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Sample records for single-molecule interfacial electron

  1. Single-molecule interfacial electron transfer dynamics of porphyrin on TiO2 nanoparticles: dissecting the interfacial electric field and electron accepting state density dependent dynamics.

    PubMed

    Rao, Vishal Govind; Dhital, Bharat; Peter Lu, H

    2015-12-01

    Single-molecule photon-stamping spectroscopy correlated with electrochemical techniques was used to dissect complex interfacial electron transfer (ET) dynamics by probing an m-ZnTCPP molecule anchored to a TiO2 NP surface while electrochemically controlling the energetically-accessible surface states of TiO2 NPs. Application of negative potential increases the electron density in TiO2 NPs, resulting in hindered forward ET and enhanced backward ET due to the changes in the interfacial electric field and the occupancy of acceptor states. PMID:26434919

  2. 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

  3. Single-molecule junctions beyond electronic transport

    NASA Astrophysics Data System (ADS)

    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.

  4. 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

  5. Can a single molecule trap the electron?

    E-print Network

    Shkrob, I A; Schlueter, John A.; Shkrob, Ilya A.

    2006-01-01

    We suggest that it might be possible to trap the electron in a cavity of a macrocycle molecule, in the same way this trapping occurs cooperatively, by several solvent molecules, in hydroxylic liquids. Such an encapsulated electron is a "molecular capacitor," in which the excess electron is largely decoupled from valence electrons in the trap. A specific design for such a trap that is based on calix[4]cyclohexanol is discussed in detail. It is shown theoretically, by ab initio and density functional theory (DFT) modeling, that one of the conformations of this molecule forms the optimum tetrahedral trap for the electron. The resulting "encapsulated electron" strikingly resembles the solvated electron in alcohols and water.

  6. Electron Transfer-Based Single Molecule Fluorescence as a Probe for Nano-Environment Dynamics

    PubMed Central

    Chen, Ruiyun; Wu, Ruixiang; Zhang, Guofeng; Gao, Yan; Xiao, Liantuan; Jia, Suotang

    2014-01-01

    Electron transfer (ET) is one of the most important elementary processes that takes place in fundamental aspects of biology, chemistry, and physics. In this review, we discuss recent research on single molecule probes based on ET. We review some applications, including the dynamics of glass-forming systems, surface binding events, interfacial ET on semiconductors, and the external field-induced dynamics of polymers. All these examples show that the ET-induced changes of fluorescence trajectory and lifetime of single molecules can be used to sensitively probe the surrounding nano-environments. PMID:24496314

  7. Single-Molecule Electronic Measurements with Metal Electrodes

    ERIC Educational Resources Information Center

    Lindsay, Stuart

    2005-01-01

    A review of concepts like tunneling through a metal-molecule-metal-junction, contrast with electrochemical and optical-charge injection, strong-coupling limit, calculations of tunnel transport, electron transfer through Redox-active molecules is presented. This is followed by a discussion of experimental approaches for single-molecule measurements.

  8. Electronic transport in benzodifuran single-molecule transistors

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    Benzodifuran (BDF) single-molecule transistors have been fabricated in electromigration break junctions for electronic measurements. The inelastic electron tunneling spectrum validates that the BDF molecule is the pathway of charge transport. The gating effect is analyzed in the framework of a single-level tunneling model combined with transition voltage spectroscopy (TVS). The analysis reveals that the highest occupied molecular orbital (HOMO) of the thiol-terminated BDF molecule dominates the charge transport through Au-BDF-Au junctions. Moreover, the energy shift of the HOMO caused by the gate voltage is the main reason for conductance modulation. In contrast, the electronic coupling between the BDF molecule and the gold electrodes, which significantly affects the low-bias junction conductance, is only influenced slightly by the applied gate voltage. These findings will help in the design of future molecular electronic devices.Benzodifuran (BDF) single-molecule transistors have been fabricated in electromigration break junctions for electronic measurements. The inelastic electron tunneling spectrum validates that the BDF molecule is the pathway of charge transport. The gating effect is analyzed in the framework of a single-level tunneling model combined with transition voltage spectroscopy (TVS). The analysis reveals that the highest occupied molecular orbital (HOMO) of the thiol-terminated BDF molecule dominates the charge transport through Au-BDF-Au junctions. Moreover, the energy shift of the HOMO caused by the gate voltage is the main reason for conductance modulation. In contrast, the electronic coupling between the BDF molecule and the gold electrodes, which significantly affects the low-bias junction conductance, is only influenced slightly by the applied gate voltage. These findings will help in the design of future molecular electronic devices. Electronic supplementary information (ESI) available: The fabrication procedure for BDF single-molecule transistors (Fig. S1); the temperature dependence of I-V characteristics of a BDF single-molecule device (Fig. S2); assignment of peaks of IET spectra to specific vibration modes (Fig. S3); the broadening of the ?(C-H) peak (~390 mV, C-H stretch of the phenyl ring) in IET spectra due to the AC modulation (Fig. S4); the I-V curves of pristine gold vacuum junctions (without BDF molecules) measured at different gate voltages (Fig. S5); gate leakage in BDF single-molecule transistors (Fig. S6); the histogram of the transition voltages at two bias polarities for BDF single-molecule devices (Fig. S7). See DOI: 10.1039/c5nr00402k

  9. Basic concepts of quantum interference and electron transport in single-molecule electronics.

    PubMed

    Lambert, C J

    2015-02-21

    This tutorial outlines the basic theoretical concepts and tools which underpin the fundamentals of phase-coherent electron transport through single molecules. The key quantity of interest is the transmission coefficient T(E), which yields the electrical conductance, current-voltage relations, the thermopower S and the thermoelectric figure of merit ZT of single-molecule devices. Since T(E) is strongly affected by quantum interference (QI), three manifestations of QI in single-molecules are discussed, namely Mach-Zehnder interferometry, Breit-Wigner resonances and Fano resonances. A simple MATLAB code is provided, which allows the novice reader to explore QI in multi-branched structures described by a tight-binding (Hückel) Hamiltonian. More generally, the strengths and limitations of materials-specific transport modelling based on density functional theory are discussed. PMID:25255961

  10. Electronic Measurements of Single-Molecule Catalysis by cAMP-Dependent Protein Kinase A

    E-print Network

    Weiss, Gregory A.

    to single-walled carbon nanotube (SWNT) electronic devices. The motions by the lysozyme active site duringElectronic Measurements of Single-Molecule Catalysis by cAMP- Dependent Protein Kinase A Patrick C-walled carbon nanotube device for long-duration monitoring. The electronic recording clearly resolves substrate

  11. Single Molecule Dissociation by Tunneling Electrons B. C. Stipe, M. A. Rezaei, and W. Ho

    E-print Network

    Persson, Mats

    Single Molecule Dissociation by Tunneling Electrons B. C. Stipe, M. A. Rezaei, and W. Ho Laboratory­ scope was used to image and dissociate single O2 molecules on the Pt(111) surface in the temperature range of 40 K to 150 K. After dissociation, the two oxygen atoms are found one to three lattice

  12. Electron Transport, Energy Transfer, and Optical Response in Single Molecule Junctions

    NASA Astrophysics Data System (ADS)

    White, Alexander

    2015-03-01

    The field of molecular electronics has grown significantly since the first measurements of single molecule conductance. The single molecule junction, a device in which two conducting leads are spanned by a single molecule, has become a powerful tool for studying charge transfer at the molecular level. While early experiments were focused on elastic electron conductance, today measurements of vibronic effects, molecular optical response, spintronics, thermal conductance, and quantum interference and decoherence effects are prominent areas of research. These new experimental advancements demand improved theoretical treatments which properly account for the interactions between different degrees of freedom: charge, electronic, vibrational, spin, etc.; all in physically relevant parameter ranges. This talk focuses on using a many-body states based approach to investigate the regime of strong interaction between these degrees of freedom, with relatively weak coupling between the molecule and the electric reservoirs created by the conducting leads. We focused on three related processes, electron transfer, electronic energy transfer and molecular excitation. In collaboraton with Boris Fainberg, Faculty of Sciences, Holon Institute of Technology; Sergei Tretiak, Theoretical Division, Center for Integrated Nanotechnologies, Los Alamos National Laboratory; and Michael Galperin, Department of Chemistry and Biochemistry, University of California San Diego.

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

    SciTech Connect

    Fratalocchi, A.; Ruocco, G.

    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.

  14. 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.

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

    SciTech Connect

    Sotthewes, Kai; Heimbuch, René Kumar, Avijit; Zandvliet, Harold J. W.; Geskin, Victor

    2014-01-01

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

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

    PubMed

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

    2012-11-21

    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 b(562) 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 b(562) 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. PMID:23069929

  17. 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.

  18. Single-molecule spectroscopy exposes hidden states in an enzymatic electron relay

    PubMed Central

    Grossman, Iris; Yuval Aviram, Haim; Armony, Gad; Horovitz, Amnon; Hofmann, Hagen; Haran, Gilad; Fass, Deborah

    2015-01-01

    The ability to query enzyme molecules individually is transforming our view of catalytic mechanisms. Quiescin sulfhydryl oxidase (QSOX) is a multidomain catalyst of disulfide-bond formation that relays electrons from substrate cysteines through two redox-active sites to molecular oxygen. The chemical steps in electron transfer have been delineated, but the conformational changes accompanying these steps are poorly characterized. Here we use single-molecule Förster resonance energy transfer (smFRET) to probe QSOX conformation in resting and cycling enzyme populations. We report the discovery of unanticipated roles for conformational changes in QSOX beyond mediating electron transfer between redox-active sites. In particular, a state of the enzyme not previously postulated or experimentally detected is shown to gate, via a conformational transition, the entrance into a sub-cycle within an expanded QSOX kinetic scheme. By tightly constraining mechanistic models, smFRET data can reveal the coupling between conformational and chemical transitions in complex enzymatic cycles. PMID:26468675

  19. Single-molecule spectroscopy exposes hidden states in an enzymatic electron relay

    NASA Astrophysics Data System (ADS)

    Grossman, Iris; Yuval Aviram, Haim; Armony, Gad; Horovitz, Amnon; Hofmann, Hagen; Haran, Gilad; Fass, Deborah

    2015-10-01

    The ability to query enzyme molecules individually is transforming our view of catalytic mechanisms. Quiescin sulfhydryl oxidase (QSOX) is a multidomain catalyst of disulfide-bond formation that relays electrons from substrate cysteines through two redox-active sites to molecular oxygen. The chemical steps in electron transfer have been delineated, but the conformational changes accompanying these steps are poorly characterized. Here we use single-molecule Förster resonance energy transfer (smFRET) to probe QSOX conformation in resting and cycling enzyme populations. We report the discovery of unanticipated roles for conformational changes in QSOX beyond mediating electron transfer between redox-active sites. In particular, a state of the enzyme not previously postulated or experimentally detected is shown to gate, via a conformational transition, the entrance into a sub-cycle within an expanded QSOX kinetic scheme. By tightly constraining mechanistic models, smFRET data can reveal the coupling between conformational and chemical transitions in complex enzymatic cycles.

  20. All-optical sensing of a single-molecule electron spin

    E-print Network

    A. O. Sushkov; N. Chisholm; I. Lovchinsky; M. Kubo; P. K. Lo; S. D. Bennett; D. Hunger; A. Akimov; R. L. Walsworth; H. Park; M. D. Lukin

    2013-11-07

    We demonstrate an all-optical method for magnetic sensing of individual molecules in ambient conditions at room temperature. Our approach is based on shallow nitrogen-vacancy (NV) centers near the surface of a diamond crystal, which we use to detect single paramagnetic molecules covalently attached to the diamond surface. The manipulation and readout of the NV centers is all-optical and provides a sensitive probe of the magnetic field fluctuations stemming from the dynamics of the electronic spins of the attached molecules. As a specific example, we demonstrate detection of a single paramagnetic molecule containing a gadolinium (Gd$^{3+}$) ion. We confirm single-molecule resolution using optical fluorescence and atomic force microscopy to co-localize one NV center and one Gd$^{3+}$-containing molecule. Possible applications include nanoscale and in vivo magnetic spectroscopy and imaging of individual molecules.

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

    SciTech Connect

    Bailey, Steven; Visontai, David; Lambert, Colin J.; Bryce, Martin R.; Frampton, Harry; Chappell, David

    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.

  2. Manipulation and characterization of thin-film interfacial chemistry: Sol-gel deposition and single molecule tracking experiments

    NASA Astrophysics Data System (ADS)

    Barhoum, Moussa

    Single molecule trajectories of 1,1'-dioctadecyl-3,3,3'3'-tetramethylindocarbo - cyanine perchlorate (DiI) fluorophores diffusing on planar supported 1,2-dimyristoyl-snglycero- 3-phosphocholine (DMPC) lipid bilayers imaged through total internal reflection fluorescence (TIRF) microscopy at different temperatures are investigated. The spatial resolution limit for detecting molecular motion is evaluated by characterizing the apparent motion which arises from the limited signal-to-noise ratio (S/N) of imaged and simulated stationary DiI molecules. Statistical criteria for reliably distinguishing molecular motion from stationary molecules using F-test statistics, including the computation of local signal-to-noise ratios are then established and used for reliably detecting subdiffraction motion of DiI molecules on DMPC. The same single molecule tracking concept is used in investigating the temperature dependence of subdiffraction diffusional confinement of single Rhodamine 6G molecules in polymer brushes of poly (N-isopropylacrylamide), pNIPAAm, above and below its lower critical solution temperature (LCST) of 32°C. Reliably distinguishing subdiffraction molecular motion from stationary events is crucial in validating the application of single molecule tracking experiment in probing nanometersized hydrophobic environments of polymer structure. A versatile and rapid sol-gel technique for the fabrication of high quality one-dimensional photonic bandgap materials was developed. Silica/titania multilayer materials are fabricated by a sol-gel chemistry route combined with dip-coating onto planar or curved substrate. A shock-cooling step immediately following the thin film heat-treatment process is introduced. The versatility of this sol-gel method is demonstrated by the fabrication of various Bragg stack-type materials with fine-tuned optical properties. Measured optical properties show good agreement with theoretical simulations confirming the high quality of these sol-gel fabricated optical materials. Finally, magnetic functionalization studies of sol-gel derived Co-ion doped titania thin films using superconducting quantum interference device (SQUID) magnetometry and an attempt to measure their magneto-optical properties using a home-built Faraday rotation setup are discussed. The experimental limitations in reliably measuring magnetization responses of these thin films are introduced and discussed in detail. The summary and outlook chapters summarize the scientific significance of each research project and briefly introduce ongoing research based on the work and the results presented in this dissertation.

  3. 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

  4. Electrical properties and mechanical stability of anchoring groups for single-molecule electronics

    PubMed Central

    Frisenda, Riccardo; Tarkuç, Simge; Galán, Elena; Perrin, Mickael L; Eelkema, Rienk; Grozema, Ferdinand C

    2015-01-01

    Summary We report on an experimental investigation of transport through single molecules, trapped between two gold nano-electrodes fabricated with the mechanically controlled break junction (MCBJ) technique. The four molecules studied share the same core structure, namely oligo(phenylene ethynylene) (OPE3), while having different aurophilic anchoring groups: thiol (SAc), methyl sulfide (SMe), pyridyl (Py) and amine (NH2). The focus of this paper is on the combined characterization of the electrical and mechanical properties determined by the anchoring groups. From conductance histograms we find that thiol anchored molecules provide the highest conductance; a single-level model fit to current–voltage characteristics suggests that SAc groups exhibit a higher electronic coupling to the electrodes, together with better level alignment than the other three groups. An analysis of the mechanical stability, recording the lifetime in a self-breaking method, shows that Py and SAc yield the most stable junctions while SMe form short-lived junctions. Density functional theory combined with non-equlibrium Green’s function calculations help in elucidating the experimental findings. PMID:26425407

  5. All-Optical Sensing of a Single-Molecule Electron Spin A. O. Sushkov,,,

    E-print Network

    Walsworth, Ronald L.

    on shallow nitrogen-vacancy (NV) centers near the surface of a diamond crystal, which we use to detect single paramagnetic molecules covalently attached to the diamond surface. The manipulation and readout of the NV of individual molecules. KEYWORDS: Nitrogen vacancy center, diamond, single-molecule spin, magnetometry, all

  6. Quantitative Connection between Ensemble Thermodynamics and Single-Molecule Kinetics: A Case Study Using Cryogenic Electron Microscopy and Single-Molecule Fluorescence Resonance Energy Transfer Investigations of the Ribosome.

    PubMed

    Kinz-Thompson, Colin D; Sharma, Ajeet K; Frank, Joachim; Gonzalez, Ruben L; Chowdhury, Debashish

    2015-08-27

    At equilibrium, thermodynamic and kinetic information can be extracted from biomolecular energy landscapes by many techniques. However, while static, ensemble techniques yield thermodynamic data, often only dynamic, single-molecule techniques can yield the kinetic data that describe transition-state energy barriers. Here we present a generalized framework based upon dwell-time distributions that can be used to connect such static, ensemble techniques with dynamic, single-molecule techniques, and thus characterize energy landscapes to greater resolutions. We demonstrate the utility of this framework by applying it to cryogenic electron microscopy (cryo-EM) and single-molecule fluorescence resonance energy transfer (smFRET) studies of the bacterial ribosomal pre-translocation complex. Among other benefits, application of this framework to these data explains why two transient, intermediate conformations of the pre-translocation complex, which are observed in a cryo-EM study, may not be observed in several smFRET studies. PMID:25785884

  7. Towards single molecule switches.

    PubMed

    Zhang, Jia Lin; Zhong, Jian Qiang; Lin, Jia Dan; Hu, Wen Ping; Wu, Kai; Xu, Guo Qin; Wee, Andrew T S; Chen, Wei

    2015-05-21

    The concept of using single molecules as key building blocks for logic gates, diodes and transistors to perform basic functions of digital electronic devices at the molecular scale has been explored over the past decades. However, in addition to mimicking the basic functions of current silicon devices, molecules often possess unique properties that have no parallel in conventional materials and promise new hybrid devices with novel functions that cannot be achieved with equivalent solid-state devices. The most appealing example is the molecular switch. Over the past decade, molecular switches on surfaces have been intensely investigated. A variety of external stimuli such as light, electric field, temperature, tunneling electrons and even chemical stimulus have been used to activate these molecular switches between bistable or even multiple states by manipulating molecular conformations, dipole orientations, spin states, charge states and even chemical bond formation. The switching event can occur either on surfaces or in break junctions. The aim of this review is to highlight recent advances in molecular switches triggered by various external stimuli, as investigated by low-temperature scanning tunneling microscopy (LT-STM) and the break junction technique. We begin by presenting the molecular switches triggered by various external stimuli that do not provide single molecule selectivity, referred to as non-selective switching. Special focus is then given to selective single molecule switching realized using the LT-STM tip on surfaces. Single molecule switches operated by different mechanisms are reviewed and discussed. Finally, molecular switches embedded in self-assembled monolayers (SAMs) and single molecule junctions are addressed. PMID:25757483

  8. Structure-dependent electronic nature of star-shaped oligothiophenes, probed by ensemble and single-molecule spectroscopy.

    PubMed

    Chung, Heejae; Narita, Tomoyuki; Yang, Jaesung; Kim, Pyosang; Takase, Masayoshi; Iyoda, Masahiko; Kim, Dongho

    2013-07-15

    We have investigated the photophysical properties of star-shaped oligothiophenes with three terthiophene arms (meta to each other, S3) or six terthiophene arms (ortho-, meta-, and para-arranged, S6) connected to an ethynylbenzene core to elucidate the relationship between their molecular structure and electronic properties by using a combination of ensemble and single-molecule spectroscopic techniques. We postulate two different conformations for molecules S3 and S6 on the basis of the X-ray structure of hexakis(5-hexyl-2-thienlyethynyl)benzene and suggest the coexistence of these conformers by using spectroscopic methods. From the steady-state spectroscopic data of compound S6, we show that the exciton is delocalized over the core structure, but that the meta-linkage in compound S3 prevents the electronic communication between the arms. However, in single-molecule spectroscopic measurements, we observed that some molecules of compound S3 showed long fluorescence lifetimes (about 1.4 ns) in the fluorescence-intensity trajectories, which indicated that ? electrons were delocalized along the meta linker. Based on these observations, we suggest that the delocalized exciton is intensely sensitive towards the dihedral angle between the core and the adjacent thiophene ring, as well as to the substituted position of the terthiophene arms. Our results highlight that the fluorescence lifetimes of compounds S3 and S6 are strongly correlated with the spatial location of their excitons, which is mainly affected by their conformation, that is, whether the innermost thiophene rings are facing each other or not. More interestingly, we observed that the difference between the degrees of ring-torsional flexibility of compounds S3 and S6 results in their sharply contrasting fluorescence properties, such as a change in fluorescence intensity as a function of temperature. PMID:23737369

  9. Charge localization on a redox-active single-molecule junction and its influence on coherent electron transport

    NASA Astrophysics Data System (ADS)

    Kastlunger, Georg; Stadler, Robert

    2013-07-01

    To adjust the charging state of a molecular metal complex in the context of a density functional theory description of coherent electron transport through single-molecule junctions, we correct for self-interaction effects by fixing the charge on a counterion, which in our calculations mimics the effect of the gate in an electrochemical scanning tunneling microscope setup, with two competing methods, namely, the generalized ?self consistent field (?SCF) technique and screening with solvation shells. One would expect a transmission peak to be pinned at the Fermi energy for a nominal charge of +1 on the molecule in the junction, but we find a more complex situation in this multicomponent system defined by the complex, the leads, the counterion, and the solvent. In particular the equilibrium charge transfer between the molecule and the leads plays an important role, which we investigate in relation to the total external charge in the context of electronegativity theory.

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

    PubMed

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

    2015-12-01

    The current state of the art in structural biology is led by NMR, X-ray crystallography and TEM investigations. These powerful tools however all rely on averaging over a large ensemble of molecules. Here, we present an alternative concept aiming at structural analysis at the single molecule level. We show that by combining electron holography and coherent diffraction imaging estimations concerning the phase of the scattered wave become needless as the phase information is extracted from the data directly and unambiguously. Performed with low-energy electrons the resolution of this lens-less microscope is just limited by the De Broglie wavelength of the electron wave and the numerical aperture, given by detector geometry. In imaging freestanding graphene, a resolution of 2Å has been achieved revealing the 660.000 unit cells of the graphene sheet from a single data set. Once applied to individual biomolecules the method shall ultimately allow for non-destructive imaging and imports the potential to distinguish between different conformations of proteins with atomic resolution. PMID:25687733

  11. Density functional theory based direct comparison of coherent tunneling and electron hopping in redox-active single-molecule junctions

    NASA Astrophysics Data System (ADS)

    Kastlunger, Georg; Stadler, Robert

    2015-03-01

    To define the conductance of single-molecule junctions with a redox functionality in an electrochemical cell, two conceptually different electron transport mechanisms, namely, coherent tunneling and vibrationally induced hopping, compete with each other, where implicit parameters of the setup such as the length of the molecule and the applied gate voltage decide which mechanism is the dominant one. Although coherent tunneling is most efficiently described within Landauer theory and the common theoretical treatment of electron hopping is based on Marcus theory, both theories are adequate for the processes they describe without introducing accuracy-limiting approximations. For a direct comparison, however, it has to be ensured that the crucial quantities obtained from electronic structure calculations, i.e., the transmission function T (E ) in Landauer theory and the transfer integral V , the reorganization energy ? , and the driving force ? G0 in Marcus theory, are derived from similar grounds, as pointed out by Nitzan and coworkers in a series of publications. In this paper our framework is a single-particle picture, for which we perform density functional theory calculations for the conductance corresponding to both transport mechanisms for junctions with the central molecule containing one, two, or three Ruthenium centers, from which we extrapolate our results in order to define the critical length of the transition point of the two regimes which we identify at 5.76nm for this type of molecular wire. We also discuss trends in the dependence on an electrochemically induced gate potential.

  12. Controlling Quantum Transport through a Single Molecule

    E-print Network

    Stafford, Charles

    Controlling Quantum Transport through a Single Molecule David M. Cardamone,* Charles A. Stafford the Aharanov-Bohm effect;8 however, for nanoscale devices such as single molecules, this is impractical due. Electronic mail: David_Cardamone@sfu.ca. Present address: Department of Physics, Simon Fraser University, BC

  13. 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.

  14. Probing single molecule dynamics

    SciTech Connect

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

    1994-07-15

    The room temperature dynamics of single sulforhodamine 101 molecules dispersed on a glass surface are investigated on two different time scales with near-field optics. On the 10[sup [minus]2] - to 10[sup 2]-second time scale, intensity fluctuations in the emission from single molecules are examined with polarization measurements, providing insight into their spectroscopic properties. On the nanosecond time scale, the fluorescence lifetimes of single molecules are measured, and their excited-state energy transfer to the aluminum coating of the near-field probe is characterized. A movie of the time-resolved emission demonstrates the feasibility of fluorescence lifetime imaging with single molecule sensitivity, picosecond temporal resolution, and a spatial resolving power beyond the diffraction limit.

  15. Electron and heat transport in porphyrin-based single-molecule transistors with electro-burnt graphene electrodes

    PubMed Central

    Sangtarash, Sara

    2015-01-01

    Summary We have studied the charge and thermal transport properties of a porphyrin-based single-molecule transistor with electro-burnt graphene electrodes (EBG) using the nonequilibrium Green’s function method and density functional theory. The porphyrin-based molecule is bound to the EBG electrodes by planar aromatic anchor groups. Due to the efficient ?–? overlap between the anchor groups and graphene and the location of frontier orbitals relative to the EBG Fermi energy, we predict HOMO-dominated transport. An on–off ratio as high as 150 is predicted for the device, which could be utilized with small gate voltages in the range of ±0.1 V. A positive thermopower of +280 ?V/K is predicted for the device at the theoretical Fermi energy. The sign of the thermopower could be changed by tuning the Fermi energy. By gating the junction and changing the Fermi energy by +10 meV, this can be further enhanced to +475 ?V/K. Although the electrodes and molecule are symmetric, the junction itself can be asymmetric due to different binding configurations at the electrodes. This can lead to rectification in the current–voltage characteristic of the junction. PMID:26199845

  16. Single Molecule Manipulation

    NASA Astrophysics Data System (ADS)

    Kiang, Ching-Hwa

    2011-10-01

    Single-molecule manipulation studies open a door for a close-up investigation of complex biological interactions at the molecular level. In these studies, single biomolecules are pulled while their force response is being monitored. The process is often nonequilibrium, and interpretation of the results has been challenging. We used the atomic force microscope to pull proteins and DNA, and determined the equilibrium properties of the molecules using the recently derived nonequilibrium work theorem. I will present applications of the technique in areas ranging from fundamental biological problems such as DNA mechanics, to complex medical processes such as the mechanical activation of von Willebrand Factor, a key protein in blood coagulation.

  17. Single-molecule Nanomagnets

    E-print Network

    Jonathan R. Friedman; Myriam P. Sarachik

    2010-08-04

    Single molecule magnets straddle the classical and quantum mechanical worlds, displaying many fascinating phenomena. They may have important technological applications in information storage and quantum computation. We review the physical properties of two prototypical molecular nanomagnets, Mn_12-acetate and Fe_8: each behaves as a rigid, spin-10 object, and exhibits tunneling between up and down directions. As temperature is lowered, the spin reversal process evolves from thermal activation to pure quantum tunneling. At low temperatures, magnetic avalanches occur in which the magnetization of an entire sample rapidly reverses. We discuss the important role that symmetry-breaking fields play in driving tunneling and in producing Berry-phase interference. Recent experimental advances indicate that quantum coherence can be maintained on time scales sufficient to allow a meaningful number of quantum computing operations to be performed. Efforts are underway to create monolayers and to address and manipulate individual molecules.

  18. 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.

  19. Single Molecule Recordings of Lysozyme Activity

    PubMed Central

    Choi, Yongki; Weiss, Gregory A.

    2013-01-01

    Single molecule bioelectronic circuits provide an opportunity to study chemical kinetics and kinetic variability with bond-by-bond resolution. To demonstrate this approach, we examined the catalytic activity of T4 lysozyme processing peptidoglycan substrates. Monitoring a single lysozyme molecule through changes in a circuit’s conductance helped elucidate unexplored and previously invisible aspects of lysozyme’s catalytic mechanism and demonstrated lysozyme to be a processive enzyme governed by 9 independent time constants. The variation of each time constant with pH or substrate crosslinking provided different insights into catalytic activity and dynamic disorder. Overall, ten lysozyme variants were synthesized and tested in single molecule circuits to dissect the transduction of chemical activity into electronic signals. Measurements show that a single amino acid with the appropriate properties is sufficient for good signal generation, proving that the single molecule circuit technique can be easily extended to other proteins. PMID:23752924

  20. Ultrafast dynamics of single molecules.

    PubMed

    Brinks, Daan; Hildner, Richard; van Dijk, Erik M H P; Stefani, Fernando D; Nieder, Jana B; Hernando, Jordi; van Hulst, Niek F

    2014-04-21

    The detection of individual molecules has found widespread application in molecular biology, photochemistry, polymer chemistry, quantum optics and super-resolution microscopy. Tracking of an individual molecule in time has allowed identifying discrete molecular photodynamic steps, action of molecular motors, protein folding, diffusion, etc. down to the picosecond level. However, methods to study the ultrafast electronic and vibrational molecular dynamics at the level of individual molecules have emerged only recently. In this review we present several examples of femtosecond single molecule spectroscopy. Starting with basic pump-probe spectroscopy in a confocal detection scheme, we move towards deterministic coherent control approaches using pulse shapers and ultra-broad band laser systems. We present the detection of both electronic and vibrational femtosecond dynamics of individual fluorophores at room temperature, showing electronic (de)coherence, vibrational wavepacket interference and quantum control. Finally, two colour phase shaping applied to photosynthetic light-harvesting complexes is presented, which allows investigation of the persistent coherence in photosynthetic complexes under physiological conditions at the level of individual complexes. PMID:24473271

  1. 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.

  2. Diamond based single molecule magnetic resonance spectroscopy

    E-print Network

    Jianming Cai; Fedor Jelezko; Martin B. Plenio; Alex Retzker

    2012-12-07

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

  3. Nanodevices for Single Molecule Studies

    NASA Astrophysics Data System (ADS)

    Craighead, H. G.; Stavis, S. M.; Samiee, K. T.

    During the last two decades, biotechnology research has resulted in progress in fields as diverse as the life sciences, agriculture and healthcare. While existing technology enables the analysis of a variety of biological systems, new tools are needed for increasing the efficiency of current methods, and for developing new ones altogether. Interest has grown in single molecule analysis for these reasons.

  4. Characterization of interfacial reactions in magnetite tunnel junctions with transmission electron microscopy

    E-print Network

    Laughlin, David E.

    transmission electron microscopy and x-ray energy dispersive spectroscopy to investigate the interfacial fully understood. Since high resolution transmission electron microscopy HRTEM has the abilityCharacterization of interfacial reactions in magnetite tunnel junctions with transmission electron

  5. 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

  6. 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

  7. Impact of Anchoring Groups on Ballistic Transport: Single Molecule vs Monolayer Junctions

    PubMed Central

    2015-01-01

    Tuning the transport properties of molecular junctions by chemically modifying the molecular structure is one of the key challenges for advancing the field of molecular electronics. In the present contribution, we investigate current–voltage characteristics of differently linked metal–molecule–metal systems that comprise either a single molecule or a molecular assembly. This is achieved by employing density functional theory in conjunction with a Green’s function approach. We show that the conductance of a molecular system with a specific anchoring group is fundamentally different depending on whether a single molecule or a continuous monolayer forms the junction. This is a consequence of collective electrostatic effects that arise from dipolar elements contained in the monolayer and from interfacial charge rearrangements. As a consequence of these collective effects, the “ideal” choice for an anchoring group is clearly different for monolayer and single molecule devices. A particularly striking effect is observed for pyridine-docked systems. These are subject to Fermi-level pinning at high molecular packing densities, causing an abrupt increase of the junction current already at small voltages. PMID:26401191

  8. Introduction to Single-Molecule Transistor

    NASA Astrophysics Data System (ADS)

    Nishijima, Mitsuaki

    Experimental and theoretical studies on the 2-terminal systems, which are related with a (3-terminal) single-molecule transistor, are reviewed. The measured current- bias-voltage (I-V) characteristics for the representative molecules are compared with the ab initio calculations. Molecular-vibration-induced loss of coherence and the change of the electron-transport mechanism are discussed. Mechanisms for rectification, negative differential resistance and switching of the 2-terminal systems are described. Shot-noise and thermopower studies are briefly mentioned.

  9. Single Molecule Detection, Analysis, and Manipulation

    E-print Network

    Walter, Nils G.

    : A Quasi-single Molecule Technique 5 5 Building Single Molecule Suspension Bridges: Optical Tweezers 5 6 and technologically critical information on the behavior of materials, the direct, real-time observation of single

  10. Mechanical studies on single molecules: general considerations

    NASA Astrophysics Data System (ADS)

    Bensimon, David; Croquette, Vincent

    2015-10-01

    The following sections are included: * Elements of molecular biology * Advantages and drawbacks of single molecule studies * Order of magnitude of the relevant parameters at the single molecule level * Single molecule manipulation techniques * Comparison of the different techniques * DNA mechanical properties * Conclusion * Bibliography

  11. Nanometer Resolution Imaging by SIngle Molecule Switching

    SciTech Connect

    Hu, Dehong; Orr, Galya

    2010-04-02

    The fluorescence intensity of single molecules can change dramatically even under constant laser excitation. The phenomenon is frequently called "blinking" and involves molecules switching between high and low intensity states.[1-3] In additional to spontaneous blinking, the fluorescence of some special fluorophores, such as cyanine dyes and photoactivatable fluorescent proteins, can be switched on and off by choice using a second laser. Recent single-molecule spectroscopy investigations have shed light on mechanisms of single molecule blinking and photoswitching. This ability to controllably switch single molecules led to the invention of a novel fluorescence microscopy with nanometer spatial resolution well beyond the diffraction limit.

  12. Single Molecule Studies of Chromatin

    SciTech Connect

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

    2006-02-06

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

  13. 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.

  14. Single Molecule Probes of Lipid Membrane Structure

    E-print Network

    Livanec, Philip W.

    2009-12-14

    structural metrics with function in biological membranes. Single-molecule fluorescence studies were used to measure membrane structure at the molecular level. Several groups have shown that polarized total internal reflection fluorescence microscopy (PTIRF...

  15. Ligand ?-radical interaction with f-shell unpaired electrons in phthalocyaninato-lanthanoid single-molecule magnets: a solution NMR spectroscopic and DFT study.

    PubMed

    Damjanovi?, Marko; Morita, Takaumi; Katoh, Keiichi; Yamashita, Masahiro; Enders, Markus

    2015-10-01

    The phthalocyaninato double-decker complexes [M(obPc)2 ](0) (M= Y(III) , Tb(III) , Dy(III) ; obPc=2,3,9,10,16,17,23,24-octabutoxyphthalocyaninato), along with their reduced ([M(obPc)2 ](-) [P(Ph)4 ](+) ; M=Tb(III) , Dy(III) ) and oxidized ([M(obPc)2 ](+) [SbCl6 ](-) (M=Y(III) , Tb(III) ) counterparts were studied with (1) H, (13) C and 2D NMR. From the NMR data of the neutral (i.e., with one unpaired electron in the ligands) and anionic Tb(III) complexes, along with the use of dispersion corrected DFT methods, it was possible to separate the metal-centered and ligand-centered contributions to the hyperfine NMR shift. These contributions to the (1) H and (13) C hyperfine NMR shifts were further analyzed in terms of pseudocontact and Fermi contact shifts. Furthermore, from a combination of NMR data and DFT calculations, we have determined the spin multiplicity of the neutral complexes [M(obPc)2 ](0) (M=Tb(III) and Dy(III) ) at room temperature. From the NMR data of the cationic Tb(III) complex, for which actually no experimental structure determination is available, we have analyzed the structural changes induced by oxidation from its neutral/anionic species and shown that the interligand distance decreases upon oxidation. The fast electron exchange process between the neutral and anionic Tb(III) double-decker complexes was also studied. PMID:26288225

  16. Quantitative Aspects of Single Molecule Microscopy

    PubMed Central

    Ober, Raimund J.; Tahmasbi, Amir; Ram, Sripad; Lin, Zhiping; Ward, E. Sally

    2015-01-01

    Single molecule microscopy is a relatively new optical microscopy technique that allows the detection of individual molecules such as proteins in a cellular context. This technique has generated significant interest among biologists, biophysicists and biochemists, as it holds the promise to provide novel insights into subcellular processes and structures that otherwise cannot be gained through traditional experimental approaches. Single molecule experiments place stringent demands on experimental and algorithmic tools due to the low signal levels and the presence of significant extraneous noise sources. Consequently, this has necessitated the use of advanced statistical signal and image processing techniques for the design and analysis of single molecule experiments. In this tutorial paper, we provide an overview of single molecule microscopy from early works to current applications and challenges. Specific emphasis will be on the quantitative aspects of this imaging modality, in particular single molecule localization and resolvability, which will be discussed from an information theoretic perspective. We review the stochastic framework for image formation, different types of estimation techniques and expressions for the Fisher information matrix. We also discuss several open problems in the field that demand highly non-trivial signal processing algorithms. PMID:26167102

  17. 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

  18. 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.

  19. Single-molecule methods to quantify adsorptive separations (Presentation Recording)

    NASA Astrophysics Data System (ADS)

    Landes, Christy

    2015-08-01

    Interfacial adsorption and transport are the chemical and physical processes that underlie separations. Although separations technology accounts for hundreds of billions of dollars in the global economy, the process is not well-understood at the mechanistic level and instead is almost always optimized empirically. One of the reasons is that access to the underlying molecular phenomena has only been available recently via single-molecule methods. There are still interesting challenges because adsorption, desorption, and transport are all dynamic processes, whereas much of the advances in super-resolution imaging have focused on imaging static materials. Our lab has focused in recent years on developing and optimizing data analysis methods for quantifying the dynamics of adsorption and transport in porous materials at nanometer-resolution spatial scales. Our methods include maximizing information content in dynamic single-molecule data and developing methods to detect change-points in binned data. My talk will outline these methods, and will address how and when they can be applied to extract dynamic details in heterogeneous materials such as porous membranes.

  20. Susanta Kumar Sarkar Single Molecule Biophysics Laboratory

    E-print Network

    fluorescence. Biomedical Optics Express 5(4), 1190­1202 (2014). Equal contributions. Patent filed by NIH. US. Single-Molecule Fluorescence. Cell 153(6):1408-1408.e1 (2013). 4. Ambika Bumb, Susanta K. Sarkar, Martin filed by NIH. US Application Serial No. 61/672996. 5. Arthur Z. Eisen, Susanta K. Sarkar, Keir C. Neuman

  1. 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.

  2. 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.

  3. Heterogeneity in Single-Molecule Observables

    E-print Network

    Kaufman, Laura

    transition temperature 1. INTRODUCTION Optical single-molecule (SM) techniques emerged more than 20 years ago with experiments mon- itoring single probe molecule behavior in solids at cryogenic temperatures (1, 2-field microscopy. These techniques have been most widely used to investigate the properties and behavior

  4. 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.

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

    SciTech Connect

    Deuis, R.L.; Subramanian, C.; Bee, J.V.

    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.

  6. Single-molecule Studies of Riboswitch Folding

    PubMed Central

    Savinov, Andrew; Perez, Christian F.; Block, Steven M.

    2014-01-01

    The folding dynamics of riboswitches are central to their ability to modulate gene expression in response to environmental cues. In most cases, a structural competition between the formation of a ligand-binding aptamer and an expression platform (or some other competing off-state) determines the regulatory outcome. Here, we review single-molecule studies of riboswitch folding and function, predominantly carried out using single-molecule FRET or optical trapping approaches. Recent results have supplied new insights into riboswitch folding energy landscapes, the mechanisms of ligand binding, the roles played by divalent ions, the applicability of hierarchical folding models, and kinetic vs. thermodynamic control schemes. We anticipate that future work, based on improved data sets and potentially combining multiple experimental techniques, will enable the development of more complete models for complex RNA folding processes. PMID:24727093

  7. Single molecule transcription profiling with AFM

    NASA Astrophysics Data System (ADS)

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

    2007-01-01

    Established techniques for global gene expression profiling, such as microarrays, face fundamental sensitivity constraints. Due to greatly increasing interest in examining minute samples from micro-dissected tissues, including single cells, unorthodox approaches, including molecular nanotechnologies, are being explored in this application. Here, we examine the use of single molecule, ordered restriction mapping, combined with AFM, to measure gene transcription levels from very low abundance samples. We frame the problem mathematically, using coding theory, and present an analysis of the critical error sources that may serve as a guide to designing future studies. We follow with experiments detailing the construction of high density, single molecule, ordered restriction maps from plasmids and from cDNA molecules, using two different enzymes, a result not previously reported. We discuss these results in the context of our calculations. Based on invited talk at the International Conference on Nanoscience and Technology 2006.

  8. Automated imaging system for single molecules

    DOEpatents

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

    2012-09-18

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

  9. Single-Molecule Imaging of Cellular Signaling

    NASA Astrophysics Data System (ADS)

    De Keijzer, Sandra; Snaar-Jagalska, B. Ewa; Spaink, Herman P.; Schmidt, Thomas

    Single-molecule microscopy is an emerging technique to understand the function of a protein in the context of its natural environment. In our laboratory this technique has been used to study the dynamics of signal transduction in vivo. A multitude of signal transduction cascades are initiated by interactions between proteins in the plasma membrane. These cascades start by binding a ligand to its receptor, thereby activating downstream signaling pathways which finally result in complex cellular responses. To fully understand these processes it is important to study the initial steps of the signaling cascades. Standard biological assays mostly call for overexpression of the proteins and high concentrations of ligand. This sets severe limits to the interpretation of, for instance, the time-course of the observations, given the large temporal spread caused by the diffusion-limited binding processes. Methods and limitations of single-molecule microscopy for the study of cell signaling are discussed on the example of the chemotactic signaling of the slime-mold Dictyostelium discoideum. Single-molecule studies, as reviewed in this chapter, appear to be one of the essential methodologies for the full spatiotemporal clarification of cellular signaling, one of the ultimate goals in cell biology.

  10. Trapping and manipulating single molecules of DNA

    NASA Astrophysics Data System (ADS)

    Shon, Min Ju

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

  11. Hybrid photodetector for single-molecule spectroscopy and microscopy

    PubMed Central

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

    2011-01-01

    We report benchmark tests of a new single-photon counting detector based on a GaAsP photocathode and an electron-bombarded avalanche photodiode developed by Hamamatsu Photonics. We compare its performance with those of standard Geiger-mode avalanche photodiodes. We show its advantages for FCS due to the absence of after-pulsing and for fluorescence lifetime measurements due to its excellent time resolution. Its large sensitive area also greatly simplifies setup alignment. Its spectral sensitivity being similar to that of recently introduced CMOS SPADs, this new detector could become a valuable tool for single-molecule fluorescence measurements, as well as for many other applications. PMID:21822361

  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. Hafnium metallocene compounds used as cathode interfacial layers for enhanced electron transfer in organic solar cells

    NASA Astrophysics Data System (ADS)

    Park, Keunhee; Oh, Seungsik; Jung, Donggeun; Chae, Heeyeop; Kim, Hyoungsub; Boo, Jin-Hyo

    2012-01-01

    We have used hafnium metallocene compounds as cathode interfacial layers for organic solar cells [OSCs]. A metallocene compound consists of a transition metal and two cyclopentadienyl ligands coordinated in a sandwich structure. For the fabrication of the OSCs, poly[3,4-ethylenedioxythiophene]:poly(styrene sulfonate), poly(3-hexylthiophene-2,5-diyl) + [6, 6]-phenyl C61 butyric acid methyl ester, bis-(ethylcyclopentadienyl)hafnium(IV) dichloride, and aluminum were deposited as a hole transport layer, an active layer, a cathode interfacial layer, and a cathode, respectively. The hafnium metallocene compound cathode interfacial layer improved the performance of OSCs compared to that of OSCs without the interfacial layer. The current density-voltage characteristics of OSCs with an interfacial layer thickness of 0.7 nm and of those without an interfacial layer showed power conversion efficiency [PCE] values of 2.96% and 2.34%, respectively, under an illumination condition of 100 mW/cm2 (AM 1.5). It is thought that a cathode interfacial layer of an appropriate thickness enhances the electron transfer between the active layer and the cathode, and thus increases the PCE of the OSCs.

  14. Hafnium metallocene compounds used as cathode interfacial layers for enhanced electron transfer in organic solar cells

    PubMed Central

    2012-01-01

    We have used hafnium metallocene compounds as cathode interfacial layers for organic solar cells [OSCs]. A metallocene compound consists of a transition metal and two cyclopentadienyl ligands coordinated in a sandwich structure. For the fabrication of the OSCs, poly[3,4-ethylenedioxythiophene]:poly(styrene sulfonate), poly(3-hexylthiophene-2,5-diyl) + [6,6]-phenyl C61 butyric acid methyl ester, bis-(ethylcyclopentadienyl)hafnium(IV) dichloride, and aluminum were deposited as a hole transport layer, an active layer, a cathode interfacial layer, and a cathode, respectively. The hafnium metallocene compound cathode interfacial layer improved the performance of OSCs compared to that of OSCs without the interfacial layer. The current density-voltage characteristics of OSCs with an interfacial layer thickness of 0.7 nm and of those without an interfacial layer showed power conversion efficiency [PCE] values of 2.96% and 2.34%, respectively, under an illumination condition of 100 mW/cm2 (AM 1.5). It is thought that a cathode interfacial layer of an appropriate thickness enhances the electron transfer between the active layer and the cathode, and thus increases the PCE of the OSCs. PMID:22230259

  15. Hafnium metallocene compounds used as cathode interfacial layers for enhanced electron transfer in organic solar cells.

