrophysics Data System (ADS)

    Teeling-Smith, Richelle M.; Johnston-Halperin, Ezekiel; Poirier, Michael G.; Hammel, P. Chris

    2013-03-01

    Electron paramagnetic resonance (EPR) is a powerful spectroscopic tool for studying the dynamics of biomolecular systems. EPR measurements on bulk samples using a commercial X-band spectrometer provide insight into atomic-scale structure and dynamics of ensembles of biomolecules. Separately, single molecule measurements of biomolecular systems allow researchers to capture heterogeneous behaviors that have revealed the molecular mechanisms behind many biological processes. We are merging these two powerful techniques to perform single molecule EPR . In this experiment, we selectively label double-stranded DNA molecules with nitrogen-vacancy (NV) center nanodiamonds and optically detect the magnetic resonance of the NV probe. Shifts and broadening of our EPR peaks indicate the changing position of the attached DNA relative to the applied magnetic field. Using this new technique, we have successfully measured the first EPR spectrum of a single biomolecule. By controlling the geometry of the diamond and the applied magnetic field, we will quantitatively determine the rotational and translational dynamics of single biomolecules. This research provides the foundation for an advanced single molecule magnetic resonance approach to studies of complex biomolecular systems.

  3. Identifying Mechanisms of Interfacial Dynamics Using Single-Molecule Tracking

    PubMed Central

    Kastantin, Mark; Walder, Robert; Schwartz, Daniel K.

    2012-01-01

    The “soft” (i.e. non-covalent) interactions between molecules and surfaces are complex and highly-varied (e.g. hydrophobic, hydrogen bonding, ionic) often leading to heterogeneous interfacial behavior. Heterogeneity can arise either from spatial variation of the surface/interface itself or from molecular configurations (i.e. conformation, orientation, aggregation state, etc.). By observing adsorption, diffusion, and desorption of individual fluorescent molecules, single-molecule tracking can characterize these types of heterogeneous interfacial behavior in ways that are inaccessible to traditional ensemble-averaged methods. Moreover, the fluorescence intensity or emission wavelength (in resonance energy transfer experiments) can be used to simultaneously track molecular configuration and directly relate this to the resulting interfacial mobility or affinity. In this feature article, we review recent advances involving the use of single-molecule tracking to characterize heterogeneous molecule-surface interactions including: multiple modes of diffusion and desorption associated with both internal and external molecular configuration, Arrhenius activated interfacial transport, spatially dependent interactions, and many more. PMID:22716995

  4. Single Molecule Spectroscopy of Electron Transfer

    SciTech Connect

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

    2009-10-20

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

  5. Single-molecule junctions beyond electronic transport.

    PubMed

    Aradhya, Sriharsha V; Venkataraman, Latha

    2013-06-01

    The idea of using individual molecules as active electronic components provided the impetus to develop a variety of experimental platforms to probe their electronic transport properties. Among these, single-molecule junctions in a metal-molecule-metal motif have contributed significantly to our fundamental understanding of the principles required to realize molecular-scale electronic components from resistive wires to reversible switches. The success of these techniques and the growing interest of other disciplines in single-molecule-level characterization are prompting new approaches to investigate metal-molecule-metal junctions with multiple probes. Going beyond electronic transport characterization, these new studies are highlighting both the fundamental and applied aspects of mechanical, optical and thermoelectric properties at the atomic and molecular scales. Furthermore, experimental demonstrations of quantum interference and manipulation of electronic and nuclear spins in single-molecule circuits are heralding new device concepts with no classical analogues. In this Review, we present the emerging methods being used to interrogate multiple properties in single molecule-based devices, detail how these measurements have advanced our understanding of the structure-function relationships in molecular junctions, and discuss the potential for future research and applications. PMID:23736215

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

    PubMed

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

    2014-11-01

    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. PMID:25099384

  7. Single-molecule electron transfer reactions in nanomaterials

    SciTech Connect

    Hu, Dehong; Lei, Chenghong; Ackerman, Eric J.

    2009-07-26

    Here we report the study of single molecule electron transfer dynamics by coupling fluorescence microscopy at a conventional electrochemical cell. The single-molecule fluorescence spectroelectrochemistry of cresyl violet in aqueous solution and on nanoparticle surface were studied. We observed that the single-molecule fluorescence intensity of cresyl violet is modulated synchronously with the cyclic voltammetric potential scanning. We attribute the fluorescence intensity change of single cresyl violet molecules to the electron transfer reaction driven by the electrochemical potential.

  8. Electronic control inside a molecule : towards single molecule devices

    NASA Astrophysics Data System (ADS)

    Lastapis, Mathieu; Fukuma, Yurie; Boland, John

    2006-03-01

    The chimerical single molecule engineering has been proven to be accessible through the use of scanning tunnelling microscopy (STM) [1]. In this field, one particularly attractive area is the study of single molecules adsorbed on semiconductor surfaces. It has been recently demonstrated that a spatial fine control of the molecular dynamics is possible through the use of tunnelling current [2]. In order to improve the electronic control of a single molecule, we are currently investigating a promising system: CaF2 on Si(111). This system has been extensively studied as a model system to deposit insulator on silicon. Here we are using this system to electronically decouple the molecule from the substrate. I will present LT STM experiments on atomically thick CaF islands on Si(111). The measured electronic properties of these islands demonstrate their potential as ideal templates to study single molecules. Finally I will present some preliminary results on N-HBC [3] adsorbed on a CaF island. [1] G. Binnig and H. Rohrer, ``In touch with atoms'', Rev. Mod. Phys. 71, S324-S330 (1999) [2] M. Lastapis et al, Science, 308, 1000 (2005) [3] S.Draper et al, JACS, 126, 8694 (2004)

  9. Contact and Length Dependent Effects in Single-Molecule Electronics

    NASA Astrophysics Data System (ADS)

    Hines, Thomas

    Understanding charge transport in single molecules covalently bonded to electrodes is a fundamental goal in the field of molecular electronics. In the past decade, it has become possible to measure charge transport on the single-molecule level using the STM break junction method. Measurements on the single-molecule level shed light on charge transport phenomena which would otherwise be obfuscated by ensemble measurements of groups of molecules. This thesis will discuss three projects carried out using STM break junction. In the first project, the transition between two different charge transport mechanisms is reported in a set of molecular wires. The shortest wires show highly length dependent and temperature invariant conductance behavior, whereas the longer wires show weakly length dependent and temperature dependent behavior. This trend is consistent with a model whereby conduction occurs by coherent tunneling in the shortest wires and by incoherent hopping in the longer wires. Measurements are supported with calculations and the evolution of the molecular junction during the pulling process is investigated. The second project reports controlling the formation of single-molecule junctions by means of electrochemically reducing two axial-diazonium terminal groups on a molecule, thereby producing direct Au-C covalent bonds in-situ between the molecule and gold electrodes. Step length analysis shows that the molecular junction is significantly more stable, and can be pulled over a longer distance than a comparable junction created with amine anchoring bonds. The stability of the junction is explained by the calculated lower binding energy associated with the direct Au-C bond compared with the Au-N bond. Finally, the third project investigates the role that molecular conformation plays in the conductance of oligothiophene single-molecule junctions. Ethyl substituted oligothiophenes were measured and found to exhibit temperature dependent conductance and transition voltage for molecules with between two and six repeat units. While the molecule with only one repeat unit shows temperature invariant behavior. Density functional theory calculations show that at higher temperatures the oligomers with multiple repeat units assume a more planar conformation, which increases the conjugation length and decreases the effective energy barrier of the junction.

  10. Single-Molecule Electronic Measurements with Metal Electrodes

    NASA Astrophysics Data System (ADS)

    Lindsay, Stuart

    2005-05-01

    The process of transferring electrons from one metal electrode to another via an intervening molecule differs from electrochemically or optically-induced electron transfer in important ways. The simplest process of ballistic electron transport with no charge localization on the molecule (tunneling) should be easy to understand quantitatively, yet experimental reports and theoretical calculations can differ by orders of magnitude. Here, we show how many of the discrepancies are resolved with measurements carefully constructed to provide data on single molecules connected to electrodes in well-defined ways. Furthermore, a number of these results are in good agreement with first-principles calculations (no adjustable parameters). The more interesting (and theoretically challenging) process of charge transport with intermediate localization by redox states can be measured in the same ways, but present theories do not yet describe these processes fully.

  11. Single-molecule resolution of protein structure and interfacial dynamics on biomaterial surfaces

    PubMed Central

    McLoughlin, Sean Yu; Kastantin, Mark; Schwartz, Daniel K.; Kaar, Joel L.

    2013-01-01

    A method was developed to monitor dynamic changes in protein structure and interfacial behavior on surfaces by single-molecule Förster resonance energy transfer. This method entails the incorporation of unnatural amino acids to site-specifically label proteins with single-molecule Förster resonance energy transfer probes for high-throughput dynamic fluorescence tracking microscopy on surfaces. Structural changes in the enzyme organophosphorus hydrolase (OPH) were monitored upon adsorption to fused silica (FS) surfaces in the presence of BSA on a molecule-by-molecule basis. Analysis of >30,000 individual trajectories enabled the observation of heterogeneities in the kinetics of surface-induced OPH unfolding with unprecedented resolution. In particular, two distinct pathways were observed: a majority population (? 85%) unfolded with a characteristic time scale of 0.10 s, and the remainder unfolded more slowly with a time scale of 0.7 s. Importantly, even after unfolding, OPH readily desorbed from FS surfaces, challenging the common notion that surface-induced unfolding leads to irreversible protein binding. This suggests that protein fouling of surfaces is a highly dynamic process because of subtle differences in the adsorption/desorption rates of folded and unfolded species. Moreover, such observations imply that surfaces may act as a source of unfolded (i.e., aggregation-prone) protein back into solution. Continuing study of other proteins and surfaces will examine whether these conclusions are general or specific to OPH in contact with FS. Ultimately, this method, which is widely applicable to virtually any protein, provides the framework to develop surfaces and surface modifications with improved biocompatibility. PMID:24235137

  12. Inelastic electron tunneling spectroscopy on single-molecule magnets

    NASA Astrophysics Data System (ADS)

    Nesbitt, J. R.; Arnason, S. B.; Hebard, A. F.; Christou, G.

    2002-03-01

    Single molecule magnets (SMMs) containing a fixed number of transition metal ions have promise in applications requiring mono-disperse nanomagnets. A well-studied example is the polynuclear metal Mn_12 complex having the general formula Mn_12O_12(O_2CR)_16(H_2O)_4. We report on the fabrication and characterization of Al-Al_2O_3/Mn_12-Pb tunnel junctions that have been prepared by spin coating oxidized Al surfaces with a methylene chloride solution containing dissolved Mn_12 molecules and then depositing Pb counterelectrodes. Inelastic electron tunneling spectroscopy (IETS) measurements were performed as a function of temperature and magnetic field on samples that showed a well-developed superconducting Pb gap at low temperatures. We compare results on three types of samples: clean unaltered samples, samples exposed to pure methylene chloride, and samples doped with Mn_12 SMMs. Progress toward the goal of identifying the vibrational modes of the Mn12 molecules and detecting the effect of magnetic field on the large spin (S=10) ground state will be described.

  13. Design and control of electron transport properties of single molecules

    PubMed Central

    Pan, Shuan; Fu, Qiang; Huang, Tian; Zhao, Aidi; Wang, Bing; Luo, Yi; Yang, Jinlong; Hou, Jianguo

    2009-01-01

    We demonstrate in this joint experimental and theoretical study how one can alter electron transport behavior of a single melamine molecule adsorbed on a Cu (100) surface by performing a sequence of elegantly devised and well-controlled single molecular chemical processes. It is found that with a dehydrogenation reaction, the melamine molecule becomes firmly bonded onto the Cu surface and acts as a normal conductor controlled by elastic electron tunneling. A current-induced hydrogen tautomerization process results in an asymmetric melamine tautomer, which in turn leads to a significant rectifying effect. Furthermore, by switching on inelastic multielectron scattering processes, mechanical oscillations of an N-H bond between two configurations of the asymmetric tautomer can be triggered with tuneable frequency. Collectively, this designed molecule exhibits rectifying and switching functions simultaneously over a wide range of external voltage. PMID:19706435

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

    SciTech Connect

    Fratalocchi, A. [PRIMALIGHT, Faculty of Electrical Engineering, Applied Mathematics and Computational Science, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900 (Saudi Arabia)] [Department of Physics, Sapienza University of Rome, P.le A. Moro 2, 00185, Rome (Italy); Ruocco, G. [Department of Physics, Sapienza University of Rome, P.le A. Moro 2, 00185, Rome (Italy)] [IPCF-CNR, c/o Department of Physics, Sapienza University, P.le Aldo Moro 2, 00185, Rome (Italy)

    2011-03-11

    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.

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

    Microsoft Academic Search

    A. Fratalocchi; G. Ruocco

    2011-01-01

    X-ray free-electron lasers (XFEL) are revolutionary photon sources, whose ultrashort, brilliant pulses are expected to allow single-molecule diffraction experiments providing structural information on the atomic length scale of nonperiodic objects. This ultimate goal, however, is currently hampered by several challenging questions basically concerning sample damage, Coulomb explosion, and the role of nonlinearity. By employing an original ab initio approach, we

  16. Localization accuracy in single molecule microscopy using electron-multiplying charge-coupled device cameras.

    PubMed

    Chao, Jerry; Ward, E Sally; Ober, Raimund J

    2012-03-15

    The electron-multiplying charge-coupled device (EMCCD) is a popular technology for imaging under extremely low light conditions. It has become widely used, for example, in single molecule microscopy experiments where few photons can be detected from the individual molecules of interest. Despite its important role in low light microscopy, however, little has been done in the way of determining how accurately parameters of interest (e.g., location of a single molecule) can be estimated from an image that it produces. Here, we develop the theory for calculating the Fisher information matrix, and hence the Cramer-Rao lower bound-based limit of the accuracy, for estimating parameters from an EMCCD image. An EMCCD operates by amplifying a weak signal that would otherwise be drowned out by the detector's readout noise as in the case of a conventional charge-coupled device (CCD). The signal amplification is a stochastic electron multiplication process, and is modeled here as a geometrically multiplied branching process. In developing our theory, we also introduce a "noise coefficient" which enables the comparison of the Fisher information of different data models via a scalar quantity. This coefficient importantly allows the selection of the best detector (e.g., EMCCD or CCD), based on factors such as the signal level, and regardless of the specific estimation problem at hand. We apply our theory to the problem of localizing a single molecule, and compare the calculated limits of the localization accuracy with the standard deviations of maximum likelihood location estimates obtained from simulated images of a single molecule. PMID:24379939

  17. Localization accuracy in single molecule microscopy using electron-multiplying charge-coupled device cameras

    PubMed Central

    Chao, Jerry; Ward, E. Sally; Ober, Raimund J.

    2012-01-01

    The electron-multiplying charge-coupled device (EMCCD) is a popular technology for imaging under extremely low light conditions. It has become widely used, for example, in single molecule microscopy experiments where few photons can be detected from the individual molecules of interest. Despite its important role in low light microscopy, however, little has been done in the way of determining how accurately parameters of interest (e.g., location of a single molecule) can be estimated from an image that it produces. Here, we develop the theory for calculating the Fisher information matrix, and hence the Cramer-Rao lower bound-based limit of the accuracy, for estimating parameters from an EMCCD image. An EMCCD operates by amplifying a weak signal that would otherwise be drowned out by the detector’s readout noise as in the case of a conventional charge-coupled device (CCD). The signal amplification is a stochastic electron multiplication process, and is modeled here as a geometrically multiplied branching process. In developing our theory, we also introduce a “noise coefficient” which enables the comparison of the Fisher information of different data models via a scalar quantity. This coefficient importantly allows the selection of the best detector (e.g., EMCCD or CCD), based on factors such as the signal level, and regardless of the specific estimation problem at hand. We apply our theory to the problem of localizing a single molecule, and compare the calculated limits of the localization accuracy with the standard deviations of maximum likelihood location estimates obtained from simulated images of a single molecule. PMID:24379939

  18. Effect of nonadiabatic electronic-vibrational interactions on the transport properties of single-molecule junctions

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

    The interaction between electronic and vibrational degrees of freedom in single-molecule junctions may result from the dependence of the electronic energies or the electronic states of the molecular bridge on the nuclear displacement. The latter mechanism leads to a direct coupling between different electronic states and is referred to as nonadiabatic electronic-vibrational coupling. Employing a perturbative nonequilibrium Green's function approach, we study the influence of nonadiabatic electronic-vibrational coupling in model molecular junctions. Thereby, we distinguish between systems with well-separated and quasidegenerate electronic levels. The results show that the nonadiabatic electronic-vibrational interaction can have a significant influence on the transport properties. The underlying mechanisms, in particular the difference between nonadiabatic and adiabatic electronic-vibrational couplings, are analyzed in some detail.

  19. Single Molecules

    NSDL National Science Digital Library

    A new molecular science journal, Single Molecules, from Wiley Interscience, "will provide researchers with a broad overview of current methods and techniques, recent applications and shortcomings of present techniques in the field of single molecules." With temporary free access, the journal's latest issue contains a few full-text articles, with more articles being regularly added. This journal is currently calling for papers.

  20. Single-Molecule Measurements of T4 Lysozyme using Carbon Nanotube Electronic Circuits

    NASA Astrophysics Data System (ADS)

    Sims, Patrick Craig

    Because of their unique electronic and chemical properties, single-walled carbon nanotubes (SWNTs) are attractive candidates for label-free, single-molecule sensing and detection applications. In this work, a field-effect transistor (FET) architecture comprised of an individual SWNT is used to transduce the conformational motion of a single T4 lysozyme protein, conjugated to the SWNT side wall, into a corresponding electrical current signal. The SWNTs are grown using chemical vapor deposition, and metal electrical contacts are formed using electron beam evaporation. Using N-(1-Pyrene)maleimide, the protein is conjugated to the SWNT side wall. After conjugation, the sensing area of the device is submerged in an electrolyte solution, and the source-drain current is measured while applying an electrolyte-gate. Analysis of the signal provided single-molecule resolution of the dynamical activity of lysozyme as it hydrolyzes macromolecular peptidoglycan, a component of bacterial cell walls. This analysis revealed seven different independent time scales that govern the activity of lysozyme, the pH dependence of these time scales, and a lower limit on the number rate-limiting steps in lysozyme's hinge opening and closing motions. Furthermore, the signals elucidated differences in how lysozyme traverses and catalyzes structurally varying peptidoglycan constructs.

  1. Fast electron transfer through a single molecule natively structured redox protein

    NASA Astrophysics Data System (ADS)

    Della Pia, Eduardo Antonio; Chi, Qijin; MacDonald, J. Emyr; Ulstrup, Jens; Jones, D. Dafydd; Elliott, Martin

    2012-10-01

    The electron transfer properties of proteins are normally measured as molecularly averaged ensembles. Through these and related measurements, proteins are widely regarded as macroscopically insulating materials. Using scanning tunnelling microscopy (STM), we present new measurements of the conductance through single-molecules of the electron transfer protein cytochrome b562 in its native conformation, under pseudo-physiological conditions. This is achieved by thiol (SH) linker pairs at opposite ends of the molecule through protein engineering, resulting in defined covalent contact between a gold surface and a platinum-iridium STM tip. Two different orientations of the linkers were examined: a long-axis configuration (SH-LA) and a short-axis configuration (SH-SA). In each case, the molecular conductance could be `gated' through electrochemical control of the heme redox state. Reproducible and remarkably high conductance was observed in this relatively complex electron transfer system, with single-molecule conductance values peaking around 18 nS and 12 nS for the SH-SA and SH-LA cytochrome b562 molecules near zero electrochemical overpotential. This strongly points to the important role of the heme co-factor bound to the natively structured protein. We suggest that the two-step model of protein electron transfer in the STM geometry requires a multi-electron transfer to explain such a high conductance. The model also yields a low value for the reorganisation energy, implying that solvent reorganisation is largely absent.The electron transfer properties of proteins are normally measured as molecularly averaged ensembles. Through these and related measurements, proteins are widely regarded as macroscopically insulating materials. Using scanning tunnelling microscopy (STM), we present new measurements of the conductance through single-molecules of the electron transfer protein cytochrome b562 in its native conformation, under pseudo-physiological conditions. This is achieved by thiol (SH) linker pairs at opposite ends of the molecule through protein engineering, resulting in defined covalent contact between a gold surface and a platinum-iridium STM tip. Two different orientations of the linkers were examined: a long-axis configuration (SH-LA) and a short-axis configuration (SH-SA). In each case, the molecular conductance could be `gated' through electrochemical control of the heme redox state. Reproducible and remarkably high conductance was observed in this relatively complex electron transfer system, with single-molecule conductance values peaking around 18 nS and 12 nS for the SH-SA and SH-LA cytochrome b562 molecules near zero electrochemical overpotential. This strongly points to the important role of the heme co-factor bound to the natively structured protein. We suggest that the two-step model of protein electron transfer in the STM geometry requires a multi-electron transfer to explain such a high conductance. The model also yields a low value for the reorganisation energy, implying that solvent reorganisation is largely absent. Electronic supplementary information (ESI) available: Experimental methods, DNA and protein sequences, additional STM statistical analysis and images, electrochemical data and It-z data analysis. See DOI: 10.1039/c2nr32131a

  2. Effects of electron-vibration coupling in transport through single molecules.

    PubMed

    Franke, Katharina J; Pascual, Jose Ignacio

    2012-10-01

    Using scanning tunneling spectroscopy, we study the transport of electrons through C(60) molecules on different metal surfaces. When electrons tunnel through a molecule, they may excite molecular vibrations. A fingerprint of these processes is a characteristic sub-structure in the differential conductance spectra of the molecular junction reflecting the onset of vibrational excitation. Although the intensity of these processes is generally weak, they become more important as the resonant character of the transport mechanism increases. The detection of single vibrational levels crucially depends on the energy level alignment and lifetimes of excited states. In the limit of large current densities, resonant electron-vibration coupling leads to an energy accumulation in the molecule, which eventually leads to its decomposition. With our experiments on C(60) we are able to depict a molecular scale picture of how electrons interact with the vibrational degrees of freedom of single molecules in different transport regimes. This understanding helps in the development of stable molecular devices, which may also carry a switchable functionality. PMID:22964796

  3. A study of planar anchor groups for graphene-based single-molecule electronics

    SciTech Connect

    Bailey, Steven; Visontai, David; Lambert, Colin J., E-mail: c.lambert@lancaster.ac.uk [Department of Physics, Lancaster University, Lancaster LA1 4YB (United Kingdom); Bryce, Martin R. [Department of Chemistry, Durham University, Durham DH1 3LE (United Kingdom)] [Department of Chemistry, Durham University, Durham DH1 3LE (United Kingdom); Frampton, Harry; Chappell, David [BP Exploration Operating Company Limited, Chertsey Road, Sunbury on Thames, Middlesex TW16 7BP (United Kingdom)] [BP Exploration Operating Company Limited, Chertsey Road, Sunbury on Thames, Middlesex TW16 7BP (United Kingdom)

    2014-02-07

    To identify families of stable planar anchor groups for use in single molecule electronics, we report detailed results for the binding energies of two families of anthracene and pyrene derivatives adsorbed onto graphene. We find that all the selected derivatives functionalized with either electron donating or electron accepting substituents bind more strongly to graphene than the parent non-functionalized anthracene or pyrene. The binding energy is sensitive to the detailed atomic alignment of substituent groups over the graphene substrate leading to larger than expected binding energies for –OH and –CN derivatives. Furthermore, the ordering of the binding energies within the anthracene and pyrene series does not simply follow the electron affinities of the substituents. Energy barriers to rotation or displacement on the graphene surface are much lower than binding energies for adsorption and therefore at room temperature, although the molecules are bound to the graphene, they are almost free to move along the graphene surface. Binding energies can be increased by incorporating electrically inert side chains and are sensitive to the conformation of such chains.

  4. Electron transport in endohedral metallofullerene Ce@C82 single-molecule transistors

    NASA Astrophysics Data System (ADS)

    Okamura, Naoya; Yoshida, Kenji; Sakata, Shuichi; Hirakawa, Kazuhiko

    2015-01-01

    We have investigated the electron transport in endohedral metallofullerene Ce@C82 single-molecule transistors (SMTs) together with that in reference C84 SMTs. The vibrational modes (bending and stretching) of the encapsulated single Ce atom in the C82 cage appear in Coulomb stability diagrams for the single-electron tunneling through Ce@C82 molecules, demonstrating the single-atom sensitivity of the transport measurements. When a bias voltage larger than 100 mV is applied across the source/drain electrodes, large hysteretic behavior is observed in the current-voltage (I-V) characteristics. At the same time, the pattern in the Coulomb stability diagram is changed. No such hysteretic behavior is observed in the I-V curves of hollow-cage C84 SMTs, even when the bias voltage exceeds 500 mV. This hysteretic change in the I-V characteristics is induced by a nanomechanical change in the configuration of the Ce@C82 molecule in the nanogap electrode due to the electric dipole that exists in Ce@C82.

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

    PubMed Central

    2011-01-01

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

  6. Flicker Noise as a Probe of Electronic Interaction at Metal-Single Molecule Interfaces.

    PubMed

    Adak, Olgun; Rosenthal, Ethan; Meisner, Jeffery; Andrade, Erick F; Pasupathy, Abhay N; Nuckolls, Colin; Hybertsen, Mark S; Venkataraman, Latha

    2015-06-10

    Charge transport properties of metal-molecule interfaces depend strongly on the character of molecule-electrode interactions. Although through-bond coupled systems have attracted the most attention, through-space coupling is important in molecular systems when, for example, through-bond coupling is suppressed due to quantum interference effects. To date, a probe that clearly distinguishes these two types of coupling has not yet been demonstrated. Here, we investigate the origin of flicker noise in single molecule junctions and demonstrate how the character of the molecule-electrode coupling influences the flicker noise behavior of single molecule junctions. Importantly, we find that flicker noise shows a power law dependence on conductance in all junctions studied with an exponent that can distinguish through-space and through-bond coupling. Our results provide a new and powerful tool for probing and understanding coupling at the metal-molecule interface. PMID:25942441

  7. Nonequilibrium electronic structure of interacting single-molecule nanojunctions: vertex corrections and polarization effects for the electron-vibron coupling.

    PubMed

    Dash, L K; Ness, H; Godby, R W

    2010-03-14

    We consider the interaction between electrons and molecular vibrations in the context of electronic transport in nanoscale devices. We present a method based on nonequilibrium Green's functions to calculate both equilibrium and nonequilibrium electronic properties of a single-molecule junction in the presence of electron-vibron interactions. We apply our method to a model system consisting of a single electronic level coupled to a single vibration mode in the molecule, which is in contact with two electron reservoirs. Higher-order diagrams beyond the usual self-consistent Born approximation (SCBA) are included in the calculations. In this paper we consider the effects of the double-exchange diagram and the diagram in which the vibron propagator is renormalized by one electron-hole bubble. We study in detail the effects of the first- and second-order diagrams on the spectral functions for a large set of parameters and for different transport regimes (resonant and off-resonant cases), both at equilibrium and in the presence of a finite applied bias. We also study the linear response (linear conductance) of the nanojunction for all the different regimes. We find that it is indeed necessary to go beyond the SCBA in order to obtain correct results for a wide range of parameters. PMID:20232953

  8. Nonequilibrium electronic structure of interacting single-molecule nanojunctions: Vertex corrections and polarization effects for the electron-vibron coupling

    NASA Astrophysics Data System (ADS)

    Dash, L. K.; Ness, H.; Godby, R. W.

    2010-03-01

    We consider the interaction between electrons and molecular vibrations in the context of electronic transport in nanoscale devices. We present a method based on nonequilibrium Green's functions to calculate both equilibrium and nonequilibrium electronic properties of a single-molecule junction in the presence of electron-vibron interactions. We apply our method to a model system consisting of a single electronic level coupled to a single vibration mode in the molecule, which is in contact with two electron reservoirs. Higher-order diagrams beyond the usual self-consistent Born approximation (SCBA) are included in the calculations. In this paper we consider the effects of the double-exchange diagram and the diagram in which the vibron propagator is renormalized by one electron-hole bubble. We study in detail the effects of the first- and second-order diagrams on the spectral functions for a large set of parameters and for different transport regimes (resonant and off-resonant cases), both at equilibrium and in the presence of a finite applied bias. We also study the linear response (linear conductance) of the nanojunction for all the different regimes. We find that it is indeed necessary to go beyond the SCBA in order to obtain correct results for a wide range of parameters.

  9. Single-molecule bioelectronics.

    PubMed

    Rosenstein, Jacob K; Lemay, Serge G; Shepard, Kenneth L

    2015-07-01

    Experimental techniques that interface single biomolecules directly with microelectronic systems are increasingly being used in a wide range of powerful applications, from fundamental studies of biomolecules to ultra-sensitive assays. In this study, we review several technologies that can perform electronic measurements of single molecules in solution: ion channels, nanopore sensors, carbon nanotube field-effect transistors, electron tunneling gaps, and redox cycling. We discuss the shared features among these techniques that enable them to resolve individual molecules, and discuss their limitations. Recordings from each of these methods all rely on similar electronic instrumentation, and we discuss the relevant circuit implementations and potential for scaling these single-molecule bioelectronic interfaces to high-throughput arrayed sensing platforms. WIREs Nanomed Nanobiotechnol 2015, 7:475-493. doi: 10.1002/wnan.1323 For further resources related to this article, please visit the WIREs website. PMID:25529538

  10. Ionic liquid based approach for single-molecule electronics with cobalt contacts.

    PubMed

    Catarelli, Samantha R; Higgins, Simon J; Schwarzacher, Walther; Mao, Bing-Wei; Yan, Jia-Wei; Nichols, Richard J

    2014-12-01

    An electrochemical method is presented for fabricating cobalt thin films for single-molecule electrical transport measurements. These films are electroplated in an aqueous electrolyte, but the crucial stages of electrochemical reduction to remove surface oxide and adsorption of alkane(di)thiol target molecules under electrochemical control to form self-assembled monolayers which protect the oxide-free cobalt surface are carried out in an ionic liquid. This approach yields monolayers on Co that are of comparable quality to those formed on Au by standard self-assembly protocols, as assessed by electrochemical methods and surface infrared spectroscopy. Using an adapted scanning tunneling microscopy (STM) method, we have determined the single-molecule conductance of cobalt/1,8-octanedithiol/cobalt junctions by employing a monolayer on cobalt and a cobalt STM tip in an ionic liquid environment and have compared the results with those of experiments using gold electrodes as a control. These cobalt substrates could therefore have future application in organic spintronic devices such as magnetic tunnel junctions. PMID:25370276

  11. Direct observation of apolipoprotein B refolding at single molecule level by ultra sensitive fluorescence microscopy and solution transmission electron microscopy

    NASA Astrophysics Data System (ADS)

    Chang, Chia-Ching; Chu, Hsueh-Liang; Lee, Hsing-Yuan; Cheng, Tsai-Mu; Chen, Gong-Shen; Chen, Fu-Rong

    2013-03-01

    Apolipoprotein (apo) B is the only protein of low-density lipoprotein (LDL). The huge size and extreme hydrophobicity of apoB make examination of its lipidation process an experimental challenge. In this study, we showed that apoB lipidation and its intermediates could be observed at single molecule level by an on-path folding process. When carboxyl-terminal-truncated mutants apoB-29 and apoB-48, representing the amino-terminal 29% and 48%, respectively, of the full-length apoB (apoB-100), were used for comparison, we observed that the refolded apoB-100 resembled both native LDL and VLDL precursors. Thus the process of lipidation recapitulates that of pre-VLDL assembly, in vitro. These results suggest that the assembly of mature VLDL requires involvement of factors in addition to apoB-100 and lipids. Using solution transmission electron microscopy (TEM), we were able to detect incorporation of hydrophobic super-paramagnetic iron oxide nanoparticles into apoB-100 particles at the initial, but not final, stage of refolding. The current study thus demonstrates that VLDL assembly can be monitored at single molecule level, too.

  12. Investigation of electron beam irradiation effect on pore formation for single molecule bio-sensor fabrication

    NASA Astrophysics Data System (ADS)

    Choi, Seong Soo; Park, Myoung Jin; Han, Chul Hee; Kim, Sung In; Yoo, Jung Ho; Park, Kyung Jin; Park, Nam Kyou; Kim, Yong Sang

    2015-03-01

    There have been tremendous interests about the fabrication of the Au plasmonic nanopore due to its capability of the nanosize optical biosensor. We have investigated the influence of low energy electron beam irradiation on an Au nanomembrane during Au nanopore formation. In this report, the influence of electron beam irradiation on the Au nanopore formation will be reported. The nanopores on the 200 nm thick Au membrane were initially fabricated using focused ion beam (FIB) and high energy electron beam techniques such as transmission electron microscopy (TEM), and field emission scanning electron microscopy (FESEM). During high energy electron beam by using TEM, either a "shrinking" or a "opening" phenomenon is reported dependent on the ratio of thickness to aperture diameter. However, for a FESEM electron beam irradiation, a shrinking phenomenon is always observed. In this report, the nanopore formation during FESEM electron beam irradiation will be reported depending upon energy absorption and thermal diffusivity.

  13. Fabrication of nanogapped single-electron transistors for transport studies of individual single-molecule magnets

    E-print Network

    del Barco, Enrique

    Fabrication of nanogapped single-electron transistors for transport studies of individual single October 2006; accepted 10 November 2006; published online 3 April 2007 Three-terminal single-electron transistor devices utilizing Al/Al2O3 gate electrodes were developed for the study of electron transport

  14. Magnetic Quantum Tunneling in a Mn12 Single-Molecule Magnet Measured With High Frequency Electron Paramagnetic Resonance

    NASA Astrophysics Data System (ADS)

    Lawrence, J.; Lee, S. C.; Kim, S.; Hill, S.; Murugesu, M.; Christou, G.

    2006-09-01

    The low temperature spin dynamics of the single-molecule magnet [Mn12O12(CH3COOH)16(H2O)4]. 2CH3COOH?4H2O, hereafter Mn12Ac, were studied using High Frequency Electron Paramagnetic Resonance (HFEPR) in order to demonstrate magnetic quantum tunneling between resonant spin projection states. We prepare the spins such that they populate only one side of the axial potential energy barrier. Using a magnetic field we cause tunneling between resonant energy states. We then use HFEPR to monitor the populations on each side of the potential energy barrier. We can estimate the tunneling relaxation time between spin projection states by plotting the area of an EPR peak as a function of wait time at a resonance field. This technique provides an alternative method to magnetometry experiments for measuring spin relaxation dynamics.

  15. Electronics and Chemistry: Varying Single Molecule Junction Conductance Using Chemical Substituents

    E-print Network

    Latha Venkataraman; Young S. Park; Adam C. Whalley Colin Nuckolls; Mark S. Hybertsen; Michael L. Steigerwald

    2007-03-16

    We measure the low bias conductance of a series of substituted benzene diamine molecules while breaking a gold point contact in a solution of the molecules. Transport through these substituted benzenes is by means of nonresonant tunneling or superexchange, with the molecular junction conductance depending on the alignment of the metal Fermi level to the closest molecular level. Electron-donating substituents, which drive the occupied molecular orbitals up, increase the junction conductance, while electron-withdrawing substituents have the opposite effect. Thus for the measured series, conductance varies inversely with the calculated ionization potential of the molecules. These results reveal that the occupied states are closest to the gold Fermi energy, indicating that the tunneling transport through these molecules is analogous to hole tunneling through an insulating film.

  16. Site-dependent electronic structures of a single molecule on a metal surface studied by scanning tunneling microscopy and spectroscopy

    NASA Astrophysics Data System (ADS)

    Katano, Satoshi; Hori, Masafumi; Kim, Yousoo; Kawai, Maki

    2014-10-01

    Single-molecule observation of the electronic structures of para-cyanobenzoate (pCB) adsorbed on Cu(1 1 0) has been performed using scanning tunneling microscopy (STM) and spectroscopy (STS). We found that pCB has two types of the adsorption site on Cu(1 1 0); i.e., two oxygen atoms of pCB are bridged between adjacent Cu atoms at the short- or long-bridge sites. STS and STS mapping revealed that the pCB adsorbed at the short-bridge site has a resonant peak at 2.0 V above the Fermi level, which is assigned to the lowest unoccupied molecular orbital (LUMO) of pCB. However, the LUMO state is shifted toward lower voltage (1.2 V) when the pCB molecule is adsorbed at the long-bridge site. The energy levels of the LUMO state, depending on the adsorption site of pCB, can thus be ascribed to the degree of the electronic interaction between pCB and the Cu substrate. The site transformation of pCB induced by the injection of tunneling electrons from the STM tip has also been presented.

  17. Structural and electronic dependence of the single-molecule-magnet behavior of dysprosium(III) complexes.

    PubMed

    Campbell, Victoria E; Bolvin, Hélène; Rivière, Eric; Guillot, Regis; Wernsdorfer, Wolfgang; Mallah, Talal

    2014-03-01

    We investigate and compare the magnetic properties of two isostructural Dy(III)-containing complexes. The Dy(III) ions are chelated by hexadentate ligands and possess two apical bidendate nitrate anions. In dysprosium(III) N,N'-bis(imine-2-yl)methylene-1,8-diamino-3,6-dioxaoctane (1), the ligand's donor atoms are two alkoxo, two pyridine, and two imine nitrogen atoms. Dysprosium(III) N,N'-bis(amine-2-yl)methylene-1,8-diamino-3,6-dioxaoctane (2) is identical with 1 except for one modification: the two imine groups have been replaced by amine groups. This change has a minute effect on the structure and a larger effect the magnetic behavior. The two complexes possess slow relaxation of the magnetization in the presence of an applied field of 1000 Oe but with a larger barrier for reorientation of the magnetization for 1 (Ueff/kB = 50 K) than for 2 (Ueff/kB = 34 K). First-principles calculations using the spin-orbit complete active-space self-consistent-field method were performed and allowed to fit the experimental magnetization data. The calculations gave the energy spectrum of the 2J + 1 sublevels issued from the J = 15/2 free-ion ground state. The lowest-lying sublevels were found to have a large contribution of MJ = ±15/2 for 1, while for 2, MJ = ±13/2 was dominant. The observed differences were attributed to a synergistic effect between the electron density of the ligand and the small structural changes provoked by a slight alteration of the coordination environment. It was observed that the stronger ligand field (imine) resulted in complex 1 with a larger energy barrier for reorientation of the magnetization than 2. PMID:24533673

  18. Single molecule laser spectroscopy

    NASA Astrophysics Data System (ADS)

    Atta, Diaa; Okasha, Ali

    2015-01-01

    In this article, we discussed some single molecule spectroscopy techniques and methods. We have chosen the simplicity in this survey based on our laboratory experience in this field. We concentrated on the imaging by both techniques the wide field and the scanning microscopes. Other imaging enhancements on the technique like extended resolution wide field, the total internal reflection imaging, and its derivatives are also reviewed. In addition to the imaging techniques, some diffusion techniques also are discussed like fluorescence correlation spectroscopy. The related methods like Forester resonance transfer, photo-induced electron transfer and anisotropy (steady state and time decay) are also discussed. In addition, we elucidated some simple details about the theory behind the FCS and its resulting curve fitting. This review is preceded by general introduction and ended with the conclusion.

  19. arXiv:1311.1801v1[cond-mat.mes-hall]7Nov2013 All-optical sensing of a single-molecule electron spin

    E-print Network

    Walsworth, Ronald L.

    superconducting quan- tum interference devices (SQUIDs) [8], semiconductor Hall effect sensors [9], and spinarXiv:1311.1801v1[cond-mat.mes-hall]7Nov2013 All-optical sensing of a single-molecule electron spin, often under am- bient, room-temperature conditions. Many state-of-the- art magnetic sensors, including

  20. Clay Nanoparticle-Supported Single-Molecule Fluorescence Spectroelectrochemistry

    SciTech Connect

    Lei, Chenghong; Hu, Dehong; Ackerman, Eric J.

    2009-02-11

    We report single-molecule fluorescence spectroelectrochemistry on a clay-modified ITO electrode using cresyl violet as a redox fluorescent probe. Ensemble averaged experiments show that cresyl violet displays well-defined cyclic voltammograms when adsorbed on the clay-modified electrode. By probing the fluorescence intensity of a single cresyl violet molecule absorbed on clay surface, we can trace the redox reaction of individual molecules induced by the cyclic voltammetric potential scanning. Inhomogeneous interfacial electron transfer dynamics of the immobilized single cresyl violet molecules on the clay-modified surface were observed.

  1. [Biophysics of single molecules].

    PubMed

    Serdiuk, I N; Deriusheva, E I

    2011-01-01

    The modern methods of research of biological molecules whose application led to the development of a new field of science, biophysics of single molecules, are reviewed. The measurement of the characteristics of single molecules enables one to reveal their individual features, and it is just for this reason that much more information can be obtained from one molecule than from the entire ensample of molecules. The high sensitivity of the methods considered in detail makes it possible to come close to the solution of the basic problem of practical importance, namely, the determination of the nucleotide sequence of a single DNA molecule. PMID:22117447

  2. Molecular spintronics using single-molecule magnets

    Microsoft Academic Search

    Lapo Bogani; Wolfgang Wernsdorfer

    2008-01-01

    A revolution in electronics is in view, with the contemporary evolution of the two novel disciplines of spintronics and molecular electronics. A fundamental link between these two fields can be established using molecular magnetic materials and, in particular, single-molecule magnets. Here, we review the first progress in the resulting field, molecular spintronics, which will enable the manipulation of spin and

  3. Towards single molecule DNA sequencing

    NASA Astrophysics Data System (ADS)

    Liu, Hao

    Single molecule DNA Sequencing technology has been a hot research topic in the recent decades because it holds the promise to sequence a human genome in a fast and affordable way, which will eventually make personalized medicine possible. Single molecule differentiation and DNA translocation control are the two main challenges in all single molecule DNA sequencing methods. In this thesis, I will first introduce DNA sequencing technology development and its application, and then explain the performance and limitation of prior art in detail. Following that, I will show a single molecule DNA base differentiation result obtained in recognition tunneling experiments. Furthermore, I will explain the assembly of a nanofluidic platform for single strand DNA translocation, which holds the promised to be integrated into a single molecule DNA sequencing instrument for DNA translocation control. Taken together, my dissertation research demonstrated the potential of using recognition tunneling techniques to serve as a general readout system for single molecule DNA sequencing application.

  4. Conductive atomic force microscopy study of single molecule electron transport through the Azurin-gold nanoparticle system

    E-print Network

    Tuscia, Università Degli Studi Della

    such as hopping, through-space, and through-bond tunnelling,4,13,14 according to distances and pathways travelled to their electron transfer, catalytic and recognition proper- ties.1 Their nanoscale dimension, along with the very

  5. Nanochannel Based Single Molecule Recycling

    PubMed Central

    Lesoine, John F.; Venkataraman, Prahnesh A.; Maloney, Peter C.; Dumont, Mark

    2012-01-01

    We present a method for measuring the fluorescence from a single molecule hundreds of times without surface immobilization. The approach is based on the use of electroosmosis to repeatedly drive a single target molecule in a fused silica nanochannel through a stationary laser focus. Single molecule fluorescence detected during the transit time through the laser focus is used to repeatedly reverse the electrical potential controlling the flow direction. Our method does not rely on continuous observation and therefore is less susceptible to fluorescence blinking than existing fluorescence-based trapping schemes. The variation in the turnaround times can be used to measure the diffusion coefficient on a single molecule level. We demonstrate the ability to recycle both proteins and DNA in nanochannels and show that the procedure can be combined with single-pair Förster energy transfer. Nanochannel-based single molecule recycling holds promise for studying conformational dynamics on the same single molecule in solution and without surface tethering. PMID:22662745

  6. Stereoelectronic switching in single-molecule junctions

    NASA Astrophysics Data System (ADS)

    Su, Timothy A.; Li, Haixing; Steigerwald, Michael L.; Venkataraman, Latha; Nuckolls, Colin

    2015-03-01

    A new intersection between reaction chemistry and electronic circuitry is emerging from the ultraminiaturization of electronic devices. Over decades chemists have developed a nuanced understanding of stereoelectronics to establish how the electronic properties of molecules relate to their conformation; the recent advent of single-molecule break-junction techniques provides the means to alter this conformation with a level of control previously unimagined. Here we unite these ideas by demonstrating the first single-molecule switch that operates through a stereoelectronic effect. We demonstrate this behaviour in permethyloligosilanes with methylthiomethyl electrode linkers. The strong ? conjugation in the oligosilane backbone couples the stereoelectronic properties of the sulfur–methylene ? bonds that terminate the molecule. Theoretical calculations support the existence of three distinct dihedral conformations that differ drastically in their electronic character. We can shift between these three species by simply lengthening or compressing the molecular junction, and, in doing so, we can switch conductance digitally between two states.

  7. Stereoelectronic switching in single-molecule junctions.

    PubMed

    Su, Timothy A; Li, Haixing; Steigerwald, Michael L; Venkataraman, Latha; Nuckolls, Colin

    2015-03-01

    A new intersection between reaction chemistry and electronic circuitry is emerging from the ultraminiaturization of electronic devices. Over decades chemists have developed a nuanced understanding of stereoelectronics to establish how the electronic properties of molecules relate to their conformation; the recent advent of single-molecule break-junction techniques provides the means to alter this conformation with a level of control previously unimagined. Here we unite these ideas by demonstrating the first single-molecule switch that operates through a stereoelectronic effect. We demonstrate this behaviour in permethyloligosilanes with methylthiomethyl electrode linkers. The strong ? conjugation in the oligosilane backbone couples the stereoelectronic properties of the sulfur-methylene ? bonds that terminate the molecule. Theoretical calculations support the existence of three distinct dihedral conformations that differ drastically in their electronic character. We can shift between these three species by simply lengthening or compressing the molecular junction, and, in doing so, we can switch conductance digitally between two states. PMID:25698330

  8. Geometric, electronic and magnetic structures of S = 19/2 and S = 20/2 thiophene-2-carboxylate functionalized Mn12 single molecule magnets.

    PubMed

    Rodriguez, Jorge H; Ziegler, Christopher J

    2015-01-01

    The geometric and magnetic structures of two structurally related, but magnetically inequivalent, single molecule magnets (SMMs) have been computationally characterized. The first SMM, with formula [Mn12O12(O2CC4H3S)16(H2O)2](-1) (I), has a half-integer spin (S(I) = 19/2) due to ferrimagnetic ordering. The second SMM, with formula Mn12O12(O2CC4H3S)16(H2O)4 (II), has an integer spin (S(II) = 20/2) and its geometric structure has been computationally predicted. Both SMMs include thiophene-2-carboxylate functional groups for potential use in molecular electronics. To determine structural and electronic differences between both SMMs, spin polarized density functional theory was applied to I and II. Hydrogen bonding of two and four Mn-bound water molecules in I and II, respectively, to thiophene-2-carboxylate oxygen atoms and inner cubane oxygen atoms is essential for structural stabilization of both complexes. The one-electron-reduction of I is concomitant with a structural asymmetry within its cubane whereby two ions, of nominal Mn(4+)(Si = 3/2) character, are inequivalent to the other two and acquire an incipient Mn(3+)(Si = 4/2) character. The geometric asymmetry in I provides an extra, albeit small, contribution to its zero field splitting and anisotropy barrier to spin reversal. Thus, despite its lower spin state, the anisotropy barrier of I is only slightly lower than that of II. PMID:25360814

  9. Fluorescence Microscopy of Single Molecules

    ERIC Educational Resources Information Center

    Zimmermann, Jan; van Dorp, Arthur; Renn, Alois

    2004-01-01

    The investigation of photochemistry and photophysics of individual quantum systems is described with the help of a wide-field fluorescence microscopy approach. The fluorescence single molecules are observed in real time.

  10. Manipulating transport through a single-molecule junction

    SciTech Connect

    Sotthewes, Kai; Heimbuch, René; Zandvliet, Harold J. W. [Physics of Interfaces and Nanomaterials, MESA Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500AE Enschede (Netherlands)] [Physics of Interfaces and Nanomaterials, MESA Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500AE Enschede (Netherlands)

    2013-12-07

    Molecular Electronics deals with the realization of elementary electronic devices that rely on a single molecule. For electronic applications, the most important property of a single molecule is its conductance. Here we show how the conductance of a single octanethiol molecule can be measured and manipulated by varying the contact's interspace. This mechanical gating of the single molecule junction leads to a variation of the conductance that can be understood in terms of a tunable image charge effect. The image charge effect increases with a decrease of the contact's interspace due to a reduction of the effective potential barrier height of 1.5 meV/pm.

  11. IPET and FETR: experimental approach for studying molecular structure dynamics by cryo-electron tomography of a single-molecule structure.

    PubMed

    Zhang, Lei; Ren, Gang

    2012-01-01

    The dynamic personalities and structural heterogeneity of proteins are essential for proper functioning. Structural determination of dynamic/heterogeneous proteins is limited by conventional approaches of X-ray and electron microscopy (EM) of single-particle reconstruction that require an average from thousands to millions different molecules. Cryo-electron tomography (cryoET) is an approach to determine three-dimensional (3D) reconstruction of a single and unique biological object such as bacteria and cells, by imaging the object from a series of tilting angles. However, cconventional reconstruction methods use large-size whole-micrographs that are limited by reconstruction resolution (lower than 20 Å), especially for small and low-symmetric molecule (<400 kDa). In this study, we demonstrated the adverse effects from image distortion and the measuring tilt-errors (including tilt-axis and tilt-angle errors) both play a major role in limiting the reconstruction resolution. Therefore, we developed a "focused electron tomography reconstruction" (FETR) algorithm to improve the resolution by decreasing the reconstructing image size so that it contains only a single-instance protein. FETR can tolerate certain levels of image-distortion and measuring tilt-errors, and can also precisely determine the translational parameters via an iterative refinement process that contains a series of automatically generated dynamic filters and masks. To describe this method, a set of simulated cryoET images was employed; to validate this approach, the real experimental images from negative-staining and cryoET were used. Since this approach can obtain the structure of a single-instance molecule/particle, we named it individual-particle electron tomography (IPET) as a new robust strategy/approach that does not require a pre-given initial model, class averaging of multiple molecules or an extended ordered lattice, but can tolerate small tilt-errors for high-resolution single "snapshot" molecule structure determination. Thus, FETR/IPET provides a completely new opportunity for a single-molecule structure determination, and could be used to study the dynamic character and equilibrium fluctuation of macromolecules. PMID:22291925

  12. 788 IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS, VOL. 10, NO. 4, JULY/AUGUST 2004 Photon-Timing Detector Module for Single-Molecule

    E-print Network

    Xie, Xiaoliang Sunney

    single-photon timing module (SPTM), based on a planar epi- taxial single photon avalanche diodes (SPAD. Index Terms--Avalanche photodiode, picosecond timing, single molecule, single photon, single and based on a statistical analysis of single-mol- ecule fluorescence lifetime trajectories essentially rely

  13. Single-molecule identification via electric current noise

    PubMed Central

    Tsutsui, Makusu; Taniguchi, Masateru; Kawai, Tomoji

    2010-01-01

    Label-free and real-time single-molecule detection may aid the development of high-throughput biosensing platforms. Molecular fluctuations are a source of noise that often hinders single-molecule identification by obscuring the fine details of molecular identity. In this study, we report molecular identification through direct observation of quantum-fluctuation-induced inelastic noise in single organic molecules. We investigated current fluctuations flowing through a single molecule that is chemically connected to two electrodes. We found increased current oscillations synchronous to electric field excitations of characteristic molecular vibrational modes that contribute to inelastic electron tunnelling. This finding demonstrates a large contribution of charge interaction with nuclear dynamics on noise properties of single-molecule bridges and suggests a potential use of inelastic noise as a valuable molecular signature for single-molecule identification. PMID:21266988

  14. Franck-Condon blockade in a single-molecule transistor.

    PubMed

    Burzurí, Enrique; Yamamoto, Yoh; Warnock, Michael; Zhong, Xiaoliang; Park, Kyungwha; Cornia, Andrea; van der Zant, Herre S J

    2014-06-11

    We investigate vibron-assisted electron transport in single-molecule transistors containing an individual Fe4 Single-Molecule Magnet. We observe a strong suppression of the tunneling current at low bias in combination with vibron-assisted excitations. The observed features are explained by a strong electron-vibron coupling in the framework of the Franck-Condon model supported by density-functional theory. PMID:24801879

  15. Correlated Single Quantum Dot Blinking and Interfacial Electron Transfer Dynamics

    PubMed Central

    Jin, Shengye; Hsiang, Jung-Cheng; Zhu, Haiming; Song, Nianhui; Dickson, Robert M.; Lian, Tianquan

    2011-01-01

    The electron transfer (ET) dynamics from core/multi-shell (CdSe/CdS3MLZnCdS2MLZnS2ML) quantum dots (QDs) to adsorbed Fluorescein (F27) molecules have been studied by single particle spectroscopy to probe the relationship between single QD interfacial electron transfer and blinking dynamics. Electron transfer from the QD to F27 and the subsequent recombination were directly observed by ensemble-averaged transient absorption spectroscopy. Single QD-F27 complexes show correlated fluctuation of fluorescence intensity and lifetime, similar to those observed in free QDs. With increasing ET rate (controlled by F27-to-QD ratio), the lifetime of on states decreases and relative contribution of off states increases. It was shown that ET is active for QDs in on states, the excited state lifetime of which reflects the ET rate, whereas in the off state QD excitons decay by Auger relaxation and ET is not a competitive quenching pathway. Thus, the blinking dynamics of single QDs modulate their interfacial ET activity. Furthermore, interfacial ET provides an additional pathway for generating off states, leading to correlated single QD interfacial ET and blinking dynamics in QD-acceptor complexes. Because blinking is a general phenomenon of single QDs, it appears that the correlated interfacial ET and blinking and the resulting intermittent ET activity are general phenomena for single QDs. PMID:21915369

  16. Kinetic equations for transport through single-molecule transistors M. Leijnse and M. R. Wegewijs

    E-print Network

    . INTRODUCTION Electron transport through single-molecule transistors SMTs has been intensively studiedKinetic equations for transport through single-molecule transistors M. Leijnse and M. R. Wegewijs the nondiagonal elements of the density matrix. As a first application, we study a single-molecule transistor

  17. Single Molecule Conductance of Oligothiophene Derivatives

    NASA Astrophysics Data System (ADS)

    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 to sample similar conformers. This work demonstrates that the conductance of bithiophene displays a strong dependence on the conformational fluctuations accessible within a given junction configuration, and that the symmetry of such small molecules can significantly influence their conductance behavior. Next, the single-molecule conductance of a family of oligothiophenes comprising one to six thiophene units was measured. An anomalous behavior was found: the peak of the conductance histogram distribution did not follow a clear exponential decay with increasing number of thiophene units in the chain. The electronic properties of the materials were characterized by optical spectroscopy and electrochemistry to gain an understanding of the factors affecting the conductance of these molecules. Different conformers in the junction were postulated to be a contributing factor to the anomalous trend in the observed conductance as a function of molecule length. Then, the electronic properties of the thiophene-1,1-dioxide unit were investigated. These motifs have become synthetically accessible in the last decade, due to Rozen's unprecedentedly potent oxidizing reagent - HOF?CH 3CN - which has been shown to be powerful yet selective enough to oxidize thiophenes in various environments. The resulting thiophene-1,1-dioxides show great promise for electronic devices. The oxidation chemistry of thiophenes was expanded and tuning of the frontier energy levels was demonstrated through combining electron poor and electron rich units. Finally, charge carriers in single-molecule junctions were shown to be tunable within a family of molecules containing these thiophene-1,1-dioxide (TDO) building blocks. Oligomers of TDO were designed in order to increase electron affinity, maintain delocalized frontier orbitals, while significantly decreasing the transport gap. Through thermopower measurements, the dominant charge carriers were shown to change from holes to electrons as the number of TDO units was increased. This resulted in a unique system in which the charge carrier depends on ba

  18. Single-molecule anisotropy imaging

    PubMed Central

    Harms, GS; Sonnleitner, M; Schutz, GJ; Gruber, HJ; Schmidt, T

    1999-01-01

    A novel method, single-molecule anisotropy imaging, has been employed to simultaneously study lateral and rotational diffusion of fluorescence-labeled lipids on supported phospholipid membranes. In a fluid membrane composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, in which the rotational diffusion time is on the order of the excited-state lifetime of the fluorophore rhodamine, a rotational diffusion constant, D(rot) = 7 x 10(7) rad(2)/s, was determined. The lateral diffusion constant, measured by direct analysis of single-molecule trajectories, was D(lat) = 3.5 x 10(-8) cm(2)/s. As predicted from the free-volume model for diffusion, the results exhibit a significantly enhanced mobility on the nanosecond time scale. For membranes of DPPC lipids in the L(beta) gel phase, the slow rotational mobility permitted the direct observation of the rotation of individual molecules characterized by D(rot) = 1.2 rad(2)/s. The latter data were evaluated by a mean square angular displacement analysis. The technique developed here should prove itself profitable for imaging of conformational motions of individual proteins on the time scale of milliseconds to seconds. PMID:10545384

  19. Single-molecule mechanics of mussel adhesion

    NASA Astrophysics Data System (ADS)

    Lee, Haeshin; Scherer, Norbert F.; Messersmith, Phillip B.

