Science.gov

Sample records for single-molecule interfacial electron

  1. Intermittent Single-Molecule Interfacial Electron Transfer Dynamics

    SciTech Connect

    Biju, Vasudevan P.; Micic, Miodrag; Hu, Dehong; Lu, H. Peter

    2004-08-04

    We report on single molecule studies of photosensitized interfacial electron transfer (ET) processes in Coumarin 343 (C343)-TiO2 nanoparticle (NP) and Cresyl Violet (CV+)-TiO2 NP systems, using time-correlated single photon counting coupled with scanning confocal fluorescence microscopy. Fluorescence intensity trajectories of individual dye molecules adsorbed on a semiconductor NP surface showed fluorescence fluctuations and blinking, with time constrants distributed from sub-milliseconds to several seconds.

  2. Single-Molecule Interfacial Electron Transfer Dynamics at Dye-Sensitized TiO2 Nanoparticles

    NASA Astrophysics Data System (ADS)

    Lu, H. Peter; Wang, Yuanmin; He, Yufan

    2009-03-01

    Interfacial electron transfer dynamics is important for environmental and catalytic reactions. Extensive ensemble-averaged studies have indicated inhomogeneous and complex dynamics of interfacial ET reaction. To characterize the inhomogeniety and the complex mechanism, we have applied single-molecule spectroscopy and correlated AFM/STM imaging to study the Interfacial ET dynamics of dye molecules adsorbed at the surface of TiO2 nanoparticles. The interfacial ET activity of individual dye molecules showed fluctuations and intermittency at time scale of milliseconds to seconds. The fluctuation dynamics were found to be inhomogeneous from molecule to molecule and from time to time, showing significant static and dynamic disorders in the dynamics. Furthermore, we have applied site-specific AFM-Raman spectroscopy on analyzing ET associated mode-specific vibrational reorganization energy barriers. Our experiments revealed site-to-site variations in the vibrational reorganization energy barriers in the interfacial ET systems. Our recent experiments on single-molecule metal-to-ligand electron transfer (3) and single-molecule STM manipulation will also be discussed.

  3. 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; Lu, H Peter

    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

  4. 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

  5. Single Molecule Electron Paramagnetic Resonance

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

  6. Probing Driving Force and Electron Accepting State Density Dependent Interfacial Electron Transfer Dynamics: Suppressed Fluorescence Blinking of Single Molecules on Indium Tin Oxide Semiconductor.

    PubMed

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

    2016-03-01

    Photoinduced, interfacial electron transfer (ET) dynamics between m-ZnTCPP and Sn-doped In2O3 (ITO) film has been studied using single-molecule photon-stamping spectroscopy. The observed ET dynamics of single m-ZnTCPP adsorbed on ITO was compared with that of m-ZnTCPP adsorbed on TiO2 NPs with and without applied electric potential. Compared to m-ZnTCPP on the TiO2 NP surface, m-ZnTCPP on the ITO surface shows a reduced lifetime as well as suppressed blinking and a quasi-continuous distribution of fluorescence intensities, presumably due to higher electron density in ITO. The higher electron density leads to the occupancy of CB acceptor states/trap states, which supports a higher backward electron transfer (BET) rate that results in a quasi-continuous distribution of fluorescence intensities. The dependence of BET rate on electron density and charge trapping is consistent with our previous observations of quasi-continuous distribution of fluorescence intensities of m-ZnTCPP on TiO2 NPs with applied negative potential across the dye-TiO2 interface. The quasi-continuous distribution of fluorescence intensities in both cases of m-ZnTCPP on the ITO surface and m-ZnTCPP on TiO2 NPs with applied negative potential indicates that the electron density in the semiconductor plays a dominant role in dictating the changes in rates of charge transfer, rather than the relative energetics between electrons in the semiconductor and the oxidized sensitizer. PMID:26468609

  7. Chemical principles of single-molecule electronics

    NASA Astrophysics Data System (ADS)

    Su, Timothy A.; Neupane, Madhav; Steigerwald, Michael L.; Venkataraman, Latha; Nuckolls, Colin

    2016-03-01

    The field of single-molecule electronics harnesses expertise from engineering, physics and chemistry to realize circuit elements at the limit of miniaturization; it is a subfield of nanoelectronics in which the electronic components are single molecules. In this Review, we survey the field from a chemical perspective and discuss the structure-property relationships of the three components that form a single-molecule junction: the anchor, the electrode and the molecular bridge. The spatial orientation and electronic coupling between each component profoundly affect the conductance properties and functions of the single-molecule device. We describe the design principles of the anchor group, the influence of the electronic configuration of the electrode and the effect of manipulating the structure of the molecular backbone and of its substituent groups. We discuss single-molecule conductance switches as well as the phenomenon of quantum interference and then trace their fundamental roots back to chemical principles.

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

    PubMed Central

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

    2012-01-01

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

  9. Single Molecule Spectroscopy of Electron Transfer

    SciTech Connect

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

    2009-10-20

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

  10. Methods and applications in single molecule electronics

    NASA Astrophysics Data System (ADS)

    Hihath, Joshua

    In recent years it has become possible to measure charge transport in a single molecule contacted to two metal electrodes. However, a thorough understanding of how a molecule behaves while contacted to two electrodes and how it interacts with its environment is still lacking. This thesis demonstrates various experimental methods for understanding and controlling charge transport in a single molecule junction and the application of these methods to various molecular systems to help elucidate the conduction mechanisms invoked. First, the conductance of DNA is examined in a controlled environment while varying the length, sequence, base-pair matching, bias, temperature, and electrochemical gate of the molecule. These studies show that the conductance of DNA is extremely sensitive to changes in length, sequence, and base-matching, but not as sensitive to temperature and electrochemical gate. Despite the variety of experimental methods applied, the subtleties of the conduction mechanism remain uncertain, and as such necessitate the development of additional tools for understanding the behavior of a single molecule junction. Next, the Conductance Screening Tool for Molecules (CSTM) is described. This is a new tool capable of creating 1000's of single molecules junctions in a matter of minutes. This tool has been used to study the conductance of alkanedithiols, molecules in an array, and single amino acid residues. This system allows for greater speed and flexibility in determining the conductance of a single molecule junction, and provides a capability for performing large-scale systematic studies of molecular systems to determine the conduction mechanism. Finally, an additional experimental method capable of extracting information about the interaction between a molecule and its environment is developed. Here, electron-phonon interactions in a single molecule contacted to two electrodes are studied. This method allows one to obtain a specific, chemical signature of a single molecule, to extract information about changes in the configuration of a single molecule junction during an experiment, and to correlate these changes with changes in the conductance of the molecule.

  11. 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

  12. Single molecules as whispering galleries for electrons

    NASA Astrophysics Data System (ADS)

    Reecht, G.; Bulou, H.; Schull, G.; Scheurer, F.

    2016-04-01

    Whispering gallery modes, well-known for acoustic and optical waves, have been shown recently for electrons in molecules on surfaces. The existence of such waves opens new possibilities for nanoelectronic devices. Here we propose a simple analytical textbook model which allows the main characteristic features of such electronic waves to be understood. The model is illustrated by two- and three-dimensional experimental situations.

  13. Single molecules as whispering galleries for electrons.

    PubMed

    Reecht, G; Bulou, H; Schull, G; Scheurer, F

    2016-04-27

    Whispering gallery modes, well-known for acoustic and optical waves, have been shown recently for electrons in molecules on surfaces. The existence of such waves opens new possibilities for nanoelectronic devices. Here we propose a simple analytical textbook model which allows the main characteristic features of such electronic waves to be understood. The model is illustrated by two- and three-dimensional experimental situations. PMID:26987969

  14. Electron Transport in Short Peptide Single Molecules

    NASA Astrophysics Data System (ADS)

    Cui, Jing; Brisendine, Joseph; Ng, Fay; Nuckolls, Colin; Koder, Ronald; Venkarataman, Latha

    We present a study of the electron transport through a series of short peptides using scanning tunneling microscope-based break junction method. Our work is motivated by the need to gain a better understanding of how various levels of protein structure contribute to the remarkable capacity of proteins to transport charge in biophysical processes such as respiration and photosynthesis. We focus here on short mono, di and tri-peptides, and probe their conductance when bound to gold electrodes in a native buffer environment. We first show that these peptides can bind to gold through amine, carboxyl, thiol and methyl-sulfide termini. We then focus on two systems (glycine and alanine) and show that their conductance decays faster than alkanes terminated by the same linkers. Importantly, our results show that the peptide bond is less conductive than a sigma carbon-carbon bond. This work was supported in part by NSF-DMR 1507440.

  15. 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

  16. Single-Molecule Electronics: Chemical and Analytical Perspectives

    NASA Astrophysics Data System (ADS)

    Nichols, Richard J.; Higgins, Simon J.

    2015-07-01

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

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

    PubMed

    Nichols, Richard J; Higgins, Simon J

    2015-01-01

    It is now possible to measure the electrical properties of single molecules using a variety of techniques including scanning probe microcopies and mechanically controlled break junctions. Such measurements can be made across a wide range of environments including ambient conditions, organic liquids, ionic liquids, aqueous solutions, electrolytes, and ultra high vacuum. This has given new insights into charge transport across molecule electrical junctions, and these experimental methods have been complemented with increasingly sophisticated theory. This article reviews progress in single-molecule electronics from a chemical perspective and discusses topics such as the molecule-surface coupling in electrical junctions, chemical control, and supramolecular interactions in junctions and gating charge transport. The article concludes with an outlook regarding chemical analysis based on single-molecule conductance. PMID:26048551

  18. 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.

  19. New Measurement Techniques and Their Applications in Single Molecule Electronics

    NASA Astrophysics Data System (ADS)

    Guo, Shaoyin

    Studying charge transport through single molecules tethered between two metal electrodes is of fundamental importance in molecular electronics. Over the years, a variety of methods have been developed in attempts of performing such measurements. However, the limitation of these techniques is still one of the factors that prohibit one from gaining a thorough understanding of single molecule junctions. Firstly, the time resolution of experiments is typically limited to milli to microseconds, while molecular dynamics simulations are carried out on the time scale of pico to nanoseconds. A huge gap therefore persists between the theory and the experiments. This thesis demonstrates a nanosecond scale measurement of the gold atomic contact breakdown process. A combined setup of DC and AC circuits is employed, where the AC circuit reveals interesting observations in nanosecond scale not previously seen using conventional DC circuits. The breakdown time of gold atomic contacts is determined to be faster than 0.1 ns and subtle atomic events are observed within nanoseconds. Furthermore, a new method based on the scanning tunneling microscope break junction (STM-BJ) technique is developed to rapidly record thousands of I-V curves from repeatedly formed single molecule junctions. 2-dimensional I-V and conductance-voltage (G-V) histograms constructed using the acquired data allow for more meaningful statistical analysis to single molecule I-V characteristics. The bias voltage adds an additional dimension to the conventional single molecule conductance measurement. This method also allows one to perform transition voltage spectra (TVS) for individual junctions and to study the correlation between the conductance and the tunneling barrier height. The variation of measured conductance values is found to be primarily determined by the poorly defined contact geometry between the molecule and metal electrodes, rather than the tunnel barrier height. In addition, the rapid I-V technique is also found useful in studying thermoelectric effect in single molecule junctions. When applying a temperature gradient between the STM tip and substrate in air, the offset current at zero bias in the I-V characteristics is a measure of thermoelectric current. The rapid I-V technique allows for statistical analysis of such offset current at different temperature gradients and thus the Seebeck coefficient of single molecule junctions is measured. Combining with single molecule TVS, the Seebeck coefficient is also found to be a measure of tunnel barrier height.

  20. Surface-bound norbornylogous bridges as molecular rulers for investigating interfacial electrochemistry and as single molecule switches.

    PubMed

    Darwish, Nadim; Paddon-Row, Michael N; Gooding, J Justin

    2014-02-18

    Electron transfer (ET) reactions through molecules attached to surfaces, whether they are through single molecules or ensembles, are the subject of much research in molecular electronics, bioelectronics, and electrochemistry. Therefore, understanding the factors that govern ET is of high importance. The availability of rigid hydrocarbon molecular scaffolds possessing well-defined configurations and lengths that can be systematically varied is crucial to the development of such devices. In this Account, we demonstrate how suitably functionalized norbornylogous (NB) systems can provide important insights into interfacial ET processes and electrical conduction through single molecules. To this end, we created NB bridges with vic-trans-bismethylenethiol groups at one end so they can assemble on gold electrodes and redox species at the distal ends. With these in hand, we then formed mixed self-assembled monolayers (SAMs) containing a small proportion of the NB bridges diluted with alkanethiols. As such, the NB bridges served as molecular rulers for probing the environment above the surface defined by the diluent species. Using this construct, we were able to measure the interfacial potential distribution above the diluent surface, and track how variation in the ionic distribution in the electrical double layer impacts ET kinetics. Using the same construct, but with a redox molecule that remains neutral in both oxidized and reduced states, we could explore the impact of the chemical environment near a surface on ET processes. These results are important, because with conventional surface constructs, ET occurs across this interfacial region. Such knowledge is therefore relevant to the design of molecular systems at surfaces involving ET. With a second family of molecules, we investigated aspects of single-molecule electrical conduction using NB bridges bearing vic-trans-bismethylenethiol groups at both ends of the bridge. This gave us insights into distance-dependent electron transport through single molecules and introduced a method of boosting the conductance of saturated molecules by incorporating aromatic moieties in their backbone. These partially conjugated NB molecules represent a new class of molecular wires with far greater stability than conventional completely conjugated molecular wires. Of particular note was our demonstration of a single molecule switch, using a NB bridge containing an embedded anthraquinone redox group, the switching mechanism being via electrochemically controlled quantum interference. PMID:24160945

  1. Single-Molecule Electronic Monitoring of DNA Polymerase Activity

    NASA Astrophysics Data System (ADS)

    Marushchak, Denys O.; Pugliese, Kaitlin M.; Turvey, Mackenzie W.; Choi, Yongki; Gul, O. Tolga; Olsen, Tivoli J.; Rajapakse, Arith J.; Weiss, Gregory A.; Collins, Philip G.

    Single-molecule techniques can reveal new spatial and kinetic details of the conformational changes occurring during enzymatic catalysis. Here, we investigate the activity of DNA polymerases using an electronic single-molecule technique based on carbon nanotube transistors. Single molecules of the Klenow fragment (KF) of polymerase I were conjugated to the transistors and then monitored via fluctuations in electrical conductance. Continuous, long-term monitoring recorded single KF molecules incorporating up to 10,000 new bases into single-stranded DNA templates. The duration of individual incorporation events was invariant across all analog and native nucleotides, indicating that the precise structure of different base pairs has no impact on the timing of incorporation. Despite similar timings, however, the signal magnitudes generated by certain analogs reveal alternate conformational states that do not occur with native nucleotides. The differences induced by these analogs suggest that the electronic technique is sensing KF's O-helix as it tests the stability of nascent base pairs.

  2. Electronic transport through single molecules: effects of strain and contacts

    NASA Astrophysics Data System (ADS)

    Chacham, Helio; Batista, Ronaldo; Mazzoni, Mario; Garzon, Ignacio; Beltran, Marcela; Ordejon, Pablo; Artacho, Emilio

    2007-03-01

    We will present theoretical investigations on single-molecule electron transport. We will focus on the following systems: a) Connected Au nanoparticles: we performed a first principles study [1] of the electronic properties of lattices of Au nanoparticles functionalized by the conjugated molecules BDMT and BDCT. Distinct behaviors of the electron hopping matrix elements between particles as a function of compression are predicted for functionalized lattices. b) Current rectification with symmetric molecules: In an interesting experiment, Reichet et al. [2] measured the current through symmetric organic molecules and obtained asymmetric IV curves when the Au contacts are pulled apart. We show, by means of first-principles calculations, that this effect can originate from the formation of small Au chains between the molecule and the Au surfaces in an asymmetric way. [1] R. J. C. Batista et al, Phys. Rev. Lett. 96, 116802 (2006). [2] J. Reichet et al., Phys. Rev. Lett. 88, 176804 (2002).

  3. Probing Electronic and Thermoelectric Properties of Single Molecule Junctions

    NASA Astrophysics Data System (ADS)

    Widawsky, Jonathan R.

    In an effort to further understand electronic and thermoelectric phenomenon at the nanometer scale, we have studied the transport properties of single molecule junctions. To carry out these transport measurements, we use the scanning tunneling microscope-break junction (STM-BJ) technique, which involves the repeated formation and breakage of a metal point contact in an environment of the target molecule. Using this technique, we are able to create gaps that can trap the molecules, allowing us to sequentially and reproducibly create a large number of junctions. By applying a small bias across the junction, we can measure its conductance and learn about the transport mechanisms at the nanoscale. The experimental work presented here directly probes the transmission properties of single molecules through the systematic measurement of junction conductance (at low and high bias) and thermopower. We present measurements on a variety of molecular families and study how conductance depends on the character of the linkage (metal-molecule bond) and the nature of the molecular backbone. We start by describing a novel way to construct single molecule junctions by covalently connecting the molecular backbone to the electrodes. This eliminates the use of linking substituents, and as a result, the junction conductance increases substantially. Then, we compare transport across silicon chains (silanes) and saturated carbon chains (alkanes) while keeping the linkers the same and find a stark difference in their electronic transport properties. We extend our studies of molecular junctions by looking at two additional aspects of quantum transport -- molecular thermopower and molecular current-voltage characteristics. Each of these additional parameters gives us further insight into transport properties at the nanoscale. Evaluating the junction thermopower allows us to determine the nature of charge carriers in the system and we demonstrate this by contrasting the measurement of amine-terminated and pyridine-terminated molecules (which exhibit hole transport and electron transport, respectively). We also report the thermopower of the highly conducting, covalently bound molecular junctions that we have recently been able to form, and learn that, because of their unique transport properties, the junction power factors, GS2, are extremely high. Finally, we discuss the measurement of molecular current-voltage curves and consider the electronic and physical effects of applying a large bias to the system. We conclude with a summary of the work discussed and an outlook on related scientific studies.

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

    PubMed Central

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  6. Single Molecule Spectroelectrochemistry of Interfacial Charge Transfer Dynamics In Hybrid Organic Solar Cell

    SciTech Connect

    Pan, Shanlin

    2014-11-16

    Our research under support of this DOE grant is focused on applied and fundamental aspects of model organic solar cell systems. Major accomplishments are: 1) we developed a spectroelectorchemistry technique of single molecule single nanoparticle method to study charge transfer between conjugated polymers and semiconductor at the single molecule level. The fluorescence of individual fluorescent polymers at semiconductor surfaces was shown to exhibit blinking behavior compared to molecules on glass substrates. Single molecule fluorescence excitation anisotropy measurements showed the conformation of the polymer molecules did not differ appreciably between glass and semiconductor substrates. The similarities in molecular conformation suggest that the observed differences in blinking activity are due to charge transfer between fluorescent polymer and semiconductor, which provides additional pathways between states of high and low fluorescence quantum efficiency. Similar spectroelectrochemistry work has been done for small organic dyes for understand their charge transfer dynamics on various substrates and electrochemical environments; 2) We developed a method of transferring semiconductor nanoparticles (NPs) and graphene oxide (GO) nanosheets into organic solvent for a potential electron acceptor in bulk heterojunction organic solar cells which employed polymer semiconductor as the electron donor. Electron transfer from the polymer semiconductor to semiconductor and GO in solutions and thin films was established through fluorescence spectroscopy and electroluminescence measurements. Solar cells containing these materials were constructed and evaluated using transient absorption spectroscopy and dynamic fluorescence techniques to understand the charge carrier generation and recombination events; 3) We invented a spectroelectorchemistry technique using light scattering and electroluminescence for rapid size determination and studying electrochemistry of single NPs in an electrochemical cell. For example, we are able to use this technique to track electroluminescence of single Au NPs, and the electrodeposition of individual Ag NPs in-situ. These metallic NPs are useful to enhance light harvesting in organic photovoltaic systems. The scattering at the surface of an indium tin oxide (ITO) working electrode was measured during a potential sweep. Utilizing Mie scattering theory and high resolution scanning electron microscopy (SEM), the scattering data were used to calculate current-potential curves depicting the electrodeposition of individual Ag NPs. The oxidation of individual presynthesized and electrodeposited Ag NPs was also investigated using fluorescence and DFS microscopies. Our work has produced 1 US provisional patent, 15 published manuscripts, 1 submitted and two additional in-writing manuscripts. 5 graduate students, 1 postdoctoral student, 1 visiting professor, and two undergraduate students have received research training in the area of electrochemistry and optical spectroscopy under support of this award.

  7. Tools for Studying Electron and Spin Transport in Single Molecules

    NASA Astrophysics Data System (ADS)

    Ralph, Daniel C.

    2005-03-01

    Experiments in the field of single-molecule electronics are challenging in part because it can be very difficult to control and characterize the device structure. Molecules contacted by metal electrodes cannot easily be imaged by microscopy techniques. Moreover, if one attempts to characterize the device structure simply by measuring a current-voltage curve, it is easy to mistake nonlinear transport across a bare tunnel junction or a metallic short for a molecular signal. I will discuss the development of a set of experimental test structures that enable the properties of a molecular device to be tuned controllably in-situ, so that the transport mechanisms can be studied more systematically and compared with theoretical predictions. My collaborators and I are developing the means to use several different types of such experimental "knobs" in coordination: electrostatic gating to shift the energy levels in a molecule, mechanical motion to adjust the molecular configuration or the molecule-electrode coupling strength, illumination with light to promote electrons to excited states or to make and break chemical bonds, and the use of ferromagnetic electrodes to study spin-polarized transport. Our work so far has provided new insights into Kondo physics, the coupling between a molecule's electronic and mechanical degrees of freedom, and spin transport through a molecule between magnetic electrodes. Collaborators: Radek Bialczak, Alex Champagne, Luke Donev, Jonas Goldsmith, Jacob Grose, Janice Guikema, Jiwoong Park, Josh Parks, Abhay Pasupathy, Jason Petta, Sara Slater, Burak Ulgut, Alexander Soldatov, H'ector Abruña, and Paul McEuen.

  8. 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

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

    PubMed

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

    2009-09-01

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

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

    PubMed

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

    2016-03-21

    Electronic devices composed of single molecules constitute the ultimate limit in the continued downscaling of electronic components. A key challenge for single-molecule electronics is to control the temperature of these junctions. Controlling heating and cooling effects in individual vibrational modes can, in principle, be utilized to increase stability of single-molecule junctions under bias, to pump energy into particular vibrational modes to perform current-induced reactions, or to increase the resolution in inelastic electron tunneling spectroscopy by controlling the life-times of phonons in a molecule by suppressing absorption and external dissipation processes. Under bias the current and the molecule exchange energy, which typically results in heating of the molecule. However, the opposite process is also possible, where energy is extracted from the molecule by the tunneling current. Designing a molecular "heat sink" where a particular vibrational mode funnels heat out of the molecule and into the leads would be very desirable. It is even possible to imagine how the vibrational energy of the other vibrational modes could be funneled into the "cooling mode," given the right molecular design. Previous efforts to understand heating and cooling mechanisms in single molecule junctions have primarily been concerned with small models, where it is unclear which molecular systems they correspond to. In this paper, our focus is on suppressing heating and obtaining current-induced cooling in certain vibrational modes. Strategies for cooling vibrational modes in single-molecule junctions are presented, together with atomistic calculations based on those strategies. Cooling and reduced heating are observed for two different cooling schemes in calculations of atomistic single-molecule junctions. PMID:27004879

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  12. Two-photon-induced hot-electron transfer to a single molecule in a scanning tunneling microscope

    SciTech Connect

    Wu, S. W.; Ho, W.

    2010-08-15

    The junction of a scanning tunneling microscope (STM) operating in the tunneling regime was irradiated with femtosecond laser pulses. A photoexcited hot electron in the STM tip resonantly tunnels into an excited state of a single molecule on the surface, converting it from the neutral to the anion. The electron-transfer rate depends quadratically on the incident laser power, suggesting a two-photon excitation process. This nonlinear optical process is further confirmed by the polarization measurement. Spatial dependence of the electron-transfer rate exhibits atomic-scale variations. A two-pulse correlation experiment reveals the ultrafast dynamic nature of photoinduced charging process in the STM junction. Results from these experiments are important for understanding photoinduced interfacial charge transfer in many nanoscale inorganic-organic structures.

  13. 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.

  14. 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.

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

    NASA Astrophysics Data System (ADS)

    Hirvonen, Liisa M.; Barber, Matthew J.; Suhling, Klaus

    2016-06-01

    Photon event centroiding in photon counting imaging and single-molecule localisation in super-resolution fluorescence microscopy share many traits. Although photon event centroiding has traditionally been performed with simple single-iteration algorithms, we recently reported that iterative fitting algorithms originally developed for single-molecule localisation fluorescence microscopy work very well when applied to centroiding photon events imaged with an MCP-intensified CMOS camera. Here, we have applied these algorithms for centroiding of photon events from an electron-bombarded CCD (EBCCD). We find that centroiding algorithms based on iterative fitting of the photon events yield excellent results and allow fitting of overlapping photon events, a feature not reported before and an important aspect to facilitate an increased count rate and shorter acquisition times.

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

    PubMed Central

    Hirvonen, Liisa M.; Barber, Matthew J.; Suhling, Klaus

    2016-01-01

    Photon event centroiding in photon counting imaging and single-molecule localisation in super-resolution fluorescence microscopy share many traits. Although photon event centroiding has traditionally been performed with simple single-iteration algorithms, we recently reported that iterative fitting algorithms originally developed for single-molecule localisation fluorescence microscopy work very well when applied to centroiding photon events imaged with an MCP-intensified CMOS camera. Here, we have applied these algorithms for centroiding of photon events from an electron-bombarded CCD (EBCCD). We find that centroiding algorithms based on iterative fitting of the photon events yield excellent results and allow fitting of overlapping photon events, a feature not reported before and an important aspect to facilitate an increased count rate and shorter acquisition times.

  17. 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.

  18. 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.

  19. 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.

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

    PubMed

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

    2016-02-01

    Adsorption sites of molecules critically determine the electric/photonic properties and the stability of heterogeneous molecule-metal interfaces. Then, selectivity of adsorption site is essential for development of the fields including organic electronics, catalysis, and biology. However, due to current technical limitations, site-selectivity, i.e., precise determination of the molecular adsorption site, remains a major challenge because of difficulty in precise selection of meaningful one among the sites. We have succeeded the single site-selection at a single-molecule junction by performing newly developed hybrid technique: simultaneous characterization of surface enhanced Raman scattering (SERS) and current-voltage (I-V) measurements. The I-V response of 1,4-benzenedithiol junctions reveals the existence of three metastable states arising from different adsorption sites. Notably, correlated SERS measurements show selectivity toward one of the adsorption sites: "bridge sites". This site-selectivity represents an essential step toward the reliable integration of individual molecules on metallic surfaces. Furthermore, the hybrid spectro-electric technique reveals the dependence of the SERS intensity on the strength of the molecule-metal interaction, showing the interdependence between the optical and electronic properties in single-molecule junctions. PMID:26728229

  1. 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.

  2. Single-Molecule Electronic Measurements of the Dynamic Flexibility of Histone Deacetylases

    NASA Astrophysics Data System (ADS)

    Froberg, James; You, Seungyong; Yu, Junru; Haldar, Manas; Sedigh, Abbas; Mallik, Sanku; Srivastava, D. K.; Choi, Yongki

    Due to their involvement in epigenetic regulation, histone deacetylases (HDACs) have gained considerable interest in designing drugs for treatment of a variety of human diseases including cancers. Recently, we applied a label-free, electronic single-molecule nano-circuit technique to gain insight into the contribution of the dynamic flexibility in HDACs structure during the course of substrates/ ligands binding and catalysis. We observed that HDAC8 has two major (dynamically interconvertible) conformational states, ``ground (catalytically unfavorable)'' and ``transition (catalytically favorable)''. In addition, we found that its cognate substrates/ligands reciprocally catalyze the transition of the ground to the transition state conformation of HDAC8. Thus, we propose that both enzymes and their substrates/ligands serve as ``catalysts'' in facilitating the structural changes of each other and promoting the overall chemical transformation reaction. Such new information provides the potential for designing a new class of mechanism-based inhibitors and activators of HDAC8 for treating human diseases.

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

    PubMed

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

    2014-02-01

    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. PMID:24511969

  4. 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.

  5. Magnetic field dependent electronic transport of Mn4 single-molecule magnet.

    NASA Astrophysics Data System (ADS)

    Haque, F.; Langhirt, M.; Henderson, J. J.; Del Barco, E.; Taguchi, T.; Christou, G.

    2010-03-01

    We have performed single-electron transport measurements on a Mn4 single-molecule magnet (SMM) in where amino groups were added to electrically protect the magnetic core and to increase the stability of the molecule when deposited on the single-electron transistor (SET) chip. A three-terminal SET with nano-gap electro-migrated gold electrodes and a naturally oxidized Aluminum back gate. Experiments were conducted at temperatures down to 230mK in the presence of high magnetic fields generated by a superconducting vector magnet. Mn4 molecules were deposited from solution to form a mono-layer. The optimum deposition time was determined by AFM analysis on atomically flat gold surfaces. We have observed Coulomb blockade an electronic excitations that curve with the magnetic field and present zero-field splitting, which represents evidence of magnetic anisotropy. Level anticrossings and large excitations slopes are associated with the behavior of molecular states with high spin values (S 9), as expected from Mn4.

  6. 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

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

    PubMed

    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

  8. 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.

  9. Electron transport in endohedral metallofullerene Ce@C{sub 82} single-molecule transistors

    SciTech Connect

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

    2015-01-26

    We have investigated the electron transport in endohedral metallofullerene Ce@C{sub 82} single-molecule transistors (SMTs) together with that in reference C{sub 84} SMTs. The vibrational modes (bending and stretching) of the encapsulated single Ce atom in the C{sub 82} cage appear in Coulomb stability diagrams for the single-electron tunneling through Ce@C{sub 82} molecules, demonstrating the single-atom sensitivity of the transport measurements. When a bias voltage larger than 100 mV is applied across the source/drain electrodes, large hysteretic behavior is observed in the current-voltage (I-V) characteristics. At the same time, the pattern in the Coulomb stability diagram is changed. No such hysteretic behavior is observed in the I-V curves of hollow-cage C{sub 84} SMTs, even when the bias voltage exceeds 500 mV. This hysteretic change in the I-V characteristics is induced by a nanomechanical change in the configuration of the Ce@C{sub 82} molecule in the nanogap electrode due to the electric dipole that exists in Ce@C{sub 82}.

  10. How to probe transverse magnetic anisotropy of a single-molecule magnet by electronic transport?

    NASA Astrophysics Data System (ADS)

    Misiorny, M.; Burzuri, E.; Gaudenzi, R.; Park, K.; Leijnse, M.; Wegewijs, M.; Paaske, J.; Cornia, A.; van der Zant, H.

    We propose an approach for in-situ determination of the transverse magnetic anisotropy (TMA) of an individual molecule by electronic transport measurements, see Phys. Rev. B 91, 035442 (2015). We study a Fe4 single-molecule magnet (SMM) captured in a gateable junction, a unique tool for addressing the spin in different redox states of a molecule. We show that, due to mixing of the spin eigenstates of the SMM, the TMA significantly manifests itself in transport. We predict and experimentally observe the pronounced intensity modulation of the Coulomb peak amplitude with the magnetic field in the linear-response transport regime, from which the TMA parameter E can be estimated. Importantly, the method proposed here does not rely on the small induced tunnelling effects and, hence, works well at temperatures and electron tunnel broadenings by far exceeding the tunnel splittings and even E itself. We deduce that the TMA for a single Fe4 molecule captured in a junction is substantially larger than the bulk value. Work supported by the Polish Ministry of Science and Education as `Iuventus Plus' project (IP2014 030973) in years 2015-2016.

  11. 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

  12. 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

  13. Fine-tuning of single-molecule conductance by tweaking both electronic structure and conformation of side substituents.

    PubMed

    Aragonès, Albert C; Darwish, Nadim; Im, JongOne; Lim, Boram; Choi, Jeongae; Koo, Sangho; Díez-Pérez, Ismael

    2015-05-18

    Herein, we describe a method to fine-tune the conductivity of single-molecule wires by employing a combination of chemical composition and geometrical modifications of multiple phenyl side groups as conductance modulators embedded along the main axis of the electronic pathway. We have measured the single-molecule conductivity of a novel series of phenyl-substituted carotenoid wires whose conductivity can be tuned with high precision over an order of magnitude range by modulating both the electron-donating character of the phenyl substituent and its dihedral angle. It is demonstrated that the electronic communication between the phenyl side groups and the molecular wire is maximized when the phenyl groups are twisted closer to the plane of the conjugated molecular wire. These findings can be refined to a general technique for precisely tuning the conductivity of molecular wires. PMID:25847688

  14. Electronic measurements of single-molecule processing by DNA polymerase I

    NASA Astrophysics Data System (ADS)

    Choi, Yongki; Olsen, Tivoli; Gul, Tolga; Corso, Brad; Dong, Chengjun; Brown, William; Weiss, Gregory; Collins, Philip

    2013-03-01

    A single-molecule nanocircuit technique is applied to continuously monitor DNA replication activity by the enzyme DNA polymerase I (Pol I). Using single copies of Pol I bound to a single-walled carbon nanotube device, an electrical signal was generated to reveal enzymatic function and dynamic variability. Continuous, single-molecule-resolution recordings were obtained for Pol I processing homopolymeric DNA templates over 10 minutes and through >10,000 DNA replication events. Processivity of up to 40 nucleotide bases was directly observed, and statistical analysis of the recordings determined key kinetic parameters for the enzyme's open and closed conformations. We observe that the closed complex forms a phosphodiester bond in a highly efficient process >99.8% of the time, with a mean duration of only 0.3 ms for all four dNTPs. The rate-limiting step for replication occurs during the enzyme's open state, but with a duration that is nearly twice as long for dATP or dTTP incorporation than for dCTP or dGTP. Taken together, the results provide a wealth of new information complementing prior work on the mechanism and dynamics of DNA polymerase.