    PubMed

    Park, Keunhee; Oh, Seungsik; Jung, Donggeun; Chae, Heeyeop; Kim, Hyoungsub; Boo, Jin-Hyo

    2012-01-01

    We have used hafnium metallocene compounds as cathode interfacial layers for organic solar cells [OSCs]. A metallocene compound consists of a transition metal and two cyclopentadienyl ligands coordinated in a sandwich structure. For the fabrication of the OSCs, poly[3,4-ethylenedioxythiophene]:poly(styrene sulfonate), poly(3-hexylthiophene-2,5-diyl) + 66-phenyl C61 butyric acid methyl ester, bis-(ethylcyclopentadienyl)hafnium(IV) dichloride, and aluminum were deposited as a hole transport layer, an active layer, a cathode interfacial layer, and a cathode, respectively. The hafnium metallocene compound cathode interfacial layer improved the performance of OSCs compared to that of OSCs without the interfacial layer. The current density-voltage characteristics of OSCs with an interfacial layer thickness of 0.7 nm and of those without an interfacial layer showed power conversion efficiency [PCE] values of 2.96% and 2.34%, respectively, under an illumination condition of 100 mW/cm2 (AM 1.5). It is thought that a cathode interfacial layer of an appropriate thickness enhances the electron transfer between the active layer and the cathode, and thus increases the PCE of the OSCs. PMID:22230259

  16. Single molecule microscopy and spectroscopy: concluding remarks.

    PubMed

    van Hulst, Niek F

    2015-12-12

    Chemistry is all about molecules: control, synthesis, interaction and reaction of molecules. All too easily on a blackboard, one draws molecules, their structures and dynamics, to create an insightful picture. The dream is to see these molecules in reality. This is exactly what "Single Molecule Detection" provides: a look at molecules in action at ambient conditions; a breakthrough technology in chemistry, physics and biology. Within the realms of the Royal Society of Chemistry, the Faraday Discussion on "Single Molecule Microscopy and Spectroscopy" was a very appropriate topic for presentation, deliberation and debate. Undoubtedly, the Faraday Discussions have a splendid reputation in stimulating scientific debates along the traditions set by Michael Faraday. Interestingly, back in the 1830's, Faraday himself pursued an experiment that led to the idea that atoms in a compound were joined by an electrical component. He placed two opposite electrodes in a solution of water containing a dissolved compound, and observed that one of the elements of the compound accumulated on one electrode, while the other was deposited on the opposite electrode. Although Faraday was deeply opposed to atomism, he had to recognize that electrical forces were responsible for the joining of atoms. Probably a direct view on the atoms or molecules in his experiment would have convinced him. As such, Michael Faraday might have liked the gathering at Burlington House in September 2015 (). Surely, with the questioning eyes of his bust on the 1(st) floor corridor, the non-believer Michael Faraday has incited each passer-by to enter into discussion and search for deeper answers at the level of single molecules. In these concluding remarks, highlights of the presented papers and discussions are summarized, complemented by a conclusion on future perspectives. PMID:26606461

  17. Single-molecule electrophoresis. Final report

    SciTech Connect

    Castro, A.; Shera, E.B.

    1996-05-22

    A novel method for the detection and identification of single molecules in solution has been devised, computer-simulated, and experimentally achieved. The technique involves the determination of electrophoretic velocities by measuring the time required by individual molecules to travel a fixed distance between two laser beams. Computer simulations of the process were performed beforehand in order to estimate the experimental feasibility of the method, and to determine the optimum values for the various experimental parameters. Examples of the use of the technique for the ultrasensitive detection and identification of rhodamine-6G, a mixture of DNA restriction fragments, and a mixture of proteins in aqueous solution are presented.

  18. Nanofabrication of electrodes with sub-5 nm spacing for transport experiments on single molecules and metal clusters

    E-print Network

    Nanofabrication of electrodes with sub-5 nm spacing for transport experiments on single molecules electrical transport properties of single molecules e.g., conjugated polymers or metal nanoclusters- tractive direction for the future development of electronic devices for several reasons. It conceptually

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

    PubMed

    Cui, Ajuan; Dong, Huanli; Hu, Wenping

    2015-12-01

    With the establishment of complementary metal-oxide-semiconductor (CMOS)-based integrated circuit technology, it has become more difficult to follow Moore's law to further downscale the size of electronic components. Devices based on various nanostructures were constructed to continue the trend in the minimization of electronics, and molecular devices are among the most promising candidates. Compared with other candidates, molecular devices show unique superiorities, and intensive studies on molecular devices have been carried out both experimentally and theoretically at the present time. Compared to two-terminal molecular devices, three-terminal devices, namely single-molecule transistors, show unique advantages both in fundamental research and application and are considered to be an essential part of integrated circuits based on molecular devices. However, it is very difficult to construct them using the traditional microfabrication techniques directly, thus new fabrication strategies are developed. This review aims to provide an exclusive way of manufacturing solid state gated nanogap electrodes, the foundation of constructing transistors of single or a few molecules. Such single-molecule transistors have the potential to be used to build integrated circuits. PMID:26450402

  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. Visualizing electromagnetic fields at the nanoscale by single molecule localization.

    PubMed

    Steuwe, Christian; Erdelyi, Miklos; Szekeres, G; Csete, M; Baumberg, Jeremy J; Mahajan, Sumeet; Kaminski, Clemens F

    2015-05-13

    Coupling of light to the free electrons at metallic surfaces allows the confinement of electric fields to subwavelength dimensions, far below the optical diffraction limit. While this is routinely used to manipulate light at the nanoscale, in electro-optic devices and enhanced spectroscopic techniques, no characterization technique for imaging the underlying nanoscopic electromagnetic fields exists, which does not perturb the field or employ complex electron beam imaging. Here, we demonstrate the direct visualization of electromagnetic fields on patterned metallic substrates at nanometer resolution, exploiting a strong "autonomous" fluorescence-blinking behavior of single molecules within the confined fields allowing their localization. Use of DNA-constructs for precise positioning of fluorescence dyes on the surface induces this distance-dependent autonomous blinking thus completely obviating the need for exogenous agents or switching methods. Mapping such electromagnetic field distributions at nanometer resolution aids the rational design of nanometals for diverse photonic applications. PMID:25915093

  2. Reversible Tuning of Interfacial and Intramolecular Charge Transfer in Individual MnPc Molecules.

    PubMed

    Zhong, Jian-Qiang; Wang, Zhunzhun; Zhang, Jia Lin; Wright, Christopher A; Yuan, Kaidi; Gu, Chengding; Tadich, Anton; Qi, Dongchen; Li, He Xing; Lai, Min; Wu, Kai; Xu, Guo Qin; Hu, Wenping; Li, Zhenyu; Chen, Wei

    2015-12-01

    The reversible selective hydrogenation and dehydrogenation of individual manganese phthalocyanine (MnPc) molecules has been investigated using photoelectron spectroscopy (PES), low-temperature scanning tunneling microscopy (LT-STM), synchrotron-based near edge X-ray absorption fine structure (NEXAFS) measurements, and supported by density functional theory (DFT) calculations. It is shown conclusively that interfacial and intramolecular charge transfer arises during the hydrogenation process. The electronic energetics upon hydrogenation is identified, enabling a greater understanding of interfacial and intramolecular charge transportation in the field of single-molecule electronics. PMID:26528623

  3. Single-molecule, single-particle fluorescence imaging of TiO2-based photocatalytic reactions.

    PubMed

    Tachikawa, Takashi; Majima, Tetsuro

    2010-12-01

    Nanostructured metal oxide semiconductors, such as TiO(2) and ZnO, have attracted great attention as the promising material for photovoltaic devices, photocatalysts for water splitting and environmental purification, sensors, batteries, etc. In this critical review, we have focused on the on-site observation of interfacial chemical reactions involving charge carriers and reactive oxygen species (ROS), such as singlet oxygen and the hydroxyl radical, generated by the photoexcitation of TiO(2) nanoparticles using single-molecule, single-particle fluorescence spectroscopy. Advanced fluorescence imaging techniques enable us to determine the location of the photocatalytically active sites that are closely related to the defects heterogeneously distributed on the surface. Consequently, this review provides a great opportunity to understand the temporal and spatial heterogeneities within an individual catalyst particle, allowing for the potential use of single-molecule, single-particle approaches in the analysis of photocatalytic reactions (189 references). PMID:20824247

  4. Toward single-molecule nanomechanical mass spectrometry

    PubMed Central

    Naik, A. K.; Hanay, M. S.; Hiebert, W. K.; Feng, X. L.; Roukes, M. L.

    2009-01-01

    Mass spectrometry (MS) provides rapid and quantitative identification of protein species with relatively low sample consumption. Yet with the trend toward biological analysis at increasingly smaller scales, ultimately down to the volume of an individual cell, MS with few-to-single molecule sensitivity will be required. Nanoelectromechanical systems (NEMS) provide unparalleled mass sensitivity, which is now sufficient for the detection of individual molecular species in real time. Here we report the first demonstration of MS based on single-biological-molecule detection with NEMS. In our NEMS-MS system, nanoparticles and protein species are introduced by electrospray injection from fluid phase in ambient conditions into vacuum and subsequently delivered to the NEMS detector by hexapole ion optics. Precipitous frequency shifts, proportional to the mass, are recorded in real time as analytes adsorb, one-by-one, onto a phase-locked, ultrahigh frequency NEMS resonator. These first NEMS-MS spectra, obtained with modest mass sensitivity from only several hundred mass adsorption events, presage the future capabilities of this approach. We also outline the substantial improvements that are feasible in the near term, some of which are unique to NEMS-MS. PMID:19581898

  5. 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

  6. Nonlinear coherent spectroscopy in the single molecule limit (Presentation Recording)

    NASA Astrophysics Data System (ADS)

    Potma, Eric O.

    2015-10-01

    Detecting coherent anti-Stokes Raman scattering (CARS) signals from signal molecules is a longstanding experimental challenge. Driving the vibrational CARS response with surface plasmon fields has proven notoriously difficult due to strong background contributions, unfavorable heat dissipation and the phase dispersion of the plasmon modes in the ensemble. In this work we overcome previous experimental limitations and demonstrate time-resolved, vibrational CARS from molecules in the low copy number limit, down to the single molecule level. Our measurements, which are performed under ambient and non-electronic resonance conditions, establish that the coherent response from vibrational modes of individual molecules can be studied experimentally, opening up a new realm of molecular spectroscopic investigations.

  7. Single-molecule chemical reactions on DNA origami

    NASA Astrophysics Data System (ADS)

    Voigt, Niels V.; Tørring, Thomas; Rotaru, Alexandru; Jacobsen, Mikkel F.; Ravnsbæk, Jens B.; Subramani, Ramesh; Mamdouh, Wael; Kjems, Jørgen; Mokhir, Andriy; Besenbacher, Flemming; Gothelf, Kurt Vesterager

    2010-03-01

    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 into DNA nanostructures and imaged. Here, we show that chemical reactions with single molecules can be performed and imaged at a local position on a DNA origami scaffold by atomic force microscopy. The high yields and chemoselectivities of successive cleavage and bond-forming reactions observed in these experiments demonstrate the feasibility of post-assembly chemical modification of DNA nanostructures and their potential use as locally addressable solid supports.

  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. From single molecule to single tubules

    NASA Astrophysics Data System (ADS)

    Guo, Chin-Lin

    2012-02-01

    Biological systems often make decisions upon conformational changes and assembly of single molecules. In vivo, epithelial cells (such as the mammary gland cells) can respond to extracellular matrix (ECM) molecules, type I collagen (COL), and switch their morphology from a lobular lumen (100-200 micron) to a tubular lumen (1mm-1cm). However, how cells make such a morphogenetic decision through interactions with each other and with COL is unclear. Using a temporal control of cell-ECM interaction, we find that epithelial cells, in response to a fine-tuned percentage of type I collagen (COL) in ECM, develop various linear patterns. Remarkably, these patterns allow cells to self-assemble into a tubule of length ˜ 1cm and diameter ˜ 400 micron in the liquid phase (i.e., scaffold-free conditions). In contrast with conventional thought, the linear patterns arise through bi-directional transmission of traction force, but not through diffusible biochemical factors secreted by cells. In turn, the transmission of force evokes a long-range (˜ 600 micron) intercellular mechanical interaction. A feedback effect is encountered when the mechanical interaction modifies cell positioning and COL alignment. Micro-patterning experiments further reveal that such a feedback is a novel cell-number-dependent, rich-get-richer process, which allows cells to integrate mechanical interactions into long-range (> 1mm) linear coordination. Our results suggest a mechanism cells can use to form and coordinate long-range tubular patterns, independent of those controlled by diffusible biochemical factors, and provide a new strategy to engineer/regenerate epithelial organs using scaffold-free self-assembly methods.

  10. Action spectroscopy for single-molecule reactions - Experiments and theory

    NASA Astrophysics Data System (ADS)

    Kim, Y.; Motobayashi, K.; Frederiksen, T.; Ueba, H.; Kawai, M.

    2015-05-01

    We review several representative experimental results of action spectroscopy (AS) of single molecules on metal surfaces using a scanning tunneling microscope (STM) by M. Kawai's group over last decade. The experimental procedures to observe STM-AS are described. A brief description of a low-temperature STM and experimental setup are followed by key experimental techniques of how to determine an onset bias voltage of a reaction and how to measure a current change associated with reactions and finally how to observe AS for single molecule reactions. The experimental results are presented for vibrationally mediated chemical transformation of trans-2-butene to 1.3-butadiene molecule and rotational motion of a single cis-2-butene molecule among four equivalent orientations on Pd(1 1 0). The AS obtained from the motion clearly detects more vibrational modes than inelastic electron tunneling spectroscopy with an STM. AS is demonstrated as a useful and novel single molecule vibrational spectroscopy. The AS for a lateral hopping of water dimer on Pt(1 1 1) is presented as an example of novelty. Several distinct vibrational modes are detected as the thresholds in the AS. The assignment of the vibrational modes determined from the analysis of the AS is made from a view of the adsorption geometry of hydrogen-bond donor or acceptor molecules in water dimer. A generic theory of STM-AS, i.e., a reaction rate or yield as a function of bias voltage, is presented using a single adsorbate resonance model for single molecule reactions induced by the inelastic tunneling current. Formulas for the reaction rate R (V) and Y (V) , i.e., reaction yield per electron Y (V) = eR (V) / I are derived. It provides a versatile framework to analyze any vibrationally mediated reactions of single adsorbates on metal surfaces. Numerical examples are presented to demonstrate generic features of the vibrational generation rate and Y (V) at different levels of approximations and to show how the effective broadening of the vibrational density of states (as described by Gaussian or Lorentzian functions) manifest themselves in Y (V) near the threshold bias voltage corresponding to a vibrational excitation responsible for reactions. A prefactor of Y (V) is explicitly derived for various types of elementary processes. Our generic formula of Y (V) also underlines the need to observe Y (V) at both bias voltage polarities, which can provide additional insight into the adsorbate projected density of states near the Fermi level within a span of the vibrational energy. The theory is applied to analysis of some highlights of the experimental results: Xe transfer, hopping of a single CO molecule on Pd(1 1 0), a dissociation of a single dimethyl disulfide (CH3S)2 and a hopping of a dissociated product, i.e., single methyl thiolate CH3S on Cu(1 1 1). It underlines that an observation of Y (V) at both bias polarities permits us to certain insight into the molecular alignment with respect to the Fermi level.

  11. Coherent State Preparation and Observation of Rabi Oscillations in a Single Molecule

    E-print Network

    Ilja Gerhardt; Gert Wrigge; Gert Zumofen; Jaesuk Hwang; Alois Renn; Vahid Sandoghdar

    2008-11-02

    We report on the excitation of single molecules via narrow zero-phonon transitions using short laser pulses. By monitoring the Stokes-shifted fluorescence, we studied the excited state population as a function of the delay time, laser intensity, and frequency detuning. A pi-pulse excitation was demonstrated with merely 500 photons, and 5 Rabi cycles were achieved at higher excitation powers. Our findings are in good agreement with theoretical calculations and provide a first step toward coherent manipulation of the electronic states of single molecules with few photons.

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

    PubMed Central

    Kitaguchi, Yuya; Habuka, Satoru; Hatta, Shinichiro; Aruga, Tetsuya; Paulsson, Magnus; Ueba, Hiromu

    2015-01-01

    Summary Mechanical methods for single-molecule control have potential for wide application in nanodevices and machines. Here we demonstrate the operation of a single-molecule switch made functional by the motion of a phenyl ring, analogous to the lever in a conventional toggle switch. The switch can be actuated by dual triggers, either by a voltage pulse or by displacement of the electrode, and electronic manipulation of the ring by chemical substitution enables rational control of the on-state conductance. Owing to its simple mechanics, structural robustness, and chemical accessibility, we propose that phenyl rings are promising components in mechanical molecular devices. PMID:26665080

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

    PubMed

    Kitaguchi, Yuya; Habuka, Satoru; Okuyama, Hiroshi; Hatta, Shinichiro; Aruga, Tetsuya; Frederiksen, Thomas; Paulsson, Magnus; Ueba, Hiromu

    2015-01-01

    Mechanical methods for single-molecule control have potential for wide application in nanodevices and machines. Here we demonstrate the operation of a single-molecule switch made functional by the motion of a phenyl ring, analogous to the lever in a conventional toggle switch. The switch can be actuated by dual triggers, either by a voltage pulse or by displacement of the electrode, and electronic manipulation of the ring by chemical substitution enables rational control of the on-state conductance. Owing to its simple mechanics, structural robustness, and chemical accessibility, we propose that phenyl rings are promising components in mechanical molecular devices. PMID:26665080

  14. Supplementary Material Free energy recovery in single molecule experiments

    E-print Network

    Ritort, Felix

    Supplementary Material Free energy recovery in single molecule experiments Single molecule force measurements (experimental setup shown in Fig. S1) can be used to determine free-energy differences between the unfolding process and using the thermodynamic relation revWG = , we can estimate the RNA folding free energy

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

    E-print Network

    Borguet, Eric

    H- based electrical sensor requires that we wire a single tailored molecule into a circuit, in other words-molecule- based pH switch/sensor that exploits the sensitivity of dye molecules to environmental pH to build metal unit. The ultimate limit would be at the single-molecule level.[1,2] To build a single-molecule p

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

    E-print Network

    Borguet, Eric

    H- based electrical sensor requires that we wire a single tailored molecule into a circuit, in other words-molecule- based pH switch/sensor that exploits the sensitivity of dye molecules to environmental pH to build metal unit. The ultimate limit would be at the single-molecule level.[1,2] To build a single-molecule p

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

    SciTech Connect

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

    2014-08-07

    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.

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

    PubMed

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

    2015-02-01

    The ability to measure the properties of proteins at the single-molecule level offers an unparalleled glimpse into biological systems at the molecular scale. The interpretation of single-molecule time series has often been rooted in statistical mechanics and the theory of Markov processes. While existing analysis methods have been useful, they are not without significant limitations including problems of model selection and parameter nonidentifiability. To address these challenges, we introduce the use of nonparametric Bayesian inference for the analysis of single-molecule time series. These methods provide a flexible way to extract structure from data instead of assuming models beforehand. We demonstrate these methods with applications to several diverse settings in single-molecule biophysics. This approach provides a well-constrained and rigorously grounded method for determining the number of biophysical states underlying single-molecule data. PMID:25650922

  19. Single-Molecule Surface-Enhanced Raman Scattering: Can STEM/ EELS Image Electromagnetic Hot Spots?

    E-print Network

    Pennycook, Steve

    Single-Molecule Surface-Enhanced Raman Scattering: Can STEM/ EELS Image Electromagnetic Hot Spots-loss spectroscopy (EELS) in a scanning transmission electron microscope (STEM) to obtain maps of the localized, the STEM/EELS plasmon maps do not show any direct signature of an electromagnetic hot spot in the gaps

  20. 31 Kohn-Sham Master Equation Approach to Transport Through Single Molecules

    E-print Network

    Burke, Kieron

    31 Kohn-Sham Master Equation Approach to Transport Through Single Molecules R. Gebauer, K. Burke. Such junctions are expected to be at the basis of future molecular-based electronic devices. But apart from in general. The theoretical modeling of molecular transport, however, is a very chal- lenging task: On one

  1. Single-molecule spectroscopy and imaging over the decades.

    PubMed

    Moerner, W E; Shechtman, Yoav; Wang, Quan

    2015-12-12

    As of 2015, it has been 26 years since the first optical detection and spectroscopy of single molecules in condensed matter. This area of science has expanded far beyond the early low temperature studies in crystals to include single molecules in cells, polymers, and in solution. The early steps relied upon high-resolution spectroscopy of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral fine structure arising directly from the position-dependent fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989 using frequency-modulation laser spectroscopy. In the early 1990s, a variety of fascinating physical effects were observed for individual molecules, including imaging of the light from 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. In the room temperature regime, researchers showed that bursts of light from single molecules could be detected in solution, leading to imaging and microscopy by a variety of methods. Studies 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. All of these early steps provided important fundamentals underpinning the development of super-resolution microscopy based on single-molecule localization and active control of emitting concentration. Current thrust areas include extensions to three-dimensional imaging with high precision, orientational analysis of single molecules, and direct measurements of photodynamics and transport properties for single molecules trapped in solution by suppression of Brownian motion. Without question, a huge variety of studies of single molecules performed by many talented scientists all over the world have extended our knowledge of the nanoscale and many microscopic mechanisms previously hidden by ensemble averaging. PMID:26616210

  2. Real-time single-molecule observations of proteins at the solid-liquid interface

    NASA Astrophysics Data System (ADS)

    Langdon, Blake Brianna

    Non-specific protein adsorption to solid surfaces is pervasive and observed across a broad spectrum of applications including biomaterials, separations, pharmaceuticals, and biosensing. Despite great interest in and considerable literature dedicated to the phenomena, a mechanistic understanding of this complex phenomena is lacking and remains controversial, partially due to the limits of ensemble-averaging techniques used to study it. Single-molecule tracking (SMT) methods allow us to study distinct protein dynamics (e.g. adsorption, desorption, diffusion, and intermolecular associations) on a molecule-by-molecule basis revealing the protein population and spatial heterogeneity inherent in protein interfacial behavior. By employing single-molecule total internal reflection fluorescence microscopy (SM-TIRFM), we have developed SMT methods to directly observe protein interfacial dynamics at the solid-liquid interface to build a better mechanistic understanding of protein adsorption. First, we examined the effects of surface chemistry (e.g. hydrophobicity, hydrogen-bonding capacity), temperature, and electrostatics on isolated protein desorption and interfacial diffusion for fibrinogen (Fg) and bovine serum albumin (BSA). Next, we directly and indirectly probed the effects of protein-protein interactions on interfacial desorption, diffusion, aggregation, and surface spatial heterogeneity on model and polymeric thin films. These studies provided many useful insights into interfacial protein dynamics including the following observations. First, protein adsorption was reversible, with the majority of proteins desorbing from all surface chemistries within seconds. Isolated protein-surface interactions were relatively weak on both hydrophobic and hydrophilic surfaces (apparent desorption activation energies of only a few kBT). However, proteins could dynamically and reversibly associate at the interface, and these interfacial associations led to proteins remaining on the surface for longer time intervals. Surface chemistry and surface spatial heterogeneity (i.e. surface sites with different binding strengths) were shown to influence adsorption, desorption, and interfacial protein-protein associations. For example, faster protein diffusion on hydrophobic surfaces increased protein-protein associations and, at higher protein surface coverage, led to proteins remaining on hydrophobic surfaces longer than on hydrophilic surfaces. Ultimately these studies suggested that surface properties (chemistry, heterogeneity) influence not only protein-surface interactions but also interfacial mobility and protein-protein associations, implying that surfaces that better control protein adsorption can be designed by accounting for these processes.

  3. Interfacial Electron Transfer and Transient Photoconductivity Studied with Terahertz Spectroscopy

    NASA Astrophysics Data System (ADS)

    Milot, Rebecca Lee

    Terahertz spectroscopy is distinguished from other far infrared and millimeter wave spectroscopies by its inherent phase sensitivity and sub-picosecond time resolution making it a versatile technique to study a wide range of physical phenomena. As THz spectroscopy is still a relatively new field, many aspects of THz generation mechanisms have not been fully examined. Using terahertz emission spectroscopy (TES), THz emission from ZnTe(110) was analyzed and found to be limited by two-photon absorption and free-carrier generation at high excitation fluences. Due to concerns about the continued use of fossil fuels, solar energy has been widely investigated as a promising source of renewable energy. Dye-sensitized solar cells (DSSCs) have been developed as a low-cost alternative to conventional photovoltaic solar cells. To solve the issues of the intermittency and inefficient transport associated with solar energy, researchers are attempting to adapt DSSCs for water oxidation and chemical fuel production. Both device designs incorporate sensitizer molecules covalently bound to metal oxide nanoparticles. The sensitizer, which is comprised of a chromophore and anchoring group, absorbs light and transfers an electron from its excited state to the conduction band of the metal oxide, producing an electric current. Using time-resolved THz spectroscopy (TRTS), an optical pump/THz probe technique, the efficiency and dynamics of electron injection from sensitizers to metal oxides was evaluated as a function of the chromophore, its anchoring group, and the metal oxide identity. Experiments for studying fully functioning DSSCs and water oxidation devices are also described. Bio-inspired pentafluorophenyl porphyrin chromophores have been designed and synthesized for use in photoelectrochemical water oxidation cells. Influences on the efficiency and dynamics of electron injection from the chromophores into TiO2 and SnO2 nanoparticles due to changes in both the central substituent to the porphyrin ring and degree of fluorination of ring substituents were analyzed. Due to the high reduction potentials of these sensitizers, injection into TiO2 was generally not observed. Injection timescales from the porphyrins into SnO2 depended strongly on the identity of the central substituent and were affected by competition with excited-state deactivation processes. The carboxylate anchoring group is commonly used to bind DSSC sensitizers to metal oxide surfaces but is typically not stable under the aqueous and oxidative conditions required for water oxidation. Electron injection efficiency and water stability of several alternative anchoring groups, including phosphonic acid, hydroxamic acid, acerylacetone, and boronic acid, were evaluated. While all of the anchoring groups exhibited water stability superior to carboxylate, the hydroxamate anchor had the best combination of ease of handling and electron injection efficiency. The effects on photoconductivity due to metal oxide morphology and the addition of dopants were also analyzed. Mixtures of anatase and rutile TiO 2 nanoparticles are known to exhibit cooperative effects which increase the efficiency of DSSCs and photocatalysis relative to the pure-phase materials. Through analysis of TRTS measurements, the mechanism of this synergistic effect was found to involve electron transfer from the lower-mobility, higher surface area rutile nanoparticles to anatase particles, resulting in a higher charge collection efficiency. In addition to morphology, doping has been investigated as a means of expanding the spectral range of visible absorption of photocatalysts. Doping ZnO nanowires with manganese(II) was found to significantly decrease the electron mobility, and doping with cobalt(II) increased the timescale for electron trapping. These differences can be understood by considering the changes to the band structure of ZnO effected by the dopants. Preliminary analyses of the solvent and electrolyte dependence on the electron injection rate and efficiency suggest that electron injection can be affected by

  4. 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.

  5. Monitoring Single-Molecule Protein Dynamics with a Carbon Nanotube Transistor

    NASA Astrophysics Data System (ADS)

    Collins, Philip G.

    2014-03-01

    Nanoscale electronic devices like field-effect transistors have long promised to provide sensitive, label-free detection of biomolecules. Single-walled carbon nanotubes press this concept further by not just detecting molecules but also monitoring their dynamics in real time. Recent measurements have demonstrated this premise by monitoring the single-molecule processivity of three different enzymes: lysozyme, protein Kinase A, and the Klenow fragment of DNA polymerase I. With all three enzymes, single molecules tethered to nanotube transistors were electronically monitored for 10 or more minutes, allowing us to directly observe a range of activity including rare transitions to chemically inactive and hyperactive conformations. The high bandwidth of the nanotube transistors further allow every individual chemical event to be clearly resolved, providing excellent statistics from tens of thousands of turnovers by a single enzyme. Initial success with three different enzymes indicates the generality and attractiveness of the nanotube devices as a new tool to complement other single-molecule techniques. Research on transduction mechanisms provides the design rules necessary to further generalize this architecture and apply it to other proteins. The purposeful incorporation of just one amino acid is sufficient to fabricate effective, single molecule sensors from a wide range of enzymes or proteins.

  6. 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

  7. 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.

  8. High Density Single-Molecule-Bead Arrays for Parallel Single Molecule Force Spectroscopy

    PubMed Central

    Barrett, Michael J.; Oliver, Piercen M.; Cheng, Peng; Cetin, Deniz; Vezenov, Dmitri

    2012-01-01

    The assembly of a highly-parallel force spectroscopy tool requires careful placement of single-molecule targets on the substrate and the deliberate manipulation of a multitude of force probes. Since the probe must approach the target biomolecule for covalent attachment, while avoiding irreversible adhesion to the substrate, the use of the polymer microsphere as force probes to create the tethered bead array poses a problem. Therefore, the interactions between the force probe and the surface must be repulsive at very short distances (< 5 nm) and attractive at long distances. To achieve this balance, the chemistry of the substrate, force probe, and solution must be tailored to control the probe-surface interactions. In addition to an appropriately designed chemistry, it is necessary to control the surface density of the target molecule in order to ensure that only one molecule is interrogated by a single force probe. We used gold-thiol chemistry to control both the substrate’s surface chemistry and the spacing of the studied molecules, through a competitive binding of the thiol-terminated DNA and an inert thiol forming a blocking layer. For our single molecule array, we modeled the forces between the probe and the substrate using DLVO theory and measured their magnitude and direction with colloidal probe microscopy. The practicality of each system was tested using a probe binding assay to evaluate the proportion of the beads remaining adhered to the surface after application of force. We have translated the results specific for our system to general guiding principles for preparation of tethered bead arrays and demonstrated the ability of this system to produce a high yield of active force spectroscopy probes in a microwell substrate. This study outlines the characteristics of the chemistry needed to create such a force spectroscopy array. PMID:22548234

  9. Understanding Enzyme Activity Using Single Molecule Tracking (Poster)

    SciTech Connect

    Liu, Y.-S.; Zeng, Y.; Luo, Y.; Xu, Q.; Himmel, M.; Smith S.; Wei, H.; Ding, S.-Y.

    2009-06-01

    This poster describes single-molecule tracking and total internal reflection fluorescence microscopy. It discusses whether the carbohydrate-binding module (CBM) moves on cellulose, how the CBM binds to cellulose, and the mechanism of cellulosome assembly.

  10. Single molecule Raman detection of enkephalin on silver colloidal particles

    E-print Network

    Kneipp, Katrin

    2004-01-01

    Enkephalin, an endogeneous substance in the human brain showing morphine?like biological functions, has been detected at the single molecule level based on the surface?enhanced Raman signal of the ring breathing mode of ...

  11. 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 ...

  12. Single-molecule localization software applied to photon counting imaging.

    PubMed

    Hirvonen, Liisa M; Kilfeather, Tiffany; Suhling, Klaus

    2015-06-01

    Centroiding in photon counting imaging has traditionally been accomplished by a single-step, noniterative algorithm, often implemented in hardware. Single-molecule localization techniques in superresolution fluorescence microscopy are conceptually similar, but use more sophisticated iterative software-based fitting algorithms to localize the fluorophore. Here, we discuss common features and differences between single-molecule localization and photon counting imaging and investigate the suitability of single-molecule localization software for photon event localization. We find that single-molecule localization software packages designed for superresolution microscopy-QuickPALM, rapidSTORM, and ThunderSTORM-can work well when applied to photon counting imaging with a microchannel-plate-based intensified camera system: photon event recognition can be excellent, fixed pattern noise can be low, and the microchannel plate pores can easily be resolved. PMID:26192667

  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. Quantitative Characterization of Filament Dynamics by Single-Molecule Lifetime

    E-print Network

    Needleman, Daniel

    CHAPTER 29 Quantitative Characterization of Filament Dynamics by Single-Molecule Lifetime University, Cambridge, Massachusetts 02138 Abstract I. Introduction to Cytoskeletal Filament Dynamics II III. Theoretical Foundations A. Equivalence to the First-Passage Time Problem B. Models of Filament

  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. Nanometer-localized multiple single-molecule fluorescence microscopy

    PubMed Central

    Qu, Xiaohui; Wu, David; Mets, Laurens; Scherer, Norbert F.

    2004-01-01

    Fitting the image of a single molecule to the point spread function of an optical system greatly improves the precision with which single molecules can be located. Centroid localization with nanometer precision has been achieved when a sufficient number of photons are collected. However, if multiple single molecules reside within a diffraction-limited spot, this localization approach does not work. This paper demonstrates nanometer-localized multiple single-molecule (NALMS) fluorescence microscopy by using both centroid localization and photobleaching of the single fluorophores. Short duplex DNA strands are used as nanoscale “rulers” to validate the NALMS microscopy approach. Nanometer accuracy is demonstrated for two to five single molecules within a diffraction-limited area. NALMS microscopy will greatly facilitate single-molecule study of biological systems because it covers the gap between fluorescence resonance energy transfer-based (<10 nm) and diffraction-limited microscopy (>100 nm) measurements of the distance between two fluorophores. Application of NALMS microscopy to DNA mapping with <10-nm (i.e., 30-base) resolution is demonstrated. PMID:15277661

  17. Interfacial valence electron localization and the corrosion resistance of Al-SiC nanocomposite.

    PubMed

    Mosleh-Shirazi, Sareh; Hua, Guomin; Akhlaghi, Farshad; Yan, Xianguo; Li, Dongyang

    2015-01-01

    Microstructural inhomogeneity generally deteriorates the corrosion resistance of materials due to the galvanic effect and interfacial issues. However, the situation may change for nanostructured materials. This article reports our studies on the corrosion behavior of SiC nanoparticle-reinforced Al6061 matrix composite. It was observed that the corrosion resistance of Al6061 increased when SiC nanoparticles were added. Overall electron work function (EWF) of the Al-SiC nanocomposite increased, along with an increase in the corrosion potential. The electron localization function of the Al-SiC nanocomposite was calculated and the results revealed that valence electrons were localized in the region of SiC-Al interface, resulting in an increase in the overall work function and thus building a higher barrier to hinder electrons in the nano-composite to participate in corrosion reactions. PMID:26667968

  18. Interfacial valence electron localization and the corrosion resistance of Al-SiC nanocomposite

    PubMed Central

    Mosleh-Shirazi, Sareh; Hua, Guomin; Akhlaghi, Farshad; Yan, Xianguo; Li, Dongyang

    2015-01-01

    Microstructural inhomogeneity generally deteriorates the corrosion resistance of materials due to the galvanic effect and interfacial issues. However, the situation may change for nanostructured materials. This article reports our studies on the corrosion behavior of SiC nanoparticle-reinforced Al6061 matrix composite. It was observed that the corrosion resistance of Al6061 increased when SiC nanoparticles were added. Overall electron work function (EWF) of the Al-SiC nanocomposite increased, along with an increase in the corrosion potential. The electron localization function of the Al-SiC nanocomposite was calculated and the results revealed that valence electrons were localized in the region of SiC-Al interface, resulting in an increase in the overall work function and thus building a higher barrier to hinder electrons in the nano-composite to participate in corrosion reactions. PMID:26667968

  19. 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.

  20. Developing Single-Molecule Technique with Microsecond Resolution

    NASA Astrophysics Data System (ADS)

    Akhterov, Maxim V.

    Molecular machines like proteins are responsible for many regulatory and catalytic functions. Specifically, molecular motions of proteins and their flexibility determine conformational states required for enzyme catalysis, signal transduction, and protein-protein interactions. However, the mechanisms for protein transitions between conformational states are often poorly understood, especially in the milli- to microsecond ranges where conventional optical techniques and computational modeling are most limited. This work describes development of an electronic single-molecule technique for monitoring microsecond motions of biological molecules. Dynamic changes of conductance through a transistor made of a single-walled carbon nanotube (SWNT-FET) report conformational changes of a protein molecule tethered to the SWNT sidewall. In principle, the high operating speed of SWNT-FETs could allow this technique to resolve molecular events with nanosecond resolution. This project focused on improving the technique to a 200 kHz effective bandwidth in order to resolve microsecond-scale dynamics. The improvement was achieved with a home-built electrochemical flow cell. By minimizing parasitic capacitance due to liquid coupling to electrodes and eliminating noise pickup, the flow cell enabled low-noise, high bandwidth measurement of molecular events as short as 2 mus. The apparatus was used to observe closing and opening motions of lysozyme. Preliminary results suggest that lysozyme has a distribution of possible velocities with the most probable speed approaching our experimental resolution of 2 mus.

  1. 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

  2. Interfacial electronic structure of vanadyl naphthalocyanine on highly ordered pyrolytic graphite

    NASA Astrophysics Data System (ADS)

    Blumenfeld, Michael L.; Steele, Mary P.; Ilyas, Nahid; Monti, Oliver L. A.

    2010-09-01

    We present a core and valence region spectroscopic analysis of the interfacial electronic structure of thin films of vanadyl naphthalocyanine (VONc) deposited onto highly oriented pyrolytic graphite (HOPG). X-ray photoelectron spectroscopy indicates the predominantly ionic character of the vanadyl metal center coordinated by the heterocycle and affords the bandgap in the thin VONc films. Valence band photoelectron spectroscopy points to the existence of three different adsorption geometries of VONc on the HOPG surface. The distribution of the different geometries can be systematically influenced in a simple post-deposition processing step, with an immediate effect on the interfacial electronic environment. We find spectroscopic evidence in the valence levels that VONc grows on HOPG most likely in a 2D-gas fashion rather than by nucleation and growth of islands. These data allow us to predict accurately the interface dipole in the case of a broad class of dipolar organic semiconductors, based simply on molecular dipole moment, polarizability and molecular diameter. This ability provides an important step towards rational optimization of energy level alignment in organic electronics.

  3. Single molecule detection using graphene electrodes

    NASA Astrophysics Data System (ADS)

    Rangel, Norma L.; Seminario, Jorge M.

    2010-06-01

    It is shown using density functional theory that the trapping of molecules between graphene electrode plates can be used to sense molecules through their vibrational fluctuations. This hypothesis is tested using water trapped in two graphene molecules connected to a potential difference. The electric current fluctuations generated through the junction correspond to the fluctuations of the vibrational modes. Since this system yield currents in a range workable by present electronic devices, there is no need for further 'molecular amplification'. Fluctuations of the three modes of water yield similar changes of potentials in the neighbourhood accessible to other molecules; therefore, vibrations from a single water molecule, as an example, or vibrations from any other molecule can be transduced into electrical currents of magnitude compatible with present silicon technology. In the particular case of the water molecule, a rectified potential signal is obtained from the fluctuations of the antisymmetric stretching mode and a simple transduction is obtained from the symmetric stretching and bending modes. It is argued that the high sensitivity is due to the strong delocalization of the frontier molecular orbitals or molecular plasmons on graphene electrodes, which guarantees the detection based on molecular potentials or molecular vibrations; these plasmon-like molecules are of major importance for the development of molecular and nano electronics.

  4. Fluorinated copper phthalocyanine nanowires for enhancing interfacial electron transport in organic solar cells.

    PubMed

    Yoon, Seok Min; Lou, Sylvia J; Loser, Stephen; Smith, Jeremy; Chen, Lin X; Facchetti, Antonio; Marks, Tobin J; Marks, Tobin

    2012-12-12

    Zinc oxide is a promising candidate as an interfacial layer (IFL) in inverted organic photovoltaic (OPV) cells due to the n-type semiconducting properties as well as chemical and environmental stability. Such ZnO layers collect electrons at the transparent electrode, typically indium tin oxide (ITO). However, the significant resistivity of ZnO IFLs and an energetic mismatch between the ZnO and the ITO layers hinder optimum charge collection. Here we report that inserting nanoscopic copper hexadecafluorophthalocyanine (F(16)CuPc) layers, as thin films or nanowires, between the ITO anode and the ZnO IFL increases OPV performance by enhancing interfacial electron transport. In inverted P3HT:PC(61)BM cells, insertion of F(16)CuPc nanowires increases the short circuit current density (J(sc)) versus cells with only ZnO layers, yielding an enhanced power conversion efficiency (PCE) of ?3.6% vs ?3.0% for a control without the nanowire layer. Similar effects are observed for inverted PTB7:PC(71)BM cells where the PCE is increased from 8.1% to 8.6%. X-ray scattering, optical, and electrical measurements indicate that the performance enhancement is ascribable to both favorable alignment of the nanowire ?-? stacking axes parallel to the photocurrent flow and to the increased interfacial layer-active layer contact area. These findings identify a promising strategy to enhance inverted OPV performance by inserting anisotropic nanostructures with ?-? stacking aligned in the photocurrent flow direction. PMID:23181741

  5. Single molecule photoluminescence excitation spectroscopy of polyfluorene

    NASA Astrophysics Data System (ADS)

    da Como, Enrico; Lupton, John

    2010-03-01

    Polyfluorene is a remarkable conjugated polymer with a uniquely rich polymorphism [1]. Because of this characteristic it can be considered as a model playground to understand structure-property relationships in conjugated polymers. Here, by low temperature single polymer chain photoluminescence excitation spectroscopy [2], we look at the spectral characteristics of the absorbing and emitting chromophores on a chain. These experiments are performed on both the ?-phase and the glassy disordered structure, elucidating the role of chain polymorphism on conformational relaxation and energy transfer. Moreover, we compare results on multichromophoric polymers with short oligomers, where a single chromophore is responsible for the optical response. These experiments illuminate directly the emergence of chromophores in conjugated polymers through delocalization: how a pi-electron system evolves from a localized molecular (oligomeric) unit into a delocalized species. [4pt] [1] Da Como Nano Lett. [0pt] [2] Walter PRL 2009

  6. Observing single molecule chemical reactions on metal nanoparticles.

    SciTech Connect

    Emory, S. R.; Ambrose, W. Patrick; Goodwin, P. M.; Keller, Richard A.

    2001-01-01

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

  7. Magnetic behaviour of TbPc2 single-molecule magnets chemically grafted on silicon surface

    PubMed Central

    Mannini, Matteo; Bertani, Federico; Tudisco, Cristina; Malavolti, Luigi; Poggini, Lorenzo; Misztal, Kasjan; Menozzi, Daniela; Motta, Alessandro; Otero, Edwige; Ohresser, Philippe; Sainctavit, Philippe; Condorelli, Guglielmo G.; Dalcanale, Enrico; Sessoli, Roberta

    2014-01-01

    Single-molecule magnets (SMMs) are among the most promising molecular systems for the development of novel molecular electronics based on the spin transport. Going beyond the investigations focused on physisorbed SMMs, in this work the robust grafting of Terbium(III) bis(phthalocyaninato) complexes to silicon surface from a diluted solution is achieved by rational chemical design yielding the formation of a partially oriented monolayer on the conducting substrate. Here, by exploiting the surface sensitivity of X-ray circular magnetic dichroism we evidence an enhancement of the magnetic bistability of this single-molecule magnet, in contrast to the dramatic reduction of the magnetic hysteresis that characterises monolayer deposits evaporated on noble and ferromagnetic metals. Photoelectron spectroscopy investigations and density functional theory analysis suggest a non-innocent role played by the silicon substrate, evidencing the potentiality of this approach for robust integration of bistable magnetic molecules in electronic devices. PMID:25109254

  8. 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

  9. Single Molecule Switches and Molecular Self-Assembly: Low Temperature STM Investigations and Manipulations

    SciTech Connect

    Iancu, Violeta

    2006-08-01

    This dissertation is devoted to single molecule investigations and manipulations of two porphyrin-based molecules, chlorophyll-a and Co-popphyrin. The molecules are absorbed on metallic substrates and studied at low temperatures using a scanning tunneling microscope. The electronic, structural and mechanical properties of the molecules are investigated in detail with atomic level precision. Chlorophyll-a is the key ingredient in photosynthesis processes while Co-porphyrin is a magnetic molecule that represents the recent emerging field of molecular spintronics. Using the scanning tunneling microscope tip and the substrate as electrodes, and the molecules as active ingredients, single molecule switches made of these two molecules are demonstrated. The first switch, a multiple and reversible mechanical switch, is realized by using chlorophyll-a where the energy transfer of a single tunneling electron is used to rotate a C-C bond of the molecule's tail on a Au(111) surface. Here, the det

  10. 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.

  11. 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.

  12. 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

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

    E-print Network

    Malý, Pavel; van Grondelle, Rienk; Man?al, Tomáš

    2015-01-01

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

  14. Evidence of natural isotopic distribution from single-molecule SERS

    E-print Network

    P. G. Etchegoin; E. C. Le Ru; M. Meyer

    2008-11-03

    We report on the observation of the natural isotopic spread of carbon from single-molecule Surface Enhanced Raman Spectroscopy (SM-SERS). By choosing a dye molecule with a very localized Raman active vibration in a cyano bond (C$\\equiv$N triple bond), we observe (in a SERS colloidal liquid) a small fraction of SM-SERS events where the frequency of the cyano mode is softened and in agreement with the effect of substituting $^{12}$C by the next most abundant $^{13}$C isotope. This example adds another demonstration of single molecule sensitivity in SERS through isotopic editing which is done, in this case, not by artificial isotopic editing but rather by nature itself. It also highlights SERS as a unique spectroscopic tool, capable of detecting an isotopic change in one atom of a single molecule.

  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. Electrochemical Single-Molecule Transistors with Optimized Gate Coupling.

    PubMed

    Osorio, Henrry M; Catarelli, Samantha; Cea, Pilar; Gluyas, Josef B G; Hartl, František; Higgins, Simon J; Leary, Edmund; Low, Paul J; Martín, Santiago; Nichols, Richard J; Tory, Joanne; Ulstrup, Jens; Vezzoli, Andrea; Milan, David C; Zeng, Qiang

    2015-11-18

    Electrochemical gating at the single molecule level of viologen molecular bridges in ionic liquids is examined. Contrary to previous data recorded in aqueous electrolytes, a clear and sharp peak in the single molecule conductance versus electrochemical potential data is obtained in ionic liquids. These data are rationalized in terms of a two-step electrochemical model for charge transport across the redox bridge. In this model the gate coupling in the ionic liquid is found to be fully effective with a modeled gate coupling parameter, ?, of unity. This compares to a much lower gate coupling parameter of 0.2 for the equivalent aqueous gating system. This study shows that ionic liquids are far more effective media for gating the conductance of single molecules than either solid-state three-terminal platforms created using nanolithography, or aqueous media. PMID:26488257

  17. 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...

  18. 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

  19. 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.