    2006-08-01

    The glue proteins secreted by marine mussels bind strongly to virtually all inorganic and organic surfaces in aqueous environments in which most adhesives function poorly. Studies of these functionally unique proteins have revealed the presence of the unusual amino acid 3,4-dihydroxy-L-phenylalanine (dopa), which is formed by posttranslational modification of tyrosine. However, the detailed binding mechanisms of dopa remain unknown, and the chemical basis for mussels' ability to adhere to both inorganic and organic surfaces has never been fully explained. Herein, we report a single-molecule study of the substrate and oxidation-dependent adhesive properties of dopa. Atomic force microscopy (AFM) measurements of a single dopa residue contacting a wet metal oxide surface reveal a surprisingly high strength yet fully reversible, noncovalent interaction. The magnitude of the bond dissociation energy as well as the inability to observe this interaction with tyrosine suggests that dopa is critical to adhesion and that the binding mechanism is not hydrogen bond formation. Oxidation of dopa, as occurs during curing of the secreted mussel glue, dramatically reduces the strength of the interaction to metal oxide but results in high strength irreversible covalent bond formation to an organic surface. A new picture of the interfacial adhesive role of dopa emerges from these studies, in which dopa exploits a remarkable combination of high strength and chemical multifunctionality to accomplish adhesion to substrates of widely varying composition from organic to metallic. 3,4-dihydroxylphenylalanine | atomic force microscopy | mussel adhesive protein

  20. Signatures of Molecular Magnetism in Single-Molecule Transport Spectroscopy

    E-print Network

    Deshmukh, Mandar M.

    single-molecule-transistor measurements on devices incorporating magnetic molecules. By studying that sequential electron tunneling may enhance the magnetic relaxation of the magnetic molecule. Single in these molecules may affect the flow of tunneling electrons. Our experiments employ the proto- typical single

  1. Coupling single molecule magnets to ferromagnetic substrates.

    PubMed

    Lodi Rizzini, A; Krull, C; Balashov, T; Kavich, J J; Mugarza, A; Miedema, P S; Thakur, P K; Sessi, V; Klyatskaya, S; Ruben, M; Stepanow, S; Gambardella, P

    2011-10-21

    We investigate the interaction of TbPc(2) single molecule magnets (SMMs) with ferromagnetic Ni substrates. Using element-resolved x-ray magnetic circular dichroism, we show that TbPc(2) couples antiferromagnetically to Ni films through ligand-mediated superexchange. This coupling is strongly anisotropic and can be manipulated by doping the interface with electron acceptor or donor atoms. We observe that the relative orientation of the substrate and molecule anisotropy axes critically affects the SMM magnetic behavior. TbPc(2) complexes deposited on perpendicularly magnetized Ni films exhibit enhanced magnetic remanence compared to SMMs in the bulk. Contrary to paramagnetic molecules pinned to a ferromagnetic support layer, we find that TbPc(2) can be magnetized parallel or antiparallel to the substrate, opening the possibility to exploit SMMs in spin valve devices. PMID:22107576

  2. Single-Molecule Studies of Protein Folding

    Microsoft Academic Search

    Alessandro Borgia; Philip M. Williams; Jane Clarke

    2008-01-01

    Although protein-folding studies began several decades ago, it is only recently that the tools to analyze protein folding at the single- molecule level have been developed. Advances in single-molecule fluorescence and force spectroscopy techniques allow investigation of the folding and dynamics of single protein molecules, both at equilibrium and as they fold and unfold. The experiments are far from simple,

  3. Single Molecule Approaches Embrace Molecular Cohorts

    PubMed Central

    Ha, Taekjip

    2013-01-01

    Enormous mechanistic insight has been gained by studying the behavior of single molecules. The same approaches used to study proteins in isolation are now being leveraged to examine the changes in functional behavior that emerge when single molecules have company. PMID:23953107

  4. Single-molecule mechanics of mussel adhesion Haeshin Lee*, Norbert F. Scherer

    E-print Network

    Scherer, Norbert F.

    irreversible covalent bond formation to an organic surface. A new picture of the interfacial adhesive role at the adhesive substrate interface has led to much speculation regard- ing its role in adhesive bonding. HoweverSingle-molecule mechanics of mussel adhesion Haeshin Lee*, Norbert F. Scherer , and Phillip B

  5. Single Molecule Probes of Lipid Membrane Structure

    E-print Network

    Livanec, Philip W.

    2009-12-14

    -M) using p-polarized excitation can reveal single-molecule orientations when spherical aberrations are introduced into the optics train. This approach was used here to measure the orientation of fluorescent lipid analogs doped into Langmuir...

  6. Vibrational Excitation in Single-Molecule Transistors: Deviation from the Simple

    E-print Network

    Heller, Eric

    Vibrational Excitation in Single-Molecule Transistors: Deviation from the Simple Franck+) in a single-molecule-transistor geometry. In (Cp)2Fen+ (n ) 0 and 1), almost no vibrations were excited during single-electron transport, whereas in (bpy)3Fen+ (n ) 1, 2, and 3), many distinct vibrations appeared

  7. Electron-induced damage of biotin studied in the gas phase and in the condensed phase at a single-molecule level

    NASA Astrophysics Data System (ADS)

    Keller, Adrian; Kopyra, Janina; Gothelf, Kurt V.; Bald, Ilko

    2013-08-01

    Biotin is an essential vitamin that is, on the one hand, relevant for the metabolism, gene expression and in the cellular response to DNA damage and, on the other hand, finds numerous applications in biotechnology. The functionality of biotin is due to two particular sub-structures, the ring structure and the side chain with carboxyl group. The heterocyclic ring structure results in the capability of biotin to form strong intermolecular hydrogen and van der Waals bonds with proteins such as streptavidin, whereas the carboxyl group can be employed to covalently bind biotin to other complex molecules. Dissociative electron attachment (DEA) to biotin results in a decomposition of the ring structure and the carboxyl group, respectively, within resonant features in the energy range 0-12 eV, thereby preventing the capability of biotin for intermolecular binding and covalent coupling to other molecules. Specifically, the fragment anions (M-H)-, (M-O)-, C3N2O-, CH2O2-, OCN-, CN-, OH- and O- are observed, and exemplarily the DEA cross section of OCN- formation is determined to be 3 × 10-19 cm2. To study the response of biotin to electrons within a complex condensed environment, we use the DNA origami technique and determine a dissociation yield of (1.1 ± 0.2) × 10-14 cm2 at 18 eV electron energy, which represents the most relevant energy for biomolecular damage induced by secondary electrons. The present results thus have important implications for the use of biotin as a label in radiation experiments.

  8. Single-molecule dynamics in nanofabricated traps

    NASA Astrophysics Data System (ADS)

    Cohen, Adam

    2009-03-01

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

  9. Convex Lens-Induced Confinement for Imaging Single Molecules

    PubMed Central

    Leslie, Sabrina R.; Fields, Alexander P.; Cohen, Adam E.

    2011-01-01

    Fluorescence imaging is used to study the dynamics of a wide variety of single molecules in solution or attached to a surface. Two key challenges in this pursuit are (1) to image immobilized single molecules in the presence of a high level of fluorescent background and (2) to image freely diffusing single molecules for long times. Strategies that perform well by one measure often perform poorly by the other. Here, we present a simple modification to a wide-field fluorescence microscope that addresses both challenges and dramatically improves single-molecule imaging. The technique of convex lens-induced confinement (CLIC) restricts molecules to a wedge-shaped gap of nanoscale depth, formed between a plano-convex lens and a planar coverslip. The shallow depth of the imaging volume leads to 20-fold greater rejection of background fluorescence than is achieved with total internal reflection fluorescence (TIRF) imaging. Elimination of out-of-plane diffusion leads to an approximately 10 000-fold longer diffusion-limited observation time per molecule than is achieved with confocal fluorescence correlation spectroscopy. The CLIC system also provides a new means to determine molecular size. The CLIC system does not require any nanofabrication, nor any custom optics, electronics, or computer control. PMID:20557026

  10. Biophysical characterization of DNA binding from single molecule force measurements

    E-print Network

    Levin, Judith G.

    Biophysical characterization of DNA binding from single molecule force measurements Kathy R Abstract Single molecule force spectroscopy is a powerful method that uses the mechanical properties of DNA. Single molecule force measurements quantitatively characterize these DNA binding mechanisms, elucidating

  11. Controlling single-molecule junction conductance by molecular interactions

    PubMed Central

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

    2015-01-01

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

  12. Controlling single-molecule junction conductance by molecular interactions.

    PubMed

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

    2015-01-01

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

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

    SciTech Connect

    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.

  14. Strongly enhanced field-dependent single-molecule electroluminescence.

    PubMed

    Lee, Tae-Hee; Gonzalez, Jose I; Dickson, Robert M

    2002-08-01

    Individual, strongly electroluminescent Ag(n) molecules (n = 2 approximately 8 atoms) have been electrically written within otherwise nonemissive silver oxide films. Exhibiting characteristic single-molecule behavior, these individual room-temperature molecules exhibit extreme electroluminescence enhancements (>10(4) vs. bulk and dc excitation on a per molecule basis) when excited with specific ac frequencies. Occurring through field extraction of electrons with subsequent reinjection and radiative recombination, single-molecule electroluminescence is enhanced by a general mechanism that avoids slow bulk material response. Thus, while we detail strong electroluminescence from single, highly fluorescent Ag(n) molecules, this mechanism also yields strong ac-excited electroluminescence from similarly prepared, but otherwise nonemissive, individual Cu nanoclusters. PMID:12149468

  15. Manipulating Kondo Temperature via Single Molecule Switching

    E-print Network

    Hla, Saw-Wai

    Manipulating Kondo Temperature via Single Molecule Switching Violeta Iancu, Aparna Deshpande the Cu(111) substrate can cause a Kondo resonance. Tunneling spectroscopy data reveal that switching from Kondo temperature from 130 to 170 K. This result demonstrates that the Kondo temperature can

  16. Manipulating, Reacting, and Constructing Single Molecules

    E-print Network

    Hla, Saw-Wai

    Manipulating, Reacting, and Constructing Single Molecules with a Scanning Tunneling Microscope Tip. The fascinating advances in atom and molecule manipulation with the scanning tunneling microscope (STM) tip allow in nanoscience and technology. The STM manipulation techniques use- ful in the molecular construction

  17. Multiplexed single-molecule assay for

    E-print Network

    Xie, Xiaoliang Sunney

    -antidigoxigenin Biotin Streptavidin Biotin-PEG Primer Increasing extension Flow force Conical lens Field stop Flow cell NA 0.45 BS L4L3 M1 L2 L1 CCD Iris Diffuser L6 L5 M2 Microscope a b c Figure 1 | Single-molecule assay

  18. Single Molecule Approaches for Two Dimensional Nanostructures

    NASA Astrophysics Data System (ADS)

    Baker, Thomas; Guo, Shajun; Koh, Weon-Kyu; Makarov, Nikolay; Fiddler, Andrew; Robel, Istvan; Klimov, Victor

    2014-03-01

    A variety of two dimensional semiconductor nanostructures have been synthesized recently by a number of different groups. Of these, nanoplatelets made of a single to few layers of material have shown interesting promise due to confinement in only a single direction. The photophysics of these types of structures show large exciton binding energies and narrow emission widths in ensemble measurements. Only a few single molecule experiments have been reported in the literature and we hope to expand the insights that single molecule techniques can provide in the understanding of these new materials. Our group has recently extended our synthetic expertise gained from quantum dots into these 2D nanoplatelets including CdSe, MoS2 and graphene. Time correlated single photon counting experiments at the single molecule level provide information on the homogenous linewidths, quantum yield variations, and fluorescence lifetimes. Furthermore, two photon correlations at zero time delay allow us to confirm the single molecule nature of the emission and potentially determine biexciton quantum yields and lifetimes.

  19. Single molecule microscopy using focal plane illumination

    Microsoft Academic Search

    Jörg Ritter; Werner Wendler; Ulrich Kubitscheck

    Single molecule fluorescence microscopy performed in spatially extended samples such as living cells usually suffers from a high fluorescence background. To overcome this problem we used a selective focal plane illumination instead of the conventional epi-illumination. By means of a custom made cylindrical lens system (NA 0.33) we created a light sheet with a Rayleigh length of 37 µm, a

  20. Single Molecule Raman Spectroscopy Under High Pressure

    NASA Astrophysics Data System (ADS)

    Fu, Yuanxi; Dlott, Dana

    2014-06-01

    Pressure effects on surface-enhanced Raman scattering spectra of Rhdoamine 6G adsorbed on silver nanoparticle surfaces was studied using a confocal Raman microscope. Colloidal silver nanoparticles were treated with Rhodamine 6G (R6G) and its isotopically substituted partner, R6G-d4. Mixed isotopomers let us identify single-molecule spectra, since multiple-molecule spectra would show vibrational transitions from both species. The nanoparticles were embedded into a poly vinyl alcohol film, and loaded into a diamond anvil cell for the high-pressure Raman scattering measurement. Argon was the pressure medium. Ambient pressure Raman scattering spectra showed few single-molecule spectra. At moderately high pressure ( 1GPa), a surprising effect was observed. The number of sites with observable spectra decreased dramatically, and most of the spectra that could be observed were due to single molecules. The effects of high pressure suppressed the multiple-molecule Raman sites, leaving only the single-molecule sites to be observed.

  1. Investigation of interfacial structures of plasma transferred arc deposited aluminium based composites by transmission electron microscopy

    SciTech Connect

    Deuis, R.L.; Subramanian, C. [Univ. of South Australia, South Australia (Australia). Ian Wark Research Inst.] [Univ. of South Australia, South Australia (Australia). Ian Wark Research Inst.; Bee, J.V. [Univ. of Adelaide, South Australia (Australia). Dept. of Mechanical Engineering] [Univ. of Adelaide, South Australia (Australia). Dept. of Mechanical Engineering

    1997-09-15

    The aim of the present work was to study the interfacial structure and associated microstructural features of three different aluminium based composites. For each composite, the nature of the interfacial structure was examined by transmission electron microscopy (TEM) and correlated to its corrosion and tribological behavior. The nature of the interfacial structures observed by this TEM investigation also help explain the variation in each composite`s tribological behavior. Generally, composites reinforced with TiC or SiC particles exhibited a lower wear rate compared to Al{sub 2}O{sub 3} containing composites. This improvement in wear rate, in part could be attributed to a better interfacial bond whether achieved by a high dislocation density at the interface or by the presence of an interfacial reaction zone. However, other factors such as reinforcement fracture toughness and morphology also play an important role in resistance to wear.

  2. Interplay between magnetic anisotropy and vibron-assisted tunneling in a single-molecule magnet transistor

    NASA Astrophysics Data System (ADS)

    Park, Kyungwha; McCaskey, Alexander; Yamamoto, Yoh; Warnock, Michael; Burzuri, Enrique; van der Zant, Herre

    2015-03-01

    Molecules trapped in single-molecule devices vibrate with discrete frequencies characteristic to the molecules, and the molecular vibrations can couple to electronic charge and/or spin degrees of freedom. For a significant electron-vibron coupling, electrons may tunnel via the vibrational excitations unique to the molecules. Recently, electron transport via individual anisotropic magnetic molecules (referred to as single-molecule magnets) has been observed in single-molecule transistors. A single-molecule magnet has a large spin moment and a large magnetic anisotropy barrier. So far, studies of electron-vibron coupling effects in single-molecule devices, are mainly for isotropic molecules. Here we investigate how the electron-vibron coupling influences electron transport via a single-molecule magnet Fe4, by using a model Hamiltonian with parameter values obtained from density-functional theory (arXiv:1411.2677). We show that the magnetic anisotropy of the Fe4 induces new features in vibrational conductance peaks and creates vibrational satellite peaks. The main and satellite peak heights have a strong, unusual dependence on the direction and magnitude of applied magnetic field, because the magnetic anisotropy barrier is comparable to vibrational energies. Funding from NSF DMR-1206354, EU FP7 program project 618082 ACMOL, advanced ERC grant (Mols@Mols). Computer resources from SDSC Trestles under DMR060009N and VT ARC.

  3. Observation of Franck-Condon Blockade in Single Molecules Gated by Local Electric Field

    NASA Astrophysics Data System (ADS)

    Zhao, Aidi; Zhou, Chunsheng; Wang, Weiyi; Tian, Guangjun; Shan, Huan; Lei, Shulai; Zhao, Yingbo; Luo, Yi; Li, Qunxiang; Wang, Bing; Hou, J. G.

    2015-03-01

    Electron transport through single molecules is greatly influenced by a discrete spectrum of vibrational modes in strong electron-vibron coupling regime. Theory predicts a current suppression at low biases known as Franck-Condon blockade. However, how Franck-Condon blockade emerges in in a real orbital-gated single molecule transistor is still elusive. In this study, by using a low-temperature scanning tunneling microscope, we report the real-space observation of Franck-Condon blockade in single molecules adsorbed on metal surfaces. The frontier molecular orbitals and charge state of the molecules are shown to be electrostatically gated by variation in the underlying surface potential and local chemical environment, allowing the observation of coulomb blockade as well as the Franck-Condon blockade. Moreover, strongly enhanced inelastic cotunneling is evidenced to dominate the electron transport in the Franck-Condon blockade regime, leading to unprecedented high-contrast single molecule vibrational spectroscopy and microscopy.

  4. Effects of interfacial properties on the ductility of polymer-supported metal films for flexible electronics

    Microsoft Academic Search

    W. Xu; T. J. Lu; F. Wang

    2010-01-01

    Polymer-supported metal films as interconnects for flexible, large area electronics may rupture when they are stretched, and the rupture strain is strongly dependent upon the film\\/substrate interfacial properties. This paper investigates the influence of interfacial properties on the ductility of polymer-supported metal films by modeling the microstructure of the metal film as well as the film\\/substrate interface using the method

  5. Single molecule transcription profiling with AFM*

    PubMed Central

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

    2009-01-01

    Established techniques for global gene expression profiling, such as microarrays, face fundamental sensitivity constraints. Due to greatly increasing interest in examining minute samples from micro-dissected tissues, including single cells, unorthodox approaches, including molecular nanotechnologies, are being explored in this application. Here, we examine the use of single molecule, ordered restriction mapping, combined with AFM, to measure gene transcription levels from very low abundance samples. We frame the problem mathematically, using coding theory, and present an analysis of the critical error sources that may serve as a guide to designing future studies. We follow with experiments detailing the construction of high density, single molecule, ordered restriction maps from plasmids and from cDNA molecules, using two different enzymes, a result not previously reported. We discuss these results in the context of our calculations. PMID:20721301

  6. Detection of single molecules in microspheres

    SciTech Connect

    Barnes, M.D.; Whitten, W.B.; Ramsey, J.M. [Oak Ridge National Lab., TN (United States); Ng, K.C. [California State Univ., Fresno, CA (United States). Dept. of Chemistry; Arnold, S. [Polytechnic Inst. of Brooklyn, NY (United States). Microparticle Photophysics Lab.

    1993-07-01

    We have investigated the use of micron-sized liquid droplets as sample medium to detect single fluorescent molecules in solution. The use of microdroplets (5--15 {mu}m diameter) offers several powerful advantages over single-molecule detection schemes involving measurements on bulk liquids where the probe volume is defined by the laser beam. In addition, cavity-quantum electrodynamical (QED) effects have been observed which influence both spontaneous emission rates and fluorescence yields of dye molecules in these microspheres.

  7. Lanthanide single molecule magnets: progress and perspective.

    PubMed

    Zhang, Peng; Zhang, Li; Tang, Jinkui

    2015-03-01

    The last few years have seen a huge renaissance in the study of single molecule magnets (SMMs) thanks to the extensive applications of lanthanide ions with large inherent anisotropy in molecular magnetism. Particularly, the recent theoretical developments and the experimental expansion into the organometallic avenue have led to an eye-catching boost in this field. Here we highlight the recent progress in this fascinating and challenging field, with emphasis on several combined experimental and theoretical studies. PMID:25641200

  8. Single-Molecule Biomechanics with Optical Methods

    Microsoft Academic Search

    Amit D. Mehta; Matthias Rief; James A. Spudich; David A. Smith; Robert M. Simmons

    1999-01-01

    duce active movement against load (forexample, "molecular motors" such as myosin,which drives muscle contraction). Anumber of "molecular machines" (for instance,DNA-processing enzymes) are nowaccessible to single-molecule observation andmanipulation. Among other obvious targetswere more passive molecules (such asbiopolymers) that respond to an applied forcein various ways. This field was initially developedby work on DNA, but more recently,it has been extended to structural...

  9. Laser-Assisted Single Molecule Refolding

    NASA Astrophysics Data System (ADS)

    Zhao, Rui; Marshall, Myles; Aleman, Elvin; Lamichhane, Rajan; Rueda, David

    2010-03-01

    In vivo, many RNA molecules can adopt multiple conformations depending on their biological context such as the HIV Dimerization Initiation Sequence (DIS) or the DsrA RNA in bacteria. It is quite common that the initial interaction between the two RNAs takes place via complementary unpaired regions, thus forming a so-called kissing complex. However, the exact kinetic mechanism by which the two RNA molecules reach the dimerized state is still not well understood. To investigate the refolding energy surface of RNA molecules, we have developed new technology based on the combination of single molecule spectroscopy with laser induced temperature jump kinetics, called Laser Assisted Single-molecule Refolding (LASR). LASR enables us to induce folding reactions of otherwise kinetically trapped RNAs at the single molecule level, and to characterize their folding landscape. LASR provides an exciting new approach to study molecular memory effects and kinetically trapped RNAs in general. LASR should be readily applicable to study DNA and protein folding as well.

  10. Promising anchoring groups for single-molecule conductance measurements.

    PubMed

    Kaliginedi, Veerabhadrarao; Rudnev, Alexander V; Moreno-García, Pavel; Baghernejad, Masoud; Huang, Cancan; Hong, Wenjing; Wandlowski, Thomas

    2014-11-21

    The understanding of the charge transport through single molecule junctions is a prerequisite for the design and building of electronic circuits based on single molecule junctions. However, reliable and robust formation of such junctions is a challenging task to achieve. In this topical review, we present a systematic investigation of the anchoring group effect on single molecule junction conductance by employing two complementary techniques, namely scanning tunneling microscopy break junction (STM-BJ) and mechanically controllable break junction (MCBJ) techniques, based on the studies published in the literature and important results from our own work. We compared conductance studies for conventional anchoring groups described earlier with the molecular junctions formed through ?-interactions with the electrode surface (Au, Pt, Ag) and we also summarized recent developments in the formation of highly conducting covalent Au-C ?-bonds using oligophenyleneethynylene (OPE) and an alkane molecular backbone. Specifically, we focus on the electron transport properties of diaryloligoyne, oligophenyleneethynylene (OPE) and/or alkane molecular junctions composed of several traditional anchoring groups, (dihydrobenzo[b]thiophene (BT), 5-benzothienyl analogue (BTh), thiol (SH), pyridyl (PY), amine (NH2), cyano (CN), methyl sulphide (SMe), nitro (NO2)) and other anchoring groups at the solid/liquid interface. The qualitative and quantitative comparison of the results obtained with different anchoring groups reveals structural and mechanistic details of the different types of single molecular junctions. The results reported in this prospective may serve as a guideline for the design and synthesis of molecular systems to be used in molecule-based electronic devices. PMID:25285778

  11. Theoretical investigation on single-molecule chiroptical spectroscopy

    SciTech Connect

    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.

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

    NASA Astrophysics Data System (ADS)

    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 lengths but different energy barrier profiles in order to elucidate electron transport in the molecular junctions. Kiguchi and Murakoshi study metallic atomic wires under electrochemical potential control. Asai reports on a theoretical study of rectification in substituted atomic wires. Finally, Weiss et al report on a new method to pattern and functionalize oxide-free germanium surfaces with self-assembled organic monolayers, which provides interfaces between inorganic semiconductors and organic molecules. Nanoelectronics, sensors and single molecule biophysics contents Biochemistry and semiconductor electronics—the next big hit for silicon?Stuart Lindsay Electrical detection of single pollen allergen particles using electrode-embedded microchannelsChihiro Kawaguchi, Tetsuya Noda, Makusu Tsutsui, Masateru Taniguchi, Satoyuki Kawano and Tomoji Kawai Quasi 3D imaging of DNA-gold nanoparticle tetrahedral structuresAvigail Stern, Dvir Rotem, Inna Popov and Danny Porath Effects of cytosine methylation on DNA charge transportJoshua Hihath, Shaoyin Guo, Peiming Zhang and Nongjian Tao Effect of electrostatics on aggregation of prion protein Sup35 peptideAlexander M Portillo, Alexey V Krasnoslobodtsev and Yuri L Lyubchenko Mapping the intracellular distribution of carbon nanotubes after targeted delivery to carcinoma cells using confocal Raman imaging as a label-free techniqueC Lamprecht, N Gierlinger, E Heister, B Unterauer, B Plochberger, M Brameshuber, P Hinterdorfer, S Hild and A Ebner Caveolae-mediated endocytosis of biocompatible gold nanoparticles in living Hela cellsXian Hao, Jiazhen Wu, Yuping Shan, Mingjun Cai, Xin Shang, Junguang Jiang and Hongda Wang Stability of an aqueous quadrupole micro-trapJae Hyun Park and Predrag S Krsti? Electron transport properties of single molecular junctions under mechanical modulationsJianfeng Zhou, Cunlan Guo and Bingqian Xu An approach to measure electromechanical properties of atomic and molecular junctionsIlya V Pobelov, Gábor Mészáros, Koji Yoshida, Artem Mishchenko, Murat Gulcur, Martin R Bryce and Thomas Wandlowski S

  13. Absorption and fluorescence of single molecules.

    PubMed

    Butter, J Y P; Hecht, B; Crenshaw, B R; Weder, C

    2006-10-21

    Simultaneous detection of single molecules by absorption and fluorescence is demonstrated using confocal microscopy at cryogenic temperature. Dynamical processes such as blinking and spectral jumping of single emitters are observed in both detection channels. The relative magnitude of fluorescence and absorption varies between molecules. In particular, we observe molecules that do not emit detectable Stokes-shifted fluorescence but show a strong absorption signal. The fact that coherent resonant scattering underlies the absorption process is demonstrated by a correlation between small linewidth and large absorption amplitude. PMID:17059286

  14. Hidden Markov Modelling of Single Molecule FRET Trajectories

    E-print Network

    Goldschmidt, Christina

    Hidden Markov Modelling of Single Molecule FRET Trajectories Life Sciences Interface DTC Short The development of single-molecule fluorescence energy transfer (FRET) microscopy has provided ground-by-eye. In this project, the application of Hidden Markov Modelling (HMM) for the anal- ysis of single-molecule FRET

  15. Cysteine engineering of polyproteins for single-molecule force spectroscopy

    E-print Network

    Dietz, Hendrik

    Cysteine engineering of polyproteins for single- molecule force spectroscopy Hendrik Dietz, Morten:10.1038/nprot.2006.12 Single-molecule methods such as force spectroscopy give experimental access understanding of enzyme activity and molecular motors1. Only recently, single-molecule methods like atomic force

  16. Interlaced Optical Force-Fluorescence Measurements for Single Molecule Biophysics

    E-print Network

    Lang, Matthew

    Interlaced Optical Force-Fluorescence Measurements for Single Molecule Biophysics Ricardo R. Brau that this scheme, interlaced optical force-fluorescence, does not compromise the trap stiffness or single molecule widely adopted for exploration of the effects of mechanical forces on single molecule systems (4

  17. Interfacial electron dynamics and hot-electron-driven surface photochemistry of carbon tetrachloride on Ag(111)

    SciTech Connect

    Ryu, Sunmin; Chang, Jinyoung; Kim, Seong Keun [School of Chemistry, Seoul National University, Seoul 151-747 (Korea, Republic of)

    2005-09-15

    We used time-resolved two-photon photoemission (2PPE) spectroscopy to investigate the photochemical behavior, the interfacial electronic structure, and the fate of photogenerated hot electron for carbon tetrachloride adsorbed on Ag(111). The photodissociation cross section was determined over a wide range of photon energy from 1.62 to 5.69 eV, which suggested a low-lying electron affinity level of adsorbed CCl{sub 4}. A CCl{sub 4}-derived unoccupied state located at 3.41 eV above the Fermi level was attributed to an image potential (IP) state based on its binding energy and effective mass. Polarization dependence of the 2PPE signal revealed that the IP state was populated by an indirect excitation process involving scattering of photoexcited hot electrons rather than direct electronic transition from a bulk band. The lifetime of the IP state was much shorter on the CCl{sub 4}-covered Ag(111) surface than on the clean one, implying that the electron in the IP state is scavenged effectively by CCl{sub 4}, probably through dissociative attachment to it. These results are significant in the sense that they provide dynamical evidence for a new relaxation pathway of the IP state in addition to the more common pathway involving back transfer of electron to the substrate.

  18. High throughput single molecule detection for monitoring biochemical reactions.

    PubMed

    Okagbare, Paul I; Soper, Steven A

    2009-01-01

    The design, performance and application of a novel optical system for high throughput single molecule detection (SMD) configured in a continuous flow format using microfluidics is reported. The system consisted of a microfabricated polymer-based multi-channel fluidic network situated within the optical path of a laser source (lambda(ex) = 660 nm) with photon transduction accomplished using an electron-multiplying charge coupled device (EMCCD) operated in a frame transfer mode that allowed tracking single molecules as they passed through a large field-of-view (FoV) illumination zone. The microfluidic device consisted of 30 microchannels possessing dimensions of 30 microm (width) x 20 microm (depth) with a 25 microm pitch. Individual molecules were electrokinetically driven through the fluidic network and excited within the wide-field illumination area with the resulting fluorescence collected via an objective and imaged onto the EMCCD camera. The detection system demonstrated sufficient sensitivity to detect single DNA molecules labeled with a fluorescent tag (AlexaFluor 660) identified through their characteristic emission wavelength and the burst of photons produced during their transit through the excitation volume. In its present configuration and fluidic architecture, the sample processing throughput was approximately 4.02 x 10(5) molecules s(-1), but could be increased dramatically through the use of narrower channels and a smaller pitch. The system was further evaluated using a single molecule-based fluorescence quenching assay for measuring the population differences between duplexed and single-stranded DNA molecules as a function of temperature for determining the duplex melting temperature, T(m). PMID:19082181

  19. Charge Transport in Azobenzene-Based Single-Molecule Junctions

    NASA Astrophysics Data System (ADS)

    Kim, Youngsang; Garcia-Lekue, Aran; Sysoiev, Dmytro; Frederiksen, Thomas; Groth, Ulrich; Scheer, Elke

    2012-11-01

    Azobenzene-derivative molecules change their conformation as a result of a cis-trans transition when exposed to ultraviolet or visible light irradiation and this is expected to induce a significant variation in the conductance of molecular devices. Despite extensive investigations carried out on this type of molecule, a detailed understanding of the charge transport for the two isomers is still lacking. We report a combined experimental and theoretical analysis of electron transport through azobenzene-derivative single-molecule break junctions with Au electrodes. Current-voltage and inelastic electron tunneling spectroscopy (IETS) measurements performed at 4.2 K are interpreted based on first-principles calculations of electron transmission and IETS spectra. This qualitative study unravels the origin of a slightly higher conductance of junctions with the cis isomer and demonstrates that IETS spectra of cis and trans forms show distinct vibrational fingerprints that can be used for identifying the isomer.

  20. Combining nanofluidics and plasmonics for single molecule detection

    NASA Astrophysics Data System (ADS)

    West, Melanie M.

    Single molecule detection is limited by the small scattering cross-section of molecules which leads to weak optical signals that can be obscured by background noise. The combination of plasmonics and nanofluidics in an integrated nano-device has the potential to provide the signal enhancement necessary for the detection of single molecules. The purpose of this investigation was to optimize the fabrication of an optofluidic device that integrates a nanochannel with a plasmonic bowtie antenna. The fluidic structure of the device was fabricated using UV-nanoimprint lithography, and the gold plasmonic antennas were fabricated using a shadow evaporation and lift-off process. The effect of electron beam lithography doses on the resolution of antenna-nanochannel configurations was studied to minimize antenna gap size while maintaining the integrity of the imprinted features. The smallest antenna gap size that was achieved was 46 nm. The antennas were characterized using dark field spectroscopy to find the resonance shift, which indicated the appropriate range for optical signal enhancement. The dark field scattering results showed antennas with a broad and well-defined resonance shift that ranged from 650--800 nm. The Raman scattering results showed the highest enhancement factor (EF = 2) for antennas with an "inverted configuration," which involved having the triangles of the antenna facing back-to-back rather than the more conventional tip-to-tip bowtie arrangement.

  1. Single Molecule Lifetime Studies of Small Clusters of Semiconductor Nanocrystals

    NASA Astrophysics Data System (ADS)

    Shepherd, Douglas; Whitcomb, Kevin; Goodwin, Peter; Gelfand, Martin; van Orden, Alan

    2009-10-01

    Enhanced fluorescence intermittency has been reported in single molecule fluorescence experiments on small clusters of semiconductor nanocrystals^1, and single Mn^2+ doped semiconductor nanocrystals^2. This behavior is attributed to electronic coupling between nanocrystals in the clusters. We report here on further studies of small clusters of semiconductor nanocrystals utilizing single molecule time-correlated single photon counting, which provides insight into the nature of the coupling. According to this analysis, clusters typically blink on a microsecond to millisecond time scale; whereas, isolated nanocrystals blink on much longer millisecond to second time scale. 1. Yu, M. and A. Van Orden, Enhanced Fluorescence Intermittency of CdSe-ZnS Quantum-Dot Clusters. Physical Review Letters, 2006. 97(23): p. 237402-4 2. Yanpeng Zhang, C.G., Javed Muhammad, David Battaglia, Xiaogang Peng and Min Xiao, Enhanced Fluorescence Intermittency in Mn-Doped Single ZnSe Quantum Dots. Journal of Physical Chemistry C, 2008. 112(51): p. 20200-20205

  2. Probing single molecule vibrations with the inelastic resonant tunneling

    NASA Astrophysics Data System (ADS)

    Sergueev, Nikolai

    2007-03-01

    Inelastic electron tunneling spectroscopy (IETS) has proven to be a valuable and powerful technique allowing identification and analysis of single molecular vibrations including those inaccessible by traditional optics measurements such as Raman and IR spectroscopies. Combined with scanning tunneling microscopy (STM) it provides a single molecule resolution. However, a comprehensive theoretical description of the electron coupling with molecular vibrations and the role it plays in conductance still remain a challenging problem. In this talk we present the first principles theory of the inelastic electron tunneling spectroscopy. Our method is based on density functional theory within Keldysh nonequilibrium Green's function formalism and allows us to treat electrons and molecular vibrations (phonons) on equal footing while computing electronic and vibrational spectrum, electron-phonon coupling, elastic and inelastic current in molecular electronic devices. The salient feature of our theory is that phonon effects on the electronic Hamiltonian are included in a self-consistent manner. Using this approach we investigate the effect of molecular vibrations on quantum transport through a C60 molecule contacted by two metallic electrodes. We demonstrate that its transport properties undergo significant changes when molecular vibrations are taken into account and show that this effect mostly originates from the resonance nature of the quantum tunneling which is expected to be true for the vast majority of the metallic electrodes. We also report a vibrational spectroscopy analysis and report those vibrational modes that contribute most to the inelastic quantum tunneling.

  3. Theory of femtosecond coherent double-pump single-molecule spectroscopy: Application to light harvesting complexes

    NASA Astrophysics Data System (ADS)

    Chen, Lipeng; Gelin, Maxim F.; Domcke, Wolfgang; Zhao, Yang

    2015-04-01

    We develop a first principles theoretical description of femtosecond double-pump single-molecule signals of molecular aggregates. We incorporate all singly excited electronic states and vibrational modes with significant exciton-phonon coupling into a system Hamiltonian and treat the ensuing system dynamics within the Davydov D1 Ansatz. The remaining intra- and inter-molecular vibrational modes are treated as a heat bath and their effect is accounted for through lineshape functions. We apply our theory to simulate single-molecule signals of the light harvesting complex II. The calculated signals exhibit pronounced oscillations of mixed electron-vibrational (vibronic) origin. Their periods decrease with decreasing exciton-phonon coupling.

  4. n and p type character of single molecule diodes

    PubMed Central

    Zoldan, Vinícius Claudio; Faccio, Ricardo; Pasa, André Avelino

    2015-01-01

    Looking for single molecule electronic devices, we have investigated the charge transport properties of individual tetra-phenylporphyrin molecules on different substrates by ultrahigh-vacuum scanning tunneling microscopy and spectroscopy and by first-principles calculations. The tetra-phenylporphyrins with a Co atom (Co-TPP) or 2 hydrogens (H2-TPP) in the central macrocycle when deposited on Cu3Au(100) substrates showed a diode-like behavior with p and n type character, respectively. After removing the central hydrogens of H2-TPP molecule with the STM tip an ohmic behavior was measured. The rectifying effect was understood from the theoretical point of view by assuming for Co-TPP HOMO conduction and for H2-TPP LUMO conduction, both selectively elected by the hybridization of states between molecule and substrate surface. PMID:25666850

  5. n and p type character of single molecule diodes

    NASA Astrophysics Data System (ADS)

    Zoldan, Vinícius Claudio; Faccio, Ricardo; Pasa, André Avelino

    2015-02-01

    Looking for single molecule electronic devices, we have investigated the charge transport properties of individual tetra-phenylporphyrin molecules on different substrates by ultrahigh-vacuum scanning tunneling microscopy and spectroscopy and by first-principles calculations. The tetra-phenylporphyrins with a Co atom (Co-TPP) or 2 hydrogens (H2-TPP) in the central macrocycle when deposited on Cu3Au(100) substrates showed a diode-like behavior with p and n type character, respectively. After removing the central hydrogens of H2-TPP molecule with the STM tip an ohmic behavior was measured. The rectifying effect was understood from the theoretical point of view by assuming for Co-TPP HOMO conduction and for H2-TPP LUMO conduction, both selectively elected by the hybridization of states between molecule and substrate surface.

  6. Charge Transport in Azobenzene-Based Single-Molecule Junctions

    NASA Astrophysics Data System (ADS)

    Garcia-Lekue, Aran; Kim, Youngsang; Sysoiev, Dmytro; Frederiksen, Thomas; Groth, Ulrich; Scheer, Elke

    2013-03-01

    The azobenzene class of molecules has become an archetype of molecular photoswitch research, due to their simple structure and the significant difference of the electronic system between their cis and trans isomers. However, a detailed understanding of the charge transport for the two isomers, when embedded in a junction with electrodes is still lacking. In order to clarify this issue, we investigate charge transport properties through single Azobenzene-ThioMethyl (AzoTM) molecules in a mechanically controlled break junction (MCBJ) system at 4.2 K. Single-molecule conductance, I-V characteristics, and IETS spectra of molecular junctions are measured and compared with first-principles transport calculations. Our studies elucidate the origin of a slightly higher conductance of junctions with cis isomer and demonstrate that IETS spectra of cis and trans forms show distinct vibrational fingerprints that can be used for identifying the isomer.

  7. n and p type character of single molecule diodes.

    PubMed

    Zoldan, Vinícius Claudio; Faccio, Ricardo; Pasa, André Avelino

    2015-01-01

    Looking for single molecule electronic devices, we have investigated the charge transport properties of individual tetra-phenylporphyrin molecules on different substrates by ultrahigh-vacuum scanning tunneling microscopy and spectroscopy and by first-principles calculations. The tetra-phenylporphyrins with a Co atom (Co-TPP) or 2 hydrogens (H2-TPP) in the central macrocycle when deposited on Cu3Au(100) substrates showed a diode-like behavior with p and n type character, respectively. After removing the central hydrogens of H2-TPP molecule with the STM tip an ohmic behavior was measured. The rectifying effect was understood from the theoretical point of view by assuming for Co-TPP HOMO conduction and for H2-TPP LUMO conduction, both selectively elected by the hybridization of states between molecule and substrate surface. PMID:25666850

  8. Microarray analysis at single molecule resolution

    PubMed Central

    Mure?an, Leila; Jacak, Jaros?aw; Klement, Erich Peter; Hesse, Jan; Schütz, Gerhard J.

    2010-01-01

    Bioanalytical chip-based assays have been enormously improved in sensitivity in the recent years; detection of trace amounts of substances down to the level of individual fluorescent molecules has become state of the art technology. The impact of such detection methods, however, has yet not fully been exploited, mainly due to a lack in appropriate mathematical tools for robust data analysis. One particular example relates to the analysis of microarray data. While classical microarray analysis works at resolutions of two to 20 micrometers and quantifies the abundance of target molecules by determining average pixel intensities, a novel high resolution approach [1] directly visualizes individual bound molecules as diffraction limited peaks. The now possible quantification via counting is less susceptible to labeling artifacts and background noise. We have developed an approach for the analysis of high-resolution microarray images. It consists first of a single molecule detection step, based on undecimated wavelet transforms, and second, of a spot identification step via spatial statistics approach (corresponding to the segmentation step in the classical microarray analysis). The detection method was tested on simulated images with a concentration range of 0.001 to 0.5 molecules per square micron and signal-to-noise ratio (SNR) between 0.9 and 31.6. For SNR above 15 the false negatives relative error was below 15%. Separation of foreground/background proved reliable, in case foreground density exceeds background by a factor of 2. The method has also been applied to real data from high-resolution microarray measurements. PMID:20123580

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

    PubMed Central

    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'. PMID:24565227

  10. Superconducting molybdenum-rhenium electrodes for single-molecule transport studies

    NASA Astrophysics Data System (ADS)

    Gaudenzi, R.; Island, J. O.; de Bruijckere, J.; Burzurí, E.; Klapwijk, T. M.; van der Zant, H. S. J.

    2015-06-01

    We demonstrate that electronic transport through single molecules or molecular ensembles, commonly based on gold (Au) electrodes, can be extended to superconducting electrodes by combining gold with molybdenum-rhenium (MoRe). This combination induces proximity-effect superconductivity in the gold to temperatures of at least 4.6 K and magnetic fields of 6 T, improving on previously reported aluminum based superconducting nanojunctions. As a proof of concept, we show three-terminal superconductive transport measurements through an individual Fe4 single-molecule magnet.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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. PMID:25106605

  13. Single-molecule nanocatalysis reveals heterogeneous reaction pathways and

    E-print Network

    Chen, Peng

    ARTICLES Single-molecule nanocatalysis reveals heterogeneous reaction pathways and catalytic in ensemble measurements. Using a single-nanoparticle single-turnover approach, we study the redox catalysis of individual colloidal Au nanoparticles in solution, using single-molecule detection of fluorogenic reactions

  14. Single-molecule spectroscopy and dynamics at room temperature

    SciTech Connect

    Xie, X.S. [Pacific Northwest National Lab., Richland, WA (United States)] [Pacific Northwest National Lab., Richland, WA (United States)

    1996-12-01

    The spirit of studying single-molecule behaviors dates back to the turn of the century. In addition to Einstein`s well-known work on Brownian motion, there has been a tradition for studying single {open_quotes}macromolecules{close_quotes} or a small number of molecules either by light scattering or by fluorescence using an optical microscope. Modern computers have allowed detailed studies of single-molecule behaviors in condensed media through molecular dynamics simulations. Optical spectroscopy offers a wealth of information on the structure, interaction, and dynamics of molecular species. With the motivation of removing {open_quotes}inhomogeneous broadening{close_quotes}, spectroscopic techniques have evolved from spectral hole burning, fluorescence line narrowing, and photo-echo to the recent pioneering work on single-molecule spectroscopy in solids at cryogenic temperatures. High-resolution spectroscopic work on single molecules relies on zero phonon lines which appear at cryogenic temperatures, and have narrow line widths and large absorption cross sections. Recent advances in near-field and confocal fluorescence have allowed not only fluorescence imaging of single molecules with high spatial resolutions but also single-molecule spectroscopy at room temperature. In this Account, the author provides a physical chemist`s perspective on experimental and theoretical developments on room-temperature single-molecule spectroscopy and dynamics, with the emphasis on the information obtainable from single-molecule experiments. 61 refs., 9 figs.

  15. Nucleosome disassembly intermediates characterized by single-molecule FRET

    E-print Network

    Langowski, Jörg

    Nucleosome disassembly intermediates characterized by single-molecule FRET Alexander Gansena,1 of mononucleosomes by quantitative single-molecule FRET with high spatial resolution, using the SELEX was induced by increasing NaCl concentration. At least 3 species with different FRET were identi- fied

  16. Single Molecule Microscopy and Hole-Burning Spectroscopy : Tools for

    E-print Network

    Schmidt, Thomas

    . A Study by Spectral Hole-Burning. 3.4Excited-State Dynamics of Mutated Antenna Complexes of PurpleSingle Molecule Microscopy and Hole-Burning Spectroscopy : Tools for the Study of Biological.2.1 Hole-Burning Spectroscopy 1.3 References Chapter 2 Single Molecule Microscopy 2.1Characterization

  17. Statistical Analysis of Single-Molecule AFM Force Spectroscopy Curves

    E-print Network

    Schmidler, Scott

    Statistical Analysis of Single-Molecule AFM Force Spectroscopy Curves Alexei Valiaev1 , Stefan from single-molecule force spectroscopy (SMFS) measurements. We apply this methodology to force observed that arise from force-induced changes in the secondary and tertiary conformation of the molecule

  18. Force and Velocity Measured for Single Molecules of RNA

    E-print Network

    Block, Steven

    Force and Velocity Measured for Single Molecules of RNA Polymerase Michelle D. Wang,* Mark J molecules of Escherichia coli RNAP were measured as progressively larger forces were applied by a feedback- force microscopy techniques capable of de- tecting movement by single molecules (2­4), and transcription

  19. Statistical Analysis of Single-Molecule AFM Force Spectroscopy Curves

    E-print Network

    Schmidler, Scott

    Statistical Analysis of Single-Molecule AFM Force Spectroscopy Curves Alexei Valiaev1,2 , Stefan-extension curves obtained from single-molecule force spectroscopy (SMFS) measurements. We apply this methodology. The force-extension curves of such molecules are often well described by statistical mechanical polymer

  20. Combined single-molecule force and fluorescence measurements for biology

    E-print Network

    Wallace, Mark

    Minireview Combined single-molecule force and fluorescence measurements for biology Mark I Wallace] carried out such an experiment using an optical trap to apply calibrated forces to a single DNA molecule Abstract Recent advances in single-molecule techniques allow the application of force to an individual

  1. Sorting Single Molecules: Application to Diagnostics and Evolutionary Biotechnology

    Microsoft Academic Search

    Manfred Eigen; Rudolf Rigler

    1994-01-01

    A method is described that provides for detection and identification of single molecules in solution. The method is based on fluoresence correlation spectroscopy, which recoords spatio-temporaal correlation among fluctuating light singles, coupled with devices for trapping single molecules in an electric field. This technique is applied to studies of molecular evolution, where it allows fast screening of large mutant spectra

  2. Interfacial Electron Transfer into Functionalized Crystalline Polyoxotitanate Nanoclusters

    E-print Network

    Coppens, Philip

    processes in a dye-sensitized solar cell. Theoretical simulations of the electron transfer of molecular adsorption are precisely defined. INTRODUCTION Dye-sensitized solar cells (DSSC) promise the dye sensitizer into the conduction band of the semiconductor substrate. Naturally, the interfaces

  3. Single Molecule Electrochemistry Fu-Ren F. Fan, Juhyoun Kwak, and Allen J. Bard*,

    E-print Network

    Kwak, Juhyoun

    by near- field scanning optical microscopy.4-8 Single-molecule detection (SMD) has also been achieved-molecule spectroscopy of molecules in solid matrices,2 the detection of individual dye molecules in solution by far-field communication,12 we reported SMD for an electroactive molecule in solution as it repeatedly undergoes electron

  4. Alkoxylated dehydrobenzo[12]annulene on Au(111): from single molecules to quantum dot molecular networks.

    PubMed

    Schouteden, Koen; Ivanova, Tsveta; Li, Zhe; Iancu, Violeta; Tahara, Kazukuni; Tobe, Yoshito; Adisoejoso, Jinne; De Feyter, Steven; Van Haesendonck, Chris; Janssens, Ewald

    2015-06-23

    We demonstrate the effective confinement of surface electrons in the pores of molecular networks formed by dehydrobenzo[12]annulene (DBA) molecules with butoxy groups (DBA-OC4) on Au(111). Investigation of the network formation starting from single molecules reveals a considerable interaction of the molecules with the substrate, which is at the origin of the observed confinement. PMID:26060847

  5. Negative differential conductance and super-Poissonian shot noise in single-molecule magnet junctions

    PubMed Central

    Xue, Hai-Bin; Liang, Jiu-Qing; Liu, Wu-Ming

    2015-01-01

    Molecular spintroinic device based on a single-molecule magnet is one of the ultimate goals of semiconductor nanofabrication technologies. It is thus necessary to understand the electron transport properties of a single-molecule magnet junction. Here we study the negative differential conductance and super-Poissonian shot noise properties of electron transport through a single-molecule magnet weakly coupled to two electrodes with either one or both of them being ferromagnetic. We predict that the negative differential conductance and super-Poissonian shot noise, which can be tuned by a gate voltage, depend sensitively on the spin polarization of the source and drain electrodes. In particular, the shot noise in the negative differential conductance region can be enhanced or decreased originating from the different formation mechanisms of negative differential conductance. The effective competition between fast and slow transport channels is responsible for the observed negative differential conductance and super-Poissonian shot noise. In addition, we further discuss the skewness and kurtosis properties of transport current in the super-Poissonian shot noise regions. Our findings suggest a tunable negative differential conductance molecular device, and the predicted properties of high-order current cumulants are very interesting for a better understanding of electron transport through single-molecule magnet junctions. PMID:25736094

  6. Single-molecule detection: applications to ultrasensitive biochemical analysis

    NASA Astrophysics Data System (ADS)

    Castro, Alonso; Shera, E. Brooks

    1995-06-01

    Recent developments in laser-based detection of fluorescent molecules have made possible the implementation of very sensitive techniques for biochemical analysis. We present and discuss our experiments on the applications of our recently developed technique of single-molecule detection to the analysis of molecules of biological interest. These newly developed methods are capable of detecting and identifying biomolecules at the single-molecule level of sensitivity. In one case, identification is based on measuring fluorescence brightness from single molecules. In another, molecules are classified by determining their electrophoretic velocities.

  7. New directions in single-molecule imaging and analysis

    PubMed Central

    Moerner, W. E.

    2007-01-01

    Optical imaging and analysis of single molecules continue to unfold as powerful ways to study the individual behavior of biological systems, unobscured by ensemble averaging. Current expansion of interest in this field is great, as evidenced by new meetings, journal special issues, and the large number of new investigators. Selected recent advances in biomolecular analysis are described, and two new research directions are summarized: superresolution imaging using single-molecule fluorescence and trapping of single molecules in solution by direct suppression of Brownian motion. PMID:17664434

  8. Reversible Aptamer-Au Plasmon Rulers for Secreted Single Molecules.

    PubMed

    Lee, Somin Eunice; Chen, Qian; Bhat, Ramray; Petkiewicz, Shayne; Smith, Jessica M; Ferry, Vivian E; Correia, Ana Luisa; Alivisatos, A Paul; Bissell, Mina J

    2015-07-01

    Plasmon rulers, consisting of pairs of gold nanoparticles, allow single-molecule analysis without photobleaching or blinking; however, current plasmon rulers are irreversible, restricting detection to only single events. Here, we present a reversible plasmon ruler, comprised of coupled gold nanoparticles linked by a single aptamer, capable of binding individual secreted molecules with high specificity. We show that the binding of target secreted molecules to the reversible plasmon ruler is characterized by single-molecule sensitivity, high specificity, and reversibility. Such reversible plasmon rulers should enable dynamic and adaptive live-cell measurement of secreted single molecules in their local microenvironment. PMID:26039492

  9. Single-molecule diodes with high rectification ratios through environmental control.

    PubMed

    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. PMID:26005998

  10. Single-molecule diodes with high rectification ratios through environmental control

    NASA Astrophysics Data System (ADS)

    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.

  11. Interfacial electron transfer dynamics of ru(II)-polypy6ridine sensitized TiO2

    SciTech Connect

    Jakubikova, Elena [Los Alamos National Laboratory; Martin, Richard L [Los Alamos National Laboratory; Batista, Enrique R [Los Alamos National Laboratory; Snoeberger, Robert C [YALE UNIV.; Batista, Victor S [YALE UNIV.

    2009-01-01

    Quantum dynamics simulations combined with density functional theory calculations are applied to study interfacial electron transfer (IET) from pyridine-4-phosphonic acid, [Ru(tpy)(tpy(PO{sub 3}H{sub 2}))]{sup 2+} and [Ru(tpy)(bpy)(H{sub 2}O)-Ru(tpy)(tpy(PO{sub 3}H{sub 2}))]{sup 4+} into the (101) surface of anatase TiO{sub 2}. IET rate from pyridine-4-phosphonic acid attached to the nanoparticle in bidentate mode ({tau} {approx} 100 fs) is an order of magnitude faster than the IET rate of the adsorbate attached in the monodentate mode ({tau} {approx} 1 ps). Upon excitation with visible light, [Ru(tpy)(tpy(PO{sub 3}H{sub 2}))]{sup 2+} attached to TiO{sub 2} in bidentate binding mode will undergo IET with the rate of {approx} 1-10 ps, which is competitive with the excited state decay into the ground state. The probability of electron injection from [Ru(tpy)(bpy)(H{sub 2}O)-Ru(tpy)(tpy(PO{sub 3}H{sub 2}))]{sup 4+} is rather low, as the excitation with visible light localizes the excited electron in the tpy-tpy bridge, which does not have favorable coupling with the TiO{sub 2} nanoparticle. The results are relevant to better understanding of the adsorbate features important for promoting efficient interfacial electron transfer into the semiconductor.