  15. Nature of Asymmetry in the Vibrational Line Shape of Single-Molecule Inelastic Electron Tunneling Spectroscopy with the STM

    NASA Astrophysics Data System (ADS)

    Xu, Chen; Chiang, Chi-lun; Han, Zhumin; Ho, W.

    2016-04-01

    Single molecule vibrational spectroscopy and microscopy was demonstrated in 1998 by inelastic electron tunneling with the scanning tunneling microscope. To date, the discussion of its application has mainly focused on the spatial resolution and the spectral energy and intensity. Here we report on the vibrational line shape for a single carbon monoxide molecule that qualitatively exhibits inversion symmetry when it is transferred from the surface to the tip. The dependence of the line shape on the molecule's asymmetric couplings in the tunnel junction can be understood from theoretical simulation and further validates the mechanisms of inelastic electron tunneling.

  16. Single-molecule bioelectronics.

    PubMed

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

  18. Real-time single-molecule electronic DNA sequencing by synthesis using polymer-tagged nucleotides on a nanopore array

    PubMed Central

    Fuller, Carl W.; Kumar, Shiv; Porel, Mintu; Chien, Minchen; Bibillo, Arek; Stranges, P. Benjamin; Dorwart, Michael; Tao, Chuanjuan; Li, Zengmin; Guo, Wenjing; Shi, Shundi; Korenblum, Daniel; Trans, Andrew; Aguirre, Anne; Liu, Edward; Harada, Eric T.; Pollard, James; Bhat, Ashwini; Cech, Cynthia; Yang, Alexander; Arnold, Cleoma; Palla, Mirkó; Hovis, Jennifer; Chen, Roger; Morozova, Irina; Kalachikov, Sergey; Russo, James J.; Kasianowicz, John J.; Davis, Randy; Roever, Stefan; Church, George M.; Ju, Jingyue

    2016-01-01

    DNA sequencing by synthesis (SBS) offers a robust platform to decipher nucleic acid sequences. Recently, we reported a single-molecule nanopore-based SBS strategy that accurately distinguishes four bases by electronically detecting and differentiating four different polymer tags attached to the 5′-phosphate of the nucleotides during their incorporation into a growing DNA strand catalyzed by DNA polymerase. Further developing this approach, we report here the use of nucleotides tagged at the terminal phosphate with oligonucleotide-based polymers to perform nanopore SBS on an α-hemolysin nanopore array platform. We designed and synthesized several polymer-tagged nucleotides using tags that produce different electrical current blockade levels and verified they are active substrates for DNA polymerase. A highly processive DNA polymerase was conjugated to the nanopore, and the conjugates were complexed with primer/template DNA and inserted into lipid bilayers over individually addressable electrodes of the nanopore chip. When an incoming complementary-tagged nucleotide forms a tight ternary complex with the primer/template and polymerase, the tag enters the pore, and the current blockade level is measured. The levels displayed by the four nucleotides tagged with four different polymers captured in the nanopore in such ternary complexes were clearly distinguishable and sequence-specific, enabling continuous sequence determination during the polymerase reaction. Thus, real-time single-molecule electronic DNA sequencing data with single-base resolution were obtained. The use of these polymer-tagged nucleotides, combined with polymerase tethering to nanopores and multiplexed nanopore sensors, should lead to new high-throughput sequencing methods. PMID:27091962

  19. Real-time single-molecule electronic DNA sequencing by synthesis using polymer-tagged nucleotides on a nanopore array.

    PubMed

    Fuller, Carl W; Kumar, Shiv; Porel, Mintu; Chien, Minchen; Bibillo, Arek; Stranges, P Benjamin; Dorwart, Michael; Tao, Chuanjuan; Li, Zengmin; Guo, Wenjing; Shi, Shundi; Korenblum, Daniel; Trans, Andrew; Aguirre, Anne; Liu, Edward; Harada, Eric T; Pollard, James; Bhat, Ashwini; Cech, Cynthia; Yang, Alexander; Arnold, Cleoma; Palla, Mirkó; Hovis, Jennifer; Chen, Roger; Morozova, Irina; Kalachikov, Sergey; Russo, James J; Kasianowicz, John J; Davis, Randy; Roever, Stefan; Church, George M; Ju, Jingyue

    2016-05-10

    DNA sequencing by synthesis (SBS) offers a robust platform to decipher nucleic acid sequences. Recently, we reported a single-molecule nanopore-based SBS strategy that accurately distinguishes four bases by electronically detecting and differentiating four different polymer tags attached to the 5'-phosphate of the nucleotides during their incorporation into a growing DNA strand catalyzed by DNA polymerase. Further developing this approach, we report here the use of nucleotides tagged at the terminal phosphate with oligonucleotide-based polymers to perform nanopore SBS on an α-hemolysin nanopore array platform. We designed and synthesized several polymer-tagged nucleotides using tags that produce different electrical current blockade levels and verified they are active substrates for DNA polymerase. A highly processive DNA polymerase was conjugated to the nanopore, and the conjugates were complexed with primer/template DNA and inserted into lipid bilayers over individually addressable electrodes of the nanopore chip. When an incoming complementary-tagged nucleotide forms a tight ternary complex with the primer/template and polymerase, the tag enters the pore, and the current blockade level is measured. The levels displayed by the four nucleotides tagged with four different polymers captured in the nanopore in such ternary complexes were clearly distinguishable and sequence-specific, enabling continuous sequence determination during the polymerase reaction. Thus, real-time single-molecule electronic DNA sequencing data with single-base resolution were obtained. The use of these polymer-tagged nucleotides, combined with polymerase tethering to nanopores and multiplexed nanopore sensors, should lead to new high-throughput sequencing methods. PMID:27091962

  20. 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 λ , and the driving force Δ 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

  2. Single molecule laser spectroscopy

    NASA Astrophysics Data System (ADS)

    Atta, Diaa; Okasha, Ali

    2015-01-01

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

  3. Single Molecule Mechanochemistry

    NASA Astrophysics Data System (ADS)

    Li, Shaowei; Zhang, Yanxing; Ho, Wilson; Wu, Ruqian; Ruqian Wu, Yanxing Zhang Team; Wilson Ho, Shaowei Li Team

    Mechanical forces can be used to trigger chemical reactions through bending and stretching of chemical bonds. Using the reciprocating movement of the tip of a scanning tunneling microscope (STM), mechanical energy can be provided to a single molecule sandwiched between the tip and substrate. When the mechanical pulse center was moved to the outer ring feature of a CO molecule, the reaction rate was significantly increased compared with bare Cu surface and over Au atoms. First, DFT calculations show that the presence of CO makes the Cu cavity more attractive toward H2 Second, H2 prefers the horizontal adsorption geometry in the Cu-Cu and Au-Cu cavities and no hybridization occurs between the antibonding states of H2 and states of Cu atoms. While H2 loses electrons from its bonding state in all three cavities, the filling of its anti-bonding state only occurs in the CO-Cu cavity. Both make the CO-Cu cavity much more effectively to chop the H2 molecule. Work was supported by the National Science Foundation Center for Chemical Innovation on Chemistry at the Space-Time Limit (CaSTL) under Grant No. CHE-1414466.

  4. Multiplexed single molecule immunoassays.

    PubMed

    Rissin, David M; Kan, Cheuk W; Song, Linan; Rivnak, Andrew J; Fishburn, Matthew W; Shao, Qichao; Piech, Tomasz; Ferrell, Evan P; Meyer, Raymond E; Campbell, Todd G; Fournier, David R; Duffy, David C

    2013-08-01

    We have developed a method that enables the multiplexed detection of proteins based on counting single molecules. Paramagnetic beads were labeled with fluorescent dyes to create optically distinct subpopulations of beads, and antibodies to specific proteins were then immobilized to individual subpopulations. Mixtures of subpopulations of beads were then incubated with a sample, and specific proteins were captured on their specific beads; these proteins were then labeled with enzymes via immunocomplex formation. The beads were suspended in enzyme substrate, loaded into arrays of femtoliter wells--or Single Molecule Arrays (Simoa)--that were integrated into a microfluidic device (the Simoa disc). The wells were then sealed with oil, and imaged fluorescently to determine: a) the location and subpopulation identity of individual beads in the femtoliter wells, and b) the presence or absence of a single enzyme associated with each bead. The images were analyzed to determine the average enzyme per bead (AEB) for each bead subpopulation that provide a quantitative parameter for determining the concentration of each protein. We used this approach to simultaneously detect TNF-α, IL-6, IL-1α, and IL-1β in human plasma with single molecule resolution at subfemtomolar concentrations, i.e., 200- to 1000-fold more sensitive than current multiplexed immunoassays. The simultaneous, specific, and sensitive measurement of several proteins using multiplexed digital ELISA could enable more reliable diagnoses of disease. PMID:23719780

  5. Single-molecule magnets

    NASA Astrophysics Data System (ADS)

    Aubin, Sheila Marie Josee

    This thesis discusses the syntheses and magnetization studies of several single-molecule magnets. These single- molecule magnets are also shown to display resonant magnetization tunneling. In chapter 1 an introduction into this area of research and similar areas of research are presented. In chapter 2 several complexes from a family of molecules with [ Mn4O3X]6+ cores are shown to behave as single-molecule magnets based on AC magnetic susceptibility measurements on microcrystalline and dilute frozen solution samples. In chapter 3 more detailed magnetic studies are reported for one complex from the Mn4 family of molecules-[ Mn4O3Cl(O2CCH3)3(dbm)3], where dbm is dibenzoylmethane. It is shown that this Mn4 complex exhibits resonant magnetization tunneling based on the observation of steps on magnetic hysteresis loops, ac magnetic susceptibility studies and the observation of a temperature-independent rate of magnetization relaxation below 0.6 K. In chapters 4 through 6 the syntheses and magnetization studies of several new Mn12 molecules with general composition [ Mn12O12(O2CR)16(H2O)4] are reported. From ac susceptibility measurements it is shown that some of these complexes exhibit much faster magnetic relaxation than others. Also, steps are observed at constant intervals of field on the magnetization hysteresis loops collected on some of these Mn12 complexes. This is evidence of field-tuned resonant magnetization tunneling.

  6. Watching single molecules dance

    NASA Astrophysics Data System (ADS)

    Mehta, Amit Dinesh

    Molecular motors convert chemical energy, from ATP hydrolysis or ion flow, into mechanical motion. A variety of increasingly precise mechanical probes have been developed to monitor and perturb these motors at the single molecule level. Several outstanding questions can be best approached at the single molecule level. These include: how far does a motor progress per energy quanta consumed? how does its reaction cycle respond to load? how many productive catalytic cycles can it undergo per diffusional encounter with its track? and what is the mechanical stiffness of a single molecule connection? A dual beam optical trap, in conjunction with in vitro ensemble motility assays, has been used to characterize two members of the myosin superfamily: muscle myosin II and chick brain myosin V. Both move the helical polymer actin, but myosin II acts in large ensembles to drive muscle contraction or cytokinesis, while myosin V acts in small numbers to transport vesicles. An optical trapping apparatus was rendered sufficiently precise to identify a myosin working stroke with 1nm or so, barring systematic errors such as those perhaps due to random protein orientations. This and other light microscopic motility assays were used to characterize myosin V: unlike myosin II this vesicle transport protein moves through many increments of travel while remaining strongly bound to a single actin filament. The step size, stall force, and travel distance of myosin V reveal a remarkably efficient motor capable of moving along a helical track for over a micrometer without significantly spiraling around it. Such properties are fully consistent with the putative role of an organelle transport motor, present in small numbers to maintain movement over long ranges relative to cellular size scales. The contrast between myosin II and myosin V resembles that between a human running on the moon and one walking on earth, where the former allows for faster motion when in larger ensembles but for less travel distance when in smaller ones.

  7. A new approach to extract multiple distinct conformers and co-existing distinct electronic properties of a single molecule by point-contact method.

    PubMed

    Bandyopadhyay, Anirban; Sahu, Satyajit; Fujita, Daisuke; Wakayama, Yutaka

    2010-03-01

    Conventionally, it is assumed that a single molecule has only one absolute electronic property. Molecular electronics, molecular machines, intelligent drugs are some of the fields that require atomic scale control of molecular properties. In spite of remarkable achievements in the last two decades, absolute control of molecular properties has not been achieved. Here, experimental evidences argue against assigning a fixed property to a molecule. A molecule might structurally accommodate itself to the new environment and its electronic properties might change accordingly. By isolating electronic properties of all the conformers of a Rose Bengal molecule one by one, a map of its complete electronic properties is drawn here. The existing concept of one absolute electronic property of a molecule is true only for those molecules, which have only one stable conformer. For others, depending on the conformer, multiple distinct electronic properties may co-exist, leading to a variable output in an electronic characterization. Thus, we present a generalized method for characterizing/resolving collective electronic properties that emerge statistically. The method could be used for designing molecular switches for collective and evolutionary information processing. PMID:20165769

  8. Ultrafast Interfacial Proton-Coupled Electron Transfer

    SciTech Connect

    Petek, Hrvoje; Zhao, Jin

    2010-12-08

    Interfaces between metallic or semiconducting solids and protic solvent adsorbates or liquids represent one of the most important, and yet hardly explored material environments for proton coupled electron transfer (PCET) processes. PCET mediated dynamical phenomena driven by light, electron, and chemical potentials are central in energy transduction processes of vast economic and environmental importance including the photocatalytic splitting of H₂O, the photo and electrochemical reduction of CO₂, and the conversion of chemical to electrical energy in fuel cells. Experimental and theoretical investigations of the dynamical aspects of PCET at solid surfaces are particularly challenging because relatively localized charges within a solvent couple in the presence of strong interfacial potentials to delocalized states of electronic continua of semiconductor or metal electrodes. Moreover, the localized charges are never the bare protons and electrons that balance chemical equations, but rather are dressed particles with associated polarization clouds inhomogeneously distributed and comprised variously of free electrons, lattice ions, and solvent molecules. The polarization clouds screen the Coulomb potential on the medium specific time scales and impose energetic costs associated with transport through the inhomogeneous region of interfaces between the solid and molecular environments. We introduce some recent theoretical studies aimed at providing an atomistic description on metal-protic solvent interface and modeling of simple processes such as the discharge of H⁺ at a metal interface. Because of the paucity of experimental research and embryonic stage of theory, our goal is to present some key theoretical concepts and early experimental efforts based primarily on a surface science approach to ultrafast electron induced dynamics. In order to introduce some key features of interfacial PCET in the strong and intermediate coupling regimes, we discuss specific examples of photoinduced dissociation of alkanes on metals and photoinduced PCET dynamics of methanol covered TiO₂ surfaces.

  9. Electronic transport in biphenyl single-molecule junctions with carbon nanotubes electrodes: The role of molecular conformation and chirality

    SciTech Connect

    Brito Silva, C. A. Jr.; Granhen, E. R.; Silva, S. J. S. da; Leal, J. F. P.; Del Nero, J.; Pinheiro, F. A.

    2010-08-15

    We investigate, by means of ab initio calculations, electronic transport in molecular junctions composed of a biphenyl molecule attached to metallic carbon nanotubes. We find that the conductance is proportional to cos{sup 2} {theta}, with {theta} the angle between phenyl rings, when the Fermi level of the contacts lies within the frontier molecular orbitals energy gap. This result, which agrees with experiments in biphenyl junctions with nonorganic contacts, suggests that the cos{sup 2} {theta} law has a more general applicability, irrespective of the nature of the electrodes. We calculate the geometrical degree of chirality of the junction, which only depends on the atomic positions, and demonstrate that it is not only proportional to cos{sup 2} {theta} but also is strongly correlated with the current through the system. These results indicate that molecular conformation plays the preponderant role in determining transport properties of biphenyl-carbon nanotubes molecular junctions.

  10. Theory of plasmon enhanced interfacial electron transfer

    NASA Astrophysics Data System (ADS)

    Wang, Luxia; May, Volkhard

    2015-04-01

    A particular attempt to improve the efficiency of a dye sensitized solar cell is it's decoration with metal nano-particles (MNP). The MNP-plasmon induced enhancement of the local field enlarges the photoexcitation of the dyes and a subsequent improvement of the charge separation efficiency may result. In a recent work (2014 J. Phys. Chem. C 118 2812) we presented a theory of plasmon enhanced interfacial electron transfer for perylene attached to a TiO2 surface and placed in the proximity of a spherical MNP. These earlier studies are generalized here to the coupling of to up to four MNPs and to the use of somewhat altered molecular parameters. If the MNPs are placed close to each other strong hybridization of plasmon excitations appears and a broad resonance to which molecular excitations are coupled is formed. To investigate this situation the whole charge injection dynamics is described in the framework of the density matrix theory. The approach accounts for optical excitation of the dye coupled to the MNPs and considers subsequent electron injection into the rutile TiO2-cluster. Using a tight-binding model for the TiO2-system with about 105 atoms the electron motion in the cluster is described. We again consider short optical excitation which causes an intermediate steady state with a time-independent overall probability to have the electron injected into the cluster. This probability is used to introduce an enhancement factor which rates the influence of the MNP. Values larger than 500 are obtained.

  11. 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

  12. Cryo-electron microscopy and single molecule fluorescent microscopy detect CD4 receptor induced HIV size expansion prior to cell entry.

    PubMed

    Pham, Son; Tabarin, Thibault; Garvey, Megan; Pade, Corinna; Rossy, Jérémie; Monaghan, Paul; Hyatt, Alex; Böcking, Till; Leis, Andrew; Gaus, Katharina; Mak, Johnson

    2015-12-01

    Viruses are often thought to have static structure, and they only remodel after the viruses have entered target cells. Here, we detected a size expansion of virus particles prior to viral entry using cryo-electron microscopy (cryo-EM) and single molecule fluorescence imaging. HIV expanded both under cell-free conditions with soluble receptor CD4 (sCD4) targeting the CD4 binding site on the HIV-1 envelope protein (Env) and when HIV binds to receptor on cellular membrane. We have shown that the HIV Env is needed to facilitate receptor induced virus size expansions, showing that the 'lynchpin' for size expansion is highly specific. We demonstrate that the size expansion required maturation of HIV and an internal capsid core with wild type stability, suggesting that different HIV compartments are linked and are involved in remodelling. Our work reveals a previously unknown event in HIV entry, and we propose that this pre-entry priming process enables HIV particles to facilitate the subsequent steps in infection. PMID:26432024

  13. A systematic study of influence of ligand substitutions on the electronic structure and magnetic properties of Mn4 single-molecule magnets.

    PubMed

    Tuan, Nguyen Anh; Katayama, Shin-ichi; Chi, Dam Hieu

    2009-01-28

    We present a density-functional theory study of the influence of ligand substitutions on the geometric structure, electronic structure, and magnetic properties of Mn4 single-molecule magnets (SMMs), in order to investigate the role of ligands in controlling these features, as well as in developing new SMMs and single-chain magnets (SCMs). Our results show that the peripheral ligands play an important role in controlling the magnetic ground-state of Mn4 SMMs. A new model is proposed to explain the spin state of manganese ions in Mn4 molecules. This model shows that the saving energy from distortion, which can be controlled by peripheral-ligand substitutions, plays a crucial role in determining the spin state of manganese ions in Mn4 molecules. The mechanism of strong exchange couplings between manganese ions in Mn4 SMMs is revealed. The strength of exchange-couplings between manganese ions in Mn4 SMMs as a function of their charge and spin state can be also controlled by substituting peripheral-ligands. The results demonstrate the possibilities of developing new Mn4-based SMMs. In addition, strong spin polarizations on peripheral ligands containing sp2-hybridized carbon sites show that using ligands containing sp2-hybridized carbon sites can enhance exchange couplings between Mn4 building blocks to develop new SMMs and SCMs which operate at high temperatures. PMID:19835095

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

    PubMed

    Rodriguez, Jorge H; Ziegler, Christopher J

    2015-01-01

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

  15. 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.

  16. Special issue: single molecule techniques.

    PubMed

    Gorris, Hans H

    2015-01-01

    Technological advances in the detection and manipulation of single molecules have enabled new insights into the function, structure and interactions of biomolecules. This Special Issue was launched to account for the rapid progress in the field of "Single Molecule Techniques". Four original research articles and seven review articles provide an introduction, as well as an in-depth discussion, of technical developments that are indispensable for the characterization of individual biomolecules. Fluorescence microscopy takes center stage in this Special Issue because it is one of the most sensitive and flexible techniques, which has been adapted in many variations to the specific demands of single molecule analysis. Two additional articles are dedicated to single molecule detection based on atomic force microscopy. PMID:26007165

  17. Interfacial electronic effects control the reaction selectivity of platinum catalysts

    NASA Astrophysics Data System (ADS)

    Chen, Guangxu; Xu, Chaofa; Huang, Xiaoqing; Ye, Jinyu; Gu, Lin; Li, Gang; Tang, Zichao; Wu, Binghui; Yang, Huayan; Zhao, Zipeng; Zhou, Zhiyou; Fu, Gang; Zheng, Nanfeng

    2016-05-01

    Tuning the electronic structure of heterogeneous metal catalysts has emerged as an effective strategy to optimize their catalytic activities. By preparing ethylenediamine-coated ultrathin platinum nanowires as a model catalyst, here we demonstrate an interfacial electronic effect induced by simple organic modifications to control the selectivity of metal nanocatalysts during catalytic hydrogenation. This we apply to produce thermodynamically unfavourable but industrially important compounds, with ultrathin platinum nanowires exhibiting an unexpectedly high selectivity for the production of N-hydroxylanilines, through the partial hydrogenation of nitroaromatics. Mechanistic studies reveal that the electron donation from ethylenediamine makes the surface of platinum nanowires highly electron rich. During catalysis, such an interfacial electronic effect makes the catalytic surface favour the adsorption of electron-deficient reactants over electron-rich substrates (that is, N-hydroxylanilines), thus preventing full hydrogenation. More importantly, this interfacial electronic effect, achieved through simple organic modifications, may now be used for the optimization of commercial platinum catalysts.

  18. Interfacial electronic effects control the reaction selectivity of platinum catalysts.

    PubMed

    Chen, Guangxu; Xu, Chaofa; Huang, Xiaoqing; Ye, Jinyu; Gu, Lin; Li, Gang; Tang, Zichao; Wu, Binghui; Yang, Huayan; Zhao, Zipeng; Zhou, Zhiyou; Fu, Gang; Zheng, Nanfeng

    2016-05-01

    Tuning the electronic structure of heterogeneous metal catalysts has emerged as an effective strategy to optimize their catalytic activities. By preparing ethylenediamine-coated ultrathin platinum nanowires as a model catalyst, here we demonstrate an interfacial electronic effect induced by simple organic modifications to control the selectivity of metal nanocatalysts during catalytic hydrogenation. This we apply to produce thermodynamically unfavourable but industrially important compounds, with ultrathin platinum nanowires exhibiting an unexpectedly high selectivity for the production of N-hydroxylanilines, through the partial hydrogenation of nitroaromatics. Mechanistic studies reveal that the electron donation from ethylenediamine makes the surface of platinum nanowires highly electron rich. During catalysis, such an interfacial electronic effect makes the catalytic surface favour the adsorption of electron-deficient reactants over electron-rich substrates (that is, N-hydroxylanilines), thus preventing full hydrogenation. More importantly, this interfacial electronic effect, achieved through simple organic modifications, may now be used for the optimization of commercial platinum catalysts. PMID:26808458

  19. Photon and electron stimulated surface dynamics of single molecules. Final report on D.O.E. No. DE-FG0295ER14563

    SciTech Connect

    Harrison, Ian

    2001-05-01

    The initial goal of this work was to build up an entirely new low-temperature scanning tunneling microscopy (STM) and ultrahigh vacuum system to examine the electron- and photon-induced chemistry of single molecules at low surface temperatures where thermal diffusion would be quenched. The photochemistry of methyl bromide on Pt(111) was first examined at 90 K using liquid nitrogen cooling. Br atoms were quite mobile even at 90 K, and were only visible by STM when coalesced along Pt step edges or in Br islands structures. The 193 nm photofragmentation of methyl bromide efficiently created monovacancies in the substrate at 90 K. It was found that at elevated temperatures there is considerable restructuring and reactive attack of the Pt surface by halogens, but for traditional, lower temperature studies of alkyl radicals prepared by thermal dissociative adsorption of alkyl iodides there is probably no problem with adsorbing I generating monovacancies on the surface. The dynamics of the ho t Br atoms formed by dissociative adsorption of Br{sub 2} was also examined. It was discovered that hot Br atoms from Br{sub 2} dissociative adsorption travel farther than hot O atoms from O{sub 2} dissociative adsorption; hot atom motion from different dissociative adsorption systems had not previously been compared for the same metal substrate. The experimental results strengthened the theoretical case that corrugation of the adsorbate/substrate potential is the key issue in determining hot atom travel. In addition, the data provided strong evidence for the transient existence of a weakly adsorbed and mobile Br{sub 2} precursor to dissociative adsorption. Some experiments imaging individual molecules at 15 K were also conducted.

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

    PubMed

    Zhang, Lei; Ren, Gang

    2012-01-01

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

  1. IPET and FETR: Experimental Approach for Studying Molecular Structure Dynamics by Cryo-Electron Tomography of a Single-Molecule Structure

    PubMed Central

    Zhang, Lei; Ren, Gang

    2012-01-01

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

  2. Electrical, Mechanical and Thermal Properties of Single Molecules

    SciTech Connect

    Tao, Nongjian

    2014-08-20

    The specific aims of the prior DOE grant are to determine the stability of a single molecule bound to two electrodes, study local heating in single molecule junctions due to electron-phonon and electron-electron interactions, measure electron-phonon interactions in single molecule wires; and explore piezoelectric properties of single molecules. We have completed all the major tasks, and also expanded naturally the scope of the project to address several other critical issues in single molecule properties, developed new experimental capabilities, and observed a number of unexpected phenomena. We summarized here some of the findings that are most relevant to the present renewal proposal. More details can be found in the publications resulted from this grant and annual progress reports.

  3. Single-Molecule DNA Analysis

    NASA Astrophysics Data System (ADS)

    Efcavitch, J. William; Thompson, John F.

    2010-07-01

    The ability to detect single molecules of DNA or RNA has led to an extremely rich area of exploration of the single most important biomolecule in nature. In cases in which the nucleic acid molecules are tethered to a solid support, confined to a channel, or simply allowed to diffuse into a detection volume, novel techniques have been developed to manipulate the DNA and to examine properties such as structural dynamics and protein-DNA interactions. Beyond the analysis of the properties of nucleic acids themselves, single-molecule detection has enabled dramatic improvements in the throughput of DNA sequencing and holds promise for continuing progress. Both optical and nonoptical detection methods that use surfaces, nanopores, and zero-mode waveguides have been attempted, and one optically based instrument is already commercially available. The breadth of literature related to single-molecule DNA analysis is vast; this review focuses on a survey of efforts in molecular dynamics and nucleic acid sequencing.

  4. 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.

  5. Manipulating transport through a single-molecule junction

    SciTech Connect

    Sotthewes, Kai; Heimbuch, René; Zandvliet, Harold J. W.

    2013-12-07

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

  6. Single molecule Raman spectra of porphycene isotopologues

    NASA Astrophysics Data System (ADS)

    Gawinkowski, Sylwester; Pszona, Maria; Gorski, Alexandr; Niedziółka-Jönsson, Joanna; Kamińska, Izabela; Nogala, Wojciech; Waluk, Jacek

    2016-02-01

    Single molecule surface-enhanced resonance Raman scattering (SERRS) spectra have been obtained for the parent porphycene (Pc-d0) and its deuterated isotopologue (Pc-d12), located on gold and silver nanoparticles. Equal populations of ``hot spots'' by the two isotopologues are observed for 1 : 1 mixtures in a higher concentration range of the single molecule regime (5 × 10-9 M). For decreasing concentrations, hot spots are preferentially populated by undeuterated molecules. This is interpreted as an indication of a lower surface diffusion coefficient of Pc-d12. The photostability of single Pc molecules placed on nanoparticles is strongly increased in comparison with polymer environments. Trans tautomeric species dominate the spectra, but the analysis of time traces reveals transient intermediates, possibly due to rare cis tautomeric forms.Single molecule surface-enhanced resonance Raman scattering (SERRS) spectra have been obtained for the parent porphycene (Pc-d0) and its deuterated isotopologue (Pc-d12), located on gold and silver nanoparticles. Equal populations of ``hot spots'' by the two isotopologues are observed for 1 : 1 mixtures in a higher concentration range of the single molecule regime (5 × 10-9 M). For decreasing concentrations, hot spots are preferentially populated by undeuterated molecules. This is interpreted as an indication of a lower surface diffusion coefficient of Pc-d12. The photostability of single Pc molecules placed on nanoparticles is strongly increased in comparison with polymer environments. Trans tautomeric species dominate the spectra, but the analysis of time traces reveals transient intermediates, possibly due to rare cis tautomeric forms. Electronic supplementary information (ESI) available: Details of estimation of the enhancement factors, additional Raman, SERS, fluorescence, and absorption spectra and maps. See DOI: 10.1039/c5nr08627b

  7. 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

  8. Quantum Oscillations in an Interfacial 2D Electron Gas.

    SciTech Connect

    Zhang, Bingop; Lu, Ping; Liu, Henan; Lin, Jiao; Ye, Zhenyu; Jaime, Marcelo; Balakirev, Fedor F.; Yuan, Huiqiu; Wu, Huizhen; Pan, Wei; Zhang, Yong

    2016-01-01

    Recently, it has been predicted that topological crystalline insulators (TCIs) may exist in SnTe and Pb1-xSnxTe thin films [1]. To date, most studies on TCIs were carried out either in bulk crystals or thin films, and no research activity has been explored in heterostructures. We present here the results on electronic transport properties of the 2D electron gas (2DEG) realized at the interfaces of PbTe/ CdTe (111) heterostructures. Evidence of topological state in this interfacial 2DEG was observed.

  9. 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 backbone length, providing a new means to tune p- and n-type transport in organic materials. Taken together, the results presented in this thesis offer an insight into how molecular symme- try and the accessible conformers within a junction have important consequences on conductance behavior. Additionally, thiophene-1,1-dioxide is shown to be an exciting unit for single molecule devices, especially when combined with electron rich thiophene flanking groups. By demon- strating, for the first time, a change in conductance pathway with molecular length, this work provides a framework for using frontier orbital levels to strategically design electronic building blocks.

  10. Single-Molecule Solvation-Shell Sensing

    NASA Astrophysics Data System (ADS)

    Leary, E.; Höbenreich, H.; Higgins, S. J.; van Zalinge, H.; Haiss, W.; Nichols, R. J.; Finch, C. M.; Grace, I.; Lambert, C. J.; McGrath, R.; Smerdon, J.

    2009-02-01

    We present a new route to single-molecule sensing via solvation shells surrounding a current-carrying backbone molecule. As an example, we show that the presence of a water solvation shell “gates” the conductance of a family of oligothiophene-containing molecular wires, and that the longer the oligothiophene, the larger is the effect. For the longest example studied, the molecular conductance is over 2 orders of magnitude larger in the presence of a shell comprising just 10 water molecules. A first principles theoretical investigation of electron transport through the molecules, using the nonequilibrium Green’s function method, shows that water molecules interact directly with the thiophene rings, significantly shifting transport resonances and greatly increasing the conductance. This reversible effect is confirmed experimentally through conductance measurements performed in the presence of moist air and dry argon.

  11. Spin blockade effect in single-molecule transistors

    NASA Astrophysics Data System (ADS)

    Luo, Guangpu; Park, Kyungwha

    Recently single-molecule transistors consisting of individual single-molecule magnets trapped between electrodes have been experimentally realized and electron transport properties through individual single-molecule magnets have been measured. For a single-molecule magnet the (2S+1)-fold degeneracy of magnetic levels in a given spin multiplet is lifted even in the absence of external magnetic field, due to the magnetic anisotropy induced by spin-orbit coupling. This anisotropic nature of single-molecule magnets allowed one to discover interesting, unexpected transport properties. A recent theoretical study showed that an Eu-based anisotropic magnetic molecule can switch its magnetic anisotropy between magnetic easy plane and easy axis upon varying the charge state of the molecule. Motivated by this report, we investigate how this switch of magnetic anisotropy influences the electron transport through the molecule, by considering sequential electron tunneling. We calculate current-voltage characteristics by solving the master equation based on the model Hamiltonians. We explore this interesting effect in the absence and presence of external magnetic field. Funding from NSF DMR-1206354.