  20. Making connections — strategies for single molecule fluorescence biophysics

    PubMed Central

    Grohmann, Dina; Werner, Finn; Tinnefeld, Philip

    2013-01-01

    Fluorescence spectroscopy and fluorescence microscopy carried out on the single molecule level are elegant methods to decipher complex biological systems; it can provide a wealth of information that frequently is obscured in the averaging of ensemble measurements. Fluorescence can be used to localise a molecule, study its binding with interaction partners and ligands, or to follow conformational changes in large multicomponent systems. Efficient labelling of proteins and nucleic acids is very important for any fluorescence method, and equally the development of novel fluorophores has been crucial in making biomolecules amenable to single molecule fluorescence methods. In this paper we review novel coupling strategies that permit site-specific and efficient labelling of proteins. Furthermore, we will discuss progressive single molecule approaches that allow the detection of individual molecules and biomolecular complexes even directly isolated from cellular extracts at much higher and much lower concentrations than has been possible so far. PMID:23769868

  1. An improved surface passivation method for single-molecule studies.

    PubMed

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

    2014-12-01

    We report a surface passivation method based on dichlorodimethylsilane (DDS)-Tween-20 for in vitro single-molecule studies, which, under the conditions tested here, more efficiently prevented nonspecific binding of biomolecules than the standard poly(ethylene glycol) surface. The DDS-Tween-20 surface was simple and inexpensive to prepare and did 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. PMID:25306544

  2. Single-molecule magnet Mn12 on graphene

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

  3. 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

  4. Single-molecule pump-probe experiments reveal variations in ultrafast energy redistribution.

    PubMed

    van Dijk, E M H P; Hernando, J; García-Parajó, M F; van Hulst, N F

    2005-08-01

    Single-molecule pump probe (SM2P) is a novel, fluorescence-based technique that allows the study of ultrafast processes on the single-molecule level. Exploiting SM2P we have observed large variations (from 1 ps to below 100 fs) in the energy redistribution times of chemically identical molecules in the same sample. Embedding the molecules in a different matrix or changing the excitation wavelength does not lead to significant changes in the average redistribution time. However, chemically different molecules exhibit different characteristic redistribution times. We therefore conclude that the process measured with the SM2P technique is dominated by intramolecular energy redistribution and not intermolecular transfer to the surrounding matrix. The matrix though is responsible for inducing conformational changes in the molecule, which affect the coupling between electronic and vibrational modes. These conformational changes are the main origin of the observed broad distribution of redistribution times. PMID:16122331

  5. Terahertz Field Enhancement and Photon-Assisted Tunneling in Single-Molecule Transistors.

    PubMed

    Yoshida, Kenji; Shibata, Kenji; Hirakawa, Kazuhiko

    2015-09-25

    We have investigated the electron transport in single-C_{60}-molecule transistors under the illumination of intense monochromatic terahertz (THz) radiation. By employing an antenna structure with a sub-nm-wide gap, we concentrate THz radiation beyond the diffraction limit and focus it onto a single molecule. Photon-assisted tunneling (PAT) in the single molecule transistors is observed in both the weak-coupling and Kondo regimes. The THz power dependence of the PAT conductance indicates that when the incident THz intensity is a few tens of mW, the THz field induced at the molecule exceeds 100??kV/cm, which is enhanced by a factor of ?10^{5} from the field in the free space. PMID:26451585

  6. Terahertz Field Enhancement and Photon-Assisted Tunneling in Single-Molecule Transistors

    NASA Astrophysics Data System (ADS)

    Yoshida, Kenji; Shibata, Kenji; Hirakawa, Kazuhiko

    2015-09-01

    We have investigated the electron transport in single-C60 -molecule transistors under the illumination of intense monochromatic terahertz (THz) radiation. By employing an antenna structure with a sub-nm-wide gap, we concentrate THz radiation beyond the diffraction limit and focus it onto a single molecule. Photon-assisted tunneling (PAT) in the single molecule transistors is observed in both the weak-coupling and Kondo regimes. The THz power dependence of the PAT conductance indicates that when the incident THz intensity is a few tens of mW, the THz field induced at the molecule exceeds 100 kV /cm , which is enhanced by a factor of ˜105 from the field in the free space.

  7. Mechanically activated switching of Si-based single-molecule junction as imaged with three-dimensional dynamic probe

    NASA Astrophysics Data System (ADS)

    Nakamura, Miki; Yoshida, Shoji; Katayama, Tomoki; Taninaka, Atsushi; Mera, Yutaka; Okada, Susumu; Takeuchi, Osamu; Shigekawa, Hidemi

    2015-10-01

    Understanding and extracting the full functions of single-molecule characteristics are key factors in the development of future device technologies, as well as in basic research on molecular electronics. Here we report a new methodology for realizing a three-dimensional (3D) dynamic probe of single-molecule conductance, which enables the elaborate 3D analysis of the conformational effect on molecular electronics, by the formation of a Si/single molecule/Si structure using scanning tunnelling microscopy (STM). The formation of robust covalent bonds between a molecule and Si electrodes, together with STM-related techniques, enables the stable and repeated control of the conformational modulation of the molecule. By 3D imaging of the conformational effect on a 1,4-diethynylbenzene molecule, a binary change in conductance with hysteresis is observed for the first time, which is considered to originate from a mechanically activated conformational change.

  8. In situ Formation of Highly Conducting Covalent Au-C Contacts for Single-Molecule Junctions

    SciTech Connect

    Cheng, Z.L.; Hybertsen, M.; Skouta, R.; Vazquez, H.; Widawsky, J.R.; Schneebeli, S.; Chen, W.; Breslow, R.; Venkataraman, L.

    2011-06-01

    Charge transport across metal-molecule interfaces has an important role in organic electronics. Typically, chemical link groups such as thiols or amines are used to bind organic molecules to metal electrodes in single-molecule circuits, with these groups controlling both the physical structure and the electronic coupling at the interface. Direct metal-carbon coupling has been shown through C60, benzene and {pi}-stacked benzene but ideally the carbon backbone of the molecule should be covalently bonded to the electrode without intervening link groups. Here, we demonstrate a method to create junctions with such contacts. Trimethyl tin (SnMe{sub 3})-terminated polymethylene chains are used to form single-molecule junctions with a break-junction technique. Gold atoms at the electrode displace the SnMe{sub 3} linkers, leading to the formation of direct Au-C bonded single-molecule junctions with a conductance that is {approx}100 times larger than analogous alkanes with most other terminations. The conductance of these Au-C bonded alkanes decreases exponentially with molecular length, with a decay constant of 0.97 per methylene, consistent with a non-resonant transport mechanism. Control experiments and ab initio calculations show that high conductances are achieved because a covalent Au-C sigma ({sigma}) bond is formed. This offers a new method for making reproducible and highly conducting metal-organic contacts.

  9. Free energy reconstruction from nonequilibrium single-molecule pulling experiments

    E-print Network

    Weeks, Eric R.

    Free energy reconstruction from nonequilibrium single-molecule pulling experiments Gerhard Hummer also drives the system away from equilibrium. Nevertheless, we show how equilibrium free energy of an extension of Jarzynski's remarkable identity between free energies and the irreversible work. Recent

  10. Single-Molecule Dynamics and Mechanisms of Metalloregulators and Metallochaperones

    E-print Network

    Chen, Peng

    , Ithaca, New York 14853, United States ABSTRACT: Understanding how cells regulate and transport metal ions-averaged measurements because of their dynamic nature, which makes it necessary to synchronize molecular actions (as" in PubMed generates >1500 publications. On the other hand, much less single-molecule studies have been

  11. Model systems for single molecule polymer Folarin Latinwoa

    E-print Network

    Schroeder, Charles

    Model systems for single molecule polymer dynamics Folarin Latinwoa and Charles M. Schroeder*ab DOI polymer dynamics. However, dsDNA is a semiflexible polymer, and the structural rigidity of the DNA double, including synthetic organic polymers. Recently, we developed single stranded DNA (ssDNA) as a new model

  12. Optical collection efficiency function in single-molecule detection experiments

    E-print Network

    Enderlein, Jörg

    Optical collection efficiency function in single-molecule detection experiments Jo¨ rg Enderlein and W. Patrick Ambrose The optical collection efficiency function for an optical system on a geometrical optics approx- imation are presented. Comparison is made with exact wave optics calculations

  13. Strong extinction of a laser beam by a single molecule

    E-print Network

    I. Gerhardt; G. Wrigge; P. Bushev; G. Zumofen; R. Pfab; V. Sandoghdar

    2006-04-24

    We present an experiment where a single molecule strongly affects the amplitude and phase of a laser field emerging from a subwavelength aperture. We achieve a visibility of -6% in direct and +10% in cross-polarized detection schemes. Our analysis shows that a close to full extinction should be possible using near-field excitation.

  14. Combining single-molecule imaging and single-channel electrophysiology.

    PubMed

    Weatherill, Eve E; Wallace, Mark I

    2015-01-16

    Combining simultaneous single-molecule fluorescence measurements of ion channel conformational change with single-channel electrophysiology would enable a direct link between structure and function. Such methods would help us to create a truly molecular "movie" of how these important biomolecules work. Here we review past and recent progress toward this goal. PMID:25026065

  15. Single-Molecule Choreography between Telomere Proteins and G Quadruplexes

    E-print Network

    Yildiz, Ahmet

    Single-Molecule Choreography between Telomere Proteins and G Quadruplexes Karl-Peter Hopfner1,2,* 1://dx.doi.org/10.1016/j.str.2014.05.011 Telomeric DNA binds proteins to protect chromosome ends, but it also adopts the binding of different telomere associated proteins. The data suggest that GQs play important roles

  16. Single Molecule Study of Cellulase Hydrolysis of Crystalline Cellulose

    SciTech Connect

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

    2009-12-01

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

  17. A Single-Molecule Study of RNA Catalysis and Folding

    E-print Network

    Herschlag, Dan

    microscopy, we studied the catalysis by and folding of individual Tetrahymena thermophila ribozyme molecules (13­21). In par- ticular, the Tetrahymena ribozyme is an in- tensely studied catalytic RNA of 400 of the catalysis by and folding of the Tetrahymena ribozyme. For the single-molecule experiments, we extended the L

  18. 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

  19. Single-molecule studies of multi-protein machines

    NASA Astrophysics Data System (ADS)

    van Oijen, Antoine

    2010-03-01

    Advances in optical imaging and molecular manipulation techniques have made it possible to observe individual enzymes and record molecular movies that provide new insight into their dynamics and reaction mechanisms. In a biological context, most of these enzymes function in concert with other enzymes in multi-protein complexes, so an important future direction will be the utilization of single-molecule techniques to unravel the orchestration of large macromolecular assemblies. Our group is developing the single-molecule tools that will make it possible to study biochemical pathways of arbitrary complexity at the single-molecule level. I will discuss results of single-molecule experiments on the replisome, the molecular machinery that is responsible for replication of DNA. We stretch individual DNA molecules and use their elastic properties to obtain dynamic information on the proteins that unwind the double helix and copy its genetic information. Furthermore, we visualize fluorescently labeled components of the replisome and thus obtain information on stochiometry and exchange kinetics. This simultaneous observation of catalytic activity and composition allows us to gain deeper insight into the structure-function relationship of the replisome.

  20. Convex Lens-Induced Confinement for Imaging Single Molecules

    E-print Network

    Cohen, Adam E.

    microscope that addresses both challenges and dramatically improves single-molecule imaging. The technique to 20-fold greater rejection of background fluorescence than is achieved with total internal reflection diffusion-limited observation time per molecule than is achieved with confocal fluorescence correlation

  1. Single Molecule Fluorescence Microscopy on Planar Supported Bilayers

    PubMed Central

    Axmann, Markus; Schütz, Gerhard J.; Huppa, Johannes B.

    2015-01-01

    In the course of a single decade single molecule microscopy has changed from being a secluded domain shared merely by physicists with a strong background in optics and laser physics to a discipline that is now enjoying vivid attention by life-scientists of all venues 1. This is because single molecule imaging has the unique potential to reveal protein behavior in situ in living cells and uncover cellular organization with unprecedented resolution below the diffraction limit of visible light 2. Glass-supported planar lipid bilayers (SLBs) are a powerful tool to bring cells otherwise growing in suspension in close enough proximity to the glass slide so that they can be readily imaged in noise-reduced Total Internal Reflection illumination mode 3,4. They are very useful to study the protein dynamics in plasma membrane-associated events as diverse as cell-cell contact formation, endocytosis, exocytosis and immune recognition. Simple procedures are presented how to generate highly mobile protein-functionalized SLBs in a reproducible manner, how to determine protein mobility within and how to measure protein densities with the use of single molecule detection. It is shown how to construct a cost-efficient single molecule microscopy system with TIRF illumination capabilities and how to operate it in the experiment. PMID:26555335

  2. Interfacial bonding and electronic structure of GaN/GaAs interface: A first-principles study

    SciTech Connect

    Cao, Ruyue; Zhang, Zhaofu; Wang, Changhong; Li, Haobo; Dong, Hong; Liu, Hui; Wang, Weichao; Xie, Xinjian

    2015-04-07

    Understanding of GaN interfacing with GaAs is crucial for GaN to be an effective interfacial layer between high-k oxides and III-V materials with the application in high-mobility metal-oxide-semiconductor field effect transistor (MOSFET) devices. Utilizing first principles calculations, here, we investigate the structural and electronic properties of the GaN/GaAs interface with respect to the interfacial nitrogen contents. The decrease of interfacial N contents leads to more Ga dangling bonds and As-As dimers. At the N-rich limit, the interface with N concentration of 87.5% shows the most stability. Furthermore, a strong band offsets dependence on the interfacial N concentration is also observed. The valance band offset of N7 with hybrid functional calculation is 0.51?eV. The electronic structure analysis shows that significant interface states exist in all the GaN/GaAs models with various N contents, which originate from the interfacial dangling bonds and some unsaturated Ga and N atoms. These large amounts of gap states result in Fermi level pinning and essentially degrade the device performance.

  3. Biophysical Variables Which Are Available from Single-Molecule Optical Studies

    NASA Astrophysics Data System (ADS)

    Moerner, W. E.

    2013-03-01

    Since the first optical detection and spectroscopy of a single molecule in a condensed phase host in 1989, a wealth of new information has been obtained from time-dependent measurements and single-molecule probability distributions. When single-molecule imaging is combined with active control of the emitter concentration, enhanced spatial resolution well beyond the optical diffraction limit can be obtained for a wide array of biophysical structures in cells. Single-molecule emitters also provide precise and accurate 3D position as well as dipole moment orientation when combined with Fourier plane processing. Examples here include the implementation of a double-helix point spread function for 3D position information (Backlund, Lew et al. PNAS (2012)), and the creation of a quadrated pupil response to sense emission dipole orientations (Backer et al. submitted 2012). If high-resolution spatial information is not needed, a machine called the Anti-Brownian ELectrokinetic (ABEL) trap provides real-time suppression of Brownian motion for single molecules in solution for extended analysis of dynamical state changes (Wang et al. Acc. Chem. Res. (2012)). With proper design of reporter fluorophore, individual electron transfer events to a single Cu atom in a redox enzyme may be sensed under turnover conditions (Goldsmith et al. PNAS (2011)). Optical counting of fluorescent ATP nucleotides on a multisubunit enzyme provides measurement of ATP number distributions, which can be used to generate a new window into enzyme cooperativity devoid of ensemble averaging (Jiang et al PNAS (2011)). With advanced control system design of feedback to enable optimal trapping performance, the ABEL trap also allows direct, simultaneous measurement of three variables: brightness, excited state lifetime, and emission spectrum, for objects as small as individual ~1-2 nm sized fluorophores in solution (Wang et al. JPCB (in press 2013)). These examples illustrate some of the wide variety of physical variables which may now be measured for single molecules in a various condensed phase environments ranging from aqueous solutions to living cells. Work supported by NIGMS and DOE-BES

  4. The optics inside an automated single molecule array analyzer

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

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

  5. 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

  6. Single-molecule DNA detection with an engineered MspA protein nanopore

    PubMed Central

    Butler, Tom Z.; Pavlenok, Mikhail; Derrington, Ian M.; Niederweis, Michael; Gundlach, Jens H.

    2008-01-01

    Nanopores hold great promise as single-molecule analytical devices and biophysical model systems because the ionic current blockades they produce contain information about the identity, concentration, structure, and dynamics of target molecules. The porin MspA of Mycobacterium smegmatis has remarkable stability against environmental stresses and can be rationally modified based on its crystal structure. Further, MspA has a short and narrow channel constriction that is promising for DNA sequencing because it may enable improved characterization of short segments of a ssDNA molecule that is threaded through the pore. By eliminating the negative charge in the channel constriction, we designed and constructed an MspA mutant capable of electronically detecting and characterizing single molecules of ssDNA as they are electrophoretically driven through the pore. A second mutant with additional exchanges of negatively-charged residues for positively-charged residues in the vestibule region exhibited a factor of ?20 higher interaction rates, required only half as much voltage to observe interaction, and allowed ssDNA to reside in the vestibule ?100 times longer than the first mutant. Our results introduce MspA as a nanopore for nucleic acid analysis and highlight its potential as an engineerable platform for single-molecule detection and characterization applications. PMID:19098105

  7. PUBLISHED ONLINE: 13 JULY 2015 | DOI: 10.1038/NPHYS3385 Gating a single-molecule transistor with

    E-print Network

    Loss, Daniel

    LETTERS PUBLISHED ONLINE: 13 JULY 2015 | DOI: 10.1038/NPHYS3385 Gating a single-molecule transistor Locane4 , Mark Thomas4 , Felix von Oppen4 , Piet W. Brouwer4 and Stefan Fölsch1 * Transistors, regardless-scale transistors, this conductance is sensitive to single electrons hopping via individual orbitals1,2 . Single

  8. Microsecond protein dynamics observed at the single-molecule level

    PubMed Central

    Otosu, Takuhiro; Ishii, Kunihiko; Tahara, Tahei

    2015-01-01

    How polypeptide chains acquire specific conformations to realize unique biological functions is a central problem of protein science. Single-molecule spectroscopy, combined with fluorescence resonance energy transfer, is utilized to study the conformational heterogeneity and the state-to-state transition dynamics of proteins on the submillisecond to second timescales. However, observation of the dynamics on the microsecond timescale is still very challenging. This timescale is important because the elementary processes of protein dynamics take place and direct comparison between experiment and simulation is possible. Here we report a new single-molecule technique to reveal the microsecond structural dynamics of proteins through correlation of the fluorescence lifetime. This method, two-dimensional fluorescence lifetime correlation spectroscopy, is applied to clarify the conformational dynamics of cytochrome c. Three conformational ensembles and the microsecond transitions in each ensemble are indicated from the correlation signal, demonstrating the importance of quantifying microsecond dynamics of proteins on the folding free energy landscape. PMID:26151767

  9. 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

  10. 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].

  11. 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

  12. Single-molecule reader for proteomics and genomics.

    PubMed

    Hesse, Jan; Wechselberger, Christian; Sonnleitner, Max; Schindler, Hansgeorg; Schütz, Gerhard J

    2002-12-25

    Recent developments in ultrasensitive fluorescence microscopy enabled the detection and detailed characterization of individual biomolecules in their native environment. New types of information can be obtained from studying individual molecules, which is not accessible from ensemble measurements. Moreover, this methodological advance matches the need of bioscience to downscale the sample amount required for screening devices. It is envisioned that concentrations as low as approximately 1000 molecules contained in a sample of 1 nl can be detected in a chip-based assay. In this review, we overview state-of-the-art single molecule microscopy with respect to its applicability to ultrasensitive screening. Quantitative estimations will be given, based on a novel apparatus designed for large area screening at single molecule sensitivity. PMID:12458002

  13. Probing DNA clamps with single-molecule force spectroscopy

    PubMed Central

    Wang, Lin; Xu, Xiaojun; Kumar, Ravindra; Maiti, Buddhadev; Liu, C. Tony; Ivanov, Ivaylo; Lee, Tae-Hee; Benkovic, Stephen J.

    2013-01-01

    Detailed mechanisms of DNA clamps in prokaryotic and eukaryotic systems were investigated by probing their mechanics with single-molecule force spectroscopy. Specifically, the mechanical forces required for the Escherichia coli and Saccharomyces cerevisiae clamp opening were measured at the single-molecule level by optical tweezers. Steered molecular dynamics simulations further examined the forces involved in DNA clamp opening from the perspective of the interface binding energies associated with the clamp opening processes. In combination with additional molecular dynamics simulations, we identified the contact networks between the clamp subunits that contribute significantly to the interface stability of the S.cerevisiae and E. coli clamps. These studies provide a vivid picture of the mechanics and energy landscape of clamp opening and reveal how the prokaryotic and eukaryotic clamps function through different mechanisms. PMID:23783571

  14. 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

  15. Microsecond protein dynamics observed at the single-molecule level.

    PubMed

    Otosu, Takuhiro; Ishii, Kunihiko; Tahara, Tahei

    2015-01-01

    How polypeptide chains acquire specific conformations to realize unique biological functions is a central problem of protein science. Single-molecule spectroscopy, combined with fluorescence resonance energy transfer, is utilized to study the conformational heterogeneity and the state-to-state transition dynamics of proteins on the submillisecond to second timescales. However, observation of the dynamics on the microsecond timescale is still very challenging. This timescale is important because the elementary processes of protein dynamics take place and direct comparison between experiment and simulation is possible. Here we report a new single-molecule technique to reveal the microsecond structural dynamics of proteins through correlation of the fluorescence lifetime. This method, two-dimensional fluorescence lifetime correlation spectroscopy, is applied to clarify the conformational dynamics of cytochrome c. Three conformational ensembles and the microsecond transitions in each ensemble are indicated from the correlation signal, demonstrating the importance of quantifying microsecond dynamics of proteins on the folding free energy landscape. PMID:26151767

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

    PubMed Central

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

    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 with an unprecedented speed and signal-to-noise ratio deep within the sample. Thereby we could directly observe and track small and large tracer molecules in aqueous solution. Furthermore, we demonstrated the feasibility to visualize the dynamics of single tracer molecules and native messenger ribonucleoprotein particles (mRNPs) in salivary gland cell nuclei of Chironomus tentans larvae up to 200 µm within the specimen with an excellent signal quality. Thus single molecule light sheet based fluorescence microscopy allows analyzing molecular diffusion and interactions in complex biological systems. PMID:20668517

  17. A Single-Molecule Study of RNA Catalysis and Folding

    NASA Astrophysics Data System (ADS)

    Zhuang, Xiaowei; Bartley, Laura E.; Babcock, Hazen P.; Russell, Rick; Ha, Taekjip; Herschlag, Daniel; Chu, Steven

    2000-06-01

    Using fluorescence microscopy, we studied the catalysis by and folding of individual Tetrahymena thermophila ribozyme molecules . The dye-labeled and surface-immobilized ribozymes used were shown to be functionally indistinguishable from the unmodified free ribozyme in solution. A reversible local folding step in which a duplex docks and undocks from the ribozyme core was observed directly in single-molecule time trajectories, allowing the determination of the rate constants and characterization of the transition state. A rarely populated docked state, not measurable by ensemble methods, was observed. In the overall folding process, intermediate folding states and multiple folding pathways were observed. In addition to observing previously established folding pathways, a pathway with an observed folding rate constant of 1 per second was discovered. These results establish single-molecule fluorescence as a powerful tool for examining RNA folding.

  18. 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

  19. High thermopower of mechanically stretched single-molecule junctions

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    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.

  20. Nanoparticle-Free Single Molecule Anti-Stokes Raman Spectroscopy

    NASA Astrophysics Data System (ADS)

    Peyser-Capadona, Lynn; Zheng, Jie; González, Jose I.; Lee, Tae-Hee; Patel, Sandeep A.; Dickson, Robert M.

    2005-02-01

    In the absence of large, plasmon-supporting nanoparticles, biocompatible dendrimer- and peptide-encapsulated few-atom Ag nanoclusters produce scaffold-specific single molecule (SM) Stokes and anti-Stokes Raman scattering. The strong SM vibrational signatures are enhanced by the Agn transitions in nanoparticle-free samples and cannot arise from plasmon enhancement. Characteristic SM-Raman intermittency is observed, with antibunching of the underlying Agn emission directly confirming the SM nature of the emissive species.

  1. Polarization forces in water deduced from single molecule data

    E-print Network

    Eugene V. Tsiper

    2004-07-08

    Intermolecular polarization interactions in water are determined using a minimal atomic multipole model constructed with distributed polarizabilities. Hydrogen bonding and other properties of water-water interactions are reproduced to fine detail by only three multipoles $\\mu_H$, $\\mu_O$, and $\\theta_O$ and two polarizabilities $\\alpha_O$ and $\\alpha_H$, which characterize a single water molecule and are deduced from single molecule data.

  2. 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

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

    PubMed

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

    2015-10-20

    Single molecule electrochemical detection (SMED) is an extremely challenging aspect of electroanalytical chemistry, requiring unconventional electrochemical cells and measurements. Here, SMED is reported using a "quad-probe" (four-channel probe) pipet cell, fabricated by depositing carbon pyrolytically into two diagonally opposite barrels of a laser-pulled quartz quadruple-barreled pipet and filling the open channels with electrolyte solution, and quasi-reference counter electrodes. A meniscus forms at the end of the probe covering the two working electrodes and is brought into contact with a substrate working electrode surface. In this way, a nanogap cell is produced whereby the two carbon electrodes in the pipet can be used to promote redox cycling of an individual molecule with the substrate. Anticorrelated currents generated at the substrate and tip electrodes, at particular distances (typically tens of nanometers), are consistent with the detection of single molecules. The low background noise realized in this droplet format opens up new opportunities in single molecule electrochemistry, including the use of ionic liquids, as well as aqueous solution, and the quantitative assessment and analysis of factors influencing redox cycling currents, due to a precisely known gap size. PMID:26398675

  4. Visualizing and controlling vibrational wave packets of single molecules.

    PubMed

    Brinks, Daan; Stefani, Fernando D; Kulzer, Florian; Hildner, Richard; Taminiau, Tim H; Avlasevich, Yuri; Müllen, Klaus; van Hulst, Niek F

    2010-06-17

    The active steering of the pathways taken by chemical reactions and the optimization of energy conversion processes provide striking examples of the coherent control of quantum interference through the use of shaped laser pulses. Experimentally, coherence is usually established by synchronizing a subset of molecules in an ensemble with ultra-short laser pulses. But in complex systems where even chemically identical molecules exist with different conformations and in diverse environments, the synchronized subset will have an intrinsic inhomogeneity that limits the degree of coherent control that can be achieved. A natural-and, indeed, the ultimate-solution to overcoming intrinsic inhomogeneities is the investigation of the behaviour of one molecule at a time. The single-molecule approach has provided useful insights into phenomena as diverse as biomolecular interactions, cellular processes and the dynamics of supercooled liquids and conjugated polymers. Coherent state preparation of single molecules has so far been restricted to cryogenic conditions, whereas at room temperature only incoherent vibrational relaxation pathways have been probed. Here we report the observation and manipulation of vibrational wave-packet interference in individual molecules at ambient conditions. We show that adapting the time and phase distribution of the optical excitation field to the dynamics of each molecule results in a high degree of control, and expect that the approach can be extended to achieve single-molecule coherent control in other complex inhomogeneous systems. PMID:20559383

  5. 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.

  6. Interfacial electronic effects in functional biolayers integrated into organic field-effect transistors

    PubMed Central

    Angione, Maria Daniela; Cotrone, Serafina; Magliulo, Maria; Mallardi, Antonia; Altamura, Davide; Giannini, Cinzia; Cioffi, Nicola; Sabbatini, Luigia; Fratini, Emiliano; Baglioni, Piero; Scamarcio, Gaetano; Palazzo, Gerardo; Torsi, Luisa

    2012-01-01

    Biosystems integration into an organic field-effect transistor (OFET) structure is achieved by spin coating phospholipid or protein layers between the gate dielectric and the organic semiconductor. An architecture directly interfacing supported biological layers to the OFET channel is proposed and, strikingly, both the electronic properties and the biointerlayer functionality are fully retained. The platform bench tests involved OFETs integrating phospholipids and bacteriorhodopsin exposed to 1–5% anesthetic doses that reveal drug-induced changes in the lipid membrane. This result challenges the current anesthetic action model relying on the so far provided evidence that doses much higher than clinically relevant ones (2.4%) do not alter lipid bilayers’ structure significantly. Furthermore, a streptavidin embedding OFET shows label-free biotin electronic detection at 10 parts-per-trillion concentration level, reaching state-of-the-art fluorescent assay performances. These examples show how the proposed bioelectronic platform, besides resulting in extremely performing biosensors, can open insights into biologically relevant phenomena involving membrane weak interfacial modifications. PMID:22493224

  7. Real-Space Imaging of Molecular Structure by Single-Molecule Inelastic Tunneling Probe

    NASA Astrophysics Data System (ADS)

    Han, Zhumin; Chiang, Chi-Lun; Xu, Chen; Ho, Wilson

    2014-03-01

    The scanning tunneling microscope is one of the most powerful tools to perform real space imaging of the electronic, magnetic, optical, and vibrational signatures of a single molecule. However, the spatial distributions of these signatures do not always relate directly to the geometric structures of the molecules. In this study, a CO molecule is transferred from the surface to a STM tip. The energy and intensity of the hindered translational mode of the CO vary when the tip is scanned across an adsorbed molecule (such as cobalt phthalocyanine). By monitoring these variations in space, we are able to resolve the geometric structure of the molecule and even subtle intramolecular and intermolecular interactions.

  8. New tools for elucidating the environmental origins of single molecule photoluminescence intermittency

    NASA Astrophysics Data System (ADS)

    Hess, Chelsea M.; Rudolph, Angela R.; Reid, Philip J.

    2015-05-01

    New experimental and analysis methods for investigating the role local environment has on photoluminescence intermittency (PI) exhibited by single luminophores are presented. Quasi-single molecule (SM) microscopy provides spatial resolution of dielectric environments within poly(vinylidene fluoride) (PVDF) films, and reveals annealing's effect on the structural phase of PVDF. New analysis methods establish that the PI exhibited by nile red (NR) SMs in PVDF are consistent with photoinduced electron transfer between NR and PVDF, where transfer rates depend on local dielectric environment. These methods should prove useful for SM studies of guest-host materials where elucidating PI contribution from the host is required.

  9. Interfacial Charge Transport in Organic Electronic Materials: the Key to a New Electronics Technology

    SciTech Connect

    Smith, D.L.; Campbell, I.H.; Davids, P.S.; Heller, C.M.; Laurich, B.K.; Crone, B.K.; Saxena, A.; Bishop, A.R.; Ferraris, J.P.; Yu, Z.G.

    1999-06-04

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at Los Alamos National Laboratory (LANL). The primary aim of this project is to obtain a basic scientific understanding of electrical transport processes at interfaces that contain an organic electronic material. Because of their processing advantages and the tunability of their electronic properties, organic electronic materials are revolutionizing major technological areas such as information display. We completed an investigation of the fundamental electronic excitation energies in the prototype conjugated polymer MEH-PPV. We completed a combined theoretical/experimental study of the energy relation between charged excitations in a conjugated polymer and the metal at a polymer/metal interface. We developed a theoretical model that explains injection currents at polymer/metal interfaces. We have made electrical measurements on devices fabricated using the conjugated polymer MEH-PPV a nd a series of metals.

  10. Electronic Coupling Dependence of Ultrafast Interfacial Electron Transfer on Nanocrystalline Thin Films and Single Crystal

    SciTech Connect

    Lian, Tianquan

    2014-04-22

    The long-term goal of the proposed research is to understand electron transfer dynamics in nanoparticle/liquid interface. This knowledge is essential to many semiconductor nanoparticle based devices, including photocatalytic waste degradation and dye sensitized solar cells.

  11. DNA replication at the single-molecule level.

    PubMed

    Stratmann, S A; van Oijen, A M

    2014-02-21

    A cell can be thought of as a highly sophisticated micro factory: in a pool of billions of molecules - metabolites, structural proteins, enzymes, oligonucleotides - multi-subunit complexes assemble to perform a large number of basic cellular tasks, such as DNA replication, RNA/protein synthesis or intracellular transport. By purifying single components and using them to reconstitute molecular processes in a test tube, researchers have gathered crucial knowledge about mechanistic, dynamic and structural properties of biochemical pathways. However, to sort this information into an accurate cellular road map, we need to understand reactions in their relevant context within the cellular hierarchy, which is at the individual molecule level within a crowded, cellular environment. Reactions occur in a stochastic fashion, have short-lived and not necessarily well-defined intermediates, and dynamically form functional entities. With the use of single-molecule techniques these steps can be followed and detailed kinetic information that otherwise would be hidden in ensemble averaging can be obtained. One of the first complex cellular tasks that have been studied at the single-molecule level is the replication of DNA. The replisome, the multi-protein machinery responsible for copying DNA, is built from a large number of proteins that function together in an intricate and efficient fashion allowing the complex to tolerate DNA damage, roadblocks or fluctuations in subunit concentration. In this review, we summarize advances in single-molecule studies, both in vitro and in vivo, that have contributed to our current knowledge of the mechanistic principles underlying DNA replication. PMID:24395040

  12. Magnetostructural correlations in Tetrairon(III) single-molecule magnets.

    PubMed

    Gregoli, Luisa; Danieli, Chiara; Barra, Anne-Laure; Neugebauer, Petr; Pellegrino, Giovanna; Poneti, Giordano; Sessoli, Roberta; Cornia, Andrea

    2009-06-22

    Tunable single-molecule magnets: The spin-level landscape in a series of Fe(III) (4) single-molecule magnets with propeller-like structure was analyzed by means of high-frequency EPR spectroscopy. The zero-field splitting parameter D of the ground S=5 spin state correlates strongly with the pitch of the propeller gamma (see picture), and thus provides a simple link between molecular structure and magnetic behavior.We report three novel tetrairon(III) single-molecule magnets with formula [Fe(4)(L)(2)(dpm)(6)] (Hdpm=2,2,6,6-tetramethylheptane-3,5-dione), prepared by using pentaerythritol monoether ligands H(3)L=R'OCH(2)C(CH(2)OH)(3) with R'=allyl (1), (R,S)-2-methyl-1-butyl (2), and (S)-2-methyl-1-butyl (3), along with a new crystal phase of the complex containing H(3)L=11-(acetylthio)-2,2-bis(hydroxymethyl)- undecan-1-ol (4). High-frequency EPR (HF-EPR) spectra at low temperature were collected on powder samples in order to determine the zero-field splitting (zfs) parameters in the ground S=5 spin state. In 1-4 and in other eight isostructural compounds previously reported, a remarkable correlation is found between the axial zfs parameter D and the pitch gamma of the propeller-like structure. The relationship is directly demonstrated by 1, which features both structurally and magnetically inequivalent molecules in the crystal. The dynamics of magnetization has been investigated by ac susceptometry, and the results analyzed by master-matrix calculations. The large rhombicities of 2 and 3 were found to be responsible for the fast magnetic relaxation observed in the two compounds. However, complex 3 shows an additional faster relaxation mechanism which is unaccounted for by the set of spin Hamiltonian parameters determined by HF-EPR. PMID:19462389

  13. Interfacial electronic structure at a metal—phthalocyanine/graphene interface: Copper—phthalocyanine versus iron—phthalocyanine

    NASA Astrophysics Data System (ADS)

    Ye, Wei-Guo; Liu, Dan; Peng, Xiao-Feng; Dou, Wei-Dong

    2013-11-01

    The energy level alignment of CuPc and FePc on single-layer graphene/Ni(111) (SLG/Ni) substrate was investigated by using ultraviolet and X-ray photoelectron spectroscopy (UPS and XPS). The highest occupied molecular orbitals (HOMOs) in a thick layer of CuPc and FePc lie at 1.04 eV and 0.90 eV, respectively, below the Fermi level of the SLG/Ni substrate. Weak adsorbate—substrate interaction leads to negligible interfacial dipole at the CuPc/SLG/Ni interface, while a large interfacial dipole (0.20 eV) was observed in the case of FePc/SLG/Ni interface, due to strong adsorbate—substrate coupling. In addition, a new interfacial electronic feature was observed for the first time in the case of FePc on SLG/Ni substrate. This interfacial state can be attributed to a charge transfer from the SLG/Ni substrate to unoccupied orbitals of FePc.

  14. 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

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

    PubMed Central

    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.

    2015-01-01

    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

  16. Conductance and Thermopower in Thiophene and Oxidized Thiophene Single-Molecule Junctions

    NASA Astrophysics Data System (ADS)

    Venkataraman, Latha

    2015-03-01

    Organic electronic materials have impacted the development of semiconducting, photovoltaic and thermoelectric devices. The precise control afforded over molecular design by organic synthesis allows for device properties to be readily tailored facilitating varied functionality. Measuring charge transfer characteristics and thermoelectric properties in organic devices and across metal-organic interfaces is of critical importance for understanding structure-function relations and single molecule measurements offer an ideal test bed for such measurements. In this talk, I will review the scanning tunneling microscope break-junction technique used to measure conductance in single-molecule devices focusing on molecular systems that have strong potential for application in organic and photovoltaic devices. Specifically, I will discuss measurements of thiophene and oxidized thiophene oligomers and illustrate how structure and conformations impact both the electronic characteristics and the dominant charge carrier in these systems. I will end this talk discussing results with a new class of thiophene derivatives where the charge carriers are changed from holes to electrons as the length of the oligomer is increased. With these measurements, we illustrate a new means to tune p- and n-type transport in organic materials.

  17. Multiphoton cascade absorption in single molecule fluorescence saturation spectroscopy.

    PubMed

    Winckler, Pascale; Jaffiol, Rodolphe

    2013-05-01

    Saturation spectroscopy is a relevant method to investigate photophysical parameters of single fluorescent molecules. Nevertheless, the impact of a gradual increase, over a broad range, of the laser excitation on the intramolecular dynamics is not completely understood, particularly concerning their fluorescence emission (the so-called brightness). Thus, we propose a comprehensive theoretical and experimental study to interpret the unexpected evolution of the brightness with the laser power taking into account the cascade absorption of two and three photons. Furthermore, we highlight the key role played by the confocal observation volume in fluorescence saturation spectroscopy of single molecules in solution. PMID:23521543

  18. The statistics of single molecule detection: An overview

    SciTech Connect

    Enderlein, J.; Robbins, D.L.; Ambrose, W.P.

    1995-12-31

    An overview of our recent results in modeling single molecule detection in fluid flow is presented. Our mathematical approach is based on a path integral representation. The model accounts for all experimental details, such as light collection, laser excitation, hydrodynamics and diffusion, and molecular photophysics. Special attention is paid to multiple molecule crossings through the detection volume. Numerical realization of the theory is discussed. Measurements of burst size distributions in single B-phycoerythrin molecule detection experiments are presented and compared with theoretical predictions.

  19. Single Molecule Studies on Dynamics in Liquid Crystals

    PubMed Central

    Täuber, Daniela; von Borczyskowski, Christian

    2013-01-01

    Single molecule (SM) methods are able to resolve structure related dynamics of guest molecules in liquid crystals (LC). Highly diluted small dye molecules on the one hand explore structure formation and LC dynamics, on the other hand they report about a distortion caused by the guest molecules. The anisotropic structure of LC materials is used to retrieve specific conformation related properties of larger guest molecules like conjugated polymers. This in particular sheds light on organization mechanisms within biological cells, where large molecules are found in nematic LC surroundings. This review gives a short overview related to the application of highly sensitive SM detection schemes in LC. PMID:24077123

  20. Detection of pathogenic DNA at the single-molecule level

    NASA Astrophysics Data System (ADS)

    Yahiatène, Idir; Klamp, Tobias; Schüttpelz, Mark; Sauer, Markus

    2011-03-01

    We demonstrate ultrasensitive detection of pathogenic DNA in a homogeneous assay at the single-molecule level applying two-color coincidence analysis. The target molecule we quantify is a 100 nucleotide long synthetic single-stranded oligonucleotide adapted from Streptococcus pneumoniae, a bacterium causing lower respiratory tract infections. Using spontaneous hybridization of two differently fluorescing Molecular Beacons we demonstrate a detection sensitivity of 100 fM (10-13M) in 30 seconds applying a simple microfluidic device with a 100 ?m channel and confocal two-color fluorescence microscopy.

  1. Stark effects after excited-state interfacial electron transfer at sensitized TiO(2) nanocrystallites.

    PubMed

    Ardo, Shane; Sun, Yali; Staniszewski, Aaron; Castellano, Felix N; Meyer, Gerald J

    2010-05-19

    Photophysical studies were performed with [Ru(dtb)(2)(dcb)](PF(6))(2) and cis-Ru(dcb)(dnb)(NCS)(2,) where dtb is 4,4'-(C(CH(3))(3))(2)-2,2'-bipyridine, dcb is 4,4'-(COOH)(2)-2,2'-bipyridine, and dnb is 4,4'-(CH(3)(CH(2))(8))(2)-2,2'-bipyridine), anchored to anatase TiO(2) particles ( approximately 15 nm in diameter) interconnected in a mesoporous, 10 mum thick film immersed in Li(+)-containing CH(3)CN electrolytes with iodide or phenothiazine donors. Pulsed-laser excitation resulted in rapid excited-state injection and donor oxidation to yield TiO(2)(e(-))s and oxidized donors, while the metal-to-ligand charge-transfer (MLCT) absorption spectrum of the Ru(II) coordination compounds differed from that which was initially excited. The spectral data were consistent with an underlying Stark effect and indicated that the surface electric field was not completely screened from the molecular sensitizer. The magnitude of the electric field was estimated to be approximately 270 MV/m from Li(+) titration experiments, corresponding to a approximately 40 mV potential drop. With iodide donors, the amplitude of the Stark effect decreased over time periods where charge recombination was absent, behavior attributed to "screening" of the electric field by interfacial ionic reorganization. The screening kinetics were nonexponential but were well described by the Kohlrausch-Williams-Watts model, from which a characteristic rate constant, tau(o)(-1), of approximately 1.5 x 10(5) s(-1) was abstracted. At least seven other sensitizers and five different cations, as well as on SnO(2) nanoparticle films, exhibited similar transient absorption behavior with iodide donor molecules indicating that the effect was quite general. In the presence of phenothiazine donors (or in the absence of an external donor), there was no clear evidence for screening, and the Stark effect disappeared concurrent with interfacial charge recombination. Complementary spectroelectrochemical studies of these same sensitized films displayed similar absorption spectra when the TiO(2) thin film was partially reduced with a forward bias. Spectral modeling in the absence of donor molecules as well as studies of TiO(2) thin films sensitized with two different Ru(II) compounds demonstrated that the electric field created by excited-state injection from one sensitizer influenced the absorption spectra of other sensitizers that had not undergone photoinduced electron injection. PMID:20423089

  2. Directional Raman Scattering from Single Molecules in the Feed Gaps of Optical Antennas

    E-print Network

    . KEYWORDS: Optical antenna, optical antenna chip, SERS enhancement, single molecule SERS, directional Raman (SERS).10-12 Reports of single molecule SERS (SMSERS)13,14 generated considerable interest but, with one the angular emission profiles of SERS at the single molecule level, showing that directional emission

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

    PubMed Central

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Mai, Danielle; Marciel, Amanda; Schroeder, Charles

    2014-03-01

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

  5. Single-molecule microscopy using tunable nanoscale confinement

    NASA Astrophysics Data System (ADS)

    McFaul, Christopher M. J.; Leith, Jason; Jia, Bojing; Michaud, François; Arsenault, Adriel; Martin, Andrew; Berard, Daniel; Leslie, Sabrina

    2013-09-01

    We present the design, construction and implementation of a modular microscopy device that transforms a basic inverted fluorescence microscope into a versatile single-molecule imaging system. The device uses Convex Lens- Induced Confinement (CLIC) to improve background rejection and extend diffusion-limited observation time. To facilitate its integration into a wide range of laboratories, this implementation of the CLIC device can use a standard flow-cell, into which the sample is loaded. By mechanically deforming the flow-cell, the device creates a tunable, wedge-shaped imaging chamber which we have modeled using finite element analysis simulations and characterized experimentally using interferometry. A powerful feature of CLIC imaging technology is the ability to examine single molecules under a continuum of applied confinement, from the nanometer to the micrometer scale. We demonstrate, using freely diffusing ?-phage DNA, that when the imposed confinement is on the scale of individual molecules their molecular conformations and diffusivity are altered significantly. To improve the flow-cell stiffness, seal, and re-usability, we have innovated the fabrication of thin PDMS-bonded flow-cells. The presented flow-cell CLIC technology can be combined with surface-lithography to provide an accessible and powerful approach to tune, trap, and image individual molecules under an extended range of imaging conditions. It is well-suited to tackling open problems in biophysics, biotechnology, nanotechnology, materials science, and chemistry.

  6. Single-molecule optical spectroscopy of autofluorescent proteins

    NASA Astrophysics Data System (ADS)

    Moerner, W. E.

    2002-12-01

    Several genetically encoded autofluorescent proteins are now available, in which the emission arises from the formation of a fluorophore directly from the amino acids of the protein sequence. These proteins are heavily used in cellular biology to assess gene expression and protein localization. The optical behavior of such proteins has recently been described in vitro at the single-molecule level. These investigations have explored several yellow-emitting mutants of the green fluorescent protein (GFP), the red-emitting DsRed protein, and the dual-GFP cameleon construct designed for fluorescence resonant energy transfer sensing of calcium ion binding. A variety of blinking, switching, and fluctuation effects have been observed, showing that several dark states are accessible after optical excitation, arising from variations in charge state, isomerization state, and photobleaching. The single-molecule spectroscopy of these systems will be surveyed by describing several illustrative examples. Although the autofluorescent proteins available at present need improvement in order to reach the performance of laser dye fluorophores, the novelty of these systems and their ease of use in biological contexts requires a continuing effort to understand the photophysical behavior.

  7. Second harmonic generation correlation spectroscopy for single molecule experiments.

    PubMed

    Liu, Jing; Irudayaraj, Joseph

    2013-11-01

    We demonstrate a single molecule detection approach to further extend the detection limit of correlation spectroscopic techniques through the Second Harmonic Generation Correlation Spectroscopy (SHGCS). SHG signals with high signal-to-noise ratio (SNR) were obtained from Barium titanium oxide, BaTiO(3) (BTO) nanocrystals (NCs) upon excitation by a femto-second laser fitted to the scanning confocal bench. The fluctuation of SHG signals from BTO NCs in transparent and turbid media was examined and their diffusion time and particle concentration were evaluated by autocorrelation. Proof-of-concept measurements indicate that water-dispersed BTO NCs at different concentrations yield an average diffusion time of 6.43 ± 0.68 ms and the detection limit of SHGCS was found to be at 814 ± 41 fM, approximately 100 folds below the detection limit of fluorescence correlation spectroscopy (FCS). The dynamics of BTO NCs was demonstrated in serum with high SNR and selectivity to show its potential applicability in biomedicine. High SNR and the sub-picomolar detection limit positions SHGCS as an excellent technique for ultralow single particle or single molecule experimentation in a complex medium. PMID:24216930

  8. Real-time single-molecule kinetics of trypsin proteolysis.

    PubMed

    Li, Jiangwei; Yeung, Edward S

    2008-11-15

    Single-molecule enzymatic kinetics and enantioselectivity were monitored in real time by using total internal reflection fluorescence microscopy. The 300-kDa poly(L-lysine) (PLL) or poly(D-lysine) (PDL) was labeled with Alexa Fluor 532 and was covalently immobilized on a dithiobis(succinimidyl undecanoate) self-assembled monolayer (DSU SAM) prepared on a gold substrate. The PLL/PDL chains were more accessible to trypsin on DSU SAM than when they were immobilized on a bare glass substrate. Short-chain PDL was further used as a blocking agent to prevent readsorption of the hydrolyzed lysine fragments. Chain shortening due to enzymatic hydrolysis resulted in the reduction of the individual fluorescence intensities. A broad distribution was obtained when 100 single-molecule half-lives were analyzed. However, the detailed hydrolysis process involved also a long-lived component and an induction period that varied significantly among molecules. Charge and steric heterogeneity at the surface are responsible for these features. In contrast, standard Michaelis-Menten fitting of the decrease in molecule numbers with time masked out all such details. PMID:18837511

  9. Watching Individual Proteins Acting on Single Molecules of DNA

    PubMed Central

    Amitani, Ichiro; Liu, Bian; Dombrowski, Christopher C.; Baskin, Ronald J.; Kowalczykowski, Stephen C.