  12. Exploring the mechanome with optical tweezers and single molecule fluorescence

    E-print Network

    Brau, Ricardo R. (Ricardo Rafael), 1979-

    2008-01-01

    The combination of optical tweezers and single molecule fluorescence into an instrument capable of making combined, coincident measurements adds an observable dimension that allows for the examination of the localized ...

  13. Modeling and analysis of single-molecule experiments

    E-print Network

    Witkoskie, James B

    2005-01-01

    Single molecule experiments offer a unique window into the molecular world. This window allows us to distinguish the behaviors of individual molecules from the behavior of bulk by observing rare events and heterogeneity ...

  14. A practical guide to single-molecule FRET

    Microsoft Academic Search

    Rahul Roy; Sungchul Hohng; Taekjip Ha

    2008-01-01

    Single-molecule fluorescence resonance energy transfer (smFRET) is one of the most general and adaptable single-molecule techniques. Despite the explosive growth in the application of smFRET to answer biological questions in the last decade, the technique has been practiced mostly by biophysicists. We provide a practical guide to using smFRET, focusing on the study of immobilized molecules that allow measurements of

  15. An Improved Surface Passivation Method for Single-Molecule Studies

    PubMed Central

    Hua, Boyang; Young Han, Kyu; Zhou, Ruobo; Kim, Hajin; Shi, Xinghua; Abeysirigunawardena, Sanjaya C.; Jain, Ankur; Singh, Digvijay; Aggarwal, Vasudha; Woodson, Sarah A.; Ha, Taekjip

    2014-01-01

    We herein report a surface passivation method for in vitro single-molecule studies, which more efficiently prevents non-specific binding of biomolecules as compared to the polyethylene glycol surface. The new surface does not perturb the behavior and activities of tethered biomolecules. It can also be used for single-molecule imaging in the presence of high concentrations of labeled species in solution. Reduction in preparation time and cost is another major advantage. PMID:25306544

  16. Single-molecule fluorescence characterization in native environment

    Microsoft Academic Search

    Thomas P. Burghardt; Katalin Ajtai

    2010-01-01

    Single-molecule detection (SMD) with fluorescence is a widely used microscopic technique for biomolecule structure and function\\u000a characterization. The modern light microscope with high numerical aperture objective and sensitive CCD camera can image the\\u000a brightly emitting organic and fluorescent protein tags with reasonable time resolution. Single-molecule imaging gives an unambiguous\\u000a bottom-up biomolecule characterization that avoids the “missing information” problem characteristic of

  17. Nano\\/micro technologies for single molecule manipulation and detection

    Microsoft Academic Search

    Tza-huei Wang; Chih-ming Ho

    2003-01-01

    A sensitive, rapid, and efficient single-molecule detection method was developed by combining fluorescence correlation spectroscopy (FCS) and on-chip molecular manipulation techniques. The highly restricted measurement volume in the FCS system significantly reduces the intrinsic background noise and facilitates single-molecule sensitivity. A microchannel integrated with multiple 3-D electrodes was fabricated and used for molecular sensing and manipulation by which individual DNA

  18. Detailed single-molecule spectroelectrochemical studies of the oxidation of conjugated polymers.

    PubMed

    Palacios, Rodrigo E; Chang, Wei-Shun; Grey, John K; Chang, Ya-Lan; Miller, William L; Lu, Chun-Yaung; Henkelman, Graeme; Zepeda, Danny; Ferraris, John; Barbara, Paul F

    2009-11-01

    Single-particle fluorescence spectroelectrochemistry was used to investigate the electrochemical oxidation of isolated, immobilized particles of the conjugated polymers BEH-PPV and MEH-PPV at an indium tin oxide (ITO) electrode immersed in an electrolyte solution. Two types of particles were investigated: (i) polymer single molecules (SM) and (ii) nanoparticle (NP) aggregates of multiple polymer single molecules. For the BEH-PPV polymer, the observation of nearly identical lowest oxidation potentials for different SM in the ensemble is evidence for effective electrostatic screening by the surrounding electrolyte solution. A combination of Monte Carlo simulations and application of Poisson-Boltzmann solvers were used to model the charging of polymer single molecules and nanoparticles in the electrochemical environment. The results indicate that the penetration of electrolyte anions into the polymer nanoparticles is necessary to produce the observed narrow fluorescence quenching vs oxidation potential curves. Finally, fluorescence-lifetime single-molecule spectroelectrochemical (SMS-EC) data revealed that at low potential an excited state reduction process (i.e., electron transfer from ITO to the polymer) is probably the dominant fluorescence quenching process. PMID:19863138

  19. Inelastic transport and low-bias rectification in a single-molecule diode.

    PubMed

    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. PMID:21932824

  20. Kondo effects and interference in transport through single molecules

    NASA Astrophysics Data System (ADS)

    Paaske, Jens; Pedersen, Kim Georg Lind; Hedegaard, Per

    2015-03-01

    Quantum transport through single molecules or quantum dot arrays with spin-degenerate ground states can be dominated by Kondo effects at low temperatures. In contrast to the single impurity case, quantum interference plays a significant role in such `multi-orbital' systems and may have a strong influence on the possible Kondo physics: deciding between single- or multi-channel screening and even ferromagnetic Kondo effect. We investigate a range of smaller molecules with source, and drain electrodes attached in different specific contacting geometries. The interacting pi-electron system is treated by means of exact diagonalization, and combining with a perturbative treatment of molecule-lead tunnel couplings, we calculate the zero-bias cotunneling conductance as a function of a gate-voltage shifting the molecular levels. We show that interference nodes cannot occur simultaneously in potential, and exchange scattering terms, which means that interference causes no conductance nodes. Nevertheless, interference nodes in the exchange scattering term may lead to a non-standard gate dependence of the Kondo temperature, as indicated by experiments. We discuss the flow towards strong coupling and the possibilities for two-channel, and/or ferromagnetic Kondo effect.

  1. Enhanced Thermoelectric Performance of Hybrid Nanoparticle-Single-Molecule Junctions

    NASA Astrophysics Data System (ADS)

    Zerah-Harush, Elinor; Dubi, Yonatan

    2015-06-01

    It was recently suggested that molecular junctions would be excellent elements for efficient and high-power thermoelectric energy-conversion devices. However, experimental measurements of thermoelectric conversion in molecular junctions indicate rather poor efficiency, raising the question of whether it is indeed possible to design a setup for molecular junctions that will exhibit enhanced thermoelectric performance. Here we suggest that hybrid single-molecule-nanoparticle junctions can serve as efficient thermoelectric converters. The introduction of a semiconducting nanoparticle introduces new tuning capabilities, which are absent in conventional metal-molecule-metal junctions. Using a generic model for the molecule and nanoparticle with realistic parameters, we demonstrate that the thermopower can be of the order of hundreds of microvolts per degree kelvin and that the thermoelectric figure of merit can reach values close to 1, an improvement of 4 orders of magnitude over existing measurements. This favorable performance persists over a wide range of experimentally relevant parameters and is robust against disorder (in the form of surface-attached molecules) and against electron decoherence at the nanoparticle-molecule interface.

  2. An all-electric single-molecule motor.

    PubMed

    Seldenthuis, Johannes S; Prins, Ferry; Thijssen, Joseph M; van der Zant, Herre S J

    2010-11-23

    Many types of molecular motors have been proposed and synthesized in recent years, displaying different kinds of motion, and fueled by different driving forces such as light, heat, or chemical reactions. We propose a new type of molecular motor based on electric field actuation and electric current detection of the rotational motion of a molecular dipole embedded in a three-terminal single-molecule device. The key aspect of this all-electronic design is the conjugated backbone of the molecule, which simultaneously provides the potential landscape of the rotor orientation and a real-time measure of that orientation through the modulation of the conductivity. Using quantum chemistry calculations, we show that this approach provides full control over the speed and continuity of motion, thereby combining electrical and mechanical control at the molecular level over a wide range of temperatures. Moreover, chemistry can be used to change all key parameters of the device, enabling a variety of new experiments on molecular motors. PMID:20936795

  3. Radio Frequency Scanning Tunneling Spectroscopy for Single-Molecule Spin Resonance

    NASA Astrophysics Data System (ADS)

    Müllegger, Stefan; Tebi, Stefano; Das, Amal K.; Schöfberger, Wolfgang; Faschinger, Felix; Koch, Reinhold

    2014-09-01

    We probe nuclear and electron spins in a single molecule even beyond the electromagnetic dipole selection rules, at readily accessible magnetic fields (few mT) and temperatures (5 K) by resonant radio-frequency current from a scanning tunneling microscope. We achieve subnanometer spatial resolution combined with single-spin sensitivity, representing a 10 orders of magnitude improvement compared to existing magnetic resonance techniques. We demonstrate the successful resonant spectroscopy of the complete manifold of nuclear and electronic magnetic transitions of up to ?Iz=±3 and ?Jz=±12 of single quantum spins in a single molecule. Our method of resonant radio-frequency scanning tunneling spectroscopy offers, atom-by-atom, unprecedented analytical power and spin control with an impact on diverse fields of nanoscience and nanotechnology.

  4. Theory of femtosecond coherent double-pump single-molecule spectroscopy: Application to light harvesting complexes.

    PubMed

    Chen, Lipeng; Gelin, Maxim F; Domcke, Wolfgang; Zhao, Yang

    2015-04-28

    We develop a first principles theoretical description of femtosecond double-pump single-molecule signals of molecular aggregates. We incorporate all singly excited electronic states and vibrational modes with significant exciton-phonon coupling into a system Hamiltonian and treat the ensuing system dynamics within the Davydov D1 Ansatz. The remaining intra- and inter-molecular vibrational modes are treated as a heat bath and their effect is accounted for through lineshape functions. We apply our theory to simulate single-molecule signals of the light harvesting complex II. The calculated signals exhibit pronounced oscillations of mixed electron-vibrational (vibronic) origin. Their periods decrease with decreasing exciton-phonon coupling. PMID:25933751

  5. Radio frequency scanning tunneling spectroscopy for single-molecule spin resonance.

    PubMed

    Müllegger, Stefan; Tebi, Stefano; Das, Amal K; Schöfberger, Wolfgang; Faschinger, Felix; Koch, Reinhold

    2014-09-26

    We probe nuclear and electron spins in a single molecule even beyond the electromagnetic dipole selection rules, at readily accessible magnetic fields (few mT) and temperatures (5 K) by resonant radio-frequency current from a scanning tunneling microscope. We achieve subnanometer spatial resolution combined with single-spin sensitivity, representing a 10 orders of magnitude improvement compared to existing magnetic resonance techniques. We demonstrate the successful resonant spectroscopy of the complete manifold of nuclear and electronic magnetic transitions of up to ?I(z)=±3 and ?J(z)=±12 of single quantum spins in a single molecule. Our method of resonant radio-frequency scanning tunneling spectroscopy offers, atom-by-atom, unprecedented analytical power and spin control with an impact on diverse fields of nanoscience and nanotechnology. PMID:25302884

  6. Massively Parallel Single-Molecule Manipulation Using Centrifugal Force

    NASA Astrophysics Data System (ADS)

    Wong, Wesley; Halvorsen, Ken

    2011-03-01

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

  7. A Multi-State Single-Molecule Switch Actuated by Rotation of an Encapsulated Cluster within a Fullerene Cage

    SciTech Connect

    Huang, Tian; Zhao, Jin; Feng, Min; Popov, Alexey A.; Yang, Shangfeng; Dunsch, Lothar; Petek, Hrvoje

    2012-11-12

    We demonstrate a single-molecule switch based on tunneling electron-driven rotation of a triangular Sc?N cluster within an icosahedral C 80 fullerene cage among three pairs of enantiomorphic configura-tions. Scanning tunneling microscopy imaging of switching within single molecules and electronic structure theory identify the conformational isomers and their isomerization pathways. Bias-dependent actionspectra and modeling identify the antisymmetric stretch vibration of Sc 3N cluster to be the gateway for energy transfer from the tunneling electrons to the cluster rotation. Hierarchical switching of conductivity through the internal cluster motion among multiple stationary states while maintaining a constant shape, is advantageous for the integration of endohedral fullerene-based single-molecule memory and logic devices into parallel molecular computing arc.

  8. Fisher information for EMCCD imaging with application to single molecule microscopy

    Microsoft Academic Search

    Jerry Chao; E. S. Ward; R. J. Ober

    2010-01-01

    Owing to its high quantum efficiency, the charge-coupled device (CCD) is an important imaging tool employed in biological applications such as single molecule microscopy. Under extremely low light conditions, however, a CCD is generally unsuitable because its readout noise can easily overwhelm the weak signal. Instead, an electron-multiplying charge-coupled device (EMCCD), which stochastically amplifies the acquired signal to drown out

  9. Conductance and Surface-Enhanced Raman Scattering of Single Molecules Utilizing Dimers of Nanoparticles

    NASA Astrophysics Data System (ADS)

    Dadosh, Tali

    In the past few years, the field of molecular electronics and in particular, the development of new techniques for contacting and measuring single molecules, has emerged, providing new insights into this field. The relatively small size of a molecule, typically of the order of 1 nm, requires innovative approaches in order to develop functioning single-molecule devices. The experimental methods currently used for single-molecule measurements provide little control over the number of molecules bridging the gap or the local electronic properties of the metal-molecule contact. In this thesis, a new approach for contacting a single molecule is presented that provides better control of these parameters. Our method is based on synthesizing a dimer structure consisting of two gold colloids connected by a thiol group to either side of the molecule. This structure is then positioned between two electrodes by electrostatic trapping and, thus, the conductance of the molecule can be measured. The fundamental questions addressed by the field of molecular electronics are as follows: "what is the conductivity of a junction containing an individual molecule and how is it affected by the molecule's specific structure?" We were able to shed some light on these questions by studying the electrical conduction through three short organic molecules that differ by their degree of conjugation. We will consider here a fully conjugated molecule, 4,4'-biphenyldithiol (BPD), Bis-(4-mercaptophenyl)-ether (BPE), in which the conjugation is broken at the center by an oxygen atom, and 1,4-benzenedimethanethiol (BDMT), where the conjugation is broken near the contacts by a methylene group. We found that the presence of localizing groups such as the oxygen in the BPE and the methylene groups in the BDMT suppresses the electrical conduction dramatically, relative to the conjugated molecule, BPD. A unique feature of the BPD molecule is the appearance of reproducible, pronounced peaks in its conductance at certain voltage values. The position of peaks in the spectrum was affected by the electrostatic environment, resulting in random gating. In view of the above developments, my thesis focuses on surface-enhanced Raman scattering (SERS) measurement of single molecules. Single-molecule spectroscopy is an emerging field that provides detailed information on molecular response, which is unavailable in measurements performed on an assembly of molecules. The obvious problem, however, in implementing most spectroscopic techniques, such as Raman scattering, is the very weak signal obtained from a single molecule. Interestingly, the Raman signal from a molecule has been shown to increase dramatically when the molecule is adsorbed to metal particles of certain types having sub-wavelength dimensions [1, 2]. This enhancement technique, known as surface-enhanced Raman scattering, can increase the Raman signal by as much as 14--15 orders of magnitude, which has been shown to be sufficient for performing single-molecule spectroscopy successfully. Dimer structures are not only attractive for conductance measurements on single-molecule devices; they could also serve as an efficient antenna system that greatly enhances the electromagnetic field at the center of the dimer, where the molecule resides. Dimers provide a basic experimental model for studying the fundamentals of the SERS enhancement, which are not well understood. Dimers have the advantage of possessing a small gap (on the order of a nanometer) that is beyond the limit of today's sophisticated lithography techniques. By utilizing the dimer structures that contain a Rhodamine 123 molecule, we were able to resolve some fundamental questions regarding the SERS enhancement mechanism. The issue of how the nanoparticles' surface plasmon properties affects the SERS enhancement was addressed both experimentally and by calculations. Moreover, it was predicted by our calculations that when the dimers consist of large nanoparticles, a non-uniform enhancement of the different molecular modes of Rhodamine 123 should o

  10. Single-molecule fluorescence characterization in native environment

    PubMed Central

    Ajtai, Katalin

    2010-01-01

    Single-molecule detection (SMD) with fluorescence is a widely used microscopic technique for biomolecule structure and function characterization. The modern light microscope with high numerical aperture objective and sensitive CCD camera can image the brightly emitting organic and fluorescent protein tags with reasonable time resolution. Single-molecule imaging gives an unambiguous bottom-up biomolecule characterization that avoids the “missing information” problem characteristic of ensemble measurements. It has circumvented the diffraction limit by facilitating single-particle localization to ~1 nm. Probes developed specifically for SMD applications extend the advantages of single-molecule imaging to high probe density regions of cells and tissues. These applications perform under conditions resembling the native biomolecule environment and have been used to detect both probe position and orientation. Native, high density SMD may have added significance if molecular crowding impacts native biomolecule behavior as expected inside the cell. PMID:21179385

  11. Tracking single molecules at work in living cells.

    PubMed

    Kusumi, Akihiro; Tsunoyama, Taka A; Hirosawa, Kohichiro M; Kasai, Rinshi S; Fujiwara, Takahiro K

    2014-07-01

    Methods for imaging and tracking single molecules conjugated with fluorescent probes, called single-molecule tracking (SMT), are now providing researchers with the unprecedented ability to directly observe molecular behaviors and interactions in living cells. Current SMT methods are achieving almost the ultimate spatial precision and time resolution for tracking single molecules, determined by the currently available dyes. In cells, various molecular interactions and reactions occur as stochastic and probabilistic processes. SMT provides an ideal way to directly track these processes by observing individual molecules at work in living cells, leading to totally new views of the biochemical and molecular processes used by cells whether in signal transduction, gene regulation or formation and disintegration of macromolecular complexes. Here we review SMT methods, summarize the recent results obtained by SMT, including related superresolution microscopy data, and describe the special concerns when SMT applications are shifted from the in vitro paradigms to living cells. PMID:24937070

  12. Analytical tools for single-molecule fluorescence imaging in cellulo

    E-print Network

    Leake, Mark

    2015-01-01

    Recent technological advances in cutting-edge ultrasensitive fluorescence microscopy have allowed single-molecule imaging experiments in living cells across all three domains of life to become commonplace. Single-molecule live-cell data is typically obtained in a low signal-to-noise ratio (SNR) regime sometimes only marginally in excess of 1, in which a combination of detector shot noise, sub-optimal probe photophysics, native cell autofluorescence and intrinsically underlying stochastic of molecules result in highly noisy datasets for which underlying true molecular behaviour is non-trivial to discern. The ability to elucidate real molecular phenomena is essential in relating experimental single-molecule observations to both the biological system under study as well as offering insight into the fine details of the physical and chemical environments of the living cell. To confront this problem of faithful signal extraction and analysis in a noise-dominated regime, the needle in a haystack challenge, such expe...

  13. Open-frame system for single-molecule microscopy

    NASA Astrophysics Data System (ADS)

    Arsenault, Adriel; Leith, Jason S.; Henkin, Gil; McFaul, Christopher M. J.; Tarling, Matthew; Talbot, Richard; Berard, Daniel; Michaud, Francois; Scott, Shane; Leslie, Sabrina R.

    2015-03-01

    We present the design and construction of a versatile, open frame inverted microscope system for wide-field fluorescence and single molecule imaging. The microscope chassis and modular design allow for customization, expansion, and experimental flexibility. We present two components which are included with the microscope which extend its basic capabilities and together create a powerful microscopy system: A Convex Lens-induced Confinement device provides the system with single-molecule imaging capabilities, and a two-color imaging system provides the option of imaging multiple molecular species simultaneously. The flexibility of the open-framed chassis combined with accessible single-molecule, multi-species imaging technology supports a wide range of new measurements in the health, nanotechnology, and materials science research sectors.

  14. The importance of surfaces in single-molecule bioscience

    PubMed Central

    Visnapuu, Mari-Liis; Duzdevich, Daniel

    2011-01-01

    The last ten years have witnessed an explosion of new techniques that can be used to probe the dynamic behavior of individual biological molecules, leading to discoveries that would not have been possible with more traditional biochemical methods. A common feature among these single-molecule approaches is the need for the biological molecules to be anchored to a solid support surface. This must be done under conditions that minimize nonspecific adsorption without compromising the biological integrity of the sample. In this review we highlight why surface attachments are a critical aspect of many single-molecule studies and we discuss current methods for anchoring biomolecules. Finally, we provide a detailed description of a new method developed by our laboratory for anchoring and organizing hundreds of individual DNA molecules on a surface, allowing “high-throughput” studies of protein–DNA interactions at the single-molecule level. PMID:18414737

  15. Detectors for single-molecule fluorescence imaging and spectroscopy

    PubMed Central

    MICHALET, X.; SIEGMUND, O.H.W.; VALLERGA, J.V.; JELINSKY, P.; MILLAUD, J.E.; WEISS, S.

    2010-01-01

    Single-molecule observation, characterization and manipulation techniques have recently come to the forefront of several research domains spanning chemistry, biology and physics. Due to the exquisite sensitivity, specificity, and unmasking of ensemble averaging, single-molecule fluorescence imaging and spectroscopy have become, in a short period of time, important tools in cell biology, biochemistry and biophysics. These methods led to new ways of thinking about biological processes such as viral infection, receptor diffusion and oligomerization, cellular signaling, protein-protein or protein-nucleic acid interactions, and molecular machines. Such achievements require a combination of several factors to be met, among which detector sensitivity and bandwidth are crucial. We examine here the needed performance of photodetectors used in these types of experiments, the current state of the art for different categories of detectors, and actual and future developments of single-photon counting detectors for single-molecule imaging and spectroscopy. PMID:20157633

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

    SciTech Connect

    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.

  17. Bacterial translocation motors investigated by single molecule techniques.

    PubMed

    Allemand, Jean-Francois; Maier, Berenike

    2009-05-01

    Translocation of DNA and protein fibers through narrow constrictions is a ubiquitous and crucial activity of bacterial cells. Bacteria use specialized machines to support macromolecular movement. A very important step toward a mechanistic understanding of these translocation machines is the characterization of their physical properties at the single molecule level. Recently, four bacterial transport processes have been characterized by nanomanipulation at the single molecule level, DNA translocation by FtsK and SpoIIIE, DNA import during transformation, and the related process of a type IV pilus retraction. With all four processes, the translocation rates, processivity, and stalling forces were remarkably high as compared with single molecule experiments with other molecular motors. Although substrates of all four processes proceed along a preferential direction of translocation, directionality has been shown to be controlled by distinct mechanisms. PMID:19243443

  18. Application of Degenerately Doped Metal Oxides in the Study of Photoinduced Interfacial Electron Transfer.

    PubMed

    Farnum, Byron H; Morseth, Zachary A; Brennaman, M Kyle; Papanikolas, John M; Meyer, Thomas J

    2015-06-18

    Degenerately doped In2O3:Sn semiconductor nanoparticles (nanoITO) have been used to study the photoinduced interfacial electron-transfer reactivity of surface-bound [Ru(II)(bpy)2(4,4'-(PO3H2)2-bpy)](2+) (RuP(2+)) molecules as a function of driving force over a range of 1.8 eV. The metallic properties of the ITO nanoparticles, present within an interconnected mesoporous film, allowed for the driving force to be tuned by controlling their Fermi level with an external bias while their optical transparency allowed for transient absorption spectroscopy to be used to monitor electron-transfer kinetics. Photoinduced electron transfer from excited-state -RuP(2+*) molecules to nanoITO was found to be dependent on applied bias and competitive with nonradiative energy transfer to nanoITO. Back electron transfer from nanoITO to oxidized -RuP(3+) was also dependent on the applied bias but without complication from inter- or intraparticle electron diffusion in the oxide nanoparticles. Analysis of the electron injection kinetics as a function of driving force using Marcus-Gerischer theory resulted in an experimental estimate of the reorganization energy for the excited-state -RuP(3+/2+*) redox couple of ?* = 0.83 eV and an electronic coupling matrix element, arising from electronic wave function overlap between the donor orbital in the molecule and the acceptor orbital(s) in the nanoITO electrode, of Hab = 20-45 cm(-1). Similar analysis of the back electron-transfer kinetics yielded ? = 0.56 eV for the ground-state -RuP(3+/2+) redox couple and Hab = 2-4 cm(-1). The use of these wide band gap, degenerately doped materials provides a unique experimental approach for investigating single-site electron transfer at the surface of oxide nanoparticles. PMID:25668488

  19. Exploring one-state downhill protein folding in single molecules

    PubMed Central

    Liu, Jianwei; Campos, Luis A.; Cerminara, Michele; Wang, Xiang; Ramanathan, Ravishankar; English, Douglas S.; Muñoz, Victor

    2012-01-01

    A one-state downhill protein folding process is barrierless at all conditions, resulting in gradual melting of native structure that permits resolving folding mechanisms step-by-step at atomic resolution. Experimental studies of one-state downhill folding have typically focused on the thermal denaturation of proteins that fold near the speed limit (ca. 106 s-1) at their unfolding temperature, thus being several orders of magnitude too fast for current single-molecule methods, such as single-molecule FRET. An important open question is whether one-state downhill folding kinetics can be slowed down to make them accessible to single-molecule approaches without turning the protein into a conventional activated folder. Here we address this question on the small helical protein BBL, a paradigm of one-state downhill thermal (un)folding. We decreased 200-fold the BBL folding-unfolding rate by combining chemical denaturation and low temperature, and carried out free-diffusion single-molecule FRET experiments with 50-?s resolution and maximal photoprotection using a recently developed Trolox-cysteamine cocktail. These experiments revealed a single conformational ensemble at all denaturing conditions. The chemical unfolding of BBL was then manifested by the gradual change of this unique ensemble, which shifts from high to low FRET efficiency and becomes broader at increasing denaturant. Furthermore, using detailed quantitative analysis, we could rule out the possibility that the BBL single-molecule data are produced by partly overlapping folded and unfolded peaks. Thus, our results demonstrate the one-state downhill folding regime at the single-molecule level and highlight that this folding scenario is not necessarily associated with ultrafast kinetics. PMID:22184219

  20. Single molecule dissociation by tunneling electrons in NO-Co-Porphyrin complex on Au(111): A novel mechanics revealed by scanning tunneling spectroscopy and first-principles thermodynamic simulation

    NASA Astrophysics Data System (ADS)

    Chang, Yunhee; Kim, Howon; Lee, Eui-Sup; Jang, Won-Jun; Kim, Yong-Hyun; Kahng, Se-Jong

    2015-03-01

    To microscopically understand the mechanisms of electron-induced NO dissociations, we performed first-principles density-functional theory (DFT) calculations for NO-CoTPP on Au(111). We explain the scanning tunneling microscopy (STM) results that the dissociations of NO were induced by both positive and negative voltage pulses with threshold voltages, +0.68 V and 0.74 V, respectively, at 0.1 nA tunneling current, showing power law relations between tunneling current and dissociation yield. To evaluate first-principles thermodynamics of the NO dissociation, we considered not only adsorption-desorption energetics, zero-point energy, and vibrational free energy at experiment temperature from first-principles, but also the chemical potential of NO gas at the cryogenic ultra-high vacuum condition. Using first-principles thermodynamics for the NO dissociation, we argue that the dissociations are induced with inelastic electron tunneling through molecular orbital resonances.

  1. Magnetic trapping of single molecules: principles, developments, and applications

    NASA Astrophysics Data System (ADS)

    Grange, W.; Strick, T. R.

    2013-09-01

    Over the last decade, magnetic trapping has emerged as a tool which can complement the optical trap in certain key biophysical assays. Through its low cost, ease of use, stability and scalability, magnetic trapping is an attractive tool for micro-rheological analysis, generation of sorting structures for microfluidics, and also single-molecule experimentation. Here we will compare and contrast optical and magnetic trapping as they pertain to singlemolecule experimentation, and in particular to the study of interactions between single molecules such as proteins and nucleic acids.

  2. Single-Molecule and Superresolution Imaging in Live Bacteria Cells

    PubMed Central

    Biteen, Julie S.; Moerner, W.E.

    2010-01-01

    Single-molecule imaging enables biophysical measurements devoid of ensemble averaging, gives enhanced spatial resolution beyond the diffraction limit, and permits superresolution reconstructions. Here, single-molecule and superresolution imaging are applied to the study of proteins in live Caulobacter crescentus cells to illustrate the power of these methods in bacterial imaging. Based on these techniques, the diffusion coefficient and dynamics of the histidine protein kinase PleC, the localization behavior of the polar protein PopZ, and the treadmilling behavior and protein superstructure of the structural protein MreB are investigated with sub-40-nm spatial resolution, all in live cells. PMID:20300204

  3. Structural dynamics of nucleosomes at single-molecule resolution.

    PubMed

    Choy, John S; Lee, Tae-Hee

    2012-10-01

    The detailed mechanisms of how DNA that is assembled around a histone core can be accessed by DNA-binding proteins for transcription, replication, or repair, remain elusive nearly 40 years after Kornberg's nucleosome model was proposed. Uncovering the structural dynamics of nucleosomes is a crucial step in elucidating the mechanisms regulating genome accessibility. This requires the deconvolution of multiple structural states within an ensemble. Recent advances in single-molecule methods enable unprecedented efficiency in examining subpopulation dynamics. In this review, we summarize studies of nucleosome structure and dynamics from single-molecule approaches and how they advance our understanding of the mechanisms that govern DNA transactions. PMID:22831768

  4. Coherent manipulation and decoherence of s=10 single-molecule magnets.

    PubMed

    Takahashi, Susumu; van Tol, Johan; Beedle, Christopher C; Hendrickson, David N; Brunel, Louis-Claude; Sherwin, Mark S

    2009-02-27

    We report coherent manipulation of S=10 Fe8 single-molecule magnets. The temperature dependence of the spin decoherence time T2 measured by high-frequency pulsed electron paramagnetic resonance indicates that strong spin decoherence is dominated by Fe8 spin bath fluctuations. By polarizing the spin bath in Fe8 single-molecule magnets at magnetic field B=4.6 T and temperature T=1.3 K, spin decoherence is significantly suppressed and extends the spin decoherence time T2 to as long as 712 ns. A second decoherence source is likely due to fluctuations of the nuclear spin bath. This hints that the spin decoherence time can be further extended via isotopic substitution to smaller nuclear magnetic moments. PMID:19257788

  5. FISHER INFORMATION FOR EMCCD IMAGING WITH APPLICATION TO SINGLE MOLECULE MICROSCOPY.

    PubMed

    Chao, Jerry; Ward, E Sally; Ober, Raimund J

    2010-01-01

    Owing to its high quantum efficiency, the charge-coupled device (CCD) is an important imaging tool employed in biological applications such as single molecule microscopy. Under extremely low light conditions, however, a CCD is generally unsuitable because its readout noise can easily overwhelm the weak signal. Instead, an electron-multiplying charge-coupled device (EMCCD), which stochastically amplifies the acquired signal to drown out the readout noise, can be used. We have previously proposed a framework for calculating the Fisher information, and hence the Cramer-Rao lower bound, for estimating parameters (e.g., single molecule location) from the images produced by an optical microscope. Here, we develop the theory that is needed for deriving, within this framework, performance measures pertaining to the estimation of parameters from an EMCCD image. Our results allow the comparison of a CCD and an EMCCD in terms of the best accuracy with which parameters can be estimated from their acquired images. PMID:22735093

  6. Single-molecule electrochemical transistor utilizing a nickel-pyridyl spinterface.

    PubMed

    Brooke, Richard J; Jin, Chengjun; Szumski, Doug S; Nichols, Richard J; Mao, Bing-Wei; Thygesen, Kristian S; Schwarzacher, Walther

    2015-01-14

    Using a scanning tunnelling microscope break-junction technique, we produce 4,4'-bipyridine (44BP) single-molecule junctions with Ni and Au contacts. Electrochemical control is used to prevent Ni oxidation and to modulate the conductance of the devices via nonredox gating--the first time this has been shown using non-Au contacts. Remarkably the conductance and gain of the resulting Ni-44BP-Ni electrochemical transistors is significantly higher than analogous Au-based devices. Ab-initio calculations reveal that this behavior arises because charge transport is mediated by spin-polarized Ni d-electrons, which hybridize strongly with molecular orbitals to form a "spinterface". Our results highlight the important role of the contact material for single-molecule devices and show that it can be varied to provide control of charge and spin transport. PMID:25456978

  7. Monitoring patterned enzymatic polymerization on DNA origami at single-molecule level

    NASA Astrophysics Data System (ADS)

    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

  8. Information-theoretical analysis of time-correlated single-photon counting measurements of single molecules

    PubMed Central

    Talaga, David S.

    2009-01-01

    Time correlated single photon counting allows luminescence lifetime information to be determined on a single molecule level. This paper develops a formalism to allow information theory analysis of the ability of luminescence lifetime measurements to resolve states in a single molecule. It analyzes the information content of the photon stream and the fraction of that information that is relevant to the state determination problem. Experimental losses of information due to instrument response, digitization, and different types of background are calculated and a procedure to determine the optimal value of experimental parameters is demonstrated. This paper shows how to use the information theoretical formalism to evaluate the number of photons required to distinguish dyes that differ only by lifetime. It extends this idea to include distinguishing molecular states that differ in the electron transfer quenching or resonant energy transfer and shows how the differences between the lifetime of signal and background can help distinguish the dye position in an excitation beam. PMID:19385684

  9. PEG-Labeled Nucleotides and Nanopore Detection for Single Molecule DNA Sequencing by Synthesis

    PubMed Central

    Kumar, Shiv; Tao, Chuanjuan; Chien, Minchen; Hellner, Brittney; Balijepalli, Arvind; Robertson, Joseph W. F.; Li, Zengmin; Russo, James J.; Reiner, Joseph E.; Kasianowicz, John J.; Ju, Jingyue

    2012-01-01

    We describe a novel single molecule nanopore-based sequencing by synthesis (Nano-SBS) strategy that can accurately distinguish four bases by detecting 4 different sized tags released from 5?-phosphate-modified nucleotides. The basic principle is as follows. As each nucleotide is incorporated into the growing DNA strand during the polymerase reaction, its tag is released and enters a nanopore in release order. This produces a unique ionic current blockade signature due to the tag's distinct chemical structure, thereby determining DNA sequence electronically at single molecule level with single base resolution. As proof of principle, we attached four different length PEG-coumarin tags to the terminal phosphate of 2?-deoxyguanosine-5?-tetraphosphate. We demonstrate efficient, accurate incorporation of the nucleotide analogs during the polymerase reaction, and excellent discrimination among the four tags based on nanopore ionic currents. This approach coupled with polymerase attached to the nanopores in an array format should yield a single-molecule electronic Nano-SBS platform. PMID:23002425

  10. Interfacial electronic properties of pentacene tuned by a molecular monolayer of C60

    NASA Astrophysics Data System (ADS)

    Liu, X.; Zhan, Y.; Braun, S.; Li, F.; Fahlman, M.

    2009-09-01

    Fine-tuning charge injection barriers between organic materials and electrodes is critical to optimize organic electronic device performance. Here we demonstrate that by modifying gold substrates with a monolayer of fullerene, significant decrease in the hole-injection barrier into pentacene films can be achieved. The insertion of the fullerene monolayer modifies the interfacial dipole and produces an interface where the pentacene molecules form a standing-up orientation with their long axis parallel to the surface normal. The latter effect lowers the vertical ionization energy of the pentacene molecules at the interface as compared to the pentacene-on-Au case, as well as improves the ?-? overlap between the pentacene molecules that will likely enhance the transport properties in corresponding devices.

  11. Single Molecules Meet Systems Biology Meals are in the Dining Room

    E-print Network

    Eddy, Sean

    Single Molecules Meet Systems Biology 09/27/11 1 NOTE: Meals are in the Dining Room Talks controls bacterial cell cycle progression 9:00 pm Refreshements available at Bob's Pub #12;Single Molecules Life at the single molecule level: Imaging and sequencing single molecules in individual cells 9:30 am

  12. Single-Molecule Devices DOI: 10.1002/ange.201308398

    E-print Network

    Borguet, Eric

    of the single- molecule pH electrical sensor by deliberately choosing two dyes (Figure 1), malachite green (MG of pararosaniline (PA, panel A) and malachite green (MG, panel B) at different pH values. At pH 5.5, both PA and MG

  13. Single-Molecule Devices DOI: 10.1002/anie.201308398

    E-print Network

    Borguet, Eric

    of the single- molecule pH electrical sensor by deliberately choosing two dyes (Figure 1), malachite green (MG of pararosaniline (PA, panel A) and malachite green (MG, panel B) at different pH values. At pH 5.5, both PA and MG

  14. A Bayesian method for single molecule, fluorescence burst analysis

    E-print Network

    Coolen, ACC "Ton"

    estimates the fluorescence lifetime (and its error) from the burst data. ©2010 Optical Society of America­ 6094 (1998). 7. W. Grange, P. Haas, A. Wild, M. A. Lieb, M. Calame, M. Hegner, and B. Hecht, "Detection. Hubner, B. Sick, B. Hecht, A. Renn, and U. P. Wild, "Single-molecule identification by spectrally

  15. Masters projects in: Single-molecule tracking of protein

    E-print Network

    Uppsala Universitet

    Masters projects in: Single-molecule tracking of protein synthesis in live E. coli cells Ribosome catalyzed protein synthesis is one of the most fundamental processes in all life forms. From decades catalyzed protein synthesis. However, we have very sparse information about the dynamics of protein

  16. The dynamics of single-molecule DNA in flow

    Microsoft Academic Search

    Eric S. G. Shaqfeh

    2005-01-01

    Within the last decade, fluorescence microscopy of single molecules of DNA in a plethora of flow fields has allowed an unprecedented examination of the dynamics of polymers in flow. As a result, new principles (e.g. “molecular individualism”) have been developed regarding these dynamics and old debates (e.g. conformational hysteresis of polymers in extensional flow) have received a fresh airing. The

  17. Statistics and Related Topics in Single-Molecule Biophysics

    PubMed Central

    Qian, Hong; Kou, S. C.

    2014-01-01

    Since the universal acceptance of atoms and molecules as the fundamental constituents of matter in the early twentieth century, molecular physics, chemistry and molecular biology have all experienced major theoretical breakthroughs. To be able to actually “see” biological macromolecules, one at a time in action, one has to wait until the 1970s. Since then the field of single-molecule biophysics has witnessed extensive growth both in experiments and theory. A distinct feature of single-molecule biophysics is that the motions and interactions of molecules and the transformation of molecular species are necessarily described in the language of stochastic processes, whether one investigates equilibrium or nonequilibrium living behavior. For laboratory measurements following a biological process, if it is sampled over time on individual participating molecules, then the analysis of experimental data naturally calls for the inference of stochastic processes. The theoretical and experimental developments of single-molecule biophysics thus present interesting questions and unique opportunity for applied statisticians and probabilists. In this article, we review some important statistical developments in connection to single-molecule biophysics, emphasizing the application of stochastic-process theory and the statistical questions arising from modeling and analyzing experimental data. PMID:25009825

  18. Light Sheet Microscopy for Single Molecule Tracking in Living Tissue

    Microsoft Academic Search

    Jörg Gerhard Ritter; Roman Veith; Andreas Veenendaal; Jan Peter Siebrasse; Ulrich Kubitscheck

    2010-01-01

    Single molecule observation in cells and tissue allows the analysis of physiological processes with molecular detail, but it still represents a major methodological challenge. Here we introduce a microscopic technique that combines light sheet optical sectioning microscopy and ultra sensitive high-speed imaging. By this approach it is possible to observe single fluorescent biomolecules in solution, living cells and even tissue

  19. Single-Molecule Spectroscopy and Imaging Studies of Protein Dynamics

    NASA Astrophysics Data System (ADS)

    Lu, H. Peter

    2012-04-01

    Enzymatic reactions and protein-protein interactions are traditionally studied at the ensemble level, despite significant static and dynamic inhomogeneities. Subtle conformational changes play a crucial role in protein functions, and these protein conformations are highly dynamic rather than being static. We applied AFM-enhanced single-molecule spectroscopy to study the mechanisms and dynamics of enzymatic reactions involved with kinase and lysozyme proteins. Enzymatic reaction turnovers and the associated structure changes of individual protein molecules were observed simultaneously in real-time by single-molecule FRET detections. Our single-molecule spectroscopy measurements of T4 lysozyme and HPPK enzymatic conformational dynamics have revealed time bunching effect and intermittent coherence in conformational state change dynamics involving in enzymatic reaction cycles. The coherent conformational state dynamics suggests that the enzymatic catalysis involves a multi-step conformational motion along the coordinates of substrate-enzyme complex formation and product releasing, presenting as an extreme dynamic behavior intrinsically related to the time bunching effect that we have reported previously. Our results of HPPK interaction with substrate support a multiple-conformational state model, being consistent with a complementary conformation selection and induced-fit enzymatic loop-gated conformational change mechanism in substrate-enzyme active complex formation. Our new approach is applicable to a wide range of single-molecule FRET measurements for protein conformational changes under enzymatic reactions.

  20. Metal Nanoparticles with Gain toward Single-Molecule Detection by

    E-print Network

    Wang, Wei Hua

    Metal Nanoparticles with Gain toward Single-Molecule Detection by Surface-Enhanced Raman Scattering we propose another route toward the goal by introducing gain medium into single metal nanoparticles and a SERS enhancement factor on the order of 1016 -1017 . KEYWORDS Metal nanoparticles, gain, surface

  1. Simultaneous single molecule atomic force and fluorescence lifetime imaging

    NASA Astrophysics Data System (ADS)

    Schulz, Olaf; Koberling, Felix; Walters, Deron; Koenig, Marcelle; Viani, Jacob; Ros, Robert

    2010-02-01

    The combination of atomic force microscopy (AFM) with single-molecule-sensitive confocal fluorescence microscopy enables a fascinating investigation into the structure, dynamics and interactions of single biomolecules or their assemblies. AFM reveals the structure of macromolecular complexes with nanometer resolution, while fluorescence can facilitate the identification of their constituent parts. In addition, nanophotonic effects, such as fluorescence quenching or enhancement due to the AFM tip, can be used to increase the optical resolution beyond the diffraction limit, thus enabling the identification of different fluorescence labels within a macromolecular complex. We present a novel setup consisting of two commercial, state-of-the-art microscopes. A sample scanning atomic force microscope is mounted onto an objective scanning confocal fluorescence lifetime microscope. The ability to move the sample and objective independently allows for precise alignment of AFM probe and laser focus with an accuracy down to a few nanometers. Time correlated single photon counting (TCSPC) gives us the opportunity to measure single-molecule fluorescence lifetimes. We will be able to study molecular complexes in the vicinity of an AFM probe on a level that has yet to be achieved. With this setup we simultaneously obtained single molecule sensitivity in the AFM topography and fluorescence lifetime imaging of YOYO-1 stained lambda-DNA samples and we showed silicon tip induced single molecule quenching on organic fluorophores.

  2. Single molecule techniques in DNA repair: a primer.

    PubMed

    Hughes, Craig D; Simons, Michelle; Mackenzie, Cassidy E; Van Houten, Bennett; Kad, Neil M

    2014-08-01

    A powerful new approach has become much more widespread and offers insights into aspects of DNA repair unattainable with billions of molecules. Single molecule techniques can be used to image, manipulate or characterize the action of a single repair protein on a single strand of DNA. This allows search mechanisms to be probed, and the effects of force to be understood. These physical aspects can dominate a biochemical reaction, where at the ensemble level their nuances are obscured. In this paper we discuss some of the many technical advances that permit study at the single molecule level. We focus on DNA repair to which these techniques are actively being applied. DNA repair is also a process that encompasses so much of what single molecule studies benefit--searching for targets, complex formation, sequential biochemical reactions and substrate hand-off to name just a few. We discuss how single molecule biophysics is poised to transform our understanding of biological systems, in particular DNA repair. PMID:24819596

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

    PubMed

    Vilfan, Igor D; Kamping, Wiecher; van den Hout, Michiel; Candelli, Andrea; Hage, Susanne; Dekker, Nynke 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 RNA-enzyme interactions. A crucial component of this research is the design and assembly of an appropriate RNA construct. Such a construct is typically subject to several criteria. First, single-molecule force spectroscopy techniques often require an RNA construct that is longer than the RNA molecules used for bulk biochemical studies. Next, the incorporation of modified nucleotides into the RNA construct is required for its surface immobilization. In addition, RNA constructs for single-molecule studies are commonly assembled from different single-stranded RNA molecules, demanding good control of hybridization or ligation. Finally, precautions to prevent RNase- and divalent cation-dependent RNA digestion must be taken. The rather limited selection of molecular biology tools adapted to the manipulation of RNA molecules, as well as the sensitivity of RNA to degradation, make RNA construct preparation a challenging task. We briefly illustrate the types of single-molecule force spectroscopy experiments that can be performed on RNA, and then present an overview of the toolkit of molecular biology techniques at one's disposal for the assembly of such RNA constructs. Within this context, we evaluate the molecular biology protocols in terms of their effectiveness in producing long and stable RNA constructs. PMID:17905817

  4. Single-Molecule Biophysics Watching & Feeling Proteins at Work

    E-print Network

    Schmidt, Thomas

    -Fluorescent Protein K Brejc et.al. PNAS 94 (1997) 2306 2 nm #12;Individual eYFP-Fusion Proteins in a Cell Membrane GSBCD ? #12;Ribozyme makes a protein from RNA #12;Enzymatic Cleavage by the Ribozyme group of Steve ChuSingle-Molecule Biophysics Watching & Feeling Proteins at Work #12;Nanostructures micrometer vs

  5. Modeling Single Molecule Fluorescence and Lasing. Final report

    SciTech Connect

    Hill, Steven C.

    1998-10-01

    In FY 1998 our efforts were in three main areas, all related to detecting single fluorescent molecules [1] and understanding their emission. (1) We completed the calculations and analysis for a paper on spatial photoselection of single molecules on the surface of a dielectric microsphere. [2] Molecules that are oriented parallel to the surface of a spherical microcavity have position-dependent excitation probabilities and a collection efficiencies. The results are different for different polarizations. (2) We completed the modeling and analysis for a paper analyzing single molecule photocount statistics in microdroplets. [3] In this paper we employed a Monte Carlo technique to simulate effects of molecular occupancy, photobleaching, and fluorophor spatial diffusion within the droplet. We discussed the optimization of detection of single molecules in microdroplets. (3) We modeled the images of single molecules in microdroplets and submitted a preliminary report of these images in a paper which also showed experimental results. [4] The computed images depend upon the molecule's position within the microsphere, its orientation and emission frequency, and on the size and refractive index of the microsphere. For this work we used and modified models and computer codes developed previously, [5] as well as developed new models and codes.

  6. A plutonium-based single-molecule magnet.

    PubMed

    Magnani, N; Colineau, E; Griveau, J-C; Apostolidis, C; Walter, O; Caciuffo, R

    2014-08-01

    The magnetic properties of the 5f(5) [tris-(tri-1-pyrazolylborato)-plutonium(III)] complex have been investigated by ac susceptibility measurements, showing it to be the first plutonium single-molecule magnet; its magnetic relaxation slows down with decreasing temperature through a thermally activated mechanism followed by a quantum tunnelling regime below 5 K. PMID:24927255

  7. Presence and spatial distribution of interfacial electronic states in LaMnO{sub 3}-SrMnO{sub 3} superlattices.

    SciTech Connect

    Shah, A. B.; Ramasse, Q. M.; May, S. J.; Kavich, J.; Wen, J. G.; Zhai, X.; Eckstein, J. N.; Freeland, J.; Bhattacharya, A.; Zuo, J. M.; Univ. of Illinois; LBNL

    2010-09-13

    We report direct evidence of interfacial states at the onset of O K edge confined to a spatial distance of 1 unit-cell full-width at half maximum at the sharp interfaces between epitaxial films of LaMnO{sub 3} and SrMnO{sub 3} from electron energy-loss spectroscopy (EELS) measurements. The interfacial states are sensitive to interface sharpness; at rough interfaces with interfacial steps of 1-2 unit cells in height, experimental data shows a reduction, or suppression, of the interfacial states. The EELS measurements were performed using a fine electron probe obtained by electron lens aberration correction. By scanning the electron probe across the interface, we are able to map the spatial distribution of the interfacial states across interfaces at high resolution.

  8. Temperature Independent Porous Nanocontainers for Single Molecule Fluorescence Studies

    PubMed Central

    Ishitsuka, Yuji; Okumus, Burak; Arslan, Sinan; Chen, Kok Hao; Ha, Taekjip

    2010-01-01

    In this work, we demonstrate the capability of using lipid vesicles biofunctionalized with protein channels to perform single molecule fluorescence measurements over a biologically relevant temperature range. Lipid vesicles can serve as an ideal nanocontainer for single molecule fluorescence measurements of bio-macromolecules. One serious limitation of the vesicle encapsulation method has been that the lipid membrane is practically impermeable to most ions and small molecules, limiting its application to observing reactions in equilibrium with the initial buffer condition. In order to permeabilize the barrier, Staphylococcal aureus toxin ?-hemolysin (aHL) channels have been incorporated into the membrane. These aHL channels have been characterized using single molecule fluorescence resonance energy transfer (smFRET) signals from vesicle encapsulated guanine-rich DNA that folds in G-quadruplex motif as well as from Rep helicase-DNA system. We show that these aHL channels are permeable to monovalent ions and small molecules, such as ATP, over the biologically relevant temperature range (17–37 °C). Ions can efficiently pass through preformed aHL channels in order to initiate DNA folding without any detectable delay. With addition of the cholesterol to the membrane, we also report 35-fold improvement in aHL channel formation efficiency making this approach more practical for wider applications. Finally, the temperature dependent single molecule enzymatic study inside these nanocontainers is demonstrated by measuring Rep helicase repetitive shuttling dynamic along a single stranded DNA at various temperature values. The permeability of the biofriendly nanocontainer over a wide range of temperature would be effectively applied to other surface-based high throughput measurements and sensors beyond the single molecule fluorescence measurements. PMID:21038883

  9. Ultrafast interfacial electron transfer from the excited state of anchored molecules into a semiconductor

    NASA Astrophysics Data System (ADS)

    Gundlach, L.; Ernstorfer, R.; Willig, F.

    Ultrafast heterogeneous electron transfer (HET) from the excited singlet state of the large organic chromophore perylene into the inorganic semiconductor rutile TiO 2 was investigated with femtosecond time-resolved two-photon photoemission (TR-2PPE). The strength of the electronic interaction between the chromophore and the semiconductor was varied by inserting different anchor/bridge groups that functioned either as electronic wire or electronic tunnelling barrier. Both anchor groups, i.e. carboxylic and phosphonic acid, formed strong chemical bonds at the TiO 2 surface. The perylene chromophore with the different anchor/bridge groups was adsorbed from solution in a dedicated ultra-high-vacuum (UHV) chamber. The adsorption geometry of the chromophore perylene was determined from angle and polarization dependent two-photon photoemission (2PPE) signals and was found to be very different for the two different anchor/bridge groups. The measured adsorption geometries are compatible with recent DFT (density functional theory) calculations by P. Persson and co-workers [M. Nilsing, S. Lunell, P. Persson, L. Ojamäe, Phosphonic acid adsorption at the TiO 2 anatase (1 0 1) surface investigated by periodic hybrid HF-DFT computations, Surf. Sci. 582 (2005) 49-60]. Two different processes contributed to the TR-2PPE transients, firstly electron transfer from the chromophore to the electronic acceptor states on the surface and secondly escape of the electrons from the surface into the bulk of the semiconductor. The latter escape process was measured separately by making the interfacial electron injection process instantaneous when the chromophore catechol was employed in place of the perylene compounds. The thus measured electron escape behavior was governed by the same time constants that have recently been predicted by Prezhdo and coworkers from time dependent DFT calculations [W.R. Duncan, W.M. Stier, O.V. Prezhdo, Ab initio nonadiabatic molecular dynamics of the ultrafast electron injection across the Alizarin-TiO 2 interface, J. Am. Chem. Soc. 127 (2005) 7941-7951]. The HET times derived from the 2PPE transients showed very good agreement with HET times measured via transient absorption (TA) on anatase TiO 2 layers. The measured energy distribution of the 2PPE signals for the injected electrons suggests that a high density of electronic acceptor states is operative in both systems and is spread over an at least 1 eV wide energy range. The acceptor states are tentatively identified with surface states created through the formation of chemical bonds between the anchor groups of the organic molecules and surface atoms of the semiconductor.

  10. Spin anisotropy effects in dimer single molecule magnets

    NASA Astrophysics Data System (ADS)

    Efremov, Dmitri V.; Klemm, Richard A.

    2006-08-01

    We present a model of homoionic, equal-spin s1 dimer single molecule magnets exhibiting D2h , C2v , or S2 molecular group symmetry, focusing upon the simplest D2h case. The spins within each dimer interact via the Heisenberg and the most general set of four quadratic anisotropic spin interactions with respective strengths J and {Jj} , and with the magnetic induction B . We solve the model exactly for s1=1/2 , and analytically for B along the crystal directions and numerically for other B directions for s1=1 and 5/2, and present M(B) curves at low T for these cases with antiferromagnetic Heisenberg couplings (J<0) . Low- T CV(B) curves for s1=1/2 and electron paramagnetic susceptibility ?(B,?) for s1=1 are also provided. For weakly anisotropic dimers, the Hartree approximation, or strong exchange limit, yields rather simple analytic formulas for M(B) and CV(B) at arbitrary s1 that accurately fit the exact solutions at sufficiently low T or large B . Low- T , large- B formulas for the inelastic neutron-scattering cross section S(B,q,?) and ?(B,?) with arbitrary s1 and B in the Hartree approximation are also given. For antiferromagnetic Heisenberg couplings (J<0) and weak anisotropy interactions (?Jj/J??1) , we provide analytic formulas for the 2s1 level-crossing magnetic inductions Bs,s1lc(?,?) , at which the low- T magnetization M(B) exhibits steps and the low- T specific heat CV(B) exhibits zeroes, surrounded by double peaks of uniform height. Strong anisotropy interactions drastically alter these behaviors, however. Our results are discussed with regard to existing experiments on s1=5/2Fe2 , s1=3/2Cr2 , and s1=1Ni2 dimers, suggesting the presence of single-ion anisotropy in three of them, but apparently without any sizeable anisotropic exchange interactions. Further experiments on single crystals of these and higher-spin dimers are therefore warranted, and we particularly urge further electron paramagnetic resonance and inelastic neutron-scattering experiments to be performed.

  11. Electron tunneling across an interfacial water layer inside an STM junction: tunneling distance, barrier height and water polarization effect

    Microsoft Academic Search

    J. R. Hahn; Y. A. Hong; H. Kang

    1998-01-01

    2   surfaces in air. The electron tunneling distance ranges from 7–20 ? when the junction resistance is of the order of 108 ?. We suggest that the unusually low value of the barrier height (<1.5 eV) originates from the three-dimensional nature of\\u000a the electron tunneling through the interfacial water layer present inside the junction. An asymmetric variation in barrier\\u000a height is observed with

  12. Identifying Single Molecule Dynamics in Real Time via Time-Resolved Coherent Anti-Stokes Raman Scattering

    NASA Astrophysics Data System (ADS)

    Yampolsky, Steven; Fishman, Dmitry; Dey, Shirshendu; Hulkko, Eero; Banik, Mayukh; Potma, Eric; Apkarian, V. Ara

    2014-03-01

    By enhancing the local response of a single molecule with a dipolar nano-antenna, the vibrational dynamics at the single molecule limit can be measured in real time, by Time-Resolved Coherent Anti-Stokes Raman Scattering (TR-CARS). Such measurements involve the preparation and subsequent probing of vibrational wavepackets on the ground electronic state. In contrast to ensemble measurements, the vibrational coherence of a single molecule is not subject to dephasing; it exhibits dynamic phase and amplitude noise due to the collapse of the wavepacket upon measurement. Continuous measurements of the amplitude noise distribution as a function of phase delay, allows the complete reconstruction of the state of the system. Under ambient conditions, repeated measurements of a single molecule coherence reduces to a statistical state of a system coupled to the thermal bath. The signature of the statistical state of a single molecule is characteristic, distinct from that of two, or three, or many; and this can be directly demonstrated through measurements. Thank You To NSF for funding the Chemistry at the Space Time Limit Center (CasTL) with (CHE-082913).