  12. Signatures of molecular magnetism in single-molecule transport spectroscopy.

    PubMed

    Jo, Moon-Ho; Grose, Jacob E; Baheti, Kanhayalal; Deshmukh, Mandar M; Sokol, Jennifer J; Rumberger, Evan M; Hendrickson, David N; Long, Jeffrey R; Park, Hongkun; Ralph, D C

    2006-09-01

    We report single-molecule-transistor measurements on devices incorporating magnetic molecules. By studying the electron-tunneling spectrum as a function of magnetic field, we are able to identify signatures of magnetic states and their associated magnetic anisotropy. A comparison of the data to simulations also suggests that sequential electron tunneling may enhance the magnetic relaxation of the magnetic molecule. PMID:16968018

  13. Single Molecule Approaches Embrace Molecular Cohorts

    PubMed Central

    Ha, Taekjip

    2013-01-01

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

  14. Metallic conductance in single-molecule junctions

    NASA Astrophysics Data System (ADS)

    van Ruitenbeek, Jan

    2010-03-01

    Through break junction techniques it has become possible to attach metallic wires to individual molecules. The actual presence of the molecule, its identity, and the numbers of molecules involved in the transport in many cases need to be deduced from measurements of current and voltage only. In parallel, several implementations of non-equilibrium Greens function approaches in combination with density functional theory have been developed in order to compute the properties of molecular junctions. For a sensitive test of the computational models there is a need for more detailed experimental observations on well-characterized model systems. In our experiments we focus on such model systems. They are simple, small molecules which have the advantage that they are relatively easy to handle in computations and they allow for more precise experimental tests at low temperatures. The molecules we have studied include H2, H2O, CO, CO2, C6H6 (benzene), and C60 contacted between Pt leads. The molecular levels hybridize strongly with the Pt metal giving rise to a high conductance. The presence of the molecules can be confirmed by the detection of vibration modes. These modes are visible in the differential conductance, dI/dV, as a function of voltage bias as fine steps at the energies eV=φn corresponding to those of the vibration modes. Further test involve isotope-substituted molecules and stretching of the molecular bridge in order to detect shifts in the energy of the modes. The conductance of a single-molecule bridge cannot be uniquely distinguished from bridges due to several parallel channels. However, by measuring shot noise, i.e. the intrinsic noise in the electron current, it is possible to show that the current is carried by a single molecule. For other molecules the measurement gives evidence that the molecule provides two, or sometimes more channels for conductance. The results are compared with state of the art non-equilibrium DFT calculations.

  15. 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.

  16. Strongly enhanced field-dependent single-molecule electroluminescence

    PubMed Central

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

    2002-01-01

    Individual, strongly electroluminescent Agn molecules (n = 2∼8 atoms) have been electrically written within otherwise nonemissive silver oxide films. Exhibiting characteristic single-molecule behavior, these individual room-temperature molecules exhibit extreme electroluminescence enhancements (>104 vs. bulk and dc excitation on a per molecule basis) when excited with specific ac frequencies. Occurring through field extraction of electrons with subsequent reinjection and radiative recombination, single-molecule electroluminescence is enhanced by a general mechanism that avoids slow bulk material response. Thus, while we detail strong electroluminescence from single, highly fluorescent Agn molecules, this mechanism also yields strong ac-excited electroluminescence from similarly prepared, but otherwise nonemissive, individual Cu nanoclusters. PMID:12149468

  17. A gate-tunable single-molecule diode.

    PubMed

    Perrin, Mickael L; Galán, Elena; Eelkema, Rienk; Thijssen, Joseph M; Grozema, Ferdinand; van der Zant, Herre S J

    2016-04-28

    In the pursuit of down-sizing electronic components, the ultimate limit is the use of single molecules as functional devices. The first theoretical proposal of such a device, predicted more than four decades ago, is the seminal Aviram-Ratner rectifier that exploits the orbital structure of the molecule. The experimental realization of single-molecule rectifiers, however, has proven to be challenging. In this work, we report on the experimental realization of a gate-tunable single-molecule rectifier with rectification ratios as high as 600. The rectification mechanism arises from the molecular structure and relies on the presence of two conjugated sites that are weakly coupled through a saturated linker. The observed gate dependence not only demonstrates tunability of the rectification ratio, it also shows that the proposed rectification mechanism based on the orbital structure is operative in the molecule. PMID:27071686

  18. Temperature dependence of charge transport in conjugated single molecule junctions

    NASA Astrophysics Data System (ADS)

    Huisman, Eek; Kamenetska, Masha; Venkataraman, Latha

    2011-03-01

    Over the last decade, the break junction technique using a scanning tunneling microscope geometry has proven to be an important tool to understand electron transport through single molecule junctions. Here, we use this technique to probe transport through junctions at temperatures ranging from 5K to 300K. We study three amine-terminated (-NH2) conjugated molecules: a benzene, a biphenyl and a terphenyl derivative. We find that amine groups bind selectively to undercoordinate gold atoms gold all the way down to 5K, yielding single molecule junctions with well-defined conductances. Furthermore, we find that the conductance of a single molecule junction increases with temperature and we present a mechanism for this temperature dependent transport result. Funded by a Rubicon Grant from The Netherlands Organisation for Scientific Research (NWO) and the NSEC program of NSF under grant # CHE-0641523.

  19. Solution-Processable Carbon Nanoelectrodes for Single-Molecule Investigations.

    PubMed

    Zhu, Jingyuan; McMorrow, Joseph; Crespo-Otero, Rachel; Ao, Geyou; Zheng, Ming; Gillin, William P; Palma, Matteo

    2016-03-01

    Here we present a solution-based assembly method for producing molecular transport junctions employing metallic single-walled carbon nanotubes as nanoelectrodes. The molecular junction conductance of a series of oligophenyls was successfully measured, highlighting the potential of an all-carbon based approach for the fabrication of solution-processable single-molecule junctions for molecular electronics. PMID:26854787

  20. Investigations on interfacial dynamics with ultrafast electron diffraction

    NASA Astrophysics Data System (ADS)

    Murdick, Ryan A.

    An ultrafast electron diffractive voltammetry (UEDV) technique is introduced, extended from ultrafast electron diffraction, to investigate the ultrafast charge transport dynamics at interfaces and in nanostructures. Rooted in Coulomb-induced refraction, formalisms are presented to quantitatively deduce the transient surface voltages (TSVs), caused by photoinduced charge redistributions at interfaces, and are applied to examine a prototypical Si/SiO2 interface, known to be susceptible to photoinduced interfacial charging The ultrafast time resolution and high sensitivity to surface charges of this electron diffractive approach allows direct elucidation of the transient effects of photoinduced hot electron transport at nanometer (˜2 nm) interfaces. Two distinctive regimes are uncovered, characterized by the time scales associated with charge separation. At the low fluence regime, the charge transfer is described by a thermally-mediated process with linear dependence on the excitation fluence. Theoretical analysis of the transient thermal properties of the carriers show that it is well-described by a direct tunneling of the laser heated electrons through the dielectric oxide layer to surface states. At higher fluences, a coherent multiphoton absorption process is invoked to directly inject electrons into the conduction band of SiO2, leading to a more efficient surface charge accumulation. A quadratic fluence dependence on this coherent, 3-photon lead electron injection is characterized by the rapid dephasing of the intermediately generated hot electrons from 2-photon absorption, limiting the yield of the consecutive 1-photon absorption by free carriers. The TSV formalism is extended beyond the simple slab geometry associated with planar surfaces (Si/SiO2), to interfaces with arbitrary geometrical features, by imposing a corrective scheme to the slab model. The validity of this treatment is demonstrated in an investigation of the charge transfer dynamics at a metal nanoparticle/self-assembled monolayer (SAM)/semiconductor interconnected structure, allowing for the elucidation of the photo-initiated charging processes (forward and backward) through the SAM, by monitoring the deflection of the associated Bragg peaks in conjunction with the UEDV extended formalism to interpret the surface voltage. The design, calibration, and implementation of a molecular beam doser (MBD), capable of layer-by-layer coverage is also presented, with preliminary investigations on interfacial ice. With the development of UEDV and implementation of the MBD, continued investigations of charge transfer in more complex interfaces can be explored, such as those pertinent to novel solar-cell device technology, as their quantum efficiencies are usually strongly dependent on an interfacial charge transfer process. As UEDV is inherently capable of probing charge and atomic motion simultaneously, systems that exhibit phenomena that are attributable to strong coupling of the atomic and electronic degrees of freedom are of particular interest for future investigations with UEDV, such as optically induced electronic phase transitions and colossal field switching in functional oxides.

  1. Low-energy cross-section calculations of single molecules by electron impact: a classical Monte Carlo transport approach with quantum mechanical description.

    PubMed

    Madsen, J R; Akabani, G

    2014-05-01

    The present state of modeling radio-induced effects at the cellular level does not account for the microscopic inhomogeneity of the nucleus from the non-aqueous contents (i.e. proteins, DNA) by approximating the entire cellular nucleus as a homogenous medium of water. Charged particle track-structure calculations utilizing this approximation are therefore neglecting to account for approximately 30% of the molecular variation within the nucleus. To truly understand what happens when biological matter is irradiated, charged particle track-structure calculations need detailed knowledge of the secondary electron cascade, resulting from interactions with not only the primary biological component-water--but also the non-aqueous contents, down to very low energies. This paper presents our work on a generic approach for calculating low-energy interaction cross-sections between incident charged particles and individual molecules. The purpose of our work is to develop a self-consistent computational method for predicting molecule-specific interaction cross-sections, such as the component molecules of DNA and proteins (i.e. nucleotides and amino acids), in the very low-energy regime. These results would then be applied in a track-structure code and thereby reduce the homogenous water approximation. The present methodology-inspired by seeking a combination of the accuracy of quantum mechanics and the scalability, robustness, and flexibility of Monte Carlo methods-begins with the calculation of a solution to the many-body Schrödinger equation and proceeds to use Monte Carlo methods to calculate the perturbations in the internal electron field to determine the interaction processes, such as ionization and excitation. As a test of our model, the approach is applied to a water molecule in the same method as it would be applied to a nucleotide or amino acid and compared with the low-energy cross-sections from the GEANT4-DNA physics package of the Geant4 simulation toolkit for the energy ranges of 7 eV to 1 keV. PMID:24731979

  2. Interfacial electron transfer into functionalized crystalline polyoxotitanate nanoclusters.

    PubMed

    Snoeberger, Robert C; Young, Karin J; Tang, Jiji; Allen, Laura J; Crabtree, Robert H; Brudvig, Gary W; Coppens, Philip; Batista, Victor S; Benedict, Jason B

    2012-05-30

    Interfacial electron transfer (IET) between a chromophore and a semiconductor nanoparticle is one of the key processes in a dye-sensitized solar cell. Theoretical simulations of the electron transfer in polyoxotitanate nanoclusters Ti(17)O(24)(OPr(i))(20) (Ti(17)) functionalized with four p-nitrophenyl acetylacetone (NPA-H) adsorbates, of which the atomic structure has been fully established by X-ray diffraction measurements, are presented. Complementary experimental information showing IET has been obtained by EPR spectroscopy. Evolution of the time-dependent photoexcited electron during the initial 5 fs after instantaneous excitation to the NPA LUMO + 1 has been evaluated. Evidence for delocalization of the excitation over multiple chromophores after excitation to the NPA LUMO + 2 state on a 15 fs time scale is also obtained. While chromophores are generally considered electronically isolated with respect to neighboring sensitizers, our calculations show that this is not necessarily the case. The present work is the most comprehensive study to date of a sensitized semiconductor nanoparticle in which the structure of the surface and the mode of molecular adsorption are precisely defined. PMID:22548416

  3. Broadband single-molecule excitation spectroscopy

    PubMed Central

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

    2016-01-01

    Over the past 25 years, single-molecule spectroscopy has developed into a widely used tool in multiple disciplines of science. The diversity of routinely recorded emission spectra does underpin the strength of the single-molecule approach in resolving the heterogeneity and dynamics, otherwise hidden in the ensemble. In early cryogenic studies single molecules were identified by their distinct excitation spectra, yet measuring excitation spectra at room temperature remains challenging. Here we present a broadband Fourier approach that allows rapid recording of excitation spectra of individual molecules under ambient conditions and that is robust against blinking and bleaching. Applying the method we show that the excitation spectra of individual molecules exhibit an extreme distribution of solvatochromic shifts and distinct spectral shapes. Importantly, we demonstrate that the sensitivity and speed of the broadband technique is comparable to that of emission spectroscopy putting both techniques side-by-side in single-molecule spectroscopy. PMID:26794035

  4. Broadband single-molecule excitation spectroscopy

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

    Over the past 25 years, single-molecule spectroscopy has developed into a widely used tool in multiple disciplines of science. The diversity of routinely recorded emission spectra does underpin the strength of the single-molecule approach in resolving the heterogeneity and dynamics, otherwise hidden in the ensemble. In early cryogenic studies single molecules were identified by their distinct excitation spectra, yet measuring excitation spectra at room temperature remains challenging. Here we present a broadband Fourier approach that allows rapid recording of excitation spectra of individual molecules under ambient conditions and that is robust against blinking and bleaching. Applying the method we show that the excitation spectra of individual molecules exhibit an extreme distribution of solvatochromic shifts and distinct spectral shapes. Importantly, we demonstrate that the sensitivity and speed of the broadband technique is comparable to that of emission spectroscopy putting both techniques side-by-side in single-molecule spectroscopy.

  5. Broadband single-molecule excitation spectroscopy.

    PubMed

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

    2016-01-01

    Over the past 25 years, single-molecule spectroscopy has developed into a widely used tool in multiple disciplines of science. The diversity of routinely recorded emission spectra does underpin the strength of the single-molecule approach in resolving the heterogeneity and dynamics, otherwise hidden in the ensemble. In early cryogenic studies single molecules were identified by their distinct excitation spectra, yet measuring excitation spectra at room temperature remains challenging. Here we present a broadband Fourier approach that allows rapid recording of excitation spectra of individual molecules under ambient conditions and that is robust against blinking and bleaching. Applying the method we show that the excitation spectra of individual molecules exhibit an extreme distribution of solvatochromic shifts and distinct spectral shapes. Importantly, we demonstrate that the sensitivity and speed of the broadband technique is comparable to that of emission spectroscopy putting both techniques side-by-side in single-molecule spectroscopy. PMID:26794035

  6. A single-molecule diode

    PubMed Central

    Elbing, Mark; Ochs, Rolf; Koentopp, Max; Fischer, Matthias; von Hänisch, Carsten; Weigend, Florian; Evers, Ferdinand; Weber, Heiko B.; Mayor, Marcel

    2005-01-01

    We have designed and synthesized a molecular rod that consists of two weakly coupled electronic π -systems with mutually shifted energy levels. The asymmetry thus implied manifests itself in a current–voltage characteristic with pronounced dependence on the sign of the bias voltage, which makes the molecule a prototype for a molecular diode. The individual molecules were immobilized by sulfur–gold bonds between both electrodes of a mechanically controlled break junction, and their electronic transport properties have been investigated. The results indeed show diode-like current–voltage characteristics. In contrast to that, control experiments with symmetric molecular rods consisting of two identical π -systems did not show significant asymmetries in the transport properties. To investigate the underlying transport mechanism, phenomenological arguments are combined with calculations based on density functional theory. The theoretical analysis suggests that the bias dependence of the polarizability of the molecule feeds back into the current leading to an asymmetric shape of the current–voltage characteristics, similar to the phenomena in a semiconductor diode. PMID:15956208

  7. Giant single-molecule anisotropic magnetoresistance at room temperature.

    PubMed

    Li, Ji-Jun; Bai, Mei-Lin; Chen, Zhao-Bin; Zhou, Xiao-Shun; Shi, Zhan; Zhang, Meng; Ding, Song-Yuan; Hou, Shi-Min; Schwarzacher, Walther; Nichols, Richard J; Mao, Bing-Wei

    2015-05-13

    We report an electrochemically assisted jump-to-contact scanning tunneling microscopy (STM) break junction approach to create reproducible and well-defined single-molecule spintronic junctions. The STM break junction is equipped with an external magnetic field either parallel or perpendicular to the electron transport direction. The conductance of Fe-terephthalic acid (TPA)-Fe single-molecule junctions is measured and a giant single-molecule tunneling anisotropic magnetoresistance (T-AMR) up to 53% is observed at room temperature. Theoretical calculations based on first-principles quantum simulations show that the observed AMR of Fe-TPA-Fe junctions originates from electronic coupling at the TPA-Fe interfaces modified by the magnetic orientation of the Fe electrodes with respect to the direction of current flow. The present study highlights new opportunities for obtaining detailed understanding of mechanisms of charge and spin transport in molecular junctions and the role of interfaces in determining the MR of single-molecule junctions. PMID:25894840

  8. 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

  9. Binding Configurations and Intramolecular Strain in Single-Molecule Devices

    NASA Astrophysics Data System (ADS)

    Rascon-Ramos, Habid

    The development of molecular-scale electronic devices has made considerable progress over the last decade, and single-molecule transistors, diodes, and wires have all been demonstrated1,2. However, despite this remarkable progress, the agreement between theoretically predicted conductance values and those measured experimentally remains limited3. One of the primary reasons for these discrepancies is that it has been difficult to determine experimentally the contact geometry and binding configuration of a single-molecule junction. In this thesis, a small-amplitude, high frequency, sinusoidal, mechanical signal is applied to a series of single-molecule devices during junction formation and breakdown. By measuring the current response at this frequency, it is possible to obtain information about the mechanical properties of the system. From these results, it is possible to determine the most likely binding and contact configurations for the molecular junction at room temperature in solution, and to obtain information about how an applied strain is distributed within the molecular junction. These results provide new insights into the complex configuration of single-molecule devices, and are in excellent agreement with previous predictions from theoretical models 4-8. *Please refer to dissertation for footnotes.

  10. Single-Molecule Studies in Live Cells.

    PubMed

    Yu, Ji

    2016-05-27

    Live-cell single-molecule experiments are now widely used to study complex biological processes such as signal transduction, self-assembly, active trafficking, and gene regulation. These experiments' increased popularity results in part from rapid methodological developments that have significantly lowered the technical barriers to performing them. Another important advance is the development of novel statistical algorithms, which, by modeling the stochastic behaviors of single molecules, can be used to extract systemic parameters describing the in vivo biochemistry or super-resolution localization of biological molecules within their physiological environment. This review discusses recent advances in experimental and computational strategies for live-cell single-molecule studies, as well as a selected subset of biological studies that have utilized these new technologies. PMID:27070321

  11. Sample preparation for single molecule localization microscopy.

    PubMed

    Allen, John R; Ross, Stephen T; Davidson, Michael W

    2013-11-21

    Single molecule localization-based optical nanoscopy was introduced in 2006, surpassing traditional diffraction-limited resolutions by an order of magnitude. Seven years later, this superresolution technique is continuing to follow a trend of increasing popularity and pervasiveness, with the proof-of-concept work long finished and commercial implementations now available. However one important aspect that tends to become lost in translation is the importance of proper sample preparation, with very few resources addressing the considerations that must be made when preparing samples for imaging with single molecule level sensitivity. Presented here is a an in-depth analysis of all aspects of sample preparation for single molecule superresolution, including both live and fixed cell preparation, choice of fluorophore, fixation and staining techniques, and imaging buffer considerations. PMID:24084850

  12. Protein folding at single-molecule resolution

    PubMed Central

    Ferreon, Allan Chris M.; Deniz, Ashok A.

    2011-01-01

    The protein folding reaction carries great significance for cellular function and hence continues to be the research focus of a large interdisciplinary protein science community. Single-molecule methods are providing new and powerful tools for dissecting the mechanisms of this complex process by virtue of their ability to provide views of protein structure and dynamics without associated ensemble averaging. This review briefly introduces common FRET and force methods, and then explores several areas of protein folding where single-molecule experiments have yielded insights. These include exciting new information about folding landscapes, dynamics, intermediates, unfolded ensembles, intrinsically disordered proteins, assisted folding and biomechanical unfolding. Emerging and future work is expected to include advances in single-molecule techniques aimed at such investigations, and increasing work on more complex systems from both the physics and biology standpoints, including folding and dynamics of systems of interacting proteins and of proteins in cells and organisms. PMID:21303706

  13. Single molecule nanometry for biological physics

    PubMed Central

    Kim, Hajin; Ha, Taekjip

    2013-01-01

    Precision measurement is a hallmark of physics but the small length scale (~ nanometer) of elementary biological components and thermal fluctuations surrounding them challenge our ability to visualize their action. Here, we highlight the recent developments in single molecule nanometry where the position of a single fluorescent molecule can be determined with nanometer precision, reaching the limit imposed by the shot noise, and the relative motion between two molecules can be determined with ~ 0.3 nm precision at ~ 1 millisecond time resolution, and how these new tools are providing fundamental insights on how motor proteins move on cellular highways. We will also discuss how interactions between three and four fluorescent molecules can be used to measure three and six coordinates, respectively, allowing us to correlate movements of multiple components. Finally, we will discuss recent progress in combining angstrom precision optical tweezers with single molecule fluorescent detection, opening new windows for multi-dimensional single molecule nanometry for biological physics. PMID:23249673

  14. Reproducible measurement of single-molecule conductivity.

    PubMed

    Cui, X D; Primak, A; Zarate, X; Tomfohr, J; Sankey, O F; Moore, A L; Moore, T A; Gust, D; Harris, G; Lindsay, S M

    2001-10-19

    A reliable method has been developed for making through-bond electrical contacts to molecules. Current-voltage curves are quantized as integer multiples of one fundamental curve, an observation used to identify single-molecule contacts. The resistance of a single octanedithiol molecule was 900 +/- 50 megohms, based on measurements on more than 1000 single molecules. In contrast, nonbonded contacts to octanethiol monolayers were at least four orders of magnitude more resistive, less reproducible, and had a different voltage dependence, demonstrating that the measurement of intrinsic molecular properties requires chemically bonded contacts. PMID:11641492

  15. Single-molecule studies of biological molecules

    NASA Astrophysics Data System (ADS)

    Lindsay, Stuart

    2005-03-01

    Structural heterogeniety, i.e., the existence of multiple nearly-degenerate conformational substates of molecules, plays a key role in biological machinery. Therefore, in order to understand many biological processes, it is necessary to examine processes at the single molecule level. This talk will describe AFM imaging of processes involved in turning on genes (1), methods for chemically-identifying single proteins (2) and methods for wiring single molecules into electrical circuits (3). .1. H. Wang et al., Biophys. J. 87, 1964--1971 (2004). 2. C. Stroh et al., Proc. Natl. Acad. Sci. (USA) 101, 12503--12507 (2004). 3. X. D. Cui et al., Science 294, 571 (2001).

  16. Single molecule fluorescence control for nanotechnology.

    PubMed

    Rueda, David; Walter, Nils G

    2005-12-01

    Nanoscience and nanotechnology are providing fresh approaches to engineer materials with practical applications such as molecular-sized therapeutic and diagnostic devices, drug delivery vehicles, environmental sensors, high-rate manufacturing platforms, and self-assembling nanomachines. In many cases, researchers are mimicking biological systems that easily achieve molecular scale control through directed self-assembly. In parallel, a revolution has occurred in the basic sciences, which utilizes recent advances in fluorescence microscopy to achieve single molecule detection capability. The future will see a merger of these two separate research thrusts, as single molecule detection will afford optimal control over the assembly and performance of individual nanoscale devices. PMID:16430133

  17. Indistinguishable photons from a single molecule.

    PubMed

    Kiraz, A; Ehrl, M; Hellerer, Th; Müstecaplioğlu, O E; Bräuchle, C; Zumbusch, A

    2005-06-10

    We report the results of coincidence counting experiments at the output, of a Michelson interferometer using the zero-phonon-line emission of a single molecule at 1.4 K. Under continuous wave excitation, we observe the absence of coincidence counts as an indication of two-photon interference. This corresponds to the observation of Hong-Ou-Mandel correlations and proves the suitability of the zero-phonon-line emission of single molecules for applications in linear optics quantum computation. PMID:16090394

  18. Life at the Single Molecule Level

    SciTech Connect

    Xie, Xiaoliang Sunny

    2011-03-04

    In a living cell, gene expression—the transcription of DNA to messenger RNA followed by translation to protein—occurs stochastically, as a consequence of the low copy number of DNA and mRNA molecules involved. Can one monitor these processes in a living cell in real time? How do cells with identical genes exhibit different phenotypes? Recent advances in single-molecule imaging in living bacterial cells allow these questions to be answered at the molecular level in a quantitative manner. It was found that rare events of single molecules can have important biological consequences.

  19. 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 π-bonding between a phenoxy molecule and a STM-tip to form and cleave one contact to the molecule. The anchoring to the other electrode is kept stable using a chalcogen atom with strong bonding to a Cu(110) substrate. These non-destructive measurements permit us to investigate the variation in single-molecule conductance under different but controlled environmental conditions. Combined with density functional theory calculations, we clarify the role of the electrostatic field in the environmental effect that influences the molecular level alignment. PMID:26135251

  20. Controlling single-molecule junction conductance by molecular interactions

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  1. The art of catching and probing single molecules.

    PubMed

    Zandvliet, Harold J W

    2012-01-01

    Probing the electronic properties of an individual molecule is a far from trivial task. In order to measure, for instance, the conductance of a single molecule, the molecule must be contacted by two nanoscopic electrodes. Here we will give two examples of how a single molecule can be caught between two metallic electrodes. In the first example the conductance of a single octanethiol molecule is measured by trapping the molecule between an atomic Pt chain on a semiconductor surface and the apex of a scanning tunneling microscope tip. In the second example a Cu-phthalocyanine molecule is caught between two adjacent nanowires on a semiconductor surface. In this 'bridge' adsorption configuration the core of the CuPc molecule, i.e. the Cu atom, is fully decoupled from the underlying substrate. The electronic properties of the core of Cu-phthalocyanine molecule are probed with scanning tunneling spectroscopy. PMID:22546191

  2. 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.

  3. A gate-tunable single-molecule diode

    NASA Astrophysics Data System (ADS)

    Perrin, Mickael L.; Galán, Elena; Eelkema, Rienk; Thijssen, Joseph M.; Grozema, Ferdinand; van der Zant, Herre S. J.

    2016-04-01

    In the pursuit of down-sizing electronic components, the ultimate limit is the use of single molecules as functional devices. The first theoretical proposal of such a device, predicted more than four decades ago, is the seminal Aviram-Ratner rectifier that exploits the orbital structure of the molecule. The experimental realization of single-molecule rectifiers, however, has proven to be challenging. In this work, we report on the experimental realization of a gate-tunable single-molecule rectifier with rectification ratios as high as 600. The rectification mechanism arises from the molecular structure and relies on the presence of two conjugated sites that are weakly coupled through a saturated linker. The observed gate dependence not only demonstrates tunability of the rectification ratio, it also shows that the proposed rectification mechanism based on the orbital structure is operative in the molecule.In the pursuit of down-sizing electronic components, the ultimate limit is the use of single molecules as functional devices. The first theoretical proposal of such a device, predicted more than four decades ago, is the seminal Aviram-Ratner rectifier that exploits the orbital structure of the molecule. The experimental realization of single-molecule rectifiers, however, has proven to be challenging. In this work, we report on the experimental realization of a gate-tunable single-molecule rectifier with rectification ratios as high as 600. The rectification mechanism arises from the molecular structure and relies on the presence of two conjugated sites that are weakly coupled through a saturated linker. The observed gate dependence not only demonstrates tunability of the rectification ratio, it also shows that the proposed rectification mechanism based on the orbital structure is operative in the molecule. Electronic supplementary information (ESI) available: DFT calculations on the DPE molecule, three-terminal measurements on the DPE molecule, additional analysis of the single-level model, three-terminal device fabrication scheme and device characterisation, and junction statistics. See DOI: 10.1039/C6NR00735J

  4. 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.

  5. 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.

  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. Automated imaging system for single molecules

    SciTech Connect

    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.

  8. Modeling of Single Molecule Cytoplasmic Dynein

    NASA Astrophysics Data System (ADS)

    Yu, Clare

    2010-03-01

    A living cell has an infrastructure much like that of a city. We will describe the transportation system that consists of roads (filaments) and molecular motors (proteins) that haul cargo along these roads. Dynein is one type of motor protein that walks along microtubules towards the nucleus of the cell. Dynein is more complicated in its structure and function than other motors. Experiments have found that, unlike other motors, dynein can take different size steps along microtubules depending on load and ATP concentration. We use Monte Carlo simulations to model the molecular motor function of cytoplasmic dynein at the single molecule level. The theory relates dynein's enzymatic properties to its mechanical force production. Our simulations reproduce the main features of recent single molecule experiments. We make testable predictions that should guide future experiments related to dynein function.

  9. Superresolution Imaging using Single-Molecule Localization

    PubMed Central

    Patterson, George; Davidson, Michael; Manley, Suliana; Lippincott-Schwartz, Jennifer

    2013-01-01

    Superresolution imaging is a rapidly emerging new field of microscopy that dramatically improves the spatial resolution of light microscopy by over an order of magnitude (∼10–20-nm resolution), allowing biological processes to be described at the molecular scale. Here, we discuss a form of superresolution microscopy based on the controlled activation and sampling of sparse subsets of photoconvertible fluorescent molecules. In this single-molecule based imaging approach, a wide variety of probes have proved valuable, ranging from genetically encodable photoactivatable fluorescent proteins to photoswitchable cyanine dyes. These have been used in diverse applications of superresolution imaging: from three-dimensional, multicolor molecule localization to tracking of nanometric structures and molecules in living cells. Single-molecule-based superresolution imaging thus offers exciting possibilities for obtaining molecular-scale information on biological events occurring at variable timescales. PMID:20055680

  10. Lanthanide single molecule magnets: progress and perspective.

    PubMed

    Zhang, Peng; Zhang, Li; Tang, Jinkui

    2015-03-01

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

  11. Iron polyoxometalate single-molecule magnets.

    PubMed

    Compain, Jean-Daniel; Mialane, Pierre; Dolbecq, Anne; Mbomekallé, Israël Martyr; Marrot, Jérôme; Sécheresse, Francis; Rivière, Eric; Rogez, Guillaume; Wernsdorfer, Wolfgang

    2009-01-01

    Iron sandwich on a tungstate bun: Two new polyoxotungstates with paramagnetic iron(III) heteroatoms (see structure, W blue, Fe yellow, O red) possess S=15/2 and S=5 ground states. Both compounds are single-molecule magnets, and the hexairon species shows large hysteresis (see picture) and quantum tunneling effects at low temperature. Electrochemical studies indicate that these species are stable in solution for a wide range of pH values. PMID:19322857

  12. Multichannel conductance of folded single-molecule wires aided by through-space conjugation.

    PubMed

    Chen, Long; Wang, Ya-Hao; He, Bairong; Nie, Han; Hu, Rongrong; Huang, Fei; Qin, Anjun; Zhou, Xiao-Shun; Zhao, Zujin; Tang, Ben Zhong

    2015-03-27

    Deciphering charge transport through multichannel pathways in single-molecule junctions is of high importance to construct nanoscale electronic devices and deepen insight into biological redox processes. Herein, we report two tailor-made folded single-molecule wires featuring intramolecular π-π stacking interactions. The scanning tunneling microscope (STM) based break-junction technique and theoretical calculations show that through-bond and through-space conjugations are integrated into one single-molecule wire, allowing for two simultaneous conducting channels in a single-molecule junction. These folded molecules with stable π-π stacking interaction offer conceptual advances in single-molecule multichannel conductance, and are perfect models for conductance studies in biological systems, organic thin films, and π-stacked columnar aggregates. PMID:25694026

  13. 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.

  14. 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.