    2011-01-01

    In traditional biochemical experiments, the behavior of individual proteins is obscured by ensemble averaging. To better understand the behavior of proteins that bind to and/or translocate on DNA, we have developed instrumentation that uses optical trapping, microfluidic solution delivery, and fluorescent microscopy to visualize either individual proteins or assemblies of proteins acting on single molecules of DNA. The general experimental design involves attaching a single DNA molecule to a polystyrene microsphere that is then used as a microscopic handle to manipulate individual DNA molecules with a laser trap. Visualization is achieved by fluorescently labeling either the DNA or the protein of interest, followed by direct imaging using high-sensitivity fluorescence microscopy. We describe the sample preparation and instrumentation used to visualize the interaction of individual proteins with single molecules of DNA. As examples, we describe the application of these methods to the study of proteins involved in recombination-mediated DNA repair, a process essential for the maintenance of genomic integrity. PMID:20580968

  10. Single molecule enzymology a la Michaelis-Menten

    E-print Network

    Ramon Grima; Nils Walter; Santiago Schnell

    2013-11-28

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

  11. 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

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

    PubMed Central

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

    2010-01-01

    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. PMID:20576476

  13. Ultra-Stable Organic Fluorophores for Single-Molecule Research

    PubMed Central

    Zheng, Qinsi; Juette, Manuel F.; Jockusch, Steffen; Wasserman, Michael R.; Zhou, Zhou; Altman, Roger B.; Blanchard, Scott C.

    2013-01-01

    Fluorescence provides a mechanism for achieving contrast in biological imaging that enables investigations of molecular structure, dynamics, and function at high spatial and temporal resolution. Small-molecule organic fluorophores have proven essential for such efforts and are widely used in advanced applications such as single-molecule and super-resolution microscopy. Yet, organic fluorophores, like all fluorescent species, exhibit instabilities in their emission characteristics, including blinking and photobleaching that limit their utility and performance. Here, we review the photophysics and photochemistry of organic fluorophores as they pertain to mitigating such instabilities, with a specific focus on the development of stabilized fluorophores through derivatization. Self-healing organic fluorophores, wherein the triplet state is intramolecularly quenched by a covalently attached protective agent, exhibit markedly improved photostabilities. We discuss the potential for further enhancements towards the goal of developing “ultra-stable” fluorophores spanning the visible spectrum and how such fluorophores are likely to impact the future of single-molecule research. PMID:24177677

  14. Single-molecule studies of bacterial protein translocation.

    PubMed

    Kedrov, Alexej; Kusters, Ilja; Driessen, Arnold J M

    2013-10-01

    In prokaryotes, a large share of the proteins are secreted from the cell through a process that requires their translocation across the cytoplasmic membrane. This process is mediated by the universally conserved Sec system with homologues in the endoplasmic reticulum and thylakoid membranes of eukaryotes. The Sec system also facilitates the membrane insertion of integral membrane proteins, an essential step along their folding pathway. In bacteria, the Sec system consists of the protein-conducting channel (SecYEG) that associates with soluble components, such as the motor protein SecA or translating ribosomes, and with integral membrane proteins, such as the heterotrimeric complex termed SecDFyajC and the YidC insertase. Over the past three decades, biochemical and structural studies have provided a comprehensive view of protein translocation, but the exact mechanistic details of this process remain to be resolved. For a number of other biomolecular systems, single-molecule biophysical analysis has efficiently complemented the conventional biochemical studies conducted in bulk, with high-sensitivity measurements probing the structure and dynamics of individual molecules in vitro and in vivo. Here, we review recent advances in studies of protein translocation employing single-molecule techniques with the aim of resolving molecular mechanisms, thereby providing a new and detailed view of the process. PMID:24024480

  15. 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

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

    SciTech Connect

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

    2007-07-05

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

  17. Common fluorescent proteins for single-molecule localization microscopy

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  18. 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.

  19. Studying the mechanism of CD47-SIRP? interactions on red blood cells by single molecule force spectroscopy

    NASA Astrophysics Data System (ADS)

    Pan, Yangang; Wang, Feng; Liu, Yanhou; Jiang, Junguang; Yang, Yong-Guang; Wang, Hongda

    2014-08-01

    The interaction forces and binding kinetics between SIRP? and CD47 were investigated by single-molecule force spectroscopy (SMFS) on both fresh and experimentally aged human red blood cells (hRBCs). We found that CD47 experienced a conformation change after oxidation, which influenced the interaction force and the position of the energy barrier between SIRP? and CD47. Our results are significant for understanding the mechanism of phagocytosis of red blood cells at the single molecule level.The interaction forces and binding kinetics between SIRP? and CD47 were investigated by single-molecule force spectroscopy (SMFS) on both fresh and experimentally aged human red blood cells (hRBCs). We found that CD47 experienced a conformation change after oxidation, which influenced the interaction force and the position of the energy barrier between SIRP? and CD47. Our results are significant for understanding the mechanism of phagocytosis of red blood cells at the single molecule level. Electronic supplementary information (ESI) available: Experimental section. See DOI: 10.1039/c4nr02889a

  20. Magnetic field dependent transport through a Mn4 single-molecule magnet

    NASA Astrophysics Data System (ADS)

    Haque, F.; Langhirt, M.; del Barco, E.; Taguchi, T.; Christou, G.

    2011-04-01

    We present a preliminary study of the single-electron transport response of a Mn4 single-molecule magnet in which pyridyl-alkoxide groups have been added to electrically protect the magnetic core and to increase the stability of the molecule during the experiments. Three-terminal single-electron transistors with nanogapped gold electrodes formed by electromigration and a naturally oxidized aluminum backgate were used to perform experiments at temperatures down to 240 mK in the presence of arbitrarily oriented magnetic fields. Coulomb blockade and electronic excitations that curve with the magnetic field and present zero-field splitting represent evidence of magnetic anisotropy. Level anticrossings and large excitation slopes are associated with the behavior of molecular states with high-spin values (S ˜ 9), as expected from Mn4.

  1. Adsorption-induced conformational isomerization of alkyl-substituted thiophene oligomers on Au(111): impact on the interfacial electronic structure.

    PubMed

    Taber, Benjamen N; Kislitsyn, Dmitry A; Gervasi, Christian F; Mannsfeld, Stefan C B; Zhang, Lei; Briseno, Alejandro L; Nazin, George V

    2015-07-22

    Alkyl-substituted quaterthiophenes on Au(111) form dimers linked by their alkyl substituents and, instead of adopting the trans conformation found in bulk oligothiophene crystals, assume cis conformations. Surprisingly, the impact of the conformation is not decisive in determining the lowest unoccupied molecular orbital energy. Scanning tunneling microscopy and spectroscopy of the adsorption geometries and electronic structures of alkyl-substituted quaterthiophenes show that the orbital energies vary substantially because of local variations in the Au(111) surface reactivity. These results demonstrate that interfacial oligothiophene conformations and electronic structures may differ substantially from those expected based on the band structures of bulk oligothiophene crystals. PMID:26153900

  2. Linker dependence of interfacial electron transfer rates in Fe(II)-polypyridine sensitized solar cells

    NASA Astrophysics Data System (ADS)

    Bowman, David N.; Mukherjee, Sriparna; Barnes, Lyndsay J.; Jakubikova, Elena

    2015-04-01

    Dye-sensitized solar cells (DSSCs) convert solar energy to electricity employing dye molecules attached to a semiconductor surface. Some of the most efficient DSSCs use Ru-based chromophores. Fe-based dyes represent a cheaper and more environmentally friendly alternative to these expensive and toxic dyes. The photoactive state of Fe-based chromophores responsible for charge-separation at the dye-semiconductor interface is, however, deactivated on a sub-picosecond time scale via the intersystem crossing (ISC) into a manifold of low-lying photo-inactive quintet states. Therefore, development of Fe-based dyes capable of fast interfacial electron transfer (IET) leading to efficient charge separation on a time scale competitive with the ISC events is important. This work investigates how linker groups anchoring a prototypical Fe-based dye [Fe(bpy-L)2(CN)2] (bpy = 2,2?-bipyridine, L = linker group) onto the TiO2 semiconductor surface influence the IET rates in the dye-semiconductor assemblies. Linker groups investigated include carboxylic acid, phosphonic acid, hydroxamate, catechol, and acetylacetonate. We employ time-dependent density functional theory (TD-DFT) to obtain absorption spectra of [Fe(bpy-L)2(CN)2] with each linker, and quantum dynamics simulations to investigate the IET rates between the dye and the (101) TiO2 anatase surface. For all attachments, TD-DFT calculations show similar absorption spectra with two main bands corresponding to the metal-to-ligand charge transfer transitions. The quantum dynamics simulations predict that the utilization of the hydroxamate linker instead of the commonly used carboxylic acid linker will lead to a more efficient IET and better photon-to-current conversion efficiencies in Fe(II)-polypyridine sensitized solar cells.

  3. Linker dependence of interfacial electron transfer rates in Fe(II)-polypyridine sensitized solar cells.

    PubMed

    Bowman, David N; Mukherjee, Sriparna; Barnes, Lyndsay J; Jakubikova, Elena

    2015-04-10

    Dye-sensitized solar cells (DSSCs) convert solar energy to electricity employing dye molecules attached to a semiconductor surface. Some of the most efficient DSSCs use Ru-based chromophores. Fe-based dyes represent a cheaper and more environmentally friendly alternative to these expensive and toxic dyes. The photoactive state of Fe-based chromophores responsible for charge-separation at the dye-semiconductor interface is, however, deactivated on a sub-picosecond time scale via the intersystem crossing (ISC) into a manifold of low-lying photo-inactive quintet states. Therefore, development of Fe-based dyes capable of fast interfacial electron transfer (IET) leading to efficient charge separation on a time scale competitive with the ISC events is important. This work investigates how linker groups anchoring a prototypical Fe-based dye [Fe(bpy-L)2(CN)2] (bpy = 2,2'-bipyridine, L = linker group) onto the TiO2 semiconductor surface influence the IET rates in the dye-semiconductor assemblies. Linker groups investigated include carboxylic acid, phosphonic acid, hydroxamate, catechol, and acetylacetonate. We employ time-dependent density functional theory (TD-DFT) to obtain absorption spectra of [Fe(bpy-L)2(CN)2] with each linker, and quantum dynamics simulations to investigate the IET rates between the dye and the (101) TiO2 anatase surface. For all attachments, TD-DFT calculations show similar absorption spectra with two main bands corresponding to the metal-to-ligand charge transfer transitions. The quantum dynamics simulations predict that the utilization of the hydroxamate linker instead of the commonly used carboxylic acid linker will lead to a more efficient IET and better photon-to-current conversion efficiencies in Fe(II)-polypyridine sensitized solar cells. PMID:25767105

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

    NASA Astrophysics Data System (ADS)

    Strano, Michael

    2009-03-01

    Nanoscale sensing elements offer promise for single molecule analyte detection in physically or biologically constrained environments. Molecular adsorption can be amplified via modulation of sharp singularities in the electronic density of states that arise from 1D quantum confinement [1]. Single-walled carbon nanotubes (SWNT), as single molecule optical sensors [2-3], offer unique advantages such as photostable near-infrared (n-IR) emission for prolonged detection through biological media, single-molecule sensitivity and, nearly orthogonal optical modes for signal transduction that can be used to identify distinct classes of analytes. Selective binding to the SWNT surface is difficult to engineer [4]. In this lecture, we will briefly review the immerging field of fluorescent diagnostics using band gap emission from SWNT. In recent work, we demonstrate that even a single pair of SWNT provides at least four optical modes that can be modulated to uniquely fingerprint chemical agents by the degree to which they alter either the emission band intensity or wavelength. We validate this identification method in vitro by demonstrating detection and identification of six genotoxic analytes, including chemotherapeutic drugs and reactive oxygen species (ROS), which are spectroscopically differentiated into four distinct classes. We also demonstrate single-molecule sensitivity in detecting hydrogen peroxide, one of the most common genotoxins and an important cellular signal. Finally, we employ our sensing and fingerprinting method of these analytes in real time within live 3T3 cells, demonstrating the first multiplexed optical detection from a nanoscale biosensor and the first label-free tool to optically discriminate between genotoxins. We will also discuss our recent efforts to fabricate biomedical sensors for real time detection of glucose and other important physiologically relevant analytes in-vivo. The response of embedded SWNT in a swellable hydrogel construct to osmotic pressure gradients will be discussed, as well as its potential as a unique transduction mechanism for a new class of implantable sensors. [4pt] [1] Saito, R., Dresselhaus, G. & Dresselhaus, M. S. Physical Properties of Carbon Nanotubes (Imperial College Press, London, 1998). [0pt] [2] Barone, P. W., Baik, S., Heller, D. A. & Strano, M. S. Near-Infrared Optical Sensors Based on Single-Walled Carbon Nanotubes. Nature Materials 4, 86-92 (2005). [0pt] [3] Jeng, E. S., Moll, A. E., Roy, A. C., Gastala, J. B. & Strano, M. S. Detection of DNA hybridization using the near infrared band-gap fluorescence of single-walled carbon nanotubes. Nano Letters 6, 371-375 (2006). [0pt] [4] Heller, D. A. et al. Optical detection of DNA conformational polymorphism on single-walled carbon nanotubes. Science 311, 508-511 (2006).

  5. Placing Single-Molecule T4 Lysozyme Enzymes on a Bacterial Cell Surface: Toward Probing Single-Molecule Enzymatic Reaction in Living Cells

    SciTech Connect

    Hu, Dehong; Lu, H PETER.

    2004-07-01

    TheT4 lysozyme enzymatic hydrolyzation reaction of bacterial cell walls is an important biological process, and single-molecule enzymatic reaction dynamics had been studied under physiological condition using purified E. Coli cell walls as substrates. Here, we report progress toward characterizing the T4 lysozyme enzymatic reaction on a living bacterial cell wall using a combined single-molecule placement and spectroscopy. Placing a dye-labeled single T4 lysozyme molecule on a targeted cell wall by using a hydrodynamic micro-injection approach, we monitored single-molecule rotational motions during binding, attachment to, and dissociation from the cell wall by tracing single-molecule fluorescence intensity time trajectories and polarization. The single-molecule attachment duration of the T4 lysozyme to the cell wall during enzymatic reactions was typically shorter than photobleaching time under physiological conditions.

  6. Single molecule thermodynamics of ATP synthesis by F$_1$-ATPase

    E-print Network

    Shoichi Toyabe; Eiro Muneyuki

    2015-01-16

    F$_\\mathrm{o}$F$_1$-ATP synthase is a factory for synthesizing ATP in virtually all cells. Its core machinery is the subcomplex F$_1$-motor (F$_1$-ATPase) and performs the reversible mechanochemical coupling. Isolated F$_1$-motor hydrolyzes ATP, which is accompanied by unidirectional rotation of its central $\\gamma$-shaft. When a strong opposing torque is imposed, the $\\gamma$-shaft rotates in the opposite direction and drives the F$_1$-motor to synthesize ATP. This mechanical-to-chemical free-energy transduction is the final and central step of the multistep cellular ATP-synthetic pathway. Here, we determined the amount of mechanical work exploited by the F$_1$-motor to synthesize an ATP molecule during forced rotations using methodology combining a nonequilibrium theory and single molecule measurements of responses to external torque. We found that the internal dissipation of the motor is negligible even during rotations far from a quasistatic process.

  7. Mechanisms of cellular proteostasis: insights from single-molecule approaches.

    PubMed

    Bustamante, Carlos J; Kaiser, Christian M; Maillard, Rodrigo A; Goldman, Daniel H; Wilson, Christian A M

    2014-01-01

    Cells employ a variety of strategies to maintain proteome homeostasis. Beginning during protein biogenesis, the translation machinery and a number of molecular chaperones promote correct de novo folding of nascent proteins even before synthesis is complete. Another set of molecular chaperones helps to maintain proteins in their functional, native state. Polypeptides that are no longer needed or pose a threat to the cell, such as misfolded proteins and aggregates, are removed in an efficient and timely fashion by ATP-dependent proteases. In this review, we describe how applications of single-molecule manipulation methods, in particular optical tweezers, are shedding new light on the molecular mechanisms of quality control during the life cycles of proteins. PMID:24895851

  8. 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.

  9. Lipid mobility in supported lipid bilayers by single molecule tracking

    NASA Astrophysics Data System (ADS)

    Kohram, Maryam; Shi, Xiaojun; Smith, Adam

    2015-03-01

    Phospholipid bilayers are the main component of cell membranes and their interaction with biomolecules in their immediate environment is critical for cellular functions. These interactions include the binding of polycationic polymers to lipid bilayers which affects many cell membrane events. As an alternative method of studying live cell membranes, we assemble a supported lipid bilayer and investigate its binding with polycationic polymers in vitro by fluorescently labeling the molecules of the supported lipid bilayer and tracking their mobility. In this work, we use single molecule tracking total internal reflection fluorescence microscopy (TIRF) to study phosphatidylinositol phosphate (PIP) lipids with and without an adsorbed polycationic polymer, quaternized polyvinylpyridine (QPVP). Individual molecular trajectories are obtained from the experiment, and a Brownian diffusion model is used to determine diffusion coefficients through mean square displacements. Our results indicate a smaller diffusion coefficient for the supported lipid bilayers in the presence of QPVP in comparison to its absence, revealing that their binding causes a decrease in lateral mobility.

  10. Measurement of work in single-molecule pulling experiments

    NASA Astrophysics Data System (ADS)

    Mossa, Alessandro; de Lorenzo, Sara; Huguet, Josep Maria; Ritort, Felix

    2009-06-01

    A main goal of single-molecule experiments is to evaluate equilibrium free energy differences by applying fluctuation relations to repeated work measurements along irreversible processes. We quantify the error that is made in a free energy estimate by means of the Jarzynski equality when the accumulated work expended on the whole system (including the instrument) is erroneously replaced by the work transferred to the subsystem consisting of the sole molecular construct. We find that the error may be as large as 100%, depending on the number of experiments and on the bandwidth of the data acquisition apparatus. Our theoretical estimate is validated by numerical simulations and pulling experiments on DNA hairpins using optical tweezers.

  11. Single-Molecule Observation of Long Jumps in Polymer Adsorption

    E-print Network

    Changqian Yu; Juan Guan; Kejia Chen; Sung Chul Bae; Steve Granick

    2013-06-22

    Single-molecule fluorescence imaging of adsorption onto initially-bare surfaces shows that polymer chains need not localize immediately after arrival. In a system optimized to present limited adsorption sites (quartz surface to which polyethylene glycol (PEG) is exposed in aqueous solution at pH = 8.2) we find that some chains diffuse back into bulk solution and re-adsorb at some distance away, sometimes multiple times before either they localize at a stable position or else diffuse away into bulk solution. This mechanism of surface diffusion is considerably more rapid than the classical model in which adsorbed polymers crawl on surfaces while the entire molecule remains adsorbed. The trajectories with jumps follow a truncated Levy distribution of step size with limiting slope -2.5, consistent with a well-defined, rapid surface diffusion coefficient over the times we observe.

  12. Identifying Transport Behavior of Single-Molecule Trajectories

    PubMed Central

    Regner, Benjamin M.; Tartakovsky, Daniel M.; Sejnowski, Terrence J.

    2014-01-01

    Models of biological diffusion-reaction systems require accurate classification of the underlying diffusive dynamics (e.g., Fickian, subdiffusive, or superdiffusive). We use a renormalization group operator to identify the anomalous (non-Fickian) diffusion behavior from a short trajectory of a single molecule. The method provides quantitative information about the underlying stochastic process, including its anomalous scaling exponent. The classification algorithm is first validated on simulated trajectories of known scaling. Then it is applied to experimental trajectories of microspheres diffusing in cytoplasm, revealing heterogeneous diffusive dynamics. The simplicity and robustness of this classification algorithm makes it an effective tool for analysis of rare stochastic events that occur in complex biological systems. PMID:25418303

  13. Single-molecule analysis of telomerase structure and function.

    PubMed

    Hengesbach, Martin; Akiyama, Benjamin M; Stone, Michael D

    2011-12-01

    The telomerase ribonucleoprotein is a specialized reverse transcriptase required to maintain protective chromosome end-capping structures called telomeres. In most cells, telomerase is not active and the natural shortening of telomeres with each round of DNA replication ultimately triggers cell growth arrest. In contrast, the presence of telomerase confers a high level of renewal capacity upon rapidly dividing cells. Telomerase is aberrantly activated in 90% of human cancers and thus represents an important target for anticancer therapeutics. However, the naturally low abundance of telomerase has hampered efforts to obtain high-resolution models for telomerase structure and function. To circumvent these challenges, single-molecule techniques have recently been employed to investigate telomerase assembly, structure, and catalysis. PMID:22057212

  14. Exploiting single-molecule transcript sequencing for eukaryotic gene prediction.

    PubMed

    Minoche, André E; Dohm, Juliane C; Schneider, Jessica; Holtgräwe, Daniela; Viehöver, Prisca; Montfort, Magda; Sörensen, Thomas Rosleff; Weisshaar, Bernd; Himmelbauer, Heinz

    2015-01-01

    We develop a method to predict and validate gene models using PacBio single-molecule, real-time (SMRT) cDNA reads. Ninety-eight percent of full-insert SMRT reads span complete open reading frames. Gene model validation using SMRT reads is developed as automated process. Optimized training and prediction settings and mRNA-seq noise reduction of assisting Illumina reads results in increased gene prediction sensitivity and precision. Additionally, we present an improved gene set for sugar beet (Beta vulgaris) and the first genome-wide gene set for spinach (Spinacia oleracea). The workflow and guidelines are a valuable resource to obtain comprehensive gene sets for newly sequenced genomes of non-model eukaryotes. PMID:26328666

  15. Single-molecule protein sequencing through fingerprinting: computational assessment

    NASA Astrophysics Data System (ADS)

    Yao, Yao; Docter, Margreet; van Ginkel, Jetty; de Ridder, Dick; Joo, Chirlmin

    2015-10-01

    Proteins are vital in all biological systems as they constitute the main structural and functional components of cells. Recent advances in mass spectrometry have brought the promise of complete proteomics by helping draft the human proteome. Yet, this commonly used protein sequencing technique has fundamental limitations in sensitivity. Here we propose a method for single-molecule (SM) protein sequencing. A major challenge lies in the fact that proteins are composed of 20 different amino acids, which demands 20 molecular reporters. We computationally demonstrate that it suffices to measure only two types of amino acids to identify proteins and suggest an experimental scheme using SM fluorescence. When achieved, this highly sensitive approach will result in a paradigm shift in proteomics, with major impact in the biological and medical sciences.

  16. Single molecule thermodynamics of ATP synthesis by F1-ATPase

    NASA Astrophysics Data System (ADS)

    Toyabe, Shoichi; Muneyuki, Eiro

    2015-01-01

    FoF1-ATP synthase is a factory for synthesizing ATP in virtually all cells. Its core machinery is the subcomplex F1-motor (F1-ATPase) and performs the reversible mechanochemical coupling. The isolated F1-motor hydrolyzes ATP, which is accompanied by unidirectional rotation of its central ? -shaft. When a strong opposing torque is imposed, the ? -shaft rotates in the opposite direction and drives the F1-motor to synthesize ATP. This mechanical-to-chemical free-energy transduction is the final and central step of the multistep cellular ATP-synthetic pathway. Here, we determined the amount of mechanical work exploited by the F1-motor to synthesize an ATP molecule during forced rotations using a methodology combining a nonequilibrium theory and single molecule measurements of responses to external torque. We found that the internal dissipation of the motor is negligible even during rotations far from a quasistatic process.

  17. X-ray induced demagnetization of single-molecule magnets

    SciTech Connect

    Dreiser, Jan; Westerström, Rasmus; Piamonteze, Cinthia; Nolting, Frithjof; Rusponi, Stefano; Brune, Harald; Yang, Shangfeng; Popov, Alexey; Dunsch, Lothar; Greber, Thomas

    2014-07-21

    Low-temperature x-ray magnetic circular dichroism measurements on the endohedral single-molecule magnet DySc{sub 2}N@C{sub 80} at the Dy M{sub 4,5} edges reveal a shrinking of the opening of the observed hysteresis with increasing x-ray flux. Time-dependent measurements show that the exposure of the molecules to x-rays resonant with the Dy M{sub 5} edge accelerates the relaxation of magnetization more than off-resonant x-rays. The results cannot be explained by a homogeneous temperature rise due to x-ray absorption. Moreover, the observed large demagnetization cross sections indicate that the resonant absorption of one x-ray photon induces the demagnetization of many molecules.

  18. Studies of a nickel-based single-molecule magnet.

    PubMed

    Andres, Hanspeter; Basler, Reto; Blake, Alexander J; Cadiou, Cyril; Chaboussant, Gregory; Grant, Craig M; Güdel, Hans-Ulrich; Murrie, Mark; Parsons, Simon; Paulsen, Carley; Semadini, Fabrizzio; Villar, Vincent; Wernsdorfer, Wolfgang; Winpenny, Richard E P

    2002-11-01

    A cyclic complex [Ni(12)(chp)(12)(O(2)CMe)(12)(thf)(6)(H(2)O)(6)] (1) has been synthesised and studied (chp=6-chloro-2-pyridonate). Complex 1 exhibits ferromagnetic exchange between the S=1 centres, giving an S=12 spin ground state. Detailed studies demonstrate that it is a single-molecule magnet with an energy barrier of approximately 10 K for reorientation of magnetisation. Resonant quantum tunnelling is also observed. The field between resonances allows accurate measurement of D, which is 0.067 K. Inelastic neutron scattering studies have allowed exchange parameters to be derived accurately, which was impossible from susceptibility data alone. Three exchange interactions are required: two ferromagnetic nearest neighbour interactions of approximately 11 and 2 cm(-1) and an anti-ferromagnetic next nearest neighbour interaction of -0.9 cm(-1). PMID:12397588

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

    E-print Network

    F. Ritort

    2006-09-15

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

  20. Fluorescent Nanoconjugate Derivatives with Enhanced Photostability for Single Molecule Imaging.

    PubMed

    Reilly, Daniel T; Kim, Sung Hoon; Katzenellenbogen, John A; Schroeder, Charles M

    2015-11-01

    Fluorescence-based imaging techniques critically rely on bright and photostable probes for precise detection of biological molecules. Recently, a new class of multichromophoric probes based on fluorescent dendrimer nanoconjugates (FDNs) was developed for single molecule fluorescence microscopy (SMFM). FDNs are generated by covalent conjugation of multiple fluorescent dyes onto macromolecular polymeric scaffolds and show marked increases in brightness and long-term photostability relative to their single organic dye constituents. Multichromophoric probes, however, are generally known to suffer from transient fluorescence emission intensities and long excursions into dark states. To overcome these issues, photostabilizers can be added to bulk solution, though some small molecule additives may exhibit poor aqueous solubility or biological toxicity. In this work, we develop enhanced FDN derivatives by covalently linking a redox-active photostabilizer (Trolox) directly onto FDN molecular scaffolds. In one approach, multiple organic dyes (Cy5) and Trolox molecules are randomly distributed on dendritic scaffolds in tunable stoichiometric amounts, and in a second approach, Cy5 dyes are covalently linked to Trolox in a precise 1:1 stoichiometry followed by covalent attachment of Cy5-Trolox conjugates onto dendrimers. In all cases, FDN-Trolox conjugates show increases in photostability, brightness, and reduced fluctuations in transient fluorescent intensity relative to FDN probes. Bulk and single molecule photophysical data for FDN probes are compared to single self-healing dye systems such as Cy5-Trolox, and as a proof-of-principle demonstration, we use FDN-Trolox derivatives for bulk immunofluorescence imaging. Overall, our work suggests that self-healed multichromophoric systems such as FDN-Trolox probes present a useful strategy for increasing fluorescent probe photostability. PMID:26461122

  1. 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.

  2. 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

  3. Theory for rates, equilibrium constants, and Brønsted slopes in F1-ATPase single molecule imaging experiments.

    PubMed

    Volkán-Kacsó, Sándor; Marcus, Rudolph A

    2015-11-17

    A theoretical model of elastically coupled reactions is proposed for single molecule imaging and rotor manipulation experiments on F1-ATPase. Stalling experiments are considered in which rates of individual ligand binding, ligand release, and chemical reaction steps have an exponential dependence on rotor angle. These data are treated in terms of the effect of thermodynamic driving forces on reaction rates, and lead to equations relating rate constants and free energies to the stalling angle. These relations, in turn, are modeled using a formalism originally developed to treat electron and other transfer reactions. During stalling the free energy profile of the enzymatic steps is altered by a work term due to elastic structural twisting. Using biochemical and single molecule data, the dependence of the rate constant and equilibrium constant on the stall angle, as well as the Børnsted slope are predicted and compared with experiment. Reasonable agreement is found with stalling experiments for ATP and GTP binding. The model can be applied to other torque-generating steps of reversible ligand binding, such as ADP and Pi release, when sufficient data become available. PMID:26483483

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

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

    2012-10-28

    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

  6. Magnetic behaviour of TbPc2 single-molecule magnets chemically grafted on silicon surface

    NASA Astrophysics Data System (ADS)

    Mannini, Matteo; Bertani, Federico; Tudisco, Cristina; Malavolti, Luigi; Poggini, Lorenzo; Misztal, Kasjan; Menozzi, Daniela; Motta, Alessandro; Otero, Edwige; Ohresser, Philippe; Sainctavit, Philippe; Condorelli, Guglielmo G.; Dalcanale, Enrico; Sessoli, Roberta

    2014-08-01

    Single-molecule magnets (SMMs) are among the most promising molecular systems for the development of novel molecular electronics based on spin transport. Going beyond investigations focused on physisorbed SMMs, in this work the robust grafting of terbium(III) bis(phthalocyaninato) complexes to a silicon surface from a diluted solution is achieved by rational chemical design yielding the formation of a partially oriented monolayer on the conducting substrate. Here by exploiting the surface sensitivity of X-ray circular magnetic dichroism, we evidence an enhancement of the magnetic bistability of this SMM, in contrast to the dramatic reduction of the magnetic hysteresis that characterizes monolayer deposits evaporated on noble and ferromagnetic metals. Photoelectron spectroscopy investigations and density functional theory analysis suggest a non-innocent role played by the silicon substrate, evidencing the potentiality of this approach for robust integration of bistable magnetic molecules in electronic devices.

  7. An approach for an advanced anode interfacial layer with electron-blocking ability to achieve high-efficiency organic photovoltaics.

    PubMed

    Yeo, Jun-Seok; Yun, Jin-Mun; Kang, Minji; Khim, Dongyoon; Lee, Seung-Hoon; Kim, Seok-Soon; Na, Seok-In; Kim, Dong-Yu

    2014-11-26

    The interfacial properties of PEDOT:PSS, pristine r-GO, and r-GO with sulfonic acid (SR-GO) in organic photovoltaic are investigated to elucidate electron-blocking property of PEDOT:PSS anode interfacial layer (AIL), and to explore the possibility of r-GO as electron-blocking layers. The SR-GO results in an optimized power conversion efficiency of 7.54% for PTB7-th:PC71BM and 5.64% for P3HT:IC61BA systems. By combining analyses of capacitance-voltage and photovoltaic-parameters dependence on light intensity, it is found that recombination process at SR-GO/active film is minimized. In contrast, the devices using r-GO without sulfonic acid show trap-assisted recombination. The enhanced electron-blocking properties in PEDOT:PSS and SR-GO AILs can be attributed to surface dipoles at AIL/acceptor. Thus, for electron-blocking, the AIL/acceptor interface should be importantly considered in OPVs. Also, by simply introducing sulfonic acid unit on r-GO, excellent contact selectivity can be realized in OPVs. PMID:25343490

  8. Investigations of electron-injection mechanisms and interfacial chemical reactions of Bphen doped with rubidium carbonate in OLEDs

    NASA Astrophysics Data System (ADS)

    Chen, Mei-Hsin; Leem, Dong-Seok; Lin, C. T.; Lee, G. R.; Pi, Tun-Wen; Kim, Jang-Joo; Wu, Chih-I.

    2008-08-01

    The effectiveness of carrier injection in electron transport layers has been investigated for high efficiency organic light emitting devices. Via ultraviolet and x-ray photoemission spectroscopy (UPS and XPS), the carrier band structures, interfacial interactions and electron-injection mechanisms are discussed. Acting as a good hole blocking layer with higher mobility for electrons, 4,7-diphenyl-1, 10-phenanthroline (Bphen) was chosen to be the electron transport layer. The performance of device used Rb2CO3 doped into Bphen is obviously better than the device even used LiF with aluminum as cathode. According to the UPS spectra, the Fermi level of Bphen after doped with the ratio of 2% and 8% rubidium carbonate (Rb2CO3) shifts toward the lowest unoccupied molecular orbital as a result of charge transfer from rubidium atom to Bphen, showing that electron-injection ability would be improved based on strong n-type doping effect. Moreover, when aluminum is deposited as a thin layer on the surface of Bphen doped with Rb2CO3, the peak around 5 eV, which is attributed to the delocalized Pi-electrons decreases as gap states appear around 2.8 eV at the top of the highest occupied molecular orbital. There are changes in the binding energy of core levels of rubidium, nitrogen and aluminum, which indicates a negative charge transfer to Bphen at the interface that could have the reduction of electroninjection barrier height. Thus, the interfacial chemical reaction leads to the excellent electron injection ability could be demonstrated.

  9. Single Molecule Screening of Disease DNA Without Amplification

    SciTech Connect

    Ji-Young Lee

    2006-12-12

    The potential of single molecule detection as an analysis tool in biological and medical fields is well recognized today. This fast evolving technique will provide fundamental sensitivity to pick up individual pathogen molecules, and therefore contribute to a more accurate diagnosis and a better chance for a complete cure. Many studies are being carried out to successfully apply this technique in real screening fields. In this dissertation, several attempts are shown that have been made to test and refine the application of the single molecule technique as a clinical screening method. A basic applicability was tested with a 100% target content sample, using electrophoretic mobility and multiple colors as identification tools. Both electrophoretic and spectral information of individual molecule were collected within a second, while the molecule travels along the flow in a capillary. Insertion of a transmission grating made the recording of the whole spectrum of a dye-stained molecule possible without adding complicated instrumental components. Collecting two kinds of information simultaneously and combining them allowed more thorough identification, up to 98.8% accuracy. Probing mRNA molecules with fluorescently labeled cDNA via hybridization was also carried out. The spectral differences among target, probe, and hybrid were interpreted in terms of dispersion distances after transmission grating, and used for the identification of each molecule. The probes were designed to have the least background when they are free, but have strong fluorescence after hybridization via fluorescence resonance energy transfer. The mRNA-cDNA hybrids were further imaged in whole blood, plasma, and saliva, to test how far a crude preparation can be tolerated. Imaging was possible with up to 50% of clear bio-matrix contents, suggesting a simple lysis and dilution would be sufficient for imaging for some cells. Real pathogen DNA of human papillomavirus (HPV) type-I6 in human genomic DNA was probed with fluorescently-labeled probe molecules and imaged. When only the probes were stained and hybridized in a vial, it had 6 orders of magnitude dynamic range with a detection limit of {approx}0.7 copy/cell. A second dye was added to lower the false positive levels. Although there was a sacrifice of two orders of magnitude in detection limit, the number of false positives was reduced to zero. HPV-16 DNA was also hybridized and detected on surface-tethered probes. When the entire human genomic DNA and HPV was labeled and hybridized, the detection limit was similar to that of one-color assay detected in capillary. However, non-specific adsorption was high, and the dynamic range was narrow because of saturation of the surface and electrostatic repulsion between hybridized targets on the surface. The second probe was introduced to lower non-specific adsorption, and the strategy succeeded in 4 orders of magnitude linear dynamic range in a log-log plot, along with 2.4 copies/cell detection limit. DNA extracts of cell lines that contained a known copy number of HPV-16 DNA were tested with the four strategies described above. The calculated numbers from observed molecule counts matched the known values. Results from the Pap test sample with added HPV DNA were similar to those of purified DNA, suggesting our method is compatible with the conventional Pap test sample collection method. Further optimization will be needed before this single molecule level detection and identification can actually be used in a real clinical lab, but it has good potential and applicability. Improvement such as automated imaging and scanning, more accurate data processing software as well as sensitive camera, should help increase the efficiency and throughput.

  10. Controlled interfacial electron dynamics in highly efficient Zn2 SnO4 -based dye-sensitized solar cells.

    PubMed

    Shin, Seong Sik; Kim, Dong Wook; Hwang, Daesub; Suk, Jae Ho; Oh, Lee Seul; Han, Byung Suh; Kim, Dong Hoe; Kim, Ju Seong; Kim, Dongho; Kim, Jin Young; Hong, Kug Sun

    2014-02-01

    Among ternary oxides, Zn2 SnO4 (ZSO) is considered for dye-sensitized solar cells (DSSCs) because of its wide bandgap, high optical transmittance, and high electrical conductivity. However, ZSO-based DSSCs have a poor performance record owing largely to the absence of systematic efforts to enhance their performance. Herein, general strategies are proposed to improve the performance of ZSO-based DSSCs involving interfacial engineering/modification of the photoanode. A conformal ZSO thin film (blocking layer) deposited at the fluorine-doped tin oxide-electrolyte interface by pulsed laser deposition suppressed the back-electron transfer effectively while maintaining a high optical transmittance, which resulted in a 22 % improvement in the short-circuit photocurrent density. Surface modification of ZSO nanoparticles (NPs) resulted in an ultrathin ZnO shell layer, a 9 % improvement in the open-circuit voltage, and a 4 % improvement in the fill factor because of the reduced electron recombination at the ZSO NPs-electrolyte interface. The ZSO-based DSSCs exhibited a faster charge injection and electron transport than their TiO2 -based counterparts, and their superior properties were not inhibited by the ZnO shell layer, which indicates their feasibility for highly efficient DSSCs. Each interfacial engineering strategy could be applied to the ZSO-based DSSC independently to lead to an improved conversion efficiency of 6 %, a very high conversion efficiency for a non-TiO2 based DSSC. PMID:24347268

  11. [Single-molecule observation of signal transduction on the plasma membrane].

    PubMed

    Iwasawa, Kokoro; Kusumi, Akihiro

    2007-02-01

    Recent advancements in single-molecule tracking methods with the nanometer-level precision allow researchers to observe the movement, recruitment, and activation of single molecules in the plasma membrane in living cells. The interaction, binding, and colocalization of two or more molecules in living cells are essential aspects of many biological molecular processes, and single-molecule technologies are very powerful tools for investigating these processes in live cells. Here, we introduce two of these investigation methods, "simultaneous, dual-color, single fluorescent molecule colocalization imaging" and" single molecule FRET(single -molecule fluorescent resonance energy transfer) ", for monitoring the colocalization or binding of two single molecules. Benchmarks have recently been established for these technologies by the research conducted in our laboratory, and thus can now be applied to wide ranges of studies for molecular interactions. PMID:17302264

  12. 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

  13. A layer-by-layer ZnO nanoparticle-PbS quantum dot self-assembly platform for ultrafast interfacial electron injection.

    PubMed

    Eita, Mohamed; Usman, Anwar; El-Ballouli, Ala'a O; Alarousu, Erkki; Bakr, Osman M; Mohammed, Omar F

    2015-01-01

    Absorbent layers of semiconductor quantum dots (QDs) are now used as material platforms for low-cost, high-performance solar cells. The semiconductor metal oxide nanoparticles as an acceptor layer have become an integral part of the next generation solar cell. To achieve sufficient electron transfer and subsequently high conversion efficiency in these solar cells, however, energy-level alignment and interfacial contact between the donor and the acceptor units are needed. Here, the layer-by-layer (LbL) technique is used to assemble ZnO nanoparticles (NPs), providing adequate PbS QD uptake to achieve greater interfacial contact compared with traditional sputtering methods. Electron injection at the PbS QD and ZnO NP interface is investigated using broadband transient absorption spectroscopy with 120 femtosecond temporal resolution. The results indicate that electron injection from photoexcited PbS QDs to ZnO NPs occurs on a time scale of a few hundred femtoseconds. This observation is supported by the interfacial electronic-energy alignment between the donor and acceptor moieties. Finally, due to the combination of large interfacial contact and ultrafast electron injection, this proposed platform of assembled thin films holds promise for a variety of solar cell architectures and other settings that principally rely on interfacial contact, such as photocatalysis. PMID:25163799

  14. Dependence of the direct electron transfer activity and adsorption kinetics of cytochrome c on interfacial charge properties.

    PubMed

    Wang, Gui-Xia; Wang, Min; Wu, Zeng-Qiang; Bao, Wen-Jing; Zhou, Yue; Xia, Xing-Hua

    2013-10-01

    With the advantages of in situ analysis and high surface sensitivity, surface-enhanced infrared absorption spectroscopy in attenuated total reflection mode (ATR-SEIRAS) combined with electrochemical methods has been employed to examine the interfacial direct electron transfer activity and adsorption kinetics of cytochrome c (cyt c). This work presents data on cyt c adsorption onto negatively charged mercaptohexanoic acid (MHA) and positively charged 6-amino-1-hexanethiol (MHN) self-assembled monolayers (SAMs) on gold nanofilm surfaces. The adsorbed cyt c displays a higher apparent electron transfer rate constant (33.5 ± 2.4 s(-1)) and apparent binding rate constant (73.1 ± 5.2 M(-1) s(-1)) at the MHA SAMs surface than those on the MHN SAMs surface. The results demonstrate that the surface charge density determines the protein adsorption kinetics, while the surface charge character determines the conformation and orientation of proteins assembled which in turn affects the direct electron transfer activity. PMID:23912152

  15. Interfacial electron transfer of glucose oxidase on poly(glutamic acid)-modified glassy carbon electrode and glucose sensing.

    PubMed

    Zhou, Xuechou; Tan, Bingcan; Zheng, Xinyu; Kong, Dexian; Li, Qinglu

    2015-11-15

    The interfacial electron transfer of glucose oxidase (GOx) on a poly(glutamic acid)-modified glassy carbon electrode (PGA/GCE) was investigated. The redox peaks measured for GOx and flavin adenine dinucleotide (FAD) are similar, and the anodic peak of GOx does not increase in the presence of glucose in a mediator-free solution. These indicate that the electroactivity of GOx is not the direct electron transfer (DET) between GOx and PGA/GCE and that the observed electroactivity of GOx is ascribed to free FAD that is released from GOx. However, efficient electron transfer occurred if an appropriate mediator was placed in solution, suggesting that GOx is active. The PGA/GCE-based biosensor showed wide linear response in the range of 0.5-5.5 mM with a low detection limit of 0.12 mM and high sensitivity and selectivity for measuring glucose. PMID:26278169

  16. Separation and counting of single molecules through nanofluidics, programmable electrophoresis, and nanoelectrode-gated tunneling and dielectric detection

    DOEpatents

    Lee, James W.; Thundat, Thomas G.

    2006-04-25

    An apparatus for carrying out the separation, detection, and/or counting of single molecules at nanometer scale. Molecular separation is achieved by driving single molecules through a microfluidic or nanofluidic medium using programmable and coordinated electric fields. In various embodiments, the fluidic medium is a strip of hydrophilic material on nonconductive hydrophobic surface, a trough produced by parallel strips of hydrophobic nonconductive material on a hydrophilic base, or a covered passageway produced by parallel strips of hydrophobic nonconductive material on a hydrophilic base together with a nonconductive cover on the parallel strips of hydrophobic nonconductive material. The molecules are detected and counted using nanoelectrode-gated electron tunneling methods, dielectric monitoring, and other methods.

  17. 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

  18. 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

  19. Flexible single molecule simulation of reaction-diffusion processes

    SciTech Connect

    Hellander, Stefan; Loetstedt, Per

    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.

  20. Extracting conformational memory from single-molecule kinetic data.

    PubMed

    Pressé, Steve; Lee, Julian; Dill, Ken A

    2013-01-17

    Single-molecule data often come in the form of stochastic time trajectories. A key question is how to extract an underlying kinetic model from the data. A traditional approach is to assume some discrete state model, that is, a model topology, and to assume that transitions between states are Markovian. The transition rates are then selected according to which ones best fit the data. However, in experiments, each apparent state can be a broad ensemble of states or can be hiding multiple interconverting states. Here, we describe a more general approach called the non-Markov memory kernel (NMMK) method. The idea is to begin with a very broad class of non-Markov models and to let the data directly select for the best possible model. To do so, we adapt an image reconstruction approach that is grounded in maximum entropy. The NMMK method is not limited to discrete state models for the data; it yields a unique model given the data, it gives error bars for the model, and it does not assume Markov dynamics. Furthermore, NMMK is less wasteful of data by letting the entire data set determine the model. When the data warrants, the NMMK gives a memory kernel that is Markovian. We highlight, by numerical example, how conformational memory extracted using this method can be translated into useful mechanistic insight. PMID:23259771

  1. De novo DNA synthesis using single molecule PCR

    PubMed Central

    Yehezkel, Tuval Ben; Linshiz, Gregory; Buaron, Hen; Kaplan, Shai; Shabi, Uri; Shapiro, Ehud

    2008-01-01

    The throughput of DNA reading (sequencing) has dramatically increased recently due to the incorporation of in vitro clonal amplification. The throughput of DNA writing (synthesis) is trailing behind, with cloning and sequencing constituting the main bottleneck. To overcome this bottleneck, an in vitro alternative for in vivo DNA cloning must be integrated into DNA synthesis methods. Here we show how a new single molecule PCR (smPCR)-based procedure can be employed as a general substitute to in vivo cloning thereby allowing for the first time in vitro DNA synthesis. We integrated this rapid and high fidelity in vitro procedure into our earlier recursive DNA synthesis and error correction procedure and used it to efficiently construct and error-correct a 1.8-kb DNA molecule from synthetic unpurified oligos completely in vitro. Although we demonstrate incorporating smPCR in a particular method, the approach is general and can be used in principle in conjunction with other DNA synthesis methods as well. PMID:18667587

  2. Profiling of Short RNAs Using Helicos Single-Molecule Sequencing

    PubMed Central

    Kapranov, Philipp; Ozsolak, Fatih; Milos, Patrice M.