  13. Dynamics and mechanisms of interfacial photoinduced electron transfer processes of third generation photovoltaics and photocatalysis.

    PubMed

    Bauer, Christophe; Teuscher, Joël; Brauer, Jan C; Punzi, Angela; Marchioro, Arianna; Ghadiri, Elham; De Jonghe, Jelissa; Wielopolski, Mateusz; Banerji, Natalie; Moser, Jacques E

    2011-01-01

    Photoinduced electron transfer (PET) across molecular/bulk interfaces has gained attention only recently and is still poorly understood. These interfaces offer an excellent case study, pertinent to a variety of photovoltaic systems, photo- and electrochemistry, molecular electronics, analytical detection, photography, and quantum confinement devices. They play in particular a key role in the emerging fields of third-generation photovoltaic energy converters and artificial photosynthetic systems aimed at the production of solar fuels, creating a need for a better understanding and theoretical treatment of the dynamics and mechanisms of interfacial PET processes. We aim to achieve a fundamental understanding of these phenomena by designing experiments that can be used to test and alter modern theory and computational modeling. One example illustrating recent investigations into the details of the ultrafast processes that form the basis for photoinduced charge separation at a molecular/bulk interface relevant to dye-sensitized solar cells is briefly presented here: Kinetics of interfacial PET and charge recombination processes were measured by fs and ns transient spectroscopy in a heterogeneous donor-bridge-acceptor (D-B-A) system, where D is a Ru(II)(terpyridyl-PO3)(NCS)3 complex, B an oligo-p-phenylene bridge, and A nanocrystalline TiO2. The forward ET reaction was found to be faster than vibrational relaxation of the vibronic excited state of the donor. Instead, the back ET occurred on the micros time scale and involved fully thermalized species. The D-A distance dependence of the electron transfer rate was studied by varying the number of p-phenylene units contained in the bridge moiety. The remarkably low damping factor beta = 0.16 angstroms(-1) observed for the ultrafast charge injection from the dye excited state into the conduction band of TiO2 is attributed to the coupling of electron tunneling with nonequilibrium vibrations redistributed on the bridge, giving rise to polaronic transport of charges from the donor ligand to the acceptor solid oxide surface. PMID:22026184

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

    PubMed Central

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

    2013-01-01

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

  15. Single-molecule studies of nucleocytoplasmic transport: from one dimension to three dimensions

    PubMed Central

    Goryaynov, Alexander; Ma, Jiong; Yang, Weidong

    2012-01-01

    In eukaryotic cells, the bidirectional trafficking of proteins and genetic materials across the double-membrane nuclear envelope is mediated by nuclear pore complexes (NPCs). A highly selective barrier formed by the phenylalanine–glycine (FG)-nucleoporin (Nup) in the NPC allows for two transport modes: passive diffusion and transport receptor-facilitated translocation. Strict regulation of nucleocytoplasmic transport is crucial for cell survival, differentiation, growth and other essential activities. However, due to the limited knowledge of the native configuration of the FG-Nup barrier and the interactions between the transiting molecules and the barrier in the NPC, the precise nucleocytoplasmic transport mechanism remains unresolved. To refine the transport mechanism, single-molecule fluorescence microscopy methods have been employed to obtain the transport kinetics of individual fluorescent molecules through the NPC and to map the interactions between transiting molecules and the FG-Nup barrier. Important characteristics of nucleocytoplasmic transport, such as transport time, transport efficiency and spatial distribution of single transiting molecules in the NPC, have been obtained that could not be measured by either ensemble average methods or conventional electron microscopy. In this critical review, we discuss the development of various single-molecule techniques and their application to nucleocytoplasmic transport in vitro and in vivo. In particular, we highlight a recent advance from one-dimensional to three-dimensional single-molecule characterization of transport through the NPC and present a comprehensive understanding of the nucleocytoplasmic transport mechanism obtained by this new technical development (105 references). PMID:22020388

  16. A single-molecule force spectroscopy study of the interactions between lectins and carbohydrates on cancer and normal cells

    NASA Astrophysics Data System (ADS)

    Zhao, Weidong; Cai, Mingjun; Xu, Haijiao; Jiang, Junguang; Wang, Hongda

    2013-03-01

    The interaction forces between carbohydrates and lectins were investigated by single-molecule force spectroscopy on both cancer and normal cells. The binding kinetics was also studied, which shows that the carbohydrate-lectin complex on cancer cells is less stable than that on normal cells.The interaction forces between carbohydrates and lectins were investigated by single-molecule force spectroscopy on both cancer and normal cells. The binding kinetics was also studied, which shows that the carbohydrate-lectin complex on cancer cells is less stable than that on normal cells. Electronic supplementary information (ESI) available: Experimental details. See DOI: 10.1039/c3nr00553d

  17. First-Principles Studies of Charge Separation in Single-Molecule Heterojunctions

    NASA Astrophysics Data System (ADS)

    Darancet, Pierre; Doak, Peter; Neaton, Jeffrey

    2010-03-01

    Single-molecule heterojunctions, consisting of donor and acceptor moieties linked by covalent bonds and coupled to metal electrodes, provide an interesting model system for understanding processes fundamental to organic solar cells, such as light absorption and charge separation. However, how the covalent contact with metallic leads influence these processes -- and metal-molecule interface electronic structure -- remains largely unknown. Using density functional theory and many-body perturbation theory, we discuss the influence of the metal contacts and binding groups on junction electronic level alignment for small asymmetric molecules containing covalently-linked moieties based on thiophene, durene and tetrafluoro-, dinitrile-, and metoxy-benzene. Implications for photocurrent and rectification are discussed.

  18. Silicon nanowire based single-molecule SERS sensor.

    PubMed

    Wang, Hui; Han, Xuemei; Ou, Xuemei; Lee, Chun-Sing; Zhang, Xiaohong; Lee, Shuit-Tong

    2013-09-01

    One-dimensional nanowire (NW) optical sensors have attracted great attention as promising nanoscale tools for applications such as probing inside living cells. However, achieving single molecule detection on NW sensors remains an interesting and unsolved problem. In the present paper, we investigate single-molecule detection (SMD) on a single SiNW based surface-enhanced Raman scattering (SERS) sensor, fabricated by controllably depositing silver nanoparticles on a SiNW (AgNP-SiNW). Both Raman spectral blinking and bi-analyte approaches are performed in aqueous solution to investigate SMD on individual SiNW SERS sensors. The results extend the functions of the SiNW sensor to SMD and provide insight into the molecule level illustration on the sensing mechanism of the nanowire sensor. PMID:23892767

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

    PubMed

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

    2015-03-01

    Inverse sandwich biphenyl complexes [(NN(TBS))Ln]2(?-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. PMID:25695369

  20. Applications of optical trapping to single molecule DNA

    SciTech Connect

    Sonek, G.J.; Berns, M.W. [Univ. of California, Irvine, CA (United States). Beckman Laser Inst. and Medical Clinic; Keller, R.A. [Los Alamos National Lab., NM (United States). Chemical Science and Technology Div.

    1997-12-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The project focused on the methodologies required to integrate optical trapping with single molecule detection (SMD) so as to demonstrate high speed sequencing through optical micromanipulation of host substrates, nucleotide cleavage, and single molecule detection. As part of this effort, the new technology of optical tweezers was applied to the confinement and manipulation of microsphere handles containing attached DNA fragments. The authors demonstrated substrate optical trapping in rapid flow streams, the fluorescence excitation and detection of fluorescently labeled nucleotides in an optical trapping system, and the epifluorescent imaging of DNA fragments in flow streams. They successfully demonstrated optical trapping in laminar flow streams and completely characterized the trapping process as functions of fluid flow velocity, chamber dimension, trapping depth, incident laser power, and fluorescence measurement geometry.

  1. High thermopower of mechanically stretched single-molecule junctions

    PubMed Central

    Tsutsui, Makusu; Morikawa, Takanori; He, Yuhui; Arima, Akihide

    2015-01-01

    Metal-molecule-metal junction is a promising candidate for thermoelectric applications that utilizes quantum confinement effects in the chemically defined zero-dimensional atomic structure to achieve enhanced dimensionless figure of merit ZT. A key issue in this new class of thermoelectric nanomaterials is to clarify the sensitivity of thermoelectricity on the molecular junction configurations. Here we report simultaneous measurements of the thermoelectric voltage and conductance on Au-1,4-benzenedithiol (BDT)-Au junctions mechanically-stretched in-situ at sub-nanoscale. We obtained the average single-molecule conductance and thermopower of 0.01 G0 and 15??V/K, respectively, suggesting charge transport through the highest occupied molecular orbital. Meanwhile, we found the single-molecule thermoelectric transport properties extremely-sensitive to the BDT bridge configurations, whereby manifesting the importance to design the electrode-molecule contact motifs for optimizing the thermoelectric performance of molecular junctions. PMID:26112999

  2. Single-molecule imaging of cytoplasmic dynein in vivo.

    PubMed

    Ananthanarayanan, Vaishnavi; Toli?, Iva M

    2015-01-01

    While early fluorescence microscopy experiments employing fluorescent probes afforded snapshots of the cell, the power of live-cell microscopy is required to understand complex dynamics in biological processes. The first successful cloning of green fluorescent protein in the 1990s paved the way for development of approaches that we now utilize for visualization in a living cell. In this chapter, we discuss a technique to observe fluorescently tagged single molecules in fission yeast. With a few simple modifications to the established total internal reflection fluorescence microscopy, cytoplasmic dynein molecules in the cytoplasm and on the microtubules can be visualized and their intracellular dynamics can be studied. We illustrate a technique to study motor behavior, which is not apparent in conventional ensemble studies of motors. In general, this technique can be employed to study single-molecule dynamics of fluorescently tagged proteins in the cell interior. PMID:25640420

  3. Single-molecule DNA sequencing technologies for future genomics research.

    PubMed

    Gupta, Pushpendra K

    2008-11-01

    During the current genomics revolution, the genomes of a large number of living organisms have been fully sequenced. However, with the advent of new sequencing technologies, genomics research is now at the threshold of a second revolution. Several second-generation sequencing platforms became available in 2007, but a further revolution in DNA resequencing technologies is being witnessed in 2008, with the launch of the first single-molecule DNA sequencer (Helicos Biosciences), which has already been used to resequence the genome of the M13 virus. This review discusses several single-molecule sequencing technologies that are expected to become available during the next few years and explains how they might impact on genomics research. PMID:18722683

  4. Single-molecule methods to study membrane receptor oligomerization.

    PubMed

    Fricke, Franziska; Dietz, Marina S; Heilemann, Mike

    2015-03-16

    Membrane receptors control fundamental cellular processes. Binding of a specific ligand to a receptor initiates communication through the membrane and activation of signaling cascades. This activation process often leads to a spatial rearrangement of receptors in the membrane at the molecular level. Single-molecule techniques contributed significantly to the understanding of receptor organization and rearrangement in membranes. Here, we review four prominent single-molecule techniques that have been applied to membrane receptors, namely, stepwise photobleaching, Förster resonance energy transfer, sub-diffraction localization microscopy and co-tracking. We discuss the requirements, benefits and limitations of each technique, discuss target labeling, present a selection of applications and results and compare the different methodologies. PMID:25521567

  5. High thermopower of mechanically stretched single-molecule junctions.

    PubMed

    Tsutsui, Makusu; Morikawa, Takanori; He, Yuhui; Arima, Akihide; Taniguchi, Masateru

    2015-01-01

    Metal-molecule-metal junction is a promising candidate for thermoelectric applications that utilizes quantum confinement effects in the chemically defined zero-dimensional atomic structure to achieve enhanced dimensionless figure of merit ZT. A key issue in this new class of thermoelectric nanomaterials is to clarify the sensitivity of thermoelectricity on the molecular junction configurations. Here we report simultaneous measurements of the thermoelectric voltage and conductance on Au-1,4-benzenedithiol (BDT)-Au junctions mechanically-stretched in-situ at sub-nanoscale. We obtained the average single-molecule conductance and thermopower of 0.01 G0 and 15??V/K, respectively, suggesting charge transport through the highest occupied molecular orbital. Meanwhile, we found the single-molecule thermoelectric transport properties extremely-sensitive to the BDT bridge configurations, whereby manifesting the importance to design the electrode-molecule contact motifs for optimizing the thermoelectric performance of molecular junctions. PMID:26112999

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

    E-print Network

    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.

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

    SciTech Connect

    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].

  8. Single Molecule Detection in Solution: Methods and Applications

    NASA Astrophysics Data System (ADS)

    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.

  9. High-throughput multispot single-molecule spectroscopy

    NASA Astrophysics Data System (ADS)

    Colyer, Ryan A.; Scalia, Giuseppe; Kim, Taiho; Rech, Ivan; Resnati, Daniele; Marangoni, Stefano; Ghioni, Massimo; Cova, Sergio; Weiss, Shimon; Michalet, Xavier

    2010-02-01

    Solution-based single-molecule spectroscopy and fluorescence correlation spectroscopy (FCS) are powerful techniques to access a variety of molecular properties such as size, brightness, conformation, and binding constants. However, this is limited to low concentrations, which results in long acquisition times in order to achieve good statistical accuracy. Data can be acquired more quickly by using parallelization. We present a new approach using a multispot excitation and detection geometry made possible by the combination of three powerful new technologies: (i) a liquid crystal spatial light modulator to produce multiple diffraction-limited excitation spots; (ii) a multipixel detector array matching the excitation pattern and (iii) a low-cost reconfigurable multichannel counting board. We demonstrate the capabilities of this technique by reporting FCS measurements of various calibrated samples as well as single-molecule burst measurements.

  10. Single-molecule near-field optical energy transfer microscopy

    Microsoft Academic Search

    W. Trabesinger; A. Kramer; M. Kreiter; B. Hecht; U. P. Wild

    2002-01-01

    The nano-optical interaction between a sharp tip and a single dipolar emitter is investigated. Changes of the excited state lifetime and the fluorescence rate of single molecules are recorded simultaneously as a function of the tip position relative to the molecule. A subdiffraction-limited area of decreased fluorescence and shortened lifetime is observed for gold-coated Si3N4 tips. The results are discussed

  11. Mechanical Single Molecule Investigations of SNARE Protein Interactions

    NASA Astrophysics Data System (ADS)

    Liu, Wei; Montana, Vedrana; Parpura, Vladimir; Mohideen, Umar

    2007-03-01

    We used an Atomic Force Microscope (AFM) to perform single molecule investigations of the SNARE (soluble N-ethyl maleimide-sensitive fusion protein attachment protein receptors) proteins, syntaxin, synaptobrevin and SNAP 25. These proteins are involved in the docking and release of neurotransmitters. The rupture force and extension of the interactions were measured. Chemical reaction rate theory was applied to obtain the energy barrier width and lifetime. Their temperature dependence was also explored.

  12. Single-Molecule Covalent Chemistry in a Protein Nanoreactor

    Microsoft Academic Search

    Hagan Bayley; Tudor Luchian; Seong-Ho Shin; Mackay B. Steffensen

    Covalent chemistry can be observed at the single-molecule level by using engineered protein pores as “nanoreactors”. By recording\\u000a the ionic current driven through single engineered alpha-hemolysin (?HL) pores in a transmembrane potential, individual bond-making\\u000a and bond-breaking steps that occur within the pore and perturb the current are monitored with sub-millisecond time-resolution.\\u000a Recently, a variety of covalent reactions of small molecules

  13. Protein Folding Transition Paths: Single Molecule Experiments, Theory and Simulations

    NASA Astrophysics Data System (ADS)

    Eaton, William

    2015-03-01

    The transition-path is the tiny fraction of an equilibrium, single-molecule trajectory when the transition over a free-energy barrier occurs between two states. In the case of protein folding, the distribution of transition paths contains all of the mechanistic information on how a protein folds and unfolds. Transition path distributions can now be predicted for fast folding proteins by all-atom molecular dynamics simulations and by an Ising-like theoretical model. Experimental information on transition paths should provide the most demanding test of both simulations and theoretical models. However, transition-paths for barrier crossings have never been observed experimentally for any molecular system in solution. Because it is a single molecule property, even determining the average transition-path time is challenging. In this presentation, I will discuss how we use measurements of Foerster resonance energy transfer in single molecule fluorescence experiments and a photon-by-photon analysis to measure average transition path times for proteins of different topology and folding rate coefficients using the Gopich/Szabo maximum likelihood method [3.4]. These results, which are surprisingly interesting, are just the first, but important, steps toward measuring intra-molecular distances during individual transition paths.

  14. RNA folding: Monte Carlo simulation and single molecule experiments

    NASA Astrophysics Data System (ADS)

    Nivon, Lucas Gregorio

    RNA plays an indispensable enzymatic and structural role in many critical cellular processes, but understanding of its folding mechanism is relatively incomplete. Here I present studies that combine computer predictions based on a simple model of folding with direct observations of single molecules to bring greater understanding to the dynamics and folding pathways of three different RNAs. Many cellular RNAs require a protein co-factor in order to function, so we first use single molecule experimental techniques to understand RNA folding in the presence of a protein co-factor, in chapter I. In parallel, a Go-based technique was developed for the simulation of RNA folding, allowing some of the first computer simulations of the process. The results of these in silico studies are reported in chapter II, for a very small (and computationally accessible) example RNA, the GCAA tetraloop, demonstrating a "zipper" pathway with a putative intermediate. This methodology is then applied to the hairpin ribozyme in chapter III, to derive a model of the folding transition state for the ribozyme and make predictions about the ribozyme dynamics. In chapter III preliminary observations are also made of the high-speed dynamics of the ribozyme in single molecule experiments using two different types of microscopy.

  15. Single-Molecule Ion Channel Conformational Dynamics in Living Cells

    NASA Astrophysics Data System (ADS)

    Lu, H. Peter

    2014-03-01

    Stochastic and inhomogeneous conformational changes regulate the function and dynamics of ion channels that are crucial for cell functions, neuronal signaling, and brain functions. Such complexity makes it difficult, if not impossible, to characterize ion channel dynamics using conventional electrical recording alone since that the measurement does not specifically interrogate the associated conformational changes but rather the consequences of the conformational changes. Recently, new technology developments on single-molecule spectroscopy, and especially, the combined approaches of using single ion channel patch-clamp electrical recording and single-molecule fluorescence imaging have provided us the capability of probing ion channel conformational changes simultaneously with the electrical single channel recording. By combining real-time single-molecule fluorescence imaging measurements with real-time single-channel electric current measurements in artificial lipid bilayers and in living cell membranes, we were able to probe single ion-channel-protein conformational changes simultaneously, and thus providing an understanding the dynamics and mechanism of ion-channel proteins at the molecular level. The function-regulating and site-specific conformational changes of ion channels are now measurable under physiological conditions in real-time, one molecule at a time. We will focus our discussion on the new development and results of real-time imaging of the dynamics of gramicidin, colicin, and NMDA receptor ion channels in lipid bilayers and living cells. Our results shed light on new perspectives of the intrinsic interplay of lipid membrane dynamics, solvation dynamics, and the ion channel functions.

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

    PubMed

    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. PMID:25453259

  17. Single molecule conformational memory extraction: p5ab RNA hairpin.

    PubMed

    Pressé, Steve; Peterson, Jack; Lee, Julian; Elms, Phillip; MacCallum, Justin L; Marqusee, Susan; Bustamante, Carlos; Dill, Ken

    2014-06-19

    Extracting kinetic models from single molecule data is an important route to mechanistic insight in biophysics, chemistry, and biology. Data collected from force spectroscopy can probe discrete hops of a single molecule between different conformational states. Model extraction from such data is a challenging inverse problem because single molecule data are noisy and rich in structure. Standard modeling methods normally assume (i) a prespecified number of discrete states and (ii) that transitions between states are Markovian. The data set is then fit to this predetermined model to find a handful of rates describing the transitions between states. We show that it is unnecessary to assume either (i) or (ii) and focus our analysis on the zipping/unzipping transitions of an RNA hairpin. The key is in starting with a very broad class of non-Markov models in order to let the data guide us toward the best model from this very broad class. Our method suggests that there exists a folding intermediate for the P5ab RNA hairpin whose zipping/unzipping is monitored by force spectroscopy experiments. This intermediate would not have been resolved if a Markov model had been assumed from the onset. We compare the merits of our method with those of others. PMID:24898871

  18. Single-molecule fluorescence spectroscopy in (bio)catalysis

    PubMed Central

    Roeffaers, Maarten B. J.; De Cremer, Gert; Uji-i, Hiroshi; Muls, Benîot; Sels, Bert F.; Jacobs, Pierre A.; De Schryver, Frans C.; De Vos, Dirk E.; Hofkens, Johan

    2007-01-01

    The ever-improving time and space resolution and molecular detection sensitivity of fluorescence microscopy offer unique opportunities to deepen our insights into the function of chemical and biological catalysts. Because single-molecule microscopy allows for counting the turnover events one by one, one can map the distribution of the catalytic activities of different sites in solid heterogeneous catalysts, or one can study time-dependent activity fluctuations of individual sites in enzymes or chemical catalysts. By experimentally monitoring individuals rather than populations, the origin of complex behavior, e.g., in kinetics or in deactivation processes, can be successfully elucidated. Recent progress of temporal and spatial resolution in single-molecule fluorescence microscopy is discussed in light of its impact on catalytic assays. Key concepts are illustrated regarding the use of fluorescent reporters in catalytic reactions. Future challenges comprising the integration of other techniques, such as diffraction, scanning probe, or vibrational methods in single-molecule fluorescence spectroscopy are suggested. PMID:17664433

  19. Viruses and Tetraspanins: Lessons from Single Molecule Approaches

    PubMed Central

    Dahmane, Selma; Rubinstein, Eric; Milhiet, Pierre-Emmanuel

    2014-01-01

    Tetraspanins are four-span membrane proteins that are widely distributed in multi-cellular organisms and involved in several infectious diseases. They have the unique property to form a network of protein-protein interaction within the plasma membrane, due to the lateral associations with one another and with other membrane proteins. Tracking tetraspanins at the single molecule level using fluorescence microscopy has revealed the membrane behavior of the tetraspanins CD9 and CD81 in epithelial cell lines, providing a first dynamic view of this network. Single molecule tracking highlighted that these 2 proteins can freely diffuse within the plasma membrane but can also be trapped, permanently or transiently, in tetraspanin-enriched areas. More recently, a similar strategy has been used to investigate tetraspanin membrane behavior in the context of human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) infection. In this review we summarize the main results emphasizing the relationship in terms of membrane partitioning between tetraspanins, some of their partners such as Claudin-1 and EWI-2, and viral proteins during infection. These results will be analyzed in the context of other membrane microdomains, stressing the difference between raft and tetraspanin-enriched microdomains, but also in comparison with virus diffusion at the cell surface. New advanced single molecule techniques that could help to further explore tetraspanin assemblies will be also discussed. PMID:24800676

  20. Single Molecule Conformational Memory Extraction: P5ab RNA Hairpin

    PubMed Central

    2015-01-01

    Extracting kinetic models from single molecule data is an important route to mechanistic insight in biophysics, chemistry, and biology. Data collected from force spectroscopy can probe discrete hops of a single molecule between different conformational states. Model extraction from such data is a challenging inverse problem because single molecule data are noisy and rich in structure. Standard modeling methods normally assume (i) a prespecified number of discrete states and (ii) that transitions between states are Markovian. The data set is then fit to this predetermined model to find a handful of rates describing the transitions between states. We show that it is unnecessary to assume either (i) or (ii) and focus our analysis on the zipping/unzipping transitions of an RNA hairpin. The key is in starting with a very broad class of non-Markov models in order to let the data guide us toward the best model from this very broad class. Our method suggests that there exists a folding intermediate for the P5ab RNA hairpin whose zipping/unzipping is monitored by force spectroscopy experiments. This intermediate would not have been resolved if a Markov model had been assumed from the onset. We compare the merits of our method with those of others. PMID:24898871

  1. Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes

    NASA Astrophysics Data System (ADS)

    Dell, Emma J.; Capozzi, Brian; Xia, Jianlong; Venkataraman, Latha; Campos, Luis M.

    2015-03-01

    To develop advanced materials for electronic devices, it is of utmost importance to design organic building blocks with tunable functionality and to study their properties at the molecular level. For organic electronic and photovoltaic applications, the ability to vary the nature of charge carriers and so create either electron donors or acceptors is critical. Here we demonstrate that charge carriers in single-molecule junctions can be tuned within a family of molecules that contain electron-deficient thiophene-1,1-dioxide (TDO) building blocks. Oligomers of TDO were designed to increase electron affinity and maintain delocalized frontier orbitals while significantly decreasing the transport gap. Through thermopower measurements we show that the dominant charge carriers change from holes to electrons as the number of TDO units is increased. This results in a unique system in which the charge carrier depends on the backbone length, and provides a new means to tune p- and n-type transport in organic materials.

  2. Electronic characteristics of the interfacial states embedded in ``buffer-free'' GaSb/GaAs (001) heterojunctions

    NASA Astrophysics Data System (ADS)

    Jallipalli, A.; Nunna, K.; Kutty, M. N.; Balakrishnan, G.; Dawson, L. R.; Huffaker, D. L.

    2009-11-01

    We report a comprehensive study of the electronic properties and compensation of the interfacial states embedded in a majority carrier electron region either on one or both sides of the "buffer-free" GaSb/GaAs (001) heterointerface. An abrupt change observed in the forward-bias current (58 mA) for a small variation in the applied bias (0.05 V) is ascribed to the compensation of the interfacial states due to electron tunneling from GaAs into GaSb. As a result, after the first sweep, the compensated interfacial states exhibit low turn-on voltage (0.35 V) and low reverse-bias currents (30 ?A at -5 V). Similar compensation is also obtained via ?-doping or annealing the diodes. The diodes analyzed in this study are useful as the heterointerface is embedded in the majority electron region resembles with that of the n-cladding region of p-i-n structures such as lasers, detectors, and solar cells.

  3. Directional bonding and asymmetry of interfacial structure in intermetallic TiAl: Combined theoretical and electron microscopy study

    Microsoft Academic Search

    R. Siegl; V. Vitek; H. Inui; K. Kishida; M. Yamaguchi

    1997-01-01

    An ordered twin boundary in the L10 TiAl alloy has been investigated by computer modelling and high-resolution electron microscopy (HREM). This combined study demonstrates the significance of directional covalent-type bonding for the interfacial structure. When using the ab-initio full-potential linear muffin-tin orbital method the stable structure exhibits a pronounced asymmetry. This structure is in an excellent agreement with HREM observations.

  4. Interfacial shear strength and thermal properties of electron beam-treated henequen fibers reinforced unsaturated polyester composites

    Microsoft Academic Search

    Yansong Pang; Donghwan Cho; Seong Ok Han; Won Ho Park

    2005-01-01

    Natural fiber henequen\\/unsaturated polyester (UPE) composites were fabricated by means of a compression molding technique\\u000a using chopped henequen fibers treated at various electron beam (EB) dosages. The interfacial shear strength (IFSS), dynamic\\u000a mechanical properties, and thermal expansion behavior were investigated through a single fiber microbonding test, fractographic\\u000a observation, dynamic mechanical analysis, and thermomechanical analysis, respectively. The results indicated that the

  5. Amorphous oxide alloys as interfacial layers with broadly tunable electronic structures for organic photovoltaic cells.

    PubMed

    Zhou, Nanjia; Kim, Myung-Gil; Loser, Stephen; Smith, Jeremy; Yoshida, Hiroyuki; Guo, Xugang; Song, Charles; Jin, Hosub; Chen, Zhihua; Yoon, Seok Min; Freeman, Arthur J; Chang, Robert P H; Facchetti, Antonio; Marks, Tobin J

    2015-06-30

    In diverse classes of organic optoelectronic devices, controlling charge injection, extraction, and blocking across organic semiconductor-inorganic electrode interfaces is crucial for enhancing quantum efficiency and output voltage. To this end, the strategy of inserting engineered interfacial layers (IFLs) between electrical contacts and organic semiconductors has significantly advanced organic light-emitting diode and organic thin film transistor performance. For organic photovoltaic (OPV) devices, an electronically flexible IFL design strategy to incrementally tune energy level matching between the inorganic electrode system and the organic photoactive components without varying the surface chemistry would permit OPV cells to adapt to ever-changing generations of photoactive materials. Here we report the implementation of chemically/environmentally robust, low-temperature solution-processed amorphous transparent semiconducting oxide alloys, In-Ga-O and Ga-Zn-Sn-O, as IFLs for inverted OPVs. Continuous variation of the IFL compositions tunes the conduction band minima over a broad range, affording optimized OPV power conversion efficiencies for multiple classes of organic active layer materials and establishing clear correlations between IFL/photoactive layer energetics and device performance. PMID:26080437

  6. Electric field induced fluorescence hysteresis of single molecules in poly(methyl methacrylate)

    NASA Astrophysics Data System (ADS)

    Zhou, Haitao; Qin, Chengbing; Chen, Ruiyun; Zhang, Guofeng; Xiao, Liantuan; Jia, Suotang

    2014-10-01

    Single molecule (SM) chips could serve as the fundamental devices in quantum information processing. In this context, a chip with the non-polar SMs of squaraine-derived rotaxanes embedded in a polar poly(methyl methacrylate) matrix was realized and the SM fluorescence hysteresis induced by the electric field was observed at room temperature. Here, we presented a model considering both of the electron transfer and space charge relaxation processes to explain the fluorescence hysteresis effect, and the model-based simulations agreed reasonably well with the experimental results.

  7. Reduction-induced switching of single-molecule conductance of fullerene derivatives.

    PubMed

    Morita, Tomoyuki; Lindsay, Stuart

    2008-08-28

    The effect of electrochemical reduction on the single-molecule conductance of fullerene C60 derivatives was studied by scanning tunneling microscopy. Three types of C60 derivatives were synthesized, a monoadduct having an amino-terminated linker and two bisadducts having two linkers at different positions (trans2 and trans3). Each C60 derivative was immobilized on a gold surface by an amino-gold linkage, confirmed by infrared reflection-absorption spectroscopy. The immobilized C60 derivatives showed reversible and multiple reduction peaks in the cyclic voltammogram in dimethylformamide (DMF) at almost the same potentials as those in solution, showing the redox properties of the molecules are intact on gold. Single-molecule conductances of the bisadducts, which can span between a scanning tunneling microscopy (STM) tip made of gold and substrate with the two linkers, were determined by the STM break-junction measurements in water and DMF. The conductances were 6.1+/-4.5 nS in water and 4.9+/-1.7 nS in DMF for the trans2 bisadduct and 8.4+/-3.4 nS in water and 7.9 nS+/-2.8 in DMF for the trans3 bisadduct. By using a potential-controlled STM setup, the tunneling current through a single molecule was recorded with sweeping the potentials of the tip and substrate. The trans2 bisadduct showed significant changes in the current when the reductions of the C60 moiety occur. Some current curves showed multiple peaks, and the other curves showed stepwise increase and decrease at the C60 reduction and subsequent reoxidation. Statistical analysis afforded stepwise switching of the conductance as the average behavior and suggested that the electron tunneling through the C60 derivative is enhanced as it accepts electrons. PMID:18681478

  8. Interfacial Interactions Pertinent to Single-Molecule and Solar-Energy Applications

    E-print Network

    Upadhyayula, Srigokul

    2013-01-01

    conformers in the “brush” polymer layer to extend away fromhydrated polymer chains are in their brush conformation. (polymer hydration is intact. Therefore, PEG is biocompatible and coatings of PEG (in brush

  9. Single molecule energetics of F1-ATPase motor.

    PubMed

    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. PMID:17158579

  10. Analytical tools for single-molecule fluorescence imaging in cellulo.

    PubMed

    Leake, M C

    2014-07-01

    Recent technological advances in cutting-edge ultrasensitive fluorescence microscopy have allowed single-molecule imaging experiments in living cells across all three domains of life to become commonplace. Single-molecule live-cell data is typically obtained in a low signal-to-noise ratio (SNR) regime sometimes only marginally in excess of 1, in which a combination of detector shot noise, sub-optimal probe photophysics, native cell autofluorescence and intrinsically underlying stochasticity of molecules result in highly noisy datasets for which underlying true molecular behaviour is non-trivial to discern. The ability to elucidate real molecular phenomena is essential in relating experimental single-molecule observations to both the biological system under study as well as offering insight into the fine details of the physical and chemical environments of the living cell. To confront this problem of faithful signal extraction and analysis in a noise-dominated regime, the 'needle in a haystack' challenge, such experiments benefit enormously from a suite of objective, automated, high-throughput analysis tools that can home in on the underlying 'molecular signature' and generate meaningful statistics across a large population of individual cells and molecules. Here, I discuss the development and application of several analytical methods applied to real case studies, including objective methods of segmenting cellular images from light microscopy data, tools to robustly localize and track single fluorescently-labelled molecules, algorithms to objectively interpret molecular mobility, analysis protocols to reliably estimate molecular stoichiometry and turnover, and methods to objectively render distributions of molecular parameters. PMID:24626744

  11. Single molecule as a local acoustic detector for mechanical oscillators.

    PubMed

    Tian, Yuxi; Navarro, Pedro; Orrit, Michel

    2014-09-26

    A single molecule can serve as a nanometer-sized detector of acoustic strain. Such a nanomicrophone has the great advantage that it can be placed very close to acoustic signal sources and high sensitivities can be achieved. We demonstrate this scheme by monitoring the fluorescence intensity of a single dibenzoterrylene molecule in an anthracene crystal attached to an oscillating tuning fork. The characterization of the vibration amplitude and of the detection sensitivity is a first step towards detection and control of nanomechanical oscillators through optical detection and feedback. PMID:25302904

  12. Single molecule probing of SNARE proteins by Atomic Force Microscopy

    PubMed Central

    Liu, Wei; Parpura, Vladimir

    2009-01-01

    Atomic Force Microscopy (AFM) in force spectroscopy mode has recently emerged as a technique of choice for studying mechanical interactions between the proteins of the core Soluble N-ethylmalmeimide-sensitive fusion protein Attachment protein REceptor (SNARE) complex. In these experiments, the rupture force, extension, spontaneous dissociation times and interaction energy for SNARE protein-protein interactions can be obtained at the single molecule level. These measurements, which are complementary to results and conclusions drawn from other techniques, improve our understanding of the role of the SNARE complex in exocytosis. PMID:19161382

  13. Two methods of temperature control for single-molecule measurements.

    PubMed

    Baker, Matthew A B; Inoue, Yuichi; Takeda, Kuniaki; Ishijima, Akihiko; Berry, Richard M

    2011-05-01

    Modern single-molecule biophysical experiments require high numerical aperture oil-immersion objectives in close contact with the sample. We introduce two methods of high numerical aperture temperature control which can be implemented on any microscope: objective temperature control using a ring-shaped Peltier device, and stage temperature control using a fluid flow cooling chip in close thermal contact with the sample. We demonstrate the efficacy of each system by showing the change in speed with temperature of two molecular motors, the bacterial flagellar motor and skeletal muscle myosin. PMID:21279639

  14. Orientation imaging of single molecules by wide-field epifluorescence microscopy

    E-print Network

    Enderlein, Jörg

    Orientation imaging of single molecules by wide-field epifluorescence microscopy Martin Bo imaging method for direct determination of single-molecule orientations is presented that uses a wide, allowing for direct determination of single-molecule orientation based on the characteristic intensity

  15. MAGNETIC QUANTUM TUNNELING AND RELATED PHENOMENA IN SINGLE MOLECULE MAGNETS Presentation

    E-print Network

    del Barco, Enrique

    MAGNETIC QUANTUM TUNNELING AND RELATED PHENOMENA IN SINGLE MOLECULE MAGNETS Presentation A A A A A A MAGNETIC QUANTUM TUNNELING AND RELATED PHENOMENA IN SINGLE MOLECULE MAGNETS MAGNETIC QUANTUM TUNNELING AND RELATED PHENOMENA IN SINGLE MOLECULE MAGNETS ENRIQUE DEL BARCOENRIQUE DEL BARCO Physics Department - New

  16. Single-Molecule Three-Color FRET with Both Negligible Spectral Overlap and Long Observation Time

    E-print Network

    Hohng, Sung Chul

    Single-Molecule Three-Color FRET with Both Negligible Spectral Overlap and Long Observation Time-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

  17. Research Highlights 1. Combination of single-molecule FRET & optical tweezers

    E-print Network

    Hohng, Sung Chul

    Research Highlights 1. Combination of single-molecule FRET & optical tweezers Understanding as little as possible. Single-molecule fluorescence resonance energy transfer (FRET) is a powerful tool to combine single-molecule FRET and optical tweezers. Prior attempts, however, exposed great technical

  18. Single-Molecule Three-Color FRET Sungchul Hohng, Chirlmin Joo, and Taekjip Ha

    E-print Network

    Hohng, Sung Chul

    Single-Molecule Three-Color FRET Sungchul Hohng, Chirlmin Joo, and Taekjip Ha Physics Department (FRET) measured at the single-molecule level can reveal conform- ational changes of biomolecules and intermolecular interactions in physiologically relevant conditions. Thus far single-molecule FRET has been

  19. Single-molecule chemical reactions: Reexamination of the Kramers approach G. Margolin1

    E-print Network

    Barkai, Eli

    Single-molecule chemical reactions: Reexamination of the Kramers approach G. Margolin1 and E; published 2 August 2005 Single-molecule chemical reactions yield insight into fluctuation phenomena.1103/PhysRevE.72.025101 PACS number s : 02.50. r, 82.37.Np, 05.40. a Chemical reaction of a single molecule

  20. Communication: Atomic force detection of single-molecule nonlinear optical vibrational spectroscopy

    E-print Network

    Mukamel, Shaul

    Communication: Atomic force detection of single-molecule nonlinear optical vibrational spectroscopy, 161107 (2014) Communication: Atomic force detection of single-molecule nonlinear optical vibrational displacement of single molecule induced by the applied force, one can look at the gradient force applied

  1. Compaction and Tensile Forces Determine the Accuracy of Folding Landscape Parameters from Single Molecule Pulling Experiments

    E-print Network

    Thirumalai, Devarajan

    , 87.80.Nj The response of biopolymers to mechanical force (f), at the single molecule level, has from single molecule force spectroscopy measurements are the f-dependent position of the transition in the analysis of the single molecule force spectroscopy data is that the molecular extension is a good reaction

  2. FEATURE ARTICLE Single Molecule Raman Spectroscopy at the Junctions of Large Ag Nanocrystals

    E-print Network

    FEATURE ARTICLE Single Molecule Raman Spectroscopy at the Junctions of Large Ag Nanocrystals Jiang because of fundamental spectroscopic issues. The invention of modern confocal single molecule techniques Raman scattering (SERS) in compact clusters of 30-70 nm Ag nanocrystals has shown single molecule Raman

  3. Single Molecule Spectroscopy and Scanning Probe Microscopy to Investigate Excited State Energy Transport in Quantum Dot Higher Order Structures

    NASA Astrophysics Data System (ADS)

    van Orden, Alan; Gelfand, Martin; Ryan, Duncan; Whitcomb, Kevin

    2014-03-01

    Single molecule fluorescence spectroscopy and scanning probe microscopy have been used to investigate small isolated clusters of CdSe/ZnS nanocrystalline quantum dots dispersed on insulating, conducting, and semiconducting surfaces. The aggregated quantum dots exhibit excited state energy transfer and charge transport which affects the time dependent autocorrelation of the photoluminescence (PL) emission intensity, photon counting statistics, blinking statistics, and PL lifetime, as observed by single molecule fluorescence spectroscopy. The structural arrangement of the nanocrystals and the electron transfer between the quantum dots and substrate can be investigated using atomic force microscopy, transmission electron microscopy, and scanning tunneling microscopy. These combined experiments provide novel perspectives on energy and electron transport in quantum dot higher order structures and the effects of structural arrangements, substrates, and attached ligands. These insights will enhance the development of technological applications of quantum dots, including bioimaging, display technology, and alternative energy technology. Research supported by NSF Grant 1059089.

  4. Visualizing helicases unwinding DNA at the single molecule level

    PubMed Central

    Fili, Natali; Mashanov, Gregory I.; Toseland, Christopher P.; Batters, Christopher; Wallace, Mark I.; Yeeles, Joseph T. P.; Dillingham, Mark S.; Webb, Martin R.; Molloy, Justin E.

    2010-01-01

    DNA helicases are motor proteins that catalyze the unwinding of double-stranded DNA into single-stranded DNA using the free energy from ATP hydrolysis. Single molecule approaches enable us to address detailed mechanistic questions about how such enzymes move processively along DNA. Here, an optical method has been developed to follow the unwinding of multiple DNA molecules simultaneously in real time. This was achieved by measuring the accumulation of fluorescent single-stranded DNA-binding protein on the single-stranded DNA product of the helicase, using total internal reflection fluorescence microscopy. By immobilizing either the DNA or helicase, localized increase in fluorescence provides information about the rate of unwinding and the processivity of individual enzymes. In addition, it reveals details of the unwinding process, such as pauses and bursts of activity. The generic and versatile nature of the assay makes it applicable to a variety of DNA helicases and DNA templates. The method is an important addition to the single-molecule toolbox available for studying DNA processing enzymes. PMID:20350930

  5. Association Kinetics from Single Molecule Force Spectroscopy Measurements

    PubMed Central

    Guo, Senli; Lad, Nimit; Ray, Chad; Akhremitchev, Boris B.

    2009-01-01

    Abstract Single molecule force spectroscopy is often used to study the dissociation of single molecules by applying mechanical force to the intermolecular bond. These measurements provide the kinetic parameters of dissociation. We present what to our knowledge is a new atomic force microscopy-based approach to obtain the activation energy of the association reaction and approximate grafting density of reactive receptors using the dependence of the probability to form molecular bonds on probe velocity when one of the interacting molecules is tethered by a flexible polymeric linker to the atomic force microscopy probe. Possible errors in the activation energy measured with this approach are considered and resulting corrections are included in the data analysis. This new approach uses the same experimental setup as traditional force spectroscopy measurements that quantify dissociation kinetics. We apply the developed methodology to measure the activation energy of biotin-streptavidin association (including a contribution from the steric factor) and obtain a value of 8 ± 1 kT. This value is consistent with the association rate measured previously in solution. Comparison with the solution-derived activation energy indicates that kinetics of biotin-streptavidin binding is mainly controlled by the reaction step. PMID:19383484

  6. New Antifouling Platform Characterized by Single-Molecule Imaging

    PubMed Central

    2015-01-01

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

  7. STM control of chemical reaction: single-molecule synthesis.

    PubMed

    Hla, Saw-Wai; Rieder, Karl-Heinz

    2003-01-01

    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. PMID:12626735

  8. Single-molecule correlated chemical probing of RNA

    PubMed Central

    Homan, Philip J.; Favorov, Oleg V.; Lavender, Christopher A.; Kursun, Olcay; Ge, Xiyuan; Busan, Steven; Dokholyan, Nikolay V.; Weeks, Kevin M.

    2014-01-01

    Complex higher-order RNA structures play critical roles in all facets of gene expression; however, the through-space interaction networks that define tertiary structures and govern sampling of multiple conformations are poorly understood. Here we describe single-molecule RNA structure analysis in which multiple sites of chemical modification are identified in single RNA strands by massively parallel sequencing and then analyzed for correlated and clustered interactions. The strategy thus identifies RNA interaction groups by mutational profiling (RING-MaP) and makes possible two expansive applications. First, we identify through-space interactions, create 3D models for RNAs spanning 80–265 nucleotides, and characterize broad classes of intramolecular interactions that stabilize RNA. Second, we distinguish distinct conformations in solution ensembles and reveal previously undetected hidden states and large-scale structural reconfigurations that occur in unfolded RNAs relative to native states. RING-MaP single-molecule nucleic acid structure interrogation enables concise and facile analysis of the global architectures and multiple conformations that govern function in RNA. PMID:25205807

  9. High contrast single molecule tracking in the pericellular coat

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

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

    2014-03-12

    Antifouling surfaces have been widely studied for their importance in medical devices and industry. Antifouling surfaces mostly achieved by methoxy-poly(ethylene glycol) (mPEG) have shown biomolecular adsorption less than 1 ng/cm(2) which was measured by surface analytical tools such as surface plasmon resonance (SPR) spectroscopy, quartz crystal microbalance (QCM), or optical waveguide lightmode (OWL) spectroscopy. Herein, we utilize a single-molecule imaging technique (i.e., an ultimate resolution) to study antifouling properties of functionalized surfaces. We found that about 600 immunoglobulin G (IgG) molecules are adsorbed. This result corresponds to ?5 pg/cm(2) adsorption, which is far below amount for the detection limit of the conventional tools. Furthermore, we developed a new antifouling platform that exhibits improved antifouling performance that shows only 78 IgG molecules adsorbed (?0.5 pg/cm(2)). The antifouling platform consists of forming 1 nm TiO2 thin layer, on which peptidomimetic antifouling polymer (PMAP) is robustly anchored. The unprecedented antifouling performance can potentially revolutionize a variety of research fields such as single-molecule imaging, medical devices, biosensors, and others. PMID:24503420

  11. Single Molecule Observation of the Cyclization of Short DNA Duplex

    NASA Astrophysics Data System (ADS)

    Akinyi, Teckla; Lee, I.-Ren; Ha, Taekjip

    2014-03-01

    In the presented work, a single molecule DNA cyclization assay was used to follow the looping kinetics of single DNA 83 bp molecules, utilizing single molecule fluorescence energy transfer (smFRET) technique. The assay was first prepared in a Na+ free condition and the majority of the DNA was in its unlooped form. A sudden Na+ jump was introduced at different concentrations (0.05-1.75M) and finally yielded DNA in its looping state by annealing the complementary single-strand overhangs of the assay. Looping and unlooping rates were obtained from the kinetic measurements. The result shows a positive and negative linear dependence of the Na+ concentration to the looping and unlooping rate, respectively, until they reach a plateau at 500 mM. The plateau persists until about 1M. For concentrations beyond 1M, an immoderate increase in looping rate is noticed while the unlooping rate does so gradually. Above 1M Na+ there is a preference of looping events that is attributed to the increase of the annealing rate of the overhangs rather than increased flexibility, consistent with earlier studies by Ibrahim Cisse et al.(2012). A protein mediated cyclization assay was also used in experiments with HU protein in which a dramatic increase in the looping rate is noticeable. However in high HU concentration, looping is prohibited implying filament formation.

  12. Single-Molecule Electrical Random Resequencing of DNA and RNA

    PubMed Central

    Ohshiro, Takahito; Matsubara, Kazuki; Tsutsui, Makusu; Furuhashi, Masayuki; Taniguchi, Masateru; Kawai, Tomoji

    2012-01-01

    Two paradigm shifts in DNA sequencing technologies—from bulk to single molecules and from optical to electrical detection—are expected to realize label-free, low-cost DNA sequencing that does not require PCR amplification. It will lead to development of high-throughput third-generation sequencing technologies for personalized medicine. Although nanopore devices have been proposed as third-generation DNA-sequencing devices, a significant milestone in these technologies has been attained by demonstrating a novel technique for resequencing DNA using electrical signals. Here we report single-molecule electrical resequencing of DNA and RNA using a hybrid method of identifying single-base molecules via tunneling currents and random sequencing. Our method reads sequences of nine types of DNA oligomers. The complete sequence of 5?-UGAGGUA-3? from the let-7 microRNA family was also identified by creating a composite of overlapping fragment sequences, which was randomly determined using tunneling current conducted by single-base molecules as they passed between a pair of nanoelectrodes. PMID:22787559

  13. Naphthalene diimides as tunable fluorophores suitable for single molecule applications

    NASA Astrophysics Data System (ADS)

    Bell, Toby D. M.; Yap, Sheryll; Jani, Chintan; Langford, Steven J.; Hofkens, Johan; De Schryver, Frans; Ghiggino, Kenneth P.

    2007-02-01

    The photophysics of two new substituted aminopropenyl naphthalene diimide (SANDI) dyes are reported. The molecules exhibit many of the photophysical properties required for fluorescence labeling applications including high photostability and high fluorescence quantum yields (> 0.5) in the visible region of the spectrum. Furthermore, the emission is sensitive to the number of substituents attached to the aromatic core, and to the surrounding environment. For example, in toluene as solvent, the mono-allyl SANDI has an emission maximum at 550 nm, whereas the di-allyl SANDI emits at 630 nm. The fluorescence decay times are in the range of ~8 - 12 ns and the Forster critical distance for fluorescence resonance energy transfer (FRET) between the mono- and di-allyl SANDI derivatives is 4.1 nm for a random donor-acceptor orientation. Single molecules of the di-allyl SANDI embedded in poly(methyl methacrylate) films show very low yields of photobleaching and very few fluorescence intermittencies or "blinks". These compounds are ideal candidates for applications at the single molecule level, for example, as FRET labels.

  14. Single molecule measurement of the “speed limit” of DNA polymerase

    PubMed Central

    Schwartz, Jerrod J.; Quake, Stephen R.

    2009-01-01

    Although DNA replication is often imagined as a regular and continuous process, the DNA polymerase enzyme is a complicated machine and can pause upon encountering physical and chemical barriers. We used single molecule measurements to make a detailed characterization of this behavior as a function of the template's secondary structure and the sequence context. Strand displacement replication through a DNA hairpin by single DNA polymerase molecules was measured in real time with near single base resolution and physiological concentrations of nucleotides. These data enabled the measurement of the intrinsic “speed limit” of DNA polymerase by separating the burst synthesis rate from pausing events. The strand displacement burst synthesis rate for Escherichia coli DNA Polymerase I (KF) was found to be an order of magnitude faster than the reported bulk strand displacement rate, a discrepancy that can be accounted for by to sequence specific pausing. The ability to follow trajectories of single molecules revealed that the burst synthesis rate is also highly stochastic and varies up to 50-fold from molecule to molecule. Surprisingly, our results allow a unified explanation of strand displacement and single strand primer extension synthesis rates. PMID:19906998

  15. Single-molecule imaging of receptor-receptor interactions.

    PubMed

    Suzuki, Kenichi G N; Kasai, Rinshi S; Fujiwara, Takahiro K; Kusumi, Akihiro

    2013-01-01

    Single-molecule imaging is a powerful tool for the study of dynamic molecular interactions in living cell plasma membranes. Herein, we describe a single-molecule imaging microscopy technique that can be used to measure lifetimes and densities of receptor dimers and oligomers. This method can be performed using a total internal reflection fluorescent microscope equipped with one or two high-sensitivity cameras. For dual-color observation, two images obtained synchronously in different colors are spatially corrected and then overlaid. Receptors must be expressed at low density in cell plasma membranes because high-density expression (>2 molecules/?m(2)) creates difficulty for tracking individual fluorescent spots. In addition, the receptors should be labeled with highly photostable fluorophores at high efficiency because short photobleaching lifetimes and low labeling efficiency of receptors reduce the probability of detecting dimers and oligomers. In this chapter, we describe methods for observing and detecting colocalization of the individual fluorescent spots of receptors labeled with fluorophores via small tags and the estimation of true dimer and oligomer lifetimes after correction with photobleaching lifetimes of fluorophores. PMID:24143988

  16. Single-Molecule Microscopy and Force Spectroscopy of Membrane Proteins

    NASA Astrophysics Data System (ADS)

    Engel, Andreas; Janovjak, Harald; Fotiadis, Dimtrios; Kedrov, Alexej; Cisneros, David; Müller, Daniel J.

    Single-molecule atomic force microscopy (AFM) provides novel ways to characterize the structure-function relationship of native membrane proteins. High-resolution AFM topographs allow observing the structure of single proteins at sub-nanometer resolution as well as their conformational changes, oligomeric state, molecular dynamics and assembly. We will review these feasibilities illustrating examples of membrane proteins in native and reconstituted membranes. Classification of individual topographs of single proteins allows understanding the principles of motions of their extrinsic domains, to learn about their local structural flexibilities and to find the entropy minima of certain conformations. Combined with the visualization of functionally related conformational changes these insights allow understanding why certain flexibilities are required for the protein to function and how structurally flexible regions allow certain conformational changes. Complementary to AFM imaging, single-molecule force spectroscopy (SMFS) experiments detect molecular interactions established within and between membrane proteins. The sensitivity of this method makes it possible to measure interactions that stabilize secondary structures such as transmembrane ?-helices, polypeptide loops and segments within. Changes in temperature or protein-protein assembly do not change the locations of stable structural segments, but influence their stability established by collective molecular interactions. Such changes alter the probability of proteins to choose a certain unfolding pathway. Recent examples have elucidated unfolding and refolding pathways of membrane proteins as well as their energy landscapes.

  17. Single-Molecule Electrical Random Resequencing of DNA and RNA

    NASA Astrophysics Data System (ADS)

    Ohshiro, Takahito; Matsubara, Kazuki; Tsutsui, Makusu; Furuhashi, Masayuki; Taniguchi, Masateru; Kawai, Tomoji

    2012-07-01

    Two paradigm shifts in DNA sequencing technologies--from bulk to single molecules and from optical to electrical detection--are expected to realize label-free, low-cost DNA sequencing that does not require PCR amplification. It will lead to development of high-throughput third-generation sequencing technologies for personalized medicine. Although nanopore devices have been proposed as third-generation DNA-sequencing devices, a significant milestone in these technologies has been attained by demonstrating a novel technique for resequencing DNA using electrical signals. Here we report single-molecule electrical resequencing of DNA and RNA using a hybrid method of identifying single-base molecules via tunneling currents and random sequencing. Our method reads sequences of nine types of DNA oligomers. The complete sequence of 5'-UGAGGUA-3' from the let-7 microRNA family was also identified by creating a composite of overlapping fragment sequences, which was randomly determined using tunneling current conducted by single-base molecules as they passed between a pair of nanoelectrodes.

  18. Biophysical characterization of DNA binding from single molecule force measurements

    NASA Astrophysics Data System (ADS)

    Chaurasiya, Kathy R.; Paramanathan, Thayaparan; McCauley, Micah J.; Williams, Mark C.

    2010-09-01

    Single molecule force spectroscopy is a powerful method that uses the mechanical properties of DNA to explore DNA interactions. Here we describe how DNA stretching experiments quantitatively characterize the DNA binding of small molecules and proteins. Small molecules exhibit diverse DNA binding modes, including binding into the major and minor grooves and intercalation between base pairs of double-stranded DNA (dsDNA). Histones bind and package dsDNA, while other nuclear proteins such as high mobility group proteins bind to the backbone and bend dsDNA. Single-stranded DNA (ssDNA) binding proteins slide along dsDNA to locate and stabilize ssDNA during replication. Other proteins exhibit binding to both dsDNA and ssDNA. Nucleic acid chaperone proteins can switch rapidly between dsDNA and ssDNA binding modes, while DNA polymerases bind both forms of DNA with high affinity at distinct binding sites at the replication fork. Single molecule force measurements quantitatively characterize these DNA binding mechanisms, elucidating small molecule interactions and protein function.