  15. Single molecule thermodynamics in biological motors.

    PubMed

    Taniguchi, Yuichi; Karagiannis, Peter; Nishiyama, Masayoshi; Ishii, Yoshiharu; Yanagida, Toshio

    2007-04-01

    Biological molecular machines use thermal activation energy to carry out various functions. The process of thermal activation has the stochastic nature of output events that can be described according to the laws of thermodynamics. Recently developed single molecule detection techniques have allowed each distinct enzymatic event of single biological machines to be characterized providing clues to the underlying thermodynamics. In this study, the thermodynamic properties in the stepping movement of a biological molecular motor have been examined. A single molecule detection technique was used to measure the stepping movements at various loads and temperatures and a range of thermodynamic parameters associated with the production of each forward and backward step including free energy, enthalpy, entropy and characteristic distance were obtained. The results show that an asymmetry in entropy is a primary factor that controls the direction in which the motor will step. The investigation on single molecule thermodynamics has the potential to reveal dynamic properties underlying the mechanisms of how biological molecular machines work. PMID:17320273

  16. Single-molecule sensing electrode embedded in-plane nanopore

    PubMed Central

    Tsutsui, Makusu; Rahong, Sakon; Iizumi, Yoko; Okazaki, Toshiya; Taniguchi, Masateru; Kawai, Tomoji

    2011-01-01

    Electrode-embedded nanopore is considered as a promising device structure for label-free single-molecule sequencing, the principle of which is based on nucleotide identification via transverse electron tunnelling current flowing through a DNA translocating through the pore. Yet, fabrication of a molecular-scale electrode-nanopore detector has been a formidable task that requires atomic-level alignment of a few nanometer sized pore and an electrode gap. Here, we report single-molecule detection using a nucleotide-sized sensing electrode embedded in-plane nanopore. We developed a self-alignment technique to form a nanopore-nanoelectrode solid-state device consisting of a sub-nanometer scale electrode gap in a 15 nm-sized SiO2 pore. We demonstrate single-molecule counting of nucleotide-sized metal-encapsulated fullerenes in a liquid using the electrode-integrated nanopore sensor. We also performed electrical identification of nucleobases in a DNA oligomer, thereby suggesting the potential use of this synthetic electrode-in-nanopore as a platform for electrical DNA sequencing. PMID:22355565

  17. Application of Recognition Tunneling in Single Molecule Identification

    NASA Astrophysics Data System (ADS)

    Zhao, Yanan

    Single molecule identification is one essential application area of nanotechnology. The application areas including DNA sequencing, peptide sequencing, early disease detection and other industrial applications such as quantitative and quantitative analysis of impurities, etc. The recognition tunneling technique we have developed shows that after functionalization of the probe and substrate of a conventional Scanning Tunneling Microscope with recognition molecules ("tethered molecule-pair" configuration), analyte molecules trapped in the gap that is formed by probe and substrate will bond with the reagent molecules. The stochastic bond formation/breakage fluctuations give insight into the nature of the intermolecular bonding at a single molecule-pair level. The distinct time domain and frequency domain features of tunneling signals were extracted from raw signals of analytes such as amino acids and their enantiomers. The Support Vector Machine (a machine-learning method) was used to do classification and predication based on the signal features generated by analytes, giving over 90% accuracy of separation of up to seven analytes. This opens up a new interface between chemistry and electronics with immediate implications for rapid Peptide/DNA sequencing and molecule identification at single molecule level.

  18. Single-molecule sensing electrode embedded in-plane nanopore.

    PubMed

    Tsutsui, Makusu; Rahong, Sakon; Iizumi, Yoko; Okazaki, Toshiya; Taniguchi, Masateru; Kawai, Tomoji

    2011-01-01

    Electrode-embedded nanopore is considered as a promising device structure for label-free single-molecule sequencing, the principle of which is based on nucleotide identification via transverse electron tunnelling current flowing through a DNA translocating through the pore. Yet, fabrication of a molecular-scale electrode-nanopore detector has been a formidable task that requires atomic-level alignment of a few nanometer sized pore and an electrode gap. Here, we report single-molecule detection using a nucleotide-sized sensing electrode embedded in-plane nanopore. We developed a self-alignment technique to form a nanopore-nanoelectrode solid-state device consisting of a sub-nanometer scale electrode gap in a 15 nm-sized SiO(2) pore. We demonstrate single-molecule counting of nucleotide-sized metal-encapsulated fullerenes in a liquid using the electrode-integrated nanopore sensor. We also performed electrical identification of nucleobases in a DNA oligomer, thereby suggesting the potential use of this synthetic electrode-in-nanopore as a platform for electrical DNA sequencing. PMID:22355565

  19. Silicon nanowire based single-molecule SERS sensor

    NASA Astrophysics Data System (ADS)

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

    2013-08-01

    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.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. Electronic supplementary information (ESI) available: Additional information on the experimental details, quantitative evaluation of the enhancement factor, and stability of the sensor. See DOI: 10.1039/c3nr01879b

  20. Interfacial polarization and internal electron tunneling effect on dielectric properties of multilayer polymer films

    NASA Astrophysics Data System (ADS)

    Tseng, Jung-Kai; Zhou, Zheng; Mackey, Matt; Carr, Joel; Baer, Eric; Zhu, Lei

    2013-03-01

    Due to large contrasts in dielectric constant and volumetric conductivity, Maxwell-Wagner-Sillars interfacial polarization is observed in poly(vinylidene fluoride) (PVDF) based multilayer films. This interfacial polarization is helpful to enhance the breakdown strength of multilayer films, because they serve as electron traps to prevent hot electron thermal runaway. In this study, the relationship between volumetric resistivity and internal electron tunneling in polysulfone (PSF)/(PVDF) multilayer film is reported. In general, resistivity decreases with decreasing the thickness of the insulating PSF layer. This is attributed to the internal electron tunneling in thin PSF layers. As a result, the electron-hole neutralization via the PSF layer decreases the interfacial polarization in the PVDF layer, resulting in a lower volumetric resistivity.

  1. 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.

  2. Single molecule microscopy and spectroscopy: concluding remarks.

    PubMed

    van Hulst, Niek F

    2015-01-01

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

  3. 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.

  4. Spin Manipulation by Creation of Single-Molecule Radical Cations

    NASA Astrophysics Data System (ADS)

    Karan, Sujoy; Li, Na; Zhang, Yajie; He, Yang; Hong, I.-Po; Song, Huanjun; Lü, Jing-Tao; Wang, Yongfeng; Peng, Lianmao; Wu, Kai; Michelitsch, Georg S.; Maurer, Reinhard J.; Diller, Katharina; Reuter, Karsten; Weismann, Alexander; Berndt, Richard

    2016-01-01

    All-trans-retinoic acid (ReA), a closed-shell organic molecule comprising only C, H, and O atoms, is investigated on a Au(111) substrate using scanning tunneling microscopy and spectroscopy. In dense arrays single ReA molecules are switched to a number of states, three of which carry a localized spin as evidenced by conductance spectroscopy in high magnetic fields. The spin of a single molecule may be reversibly switched on and off without affecting its neighbors. We suggest that ReA on Au is readily converted to a radical by the abstraction of an electron.

  5. Hybrid photodetector for single-molecule spectroscopy and microscopy

    NASA Astrophysics Data System (ADS)

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

    2008-02-01

    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.

  6. Theoretical investigation on single-molecule chiroptical spectroscopy

    SciTech Connect

    Wakabayashi, M.; Yokojima, S.; Fukaminato, T.; Ogata, K.; Nakamura, S.

    2013-12-10

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

  7. Spin coherence in a Mn3 single-molecule magnet

    NASA Astrophysics Data System (ADS)

    Abeywardana, Chathuranga; Mowson, Andrew M.; Christou, George; Takahashi, Susumu

    2016-01-01

    Spin coherence in single crystals of the spin S = 6 single-molecule magnet (SMM) [Mn3O(O2CEt)3(mpko)3]+ (abbreviated Mn3) has been investigated using 230 GHz electron paramagnetic resonance spectroscopy. Coherence in Mn3 was uncovered by significantly suppressing dipolar contribution to the decoherence with complete spin polarization of Mn3 SMMs. The temperature dependence of spin decoherence time (T2) revealed that the dipolar decoherence is the dominant source of decoherence in Mn3 and T2 can be extended up to 267 ns by quenching the dipolar decoherence.

  8. 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

  9. Single-molecule studies of collagen mechanics

    NASA Astrophysics Data System (ADS)

    Forde, Nancy; Rezaei, Naghmeh; Kirkness, Michael

    Collagen is the fundamental structural protein in vertebrates. Its triple helical structure at the molecular level is believed to be strongly related to its mechanical role in connective tissues. However, the mechanics of collagen at the single-molecule level remain contentious. Estimates of its persistence length span an order of magnitude, from 15-180 nm for this biopolymer of 300 nm contour length. How collagen responds to applied force is also controversial, with different single-molecule studies suggesting one of three different responses: extending entropically, overwinding, or unwinding, all at forces below 10 pN. Using atomic force microscopy to image collagens deposited from solution, we find that their flexibility depends strongly on ionic strength and pH. To study force-dependent structural changes, we are performing highly parallelized enzymatic cleavage assays of triple helical collagen in our new compact centrifuge force microscope. Because proteolytic cleavage requires a locally unwound triple helix, these experiments are revealing how local collagen structure changes in response to applied force. Our results can help to resolve long-standing debates about collagen mechanics and structure at the molecular level.

  10. Photobleaching Pathways in Single Molecule FRET Experiments

    PubMed Central

    Kong, Xiangxu; Nir, Eyal; Hamadani, Kambiz; Weiss, Shimon

    2008-01-01

    In order to acquire accurate structural and dynamical information on complex biomolecular machines using single-molecule fluorescence resonance energy transfer (sm-FRET), a large flux of donor and acceptor photons are needed. To achieve such fluxes one may use higher laser excitation intensity, however this induces increased rates of photobleaching. Anti-oxidants additives have been extensively used for reducing acceptor’s photobleaching. Here we focus on deciphering the initial step along the photobleaching pathway. Utilizing an array of recently-developed single molecule and ensemble spectroscopies, and doubly-labeled Acyl-CoA binding protein and double-stranded DNA as model systems, we study these photobleaching pathways which place fundamental limitations on sm-FRET experiments. We find that: (i) acceptor photobleaching scales with FRET efficiency; (ii) acceptor photobleaching is enhanced under picosecond pulsed (vs. continuous wave) excitation; and (iii) acceptor photobleaching scales with the intensity of only the short wavelength (donor) excitation laser. We infer from these findings that the main pathway for acceptor’s photobleaching is through absorption of a short wavelength photon from the acceptor’s first excited singlet state and that donor’s photobleaching is usually not a concern. We conclude by suggesting using short pulses for donor excitation, among other possible remedies, for reducing acceptor’s photobleaching in sm-FRET measurements. PMID:17375921

  11. Electric field breakdown in single molecule junctions.

    PubMed

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

    2015-04-22

    Here we study the stability and rupture of molecular junctions under high voltage bias at the single molecule/single bond level using the scanning tunneling microscope-based break-junction technique. We synthesize carbon-, silicon-, and germanium-based molecular wires terminated by aurophilic linker groups and study how the molecular backbone and linker group affect the probability of voltage-induced junction rupture. First, we find that junctions formed with covalent S-Au bonds are robust under high voltage and their rupture does not demonstrate bias dependence within our bias range. In contrast, junctions formed through donor-acceptor bonds rupture more frequently, and their rupture probability demonstrates a strong bias dependence. Moreover, we find that the junction rupture probability increases significantly above ∼1 V in junctions formed from methylthiol-terminated disilanes and digermanes, indicating a voltage-induced rupture of individual Si-Si and Ge-Ge bonds. Finally, we compare the rupture probabilities of the thiol-terminated silane derivatives containing Si-Si, Si-C, and Si-O bonds and find that Si-C backbones have higher probabilities of sustaining the highest voltage. These results establish a new method for studying electric field breakdown phenomena at the single molecule level. PMID:25675085

  12. Single Molecule and Single Cell Epigenomics

    PubMed Central

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

    2014-01-01

    Dynamically regulated changes in chromatin states are vital for normal development and can produce disease when they go awry. Accordingly, much effort has been devoted to characterizing these states under normal and pathological conditions. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the most widely used method to characterize where in the genome transcription factors, modified histones, modified nucleotides and chromatin binding proteins are found; bisulfite sequencing (BS-seq) and its variants are commonly used to characterize the locations of DNA modifications. Though very powerful, these methods are not without limitations. Notably, they are best at characterizing one chromatin feature at a time, yet chromatin features arise and function in combination. Investigators commonly superimpose separate ChIP-seq or BS-seq datasets, and then infer where chromatin features are found together. While these inferences might be correct, they can be misleading when the chromatin source has distinct cell types, or when a given cell type exhibits any cell to cell variation in chromatin state. These ambiguities can be eliminated by robust methods that directly characterize the existence and genomic locations of combinations of chromatin features in very small inputs of cells or ideally, single cells. Here we review single molecule epigenomic methods under development to overcome these limitations, the technical challenges associated with single molecule methods and their potential application to single cells. PMID:25204781

  13. 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 Krstić 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 Single-molecule conductance determinations on HS(CH2)4O(CH2)4SH and HS(CH2)2O(CH2)2O(CH2)2SH, and comparison with alkanedithiols of the same lengthLisa E Scullion, Edmund Leary, Simon J Higgins and Richard J Nichols Metal atomic contact under electrochemical potential controlManabu Kiguchi and Kei Murakoshi Rectification in substituted atomic wires: a theoretical insightYoshihiro Asai High-fidelity chemical patterning on oxide-free germaniumJ Nathan Hohman, Moonhee Kim, Jeffrey A Lawrence, Patrick D McClanahan and Paul S Weiss

  14. Theory of single molecule emission spectroscopy

    SciTech Connect

    Bel, Golan; Brown, Frank L. H.

    2015-05-07

    A general theory and calculation framework for the prediction of frequency-resolved single molecule photon counting statistics is presented. Expressions for the generating function of photon counts are derived, both for the case of naive “detection” based solely on photon emission from the molecule and also for experimentally realizable detection of emitted photons, and are used to explicitly calculate low-order photon-counting moments. The two cases of naive detection versus physical detection are compared to one another and it is demonstrated that the physical detection scheme resolves certain inconsistencies predicted via the naive detection approach. Applications to two different models for molecular dynamics are considered: a simple two-level system and a two-level absorber subject to spectral diffusion.

  15. Single-Molecule Gold-Nanoparticle Tracking

    PubMed Central

    Dunn, Alexander R.; Spudich, James A.

    2016-01-01

    Gold nanoparticles, like single fluorophores, can be used to locate single molecules with nanometer accuracy. Unlike an optical trap, the gold particle label does not exert an external load, which is important for studying diffusive processes. Thus, a gold particle can be used analogously to a single fluorophore, providing similar information but with submillisecond time resolution. The features of gold-nanoparticle tracking (high temporal resolution, small label size, and lack of applied force) facilitate the characterization of structural properties of short-lived intermediates, as shown by our work with myosin V. This protocol provides details for gold-nanoparticle-tracking experiments, including flow cell construction, microscopy, and data analysis, along with a brief outline of actin and myosin preparation. Although details particular to our experiment are given, the approach should be generally applicable. PMID:22135665

  16. Single-molecule studies using magnetic traps.

    PubMed

    Lionnet, Timothée; Allemand, Jean-François; Revyakin, Andrey; Strick, Terence R; Saleh, Omar A; Bensimon, David; Croquette, Vincent

    2012-01-01

    In recent years, techniques have been developed to study and manipulate single molecules of DNA and other biopolymers. In one such technique, the magnetic trap, a single DNA molecule is bound at one end to a glass surface and at the other to a magnetic microbead. Small magnets, whose position and rotation can be controlled, pull on and rotate the microbead. This provides a simple method to stretch and twist the molecule. The system allows one to apply and measure forces ranging from 10(-3) to >100 pN. In contrast to other techniques, the force measurement is absolute and does not require calibration of the sensor. In this article, we describe the principle of the magnetic trap, as well as its use in the measurement of the elastic properties of DNA and the study of DNA-protein interactions. PMID:22194259

  17. Single-molecule spectroscopy using microfluidic platforms.

    PubMed

    Kim, Samuel; Zare, Richard N

    2010-01-01

    Microfluidics serves as a convenient platform for single-molecule experiments by providing manipulation of small amounts of liquids and micron-sized particles. An adapted version of capillary electrophoresis (CE) on a microchip can be utilized to separate chemical species with high resolution based on their ionic mobilities (i.e., charges and sizes), but identification of separated species is not trivial, especially for complex mixtures of sticky biomolecules. We describe here how to use a surfactant mixture system for CE on a poly(dimethylsiloxane) (PDMS) microchip, capture separated peaks within a 50-pl chamber using microvalves, analyze the fluorescence signals with correlation spectroscopy to extract molecular diffusion characteristics, and to identify the biomolecular clusters in a model immunocomplex system. PMID:20580962

  18. Variation in the Single-Molecule Conductance of Oligothiophenes

    NASA Astrophysics Data System (ADS)

    Capozzi, Brian; Dell, Emma; Dubay, Kateri; Moreno, Jose; Berkelbach, Timothy; Reichman, David; Campos, Luis; Venkataraman, Latha

    2013-03-01

    Thiophenes are ubiquitous in organic electronic and photovoltaic applications; yet, they have received minimal attention in single molecule transport studies. Here, we carry out single molecule conductance measurements on a family of methyl sulfide-terminated oligothiophenes using the scanning tunneling microscope based break-junction technique. We find a non-exponential decay in conductance with the number of thiophene units (2 through 6) in the chain, which cannot be explained by a simple tunneling or hopping mechanism. We also find that the oligothiophenes exhibit a rather broad conductance distribution when compared to oligophenyls. Using a combination of experiment and molecular dynamics simulations, we show that this increased breadth is most likely due to different thiophene confomers sampled in the experiments, which do not necessarily maintain conjugation along the backbone. These measurements therefore reinforce the importance of conformation and conjugation effects in thiophene-based organic electronic devices where highly conducting molecular components are required. The experimental work was funded by NSF-DMR-1206202 and the theory was funded by the EFRC program of the U.S. Department of Energy under Award No. DESC0001085.

  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. High throughput single molecule detection for monitoring biochemical reactions.

    PubMed

    Okagbare, Paul I; Soper, Steven A

    2009-01-01

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

  1. Bringing single-molecule spectroscopy to macromolecular protein complexes

    PubMed Central

    Joo, Chirlmin; Fareh, Mohamed; Kim, V. Narry

    2013-01-01

    Single-molecule fluorescence spectroscopy offers real-time, nanometer-resolution information. Over the past two decades, this emerging single-molecule technique has been rapidly adopted to investigate the structural dynamics and biological functions of proteins. Despite this remarkable achievement, single-molecule fluorescence techniques must be extended to macromolecular protein complexes that are physiologically more relevant for functional studies. In this review, we present recent major breakthroughs for investigating protein complexes within cell extracts using single-molecule fluorescence. We outline the challenges, future prospects and potential applications of these new single-molecule fluorescence techniques in biological and clinical research. PMID:23200186

  2. Single-Molecule STM Studies on Atomically-Flat Nanoparticles

    NASA Astrophysics Data System (ADS)

    Dahayanaka, D. H.; Kelle, D. W.; Wasielewski, D. J.; Day, E. S.; White, D. R.; Bumm, L. A.; Waite, C. M.; Moore, J. L.; Halterman, R. L.

    2006-03-01

    The scanning tunneling microscope (STM) has been broadly applied to measure electronic characteristics of individual molecules supported in an inert monolayer matrix, which is typically grown on gold thin films on mica or bulk single crystal substrates. Although these substrates are excellent for electronic measurements, they have serious disadvantages for optical measurements because they are not optically transparent and the metal surface can quench the molecular excited state. We demonstrate that single molecule electronic measurements can also be performed using atomically-flat gold nanoparticles (FGNPs) supported on indium tin oxide coated glass as a replacement for the typical gold substrate. These substrates are optically transparent and each of the FGNP ``nanosubstrates'' is an optically resonant photonic antenna, thus they have the added advantage that optical measurements can be performed.

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

    PubMed

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

    2016-01-13

    Structure, dynamics, and coupling involving single-molecules determine function in catalytic, electronic or biological systems. While vibrational spectroscopy provides insight into molecular structure, rapid fluctuations blur the molecular trajectory even in single-molecule spectroscopy, analogous to spatial averaging in measuring large ensembles. To gain insight into intramolecular coupling, substrate coupling, and dynamic processes, we use tip-enhanced Raman spectroscopy (TERS) at variable and cryogenic temperatures, to slow and control the motion of a single molecule. We resolve intrinsic line widths of individual normal modes, allowing detailed and quantitative investigation of the vibrational modes. From temperature dependent line narrowing and splitting, we quantify ultrafast vibrational dephasing, intramolecular coupling, and conformational heterogeneity. Through statistical correlation analysis of fluctuations of individual modes, we observe rotational motion and spectral fluctuations of the molecule. This work demonstrates single-molecule vibrational spectroscopy beyond chemical identification, opening the possibility for a complete picture of molecular motion ranging from femtoseconds to minutes. PMID:26679007

  4. Theoretical/Computational Probes of Homogeneous and Interfacial Electron Transfer: Electronic Structure and Energetics

    NASA Astrophysics Data System (ADS)

    Newton, Marshall

    2008-03-01

    Theoretical and computational techniques are used to elucidate the physical and chemical factors that control the kinetics of homogeneous and interfacial electron-transfer (ET) reactions. These latter include systems for which standard rate constants (k^0(l)) have been measured electrochemically for ET between substrate Au electrodes and redox couples attached to the electrode surfaces by variable lengths (l) of oligomethylene (OM), oligophenylenevinylene (OPV) and oligophenyleneethynylene (OPE) bridges. These oligomers, spanning a range of ˜ 1-4 nm, are components of mixed self-assembled monolayers (SAMs), coupled to the substrate via S atom linkers. The mechanistic analysis of the kinetic behavior, including polaron-based activation and electronic tunneling, is supported by calculations of electronic structure and molecular and medium energetics. Band structure calculations for neat phenylthiolate SAMs on Au and Cu susbstrates were used to probe the properties of the interface, including surface dipole layer and work function, the electronic nature of the `thiolate' linker atoms, and the competition between direct and substrate-mediated coupling.

  5. Detection of Steps in Single Molecule Data

    PubMed Central

    Aggarwal, Tanuj; Materassi, Donatello; Davison, Robert; Hays, Thomas; Salapaka, Murti

    2013-01-01

    Over the past few decades, single molecule investigations employing optical tweezers, AFM and TIRF microscopy have revealed that molecular behaviors are typically characterized by discrete steps or events that follow changes in protein conformation. These events, that manifest as steps or jumps, are short-lived transitions between otherwise more stable molecular states. A major limiting factor in determining the size and timing of the steps is the noise introduced by the measurement system. To address this impediment to the analysis of single molecule behaviors, step detection algorithms incorporate large records of data and provide objective analysis. However, existing algorithms are mostly based on heuristics that are not reliable and lack objectivity. Most of these step detection methods require the user to supply parameters that inform the search for steps. They work well, only when the signal to noise ratio (SNR) is high and stepping speed is low. In this report, we have developed a novel step detection method that performs an objective analysis on the data without input parameters, and based only on the noise statistics. The noise levels and characteristics can be estimated from the data providing reliable results for much smaller SNR and higher stepping speeds. An iterative learning process drives the optimization of step-size distributions for data that has unimodal step-size distribution, and produces extremely low false positive outcomes and high accuracy in finding true steps. Our novel methodology, also uniquely incorporates compensation for the smoothing affects of probe dynamics. A mechanical measurement probe typically takes a finite time to respond to step changes, and when steps occur faster than the probe response time, the sharp step transitions are smoothed out and can obscure the step events. To address probe dynamics we accept a model for the dynamic behavior of the probe and invert it to reveal the steps. No other existing method addresses the impact of probe dynamics on step detection. Importantly, we have also developed a comprehensive set of tools to evaluate various existing step detection techniques. We quantify the performance and limitations of various step detection methods using novel evaluation scales. We show that under these scales, our method provides much better overall performance. The method is validated on different simulated test cases, as well as experimental data. PMID:23956798

  6. 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

  7. Single-Molecule Investigations of RNA Dissociation

    PubMed Central

    Green, Nicola H.; Williams, Philip M.; Wahab, Omar; Davies, Martyn C.; Roberts, Clive J.; Tendler, Saul J. B.; Allen, Stephanie

    2004-01-01

    Given the essential cellular roles for ribonucleic acids (RNAs) it is important to understand the stability of three-dimensional structures formed by these molecules. This study aims to investigate the dissociation energy landscape for simple RNA structures via atomic-force-microscopy-based single-molecule force-spectroscopy measurements. This approach provides details on the locations and relative heights of the energy barriers to dissociation, and thus information upon the relative kinetic stabilities of the formed complexes. Our results indicate that a simple dodecamer RNA helix undergoes a forced dissociation process similar to that previously observed for DNA oligonucleotides. Incorporating a UCU bulge motif is found to introduce an additional energy barrier closer to the bound state, and also to destabilize the duplex. In the absence of magnesium ions a duplex containing this UCU bulge is destabilized and a single, shorter duplex is formed. These results reveal that a bulge motif impacts upon the forced dissociation of RNA and produces an energy landscape sensitive to the presence of magnesium ions. Interestingly, the obtained data compare well with previously reported ensemble measurements, illustrating the potential of this approach to improve our understanding of RNA stability and dissociation kinetics. PMID:15189877

  8. Single molecule force spectroscopy of asphaltene aggregates.

    PubMed

    Long, Jun; Xu, Zhenghe; Masliyah, Jacob H

    2007-05-22

    Asphaltene aggregation and deposition cause severe problems in nearly all phases of petroleum processing. To resolve those problems, understanding the aggregation mechanisms is a prerequisite and has attracted the interest of a great number of investigators. However, to date, the nature and extent of asphaltene aggregation remain widely debated. In the present study, we attempt to investigate asphaltene aggregation from a completely new perspective. The technique of single molecule force spectroscopy (SMFS) was used to investigate the response of single asphaltene aggregates under an external pulling force. Force curves representing the stretching of single asphaltene aggregates were obtained in simple electrolyte solutions (KCl and calcium) and organic solvents (toluene and heptane). These force curves were well-fitted by the modified worm-like chain model, indicating that those asphaltene aggregates acted like long-chain polymers under pulling by an external force. It was found that lower solution pH values and the presence of divalent cations resulted in a lower bending rigidity of the formed aggregates. The information retrieved from the force curves suggests that asphaltene molecules with a structure featuring small aromatic clusters connected by aliphatic chains do exist and that asphaltene aggregation could occur through a linear polymerization mechanism. The current study extends the application scope of SMFS. PMID:17441741

  9. Correlated Fluorescence Parameters of Single Molecules

    NASA Astrophysics Data System (ADS)

    Gradinaru, Claudiu; Chandler, David; Hayden, Carl

    2007-03-01

    A novel detection system is used in a confocal optical microscope for measuring correlated fluorescence lifetimes and spectra. Fluorescence photons emitted from a sample are imaged through a dispersive optical system onto a time- and position-sensitive detector. For each photon the apparatus records the wavelength, the emission time relative to the laser excitation pulse and the absolute detection time, so that correlations among all the fluorescence properties are maintained. A histogram over many photons can generate a full fluorescence spectrum and a correlated decay plot at every pixel in a fluorescence image. The complex data structure allows mapping the time-dependent distribution of multiple fluorescent species in a sample and enables monitoring the dynamics of single molecules on a time scale that spans from picoseconds to minutes. Unique correlations between intensity, spectrum and lifetime prove useful for tracking changes in the nanoenvironment of fluorescent probes. The detection method also provides a more complete description of the fluorescence resonance energy transfer (FRET) than conventional microscopy techniques, as demonstrated by single-pair FRET experiments between dyes spaced apart by short peptides and by dsDNA chains.

  10. Single-Molecule Manipulation Using Optical Traps

    NASA Astrophysics Data System (ADS)

    Woodside, Michael T.; Valentine, Megan T.

    One of the most sensitive tools for manipulating single molecules and measuring their properties is the optical trap, also known as optical tweezers. Consisting essentially of a strongly focused light beam, optical traps were first developed and demonstrated in the 1970s and 1980s by Arthur Ashkin and colleagues (Ashkin et al. 1986). These early pioneers showed that micron-sized dielectric particles could be held and manipulated in solution by using optical forces to create a stable, three-dimensional potential well. Since then, optical trapping instrumentation has been refined and developed such that piconewton forces are now routinely applied, while at the same time measuring the resultant displacements to nanometre or even angström resolution. As a result of these advances, optical traps have been applied widely, from cytometry to the study of mesoscopic colloids and polymers and of course the properties of single biological macromolecules. This chapter begins with a description of the theory and design of optical traps, followed by an illustrative discussion of applications to the study of structure formation and molecular motors, a description of typical "tricks of the trade" for using optical traps, and a brief look at techniques for extending the capabilities of traps.

  11. Theory of the Control of Ultrafast Interfacial Electron Transfer

    NASA Astrophysics Data System (ADS)

    Rasmussen, Andrew Musso

    This dissertation describes the theoretial exploration of electron transfer (ET) processes at the interface between bulk and molecular or nanoscale materials. Analysis of simple model Hamiltonians, those for the two- and three-level electronic systems as well as for a single electronic level coupled to a continuum, inform an understanding of electron transfer in nontrivial systems. A new treatment of the three-level system at an undergraduate level encapsulates the hopping and superexchange mechanisms of electron transfer. The elegance of the behavior of ET from a single-level/continuum system precedes a treatment of the reverse process---quasicontinuum-to-discrete level ET. This reverse process, relevant to ET from a bulk material to a semiconductor quantum dot (QD) offers a handle for the coherent control of ET at an interface: the shape of an electronic wavepacket within the quasicontinuum. An extension of the single-level-to-continuum ET process is the injection of an electron from a QD to a wide-bandgap semiconductor nanoparticle (NP). We construct a minimal model to explain trends in ET rates at the QD/NP interface as a function of QD size. Finally, we propose a scheme to gate ET through a molecular junction via the coherent control of the torsional mode(s) of a linking molecule within the junction.

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  13. Microarray analysis at single molecule resolution

    PubMed Central

    Mureşan, Leila; Jacak, Jarosław; 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

  14. 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.

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

    PubMed Central

    2013-01-01

    At scales below micrometers, Brownian motion dictates most of the behaviors. The simple observation of a colloid is striking: a permanent and random motion is seen, whereas inertial forces play a negligible role. This Physics, where velocity is proportional to force, has opened new horizons in biology. The random feature is challenged in living systems where some proteins - molecular motors - have a directed motion whereas their passive behaviors of colloid should lead to a Brownian motion. Individual proteins, polymers of living matter such as DNA, RNA, actin or microtubules, molecular motors, all these objects can be viewed as chains of colloids. They are submitted to shocks from molecules of the solvent. Shapes taken by these biopolymers or dynamics imposed by motors can be measured and modeled from single molecules to their collective effects. Thanks to the development of experimental methods such as optical tweezers, Atomic Force Microscope (AFM), micropipettes, and quantitative fluorescence (such as Förster Resonance Energy Transfer, FRET), it is possible to manipulate these individual biomolecules in an unprecedented manner: experiments allow to probe the validity of models; and a new Physics has thereby emerged with original biological insights. Theories based on statistical mechanics are needed to explain behaviors of these systems. When force-extension curves of these molecules are extracted, the curves need to be fitted with models that predict the deformation of free objects or submitted to a force. When velocity of motors is altered, a quantitative analysis is required to explain the motions of individual molecules under external forces. This lecture will give some elements of introduction to the lectures of the session 'Nanophysics for Molecular Biology'. PMID:24565227

  16. 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

  17. n and p type character of single molecule diodes

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

  18. 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.

  19. 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 several components of a DSSC or water oxidation cell in addition to the sensitizer and metal oxide. Performing TRTS studies on fully assembled devices will therefore be essential for determining the relationship between electron injection and device efficiency.

  20. 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.

  1. Interfacial electronic charge transfer and density of states in short period Cu/Cr multilayers

    SciTech Connect

    Bello, A.F.; Van Buuren, T.; Kepesis, J.E.; Barbee, T.W., Jr.

    1998-04-01

    Nanometer period metallic multilayers are ideal structures to investigate electronic phenomena at interfaces between metal films since interfacial atoms comprise a large atomic fraction of the samples. The multilayers studied were fabricated by magnetron sputtering and consist of bilayers from 1.9 mn to 3.3 mn. X-ray diffraction, cross-section TEM and plan-view TEM show the Cu layers to have a BCC structure Cu in contrast to its equilibrium FCC structure. The electronic structure of the Cu and the Cr layers in several samples of thin Cu/Cr multilayers were studied using x-ray absorption spectroscopy (XAS). Total electron yield was measured and used to study the white lines at the Cu L{sub 2} and L{sub 3} absorption edges. The white lines at the Cu absorption edges are strongly related to the unoccupied d-orbitals and are used to calculate the amount of charge transfer between the Cr and Cu atoms in interfaces. Analysis of the Cu white lines show a charge transfer of 0.026 electrons/interfacial Cu atom to the interfacial Cr atoms. In the Cu XAS spectra we also observe a van Hove singularity between the L{sub 2} and L{sub 3} absorption edges as expected from the structural analysis. The absorption spectra are compared to partial density of states obtained from a full-potential linear muffin-tin orbital calculation. The calculations confirm the presence of charge transfer and indicate that it is localized to the first two interfacial layers in both Cu and Cr.

  2. Microscopes for Fluorimeters: The Era of Single Molecule Measurements

    PubMed Central

    Vale, Ronald D.