    2012-01-01

    The importance of short (<200 nt) RNAs in cell biogenesis has been well documented. These short RNAs include crucial classes of molecules such as transfer RNAs, small nuclear RNA, microRNAs, and many others (reviewed in Storz et al., Annu Rev Biochem 74:199–217, 2005; Ghildiyal and Zamore, Nat Rev Genet 10:94–108, 2009). Furthermore, the realm of functional RNAs that fall within this size range is growing to include less well-characterized RNAs such as short RNAs found at the promoters and 3? termini of genes (Affymetrix ENCODE Transcriptome Project et al., Nature 457:1028–1032, 2009; Davis and Ares, Proc Natl Acad Sci USA 103:3262–3267, 2006; Kapranov et al., Science 316:1484–1488, 2007; Taft et al., Nat Genet 41:572–578, 2009; Kapranov et al., Nature 466:642–646, 2010), short RNAs involved in paramutation (Rassoulzadegan et al., Nature 441:469–474, 2006), and others (reviewed in Kawaji and Hayashizaki, PLoS Genet 4:e22, 2008). Discovery and accurate quantification of these RNA molecules, less than 200 bases in size, is thus an important and also challenging aspect of understanding the full repertoire of cellular and extracellular RNAs. Here, we describe the strategies and procedures we developed to profile short RNA species using single-molecule sequencing (SMS) and the advantages SMS offers. PMID:22144202

  3. Nonlinear response of single-molecule nanomagnets: Equilibrium and dynamical

    NASA Astrophysics Data System (ADS)

    López-Ruiz, R.; Luis, F.; González, V.; Millán, A.; García-Palacios, J. L.

    2005-12-01

    We present an experimental study of the nonlinear susceptibility of Mn12 single-molecule magnets. We investigate both their thermal-equilibrium and dynamical nonlinear responses. The equilibrium results show the sensitivity of the nonlinear susceptibility to the magnetic anisotropy, which is nearly absent in the linear response for axes distributed at random. The nonlinear dynamic response of Mn12 was recently found to be very large, displaying peaks reversed with respect to classical superparamagnets [F. Luis , Phys. Rev. Lett. 92, 107201 (2004)]. Here we corroborate the proposed explanation—the strong field dependence of the relaxation rate due to the detuning of tunnel energy levels. This is done by studying the orientational dependence of the nonlinear susceptibility, which permits us to isolate the quantum detuning contribution. Besides, from the analysis of the longitudinal and transverse contributions we estimate a bound for the decoherence time due to the coupling to the phonon bath, which is much shorter than the energy-level lifetimes.

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

    NASA Astrophysics Data System (ADS)

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

    2011-03-01

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

  5. Quantitative structural information from single-molecule FRET.

    PubMed

    Beckers, M; Drechsler, F; Eilert, T; Nagy, J; Michaelis, J

    2015-12-12

    Single-molecule studies can be used to study biological processes directly and in real-time. In particular, the fluorescence energy transfer between reporter dye molecules attached to specific sites on macromolecular complexes can be used to infer distance information. When several measurements are combined, the information can be used to determine the position and conformation of certain domains with respect to the complex. However, data analysis schemes that include all experimental uncertainties are highly complex, and the outcome depends on assumptions about the state of the dye molecules. Here, we present a new analysis algorithm using Bayesian parameter estimation based on Markov Chain Monte Carlo sampling and parallel tempering termed Fast-NPS that can analyse large smFRET networks in a relatively short time and yields the position of the dye molecules together with their respective uncertainties. Moreover, we show what effects different assumptions about the dye molecules have on the outcome. We discuss the possibilities and pitfalls in structure determination based on smFRET using experimental data for an archaeal transcription pre-initiation complex, whose architecture has recently been unravelled by smFRET measurements. PMID:26407323

  6. A single molecule study of cellulase hydrolysis of crystalline cellulose

    NASA Astrophysics Data System (ADS)

    Liu, Yu-San; Luo, Yonghua; Baker, John O.; Zeng, Yining; Himmel, Michael E.; Smith, Steve; Ding, Shi-You

    2010-02-01

    Cellobiohydrolase-I (CBH I), a processive exoglucanase secreted by Trichoderma reesei, is one of the key enzyme components in a commercial cellulase mixture currently used for processing biomass to biofuels. CBH I contains a family 7 glycoside hydrolase catalytic module, a family 1 carbohydrate-binding module (CBM), and a highlyglycosylated linker peptide. It has been proposed that the CBH I cellulase initiates the hydrolysis from the reducing end of one cellulose chain and successively cleaves alternate ?-1,4-glycosidic bonds to release cellobiose as its principal end product. The role each module of CBH I plays in the processive hydrolysis of crystalline cellulose has yet to be convincingly elucidated. In this report, we use a single-molecule approach that combines optical (Total Internal Reflection Fluorescence microscopy, or TIRF-M) and non-optical (Atomic Force Microscopy, or AFM) imaging techniques to analyze the molecular motion of CBM tagged with green fluorescence protein (GFP), and to investigate the surface structure of crystalline cellulose and changes made in the structure by CBM and CBH I. The preliminary results have revealed a confined nanometer-scale movement of the TrCBM1-GFP bound to cellulose, and decreases in cellulose crystal size as well as increases in surface roughness during CBH I hydrolysis of crystalline cellulose.

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

    PubMed Central

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

    2014-01-01

    In contrast with advances in massively parallel DNA sequencing1, high-throughput protein analyses2-4 are often limited by ensemble measurements, individual analyte purification and hence compromised quality and cost-effectiveness. Single-molecule (SM) protein detection achieved using optical methods5 is limited by the number of spectrally nonoverlapping chromophores. Here, we introduce a single molecular interaction-sequencing (SMI-Seq) technology for parallel protein interaction profiling leveraging SM advantages. DNA barcodes are attached to proteins collectively via ribosome display6 or individually via enzymatic conjugation. Barcoded proteins are assayed en masse in aqueous solution and subsequently immobilized in a polyacrylamide (PAA) thin film to construct a random SM array, where barcoding DNAs are amplified into in situ polymerase colonies (polonies)7 and analyzed by DNA sequencing. This method allows precise quantification of various proteins with a theoretical maximum array density of over one million polonies per square millimeter. Furthermore, protein interactions can be measured based on the statistics of colocalized polonies arising from barcoding DNAs of interacting proteins. Two demanding applications, G-protein coupled receptor (GPCR) and antibody binding profiling, were demonstrated. SMI-Seq enables “library vs. library” screening in a one-pot assay, simultaneously interrogating molecular binding affinity and specificity. PMID:25252978

  8. Fingerprinting polysaccharides with single-molecule atomic force microscopy.

    PubMed

    Marszalek, P E; Li, H; Fernandez, J M

    2001-03-01

    We report the use of an atomic force microscopy (AFM)-based force spectroscopy technique to identify, at the single-molecule level, the components of mixtures of polysaccharides. Previously, we showed that the elasticity of certain types of polysaccharides is governed by force-induced conformational transitions of the pyranose ring. These transitions produce atomic fingerprints in the force-extension spectrum that are characteristic of the ground-energy conformation of the pyranose ring and the type of glycosidic linkages. Using this approach we find that commercially available agarose and lambda-carrageenan contain molecules that, when stretched in an atomic force microscope, produce a force spectrum characteristic of alpha-(1-->4) d-glucans. We have identified these molecules as amylopectin or floridean starch, a storage polysaccharide in algae. Our methodology can identify individual polysaccharide molecules in solution, which is not possible by any other spectroscopic technique, and therefore is an important addition to the arsenal of analytical techniques used in carbohydrate research. PMID:11231560

  9. Single-Molecule Manipulation Studies of a Mechanically Activated Protein

    NASA Astrophysics Data System (ADS)

    Botello, Eric; Harris, Nolan; Choi, Huiwan; Bergeron, Angela; Dong, Jing-Fei; Kiang, Ching-Hwa

    2009-10-01

    Plasma von Willebrand factor (pVWF) is the largest multimeric adhesion ligand found in human blood and must be adhesively activated by exposure to shear stress, like at sites of vascular injury, to initiate blood clotting. Sheared pVWF (sVWF) will undergo a conformational change from a loose tangled coil to elongated strings forming adhesive fibers by binding with other sVWF. VWF's adhesion activity is also related to its length, with the ultra-large form of VWF (ULVWF) being hyper-actively adhesive without exposure to shear stress; it has also been shown to spontaneously form fibers. We used single molecule manipulation techniques with the AFM to stretch pVWF, sVWF and ULVWF and monitor the forces as a function of molecular extension. We showed a similar increase in resistance to unfolding for sVWF and ULVWF when compared to pVWF. This mechanical resistance to forced unfolding is reduced when other molecules known to disrupt their fibril formation are present. Our results show that sVWF and ULVWF domains unfold at higher forces than pVWF, which is consistent with the hypothesis that shear stress induces lateral association that alters adhesion activity of pVWF.

  10. Analysis and Interpretation of Single Molecule Protein Unfolding Kinetics

    NASA Astrophysics Data System (ADS)

    Lannon, Herbert; Brujic, Jasna

    2012-02-01

    The kinetics of protein unfolding under a stretching force has been extensively studied by atomic force microscopy (AFM) over the past decade [1]. Experimental artifacts at the single molecule level introduce uncertainties in the data analysis that have led to several competing physical models for the unfolding process. For example, the unfolding dynamics of the protein ubiquitin under constant force has been described by probability distributions as diverse as exponential [2,3], a sum of exponentials, log-normal [4], and more recently a function describing static disorder in the Arrhenius model [5]. A new method for data analysis is presented that utilizes maximum likelihood estimation (MLE) combined with other traditional statistical tests to unambiguously rank the consistency of these and other models with the experimental data. These techniques applied to the ubiquitin unfolding data shows that the probability of unfolding is best fit with a stretched exponential distribution, with important implications on the complexity of the mechanism of protein unfolding. [4pt] [1] Carrion-Vazquez, et. al. Springer Series in Biophys. 2006 [0pt] [2] Fernandez et. al. Science 2004 [0pt] [3] Brujic et. al. Nat. Phys 2006 [0pt] [4] Garcia-Manyes et. al. Biophys. J. 2007 [0pt] [5] Kuo et. al. PNAS 2010

  11. Single-Molecule Spectroscopic Investigations of RNA Structural Dynamics

    NASA Astrophysics Data System (ADS)

    Fiore, Julie L.; Nesbitt, David J.

    2007-03-01

    To function properly, catalytic RNAs (ribozymes) fold into specific three-dimensional shapes stabilized by multiple tertiary interactions. However, only limited information is available on the contributions of individual tertiary contacts to RNA conformational dynamics. The Tetrahymena ribozymes's P4--P6 domain forms a hinged, ``candy-cane'' structure with parallel helices clamped by two motifs, the GAAA tetraloop-tetraloop receptor and adenosine (A)-rich bulge--P4 helix interactions. Previously, we characterized RNA folding due to a tetraloop-receptor interaction. In this study, we employ time-resolved single-molecule FRET methods to probe A-rich bulge induced structural dynamics. Specifically, fluorescently labeled RNA constructs excited by a pulsed 532 nm laser are detected in the confocal region of an inverted microscope, with each photon sorted by arrival time, color and polarization. We resolve the kinetic dependence of A-rich bulge-P4 helix docking/undocking on cationic environment (e.g. Na^+ and Mg^2+ concentration.) At saturating [Mg^2+], the docked structure appears only weakly stabilized, while only 50% of the molecules exhibit efficient folding.

  12. Single-molecule localization microscopy using mCherry.

    PubMed

    Winterflood, Christian M; Ewers, Helge

    2014-11-10

    We demonstrate the potential of the commonly used red fluorescent protein mCherry for single-molecule super-resolution imaging. mCherry can be driven into a light-induced dark state in the presence of a thiol from which it can recover spontaneously or by irradiation with near UV light. We show imaging of subcellular protein structures such as microtubules and the nuclear pore complex with a resolution below 40 nm. We were able to image the C-terminus of the nuclear pore protein POM121, which is on the inside of the pore and not readily accessible for external labeling. The photon yield for mCherry is comparable to that of the latest optical highlighter fluorescent proteins. Our findings show that the widely used mCherry red fluorescent protein and the vast number of existing mCherry fusion proteins are readily amenable to super-resolution imaging. This obviates the need for generating novel protein fusions that may compromise function or the need for external fluorescent labeling. PMID:25111075

  13. Single molecule analysis of Trypanosoma brucei DNA replication dynamics

    PubMed Central

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

    2015-01-01

    Eukaryotic genome duplication relies on origins of replication, distributed over multiple chromosomes, to initiate DNA replication. A recent genome-wide analysis of Trypanosoma brucei, the etiological agent of sleeping sickness, localized its replication origins to the boundaries of multigenic transcription units. To better understand genomic replication in this organism, we examined replication by single molecule analysis of replicated DNA. We determined the average speed of replication forks of procyclic and bloodstream form cells and we found that T. brucei DNA replication rate is similar to rates seen in other eukaryotes. We also analyzed the replication dynamics of a central region of chromosome 1 in procyclic forms. We present evidence for replication terminating within the central part of the chromosome and thus emanating from both sides, suggesting a previously unmapped origin toward the 5? extremity of chromosome 1. Also, termination is not at a fixed location in chromosome 1, but is rather variable. Importantly, we found a replication origin located near an ORC1/CDC6 binding site that is detected after replicative stress induced by hydroxyurea treatment, suggesting it may be a dormant origin activated in response to replicative stress. Collectively, our findings support the existence of more replication origins in T. brucei than previously appreciated. PMID:25690894

  14. 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

  15. 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.

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

    PubMed Central

    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

  17. Electrostatic and Steric Interactions Determine Bacteriorhodopsin Single-Molecule Biomechanics

    PubMed Central

    Voïtchovsky, Kislon; Contera, Sonia Antoranz; Ryan, J. F.

    2007-01-01

    Bacteriorhodopsin (bR) is a haloarchaeal membrane protein that converts the energy of single photons into large structural changes to directionally pump protons across purple membrane. This is achieved by a complex combination of local dynamic interactions controlling bR biomechanics at the submolecular level, producing efficient amplification of the retinal photoisomerization. Using single molecule force spectroscopy at different salt concentrations, we show that tryptophan (Trp) residues use steric specific interactions to create a rigid scaffold in bR extracellular region and are responsible for the main unfolding barriers. This scaffold, which encloses the retinal, controls bR local mechanical properties and anchors the protein into the membrane. Furthermore, the stable Trp-based network allows ion binding to two specific sites on the extracellular loops (BC and FG), which are involved in proton release and lateral transport. In contrast, the cytoplasmic side of bR is mainly governed by relatively weak nonspecific electrostatic interactions that provide the flexibility necessary for large cytoplasmic structural rearrangements during the photocycle. The presence of an extracellular Trp-based network tightly enclosing the retinal seems common to most haloarchaeal rhodopsins, and could be relevant to their exceptional efficiency. PMID:17513362

  18. Extracting Conformational Memory from Single-Molecule Kinetic Data

    PubMed Central

    Lee, Julian; Dill, Ken A.

    2013-01-01

    Single-molecule data often comes in the form of stochastic time trajectories. A key question is how to extract an underlying kinetic model from the data. A traditional approach is to assume some discrete state model, i.e. a model topology, and to assume that transitions between states are Markovian. The transition rates are then selected according to which best fit the data. However in experiments, each apparent state can be a broad ensemble of states or can be hiding multiple inter-converting states. Here we describe a more general approach called the non-Markov Memory Kernel (NMMK) method. The idea is to begin with a very broad class of non-Markov models and to let the data directly select for the best possible model. To do so, we adapt an image reconstruction approach that is grounded in Maximum Entropy. The NMMK method is not limited to discrete state models for the data; it yields a unique model given the data; it gives error bars for the model; it does not assume Markov dynamics. Furthermore, NMMK is less wasteful of data by letting the entire data set determine the model. When the data warrants, the NMMK gives a memory kernel that is Markovian. We highlight, by numerical example, how conformational memory extracted using this method can be translated into useful mechanistic insight. PMID:23259771

  19. Single Molecule Visualization of DNA in Pure Shear Flow

    NASA Astrophysics Data System (ADS)

    Smith, Connie; Duggal, Rajat; Pasquali, Matteo

    2003-03-01

    Polymers are ever-present in society from plastic bottles to DNA. The study of single molecule dynamics will provide the opportunity for advances in fields from synthetic polymer coatings to gene therapy. Many applications involve flow of dilute polymer solutions in viscous solvents. These long, flexible polymer chains (DNA) are coiled at rest in solution. The configuration of the molecules is altered by the applied flow which, in turn, affects the dynamics of the flow. Control of flow allows for manipulation of the DNA molecules. Our apparatus consists of a rectangular channel that has been plasma etched into a silicon wafer with pressure driven flow (pulse-free syringe pump). The dynamics of the DNA molecules in flow are monitored using fluorescence microscopy and digital imaging. The flow channel was designed to allow for visualization of the molecules in the plane defined by velocity and velocity gradient instead of the plane identified by the velocity and the vorticity (previously studied by Smith et al (1999) and LeDuc et al (1999)). Moreover, we can visualize the DNA in a flow where the velocity gradient is not uniform. The individual and average conformations (size and orientation) of the flowing DNA molecules are being studied as a function of the Weissenberg number (product of strain rate and DNA relaxation time) and distance from the channel walls.

  20. 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.

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

    SciTech Connect

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

    2014-05-28

    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.

  2. 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

  3. 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}3Cl]?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

  4. Partial Nitrogen Atom Transfer: A New Synthetic Tool to Design Single-Molecule Magnets.

    PubMed

    Ding, Mei; Rouzières, Mathieu; Losovyj, Yaroslav; Pink, Maren; Clérac, Rodolphe; Smith, Jeremy M

    2015-09-21

    Incomplete nitrogen atom transfer from the iron(IV) nitride complex PhB(MesIm)3Fe?N to the vanadium(III) complex V(Mes)3(THF) quantitatively provides the bimetallic complex PhB(MesIm)3Fe-N?V(Mes)3. Structural and spectroscopic characterizations reveal that the nitride ligand forms a linear bridge between V(V) and high-spin Fe(II) metal ions, confirming that atom transfer is accompanied by electron transfer. In the presence of an applied dc field, the complex displays slow relaxation of the magnetization, revealing its single-molecule magnet properties with an estimation of the energy barrier at about 10 K. This complex establishes a synthetic principle for the assembly of paramagnetic complexes bridged by nitride ligands. PMID:26322964

  5. 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

  6. A Mononuclear Uranium(IV) Single-Molecule Magnet with an Azobenzene Radical Ligand.

    PubMed

    Antunes, Maria A; Coutinho, Joana T; Santos, Isabel C; Marçalo, Joaquim; Almeida, Manuel; Baldoví, José J; Pereira, Laura C J; Gaita-Ariño, Alejandro; Coronado, Eugenio

    2015-12-01

    A tetravalent uranium compound with a radical azobenzene ligand, namely, [{(SiMe2 NPh)3 -tacn}U(IV) (?(2) -N2 Ph2 (.) )] (2), was obtained by one-electron reduction of azobenzene by the trivalent uranium compound [U(III) {(SiMe2 NPh)3 -tacn}] (1). Compound 2 was characterized by single-crystal X-ray diffraction and (1) H?NMR, IR, and UV/Vis/NIR spectroscopy. The magnetic properties of 2 and precursor 1 were studied by static magnetization and ac susceptibility measurements, which for the former revealed single-molecule magnet behaviour for the first time in a mononuclear U(IV) compound, whereas trivalent uranium compound 1 does not exhibit slow relaxation of the magnetization at low temperatures. A first approximation to the magnetic behaviour of these compounds was attempted by combining an effective electrostatic model with a phenomenological approach using the full single-ion Hamiltonian. PMID:26536849

  7. Low Temperature Scanning Tunneling Spectroscopy of isolated Mn12-Ph Single Molecule Magnets

    NASA Astrophysics Data System (ADS)

    Reaves, K.; Han, P.; Iwaya, K.; Hitosugi, T.; Packwood, D.; Katzgraber, H. G.; Zhao, H.; Dunbar, K. R.; Kim, K.; Teizer, W.

    2015-03-01

    We study Mn12O12(C6H5COO)16(H2O)4 (Mn12-Ph) single-molecule magnets on a Cu(111) surface using scanning tunneling microscopy and scanning tunneling spectroscopy at cryogenic temperatures (T < 6K). We report the observation of Mn12-Ph in isolation and in thin films, deposited through in situ vacuum spray deposition onto clean Cu(111). The tunneling current of isolated Mn12-Ph, normalized with respect to the Cu background, shows a strong bias voltage dependence within the molecular interior. The qualitative features of these I vs.V curves differ by spatial location in several intriguing ways (e.g. fixed junction impedance with increasing bias voltages). We explore these normalized I vs. V curves and present a phenomenological explanation for the observed behaviors, corresponding to the physical and electronic structure within the molecule. Funding from WPI-AIMR.

  8. A CMOS enhanced solid-state nanopore based single molecule detection platform.

    PubMed

    Chen, Chinhsuan; Yemenicioglu, Sukru; Uddin, Ashfaque; Corgliano, Ellie; Theogarajan, Luke

    2013-01-01

    Solid-state nanopores have emerged as a single molecule label-free electronic detection platform. Existing transimpedance stages used to measure ionic current nanopores suffer from dynamic range limitations resulting from steady-state baseline currents. We propose a digitally-assisted baseline cancellation CMOS platform that circumvents this issue. Since baseline cancellation is a form of auto-zeroing, the 1/f noise of the system is also reduced. Our proposed design can tolerate a steady state baseline current of 10µA and has a usable bandwidth of 750kHz. Quantitative DNA translocation experiments on 5kbp DNA was performed using a 5nm silicon nitride pore using both the CMOS platform and a commercial system. Comparison of event-count histograms show that the CMOS platform clearly outperforms the commercial system, allowing for unambiguous interpretation of the data. PMID:24109650

  9. 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.

  10. 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

  11. 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.

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

    SciTech Connect

    Gangineni, R. B.; Negulescu, B.; Baraduc, C.; Gaudin, G.

    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.

  13. Water-Stable, Hydroxamate Anchors for Functionalization of TiO2 Surfaces with Ultrafast Interfacial Electron Transfer

    SciTech Connect

    McNamara, W.R.; Milot, R.L.; Song, H.; Snoeberger III, R.C.; Batista, Victor S.; Schmuttenmaer, C.A.; Brudvig, Gary W; Crabtree, Robert H

    2010-01-01

    A novel class of derivatized hydroxamic acid linkages for robust sensitization of TiO{sub 2} nanoparticles (NPs) under various aqueous conditions is described. The stability of linkages bound to metal oxides under various conditions is important in developing photocatalytic cells which incorporate transition metal complexes for solar energy conversion. In order to compare the standard carboxylate anchor to hydroxamates, two organic dyes differing only in anchoring groups were synthesized and attached to TiO{sub 2} NPs. At acidic, basic, and close to neutral pH, hydroxamic acid linkages resist detachment compared to the labile carboxylic acids. THz spectroscopy was used to compare ultrafast interfacial electron transfer (IET) into the conduction band of TiO{sub 2} for both linkages and found similar IET characteristics. Observable electron injection and stronger binding suggest that hydroxamates are a suitable class of anchors for designing water stable molecules for functionalizing TiO{sub 2}.

  14. Partially condensed DNA conformations observed by single molecule fluorescence microscopy.

    PubMed Central

    Serwer, P; Hayes, S J

    2001-01-01

    To detect partially condensed conformations of a double-stranded DNA molecule, single molecule fluorescence microscopy is performed here. The single DNA molecules are ethidium stained, 670 kilobase pair bacteriophage G genomes that are observed both during and after expulsion from capsids. Expulsion occurs in an agarose gel. Just after expulsion, the entire G DNA molecule typically has a partially condensed conformation not previously described (called a balloon). A balloon subsequently extrudes a filamentous segment of DNA. The filamentous segment becomes gently elongated via diffusion into the network that forms the agarose gel. The elongated DNA molecule usually has bright spots that undergo both appearance/disappearance and apparent motion. These spots are called dynamic spots. A dynamic spot is assumed to be the image of a zone of partially condensed DNA segments (globule). The positions of globules along an elongated DNA molecule 1) are restricted primarily to time-stable regions with comparatively high thermal motion-induced, micrometer-scale bending of the DNA molecule and 2) move within a given region on a time scale smaller than the time scale of recording. Less mobile globules are observed when either magnesium cation or ethanol is added before gel-embedding DNA molecules. These observations are explained by globules induced at equilibrium by a bending-dependent, inter-DNA segment force. Theory has previously predicted that globules are induced by electrostatic forces along an electrically charged polymer at equilibrium. The hypothesis is proposed that intracellular DNA globules assist action-at-a-distance during DNA metabolism. PMID:11721002

  15. Improved single molecule force spectroscopy using micromachined cantilevers.

    PubMed

    Bull, Matthew S; Sullan, Ruby May A; Li, Hongbin; Perkins, Thomas T

    2014-05-27

    Enhancing the short-term force precision of atomic force microscopy (AFM) while maintaining excellent long-term force stability would result in improved performance across multiple AFM modalities, including single molecule force spectroscopy (SMFS). SMFS is a powerful method to probe the nanometer-scale dynamics and energetics of biomolecules (DNA, RNA, and proteins). The folding and unfolding rates of such macromolecules are sensitive to sub-pN changes in force. Recently, we demonstrated sub-pN stability over a broad bandwidth (?f = 0.01-16 Hz) by removing the gold coating from a 100 ?m long cantilever. However, this stability came at the cost of increased short-term force noise, decreased temporal response, and poor sensitivity. Here, we avoided these compromises while retaining excellent force stability by modifying a short (L = 40 ?m) cantilever with a focused ion beam. Our process led to a ?10-fold reduction in both a cantilever's stiffness and its hydrodynamic drag near a surface. We also preserved the benefits of a highly reflective cantilever while mitigating gold-coating induced long-term drift. As a result, we extended AFM's sub-pN bandwidth by a factor of ?50 to span five decades of bandwidth (?f ? 0.01-1000 Hz). Measurements of mechanically stretching individual proteins showed improved force precision coupled with state-of-the-art force stability and no significant loss in temporal resolution compared to the stiffer, unmodified cantilever. Finally, these cantilevers were robust and were reused for SFMS over multiple days. Hence, we expect these responsive, yet stable, cantilevers to broadly benefit diverse AFM-based studies. PMID:24670198

  16. Integration of biological ion channels onto optically addressable micro-fluidic electrode arrays for single molecule characterization.

    SciTech Connect

    Brozik, Susan Marie; Frink, Laura J. Douglas; Bachand, George David; Keller, David J.; Patrick, Elizabeth L.; Marshall, Jason A.; Ortiz, Theodore P.; Meyer, Lauren A.; Davis, Ryan W.; Brozik, James A.; Flemming, Jeb Hunter

    2004-12-01

    The challenge of modeling the organization and function of biological membranes on a solid support has received considerable attention in recent years, primarily driven by potential applications in biosensor design. Affinity-based biosensors show great promise for extremely sensitive detection of BW agents and toxins. Receptor molecules have been successfully incorporated into phospholipid bilayers supported on sensing platforms. However, a collective body of data detailing a mechanistic understanding of membrane processes involved in receptor-substrate interactions and the competition between localized perturbations and delocalized responses resulting in reorganization of transmembrane protein structure, has yet to be produced. This report describes a systematic procedure to develop detailed correlation between (recognition-induced) protein restructuring and function of a ligand gated ion channel by combining single molecule fluorescence spectroscopy and single channel current recordings. This document is divided into three sections: (1) reported are the thermodynamics and diffusion properties of gramicidin using single molecule fluorescence imaging and (2) preliminary work on the 5HT{sub 3} serotonin receptor. Thirdly, we describe the design and fabrication of a miniaturized platform using the concepts of these two technologies (spectroscopic and single channel electrochemical techniques) for single molecule analysis, with a longer term goal of using the physical and electronic changes caused by a specific molecular recognition event as a transduction pathway in affinity based biosensors for biotoxin detection.

  17. Introduction to Single Molecule Imaging and Mechanics: Seeing and Touching Molecules One at a Time

    E-print Network

    Walter, Nils G.

    with the goal of having them present the current state-of-the-art of these single molecule methods to the mean values but also the higher moments of the kinetic coefficients that characterize a dynamic process. Furthermore, single molecule methods can give access to nonuniform kinetic behavior as well as transient

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

    DOEpatents

    Sansinena, Jose-Maria (Los Alamos, NM); Redondo, Antonio (Los Alamos, NM); Olazabal, Virginia (Los Alamos, NM); Hoffbauer, Mark A. (Los Alamos, NM); Akhadov, Elshan A. (Los Alamos, NM)

    2009-12-29

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

  19. A single-molecule characterization of p53 search on DNA

    E-print Network

    A single-molecule characterization of p53 search on DNA Anahita Tafvizia,b , Fang Huangc,3 , Alan R (sent for review August 9, 2010) The tumor suppressor p53 slides along DNA while searching for its coordination with the core DNA- binding domain is highly debated. Here we use single-molecule techniques

  20. Single-molecule studies of fork dynamics in Escherichia coli DNA replication

    E-print Network

    Single-molecule studies of fork dynamics in Escherichia coli DNA replication Nathan A Tanner1,4 & Antoine M van Oijen1 We present single-molecule studies of the Escherichia coli replication machinery. We and leading-strand synthesis. When coupled to the replicative helicase DnaB, Pol III mediates leading

  1. Gating of single molecule junction conductance by charge transfer complex formation

    NASA Astrophysics Data System (ADS)

    Vezzoli, Andrea; Grace, Iain; Brooke, Carly; Wang, Kun; Lambert, Colin J.; Xu, Bingqian; Nichols, Richard J.; Higgins, Simon J.

    2015-11-01

    The solid-state structures of organic charge transfer (CT) salts are critical in determining their mode of charge transport, and hence their unusual electrical properties, which range from semiconducting through metallic to superconducting. In contrast, using both theory and experiment, we show here that the conductance of metal |single molecule| metal junctions involving aromatic donor moieties (dialkylterthiophene, dialkylbenzene) increase by over an order of magnitude upon formation of charge transfer (CT) complexes with tetracyanoethylene (TCNE). This enhancement occurs because CT complex formation creates a new resonance in the transmission function, close to the metal contact Fermi energy, that is a signal of room-temperature quantum interference.The solid-state structures of organic charge transfer (CT) salts are critical in determining their mode of charge transport, and hence their unusual electrical properties, which range from semiconducting through metallic to superconducting. In contrast, using both theory and experiment, we show here that the conductance of metal |single molecule| metal junctions involving aromatic donor moieties (dialkylterthiophene, dialkylbenzene) increase by over an order of magnitude upon formation of charge transfer (CT) complexes with tetracyanoethylene (TCNE). This enhancement occurs because CT complex formation creates a new resonance in the transmission function, close to the metal contact Fermi energy, that is a signal of room-temperature quantum interference. Electronic supplementary information (ESI) available: Synthesis of 1c; experimental details of conductance measurements, formation of charge transfer complexes of 1c and 2 in solution; further details of theoretical methods. See DOI: 10.1039/c5nr04420k

  2. Reversible gating of smart plasmonic molecular traps using thermoresponsive polymers for single-molecule detection.

    PubMed

    Zheng, Yuanhui; Soeriyadi, Alexander H; Rosa, Lorenzo; Ng, Soon Hock; Bach, Udo; Justin Gooding, J

    2015-01-01

    Single-molecule surface-enhanced Raman spectroscopy (SERS) has attracted increasing interest for chemical and biochemical sensing. Many conventional substrates have a broad distribution of SERS enhancements, which compromise reproducibility and result in slow response times for single-molecule detection. Here we report a smart plasmonic sensor that can reversibly trap a single molecule at hotspots for rapid single-molecule detection. The sensor was fabricated through electrostatic self-assembly of gold nanoparticles onto a gold/silica-coated silicon substrate, producing a high yield of uniformly distributed hotspots on the surface. The hotspots were isolated with a monolayer of a thermoresponsive polymer (poly(N-isopropylacrylamide)), which act as gates for molecular trapping at the hotspots. The sensor shows not only a good SERS reproducibility but also a capability to repetitively trap and release molecules for single-molecular sensing. The single-molecule sensitivity is experimentally verified using SERS spectral blinking and bianalyte methods. PMID:26549539

  3. TOPICAL REVIEW: Surfing on a new wave of single-molecule fluorescence methods

    NASA Astrophysics Data System (ADS)

    Hohlbein, Johannes; Gryte, Kristofer; Heilemann, Mike; Kapanidis, Achillefs N.

    2010-09-01

    Single-molecule fluorescence microscopy is currently one of the most popular methods in the single-molecule toolbox. In this review, we discuss recent advances in fluorescence instrumentation and assays: these methods are characterized by a substantial increase in complexity of the instrumentation or biological samples involved. Specifically, we describe new multi-laser and multi-colour fluorescence spectroscopy and imaging techniques, super-resolution microscopy imaging and the development of instruments that combine fluorescence detection with other single-molecule methods such as force spectroscopy. We also highlight two pivotal developments in basic and applied biosciences: the new information available from detection of single molecules in single biological cells and exciting developments in fluorescence-based single-molecule DNA sequencing.

  4. Reversible gating of smart plasmonic molecular traps using thermoresponsive polymers for single-molecule detection

    PubMed Central

    Zheng, Yuanhui; Soeriyadi, Alexander H.; Rosa, Lorenzo; Ng, Soon Hock; Bach, Udo; Justin Gooding, J.

    2015-01-01

    Single-molecule surface-enhanced Raman spectroscopy (SERS) has attracted increasing interest for chemical and biochemical sensing. Many conventional substrates have a broad distribution of SERS enhancements, which compromise reproducibility and result in slow response times for single-molecule detection. Here we report a smart plasmonic sensor that can reversibly trap a single molecule at hotspots for rapid single-molecule detection. The sensor was fabricated through electrostatic self-assembly of gold nanoparticles onto a gold/silica-coated silicon substrate, producing a high yield of uniformly distributed hotspots on the surface. The hotspots were isolated with a monolayer of a thermoresponsive polymer (poly(N-isopropylacrylamide)), which act as gates for molecular trapping at the hotspots. The sensor shows not only a good SERS reproducibility but also a capability to repetitively trap and release molecules for single-molecular sensing. The single-molecule sensitivity is experimentally verified using SERS spectral blinking and bianalyte methods. PMID:26549539

  5. Reversible gating of smart plasmonic molecular traps using thermoresponsive polymers for single-molecule detection

    NASA Astrophysics Data System (ADS)

    Zheng, Yuanhui; Soeriyadi, Alexander H.; Rosa, Lorenzo; Ng, Soon Hock; Bach, Udo; Justin Gooding, J.

    2015-11-01

    Single-molecule surface-enhanced Raman spectroscopy (SERS) has attracted increasing interest for chemical and biochemical sensing. Many conventional substrates have a broad distribution of SERS enhancements, which compromise reproducibility and result in slow response times for single-molecule detection. Here we report a smart plasmonic sensor that can reversibly trap a single molecule at hotspots for rapid single-molecule detection. The sensor was fabricated through electrostatic self-assembly of gold nanoparticles onto a gold/silica-coated silicon substrate, producing a high yield of uniformly distributed hotspots on the surface. The hotspots were isolated with a monolayer of a thermoresponsive polymer (poly(N-isopropylacrylamide)), which act as gates for molecular trapping at the hotspots. The sensor shows not only a good SERS reproducibility but also a capability to repetitively trap and release molecules for single-molecular sensing. The single-molecule sensitivity is experimentally verified using SERS spectral blinking and bianalyte methods.

  6. Comparison of hydrolytic and non-hydrolytic atomic layer deposition chemistries: Interfacial electronic properties at alumina-silicon interfaces

    NASA Astrophysics Data System (ADS)

    Marstell, Roderick J.; Strandwitz, Nicholas C.

    2015-11-01

    We report the differences in the passivation and electronic properties of aluminum oxide (Al2O3) deposited on silicon via traditional hydrolytic atomic layer deposition (ALD) and non-hydrolytic (NH) ALD chemistries. Traditional films were grown using trimethylaluminum (TMA) and water and NHALD films grown using TMA and isopropanol at 300 °C. Hydrolytically grown ALD films contain a smaller amount of fixed charge than NHALD films (oxide fixed charge Qf Traditional = -8.1 × 1011 cm-2 and Qf NHALD = -3.6 × 1012 cm-2), and a larger degree of chemical passivation than NHALD films (density of interface trap states, Dit Traditional = 5.4 × 1011 eV-1 cm-2 and Dit NHALD = 2.9 × 1012 eV-1 cm-2). Oxides grown with both chemistries were found to have a band gap of 7.1 eV. The conduction band offset was 3.21 eV for traditionally grown films and 3.38 eV for NHALD. The increased Dit for NHALD films may stem from carbon impurities in the oxide layer that are at and near the silicon surface, as evidenced by both the larger trap state time constant (?Traditional = 2.2 × 10-9 s and ?NHALD = 1.7 × 10-7 s) and the larger carbon concentration. We have shown that the use of alcohol-based oxygen sources in NHALD chemistry can significantly affect the resulting interfacial electronic behavior presenting an additional parameter for understanding and controlling interfacial electronic properties at semiconductor-dielectric interfaces.

  7. Ab Initio Modeling of Fe(II) Adsorption and Interfacial Electron Transfer at Goethite (?-FeOOH) Surfaces

    SciTech Connect

    Alexandrov, Vitali Y.; Rosso, Kevin M.

    2015-01-01

    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 Fe2+(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.

  8. Influence of the electron-phonon interfacial conductance on the thermal transport at metal/dielectric interfaces.

    PubMed

    Lombard, J; Detcheverry, F; Merabia, S

    2015-01-14

    Thermal boundary conductance at a metal-dielectric interface is a quantity of prime importance for heat management at the nanoscale. While the boundary conductance is usually ascribed to the coupling between metal phonons and dielectric phonons, in this work we examine the influence of a direct coupling between the metal electrons and the dielectric phonons. The effect of electron-phonon processes is generally believed to be resistive and tends to decrease the overall thermal boundary conductance as compared to the phonon-phonon conductance ?(p). Here, we find that the effect of a direct electron-phonon interfacial coupling ?(e) is to enhance the effective thermal conductance between the metal and the dielectric. Resistive effects turn out to be important only for thin films of metals that have a low electron-phonon coupling strength. Two approaches are explored to reach these conclusions. First, we present an analytical solution of the two-temperature model to compute the effective conductance which accounts for all the relevant energy channels, as a function of ?(e), ?(p) and the electron-phonon coupling factor G. Second, we use numerical resolution to examine the influence of ?(e) on two realistic cases: a gold film on silicon or silica substrates. We point out the implications for the interpretation of time-resolved thermoreflectance experiments. PMID:25425559

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

    PubMed

    Nelson, A J; Hess, S T

    2014-04-01

    Resolution describes the smallest details within a sample that can be recovered by a microscope lens system. For optical microscopes detecting visible light, diffraction limits the resolution to ?200-250 nm. In contrast, localization measures the position of an isolated object using its image. Single fluorescent molecules can be localized with an uncertainty of a few tens of nanometres, and in some cases less than one nanometre. Superresolution fluorescence localization microscopy (SRFLM) images and localizes fluorescent molecules in a sample. By controlling the visibility of the fluorescent molecules with light, it is possible to cause a sparse subset of the tags to fluoresce and be spatially separated from each other. A movie is acquired with a camera, capturing images of many sets of visible fluorescent tags over a period of time. The movie is then analysed by a computer whereby all of the single molecules are independently measured, and their positions are recorded. When the coordinates of a sufficient number of molecules are collected, an image can be rendered by plotting the coordinates of the localized molecules. The spatial resolution of these rendered images can be better than 20 nm, roughly an order of magnitude better than the diffraction limited resolution. The invention of SRFLM has led to an explosion of related techniques. Through the use of specialized optics, the fluorescent signal can be split into multiple detection channels. These channels can capture additional information such as colour (emission wavelength), orientation and three-dimensional position of the detected molecules. Measurement of the colour of the detected fluorescence can allow researchers to distinguish multiple types of fluorescent tags and to study the interaction between multiple molecules of interest. Three-dimensional imaging and determination of molecular orientations offer insight into structural organization of the sample. SRFLM is compatible with living samples and has helped to illuminate many dynamic biological processes, such as the trajectories of molecules within living cells. This review discusses the concept and process of SRFLM imaging and investigates recent advances in SRFLM functionality. Since its announcement in 2006, SRFLM has been quickly adopted and modified by many researchers to help investigate questions whose answers lie below the diffraction limit. The versatility of the SRFLM technique has great promise for improving our understanding of cell biology at the molecular level. PMID:24611627

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

    SciTech Connect

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

    2009-06-04

    Single-molecule magnets (SMMs) have been the subject of much interest in recent years because their molecular nature and inherent physical properties allow the crossover between classical and quantum physics to be observed. The macroscopic observation of quantum phenomena - tunneling between different spin states, quantum interference between tunnel paths - not only allows scientists to study quantum mechanical laws in great detail, but also provides model systems with which to investigate the possible implementation of spin-based solid state qubits and molecular spintronics. The isolation of small, simple SMMs is therefore an exciting prospect. To date almost all SMMs have been made via the self-assembly of 3d metal ions in the presence of bridging/chelating organic ligands. However, very recently an exciting new class of SMMs, based on 3d metal clusters (or single lanthanide ions) housed within polyoxometalates, has appeared. These types of molecule, in which the SMM is completely encapsulated within (or shrouded by) a 'protective' organic or inorganic sheath have much potential for design and manipulation: for example, for the removal of unwanted dipolar interactions, the introduction of redox activity, or to simply aid functionalization for surface grafting. Calix[4]arenes are cyclic (typically bowl-shaped) polyphenols that have been used extensively in the formation of versatile self-assembled supramolecular structures. Although many have been reported, p-{sup t}But-calix[4]arene and calix[4]arene (TBC4 and C4 respectively, Figure 1A) are frequently encountered due to (a) synthetic accessibility, and (b) vast potential for alteration at either the upper or lower rim of the macrocyclic framework. Within the field of supramolecular chemistry, TBC4 is well known for interesting polymorphic behavior and phase transformations within anti-parallel bi-layer arrays, while C4 often forms self-included trimers. The polyphenolic nature of calix[n]arenes (where n = 4-8) also suggests they should be excellent candidates as ligands for the isolation of molecular magnets, but to date their use in the isolation of paramagnetic cluster compounds is rather limited. Herein we present the first Mn cluster and the first SMM to be isolated using any methylene bridged calix[n]arene - a ferromagnetically coupled mixed-valence [Mn{sub 2}{sup III}Mn{sub 2}{sup II}] complex housed between either two TBC4s or two C4s.

  11. 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.

  12. Single Molecule Spectroscopy of Amino Acids and Peptides by Recognition Tunneling

    PubMed Central

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

    2014-01-01

    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 and measuring the electron tunneling 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 tunneling technique, we are able to identify D, 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. PMID:24705512

  13. Single-molecule surface studies of fibrinogen and DNA on semiconductors

    NASA Astrophysics Data System (ADS)

    Kong, Xianhua

    Understanding of protein adsorption onto non-biological substrates is of fundamental interest in science, but also has great potential technological applications in medical devices and biosensors. This study explores the non-specific interaction, at the single molecule level, of a blood protein and DNA with semiconductor surfaces through the use of a custom built, non rastering electron emission microscope and a scanning probe microscope. The specifics and history of electron emission are described as well as the equipment used in this study. The protein examined in this study is human plasma fibrinogen, which plays an important role in haemostatis and thrombosis, and deoxyribonucleic acid (DNA) is also studied. A novel technique for determining the photothreshold of biomolecules on single molecule level is developed and applied to fibrinogen molecules adsorbed on oxidized silicon surfaces, using photo-electron emission microscopy (PEEM). Three theoretical models are employed and compared to analyze the experimental photothreshold data. The non-specific adsorption of human plasma fibrinogen on oxidized p- and n- type silicon (100) surfaces is investigated to characterize both hydrophobic interactions and electrostatic forces. The experimental results indicate that hydrophobic interactions are one of the driving forces for protein adsorption and the electrostatic interactions also play a role in the height of the fibrinogen molecules adsorbed on the surface. PEEM images establish a photo threshold of 5.0 +/- 0.2 eV for fibrinogen on both n-type and p-type Si (100) surfaces. We suggest that the photothreshold results from surface state associated Fermi level (EF) pinning and there exists negative charge transfer from the adsorbed fibrinogen onto the p-type silicon substrates, while on n-type silicon substrates negative charge is transferred in the opposite direction. The adsorption of deoxyribonucleic acid (DNA) on mica and silicon is studied in liquid and ambient environments with atomic force microscopy (AFM). Its interactions with fibrinogen proteins co-adsorbed on surfaces exhibit an interesting desorption effect. The photoelectric imaging of DNA adsorbed on silicon is studied in ultra-high vacuum. A contrast reversal is observed on Si (111) depending on different surface pretreatments, which we suggest is due to the surface states induced photoemission. Several semiconductor materials, including Si(100), Si (111), diamond-like carbon (DLC) films, single crystal diamond (SCD) (100), nano-crystalline diamond (NCD) films, silicon carbide (SiC) (0001), and graphene, are examined for biocompatibility in applications such as medical implants and biosensors. In conjunction with other studies in the literature, we suggest that DLC, NCD, and SiC are suitable for biosensor applications.

  14. Fast recognition of single molecules based on single event photon statistics

    E-print Network

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

    2007-08-02

    Mandel Q-parameter, which is determined from single event photon statistics, provides an alternative to differentiate single-molecule with fluorescence detection. In this work, by using the Q-parameter of the sample fluorescence compared to that of an ideal double-molecule system with the same average photon number, we present a novel and fast approach for identifying single molecules based on single event photon statistics analyses, compared with commonly used two-time correlation measurements. The error estimates for critical values of photon statistics are also presented for single-molecule determination.

  15. Comparative study on the interfacial electron transfer of zinc porphyrins with meso-?-extension at a 2(n) pattern.

    PubMed

    Fan, Yanru; Huang, Yu; Jiang, Yuan; Ning, Xingming; Wang, Xuemei; Shan, Duoliang; Lu, Xiaoquan

    2016-01-15

    Three zinc-tetraarylporphyrins were prepared in order to investigate the effects of systematic meso-?-extension on the redox behaviors and interfacial electron transfer kinetics. The meso-?-extension increased at a 2(n) pattern, where 2(n) was the benzene ring number in an aryl group and the aryl group represented phenyl, naphthyl and pyrenyl group, respectively. The structures of zinc-tetraarylporphyrins and hydroquinone were optimized by using density functional theory. The bimolecular reactions between zinc-tetraarylporphyrins and hydroquinone at the liquid-liquid interface were studied by using scanning electrochemical microscopy. There was an inverse electron transfer rate-overall driving force dependence by comparison of three bimolecular reactions. It was suggested that the formation of a precursor between zinc-tetraarylporphyrin cation and hydroquinone was deeply influenced by the increasing steric hindrance from phenyl group to pyrenyl group. The electron transfer rate constant depended strongly on the overall driving force for each bimolecular reaction, with transfer coefficients of 0.41, 0.37 and 0.39. PMID:26439289

  16. Single-molecule comparison of DNA Pol I activity with native and analog nucleotides

    NASA Astrophysics Data System (ADS)

    Gul, Osman; Olsen, Tivoli; Choi, Yongki; Corso, Brad; Weiss, Gregory; Collins, Philip

    2014-03-01

    DNA polymerases are critical enzymes for DNA replication, and because of their complex catalytic cycle they are excellent targets for investigation by single-molecule experimental techniques. Recently, we studied the Klenow fragment (KF) of DNA polymerase I using a label-free, electronic technique involving single KF molecules attached to carbon nanotube transistors. The electronic technique allowed long-duration monitoring of a single KF molecule while processing thousands of template strands. Processivity of up to 42 nucleotide bases was directly observed, and statistical analysis of the recordings determined key kinetic parameters for the enzyme's open and closed conformations. Subsequently, we have used the same technique to compare the incorporation of canonical nucleotides like dATP to analogs like 1-thio-2'-dATP. The analog had almost no affect on duration of the closed conformation, during which the nucleotide is incorporated. On the other hand, the analog increased the rate-limiting duration of the open conformation by almost 40%. We propose that the thiolated analog interferes with KF's recognition and binding, two key steps that determine its ensemble turnover rate.