  19. Single Molecule Studies of Energy Transfer in Semiconductor Nanocrystal Clusters

    NASA Astrophysics Data System (ADS)

    Shepherd, Douglas; Whitcomb, Kevin; Goodwin, Peter; Gelfand, Martin; van Orden, Alan

    2010-03-01

    Enhanced fluorescence intermittency has been reported in single molecule fluorescence experiments on small clusters of semiconductor nanocrystals^1 (NCs). We report here on studies of small clusters of NCs by single molecule time-correlated single photon counting. According to this analysis, clusters typically blink on a microsecond to millisecond time scale; whereas, isolated NCs blink on a much longer millisecond to second time scale. A fast-decay component in the cluster fluorescence lifetime, not present in single NCs, is correlated with low fluorescence intensity. A model based on nonradiative energy transfer to NCs with smaller bandgap, combined with independent blinking for the NCs in the cluster, accounts for the main experimental features. In this model the smallest-gap NC dominates the emission properties, in particular the ``off'' time distribution of the cluster, which experimentally resembles that for a single NC. [1] Yu, M. and A. Van Orden, Enhanced Fluorescence Intermittency of CdSe-ZnS Quantum-Dot Cluster, Physical Review Letters, 2006 237402-4

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

    PubMed

    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. PMID:25622229

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

    NASA Astrophysics Data System (ADS)

    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.

  2. Transport properties of a single-molecule diode.

    PubMed

    Lörtscher, Emanuel; Gotsmann, Bernd; Lee, Youngu; Yu, Luping; Rettner, Charles; Riel, Heike

    2012-06-26

    Charge transport through single diblock dipyrimidinyl diphenyl molecules consisting of a donor and acceptor moiety was measured in the low-bias regime and as a function of bias at different temperatures using the mechanically controllable break-junction technique. Conductance histograms acquired at 10 mV reveal two distinct peaks, separated by a factor of 1.5, representing the two orientations of the single molecule with respect to the applied bias. The current-voltage characteristics exhibit a temperature-independent rectification of up to a factor of 10 in the temperature range between 300 and 50 K with single-molecule currents of 45-70 nA at ±1.5 V. The current-voltage characteristics are discussed using a semiempirical model assuming a variable coupling of the molecular energy levels as well as a nonsymmetric voltage drop across the molecular junction, thus shifting the energy levels accordingly. The excellent agreement of the data with the proposed model suggests that the rectification originates from an asymmetric Coulomb blockade in combination with an electric-field-induced level shifting. PMID:22582743

  3. Surface Passivation for Single-molecule Protein Studies

    PubMed Central

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

    2014-01-01

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

  4. Nanoscale characterization of interfacial electronic properties and degradation mechanisms of organic thin films for electroluminescence displays

    NASA Astrophysics Data System (ADS)

    Xu, Mingsheng

    For the first time, the promising organic light-emitting diode (OLED), indium tin oxide (ITO)/copper phthalocyanine (CuPc)/N,N '-di(naphthalene-l-yl)-N,N'-diphthalbenzidine (NPB)/tris(8-quinolinolatoline) aluminum (Alq3) (ITO/CuPc/NPB/Alq 3), has been selected for investigating its interfacial properties, and morphological degradation mechanisms induced by moisture and temperature through the systematic visualization by the state-of-the-art scanning probe microscopy (SPM). The motivation of this thesis lies in the importance of the OLED interfaces associated with the OLED's quantum efficiency, and morphological alteration in respect to device lifetime and luminance. Variable-temperature ultrahigh vacuum scanning tunnelling microscopy and spectroscopy (VT-UHV/STM and STS) are used to investigate the interfacial electronic properties at the Au(111)/CuPc interface. The energy band gap of CuPc ultrathin films on Au(111) measured by the charge injection from the STM tip into the highest occupied molecular orbitals (HOMO) and the lowest unoccupied molecular orbitals (LUMO) levels of CuPc is ˜1.9--2.1 eV, which is comparable to the optical band gap (˜1.7 eV). This result indicates that a dipole layer and/or image forces is present right at the Au(111)/CuPc interface, and confirms that the common vacuum level alignment at the interface is invalid. Also, it is found that the morphological features probably affect the tunnelling current. To scrutinize the degradation associated with morphological variations of the Alga-based OLED structures, a variable-temperature tapping mode atomic force microscope (VT-AFM) and other complementary techniques such as thickness-shear mode (TSM) acoustic wave mass sensor and micro-Raman spectroscopy have been employed to sift the degradation mechanisms induced by ambient atmosphere and Joule heating. A volatile species released from the Alq3 thin films under exposure to moisture has been traced by the TSM acoustic wave mass sensor. This volatile species is most likely to be the freed 8-quinolinolatoline (8-Hq), a product of the reaction by Alq3 with water. As a result, the degradation mechanisms associated with morphological change of Alq 3 thin film by moisture are the crystallization of Alq3, the hydration of Alq3, and the reaction by Alq3 complex with moisture. Moreover, it has been visualized that the hydrated Alq 3 can be transformed into crystalline Alq3 structures and dark holes by the captioned reactions. Similarly, the ambient-induced morphological changes of ITO/CuPc, ITO/CuPc/NPB and ITO/CuPc/NPB/Alq3 structures have also been investigated. It is found that indium diffusion from the ITO substrate into organic layers possibly exists. After stored in an ambient atmosphere, crystallization of NPB thin films takes place. Photoluminescence (PL) investigation and local current map of the various degrading/degraded thin films suggest that the morphological changes, e.g., the formation of dark holes and Alq3 crystalline structures, essentially affect the PL and electrical characteristics. (Abstract shortened by UMI.)

  5. Simultaneous, Coincident Optical Trapping and Single-Molecule Fluorescence

    PubMed Central

    Lang, Matthew J.; Fordyce, Polly M.; Engh, Anita M.; Neuman, Keir C.; Block, Steven M.

    2006-01-01

    We constructed a microscope-based instrument capable of simultaneous, spatially coincident optical trapping and single-molecule fluorescence. The capabilities of this apparatus were demonstrated by studying the force-induced strand separation of a dye-labeled, 15-basepair region of double stranded DNA, with force applied either parallel (“unzipping” mode) or perpendicular (“shearing” mode) to the long axis of the region. Mechanical transitions corresponding to DNA hybrid rupture occurred simultaneously with discontinuous changes in the fluorescence emission. The rupture force was strongly dependent on the direction of applied force, indicating the existence of distinct unbinding pathways for the two force-loading modes. From the rupture force histograms, we determined the distance to the thermodynamic transition state and the thermal off rates in the absence of load for both processes. PMID:15782176

  6. Progress towards DNA sequencing at the single molecule level

    SciTech Connect

    Goodwin, P.M.; Affleck, R.L.; Ambrose, W.P. [and others

    1995-12-01

    We describe progress towards sequencing DNA at the single molecule level. Our technique involves incorporation of fluorescently tagged nucleotides into a targeted sequence, anchoring the labeled DNA strand in a flowing stream, sequential exonuclease digestion of the DNA strand, and efficient detection and identification of single tagged nucleotides. Experiments demonstrating strand specific exonuclease digestion of fluorescently labeled DNA anchored in flow as well as the detection of single cleaved fluorescently tagged nucleotides from a small number of anchored DNA fragments axe described. We find that the turnover rate of Esherichia coli exonuclease III on fluorescently labeled DNA in flow at 36{degree}C is {approximately}7 nucleotides per DNA strand per second, which is approximately the same as that measured for this enzyme on native DNA under static, saturated (excess enzyme) conditions. Experiments demonstrating the efficient detection of single fluorescent molecules delivered electrokinetically to a {approximately}3 pL probe volume are also described.

  7. Three dimensional single molecule localization using a phase retrieved pupilfunction

    PubMed Central

    Liu, Sheng; Kromann, Emil B.; Krueger, Wesley D.; Bewersdorf, Joerg; Lidke, Keith A.

    2013-01-01

    Localization-based superresolution imaging is dependent on finding the positions of individualfluorophores in a sample by fitting the observed single-molecule intensity pattern to the microscopepoint spread function (PSF). For three-dimensional imaging, system-specific aberrations of theoptical system can lead to inaccurate localizations when the PSF model does not account for theseaberrations. Here we describe the use of phase-retrieved pupil functions to generate a more accuratePSF and therefore more accurate 3D localizations. The complex-valued pupil function containsinformation about the system-specific aberrations and can thus be used to generate the PSF forarbitrary defocus. Further, it can be modified to include depth dependent aberrations. We describethe phase retrieval process, the method for including depth dependent aberrations, and a fastfitting algorithm using graphics processing units. The superior localization accuracy of the pupilfunction generated PSF is demonstrated with dual focal plane 3D superresolution imaging ofbiological structures. PMID:24514501

  8. Quantitative single-molecule imaging by confocal laser scanning microscopy.

    PubMed

    Vukojevic, Vladana; Heidkamp, Marcus; Ming, Yu; Johansson, Björn; Terenius, Lars; Rigler, Rudolf

    2008-11-25

    A new approach to quantitative single-molecule imaging by confocal laser scanning microscopy (CLSM) is presented. It relies on fluorescence intensity distribution to analyze the molecular occurrence statistics captured by digital imaging and enables direct determination of the number of fluorescent molecules and their diffusion rates without resorting to temporal or spatial autocorrelation analyses. Digital images of fluorescent molecules were recorded by using fast scanning and avalanche photodiode detectors. In this way the signal-to-background ratio was significantly improved, enabling direct quantitative imaging by CLSM. The potential of the proposed approach is demonstrated by using standard solutions of fluorescent dyes, fluorescently labeled DNA molecules, quantum dots, and the Enhanced Green Fluorescent Protein in solution and in live cells. The method was verified by using fluorescence correlation spectroscopy. The relevance for biological applications, in particular, for live cell imaging, is discussed. PMID:19011092

  9. The bright future of single-molecule fluorescence imaging

    PubMed Central

    Juette, Manuel F.; Terry, Daniel S.; Wasserman, Michael R.; Zhou, Zhou; Altman, Roger B.; Zheng, Qinsi; Blanchard, Scott C.

    2014-01-01

    Single-molecule Förster resonance energy transfer (smFRET) is an essential and maturing tool to probe biomolecular interactions and conformational dynamics in vitro and, increasingly, in living cells. Multi-color smFRET enables the correlation of multiple such events and the precise dissection of their order and timing. However, the requirements for good spectral separation, high time resolution, and extended observation times place extraordinary demands on the fluorescent labels used in such experiments. Together with advanced experimental designs and data analysis, the development of long-lasting, non-fluctuating fluorophores is therefore proving key to progress in the field. Recently developed strategies for obtaining ultra-stable organic fluorophores spanning the visible spectrum are underway that will enable multi-color smFRET studies to deliver on their promise of previously unachievable biological insights. PMID:24956235

  10. New Insights into the Spliceosome by Single Molecule Fluorescence Microscopy

    PubMed Central

    Hoskins, Aaron A.; Gelles, Jeff; Moore, Melissa J.

    2011-01-01

    Splicing is an essential eukaryotic process in which introns are excised from precursors to messenger RNAs and exons ligated together. This reaction is catalyzed by a multi-MegaDalton machine called the spliceosome, composed of 5 small nuclear RNAs (snRNAs) and a core set of ~100 proteins minimally required for activity. Due to the spliceosome’s size, its low abundance in cellular extracts, and its highly dynamic assembly pathway, analysis of the kinetics of splicing and the conformational rearrangements occurring during spliceosome assembly and disassembly has proven extraordinarily challenging. Here, we review recent progress in combining chemical biology methodologies with single molecule fluorescence techniques to provide a window into splicing in real time. These methods complement ensemble measurements of splicing in vivo and in vitro to facilitate kinetic dissection of pre-mRNA splicing. PMID:22057211

  11. Ultrasensitive nucleic acid sequence detection by single-molecule electrophoresis

    SciTech Connect

    Castro, A; Shera, E.B.

    1996-09-01

    This is the final report of a one-year laboratory-directed research and development project at Los Alamos National Laboratory. There has been considerable interest in the development of very sensitive clinical diagnostic techniques over the last few years. Many pathogenic agents are often present in extremely small concentrations in clinical samples, especially at the initial stages of infection, making their detection very difficult. This project sought to develop a new technique for the detection and accurate quantification of specific bacterial and viral nucleic acid sequences in clinical samples. The scheme involved the use of novel hybridization probes for the detection of nucleic acids combined with our recently developed technique of single-molecule electrophoresis. This project is directly relevant to the DOE`s Defense Programs strategic directions in the area of biological warfare counter-proliferation.

  12. Processive cytoskeletal motors studied with single-molecule fluorescence techniques.

    PubMed

    Belyy, Vladislav; Yildiz, Ahmet

    2014-10-01

    Processive cytoskeletal motors from the myosin, kinesin, and dynein families walk on actin filaments and microtubules to drive cellular transport and organization in eukaryotic cells. These remarkable molecular machines are able to take hundreds of successive steps at speeds of up to several microns per second, allowing them to effectively move vesicles and organelles throughout the cytoplasm. Here, we focus on single-molecule fluorescence techniques and discuss their wide-ranging applications to the field of cytoskeletal motor research. We cover both traditional fluorescence and sub-diffraction imaging of motors, providing examples of how fluorescence data can be used to measure biophysical parameters of motors such as coordination, stepping mechanism, gating, and processivity. We also outline some remaining challenges in the field and suggest future directions. PMID:24882363

  13. A Molecular Tuning Fork in Single-Molecule Mechanochemical Sensing.

    PubMed

    Mandal, Shankar; Koirala, Deepak; Selvam, Sangeetha; Ghimire, Chiran; Mao, Hanbin

    2015-06-22

    The separate arrangement of target recognition and signal transduction in conventional biosensors often compromises the real-time response and can introduce additional noise. To address these issues, we combined analyte recognition and signal reporting by mechanochemical coupling in a single-molecule DNA template. We incorporated a DNA hairpin as a mechanophore in the template, which, under a specific force, undergoes stochastic transitions between folded and unfolded hairpin structures (mechanoescence). Reminiscent of a tuning fork that vibrates at a fixed frequency, the device was classified as a molecular tuning fork (MTF). By monitoring the lifetime of the folded and unfolded hairpins with equal populations, we were able to differentiate between the mono- and bivalent binding modes during individual antibody-antigen binding events. We anticipate these mechanospectroscopic concepts and methods will be instrumental for the development of novel bioanalyses. PMID:25960021

  14. Single-molecule denaturation mapping of DNA in nanofluidic channels

    PubMed Central

    Reisner, Walter; Larsen, Niels B.; Silahtaroglu, Asli; Kristensen, Anders; Tommerup, Niels; Tegenfeldt, Jonas O.; Flyvbjerg, Henrik

    2010-01-01

    Here we explore the potential power of denaturation mapping as a single-molecule technique. By partially denaturing YOYO®-1-labeled DNA in nanofluidic channels with a combination of formamide and local heating, we obtain a sequence-dependent “barcode” corresponding to a series of local dips and peaks in the intensity trace along the extended molecule. We demonstrate that this structure arises from the physics of local denaturation: statistical mechanical calculations of sequence-dependent melting probability can predict the barcode to be observed experimentally for a given sequence. 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. PMID:20616076

  15. Single-molecule paleoenzymology probes the chemistry of resurrected enzymes.

    PubMed

    Perez-Jimenez, Raul; Inglés-Prieto, Alvaro; Zhao, Zi-Ming; Sanchez-Romero, Inmaculada; Alegre-Cebollada, Jorge; Kosuri, Pallav; Garcia-Manyes, Sergi; Kappock, T Joseph; Tanokura, Masaru; Holmgren, Arne; Sanchez-Ruiz, Jose M; Gaucher, Eric A; Fernandez, Julio M

    2011-05-01

    It is possible to travel back in time at the molecular level by reconstructing proteins from extinct organisms. Here we report the reconstruction, based on sequence predicted by phylogenetic analysis, of seven Precambrian thioredoxin enzymes (Trx) dating back between ~1.4 and ~4 billion years (Gyr). The reconstructed enzymes are up to 32 °C more stable than modern enzymes, and the oldest show markedly higher activity than extant ones at pH 5. We probed the mechanisms of reduction of these enzymes using single-molecule force spectroscopy. From the force dependency of the rate of reduction of an engineered substrate, we conclude that ancient Trxs use chemical mechanisms of reduction similar to those of modern enzymes. Although Trx enzymes have maintained their reductase chemistry unchanged, they have adapted over 4 Gyr to the changes in temperature and ocean acidity that characterize the evolution of the global environment from ancient to modern Earth. PMID:21460845

  16. Single-Molecule Tracking of Polymer Surface Diffusion

    NASA Astrophysics Data System (ADS)

    Skaug, Michael; Mabry, Joshua; Schwartz, Daniel

    2014-03-01

    The mobility of polymers adsorbed on a solid surface is important in thin film formation, adhesion phenomena and biosensing applications, but it is still poorly understood. We used single-molecule fluorescence experiments to follow the motion of isolated polyethylene glycol chains adsorbed at a hydrophobic solid-aqueous interface. We found that molecules moved on the surface via a continuous time random walk mechanism, where periods of immobilization were punctuated by flights through the bulk liquid. The dependence of surface mobility on molecular weight suggested that surface-adsorbed polymers maintained effectively three-dimensional surface conformations. These results indicate that polymer surface diffusion, rather than occurring in the two dimensions of the interface, is dominated by a three-dimensional mechanism that leads to large surface displacements and significant bulk-surface coupling. The authors acknowledge support from the U.S. Department of Energy Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division (DE-SC0001854).

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

    PubMed

    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. PMID:25562308

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

    E-print Network

    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.

  19. Nonlinear irreversible thermodynamics of single-molecule experiments

    NASA Astrophysics Data System (ADS)

    Santamaría-Holek, I.; López-Alamilla, N. J.; Hidalgo-Soria, M.; Pérez-Madrid, A.

    2015-06-01

    Irreversible thermodynamics of single-molecule experiments subject to external constraining forces of a mechanical nature is presented. Extending Onsager's formalism to the nonlinear case of systems under nonequilibrium external constraints, we are able to calculate the entropy production and the general nonlinear kinetic equations for the variables involved. In particular, we analyze the case of RNA stretching protocols obtaining critical oscillations between different configurational 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.

  20. Single Molecule Detection Using Surface-Enhanced Raman Scattering (SERS)

    SciTech Connect

    Kneipp, K.; Wang, Y.; Kneipp, H.; Perelman, L.T.; Itzkan, I.; Dasari, R.R.; Feld, M.S. [George R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)] [George R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); [Department of Physics, Technical University of Berlin, D 10623 Berlin (Germany)

    1997-03-01

    By exploiting the extremely large effective cross sections (10{sup -17}{endash}10{sup -16}cm{sup 2}/molecule) available from surface-enhanced Raman scattering (SERS), we achieved the first observation of single molecule Raman scattering. Measured spectra of a single crystal violet molecule in aqueous colloidal silver solution using one second collection time and about 2{times}10{sup 5}W/cm{sup 2} nonresonant near-infrared excitation show a clear {open_quotes}fingerprint{close_quotes} of its Raman features between 700 and 1700cm{sup -1}. Spectra observed in a time sequence for an average of 0.6 dye molecule in the probed volume exhibited the expected Poisson distribution for actually measuring 0, 1, 2, or 3 molecules. {copyright} {ital 1997} {ital The American Physical Society}

  1. Super-Resolution Fluorescence Imaging with Single Molecules

    PubMed Central

    Sahl, Steffen J.; Moerner, W. E.

    2013-01-01

    The ability to detect, image and localize single molecules optically with high spatial precision by their fluorescence enables an emergent class of super-resolution microscopy methods which have overcome the longstanding diffraction barrier for far-field light-focusing optics. Achieving spatial resolutions of 20–40 nm or better in both fixed and living cells, these methods are currently being established as powerful tools for minimally-invasive spatiotemporal analysis of structural details in cellular processes which benefit from enhanced resolution. Briefly covering the basic principles, this short review then summarizes key recent developments and application examples of two- and three-dimensional (3D) multi-color techniques and faster time-lapse schemes. The prospects for quantitative imaging – in terms of its ability to correct for dipole-emission-induced systematic localization errors and to provide accurate counts of molecular copy numbers within nanoscale cellular domains – are discussed. PMID:23932284

  2. Single Molecule Manipulation and Spectroscopy of Chlorophyll-a from Spinach

    NASA Astrophysics Data System (ADS)

    Benson, Jessica-Jones

    2005-03-01

    Chlorophyll-a, a molecule produced from `Spinach', adsorbed on a Au(111) surface has been investigated by using an ultra-high-vacuum low-temperature scanning-tunneling-microscope (UHV-LT-STM) at liquid helium temperatures. Studies are carried out both on isolated single molecules and on self-assembled molecular layers. The tunneling I-V and dI-dV spectroscopy of chlorophyll-a elucidate electronic properties of single molecule, such as the HOMO-LOMO gap and molecular orbital states. Mechanical stability of the chlorophyll-a is examined by using STM lateral manipulation (1,2). Here, the STM tip is placed just a few angstrom separation from the molecule to increase the tip-molecule interaction. Then the tip is laterally scanned across the surface resulting in pulling of the molecule. The detailed molecule movement is directly monitored through the corresponding STM-tip height signals. Our results reveal that the spinach molecule is a promising candidate for environmental friendly nano-device applications. (1). S.-W. Hla, K.-H. Rieder, Ann. Rev. Phys. Chem. 54 (2003) 307-330. (2). S.-W. Hla, et al. Phys. Rev. Lett. 93 (2004), 208302. This work is financially supported by the US-DOE grant DE-FG02-02ER46012.

  3. Nanopore arrays in a silicon membrane for parallel single-molecule detection: DNA translocation.

    PubMed

    Zhang, Miao; Schmidt, Torsten; Jemt, Anders; Sahlén, Pelin; Sychugov, Ilya; Lundeberg, Joakim; Linnros, Jan

    2015-08-01

    Optical nanopore sensing offers great potential in single-molecule detection, genotyping, or DNA sequencing for high-throughput applications. However, one of the bottle-necks for fluorophore-based biomolecule sensing is the lack of an optically optimized membrane with a large array of nanopores, which has large pore-to-pore distance, small variation in pore size and low background photoluminescence (PL). Here, we demonstrate parallel detection of single-fluorophore-labeled DNA strands (450 bps) translocating through an array of silicon nanopores that fulfills the above-mentioned requirements for optical sensing. The nanopore array was fabricated using electron beam lithography and anisotropic etching followed by electrochemical etching resulting in pore diameters down to ?7 nm. The DNA translocation measurements were performed in a conventional wide-field microscope tailored for effective background PL control. The individual nanopore diameter was found to have a substantial effect on the translocation velocity, where smaller openings slow the translocation enough for the event to be clearly detectable in the fluorescence. Our results demonstrate that a uniform silicon nanopore array combined with wide-field optical detection is a promising alternative with which to realize massively-parallel single-molecule detection. PMID:26180050

  4. Observing Lysozyme's Closing and Opening Motions by High-Resolution Single-Molecule Enzymology.

    PubMed

    Akhterov, Maxim V; Choi, Yongki; Olsen, Tivoli J; Sims, Patrick C; Iftikhar, Mariam; Gul, O Tolga; Corso, Brad L; Weiss, Gregory A; Collins, Philip G

    2015-06-19

    Single-molecule techniques can monitor the kinetics of transitions between enzyme open and closed conformations, but such methods usually lack the resolution to observe the underlying transition pathway or intermediate conformational dynamics. We have used a 1 MHz bandwidth carbon nanotube transistor to electronically monitor single molecules of the enzyme T4 lysozyme as it processes substrate. An experimental resolution of 2 ?s allowed the direct recording of lysozyme's opening and closing transitions. Unexpectedly, both motions required 37 ?s, on average. The distribution of transition durations was also independent of the enzyme's state: either catalytic or nonproductive. The observation of smooth, continuous transitions suggests a concerted mechanism for glycoside hydrolysis with lysozyme's two domains closing upon the polysaccharide substrate in its active site. We distinguish these smooth motions from a nonconcerted mechanism, observed in approximately 10% of lysozyme openings and closings, in which the enzyme pauses for an additional 40-140 ?s in an intermediate, partially closed conformation. During intermediate forming events, the number of rate-limiting steps observed increases to four, consistent with four steps required in the stepwise, arrow-pushing mechanism. The formation of such intermediate conformations was again independent of the enzyme's state. Taken together, the results suggest lysozyme operates as a Brownian motor. In this model, the enzyme traces a single pathway for closing and the reverse pathway for enzyme opening, regardless of its instantaneous catalytic productivity. The observed symmetry in enzyme opening and closing thus suggests that substrate translocation occurs while the enzyme is closed. PMID:25763461

  5. Multiscale complex network of protein conformational fluctuations in single-molecule time series

    PubMed Central

    Li, Chun-Biu; Yang, Haw; Komatsuzaki, Tamiki

    2008-01-01

    Conformational dynamics of proteins can be interpreted as itinerant motions as the protein traverses from one state to another on a complex network in conformational space or, more generally, in state space. Here we present a scheme to extract a multiscale state space network (SSN) from a single-molecule time series. Analysis by this method enables us to lift degeneracy—different physical states having the same value for a measured observable—as much as possible. A state or node in the network is defined not by the value of the observable at each time but by a set of subsequences of the observable over time. The length of the subsequence can tell us the extent to which the memory of the system is able to predict the next state. As an illustration, we investigate the conformational fluctutation dynamics probed by single-molecule electron transfer (ET), detected on a photon-by-photon basis. We show that the topographical features of the SSNs depend on the time scale of observation; the longer the time scale, the simpler the underlying SSN becomes, leading to a transition of the dynamics from anomalous diffusion to normal Brownian diffusion. PMID:18178627

  6. Dwell time analysis of a single-molecule mechanochemical reaction.

    PubMed

    Szoszkiewicz, Robert; Ainavarapu, Sri Rama Koti; Wiita, Arun P; Perez-Jimenez, Raul; Sanchez-Ruiz, Jose M; Fernandez, Julio M

    2008-02-19

    Force-clamp spectroscopy is a novel technique for studying mechanochemistry at the single-bond level. Single disulfide bond reduction events are accurately detected as stepwise increases in the length of polyproteins that contain disulfide bonds and that are stretched at a constant force with the cantilever of an atomic force microscope (AFM). The kinetics of this reaction has been measured from single-exponential fits to ensemble averages of the reduction events. However, exponential fits are notoriously ambiguous to use in cases of kinetic data showing multiple reaction pathways. Here we introduce a dwell time analysis technique, of widespread use in the single ion channel field, that we apply to the examination of the kinetics of reduction of disulfide bonds measured from single-molecule force-clamp spectroscopy traces. In this technique, exponentially distributed dwell time data is plotted as a histogram with a logarithmic time scale and a square root ordinate. The advantage of logarithmic histograms is that exponentially distributed dwell times appear as well-defined peaks in the distribution, greatly enhancing our ability to detect multiple kinetic pathways. We apply this technique to examine the distribution of dwell times of 4488 single disulfide bond reduction events measured in the presence of two very different kinds of reducing agents: tris-(2-carboxyethyl)phosphine hydrochloride (TCEP) and the enzyme thioredoxin (TRX). A different clamping force is used for each reducing agent to obtain distributions of dwell times on a similar time scale. In the case of TCEP, the logarithmic histogram of dwell times showed a single peak, corresponding to a single reaction mechanism. By contrast, similar experiments done with TRX showed two well-separated peaks, marking two distinct modes of chemical reduction operating simultaneously. These experiments demonstrate that dwell time analysis techniques are a powerful approach to studying chemical reactions at the single-molecule level. PMID:17999545

  7. Imaging single molecules using total internal reflection fluorescence microscopy (TIRFM).

    PubMed

    Reck-Peterson, Samara L; Derr, Nathan D; Stuurman, Nico

    2010-03-01

    Total internal reflection fluorescence microscopy (TIRFM) allows fluorescent molecules to be visualized with an unparalleled signal-to-noise ratio. This is achieved by illuminating only the molecules that are within a thin volume near the coverslip surface but not those that are deeper in solution. Using this technique, fluorescent molecules within approximately 100 nm of the coverslip can be visualized, and single molecules that are separated by a distance greater than the diffraction limit (approximately 200 nm) can be individually resolved. The application of centroid-tracking methods allows subdiffraction-limited localization precision as low as 1 nm. Additionally, by combining centroid-tracking methods with recent advances in fluorophore technology and imaging methods, even those molecules that are present at high concentrations and closer to one another than the diffraction limit can be individually imaged. TIRF is ideally suited for studying protein dynamics on or near the plasma membrane. Although TIRFM was pioneered in the 1980s, it was not until the mid-1990s that single biological molecules were imaged directly. The explosion of new fluorescent proteins, new organic dyes, and quantum dots (Qdots), along with commercially available TIRFMs, has made this technique increasingly useful and accessible to biologists. In this review, we first describe the theory of TIRFM. We then give a detailed description of important considerations for setting up a TIRFM, based on commercially available systems, and review considerations for purification and labeling of proteins. Finally, we discuss new techniques that allow single molecules to be imaged at cellular concentrations and with super-resolution localization. PMID:20194477

  8. Determining serpin conformational distributions with single molecule fluorescence.

    PubMed

    Mushero, Nicole; Gershenson, Anne

    2011-01-01

    Conformational plasticity is key to inhibitory serpin function, and this plasticity gives serpins relatively easy access to alternative, dysfunctional conformations. Thus, a given serpin population may contain both functional and dysfunctional proteins. Single molecule fluorescence (SMF), with its ability to interrogate one fluorescently labeled protein at a time, is a powerful method for elucidating conformational distributions and monitoring how these distributions change over time. SMF and related methods have been particularly valuable for characterizing serpin polymerization. Fluorescence correlation spectroscopy experiments have revealed a second lag phase during in vitro ?(1)-antitrypsin polymerization associated with the formation of smaller oligomers that then condense to form longer polymers [Purkayastha, P., Klemke, J. W., Lavender, S., Oyola, R., Cooperman, B. S., and Gai, F. (2005). Alpha 1-antitrypsin polymerization: A fluorescence correlation spectroscopic study. Biochemistry44, 2642-2649.]. SMF studies of in vitro neuroserpin polymerization have confirmed that a monomeric intermediate is required for polymer formation while providing a test of proposed polymerization mechanisms [Chiou, A., Hägglöf, P., Orte, A., Chen, A. Y., Dunne, P. D., Belorgey, D., Karlsson-Li, S., Lomas, D., and Klenerman, D. (2009). Probing neuroserpin polymerization and interaction with amyloid-beta peptides using single molecule fluorescence. Biophys. J.97, 2306-2315.]. SMF has also been used to monitor protease-serpin interactions. Single pair Förster resonance energy transfer studies of covalent protease-serpin complexes suggest that the extent of protease structural disruption in the complex is protease dependent [Liu, L., Mushero, N., Hedstrom, L., and Gershenson, A. (2006). Conformational distributions of protease-serpin complexes: A partially translocated complex. Biochemistry45, 10865-10872.]. SMF techniques are still evolving and the combination of SMF with encapsulation methods has the potential to provide more detailed information on the conformational changes associated with serpin polymerization, protease-serpin complex formation, and serpin folding. PMID:22078542

  9. Solution, surface, and single molecule platforms for the study of DNA-mediated charge transport

    PubMed Central

    Muren, Natalie B.; Olmon, Eric D.; Barton, Jacqueline K.

    2012-01-01

    The structural core of DNA, a continuous stack of aromatic heterocycles, the base pairs, which extends down the helical axis, gives rise to the fascinating electronic properties of this molecule that is so critical for life. Our laboratory and others have developed diverse experimental platforms to investigate the capacity of DNA to conduct charge, termed DNA-mediated charge transport (DNA CT). Here, we present an overview of DNA CT experiments in solution, on surfaces, and with single molecules that collectively provide a broad and consistent perspective on the essential characteristics of this chemistry. DNA CT can proceed over long molecular distances but is remarkably sensitive to perturbations in base pair stacking. We discuss how this foundation, built with data from diverse platforms, can be used both to inform a mechanistic description of DNA CT and to inspire the next platforms for its study: living organisms and molecular electronics. PMID:22850865

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

    PubMed Central

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

    2014-01-01

    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 the 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 on developing lab-on-a-chip techniques for single-molecule studies and expound our thoughts on the near future of on-chip single-molecule studies. PMID:23670195

  11. Interfacial electronic transport phenomena in single crystalline Fe-MgO-Fe thin barrier junctions

    SciTech Connect

    Gangineni, R. B., E-mail: rameshg.phy@pondiuni.edu.in [Department of Physics, School of Physical, Chemical and Applied Sciences, Pondicherry University, R. V. Nagar, Kalapet, Pondicherry 605 014 (India); SPINTEC, UMR 8191 CEA/CNRS/UJF-Grenoble 1/Grenoble INP, INAC, 17 rue des Martyrs, F-38054 Grenoble Cedex (France); Bellouard, C., E-mail: christine.bellouard@ijl.nancy-universite.fr; Duluard, A. [Institut Jean Lamour, UMR 7198, CNRS-Université de Lorraine, BP 239, 54506 Vandoeuvre (France); Negulescu, B. [Institut Jean Lamour, UMR 7198, CNRS-Université de Lorraine, BP 239, 54506 Vandoeuvre (France); UFR de Sciences et Techniques, Matériaux, microélectronique, acoustique, nanotechnologies (GREMAN), University François Rabelais, Parc de Grandmont, 37200 Tours (France); Baraduc, C.; Gaudin, G. [SPINTEC, UMR 8191 CEA/CNRS/UJF-Grenoble 1/Grenoble INP, INAC, 17 rue des Martyrs, F-38054 Grenoble Cedex (France); Tiusan, C., E-mail: coriolan.tiusan@phys.utcluj.ro [Institut Jean Lamour, UMR 7198, CNRS-Université de Lorraine, BP 239, 54506 Vandoeuvre (France); Department of Physics and Chemistry, Center of Superconductivity, Spintronics and Surface Science, Technical University of Cluj Napoca, Str. Memorandumului No. 28, RO-400114 Cluj-Napoca (Romania)

    2014-05-05

    Spin filtering effects in nano-pillars of Fe-MgO-Fe single crystalline magnetic tunnel junctions are explored with two different sample architectures and thin MgO barriers (thickness: 3–8 monolayers). The two architectures, with different growth and annealing conditions of the bottom electrode, allow tuning the quality of the bottom Fe/MgO interface. As a result, an interfacial resonance states (IRS) is observed or not depending on this interface quality. The IRS contribution, observed by spin polarized tunnel spectroscopy, is analyzed as a function of the MgO barrier thickness. Our experimental findings agree with theoretical predictions concerning the symmetry of the low energy (0.2?eV) interfacial resonance states: a mixture of ?{sub 1}-like and ?{sub 5}-like symmetries.

  12. Interfacial electron and phonon scattering processes in high-powered nanoscale applications.

    SciTech Connect

    Hopkins, Patrick E.

    2011-10-01

    The overarching goal of this Truman LDRD project was to explore mechanisms of thermal transport at interfaces of nanomaterials, specifically linking the thermal conductivity and thermal boundary conductance to the structures and geometries of interfaces and boundaries. Deposition, fabrication, and post possessing procedures of nanocomposites and devices can give rise to interatomic mixing around interfaces of materials leading to stresses and imperfections that could affect heat transfer. An understanding of the physics of energy carrier scattering processes and their response to interfacial disorder will elucidate the potentials of applying these novel materials to next-generation high powered nanodevices and energy conversion applications. An additional goal of this project was to use the knowledge gained from linking interfacial structure to thermal transport in order to develop avenues to control, or 'tune' the thermal transport in nanosystems.

  13. Compact Quantum Dots for Single-molecule Imaging

    PubMed Central

    Smith, Andrew M.; Nie, Shuming

    2012-01-01

    Single-molecule imaging is an important tool for understanding the mechanisms of biomolecular function and for visualizing the spatial and temporal heterogeneity of molecular behaviors that underlie cellular biology 1-4. To image an individual molecule of interest, it is typically conjugated to a fluorescent tag (dye, protein, bead, or quantum dot) and observed with epifluorescence or total internal reflection fluorescence (TIRF) microscopy. While dyes and fluorescent proteins have been the mainstay of fluorescence imaging for decades, their fluorescence is unstable under high photon fluxes necessary to observe individual molecules, yielding only a few seconds of observation before complete loss of signal. Latex beads and dye-labeled beads provide improved signal stability but at the expense of drastically larger hydrodynamic size, which can deleteriously alter the diffusion and behavior of the molecule under study. Quantum dots (QDs) offer a balance between these two problematic regimes. These nanoparticles are composed of semiconductor materials and can be engineered with a hydrodynamically compact size with exceptional resistance to photodegradation 5. Thus in recent years QDs have been instrumental in enabling long-term observation of complex macromolecular behavior on the single molecule level. However these particles have still been found to exhibit impaired diffusion in crowded molecular environments such as the cellular cytoplasm and the neuronal synaptic cleft, where their sizes are still too large 4,6,7. Recently we have engineered the cores and surface coatings of QDs for minimized hydrodynamic size, while balancing offsets to colloidal stability, photostability, brightness, and nonspecific binding that have hindered the utility of compact QDs in the past 8,9. The goal of this article is to demonstrate the synthesis, modification, and characterization of these optimized nanocrystals, composed of an alloyed HgxCd1-xSe core coated with an insulating CdyZn1-yS shell, further coated with a multidentate polymer ligand modified with short polyethylene glycol (PEG) chains (Figure 1). Compared with conventional CdSe nanocrystals, HgxCd1-xSe alloys offer greater quantum yields of fluorescence, fluorescence at red and near-infrared wavelengths for enhanced signal-to-noise in cells, and excitation at non-cytotoxic visible wavelengths. Multidentate polymer coatings bind to the nanocrystal surface in a closed and flat conformation to minimize hydrodynamic size, and PEG neutralizes the surface charge to minimize nonspecific binding to cells and biomolecules. The end result is a brightly fluorescent nanocrystal with emission between 550-800 nm and a total hydrodynamic size near 12 nm. This is in the same size range as many soluble globular proteins in cells, and substantially smaller than conventional PEGylated QDs (25-35 nm). PMID:23093375

  14. Photophysical Properties of Acene DCDHF Fluorophores: Long-Wavelength Single-Molecule Emitters Designed for Cellular Imaging

    PubMed Central

    Lord, Samuel J.; Lu, Zhikuan; Wang, Hui; Willets, Katherine A.; Schuck, P. James; Lee, Hsiao-lu D.; Nishimura, Stefanie Y.; Twieg, Robert J.; Moerner, W. E.

    2009-01-01

    We report the solvatochromic, viscosity-sensitive, and single-molecule photophysics of the fluorophores DCDHF-N-6 and DCDHF-A-6. These molecules are members of the dicyanomethylenedihydrofuran (DCDHF) class of single-molecule emitters that contain an amine electron donor and a DCDHF acceptor linked by a conjugated unit; DCDHF-N-6 and DCDHF-A-6 have naphthalene- and anthracene-conjugated linkers, respectively. These molecules maintain the beneficial photophysics of the phenylene-linked DCDHF (i.e., photostability, emission wavelength dependence on solvent polarity, and quantum yield sensitivity to solvent viscosity), yet offer absorption and emission at longer wavelengths that are more appropriate for cellular imaging. We demonstrate that these new fluorophores are less photolabile in an aqueous environment than several other commonly used dyes (rhodamine 6G, Texas Red, and fluorescein). Finally, we image single copies of the acene DCDHFs diffusing in the plasma membrane of living cells. PMID:17718454

  15. Single-Molecule Tracking in Living Cells Using Single Quantum Dot Applications

    PubMed Central

    Baba, Koichi; Nishida, Kohji

    2012-01-01

    Revealing the behavior of single molecules in living cells is very useful for understanding cellular events. Quantum dot probes are particularly promising tools for revealing how biological events occur at the single molecule level both in vitro and in vivo. In this review, we will introduce how single quantum dot applications are used for single molecule tracking. We will discuss how single quantum dot tracking has been used in several examples of complex biological processes, including membrane dynamics, neuronal function, selective transport mechanisms of the nuclear pore complex, and in vivo real-time observation. We also briefly discuss the prospects for single molecule tracking using advanced probes. PMID:22896768

  16. Frequency domain Fourier transform THz-EPR on single molecule magnets using coherent synchrotron radiation.

    PubMed

    Schnegg, Alexander; Behrends, Jan; Lips, Klaus; Bittl, Robert; Holldack, Karsten

    2009-08-21

    Frequency domain Fourier transform THz electron paramagnetic resonance (FD-FT THz-EPR) based on coherent synchrotron radiation (CSR) is presented as a novel tool to ascertain very large zero field splittings in transition metal ion complexes. A description of the FD-FT THz-EPR at the BESSY II storage ring providing CSR in a frequency range from 5 cm(-1) up to 40 cm(-1) at external magnetic fields from -10 T to +10 T is given together with first measurements on the single molecule magnet Mn(12)Ac where we studied DeltaM(S) = +/-1 spin transition energies as a function of the external magnetic field and temperature. PMID:19639156

  17. Time-, frequency-, and wavevector-resolved x-ray diffraction from single molecules

    PubMed Central

    Bennett, Kochise; Biggs, Jason D.; Zhang, Yu; Dorfman, Konstantin E.; Mukamel, Shaul

    2014-01-01

    Using a quantum electrodynamic framework, we calculate the off-resonant scattering of a broadband X-ray pulse from a sample initially prepared in an arbitrary superposition of electronic states. The signal consists of single-particle (incoherent) and two-particle (coherent) contributions that carry different particle form factors that involve different material transitions. Single-molecule experiments involving incoherent scattering are more influenced by inelastic processes compared to bulk measurements. The conditions under which the technique directly measures charge densities (and can be considered as diffraction) as opposed to correlation functions of the charge-density are specified. The results are illustrated with time- and wavevector-resolved signals from a single amino acid molecule (cysteine) following an impulsive excitation by a stimulated X-ray Raman process resonant with the sulfur K-edge. Our theory and simulations can guide future experimental studies on the structures of nano-particles and proteins. PMID:24880284

  18. Resonant transport and electrostatic effects in single-molecule electrical junctions

    NASA Astrophysics Data System (ADS)

    Brooke, Carly; Vezzoli, Andrea; Higgins, Simon J.; Zotti, Linda A.; Palacios, J. J.; Nichols, Richard J.

    2015-05-01

    In this contribution we demonstrate structural control over a transport resonance in HS (CH2)n[1 ,4 -C6H4] (CH2)nSH (n =1 , 3, 4, 6) metal-molecule-metal junctions, fabricated and tested using the scanning tunneling microscopy-based I (z ) method. The Breit-Wigner resonance originates from one of the arene ? -bonding orbitals, which sharpens and moves closer to the contact Fermi energy as n increases. Varying the number of methylene groups thus leads to a very shallow decay of the conductance with the length of the molecule. We demonstrate that the electrical behavior observed here can be straightforwardly rationalized by analyzing the effects caused by the electrostatic balance created at the metal-molecule interface. Such resonances offer future prospects in molecular electronics in terms of controlling charge transport over longer distances, and also in single-molecule conductance switching if the resonances can be externally gated.

  19. A Trigonal-Pyramidal Erbium(III) Single-Molecule Magnet.

    PubMed

    Brown, Andrew J; Pinkowicz, Dawid; Saber, Mohamed R; Dunbar, Kim R

    2015-05-11

    Given the recent advent of mononuclear single-molecule magnets (SMMs), a rational approach based on lanthanides with axially elongated f-electron charge cloud (prolate) has only recently received attention. We report herein a new SMM, [Li(THF)4 [Er{N(SiMe3 )2 }3 Cl]?2?THF, which exhibits slow relaxation of the magnetization under zero dc field with an effective barrier to the reversal of magnetization (?Eeff /kB =63.3?K) and magnetic hysteresis up to 3?K at a magnetic field sweep rate of 34.6?Oe?s(-1) . This work questions the theory that oblate or prolate lanthanides must be stabilized with the appropriate ligand framework in order for SMM behavior to be favored. PMID:25809280

  20. A theoretical model for single-molecule incoherent scanning tunneling spectroscopy

    NASA Astrophysics Data System (ADS)

    Raza, H.

    2008-11-01

    Single-molecule scanning tunneling spectroscopy (STS), with dephasing due to elastic and inelastic scattering, is of some current interest. Motivated by this, we report an extended Hückel theory (EHT)-based mean-field non-equilibrium Green's function (NEGF) transport model with electron-phonon scattering treated within the self-consistent Born approximation (SCBA). Furthermore, a procedure based on EHT basis set modification is described. We use this model to study the effect of the temperature-dependent dephasing due to low lying modes in the far-infrared range for which \\hbar \\omega \\ll k_{\\mathrm {B}}T , on the resonant conduction through the highest occupied molecular orbital (HOMO) level of a phenyl dithiol molecule bonded to fcc-Au(111) contact. We finally propose to include dephasing in room temperature molecular resonant conduction calculations.

  1. Tuning the thermoelectric properties of a single-molecule junction by mechanical stretching.

    PubMed

    Torres, Alberto; Pontes, Renato B; da Silva, Antônio J R; Fazzio, Adalberto

    2015-02-21

    We theoretically investigate, as a function of the stretching, the behaviour of the thermoelectric properties - the Seebeck coefficient (S), the electronic heat conductance (?el) and the figure of merit (ZT) - of a molecule-based junction composed of a benzene-1,4-dithiolate molecule (BDT) coupled to Au(111) surfaces at room temperature. We show that the thermoelectric properties of a single molecule junction can be tuned by mechanic stretching. The Seebeck coefficient is positive, indicating that it is dominated by the HOMO. Furthermore, it increases as the HOMO level, which is associated to the sulphur atom, tends towards energies close to the Fermi energy. By modelling the transmission coefficient of the system as a single Lorentzian peak, we propose a scheme to obtain the maximum ZT of any molecular junction. PMID:25612893

  2. Single molecule studies reveal new mechanisms for microtubule severing

    NASA Astrophysics Data System (ADS)

    Ross, Jennifer; Diaz-Valencia, Juan Daniel; Morelli, Margaret; Zhang, Dong; Sharp, David

    2011-03-01

    Microtubule-severing enzymes are hexameric complexes made from monomeric enzyme subunits that remove tubulin dimers from the microtubule lattice. Severing proteins are known to remodel the cytoskeleton during interphase and mitosis, and are required in proper axon morphology and mammalian bone and cartilage development. We have performed the first single molecule imaging to determine where and how severing enzymes act to cut microtubules. We have focused on the original member of the group, katanin, and the newest member, fidgetin to compare their biophysical activities in vitro. We find that, as expected, severing proteins localize to areas of activity. Interestingly, the association is very brief: they do not stay bound nor do they bind cooperatively at active sites. The association duration changes with the nucleotide content, implying that the state in the catalytic cycle dictates binding affinity with the microtubule. We also discovered that, at lower concentrations, both katanin and fidgetin can depolymerize taxol-stabilized microtubules by removing terminal dimers. These studies reveal the physical regulation schemes to control severing activity in cells, and ultimately regulate cytoskeletal architecture. This work is supported by the March of Dimes Grant #5-FY09-46.

  3. Mechanical Properties of ?-Catenin Revealed by Single-Molecule Experiments

    PubMed Central

    Valbuena, Alejandro; Vera, Andrés Manuel; Oroz, Javier; Menéndez, Margarita; Carrión-Vázquez, Mariano

    2012-01-01

    ?-catenin is a central component of the adaptor complex that links cadherins to the actin cytoskeleton in adherens junctions and thus, it is a good candidate to sense and transmit mechanical forces to trigger specific changes inside the cell. To fully understand its molecular physiology, we must first investigate its mechanical role in mechanotransduction within the cadherin system. We have studied the mechanical response of ?-catenin to stretching using single-molecule force spectroscopy and molecular dynamics. Unlike most proteins analyzed to date, which have a fixed mechanical unfolding pathway, the ?-catenin armadillo repeat region (ARM) displays low mechanostability and multiple alternative unfolding pathways that seem to be modulated by its unstructured termini. These results are supported by steered molecular dynamics simulations, which also predict its mechanical stabilization and unfolding pathway restrictions when the contiguous ?-helix of the C-terminal unstructured region is included. Furthermore, simulations of the ARM/E-cadherin cytosolic tail complex emulating the most probable stress geometry occurring in vivo show a mechanical stabilization of the interaction whose magnitude correlates with the length of the stretch of the cadherin cytosolic tail that is in contact with the ARM region. PMID:23083718

  4. Single-molecule analysis of the full transcription cycle

    NASA Astrophysics Data System (ADS)

    Strick, Terence

    2005-03-01

    By monitoring the extension of a mechanically stretched, supercoiled DNA molecule containing a single bacterial promoter, we have been able to directly observe in real time the change in DNA extension associated with topological unwinding of ˜1 helical turn of promoter DNA by RNAP during transcription initiation. We find that this stage of transcription initiation is extremely sensitive to the torque acting on the supercoiled DNA. Upon addition of limited sets of nucleotides, changes in the polymerase/promoter interaction which are related to the process of abortive initiation can be studied in detail. Upon addition of the full set of nucleotides, the subsequent stages of transcription -- promoter escape, productive elongation and transcription termination -- can also be observed in real-time. The changes in DNA topology which occur at each of these stages have been determined, and these results provide for the first global view of the entire transcription cycle at the resolution of single molecules. Co-authors: Richard H. Ebright, Chen-Yu Liu and Andrey Revyakin, HHMI & Waksman Institute, Rutgers University.

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

    PubMed Central

    Lagerholm, B. Christoffer

    2012-01-01

    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 ?-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 ?-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. PMID:22952963

  6. Single Molecule Magnetic Force Detection with a Carbon Nanotube Resonator

    NASA Astrophysics Data System (ADS)

    Willick, Kyle; Walker, Sean; Baugh, Jonathan

    2015-03-01

    Single molecule magnets (SMMs) sit at the boundary between macroscopic magnetic behaviour and quantum phenomena. Detecting the magnetic moment of an individual SMM would allow exploration of this boundary, and could enable technological applications based on SMMs such as quantum information processing. Detection of these magnetic moments remains an experimental challenge, particularly at the time scales of relaxation and decoherence. We present a technique for sensitive magnetic force detection that should permit such measurements. A suspended carbon nanotube (CNT) mechanical resonator is combined with a magnetic field gradient generated by a ferromagnetic gate electrode, which couples the magnetic moment of a nanomagnet to the resonant motion of the CNT. Numerical calculations of the mechanical resonance show that resonant frequency shifts on the order of a few kHz arise due to single Bohr magneton changes in magnetic moment. A signal-to-noise analysis based on thermomechanical noise shows that magnetic switching at the level of a Bohr magneton can be measured in a single shot on timescales as short as 10 ?s. This sensitivity should enable studies of the spin dynamics of an isolated SMM, within the spin relaxation timescales for many available SMMs. Supported by NSERC.

  7. Locked nucleic acid oligomers as handles for single molecule manipulation

    PubMed Central

    Berezney, John P.; Saleh, Omar A.

    2014-01-01

    Single-molecule manipulation (SMM) techniques use applied force, and measured elastic response, to reveal microscopic physical parameters of individual biomolecules and details of biomolecular interactions. A major hurdle in the application of these techniques is the labeling method needed to immobilize biomolecules on solid supports. A simple, minimally-perturbative labeling strategy would significantly broaden the possible applications of SMM experiments, perhaps even allowing the study of native biomolecular structures. To accomplish this, we investigate the use of functionalized locked nucleic acid (LNA) oligomers as biomolecular handles that permit sequence-specific binding and immobilization of DNA. We find these probes form bonds with DNA with high specificity but with varied stability in response to the direction of applied mechanical force: when loaded in a shear orientation, the bound LNA oligomers were measured to be two orders of magnitude more stable than when loaded in a peeling, or unzipping, orientation. Our results show that LNA provides a simple, stable means to functionalize dsDNA for manipulation. We provide design rules that will facilitate their use in future experiments. PMID:25159617

  8. Flexible single molecule simulation of reaction-diffusion processes

    SciTech Connect

    Hellander, Stefan, E-mail: stefan.hellander@it.uu.s [Division of Scientific Computing, Department of Information Technology, Uppsala University, P.O. Box 337, SE-75105 Uppsala (Sweden); Loetstedt, Per, E-mail: perl@it.uu.s [Division of Scientific Computing, Department of Information Technology, Uppsala University, P.O. Box 337, SE-75105 Uppsala (Sweden)

    2011-05-10

    An algorithm is developed for simulation of the motion and reactions of single molecules at a microscopic level. The molecules diffuse in a solvent and react with each other or a polymer and molecules can dissociate. Such simulations are of interest e.g. in molecular biology. The algorithm is similar to the Green's function reaction dynamics (GFRD) algorithm by van Zon and ten Wolde where longer time steps can be taken by computing the probability density functions (PDFs) and then sample from the distribution functions. Our computation of the PDFs is much less complicated than GFRD and more flexible. The solution of the partial differential equation for the PDF is split into two steps to simplify the calculations. The sampling is without splitting error in two of the coordinate directions for a pair of molecules and a molecule-polymer interaction and is approximate in the third direction. The PDF is obtained either from an analytical solution or a numerical discretization. The errors due to the operator splitting, the partitioning of the system, and the numerical approximations are analyzed. The method is applied to three different systems involving up to four reactions. Comparisons with other mesoscopic and macroscopic models show excellent agreement.

  9. FPGA for single-molecule recycling in a nanochannel

    NASA Astrophysics Data System (ADS)

    Behery, Sultan; Wang, Bo; Canfield, Brian; Davis, Lloyd

    2013-03-01

    Single-molecule (SM) trapping and detection experiments are important in studying biophysical processes on the molecular level. As an SM is too small for optical trapping, prolonged observation requires measurement of the position and active feedback to counteract diffusion. In previous work, a custom-built Field Programmable Gate Array (FPGA) circuit board was developed for SM detection and real-time electrokinetic trapping in a fused silica nanochannel. The FPGA was used as part of a feedback system to control the voltage for electrokinetic movement of solution along the nanochannel in response to the time stamps of individual photons from the excited SM. Other researchers have since shown that alternating the flow in a nanochannel can be used to recycle an SM through a stationary laser focus for repeated observations and that the times between each passage yield a measurement of the molecule's diffusion. Improved measurements could be obtained by use of an FPGA for more precisely timed flow control. Therefore, we are now adapting the FPGA for SM trapping to use algorithms tested in a Monte Carlo simulation of SM recycling in an attempt to extend existing capabilities. This presentation discusses the custom-built FPGA board, algorithms, and ongoing nanochannel experiments.