    2009-01-01

    As transforming as the first atomic resolution view of myoglobin in the late 1950s, scientists can now use a suite of single molecule technologies to watch protein macromolecular machines executing their functions “in real time.” This Essay highlights applications and challenges of single molecule studies in structural biology, cell biology, and biotechnology. PMID:19041739

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

    PubMed

    Jadhav, Vivek S; Brüggemann, Dorothea; Wruck, Florian; Hegner, Martin

    2016-01-01

    DNA handles are often used as spacers and linkers in single-molecule experiments to isolate and tether RNAs, proteins, enzymes and ribozymes, amongst other biomolecules, between surface-modified beads for nanomechanical investigations. Custom DNA handles with varying lengths and chemical end-modifications are readily and reliably synthesized en masse, enabling force spectroscopic measurements with well-defined and long-lasting mechanical characteristics under physiological conditions over a large range of applied forces. Although these chemically tagged DNA handles are widely used, their further individual modification with protein receptors is less common and would allow for additional flexibility in grabbing biomolecules for mechanical measurements. In-depth information on reliable protocols for the synthesis of these DNA-protein hybrids and on their mechanical characteristics under varying physiological conditions are lacking in literature. Here, optical tweezers are used to investigate different protein-labelled DNA handles in a microfluidic environment under different physiological conditions. Digoxigenin (DIG)-dsDNA-biotin handles of varying sizes (1000, 3034 and 4056 bp) were conjugated with streptavidin or neutravidin proteins. The DIG-modified ends of these hybrids were bound to surface-modified polystyrene (anti-DIG) beads. Using different physiological buffers, optical force measurements showed consistent mechanical characteristics with long dissociation times. These protein-modified DNA hybrids were also interconnected in situ with other tethered biotinylated DNA molecules. Electron-multiplying CCD (EMCCD) imaging control experiments revealed that quantum dot-streptavidin conjugates at the end of DNA handles remain freely accessible. The experiments presented here demonstrate that handles produced with our protein-DNA labelling procedure are excellent candidates for grasping single molecules exposing tags suitable for molecular recognition in time-critical molecular motor studies. PMID:26925362

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

    PubMed Central

    Wruck, Florian

    2016-01-01

    Summary DNA handles are often used as spacers and linkers in single-molecule experiments to isolate and tether RNAs, proteins, enzymes and ribozymes, amongst other biomolecules, between surface-modified beads for nanomechanical investigations. Custom DNA handles with varying lengths and chemical end-modifications are readily and reliably synthesized en masse, enabling force spectroscopic measurements with well-defined and long-lasting mechanical characteristics under physiological conditions over a large range of applied forces. Although these chemically tagged DNA handles are widely used, their further individual modification with protein receptors is less common and would allow for additional flexibility in grabbing biomolecules for mechanical measurements. In-depth information on reliable protocols for the synthesis of these DNA–protein hybrids and on their mechanical characteristics under varying physiological conditions are lacking in literature. Here, optical tweezers are used to investigate different protein-labelled DNA handles in a microfluidic environment under different physiological conditions. Digoxigenin (DIG)-dsDNA-biotin handles of varying sizes (1000, 3034 and 4056 bp) were conjugated with streptavidin or neutravidin proteins. The DIG-modified ends of these hybrids were bound to surface-modified polystyrene (anti-DIG) beads. Using different physiological buffers, optical force measurements showed consistent mechanical characteristics with long dissociation times. These protein-modified DNA hybrids were also interconnected in situ with other tethered biotinylated DNA molecules. Electron-multiplying CCD (EMCCD) imaging control experiments revealed that quantum dot–streptavidin conjugates at the end of DNA handles remain freely accessible. The experiments presented here demonstrate that handles produced with our protein–DNA labelling procedure are excellent candidates for grasping single molecules exposing tags suitable for molecular recognition in time-critical molecular motor studies. PMID:26925362

  5. 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

  6. Analyzing Single-Molecule Time Series via Nonparametric Bayesian Inference

    PubMed Central

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

    2015-01-01

    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

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

    PubMed

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

    2015-01-01

    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

  8. 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

  9. 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

  10. 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

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

    SciTech Connect

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

    2015-06-01

    We demonstrate that electronic transport through single molecules or molecular ensembles, commonly based on gold (Au) electrodes, can be extended to superconducting electrodes by combining gold with molybdenum-rhenium (MoRe). This combination induces proximity-effect superconductivity in the gold to temperatures of at least 4.6 K and magnetic fields of 6 T, improving on previously reported aluminum based superconducting nanojunctions. As a proof of concept, we show three-terminal superconductive transport measurements through an individual Fe{sub 4} single-molecule magnet.

  12. Evidence on single-molecule transport in electrostatically-gated molecular transistors

    NASA Astrophysics Data System (ADS)

    Bldea, Ioan; Kppel, Horst

    2012-03-01

    We show that, if adequately formulated for molecular electronics, the barrier picture can quantitatively reproduce the currents and describe the orbital gating in the molecular transistors fabricated by Song et al. [H. Song, Y. Kim, Y.H. Jang, H. Jeong, M.A. Reed, T. Lee, Nature 462 (2009) 1039]. Based on our results, we demonstrate (i) that the measured current represents the contribution of a single molecule, and (ii) the linear dependence of the molecular orbital energy offset ?g on the voltage Vt at the Fowler-Nordheim minimum, validating thereby the transition voltage spectroscopy for the gated single molecule devices of Song et al.

  13. 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.

  14. 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.

  15. Single-molecule redox blinking of perylene diimide derivatives in water.

    PubMed

    Cordes, Thorben; Vogelsang, Jan; Anaya, Milena; Spagnuolo, Carla; Gietl, Andreas; Summerer, Wolfram; Herrmann, Andreas; Müllen, Klaus; Tinnefeld, Philip

    2010-02-24

    Dynamic developments in ultrasensitive and superresolution fluorescence microscopy call for improved fluorescence markers with increased photostability and new functionalities. We used single-molecule spectroscopy to study water-soluble perylene dicarboximide fluorophores (PDI), which were immobilized in aqueous buffer by attaching the fluorophore to DNA. Under these conditions bright fluorescence, comparable to that of single-molecule compatible organic fluorophores, is observed with homogeneous spectral and fluorescence decay time distributions. We additionally show how the fluorescence of the PDI can be controlled through photoinduced electron-transfer reactions by using different concentrations of reductants and oxidants, yielding either blinking or stable emission. We explain these properties by the redox potentials of PDI and the recently introduced ROXS (reducing and oxidizing system) concept. Finally, we evaluate how this fluorescence control of PDIs can be used for superresolution "Blink-Microscopy" in aqueous or organic media and more generally for single-molecule spectroscopy. PMID:20121094

  16. Synthesis of 1,2-biphenylethane based single-molecule diodes.

    PubMed

    Galán, Elena; Perrin, Mickael L; Lutz, Martin; van der Zant, Herre S J; Grozema, Ferdinand C; Eelkema, Rienk

    2016-02-16

    We have described the synthesis of novel biphenylethane-based wires for molecular electronics. Exceptional single-molecule diode behavior was predicted for unsymmetrically substituted biphenylethane derivatives, synthesized here using the so far unexplored unsymmetrically substituted 1,2-bis(4-bromophenyl)ethanes as key intermediates, which were obtained from the corresponding tolane precursor by selective hydrogenation. PMID:26809645

  17. Probing interfacial electron dynamics with time-resolved X-ray spectroscopy

    NASA Astrophysics Data System (ADS)

    Neppl, Stefan

    2015-05-01

    Time-resolved core-level spectroscopy techniques using laser pulses to initiate and short X-ray pulses to probe photo-induced processes have the potential to provide electronic state- and atomic site-specific insight into fundamental electron dynamics at complex interfaces. We describe the implementation of femto- and picosecond time-resolved photoelectron spectroscopy at the Linac Coherent Light Source (LCLS) and at the Advanced Light Source (ALS) in order to follow light-driven electron dynamics at dye-semiconductor interfaces on femto- to nanosecond timescales, and from the perspective of individual atomic sites. A distinct transient binding-energy shift of the Ru3d photoemission lines originating from the metal centers of N3 dye-molecules adsorbed on nanoporous ZnO is observed 500 fs after resonant HOMO-LUMO excitation with a visible laser pulse. This dynamical chemical shift is accompanied by a characteristic surface photo-voltage response of the semiconductor substrate. The two phenomena and their correlation will be discussed in the context of electronic bottlenecks for efficient interfacial charge-transfer and possible charge recombination and relaxation pathways leading to the neutralization of the transiently oxidized dye following ultrafast electron injection. First steps towards in operando time-resolved X-ray absorption spectroscopy techniques to monitor interfacial chemical dynamics will be presented.

  18. Single-molecule imaging at high hydrostatic pressure

    NASA Astrophysics Data System (ADS)

    Vass, Hugh; Lucas Black, S.; Flors, Cristina; Lloyd, Diarmuid; Bruce Ward, F.; Allen, Rosalind J.

    2013-04-01

    Direct microscopic fluorescence imaging of single molecules can provide a wealth of mechanistic information, but up to now, it has not been possible under high pressure conditions, due to limitations in microscope pressure cell design. We describe a pressure cell window design that makes it possible to image directly single molecules at high hydrostatic pressure. We demonstrate our design by imaging single molecules of Alexa Fluor 647 dye bound to DNA, at 120 and 210 bar, and following their fluorescence photodynamics. We further show that the failure pressure of this type of pressure cell window can be in excess of 1 kbar.

  19. Microscopy beyond the diffraction limit using actively controlled single molecules

    PubMed Central

    MOERNER, W.E.

    2013-01-01

    Summary In this short review, the general principles are described for obtaining microscopic images with resolution beyond the optical diffraction limit with single molecules. Although it has been known for several decades that single-molecule emitters can blink or turn on and off, in recent work the addition of on/off control of molecular emission to maintain concentrations at very low levels in each imaging frame combined with sequential imaging of sparse subsets has enabled the reconstruction of images with resolution far below the optical diffraction limit. Single-molecule active control microscopy provides a powerful window into information about nanoscale structures that was previously unavailable. PMID:22582796

  20. 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.

  1. Experimental demonstration of a single-molecule electric motor.

    PubMed

    Tierney, Heather L; Murphy, Colin J; Jewell, April D; Baber, Ashleigh E; Iski, Erin V; Khodaverdian, Harout Y; McGuire, Allister F; Klebanov, Nikolai; Sykes, E Charles H

    2011-10-01

    For molecules to be used as components in molecular machines, methods that couple individual molecules to external energy sources and that selectively excite motion in a given direction are required. Significant progress has been made in the construction of molecular motors powered by light and by chemical reactions, but electrically driven motors have not yet been built, despite several theoretical proposals for such motors. Here we report that a butyl methyl sulphide molecule adsorbed on a copper surface can be operated as a single-molecule electric motor. Electrons from a scanning tunnelling microscope are used to drive the directional motion of the molecule in a two-terminal setup. Moreover, the temperature and electron flux can be adjusted to allow each rotational event to be monitored at the molecular scale in real time. The direction and rate of the rotation are related to the chiralities of both the molecule and the tip of the microscope (which serves as the electrode), illustrating the importance of the symmetry of the metal contacts in atomic-scale electrical devices. PMID:21892165

  2. Donor-Dependent Kinetics of Interfacial Proton-Coupled Electron Transfer.

    PubMed

    Jackson, Megan N; Surendranath, Yogesh

    2016-03-01

    The effect of the proton donor on the kinetics of interfacial concerted proton-electron transfer (CPET) to polycrystalline Au was probed indirectly by studying the rate of hydrogen evolution from trialkylammonium donors with different steric profiles, but the same pKa. Detailed kinetic studies point to a mechanism for HER catalysis that involves rate-limiting CPET from the proton donor to the electrode surface, allowing this catalytic reaction to serve as a proxy for the rate of interfacial CPET. In acetonitrile electrolyte, triethylammonium (TEAH(+)) displays up to 20-fold faster CPET kinetics than diisopropylethylammonium (DIPEAH(+)) at all measured potentials. In aqueous electrolyte, this steric constraint is largely lifted, suggesting a key role for water in mediating interfacial CPET. In acetonitrile, TEAH(+) also displays a much larger transfer coefficient (β = 0.7) than DIPEAH(+) (β = 0.4), and TEAH(+) displays a potential-dependent H/D kinetic isotope effect that is not observed for DIPEAH(+). These results demonstrate that proton donor structure strongly impacts the free energy landscape for CPET to extended solid surfaces and highlight the crucial role of the proton donor in the kinetics of electrocatalytic energy conversion reactions. PMID:26862666

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

    SciTech Connect

    Jakubikova, Elena; Martin, Richard L; Batista, Enrique R; Snoeberger, Robert C; Batista, Victor S

    2009-01-01

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

  4. Large Conductance Switching in a Single-Molecule Device through Room Temperature Spin-Dependent Transport.

    PubMed

    Aragonès, Albert C; Aravena, Daniel; Cerdá, Jorge I; Acís-Castillo, Zulema; Li, Haipeng; Real, José Antonio; Sanz, Fausto; Hihath, Josh; Ruiz, Eliseo; Díez-Pérez, Ismael

    2016-01-13

    Controlling the spin of electrons in nanoscale electronic devices is one of the most promising topics aiming at developing devices with rapid and high density information storage capabilities. The interface magnetism or spinterface resulting from the interaction between a magnetic molecule and a metal surface, or vice versa, has become a key ingredient in creating nanoscale molecular devices with novel functionalities. Here, we present a single-molecule wire that displays large (>10000%) conductance switching by controlling the spin-dependent transport under ambient conditions (room temperature in a liquid cell). The molecular wire is built by trapping individual spin crossover Fe(II) complexes between one Au electrode and one ferromagnetic Ni electrode in an organic liquid medium. Large changes in the single-molecule conductance (>100-fold) are measured when the electrons flow from the Au electrode to either an α-up or a β-down spin-polarized Ni electrode. Our calculations show that the current flowing through such an interface appears to be strongly spin-polarized, thus resulting in the observed switching of the single-molecule wire conductance. The observation of such a high spin-dependent conductance switching in a single-molecule wire opens up a new door for the design and control of spin-polarized transport in nanoscale molecular devices at room temperature. PMID:26675052

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

    PubMed Central

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

    2015-01-01

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

  6. Single-molecule 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

  7. 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.

  8. 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

  9. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    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.

  11. 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

  12. Massively parallel single-molecule manipulation using centrifugal force.

    PubMed

    Halvorsen, Ken; Wong, Wesley P

    2010-06-01

    Precise manipulation of single molecules has already led to remarkable insights in physics, chemistry, biology, and medicine. However, widespread adoption of single-molecule techniques has been impeded by equipment cost and the laborious nature of making measurements one molecule at a time. We have solved these issues by developing an approach that enables massively parallel single-molecule force measurements using centrifugal force. This approach is realized in an instrument that we call the centrifuge force microscope in which objects in an orbiting sample are subjected to a calibration-free, macroscopically uniform force-field while their micro-to-nanoscopic motions are observed. We demonstrate high-throughput single-molecule force spectroscopy with this technique by performing thousands of rupture experiments in parallel, characterizing force-dependent unbinding kinetics of an antibody-antigen pair in minutes rather than days. Additionally, we verify the force accuracy of the instrument by measuring the well-established DNA overstretching transition at 66 +/- 3 pN. With significant benefits in efficiency, cost, simplicity, and versatility, single-molecule centrifugation has the potential to expand single-molecule experimentation to a wider range of researchers and experimental systems. PMID:20513382

  13. Activating "Invisible" Glue: Using Electron Beam for Enhancement of Interfacial Properties of Graphene-Metal Contact.

    PubMed

    Kim, Songkil; Russell, Michael; Kulkarni, Dhaval D; Henry, Mathias; Kim, Steve; Naik, Rajesh R; Voevodin, Andrey A; Jang, Seung Soon; Tsukruk, Vladimir V; Fedorov, Andrei G

    2016-01-26

    Interfacial contact of two-dimensional graphene with three-dimensional metal electrodes is crucial to engineering high-performance graphene-based nanodevices with superior performance. Here, we report on the development of a rapid "nanowelding" method for enhancing properties of interface to graphene buried under metal electrodes using a focused electron beam induced deposition (FEBID). High energy electron irradiation activates two-dimensional graphene structure by generation of structural defects at the interface to metal contacts with subsequent strong bonding via FEBID of an atomically thin graphitic interlayer formed by low energy secondary electron-assisted dissociation of entrapped hydrocarbon contaminants. Comprehensive investigation is conducted to demonstrate formation of the FEBID graphitic interlayer and its impact on contact properties of graphene devices achieved via strong electromechanical coupling at graphene-metal interfaces. Reduction of the device electrical resistance by ∼50% at a Dirac point and by ∼30% at the gate voltage far from the Dirac point is obtained with concurrent improvement in thermomechanical reliability of the contact interface. Importantly, the process is rapid and has an excellent insertion potential into a conventional fabrication workflow of graphene-based nanodevices through single-step postprocessing modification of interfacial properties at the buried heterogeneous contact. PMID:26741645

  14. Quantum dots for quantitative imaging: from single molecules to tissue

    PubMed Central

    Vu, Tania Q.; Lam, Wai Yan; Hatch, Ellen W.; Lidke, Diane S.

    2015-01-01

    Since their introduction to biological imaging, quantum dots (QDs) have progressed from a little known, but attractive technology to one that has gained broad application in many areas of biology. The versatile properties of these fluorescent nanoparticles have allowed investigators to conduct biological studies with extended spatiotemporal capabilities that were previously not possible. In this review, we focus on QD applications that provide enhanced quantitative information on protein dynamics and localization, including single particle tracking (SPT) and immunohistochemistry (IHC), and finish by examining prospects of upcoming applications, such as correlative light and electron microscopy (CLEM) and super-resolution. Advances in single molecule imaging, including multi-color and 3D QD tracking, have provided new insights into the mechanisms of cell signaling and protein trafficking. New forms of QD tracking in vivo have allowed for observation of biological processes with molecular level resolution in the physiological context of the whole animal. Further methodological development of multiplexed QD-based immunohistochemistry assays are allowing more quantitative analysis of key proteins in tissue samples. These advances highlight the unique quantitative data sets that QDs can provide to further our understanding of biological and disease processes. PMID:25620410

  15. Reliable anchoring groups for single-molecule junctions

    NASA Astrophysics Data System (ADS)

    González, M. Teresa; Leary, Edmund; Evangeli, Charalambos; Arroyo, Carlos; Rubio-Bollinger, Gabino; Agraïit, Nicolás

    2012-02-01

    In the field of molecular electronics, thiols have been extensively used as the most common anchoring groups to bind molecules to gold electrodes. However, other anchoring groups as amines can provide interesting advantages. Recently, C-60 has been also proposed as a possible very efficient binding group. In this talk, I will present our studies on molecular junctions formed by thiol-, amine-, and C-60-terminated molecules. We use a STM (scanning tunneling microscope) break-junction technique to create and characterized single-molecule junctions both in ambient and liquid environment. We compare thiols and amines on the alkane family and an oligo(phenylene ethynylene). Our study of the molecular-junction stretching length allows us to conclude that thiols affect atomic rearrangement at the electrodes significantly more than amines. Using C-60-terminated molecules, we have recently introduced a new technique for controllably wiring one molecule at a time. We first get STM images to located isolated molecules on a gold substrate, which are then specifically targeted and contacted using a STM gold tip. This technique offers a significant improvement over other techniques, as it guaranties that one and only one molecule is contacted at a time between the electrodes.

  16. Gold plasmonic effects on charge transport through single molecule junctions

    NASA Astrophysics Data System (ADS)

    Adak, Olgun; Venkataraman, Latha

    2014-03-01

    We study the impact of surface plasmon polaritons, the coupling of electromagnetic waves to collective electron oscillations on metal surfaces, on the conductance of single-molecule junctions. We use a scanning-tunneling microscope based break junction setup that is built into an optical microscope to form molecular junctions. Coherent 685nm light is used to illuminate the molecular junctions formed with 4,4'-bipyridine with diffraction limited focusing performance. We employ a lock-in type technique to measure currents induced by light. Furthermore, the thermal expansion due to laser heating is mimicked by mechanically modulating inter-electrode separation. For each junction studied, we measure current, and use AC techniques to determine molecular junction resonance levels and coupling strengths. We use a cross correlations analysis technique to analyze and compare the effect of light to that of the mechanical modulation. Our results show that junction transmission characteristics are not altered under illumination, within the resolution of our instrument. We argue that photo-currents measured with lock-in techniques in these kinds of structures are due to thermal effects. This work was funded by the Center for Re-Defining Photovoltaic Efficiency through Molecule Scale Control, an EFRC funded by the US Department of Energy, Office of Basic Energy Sciences under Contract No. DESC0001085.

  17. 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.

  18. Single-Molecule Conductance of Viologen-Cucurbit[8]uril Host-Guest Complexes.

    PubMed

    Zhang, Wei; Gan, Shiyu; Vezzoli, Andrea; Davidson, Ross J; Milan, David C; Luzyanin, Konstantin V; Higgins, Simon J; Nichols, Richard J; Beeby, Andrew; Low, Paul J; Li, Buyi; Niu, Li

    2016-05-24

    The local molecular environment is a critical factor which should be taken into account when measuring single-molecule electrical properties in condensed media or in the design of future molecular electronic or single molecule sensing devices. Supramolecular interactions can be used to control the local environment in molecular assemblies and have been used to create microenvironments, for instance, for chemical reactions. Here, we use supramolecular interactions to create microenvironments which influence the electrical conductance of single molecule wires. Cucurbit[8]uril (CB[8]) with a large hydrophobic cavity was used to host the viologen (bipyridinium) molecular wires forming a 1:1 supramolecular complex. Significant increases in the viologen wire single molecule conductances are observed when it is threaded into CB[8] due to large changes of the molecular microenvironment. The results were interpreted within the framework of a Marcus-type model for electron transfer as arising from a reduction in outer-sphere reorganization energy when the viologen is confined within the hydrophobic CB[8] cavity. PMID:27055002

  19. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  1. Towards physiological complexity with in vitro single-molecule biophysics

    PubMed Central

    Duzdevich, Daniel; Greene, Eric C.

    2013-01-01

    Single-molecule biology has matured in recent years, driven to greater sophistication by the development of increasingly advanced experimental techniques. A progressive appreciation for its unique strengths is attracting research that spans an exceptionally broad swath of physiological phenomena—from the function of nucleosomes to protein diffusion in the cell membrane. Newfound enthusiasm notwithstanding, the single-molecule approach is limited to an intrinsically defined set of biological questions; such limitation applies to all experimental approaches, and an explicit statement of the boundaries delineating each set offers a guide to most fruitfully orienting in vitro single-molecule research in the future. Here, we briefly describe a simple conceptual framework to categorize how submolecular, molecular and intracellular processes are studied. We highlight the domain of single-molecule biology in this scheme, with an emphasis on its ability to probe various forms of heterogeneity inherent to populations of discrete biological macromolecules. We then give a general overview of our high-throughput DNA curtain methodology for studying protein–nucleic acid interactions, and by contextualizing it within this framework, we explore what might be the most enticing avenues of future research. We anticipate that a focus on single-molecule biology's unique strengths will suggest a new generation of experiments with greater complexity and more immediately translatable physiological relevance. PMID:23267187

  2. Sizing up single-molecule enzymatic conformational dynamics.

    PubMed

    Lu, H Peter

    2014-02-21

    Enzymatic reactions and related protein conformational dynamics are complex and inhomogeneous, playing crucial roles in biological functions. The relationship between protein conformational dynamics and enzymatic reactions has been a fundamental focus in modern enzymology. It is extremely difficult to characterize and analyze such complex dynamics in an ensemble-averaged measurement, especially when the enzymes are associated with multiple-step, multiple-conformation complex chemical interactions and transformations. Beyond the conventional ensemble-averaged studies, real-time single-molecule approaches have been demonstrated to be powerful in dissecting the complex enzymatic reaction dynamics and related conformational dynamics. Single-molecule enzymology has come a long way since the early demonstrations of the single-molecule spectroscopy studies of enzymatic dynamics about two decades ago. The rapid development of this fundamental protein dynamics field is hand-in-hand with the new development of single-molecule imaging and spectroscopic technology and methodology, theoretical model analyses, and correlations with biological preparation and characterization of the enzyme protein systems. The complex enzymatic reactions can now be studied one molecule at a time under physiological conditions. Most exciting developments include active manipulation of enzymatic conformational changes and energy landscape to regulate and manipulate the enzymatic reactivity and associated conformational dynamics, and the new advancements have established a new stage for studying complex protein dynamics beyond by simply observing but by actively manipulating and observing the enzymatic dynamics at the single-molecule sensitivity temporally and spatially. PMID:24306450

  3. Observing single-molecule chemical reactions on metal nanoparticles

    NASA Astrophysics Data System (ADS)

    Emory, Steven R.; Ambrose, W. Patrick; Goodwin, Peter M.; Keller, Richard A.

    2001-06-01

    We report on 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 scatters (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 bread SERS vibrational bands at 1592 cm-1 and 1340 cm-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 measurement 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.

  4. Single-Molecule Protein Conformational Dynamics in Cell Signaling

    SciTech Connect

    Lu, H PETER.

    2004-08-22

    We have demonstrated the application of single-molecule imaging and ultrafast spectroscopy to probe protein conformational dynamics in solution and in lipid bilayers. Dynamic protein-protein interactions involve significant conformational motions that initiate chain reactions leading to specific cellular responses. We have carried out a single molecule study of dynamic protein-protein interactions in a GTPase intracellular signaling protein Cdc42 in complex with a downstream effector protein, WASP. We were able to probe hydrophobic interactions significant to Cdc42/WASP recognition. Single molecule fluorescence intensity and polarization measurements have revealed the dynamic and inhomogeneous nature of protein-protein interactions within the Cdc42/WASP complex that is characterized by structured distributions of conformational fluctuation rates. Conducting a single-molecule fluorescence anisotropy study of calmodulin (CaM), a regulatory protein for calcium-dependent cell signaling, we were able to probe CaM conformational dynamics at a wide time scale. In this study, CaM contains a site-specifically inserted tetra-cysteine motif that reacted with FlAsH, a biarsenic fluorescein derivative that can be rotationally locked to the host protein. The study provided direct characterization of the nanosecond motions of CaM tethered to a biologically compatible surface under physiological buffer solution. The unique technical approaches are applicable of studying single-molecule dynamics of protein conformational motions and protein-protein interactions at a wide time range without the signal convolution of probe-dye molecule motions

  5. Massively Parallel Single-Molecule Manipulation Using Centrifugal Force

    NASA Astrophysics Data System (ADS)

    Wong, Wesley; Halvorsen, Ken

    2011-03-01

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

  6. Single-molecule designs for electric switches and rectifiers.

    PubMed

    Kornilovitch, Pavel; Bratkovsky, Alexander; Williams, Stanley

    2003-12-01

    A design for molecular rectifiers is proposed. Current rectification is based on the spatial asymmetry of a molecule and requires only one resonant conducting molecular orbital. Rectification is caused by asymmetric coupling of the orbital to the electrodes, which results in asymmetric movement of the two Fermi levels with respect to the orbital under external bias. Results from numerical studies of the family of suggested molecular rectifiers, HS-(CH(2))(n)-C(6)H(4)(CH(2))(m)SH, are presented. Current rectification ratios in excess of 100 are achievable for n = 2 and m > 6. A class of bistable stator-rotor molecules is proposed. The stationary part connects the two electrodes and facilitates electron transport between them. The rotary part, which has a large dipole moment, is attached to an atom of the stator via a single sigma bond. Electrostatic bonds formed between the oxygen atom of the rotor and hydrogen atoms of the stator make the symmetric orientation of the dipole unstable. The rotor has two potential minima with equal energy for rotation about the sigma bond. The dipole can be flipped between the two states by an external electric field. Both rotor-orientation states have asymmetric current-voltage characteristics that are the reverse of each other, so they are distinguishable electrically. Theoretical results on conformation, energy barriers, retention times, switching voltages, and current-voltage characteristics are presented for a particular stator-rotor molecule. Such molecules could be the base for single-molecule switches, reversible diodes, and other molecular electronic devices. PMID:14976019

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

    PubMed

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

    2012-05-01

    The observation of interference patterns in double-slit experiments with massive particles is generally regarded as the ultimate demonstration of the quantum nature of these objects. Such matter-wave interference has been observed for electrons, neutrons, atoms and molecules and, in contrast to classical physics, quantum interference can be observed when single particles arrive at the detector one by one. The build-up of such patterns in experiments with electrons has been described as the "most beautiful experiment in physics". Here, we show how a combination of nanofabrication and nano-imaging allows us to record the full two-dimensional build-up of quantum interference patterns in real time for phthalocyanine molecules and for derivatives of phthalocyanine molecules, which have masses of 514 AMU and 1,298 AMU respectively. A laser-controlled micro-evaporation source was used to produce a beam of molecules with the required intensity and coherence, and the gratings were machined in 10-nm-thick silicon nitride membranes to reduce the effect of van der Waals forces. Wide-field fluorescence microscopy detected the position of each molecule with an accuracy of 10 nm and revealed the build-up of a deterministic ensemble interference pattern from single molecules that arrived stochastically at the detector. In addition to providing this particularly clear demonstration of wave-particle duality, our approach could also be used to study larger molecules and explore the boundary between quantum and classical physics. PMID:22447163

  8. 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

  9. Open-frame system for single-molecule microscopy

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  10. Open-frame system for single-molecule microscopy.

    PubMed

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

    2015-03-01

    We present the design and construction of a versatile, open frame inverted microscope system for wide-field fluorescence and single molecule imaging. The microscope chassis and modular design allow for customization, expansion, and experimental flexibility. We present two components which are included with the microscope which extend its basic capabilities and together create a powerful microscopy system: A Convex Lens-induced Confinement device provides the system with single-molecule imaging capabilities, and a two-color imaging system provides the option of imaging multiple molecular species simultaneously. The flexibility of the open-framed chassis combined with accessible single-molecule, multi-species imaging technology supports a wide range of new measurements in the health, nanotechnology, and materials science research sectors. PMID:25832232

  11. Quantum dots find their stride in single molecule tracking

    PubMed Central

    Bruchez, Marcel P.

    2011-01-01

    Thirteen years after the demonstration of quantum dots as biological imaging agents, and nine years after the initial commercial introduction of bioconjugated quantum dots, the brightness and photostability of the quantum dots has enabled a range of investigations using single molecule tracking. These materials are being routinely utilized by a number of groups to track the dynamics of single molecules in reconstituted biophysical systems and on living cells, and are especially powerful for investigations of single molecules over long timescales with short exposure times and high pointing accuracy. New approaches are emerging where the quantum dots are used as “hard-sphere” probes for intracellular compartments. Innovations in quantum dot surface modification are poised to substantially expand the utility of these materials. PMID:22055494

  12. Detectors for single-molecule fluorescence imaging and spectroscopy.

    PubMed

    Michalet, X; Siegmund, O H W; Vallerga, J V; Jelinsky, P; Millaud, J E; Weiss, S

    2007-01-01

    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

  13. 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, ξ, 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

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

    PubMed Central

    Chen, Peng; Keller, Aaron M.; Joshi, Chandra P.; Martell, Danya J.; Andoy, Nesha May; Benítez, Jaime J.; Chen, Tai-Yen; Santiago, Ace George; Yang, Feng

    2013-01-01

    Understanding how cells regulate and transport metal ions is an important goal in the field of bioinorganic chemistry, a frontier research area that resides at the interfaces of chemistry and biology. This Current Topics article reviews recent advances from the authors' group in using single-molecule fluorescence imaging techniques to identify the mechanisms of metal homeostatic proteins, including metalloregulators and metallochaperones. It emphasizes the novel mechanistic insights into how dynamic protein–DNA and protein–protein interactions offer efficient pathways for MerR-family metalloregulators and copper chaperones to fulfill their functions. The article also summarizes other related single-molecule studies of bioinorganic systems, and gives an outlook toward single-molecule imaging of metalloprotein functions in living cells. PMID:24053279

  15. Fully automated single-molecule force spectroscopy for screening applications.

    PubMed

    Struckmeier, Jens; Wahl, Reiner; Leuschner, Mirko; Nunes, Joao; Janovjak, Harald; Geisler, Ulrich; Hofmann, Gerd; Jähnke, Torsten; Müller, Daniel J

    2008-09-24

    With the introduction of single-molecule force spectroscopy (SMFS) it has become possible to directly access the interactions of various molecular systems. A bottleneck in conventional SMFS is collecting the large amount of data required for statistically meaningful analysis. Currently, atomic force microscopy (AFM)-based SMFS requires the user to tediously 'fish' for single molecules. In addition, most experimental and environmental conditions must be manually adjusted. Here, we developed a fully automated single-molecule force spectroscope. The instrument is able to perform SMFS while monitoring and regulating experimental conditions such as buffer composition and temperature. Cantilever alignment and calibration can also be automatically performed during experiments. This, combined with in-line data analysis, enables the instrument, once set up, to perform complete SMFS experiments autonomously. PMID:21832579

  16. Single-Molecule Total Internal Reflection Fluorescence Microscopy.

    PubMed

    Kudalkar, Emily M; Davis, Trisha N; Asbury, Charles L

    2016-01-01

    The advent of total internal reflection fluorescence (TIRF) microscopy has permitted visualization of biological events on an unprecedented scale: the single-molecule level. Using TIRF, it is now possible to view complex biological interactions such as cargo transport by a single molecular motor or DNA replication in real time. TIRF allows for visualization of single molecules by eliminating out-of-focus fluorescence and enhancing the signal-to-noise ratio. TIRF has been instrumental for studying in vitro interactions and has also been successfully implemented in live-cell imaging. Visualization of cytoskeletal structures and dynamics at the plasma membrane, such as endocytosis, exocytosis, and adhesion, has become much clearer using TIRF microscopy. Thanks to recent advances in optics and commercial availability, TIRF microscopy is becoming an increasingly popular and user-friendly technique. In this introduction, we describe the fundamental properties of TIRF microscopy and the advantages of using TIRF for single-molecule investigation. PMID:27140922

  17. 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.