  17. Single-molecule in vivo imaging of bacterial respiratory complexes indicates delocalized oxidative phosphorylation.

    PubMed

    Llorente-Garcia, Isabel; Lenn, Tchern; Erhardt, Heiko; Harriman, Oliver L; Liu, Lu-Ning; Robson, Alex; Chiu, Sheng-Wen; Matthews, Sarah; Willis, Nicky J; Bray, Christopher D; Lee, Sang-Hyuk; Shin, Jae Yen; Bustamante, Carlos; Liphardt, Jan; Friedrich, Thorsten; Mullineaux, Conrad W; Leake, Mark C

    2014-06-01

    Chemiosmotic energy coupling through oxidative phosphorylation (OXPHOS) is crucial to life, requiring coordinated enzymes whose membrane organization and dynamics are poorly understood. We quantitatively explore localization, stoichiometry, and dynamics of key OXPHOS complexes, functionally fluorescent protein-tagged, in Escherichia coli using low-angle fluorescence and superresolution microscopy, applying single-molecule analysis and novel nanoscale co-localization measurements. Mobile 100-200nm membrane domains containing tens to hundreds of complexes are indicated. Central to our results is that domains of different functional OXPHOS complexes do not co-localize, but ubiquinone diffusion in the membrane is rapid and long-range, consistent with a mobile carrier shuttling electrons between islands of different complexes. Our results categorically demonstrate that electron transport and proton circuitry in this model bacterium are spatially delocalized over the cell membrane, in stark contrast to mitochondrial bioenergetic supercomplexes. Different organisms use radically different strategies for OXPHOS membrane organization, likely depending on the stability of their environment. PMID:24513194

  18. Molecular quantum spintronics: supramolecular spin valves based on single-molecule magnets and carbon nanotubes.

    PubMed

    Urdampilleta, Matias; Nguyen, Ngoc-Viet; Cleuziou, Jean-Pierre; Klyatskaya, Svetlana; Ruben, Mario; Wernsdorfer, Wolfgang

    2011-01-01

    We built new hybrid devices consisting of chemical vapor deposition (CVD) grown carbon nanotube (CNT) transistors, decorated with TbPc(2) (Pc = phthalocyanine) rare-earth based single-molecule magnets (SMMs). The drafting was achieved by tailoring supramolecular ?-? interactions between CNTs and SMMs. The magnetoresistance hysteresis loop measurements revealed steep steps, which we can relate to the magnetization reversal of individual SMMs. Indeed, we established that the electronic transport properties of these devices depend strongly on the relative magnetization orientations of the grafted SMMs. The SMMs are playing the role of localized spin polarizer and analyzer on the CNT electronic conducting channel. As a result, we measured magneto-resistance ratios up to several hundred percent. We used this spin valve effect to confirm the strong uniaxial anisotropy and the superparamagnetic blocking temperature (T(B) ~ 1 K) of isolated TbPc(2) SMMs. For the first time, the strength of exchange interaction between the different SMMs of the molecular spin valve geometry could be determined. Our results introduce a new design for operable molecular spintronic devices using the quantum effects of individual SMMs. PMID:22072910

  19. Voltage tuning of vibrational mode energies in single-molecule junctions

    PubMed Central

    Li, Yajing; Doak, Peter; Kronik, Leeor; Neaton, Jeffrey B.; Natelson, Douglas

    2014-01-01

    Vibrational modes of molecules are fundamental properties determined by intramolecular bonding, atomic masses, and molecular geometry, and often serve as important channels for dissipation in nanoscale processes. Although single-molecule junctions have been used to manipulate electronic structure and related functional properties of molecules, electrical control of vibrational mode energies has remained elusive. Here we use simultaneous transport and surface-enhanced Raman spectroscopy measurements to demonstrate large, reversible, voltage-driven shifts of vibrational mode energies of C60 molecules in gold junctions. C60 mode energies are found to vary approximately quadratically with bias, but in a manner inconsistent with a simple vibrational Stark effect. Our theoretical model instead suggests that the mode shifts are a signature of bias-driven addition of electronic charge to the molecule. These results imply that voltage-controlled tuning of vibrational modes is a general phenomenon at metal–molecule interfaces and is a means of achieving significant shifts in vibrational energies relative to a pure Stark effect. PMID:24474749

  20. 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) (H3pPy=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 s(eff)=0 spins and lead to negligible intrachain communication. By contrast, the mixed-valent bridges (s=3/2, s(eff)=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

  1. Detecting the barium daughter in 136Xe 0-??? decay using single-molecule fluorescence imaging techniques

    NASA Astrophysics Data System (ADS)

    Nygren, David R.

    2015-11-01

    Single-molecule fluorescent imaging may provide an avenue to efficiently detect the Ba++ daughter atom in the decay 136Xe ? Ba + 2e?, and, unambiguously associate the birth point in space within the electron trajectories of the decay event. Chelation of doubly-charged alkaline earth elements such as calcium and barium by certain precursor molecules converts the resulting complex from a non-fluorescent to a fluorescent state. Repeated photo-excitation of a single fluorescent complex reveals both presence and location with high precision. This technique, widespread now in biochemistry, biophysics and biology, may permit a similar discriminating response in a large high-pressure xenon gas TPC for the Ba++ ion from xenon double-beta decay. The TPC measures the event time and energy of the two nascent electrons, as well as topology and position in 3-D from their trajectories in the gas. Measurement of the 2-D location of the molecular ion after arrival at the cathode plane permits an association of ion with the event. Demonstration of an efficient, highly specific detection of the barium daughter would provide a long-sought pathway to a background-free result in the search for this decay mode, of central importance for determining the nature of the neutrino.

  2. Monitoring Single-Molecule Reactivity on a Carbon Nanotube

    E-print Network

    Weiss, Gregory A.

    previously demonstrated using silicon nanowire electronic devices.7-10 For example, Patolsky et al. reported microelectronics, prototype nano- electronic devices based on nanowires, carbon nanotubes, and clusters generally as ultrasen- sitive chemical and biological sensors. For example, by tailoring the surface chemistry

  3. 10.1117/2.1201009.003163 Single-molecule fluorescence

    E-print Network

    Michalet, Xavier

    combined with a microchan- nel plate to amplify each photo-electron.4 A position-sensitive Figure 1 ( ). A position-sensitive anode determines the position (X, Y) of the electron cloud. A clock provides coarse tim future in biology.5 This photon-counting camera is also an excellent fluorescence-lifetime imaging device

  4. 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.

  5. Thermodynamics for Single-Molecule Stretching Experiments J. M. Rubi,*, D. Bedeaux, and S. Kjelstrup

    E-print Network

    Kjelstrup, Signe

    Thermodynamics for Single-Molecule Stretching Experiments J. M. Rubi,*, D. Bedeaux, and S to construct nonequilibrium thermodynamics for systems too small to be considered thermodynamically be viewed as a large thermodynamic system, we discuss the validity of nonequilibrium thermodynamics

  6. Modeling and simulation of stochastic phenomena in carbon nanotube-based single molecule sensors

    E-print Network

    Ulissi, Zachary Ward

    2015-01-01

    Shrinking sensors to the nanoscale introduces novel selectivity mechanisms and enables the ultimate sensitivity limit, single-molecule detection. Single-walled carbon nanotubes, with a bright fluorescence signal and no ...

  7. Mn12-acetate: a prototypical single molecule magnet K.M. Mertesa

    E-print Network

    Zeldov, Eli

    to as single molecule magnets. These organic materials contain a very large (Avogadro's) number of nearly to measurement. Indeed, there have been a number of remarkable findings in Mn12 and Fe8: regular steps

  8. 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 ...

  9. A label-free untethered approach to single-molecule protein binding kinetics.

    PubMed

    Al Balushi, Ahmed A; Gordon, Reuven

    2014-10-01

    Single molecule approaches provide rich real-time dynamics of molecular interactions that are not accessible to ensemble measurements. Previous single molecule studies have relied on labeling and tethering, which alters the natural state of the protein. Here we use the double-nanohole (DNH) optical tweezer approach to measure protein binding kinetics at the single molecule level in a label-free, free-solution (untethered) way. The binding kinetics of human serum albumin (HSA) to tolbutamide and to phenytoin are in quantitative agreement with previous measurements, and our single-molecule approach reveals a biexponential behavior characteristic of a multistep process. The DNH optical tweezer is an inexpensive platform for studying the real-time binding kinetics of protein-small molecule interactions in a label-free, free-solution environment, which will be of interest to future studies including drug discovery. PMID:25211555

  10. 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 ...

  11. NANOFLUIDIC SINGLE MOLECULE DETECTION (SMD) FOR PROTEIN DETECTION AND INTERACTION DYNAMICS STUDY 

    E-print Network

    Jing, Nan

    2010-07-14

    The objective of this work is to develop a micro/nanofluidic-based single molecule detection (SMD) scheme, which would allow us to inspect individual protein or protein complex study protein-protein interactions and their dynamics. This is a...

  12. Single-molecule analysis of DNA replication in Xenopus egg extracts Hasan Yardimci a

    E-print Network

    Single-molecule analysis of DNA replication in Xenopus egg extracts Hasan Yardimci a , Anna B in a soluble Xenopus leavis egg extract replication system and subsequent visualization of replication products

  13. Alignment of micro-crystals of Mn12-acetate and direct observation of single molecules thereof 

    E-print Network

    Seo, Dongmin

    2009-05-15

    OF MICRO-CRYSTALS OF MN 12 -ACETATE AND DIRECT OBSERVATION OF SINGLE MOLECULES THEREOF A Dissertation by DONGMIN SEO Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements... for the degree of DOCTOR OF PHILOSOPHY December 2007 Major Subject: Physics ALIGNMENT OF MICRO-CRYSTALS OF MN 12 -ACETATE AND DIRECT OBSERVATION OF SINGLE MOLECULES THEREOF A Dissertation by DONGMIN SEO Submitted to the Office...

  14. 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.

  15. Peptide Nucleic Acids as Tools for Single-Molecule Sequence Detection and Manipulation

    PubMed Central

    Zohar, Hagar; Hetherington, Craig L.; Bustamante, Carlos J.; Muller, Susan J.

    2012-01-01

    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. PMID:20923183

  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. 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.

  18. A family of enneanuclear iron(II) single-molecule magnets.

    PubMed

    Boudalis, Athanassios K; Sanakis, Yiannis; Clemente-Juan, Juan Modesto; Donnadieu, Bruno; Nastopoulos, Vassilios; Mari, Alain; Coppel, Yanick; Tuchagues, Jean-Pierre; Perlepes, Spyros P

    2008-01-01

    Complexes [Fe9(X)2-(O2CMe)8{(2-py)2CO2}4] (X(-)=OH(-) (1), N3(-) (2), and NCO(-) (3)) have been prepared by a route previously employed for the synthesis of analogous Co(9) and Ni(9) complexes, involving hydroxide substitution by pseudohalides (N3(-), NCO(-)). As indicated by DC magnetic susceptibility measurements, this substitution induced higher ferromagnetic couplings in complexes 2 and 3, leading to higher ground spin states compared to that of 1. Variable-field experiments have shown that the ground state is not well isolated from excited states, as a result of which it cannot be unambiguously determined. AC susceptometry has revealed out-of-phase signals, which suggests that these complexes exhibit a slow relaxation of magnetization that follows Arrhenius behavior, as observed in single-molecule magnets, with energy barriers of 41 K for 2 (tau 0=3.4 x 10(-12) s) and 44 K for 3 (tau 0=2.0 x 10(-11) s). Slow magnetic relaxation has also been observed by zero-field 57Fe Mössbauer spectroscopy. Characteristic integer-spin electron paramagnetic resonance (EPR) signals have been observed at X-band for 1, whereas 2 and 3 were found to be EPR-silent at this frequency. 1H NMR spectrometry in CD3CN has shown that complexes 1-3 are stable in solution. PMID:18213674

  19. A Redox Responsive, Fluorescent Supramolecular Metallohydrogel Consists of Nanofibers with Single-Molecule Width

    PubMed Central

    Zhang, Ye; Zhang, Bei; Kuang, Yi; Gao, Yuan; Shi, Junfeng; Zhang, Xixiang; Xu, Bing

    2013-01-01

    The integration of a tripeptide derivative, which is a versatile self-assembly motif, with a ruthenium(II)tris(bipyridine) complex affords the first supramolecular metallo-hydrogelator that not only self-assembles in water to form a hydrogel, but also exhibits gel-sol transition upon oxidation of the metal center. Surprisingly, the incorporation of the metal complex in the hydrogelator results in the nanofibers, formed by the self-assembly of the hydrogelator in water, to have the width of a single molecule of the hydrogelator. These results illustrate that metal complexes, besides being able to impart rich optical, electronic, redox or magnetic properties to supramolecular hydrogels, offer a unique geometrical control to pre-arrange the self-assembly motif prior to self-assembling. The use of metal complexes to modulate the dimensionality of intermolecular interactions may also help elucidate the interactions of the molecular nanofibers with other molecules, thus facilitating the development of supramolecular hydrogel materials for a wide range of applications. PMID:23521132

  20. Experimental and theoretical investigations of four 3d-4f butterfly single-molecule magnets.

    PubMed

    Zou, Hua-Hong; Sheng, Liang-Bing; Liang, Fu-Pei; Chen, Zi-Lu; Zhang, Yi-Quan

    2015-11-14

    The syntheses, structures, and characterization of four 3d-4f butterfly clusters are described. With different polyhydroxy Schiff-base ligands 2-(((2-hydroxy-3-methoxyphenyl)methylene)amino)-2-(hydroxymethyl)-1,3-propanediol (H4L1) and 2-(2,3-dihydroxpropyliminomethyl)-6-methoxyphenol (H3L2), three heterotetranuclear NiLn complexes (NiDy-L1 (1), NiTb-L2 (2), NiDy-L2 (3)) and one heterohexanuclear CoDy complex (4) were obtained. The three heterotetranuclear NiLn complexes display a central planar butterfly topology. The heterohexanuclear complex was built from butterfly CoDy clusters and two Dy(III) ions by the bridging of pivalate. The vertices of the body positions of the butterfly are occupied by transition metal ions in all four complexes. Magnetic analyses indicate that the complexes exhibit typical single-molecule magnet behaviour with anisotropy barriers of 33.7 cm(-1), 60.3 cm(-1), 39.6 cm(-1), and 18.4 cm(-1) for 1-4, respectively. Ab initio calculations were performed on these complexes, and the low lying electronic structure of each Ln(III) (Ln = Dy, Tb) ion and the magnetic interactions were determined. It was found that the two Ln ions may have much more contribution to the total relaxation barrier through the stronger 3d-4f exchange couplings compared to weak Ln-Ln interactions. PMID:26443303

  1. 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

  2. Supporting Information Mass Action at the Single-Molecule Level

    E-print Network

    Cohen, Adam E.

    of photobleaching Figure S5. Counting of fluorescent dyes in a dimple Figure S6. Reproducible filling of dimples Part IV. Measurement of interaction using red-green correlation Table S3. DNA sequences Figure S7 voltage of 30 kV and an electron dose in the range of 700­1,200 C/cm2 . Typically 40 dimple arrays were

  3. Design and development of a field-deployable single-molecule detector (SMD) for the analysis of molecular markers†

    PubMed Central

    Emory, Jason M.; Peng, Zhiyong; Young, Brandon; Hupert, Mateusz L.; Rousselet, Arnold; Patterson, Donald; Ellison, Brad; Soper, Steven A.

    2012-01-01

    Single-molecule detection (SMD) has demonstrated some attractive benefits for many types of biomolecular analyses including enhanced processing speed by eliminating processing steps, elimination of ensemble averaging and single-molecule sensitivity. However, it's wide spread use has been hampered by the complex instrumentation required for its implementation when using fluorescence as the readout modality. We report herein a simple and compact fluorescence single-molecule instrument that is straightforward to operate and consisted of fiber optics directly coupled to a microfluidic device. The integrated fiber optics served as waveguides to deliver the laser excitation light to the sample and collecting the resulting emission, simplifying the optical requirements associated with traditional SMD instruments by eliminating the need for optical alignment and simplification of the optical train. Additionally, the use of a vertical cavity surface emitting laser and a single photon avalanche diode serving as the excitation source and photon transducer, respectively, as well as a field programmable gate array (FPGA) integrated into the processing electronics assisted in reducing the instrument footprint. This small footprint SMD platform was tested using fluorescent microspheres and single AlexaFluor 660 molecules to determine the optimal operating parameters and system performance. As a demonstration of the utility of this instrument for biomolecular analyses, molecular beacons (MBs) were designed to probe bacterial cells for the gene encoding Gram-positive species. The ability to monitor biomarkers using this simple and portable instrument will have a number of important applications, such as strain-specific detection of pathogenic bacteria or the molecular diagnosis of diseases requiring rapid turn-around-times directly at the point-of-use. PMID:22005669

  4. Interfacial electronic structure of copper phthalocyanine and copper hexadecafluorophthalocyanine studied by photoemission

    NASA Astrophysics Data System (ADS)

    Lau, K. M.; Tang, J. X.; Sun, H. Y.; Lee, C. S.; Lee, S. T.; Yan, Donghang

    2006-04-01

    Electronic structures of the heterojunction between copper phthalocyanine (CuPc) and copper hexadecafluorophthalocyanine (F16CuPc) were studied with ultraviolet photoemission spectroscopy. Band bending and an interface dipole were observed at the interface due to the formation of an electron accumulation layer and a depletion layer in F16CuPc and CuPc, respectively. Such an energy level alignment leads to interesting ambipolar characteristics for application of the CuPc /F16CuPc junction in organic field-effect transistors.

  5. 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.

  6. Visualizing Electromagnetic Fields at the Nanoscale by Single Molecule Localization

    E-print Network

    Steuwe, Christian; Erdelyi, Miklos; Szekeres, G.; Csete, M.; Baumberg, Jeremy J.; Mahajan, Sumeet; Kaminski, Clemens F.

    2015-04-27

    , L.; Michael, J. R., Scanning electron microscopy and X-ray microanalysis. Springer: 2003. 13. Hofmann, C. E.; Vesseur, E. J. R.; Sweatlock, L. A.; Lezec, H. J.; García de Abajo, F. J.; Polman, A.; Atwater, H. A. Nano Lett. 2007, 7, 3612-3617. 14... .; Bartlett, P. N.; Baumberg, J. J.; Kelf, T. A.; Sugawara, Y.; Russell, A. E. Faraday Discuss. 2006, 132, 191-199. 33. Chan, V.; Graves, D. J.; Fortina, P.; McKenzie, S. E. Langmuir 1997, 13, 320-329. 34. Rant, U.; Arinaga, K.; Fujita, S.; Yokoyama, N...

  7. 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.

  8. Probing Interfacial Electronic States in CdSe Quantum Dots using Second Harmonic Generation Spectroscopy

    SciTech Connect

    Doughty, Benjamin L; Ma, Yingzhong; Shaw, Robert W

    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.

  9. 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

  10. High-efficiency inverted organic solar cells with polyethylene oxide-modified Zn-doped TiO2 as an interfacial electron transport layer.

    PubMed

    Thambidurai, M; Kim, Jun Young; Ko, Youngjun; Song, Hyung-Jun; Shin, Hyeonwoo; Song, Jiyun; Lee, Yeonkyung; Muthukumarasamy, N; Velauthapillai, Dhayalan; Lee, Changhee

    2014-08-01

    High efficiency inverted organic solar cells are fabricated using the PTB7:PC71BM polymer by incorporating Zn-doped TiO2 (ZTO) and 0.05 wt% PEO:ZTO as interfacial electron transport layers. The 0.05 wt% PEO-modified ZTO device shows a significantly increased power conversion efficiency (PCE) of 8.10%, compared to that of the ZTO (7.67%) device. PMID:24976080

  11. Single Molecule Transistor based Nanopore for the detection of Nicotine

    E-print Network

    Ray, S J

    2015-01-01

    A nanopore based detection methodology was proposed and investigated for the detection of Nicotine. This technique uses a Single Molecular Transistor (SMT) working as a nanopore operational in the Coulomb Blockade regime. When the Nicotine molecule is pulled through the nanopore area surrounded by the Source(S), Drain(D) and Gate electrodes, the charge stability diagram can detect the presence of the molecule and is unique for a specific molecular structure. Due to the weak coupling between the different electrodes which is set by the nanopore size, the molecular energy states stay almost unaffected by the electrostatic environment that can be realised from the charge stability diagram. Identification of different orientation and position of the Nicotine molecule within the nanopore area can be made from specific regions of overlap between different charge states on the stability diagram that could be used as an electronic fingerprint for detection. This method could be advantageous and useful to detect the p...

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

    PubMed Central

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

    2014-01-01

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

  13. 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.

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

    NASA Astrophysics Data System (ADS)

    Wang, Bo; Davis, Lloyd

    2014-03-01

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

  15. 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

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

    PubMed

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

    2014-11-01

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

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

    NASA Astrophysics Data System (ADS)

    Moerner, W. E. William E.

    2015-10-01

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

  18. 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

  19. Step Detection in Single-Molecule Real Time Trajectories Embedded in Correlated Noise

    PubMed Central

    Arunajadai, Srikesh G.; Cheng, Wei

    2013-01-01

    Single-molecule real time trajectories are embedded in high noise. To extract kinetic or dynamic information of the molecules from these trajectories often requires idealization of the data in steps and dwells. One major premise behind the existing single-molecule data analysis algorithms is the Gaussian ‘white’ noise, which displays no correlation in time and whose amplitude is independent on data sampling frequency. This so-called ‘white’ noise is widely assumed but its validity has not been critically evaluated. We show that correlated noise exists in single-molecule real time trajectories collected from optical tweezers. The assumption of white noise during analysis of these data can lead to serious over- or underestimation of the number of steps depending on the algorithms employed. We present a statistical method that quantitatively evaluates the structure of the underlying noise, takes the noise structure into account, and identifies steps and dwells in a single-molecule trajectory. Unlike existing data analysis algorithms, this method uses Generalized Least Squares (GLS) to detect steps and dwells. Under the GLS framework, the optimal number of steps is chosen using model selection criteria such as Bayesian Information Criterion (BIC). Comparison with existing step detection algorithms showed that this GLS method can detect step locations with highest accuracy in the presence of correlated noise. Because this method is automated, and directly works with high bandwidth data without pre-filtering or assumption of Gaussian noise, it may be broadly useful for analysis of single-molecule real time trajectories. PMID:23533612

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

    SciTech Connect

    Rombach-Riegraf, Verena; Oswald, Peter; Bienert, Roland; Petersen, Jan; Domingo, M.P.; Pardo, Julian; Fundacion Aragon I-D , Gobierno de Aragon, Zaragoza; Immune Effector Cells Group, Aragon Health Research Institute , Biomedical Research Centre of Aragon Fundacion Aragon I-D - ARAID, Gobierno de Aragon, Zaragoza ; Graeber, P.; Galvez, E.M.

    2013-01-04

    Highlights: Black-Right-Pointing-Pointer It is possible to eliminate the blinking effect of a water-soluble QD. Black-Right-Pointing-Pointer We provide a direct method to study protein function and dynamics at the single level. Black-Right-Pointing-Pointer QD, potent tool for single molecule studies of biochemical and biological processes. -- Abstract: Luminescent semiconductor nanocrystals (quantum dots, QD) have unique photo-physical properties: high photostability, brightness and narrow size-tunable fluorescence spectra. Due to their unique properties, QD-based single molecule studies have become increasingly more popular during the last years. However QDs show a strong blinking effect (random and intermittent light emission), which may limit their use in single molecule fluorescence studies. QD blinking has been widely studied and some hypotheses have been done to explain this effect. Here we summarise what is known about the blinking effect in QDs, how this phenomenon may affect single molecule studies and, on the other hand, how the 'on'/'off' states can be exploited in diverse experimental settings. In addition, we present results showing that site-directed binding of QD to cysteine residues of proteins reduces the blinking effect. This option opens a new possibility of using QDs to study protein-protein interactions and dynamics by single molecule fluorescence without modifying the chemical composition of the solution or the QD surface.

  1. 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

  2. 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

  3. Origin of high- and low-conductance traces in alkanediisothiocyanate single-molecule contacts

    NASA Astrophysics Data System (ADS)

    Luzhbin, D. A.; Kaun, C.-C.

    2010-01-01

    Zero-bias transport properties of alkanediisothiocyanate [-SCN-(CH2)n-NCS-,n=4,6,8] molecules anchored to various quasi-one-dimensional Au(111) electrodes are studied by an ab initio method within a standard two-probe methodology based on the density-functional theory and the nonequilibrium Green’s functions formalism. We have shown that the high-/low-conductance traces observed in STM break-junction experiments on this molecular species can be clearly related to the difference in the electronic structures between the molecular contacts with different geometric configurations of the near-interface planes of the electrodes. The difference in transport properties of alkanediisothiocyanate single-molecule junctions can be understood in terms of the distribution of the surface states, emerging in the energy gap of the alkanes due to the electrode environment. A general feature of the high-conductance junctions is a number of closely located surface states around the Fermi energy, well coupled to the scattering states of the junctions. These well-coupled states broaden the transmission peaks responsible for conductance, increasing their amplitudes at the Fermi energy, while the sparser distribution of the surface states gives sharper peaks with smaller amplitudes at the Fermi energy, naturally representing the low-conductance junctions. The effects of changing the end groups, junction distance, and electrode cross-section are also investigated and analyzed in terms of changes in the electronic structure of the molecular junctions. A comparison with the available experimental data is also provided.

  4. Single molecule transistor based nanopore for the detection of nicotine

    SciTech Connect

    Ray, S. J.

    2014-12-28

    A nanopore based detection methodology was proposed and investigated for the detection of Nicotine. This technique uses a Single Molecular Transistor working as a nanopore operational in the Coulomb Blockade regime. When the Nicotine molecule is pulled through the nanopore area surrounded by the Source(S), Drain (D), and Gate electrodes, the charge stability diagram can detect the presence of the molecule and is unique for a specific molecular structure. Due to the weak coupling between the different electrodes which is set by the nanopore size, the molecular energy states stay almost unaffected by the electrostatic environment that can be realised from the charge stability diagram. Identification of different orientation and position of the Nicotine molecule within the nanopore area can be made from specific regions of overlap between different charge states on the stability diagram that could be used as an electronic fingerprint for detection. This method could be advantageous and useful to detect the presence of Nicotine in smoke which is usually performed using chemical chromatography techniques.

  5. Single molecule transistor based nanopore for the detection of nicotine

    NASA Astrophysics Data System (ADS)

    Ray, S. J.

    2014-12-01

    A nanopore based detection methodology was proposed and investigated for the detection of Nicotine. This technique uses a Single Molecular Transistor working as a nanopore operational in the Coulomb Blockade regime. When the Nicotine molecule is pulled through the nanopore area surrounded by the Source(S), Drain (D), and Gate electrodes, the charge stability diagram can detect the presence of the molecule and is unique for a specific molecular structure. Due to the weak coupling between the different electrodes which is set by the nanopore size, the molecular energy states stay almost unaffected by the electrostatic environment that can be realised from the charge stability diagram. Identification of different orientation and position of the Nicotine molecule within the nanopore area can be made from specific regions of overlap between different charge states on the stability diagram that could be used as an electronic fingerprint for detection. This method could be advantageous and useful to detect the presence of Nicotine in smoke which is usually performed using chemical chromatography techniques.

  6. 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).

  7. 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

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

    PubMed

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

    2015-08-01

    We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality. PMID:26121404

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

    PubMed Central

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

    2015-01-01

    We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality. PMID:26121404

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

    PubMed

    Li, Gene-Wei; Xie, X Sunney

    2011-07-21

    Gene expression originates from individual DNA molecules within living cells. Like many single-molecule processes, gene expression and regulation are stochastic, that is, sporadic in time. This leads to heterogeneity in the messenger-RNA and protein copy numbers in a population of cells with identical genomes. With advanced single-cell fluorescence microscopy, it is now possible to quantify transcriptomes and proteomes with single-molecule sensitivity. Dynamic processes such as transcription-factor binding, transcription and translation can be monitored in real time, providing quantitative descriptions of the central dogma of molecular biology and the demonstration that a stochastic single-molecule event can determine the phenotype of a cell. PMID:21776076

  11. Probing the dynamics of growth factor receptor by single-molecule fluorescence imaging.

    PubMed

    Sun, Yahong; Li, Nan; Fang, Xiaohong

    2015-09-01

    Single-molecule fluorescence imaging with living cells offers a new approach to visualize and monitor individual proteins during their cellular activities. It facilities the study of cell signaling proteins whose structures and interactions are highly temporal and spatial regulated. In this review, we will mainly present our recent work on probing the dynamics of two types of important transmembrane growth factor receptors, transforming growth factor ? receptors and epidermal growth factor receptors, by single-molecule fluorescence microscopy. This includes the characterization of receptor stoichiometry, monomer-dimer interconversion kinetics, effects of microenvironment on receptor membrane diffusion, and intracellular transportation under different signaling conditions. Related studies on these receptors from other groups, as well as the method developments, will be also discussed. Single-molecule study helps to achieve a better understanding of the molecular mechanism of receptor activation, endocytosis and other molecular events in transmembrane signaling. PMID:25963927

  12. Mechanism of transcriptional repression at a bacterial promoter by analysis of single molecules.

    PubMed

    Sanchez, Alvaro; Osborne, Melisa L; Friedman, Larry J; Kondev, Jane; Gelles, Jeff

    2011-10-01

    The molecular basis for regulation of lactose metabolism in Escherichia coli is well studied. Nonetheless, the physical mechanism by which the Lac repressor protein prevents transcription of the lactose promoter remains unresolved. Using multi-wavelength single-molecule fluorescence microscopy, we visualized individual complexes of fluorescently tagged RNA polymerase holoenzyme bound to promoter DNA. Quantitative analysis of the single-molecule observations, including use of a novel statistical partitioning approach, reveals highly kinetically stable binding of polymerase to two different sites on the DNA, only one of which leads to transcription. Addition of Lac repressor directly demonstrates that bound repressor prevents the formation of transcriptionally productive open promoter complexes; discrepancies in earlier studies may be attributable to transcriptionally inactive polymerase binding. The single-molecule statistical partitioning approach is broadly applicable to elucidating mechanisms of regulatory systems including those that are kinetically rather than thermodynamically controlled. PMID:21829165

  13. Bifunctional nanoarrays for probing the immune response at the single-molecule level

    PubMed Central

    Cai, Haogang; Depoil, David; Palma, Matteo; Sheetz, Michael P.; Dustin, Michael L.; Wind, Shalom J.

    2013-01-01

    Bifunctional nanoarrays were created to simulate the immunological synapse and probe the T-cell immune response at the single-molecule level. Sub-5?nm AuPd nanodot arrays were fabricated using both e-beam and nanoimprint lithography. The nanoarrays were then functionalized by two costimulatory molecules: antibody UCHT1 Fab, which binds to the T-cell receptor (TCR) and activates the immune response, bound to metallic nanodots; and intercellular adhesion molecule-1, which enhances cell adhesion, on the surrounding area. Initial T-cell experiments show successful attachment and activation on the bifunctional nanoarrays. This nanoscale platform for single-molecule control of TCR in living T-cells provides a new approach to explore how its geometric arrangement affects T-cell activation and behavior, with potential applications in immunotherapy. This platform also serves as a general model for single-molecule nanoarrays where more than one molecular species is required. PMID:24353927

  14. 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.

  15. 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.

  16. Magneto-ionic control of interfacial magnetism

    E-print Network

    Bauer, Uwe

    In metal/oxide heterostructures, rich chemical electronic magnetic and mechanical properties can emerge from interfacial chemistry and structure. The possibility to dynamically control interface characteristics with an ...

  17. Interfacial reactions of glasses for biomedical application by scanning transmission electron microscopy and microanalysis.

    PubMed

    Banchet, V; Michel, J; Jallot, E; Wortham, L; Bouthors, S; Laurent-Maquin, D; Balossier, G

    2006-05-01

    Short-term physico-chemical reactions at the interface between bioactive glass particles and biological fluids are studied for three glasses with different bioactive properties; these glasses are in the SiO(2)-Na(2)O-CaO-P(2)O(5)-K(2)O-Al(2)O(3)-MgO system. Our aim is to show the difference between the mechanisms of their surface reactions. The relation between the composition and the bioactive properties of these glasses is also discussed. The elemental analysis is performed at the submicrometer scale by scanning transmission electron microscopy associated with energy-dispersive X-ray spectroscopy and electron energy loss spectroscopy. After different immersion times (ranging from 0 to 96 h) of bioactive glass particles in a simulated biological solution, results show the formation of different surface layers at the glass periphery in the case of two bioactive glasses (A9 and BVA). For the third glass (BVH) we do not observe any surface layer formation or any modification of the glass composition. For the two other glasses (A9 and BVA), we observe the presence of different layers: an already observed (Si, O, Al) rich layer at the periphery, a previously demonstrated thin (Si, O) layer formed on top of the (Si, O, Al) layer and a (Ca, P) layer. We determine the different steps of the mechanisms of the surface reactions, which appear to be similar in these glasses, and compare the physico-chemical reactions and kinetics using the different immersion times. The A9 glass permits the observation of all important steps of the surface reactions which lead to bioactivity. This study shows the important relationship between composition and bioactivity which can determine the medical applicability of the glass. PMID:16701894

  18. Single Molecule and Collective Dynamics of Motor Protein Coupled with Mechano-Sensitive Chemical Reaction

    NASA Astrophysics Data System (ADS)

    Iwaki, Mitsuhiro; Marcucci, Lorenzo; Togashi, Yuichi; Yanagida, Toshio

    2013-12-01

    Motor proteins such as myosin and kinesin hydrolyze ATP into ADP and Pi to convert chemical energy into mechanical work. This resultsin various motile processes like muscle contraction, vesicle transport and cell division. Recent single molecule experiments have revealed that external load applied to these motor proteins perturb not only the mechanical motion, but the ATP hydrolysis cycle as well, making these molecules mechano-enzymes. Here, we describe our single molecule detection techniques to reveal the mechano-enzymatic properties of myosin and introduce recent progress from both experimental and theoretical approaches at the single- and multiple-molecule level.

  19. Redox cycling and kinetic analysis of single molecules of solution-phase nitrite reductase

    PubMed Central

    Goldsmith, Randall H.; Tabares, Leandro C.; Kostrz, Dorota; Dennison, Christopher; Aartsma, Thijs J.; Canters, G. W.; Moerner, W. E.

    2011-01-01

    Single-molecule measurements are a valuable tool for revealing details of enzyme mechanisms by enabling observation of unsynchronized behavior. However, this approach often requires immobilizing the enzyme on a substrate, a process which may alter enzyme behavior. We apply a microfluidic trapping device to allow, for the first time, prolonged solution-phase measurement of single enzymes in solution. Individual redox events are observed for single molecules of a blue nitrite reductase and are used to extract the microscopic kinetic parameters of the proposed catalytic cycle. Changes in parameters as a function of substrate concentration are consistent with a random sequential substrate binding mechanism. PMID:21969548

  20. Study of the interfacial reactions between a bioactive apatite-mullite glass-ceramic coating and titanium substrates using high angle annular dark field transmission electron microscopy.

    PubMed

    Stanton, Kenneth T; O'Flynn, Kevin P; Nakahara, Shohei; Vanhumbeeck, Jean-François; Delucca, John M; Hooghan, Bobby

    2009-04-01

    Glass of generic composition SiO(2) . Al(2)O(3) . P(2)O(5) . CaO . CaF(2) will crystallise predominantly to apatite and mullite upon heat-treatment. Such ceramics are bioactive, osseoconductive, and have a high resistance to fracture. As a result, they are under investigation for use as biomedical device coatings, and in particular for orthopaedic implants. Previous work has shown that the material can be successfully enamelled to titanium with an interfacial reaction zone produced during heat treatment. The present study uses high angle annular dark field transmission electron microscopy (HAADF-TEM) to conduct a detailed examination of this region. Results show evidence of complex interfacial reactions following the diffusion of titanium into an intermediate layer and the production of titanium silicides and titanium phosphides. These results confirm previously hypothesised mechanisms for the bonding of silicate bioceramics with titanium alloys. PMID:19034617

  1. Transmission electron microscopy and ab initio calculations to relate interfacial intermixing and the magnetism of core/shell nanoparticles

    SciTech Connect

    Chi, C.-C.; Hsiao, C.-H.; Ouyang, Chuenhou; Skoropata, E.; Lierop, J. van

    2015-05-07

    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 Co{sup 2+} 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.

  2. 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].

  3. Interfacial Scattering in Magnetic Multilayers

    NASA Astrophysics Data System (ADS)

    Stewart, D. A.; Zhang, X.-G.; Butler, W. H.

    2001-03-01

    The role of interfacial scattering in magnetic multilayers and its effects on transport and giant magnetoresistance are examined. The interfacial region is modeled as a randomly disordered alloy layer. The calculations were performed for a ComidCu multilayer using the Coherent Potential Approximation (CPA) in a layered Koringa-Kohn-Rostoker (LKKR) framework. The effect of this interfacial disorder on the multilayer non-local conductivity for different values of the electron momentum parallel to the layers, k_||, is explored. The influences of the interfacial layer thickness and k_|| on the non-local conductivity are also determined. A semi-classical boltzmann model for non-local conductivity is developed which incorporates the effects of surface roughness. The two approaches are compared and a k_|| dependent specularity parameter is obtained that varies with the disorder and thickness of the interfacial layer.

  4. Giant magnetoresistance as a probe of interfacial electronic character (invited) (abstract)

    NASA Astrophysics Data System (ADS)

    Parkin, S. S. P.

    1996-04-01

    The giant magnetoresistance (GMR) effect exhibited by magnetic multilayers and related structures is very sensitive to the nature of the interfaces between the magnetic and nonmagnetic layers. We have explored the dependence of GMR on the electronic character of these interfaces by inserting additional thin magnetic layers at the interfaces. Insertion of thin Co layers in Ni-Fe/Cu/Ni-Fe or thin Ni-Fe layers in Co/Cu/Cu exchange biased sandwiches leads to an increase or decrease, respectively, in the magnitude of the GMR effect; the variation is monotonic with thickness of the inserted layer. In contrast, insertion of thin layers of Fe at the Ni-Fe/Cu interfaces in Ni-Fe/Cu/Ni-Fe exchange biased sandwich structure results in a nonmonotonic variation of GMR with Fe layer thickness; for intermediate thicknesses in particular the GMR is substantially reduced. The magnetism and structure of the Fe layers is explored in related sputter-deposited single-crystalline Ni/Fe/Cu thin-film structures prepared using thin Fe/Pt seed layers grown at high temperatures on single crystalline polished wafers of MgO(100), MgO(110), and (0001)Al2O3. The magnetism of the Ni, Fe, and Cu layers is examined using x-ray magnetic circular dichroism (XMCD) and the structure of the Fe is analyzed using extended x-ray absorption fine structure (EXAFS) studies. These experiments show that the Fe moment varies nonmonotonically with thickness resulting from a structural phase transition from fcc to bcc Fe with increasing thickness. The Fe displays a very small magnetic moment for an intermediate range of Fe thickness for which the Fe structure is fcc. This range of thickness depends on the crystalline orientation of the Fe. It is within this same range of thickness that the GMR is suppressed in related exchange biased sandwich structures. Interestingly we find that such nonferromagnetic layers of fcc Fe can be used as spacer layers in magnetic multilayers of, for example, Ni/Fe. These multilayers display both antiferromagnetic interlayer coupling of the Ni layers and giant magnetoresistance, which each oscillate as a function of Fe thickness.

  5. Solvent Isotope Effects on Interfacial Protein Electron Transfer in Crystals and Electode Films

    SciTech Connect

    Kang,S.; Hoke, K.; Crane, B.

    2006-01-01

    D{sub 2}O-grown crystals of yeast zinc porphyrin substituted cytochrome c peroxidase (ZnCcP) in complex with yeast iso-1-cytochrome c (yCc) diffract to higher resolution (1.7 Angstroms) and pack differently than H{sub 2}O-grown crystals (2.4-3.0 Angstroms). Two ZnCcP's bind the same yCc (porphyrin-to-porphyrin separations of 19 and 29 Angstroms), with one ZnCcP interacting through the same interface found in the H{sub 2}O crystals. The triplet excited-state of at least one of the two unique ZnCcP's is quenched by electron transfer (ET) to Fe(III)yCc (k{sub e} = 220 s{sup -1}). Measurement of thermal recombination ET between Fe(II)yCc and ZnCcP+ in the H{sub 2}O-treated crystals has both slow and fast components that differ by 2 orders of magnitude (k{sub eb}{sup 1}= 2200 s{sup -1}, k{sub eb}{sup 2}= 30 s{sup -1}). Back ET in H{sub 2}O-grown crystals is too fast for observation, but soaking H{sub 2}O-grown crystals in D{sub 2}O for hours generates slower back ET, with kinetics similar to those of the D{sub 2}O-grown crystals (k{sub eb}{sup 1} = 7000 s{sup -1}, k{sub eb}{sup 2}= 100 s{sup -1}). Protein-film voltammetry of yCc adsorbed to mixed alkanethiol monolayers on gold electrodes shows slower ET for D{sub 2}O-grown yCc films than for H{sub 2}O-grown films (k{sub H} = 800 s{sup -1}; k{sub D} = 540 s{sup -1} at 20 C). Soaking H{sub 2}O- or D{sub 2}O-grown films in the counter solvent produces an immediate inverse isotope effect that diminishes over hours until the ET rate reaches that found in the counter solvent. Thus, D{sub 2}O substitution perturbs interactions and ET between yCc and either CcP or electrode films. The effects derive from slow exchanging protons or solvent molecules that in the crystal produce only small structural changes.

  6. Quantitatively probing propensity for structural transitions in engineered virus nanoparticles by single-molecule mechanical analysis

    NASA Astrophysics Data System (ADS)

    Castellanos, Milagros; Carrillo, Pablo J. P.; Mateu, Mauricio G.

    2015-03-01

    Viruses are increasingly being studied from the perspective of fundamental physics at the nanoscale as biologically evolved nanodevices with many technological applications. In viral particles of the minute virus of mice (MVM), folded segments of the single-stranded DNA genome are bound to the capsid inner wall and act as molecular buttresses that increase locally the mechanical stiffness of the particle. We have explored whether a quantitative linkage exists in MVM particles between their DNA-mediated stiffening and impairment of a heat-induced, virus-inactivating structural change. A series of structurally modified virus particles with disrupted capsid-DNA interactions and/or distorted capsid cavities close to the DNA-binding sites were engineered and characterized, both in classic kinetics assays and by single-molecule mechanical analysis using atomic force microscopy. The rate constant of the virus inactivation reaction was found to decrease exponentially with the increase in elastic constant (stiffness) of the regions closer to DNA-binding sites. The application of transition state theory suggests that the height of the free energy barrier of the virus-inactivating structural transition increases linearly with local mechanical stiffness. From a virological perspective, the results indicate that infectious MVM particles may have acquired the biological advantage of increased survival under thermal stress by evolving architectural elements that rigidify the particle and impair non-productive structural changes. From a nanotechnological perspective, this study provides proof of principle that determination of mechanical stiffness and its manipulation by protein engineering may be applied for quantitatively probing and tuning the conformational dynamics of virus-based and other protein-based nanoassemblies.Viruses are increasingly being studied from the perspective of fundamental physics at the nanoscale as biologically evolved nanodevices with many technological applications. In viral particles of the minute virus of mice (MVM), folded segments of the single-stranded DNA genome are bound to the capsid inner wall and act as molecular buttresses that increase locally the mechanical stiffness of the particle. We have explored whether a quantitative linkage exists in MVM particles between their DNA-mediated stiffening and impairment of a heat-induced, virus-inactivating structural change. A series of structurally modified virus particles with disrupted capsid-DNA interactions and/or distorted capsid cavities close to the DNA-binding sites were engineered and characterized, both in classic kinetics assays and by single-molecule mechanical analysis using atomic force microscopy. The rate constant of the virus inactivation reaction was found to decrease exponentially with the increase in elastic constant (stiffness) of the regions closer to DNA-binding sites. The application of transition state theory suggests that the height of the free energy barrier of the virus-inactivating structural transition increases linearly with local mechanical stiffness. From a virological perspective, the results indicate that infectious MVM particles may have acquired the biological advantage of increased survival under thermal stress by evolving architectural elements that rigidify the particle and impair non-productive structural changes. From a nanotechnological perspective, this study provides proof of principle that determination of mechanical stiffness and its manipulation by protein engineering may be applied for quantitatively probing and tuning the conformational dynamics of virus-based and other protein-based nanoassemblies. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr07046a

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

    NASA Astrophysics Data System (ADS)

    Ha, Taekjip; Tinnefeld, Philip

    2012-05-01

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

  8. Biophysical Journal Volume 84 February 2003 733738 733 Relating Single-Molecule Measurements to Thermodynamics

    E-print Network

    Swigon, David

    to Thermodynamics David Keller,* David Swigon,y and Carlos Bustamantez§{ *Department of Chemistry, University of New ensembles of molecules are routinely interpreted using thermodynamics, but the normal rules of thermodynamics may not apply to measurements made on single molecules. Using a polymer stretching experiment

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

    E-print Network

    Chen, Peng

    reaction. For both nanocatalysts, the distributions of the microscopic reaction time from a single catalystSingle-Molecule Kinetics Reveals a Hidden Surface Reaction Intermediate in Single and characterizing reaction inter- mediates is not only important and powerful for elucidating reaction mechanisms

  10. Recovery of Free Energy Branches in Single Molecule Experiments Ivan Junier,1

    E-print Network

    Ritort, Felix

    Recovery of Free Energy Branches in Single Molecule Experiments Ivan Junier,1 Alessandro Mossa,2 19 February 2009) We present a method for determining the free energy of coexisting states from use optical tweezers to determine the free energy branches of the native and unfolded states of a two

  11. the unfolding of fibrin(ogen) domains has been measured by single-molecule atomic

    E-print Network

    Connolly Jr, Harold C.

    the unfolding of fibrin(ogen) domains has been measured by single-molecule atomic force microscopy the use of coarse-grained methods. Knowing which fibrin domains are mechanically stable and which domains for these efforts. Clots including platelets are more complex, because the platelets control fibrin polymerization

  12. Microfluidic separation and capture of analytes for single-molecule spectroscopy{

    E-print Network

    Zare, Richard N.