  10. Whole-mount single molecule FISH method for zebrafish embryo.

    PubMed

    Oka, Yuma; Sato, Thomas N

    2015-01-01

    Noise in gene expression renders cells more adaptable to changing environment by imposing phenotypic and functional heterogeneity on genetically identical individual cells. Hence, quantitative measurement of noise in gene expression is essential for the study of biological processes in cells. Currently, there are two complementary methods for quantitatively measuring noise in gene expression at the single cell level: single molecule FISH (smFISH) and single cell qRT-PCR (or single cell RNA-seq). While smFISH has been developed for culture cells, tissue sections and whole-mount invertebrate organisms, the method has not been reported for whole-mount vertebrate organisms. Here, we report an smFISH method that is suitable for whole-mount zebrafish embryo, a popular vertebrate model organism for the studies of development, physiology and disease. We show the detection of individual transcripts for several cell-type specific and ubiquitously expressed genes at the single cell level in whole-mount zebrafish embryo. We also demonstrate that the method can be adapted to detect two different genes in individual cells simultaneously. The whole-mount smFISH method described in this report is expected to facilitate the study of noise in gene expression and its role in zebrafish, a vertebrate animal model relevant to human biology. PMID:25711926

  11. Optical Microcavity: Sensing down to Single Molecules and Atoms

    PubMed Central

    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. PMID:22319393

  12. Single Molecule Approaches to Studying Heterogeneity in Molecular Supercooled Liquids

    NASA Astrophysics Data System (ADS)

    Kaufman, Laura

    2014-03-01

    Supercooled liquids display behaviors consistent with the presence of heterogeneous dynamics. We investigate the length scales over which such heterogeneities exist and the time scales over which they persist using single molecule (SM) fluorescence microscopy. In previous work, multiple perylene diimide (PDI) probes were employed to investigate whether probe properties affected breadth of heterogeneity reported in the fragile supercooled liquid ortho-terphenyl (OTP) as well as in less fragile supercooled glycerol. In both cases, the fastest rotating probes reported the greatest breadth of heterogeneity in the host, regardless of physical probe size, suggesting slow probes were averaging over dynamic changes in the environment in time. Here, we introduce a new set of BODIPY-core based probes that are both smaller and more quickly rotating in OTP than the PDI probes. These probes show qualitatively different behavior than the PDI probes, reporting more spatial and temporal heterogeneity than previously studied probes. The newly employed probes open the door to studying the full range of consequences of dynamic heterogeneity in supercooled liquids on the molecular length scale.

  13. Single-molecule force spectroscopy: Practical limitations beyond Bell's model

    E-print Network

    Sebastian Getfert; Mykhaylo Evstigneev; Peter Reimann

    2008-05-19

    Single-molecule force spectroscopy experiments, as well as a number of other physical systems, are governed by thermally activated transitions out of a metastable state under the action of a steadily increasing external force. The main observable in such experiments is the distribution of the forces, at which the escape events occur. The challenge in interpreting the experimental data is to relate them to the microscopic system properties. We work out a maximum likelihood approach and show that it is the optimal method to tackle this problem. When fitting actual experimental data it is unavoidable to assume some functional form for the force-dependent escape rate. We consider a quite general and common such functional form and demonstrate by means of data from a realistic computer experiment that the maximum number of fit parameters that can be determined reliably is three. They are related to the force-free escape rate and the position and height of the activation barrier. Furthermore, the results for the first two of these fit parameters show little dependence on the assumption about the manner in which the barrier decreases with the applied force, while the last one, the barrier height in the absence of force, depends strongly on this assumption.

  14. Single Molecule Visualization of DNA in Wicking Flows

    NASA Astrophysics Data System (ADS)

    Delong, Chad; Hoagland, David

    2006-03-01

    An understanding of polymers in flow through micro- and nano-structured materials is critical to the success of bioseparations (proteins, DNA, etc.). An open, nanofluidic system has been developed to drive flow through a packed bed of colloidal particles using capillary forces (wicking), allowing the study of polymer dynamics in the absence of the electric field is typically used to drive micro- and nano-fluidic flows. This is especially important when dealing with charged molecules whose confirmation can be affected by the electric field or those insoluble in water. Single molecule imaging is performed in this system on fluorescently labeled DNA using an optical microscope equipped with a fluorescent light source, image intensifier, and CCD camera. Chain elongation in the flow depends sharply on flow rate, with fully relaxed configurations observed below a critical flow rate. At high flow rates, flow induced degradation can be seen. Molecular entanglements with the separation matrix cause molecular weight separation because longer molecules elongate in the flow and become entangled, leading to a longer retention time.

  15. Spin Anisotropy Effects in Dimer Single Molecule Magnets

    NASA Astrophysics Data System (ADS)

    Efremov, Dmitri; Klemm, Richard

    2006-03-01

    We present a model of equal spin s1 dimer single molecule magnets. The spins within each dimer interact via the Heisenberg and the most general set of four quadratic anisotropic spin interactions with respective strengths J and Jj, and with the magnetic induction B. For antiferromagnetic Heisenberg couplings (J<0) and weak anisotropy interactions (|Jj/J|1), the low temperature T magnetization M(B) exhibits 2s1 steps, the height and midpoint slope of the sth step differing from their isotropic limits by corrections of O(Jj/J)^2, but the position occurring at the energy level-crossing magnetic induction Bs,s1^lc(,), where , define the direction of B. We solve the model exactly for s1=1/2, 1, and 5/2. For weakly anisotropic dimers, the Hartree approximation yields analytic formulas for M(B) and CV(B) at arbitrary s1 that accurately fit the exact solutions at sufficiently low T or large B. Low-T formulas for the inelastic neutron scattering S(q,?) and the EPR ?(?) in an extended Hartree approximation are given. Our results are discussed with regard to existing experiments on s1=5/2 Fe2 dimers, suggesting further experiments on single crystals of these and some s1=9/2 [Mn4]2 dimers are warranted.

  16. Flexible single molecule simulation of reaction-diffusion processes

    NASA Astrophysics Data System (ADS)

    Hellander, Stefan; Lötstedt, Per

    2011-05-01

    An algorithm is developed for simulation of the motion and reactions of single molecules at a microscopic level. The molecules diffuse in a solvent and react with each other or a polymer and molecules can dissociate. Such simulations are of interest e.g. in molecular biology. The algorithm is similar to the Green's function reaction dynamics (GFRD) algorithm by van Zon and ten Wolde where longer time steps can be taken by computing the probability density functions (PDFs) and then sample from the distribution functions. Our computation of the PDFs is much less complicated than GFRD and more flexible. The solution of the partial differential equation for the PDF is split into two steps to simplify the calculations. The sampling is without splitting error in two of the coordinate directions for a pair of molecules and a molecule-polymer interaction and is approximate in the third direction. The PDF is obtained either from an analytical solution or a numerical discretization. The errors due to the operator splitting, the partitioning of the system, and the numerical approximations are analyzed. The method is applied to three different systems involving up to four reactions. Comparisons with other mesoscopic and macroscopic models show excellent agreement.

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

    NASA Astrophysics Data System (ADS)

    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. Interfacial Electronic Structure of the Dipolar Vanadyl Naphthalocyanine on Au (111): “Push-back” vs Dipolar Effects

    SciTech Connect

    Terentjevs, Aleksandrs [National Nanotechnology Lab. (NNL), Istituto Nanoscienze-CNR, Lecce (Italy); Steele, Mary P. [Univ. of Arizona, Tucson, AZ (United States); Blumenfeld, Michael L. [Univ. of Arizona, Tucson, AZ (United States); Ilyas, Nahid [Univ. of Arizona, Tucson, AZ (United States); Kelly, Leah L. [Univ. of Arizona, Tucson, AZ (United States); Fabiano, Eduardo [National Nanotechnology Lab. (NNL), Istituto Nanoscienze-CNR, Lecce (Italy); Monti, Oliver L.A. [Univ. of Arizona, Tucson, AZ (United States); Della Sala, Fabio [Center for Biomolecular Nanotechnologies, Istituto Italiano di Tecnologia (IIT), Lecce (Italy)

    2011-11-03

    We investigate the interfacial electronic structure of the dipolar organic semiconductor vanadyl naphthalocyanine on Au(111) in a combined computational and experimental approach to understand the role of the permanent molecular dipole moment on energy-level alignment at this interface. First-principles Density Functional Theory (DFT) calculations on such large systems are challenging, due to the large computational cost and the need to accurately consider dispersion interactions. Our DFT results with dispersion correction show a molecular deformation upon adsorption but no strong chemical bond formation. Ultraviolet photoelectron spectroscopy measurements show a considerable workfunction change of ?0.73(2) eV upon growth of the first monolayer, which is well reproduced by the DFT calculations. This shift originates from a large electron density “push-back” effect at the gold surface, whereas the large out-of-plane vanadyl dipole moment plays only a minor role.

  19. Functional metalloproteins integrated with conductive substrates: detecting single molecules and sensing individual recognition events.

    PubMed

    Bonanni, B; Andolfi, L; Bizzarri, A R; Cannistraro, S

    2007-05-17

    In the past decade, there has been significant interest in the integration of biomaterials with electronic elements: combining biological functions of biomolecules with nanotechnology offers new perspectives for implementation of ultrasensitive hybrid nanodevices. In particular, great attention has been devoted to redox metalloproteins, since they possess unique characteristics, such as electron-transfer capability, possibility of gating redox activity, and nanometric size, which make them appealing for bioelectronics applications at the nanoscale. The reliable connection of redox proteins to electrodes, aimed at ensuring good electrical contact with the conducting substrate besides preserving protein functionality, is a fundamental step for designing a hybrid nanodevice and calls for a full characterization of the immobilized proteins, possibly at the single-molecule level. Here, we describe how a multitechnique approach, based on several scanning probe microscopy techniques, may provide a comprehensive characterization of different metalloproteins on metal electrodes, disclosing unique information not only about morphological properties of the adsorbed molecules but also about the effectiveness of electrical coupling with the conductive substrate, or even concerning the preserved biorecognition capability upon adsorption. We also show how the success of an immobilization strategy, which is of primary importance for optimal integration of metalloproteins with a metal electrode, can be promptly assessed by means of the proposed approach. Besides the characterization aspect, the complementary employment of the proposed techniques deserves major potentialities for ultrasensitive detection of adsorbed biomolecules. In particular, it is shown how sensing of single metalloproteins may be optimized by monitoring the most appropriate observable. Additionally, we suggest how the combination of several experimental techniques might offer increased versatility, real-time response, and wide applicability as a detection method, once a reproducible correlation among signals coming from different single-molecule techniques is established. PMID:17425359

  20. Interfacial Coupling and Electronic Structure of Two-Dimensional Silicon Grown on the Ag(111) Surface at High Temperature.

    PubMed

    Feng, Jiagui; Wagner, Sean R; Zhang, Pengpeng

    2015-01-01

    Freestanding silicene, a monolayer of Si arranged in a honeycomb structure, has been predicted to give rise to massless Dirac fermions, akin to graphene. However, Si structures grown on a supporting substrate can show properties that strongly deviate from the freestanding case. Here, combining scanning tunneling microscopy/spectroscopy and differential conductance mapping, we show that the electrical properties of the phase of few-layer Si grown on Ag(111) strongly depend on film thickness, where the electron phase coherence length decreases and the free-electron-like surface state gradually diminishes when approaching the interface. These features are presumably attributable to the inelastic inter-band electron-electron scattering originating from the overlap between the surface state, interface state and the bulk state of the substrate. We further demonstrate that the intrinsic electronic structure of the as grown phase is identical to that of the R30° reconstructed Ag on Si(111), both of which exhibit the parabolic energy-momentum dispersion relation with comparable electron effective masses. These findings highlight the essential role of interfacial coupling on the properties of two-dimensional Si structures grown on supporting substrates, which should be thoroughly scrutinized in pursuit of silicene. PMID:26084916

  1. Ab initio modeling of Fe(ii) adsorption and interfacial electron transfer at goethite (?-FeOOH) surfaces.

    PubMed

    Alexandrov, Vitaly; Rosso, Kevin M

    2015-05-27

    Goethite (?-FeOOH) surfaces represent one of the most ubiquitous redox-active interfaces in the environment, playing an important role in biogeochemical metal cycling and contaminant residence in the subsurface. Fe(ii)-catalyzed recrystallization of goethite is a fundamental process in this context, but the proposed Fe(ii)aq-Fe(iii)goethite electron and iron atom exchange mechanism of recrystallization remains poorly understood at the atomic level. We examine the adsorption of aqueous Fe(ii) and subsequent interfacial electron transfer (ET) between adsorbed Fe(ii) and structural Fe(iii) at the (110) and (021) goethite surfaces using density functional theory calculations including Hubbard U corrections (DFT + U) aided by ab initio molecular dynamics simulations. We investigate various surface sites for the adsorption of Fe(2+)(H2O)6 in different coordination environments. Calculated energies for adsorbed complexes at both surfaces favor monodentate complexes with reduced 4- and 5-fold coordination over higher-dentate structures and 6-fold coordination. The hydrolysis of H2O ligands is observed for some pre-ET adsorbed Fe(ii) configurations. ET from the adsorbed Fe(ii) into the goethite lattice is calculated to be energetically uphill always, but simultaneous proton transfer from H2O ligands of the adsorbed complexes to the surface oxygen species stabilizes post-ET states. We find that surface defects such as oxygen vacancies near the adsorption site also can stabilize post-ET states, enabling the Fe(ii)aq-Fe(iii)goethite interfacial electron transfer reaction implied from experiments to proceed. PMID:25968615

  2. Single-molecule manipulation measurements of polymer/solution interactions

    NASA Astrophysics Data System (ADS)

    Dittmore, Andrew N.

    Because the properties of soft materials emerge from the physics of the constituent polymers, we are motivated to characterize chain molecules at a fundamental level. We build upon the magnetic tweezers single-molecule manipulation technique, which involves measuring the distance between the ends of a polymer in real time and with nanometer precision while applying stable magnetic stretching forces in the piconewton range. Here we demonstrate new applications of this technique, specifically by measuring the interactions between a polymer and the surrounding solvent. First, through low-force elastic measurements, we determine a range of fundamental parameters that quantify solvent quality and chain structure. We present a force-solvent phase diagram to summarize these parameters and our experimental data, and discuss where PEG, DNA, RNA, and proteins fit into the diagram. The unstructured and structured states of a biomolecule reside at opposite ends of the diagram, indicating that folding is accompanied by a change in the character of the solvent. We therefore chose to investigate the local solvent change that occurs when a charged biomolecule folds. We present a thermodynamic framework for measuring the uptake of counterions that accompanies nucleic acid folding. Our measurements of a simple DNA hairpin identify potential shortcomings in thermodynamic parameters of MFOLD, the most widely used predictive software for nucleic acids. Finally, we present a variety of polymer immobilization schemes, achieve low-noise measurements with a strong magnet design, identify new assays, and provide technical guidance that may be useful to those interested in pursuing future magnetic tweezers experiments.

  3. Novel Polymer Linkers for Single Molecule AFM Force Spectroscopy

    PubMed Central

    Tong, Zenghan; Mikheikin, Andrey; Krasnoslobodtsev, Alexey; Lv, Zhengjian; Lyubchenko, Yuri L.

    2013-01-01

    Flexible polymer linkers play an important role in various imaging and probing techniques that require surface immobilization, including atomic force microscopy (AFM). In AFM force spectroscopy, polymer linkers are necessary for the covalent attachment of molecules of interest to the AFM tip and the surface. The polymer linkers tether the molecules and provide their proper orientation in probing experiments. Additionally, the linkers separate specific interactions from nonspecific short-range adhesion and serve as a reference point for the quantitative analysis of single molecule probing events. In this report, we present our results on the synthesis and testing of a novel polymer linker and the identification of a number of potential applications for its use in AFM force spectroscopy experiments. The synthesis of the linker is based on the well-developed phosphoramidate (PA) chemistry that allows the routine synthesis of linkers with predetermined lengths and PA composition. These linkers are homogeneous in length and can be terminated with various functional groups. PA linkers with different functional groups were synthesized and tested in experimental systems utilizing different immobilization chemistries. We probed interactions between complementary DNA oligonucleotides; DNA and protein complexes formed by the site-specific binding protein SfiI; and interactions between amyloid peptide (A?42). The results of the AFM force spectroscopy experiments validated the feasibility of the proposed approach for the linker design and synthesis. Furthermore, the properties of the tether (length, functional groups) can be adjusted to meet the specific requirements for different force spectroscopy experiments and system characteristics, suggesting that it could be used for a large number of various applications. PMID:23624104

  4. Modulation of intermolecular interactions in single-molecule magnets

    NASA Astrophysics Data System (ADS)

    Heroux, Katie Jeanne

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

  5. Asymmetric nanopore membranes: Single molecule detection and unique transport properties

    NASA Astrophysics Data System (ADS)

    Bishop, Gregory William

    Biological systems rely on the transport properties of transmembrane channels. Such pores can display selective transport by allowing the passage of certain ions or molecules while rejecting others. Recent advances in nanoscale fabrication have allowed the production of synthetic analogs of such channels. Synthetic nanopores (pores with a limiting dimension of 1--100 nm) can be produced in a variety of materials by several different methods. In the Martin group, we have been exploring the track-etch method to produce asymmetric nanopores in thin films of polymeric or crystalline materials. Asymmetric nanopores are of particular interest due to their ability to serve as ion-current rectifiers. This means that when a membrane that contains such a pore or collection of pores is used to separate identical portions of electrolyte solution, the magnitude of the ionic current will depend not only on the magnitude of the applied potential (as expected) but also the polarity. Ion-current rectification is characterized by an asymmetric current--potential response. Here, the interesting transport properties of asymmetric nanopores (ion-current rectification and the related phenomenon of electroosmotic flow rectification) are explored. The effects of pore shape and pore density on these phenomena are investigated. Membranes that contain a single nanopore can serve as platforms for the single-molecule sensing technique known as resistive pulse sensing. The resistive-pulse sensing method is based on the Coulter principle. Thus, the selectivity of the technique is based largely upon size, making the analysis of mixtures by this method difficult in many cases. Here, the surface of a single nanopore membrane is modified with a molecular recognition agent in an attempt to obtain a more selective resistive-pulse sensor for a specific analyte.

  6. Nucleosome disassembly intermediates characterized by single-molecule FRET

    PubMed Central

    Gansen, Alexander; Valeri, Alessandro; Hauger, Florian; Felekyan, Suren; Kalinin, Stanislav; Tóth, Katalin; Langowski, Jörg; Seidel, Claus A. M.

    2009-01-01

    The nucleosome has a central role in the compaction of genomic DNA and the control of DNA accessibility for transcription and replication. To help understanding the mechanism of nucleosome opening and closing in these processes, we studied the disassembly of mononucleosomes by quantitative single-molecule FRET with high spatial resolution, using the SELEX-generated “Widom 601” positioning sequence labeled with donor and acceptor fluorophores. Reversible dissociation was induced by increasing NaCl concentration. At least 3 species with different FRET were identified and assigned to structures: (i) the most stable high-FRET species corresponding to the intact nucleosome, (ii) a less stable mid-FRET species that we attribute to a first intermediate with a partially unwrapped DNA and less histones, and (iii) a low-FRET species characterized by a very broad FRET distribution, representing highly unwrapped structures and free DNA formed at the expense of the other 2 species. Selective FCS analysis indicates that even in the low-FRET state, some histones are still bound to the DNA. The interdye distance of 54.0 ? measured for the high-FRET species corresponds to a compact conformation close to the known crystallographic structure. The coexistence and interconversion of these species is first demonstrated under non-invasive conditions. A geometric model of the DNA unwinding predicts the presence of the observed FRET species. The different structures of these species in the disassembly pathway map the energy landscape indicating major barriers for 10-bp and minor ones for 5-bp DNA unwinding steps. PMID:19706432

  7. Nucleosome disassembly intermediates characterized by single-molecule FRET.

    PubMed

    Gansen, Alexander; Valeri, Alessandro; Hauger, Florian; Felekyan, Suren; Kalinin, Stanislav; Tóth, Katalin; Langowski, Jörg; Seidel, Claus A M

    2009-09-01

    The nucleosome has a central role in the compaction of genomic DNA and the control of DNA accessibility for transcription and replication. To help understanding the mechanism of nucleosome opening and closing in these processes, we studied the disassembly of mononucleosomes by quantitative single-molecule FRET with high spatial resolution, using the SELEX-generated "Widom 601" positioning sequence labeled with donor and acceptor fluorophores. Reversible dissociation was induced by increasing NaCl concentration. At least 3 species with different FRET were identified and assigned to structures: (i) the most stable high-FRET species corresponding to the intact nucleosome, (ii) a less stable mid-FRET species that we attribute to a first intermediate with a partially unwrapped DNA and less histones, and (iii) a low-FRET species characterized by a very broad FRET distribution, representing highly unwrapped structures and free DNA formed at the expense of the other 2 species. Selective FCS analysis indicates that even in the low-FRET state, some histones are still bound to the DNA. The interdye distance of 54.0 A measured for the high-FRET species corresponds to a compact conformation close to the known crystallographic structure. The coexistence and interconversion of these species is first demonstrated under non-invasive conditions. A geometric model of the DNA unwinding predicts the presence of the observed FRET species. The different structures of these species in the disassembly pathway map the energy landscape indicating major barriers for 10-bp and minor ones for 5-bp DNA unwinding steps. PMID:19706432

  8. Time resolved single molecule spectroscopy of semiconductor quantum dot/conjugated organic hybrid nanostructures

    NASA Astrophysics Data System (ADS)

    Odoi, Michael Yemoh

    Single molecule studies on CdSe quantum dots functionalized with oligo-phenylene vinylene ligands (CdSe-OPV) provide evidence of strong electronic communication that facilitate charge and energy transport between the OPV ligands and the CdSe quantum dot core. This electronic interaction greatly modify, the photoluminescence properties of both bulk and single CdSe-OPV nanostructure thin film samples. Size-correlated wide-field fluorescence imaging show that blinking suppression in single CdSe-OPV is linked to the degree of OPV coverage (inferred from AFM height scans) on the quantum dot surface. The effect of the complex electronic environment presented by photoexcited OPV ligands on the excited state property of CdSe-OPV is measured with single photon counting and photon-pair correlation spectroscopy techniques. Time-tagged-time-resolved (TTTR) single photon counting measurements from individual CdSe-OPV nanostructures, show excited state lifetimes an order of magnitude shorter relative to conventional ZnS/CdSe quantum dots. Second-order intensity correlation measurements g(2)(tau) from individual CdSe-OPV nanostructures point to a weak multi-excitonic character with a strong wavelength dependent modulation depth. By tuning in and out of the absorption of the OPV ligands we observe changes in modulation depth from g(2) (0) ? 0.2 to 0.05 under 405 and 514 nm excitation respectively. Defocused images and polarization anisotropy measurements also reveal a well-defined linear dipole emission pattern in single CdSe-OPV nanostructures. These results provide new insights into to the mechanism behind the electronic interactions in composite quantum dot/conjugated organic composite systems at the single molecule level. The observed intensity flickering , blinking suppression and associated lifetime/count rate and antibunching behaviour is well explained by a Stark interaction model. Charge transfer from photo-excitation of the OPV ligands to the surface of the CdSe quantum dot core, mixes electron/holes states and lifts the degeneracy in the band edge bright exciton state, which induces a well define linear dipole behaviour in single CdSe-OPV nanostructures. The shift in the electron energies also affects Auger assisted hole trapping rates, suppress access to dark states and reduce the excited state lifetime.

  9. Single-Molecule Tracking of Inositol Trisphosphate Receptors Reveals Different Motilities and Distributions

    E-print Network

    Parker, Ian

    have shown that the majority of IP3Rs are freely motile. To address this discrepancy, we applied single-molecule imaging to locate and track type 1 IP3Rs tagged with a photoswitchable fluorescent protein and expressedArticle Single-Molecule Tracking of Inositol Trisphosphate Receptors Reveals Different Motilities

  10. Do-it-yourself guide: how to use the modern single-molecule toolkit

    E-print Network

    Walter, Nils G.

    Do-it-yourself guide: how to use the modern single-molecule toolkit Nils G Walter, Cheng-Yen Huang the modern biosciences. Here we survey the current state of the art in single-molecule tools including/or transient species along a reaction pathway, which are typically averaged out in ensemble measurements; (vi

  11. On detailed balance and reversibility of semi-Markov processes and single-molecule enzyme kinetics

    E-print Network

    Miekisz, Jacek

    On detailed balance and reversibility of semi-Markov processes and single- molecule enzyme kinetics://jmp.aip.org/about/rights_and_permissions #12;On detailed balance and reversibility of semi-Markov processes and single-molecule enzyme kinetics-Markov processes have found increasing applications in modeling the kinet- ics of single enzyme molecules. Detailed

  12. High-density single-molecule analysis of cell surface dynamics in C. elegans embryos

    E-print Network

    Cai, Long

    High-density single-molecule analysis of cell surface dynamics in C. elegans embryos Francois B in GFP::Actin embryos. Supplementary Figure 3 Tunable and high-density sampling of single molecule vs axial position, measured across the field of illumination in a GFP::Utrophin embryo during

  13. Single-molecule FRET experiments with a red-enhanced custom technology SPAD

    E-print Network

    Michalet, Xavier

    Single-molecule FRET experiments with a red-enhanced custom technology SPAD Francesco Panzerib, Italy ABSTRACT Single-molecule fluorescence spectroscopy of freely diffusing molecules in solution is a powerful tool used to investigate the properties of individual molecules. Single-Photon Avalanche Diodes

  14. Single-Molecule Kinetics of Nanoparticle Catalysis , Hao Shen, Guokun Liu, and Peng Chen

    E-print Network

    Chen, Peng

    #12;Single-Molecule Kinetics of Nanoparticle Catalysis Weilin Xu , Hao Shen, Guokun Liu, and Peng to characterize in ensemble-averaged measurements. The single-molecule approach enables studying the catalysis of nanoparticles at the single-particle level with real-time single-turnover resolution. This article reviews our

  15. Single-Molecule Kinetics Reveals a Hidden Surface Reaction Intermediate in Single-Nanoparticle Catalysis

    E-print Network

    Chen, Peng

    Single-Molecule Kinetics Reveals a Hidden Surface Reaction Intermediate in Single polydispersion in reaction kinetics. Here we use single-molecule fluorescence microscopy to study two.3 nm pseudospherical Au nanoparticlesat the single-particle, single- turnover resolution in catalyzing

  16. Single-Molecule Fluorescence Spectroscopy: New Probes of Protein Function and Dynamics

    NSDL National Science Digital Library

    PhD Carey K. Johnson (University of Kansas Department of Chemistry)

    2005-02-01

    Single-molecule fluorescence methods provide new tools for the study of biological systems. Single-pair fluorescence resonance energy transfer has provided detailed information about dynamics and structure of the Ca2+-signaling protein calmodulin. Single-molecule polarization modulation spectroscopy has probed the mechanism by which calmodulin activates the plasma membrane Ca2+ pump

  17. Complex RNA Folding Kinetics Revealed by Single-Molecule FRET and Hidden Markov Models

    E-print Network

    Complex RNA Folding Kinetics Revealed by Single-Molecule FRET and Hidden Markov Models Bettina G a hidden Markov model and optimization procedure for photon-based single-molecule FRET data, which takes (low-FRET) and compact (high-FRET) states. Five states were consistently and independently identified

  18. Supplementary Information for: Complex RNA folding kinetics revealed by single molecule FRET and hidden Markov models

    E-print Network

    Supplementary Information for: Complex RNA folding kinetics revealed by single molecule FRET (hidden states). The states are not associated with a single FRET value of the signal but to a value range emission process, which gives rise to the ob- served photon-by-photon trace in a single-molecule FRET

  19. Single-Molecule FRET Reveals the Native-State Dynamics of the IB Ankyrin Repeat Domain

    E-print Network

    Komives, Elizabeth A.

    Single-Molecule FRET Reveals the Native-State Dynamics of the IB Ankyrin Repeat Domain Jorge A single-molecule fluorescence resonance energy transfer (smFRET) studies in which the second and sixth ankyrin repeats (ARs) of IB were labeled with FRET pairs showed slow fluctuations as if the IB AR domain

  20. Electromagnetic Torque Tweezers: A Versatile Approach for Measurement of Single-Molecule Twist and Torque

    E-print Network

    Dekker, Nynke

    Electromagnetic Torque Tweezers: A Versatile Approach for Measurement of Single-Molecule Twist of freedom. Here we present electromagnetic torque tweezers (eMTT) that combine permanent and electromagnets from single-molecules to living cells. KEYWORDS: Electromagnetic torque tweezers, torque spectroscopy

  1. Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic

    E-print Network

    Ritort, Felix

    Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy Keir C Neuman1 & Attila Nagy2 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

  2. A correlation force spectrometer for single molecule measurements under tensile load

    E-print Network

    Paul, Mark

    A correlation force spectrometer for single molecule measurements under tensile load Milad Radiom,1.15­20 Comparing the dual trap technique with atomic force microscopy (AFM) single molecule force correlation force spectroscopy (CFS). We describe an instrument that is designed for characterizing

  3. Compaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experiments

    E-print Network

    Thirumalai, Devarajan

    ,87.64.Dz The response of biopolymers to mechanical force (f), at the single molecule level, has single molecule force spectroscopy (SMFS) measurements are f-dependent position of the transition stateCompaction and tensile forces determine the accuracy of folding landscape parameters from single

  4. A two-state kinetic model for the unfolding of single molecules by mechanical force

    E-print Network

    Ritort, Felix

    A two-state kinetic model for the unfolding of single molecules by mechanical force F. Ritort , C investigate the work dissipated during the irreversible unfold- ing of single molecules by mechanical force molecule of DNA to stretch it from a coil to an extended form, and force is applied to DNA or RNA hairpins

  5. Probing protein conformations at the oil dropletwater interface using single-molecule force spectroscopy

    E-print Network

    Dutcher, John

    Probing protein conformations at the oil droplet­water interface using single-molecule force atomic force microscopy (AFM) imaging and single molecule force spectroscopy (SMFS) to study b to fully extend the molecules, the spacing between sawtooth peaks in the force­distance curves

  6. Extracting Kinetics from Single-Molecule Force Spectroscopy: Nanopore Unzipping of DNA Hairpins

    E-print Network

    Meller, Amit

    Extracting Kinetics from Single-Molecule Force Spectroscopy: Nanopore Unzipping of DNA Hairpins, Massachusetts ABSTRACT Single-molecule force experiments provide powerful new tools to explore biomolecular (SM) experiments forces can be exerted directly on individual molecules and their response can

  7. Coherent Manipulation and Decoherence of S=10 Single-Molecule Magnets

    NASA Astrophysics Data System (ADS)

    Takahashi, Susumu

    2009-03-01

    A single crystal of high-spin single-molecule magnets (SMMs) is an attractive testbed for quantum science and technologies. High-spin SMMs are suitable for applications to dense quantum memory and computing devices. Because SMM clusters are identical and interact weakly, the ensemble properties of single crystals of SMMs reflect the properties of a single cluster. However coherent manipulation of high-spin SMM crystals has never been demonstrated due to strong spin decoherence. For spins in the solid state, an interaction with fluctuations of surrounding spin bath is a major source of spin decoherence. One approach to reduce spin bath fluctuations is to bring the spin bath into a well-known quantum state that exhibits little or no fluctuations. A prime example is the case of a fully polarized spin bath. In diamond, spin decoherence has been quenched using high-frequency pulsed electron paramagnetic resonance (EPR) [1]. We present coherent manipulation and decoherence of a single-crystal of S=10 Fe8 SMMs. Through polarizing a spin bath in Fe8 single-molecule magnets at 4.6 T and 1.3 K, we demonstrate that spin decoherence is significantly suppressed to extend the spin decoherence time (T2) up to 700 ns [2]. Investigation of temperature dependence of spin relaxation times reveals the nature of spin decoherence. This work is collaboration with J. van Tol, C. C. Beedle, D. N. Hendrickson, L.-C. Brunel, and M. S. Sherwin.[4pt] [1] S. Takahashi, R. Hanson, J. van Tol, M. S. Sherwin, and D. D. Awschalom, Phys. Rev. Lett. 101, 047601 (2008).[0pt] [2] S. Takahashi, J. van Tol, C. C. Beedle, D. N. Hendrickson, L.-C. Brunel, and M. S. Sherwin, arXiv: 0810.1254.

  8. Manipulating Protein Conformations by Single-Molecule AFM-FRET Nanoscopy

    PubMed Central

    He, Yufan; Lu, Maolin; Cao, Jin; Lu, H. Peter

    2013-01-01

    Combining atomic force microscopy and fluorescence resonance energy transfer spectroscopy (AFM-FRET), we have developed a single-molecule AFM-FRET nanoscopy approach capable of effectively pinpointing and mechanically manipulating a targeted dye-labeled single protein in a large sampling area, and simultaneously monitoring the conformational changes of the targeted protein by recording single-molecule FRET time trajectories. We have further demonstrated an application of using this nanoscopy on manipulation of single-molecule protein conformation and simultaneous single-molecule FRET measurement of a Cy3–Cy5 labeled kinase enzyme, HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase). By analyzing time-resolved FRET trajectories and correlated AFM force pulling curves of the targeted single-molecule enzyme, we are able to observe the protein conformational changes of a specific coordination by AFM mechanic force pulling. PMID:22276737

  9. Controlling orbital-selective Kondo effects in a single molecule through coordination chemistry.

    PubMed

    Tsukahara, Noriyuki; Minamitani, Emi; Kim, Yousoo; Kawai, Maki; Takagi, Noriaki

    2014-08-01

    Iron(II) phthalocyanine (FePc) molecule causes novel Kondo effects derived from the unique electronic structure of multi-spins and multi-orbitals when attached to Au(111). Two unpaired electrons in the d(z)(2) and the degenerate d? orbitals are screened stepwise, resulting in spin and spin+orbital Kondo effects, respectively. We investigated the impact on the Kondo effects of the coordination of CO and NO molecules to the Fe(2+) ion as chemical stimuli by using scanning tunneling microscopy (STM) and density functional theory calculations. The impacts of the two diatomic molecules are different from each other as a result of the different electronic configurations. The coordination of CO converts the spin state from triplet to singlet, and then the Kondo effects completely disappear. In contrast, an unpaired electron survives in the molecular orbital composed of Fe d(z)(2) and NO 5? and 2?* orbitals for the coordination of NO, causing a sharp Kondo resonance. The isotropic magnetic response of the peak indicates the origin is the spin Kondo effect. The diatomic molecules attached to the Fe(2+) ion were easily detached by applying a pulsed voltage at the STM junction. These results demonstrate that the single molecule chemistry enables us to switch and control the spin and the many-body quantum states reversibly. PMID:25106595

  10. Nanoelectrical analysis of single molecules and atomic-scale materials at the solid/liquid interface.

    PubMed

    Nirmalraj, Peter; Thompson, Damien; Molina-Ontoria, Agustín; Sousa, Marilyne; Martín, Nazario; Gotsmann, Bernd; Riel, Heike

    2014-10-01

    Evaluating the built-in functionality of nanomaterials under practical conditions is central for their proposed integration as active components in next-generation electronics. Low-dimensional materials from single atoms to molecules have been consistently resolved and manipulated under ultrahigh vacuum at low temperatures. At room temperature, atomic-scale imaging has also been performed by probing materials at the solid/liquid interface. We exploit this electrical interface to develop a robust electronic decoupling platform that provides precise information on molecular energy levels recorded using in situ scanning tunnelling microscopy/spectroscopy with high spatial and energy resolution in a high-density liquid environment. Our experimental findings, supported by ab initio electronic structure calculations and atomic-scale molecular dynamics simulations, reveal direct mapping of single-molecule structure and resonance states at the solid/liquid interface. We further extend this approach to resolve the electronic structure of graphene monolayers at atomic length scales under standard room-temperature operating conditions. PMID:25129620

  11. 688 IEEE ELECTRON DEVICE LETTERS, VOL. 27, NO. 8, AUGUST 2006 Impact of the Interfacial Layer on the Low-Frequency

    E-print Network

    Misra, Durgamadhab "Durga"

    the main source of 1/f noise not only on pMOS devices, as usually observed, but also on nMOS devices. 2688 IEEE ELECTRON DEVICE LETTERS, VOL. 27, NO. 8, AUGUST 2006 Impact of the Interfacial Layer] for EOT devices. For pMOS devices, the major noise mechanism is found to be mobility

  12. Spectroelectrochemical investigation of intramolecular and interfacial electron-transfer rates reveals differences between nitrite reductase at rest and during turnover.

    PubMed

    Krzemi?ski, ?ukasz; Ndamba, Lionel; Canters, Gerard W; Aartsma, Thijs J; Evans, Stephen D; Jeuken, Lars J C

    2011-09-28

    A combined fluorescence and electrochemical method is described that is used to simultaneously monitor the type-1 copper oxidation state and the nitrite turnover rate of a nitrite reductase (NiR) from Alcaligenes faecalis S-6. The catalytic activity of NiR is measured electrochemically by exploiting a direct electron transfer to fluorescently labeled enzyme molecules immobilized on modified gold electrodes, whereas the redox state of the type-1 copper site is determined from fluorescence intensity changes caused by Fo?rster resonance energy transfer (FRET) between a fluorophore attached to NiR and its type-1 copper site. The homotrimeric structure of the enzyme is reflected in heterogeneous interfacial electron-transfer kinetics with two monomers having a 25-fold slower kinetics than the third monomer. The intramolecular electron-transfer rate between the type-1 and type-2 copper site changes at high nitrite concentration (?520 ?M), resulting in an inhibition effect at low pH and a catalytic gain in enzyme activity at high pH. We propose that the intramolecular rate is significantly reduced in turnover conditions compared to the enzyme at rest, with an exception at low pH/nitrite conditions. This effect is attributed to slower reduction rate of type-2 copper center due to a rate-limiting protonation step of residues in the enzyme's active site, gating the intramolecular electron transfer. PMID:21863850

  13. Solid-phase single molecule biosensing using dual-color colocalization of fluorescent quantum dot nanoprobes

    NASA Astrophysics Data System (ADS)

    Liu, Jianbo; Yang, Xiaohai; Wang, Kemin; Wang, Qing; Liu, Wei; Wang, Dong

    2013-10-01

    The development of solid-phase surface-based single molecule imaging technology has attracted significant interest during the past decades. Here we demonstrate a sandwich hybridization method for highly sensitive detection of a single thrombin protein at a solid-phase surface based on the use of dual-color colocalization of fluorescent quantum dot (QD) nanoprobes. Green QD560-modified thrombin binding aptamer I (QD560-TBA I) were deposited on a positive poly(l-lysine) assembled layer, followed by bovine serum albumin blocking. It allowed the thrombin protein to mediate the binding of the easily detectable red QD650-modified thrombin binding aptamer II (QD650-TBA II) to the QD560-TBA I substrate. Thus, the presence of the target thrombin can be determined based on fluorescent colocalization measurements of the nanoassemblies, without target amplification or probe separation. The detection limit of this assay reached 0.8 pM. This fluorescent colocalization assay has enabled single molecule recognition in a separation-free detection format, and can serve as a sensitive biosensing platform that greatly suppresses the nonspecific adsorption false-positive signal. This method can be extended to other areas such as multiplexed immunoassay, single cell analysis, and real time biomolecule interaction studies.The development of solid-phase surface-based single molecule imaging technology has attracted significant interest during the past decades. Here we demonstrate a sandwich hybridization method for highly sensitive detection of a single thrombin protein at a solid-phase surface based on the use of dual-color colocalization of fluorescent quantum dot (QD) nanoprobes. Green QD560-modified thrombin binding aptamer I (QD560-TBA I) were deposited on a positive poly(l-lysine) assembled layer, followed by bovine serum albumin blocking. It allowed the thrombin protein to mediate the binding of the easily detectable red QD650-modified thrombin binding aptamer II (QD650-TBA II) to the QD560-TBA I substrate. Thus, the presence of the target thrombin can be determined based on fluorescent colocalization measurements of the nanoassemblies, without target amplification or probe separation. The detection limit of this assay reached 0.8 pM. This fluorescent colocalization assay has enabled single molecule recognition in a separation-free detection format, and can serve as a sensitive biosensing platform that greatly suppresses the nonspecific adsorption false-positive signal. This method can be extended to other areas such as multiplexed immunoassay, single cell analysis, and real time biomolecule interaction studies. Electronic supplementary information (ESI) available: Absorbance and fluorescence spectra of quantum dot nanoprobes, electrophoresis analysis, and experimental setup for fluorescence imaging with dual channels. See DOI: 10.1039/c3nr03291d

  14. Single-molecule spectroscopy of amino acids and peptides by recognition tunnelling

    NASA Astrophysics Data System (ADS)

    Zhao, Yanan; Ashcroft, Brian; Zhang, Peiming; Liu, Hao; Sen, Suman; Song, Weisi; Im, Jongone; Gyarfas, Brett; Manna, Saikat; Biswas, Sovan; Borges, Chad; Lindsay, Stuart

    2014-06-01

    The human proteome has millions of protein variants due to alternative RNA splicing and post-translational modifications, and variants that are related to diseases are frequently present in minute concentrations. For DNA and RNA, low concentrations can be amplified using the polymerase chain reaction, but there is no such reaction for proteins. Therefore, the development of single-molecule protein sequencing is a critical step in the search for protein biomarkers. Here, we show that single amino acids can be identified by trapping the molecules between two electrodes that are coated with a layer of recognition molecules, then measuring the electron tunnelling current across the junction. A given molecule can bind in more than one way in the junction, and we therefore use a machine-learning algorithm to distinguish between the sets of electronic `fingerprints' associated with each binding motif. With this recognition tunnelling technique, we are able to identify D and L enantiomers, a methylated amino acid, isobaric isomers and short peptides. The results suggest that direct electronic sequencing of single proteins could be possible by sequentially measuring the products of processive exopeptidase digestion, or by using a molecular motor to pull proteins through a tunnel junction integrated with a nanopore.

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

    PubMed

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

    2014-01-01

    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. PMID:25271426

  16. Experimental approaches for addressing fundamental biological questions in living, functioning cells with single molecule precision

    PubMed Central

    Lenn, Tchern; Leake, Mark C.

    2012-01-01

    In recent years, single molecule experimentation has allowed researchers to observe biological processes at the sensitivity level of single molecules in actual functioning, living cells, thereby allowing us to observe the molecular basis of the key mechanistic processes in question in a very direct way, rather than inferring these from ensemble average data gained from traditional molecular and biochemical techniques. In this short review, we demonstrate the impact that the application of single molecule bioscience experimentation has had on our understanding of various cellular systems and processes, and the potential that this approach has for the future to really address very challenging and fundamental questions in the life sciences. PMID:22773951

  17. Development of new microscope unit for single molecule spectroscopy under various ambient conditions

    NASA Astrophysics Data System (ADS)

    Yamada, T.; Kaji, T.; Ueda, R.; Otomo, A.

    2013-03-01

    This paper introduces techniques we previously developed for single molecule spectroscopy and continues on to describe our studies on dipole orientation imaging of single molecules under various ambient conditions. In these studies, we successfully obtained defocused images of single perylene diimide (PDI) molecules under air, high-vacuum, and pure N2 gas conditions by utilizing the advantages of our new microscope unit. The studies are positioned as one of the important applications of our microscope unit for single molecule spectroscopy. We expect a wide range of applications for this unit for various microscope measurements for many types of materials.

  18. Molecular processes studied at a single-molecule level using DNA origami nanostructures and atomic force microscopy.

    PubMed

    Bald, Ilko; Keller, Adrian

    2014-01-01

    DNA origami nanostructures allow for the arrangement of different functionalities such as proteins, specific DNA structures, nanoparticles, and various chemical modifications with unprecedented precision. The arranged functional entities can be visualized by atomic force microscopy (AFM) which enables the study of molecular processes at a single-molecular level. Examples comprise the investigation of chemical reactions, electron-induced bond breaking, enzymatic binding and cleavage events, and conformational transitions in DNA. In this paper, we provide an overview of the advances achieved in the field of single-molecule investigations by applying atomic force microscopy to functionalized DNA origami substrates. PMID:25191873

  19. Self-Doping, O2-Stable, n-Type Interfacial Layer for Organic Electronics

    SciTech Connect

    Reilly, T. H. III; Hains, A. W.; Chen, H. Y.; Gregg, B. A.

    2012-04-01

    Solid films of a water-soluble dicationic perylene diimide salt, perylene bis(2-ethyltrimethylammonium hydroxide imide), Petma{sup +}OH{sup -}, are strongly doped n-type by dehydration and reversibly de-doped by hydration. The hydrated films consist almost entirely of the neutral perylene diimide, PDI, while the dehydrated films contain {approx}50% PDI anions. The conductivity increases by five orders of magnitude upon dehydration, probably limited by film roughness, while the work function decreases by 0.74 V, consistent with an n-type doping density increase of {approx}12 orders of magnitude. Remarkably, the PDI anions are stable in dry air up to 120 C. The work function of the doped film, {phi} (3.96 V vs. vacuum), is unusually negative for an O{sub 2}-stable contact. Petma{sup +} OH{sup -} is also characterized as an interfacial layer, IFL, in two different types of organic photovoltaic cells. Results are comparable to state of the art cesium carbonate IFLs, but may improve if film morphology can be better controlled. The films are stable and reversible over many months in air and light. The mechanism of this unusual self-doping process may involve the change in relative potentials of the ions in the film caused by their deshielding and compaction as water is removed, leading to charge transfer when dry.

  20. Fabrication of metallized nanopores in silicon nitride membranes for single-molecule sensing.

    PubMed

    Wei, Ruoshan; Pedone, Daniel; Zürner, Andreas; Döblinger, Markus; Rant, Ulrich

    2010-07-01

    The fabrication and characterization of a metallized nanopore structure for the sensing of single molecules is described. Pores of varying diameters (>10 nm) are patterned into free-standing silicon nitride membranes by electron-beam lithography and reactive ion etching. Structural characterization by transmission electron microscopy (TEM) and tomography reveals a conical pore shape with a 40 degrees aperture. Metal films of Ti/Au are vapor deposited and the pore shape and shrinking are studied as a function of evaporated film thickness. TEM tomography analysis confirms metalization of the inner pore walls as well as conservation of the conical pore shape. In electrical measurements of the transpore current in aqueous electrolyte solution, the pores feature very low noise. The applicability of the metallized pores for stochastic sensing is demonstrated in real-time translocation experiments of single lambda-DNA molecules. We observe exceptionally long-lasting current blockades with a fine structure of distinct current levels, suggesting an attractive interaction between the DNA and the PEGylated metallic pore walls. PMID:20564484

  1. Redox-Controlled Exchange Bias in a Supramolecular Chain of Fe4 Single-Molecule Magnets.

    PubMed

    Nava, Andrea; Rigamonti, Luca; Zangrando, Ennio; Sessoli, Roberta; Wernsdorfer, Wolfgang; Cornia, Andrea

    2015-07-20

    Tetrairon(III) single-molecule magnets [Fe4 (pPy)2 (dpm)6 ] (1) (H3 pPy=2-(hydroxymethyl)-2-(pyridin-4-yl)propane-1,3-diol, Hdpm=dipivaloylmethane) have been deliberately organized into supramolecular chains by reaction with Ru(II) Ru(II) or Ru(II) Ru(III) paddlewheel complexes. The products [Fe4 (pPy)2 (dpm)6 ][Ru2 (OAc)4 ](BF4 )x with x=0 (2?a) or x=1 (2?b) differ in the electron count on the paramagnetic diruthenium bridges and display hysteresis loops of substantially different shape. Owing to their large easy-plane anisotropy, the s=1 diruthenium(II,II) units in 2?a act as effective seff =0 spins and lead to negligible intrachain communication. By contrast, the mixed-valent bridges (s=3/2, seff =1/2) in 2?b introduce a significant exchange bias, with concomitant enhancement of the remnant magnetization. Our results suggest the possibility to use electron transfer to tune intermolecular communication in redox-responsive arrays of SMMs. PMID:26096860

  2. Ab initio study of the thermopower of biphenyl-based single-molecule junctions

    NASA Astrophysics Data System (ADS)

    Bürkle, M.; Zotti, L. A.; Viljas, J. K.; Vonlanthen, D.; Mishchenko, A.; Wandlowski, T.; Mayor, M.; Schön, G.; Pauly, F.

    2012-09-01

    By employing ab initio electronic-structure calculations combined with the nonequilibrium Green's function technique, we study the dependence of the thermopower Q on the conformation in biphenyl-based single-molecule junctions. For the series of experimentally available biphenyl molecules, alkyl side chains allow us to gradually adjust the torsion angle ? between the two phenyl rings from 0? to 90? and to control in this way the degree of ?-electron conjugation. Studying different anchoring groups and binding positions, our theory predicts that the absolute values of the thermopower decrease slightly towards larger torsion angles, following an a+bcos2? dependence. The anchoring group determines the sign of Q and a,b simultaneously. Sulfur and amine groups give rise to Q,a,b>0, while for cyano, Q,a,b<0. The different binding positions can lead to substantial variations of the thermopower mostly due to changes in the alignment of the frontier molecular orbital levels and the Fermi energy. We explain our ab initio results in terms of a ?-orbital tight-binding model and a minimal two-level model, which describes the pair of hybridizing frontier orbital states on the two phenyl rings. The variations of the thermopower with ? seem to be within experimental resolution.

  3. On single-molecule DNA sequencing with atomic force microscopy using functionalized carbon nanotube probes

    E-print Network

    Burns, Daniel James

    2004-01-01

    A novel DNA sequencing method is proposed based on the specific binding nature of nucleotides and measured by an atomic force microscope (AFM). A single molecule of DNA is denatured and immobilized on an atomically fiat ...

  4. Theoretical study of single-molecule spectroscopy and vibrational spectroscopy in condensed phases

    E-print Network

    Yang, Shilong, 1975-

    2005-01-01

    In this thesis, theoretical models and computer simulations are employed to study several problems of single-molecule spectroscopy and vibrational spectroscopy in condensed phases. The first part of the thesis concentrates ...

  5. Single molecule quantitation and sequencing of rare translocations using microfluidic nested digital PCR

    E-print Network

    Shuga, Joe; Zeng, Yong; Novak, Richard; Lan, Qing; Tang, Xiaojiang; Rothman, Nathaniel; Vermeulen, Roel; Li, Laiyu; Hubbard, Alan; Zhang, Luoping; Mathies, Richard A.; Smith, Martyn T.

    2013-06-23

    of individual tumors. Here, we report the development and application of a bead-based hemi-nested microfluidic droplet digital PCR (dPCR) technology to achieve ‘quantitative’ measurement and single-molecule sequencing of somatically acquired carcinogenic...

  6. Dissecting Single-Molecule Signal Transduction in Carbon Nanotube Circuits with Protein Engineering

    E-print Network

    Weiss, Gregory A.

    Dissecting Single-Molecule Signal Transduction in Carbon Nanotube Circuits with Protein Engineering dissected using eight di erent lysozyme variants synthesized by protein engineering. The data prove that e

  7. The chemical dynamics of nanosensors capable of single-molecule detection

    E-print Network

    Boghossian, Ardemis A.

    Recent advances in nanotechnology have produced the first sensor transducers capable of resolving the adsorption and desorption of single molecules. Examples include near infrared fluorescent single-walled carbon nanotubes ...

  8. Probing single molecule orientations in model lipid membranes with near-field scanning optical microscopy

    E-print Network

    Hollars, Christopher W.; Dunn, Robert C.

    2000-02-01

    Single molecule near-field fluorescence measurements are utilized to characterize the molecular level structure in Langmuir–Blodgett monolayers of L-?-dipalmitoylphosphatidylcholine (DPPC).Monolayers incorporating 3×10?4 mol?% of the fluorescent...

  9. Coherent anti-Stokes Raman scattering with single-molecule sensitivity using a plasmonic Fano resonance

    NASA Astrophysics Data System (ADS)

    Zhang, Yu; Zhen, Yu-Rong; Neumann, Oara; Day, Jared K.; Nordlander, Peter; Halas, Naomi J.

    2014-07-01

    Plasmonic nanostructures are of particular interest as substrates for the spectroscopic detection and identification of individual molecules. Single-molecule sensitivity Raman detection has been achieved by combining resonant molecular excitation with large electromagnetic field enhancements experienced by a molecule associated with an interparticle junction. Detection of molecules with extremely small Raman cross-sections (~10-30?cm2 sr-1), however, has remained elusive. Here we show that coherent anti-Stokes Raman spectroscopy (CARS), a nonlinear spectroscopy of great utility and potential for molecular sensing, can be used to obtain single-molecule detection sensitivity, by exploiting the unique light harvesting properties of plasmonic Fano resonances. The CARS signal is enhanced by ~11 orders of magnitude relative to spontaneous Raman scattering, enabling the detection of single molecules, which is verified using a statistically rigorous bi-analyte method. This approach combines unprecedented single-molecule spectral sensitivity with plasmonic substrates that can be fabricated using top-down lithographic strategies.

  10. Ultra high-throughput single molecule spectroscopy with a 1024 pixel SPAD

    E-print Network

    Michalet, Xavier

    , structural biochemistry, and single-protein tracking in live cells, yielding insights into outstanding@chem.ucla.edu, Phone: 1-310-794-6693, Fax: 1-310-267-4672 Invited Paper Single Molecule Spectroscopy and Imaging IV

  11. Controlled spontaneous emission of single molecules in a two-dimensional photonic band gap.

    PubMed

    Kaji, Takahiro; Yamada, Toshiki; Ito, Syoji; Miyasaka, Hiroshi; Ueda, Rieko; Inoue, Shin-ichiro; Otomo, Akira

    2013-01-01

    We have established a new platform to control the rate of spontaneous emission (SE) of organic molecules in the visible-light region using a combination of a two-dimensional (2D) photonic crystal (PC) slab made of TiO(2) and a single-molecule measurement method. The SE from single molecules of a perylenediimide derivative was effectively inhibited via a radiation field controlled by the 2D PC slab, which has a photonic band gap (PBG) for transverse-electric (TE)-polarized light. The fluorescence lifetimes of the single molecules were extended up to 5.5 times (28.6 ns) by the PBG effect. This result appears to be the first demonstration of drastic lifetime elongation for single molecules due to a PBG effect. PMID:23253079

  12. Interfacial electronic structure at the CH3NH3PbI3/MoOx interface

    NASA Astrophysics Data System (ADS)

    Liu, Peng; Liu, Xiaoliang; Lyu, Lu; Xie, Haipeng; Zhang, Hong; Niu, Dongmei; Huang, Han; Bi, Cheng; Xiao, Zhengguo; Huang, Jinsong; Gao, Yongli

    2015-05-01

    Interfacial electronic properties of the CH3NH3PbI3 (MAPbI3)/MoOx interface are investigated using ultraviolet photoemission spectroscopy and X-ray photoemission spectroscopy. It is found that the pristine MAPbI3 film coated onto the substrate of poly (3,4-ethylenedioxythiophene) poly(styrenesulfonate)/indium tin oxide by two-step method behaves as an n-type semiconductor, with a band gap of ˜1.7 eV and a valence band edge of 1.40 eV below the Fermi energy (EF). With the MoOx deposition of 64 Å upon MAPbI3, the energy levels of MAPbI3 shift toward higher binding energy by 0.25 eV due to electron transfer from MAPbI3 to MoOx. Its conduction band edge is observed to almost pin to the EF, indicating a significant enhancement of conductivity. Meanwhile, the energy levels of MoOx shift toward lower binding energy by ˜0.30 eV, and an interface dipole of 2.13 eV is observed at the interface of MAPbI3/MoOx. Most importantly, the chemical reaction taking place at this interface results in unfavorable interface energy level alignment for hole extraction. A potential barrier of ˜1.36 eV observed for hole transport will impede the hole extraction from MAPbI3 to MoOx. On the other hand, a potential barrier of ˜0.14 eV for electron extraction is too small to efficiently suppress electrons extracted from MAPbI3 to MoOx. Therefore, such an interface is not an ideal choice for hole extraction in organic photovoltaic devices.