  18. Extending Single-Molecule Microscopy Using Optical Fourier Processing

    PubMed Central

    2015-01-01

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

  19. 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

  20. Single-molecule decoding of combinatorially modified nucleosomes.

    PubMed

    Shema, Efrat; Jones, Daniel; Shoresh, Noam; Donohue, Laura; Ram, Oren; Bernstein, Bradley E

    2016-05-01

    Different combinations of histone modifications have been proposed to signal distinct gene regulatory functions, but this area is poorly addressed by existing technologies. We applied high-throughput single-molecule imaging to decode combinatorial modifications on millions of individual nucleosomes from pluripotent stem cells and lineage-committed cells. We identified definitively bivalent nucleosomes with concomitant repressive and activating marks, as well as other combinatorial modification states whose prevalence varies with developmental potency. We showed that genetic and chemical perturbations of chromatin enzymes preferentially affect nucleosomes harboring specific modification states. Last, we combined this proteomic platform with single-molecule DNA sequencing technology to simultaneously determine the modification states and genomic positions of individual nucleosomes. This single-molecule technology has the potential to address fundamental questions in chromatin biology and epigenetic regulation. PMID:27151869

  1. Methods of single-molecule fluorescence spectroscopy and microscopy

    NASA Astrophysics Data System (ADS)

    Moerner, W. E.; Fromm, David P.

    2003-08-01

    Optical spectroscopy at the ultimate limit of a single molecule has grown over the past dozen years into a powerful technique for exploring the individual nanoscale behavior of molecules in complex local environments. Observing a single molecule removes the usual ensemble average, allowing the exploration of hidden heterogeneity in complex condensed phases as well as direct observation of dynamical state changes arising from photophysics and photochemistry, without synchronization. This article reviews the experimental techniques of single-molecule fluorescence spectroscopy and microscopy with emphasis on studies at room temperature where the same single molecule is studied for an extended period. Key to successful single-molecule detection is the need to optimize signal-to-noise ratio, and the physical parameters affecting both signal and noise are described in detail. Four successful microscopic methods including the wide-field techniques of epifluorescence and total internal reflection, as well as confocal and near-field optical scanning microscopies are described. In order to extract the maximum amount of information from an experiment, a wide array of properties of the emission can be recorded, such as polarization, spectrum, degree of energy transfer, and spatial position. Whatever variable is measured, the time dependence of the parameter can yield information about excited state lifetimes, photochemistry, local environmental fluctuations, enzymatic activity, quantum optics, and many other dynamical effects. Due to the breadth of applications now appearing, single-molecule spectroscopy and microscopy may be viewed as useful new tools for the study of dynamics in complex systems, especially where ensemble averaging or lack of synchronization may obscure the details of the process under study.

  2. Single-Molecule Stochastic Analysis of Channeling Enzyme Tryptophan Synthase.

    PubMed

    Loutchko, Dimitri; Gonze, Didier; Mikhailov, Alexander S

    2016-03-10

    The channeling enzyme tryptophan synthase provides a paradigmatic example of a chemical nanomachine. It possesses two active centers and, as a single molecule, catalyzes 13 different reaction steps with a complex pattern of allosteric regulation and with an intermediate product channeled from one active center to another. Here, the first single-molecule stochastic model of the enzyme is proposed and analyzed. All its transition rate constants were deduced from the experimental data available, and no fitting parameters were thus employed. Numerical simulations reveal strong correlations in the states of the active centers and the emergent synchronization of intramolecular processes in tryptophan synthase. PMID:26863529

  3. Deciphering Complexity in Molecular Biophysics with Single-Molecule Resolution.

    PubMed

    Deniz, Ashok A

    2016-01-29

    The structural features and dynamics of biological macromolecules underlie the molecular biology and correct functioning of cells. However, heterogeneity and other complexity of these molecules and their interactions often lead to loss of important information in traditional biophysical experiments. Single-molecule methods have dramatically altered the conceptual thinking and experimental tests available for such studies, leveraging their ability to avoid ensemble averaging. Here, I discuss briefly the rise of fluorescence single-molecule methods over the past two decades, a few key applications, and end with a view to challenges and future prospects. PMID:26707199

  4. Lucky Imaging: Improved Localization Accuracy for Single Molecule Imaging

    PubMed Central

    Cronin, Bríd; de Wet, Ben; Wallace, Mark I.

    2009-01-01

    We apply the astronomical data-analysis technique, Lucky imaging, to improve resolution in single molecule fluorescence microscopy. We show that by selectively discarding data points from individual single-molecule trajectories, imaging resolution can be improved by a factor of 1.6 for individual fluorophores and up to 5.6 for more complex images. The method is illustrated using images of fluorescent dye molecules and quantum dots, and the in vivo imaging of fluorescently labeled linker for activation of T cells. PMID:19348772

  5. Single molecule techniques for the study of membrane proteins.

    PubMed

    García-Sáez, Ana J; Schwille, Petra

    2007-08-01

    Single molecule techniques promise novel information about the properties and behavior of individual particles, thus enabling access to molecular heterogeneities in biological systems. Their recent developments to accommodate membrane studies have significantly deepened the understanding of membrane proteins. In this short review, we will describe the basics of the three most common single-molecule techniques used on membrane proteins: fluorescence correlation spectroscopy, single particle tracking, and atomic force microscopy. We will discuss the most relevant findings made during the recent years and their contribution to the membrane protein field. PMID:17497147

  6. Extracting conformational information from single molecule photon statistics.

    PubMed

    Peng, Yonggang; Yang, Chuanlu; Zheng, Yujun

    2016-02-14

    In this paper, we describe the approach of resonant trajectories of photon emission (Traj〈N〉 and TrajQ) in the conformational coordinate X and external field frequency ωL space to extract the conformational information of single molecule. The Smoluchowski equation is employed to describe the conformational dynamics of the single molecule in complex environments. This approach is applied to single Thioflavin T (ThT) molecule, and our results are in excellent agreement with the results of ab initio simulations. PMID:26874487

  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. 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

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

    SciTech Connect

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

    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 D{sub 1} 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.

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

    PubMed

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

    2014-08-01

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

  11. The Single Molecule Imaging Approach to Membrane Protein Stoichiometry

    PubMed Central

    Hallworth, Richard; Nichols, Michael G.

    2013-01-01

    Recent technical advances have enabled the imaging of single fluorescent molecules. The application of single molecule visualization techniques has opened up new avenues of experimentation in biology at the molecular level. In this article, we review the application of single fluorescent molecule visualization and analysis to an important problem, that of sub-unit stoichiometry in membrane proteins, with particular emphasis on our approach. Single fluorescent molecules, coupled to fluorescent proteins, are localized in the membranes of cells. The molecules are then exposed to continuous low-level excitation until their fluorescence emissions reach background levels. The high sensitivity of modern instrumentation has enabled direct observations of discrete step decreases in the fluorescence of single molecules, which represent the bleaching of single fluorophores. By counting the number of steps over a large number of single molecules, an average step count is determined, from which the stoichiometry is deduced using a binomial model. We examined the stoichiometry of a protein, prestin, that is central to mammalian hearing. We discuss how we prepared, identified and imaged single molecules of prestin. The methodological considerations behind our approach are described and compared to similar procedures in other laboratories. PMID:22831749

  12. 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

  13. Single molecule thermodynamics and nanopore-based thermometry

    NASA Astrophysics Data System (ADS)

    Reiner, Joseph E.; Robertson, Joseph W. F.; Burden, Lisa K.; Burden, Daniel L.; Kasianowicz, John J.

    2012-02-01

    The nanopore-based resistive pulse method measures the reduction in ionic current caused by the interaction of single molecules with the pore. It has great promise in addressing problems across a range of fields that include biomedicine and genomics. The technique requires the residence time of the molecules in the pore to exceed the inverse bandwidth of the detection system (˜ 10 μs). Efforts are underway to improve this by molecular modification of the pore wall, but little effort has focused on modifying the solution conditions in and around the pore. We address this issue by precisely controlling the solution temperature around a protein ion channel (alpha hemolysin) via laser-induced heating of gold nanoparticles. In this technique, the nanopore serves dual roles as both a highly local thermometer and single molecule sensor. Preliminary data suggests that the solution temperature can be controlled over a wide range, the nanopore conductance can be used to directly measure rapid changes in temperature, and the temperature change can dramatically alter the interaction kinetics of single molecules with the nanopore. The method will improve the development of biochip sensors and lead to a new platform for single molecule thermodynamic studies.

  14. Biology and polymer physics at the single-molecule level.

    PubMed

    Chu, Steven

    2003-04-15

    The ability to look at individual molecules has given us new insights into molecular processes. Examples of our recent work are given to illustrate how behaviour that may otherwise be hidden from view can be clearly seen in single-molecule experiments. PMID:12871618

  15. 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

  16. Modeling single molecule detection probabilities in microdroplets. Final report

    SciTech Connect

    Hill, S.C.

    1996-03-01

    Numerical tools for modeling the fluorescence collected from a single molecule within a microsphere as a function of it`s position and orientation, the size of the droplet, the numerical aperture of the lens, the detection geometry, type of illumination, and the linewidth of the emitting molecule, are described.

  17. Conformational transitions monitored for single molecules in solution.

    PubMed Central

    Edman, L; Mets, U; Rigler, R

    1996-01-01

    Phenomena that can be observed for a large number of molecules may not be understood if it is not possible to observe the events on the single-molecule level. We measured the fluorescence lifetimes of individual tetramethylrhodamine molecules, linked to an 18-mer deoxyribonucleotide sequence specific for M13 DNA, by time-resolved, single-photon counting in a confocal fluorescence microscope during Brownian motion in solution. When many molecules were observed, a biexponential fluorescence decay was observed with equal amplitudes. However, on the single-molecule level, the fraction of one of the amplitudes spanned from 0 to unity for a collection of single-molecule detections. Further analysis by fluorescence correlation spectroscopy made on many molecules revealed a process that obeys a stretched exponential relaxation law. These facts, combined with previous evidence of the quenching effect of guanosine on rhodamines, indicate that the tetramethylrhodamine molecule senses conformational transitions as it associates and dissociates to a guanosine-rich area. Thus, our results reveal conformational transitions in a single molecule in solution under conditions that are relevant for biological processes. PMID:8692883

  18. 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.

  19. 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

  20. Deconvolving Single-Molecule Intensity Distributions for Quantitative Microscopy Measurements

    PubMed Central

    Mutch, Sarah A.; Fujimoto, Bryant S.; Kuyper, Christopher L.; Kuo, Jason S.; Bajjalieh, Sandra M.; Chiu, Daniel T.

    2007-01-01

    In fluorescence microscopy, images often contain puncta in which the fluorescent molecules are spatially clustered. This article describes a method that uses single-molecule intensity distributions to deconvolve the number of fluorophores present in fluorescent puncta as a way to “count” protein number. This method requires a determination of the correct statistical relationship between the single-molecule and single-puncta intensity distributions. Once the correct relationship has been determined, basis histograms can be generated from the single-molecule intensity distribution to fit the puncta distribution. Simulated data were used to demonstrate procedures to determine this relationship, and to test the methodology. This method has the advantages of single-molecule measurements, providing both the mean and variation in molecules per puncta. This methodology has been tested with the avidin-biocytin binding system for which the best-fit distribution of biocytins in the sample puncta was in good agreement with a bulk determination of the avidin-biocytin binding ratio. PMID:17259276

  1. 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.

  2. Ultrafast Interfacial Electron and Hole Transfer from CsPbBr3 Perovskite Quantum Dots.

    PubMed

    Wu, Kaifeng; Liang, Guijie; Shang, Qiongyi; Ren, Yueping; Kong, Degui; Lian, Tianquan

    2015-10-14

    Recently reported colloidal lead halide perovskite quantum dots (QDs) with tunable photoluminescence (PL) wavelengths covering the whole visible spectrum and exceptionally high PL quantum yields (QYs, 50-90%) constitute a new family of functional materials with potential applications in light-harvesting and -emitting devices. By transient absorption spectroscopy, we show that the high PL QYs (∼79%) can be attributed to negligible electron or hole trapping pathways in CsPbBr3 QDs: ∼94% of lowest excitonic states decayed with a single-exponential time constant of 4.5 ± 0.2 ns. Furthermore, excitons in CsPbBr3 QDs can be efficiently dissociated in the presence of electron or hole acceptors. The half-lives of electron transfer (ET) to benzoquinone and subsequent charge recombination are 65 ± 5 ps and 2.6 ± 0.4 ns, respectively. The half-lives for hole transfer (HT) to phenothiazine and the subsequent charge recombination are 49 ± 6 ps and 1.0 ± 0.2 ns, respectively. The lack of electron and hole traps and fast interfacial ET and HT rates are key properties that may enable the development of efficient lead halide perovskite QDs-based light-harvesting and -emitting devices. PMID:26414242

  3. 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.

  4. Fluorescence-force spectroscopy at the single molecule level

    NASA Astrophysics Data System (ADS)

    Zhou, Ruobo

    During the past decade, various powerful single-molecule techniques have evolved and helped to address important questions in life sciences. As the single molecule techniques become mature, there is increasingly pressing need to maximize the information content of the analysis in order to be able to study more complex systems that better approximate in-vivo conditions. Here, we develop a fluorescence-force spectroscopy method to combine single-molecule fluorescence spectroscopy with optical tweezers. Optical tweezers are used to manipulate and observe mechanical properties on the nanometer scale and piconewton force range. However, once the force range is in the low piconewton range or less, the spatial resolution of optical tweezers decreases significantly. In combination with fluorescence spectroscopy, like single molecule Forster (or fluorescence) resonance energy transfer (FRET) whose detectable distance range is approximately 3-10 nm, we are able to observe nanometer fluctuations and internal conformational changes in a low-force regime. The possibility to place fluorescent labels at nearly any desired position and a sophisticated design of the experiment increases the amount of information that can be extracted in contrast to pure mechanical or fluorescence experiments. We demonstrate the applications of this method to various biological systems including: 1) to measure the effect of very low forces on the nanometer scale conformational transitions of the DNA four-way (Holliday) junction; 2) to dissect protein diffusion and dissociation mechanisms on single stranded DNA, 3) to calibrate FRET-based in-vivo force sensors and 4) to study mechanical unfolding of single proteins. The results could not have been obtained with fluorescence or force measurement alone, and clearly demonstrates the power and generality of our approach. Finally, we show that self-quenching of two identical fluorophores can be used to detect small conformational dynamics corresponding to sub-nanometer distance changes of single molecules in a FRET-insensitive short range (< 3 nm), extending the detectable distance range of our fluorescence-force spectroscopy method.

  5. Interfacial ultramorphology evaluation of resin luting cements to dentin: a correlative scanning electron microscopy and transmission electron microscopy analysis.

    PubMed

    Aguiar, Thaiane Rodrigues; Vermelho, Paulo Moreira; Andr, Carolina Bosso; Giannini, Marcelo

    2013-12-01

    The objective of this study was to analyze the dentin-resin cements interfacial ultramorphologies using two different methods: scanning (SEM) and transmission electron microscopy (TEM). Four commercial products were evaluated: two conventional cementing system (RelyX ARC/Adper Scotchbond Multi-Purpose Plus, 3M ESPE and Clearfil Esthetic Cement/DC Bond, Kuraray) and two self-adhesive resin cements (RelyX Unicem, 3M ESPE and Clearfil SA Cement, Kuraray). Prepolymerized resin disks (Sinfony, 3M ESPE) were cemented on oclusal dentin surfaces of 24 third human molars, simulating the indirect restorations. After 24 h, teeth were sectioned into 0.9-mm thick slabs and processed for microscopy analyses (SEM or TEM/ n = 3). Qualitative characterization of dentin-resin cement interface was performed. Hybrid layer formation with long and dense resin tags was observed only for RelyX ARC cementing system. Clearfil Esthetic Cement/DC Bond system revealed few and short resin tags formation, whereas no hybridization and resin tags were detected for self-adhesive resin cements. Some interfacial regions exhibited that the self-adhesive resin cements were not bonded to dentin, presenting bubbles or voids at the interfaces. In conclusion, TEM and SEM bonding interface analyses showed ultramorphological variations among resin cements, which are directly related to dental bonding strategies used for each resin cement tested. PMID:24030836

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

    NASA Astrophysics Data System (ADS)

    Okholm, A. H.; Aslan, H.; Besenbacher, F.; Dong, M.; Kjems, J.

    2015-06-01

    DNA origami has been used to orchestrate reactions with nano-precision using a variety of biomolecules. Here, the dynamics of albumin-assisted, localized single-molecule DNA polymerization by terminal deoxynucleotidyl transferase on a 2D DNA origami are monitored using AFM in liquid. Direct visualization of the surface activity revealed the mechanics of growth.DNA origami has been used to orchestrate reactions with nano-precision using a variety of biomolecules. Here, the dynamics of albumin-assisted, localized single-molecule DNA polymerization by terminal deoxynucleotidyl transferase on a 2D DNA origami are monitored using AFM in liquid. Direct visualization of the surface activity revealed the mechanics of growth. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr01945a

  7. The enzyme mechanism of nitrite reductase studied at single-molecule level

    PubMed Central

    Kuznetsova, Sofya; Zauner, Gerhild; Aartsma, Thijs J.; Engelkamp, Hans; Hatzakis, Nikos; Rowan, Alan E.; Nolte, Roeland J. M.; Christianen, Peter C. M.; Canters, Gerard W.

    2008-01-01

    A generic method is described for the fluorescence “readout” of the activity of single redox enzyme molecules based on Förster resonance energy transfer from a fluorescent label to the enzyme cofactor. The method is applied to the study of copper-containing nitrite reductase from Alcaligenes faecalis S-6 immobilized on a glass surface. The parameters extracted from the single-molecule fluorescence time traces can be connected to and agree with the macroscopic ensemble averaged kinetic constants. The rates of the electron transfer from the type 1 to the type 2 center and back during turnover exhibit a distribution related to disorder in the catalytic site. The described approach opens the door to single-molecule mechanistic studies of a wide range of redox enzymes and the precise investigation of their internal workings. PMID:18303118

  8. Pushing single molecule techniques to microsecond resolution proves that T4 Lysozyme is a Brownian ratchet

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    Single-molecule techniques can monitor conformational dynamics of proteins, but such methods usually lack the resolution to directly observe conformational pathways or intermediate conformational states. We have recently described a single-molecule electronic technique that breaks this barrier. Using a 1 MHz-bandwidth carbon nanotube transistor, the transition pathways between open and closed conformations of T4 lysozyme have been recorded with a microsecond resolution. We directly resolve a smooth, continuous transition with an average duration of 37 microseconds. Unexpectedly, the mechanical closing and re-opening of the enzyme have identical distributions of transition durations, and the motion is independent of the enzyme catalyzing the substrate. These results illustrate the principle of microscopic reversibility applied to a Brownian ratchet, with lysozyme tracing a single pathway for closing and the reverse pathway for enzyme opening, regardless of its instantaneous catalytic productivity.

  9. Single-molecule spectroscopy reveals how calmodulin activates NO synthase by controlling its conformational fluctuation dynamics

    PubMed Central

    He, Yufan; Haque, Mohammad Mahfuzul; Stuehr, Dennis J.; Lu, H. Peter

    2015-01-01

    Mechanisms that regulate the nitric oxide synthase enzymes (NOS) are of interest in biology and medicine. Although NOS catalysis relies on domain motions, and is activated by calmodulin binding, the relationships are unclear. We used single-molecule fluorescence resonance energy transfer (FRET) spectroscopy to elucidate the conformational states distribution and associated conformational fluctuation dynamics of the two electron transfer domains in a FRET dye-labeled neuronal NOS reductase domain, and to understand how calmodulin affects the dynamics to regulate catalysis. We found that calmodulin alters NOS conformational behaviors in several ways: It changes the distance distribution between the NOS domains, shortens the lifetimes of the individual conformational states, and instills conformational discipline by greatly narrowing the distributions of the conformational states and fluctuation rates. This information was specifically obtainable only by single-molecule spectroscopic measurements, and reveals how calmodulin promotes catalysis by shaping the physical and temporal conformational behaviors of NOS. PMID:26311846

  10. Rectifications in organic single-molecule diodes alkanethiolate-terminated heterocyclics

    NASA Astrophysics Data System (ADS)

    An, Yipeng; Zhang, Mengjun; Wang, Tianxing; Wang, Guangtao; Fu, Zhaoming

    2016-02-01

    Based on the non-equilibrium Green's function formalism combined with the ab initio density functional theory, we investigate the rectifying behaviors of the organic single-molecule S(CH2)11-terminated with a variety of heterocyclics (i.e., BIPY, PHE, PHEPY, and PYR) coupled with two semi-infinite Au electrodes. Our quantum transport calculation results show that the BIPY and PHE nanojunctions show the high-efficiency rectifying effects. While, differently, the current-voltage (I-V) curves of PHEPY and PYR nanojunctions display the insulating and linear characters, respectively. The corresponding electronic transport mechanisms are analyzed in detail. Our calculation results demonstrate that these investigated organic single-molecule nanojunctions have the potential applications in rectifiers and molecular wires.

  11. 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.

  12. Energy-Level Alignment for Single-Molecule Conductance of Extended Metal-Atom Chains.

    PubMed

    Ting, Ta-Cheng; Hsu, Liang-Yan; Huang, Min-Jie; Horng, Er-Chien; Lu, Hao-Cheng; Hsu, Chan-Hsiang; Jiang, Ching-Hong; Jin, Bih-Yaw; Peng, Shie-Ming; Chen, Chun-Hsien

    2015-12-21

    The use of single-molecule junctions for various functions constitutes a central goal of molecular electronics. The functional features and the efficiency of electron transport are dictated by the degree of energy-level alignment (ELA), that is, the offset potential between the electrode Fermi level and the frontier molecular orbitals. Examples manifesting ELA are rare owing to experimental challenges and the large energy barriers of typical model compounds. In this work, single-molecule junctions of organometallic compounds with five metal centers joined in a collinear fashion were analyzed. The single-molecule i-V scans could be conducted in a reliable manner, and the EFMO levels were electrochemically accessible. When the electrode Fermi level (EF ) is close to the frontier orbitals (EFMO ) of the bridging molecule, larger conductance was observed. The smaller |EF -EFMO | gap was also derived quantitatively, unambiguously confirming the ELA. The mechanism is described in terms of a two-level model involving co-tunneling and sequential tunneling processes. PMID:26546238

  13. 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.

  14. Dynamics of interfacial electron-transfer processes in colloidal semiconductor systems

    SciTech Connect

    Duonghong, D.; Ransden, J.; Gratzel, M.

    1982-06-02

    The dynamics of interfacial electron-transfer reactions were studied with colloidal Ti0/sub 2/ and CdS particles, which form transparent aqueous dipersions. Excitation of the semiconductor was carried out by a nanosecond laser flash and subsequent conduction-band electron (e/sup -//sub CB/ and hole (h/sup +/) transfer reactions to solution species examined by kinetic spectroscopy. Methylviologen (MV/sup 2 +/) was employed as an electron acceptor and thiocyanate or phenothiazine derivative as a hole scavenger. Excitation of colloidal Ti0/sub 2/ leads to long-lived e/sup -//sub CB/ whose rate of reaction with MV/sup 2 +/ is strongly influenced by the MV/sup 2 +/ concentration and pH. The pH effect on the yield of MV/sup +/ can be exploited to derive the flat-band potential of the particle for which a value of E/sub fb/ = 0.130 - 0.059(pH) V (vs. NHE) was obtained. In the case of colloidal CdS the lifetime of the electron-hole pair was determined as 0.3 ns from time-resolved fluorescence spectroscopy.Only donors or acceptors adsorbed onto the particle surface can intervene as h/sup +/ or e/sup -//sub CB/ scavengers, respectively. Experiments with Pt-loaded CdS established the competition of catalytic H/sub 2/ production by e/sup -//sub CB/ with electron transfer to adsorbed MV/sup 2 +/. RuO/sub 2/ deposits are shown to enhance hole transfer from the valence band to solution species.

  15. Dynamic Chromatin Regulation from a Single Molecule Perspective.

    PubMed

    Fierz, Beat

    2016-03-18

    Chromatin regulatory processes, like all biological reactions, are dynamic and stochastic in nature but can give rise to stable and inheritable changes in gene expression patterns. A molecular understanding of those processes is key for fundamental biological insight into gene regulation, epigenetic inheritance, lineage determination, and therapeutic intervention in the case of disease. In recent years, great progress has been made in identifying important molecular players involved in key chromatin regulatory pathways. Conversely, we are only beginning to understand the dynamic interplay between protein effectors, transcription factors, and the chromatin substrate itself. Single-molecule approaches employing both highly defined chromatin substrates in vitro, as well as direct observation of complex regulatory processes in vivo, open new avenues for a molecular view of chromatin regulation. This review highlights recent applications of single-molecule methods and related techniques to investigate fundamental chromatin regulatory processes. PMID:26565113

  16. 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 μV/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

  17. Single-Molecule Observation of Prokaryotic DNA Replication

    PubMed Central

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

    2010-01-01

    Recent advances in optical imaging and molecular manipulation techniques have made it possible to observe the activity of individual enzymes and study the dynamic properties of processes that are challenging to elucidate using ensemble-averaging techniques. The use of single-molecule approaches has proven to be particularly successful in the study of the dynamic interactions between the components at the replication fork. In this section, we describe the methods necessary for in vitro single-molecule studies of prokaryotic replication systems. Through these experiments, accurate information can be obtained on the rates and processivities of DNA unwinding and polymerization. The ability to monitor in real time the progress of a single replication fork allows for the detection of short-lived, intermediate states that would be difficult to visualize in bulk-phase assays. PMID:19563119

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

    NASA Astrophysics Data System (ADS)

    Otosu, Takuhiro; Ishii, Kunihiko; Tahara, Tahei

    2015-07-01

    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.

  19. Single molecule study of ClpP enzymatic activity

    NASA Astrophysics Data System (ADS)

    Mazouchi, Amir; Yu, Angela; Houry, Walid; Gradinaru, Claudiu

    2009-03-01

    Elementary processes that form the basis of biological activities pass through a number of short-lived intermediate states while progressing from initial state to final state. Single-molecule techniques, unlike ensemble averaging measurements, are often able to resolve these transient states. ClpP, a known target of antibacterial drugs like acydepsipeptides (ADEPs), is a classical representative of serine proteases, enzymes that cleave peptide bonds in proteins. We performed single-molecule fluorescence measurements including burst spectroscopy and fluorescence correlation spectroscopy (FCS) to address unknown aspects of this degradation process. Our study reveals important molecular details of protein degradation, such as the enzyme-substrate binding rate, the lifetime distribution of the conjugated state and the probability of substrate cleavage upon conjugation.

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

    PubMed

    Hatzakis, Nikos S

    2014-02-01

    Biomolecular interactions regulate a plethora of vital cellular processes, including signal transduction, metabolism, catalysis and gene regulation. Regulation is encoded in the molecular properties of the constituent proteins; distinct conformations correspond to different functional outcomes. To describe the molecular basis of this behavior, two main mechanisms have been advanced: 'induced fit' and 'conformational selection'. Our understanding of these models relies primarily on NMR, computational studies and kinetic measurements. These techniques report the average behavior of a large ensemble of unsynchronized molecules, often masking intrinsic dynamic behavior of proteins and biologically significant transient intermediates. Single molecule measurements are emerging as a powerful tool for characterizing protein function. They offer the direct observation and quantification of the activity, abundance and lifetime of multiple states and transient intermediates in the energy landscape, that are typically averaged out in non-synchronized ensemble measurements. Here we survey new insights from single molecule studies that advance our understanding of the molecular mechanisms underlying biomolecular recognition. PMID:24342874

  1. Three-dimensional molecular modeling with single molecule FRET.

    PubMed

    Brunger, Axel T; Strop, Pavel; Vrljic, Marija; Chu, Steven; Weninger, Keith R

    2011-03-01

    Single molecule fluorescence energy transfer experiments enable investigations of macromolecular conformation and folding by the introduction of fluorescent dyes at specific sites in the macromolecule. Multiple such experiments can be performed with different labeling site combinations in order to map complex conformational changes or interactions between multiple molecules. Distances that are derived from such experiments can be used for determination of the fluorophore positions by triangulation. When combined with a known structure of the macromolecule(s) to which the fluorophores are attached, a three-dimensional model of the system can be determined. However, care has to be taken to properly derive distance from fluorescence energy transfer efficiency and to recognize the systematic or random errors for this relationship. Here we review the experimental and computational methods used for three-dimensional modeling based on single molecule fluorescence resonance transfer, and describe recent progress in pushing the limits of this approach to macromolecular complexes. PMID:20837146

  2. Three-dimensional Molecular Modeling with Single Molecule FRET

    PubMed Central

    Brunger, Axel T.; Strop, Pavel; Vrljic, Marija; Chu, Steven; Weninger, Keith R.

    2011-01-01

    Single molecule fluorescence energy transfer experiments enable investigations of macromolecular conformation and folding by the introduction of fluorescent dyes at specific sites in the macromolecule. Multiple such experiments can be performed with different labeling site combinations in order to map complex conformational changes or interactions between multiple molecules. Distances that are derived from such experiments can be used for determination of the fluorophore positions by triangulation. When combined with a known structure of the macromolecule(s) to which the fluorophores are attached, a three-dimensional model of the system can be determined. However, care has to be taken to properly derive distance from fluorescence energy transfer efficiency and to recognize the systematic or random errors for this relationship. Here we review the experimental and computational methods used for three-dimensional modeling based on single molecule fluorescence resonance transfer, and describe recent progress in pushing the limits of this approach to macromolecular complexes. PMID:20837146

  3. 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].

  4. Visualizing Cellular Machines with Colocalization Single Molecule Microscopy

    PubMed Central

    Larson, Joshua D.; Rodgers, Margaret L.

    2013-01-01

    Many of the cell's macromolecular machines contain multiple components that transiently associate with one another. This compositional and dynamic complexity presents a challenge for understanding how these machines are constructed and function. Colocalization single molecule spectroscopy enables simultaneous observation of individual components of these machines in real-time and grants a unique window into processes that are typically obscured in ensemble assays. Colocalization experiments can yield valuable information about assembly pathways, compositional heterogeneity, and kinetics that together contribute to the development of richly detailed reaction mechanisms. This review focuses on recent advances in colocalization single molecule spectroscopy and how this technique has been applied to enhance our understanding of transcription, RNA splicing, and translation. PMID:23970346

  5. 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.

  6. Applications of optical trapping to single molecule DNA

    SciTech Connect

    Sonek, G.J.; Berns, M.W.; Keller, R.A.

    1997-12-01

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

  7. High-Resolution, Single-Molecule Measurements of Biomolecular Motion

    PubMed Central

    Greenleaf, William J.; Woodside, Michael T.; Block, Steven M.

    2007-01-01

    Many biologically important macromolecules undergo motions that are essential to their function. Biophysical techniques can now resolve the motions of single molecules down to the nanometer scale or even below, providing new insights into the mechanisms that drive molecular movements. This review outlines the principal approaches that have been used for high-resolution measurements of single-molecule motion, including centroid tracking, fluorescence resonance energy transfer, magnetic tweezers, atomic force microscopy, and optical traps. For each technique, the principles of operation are outlined, the capabilities and typical applications are examined, and various practical issues for implementation are considered. Extensions to these methods are also discussed, with an eye toward future application to outstanding biological problems. PMID:17328679

  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. 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.

  10. 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

  11. Hydration effects on membrane structure probed by single molecule orientations.

    PubMed

    Huckabay, Heath A; Dunn, Robert C

    2011-03-15

    Single molecule fluorescence measurements are used to probe the structural changes in glass-supported DPPC bilayers as a function of relative humidity (RH). Defocused polarized total internal reflection fluorescence microscopy is employed to determine the three-dimensional orientation of the fluorescent lipid analogue BODIPY-PC, doped into DPPC membranes in trace amounts. Supported DPPC bilayers formed using vesicle fusion and Langmuir-Blodgett/Langmuir-Schäfer (LB/LS) transfer are compared and show similar trends as a function of relative humidity. Population histograms of the emission dipole tilt angle reveal bimodal distributions as observed previously for BODIPY-PC in DPPC. These distributions are dominated by large populations of BODIPY-PC molecules with emission dipoles oriented parallel (≥81°) and normal (≤10°) to the membrane plane, with less than 25% oriented at intermediate tilts. As the relative humidity is increased from 13% to 95%, the population of molecules oriented normal to the surface decreases with a concomitant increase in those oriented parallel to the surface. The close agreement in trends observed for bilayers formed from vesicle fusion and LB/LS transfer supports the assignment of an equivalent surface pressure of 23 mN/m for bilayers formed from vesicle fusion. At each RH condition, a small population of BODIPY-PC dye molecules are laterally mobile in both bilayer preparations. This population exponentially increases with RH but never exceeds 6% of the total population. Interestingly, even under conditions where there is little lateral diffusion, fluctuations in the single molecule orientations can be observed which suggests there is appreciable freedom in the acyl chain region. Dynamic measurements of single molecule orientation changes, therefore, provide a new view into membrane properties at the single molecule level. PMID:21319764

  12. Microfluidic Device for Single-Molecule Experiments with Enhanced Photostability

    PubMed Central

    Lemke, Edward A.; Gambin, Yann; Vandelinder, Virginia; Brustad, Eric M.; Liu, Hsiao-Wei; Schultz, Peter G.