    Microfluidic separation and capture of analytes for single-molecule spectroscopy{ Samuel Kim,a Bo labeled biological molecules is separated electrophoretically on a chip and the constituent molecules specific labeling for quantitative data analysis. Therefore, a purification/separation procedure is usually

  13. Focus on Function: Single Molecule RNA Enzymology Mark A. Ditzler,1

    E-print Network

    Walter, Nils G.

    on their size: small self-cleaving RNAs (\\200 nucleotides), medium-sized self-splicing introns, and largerReview Focus on Function: Single Molecule RNA Enzymology Mark A. Ditzler,1 Elvin A. Alema´n,2 David@wiley. com INTRODUCTION A detailed understanding of the biopolymer ribonu- cleic acid (RNA) is of great

  14. Silver nanoparticles self assembly as SERS substrates with near single molecule detection limit

    E-print Network

    Brolo, Alexandre G.

    Silver nanoparticles self assembly as SERS substrates with near single molecule detection limit as an Advance Article on the web 15th July 2009 DOI: 10.1039/b904744a Highly sensitive SERS substrates distribution of Ag NPs aggregates as the deposition number increased. Surface-enhanced Raman scattering (SERS

  15. SINGLE MOLECULE DETECTION OF TUBERCULOSIS NUCLEIC ACID USING DARK FIELD TETHERED PARTICLE MOTION

    E-print Network

    van Vliet, Lucas J.

    SINGLE MOLECULE DETECTION OF TUBERCULOSIS NUCLEIC ACID USING DARK FIELD TETHERED PARTICLE MOTION for tuberculosis nucleic acid detection re- quire amplification and labeling before detection is possible. We of an exquisitely sensitive method of detecting the presence of nucleic acids derived from human pathogens directly

  16. Single-Molecule Microscopy Studies of Electric-Field Poling in Chromophore-Polymer Composite Materials

    E-print Network

    Reid, Philip J.

    Single-Molecule Microscopy Studies of Electric-Field Poling in Chromophore-Polymer Composite electrooptic devices based on chromophore-polymer composite materials is to improve chromophore ordering electric field, applied at temperatures near the Tg of the polymer host, a process referred to as "poling

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

    E-print Network

    Economou, Tassos

    be monitored in real time, providing quantitative descriptions of the central dogma of molecular biologyCentral dogma at the single-molecule level in living cells Gene-Wei Li1 & X. Sunney Xie1 Gene-molecule technique in biology10 . However, in this case, stochastic chemical reaction events of a single

  18. SINGLE MOLECULE DETECTION OF TUBERCULOSIS NUCLEIC ACID USING DARK FIELD TETHERED PARTICLE MOTION

    E-print Network

    Rieger, Bernd

    SINGLE MOLECULE DETECTION OF TUBERCULOSIS NUCLEIC ACID USING DARK FIELD TETHERED PARTICLE MOTION for tuberculosis nucleic acid detection re- quire amplification and labeling before detection is possible. We of a range of infections (for example active tuberculosis) a nucleic acid Corresponding author: s

  19. Single-Molecule Conductance in Atomically Precise Germanium Timothy A. Su,,

    E-print Network

    Single-Molecule Conductance in Atomically Precise Germanium Wires Timothy A. Su,,§ Haixing Li conductivity of bulk-scale group 14 materials such as diamond carbon, silicon, and germanium is well understood, which rely so heavily on silicon and germanium, begin to resemble ornate molecules rather than extended

  20. Optical Detection and Manipulation of Single Molecules in Room-Temperature Solutions

    E-print Network

    CONCEPTS Optical Detection and Manipulation of Single Molecules in Room-Temperature Solutions. Keywords: single-moleculedetection - single-moleculema- nipulation - laser-induced fluorescence * optical, frcquency-modulated optical ab- sorption and fluorescence excitation have been used to investi- gate

  1. 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. This study provides insight into structural changes of this protein when adsorbed onto an oil­water interface, and demonstrates the potential of SMFS as a tool to study the structure of proteins that are important in complex

  2. Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments

    E-print Network

    Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments of GFP that is used as a marker in cell biology and biotechnology. By engineering internal disulfide bonds at selected positions in the GFP structure, mechanical unfolding routes are precisely controlled

  3. Exploring the energy landscape of GFP by single-molecule mechanical experiments

    E-print Network

    Dietz, Hendrik

    Exploring the energy landscape of GFP by single-molecule mechanical experiments Hendrik Dietz single GFP molecules from the native state through their complex energy landscape into the completely unfolded state. Unlike many smaller proteins, mechanical GFP unfolding proceeds by means of two subsequent

  4. Detecting Molecular Fingerprints in Single Molecule Force Spectroscopy Using Pattern Recognition

    E-print Network

    , force spectroscopy, AFM, pattern recognition, GFP One of the most fundamental and challenging problems. The folding process of proteins is generally described as diffusion in a high dimensional energy-landscape.1) Recent advances in single molecule force spectroscopy have made it possible to explore the energy

  5. Single-molecule studies of repressorDNA interactions show long-range interactions

    E-print Network

    Wang, Yan Mei

    other; and (iii) energy transfer between GFP­LacI and the dye (BOBO-3, dimeric cyanine nucleic acid performed single-molecule studies of GFP­LacI repressor proteins bound to bacteriophage DNA containing a 256 concentration used in our experiments, all 256 sites would be occupied by two GFP­LacI monomers (Fig. 1b

  6. Multicolour single molecule emission and excitation spectroscopy reveals extensive spectral shifts.

    PubMed

    Piatkowski, Lukasz; Gellings, Esther; van Hulst, Niek F

    2015-12-12

    We explore the distribution and shape of single molecule spectra at room temperature, when embedded in a polymer host. Multicolour excitation and emission spectroscopy is implemented to capture the full inhomogeneous distribution. We observe dramatic spectral changes in a distribution of single quaterrylene diimide (QDI) molecules isolated in a PMMA matrix. The molecules are strongly blue shifted with respect to the ensemble absorption maximum and spread over a staggering 200 nm range. Despite these strong shifts, the shape of the emission spectra does not differ much between individual molecules. We demonstrate that a considerable number of molecules may be invisible in single molecule experiments, as they typically rely on only a single excitation wavelength, which predetermines which subensemble is probed in the experiment. Lastly, we make a first step towards single molecule excitation spectroscopy under ambient conditions, which allows us to determine the spectral range at which individual molecules absorb light most efficiently. We show how single molecule emission and excitation spectroscopies can complement each other and a combination of both techniques can help in understanding the origin of underlaying spectral properties of individual molecules. PMID:26407189

  7. Single molecule experiments in biophysics: exploring the thermal behavior of nonequilibrium small systems

    E-print Network

    Ritort, Felix

    molecular tasks under nonequilibrium conditions [2]. Often the innermost workings of such machines is poorlySingle molecule experiments in biophysics: exploring the thermal behavior of nonequilibrium small applied to biomolecules contributes to our understanding of the nonequilibrium thermal behavior of small

  8. Single molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update

    PubMed Central

    Widom, Julia R.; Dhakal, Soma; Heinicke, Laurie A.; Walter, Nils G.

    2015-01-01

    Toxicology is the highly interdisciplinary field studying the adverse effects of chemicals on living organisms. It requires sensitive tools to detect such effects. After their initial implementation during the 1990s, single-molecule fluorescence detection tools were quickly recognized for their potential to contribute greatly to many different areas of scientific inquiry. In the intervening time, technical advances in the field have generated ever-improving spatial and temporal resolution, and have enabled the application of single-molecule fluorescence to increasingly complex systems, such as live cells. In this review, we give an overview of the optical components necessary to implement the most common versions of single-molecule fluorescence detection. We then discuss current applications to enzymology and structural studies, systems biology, and nanotechnology, presenting the technical considerations that are unique to each area of study, along with noteworthy recent results. We also highlight future directions that have the potential to revolutionize these areas of study by further exploiting the capabilities of single-molecule fluorescence microscopy. PMID:25212907

  9. Mechanical Coupling between Myosin Molecules Causes Differences between Ensemble and Single-Molecule Measurements

    E-print Network

    Peskin, Charles S.

    , hydrolyzing ATP to power the relative sliding of actin filaments. The technological advances that have enabled-stroke), which moves actin. When unbound (or weakly bound), myosin hydrolyzes ATP and reverses the power and hydrolyzing ATP in the process. The recent development of single molecule measurements has allowed mechanical

  10. Room-Temperature Fluorescence Imaging and Spectroscopy of Single Molecules by Two-Photon Excitation

    E-print Network

    Xie, Xiaoliang Sunney

    molecules. With one-photon fluorescence excitation, detection of single molecules in solution,2-6 imaging on a glass substrate by two-photon excitation with femtosecond pulses from a mode-locked Ti:sapphire laser of photobleaching rates is made between one-photon and two- photon excitation schemes. Introduction Recently two

  11. Single-Molecule Protein Unfolding and Translocation by an ATP-Fueled

    E-print Network

    Lang, Matthew

    Single-Molecule Protein Unfolding and Translocation by an ATP-Fueled Proteolytic Machine Marie ATP-powered proteases for protein- quality control and regulation. In the ClpXP protease, Clp with ClpXP. INTRODUCTION In all organisms, AAA+ family molecular machines harness the energy of ATP binding

  12. Dynamics of Single-Molecule Rotations on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

    E-print Network

    dynamics simulations and simple models to investigate what factors influence single-molecule rotations of these biological machines have stimulated multiple efforts to develop analogous manmade nanoscale devices been achieved,11,15-29 a direct application of these nanoscale machines is still limited due

  13. Frontiers in Laser Cooling, Single-Molecule Biophysics, and Enrgy Science: A Talk by Carl Wieman

    ScienceCinema

    Wieman, Carl

    2011-04-13

    Carl Wieman presents a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

  14. 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 ...

  15. Single-Molecule FRET Studies of HIV TAR-DNA Hairpin Unfolding Jixin Chen,

    E-print Network

    conserved among HIV isolates, indicating a strong selection pressure to maintain its structure.5 ThusSingle-Molecule FRET Studies of HIV TAR-DNA Hairpin Unfolding Dynamics Jixin Chen, Nitesh K. Poddar *S Supporting Information ABSTRACT: We directly measure the dynamics of the HIV trans

  16. Electrical Readout of Individual Nuclear Spin Trajectories in a Single-Molecule Magnet Spin Transistor

    E-print Network

    Transistor S. Thiele,1 R. Vincent,1 M. Holzmann,2 S. Klyatskaya,3 M. Ruben,3,4 F. Balestro,1 and W nuclear spin. The device, a TbPc2 single-molecule magnet spin transistor, detects the four different suggests that the relaxation times are limited by the current tunneling through the transistor, which opens

  17. Single-Molecule Spectroscopy of Cold Denaturation and the Temperature-Induced Collapse of Unfolded Proteins

    E-print Network

    Schuler, Ben

    Single-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 between these observations, we investigated the unfolded state of yeast frataxin, whose cold denaturation

  18. Single-molecule denaturation and degradation of proteins by the AAA ClpXP protease

    E-print Network

    Lang, Matthew

    Single-molecule denaturation and degradation of proteins by the AAA ClpXP protease Yongdae Shina,1 proteins, and then uses cycles of ATP hydrolysis to denature any native structure and to translocate assays to probe the kinetics of protein denaturation and degradation by ClpXP. These assays employ

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

    E-print Network

    Michalet, Xavier

    -spot excitation, fast multi-pixel detection, algorithms to handle many channels and suitable software to processUltra high-throughput single molecule spectroscopy with a 1024 pixel SPAD Ryan A. Colyera on silicon spatial light modulator (LCOS-SLM) and a novel standard CMOS 1024 pixel SPAD array, opening

  20. 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

  1. Single molecule fluorescence methodologies for investigating transcription factor binding kinetics to nucleosomes and DNA

    E-print Network

    Poirier, Michael

    Single molecule fluorescence methodologies for investigating transcription factor binding kinetics and dissociation kinet- ics of DNA binding proteins with naked and nucleosomal DNA are essential for understanding methodologies for quantifying the binding and dissociation kinetics of transcription factors at a target site

  2. Efficient coupling of photons to a single molecule and the observation of its

    E-print Network

    Loss, Daniel

    :10.1038/nphys812 Single dye molecules at cryogenic temperatures exhibit many spectroscopic phenomena quantum optics. However, the existing techniques for their detection have either sacrificed information are eliminated at cryogenic temperatures. A key technological hurdle in resonant spectroscopy of single molecules

  3. DOI: 10.1002/ijch.201100102 Single-Molecule Studies of HIV-1 Protease Catalysis

    E-print Network

    Myong, Sua

    Protein Synthesis Vladimir Yu. Torbeev,[a] Su-A Myong,[b] Taekjip Ha,[b] and Stephen B. H. Kent*[a] 1 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

  4. Single-molecule insights into retention at a reversed-phase chromatographic interface.

    PubMed

    Mabry, Joshua N; Skaug, Michael J; Schwartz, Daniel K

    2014-10-01

    The efficiency of chromatographic separations decreases markedly when peaks exhibit asymmetry (e.g., "peak tailing"). Theoretically, these effects can arise from heterogeneous adsorption kinetics. To investigate the nature and consequences of such heterogeneity, we used a combination of single-molecule imaging and reversed-phase liquid chromatography (RPLC). In both single-molecule and macroscopic RPLC experiments, the stationary phase was hydrophobic end-capped (trimethylsilyl-functionalized) silica, which we exposed to different methanol/water solutions (50%-62% methanol), containing a fluorescent fatty acid analyte. Super-resolution maps based on single-molecule observations revealed rare, strong adsorption sites with activity that varied significantly with methanol concentration. The adsorption and desorption kinetics on the strong sites were heterogeneous and positively correlated, suggesting a broad underlying distribution of site binding energies. Adsorption equilibrium on the strong sites was more sensitive to solution conditions than overall retention measured in RPLC experiments, suggesting that the effect of strong sites on the overall adsorption kinetics should change with solution conditions. Interestingly, in RPLC experiments, peak tailing had a nonmonotonic dependence on methanol concentration within the range studied. Using the stochastic model of chromatography, we showed quantitatively that our single-molecule kinetic results were consistent with this macroscopic trend. This approach to identifying and quantifying adsorption sites should be useful for designing better chromatographic separations and for identifying the role of heterogeneous surface chemistry in molecular dynamics. PMID:25188676

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

    E-print Network

    Walter, Nils G.

    Institute of Physics. Related Articles Supercontinuum ultra wide range confocal microscope for reflectance) High-throughput scanning confocal microscope for single molecule analysis Appl. Phys. Lett. 84, 1216 (2004) Improvement of detected intensity in confocal microscopy by using reflecting optical system Rev

  6. Single-molecule fluorescence detection: Autocorrelation criterion and experimental realization with phycoerythrin

    SciTech Connect

    Peck, K.; Stryer, L.; Glazer, A.N.; Mathies, R.A. )

    1989-06-01

    A theory for single-molecule fluorescence detection is developed and then used to analyze data from subpicomolar solutions of B-phycoerythrin (PE). The distribution of detected counts is the convolution of a Poissonian continuous background with bursts arising from the passage of individual fluorophores through the focused laser beam. The autocorrelation function reveals single-molecule events and provides a criterion for optimizing experimental parameters. The transit time of fluorescent molecules through the 120-fl imaged volume was 800 {mu}s. The optimal laser power gave an incident intensity of 1.8 {times} 10{sup 23} photo{center dot}cm{sup minus2}{center dot}s{sup {minus}1}, corresponding to a mean time of 1.1 ns between absorptions. The mean incremental count rate was 1.5 per 100 {mu}s for PE monomers and 3.0 for PE dimers above a background count rate of 1.0. The distribution of counts and the autocorrelation function for 200 fM monomer and 100 fM dimer demonstrate that single-molecule detection was achieved. At this concentration, the mean occupancy was 0.014 monomer molecules in the probed volume. A hard-wired version of this detection system was used to measure the concentration of PE down to 1 fM. This single-molecule counter is 3 orders of magnitude more sensitive than conventional fluorescence detection systems.

  7. Stochastic gene expression: from single molecules to the Benjamin B Kaufmann1,2

    E-print Network

    Timmer, Jens

    Stochastic gene expression: from single molecules to the proteome Benjamin B Kaufmann1 and degradation of mRNAs, but several lines of evidence suggest that infrequent gene activation events also bear to be correlated for chromosomally proximal genes, suggesting the existence of an upstream player. Addresses 1

  8. First principle study of the effect of defects on performance of single-molecule pentacene field effect transistors

    NASA Astrophysics Data System (ADS)

    Ghosh, Bahniman; Gramin, Akash

    2015-07-01

    In this work, we have performed first principle study on a single-molecule pentacene field effect transistor and studied various oxygen- and hydrogen-induced defects in the same device configuration. Further, we have investigated the effect of these defects on the various electronic transport properties of the device and compared them with those of the original device along with reporting the negative differential region window and the peak-to-valley ratio in different cases. For this purpose, we have applied the density functional theory in conjugation with non-equilibrium green's function (NEGF) formalism on a 14.11 Å pentacene device to obtain the I-V characteristics, conductance curves and transmission spectra in various device scenarios.

  9. Microstructure, phase transition, and interfacial chemistry of Gd{sub 2}O{sub 3}/Si(111) grown by electron-beam physical vapor deposition

    SciTech Connect

    Weng Xiaojun; Grave, Daniel A.; Hughes, Zachary R.; Wolfe, Douglas E.; Robinson, Joshua A.

    2012-07-15

    The effects of growth temperature, film thickness, and oxygen flux on the microstructure, phase transition, and interfacial chemistry of gadolinium oxide (Gd{sub 2}O{sub 3}) films grown on Si(111) substrates by electron-beam physical vapor deposition were investigated using a combination of transmission electron microscopy (TEM), electron diffraction, scanning TEM, x-ray energy dispersive spectrometry, and electron energy loss spectrometry. The authors find that a low growth temperature (250 Degree-Sign C) and a high oxygen flux (200 sccm) led to a small grain size and a high porosity of the Gd{sub 2}O{sub 3} film. Lowering the oxygen flux to 50 sccm led to reduced film porosity, presumably due to the increased diffusion length of the Gd atoms on the surface. Increasing the growth temperature to 650 Degree-Sign C resulted in a film with large columnar grains and elongated pores at the grain boundaries. Thin films grown at 250 Degree-Sign C consisted of cubic Gd{sub 2}O{sub 3}, but thermodynamically less stable monoclinic phase formed as the film thickness increased. Lowering the oxygen flux apparently further promoted the formation of the monoclinic phase. Furthermore, monoclinic phase dominated in the films grown at 650 Degree-Sign C. Such phase transitions may be related to the stress evolution of the films at different temperatures, thicknesses, and oxygen fluxes. Enhanced Gd{sub 2}O{sub 3}/Si interfacial reaction was observed as the growth temperature, film thickness, and oxygen flux increased. Moreover, oxygen was found to play a crucial role in the Gd{sub 2}O{sub 3}/Si interfacial reaction and the formation of Gd-Si-O interface layers, which proceeded by the reaction of excess oxygen with Si followed by the intermixing of SiO{sub x} and Gd{sub 2}O{sub 3}.

  10. Molecular spintronics based on single-molecule magnets composed of multiple-decker phthalocyaninato terbium(III) complex.

    PubMed

    Katoh, Keiichi; Isshiki, Hironari; Komeda, Tadahiro; Yamashita, Masahiro

    2012-06-01

    Unlike electronics, which is based on the freedom of the charge of an electron whose memory is volatile, spintronics is based on the freedom of the charge, spin, and orbital of an electron whose memory is non-volatile. Although in most GMR, TMR, and CMR systems, bulk or classical magnets that are composed of transition metals are used, this Focus Review considers the growing use of single-molecule magnets (SMMs) that are composed of multinuclear metal complexes and nanosized magnets, which exhibit slow magnetic-relaxation processes and quantum tunneling. Molecular spintronics, which combines spintronics and molecular electronics, is an emerging field of research. Using molecules is advantageous because their electronic and magnetic properties can be manipulated under specific conditions. Herein, recent developments in [LnPc]-based multiple-decker SMMs on surfaces for molecular spintronic devices are presented. First, we discuss the strategies for preparing single-molecular-memory devices by using SMMs. Next, we focus on the switching of the Kondo signal of [LnPc]-based multiple-decker SMMs that are adsorbed onto surfaces, their characterization by using STM and STS, and the relationship between the molecular structure, the electronic structure, and the Kondo resonance of [TbPc(2)]. Finally, the field-effect-transistor (FET) properties of surface-adsorbed [LnPc(2)] and [Ln(2)Pc(3)] cast films are reported, which is the first step towards controlling SMMs through their spins for applications in single-molecular memory and spintronics devices. PMID:22514153

  11. High-efficiency inverted organic solar cells with polyethylene oxide-modified Zn-doped TiO2 as an interfacial electron transport layer

    NASA Astrophysics Data System (ADS)

    Thambidurai, M.; Kim, Jun Young; Ko, Youngjun; Song, Hyung-Jun; Shin, Hyeonwoo; Song, Jiyun; Lee, Yeonkyung; Muthukumarasamy, N.; Velauthapillai, Dhayalan; Lee, Changhee

    2014-07-01

    High efficiency inverted organic solar cells are fabricated using the PTB7:PC71BM polymer by incorporating Zn-doped TiO2 (ZTO) and 0.05 wt% PEO:ZTO as interfacial electron transport layers. The 0.05 wt% PEO-modified ZTO device shows a significantly increased power conversion efficiency (PCE) of 8.10%, compared to that of the ZTO (7.67%) device.High efficiency inverted organic solar cells are fabricated using the PTB7:PC71BM polymer by incorporating Zn-doped TiO2 (ZTO) and 0.05 wt% PEO:ZTO as interfacial electron transport layers. The 0.05 wt% PEO-modified ZTO device shows a significantly increased power conversion efficiency (PCE) of 8.10%, compared to that of the ZTO (7.67%) device. Electronic supplementary information (ESI) available: Experimental part, UPS spectra, absorption spectra, XPS spectra, J-V characteristics, IPCE spectra, AFM, and PL spectra. See DOI: 10.1039/c4nr02780a

  12. Coherent Anti-Stokes Raman Scattering Spectroscopy of Single Molecules in Solution

    SciTech Connect

    Sunney Xie, Wei Min, Chris Freudiger, Sijia Lu

    2012-01-18

    During this funding period, we have developed two breakthrough techniques. The first is stimulated Raman scattering microscopy, providing label-free chemical contrast for chemical and biomedical imaging based on vibrational spectroscopy. Spontaneous Raman microscopy provides specific vibrational signatures of chemical bonds, but is often hindered by low sensitivity. We developed a three-dimensional multiphoton vibrational imaging technique based on stimulated Raman scattering (SRS). The sensitivity of SRS imaging is significantly greater than that of spontaneous Raman microscopy, which is achieved by implementing high-frequency (megahertz) phase-sensitive detection. SRS microscopy has a major advantage over previous coherent Raman techniques in that it offers background-free and readily interpretable chemical contrast. We demonstrated a variety of biomedical applications, such as differentiating distributions of omega-3 fatty acids and saturated lipids in living cells, imaging of brain and skin tissues based on intrinsic lipid contrast, and monitoring drug delivery through the epidermis. This technology offers exciting prospect for medical imaging. The second technology we developed is stimulated emission microscopy. Many chromophores, such as haemoglobin and cytochromes, absorb but have undetectable fluorescence because the spontaneous emission is dominated by their fast non-radiative decay. Yet the detection of their absorption is difficult under a microscope. We use stimulated emission, which competes effectively with the nonradiative decay, to make the chromophores detectable, as a new contrast mechanism for optical microscopy. We demonstrate a variety of applications of stimulated emission microscopy, such as visualizing chromoproteins, non-fluorescent variants of the green fluorescent protein, monitoring lacZ gene expression with a chromogenic reporter, mapping transdermal drug distribu- tions without histological sectioning, and label-free microvascular imaging based on endogenous contrast of haemoglobin. For all these applications, sensitivity is orders of magnitude higher than for spontaneous emission or absorption contrast, permitting nonfluorescent reporters for molecular imaging. Although we did not accomplish the original goal of detecting single-molecule by CARS, our quest for high sensitivity of nonlinear optical microscopy paid off in providing the two brand new enabling technologies. Both techniques were greatly benefited from the use of high frequency modulation for microscopy, which led to orders of magnitude increase in sensitivity. Extensive efforts have been made on optics and electronics to accomplish these breakthroughs.

  13. 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.

  14. Spectral imaging of single molecules by transmission grating-based epi-fluorescencs microscopy

    SciTech Connect

    Han, Rui; Zhang, YeWang; Dong, Xiuling; Gai, Hongwei; Yeung, Edward S.

    2008-06-16

    A spectral imaging method of single protein molecules labeled with a single fluorophore is presented. The method is based on a transmission grating and a routine fluorescence microscope. The bovine serum albumin (BSA) and antiBSA molecules labeled with Alexa Fluor 488 and Alexa Fluor 594, respectively, are used as the model proteins. The fluorescence of single molecules is dispersed into zeroth-order spectrum and first-order spectrum by the transmission grating. Results show that the fluorescence emission spectrum of single molecule converted from the first-order spectral imaging is in good agreement with the bulk fluorescence spectrum. The spectral resolution of 2.4 nm/pixel is obtained, which is sufficient for identifying the molecular species in a multicomponent system.

  15. Rapid prototyping of multichannel microfluidic devices for single-molecule DNA curtain imaging.

    PubMed

    Robison, Aaron D; Finkelstein, Ilya J

    2014-05-01

    Single-molecule imaging and manipulation of biochemical reactions continues to reveal numerous biological insights. To facilitate these studies, we have developed and implemented a high-throughput approach to organize and image hundreds of individual DNA molecules at aligned diffusion barriers. Nonetheless, obtaining statistically relevant data sets under a variety of reaction conditions remains challenging. Here, we present a method for integrating high-throughput single-molecule "DNA curtain" imaging with poly(dimethylsiloxane) (PDMS)-based microfluidics. Our benchtop fabrication method can be accomplished in minutes with common tools found in all molecular biology laboratories. We demonstrate the utility of this approach by simultaneous imaging of two independent biochemical reaction conditions in a laminar flow device. In addition, five different reaction conditions can be observed concurrently in a passive linear gradient generator. Combining rapid microfluidic fabrication with high-throughput DNA curtains greatly expands our capability to interrogate complex biological reactions. PMID:24734940

  16. Single-Molecule Detection of Thionine on Aggregated Gold Nanoparticles by Surface Enhanced Raman Scattering

    SciTech Connect

    Ruan, Chuanmin; Wang, Wei; Gu, Baohua

    2007-01-01

    We report observations of single molecule detection of thionine and its dynamic interactions on aggregated gold nanoparticle clusters using surface enhanced Raman scattering (SERS). Spectral intensities were found to be independent of the size of Au nanoparticles studied (from 17 to 80 nm) at thionine concentration below 10-12 M or at single molecule concentration levels. Raman line separations and, in particular, spectral fluctuations and blinking also were observed, suggesting temporal changes in single molecular motion and/or arrangements of thionine on Au nanoparticle surfaces. In contrast, by using dispersed Au nanoparticles, only ensemble SERS spectra could be observed at relatively high concentrations (>10-8 M thionine), and spectral intensities varied with the size of Au nanoparticles.

  17. Exploring bacterial cell biology with single-molecule tracking and super-resolution imaging

    PubMed Central

    Gahlmann, Andreas; Moerner, W. E.

    2014-01-01

    The ability to detect single molecules in live bacterial cells enables us to probe biological events one molecule at a time and thereby gain knowledge of the activities of intracellular molecules that remain obscure in conventional ensemble-averaged measurements. Single-molecule fluorescence tracking and super-resolution imaging are thus providing a new window into bacterial cells and facilitating the elucidation of cellular processes at an unprecedented level of sensitivity, specificity and spatial resolution. In this Review, we consider what these technologies have taught us about the bacterial cytoskeleton, nucleoid organization and the dynamic processes of transcription and translation, and we also highlight the methodological improvements that are needed to address a number of experimental challenges in the field. PMID:24336182

  18. Detection of Single Molecules Illuminated by a Light-Emitting Diode

    PubMed Central

    Gerhardt, Ilja; Mai, Lijian; Lamas-Linares, Antía; Kurtsiefer, Christian

    2011-01-01

    Optical detection and spectroscopy of single molecules has become an indispensable tool in biological imaging and sensing. Its success is based on fluorescence of organic dye molecules under carefully engineered laser illumination. In this paper we demonstrate optical detection of single molecules on a wide-field microscope with an illumination based on a commercially available, green light-emitting diode. The results are directly compared with laser illumination in the same experimental configuration. The setup and the limiting factors, such as light transfer to the sample, spectral filtering and the resulting signal-to-noise ratio are discussed. A theoretical and an experimental approach to estimate these parameters are presented. The results can be adapted to other single emitter and illumination schemes. PMID:22346610

  19. Single-Molecule Imaging of Fluorescent Proteins Expressed in Living Cells

    NASA Astrophysics Data System (ADS)

    Hibino, Kayo; Hiroshima, Michio; Takahashi, Masahiro; Sako, Yasushi

    This chapter focuses on single-molecule imaging (SMI) in living cells using green fluorescent protein (GFP) or its related fluorescent protein tags (GFPs). Use of GFPs is a convenient technique to achieve molecular imaging of most proteins in living cells. However, because of difficulties in preparing samples suitable for SMI and the instability of fluorescence signals, special care is required for SMI using GFPs in living cells. Techniques for vector preparation, protein expression, sample preparation, microscopy, and image processing for SMI of GFPs in living cells are discussed in this chapter, along with examples of imaging applications. Double labeling of single molecules and single-pair fluorescent resonance energy transfer (spFRET) are possible in living cells using GFP and YFP as fluorescent tags. The limitations of SMI using GFPs are also discussed.

  20. Time-Resolved Measurement of Vibrational Coherences in the Single Molecule Limit

    NASA Astrophysics Data System (ADS)

    Yampolsky, Steven

    Time-resolved, surface-enhanced, coherent anti-Stokes Raman spectroscopy (tr-SECARS) is ideally suited for preparing and interrogating vibrational coherences on single molecules. We have succeeded in the rst demonstration of this concept through measurements carried out on molecules attached to gold nanosphere pairs which act as plasmonic nano-dumbell antennae. The tr-SECARS traces provide unique signatures of coherent evolution in discrete ensembles. The signals are characterized by phase and amplitude noise, which can be cast in terms of amplitude probability distribution functions (PDF), which allow rigorous distinction between single, few, and many molecule coherences. We give a brief background on tr-CARS, the experimental system for carrying out tr-SECARS and the analysis of the results in terms of PDFs. The analysis makes it clear that we have, for the rst time, observed the coherent vibrational motion of a single molecule.

  1. Single-molecule imaging of telomerase reverse transcriptase in human telomerase holoenzyme and minimal RNP complexes.

    PubMed

    Wu, Robert Alexander; Dagdas, Yavuz S; Yilmaz, S Tunc; Yildiz, Ahmet; Collins, Kathleen

    2015-01-01

    Telomerase synthesizes chromosome-capping telomeric repeats using an active site in telomerase reverse transcriptase (TERT) and an integral RNA subunit template. The fundamental question of whether human telomerase catalytic activity requires cooperation across two TERT subunits remains under debate. In this study, we describe new approaches of subunit labeling for single-molecule imaging, applied to determine the TERT content of complexes assembled in cells or cell extract. Surprisingly, telomerase reconstitutions yielded heterogeneous DNA-bound TERT monomer and dimer complexes in relative amounts that varied with assembly and purification method. Among the complexes, cellular holoenzyme and minimal recombinant enzyme monomeric for TERT had catalytic activity. Dimerization was suppressed by removing a TERT domain linker with atypical sequence bias, which did not inhibit cellular or minimal enzyme assembly or activity. Overall, this work defines human telomerase DNA binding and synthesis properties at single-molecule level and establishes conserved telomerase subunit architecture from single-celled organisms to humans. PMID:26457608

  2. A Stochastic Single-Molecule Event Triggers Phenotype Switching of a Bacterial Cell

    NASA Astrophysics Data System (ADS)

    Xie, Sunney; Choi, Paul; Cai, Long

    2009-03-01

    By monitoring fluorescently labeled lactose permease with single-molecule sensitivity, we investigated the molecular mechanism of how an Escherichia coli cell with the lac operon switches from one phenotype to another. At intermediate inducer concentrations, a population of genetically identical cells exhibits two phenotypes: induced cells with highly fluorescent membranes and uninduced cells with a small number of membrane-bound permeases. We found that this basal-level expression results from partial dissociation of the tetrameric lactose repressor from one of its operators on looped DNA. In contrast, infrequent events of complete dissociation of the repressor from DNA result in large bursts of permease expression that trigger induction of the lac operon. Hence, a stochastic single-molecule event determines a cell's phenotype.

  3. A stochastic single-molecule event triggers phenotype switching of a bacterial cell.

    PubMed

    Choi, Paul J; Cai, Long; Frieda, Kirsten; Xie, X Sunney

    2008-10-17

    By monitoring fluorescently labeled lactose permease with single-molecule sensitivity, we investigated the molecular mechanism of how an Escherichia coli cell with the lac operon switches from one phenotype to another. At intermediate inducer concentrations, a population of genetically identical cells exhibits two phenotypes: induced cells with highly fluorescent membranes and uninduced cells with a small number of membrane-bound permeases. We found that this basal-level expression results from partial dissociation of the tetrameric lactose repressor from one of its operators on looped DNA. In contrast, infrequent events of complete dissociation of the repressor from DNA result in large bursts of permease expression that trigger induction of the lac operon. Hence, a stochastic single-molecule event determines a cell's phenotype. PMID:18927393

  4. 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.

  5. Current rectification in a single molecule diode: the role of electrode coupling

    NASA Astrophysics Data System (ADS)

    Sherif, Siya; Rubio-Bollinger, Gabino; Pinilla-Cienfuegos, Elena; Coronado, Eugenio; Cuevas, Juan Carlos; Agraït, Nicolás

    2015-07-01

    We demonstrate large rectification ratios (\\gt 100) in single-molecule junctions based on a metal-oxide cluster (polyoxometalate), using a scanning tunneling microscope (STM) both at ambient conditions and at low temperature. These rectification ratios are the largest ever observed in a single-molecule junction, and in addition these junctions sustain current densities larger than 105 A cm-2. By following the variation of the I-V characteristics with tip-molecule separation we demonstrate unambiguously that rectification is due to asymmetric coupling to the electrodes of a molecule with an asymmetric level structure. This mechanism can be implemented in other type of molecular junctions using both organic and inorganic molecules and provides a simple strategy for the rational design of molecular diodes.

  6. Aptamer-based single-molecule imaging of insulin receptors in living cells

    NASA Astrophysics Data System (ADS)

    Chang, Minhyeok; Kwon, Mijin; Kim, Sooran; Yunn, Na-Oh; Kim, Daehyung; Ryu, Sung Ho; Lee, Jong-Bong

    2014-05-01

    We present a single-molecule imaging platform that quantitatively explores the spatiotemporal dynamics of individual insulin receptors in living cells. Modified DNA aptamers that specifically recognize insulin receptors (IRs) with a high affinity were selected through the SELEX process. Using quantum dot-labeled aptamers, we successfully imaged and analyzed the diffusive motions of individual IRs in the plasma membranes of a variety of cell lines (HIR, HEK293, HepG2). We further explored the cholesterol-dependent movement of IRs to address whether cholesterol depletion interferes with IRs and found that cholesterol depletion of the plasma membrane by methyl-?-cyclodextrin reduces the mobility of IRs. The aptamer-based single-molecule imaging of IRs will provide better understanding of insulin signal transduction through the dynamics study of IRs in the plasma membrane.

  7. 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

  8. Reduced dyes enhance single-molecule localization density for live superresolution imaging.

    PubMed

    Carlini, Lina; Benke, Alexander; Reymond, Luc; Lukinavi?ius, Gražvydas; Manley, Suliana

    2014-03-17

    Cell-permeable rhodamine dyes are reductively quenched by NaBH4 into a non-fluorescent leuco-rhodamine form. Quenching is reversible, and their fluorescence is recovered when the dyes are oxidized. In living cells, oxidation occurs spontaneously, and can result in up to ten-fold higher densities of single molecule localizations, and more photons per localization as compared with unmodified dyes. These two parameters directly impact the achievable resolution, and we see a significant improvement in the quality of live-cell point-localization super-resolution images taken with reduced dyes. These improvements carry over to increase the density of trajectories for single-molecule tracking experiments. PMID:24554553

  9. Camera-based single-molecule FRET detection with improved time resolution.

    PubMed

    Farooq, Shazia; Hohlbein, Johannes

    2015-10-14

    The achievable time resolution of camera-based single-molecule detection is often limited by the frame rate of the camera. Especially in experiments utilizing single-molecule Förster resonance energy transfer (smFRET) to probe conformational dynamics of biomolecules, increasing the frame rate by either pixel-binning or cropping the field of view decreases the number of molecules that can be monitored simultaneously. Here, we present a generalised excitation scheme termed stroboscopic alternating-laser excitation (sALEX) that significantly improves the time resolution without sacrificing highly parallelised detection in total internal reflection fluorescence (TIRF) microscopy. In addition, we adapt a technique known from diffusion-based confocal microscopy to analyse the complex shape of FRET efficiency histograms. We apply both sALEX and dynamic probability distribution analysis (dPDA) to resolve conformational dynamics of interconverting DNA hairpins in the millisecond time range. PMID:26439729

  10. 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

  11. Chemical structure imaging of a single molecule by atomic force microscopy at room temperature

    PubMed Central

    Iwata, Kota; Yamazaki, Shiro; Mutombo, Pingo; Hapala, Prokop; Ondrá?ek, Martin; Jelínek, Pavel; Sugimoto, Yoshiaki

    2015-01-01

    Atomic force microscopy is capable of resolving the chemical structure of a single molecule on a surface. In previous research, such high resolution has only been obtained at low temperatures. Here we demonstrate that the chemical structure of a single molecule can be clearly revealed even at room temperature. 3,4,9,10-perylene tetracarboxylic dianhydride, which is strongly adsorbed onto a corner-hole site of a Si(111)–(7 × 7) surface in a bridge-like configuration is used for demonstration. Force spectroscopy combined with first-principle calculations clarifies that chemical structures can be resolved independent of tip reactivity. We show that the submolecular contrast over a central part of the molecule is achieved in the repulsive regime due to differences in the attractive van der Waals interaction and the Pauli repulsive interaction between different sites of the molecule. PMID:26178193

  12. Crypto-tomography: the data assembly challenge in single-molecule diffraction

    NASA Astrophysics Data System (ADS)

    Elser, Veit

    2007-03-01

    In the absence of a molecular alignment mechanism, the diffraction patterns collected in single-molecule XFEL experiments will sample randomly oriented, 2D slices of a 3D data set. The signal to noise ratio in the individual slices will be so low that the relative orientations of any two will be poorly determined. This talk describes a new strategy for data assembly, where the relationships among multiple slices are determined collectively.

  13. Single molecule magnet behaviour in a rare trinuclear {Cr(III)Dy} methoxo-bridged complex.

    PubMed

    Car, Pierre-Emmanuel; Favre, Annaïck; Caneschi, Andrea; Sessoli, Roberta

    2015-09-28

    The reaction of the chromium(iii) chloride tetrahydrofuran complex with the dipivaloylmethane ligand, the lanthanide alcoholic salt DyCl3·CH3OH and the 1,1,1-tris(hydroxymethyl)-ethane ligand resulted in the formation of a new trinuclear chromium-dysprosium complex. Magnetic investigations revealed that the new 3d-4f complex exhibits single molecule magnet behaviour. PMID:26282265

  14. Single-molecule magnet behaviour in polynuclear assembly of trivalent cerium ions with polyoxomolybdates.

    PubMed

    Khélifa, A Ben; Belkhiria, M Salah; Huang, G; Freslon, S; Guillou, O; Bernot, K

    2015-10-01

    An isopolyoxomolybdate-based POM is coordinated to trivalent cerium ions to afford a hybrid complex namely, [Ce(dmso)8][Ce(?2-NO3)2(dmso)4(?-Mo8O26)0.5][Mo6O19]. The original electrostatic environment created around the Ce(III) by its coordination to the isopolyoxomolybdate core induces complex single-molecule magnet behavior. PMID:26314612

  15. Testing Landscape Theory for Biomolecular Processes with Single Molecule Fluorescence Spectroscopy

    NASA Astrophysics Data System (ADS)

    Truex, Katherine; Chung, Hoi Sung; Louis, John M.; Eaton, William A.

    2015-07-01

    Although Kramers' theory for diffusive barrier crossing on a 1D free energy profile plays a central role in landscape theory for complex biomolecular processes, it has not yet been rigorously tested by experiment. Here we test this 1D diffusion scenario with single molecule fluorescence measurements of DNA hairpin folding. We find an upper bound of 2.5 ? s for the average transition path time, consistent with the predictions by theory with parameters determined from optical tweezer measurements.

  16. On the Uncertainty in Single Molecule Fluorescent Lifetime and Energy Emission Measurements

    NASA Technical Reports Server (NTRS)

    Brown, Emery N.; Zhang, Zhenhua; McCollom, Alex D.

    1996-01-01

    Time-correlated single photon counting has recently been combined with mode-locked picosecond pulsed excitation to measure the fluorescent lifetimes and energy emissions of single molecules in a flow stream. Maximum likelihood (ML) and least squares methods agree and are optimal when the number of detected photons is large, however, in single molecule fluorescence experiments the number of detected photons can be less than 20, 67 percent of those can be noise, and the detection time is restricted to 10 nanoseconds. Under the assumption that the photon signal and background noise are two independent inhomogeneous Poisson processes, we derive the exact joint arrival time probability density of the photons collected in a single counting experiment performed in the presence of background noise. The model obviates the need to bin experimental data for analysis, and makes it possible to analyze formally the effect of background noise on the photon detection experiment using both ML or Bayesian methods. For both methods we derive the joint and marginal probability densities of the fluorescent lifetime and fluorescent emission. The ML and Bayesian methods are compared in an analysis of simulated single molecule fluorescence experiments of Rhodamine 110 using different combinations of expected background noise and expected fluorescence emission. While both the ML or Bayesian procedures perform well for analyzing fluorescence emissions, the Bayesian methods provide more realistic measures of uncertainty in the fluorescent lifetimes. The Bayesian methods would be especially useful for measuring uncertainty in fluorescent lifetime estimates in current single molecule flow stream experiments where the expected fluorescence emission is low. Both the ML and Bayesian algorithms can be automated for applications in molecular biology.

  17. On the uncertainty in single molecule fluorescent lifetime and energy emission measurements

    NASA Technical Reports Server (NTRS)

    Brown, Emery N.; Zhang, Zhenhua; Mccollom, Alex D.

    1995-01-01

    Time-correlated single photon counting has recently been combined with mode-locked picosecond pulsed excitation to measure the fluorescent lifetimes and energy emissions of single molecules in a flow stream. Maximum likelihood (ML) and least square methods agree and are optimal when the number of detected photons is large however, in single molecule fluorescence experiments the number of detected photons can be less than 20, 67% of those can be noise and the detection time is restricted to 10 nanoseconds. Under the assumption that the photon signal and background noise are two independent inhomogeneous poisson processes, we derive the exact joint arrival time probably density of the photons collected in a single counting experiment performed in the presence of background noise. The model obviates the need to bin experimental data for analysis, and makes it possible to analyze formally the effect of background noise on the photon detection experiment using both ML or Bayesian methods. For both methods we derive the joint and marginal probability densities of the fluorescent lifetime and fluorescent emission. the ML and Bayesian methods are compared in an analysis of simulated single molecule fluorescence experiments of Rhodamine 110 using different combinations of expected background nose and expected fluorescence emission. While both the ML or Bayesian procedures perform well for analyzing fluorescence emissions, the Bayesian methods provide more realistic measures of uncertainty in the fluorescent lifetimes. The Bayesian methods would be especially useful for measuring uncertainty in fluorescent lifetime estimates in current single molecule flow stream experiments where the expected fluorescence emission is low. Both the ML and Bayesian algorithms can be automated for applications in molecular biology.

  18. SDmixer—a versatile software tool for spectral demixing of multicolor single molecule localization data

    NASA Astrophysics Data System (ADS)

    Tadeus, Georgi; Lampe, André; Schmoranzer, Jan

    2015-09-01

    Spectral demixing (SD) offers multicolor single molecule localization microscopy (SMLM) with low crosstalk and without the need to correct for registration errors. Here, we present SDmixer, a versatile, open-source software tool that enables any laboratory to perform rapid SD-based multicolor SMLM. A graphic user interface allows non-experts to process 2D or 3D data sets from any SML software and to reconstruct the super-resolved multicolor images with flexible output options.