  13. Statistics of Single-Molecule Detection Jo1rg Enderlein,* David L. Robbins, W. Patrick Ambrose, Peter M. Goodwin, and

    E-print Network

    Enderlein, Jörg

    Statistics of Single-Molecule Detection Jo1rg Enderlein,* David L. Robbins, W. Patrick Ambrose for the calculation of the photon detection statistics in single-molecule detection experiments is presented detection statistics in single- molecule detection experiments in a fluid flow. Using a path integral

  14. Targeting, resolving and quantifying cellular structures by single-molecule localization microscopy

    PubMed Central

    Sibarita, Jean-Baptiste; Heilemann, Mike

    2012-01-01

    The second ‘Single Molecule Localization Microscopy' symposium was held in August 2012 at the École Polytechnique Fédérale de Lausanne in Switzerland. During two and a half days, around 100 researchers from across the globe, and in disciplines spanning physics, biology, chemistry and computer science, gathered to discuss the developments in single-molecule super-resolution imaging and its applications to address important biological questions. PMID:23146894

  15. Nanoscale surface-enhanced resonance Raman scattering spectroscopy of single molecules on isolated silver clusters

    Microsoft Academic Search

    Alfred J. Meixner; Tim Vosgröne; Marcus Sackrow

    2001-01-01

    Surface-enhanced resonance Raman scattering (SERRS) of rhodamine 6G (R6G) adsorbed on isolated colloidal silver clusters has been studied down to the single-molecule level with a high-resolution confocal optical microscope equipped with a spectrometer and a cooled CCD-camera. At the single-molecule level the SERRS-spectra recorded as a function of time reveal inhomogeneous behaviour such as on\\/off blinking, spectral diffusion and intensity

  16. SINGLE MOLECULE APPROACHES TO BIOLOGY, 2010 GORDON RESEARCH CONFERENCE, JUNE 27-JULY 2, 2010, ITALY

    SciTech Connect

    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 Tuscany, provides an avenue for scientists from different disciplines to interact and brainstorm and promotes cross-disciplinary collaborations directed toward compelling biological problems.

  17. Peptide Nucleic Acids as Tools for Single-Molecule Sequence Detection and Manipulation

    NASA Astrophysics Data System (ADS)

    Zohar, Hagar; Hetherington, Craig; Bustamante, Carlos; Muller, Susan

    2011-03-01

    The ability to strongly and sequence-specifically attach modifications such as fluorophores and haptens to individual double-stranded (ds) DNA molecules is critical to a variety of single-molecule experiments. We propose using modified peptide nucleic acids (PNAs) for this purpose and implement them in two model single-molecule experiments where individual DNA molecules are manipulated via microfluidic flow and optical tweezers, respectively. We demonstrate that PNAs are versatile and robust sequence-specific tethers.

  18. Extracting physics of life at the molecular level: A review of single-molecule data analyses

    NASA Astrophysics Data System (ADS)

    Colomb, Warren; Sarkar, Susanta K.

    2015-06-01

    Studying individual biomolecules at the single-molecule level has proved very insightful recently. Single-molecule experiments allow us to probe both the equilibrium and nonequilibrium properties as well as make quantitative connections with ensemble experiments and equilibrium thermodynamics. However, it is important to be careful about the analysis of single-molecule data because of the noise present and the lack of theoretical framework for processes far away from equilibrium. Biomolecular motion, whether it is free in solution, on a substrate, or under force, involves thermal fluctuations in varying degrees, which makes the motion noisy. In addition, the noise from the experimental setup makes it even more complex. The details of biologically relevant interactions, conformational dynamics, and activities are hidden in the noisy single-molecule data. As such, extracting biological insights from noisy data is still an active area of research. In this review, we will focus on analyzing both fluorescence-based and force-based single-molecule experiments and gaining biological insights at the single-molecule level. Inherently nonequilibrium nature of biological processes will be highlighted. Simulated trajectories of biomolecular diffusion will be used to compare and validate various analysis techniques.

  19. Interfacial electron density profile in Nb\\/Si bilayer films: an X-ray reflectivity study

    Microsoft Academic Search

    N. Suresh; Rachana Thakur; D. M. Phase; S. M. Chaudhari

    2004-01-01

    This article describes a systematic study of the nature of interfaces involved in a Nb layer deposited on Si (Nb-on-Si) and Si layer deposited on Nb (Si-on-Nb) bilayer films by using a UHV electron beam evaporation technique, having individual layer thickness of 35 and 100Å each. By using Grazing angle X-ray reflectivity and adopting a proper modelling technique the electron

  20. Self-contained Kondo effect in single molecules

    SciTech Connect

    Booth, Corwin H.; Walter, Marc D.; Daniel, Million; Lukens, WayneW.; Andersen, Richard A.

    2005-04-25

    Kondo coupling of f and conduction electrons is a common feature of f-electron intermetallics. Similar effects should occur in carbon ring systems (metallocenes). Evidence for Kondo coupling in Ce(C{sub 8}H{sub 8}){sub 2} (cerocene) and the ytterbocene Cp*{sub 2}Yb(bipy) is reported from magnetic susceptibility and L{sub III}-edge x-ray absorption spectroscopy. These well-defined systems provide a new way to study the Kondo effect on the nanoscale, should generate insight into the Anderson Lattice problem, and indicate the importance of this often-ignored contribution to bonding in organometallics.

  1. Length-dependent thermopower of highly conducting Au-C bonded single molecule junctions.

    PubMed

    Widawsky, J R; Chen, W; Vázquez, H; Kim, T; Breslow, R; Hybertsen, M S; Venkataraman, L

    2013-06-12

    We report the simultaneous measurement of conductance and thermopower of highly conducting single-molecule junctions using a scanning tunneling microscope-based break-junction setup. We start with molecular backbones (alkanes and oligophenyls) terminated with trimethyltin end groups that cleave off in situ to create junctions where terminal carbons are covalently bonded to the Au electrodes. We apply a thermal gradient across these junctions and measure their conductance and thermopower. Because of the electronic properties of the highly conducting Au-C links, the thermoelectric properties and power factor are very high. Our results show that the molecular thermopower increases nonlinearly with the molecular length while conductance decreases exponentially with increasing molecular length. Density functional theory calculations show that a gateway state representing the Au-C covalent bond plays a key role in the conductance. With this as input, we analyze a series of simplified models and show that a tight-binding model that explicitly includes the gateway states and the molecular backbone states accurately captures the experimentally measured conductance and thermopower trends. PMID:23682792

  2. Single-molecule protein arrays enabled by scanning probe block copolymer lithography

    PubMed Central

    Chai, Jinan; Wong, Lu Shin; Giam, Louise; Mirkin, Chad A.

    2011-01-01

    The ability to control the placement of individual protein molecules on surfaces could enable advances in a wide range of areas, from the development of nanoscale biomolecular devices to fundamental studies in cell biology. Such control, however, remains a challenge in nanobiotechnology due to the limitations of current lithographic techniques. Herein we report an approach that combines scanning probe block copolymer lithography with site-selective immobilization strategies to create arrays of proteins down to the single-molecule level with arbitrary pattern control. Scanning probe block copolymer lithography was used to synthesize individual sub-10-nm single crystal gold nanoparticles that can act as scaffolds for the adsorption of functionalized alkylthiol monolayers, which facilitate the immobilization of specific proteins. The number of protein molecules that adsorb onto the nanoparticles is dependent upon particle size; when the particle size approaches the dimensions of a protein molecule, each particle can support a single protein. This was demonstrated with both gold nanoparticle and quantum dot labeling coupled with transmission electron microscopy imaging experiments. The immobilized proteins remain bioactive, as evidenced by enzymatic assays and antigen-antibody binding experiments. Importantly, this approach to generate single-biomolecule arrays is, in principle, applicable to many parallelized cantilever and cantilever-free scanning probe molecular printing methods. PMID:22106270

  3. Engineering nanostructures by binding single molecules to single-walled carbon nanotubes.

    PubMed

    Sharkey, J Joseph; Stranks, Samuel D; Huang, Jian; Alexander-Webber, Jack A; Nicholas, Robin J

    2014-12-23

    Organic and hybrid organic-inorganic systems are promising candidates for low cost photovoltaics. Recently, perovskite-based systems have been attracting a large amount of research attention, where the highest performing devices employ a small molecule (2,2',7,7'-tetrakis(N,N-di-p-methoxyphenyl-amine)-9,9'-spirobifluorene) (Spiro-OMeTAD) hole transporter. Here, we demonstrate the production of single-walled carbon nanotube (SWNT)/single molecule nanostructures using a simple solution processing technique for effective and strong binding of Spiro-OMeTAD to individual polymer-wrapped SWNTs. These small molecules bind very strongly, which causes both large mechanical strain of the nanotubes and also improves the separation of individual SWNTs, thus improving the nanotube photoluminescence quantum efficiency by 1 order of magnitude compared to simple polymer-nanotube nanohybrids. Using absorption and photoluminescence measurements, we show that there is a dramatic variation in the electronic properties of the polymer-NT nanocomposites due to the band alignment formed with Spiro-OMeTAD. These self-assembled nanocomposites offer the potential for integration into high performance optoelectronic such as photovoltaic cells and light emission devices. PMID:25437329

  4. Origin and spectroscopic determination of trigonal anisotropy in a heteronuclear single-molecule magnet

    NASA Astrophysics Data System (ADS)

    Sorace, L.; Boulon, M.-E.; Totaro, P.; Cornia, A.; Fernandes-Soares, J.; Sessoli, R.

    2013-09-01

    W-band (? ? 94 GHz) electron paramagnetic resonance (EPR) spectroscopy was used for a single-crystal study of a star-shaped Fe3Cr single-molecule magnet (SMM) with crystallographically imposed trigonal symmetry. The high resolution and sensitivity accessible with W-band EPR allowed us to determine accurately the axial zero-field splitting terms for the ground (S = 6) and first two excited states (S = 5 and S = 4). Furthermore, spectra recorded by applying the magnetic field perpendicular to the trigonal axis showed a ?/6 angular modulation. This behavior is a signature of the presence of trigonal transverse magnetic anisotropy terms whose values had not been spectroscopically determined in any SMM prior to this work. Such in-plane anisotropy could only be justified by dropping the so-called “giant spin approach” and by considering a complete multispin approach. From a detailed analysis of experimental data with the two models, it emerged that the observed trigonal anisotropy directly reflects the structural features of the cluster, i.e., the relative orientation of single-ion anisotropy tensors and the angular modulation of single-ion anisotropy components in the hard plane of the cluster. Finally, since high-order transverse anisotropy is pivotal in determining the spin dynamics in the quantum tunneling regime, we have compared the angular dependence of the tunnel splitting predicted by the two models upon application of a transverse field (Berry-phase interference).

  5. Theory of action spectroscopy for single-molecule reactions induced by vibrational excitations with STM

    NASA Astrophysics Data System (ADS)

    Frederiksen, T.; Paulsson, M.; Ueba, H.

    2014-01-01

    A theory of action spectroscopy, i.e., a reaction rate or yield as a function of bias voltage, is presented for single-molecule reactions induced by the inelastic tunneling current with a scanning tunneling microscope. A formula for the reaction yield is derived using the adsorbate resonance model, which provides a versatile tool to analyze vibrationally mediated reactions of single adsorbates on conductive surfaces. This allows us to determine the energy quantum of the excited vibrational mode, the effective broadening of the vibrational density of states (as described by Gaussian or Lorentzian functions), and a prefactor characterizing the elementary process behind the reaction. The underlying approximations are critically discussed. We point out that observation of reaction yields at both bias voltage polarities can provide additional insight into the adsorbate density of states near the Fermi level. As an example, we apply the theory to the case of flip motion of a hydroxyl dimer (OD)2 on Cu(110) which was experimentally observed by Kumagai et al. [Phys. Rev. B 79, 035423 (2009), 10.1103/PhysRevB.79.035423]. In combination with density functional theory calculations for the vibrational modes, the vibrational damping due to electron-hole pair generation, and the potential energy landscape for the flip motion, a detailed microscopic picture for the switching process is established. This picture reveals that the predominant mechanism is excitation of the OD stretch modes which couple anharmonically to the low-energy frustrated rotation mode.

  6. Impact of Electrode Density of States on Transport through Pyridine-Linked Single Molecule Junctions.

    PubMed

    Adak, Olgun; Korytár, Richard; Joe, Andrew Y; Evers, Ferdinand; Venkataraman, Latha

    2015-06-10

    We study the impact of electrode band structure on transport through single-molecule junctions by measuring the conductance of pyridine-based molecules using Ag and Au electrodes. Our experiments are carried out using the scanning tunneling microscope based break-junction technique and are supported by density functional theory based calculations. We find from both experiments and calculations that the coupling of the dominant transport orbital to the metal is stronger for Au-based junctions when compared with Ag-based junctions. We attribute this difference to relativistic effects, which result in an enhanced density of d-states at the Fermi energy for Au compared with Ag. We further show that the alignment of the conducting orbital relative to the Fermi level does not follow the work function difference between two metals and is different for conjugated and saturated systems. We thus demonstrate that the details of the molecular level alignment and electronic coupling in metal-organic interfaces do not follow simple rules but are rather the consequence of subtle local interactions. PMID:26020454

  7. Reducing background contributions in fluorescence fluctuation time-traces for single-molecule measurements in solution.

    PubMed

    Földes-Papp, Zeno; Liao, Shih-Chu Jeff; You, Tiefeng; Barbieri, Beniamino

    2009-08-01

    We first report on the development of new microscope means that reduce background contributions in fluorescence fluctuation methods: i) excitation shutter, ii) electronic switches, and iii) early and late time-gating. The elements allow for measuring molecules at low analyte concentrations. We first found conditions of early and late time-gating with time-correlated single-photon counting that made the fluorescence signal as bright as possible compared with the fluctuations in the background count rate in a diffraction-limited optical set-up. We measured about a 140-fold increase in the amplitude of autocorrelated fluorescence fluctuations at the lowest analyte concentration of about 15 pM, which gave a signal-to-background advantage of more than two-orders of magnitude. The results of this original article pave the way for single-molecule detection in solution and in live cells without immobilization or hydrodynamic/electrokinetic focusing at longer observation times than are currently available. PMID:19689322

  8. Observation and electric current control of a local spin in a single-molecule magnet

    PubMed Central

    Komeda, Tadahiro; Isshiki, Hironari; Liu, Jie; Zhang, Yan-Feng; Lorente, Nicolás; Katoh, Keiichi; Breedlove, Brian K.; Yamashita, Masahiro

    2011-01-01

    In molecular spintronics, the spin state of a molecule may be switched on and off by changing the molecular structure. Here, we switch on and off the molecular spin of a double-decker bis(phthalocyaninato)terbium(III) complex (TbPc2) adsorbed on an Au(111) surface by applying an electric current via a scanning tunnelling microscope. The dI/dV curve of the tunnelling current recorded onto a TbPc2 molecule shows a Kondo peak, the origin of which is an unpaired spin of a ?-orbital of a phthalocyaninato (Pc) ligand. By applying controlled current pulses, we could rotate the upper Pc ligand in TbPc2, leading to the disappearance and reappearance of the Kondo resonance. The rotation shifts the molecular frontier-orbital energies, quenching the ?-electron spin. Reversible switching between two stable ligand orientations by applying a current pulse should make it possible to code information at the single-molecule level. PMID:21364556

  9. A Single-Molecule Phonon Field-Effect Transistor

    Microsoft Academic Search

    Marcos Menezes; Brenda Moreira; Jordan Del Nero; Rodrigo Capaz

    2009-01-01

    Controlling phonons in the same way we control electrons in materials has been an old but elusive dream for physicists. In particular, it would be extremely desirable to control the thermal (phonon) flux between two reservoirs using a gate electric field, i.e., to construct a field-effect transistor for phonons. However, in most materials, electric fields do not couple strongly to

  10. Kondo resonance in a single-molecule transistor

    E-print Network

    .............................................................. Kondo resonance in a single-order tunnelling and correlated electron motion give rise to new phenomena9­19 , including the Kondo resonance10­16 . To date, all of the studies of Kondo phenomena in quantum dots have been performed on systems where

  11. Mechanically controlled molecular orbital alignment in single molecule junctions

    NASA Astrophysics Data System (ADS)

    Bruot, Christopher; Hihath, Joshua; Tao, Nongjian

    2012-01-01

    Research in molecular electronics often involves the demonstration of devices that are analogous to conventional semiconductor devices, such as transistors and diodes, but it is also possible to perform experiments that have no parallels in conventional electronics. For example, by applying a mechanical force to a molecule bridged between two electrodes, a device known as a molecular junction, it is possible to exploit the interplay between the electrical and mechanical properties of the molecule to control charge transport through the junction. 1,4'-Benzenedithiol is the most widely studied molecule in molecular electronics, and it was shown recently that the molecular orbitals can be gated by an applied electric field. Here, we report how the electromechanical properties of a 1,4'-benzenedithiol molecular junction change as the junction is stretched and compressed. Counterintuitively, the conductance increases by more than an order of magnitude during stretching, and then decreases again as the junction is compressed. Based on simultaneously recorded current-voltage and conductance-voltage characteristics, and inelastic electron tunnelling spectroscopy, we attribute this finding to a strain-induced shift of the highest occupied molecular orbital towards the Fermi level of the electrodes, leading to a resonant enhancement of the conductance. These results, which are in agreement with the predictions of theoretical models, also clarify the origins of the long-standing discrepancy between the calculated and measured conductance values of 1,4'-benzenedithiol, which often differ by orders of magnitude.

  12. Single-molecule chemical reactions on DNA origami

    Microsoft Academic Search

    Niels V. Voigt; Thomas Tørring; Alexandru Rotaru; Mikkel F. Jacobsen; Jens B. Ravnsbæk; Ramesh Subramani; Wael Mamdouh; Jørgen Kjems; Andriy Mokhir; Flemming Besenbacher; Kurt Vesterager Gothelf

    2010-01-01

    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

  13. Interfacial electronic structure for Ca and an electroluminescent polymer: Poly (2,5-diheptyl-1,4-phenylene-alt-2,5-thienylene)

    Microsoft Academic Search

    Aparna Rajagopal; Norbert Koch; Jacques Ghijsen; Robert L. Johnson; K. Kaeriyama; Günther Leising; Jean-Jacques Pireaux

    2000-01-01

    X-ray photoemission spectroscopy (XPS) and ultraviolet photoelectron spectroscopy (UPS) have been used to investigate the evolution of the interfacial electronic structure of a blue light-emitting polymer: poly (2,5-diheptyl-1,4-phenylene-alt-2,5-thienylene) (PDHPT) as a function of Ca metal coverage. UPS results show a decrease in intensity of the highest molecular orbital-derived feature of the polymer upon Ca deposition and a decrease in work

  14. CRADA Final Report for CRADA No. ORNL99-0544, Interfacial Properties of Electron Beam Cured Composites

    SciTech Connect

    Janke, C.J.

    2005-10-17

    Electron beam (EB) curing is a technology that promises, in certain applications, to deliver lower cost and higher performance polymer matrix composite (PMC) structures compared to conventional thermal curing processes. PMCs enhance performance by making products lighter, stronger, more durable, and less energy demanding. They are essential in weight- and performance-dominated applications. Affordable PMCs can enhance US economic prosperity and national security. US industry expects rapid implementation of electron beam cured composites in aircraft and aerospace applications as satisfactory properties are demonstrated, and implementation in lower performance applications will likely follow thereafter. In fact, at this time and partly because of discoveries made in this project, field demonstrations are underway that may result in the first fielded applications of electron beam cured composites. Serious obstacles preventing the widespread use of electron beam cured PMCs in many applications are their relatively poor interfacial properties and resin toughness. The composite shear strength and resin toughness of electron beam cured carbon fiber reinforced epoxy composites were about 25% and 50% lower, respectively, than those of thermally cured composites of similar formulations. The essential purpose of this project was to improve the mechanical properties of electron beam cured, carbon fiber reinforced epoxy composites, with a specific focus on composite shear properties for high performance aerospace applications. Many partners, sponsors, and subcontractors participated in this project. There were four government sponsors from three federal agencies, with the US Department of Energy (DOE) being the principal sponsor. The project was executed by Oak Ridge National Laboratory (ORNL), NASA and Department of Defense (DOD) participants, eleven private CRADA partners, and two subcontractors. A list of key project contacts is provided in Appendix A. In order to properly manage the large project team and properly address the various technical tasks, the CRADA team was organized into integrated project teams (IPT's) with each team focused on specific research areas. Early in the project, the end user partners developed ''exit criteria'', recorded in Appendix B, against which the project's success was to be judged. The project team made several important discoveries. A number of fiber coatings or treatments were developed that improved fiber-matrix adhesion by 40% or more, according to microdebond testing. The effects of dose-time and temperature-time profiles during the cure were investigated, and it was determined that fiber-matrix adhesion is relatively insensitive to the irradiation procedure, but can be elevated appreciably by thermal postcuring. Electron beam curable resin properties were improved substantially, with 80% increase in electron beam 798 resin toughness, and {approx}25% and 50% improvement, respectively, in ultimate tensile strength and ultimate tensile strain vs. earlier generation electron beam curable resins. Additionally, a new resin electron beam 800E was developed with generally good properties, and a very notable 120% improvement in transverse composite tensile strength vs. earlier generation electron beam cured carbon fiber reinforced epoxies. Chemical kinetics studies showed that reaction pathways can be affected by the irradiation parameters, although no consequential effects on material properties have been noted to date. Preliminary thermal kinetics models were developed to predict degree of cure vs. irradiation and thermal parameters. These models are continually being refined and validated. Despite the aforementioned impressive accomplishments, the project team did not fully realize the project objectives. The best methods for improving adhesion were combined with the improved electron beam 3K resin to make prepreg and uni-directional test laminates from which composite properties could be determined. Nevertheless, only minor improvements in the composite shear strength, and moderate improvements i

  15. Interfacial Properties of Ultrathin- Film Metal Electrodes: Studies by Combined Electron Spectroscopy and Electrochemistry 

    E-print Network

    Cummins, Kyle

    2012-07-16

    A pair of studies investigating the deposition and surface chemical properties of ultrathin metal films were pursued: (i) Pt-Co alloys on Mo(110); and (ii) Pd on Pt(111). Experimental measurement was based on a combination of electron spectroscopy...

  16. Beyond vibrationally mediated electron transfer: interfacial charge injection on a sub-10-fs time scale

    NASA Astrophysics Data System (ADS)

    Huber, Robert; Moser, Jacques E.; Gratzel, Michael; Wachtveitl, Josef L.

    2003-12-01

    The electron transfer (ET) from organic dye molecules to semiconductor-colloidal systems is characterized by a special energetic situation with a charge transfer reaction from a system of discrete donor levels to a continuum of acceptor states. If these systems show a strong electronic coupling they are amongst the fastest known ET systems with transfer times of less than 10 fs. In the first part a detailed discussion of the direct observation of an ET reaction with a time constant of about 6 fs will be given, with an accompanying argumentation concerning possible artifacts or other interfering signal contributions. In a second part we will try to give a simple picture for the scenario of such superfast ET reactions and one main focus will be the discussion of electronic dephasing and its consequences for the ET reaction. The actual ET process can be understood as a kind of dispersion process of the initially located electron into the colloid representing a real motion of charge density from the alizarin to the colloid.

  17. Probing Interfacial Electronic States in CdSe Quantum Dots using Second Harmonic Generation Spectroscopy

    SciTech Connect

    Doughty, Benjamin L [ORNL; Ma, Yingzhong [ORNL; Shaw, Robert W [ORNL

    2015-01-01

    Understanding and rationally controlling the properties of nanomaterial surfaces is a rapidly expanding field of research due to the dramatic role they play on the optical and electronic properties vital to light harvesting, emitting and detection technologies. This information is essential to the continued development of synthetic approaches designed to tailor interfaces for optimal nanomaterial based device performance. In this work, closely spaced electronic excited states in model CdSe quantum dots (QDs) are resolved using second harmonic generation (SHG) spectroscopy, and the corresponding contributions from surface species to these states are assessed. Two distinct spectral features are observed in the SHG spectra, which are not readily identified in linear absorption and photoluminescence excitation spectra. These features include a weak band at 395 6 nm, which coincides with transitions to the 2S1/2 1Se state, and a much more pronounced band at 423 4 nm arising from electronic transitions to the 1P3/2 1Pe state. Chemical modification of the QD surfaces through oxidation resulted in disappearance of the SHG band corresponding to the 1P3/2 1Pe state, indicating prominent surface contributions. Signatures of deep trap states localized on the surfaces of the QDs are also observed. We further find that the SHG signal intensities depend strongly on the electronic states being probed and their relative surface contributions, thereby offering additional insight into the surface specificity of SHG signals from QDs.

  18. First-Principles Studies of Single-Molecule Photovoltaics

    NASA Astrophysics Data System (ADS)

    Doak, Peter; Segalman, R. A.; Tilley, T. D.; Neaton, J. B.

    2009-03-01

    Organic photovoltaics consist of electron donor and acceptor polymers or molecules blended together, and are promising inexpensive, lightweight alternatives to conventional silicon solar cells. However, many of the physical processes responsible for their poor efficiencies are not well understood. Here, using first-principles calculations based on density functional theory, including self-energy corrections within the GW approximation and a discussion of excitonic effects, we examine the relationship between molecular structure and electronic level alignment at a covalent donor-acceptor interface. We consider small asymmetric molecules subdivided into discrete covalently linked moieties based on thiophene, tetrafluorobenzene, pyridine, and durene. Excited states of each of these moieties, as well as their covalently-linked combinations, are computed and discussed in the context of their ability to absorb photons and separate charge. Work supported in part by the DOE Helios SERC. Computational resources provided by NERSC.

  19. The Use of Ultrashort Picosecond Laser Pulses to Generate Quantum Optical Properties of Single Molecules in Biophysics

    NASA Astrophysics Data System (ADS)

    Ly, Sonny

    Generation of quantum optical states from ultrashort laser-molecule interactions have led to fascinating discoveries in physics and chemistry. In recent years, these interactions have been extended to probe phenomena in single molecule biophysics. Photons emitted from a single fluorescent molecule contains important properties about how the molecule behave and function in that particular environment. Analysis of the second order coherence function through fluorescence correlation spectroscopy plays a pivotal role in quantum optics. At very short nanosecond timescales, the coherence function predicts photon antibunching, a purely quantum optical phenomena which states that a single molecule can only emit one photon at a time. Photon antibunching is the only direct proof of single molecule emission. From the nanosecond to microsecond timescale, the coherence function gives information about rotational diffusion coefficients, and at longer millisecond timescales, gives information regarding the translational diffusion coefficients. In addition, energy transfer between molecules from dipole-dipole interaction results in FRET, a highly sensitive method to probe conformational dynamics at nanometer distances. Here I apply the quantum optical techniques of photon antibunching, fluorescence correlation spectroscopy and FRET to probe how lipid nanodiscs form and function at the single molecule level. Lipid nanodiscs are particles that contain two apolipoprotein (apo) A-I circumventing a lipid bilayer in a belt conformation. From a technological point of view, nanodiscs mimics a patch of cell membrane that have recently been used to reconstitute a variety of membrane proteins including cytochrome P450 and bacteriorhodopsin. They are also potential drug transport vehicles due to its small and stable 10nm diameter size. Biologically, nanodiscs resemble to high degree, high density lipoproteins (HDL) in our body and provides a model platform to study lipid-protein interactions and their dynamic formation to lipoprotein particles without having to extract from human blood plasma. Although HDL has been studied extensively within the last thirty years, many questions still remain regarding the structure of apoA-I, the protein associated exclusively with it. Despite our ability to detect and image these nanodiscs by blotting, atomic force microscopy (AFM), or electron microscopy (EM), many basic properties such as their specific hydrated shape in solution, or the precise conformation of the apolipoproteins surrounding the particles are still unknown. The dynamic interactions of apoA-I with lipids are also rather poorly understood on a fundamental level, and are only characterized in bulk (biochemical blotting) or stationary methods (AFM, EM), making it impossible to study individual steps with high spatial or temporal resolution.

  20. Interfacial Properties of Ultrathin- Film Metal Electrodes: Studies by Combined Electron Spectroscopy and Electrochemistry

    E-print Network

    Cummins, Kyle

    2012-07-16

    gratitude to my mentor and advisor, Dr. M. P. Soriaga, for the countless hours of collaboration and advice. Imparted to me, through his encouragement and scholastic stewardship, were the virtues of academic creativity and intellectual accountability. A.... viii NOMENCLATURE ADC Analog-to-Digital Converter AES Auger Electron Spectroscopy CE Counter Electrode CHA Concentric Hemispheric Analyzer CMA Cylindrical Mirror Analyzer CPD Controlled-Potential Deposition CV Cyclic Voltammetry...

  1. Preparation of zinc sulfide nanocrystallites from single-molecule precursors

    NASA Astrophysics Data System (ADS)

    Palve, Anil M.; Garje, Shivram S.

    2011-07-01

    Zinc sulfide nanocrystallites were prepared using Zinc(II) thiosemicarbazone complexes of the types Zn(L) 2 and ZnCl 2(LH) 2 (where, LH=thiosemicarbazones of cinnamaldehyde, 4-chlorobenzaldehyde, indol-3-carboxaldehyde and thiophene-2-carboxaldehyde) as single source precursors by solvothermal decomposition in ethylene glycol and ethylene diamine in few cases. The materials were characterized by powder X-ray diffraction (XRD), transmission electron microscopy (TEM), selected area electron diffraction, energy dispersive X-ray analysis and UV-vis and IR spectroscopy. Solvothermal decomposition in ethylene glycol resulted in the formation of hexagonal ZnS (JCPDS: 36-1450) as evident from the XRD patterns. However, XRD shows formation of hybrid material, ZnS 0.5EN in case of solvothermal decomposition in ethylenediamine. Infrared spectra authenticate the capping of ethylene glycol and ethylenediamine on ZnS and ZnS 0.5EN, respectively. TEM images showed formation of spherical nanoparticles for the materials obtained from ethylene glycol, whereas plate-like morphology is observed in case of materials obtained from ethylene diamine. The blue shift of absorption bands compared to bands of bulk materials in the UV-vis spectra supports the formation of smaller particles.

  2. The bulk and interfacial electronic and chemical structure of amorphous hydrogenated boron carbide

    NASA Astrophysics Data System (ADS)

    Driver, Marcus Sky

    The chemical and electronic structure, as related to the surface, interface and bulk of amorphous hydrogenated boron carbide (a-BxC:H y), is of interest in neutron detection and microelectronics. This dissertation investigates the chemical and electronic structure of semiconducting thin-film a-BxC:Hy grown by plasma enhanced chemical vapor deposition (PECVD) of ortho-carborane (1,2-C2B10H12). Experimental methods used include: x-ray and ultraviolet photoelectron spectroscopies (XPS/UPS) and x-ray absorption/emission spectroscopies (XAS/XES). These methods were used to investigate the chemical species, bonding and hybridizations, and band gaps of a-BxC:Hy prepared or treated under varying conditions. Additionally, a detailed examination of the formation of Schottky barriers was implemented. Throughout this dissertation the chemical structure was studied. One study was to understand various growth conditions. The effects of the PECVD growth parameters were evaluated by comparing changes in atomic percentages (at.%'s) between thin-films from various substrate temperatures. Additionally, detailed studies of the photoelectron core level under two different growth conditions were undertaken to evaluate the effects of pre-/post- argon ion etching (Ar+) for the following: the chemical structural change for both an as grown (AG) and in-situ thermal treatment (500°C), and post Ar+ etch of samples thermally treated ranging from as grown to 850°C. The as grown and in-situ treated samples were used in conjunction to determine the formation of the Schottky barrier. The electronic structure was determined by the changes within the valence band of the thermally treated samples and formation of Schottky barrier. Thermally treated samples (as grown to 850°C) were further evaluated with respect to their occupied and unoccupied electronic states. The atomic percentage gave a stoichiometry range for a-B xC:Hy (given as x=1.5 to 3.0 with y= decreases with thermal treatment and Oz: z= 0.2 to 0.5). Studies of films with respect to thermal treatment reveal two discrete state changes that occur at 400°C and 850°C These changes are due to segregation of carbon and oxygen by the reorganization of the hydrocarbon chains between icosahedra. Additionally, the Schottky barrier study indicates that a clean surface was necessary before deposition of an ohmic contact and from the metals studied. Such studies are important to applications for high temperature thermoelectric converters, high-efficiency direct-conversion solid-state neutron detectors and microelectronics.

  3. Experimental and Computational Characterization of Biological Liquid Crystals: A Review of Single-Molecule Bioassays

    PubMed Central

    Eom, Kilho; Yang, Jaemoon; Park, Jinsung; Yoon, Gwonchan; Soo Sohn, Young; Park, Shinsuk; Yoon, Dae Sung; Na, Sungsoo; Kwon, Taeyun

    2009-01-01

    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. PMID:19865530

  4. Influencing the properties of dysprosium single-molecule magnets with phosphorus donor ligands

    PubMed Central

    Pugh, Thomas; Tuna, Floriana; Ungur, Liviu; Collison, David; McInnes, Eric J.L.; Chibotaru, Liviu F.; Layfield, Richard A.

    2015-01-01

    Single-molecule magnets are a type of coordination compound that can retain magnetic information at low temperatures. Single-molecule magnets based on lanthanides have accounted for many important advances, including systems with very large energy barriers to reversal of the magnetization, and a di-terbium complex that displays magnetic hysteresis up to 14?K and shows strong coercivity. Ligand design is crucial for the development of new single-molecule magnets: organometallic chemistry presents possibilities for using unconventional ligands, particularly those with soft donor groups. Here we report dysprosium single-molecule magnets with neutral and anionic phosphorus donor ligands, and show that their properties change dramatically when varying the ligand from phosphine to phosphide to phosphinidene. A phosphide-ligated, trimetallic dysprosium single-molecule magnet relaxes via the second-excited Kramers' doublet, and, when doped into a diamagnetic matrix at the single-ion level, produces a large energy barrier of 256?cm?1 and magnetic hysteresis up to 4.4?K. PMID:26130418

  5. Investigation of RNA Polymerase I Transcription under Force-Free Condition by Single Molecule Technique

    NASA Astrophysics Data System (ADS)

    Ucuncuoglu, Suleyman; Schneider, David A.; Dunlap, David; Finzi, Laura

    2014-03-01

    RNA Polymerase I (Pol I) conducts more than 60% of all the transcriptional activity in cells and also is responsible for synthesizing the RNA structure of the ribosome in eukaryotic cells. It is evident in many studies that Pol I transcription is affected by tumor suppressors and oncogenes which makes Pol I as a target for the anticancer therapeutics. The mechanistic pathways and kinetics of the Pol I transcription needs to be understood more precisely. Even though previous bulk studies measured the kinetics of the Pol I transcription, the results may hinder the intermediate states such as processivity and pausing during elongation. Here we used the single molecule approach to show that Pol I pauses more than Pol II during elongation step by using a novel single molecule instrument, multiplexed tethered particle motion microscopy (TPM). Our in-house developed TPM equipment is able to concurrently observe hundreds of single molecules. TPM technique has a major advantage to observe pausing under force-free condition unlike other single molecule techniques such as magnetic tweezers and optical tweezers. We also report that the processivity of Pol I is very low where only one out of fifteen transcription event reached the run-off site. We anticipate that our single molecule assays paved the way for observing more sophisticated aspects of Pol I transcription and it's relation with initiation and transcriptional factors.

  6. Combined versatile high-resolution optical tweezers and single-molecule fluorescence microscopy

    PubMed Central

    Sirinakis, George; Ren, Yuxuan; Gao, Ying; Xi, Zhiqun; Zhang, Yongli

    2012-01-01

    Optical trapping and single-molecule fluorescence are two major single-molecule approaches. Their combination has begun to show greater capability to study more complex systems than either method alone, but met many fundamental and technical challenges. We built an instrument that combines base-pair resolution dual-trap optical tweezers with single-molecule fluorescence microscopy. The instrument has complementary design and functionalities compared with similar microscopes previously described. The optical tweezers can be operated in constant force mode for easy data interpretation or in variable force mode for maximum spatiotemporal resolution. The single-molecule fluorescence detection can be implemented in either wide-field or confocal imaging configuration. To demonstrate the capabilities of the new instrument, we imaged a single stretched ? DNA molecule and investigated the dynamics of a DNA hairpin molecule in the presence of fluorophore-labeled complementary oligonucleotide. We simultaneously observed changes in the fluorescence signal and pauses in fast extension hopping of the hairpin due to association and dissociation of individual oligonucleotides. The combined versatile microscopy allows for greater flexibility to study molecular machines or assemblies at a single-molecule level. PMID:23020384

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

    PubMed

    Moerner, W E William E

    2015-07-01

    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 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. PMID:26088273

  8. Influencing the properties of dysprosium single-molecule magnets with phosphorus donor ligands.

    PubMed

    Pugh, Thomas; Tuna, Floriana; Ungur, Liviu; Collison, David; McInnes, Eric J L; Chibotaru, Liviu F; Layfield, Richard A

    2015-01-01

    Single-molecule magnets are a type of coordination compound that can retain magnetic information at low temperatures. Single-molecule magnets based on lanthanides have accounted for many important advances, including systems with very large energy barriers to reversal of the magnetization, and a di-terbium complex that displays magnetic hysteresis up to 14?K and shows strong coercivity. Ligand design is crucial for the development of new single-molecule magnets: organometallic chemistry presents possibilities for using unconventional ligands, particularly those with soft donor groups. Here we report dysprosium single-molecule magnets with neutral and anionic phosphorus donor ligands, and show that their properties change dramatically when varying the ligand from phosphine to phosphide to phosphinidene. A phosphide-ligated, trimetallic dysprosium single-molecule magnet relaxes via the second-excited Kramers' doublet, and, when doped into a diamagnetic matrix at the single-ion level, produces a large energy barrier of 256?cm(-1) and magnetic hysteresis up to 4.4?K. PMID:26130418

  9. Closing the gap between single molecule and bulk FRET analysis of nucleosomes.

    PubMed

    Gansen, Alexander; Hieb, Aaron R; Böhm, Vera; Tóth, Katalin; Langowski, Jörg

    2013-01-01

    Nucleosome structure and stability affect genetic accessibility by altering the local chromatin morphology. Recent FRET experiments on nucleosomes have given valuable insight into the structural transformations they can adopt. Yet, even if performed under seemingly identical conditions, experiments performed in bulk and at the single molecule level have given mixed answers due to the limitations of each technique. To compare such experiments, however, they must be performed under identical conditions. Here we develop an experimental framework that overcomes the conventional limitations of each method: single molecule FRET experiments are carried out at bulk concentrations by adding unlabeled nucleosomes, while bulk FRET experiments are performed in microplates at concentrations near those used for single molecule detection. Additionally, the microplate can probe many conditions simultaneously before expending valuable instrument time for single molecule experiments. We highlight this experimental strategy by exploring the role of selective acetylation of histone H3 on nucleosome structure and stability; in bulk, H3-acetylated nucleosomes were significantly less stable than non-acetylated nucleosomes. Single molecule FRET analysis further revealed that acetylation of histone H3 promoted the formation of an additional conformational state, which is suppressed at higher nucleosome concentrations and which could be an important structural intermediate in nucleosome regulation. PMID:23637734

  10. Closing the Gap between Single Molecule and Bulk FRET Analysis of Nucleosomes

    PubMed Central

    Gansen, Alexander; Hieb, Aaron R.; Böhm, Vera; Tóth, Katalin; Langowski, Jörg

    2013-01-01

    Nucleosome structure and stability affect genetic accessibility by altering the local chromatin morphology. Recent FRET experiments on nucleosomes have given valuable insight into the structural transformations they can adopt. Yet, even if performed under seemingly identical conditions, experiments performed in bulk and at the single molecule level have given mixed answers due to the limitations of each technique. To compare such experiments, however, they must be performed under identical conditions. Here we develop an experimental framework that overcomes the conventional limitations of each method: single molecule FRET experiments are carried out at bulk concentrations by adding unlabeled nucleosomes, while bulk FRET experiments are performed in microplates at concentrations near those used for single molecule detection. Additionally, the microplate can probe many conditions simultaneously before expending valuable instrument time for single molecule experiments. We highlight this experimental strategy by exploring the role of selective acetylation of histone H3 on nucleosome structure and stability; in bulk, H3-acetylated nucleosomes were significantly less stable than non-acetylated nucleosomes. Single molecule FRET analysis further revealed that acetylation of histone H3 promoted the formation of an additional conformational state, which is suppressed at higher nucleosome concentrations and which could be an important structural intermediate in nucleosome regulation. PMID:23637734

  11. Conformational switching in a light-harvesting protein as followed by single-molecule spectroscopy.

    PubMed

    Gall, Andrew; Ilioaia, Cristian; Krüger, Tjaart P J; Novoderezhkin, Vladimir I; Robert, Bruno; van Grondelle, Rienk

    2015-06-01

    Among the ultimate goals of protein physics, the complete, experimental description of the energy paths leading to protein conformational changes remains a challenge. Single protein fluorescence spectroscopy constitutes an approach of choice for addressing protein dynamics, and, among naturally fluorescing proteins, light-harvesting (LH) proteins from purple bacteria constitute an ideal object for such a study. LHs bind bacteriochlorophyll a molecules, which confer on them a high intrinsic fluorescence yield. Moreover, the electronic properties of these pigment-proteins result from the strong excitonic coupling between their bound bacteriochlorophyll a molecules in combination with the large energetic disorder due to slow fluctuations in their structure. As a result, the position and probability of their fluorescence transition delicately depends on the precise realization of the disorder of the set of bound pigments, which is governed by the LH protein dynamics. Analysis of these parameters using time-resolved single-molecule fluorescence spectroscopy thus yields direct access to the protein dynamics. Applying this technique to the LH2 protein from Rhodovulum (Rdv.) sulfidophilum, the structure-and consequently the fluorescence properties-of which depends on pH, allowed us to follow a single protein, pH-induced, reversible, conformational transition. Hence, for the first time, to our knowledge, a protein transition can be visualized through changes in the electronic structure of the intrinsic cofactors, at a level of a single LH protein, which opens a new, to our knowledge, route for understanding the changes in energy landscape that underlie protein function and adaptation to the needs of living organisms. PMID:26039172

  12. Electronic and Interfacial Properties of PD/6H-SiC Schottky Diode Gas Sensors

    NASA Technical Reports Server (NTRS)

    Chen, Liang-Yu; Hunter, Gary W.; Neudeck, Philip G.; Bansal, Gaurav; Petit, Jeremy B.; Knight, Dak; Liu, Chung-Chiun; Wu, Qinghai

    1996-01-01

    Pd/SiC Schottky diodes detect hydrogen and hydrocarbons with high sensitivity. Variation of the diode temperature from 100 C to 200 C shows that the diode sensitivity to propylene is temperature dependent. Long-term heat treating at 425 C up to 140 hours is carried out to determine the effect of extended heat treating on the diode properties and gas sensitivity. The heat treating significantly affects the diode's capacitive characteristics, but the diode's current carrying characteristics are much more stable with a large response to hydrogen. Scanning Electron Microscopy and X-ray Spectrometry studies of the Pd surface after the heating show cluster formation and background regions with grain structure observed in both regions. The Pd and Si concentrations vary between grains. Auger Electron Spectroscopy depth profiles revealed that the heat treating promoted interdiffusion and reaction between the Pd and SiC dw broadened the interface region. This work shows that Pd/SiC Schottky diodes have significant potential as high temperature gas sensors, but stabilization of the structure is necessary to insure their repeatability in long-term, high temperature applications.

  13. Comparing electron recombination via interfacial modifications in dye-sensitized solar cells.

    PubMed

    Li, Luping; Chen, Shikai; Xu, Cheng; Zhao, Yang; Rudawski, Nicholas G; Ziegler, Kirk J

    2014-12-10

    Establishing a blocking layer between the interfaces of the photoanode is an effective approach to improve the performance of dye-sensitized solar cells (DSSCs). In this work, HfO2 blocking layers are deposited via atomic layer deposition (ALD) onto tin-doped indium oxide (ITO) and TiO2. In both cases, addition of the blocking layer increases cell efficiencies to greater than 7%. The improved performance for a HfO2 layer inserted between the ITO/TiO2 interface is associated with an energy barrier that reduces electron recombination. HfO2 blocking layers between the TiO2/dye interface show more complex behavior and are more sensitive to the number of ALD cycles. For thin blocking layers on TiO2, the improved device performance is attributed to the passivation of surface states in TiO2. A distinct transition in dark current and electron lifetime are observed after 4 ALD cycles. These changes to performance indicate thick HfO2 layers on TiO2 formed an energy barrier that significantly hinders cell performance. PMID:25412271

  14. Photosensitization of nanoparticulate TiO2 using a Re(I)-polypyridyl complex: studies on interfacial electron transfer in the ultrafast time domain.

    PubMed

    Kar, Prasenjit; Banerjee, Tanmay; Verma, Sandeep; Sen, Anik; Das, Amitava; Ganguly, Bishwajit; Ghosh, Hirendra N

    2012-06-14

    We have synthesized a new photoactive rhenium(i)-complex having a pendant catechol functionality [Re(CO)(3)Cl(L)] (1) (L is 4-[2-(4'-methyl-2,2'-bipyridinyl-4-yl)vinyl]benzene-1,2-diol) for studying the dynamics of the interfacial electron transfer between nanoparticulate TiO(2) and the photoexcited states of this Re(i)-complex using femtosecond transient absorption spectroscopy. Our steady state absorption studies revealed that complex 1 can bind strongly to TiO(2) surfaces through the catechol functionality with the formation of a charge transfer (CT) complex, which has been confirmed by the appearance of a new red-shifted CT band. The longer wavelength absorption band for 1, bound to TiO(2) through the proposed catecholate functionality, could also be explained based on the DFT calculations. Dynamics of the interfacial electron transfer between 1 and TiO(2) nanoparticles was investigated by studying kinetics at various wavelengths in the visible and near infrared regions. Electron injection into the conduction band of the nanoparticulate TiO(2) was confirmed by detection of the conduction band electron in TiO(2) ([e(-)](TiO(2)(CB))) and the cation radical of the adsorbed dye (1?(+)) in real time as monitored by transient absorption spectroscopy. A single exponential and pulse-width limited (<100 fs) electron injection was observed. Back electron transfer dynamics was determined by monitoring the decay kinetics of 1?(+) and . PMID:22549294

  15. Plasmon Mapping in Metallic Nanostructures and its Application to Single Molecule Surface Enhanced Raman Scattering: Imaging Electromagnetic Hot-Spots and Analyte Location

    SciTech Connect

    Camden, Jon P

    2013-07-16

    A major component of this proposal is to elucidate the connection between optical and electron excitation of plasmon modes in metallic nanostructures. These accomplishments are reported: developed a routine protocol for obtaining spatially resolved, low energy EELS spectra, and resonance Rayleigh scattering spectra from the same nanostructures.; correlated optical scattering spectra and plasmon maps obtained using STEM/EELS.; and imaged electromagnetic hot spots responsible for single-molecule surface-enhanced Raman scattering (SMSERS).

  16. Dye-controlled interfacial electron transfer for high-current indium tin oxide photocathodes.

    PubMed

    Huang, Zhongjie; He, Mingfu; Yu, Mingzhe; Click, Kevin; Beauchamp, Damian; Wu, Yiying

    2015-06-01

    Efficient sensitized photocathodes are highly desired for solar fuels and tandem solar cells, yet the development is hindered by the scarcity of suitable p-type semiconductors. The generation of high cathodic photocurrents by sensitizing a degenerate n-type semiconductor (tin-doped indium oxide; ITO) is reported. The sensitized mesoporous ITO electrodes deliver cathodic photocurrents of up to 5.96±0.19?mA?cm(-2) , which are close to the highest record in conventional p-type sensitized photocathodes. This is realized by the rational selection of dyes with appropriate energy alignments with ITO. The energy level alignment between the highest occupied molecular orbital of the sensitizer and the conduction band of ITO is crucial for efficient hole injection. Transient absorption spectroscopy studies demonstrate that the cathodic photocurrent results from reduction of the photoexcited sensitizer by free electrons in ITO. Our results reveal a new perspective toward the selection of electrode materials for sensitized photocathodes. PMID:25907357

  17. Origin of Enhanced Hole Injection in Organic Light-Emitting Diodes with an Electron-Acceptor Doping Layer: p-Type Doping or Interfacial Diffusion?

    PubMed

    Zhang, Lei; Zu, Feng-Shuo; Deng, Ya-Li; Igbari, Femi; Wang, Zhao-Kui; Liao, Liang-Sheng

    2015-06-10

    The electrical doping nature of a strong electron acceptor, 1,4,5,8,9,11-hexaazatriphenylene hexacarbonitrile (HATCN), is investigated by doping it in a typical hole-transport material, N,N'-bis(naphthalen-1-yl)-N,N'-diphenylbenzidine (NPB). A better device performance of organic light-emitting diodes (OLEDs) was achieved by doping NPB with HATCN. The improved performance could, in principle, arise from a p-type doping effect in the codeposited thin films. However, physical characteristics evaluations including UV-vis absorption, Fourier transform infrared absorption, and X-ray photoelectron spectroscopy demonstrated that there was no obvious evidence of charge transfer in the NPB:HATCN composite. The performance improvement in NPB:HATCN-based OLEDs is mainly attributed to an interfacial modification effect owing to the diffusion of HATCN small molecules. The interfacial diffusion effect of the HATCN molecules was verified by the in situ ultraviolet photoelectron spectroscopy evaluations. PMID:25970499

  18. High-throughput single-molecule fluorescence spectroscopy using parallel detection

    PubMed Central

    Michalet, X.; Colyer, R. A.; Scalia, G.; Kim, T.; Levi, Moran; Aharoni, Daniel; Cheng, Adrian; Guerrieri, F.; Arisaka, Katsushi; Millaud, Jacques; Rech, I.; Resnati, D.; Marangoni, S.; Gulinatti, A.; Ghioni, M.; Tisa, S.; Zappa, F.; Cova, S.; Weiss, S.

    2011-01-01

    Solution-based single-molecule fluorescence spectroscopy is a powerful new experimental approach with applications in all fields of natural sciences. The basic concept of this technique is to excite and collect light from a very small volume (typically femtoliter) and work in a concentration regime resulting in rare burst-like events corresponding to the transit of a single-molecule. Those events are accumulated over time to achieve proper statistical accuracy. Therefore the advantage of extreme sensitivity is somewhat counterbalanced by a very long acquisition time. One way to speed up data acquisition is parallelization. Here we will discuss a general approach to address this issue, using a multispot excitation and detection geometry that can accommodate different types of novel highly-parallel detector arrays. We will illustrate the potential of this approach with fluorescence correlation spectroscopy (FCS) and single-molecule fluorescence measurements obtained with different novel multipixel single-photon counting detectors. PMID:21625288

  19. Single-Molecule Fluorescence Using Nucleotide Analogs: A Proof-of-Principle

    PubMed Central

    2015-01-01

    Fluorescent nucleotide analogues, such as 2-aminopurine (2AP) and pyrrolo-C (PyC), have been extensively used to study nucleic acid local conformational dynamics in bulk experiments. Here we present a proof-of-principle approach using 2AP and PyC fluorescence at the single-molecule level. Our data show that ssDNA, dsDNA, or RNA containing both 2AP and PyC can be monitored using single-molecule fluorescence and a click chemistry immobilization method. We demonstrate that this approach can be used to monitor DNA and RNA in real time. This is the first reported assay using fluorescent nucleotide analogs at the single-molecule level. We anticipate that single 2AP or PyC fluorescence will have numerous applications in studies of DNA and RNA, including protein-induced base-flipping dynamics in protein–nucleic acid complexes. PMID:24803990

  20. Seeing a single molecule vibrate through time-resolved coherent anti-Stokes Raman scattering

    NASA Astrophysics Data System (ADS)

    Yampolsky, Steven; Fishman, Dmitry A.; Dey, Shirshendu; Hulkko, Eero; Banik, Mayukh; Potma, Eric O.; Apkarian, Vartkess A.

    2014-08-01

    The motion of chemical bonds within molecules can be observed in real time in the form of vibrational wave packets prepared and interrogated through ultrafast nonlinear spectroscopy. Such nonlinear optical measurements are commonly performed on large ensembles of molecules and, as such, are limited to the extent that ensemble coherence can be maintained. Here, we describe vibrational wave packet motion on single molecules, recorded through time-resolved, surface-enhanced, coherent anti-Stokes Raman scattering. The sensitivity required to detect the motion of a single molecule under ambient conditions is achieved by equipping the molecule with a dipolar nano-antenna (a gold dumbbell). In contrast with measurements in ensembles, the vibrational coherence on a single molecule does not undergo pure dephasing. It develops phase fluctuations with characteristic statistics. We present the time evolution of discretely sampled statistical states, and highlight the unique information content in the characteristic, early-time probability distribution function of the signal.

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

    PubMed

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

    2015-07-22

    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. PMID:26132347

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

    SciTech Connect

    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.

  3. Orientational control over nitrite reductase on modified gold electrode and its effects on the interfacial electron transfer.

    PubMed

    Krzemi?ski, Lukasz; Cronin, Samuel; Ndamba, Lionel; Canters, Gerard W; Aartsma, Thijs J; Evans, Stephen D; Jeuken, Lars J C

    2011-11-01

    Recently, studies have been reported in which fluorescently labeled redox proteins have been studied with a combination of spectroscopy and electrochemistry. In order to understand the effect of the dye on the protein-electrode interaction, voltammetry and surface analysis have been performed on protein films of dye-labeled and unlabeled forms of a cysteine-surface variant (L93C) and the wild type (wt) of the copper containing nitrite reductase (NiR) from Alcaligenes faecalis S6. The protein has been adsorbed onto gold electrodes modified with self-assembled monolayers (SAMs) made up of 6-mercaptohexanol (6-OH) and mixtures of various octanethiols. Electrochemical and surface-analytical techniques were utilized to explore the influence of the SAM composition on wt and L93C NiR enzyme activity and the orientation of the enzyme molecules with respect to the electrode/SAM. The unlabeled L93C NiR enzyme is only electroactive on mixed SAMs composed of positive 8-aminooctanethiol (8-NH(2)) and 8-mercaptooctanol (8-OH). No enzymatic activity is observed on SAMs consisting of pure 6-OH, 8-OH, or pure 8-NH(2). Modification of L93C NiR with the ATTO 565 dye resulted in enzymatic activity on SAMs of 6-OH, but not on SAMs of 8-OH. Quartz crystal microbalance with dissipation measurements show that well-ordered and rigid protein films (single orientation of the protein) are formed when NiR is electroactive. By contrast, electrode-NiR combinations for which no electrochemical activity is observed still have NiR adsorbed on the surfaces, but a less-structured and water-rich film is formed. For the unlabeled L93C NiR, bilayer formation is observed, suggesting that the Cys93 residue is orientated away from the surface and able to form disulfide bridges to a second layer of L93C NiR. The results indicate that interfacial electron transfer is only possible if the negatively charged surface patch surrounding the electron-entry site of NiR is directed toward the electrode. This can be achieved either by introducing positive charges in the SAM or, when the SAM does not carry a charge, by labeling the enzyme with an ATTO 565 dye, which has some hydrophobic character, close to the electron entry site of the NiR. PMID:21939276

  4. Transmission electron microscopy and ab initio calculations to relate interfacial intermixing and the magnetism of core/shell nanoparticles

    NASA Astrophysics Data System (ADS)

    Chi, C.-C.; Hsiao, C.-H.; Skoropata, E.; van Lierop, J.; Ouyang, Chuenhou Hao

    2015-05-01

    Significant efforts towards understanding bi-magnetic core-shell nanoparticles are underway currently as they provide a pathway towards properties unavailable with single-phased systems. Recently, we have demonstrated that the magnetism of ?-Fe2O3/CoO core-shell nanoparticles, in particular, at high temperatures, originates essentially from an interfacial doped iron-oxide layer that is formed by the migration of Co2+ from the CoO shell into the surface layers of the ?-Fe2O3 core [Skoropata et al., Phys. Rev. B 89, 024410 (2014)]. To examine directly the nature of the intermixed layer, we have used high-resolution transmission electron microscopy (HRTEM) and first-principles calculations to examine the impact of the core-shell intermixing at the atomic level. By analyzing the HRTEM images and energy dispersive spectra, the level and nature of intermixing was confirmed, mainly as doping of Co into the octahedral site vacancies of ?-Fe2O3. The average Co doping depths for different processing temperatures (150 °C and 235 °C) were 0.56 nm and 0.78 nm (determined to within 5% through simulation), respectively, establishing that the amount of core-shell intermixing can be altered purposefully with an appropriate change in synthesis conditions. Through first-principles calculations, we find that the intermixing phase of ?-Fe2O3 with Co doping is ferromagnetic, with even higher magnetization as compared to that of pure ?-Fe2O3. In addition, we show that Co doping into different octahedral sites can cause different magnetizations. This was reflected in a change in overall nanoparticle magnetization, where we observed a 25% reduction in magnetization for the 235 °C versus the 150 °C sample, despite a thicker intermixed layer.