    2009-01-01

    A microfluidic device made of PDMS addresses key limitations in single-molecule fluorescence experiments by providing high dye photostability and low sample sticking. Photobleaching is dramatically reduced by deoxygenation via gas diffusion through porous channel walls. Rapid buffer exchange in a laminar sheath flow followed by optical interrogation minimizes surface-sample contacts, and allows the in situ addition and combination of other reagents. PMID:19772358

  13. 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.

  14. 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.

  15. Single-Molecule Studies of Actin Assembly and Disassembly Factors

    PubMed Central

    Smith, Benjamin A.; Gelles, Jeff; Goode, Bruce L.

    2014-01-01

    The actin cytoskeleton is very dynamic and highly regulated by multiple associated proteins in vivo. Understanding how this system of proteins functions in the processes of actin network assembly and disassembly requires methods to dissect the mechanisms of activity of individual factors and of multiple factors acting in concert. The advent of single-filament and single-molecule fluorescence imaging methods has provided a powerful new approach to discovering actin-regulatory activities and obtaining direct, quantitative insights into the pathways of molecular interactions that regulate actin network architecture and dynamics. Here we describe techniques for acquisition and analysis of single-molecule data, applied to the novel challenges of studying the filament assembly and disassembly activities of actin-associated proteins in vitro. We discuss the advantages of single-molecule analysis in directly visualizing the order of molecular events, measuring the kinetic rates of filament binding and dissociation, and studying the coordination among multiple factors. The methods described here complement traditional biochemical approaches in elucidating actin-regulatory mechanisms in reconstituted filamentous networks. PMID:24630103

  16. Towards Single-Molecule Optical Mapping of the Epigenome

    PubMed Central

    Levy-Sakin, Michal; Grunwald, Assaf; Kim, Soohong; Gassman, Natalie R.; Gottfried, Anna; Antelman, Josh; Kim, Younggyu; Ho, Sam; Samuel, Robin; Michalet, Xavier; Lin, Ron R.; Dertinger, Thomas; Kim, Andrew S.; Chung, Sangyoon; Colyer, Ryan A.; Weinhold, Elmar; Weiss, Shimon; Ebenstein, Yuval

    2014-01-01

    The last decade has seen an explosive growth in the utilization of single-molecule techniques for the study of complex systems. The ability to resolve phenomena otherwise masked by ensemble averaging has made these approaches especially attractive for the study of biological systems, where stochastic events lead to inherent inhomogeneity on the population level. The complex composition of the genome has made it an ideal system to study on the single-molecule level and methods aimed at resolving genetic information from long, individual, genomic DNA molecules have been in use for the last 30 years. These methods, and particularly optical based mapping of DNA, have been instrumental in highlighting genomic variation and contributed significantly to the assembly of many genomes including the human genome. Nanotechnology and nanoscopy have been a strong driving force for advancing genomic mapping approaches, allowing both better manipulation of DNA on the nano-scale and enhanced optical resolving power for analysis of genomic information. In the very last years, these developments have been adopted also for epigenetic studies. The common principle for these studies is the use of advanced optical microscopy for the detection of fluorescently labeled epigenetic marks on long, extended DNA molecules. Here we will discuss recent single-molecule studies for the mapping of chromatin composition and epigenetic DNA modifications, such as DNA methylation. PMID:24328256

  17. Viruses and Tetraspanins: Lessons from Single Molecule Approaches

    PubMed Central

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

    2014-01-01

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

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

    PubMed

    Malý, Pavel; Gruber, J Michael; van Grondelle, Rienk; Mančal, Tomáš

    2016-01-01

    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 chlorophylls, Lut 1 can act as an efficient fluorescence quencher in LHCII. PMID:27189196

  19. Semisynthetic protein nanoreactor for single-molecule chemistry

    PubMed Central

    Lee, Joongoo; Bayley, Hagan

    2015-01-01

    The covalent chemistry of individual reactants bound within a protein pore can be monitored by observing the ionic current flow through the pore, which acts as a nanoreactor responding to bond-making and bond-breaking events. In the present work, we incorporated an unnatural amino acid into the α-hemolysin (αHL) pore by using solid-phase peptide synthesis to make the central segment of the polypeptide chain, which forms the transmembrane β-barrel of the assembled heptamer. The full-length αHL monomer was obtained by native chemical ligation of the central synthetic peptide to flanking recombinant polypeptides. αHL pores with one semisynthetic subunit were then used as nanoreactors for single-molecule chemistry. By introducing an amino acid with a terminal alkyne group, we were able to visualize click chemistry at the single-molecule level, which revealed a long-lived (4.5-s) reaction intermediate. Additional side chains might be introduced in a similar fashion, thereby greatly expanding the range of single-molecule covalent chemistry that can be investigated by the nanoreactor approach. PMID:26504203

  20. Single-molecule imaging of hyaluronan in human synovial fluid

    NASA Astrophysics Data System (ADS)

    Kappler, Joachim; Kaminski, Tim P.; Gieselmann, Volkmar; Kubitscheck, Ulrich; Jerosch, Jörg

    2010-11-01

    Human synovial fluid contains a high concentration of hyaluronan, a high molecular weight glycosaminoglycan that provides viscoelasticity and contributes to joint lubrication. In osteoarthritis synovial fluid, the concentration and molecular weight of hyaluronan decrease, thus impairing shock absorption and lubrication. Consistently, substitution of hyaluronan (viscosupplementation) is a widely used treatment for osteoarthritis. So far, the organization and dynamics of hyaluronan in native human synovial fluid and its action mechanism in viscosupplementation are poorly characterized at the molecular level. Here, we introduce highly sensitive single molecule microscopy to analyze the conformation and interactions of fluorescently labeled hyaluronan molecules in native human synovial fluid. Our findings are consistent with a random coil conformation of hyaluronan in human synovial fluid, and point to specific interactions of hyaluronan molecules with the synovial fluid matrix. Furthermore, single molecule microscopy is capable of detecting the breakdown of the synovial fluid matrix in osteoarthritis. Thus, single molecule microscopy is a useful new method to probe the structure of human synovial fluid and its changes in disease states like osteoarthritis.

  1. Nonequilibrium Single Molecule Protein Folding in a Coaxial Mixer

    PubMed Central

    Hamadani, Kambiz M.; Weiss, Shimon

    2008-01-01

    We have developed a continuous-flow mixing device suitable for monitoring bioconformational reactions at the single-molecule level with a response time of ∼10 ms under single-molecule flow conditions. Its coaxial geometry allows three-dimensional hydrodynamic focusing of sample fluids to diffraction-limited dimensions where diffusional mixing is rapid and efficient. The capillary-based design enables rapid in-lab construction of mixers without the need for expensive lithography-based microfabrication facilities. In-line filtering of sample fluids using granulated silica particles virtually eliminates clogging and extends the lifetime of each device to many months. In this article, to determine both the distance-to-time transfer function and the instrument response function of the device we characterize its fluid flow and mixing properties using both fluorescence cross-correlation spectroscopy velocimetry and finite element fluid dynamics simulations. We then apply the mixer to single molecule FRET protein folding studies of Chymotrypsin Inhibitor protein 2. By transiently populating the unfolded state of Chymotrypsin Inhibitor Protein 2 (CI2) under nonequilibrium in vitro refolding conditions, we spatially and temporally resolve the denaturant-dependent nonspecific collapse of the unfolded state from the barrier-limited folding transition of CI2. Our results are consistent with previous CI2 mixing results that found evidence for a heterogeneous unfolded state consisting of cis- and trans-proline conformers. PMID:18339751

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

    PubMed

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

    2014-06-19

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

  3. Semisynthetic protein nanoreactor for single-molecule chemistry.

    PubMed

    Lee, Joongoo; Bayley, Hagan

    2015-11-10

    The covalent chemistry of individual reactants bound within a protein pore can be monitored by observing the ionic current flow through the pore, which acts as a nanoreactor responding to bond-making and bond-breaking events. In the present work, we incorporated an unnatural amino acid into the α-hemolysin (αHL) pore by using solid-phase peptide synthesis to make the central segment of the polypeptide chain, which forms the transmembrane β-barrel of the assembled heptamer. The full-length αHL monomer was obtained by native chemical ligation of the central synthetic peptide to flanking recombinant polypeptides. αHL pores with one semisynthetic subunit were then used as nanoreactors for single-molecule chemistry. By introducing an amino acid with a terminal alkyne group, we were able to visualize click chemistry at the single-molecule level, which revealed a long-lived (4.5-s) reaction intermediate. Additional side chains might be introduced in a similar fashion, thereby greatly expanding the range of single-molecule covalent chemistry that can be investigated by the nanoreactor approach. PMID:26504203

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

    PubMed Central

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

    2007-01-01

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

  5. Designer Plasmonics Nanostructures Approaching Single Molecule Raman Scattering

    NASA Astrophysics Data System (ADS)

    Gordon, Reuven; Min, Qiao; Andrade, Gustavo F. S.; Brolo, Alexandre G.

    2010-03-01

    Since the early reports of single molecule Raman scattering detection using randomly roughened metal substrates [Phys. Rev. Lett. 78, 1667 - 1670 (1997), Science 21, 275(5303), 1102 - 1106 (1997)], there has been considerable interest in achieving single molecule Raman spectroscopy from fabricated nanostructures that are not random. Such designer plasmonic nanostructures have the advantages of improved control over the near-field enhancement magnitude, deterministic placement of the local-field hot-spots, optimized collection efficiency and greater reproducibility. Previously, we have created a metal nanostructures with measured 20 molecule Raman signal limit of detection [J. Phys. Chem. C 112 (39), 15098-15101, (2008)]. To achieve the desired near-field electric field enhancements, those nanostructures contained familiar elements to the plasmonic community: concentric focusing rings and subwavelength focusing tapers. Here, we will describe improved designs that have enabled us to improve those results by a factor of 6. We will also show polarization dependent studies that clearly demonstrate the plasmonic nature of the subwavelength focusing structures, including experimental polarization-resolved Raman spectroscopy maps. We are beginning statistical analysis experiments to determine if single molecule Raman is present in these nanostructures.

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

    PubMed

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

    2014-12-15

    From the onset of the first microscopic visualization of single fluorescent molecules in living cells at the beginning of this century, to the present, almost routine application of single molecule microscopy, the method has well-proven its ability to contribute unmatched detailed insight into the heterogeneous and dynamic molecular world life is composed of. Except for investigations on bacteria and yeast, almost the entire story of success is based on studies on adherent mammalian 2D cell cultures. However, despite this continuous progress, the technique was not able to keep pace with the move of the cell biology community to adapt 3D cell culture models for basic research, regenerative medicine, or drug development and screening. In this review, we will summarize the progress, which only recently allowed for the application of single molecule microscopy to 3D cell systems and give an overview of the technical advances that led to it. While initially posing a challenge, we finally conclude that relevant 3D cell models will become an integral part of the on-going success of single molecule microscopy. PMID:25453259

  7. 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

  8. "Sticky electrons" transport and interfacial transfer of electrons in the dye-sensitized solar cell.

    PubMed

    Peter, Laurence

    2009-11-17

    Dye-sensitized solar cells (DSCs, also known as Gratzel cells) mimic the photosynthetic process by using a sensitizer dye to harvest light energy to generate electrical power. Several functional features of these photochemical devices are unusual, and DSC research offers a rewarding arena in which to test new ideas, new materials, and new methodologies. Indeed, one of the most attractive chemical features of the DSC is that the basic concept can be used to construct a range of devices, replacing individual components with alternative materials. Despite two decades of increasing research activity, however, many aspects of the behavior of electrons in the DSC remain puzzling. In this Account, we highlight current understanding of the processes involved in the functioning of the DSC, with particular emphasis on what happens to the electrons in the mesoporous film following the injection step. The collection of photoinjected electrons appears to involve a random walk process in which electrons move through the network of interconnected titanium dioxide nanoparticles while undergoing frequent trapping and detrapping. During their passage to the cell contact, electrons may be lost by transfer to tri-iodide species in the redox electrolyte that permeates the mesoporous film. Competition between electron collection and back electron transfer determines the performance of a DSC: ideally, all injected electrons should be collected without loss. This Account then goes on to survey recent experimental and theoretical progress in the field, placing particular emphasis on issues that need to be resolved before we can gain a clear picture of how the DSC works. Several important questions about the behavior of "sticky" electrons, those that undergo multiple trapping and detrapping, in the DSC remain unanswered. The most fundamental of these concerns is the nature of the electron traps that appear to dominate the time-dependent photocurrent and photovoltage response of DSCs. The origin of the nonideality factor in the relationship between the intensity and the DSC photovoltage is also unclear, as is the discrepancy in electron diffusion length values determined by steady-state and non-steady-state methods. With these unanswered questions, DSC research is likely to remain an active and fruitful area for some years to come. PMID:19637905

  9. Ensemble and Single-Molecule Studies on Fluorescence Quenching in Transition Metal Bipyridine-Complexes

    PubMed Central

    Brox, Dominik; Kiel, Alexander; Wörner, Svenja Johanna; Pernpointner, Markus; Comba, Peter; Martin, Bodo; Herten, Dirk-Peter

    2013-01-01

    Beyond their use in analytical chemistry fluorescent probes continuously gain importance because of recent applications of single-molecule fluorescence spectroscopy to monitor elementary reaction steps. In this context, we characterized quenching of a fluorescent probe by different metal ions with fluorescence spectroscopy in the bulk and at the single-molecule level. We apply a quantitative model to explain deviations from existing standard models for fluorescence quenching. The model is based on a reversible transition from a bright to a dim state upon binding of the metal ion. We use the model to estimate the stability constants of complexes with different metal ions and the change of the relative quantum yield of different reporter dye labels. We found ensemble data to agree widely with results from single-molecule experiments. Our data indicates a mechanism involving close molecular contact of dye and quenching moiety which we also found in molecular dynamics simulations. We close the manuscript with a discussion of possible mechanisms based on Förster distances and electrochemical potentials which renders photo-induced electron transfer to be more likely than Förster resonance energy transfer. PMID:23483966

  10. Probing Single-Molecule Dissociations from a Bimolecular Complex NO-Co-Porphyrin.

    PubMed

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

    2015-07-28

    Axial coordinations of diatomic NO molecules to metalloporphyrins play key roles in dynamic processes of biological functions such as blood pressure control and immune response. Probing such reactions at the single molecule level is essential to understand their physical mechanisms but has been rarely performed. Here we report on our single molecule dissociation experiments of diatomic NO from NO-Co-porphyrin complexes describing its dissociation mechanisms. Under tunneling junctions of scanning tunneling microscope, both positive and negative energy pulses gave rise to dissociations of NO with threshold voltages, +0.68 and -0.74 V at 0.1 nA tunneling current on Au(111). From the observed power law relations between dissociation rate and tunneling current, we argue that the dissociations were inelastically induced with molecular orbital resonances by stochastically tunneling electrons, which is supported with our density functional theory calculations. Our study shows that single molecule dissociation experiments can be used to probe reaction mechanisms in a variety of axial coordinations between small molecules and metalloporphyrins. PMID:26172541

  11. 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

  12. Single-Molecule Diodes with High On/Off Ratios Through Environmental Control

    NASA Astrophysics Data System (ADS)

    Capozzi, Brian; Xia, Jianlong; Dell, Emma; Adak, Olgun; Liu, Zhen-Fei; Neaton, Jeffrey; Campos, Luis; Venkataraman, Latha

    2015-03-01

    Single-Molecule diodes were first proposed with an asymmetric molecule comprising a donor-bridge-acceptor architecture to mimic a semiconductor p-n junction. Progress in molecular electronics has led to the realization of several single-molecule diodes; these have relied on asymmetric molecular backbones, asymmetric molecule-electrode linkers, or asymmetric electrode materials. Despite these advances, molecular diodes have had limited potential for functional applications due to several pitfalls, including low rectification ratios (``on''/``off'' current ratios <10). Here, we introduce a powerful approach for inducing rectification in conventionally symmetric single-molecule junctions, taking advantage of environmental factors about the junction. By utilizing an asymmetric environment instead of an asymmetric molecule, we reproducibly achieve high rectification ratios at low operating voltages for molecular junctions based on a family of symmetric small-gap molecules. This technique serves as an unconventional approach for developing functional molecular-scale devices and probing their charge transport characteristics. Furthermore, this technique should be applicable to other nanoscale devices, providing a general route for tuning device properties.

  13. Single-molecule studies of unconventional motor protein myosin VI

    NASA Astrophysics Data System (ADS)

    Kim, HyeongJun

    Myosin VI is one of the myosin superfamily members that are actin-based molecular motors. It has received special attention due to its distinct features as compared to other myosins, such as its opposite directionality and a much larger step size than expected given the length of its "leg". This dissertation presents the author.s graduate work of several single-molecule studies on myosin VI. Special attention was paid to some of myosin VI.s tail domains that consist of proximal tail (PT), medial tail (MT), distal tail (DT) domains and cargo-binding domain (CBD). The functional form of myosin VI in cells is still under debate. Although full length myosin VI proteins in cytosolic extracts of cells were monomers from earlier studies, there are several reasons why it is now believed that myosin VI could exist as a dimer. If this is true and dimerization occurs, the next logical question would be which parts of myosin VI are dimerization regions? One model claimed that the CBD is the sole dimerization region. A competing model claimed that there must be another region that could be involved in dimerization, based on their observation that a construct without the CBD could still dimerize. Our single-molecule experiment with progressively truncated myosin VI constructs showed that the MT domain is a dimerization region, supporting the latter model. Additional single-molecule experiments and molecular dynamics (MD) simulation done with our collaborators suggest that electrostatic salt bridges formed between positive and negative amino acid residues are mainly responsible for the MT domain dimerization. After resolving this, we are left with another important question which is how myosin VI can take such a large step. Recent crystal structure showed that one of the tail domains preceding the MT domain, called the PT domain, is a three-helix bundle. The most easily conceivable way might be an unfolding of the three-helix bundle upon dimerization, allowing the protein to stretch and reach a larger distance. The single-molecule stepping data with mutant full-length construct that lacks two helices out of three in the PT domain tell that it is indeed the case. In this dissertation, more details of myosin VI PT/MT domain experiments will be explored along with background information on the single-molecule experiment methods used in these studies.

  14. Intracellular bottom-up generation of targeted nanosensors for single-molecule imaging

    NASA Astrophysics Data System (ADS)

    Hou, Yanyan; Arai, Satoshi; Kitaguchi, Tetsuya; Suzuki, Madoka

    2016-02-01

    Organic dyes are useful tools for sensing cellular activities but unfavorable in single-molecule imaging, whereas quantum dots (QDs) are widely applied in single-molecule imaging but with few sensing applications. Here, to visualize cellular activities by monitoring the response of a single probe in living cells, we propose a bottom-up approach to generate nanoprobes where four organic dyes are conjugated to tetravalent single-chain avidin (scAVD) proteins via an intracellular click reaction. We demonstrate that the nanoprobes, exhibiting increased brightness and enhanced photostability, were detectable as single dots in living cells. The ease of intracellular targeting allowed the tracking of endoplasmic reticulum (ER) remodeling with nanometer spatial resolution. Conjugating thermosensitive dyes generated temperature-sensitive nanoprobes on ER membranes that successfully monitored local temperature changes in response to external heat pulses. Our approach is potentially a suitable tool for visualizing localized cellular activities with single probe sensitivity in living cells.Organic dyes are useful tools for sensing cellular activities but unfavorable in single-molecule imaging, whereas quantum dots (QDs) are widely applied in single-molecule imaging but with few sensing applications. Here, to visualize cellular activities by monitoring the response of a single probe in living cells, we propose a bottom-up approach to generate nanoprobes where four organic dyes are conjugated to tetravalent single-chain avidin (scAVD) proteins via an intracellular click reaction. We demonstrate that the nanoprobes, exhibiting increased brightness and enhanced photostability, were detectable as single dots in living cells. The ease of intracellular targeting allowed the tracking of endoplasmic reticulum (ER) remodeling with nanometer spatial resolution. Conjugating thermosensitive dyes generated temperature-sensitive nanoprobes on ER membranes that successfully monitored local temperature changes in response to external heat pulses. Our approach is potentially a suitable tool for visualizing localized cellular activities with single probe sensitivity in living cells. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr08012f

  15. Influence of phonon-associated tunneling rate on transport through a single-molecule transistor

    NASA Astrophysics Data System (ADS)

    Tang, Ying-Tsan; Chuu, Der-San; Lin, Kao-Chin

    2011-01-01

    We study the electronic transport through a single-molecule transistor (SMT) by considering the phonon-associated tunneling rate. We find that the electron-phonon interaction (EPI) changes the constant conductivities of the leads into a multi-channel structure of single vibration frequency. This interference of the multi-channel tunneling process results in a bias-dependent tunneling rate and obscures the conductance peaks at large bias voltage. The bias-dependent tunneling rate further causes a remarkable conductivity gap between the chemical potential of the leads ( n=0) and the first phonon sideband ( n=1). These anomalies are consistent with the experimental observations in transport experiments.

  16. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

  18. Advances in magnetic tweezers for single molecule and cell biophysics.

    PubMed

    Kilinc, Devrim; Lee, Gil U

    2014-01-01

    Magnetic tweezers (MTW) enable highly accurate forces to be transduced to molecules to study mechanotransduction at the molecular or cellular level. We review recent MTW studies in single molecule and cell biophysics that demonstrate the flexibility of this technique. We also discuss technical advances in the method on several fronts, i.e., from novel approaches for the measurement of torque to multiplexed biophysical assays. Finally, we describe multi-component nanorods with enhanced optical and magnetic properties and discuss their potential as future MTW probes. PMID:24263142

  19. Single molecule labeling of an atomic force microscope cantilever tip

    PubMed Central

    Liu, Jianwei; Butte, Manish J.

    2012-01-01

    In this paper, we present a method to functionalize the very apex of an atomic force microscope cantilever with a single or a few molecules. In force spectroscopy or interaction mapping, the cantilever must be functionalized with only a few molecules to avoid noise or spurious measurements. Here, we covalently attached single molecules to the cantilever by touching it to a paper wetted with a solution of quantum dots. The paper competes with wicking up the hydrophilic surface of the tip. This method has broad applications in scanning probe microscopy where small numbers of molecules are needed on the tip. PMID:23152642

  20. Reversible Positioning of Single Molecules inside Zero-Mode Waveguides

    PubMed Central

    2015-01-01

    We have developed a hybrid nanopore/zero-mode waveguide device for single-molecule fluorescence and DNA sequencing applications. The device is a freestanding solid-state membrane with sub-5 nm nanopores that reversibly delivers individual biomolecules to the base of 70 nm diameter waveguides for interrogation. Rapid and reversible molecular loading is achieved by controlling the voltage across the device. Using this device we demonstrate protein and DNA loading with efficiency that is orders of magnitude higher than diffusion-based molecular loading. PMID:25209321

  1. Multiplexed single-molecule force spectroscopy using a centrifuge

    PubMed Central

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

    2016-01-01

    We present a miniature centrifuge force microscope (CFM) that repurposes a benchtop centrifuge for high-throughput single-molecule experiments with high-resolution particle tracking, a large force range, temperature control and simple push-button operation. Incorporating DNA nanoswitches to enable repeated interrogation by force of single molecular pairs, we demonstrate increased throughput, reliability and the ability to characterize population heterogeneity. We perform spatiotemporally multiplexed experiments to collect 1,863 bond rupture statistics from 538 traceable molecular pairs in a single experiment, and show that 2 populations of DNA zippers can be distinguished using per-molecule statistics to reduce noise. PMID:26984516

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

    PubMed

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

    2016-01-01

    We present a miniature centrifuge force microscope (CFM) that repurposes a benchtop centrifuge for high-throughput single-molecule experiments with high-resolution particle tracking, a large force range, temperature control and simple push-button operation. Incorporating DNA nanoswitches to enable repeated interrogation by force of single molecular pairs, we demonstrate increased throughput, reliability and the ability to characterize population heterogeneity. We perform spatiotemporally multiplexed experiments to collect 1,863 bond rupture statistics from 538 traceable molecular pairs in a single experiment, and show that 2 populations of DNA zippers can be distinguished using per-molecule statistics to reduce noise. PMID:26984516

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

    PubMed

    Tian, Yuxi; Navarro, Pedro; Orrit, Michel

    2014-09-26

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

  4. Single Molecule as a Local Acoustic Detector for Mechanical Oscillators

    NASA Astrophysics Data System (ADS)

    Tian, Yuxi; Navarro, Pedro; Orrit, Michel

    2014-09-01

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

  5. 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 μm channel and confocal two-color fluorescence microscopy.

  6. 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

  7. Multiplexed single-molecule force spectroscopy using a centrifuge

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  8. Ultrafast Photoinduced Interfacial Proton Coupled Electron Transfer from CdSe Quantum Dots to 4,4'-Bipyridine.

    PubMed

    Chen, Jinquan; Wu, Kaifeng; Rudshteyn, Benjamin; Jia, Yanyan; Ding, Wendu; Xie, Zhao-Xiong; Batista, Victor S; Lian, Tianquan

    2016-01-27

    Pyridine and derivatives have been reported as efficient and selective catalysts for the electrochemical and photoelectrochemical reduction of CO2 to methanol. Although the catalytic mechanism remains a subject of considerable recent debate, most proposed models involve interfacial proton coupled electron transfer (PCET) to electrode-bound catalysts. We report a combined experimental and theoretical study of the photoreduction of 4,4'-bipyridium (bPYD) using CdSe quantum dots (QDs) as a model system for interfacial PCET. We observed ultrafast photoinduced PCET from CdSe QDs to form doubly protonated [bPYDH2](+•) radical cations at low pH (4-6). Through studies of the dependence of PCET rate on isotopic substitution, pH and bPYD concentration, the radical formation mechanism was identified to be a sequential interfacial electron and proton transfer (ET/PT) process with a rate-limiting pH independent electron transfer rate constant, kint, of 1.05 ± 0.13 × 10(10) s(-1) between a QD and an adsorbed singly protonated [bPYDH](+). Theoretical studies of the adsorption of [bPYDH](+) and methylviologen on QD surfaces revealed important effects of hydrogen bonding with the capping ligand (3-mercaptopropionic acid) on binding geometry and interfacial PCET. In the presence of sacrificial electron donors, this system was shown to be capable of generating [bPYDH2](+•) radical cations under continuous illumination at 405 nm with a steady-state photoreduction quantum yield of 1.1 ± 0.1% at pH 4. The mechanism of bPYD photoreduction reported in this work may provide useful insights into the catalytic roles of pyridine and pyridine derivatives in the electrochemical and photoelectrochemical reduction of CO2. PMID:26713752

  9. Rational design of DNA-actuated enzyme nanoreactors guided by single molecule analysis

    NASA Astrophysics Data System (ADS)

    Dhakal, Soma; Adendorff, Matthew R.; Liu, Minghui; Yan, Hao; Bathe, Mark; Walter, Nils G.

    2016-01-01

    The control of enzymatic reactions using nanoscale DNA devices offers a powerful application of DNA nanotechnology uniquely derived from actuation. However, previous characterization of enzymatic reaction rates using bulk biochemical assays reported suboptimal function of DNA devices such as tweezers. To gain mechanistic insight into this deficiency and to identify design rules to improve their function, here we exploit the synergy of single molecule imaging and computational modeling to characterize the three-dimensional structures and catalytic functions of DNA tweezer-actuated nanoreactors. Our analysis revealed two important deficiencies - incomplete closure upon actuation and conformational heterogeneity. Upon rational redesign of the Holliday junctions located at their hinge and arms, we found that the DNA tweezers could be more completely and uniformly closed. A novel single molecule enzyme assay was developed to demonstrate that our design improvements yield significant, independent enhancements in the fraction of active enzyme nanoreactors and their individual substrate turnover frequencies. The sequence-level design strategies explored here may aid more broadly in improving the performance of DNA-based nanodevices including biological and chemical sensors.The control of enzymatic reactions using nanoscale DNA devices offers a powerful application of DNA nanotechnology uniquely derived from actuation. However, previous characterization of enzymatic reaction rates using bulk biochemical assays reported suboptimal function of DNA devices such as tweezers. To gain mechanistic insight into this deficiency and to identify design rules to improve their function, here we exploit the synergy of single molecule imaging and computational modeling to characterize the three-dimensional structures and catalytic functions of DNA tweezer-actuated nanoreactors. Our analysis revealed two important deficiencies - incomplete closure upon actuation and conformational heterogeneity. Upon rational redesign of the Holliday junctions located at their hinge and arms, we found that the DNA tweezers could be more completely and uniformly closed. A novel single molecule enzyme assay was developed to demonstrate that our design improvements yield significant, independent enhancements in the fraction of active enzyme nanoreactors and their individual substrate turnover frequencies. The sequence-level design strategies explored here may aid more broadly in improving the performance of DNA-based nanodevices including biological and chemical sensors. Electronic supplementary information (ESI) available: Details of the DNA sequences, assembly, and bulk characterization of all DNA tweezers; details of the smFRET characterization of the tweezers; additional AFM images; detailed results of MD simulation; bulk measurement of tweezer-scaffolded G6pDH activity; and single molecule measurements of tweezer-scaffolded G6pDH activity. See DOI: 10.1039/c5nr07263h

  10. 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.

  11. Cationic Mn4 single-molecule magnet with a sterically isolated core.

    PubMed

    Heroux, Katie J; Quddusi, Hajrah M; Liu, Junjie; O'Brien, James R; Nakano, Motohiro; del Barco, Enrique; Hill, Stephen; Hendrickson, David N

    2011-08-15

    The synthesis, structure, and magnetic properties of a ligand-modified Mn(4) dicubane single-molecule magnet (SMM), [Mn(4)(Bet)(4)(mdea)(2)(mdeaH)(2)](BPh(4))(4), are presented, where the cationic SMM units are significantly separated from neighboring molecules in the crystal lattice. There are no cocrystallized solvate molecules, making it an ideal candidate for single-crystal magnetization hysteresis and high-frequency electron paramagnetic resonance studies. Increased control over intermolecular interactions in such materials is a crucial factor in the future application of SMMs. PMID:21751785

  12. Kinetic Measurements on Single-molecule Disulfide Bond Cleavage

    PubMed Central

    Liang, Jian; Fernández, Julio M.

    2011-01-01

    We use single-molecule force clamp spectroscopy (SMFCS) to explore the reactivity of tris(2-carboxyethyl)phosphine (TCEP), 1, 4-DL-dithiothreitol (DTT) and hydrosulfide anion (HS-) on disulfide bonds within a mechanically stretched polypeptide. The single-bond level bimolecular nucleophilic substitution (SN2) events are recorded at a series of precisely-controlled temperatures so that the Arrhenius kinetic parameters, i.e. the height of the activation energy barrier (Ea) and the attempting frequency (A) of the chemical reactions, can be determined. The values of A are typically at the order of 107 M-1s-1, which is far lower than that predicted by the transition-state theory, in which A is given by kBT/h and around 1012 M-1s-1 at room temperature. Furthermore, Ea is derived to be 30-40 kJ/mol, which can be lowered by ~6-8% with every 100 pN mechanical force applied. The correlation of the A and Ea with the molecular structures reveals that the relative magnitude of these two parameters cannot be simply judged from the size of the molecule or the nucleophilicity of the attacking atom. The comparison of the influences on the reaction rate induced by force and temperature indicates an equivalent accelerating effect by every 50 pN or 10 K increment, giving for the first time the relationship between mechanical and thermal effects on a single-molecule SN2 chemical reaction. PMID:21341766

  13. DCDHF Fluorophores for Single-Molecule Imaging in Cells**

    PubMed Central

    Lord, Samuel J.; Conley, Nicholas R.; Lee, Hsiao-lu D.; Nishimura, Stefanie Y.; Pomerantz, Andrea K.; Willets, Katherine A.; Lu, Zhikuan; Wang, Hui; Liu, Na; Samuel, Reichel; Weber, Ryan; Semyonov, Alexander; He, Meng; Twieg, Robert J.; Moerner, W. E.