  19. Electrochemical single-molecule detection in aqueous solution using self-aligned nanogap transducers.

    PubMed

    Kang, Shuo; Nieuwenhuis, Ab F; Mathwig, Klaus; Mampallil, Dileep; Lemay, Serge G

    2013-12-23

    Electrochemical detection of individual molecular tags in nanochannels may enable cost-effective, massively parallel analysis and diagnostics platforms. Here we demonstrate single-molecule detection of prototypical analytes in aqueous solution based on redox cycling in 40 nm nanogap transducers. These nanofluidic devices are fabricated using standard microfabrication techniques combined with a self-aligned approach that minimizes gap size and dead volume. We demonstrate the detection of three common redox mediators at physiological salt concentrations. PMID:24279688

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

    PubMed

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

    2010-02-01

    Although single-molecule fluorescence spectroscopy was first demonstrated at near-absolute zero temperatures (1.8 K), the field has since advanced to include room-temperature observations, largely owing to the use of objective lenses with high numerical aperture, brighter fluorophores and more sensitive detectors. This has opened the door for many chemical and biological systems to be studied at native temperatures at the single-molecule level both in vitro and in vivo. However, it is difficult to study systems and phenomena at temperatures above 37 degrees C, because the index-matching fluids used with high-numerical-aperture objective lenses can conduct heat from the sample to the lens, and sustained exposure to high temperatures can cause the lens to fail. Here, we report that TiO(2) colloids with diameters of 2 microm and a high refractive index can act as lenses that are capable of single-molecule imaging at 70 degrees C when placed in immediate proximity to an emitting molecule. The optical system is completed by a low-numerical-aperture optic that can have a long working distance and an air interface, which allows the sample to be independently heated. Colloidal lenses were used for parallel imaging of surface-immobilized single fluorophores and for real-time single-molecule measurements of mesophilic and thermophilic enzymes at 70 degrees C. Fluorophores in close proximity to TiO(2) also showed a 40% increase in photostability due to a reduction of the excited-state lifetime. PMID:20023643

  1. A single molecule magnet to single molecule magnet transformation via a solvothermal process: Fe4Dy2 ? Fe6Dy3.

    PubMed

    Chen, Sihuai; Mereacre, Valeriu; Anson, Christopher E; Powell, Annie K

    2015-12-14

    Two series of heterometallic Fe(III)-Ln(III) compounds, [FeLn(?3-OH)2(mdea)4(m-NO2C6H4COO)8]·3MeCN where Ln = Y () and Dy () and [FeLn(?4-O)3(?3-O)(mdea)5(m-NO2C6H4COO)9]·3MeCN where Ln = Y () and Dy (), were synthesized. Compounds and were obtained under ambient conditions, whereas and were obtained via a solvothermal transformation process by heating or at 120 °C in MeCN. The magnetic properties of all four compounds have been measured and show that compounds and containing Dy(III) ions exhibit slow relaxation of magnetization characteristic of Single Molecule Magnetic (SMM) behaviour. PMID:26599423

  2. Single-molecule nucleic acid interactions monitored on a label-free microcavity biosensor platform.

    PubMed

    Baaske, Martin D; Foreman, Matthew R; Vollmer, Frank

    2014-11-01

    Biosensing relies on the detection of molecules and their specific interactions. It is therefore highly desirable to develop transducers exhibiting ultimate detection limits. Microcavities are an exemplary candidate technology for demonstrating such a capability in the optical domain and in a label-free fashion. Additional sensitivity gains, achievable by exploiting plasmon resonances, promise biosensing down to the single-molecule level. Here, we introduce a biosensing platform using optical microcavity-based sensors that exhibits single-molecule sensitivity and is selective to specific single binding events. Whispering gallery modes in glass microspheres are used to leverage plasmonic enhancements in gold nanorods for the specific detection of nucleic acid hybridization, down to single 8-mer oligonucleotides. Detection of single intercalating small molecules confirms the observation of single-molecule hybridization. Matched and mismatched strands are discriminated by their interaction kinetics. Our platform allows us to monitor specific molecular interactions transiently, hence mitigating the need for high binding affinity and avoiding permanent binding of target molecules to the receptors. Sensor lifetime is therefore increased, allowing interaction kinetics to be statistically analysed. PMID:25173831

  3. Single-molecule nucleic acid interactions monitored on a label-free microcavity biosensor platform

    NASA Astrophysics Data System (ADS)

    Baaske, Martin D.; Foreman, Matthew R.; Vollmer, Frank

    2014-11-01

    Biosensing relies on the detection of molecules and their specific interactions. It is therefore highly desirable to develop transducers exhibiting ultimate detection limits. Microcavities are an exemplary candidate technology for demonstrating such a capability in the optical domain and in a label-free fashion. Additional sensitivity gains, achievable by exploiting plasmon resonances, promise biosensing down to the single-molecule level. Here, we introduce a biosensing platform using optical microcavity-based sensors that exhibits single-molecule sensitivity and is selective to specific single binding events. Whispering gallery modes in glass microspheres are used to leverage plasmonic enhancements in gold nanorods for the specific detection of nucleic acid hybridization, down to single 8-mer oligonucleotides. Detection of single intercalating small molecules confirms the observation of single-molecule hybridization. Matched and mismatched strands are discriminated by their interaction kinetics. Our platform allows us to monitor specific molecular interactions transiently, hence mitigating the need for high binding affinity and avoiding permanent binding of target molecules to the receptors. Sensor lifetime is therefore increased, allowing interaction kinetics to be statistically analysed.

  4. Modification of a single-molecule AFM probe with highly defined surface functionality

    PubMed Central

    Khanal, Ashok

    2014-01-01

    Summary Single-molecule force spectroscopy with an atomic force microscope has been widely used to study inter- and intramolecular interactions. To obtain data consistent with single molecular events, a well-defined method is critical to limit the number of molecules at the apex of an AFM probe to one or to a few. In this paper, we demonstrate an easy method for single-molecule probe modification by using the Cu-catalyzed alkyne–azide cycloaddition reaction. Excess terminal alkynes were covalently attached to the probe, and a bi-functional molecule containing an azide at one end and a carboxylic acid at the other was dissolved in the reaction solution. By simply contacting the probe and the Cu substrate, controlled carboxylation on the probe apex could be achieved, since the ‘click’ reaction requires the co-exist of alkyne, azide and Cu(I). The finite contact area would result in a highly defined surface functionality of the probe down to single molecule level with high reproducibility. PMID:25551040

  5. Nanopore sensing at ultra-low concentrations using single-molecule dielectrophoretic trapping.

    PubMed

    Freedman, Kevin J; Otto, Lauren M; Ivanov, Aleksandar P; Barik, Avijit; Oh, Sang-Hyun; Edel, Joshua B

    2016-01-01

    Single-molecule techniques are being developed with the exciting prospect of revolutionizing the healthcare industry by generating vast amounts of genetic and proteomic data. One exceptionally promising route is in the use of nanopore sensors. However, a well-known complexity is that detection and capture is predominantly diffusion limited. This problem is compounded when taking into account the capture volume of a nanopore, typically 10(8)-10(10) times smaller than the sample volume. To rectify this disproportionate ratio, we demonstrate a simple, yet powerful, method based on coupling single-molecule dielectrophoretic trapping to nanopore sensing. We show that DNA can be captured from a controllable, but typically much larger, volume and concentrated at the tip of a metallic nanopore. This enables the detection of single molecules at concentrations as low as 5?fM, which is approximately a 10(3) reduction in the limit of detection compared with existing methods, while still maintaining efficient throughput. PMID:26732171

  6. Label-free field-effect-based single-molecule detection of DNA hybridization kinetics

    PubMed Central

    Sorgenfrei, Sebastian; Chiu, Chien-yang; Gonzalez, Ruben L.; Yu, Young-Jun; Kim, Philip; Nuckolls, Colin; Shepard, Kenneth L.

    2013-01-01

    Probing biomolecules at the single-molecule level can provide useful information about molecular interactions, kinetics and motions that is usually hidden in ensemble measurements. Techniques with improved sensitivity and time resolution are required to explore fast biomolecular dynamics. Here, we report the first observation of DNA hybridization at the single-molecule level using a carbon nanotube field-effect transistor. By covalently attaching a single-stranded probe DNA sequence to a point defect in a carbon nanotube, we are able to measure two-level fluctuations in the nanotube conductance due to reversible hybridizing and melting of a complementary DNA target. The kinetics are studied as a function of temperature, allowing the measurement of rate constants, melting curves and activation energies for different sequences and target concentrations. The kinetics show non-Arrhenius behavior, in agreement with DNA hybridization experiments using fluorescence correlation spectroscopy. This technique is label-free and has the potential for studying single-molecule dynamics at sub-microsecond time-scales. PMID:21258331

  7. Optimized straight forward procedure for covalent surface immobilization of different biomolecules for single molecule applications.

    PubMed

    Janissen, Richard; Oberbarnscheidt, Leoni; Oesterhelt, Filipp

    2009-07-01

    Covalent chemisorption of biomolecules to surfaces with high density and low unspecific background is prerequisite for most optical and mechanical single molecule experiments and accordingly, many recipes have been developed. However, new establishment of the surface functionalization process in the lab usually is still difficult and time consuming due to the complex procedures containing many pitfalls. Therefore, based on the known recipes, we developed and optimized a simple straight forward protocol. We demonstrated it resulting in a high density of the coupled biomolecules, homogeneous surfaces and a low unspecific background when binding nucleic acids, peptides and proteins. The protocol was optimized for borosilicate cover glasses and silicon nitride atomic force microscope cantilevers commonly used in single molecule experiments and takes advantage of commonly used chemicals. It consists of only four steps, silanol group generation, amination, grafting of poly(ethylene glycol) to the surface and biomolecule coupling. All individual steps were optimized comparing different variations partially described in the literature. Finally, a detailed description is provided which allows avoiding most sources of contamination, often being a main hurdle on the way to single molecule experiments. PMID:19329289

  8. High-Throughput Universal DNA Curtain Arrays for Single-Molecule Fluorescence Imaging

    PubMed Central

    Gallardo, Ignacio F.; Pasupathy, Praveenkumar; Brown, Maxwell; Manhart, Carol M.; Neikirk, Dean P.; Alani, Eric; Finkelstein, Ilya J.

    2015-01-01

    Single-molecule studies of protein–DNA interactions have shed critical insights into the molecular mechanisms of nearly every aspect of DNA metabolism. The development of DNA curtains—a method for organizing arrays of DNA molecules on a fluid lipid bilayer—has greatly facilitated these studies by increasing the number of reactions that can be observed in a single experiment. However, the utility of DNA curtains is limited by the challenges associated with depositing nanometer-scale lipid diffusion barriers onto quartz microscope slides. Here, we describe a UV lithography-based method for large-scale fabrication of chromium (Cr) features and organization of DNA molecules at these features for high-throughput single-molecule studies. We demonstrate this approach by assembling 792 independent DNA arrays (containing >900 000 DNA molecules) within a single microfluidic flowcell. As a first proof of principle, we track the diffusion of Mlh1-Mlh3—a heterodimeric complex that participates in DNA mismatch repair and meiotic recombination. To further highlight the utility of this approach, we demonstrate a two-lane flowcell that facilitates concurrent experiments on different DNA substrates. Our technique greatly reduces the challenges associated with assembling DNA curtains and paves the way for the rapid acquisition of large statistical data sets from individual single-molecule experiments. PMID:26325477

  9. Interaction of dihydrofolate reductase with methotrexate: Ensemble and single-molecule kinetics

    NASA Astrophysics Data System (ADS)

    Rajagopalan, P. T. Ravi; Zhang, Zhiquan; McCourt, Lynn; Dwyer, Mary; Benkovic, Stephen J.; Hammes, Gordon G.

    2002-10-01

    The thermodynamics and kinetics of the interaction of dihydrofolate reductase (DHFR) with methotrexate have been studied by using fluorescence, stopped-flow, and single-molecule methods. DHFR was modified to permit the covalent addition of a fluorescent molecule, Alexa 488, and a biotin at the N terminus of the molecule. The fluorescent molecule was placed on a protein loop that closes over methotrexate when binding occurs, thus causing a quenching of the fluorescence. The biotin was used to attach the enzyme in an active form to a glass surface for single-molecule studies. The equilibrium dissociation constant for the binding of methotrexate to the enzyme is 9.5 nM. The stopped-flow studies revealed that methotrexate binds to two different conformations of the enzyme, and the association and dissociation rate constants were determined. The single-molecule investigation revealed a conformational change in the enzyme-methotrexate complex that was not observed in the stopped-flow studies. The ensemble averaged rate constants for this conformation change in both directions is about 2-4 s1 and is attributed to the opening and closing of the enzyme loop over the bound methotrexate. Thus the mechanism of methotrexate binding to DHFR involves multiple steps and protein conformational changes.

  10. Single-molecule fluorescence study of the inhibition of the oncogenic functionality of STAT3

    NASA Astrophysics Data System (ADS)

    Liu, Baoxu; Badali, Daniel; Fletcher, Steven; Avadisian, Miriam; Gunning, Patrick; Gradinaru, Claudiu

    2009-06-01

    Signal-Transducer-and-Activator-of-Transcription 3 (STAT3) protein plays an important role in the onset of cancers such as leukemia and lymphoma. In this study, we aim to test the effectiveness of a novel peptide drug designed to tether STAT3 to the phospholipid bilayer of the cell membrane and thus inhibit unwanted transcription. As a first step, STAT3 proteins were successfully labelled with tetramethylrhodamine (TMR), a fluorescent dye with suitable photostability for single molecule studies. The effectiveness of labelling was determined using fluorescence correlation spectroscopy in a custom built confocal microscope, from which diffusion times and hydrodynamic radii of individual proteins were determined. A newly developed fluorescein derivative label (F-NAc) has been designed to be incorporated into the structure of the peptide drug so that peptide-STAT3 interactions can be examined. This dye is spectrally characterized and is found to be well suited for its application to this project, as well as other single-molecule studies. The membrane localization via high-affinity cholesterol-bound small-molecule binding agents can be demonstrated by encapsulating TMR-labeled STAT3 and inhibitors within a vesicle model cell system. To this end, unilaminar lipid vesicles were examined for size and encapsulation ability. Preliminary results of the efficiency and stability of the STAT3 anchoring in lipid membranes obtained via quantitative confocal imaging and single-molecule spectroscopy using a custom-built multiparameter fluorescence microscope are reported here.

  11. Single-molecule kinetics under force: probing protein folding and enzymatic activity with optical tweezers

    NASA Astrophysics Data System (ADS)

    Wong, Wesley

    2010-03-01

    Weak non-covalent bonds between and within single molecules govern many aspects of biological structure and function (e.g. DNA base-paring, receptor-ligand binding, protein folding, etc.) In living systems, these interactions are often subject to mechanical forces, which can greatly alter their kinetics and activity. My group develops and applies novel single-molecule manipulation techniques to explore and quantify these force-dependent kinetics. Using optical tweezers, we have quantified the force-dependent unfolding and refolding kinetics of different proteins, including the cytoskeletal protein spectrin in collaboration with E. Evans's group [1], and the A2 domain of the von Willebrand factor blood clotting protein in collaboration with T. Springer's group [2]. Furthermore, we have studied the kinetics of the ADAMTS13 enzyme acting on a single A2 domain, and have shown that physiolgical forces in the circulation can act as a cofactor for enzymatic cleavage, regulating hemostatic activity [2]. References: 1. E. Evans, K. Halvorsen, K. Kinoshita, and W.P. Wong, Handbook of Single Molecule Biophysics, P. Hinterdorfer, ed., Springer (2009). 2. X. Zhang, K. Halvorsen, C.-Z. Zhang, W.P. Wong, and T.A. Springer, Science 324 (5932), 1330-1334 (2009).

  12. Single molecule fluorescence resonance energy transfer scanning near-field optical microscopy: potentials and challenges.

    PubMed

    Sekatskii, S K; Dukenbayev, K; Mensi, M; Mikhaylov, A G; Rostova, E; Smirnov, A; Suriyamurthy, N; Dietler, G

    2015-12-12

    A few years ago, single molecule Fluorescence Resonance Energy Transfer Scanning Near-Field Optical Microscope (FRET SNOM) images were demonstrated using CdSe semiconductor nanocrystal-dye molecules as donor-acceptor pairs. Corresponding experiments reveal the necessity to exploit much more photostable fluorescent centers for such an imaging technique to become a practically used tool. Here we report the results of our experiments attempting to use nitrogen vacancy (NV) color centers in nanodiamond (ND) crystals, which are claimed to be extremely photostable, for FRET SNOM. All attempts were unsuccessful, and as a plausible explanation we propose the absence (instability) of NV centers lying close enough to the ND border. We also report improvements in SNOM construction that are necessary for single molecule FRET SNOM imaging. In particular, we present the first topographical images of single strand DNA molecules obtained with fiber-based SNOM. The prospects of using rare earth ions in crystals, which are known to be extremely photostable, for single molecule FRET SNOM at room temperature and quantum informatics at liquid helium temperatures, where FRET is a coherent process, are also discussed. PMID:26407105

  13. Wafer-scale metasurface for total power absorption, local field enhancement and single molecule Raman spectroscopy

    PubMed Central

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

    2013-01-01

    The ability to detect molecules at low concentrations is highly desired for applications that range from basic science to healthcare. Considerable interest also exists for ultrathin materials with high optical absorption, e.g. for microbolometers and thermal emitters. Metal nanostructures present opportunities to achieve both purposes. Metal nanoparticles can generate gigantic field enhancements, sufficient for the Raman spectroscopy of single molecules. Thin layers containing metal nanostructures (“metasurfaces”) can achieve near-total power absorption at visible and near-infrared wavelengths. Thus far, however, both aims (i.e. single molecule Raman and total power absorption) have only been achieved using metal nanostructures produced by techniques (high resolution lithography or colloidal synthesis) that are complex and/or difficult to implement over large areas. Here, we demonstrate a metasurface that achieves the near-perfect absorption of visible-wavelength light and enables the Raman spectroscopy of single molecules. Our metasurface is fabricated using thin film depositions, and is of unprecedented (wafer-scale) extent. PMID:24091825

  14. Single-stranded DNA scanning and deamination with Single molecule resolution

    NASA Astrophysics Data System (ADS)

    Rueda, David

    2012-04-01

    Over the past decade, single-molecule fluorescence resonance energy transfer spectroscopy (smFRET) has become an increasingly popular tool to study the structural dynamics of biopolymers, such as DNA, RNA and proteins. The most attractive aspect of single-molecule experiments is that, unlike ensemble-averaged techniques, they directly reveal the structural dynamics of individual molecules, which would otherwise be hidden in ensemble-averaged experiments. Here, we will present a novel single molecule assay to study, for the first time, scanning of an enzyme (APOBEC3G, involved in the defense against HIV) on single stranded DNA (ssDNA). We have investigated the ssDNA scanning and activity of Apo3G with smFRET. Our data show that Apo3G scans ssDNA randomly and bidirectionally with average excursion lengths of ˜ 10 å and ˜1 s-1 scanning rates. Apo3G quasi-localization is observed on highly reactive motifs located near the one end of the ssDNA. Motif-dependent ssDNA bending is also observed, where the bending is maximal for highly reactive targets located near the DNA end. Interestingly, both the Apo3G scanning and Apo3G-induced ssDNA bending is reduced with lowered ionic strength, indicating that Apo3G motion on ssDNA is facilitated by salt by reducing `electrostatic friction'. Although scanning is random, asymmetric catalytic orientation may be the reason for Apo3G directional activity.

  15. [The principle and application of the single-molecule real-time sequencing technology].

    PubMed

    Yanhu, Liu; Lu, Wang; Li, Yu

    2015-03-01

    Last decade witnessed the explosive development of the third-generation sequencing strategy, including single-molecule real-time sequencing (SMRT), true single-molecule sequencing (tSMSTM) and the single-molecule nanopore DNA sequencing. In this review, we summarize the principle, performance and application of the SMRT sequencing technology. Compared with the traditional Sanger method and the next-generation sequencing (NGS) technologies, the SMRT approach has several advantages, including long read length, high speed, PCR-free and the capability of direct detection of epigenetic modi?cations. However, the disadvantage of its low accuracy, most of which resulted from insertions and deletions, is also notable. So, the raw sequence data need to be corrected before assembly. Up to now, the SMRT is a good fit for applications in the de novo genomic sequencing and the high-quality assemblies of small genomes. In the future, it is expected to play an important role in epigenetics, transcriptomic sequencing, and assemblies of large genomes. PMID:25787000

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

    PubMed

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

    2014-11-27

    In contrast with advances in massively parallel DNA sequencing, high-throughput protein analyses are often limited by ensemble measurements, individual analyte purification and hence compromised quality and cost-effectiveness. Single-molecule protein detection using optical methods is limited by the number of spectrally non-overlapping chromophores. Here we introduce a single-molecular-interaction sequencing (SMI-seq) technology for parallel protein interaction profiling leveraging single-molecule advantages. DNA barcodes are attached to proteins collectively via ribosome display or individually via enzymatic conjugation. Barcoded proteins are assayed en masse in aqueous solution and subsequently immobilized in a polyacrylamide thin film to construct a random single-molecule array, where barcoding DNAs are amplified into in situ polymerase colonies (polonies) and analysed by DNA sequencing. This method allows precise quantification of various proteins with a theoretical maximum array density of over one million polonies per square millimetre. Furthermore, protein interactions can be measured on the basis of the statistics of colocalized polonies arising from barcoding DNAs of interacting proteins. Two demanding applications, G-protein coupled receptor and antibody-binding profiling, are demonstrated. SMI-seq enables 'library versus library' screening in a one-pot assay, simultaneously interrogating molecular binding affinity and specificity. PMID:25252978

  17. Electronic Structure and Ferromagnetism Modulation in Cu/Cu2O Interface: Impact of Interfacial Cu Vacancy and Its Diffusion

    NASA Astrophysics Data System (ADS)

    Li, Hao-Bo; Wang, Weichao; Xie, Xinjian; Cheng, Yahui; Zhang, Zhaofu; Dong, Hong; Zheng, Rongkun; Wang, Wei-Hua; Lu, Feng; Liu, Hui

    2015-10-01

    Cu/Cu2O composite structures have been discovered to show sizable ferromagnetism (FM) with the potential applications in spintronic devices. To date, there is no consensus on the FM origin in Cu/Cu2O systems. Here, first principles calculations are performed on the interface structure to explore the microscopic mechanism of the FM. It is found that only the Cu vacancy (VCu) adjacent to the outermost Cu2O layer induces a considerable magnetic moment, mostly contributed by 2p orbitals of the nearest-neighbor oxygen atom (ONN) with two dangling bonds and 3d orbitals of the Cu atoms bonding with the ONN. Meanwhile, the charge transfer from Cu to Cu2O creates higher density of states at the Fermi level and subsequently leads to the spontaneous FM. Furthermore, the FM could be modulated by the amount of interfacial VCu, governed by the interfacial Cu diffusion with a moderate energy barrier (~1.2?eV). These findings provide insights into the FM mechanism and tuning the FM via interfacial cation diffusion in the Cu/Cu2O contact.

  18. Electronic Structure and Ferromagnetism Modulation in Cu/Cu2O Interface: Impact of Interfacial Cu Vacancy and Its Diffusion

    PubMed Central

    Li, Hao-Bo; Wang, Weichao; Xie, Xinjian; Cheng, Yahui; Zhang, Zhaofu; Dong, Hong; Zheng, Rongkun; Wang, Wei-Hua; Lu, Feng; Liu, Hui

    2015-01-01

    Cu/Cu2O composite structures have been discovered to show sizable ferromagnetism (FM) with the potential applications in spintronic devices. To date, there is no consensus on the FM origin in Cu/Cu2O systems. Here, first principles calculations are performed on the interface structure to explore the microscopic mechanism of the FM. It is found that only the Cu vacancy (VCu) adjacent to the outermost Cu2O layer induces a considerable magnetic moment, mostly contributed by 2p orbitals of the nearest-neighbor oxygen atom (ONN) with two dangling bonds and 3d orbitals of the Cu atoms bonding with the ONN. Meanwhile, the charge transfer from Cu to Cu2O creates higher density of states at the Fermi level and subsequently leads to the spontaneous FM. Furthermore, the FM could be modulated by the amount of interfacial VCu, governed by the interfacial Cu diffusion with a moderate energy barrier (~1.2?eV). These findings provide insights into the FM mechanism and tuning the FM via interfacial cation diffusion in the Cu/Cu2O contact. PMID:26478505

  19. Electronic Structure and Ferromagnetism Modulation in Cu/Cu2O Interface: Impact of Interfacial Cu Vacancy and Its Diffusion.

    PubMed

    Li, Hao-Bo; Wang, Weichao; Xie, Xinjian; Cheng, Yahui; Zhang, Zhaofu; Dong, Hong; Zheng, Rongkun; Wang, Wei-Hua; Lu, Feng; Liu, Hui

    2015-01-01

    Cu/Cu2O composite structures have been discovered to show sizable ferromagnetism (FM) with the potential applications in spintronic devices. To date, there is no consensus on the FM origin in Cu/Cu2O systems. Here, first principles calculations are performed on the interface structure to explore the microscopic mechanism of the FM. It is found that only the Cu vacancy (VCu) adjacent to the outermost Cu2O layer induces a considerable magnetic moment, mostly contributed by 2p orbitals of the nearest-neighbor oxygen atom (ONN) with two dangling bonds and 3d orbitals of the Cu atoms bonding with the ONN. Meanwhile, the charge transfer from Cu to Cu2O creates higher density of states at the Fermi level and subsequently leads to the spontaneous FM. Furthermore, the FM could be modulated by the amount of interfacial VCu, governed by the interfacial Cu diffusion with a moderate energy barrier (~1.2?eV). These findings provide insights into the FM mechanism and tuning the FM via interfacial cation diffusion in the Cu/Cu2O contact. PMID:26478505

  20. Interfacial reactions between titanium and borate glass

    SciTech Connect

    Brow, R.K.; Saha, S.K.; Goldstein, J.I.

    1992-12-31

    Interfacial reactions between melts of several borate glasses and titanium have been investigated by analytical scanning electron microscopy (SEM) and x-ray photoelectron spectroscopy (XPS). A thin titanium boride interfacial layer is detected by XPS after short (30 minutes) thermal treatments. ASEM analyses after longer thermal treatments (8--120 hours) reveal boron-rich interfacial layers and boride precipitates in the Ti side of the interface.

  1. Magnetic interaction between a radical spin and a single-molecule magnet in a molecular spin-valve.

    PubMed

    Urdampilleta, Matias; Klayatskaya, Svetlana; Ruben, Mario; Wernsdorfer, Wolfgang

    2015-04-28

    Molecular spintronics using single molecule magnets (SMMs) is a fast growing field of nanoscience that proposes to manipulate the magnetic and quantum information stored in these molecules. Herein we report evidence of a strong magnetic coupling between a metallic ion and a radical spin in one of the most extensively studied SMMs: the bis(phtalocyaninato)terbium(III) complex (TbPc2). For that we use an original multiterminal device comprising a carbon nanotube laterally coupled to the SMMs. The current through the device, sensitive to magnetic interactions, is used to probe the magnetization of a single Tb ion. Combining this electronic read-out with the transverse field technique has allowed us to measure the interaction between the terbium ion, its nuclear spin, and a single electron located on the phtalocyanine ligands. We show that the coupling between the Tb and this radical is strong enough to give extra resonances in the hysteresis loop that are not observed in the anionic form of the complex. The experimental results are then modeled by diagonalization of a three-spins Hamiltonian. This strong coupling offers perspectives for implementing nuclear and electron spin resonance techniques to perform basic quantum operations in TbPc2. PMID:25858088

  2. New single-molecule magnet based on Mn12 oxocarboxylate clusters with mixed carboxylate ligands, [Mn12O12(CN-o-C6H4CO2)12(CH3CO2)4(H2O)4]*8CH2Cl2: synthesis, crystal and electronic structure, magnetic properties

    E-print Network

    Kushch, Lyudmila A; Dmitriev, Alexey I; Yagubskii, Eduard B; Koplak, Oksana V; Zorina, Leokadiya V; Boukhvalov, Danil W

    2012-01-01

    A new high symmetry Mn12 oxocarboxylate cluster [Mn12O12(CN-o-C6H4CO2)12(CH3CO2)4(H2O)4]*8CH2Cl2 (1) with mixed carboxylate ligands is reported. It was synthesized by the standard carboxylate substitution method. 1 crystallizes in the tetragonal space group I41/a. Complex 1 contains a [Mn12O12] core with eight CN-o-C6H4CO2 ligands in the axial positions, four CH3CO2 and four CN-o-C6H4CO2 those in equatorial positions. Four H2O molecules are bonded to four Mn atoms in an alternating up, down, up, down arrangement indicating 1:1:1:1 isomer. The Mn12 molecules in 1 are self-assembled by complementary hydrogen C-H...N bonds formed with participation of the axial o-cyanobenzoate ligands of the adjacent Mn12 clusters. The lattice solvent molecules (CH2Cl2) are weakly interacted with Mn12 units that results in solvent loss immediately after removal of the crystals from the mother liquor. The electronic structure and the intramolecular exchange parameters have been calculated. Mn 3d bands of 1 are rather broad and ce...

  3. Exploring the time-scale of photo-initiated interfacial electron transfer through first-principles interpretation of ultrafast X-ray spectroscopy (Presentation Recording)

    NASA Astrophysics Data System (ADS)

    Prendergast, David; Pemmaraju, Sri Chaitanya Das

    2015-09-01

    With the advent of X-ray free electron lasers and table-top high-harmonic-generation X-ray sources, we can now explore changes in electronic structure on ultrafast time scales -- at or less than 1ps. Transient X-ray spectroscopy of this kind provides a direct probe of relevant electronic levels related to photoinitiated processes and associated interfacial electron transfer as the initial step in solar energy conversion. However, the interpretation of such spectra is typically fraught with difficulty, especially since we rarely have access to spectral standards for nonequilibrium states. To this end, direct first-principles simulations of X-ray absorption spectra can provide the necessary connection between measurements and reliable models of the atomic and electronic structure. We present examples of modeling excited states of materials interfaces relevant to solar harvesting and their corresponding X-ray spectra in either photoemission or absorption modalities. In this way, we can establish particular electron transfer mechanisms to reveal detailed working principles of materials systems in solar applications and provide insight for improved efficiency.

  4. Single-molecule di usion in a periodic potential at a solidliquid interface

    E-print Network

    Lindenberg, Katja

    atomic/molecular dimensions, and may provide a new way to understand and control solid­liquid interfacial­7 which are critical to biomaterial surface design8,9 and biosensor and microarray technologies.10

  5. Fluorescence spectroscopy of single molecules at room temperature and its applications

    SciTech Connect

    Ha, Taekjip

    1996-12-01

    We performed fluorescence spectroscopy of single and pairs of dye molecules on a surface at room temperature. Near field scanning optical microscope (NSOM) and far field scanning optical microscope with multi-color excitation/detection capability were built. The instrument is capable of optical imaging with 100nm resolution and has the sensitivity necessary for single molecule detection. A variety of dynamic events which cannot be observed from an ensemble of molecules is revealed when the molecules are probed one at a time. They include (1) spectral jumps correlated with dark states, (2) individually resolved quantum jumps to and from the meta-stable triplet state, (3) rotational jumps due to desorption/readsorption events of single molecules on the surface. For these studies, a computer controlled optical system which automatically and rapidly locates and performs spectroscopic measurements on single molecules was developed. We also studied the interaction between closely spaced pairs of molecules. In particular, fluorescence resonance energy transfer between a single resonant pair of donor and acceptor molecules was measured. Photodestruction dynamics of the donor or acceptor were used to determine the presence and efficiency of energy transfer Dual molecule spectroscopy was extended to a non-resonant pair of molecules to obtain high resolution differential distance information. By combining NSOM and dual color scheme, we studied the co-localization of parasite proteins and host proteins on a human red blood cell membrane infected with malaria. These dual-molecule techniques can be used to measure distances, relative orientations, and changes in distances/orientations of biological macromolecules with very good spatial, angular and temporal resolutions, hence opening new capabilities in the study of such systems.

  6. Interaction of cholesterol in ternary lipid mixtures investigated using single-molecule fluorescence.

    PubMed

    DeWitt, Brittany N; Dunn, Robert C

    2015-01-27

    Fluorescence measurements of the sterol analog 23-(dipyrrometheneboron difluoride)-24-norcholesterol (BODIPY-cholesterol) are used to compare the effects of cholesterol (Chol) in monolayers of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC)/1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC)/Chol and chicken egg sphingomyelin (SM)/DOPC/Chol. Monolayers are formed using the Langmuir-Blodgett technique and compared at surface pressures of 8 and 30 mN/m. In particular, these ternary lipid mixtures are compared using both ensemble and single-molecule fluorescence measurements of BODIPY-cholesterol. In mixed monolayers incorporating 0.10 mol % BODIPY-cholesterol, fluorescence microscopy measurements as a function of cholesterol added reveal similar trends in monolayer phase structure for both DPPC/DOPC/Chol and SM/DOPC/Chol films. With a probe concentration reduced to ?10(-8) mol % BODIPY-cholesterol, single-molecule fluorescence measurements using defocused polarized total internal reflection microscopy are used to characterize the orientations of BODIPY-cholesterol in the monolayers. Population histograms of the BODIPY emission dipole tilt angle away from the membrane normal reveal distinct insertion geometries with a preferred angle observed near 78°. The measured angles and populations are relatively insensitive to added cholesterol and changes in surface pressure for monolayers of SM/DOPC/Chol. For monolayers of DPPC/DOPC/Chol, however, the single-molecule measurements reveal significant changes in the BODIPY-cholesterol insertion geometry when the surface pressure is increased to 30 mN/m. These changes are discussed in terms of a squeeze-out mechanism for BODIPY-cholesterol in these monolayers and provide insight into the partitioning and arrangement of BODIPY-cholesterol in ternary lipid mixtures. PMID:25531175

  7. Single Molecule Visualization of Protein-DNA Complexes: Watching Machines at Work

    NASA Astrophysics Data System (ADS)

    Kowalczykowski, Stephen

    2013-03-01

    We can now watch individual proteins acting on single molecules of DNA. Such imaging provides unprecedented interrogation of fundamental biophysical processes. Visualization is achieved through the application of two complementary procedures. In one, single DNA molecules are attached to a polystyrene bead and are then captured by an optical trap. The DNA, a worm-like coil, is extended either by the force of solution flow in a micro-fabricated channel, or by capturing the opposite DNA end in a second optical trap. In the second procedure, DNA is attached by one end to a glass surface. The coiled DNA is elongated either by continuous solution flow or by subsequently tethering the opposite end to the surface. Protein action is visualized by fluorescent reporters: fluorescent dyes that bind double-stranded DNA (dsDNA), fluorescent biosensors for single-stranded DNA (ssDNA), or fluorescently-tagged proteins. Individual molecules are imaged using either epifluorescence microscopy or total internal reflection fluorescence (TIRF) microscopy. Using these approaches, we imaged the search for DNA sequence homology conducted by the RecA-ssDNA filament. The manner by which RecA protein finds a single homologous sequence in the genome had remained undefined for almost 30 years. Single-molecule imaging revealed that the search occurs through a mechanism termed ``intersegmental contact sampling,'' in which the randomly coiled structure of DNA is essential for reiterative sampling of DNA sequence identity: an example of parallel processing. In addition, the assembly of RecA filaments on single molecules of single-stranded DNA was visualized. Filament assembly requires nucleation of a protein dimer on DNA, and subsequent growth occurs via monomer addition. Furthermore, we discovered a class of proteins that catalyzed both nucleation and growth of filaments, revealing how the cell controls assembly of this protein-DNA complex.

  8. Single-molecule mobility and spectral measurements in submicrometer fluidic channels

    NASA Astrophysics Data System (ADS)

    Stavis, Samuel M.; Edel, Joshua B.; Li, Yougen; Samiee, Kevan T.; Luo, Dan; Craighead, Harold G.

    2005-08-01

    Electrophoretic mobility differences of biological molecules are frequently exploited to physically separate and subsequently identify the components of a mixture. We present a method to rapidly identify single molecules by measuring both their mobility and fluorescence emission under continuous flow without separation. Submicrometer fluidic channels were used to detect individual nucleic-acid-engineered fluorescent labels driven electrokinetically in free solution. Two separate focal volumes along the length of the fluidic channel collected spectral, spatial, and temporal information from the passage of fluorescent labels through the channel. One focal volume was defined by a focused 488-nm-wavelength laser and the other by a focused 568-nm laser. The subfemtoliter focal volumes resulted in signal-to-noise ratios sufficient for single-fluorophore detection, and the two excitation wavelengths enabled detection of multicolor fluorescent labels and discrimination of single-color detection events. Each fluorescent label was uniformly excited and analyzed as it passed through the channel. Flow control facilitated high throughput at low concentrations, as well as a balance of several experimental parameters. Two fluorescent labels were considered for identification by single-molecule mobility measurements. Approximately 81% of fluorescent labels of one variety and 77% of the other were found to be identifiable based on their mobility alone. As implemented, this method could be used in conjunction with spectral analysis of fluorescent labels to enhance the resolution of single-molecule identification. Ultimately, this technique could be used autonomously to detect biomolecules bound to fluorescent labels and to identify similarly labeled biomolecules by their mobility.

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

    NASA Astrophysics Data System (ADS)

    Hollars, Christopher W.; Dunn, Robert C.

    2000-05-01

    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 lipid analog N-(6-tetramethylrhodaminethiocarbamoyl)-1,2-dihexadecanoyl-sn- glycero-3-phosphoethanolamine, triethylammonium salt (TRITC-DHPE) are transferred onto a freshly cleaved mica surface at low (?=8 mN/m) and high (?=30 mN/m) surface pressures. The near-field fluorescence images exhibit shapes in the single molecule images that are indicative of the lipid analog probe orientation within the films. Modeling the fluorescence patterns yields the single molecule tilt angle distribution in the monolayers which indicates that the majority of the molecules are aligned with their absorption dipole moment pointed approximately normal to the membrane plane. Histograms of the data indicate that the average orientation of the absorption dipole moment is 2.2° (?=4.8°) in monolayers transferred at ?=8 mN/m and 2.4° (?=5.0°) for monolayers transferred at ?=30 mN/m. There is no statistical difference in the mean tilt angle or distribution for the two monolayer conditions studied. The insensitivity of tilt angle to film surface pressure may arise from small chromophore doped domains of trapped liquid-expanded lipid phase remaining at high surface pressure. There is no evidence in the near-field fluorescence images for probe molecules oriented with their dipole moment aligned parallel with the membrane plane. We do, however, find a small but significant population of probe molecules (˜13%) with tilt angles greater than 16°. Comparison of the simultaneously collected near-field fluorescence and force images suggests that these large angle orientations are not the result of significant defects in the films. Instead, this small population may represent a secondary insertion geometry for the probe molecule into the lipid monolayer.

  10. SNSMIL, a real-time single molecule identification and localization algorithm for super-resolution fluorescence microscopy

    PubMed Central

    Tang, Yunqing; Dai, Luru; Zhang, Xiaoming; Li, Junbai; Hendriks, Johnny; Fan, Xiaoming; Gruteser, Nadine; Meisenberg, Annika; Baumann, Arnd; Katranidis, Alexandros; Gensch, Thomas

    2015-01-01

    Single molecule localization based super-resolution fluorescence microscopy offers significantly higher spatial resolution than predicted by Abbe’s resolution limit for far field optical microscopy. Such super-resolution images are reconstructed from wide-field or total internal reflection single molecule fluorescence recordings. Discrimination between emission of single fluorescent molecules and background noise fluctuations remains a great challenge in current data analysis. Here we present a real-time, and robust single molecule identification and localization algorithm, SNSMIL (Shot Noise based Single Molecule Identification and Localization). This algorithm is based on the intrinsic nature of noise, i.e., its Poisson or shot noise characteristics and a new identification criterion, QSNSMIL, is defined. SNSMIL improves the identification accuracy of single fluorescent molecules in experimental or simulated datasets with high and inhomogeneous background. The implementation of SNSMIL relies on a graphics processing unit (GPU), making real-time analysis feasible as shown for real experimental and simulated datasets. PMID:26098742

  11. Bacterial protein complexes studied by single-molecule imaging and single-cell micromanipulation techniques in microfluidic devices 

    E-print Network

    Reuter, Marcel

    2010-06-28

    Biological systems of bacteria were investigated at the single-cell and single-molecule level. Additionally, aspects of the techniques employed were studied. A unifying theme in each project is the reliance on optical ...

  12. Microfluidic mixing for non-equilibrium single-molecule optical spectroscopy

    NASA Astrophysics Data System (ADS)

    Pfeil, Shawn H.

    We describe a series of experiments made possible by the combination of single-molecule fluorescence spectroscopy and microfluidic mixing. To perform these measurements, a microfluidic sample handling system was developed and characterized. This system allows observation at times as early as 2.4 ms after a reaction is triggered, which is an more than an order of magnitude earlier than previous microfabricated devices. Dilutions as high as 1:19 (v/v) are achieved, allowing measurements of molecular refolding in native conditions. The interconversion of subpopulations, masked by averaging in ensemble measurements, is observed. This technology also facilitates ultra-sensitive chemiluminescence measurements, using only microliters of sample. Microfluidics are designed and fabricated to extend single-molecule measurements to samples out of equilibrium. The system is optimized for sensitive optical detection and experimental convenience. Channels are replica-molded in poly-dimethyl-siloxane (PDMS) elastomer and sealed to coverglass. The resulting devices are compatible with a broad range of chemicals, and exhibit low background fluorescence. The combination of continuous flow, which decouples reaction progress from measurement duration, with low background enables single molecules to be probed at well defined times after a reaction is triggered. Fluid delivery and pressure connections are made using an interface optimized for rapid assembly, rapid sample exchange, and modular device replacement, while providing access for high numerical aperture optics. The kinetics of Csp, the cold shock protein from Thermotoga maritima, are studied with the mixer. An order of magnitude decrease in deadtime puts a new upper limit of 4.6 ms on the time required for collapse after mixing. This result is in agreement with indirect measurements of chain reconfiguration time, which suggest collapse happens on the timescale of 10--100 ns. Measurements of the kinetics of a DNA sequence that binds cocaine put a lower bound on its folding rate of 100 s-1. Single-Molecule measurements at equilibrium, in conjunction with ensemble measurements, demonstrate that this system can be described thermodynamically with a two-state model. In addition, standard free energy changes for folding, in the presence and absence of 1 mM cocaine, are obtained. Ensemble chemiluminescence experiments demonstrate the broad applicability of themixing system. The luciferase-luciferin system from Photinus pyralis, the North American firefly, is studied. Kinetically resolved chemiluminescence measurements are performed using only 50 femtomoles of target, and microliters of sample. This compares favorably to stopped-flow, which requires milliliters of sample and picomoles of target.

  13. Single-Molecule Imaging of Signal Transduction via GPI-Anchored Receptors.

    PubMed

    Suzuki, Kenichi G N

    2016-01-01

    Lipid rafts have been drawing extensive attention as a signaling platform. To investigate molecular interactions in lipid rafts, we often need to observe molecules in the plasma membranes of living cells because chemical fixation and subsequent immunostaining with divalent or multivalent antibodies may change the location of the target molecules. In this chapter, we describe how to examine dynamics of raft-associated glycosylphosphatidylinositol (GPI)-anchored receptors and interactions of the receptors with downstream signaling molecules by single-particle tracking or single-molecule imaging techniques. PMID:26552688

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

    SciTech Connect

    Saurabh, Prasoon Mukamel, Shaul

    2014-04-28

    Atomic Force Microscopy (AFM) allows for a highly sensitive detection of spectroscopic signals. This has been first demonstrated for NMR of a single molecule and recently extended to stimulated Raman in the optical regime. We theoretically investigate the use of optical forces to detect time and frequency domain nonlinear optical signals. We show that, with proper phase matching, the AFM-detected signals closely resemble coherent heterodyne-detected signals. Applications are made to AFM-detected and heterodyne-detected vibrational resonances in Coherent Anti-Stokes Raman Spectroscopy (?{sup (3)}) and sum or difference frequency generation (?{sup (2)})

  15. Ultrahigh spin thermopower and pure spin current in a single-molecule magnet

    PubMed Central

    Luo, Bo; Liu, Juan; Lü, Jing-Tao; Gao, Jin-Hua; Yao, Kai-Lun

    2014-01-01

    Using the non-equilibrium Green's function (NEGF) formalism within the sequential regime, we studied ultrahigh spin thermopower and pure spin current in single-molecule magnet(SMM), which is attached to nonmagnetic metal wires with spin bias and angle (?) between the easy axis of SMM and the spin orientation in the electrodes. A pure spin current can be generated by tuning the gate voltage and temperature difference with finite spin bias and the arbitrary angle except of . In the linear regime, large thermopower can be obtained by modifying Vg and the angles (?). These results are useful in fabricating and advantaging SMM devices based on spin caloritronics. PMID:24549224

  16. Experimental Free Energy Surface Reconstruction From Single-Molecule Force Spectroscopy Using Jarzynski's Equality

    E-print Network

    Nolan C. Harris; Yang Song; Ching-Hwa Kiang

    2007-07-03

    We used the atomic force microscope to manipulate and unfold individual molecules of the titin I27 domain and reconstructed its free energy surface using Jarzynski's equality. The free energy surface for both stretching and unfolding was reconstructed using an exact formula that relates the nonequilibrium work fluctuations to the molecular free energy. In addition, the unfolding free energy barrier, i.e. the activation energy, was directly obtained from experimental data for the first time. This work demonstrates that Jarzynski's equality can be used to analyze nonequilibrium single-molecule experiments, and to obtain the free energy surfaces for molecular systems, including interactions for which only nonequilibrium work can be measured.

  17. Bias voltage induced resistance switching effect in single-molecule magnets’ tunneling junction

    NASA Astrophysics Data System (ADS)

    Zhang, Zhengzhong; Jiang, Liang

    2014-09-01

    An electric-pulse-induced reversible resistance change effect in a molecular magnetic tunneling junction, consisting of a single-molecule magnet (SMM) sandwiched in one nonmagnetic and one ferromagnetic electrode, is theoretically investigated. By applying a time-varying bias voltage, the SMM's spin orientation can be manipulated with large bias voltage pulses. Moreover, the different magnetic configuration at high-resistance/low-resistance states can be ‘read out’ by utilizing relative low bias voltage. This device scheme can be implemented with current technologies (Khajetoorians et al 2013 Science 339 55) and has potential application in molecular spintronics and high-density nonvolatile memory devices.

  18. Renormalization of Molecular Energy Levels in Single-Molecule Nanojunctions: An Ab-initio Approach

    NASA Astrophysics Data System (ADS)

    Parashar, Sweta; Srivastava, Pankaj; Pattanaik, Manisha

    2015-02-01

    Using first-principle calculations based on Density Functional Theory (DFT) in conjunction with the Non-Equilibrium Greens Functions (NEGF) technique, we have studied the effect of electrostatic environment in molecular energy levels of single-molecule transistors. This approach is applied to three polycyclic aromatic hydrocarbons (PAHs) anthracene, tetracene and pentacene, for calculating charging energies of molecular systems weakly coupled to an electrostatic environment. The result shows renormalization of molecular energy levels in an electrostatic environment. Further, it is observed that on increasing the number of aromatic rings, the addition energy value decreases which increases the conductivity of the system. Subsequently charge stability diagram for PAHs has been obtained.

  19. Splitting Probabilities as a Test of Reaction Coordinate Choice in Single-Molecule Experiments

    NASA Astrophysics Data System (ADS)

    Chodera, John D.; Pande, Vijay S.

    2011-08-01

    To explain the observed dynamics in equilibrium single-molecule measurements of biomolecules, the experimental observable is often chosen as a putative reaction coordinate along which kinetic behavior is presumed to be governed by diffusive dynamics. Here, we invoke the splitting probability as a test of the suitability of such a proposed reaction coordinate. Comparison of the observed splitting probability with that computed from the kinetic model provides a simple test to reject poor reaction coordinates. We demonstrate this test for a force spectroscopy measurement of a DNA hairpin.

  20. Gating of single molecule junction conductance by charge transfer complex formation.

    PubMed

    Vezzoli, Andrea; Grace, Iain; Brooke, Carly; Wang, Kun; Lambert, Colin J; Xu, Bingqian; Nichols, Richard J; Higgins, Simon J

    2015-12-01

    The solid-state structures of organic charge transfer (CT) salts are critical in determining their mode of charge transport, and hence their unusual electrical properties, which range from semiconducting through metallic to superconducting. In contrast, using both theory and experiment, we show here that the conductance of metal |single molecule| metal junctions involving aromatic donor moieties (dialkylterthiophene, dialkylbenzene) increase by over an order of magnitude upon formation of charge transfer (CT) complexes with tetracyanoethylene (TCNE). This enhancement occurs because CT complex formation creates a new resonance in the transmission function, close to the metal contact Fermi energy, that is a signal of room-temperature quantum interference. PMID:26510687