  5. Chemically functionalized carbon films for single molecule imaging

    PubMed Central

    Llaguno, Marc C.; Xu, Hui; Shi, Liang; Huang, Nian; Zhang, Hong; Liu, Qinghua; Jiang, Qiu-Xing

    2014-01-01

    Many biological complexes are naturally low in abundance and pose a significant challenge to their structural and functional studies. Here we describe a new method that utilizes strong oxidation and chemical linkage to introduce a high density of bioactive ligands onto nanometer-thick carbon films and enable selective enrichment of individual macromolecular complexes at subnanogram levels. The introduced ligands are physically separated. Ni-NTA, Protein G and DNA/RNA oligonucleotides were covalently linked to the carbon surface. They embody negligible mass and their stability makes the functionalized films able to survive long-term storage and tolerate variations in pH, temperature, salts, detergents, and solvents. We demonstrated the application of the new method to the electron microscopic imaging of the substrate-bound C3PO, an RNA-processing enzyme important for the RNA interference pathway. On the ssRNA-linked carbon surface, the formation of C3PO oligomers at subnanomolar concentrations likely mimics their assembly onto ssRNA substrates presented by their native partners. Interestingly, the 3D reconstructions by negative stain EM reveal a side port in the C3PO/ssRNA complex, and the 15 Å cryoEM map showed extra density right above the side port, which probably represents the ssRNA. These results suggest a new way for ssRNAs to interact with the active sites of the complex. Together our data demonstrate that the surface-engineered carbon films are suitable for selectively enriching low-abundance biological complexes at nanomolar level and for developing novel applications on a large number of surface-presented molecules. PMID:24457027

  6. Determination of the characteristic interfacial electronic states of {111} Cu-MgO interfaces by ELNES

    NASA Astrophysics Data System (ADS)

    Imhoff, D.; Laurent, S.; Colliex, C.; Backhaus-Ricoult, M.

    1999-01-01

    The chemical bonding of different \\{111\\} Cu MgO interfaces obtained by internal oxidation of (Cu, Mg) alloys at T = 900 ^circC and for an high oxygen activity of a_o_2=10^{-8}, is studied by transmission electron energy loss spectroscopy (EELS) at high spatial resolution. For polar \\{111\\} interfaces (Cu and MgO in topotactical or pseudotwin orientation), it is shown that the terminating lattice plane in magnesia is occupied by oxygen atoms. An important charge transfer is identified at the interface, yielding Cu L ELNES features corresponding to those of Cu^{1+} (Cu(I)) in its oxide. O K edge fine structures at the interface are also modified: an edge enlargement and the presence of a low energy shoulder confirm the bonding of oxygen to Cu^{1+}. Consistent with these results, the Mg L edge is never modified compared to the MgO bulk phase. Specifically adapted to the heterophase interfaces, a spatial difference method, based on normalised spectra (NSD), is applied to estimate the relative contribution of the ELNES signal in the interface area. In the present case of high oxygen activity, the number of copper atoms in the Cu(I) oxidized state corresponds to a total occupancy of the outermost metal plane at the interface.

  7. 3D single molecule tracking and superresolution microscopy using multifocal plane microscopy.

    PubMed

    Ram, Sripad; Ward, E Sally; Ober, Raimund J

    2012-12-31

    The study of cellular processes in three-dimensions is severely limited by the lack of imaging methodologies that allow for fast 3D tracking of cellular events and 3D superresolution imaging of sub-cellular structures. We have developed a 3D imaging modality, multifocal plane microscopy (MUM), that provides a powerful approach for 3D single molecule tracking and 3D superresolution microscopy. Here we review the technical challenges associated with 3D single molecule localization that is fundamental to both 3D tracking and 3D superresolution, and discuss how MUM overcomes these problems. PMID:24443677

  8. Single-molecule imaging of organic semiconductors: Toward nanoscale insights into photophysics and molecular packing

    NASA Astrophysics Data System (ADS)

    Shepherd, W. E. B.; Grollman, R.; Robertson, A.; Paudel, K.; Hallani, R.; Loth, M. A.; Anthony, J. E.; Ostroverkhova, O.

    2015-06-01

    Photophysical properties of functionalized anthradithiophene (ADT) and pentacene (Pn) derivatives, as well as energy and charge transfer properties of donor-acceptor (D/A) pairs of these derivatives, are presented. The molecules studied were imaged on the single-molecule level in a polymeric and in a functionalized benzothiophene (BTBTB) crystalline host using room-temperature wide-field epifluorescence microscopy. The BTBTB host imposed orientational constraints on the guest molecules, depending on their functionalization. Flexibility of functionalization of both guest (ADT, Pn) and host (BTBTB) molecules can be used for systematic studies of nanoscale morphology and photophysics of D/A organic semiconductor bulk heterojunctions using single-molecule fluorescence microscopy.

  9. Single-molecule fluorescence imaging of the remote TiO2 photocatalytic oxidation.

    PubMed

    Naito, Kazuya; Tachikawa, Takashi; Fujitsuka, Mamoru; Majima, Tetsuro

    2005-12-15

    The remote TiO2 photocatalytic oxidation reaction of single dyes has been investigated by the single-molecule fluorescent imaging technique. The present results suggest that the active oxygen species (Ox) is most probably the .OH radical, which is generated from the photodecomposition of H2O2 by UV light. The analyses of the number, intensity, and spectrum of individual fluorescence spots at the single-molecule level also indicate that unoxidized and oxidized dyes exist during the bleaching processes of single dyes. PMID:16375274

  10. Stoichiometry of the ?-complementation reaction of Escherichia coli ?-galactosidase as revealed through single-molecule studies.

    PubMed

    Mogalisetti, Pratyusha; Walt, David R

    2015-03-01

    The ?-complementation reaction of ?-galactosidase was studied at single-molecule resolution using arrays of femtoliter-sized wells. Single molecules of the complementation species were observed to be stable for long periods of time, demonstrating that the ?-complementation reaction is irreversible. By directly counting the number of active molecules formed in the complementation reaction when different concentrations of enzyme acceptor (EA) and enzyme donor (ED) are used, we deduce that the EA:ED ratio in the complementation species is 4:1. PMID:25668156

  11. Nanoscale arrangement of proteins by single-molecule cut-and-paste.

    PubMed

    Strackharn, Mathias; Pippig, Diana A; Meyer, Philipp; Stahl, Stefan W; Gaub, Hermann E

    2012-09-19

    Protein-based nanostructures are key to the organization of life and it is their precise arrangement, which determines their specific functions. A single-molecule approach for the directed assembly of protein arrangements allows for a controlled composition of systems based on protein components. Applying antibodies and antigenic peptide tags we utilized the Single-Molecule Cut-and-Paste (SMC&P) technique for the handling of single proteins. Protein-DNA complexes could be arranged to complex patterns with the functionality of the protein part remaining unimpaired. PMID:22950442

  12. Single molecule data under scrutiny. Comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb & S.K. Sarkar

    NASA Astrophysics Data System (ADS)

    Wohland, Thorsten

    2015-06-01

    Single Molecule Detection and Spectroscopy have grown from their first beginnings into mainstream, mature research areas that are widely applied in the biological sciences. However, despite the advances in technology and the application of many single molecule techniques even in in vivo settings, the data analysis of single molecule experiments is complicated by noise, systematic errors, and complex underlying processes that are only incompletely understood. Colomb and Sarkar provide in this issue an overview of single molecule experiments and the accompanying problems in data analysis, which have to be overcome for a proper interpretation of the experiments [1].

  13. Single-Molecule Spectroscopy of Cold Denaturation and the Temperature-Induced Collapse of Unfolded Proteins

    E-print Network

    Schuler, Ben

    of cold denaturation are still under debate, but the most common interpretation of the originSingle-Molecule Spectroscopy of Cold Denaturation and the Temperature-Induced Collapse of Unfolded that cold- denatured proteins are more expanded than heat- denatured proteins. To clarify the connection

  14. Scaffolding Carbon Nanotubes into Single-Molecule Circuitry Brett R. Goldsmith1

    E-print Network

    Weiss, Gregory A.

    . INTRODUCTION Chemical, biological, and even mechanical sensor prototypes are all currently explored as possible, not enough is known about the underlying mechanisms to control or tailor this sensitivity. By limiting site (3). In this limit, a CNT circuit can be used to directly transduce single-molecule interactions

  15. Biased Diffusion, Optical Trapping, and Manipulation of Single Molecules in Solution

    E-print Network

    Zare, Richard N.

    possibilities. In this communication, we present our investigation of the diffusional behavior of a single molecule near the focal volume of a confocal fluorescence microscope. We report the first direct optical action of the radiation field on DNA. In confocal fluorescence microscopy, the entrance of a single

  16. Mechanical Design of the First Proximal Ig Domain of Human Cardiac Titin Revealed by Single Molecule

    E-print Network

    Fernandez, Julio M.

    University New York, NY 10027, USA The elastic I-band part of muscle protein titin contains two tandem significant differences between the mechanical unfolding of the I1 and I27 modules. Our study illustrates. Keywords: I1 Ig domain; titin; mechanical unfolding; AFM; single molecule*Corresponding author Introduction

  17. Determining the elastic properties of aptamer-ricin single molecule multiple pathways

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ricin and an anti-ricin aptamer showed three stable binding conformations with their special chemomechanical properties. The elastic properties of the ricin-aptamer single-molecule interactions were investigated by the dynamic force spectroscopy (DFS). The worm-like-chain model and Hook’s law were ...

  18. Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy

    PubMed Central

    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

  19. Self-Contained Kondo Effect in Single Molecules C. H. Booth,1

    E-print Network

    Booth, Corwin H.

    Self-Contained Kondo Effect in Single Molecules C. H. Booth,1 M. D. Walter,1 M. Daniel,1 W. W 94720, USA (Received 12 May 2005; published 19 December 2005) Kondo coupling of f and conduction systems (metallocenes). Evidence for Kondo coupling in CeC8H82 (cerocene) and the ytterbocene Cp 2Ybbipy

  20. Nanopipette Delivery of Individual Molecules to Cellular Compartments for Single-Molecule Fluorescence Tracking

    Microsoft Academic Search

    Andreas Bruckbauer; Peter James; Dejian Zhou; Ji Won Yoon; David Excell; Yuri Korchev; Roy Jones; David Klenerman

    2007-01-01

    We have developed a new method, using a nanopipette, for controlled voltage-driven delivery of individual fluorescently labeled probe molecules to the plasma membrane which we used for single-molecule fluorescence tracking (SMT). The advantages of the method are 1), application of the probe to predefined regions on the membrane; 2), release of only one or a few molecules onto the cell

  1. Stochastic-trajectories and nonPoisson kinetics in single-molecule spectroscopy

    E-print Network

    Mukamel, Shaul

    and Engineering, University of Rochester, Rochester, New York 14627 Received 1 June 1999; accepted 29 July 1999-9606 99 01340-9 I. INTRODUCTION Recent advances in fluorescence detection and micros- copy allow the studies of single molecules in complex con- densed phase environments at cryogenic as well as room

  2. Monitoring patterned enzymatic polymerization on DNA origami at single-molecule level.

    PubMed

    Okholm, A H; Aslan, H; Besenbacher, F; Dong, M; Kjems, J

    2015-07-01

    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. PMID:26061114

  3. An Automated Two-Dimensional Optical Force Clamp for Single Molecule Studies

    E-print Network

    Asbury, Chip

    force microscopy (to 4 nm), a two-dimensional raster scan to calibrate position detector responseAn Automated Two-Dimensional Optical Force Clamp for Single Molecule Studies Matthew J. Lang a microtubule. The instrument can be operated as a two-dimensional force clamp, applying loads of fixed

  4. Single-molecule spectroscopy of protein folding in a chaperonin cage

    E-print Network

    Lipman, Everett A.

    Single-molecule spectroscopy of protein folding in a chaperonin cage Hagen Hofmanna , Frank for avoiding protein aggregation in vivo, but it is still unclear how they affect protein folding mechanisms In the recent past, a large number of components have been identified that control and modulate protein folding

  5. Single-molecule protein folding: Diffusion fluorescence resonance energy transfer studies

    E-print Network

    Croquette, Vincent

    Single-molecule protein folding: Diffusion fluorescence resonance energy transfer studies for protein folding studies and has been extensively stud- ied, both experimentally (at the ensemble level concentration. It is shown that new infor- mation about different aspects of the protein folding reaction can

  6. Rapid analysis of specific DNA sequences by Fluorescent single-molecule detection

    SciTech Connect

    Castro, A. (Alonso)

    2002-01-01

    We have developed a technique for the detection of specific nucleic acid sequences at the single molecule level of sensitivity. This method is based on the synthesis of a highly fluorescent reporter molecule using the target nucleic acid as a template.

  7. Employment of triketones to construct a dysprosium(III) single-molecule magnet.

    PubMed

    Wang, Chao; Lin, Shuang-Yan; Wu, Jianfeng; Yuan, Sen-Wen; Tang, Jinkui

    2015-03-14

    The initial employment of a triketone ligand in 4f coordination chemistry afforded a series of dinuclear complexes. Magnetic studies revealed that an antiferromagnetic interaction exists in a digadolinium(III) compound, while a dysprosium(III) constructed complex exhibits single-molecule magnet (SMM) behaviour at low temperatures with an energy barrier of 86.8 K. PMID:25662367

  8. Mechanical design of proteins studied by single-molecule force spectroscopy and protein engineering

    Microsoft Academic Search

    Mariano Carrion-Vazquez; Andres F. Oberhauser; Thomas E. Fisher; Piotr E. Marszalek; Hongbin Li; Julio M. Fernandez

    2000-01-01

    Mechanical unfolding and refolding may regulate the molecular elasticity of modular proteins with mechanical functions. The development of the atomic force microscopy (AFM) has recently enabled the dynamic measurement of these processes at the single-molecule level. Protein engineering techniques allow the construction of homomeric polyproteins for the precise analysis of the mechanical unfolding of single domains. ?-Helical domains are mechanically

  9. PhD studentship: "DNA Nanotechnology: biochips for single-molecule biological investigations"

    E-print Network

    Chittka, Lars

    , and nanofabrication techniques. He/she will carry out investigations via fluorescence microscopy and scanning probe nanostructures for a variety of different applications in nanoscience and nanotechnology, ranging from scaffoldsPhD studentship: "DNA Nanotechnology: biochips for single- molecule biological investigations

  10. Single-molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update.

    PubMed

    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. PMID:25212907

  11. Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy

    Microsoft Academic Search

    Attila Nagy; Keir C Neuman

    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. Here we describe these techniques and illustrate them with examples highlighting current capabilities and limitations.

  12. Visualizing and quantifying protein polySUMOylation at the single-molecule level.

    PubMed

    Yang, Yong; Zhang, Chun-yang

    2014-01-21

    Protein polySUMOylation, the attachment of small ubiquitin-like modifier (SUMO) chains to the target protein, is associated with a variety of physiological processes. However, the analysis of protein polySUMOylation is often complicated by the heterogeneity of SUMO-target conjugates. Here, we develop a new strategy to visualize and quantify polySUMOylation at the single-molecule level by integrating the tetracysteine (TC) tag labeling technology and total internal reflection fluorescence (TIRF)-based single-molecule imaging. As a proof-of-concept, we employ the human SUMO-2 as the model. The addition of TC tag to SUMO-2 can specifically translate the SUMO-mediated modification into visible fluorescence signal without disturbing the function of SUMO-2. The SUMO monomers display homogeneous fluorescence spots at the single-molecule level, whereas the mixed SUMO chains exhibit nonuniform fluorescence spots with a wide range of intensities. Analysis of the number and the brightness of fluorescence spots enable quantitative measurement of the polySUMOylation degree inside the cells under different physiological conditions. Due to the frequent occurrence of posttranslational modification by polymeric chains in cells, this single-molecule strategy has the potential to be broadly applied for studying protein posttranslational modification in normal cellular physiology and disease etiology. PMID:24383460

  13. A triangular dysprosium with asymmetric central caps featuring ferromagnetic coupling and single-molecule magnet behaviour.

    PubMed

    Shen, Si; Xue, Shufang; Lin, Shuang-Yan; Zhao, Lang; Tang, Jinkui

    2013-08-01

    A new Dy3 triangle bridged by a deprotonated alkoxyl group of a Schiff-base ligand together with a ?3-OH group has been prepared, in which intramolecular ferromagnetic interactions and single molecule magnet behaviour have been observed. PMID:23764730

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

    PubMed

    Bavishi, Krutika; Hatzakis, Nikos S

    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 in deciphering mechanisms that underlie protein folding, structural and functional dynamics by single molecule fluorescence microscopy techniques. We will discuss a few selected examples highlighting the power of the emerging techniques and finally discuss the future improvements and directions. PMID:25429564

  15. Optical Detection and Manipulation of Single Molecules in Room-Temperature Solutions

    E-print Network

    Zare, Richard N.

    CONCEPTS Optical Detection and Manipulation of Single Molecules in Room-Temperature Solutions molecules in solution at room temperature can be trapped and detected by observation of fluorescent pho on single enzymes, for example, have revealed very different catalytic rates for individual enzyme molecule

  16. Long-Lived Intracellular Single-Molecule Fluorescence Using Electroporated Molecules

    PubMed Central

    Crawford, Robert; Torella, Joseph P.; Aigrain, Louise; Plochowietz, Anne; Gryte, Kristofer; Uphoff, Stephan; Kapanidis, Achillefs N.

    2013-01-01

    Studies of biomolecules in vivo are crucial to understand their function in a natural, biological context. One powerful approach involves fusing molecules of interest to fluorescent proteins to study their expression, localization, and action; however, the scope of such studies would be increased considerably by using organic fluorophores, which are smaller and more photostable than their fluorescent protein counterparts. Here, we describe a straightforward, versatile, and high-throughput method to internalize DNA fragments and proteins labeled with organic fluorophores into live Escherichia coli by employing electroporation. We studied the copy numbers, diffusion profiles, and structure of internalized molecules at the single-molecule level in vivo, and were able to extend single-molecule observation times by two orders of magnitude compared to green fluorescent protein, allowing continuous monitoring of molecular processes occurring from seconds to minutes. We also exploited the desirable properties of organic fluorophores to perform single-molecule Förster resonance energy transfer measurements in the cytoplasm of live bacteria, both for DNA and proteins. Finally, we demonstrate internalization of labeled proteins and DNA into yeast Saccharomyces cerevisiae, a model eukaryotic system. Our method should broaden the range of biological questions addressable in microbes by single-molecule fluorescence. PMID:24314075

  17. Fast dynamics of supercoiled DNA revealed by single-molecule experiments

    E-print Network

    Dekker, Nynke

    on the hydrodynamic drag opposing plectoneme removal, and thus provide a quantitative baseline for the dynamicsFast dynamics of supercoiled DNA revealed by single-molecule experiments Aure´lien Crut*, Daniel A for review January 14, 2007) The dynamics of supercoiled DNA play an important role in various cellular

  18. Influence of fluorescent tag on the motility properties of kinesin-1 in single-molecule assays.

    PubMed

    Norris, Stephen R; Núñez, Marcos F; Verhey, Kristen J

    2015-03-10

    Molecular motors such as kinesin and dynein use the energy derived from ATP hydrolysis to walk processively along microtubule tracks and transport various cargoes inside the cell. Recent advancements in fluorescent protein (FP) research enable motors to be fluorescently labeled such that single molecules can be visualized inside cells in multiple colors. The performance of these fluorescent tags can vary depending on their spectral properties and a natural tendency for oligomerization. Here we present a survey of different fluorescent tags fused to kinesin-1 and studied by single-molecule motility assays of mammalian cell lysates. We tested eight different FP tags and found that seven of them display sufficient fluorescence intensity and photostability to visualize motility events. Although none of the FP tags interfere with the enzymatic properties of the motor, four of the tags (EGFP, monomeric EGFP, tagRFPt, and mApple) cause aberrantly long motor run lengths. This behavior is unlikely to be due to electrostatic interactions and is probably caused by tag-dependent oligomerization events that appear to be facilitated by fusion to the dimeric kinesin-1. We also compared the single-molecule performance of various fluorescent SNAP and HALO ligands. We found that although both green and red SNAP ligands provide sufficient fluorescent signal, only the tetramethyl rhodamine (TMR) HALO ligand provides sufficient signal for detection in these assays. This study will serve as a valuable reference for choosing fluorescent labels for single-molecule motility assays. PMID:25762325

  19. Evidence of Disorder in Biological Molecules from Single Molecule Pulling Experiments Changbong Hyeon,1,*

    E-print Network

    Thirumalai, Devarajan

    Evidence of Disorder in Biological Molecules from Single Molecule Pulling Experiments Changbong-722, Korea 2 Institute for Physical Science and Technology, University of Maryland, College Park, Maryland of fluctuations--a measure of dynamical disorder--is comparable to or smaller than the rate of force

  20. DOI: 10.1002/ijch.201100102 Single-Molecule Studies of HIV-1 Protease Catalysis

    E-print Network

    Myong, Sua

    and substrate-derived inhibitors prepared by solid phase peptide synthesis. Chemical protein synthesis was used peptide and protein synthesis for single-molecule studies of enzyme catalysis. Keywords: chemical protein Protein Synthesis Vladimir Yu. Torbeev,[a] Su-A Myong,[b] Taekjip Ha,[b] and Stephen B. H. Kent*[a] 1

  1. Investigation of the numerics of point spread function integration in single molecule localization.

    PubMed

    Chao, Jerry; Ram, Sripad; Lee, Taiyoon; Ward, E Sally; Ober, Raimund J

    2015-06-29

    The computation of point spread functions, which are typically used to model the image profile of a single molecule, represents a central task in the analysis of single molecule microscopy data. To determine how the accuracy of the computation affects how well a single molecule can be localized, we investigate how the fineness with which the point spread function is integrated over an image pixel impacts the performance of the maximum likelihood location estimator. We consider both the Airy and the two-dimensional Gaussian point spread functions. Our results show that the point spread function needs to be adequately integrated over a pixel to ensure that the estimator closely recovers the true location of the single molecule with an accuracy that is comparable to the best possible accuracy as determined using the Fisher information formalism. Importantly, if integration with an insufficiently fine step size is carried out, the resulting estimates can be significantly different from the true location, particularly when the image data is acquired at relatively low magnifications. We also present a methodology for determining an adequate step size for integrating the point spread function. PMID:26191698

  2. Single-molecule analysis of cell surface dynamics in Caenorhabditis elegans embryos.

    PubMed

    Robin, François B; McFadden, William M; Yao, Baixue; Munro, Edwin M

    2014-06-01

    We describe a general, versatile and minimally invasive method to image single molecules near the cell surface that can be applied to any GFP-tagged protein in Caenorhabditis elegans embryos. We exploited tunable expression via RNAi and a dynamically exchanging monomer pool to achieve fast, continuous single-molecule imaging at optimal densities with signal-to-noise ratios adequate for robust single-particle tracking (SPT). We introduce a method called smPReSS, single-molecule photobleaching relaxation to steady state, that infers exchange rates from quantitative analysis of single-molecule photobleaching kinetics without using SPT. Combining SPT and smPReSS allowed for spatially and temporally resolved measurements of protein mobility and exchange kinetics. We used these methods to (i) resolve distinct mobility states and spatial variation in exchange rates of the polarity protein PAR-6 and (ii) measure spatiotemporal modulation of actin filament assembly and disassembly. These methods offer a promising avenue to investigate dynamic mechanisms that pattern the embryonic cell surface. PMID:24727651

  3. Molecular Self-Assembly of Jointed Molecules on a Metallic Substrate: From Single Molecule to Monolayer**

    E-print Network

    Paris-Sud XI, Université de

    Molecular Self-Assembly of Jointed Molecules on a Metallic Substrate: From Single Molecule microscopy, molecular mechanics calculations, self-assembly. 1 hal-00080899,version1-21Jun2006 Author molecules adsorbed on metallic substrates. In this situation, self-assembled structures can be understood

  4. Optimal 3D single-molecule super-resolution microscopy with engineered point spread functions

    Microsoft Academic Search

    Sean Quirin; Ginni Grover; Rafael Piestun

    2012-01-01

    Three-dimensional single-molecule localization is a fundamental problem in biological and biophysical experiments such as super-resolution microscopy. Point spread function engineering accompanied by corresponding reconstruction procedures provides a unique approach to increase localization precision. Joint optical\\/digital design and image reconstruction are investigated.

  5. Double-helix microscopy for wide-field 3D single-molecule fluorescence imaging

    Microsoft Academic Search

    Ginni Sharma; S. R. P. Pavani; S. Quirin; R. Piestun

    2010-01-01

    We present methods to improve the localization accuracy in wide-field 3D single-molecule double-helix microscopy. We analyze the optical efficiency of the system, the fundamental limit for 3D localization, the estimation algorithms, and polarization sensitive detection.

  6. Constructing an Array of Anchored Single-Molecule Rotors on Gold Surfaces Y. Y. Zhang,1

    E-print Network

    Gao, Hongjun

    atom of the molecule and a gold adatom at the surface, which gives them a well- defined contact while for the plane waves was 400 eV. In structural relaxations, all atoms except for the bottom two gold layers wereConstructing an Array of Anchored Single-Molecule Rotors on Gold Surfaces L. Gao,1 Q. Liu,1 Y. Y

  7. Single molecule biochemistry using optical tweezers Amit D. Mehta*, Katherine A. Pullen, James A. Spudich

    E-print Network

    Spudich, James A.

    studied example is kinesin, a two-headed motor observed to transport vesicles along microtubules. A single Biochemical Societies. Key words: Optical trap; Single molecule; Myosin; Kinesin; Titin 1. Introduction kinesin molecule can move along its microtubule track for micrometres before dissociating [3

  8. Accurate Single Molecule FRET Efficiency Determination for Surface Immobilized DNA Using Maximum Likelihood Calculated Lifetimes

    E-print Network

    Accurate Single Molecule FRET Efficiency Determination for Surface Immobilized DNA Using Maximum of surface immobilized double-stranded DNA coupled with a tetramethylrhodmaine and Cy5 FRET pair were these methods for the case of immobilized SM in conjunction with SM fluorescence resonance energy transfer (sm-FRET

  9. Analysis of single-molecule FRET trajectories of transcription complexes based on Hidden-Markov Modelling

    E-print Network

    Goldschmidt, Christina

    Analysis of single-molecule FRET trajectories of transcription complexes based on Hidden resonance energy transfer (FRET) and alternating-laser excitation (ALEX) tools to probe RNAP structure. At Oxford, the Kapanides group improved the temporal resolution of the TIRF assay: by monitoring FRET (using

  10. Probing Protein Fluctuations, Folding and Misfolding at Single-molecule Resolution

    NASA Astrophysics Data System (ADS)

    Deniz, Ashok

    2010-03-01

    The conformational fluctuations and folding of proteins are key for their function in cells and organisms. Conversely, misfolding and aggregation can cause disease, although amyloids with functional significance are also being identified. To better understand these aspects of protein biophysics, we utilize single-molecule fluorescence and complementary methods to directly study complex protein dynamics, structural distributions, and conformational transitions. In one example, we used these methods to investigate disorder and disorder-to-order transitions in intrinsically disordered proteins (IDPs). IDPs are an interesting class of proteins which are relatively unstructured in isolation, but can often fold by interacting with binding partners. These complex systems are increasingly found to play major roles in biology and disease. In one case, we used a combination of single-molecule FRET (smFRET), coincidence and correlation analyses to probe the native structural features of a yeast protein Sup35, whose amyloid state is believed to be used in a beneficial context in yeast. We find that the monomeric protein populates a compact and rapidly fluctuating ensemble of conformations. In another case, we studied the binding-coupled folding of the IDP alpha-synuclein, whose misfolding and aggregation have been linked to Parkinson's disease. Single-molecule measurements directly revealed a complex multi-state folding landscape for this protein. Observations of a transient folding intermediate using microfluidic mixing, and links to misfolding and aggregation will also be discussed. Our results highlight single-molecule methodology that is broadly applicable to map protein folding and misfolding landscapes.

  11. Enhancement and Quenching of Single-Molecule Fluorescence Pascal Anger, Palash Bharadwaj, and Lukas Novotny*

    E-print Network

    Novotny, Lukas

    Enhancement and Quenching of Single-Molecule Fluorescence Pascal Anger, Palash Bharadwaj, and Lukas to a laser-irradiated gold nanoparticle. The local field enhancement leads to an increased excitation rate). Because of these competing effects, previous experiments showed either fluorescence enhancement

  12. Quantifying and Optimizing Single-Molecule Switching Nanoscopy at High Speeds

    PubMed Central

    Lin, Yu; Long, Jane J.; Huang, Fang; Duim, Whitney C.; Kirschbaum, Stefanie; Zhang, Yongdeng; Schroeder, Lena K.; Rebane, Aleksander A.; Velasco, Mary Grace M.; Virrueta, Alejandro; Moonan, Daniel W.; Jiao, Junyi; Hernandez, Sandy Y.; Zhang, Yongli; Bewersdorf, Joerg

    2015-01-01

    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. PMID:26011109

  13. Magnetic cooling at a single molecule level: a spectroscopic investigation of isolated molecules on a surface.

    PubMed

    Corradini, Valdis; Ghirri, Alberto; Candini, Andrea; Biagi, Roberto; del Pennino, Umberto; Dotti, Gianluca; Otero, Edwige; Choueikani, Fadi; Blagg, Robin J; McInnes, Eric J L; Affronte, Marco

    2013-05-28

    A sub-monolayer distribution of isolated molecular Fe14 (bta)6 nanomagnets is deposited intact on a Au(111) surface and investigated by X-ray magnetic circular dichroism spectroscopy. The entropy variation with respect to the applied magnetic field is extracted from the magnetization curves and evidences high magnetocaloric values at the single molecule level. PMID:23580458

  14. Single-molecule chemical reactions tracked at the atomic-bond level.

    PubMed

    Lu, Jiong; Loh, Kian Ping

    2013-12-16

    On the right track: Recent advances in noncontact atomic force microscopy (nc-AFM) have enabled the bond-resolved imaging of reaction pathways. In particular, unprecedented insights into complex enediyne cyclization cascades on silver surfaces were gained by single-molecule imaging. PMID:24155108

  15. New photon-counting detectors for single-molecule fluorescence spectroscopy and imaging

    PubMed Central

    Michalet, X.; Colyer, R. A.; Scalia, G.; Weiss, S.; Siegmund, Oswald H. W.; Tremsin, Anton S.; Vallerga, John V.; Villa, F.; Guerrieri, F.; Rech, I.; Gulinatti, A.; Tisa, S.; Zappa, F.; Ghioni, M.; Cova, S.

    2013-01-01

    Solution-based single-molecule fluorescence spectroscopy is a powerful new experimental approach with applications in all fields of natural sciences. Two typical geometries can be used for these experiments: point-like and widefield excitation and detection. In point-like geometries, the basic concept is to excite and collect light from a very small volume (typically femtoliter) and work in a concentration regime resulting in rare burst-like events corresponding to the transit of a single-molecule. Those events are accumulated over time to achieve proper statistical accuracy. Therefore the advantage of extreme sensitivity is somewhat counterbalanced by a very long acquisition time. One way to speed up data acquisition is parallelization. Here we will discuss a general approach to address this issue, using a multispot excitation and detection geometry that can accommodate different types of novel highly-parallel detector arrays. We will illustrate the potential of this approach with fluorescence correlation spectroscopy (FCS) and single-molecule fluorescence measurements. In widefield geometries, the same issues of background reduction and single-molecule concentration apply, but the duration of the experiment is fixed by the time scale of the process studied and the survival time of the fluorescent probe. Temporal resolution on the other hand, is limited by signal-to-noise and/or detector resolution, which calls for new detector concepts. We will briefly present our recent results in this domain. PMID:24729836

  16. Label-free single-molecule detection of DNA-hybridization kinetics with a carbon nanotube

    E-print Network

    Hone, James

    -dimensional conductors such as single-walled carbon nano- tubes act as high-gain field-effect sensors, in which with specific adsorption and coated nano- tubes11 or non-specific adsorption with pristine nanotubes12 haveLabel-free single-molecule detection of DNA- hybridization kinetics with a carbon nanotube field

  17. Time-dependent study of single-molecule SERS signal from yeast cytochrome c

    E-print Network

    Tuscia, Università Degli Studi Della

    Time-dependent study of single-molecule SERS signal from yeast cytochrome c Ines Delfino *, Anna; accepted 17 February 2006 Available online 6 March 2006 Abstract A study of cytochrome c from Saccharomyces-molecule; Cytochrome c; SERS; Correlation analysis 1. Introduction In recent years, an exponentially growing interest

  18. Single Molecule Recognition between Cytochrome C 551 and Gold-Immobilized Azurin by Force Spectroscopy

    E-print Network

    Tuscia, Università Degli Studi Della

    Single Molecule Recognition between Cytochrome C 551 and Gold-Immobilized Azurin by Force allowed investigating the interaction between two redox partners, Azurin and Cytochrome C 551. Azurin has been directly chemisorbed on a gold electrode whereas cytochrome c has been linked to the atomic force

  19. New photon-counting detectors for single-molecule fluorescence spectroscopy and imaging

    E-print Network

    Michalet, Xavier

    the advantage of extreme sensitivity is somewhat counterbalanced by a very long acquisition time. One way to speed up data acquisition is parallelization. Here we will discuss a general approach to address a single molecule needs to large enough be detectable by the photon sensor; (ii) Signals from different

  20. Size-Dependent Catalytic Activity and Dynamics of Gold Nanoparticles at the Single-Molecule Level

    E-print Network

    Chen, Peng

    Size-Dependent Catalytic Activity and Dynamics of Gold Nanoparticles at the Single-Molecule Level from their nanometer size, which gives them increased surface-to-volume ratios and chemical potentials. The size of nanoparticles is thus pivotal for their catalytic properties. Here, we use single

  1. A dinuclear cobalt complex featuring unprecedented anodic and cathodic redox switches for single-molecule magnet activity.

    PubMed

    Fortier, Skye; Le Roy, Jennifer J; Chen, Chun-Hsing; Vieru, Veacheslav; Murugesu, Muralee; Chibotaru, Liviu F; Mindiola, Daniel J; Caulton, Kenneth G

    2013-10-01

    One-electron oxidation or reduction of the paramagnetic dinuclear Co(II) complex dmp2Nin{Co[N(SiMe3)2]}2 (1; dmp2Nin(2-) = bis(2,6-dimethylphenyl)nindigo), by fully reversible chemical or electrochemical methods, generates the radical salts [1(OEt2)](+) and [1](-), respectively. Full structural and magnetic analyses reveal the locus of the redox changes to be nindigo-based, thus giving rise to ligand-centered radicals sandwiched between two paramagnetic and low-coordinate Co(II) centers. The presence of these sandwiched radicals mediates magnetic coupling between the high-spin (S = 3/2) cobalt ions, which gives rise to single-molecule magnet (SMM) activity in both the oxidized ([1(OEt2)](+)) and reduced ([1](-)) states. This feature represents the first example of a SMM exhibiting fully reversible, dual "ON/OFF" switchability in both the cathodic and anodic states. PMID:23991708

  2. Control of photosensitized electron transfer reactions in organized interfacial systems: vesicles, water-in-oil microemulsions, and colloidal silicon dioxide particles

    SciTech Connect

    Wilner, I.; Laane, C.; Otvos, J.W.; Calvin, M.

    1982-01-01

    The separation of photoproducts formed in photosensitized electron transfer reactions is essential for efficient energy conversion and storage. The organization of the components involved in the photoinduced process in interfacial systems leads to efficient compartmentalization of the products. Several interfacial systems, e.g., lipid bilayer membranes (vesicles), water-in-oil microemulsions and a solid SiO/sub 2/ colloidal interface, have been designed to accomplish this goal. An electron transfer across a lipid bilayer membrane leading to the separation of the photoproducts at opposite sides of the membrane is facilitated by establishing a transmembrane potential and organizing the cotransport of cations with specific carriers. In the water-in-oil microemulsion the separation of photoproducts is achieved by means of the hydrophilic-hydrophobic nature of the products. Photosensitized electron transfer reactions analogous to those occurring in the two half-cells are presented. The colloidal SiO/sub 2/ particles provice a charged interface that interacts with charged photoproducts. The photosensitized reduction of a neutral acceptor, propylviologen sulfonate (PVS/sup 0/) by positively charged sensitizers such as Ru(bipy)/sub 3//sup 2 +/ and Zn-tetramethylpyridinium porphyrin, Zu-TMPyP/sup 4 +/, is described. The effect of the SiO/sub 2/ interface is attributed to a high surface potential that results in the separation of the intermediate photoproducts. The quantum yields of the photosensitized reactions are correlated to the interfacial surface potential and the electrical effects of other charged interfaces such as micelles are compared with those of SiO/sub 2/. The possible utilization of the energy stored in the stabilized photoproducts in further chemical reactions is discussed. Special attention is given to the photodecomposition of water as a reaction route. 12 figures.

  3. Comparative single-molecule and ensemble myosin enzymology: sulfoindocyanine ATP and ADP derivatives.

    PubMed Central

    Oiwa, K; Eccleston, J F; Anson, M; Kikumoto, M; Davis, C T; Reid, G P; Ferenczi, M A; Corrie, J E; Yamada, A; Nakayama, H; Trentham, D R

    2000-01-01

    Single-molecule and macroscopic reactions of fluorescent nucleotides with myosin have been compared. The single-molecule studies serve as paradigms for enzyme-catalyzed reactions and ligand-receptor interactions analyzed as individual stochastic processes. Fluorescent nucleotides, called Cy3-EDA-ATP and Cy5-EDA-ATP, were derived by coupling the dyes Cy3.29.OH and Cy5.29.OH (compounds XI and XIV, respectively, in, Bioconjug. Chem. 4:105-111)) with 2'(3')-O-[N-(2-aminoethyl)carbamoyl]ATP (EDA-ATP). The ATP(ADP) analogs were separated into their respective 2'- and 3'-O-isomers, the interconversion rate of which was 30[OH(-)] s(-1) (0.016 h(-1) at pH 7.1) at 22 degrees C. Macroscopic studies showed that 2'(3')-O-substituted nucleotides had properties similar to those of ATP and ADP in their interactions with myosin, actomyosin, and muscle fibers, although the ATP analogs did not relax muscle as well as ATP did. Significant differences in the fluorescence intensity of Cy3-nucleotide 2'- and 3'-O-isomers in free solution and when they interacted with myosin were evident. Single-molecule studies using total internal reflection fluorescence microscopy showed that reciprocal mean lifetimes of the nucleotide analogs interacting with myosin filaments were one- to severalfold greater than predicted from macroscopic data. Kinetic and equilibrium data of nucleotide-(acto)myosin interactions derived from single-molecule microscopy now have a biochemical and physiological framework. This is important for single-molecule mechanical studies of motor proteins. PMID:10827983

  4. Optimization of Cell Morphology Measurement via Single-Molecule Tracking PALM

    PubMed Central

    Frost, Nicholas A.; Lu, Hsiangmin E.; Blanpied, Thomas A.

    2012-01-01

    In neurons, the shape of dendritic spines relates to synapse function, which is rapidly altered during experience-dependent neural plasticity. The small size of spines makes detailed measurement of their morphology in living cells best suited to super-resolution imaging techniques. The distribution of molecular positions mapped via live-cell Photoactivated Localization Microscopy (PALM) is a powerful approach, but molecular motion complicates this analysis and can degrade overall resolution of the morphological reconstruction. Nevertheless, the motion is of additional interest because tracking single molecules provides diffusion coefficients, bound fraction, and other key functional parameters. We used Monte Carlo simulations to examine features of single-molecule tracking of practical utility for the simultaneous determination of cell morphology. We find that the accuracy of determining both distance and angle of motion depend heavily on the precision with which molecules are localized. Strikingly, diffusion within a bounded region resulted in an inward bias of localizations away from the edges, inaccurately reflecting the region structure. This inward bias additionally resulted in a counterintuitive reduction of measured diffusion coefficient for fast-moving molecules; this effect was accentuated by the long camera exposures typically used in single-molecule tracking. Thus, accurate determination of cell morphology from rapidly moving molecules requires the use of short integration times within each image to minimize artifacts caused by motion during image acquisition. Sequential imaging of neuronal processes using excitation pulses of either 2 ms or 10 ms within imaging frames confirmed this: processes appeared erroneously thinner when imaged using the longer excitation pulse. Using this pulsed excitation approach, we show that PALM can be used to image spine and spine neck morphology in living neurons. These results clarify a number of issues involved in interpretation of single-molecule data in living cells and provide a method to minimize artifacts in single-molecule experiments. PMID:22570741

  5. Electron-phonon mediated dephasing inElectron-phonon mediated dephasing in electronic systems driven out-of-electronic systems driven out-of-

    E-print Network

    Marini, Andrea

    Single-molecule (Hwang. Nature, 2009) and Carbon Nanotube (Tans, Nature, 1998) optical transistors Severe;Expertimental evidences (I): A single molecule transistorExpertimental evidences (I): A single molecule transistor A transistor is a semiconductor device used to amplify and switch electronic signals and power

  6. Synthesis and characterization of single-molecule magnets: manganese-acetate, iron-bromium, and analogs

    NASA Astrophysics Data System (ADS)

    North, Jeremy Micah

    This dissertation describes the synthesis and characterization of two new compounds that are among the most studied materials in solid state chemistry over the past eight or so years. The compounds investigated are [Mn12O12(CH3COO)16(H2O) 4]·2CH3COOH·4H2O (Mn12-ac), [(C6H15N3)6Fe8O 2(OH)12]Br7(H2O)Br·8H2 O (Fe8Br8), and several of their analogs. All of these compounds exhibit unusual magnetic ground states, with high electron spin, S = 10, and the novel phenomenon of magnetic quantum tunneling (MQT), whose origin is still not fully understood. We developed methods of growing large, high quality crystals, perhaps the best ones in the literature. We then investigated these materials using electrical conductivity measurements, Raman and infrared spectroscopy, and high-frequency electron paramagnetic resonance (EPR) spectroscopy, and obtained results that should elicit further theoretical and experimental investigations. Chapter 1 provides a general introduction to the field of study, the topic of single molecule magnets. It summarizes the general properties of these materials and lays the foundation for the studies outlined. Chapter 2 discusses the synthesis of the materials studied and describes the experimental parameters of each of the techniques used for characterization. Chapter 3 reports electrical conductivity measurements on Mn12-ac, and Fe 8Br8, which establish these materials as semiconductors. It also describes measurements that show the photoconductive properties of Mn12-ac. Chapter 4 presents Raman and infrared spectroscopy measurements on both materials. Through the use of model compounds and theoretical calculations we were able to assign the majority of the modes in Mn12-ac and Fe8Br8. These data report the frequencies of several low-lying vibrations that might be important in the mechanism of MQT. The results of high-frequency single crystal EPR measurements of Mn12-ac are reported in Chapter 5. These measurements have shown evidence for a distribution of tilts in the magnetic easy axes of Mn12-ac, which could help to explain the mechanism by which magnetic quantum tunneling occurs in this system. Finally, Chapter 6 reports and summarizes the main conclusions of this dissertation. Taken together, these results should constitute a significant step in our understanding of the unusual properties of these materials, such as MQT, and should also elicit further theoretical and experimental investigations.

  7. High-throughput scanning confocal microscope for single molecule Chandran R. Sabanayagam, John S. Eid, and Amit Mellera)

    E-print Network

    Meller, Amit

    High-throughput scanning confocal microscope for single molecule analysis Chandran R. Sabanayagam and programmable confocal microscope that can acquire upwards of 103 single-molecule fluorescence resonance energy transfer FRET time traces is presented. The microscope augments the capabilities of current instruments

  8. Single Molecule Force Spectroscopy of Salt-dependent Bacteriophage T7 Gene 2.5 Protein Binding to

    E-print Network

    Richardson, Charles C.

    Single Molecule Force Spectroscopy of Salt-dependent Bacteriophage T7 Gene 2.5 Protein Binding by single molecule force spectroscopy. T7 gp2.5- 26C, lacking 26 acidic C-terminal residues, also reduces of single DNA molecules by stretch- ing the molecules and measuring the required force for a given extension

  9. Forces and conductances in a single-molecule bipyridine junction R. Stadler, K. S. Thygesen, and K. W. Jacobsen

    E-print Network

    Thygesen, Kristian

    Forces and conductances in a single-molecule bipyridine junction R. Stadler, K. S. Thygesen, and K force, indicating that the contacts consist of single molecules. Such bipyridine junctions of several proper- ties forces and conductances for junctions of single aro- matic molecules, and ii pyridine

  10. Arrayed lipid bilayer chambers allow single-molecule analysis of membrane transporter activity

    PubMed Central

    Watanabe, Rikiya; Soga, Naoki; Fujita, Daishi; Tabata, Kazuhito V.; Yamauchi, Lisa; Hyeon Kim, Soo; Asanuma, Daisuke; Kamiya, Mako; Urano, Yasuteru; Suga, Hiroaki; Noji, Hiroyuki

    2014-01-01

    Nano- to micron-size reaction chamber arrays (femtolitre chamber arrays) have facilitated the development of sensitive and quantitative biological assays, such as single-molecule enzymatic assays, digital PCR and digital ELISA. However, the versatility of femtolitre chamber arrays is limited to reactions that occur in aqueous solutions. Here we report an arrayed lipid bilayer chamber system (ALBiC) that contains sub-million femtolitre chambers, each sealed with a stable 4-?m-diameter lipid bilayer membrane. When reconstituted with a limiting amount of the membrane transporter proteins ?-hemolysin or F0F1-ATP synthase, the chambers within the ALBiC exhibit stochastic and quantized transporting activities. This demonstrates that the single-molecule analysis of passive and active membrane transport is achievable with the ALBiC system. This new platform broadens the versatility of femtolitre chamber arrays and paves the way for novel applications aimed at furthering our mechanistic understanding of membrane proteins’ function. PMID:25058452

  11. Aptamer-Encoded Nanopore for Ultrasensitive Detection of Bioterrorist Agent Ricin at Single-Molecule Resolution

    PubMed Central

    Gu, Li-Qun; Ding, Shu; Gao, Changlu

    2011-01-01

    The molecular-scale pore structure, called nanopore, can be formed from protein ion channels by genetic engineering or fabricated on solid substrates using fashion nanotechnology. Target molecules in interaction with the functionalized lumen of nanopore, can produce characteristic changes in the pore conductance, which act as fingerprints, allowing us to identify single molecules and simultaneously quantify each target species in the mixture. Nanopore sensors have been created for tremendous biomedical detections, with targets ranging from metal ions, drug compounds and cellular second messengers, to proteins and DNAs. Here we will review our recent discoveries with a lab-in-hand glass nanopore: single-molecule discrimination of chiral enantiomers with a trapped cyclodextrin, and sensing of bioterrorist agent ricin. PMID:19964179

  12. Single molecule detection of 4-dimethylaminoazobenzene by surface-enhanced Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    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.

  13. Single molecule fluorescence spectroscopy of pH sensitive oligonucleotide switches.

    PubMed

    Kolaric, Branko; Sliwa, Michel; Brucale, Marco; Vallée, Renaud A L; Zuccheri, Giampaolo; Samori, Bruno; Hofkens, Johan; De Schryver, Frans C

    2007-06-01

    Several authors demonstrated that an oligonucleotide based pH-sensitive construct can act as a switch between an open and a closed state by changing the pH. To validate this process, specially designed fluorescence dye-quencher substituted oligonucleotide constructs were developed to probe the switching between these two states. This paper reports on bulk and single molecule fluorescence investigations of a duplex-triplex pH sensitive oligonucleotide switch. On the bulk level, only a partial quenching of the fluorescence is observed, similarly to what is observed for other published switches and is supposed to be due to intermolecular interactions between oligonucleotide strands. On the single molecule level, each DNA-based nanometric construct shows a complete switching. These observations suggest the tendency of the DNA construct to associate at high concentration. PMID:17549262

  14. A scheme for a single molecule phase-shift gate in a solid matrix.

    PubMed

    Cui, Xiao-Dong; Zheng, Yujun

    2015-06-01

    We propose a feasible scheme to implement a phase-shift gate 100e(i?) based on a two-state single molecule in a solid matrix, where ? is a geometric phase controlled through a fast on-resonant laser field and a slow off-resonant radio-frequency field. In our scheme, a non-Hermitian quantum model is employed to characterize the single molecule in a solid matrix including the spontaneous decay effect. By the coupling between the radio-frequency field and the two-state permanent dipole difference resulting from the solid matrix, the spontaneous decay fatal to the preservation of geometric phase can be effectively suppressed for a considerably long waiting time. PMID:26049500

  15. A Simple Method for GFP- and RFP-based Dual Color Single-Molecule Localization Microscopy.

    PubMed

    Platonova, Evgenia; Winterflood, Christian M; Ewers, Helge

    2015-06-19

    The recent development of single-molecule localization-based super-resolution techniques has afforded a resolution in the nanometer range in light microscopy. The ability to resolve biological structures on this scale by multicolor techniques faces significant challenges which have prevented their widespread use. Here, we provide a generic approach for high-quality simultaneous two-color single-molecule localization microscopy imaging of any combination of GFP- and RFP-tagged proteins with the use of nanobodies. Our method addresses a number of common issues related to two-color experiments, including accuracy and density of labeling as well as chromatic aberration and color-crosstalk with only minimal technical requirements. We demonstrate two-color imaging of various nanoscopic structures and show a compound resolution down to the limit routinely achieved only in a single color. PMID:25806422

  16. Optical and electrical detection of single-molecule translocation through carbon nanotubes.

    PubMed

    Song, Weisi; Pang, Pei; He, Jin; Lindsay, Stuart

    2013-01-22

    Ion current through a single-walled carbon nanotube (SWCNT) was monitored at the same time as fluorescence was recorded from charged dye molecules translocating through the SWCNT. Fluorescence bursts generally follow ion current peaks with a delay time consistent with diffusion from the end of the SWCNT to the fluorescence collection point. The fluorescence amplitude distribution of the bursts is consistent with single-molecule signals. Thus each peak in the ion current flowing through the SWCNT is associated with the translocation of a single molecule. Ion current peaks (as opposed to blockades) were produced by both positively (Rhodamine 6G) and negatively (Alexa 546) charged molecules, showing that the charge filtering responsible for the current bursts is caused by the molecules themselves. PMID:23248975

  17. Single-molecule analysis of chirality in a multicomponent reaction network

    NASA Astrophysics Data System (ADS)

    Steffensen, Mackay B.; Rotem, Dvir; Bayley, Hagan

    2014-07-01

    Single-molecule approaches to chemical reaction analysis can provide information that is not accessible by studying ensemble systems. Changes in the molecular structures of compounds tethered to the inner wall of a protein pore are known to affect the current carried through the pore by aqueous ions under a fixed applied potential. Here, we use this approach to study the substitution reactions of arsenic(III) compounds with thiols, stretching the limits of the protein pore technology to track the interconversion of seven reaction components in a network that comprises interconnected Walden cycles. Single-molecule pathway analysis of ‘allowed’ and ‘forbidden’ reactions reveals that sulfur-sulfur substitution occurs with stereochemical inversion at the arsenic centre. Hence, we demonstrate that the nanoreactor approach can be a valuable technique for the analysis of dynamic reaction systems of relevance to biology.

  18. Linking enzyme conformational dynamics to catalytic function with single-molecule FRET

    NASA Astrophysics Data System (ADS)

    Tan, Yan-Wen; Hanson, Jeffrey A.; Duderstadt, Karl; Bhattacharyya, Sucharita; Yang, Haw

    2008-03-01

    Many enzymes endure sizable conformational remodeling on a timescale comparable to their catalytic cycle. These conformational dynamics may be critical to the enzymes' catalytic function. In adenylate kinase (AK) from E. coli, this involves a large-amplitude rearrangement of the enzyme's lid domain. We use high-resolution single-molecule FRET developed in our laboratory to measure AK's domain movements on its catalytic timescale. We utilize maximum entropy-based methods to remove photon-counting noise from raw data, so that the enzyme's entire conformational distribution can be quantitatively recovered without a presumed model. Multiple sequence alignment suggests regularities between the conserved residues and their structural-functional roles. Armed with precise single-molecule FRET dynamics measurements and comprehensive bulk kinetic studies of the mechanism, we were able to quantitatively correlate AK's stochastic lid dynamics with its deterministic catalytic rates. Implications on the structure-function conservation and protein engineering will be discussed.

  19. Geometric-phase interference in a Mn12 single-molecule magnet with fourfold rotational symmetry.

    PubMed

    Adams, S T; da Silva Neto, E H; Datta, S; Ware, J F; Lampropoulos, C; Christou, G; Myaesoedov, Y; Zeldov, E; Friedman, Jonathan R

    2013-02-22

    We study the magnetic relaxation rate ? of the single-molecule magnet Mn(12)-tBuAc as a function of the magnetic field component H(T) transverse to the molecule's easy axis. When the spin is near a magnetic quantum tunneling resonance, we find that ? increases abruptly at certain values of H(T). These increases are observed just beyond values of H(T) at which a geometric-phase interference effect suppresses tunneling between two excited energy levels. The effect is washed out by rotating H(T) away from the spin's hard axis, thereby suppressing the interference effect. Detailed numerical calculations of ? using the known spin Hamiltonian accurately reproduce the observed behavior. These results are the first experimental evidence for geometric-phase interference in a single-molecule magnet with true fourfold symmetry. PMID:23473196

  20. A simple procedure to improve the surface passivation for single molecule fluorescence studies

    NASA Astrophysics Data System (ADS)

    Pan, Hai; Xia, Yifan; Qin, Meng; Cao, Yi; Wang, Wei

    2015-07-01

    The single-molecule fluorescence technique is becoming a general and mature tool to probe interactions and dynamics of biomolecules with ultra high precision and accuracy. However, nonspecific adsorption of biomolecules to the flow cells remains a major experimental riddle for the study of many complex biological systems, especially those exhibiting low binding affinity and presenting with weakly populated intermediates. Many novel surface passivation methods have been introduced to reduce nonspecific interactions. Here, we present an effective and inexpensive method to significantly reduce nonspecific binding of biomolecules in conventional poly (ethylene glycol) (PEG)–based surface passivation protocols, without additional exogenous effects. In particular, we propose a simple 10 min Tween-20 treatment for the PEG passivated surface, which could further increase the hydrophilicity of the surface and thus promote passivation efficacy by about 5 to 10 times. We anticipate that this new procedure will find broad practical applications and extend the current reaches of single-molecule fluorescence studies.