    2009-01-01

    There is a persistent need for small-molecule fluorescent labels optimized for single-molecule imaging in the cellular environment. Application of these labels comes with a set of strict requirements: strong absorption, efficient and stable emission, water solubility and membrane permeability, low background emission, and red-shifted absorption to avoid cell autofluorescence. We have designed and characterized several fluorophores, termed “DCDHF” fluorophores, for use in live-cell imaging based on the push–pull design: an amine donor group and a 2-dicyanomethylene-3-cyano-2,5-dihydrofuran (DCDHF) acceptor group, separated by a π-rich conjugated network. In general, the DCDHF fluorophores are comparatively photostable, sensitive to local environment, and their chemistries and photophysics are tunable to optimize absorption wavelength, membrane affinity, and solubility. Especially valuable are fluorophores with sophisticated photophysics for applications requiring additional facets of control, such as photoactivation. For example, we have reengineered a red-emitting DCDHF fluorophore so that it is dark until photoactivated with a short burst of low-intensity violet light. This molecule and its relatives provide a new class of bright photoactivatable small-molecule fluorophores, which are needed for super-resolution imaging schemes that require active control (here turning-on) of single-molecule emission. PMID:19025732

  14. New assay for multiple single molecule enzyme kinetics

    NASA Astrophysics Data System (ADS)

    Lee, Alan I.; Brody, James P.

    2005-03-01

    A population of identical proteins has the same amino acid sequence, but there may be subtle differences in local folding that lead to variations in activity. Single molecule studies allow us to understand these subtle differences. Single molecule experiments are usually time consuming and difficult because only a few molecules are observed in one experiment. To address this problem, we have developed an assay where we can simultaneously measure the activity of multiple individual molecules of a protease, α-chymotrypsin. The assay utilizes a synthetic chymotrypsin substrate that is non-fluorescent before cleavage by chymotrypsin, but is intensely fluorescent after. To study the activity of individual enzymes, the enzyme and substrate are encapsulated in micron-sized droplets of water surrounded by silicone oil. On average, each micro-droplet contains less than one enzyme. The fluorescence of these droplets is recorded over time using a microscope and a CCD camera system. Software tracks individual droplets over time and records fluorescence. The kinetics of individual chymotrypsin molecules is calculated through the increase of fluorescence intensity of the same individual droplet over time. The activity profiles of the individual enzymes and the bulk sample of the enzyme are very similar. This validates the assay and demonstrates that the average of a few individual molecules can be representative of the behavior of the bulk population.

  15. 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

  16. 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

  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. Single Molecule Observation of the Cyclization of Short DNA Duplex

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  19. 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.

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

    NASA Astrophysics Data System (ADS)

    Lee, M. Ann; Dunn, Robert C.

    1997-03-01

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

  1. Single-molecule super-resolution light-sheet microscopy.

    PubMed

    Hu, Ying S; Zimmerley, Maxwell; Li, Yu; Watters, Robin; Cang, Hu

    2014-03-17

    Single-molecule super-resolution imaging is a new promising tool for investigation of sub-cellular structures. Concurrently, light-sheet microscopy, also known as selective plane illumination microscopy (SPIM), has gained rapid favor with the imaging community in developmental biology due to its fast speed, high contrast, deep penetration, and low phototoxicity. While nearly a dozen reviews thoroughly describe the development of light-sheet microscopy and its technological breakthroughs with a main focus on improving the 3D imaging speed of fish embryos, central nervous system, and other tissues, few have addressed the potential of combining light-sheet microscopy and localization-based super-resolution imaging to achieve sub-diffraction-limited resolution. Adapting light-sheet illumination for single-molecule imaging presents unique challenges for instrumentation and reconstruction algorithms. In this Minireview, we provide an overview of the recent developments that address these challenges. We compare different approaches in super-resolution and light-sheet imaging, address advantages and limitations in each approach, and outline future directions of this emerging field. PMID:24615819

  2. 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

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

    NASA Astrophysics Data System (ADS)

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

    2012-07-01

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

  4. Single molecule studies of the neuronal SNARE fusion machinery

    PubMed Central

    Brunger, Axel T.; Weninger, Keith; Bowen, Mark; Chu, Steven

    2010-01-01

    SNAREs are essential components of the machinery for Ca2+-triggered fusion of synaptic vesicles with the plasma membrane, resulting in neurotransmitter release into the synaptic cleft. While much is known about their biophysical and structural properties and their interactions with accessory proteins such as the Ca2+ sensor synaptotagmin, their precise role in membrane fusion remains an enigma. Ensemble studies of liposomes with reconstituted SNAREs have demonstrated that SNAREs and accessory proteins can trigger lipid mixing/fusion, but the inability to study individual fusion events has precluded molecular insights into the fusion process. Thus, this field is ripe for studies with single molecule methodology. In this review we discuss first applications of single-molecule approaches to observe reconstituted SNAREs, their complexes, associated proteins, and their effect on biological membranes. Some of the findings are provocative, such the possibility of parallel and anti-parallel SNARE complexes, or vesicle docking with only syntaxin and synaptobrevin, but have been confirmed by other experiments. PMID:19489736

  5. Single-molecule studies of the neuronal SNARE fusion machinery.

    PubMed

    Brunger, Axel T; Weninger, Keith; Bowen, Mark; Chu, Steven

    2009-01-01

    SNAREs are essential components of the machinery for Ca(2+)-triggered fusion of synaptic vesicles with the plasma membrane, resulting in neurotransmitter release into the synaptic cleft. Although much is known about their biophysical and structural properties and their interactions with accessory proteins such as the Ca(2+) sensor synaptotagmin, their precise role in membrane fusion remains an enigma. Ensemble studies of liposomes with reconstituted SNAREs have demonstrated that SNAREs and accessory proteins can trigger lipid mixing/fusion, but the inability to study individual fusion events has precluded molecular insights into the fusion process. Thus, this field is ripe for studies with single-molecule methodology. In this review, we discuss applications of single-molecule approaches to observe reconstituted SNAREs, their complexes, associated proteins, and their effect on biological membranes. Some of the findings are provocative, such as the possibility of parallel and antiparallel SNARE complexes or of vesicle docking with only syntaxin and synaptobrevin, but have been confirmed by other experiments. PMID:19489736

  6. Single-Molecule High-Resolution Colocalization of Single Probes

    PubMed Central

    Churchman, L. Stirling; Spudich, James A.

    2016-01-01

    Colocalization of fluorescent probes is commonly used in cell biology to discern the proximity of two proteins in the cell. Considering that the resolution limit of optical microscopy is on the order of 250 nm, there has not been a need for high-resolution colocalization techniques. However, with the advent of higher resolution techniques for cell biology and single-molecule biophysics, colocalization must also improve. For diffraction-limited applications, a geometric transformation (i.e., translation, scaling, and rotation) is typically applied to one color channel to align it with the other; however, to achieve high-resolution colocalization, this is not sufficient. Single-molecule high-resolution colocalization (SHREC) of single probes uses the local weighted mean transformation to achieve a colocalization resolution of at least 10 nm. This protocol describes the acquisition of registration data and the analysis required to obtain a high-resolution mapping between imaging channels. The total internal reflection fluorescence microscope (TIRFM) system described is designed to excite and image the fluorescent probes Cy3 and Cy5. Modifications may be required depending on the requirements of the individual study. PMID:22301661

  7. 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.

  8. 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.

  9. 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 λ-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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

    PubMed

    Kushch, L A; Sasnovskaya, V D; Dmitriev, A I; Yagubskii, E B; Koplak, O V; Zorina, L V; Boukhvalov, D W

    2012-11-28

    A new high symmetry Mn(12) oxocarboxylate cluster [Mn(12)O(12)(CN-o-C(6)H(4)CO(2))(12)(CH(3)CO(2))(4)(H(2)O)(4)]·8CH(2)Cl(2) (1) with mixed carboxylate ligands is reported. It was synthesized by the standard carboxylate substitution method. 1 crystallizes in the tetragonal space group I4(1)/a. Complex 1 contains a [Mn(12)O(12)] core with eight CN-o-C(6)H(4)CO(2) ligands in the axial positions, four CH(3)CO(2) and four CN-o-C(6)H(4)CO(2) in equatorial positions. Four H(2)O molecules are bonded to four Mn atoms in an alternating up, down, up, down arrangement indicating a 1 : 1 : 1 : 1 isomer. The Mn(12) 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 Mn(12) clusters. The lattice solvent molecules (CH(2)Cl(2)) are weakly interacted with Mn(12) 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 the center of gravity of the bands shifts down from the Fermi level. The overlap between Mn 3d bands and 2p ones of the oxygen atoms from the carboxylate bridges is higher than in the parent Mn(12)-acetate cluster. These changes in the electronic structure provide a significant difference in the exchange interactions in comparison to Mn(12)-acetate. The magnetic properties have been studied on a dried (solvent-free) polycrystalline sample of 1. The dc magnetic susceptibility measurements in the 2-300 K temperature range support a high-spin ground state (S = 10). A bifurcation of temperature dependencies of magnetization taken under zero field cooled and field cooled conditions observed below 4.5 K is due to slow magnetization relaxation. Magnetization versus applied dc field exhibited a stepwise hysteresis loop at 2 K. The ac magnetic susceptibility data revealed the frequency dependent out-of-phase (χ(M)'') signals characteristic of single-molecule magnets. PMID:23059752

  14. Single-molecule light emission at room temperature on a wide-band-gap semiconductor

    NASA Astrophysics Data System (ADS)

    Yang, H.; Mayne, A. J.; Comtet, G.; Dujardin, G.; Kuk, Y.; Nagarajan, S.; Gourdon, A.

    2014-09-01

    Room-temperature light emission from single chemisorbed perylene based molecules adsorbed on silicon carbide (SiC) is probed by scanning tunneling microscopy (STM). A new approach to STM-induced luminescence of a single molecule is explored using a wide-band-gap semiconductor to decouple electronically the molecule from the surface. After molecular adsorption, the lowest unoccupied molecular orbital and the highest occupied molecular orbital (HOMO) both lie within the bulk band gap and below the Fermi level of the substrate. The maximum photon energy of the light emission from the molecule shows a fixed shift of 1.5 eV relative to the maximum energy of the tunnel electrons. This is consistent with the photons being generated by inelastic electron tunneling between the HOMO and the unoccupied electronic states of the STM tip.

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

    NASA Astrophysics Data System (ADS)

    Xu, Mingsheng

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

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

    PubMed Central

    Belyy, Vladislav; Yildiz, Ahmet

    2014-01-01

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

  17. Nonlinear irreversible thermodynamics of single-molecule experiments.

    PubMed

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

    2015-06-01

    Irreversible thermodynamics of single-molecule experiments subject to external constraining forces of a mechanical nature is presented. Extending Onsager's formalism to the nonlinear case of systems under nonequilibrium external constraints, we are able to calculate the entropy production and the general nonlinear kinetic equations for the variables involved. In particular, we analyze the case of RNA stretching protocols obtaining critical oscillations between different configurational states when forced by external means to remain in the unstable region of its free-energy landscape, as observed in experiments. We also calculate the entropy produced during these hopping events and show how resonant phenomena in stretching experiments of single RNA macromolecules may arise. We also calculate the hopping rates using Kramer's approach obtaining a good comparison with experiments. PMID:26172743

  18. 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.

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

    PubMed Central

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

    2013-01-01

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

  20. Single-Molecule Detection in Micron-Sized Capillaries

    NASA Astrophysics Data System (ADS)

    Ball, David A.; Shen, Guoqing; Davis, Lloyd M.

    2004-11-01

    The detection of individual molecules in solution by laser-induced fluorescence is becoming an increasingly important tool for biophysics research and biotechnology applications. In a typical single-molecule detection (SMD) experiment, diffusion is the dominant mode of transport of fluorophores through the focused laser beam. In order to more rapidly process a large number of slowly diffusing bio-molecules for applications in pharmaceutical drug discovery, a flow can be introduced within a capillary. If the flow speed is sufficient, bio-molecules will be carried through the probe volume significantly faster than by diffusion alone. Here we discuss SMD near the tip of, and in, such micron-sized capillaries, with a high numerical-aperture microscope objective used for confocal-epi-illumination along the axis of the capillary. Problems such as molecular adsorption to the glass are also addressed.

  1. Eukaryotic transcriptional dynamics: from single molecules to cell populations

    PubMed Central

    Coulon, Antoine; Chow, Carson C.; Singer, Robert H.; Larson, Daniel R.

    2013-01-01

    Transcriptional regulation is achieved through combinatorial interactions between regulatory elements in the human genome and a vast range of factors that modulate the recruitment and activity of RNA polymerase. Experimental approaches for studying transcription in vivo now extend from single-molecule techniques to genome-wide measurements. Parallel to these developments is the need for testable quantitative and predictive models for understanding gene regulation. These conceptual models must also provide insight into the dynamics of transcription and the variability that is observed at the single-cell level. In this Review, we discuss recent results on transcriptional regulation and also the models those results engender. We show how a non-equilibrium description informs our view of transcription by explicitly considering time-and energy-dependence at the molecular level. PMID:23835438

  2. Continuous base identification for single-molecule nanopore DNA sequencing

    NASA Astrophysics Data System (ADS)

    Clarke, James; Wu, Hai-Chen; Jayasinghe, Lakmal; Patel, Alpesh; Reid, Stuart; Bayley, Hagan

    2009-04-01

    A single-molecule method for sequencing DNA that does not require fluorescent labelling could reduce costs and increase sequencing speeds. An exonuclease enzyme might be used to cleave individual nucleotide molecules from the DNA, and when coupled to an appropriate detection system, these nucleotides could be identified in the correct order. Here, we show that a protein nanopore with a covalently attached adapter molecule can continuously identify unlabelled nucleoside 5'-monophosphate molecules with accuracies averaging 99.8%. Methylated cytosine can also be distinguished from the four standard DNA bases: guanine, adenine, thymine and cytosine. The operating conditions are compatible with the exonuclease, and the kinetic data show that the nucleotides have a high probability of translocation through the nanopore and, therefore, of not being registered twice. This highly accurate tool is suitable for integration into a system for sequencing nucleic acids and for analysing epigenetic modifications.

  3. Kinesin regulation dynamics through cargo delivery, a single molecule investigation

    NASA Astrophysics Data System (ADS)

    Kovacs, Anthony; Kessler, Jonathan; Lin, Huawen; Dutcher, Susan; Wang, Yan Mei

    2015-03-01

    Kinesins are microtubule-based motors that deliver cargo to their destinations in a highly regulated manner. Although in recent years numerous regulators of cargo delivery have been identified, the regulation mechanism of kinesin through the cargo delivery and recycling process is not known. By performing single molecule fluorescence imaging measurements in Chlamydomonas flagella, which are 200 nm in diameter, 10 microns in length, and contain 9 sets of microtubule doublets, we tracked the intraflagellar transport (IFT) trains, BBSome cargo, and kinesin-2 motors through the cargo delivery process and determined the aforementioned dynamics. Upon arrival at the microtubule plus end at the flagellar tip, (1) IFT trains and BBSome cargo remain intact, dissociate together from kinesins and microtubules, and diffuse along flagellar membrane for a mean of 2.3 sec before commencing retrograde travel. (2) Kinesin motors remain bound to and diffuse along microtubules for 1.3 sec before dissociating into the flagellar lumen for recycling.

  4. Single Molecule Stepping and Structural Dynamics of Myosin X

    PubMed Central

    Sun, Yujie; Sato, Osamu; Ruhnow, Felix; Arsenault, Mark E.; Ikebe, Mitsuo; Goldman, Yale E.

    2010-01-01

    Myosin X is an unconventional myosin with puzzling motility properties. We studied the motility of dimerized myosin X using single molecule fluorescence techniques – polTIRF, FIONA, and Parallax to measure rotation angles and 3-dimensional position of the molecule during its walk. It was found that Myosin X steps processively in a hand-over-hand manner following a left-handed helical path along both single actin filaments and bundles. Its step size and velocity are smaller on actin bundles than individual filaments, suggesting myosin X often steps onto neighboring filaments in a bundle. The data suggest that a previously postulated single α-helical domain mechanically extends the 3-IQ motif lever arm and either the neck-tail hinge or the tail is flexible. These structural features, in conjunction with the membrane and microtubule binding domains, enable myosin X to perform multiple functions on varied actin structures in cells. PMID:20364131

  5. Bayesian cluster identification in single-molecule localization microscopy data.

    PubMed

    Rubin-Delanchy, Patrick; Burn, Garth L; Griffi, Juliette; Williamson, David J; Heard, Nicholas A; Cope, Andrew P; Owen, Dylan M

    2015-11-01

    Single-molecule localization-based super-resolution microscopy techniques such as photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM) produce pointillist data sets of molecular coordinates. Although many algorithms exist for the identification and localization of molecules from raw image data, methods for analyzing the resulting point patterns for properties such as clustering have remained relatively under-studied. Here we present a model-based Bayesian approach to evaluate molecular cluster assignment proposals, generated in this study by analysis based on Ripley's K function. The method takes full account of the individual localization precisions calculated for each emitter. We validate the approach using simulated data, as well as experimental data on the clustering behavior of CD3?, a subunit of the CD3 T cell receptor complex, in resting and activated primary human T cells. PMID:26436479

  6. Single molecule targeted sequencing for cancer gene mutation detection.

    PubMed

    Gao, Yan; Deng, Liwei; Yan, Qin; Gao, Yongqian; Wu, Zengding; Cai, Jinsen; Ji, Daorui; Li, Gailing; Wu, Ping; Jin, Huan; Zhao, Luyang; Liu, Song; Ge, Liangjin; Deem, Michael W; He, Jiankui

    2016-01-01

    With the rapid decline in cost of sequencing, it is now affordable to examine multiple genes in a single disease-targeted clinical test using next generation sequencing. Current targeted sequencing methods require a separate step of targeted capture enrichment during sample preparation before sequencing. Although there are fast sample preparation methods available in market, the library preparation process is still relatively complicated for physicians to use routinely. Here, we introduced an amplification-free Single Molecule Targeted Sequencing (SMTS) technology, which combined targeted capture and sequencing in one step. We demonstrated that this technology can detect low-frequency mutations using artificially synthesized DNA sample. SMTS has several potential advantages, including simple sample preparation thus no biases and errors are introduced by PCR reaction. SMTS has the potential to be an easy and quick sequencing technology for clinical diagnosis such as cancer gene mutation detection, infectious disease detection, inherited condition screening and noninvasive prenatal diagnosis. PMID:27193446

  7. Subnanometre enzyme mechanics probed by single-molecule force spectroscopy

    PubMed Central

    Pelz, Benjamin; Žoldák, Gabriel; Zeller, Fabian; Zacharias, Martin; Rief, Matthias

    2016-01-01

    Enzymes are molecular machines that bind substrates specifically, provide an adequate chemical environment for catalysis and exchange products rapidly, to ensure fast turnover rates. Direct information about the energetics that drive conformational changes is difficult to obtain. We used subnanometre single-molecule force spectroscopy to study the energetic drive of substrate-dependent lid closing in the enzyme adenylate kinase. Here we show that in the presence of the bisubstrate inhibitor diadenosine pentaphosphate (AP5A), closing and opening of both lids is cooperative and tightly coupled to inhibitor binding. Surprisingly, binding of the substrates ADP and ATP exhibits a much smaller energetic drive towards the fully closed state. Instead, we observe a new dominant energetic minimum with both lids half closed. Our results, combining experiment and molecular dynamics simulations, give detailed mechanical insights into how an enzyme can cope with the seemingly contradictory requirements of rapid substrate exchange and tight closing, to ensure efficient catalysis. PMID:26906294

  8. 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

  9. 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.

  10. 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.

  11. Enhancing single molecule imaging in optofluidics and microfluidics.

    PubMed

    Vasdekis, Andreas E; Laporte, Gregoire P J

    2011-01-01

    Microfluidics and optofluidics have revolutionized high-throughput analysis and chemical synthesis over the past decade. Single molecule imaging has witnessed similar growth, due to its capacity to reveal heterogeneities at high spatial and temporal resolutions. However, both resolution types are dependent on the signal to noise ratio (SNR) of the image. In this paper, we review how the SNR can be enhanced in optofluidics and microfluidics. Starting with optofluidics, we outline integrated photonic structures that increase the signal emitted by single chromophores and minimize the excitation volume. Turning then to microfluidics, we review the compatible functionalization strategies that reduce noise stemming from non-specific interactions and architectures that minimize bleaching and blinking. PMID:21954349

  12. Subnanometre enzyme mechanics probed by single-molecule force spectroscopy.

    PubMed

    Pelz, Benjamin; oldk, Gabriel; Zeller, Fabian; Zacharias, Martin; Rief, Matthias

    2016-01-01

    Enzymes are molecular machines that bind substrates specifically, provide an adequate chemical environment for catalysis and exchange products rapidly, to ensure fast turnover rates. Direct information about the energetics that drive conformational changes is difficult to obtain. We used subnanometre single-molecule force spectroscopy to study the energetic drive of substrate-dependent lid closing in the enzyme adenylate kinase. Here we show that in the presence of the bisubstrate inhibitor diadenosine pentaphosphate (AP5A), closing and opening of both lids is cooperative and tightly coupled to inhibitor binding. Surprisingly, binding of the substrates ADP and ATP exhibits a much smaller energetic drive towards the fully closed state. Instead, we observe a new dominant energetic minimum with both lids half closed. Our results, combining experiment and molecular dynamics simulations, give detailed mechanical insights into how an enzyme can cope with the seemingly contradictory requirements of rapid substrate exchange and tight closing, to ensure efficient catalysis. PMID:26906294

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

    NASA Astrophysics Data System (ADS)

    Liu, Yun; Garg, Anupam

    2016-03-01

    Tunneling between the two lowest energy levels of single molecule magnets with Ising type anisotropy, accompanied by the emission or absorption of phonons, is considered. Quantitatively accurate calculations of the rates for such tunneling are performed for a model Hamiltonian especially relevant to the best studied example, Fe8. Two different methods are used: high-order perturbation theory in the spin-phonon interaction and the non-Ising-symmetric parts of the spin Hamiltonian, and a novel semiclassical approach based on spin-coherent-state-path-integral instantons. The methods are found to be in good quantitative agreement with other, and consistent with previous approaches to the problem. The implications of these results for magnetization of molecular solids of these molecules are discussed briefly.

  14. Progress towards DNA sequencing at the single molecule level

    SciTech Connect

    Goodwin, P.M.; Affleck, R.L.; Ambrose, W.P.

    1995-12-01

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

  15. Subnanometre enzyme mechanics probed by single-molecule force spectroscopy

    NASA Astrophysics Data System (ADS)

    Pelz, Benjamin; Žoldák, Gabriel; Zeller, Fabian; Zacharias, Martin; Rief, Matthias

    2016-02-01

    Enzymes are molecular machines that bind substrates specifically, provide an adequate chemical environment for catalysis and exchange products rapidly, to ensure fast turnover rates. Direct information about the energetics that drive conformational changes is difficult to obtain. We used subnanometre single-molecule force spectroscopy to study the energetic drive of substrate-dependent lid closing in the enzyme adenylate kinase. Here we show that in the presence of the bisubstrate inhibitor diadenosine pentaphosphate (AP5A), closing and opening of both lids is cooperative and tightly coupled to inhibitor binding. Surprisingly, binding of the substrates ADP and ATP exhibits a much smaller energetic drive towards the fully closed state. Instead, we observe a new dominant energetic minimum with both lids half closed. Our results, combining experiment and molecular dynamics simulations, give detailed mechanical insights into how an enzyme can cope with the seemingly contradictory requirements of rapid substrate exchange and tight closing, to ensure efficient catalysis.

  16. Single-cell and single-molecule laser biotechnology

    NASA Astrophysics Data System (ADS)

    Greulich, Karl O.; Bauer, Eckhard; Fiedler, Ursula; Hoyer, Carsten; Koenig, Karsten; Monajembashi, Shamci

    1996-01-01

    While lasers have found a wide field of application in the analysis of cells and biomolecules, their use in manipulation is less common. Now, new applications of lasers are emerging, which aim at cells and even molecules as biotechnological individuals: For example, in single cell gel electrophoresis individual cells are irradiated by UV laser pulses which cause radiation damage to DNA. When the whole cell is positioned in an electric field and the UV induced damages are converted into DNA strand breaks, the resulting DNA fragments are eluted out of the cell nucleus. Small fragments are running further than large ones. After staining of the DNA fragments, the cell has the appearance like a comet (therefore comet assay). The tail moment, a parameter quantifying the shape of the tail, gives information on the degree of DNA damage. The kinetics of DNA damage induction can be described by a type of exponential law with parameters which are related to radiation sensitivity of the DNA. A further emerging technique aims at DNA as a molecular individuum. One pivotal step for single molecule DNA analysis is single molecule handling. For that purpose, a DNA molecule is coupled to a micrometer sized polystyrene bead, either via an avidin-biotin bridge or, more specifically, by strand recognition, and labeled with fluorescence dyes such as DAPI. In order to visualize the dynamics of individual DNA molecules, highly sensitive video processing and single photon counting is required. Moving the polystyrene bead using optical tweezers, the molecule can be deformed, i.e., bent, turned or stretched. Using a laser microbeam, the same individual molecule can be cut into smaller portions.

  17. Determining Serpin Conformational Distributions with Single Molecule Fluorescence

    PubMed Central

    Mushero, Nicole; Gershenson, Anne

    2012-01-01

    Conformational plasticity is key to inhibitory serpin function, and this plasticity gives serpins relatively easy access to alternative, dysfunctional conformations. Thus, a given serpin population may contain both functional and dysfunctional proteins. Single molecule fluorescence (SMF), with its ability to interrogate one fluorescently labeled protein at a time, is a powerful method for elucidating conformational distributions and monitoring how these distributions change over time. SMF and related methods have been particularly valuable for characterizing serpin polymerization. Fluorescence correlation spectroscopy experiments have revealed a second lag phase during in vitro α1-antitrypsin polymerization associated with the formation of smaller oligomers that then condense to form longer polymers [Purkayastha, P., Klemke, J. W., Lavender, S., Oyola, R., Cooperman, B. S., and Gai, F. (2005). Alpha 1-antitrypsin polymerization: A fluorescence correlation spectroscopic study. Biochemistry 44, 2642–2649.]. SMF studies of in vitro neuroserpin polymerization have confirmed that a monomeric intermediate is required for polymer formation while providing a test of proposed polymerization mechanisms [Chiou, A., Hägglöf, P., Orte, A., Chen, A. Y., Dunne, P. D., Belorgey, D., Karlsson-Li, S., Lomas, D., and Klenerman, D. (2009)]. Probing neuroserpin polymerization and interaction with amyloid-beta peptides using single molecule fluorescence. Biophys. J. 97, 2306–2315.]. SMF has also been used to monitor protease–serpin interactions. Single pair Förster resonance energy transfer studies of covalent protease–serpin complexes suggest that the extent of protease structural disruption in the complex is protease dependent [Liu, L., Mushero, N., Hedstrom, L., and Gershenson, A. (2006). Conformational distributions of protease-serpin complexes: A partially translocated complex. Biochemistry 45, 10865–10872.]. SMF techniques are still evolving and the combination of SMF with encapsulation methods has the potential to provide more detailed information on the conformational changes associated with serpin polymerization, protease–serpin complex formation, and serpin folding. PMID:22078542

  18. Femtosecond coherence and quantum control of single molecules at room temperature

    NASA Astrophysics Data System (ADS)

    Hildner, Richard; Brinks, Daan; van Hulst, Niek F.

    2011-02-01

    Quantum-mechanical phenomena, such as electronic coherence and entanglement, play a key role in several remarkably efficient natural processes including ultrafast electronic energy transfer and charge separation in photosynthetic light-harvesting. To gain insight into such dynamic processes of biomolecules it is vital to reveal relations between structural and quantum-mechanical properties. However, ensemble experiments targeting ultrafast coherences are hampered by the large intrinsic heterogeneity in these systems at physiological conditions, and single-molecule techniques have not been available until now. Here we show, by employing femtosecond pulse-shaping techniques, that quantum coherences in single organic molecules can be created, probed and manipulated at ambient conditions even in highly disordered solid environments. We find broadly distributed coherence decay times for different individual molecules giving direct insight into the structural heterogeneity of the local surroundings. Most importantly, we induce Rabi oscillations and control the coherent superposition state in a single molecule, thus carrying out a basic femtosecond single-qubit operation at room temperature.

  19. 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.

  20. 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).

  1. 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.

  2. Subnanometre single-molecule localization, registration and distance measurements.

    PubMed

    Pertsinidis, Alexandros; Zhang, Yunxiang; Chu, Steven

    2010-07-29

    Remarkable progress in optical microscopy has been made in the measurement of nanometre distances. If diffraction blurs the image of a point object into an Airy disk with a root-mean-squared (r.m.s.) size of s = 0.44lambda/2NA (approximately 90 nm for light with a wavelength of lambda = 600 nm and an objective lens with a numerical aperture of NA = 1.49), limiting the resolution of the far-field microscope in use to d = 2.4s approximately = 200 nm, additional knowledge about the specimen can be used to great advantage. For example, if the source is known to be two spatially resolved fluorescent molecules, the distance between them is given by the separation of the centres of the two fluorescence images. In high-resolution microwave and optical spectroscopy, there are numerous examples where the line centre is determined with a precision of less than 10(-6) of the linewidth. In contrast, in biological applications the brightest single fluorescent emitters can be detected with a signal-to-noise ratio of approximately 100, limiting the centroid localization precision to s(loc) > or = 1% (> or = 1 nm) of the r.m.s. size, s, of the microscope point spread function (PSF). Moreover, the error in co-localizing two or more single emitters is notably worse, remaining greater than 5-10% (5-10 nm) of the PSF size. Here we report a distance resolution of s(reg) = 0.50 nm (1sigma) and an absolute accuracy of s(distance) = 0.77 nm (1sigma) in a measurement of the separation between differently coloured fluorescent molecules using conventional far-field fluorescence imaging in physiological buffer conditions. The statistical uncertainty in the mean for an ensemble of identical single-molecule samples is limited only by the total number of collected photons, to s(loc) approximately 0.3 nm, which is approximately 3 x 10(-3) times the size of the optical PSF. Our method may also be used to improve the resolution of many subwavelength, far-field imaging methods such as those based on co-localization of molecules that are stochastically switched on in space. The improved resolution will allow the structure of large, multisubunit biological complexes in biologically relevant environments to be deciphered at the single-molecule level. PMID:20613725

  3. Compact quantum dots for single-molecule imaging.

    TOXLINE Toxicology Bibliographic Information

    Smith AM; Nie S

    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).

  4. 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 Δ{sub 1}-like and Δ{sub 5}-like symmetries.

  5. 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.

  6. 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.

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

    NASA Astrophysics Data System (ADS)

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

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

  8. Single-molecule imaging of DNA polymerase I (Klenow fragment) activity by atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Chao, J.; Zhang, P.; Wang, Q.; Wu, N.; Zhang, F.; Hu, J.; Fan, C. H.; Li, B.

    2016-03-01

    We report a DNA origami-facilitated single-molecule platform that exploits atomic force microscopy to study DNA replication. We imaged several functional activities of the Klenow fragment of E. coli DNA polymerase I (KF) including binding, moving, and dissociation from the template DNA. Upon completion of these actions, a double-stranded DNA molecule was formed. Furthermore, the direction of KF activities was captured and then confirmed by shifting the KF binding sites on the template DNA.We report a DNA origami-facilitated single-molecule platform that exploits atomic force microscopy to study DNA replication. We imaged several functional activities of the Klenow fragment of E. coli DNA polymerase I (KF) including binding, moving, and dissociation from the template DNA. Upon completion of these actions, a double-stranded DNA molecule was formed. Furthermore, the direction of KF activities was captured and then confirmed by shifting the KF binding sites on the template DNA. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr06544e

  9. Intramolecular Interactions of Highly π-Conjugated Perylenediimide Oligomers Probed by Single-Molecule Spectroscopy.

    PubMed

    Cho, Jae-Won; Yoo, Hyejin; Lee, Ji-Eun; Yan, Qifan; Zhao, Dahui; Kim, Dongho

    2014-11-01

    Highly π-conjugated perylenediimide (PDI) oligomers are promising low band gap organic materials for various applications in optoelectronics. In this work, individual fluorescence dynamics of ethynylene- and butadiynylene-bridged dimeric and trimeric PDIs (PEP, PBP, and PEPEP) were monitored and analyzed by single-molecule fluorescence spectroscopy to gain information on the degree of extension of π-conjugation through the acetylene bridge in PDI multichromophores. The simultaneous measurements of fluorescence intensity, lifetime, and spectrum indicate a sequential decrease in π-conjugation upon photobleaching of PDI monomer units. Furthermore, Huang-Rhys (HR) factors, S, are obtained to evaluate the degree of electronic coupling in view of π-conjugation and overall rigidity between the PDI units in PDI oligomers at the single-molecule level. In addition, butadiynylene-bridged dimeric PDI (PBP) reveals conformational heterogeneity due to the long butadiynylene linker. These results suggest a new way to control the photophysical properties of the PDI multichromophoric system by expansion of π-conjugation and modification with different linker groups. PMID:26278766

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

    PubMed Central

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

    2012-01-01

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

  11. Quantum Dot Spin Valves Controlled by Single Molecule Magnets

    NASA Astrophysics Data System (ADS)

    Rostamzadeh Renani, Fatemeh; Kirczenow, George

    2013-03-01

    We explore theoretically for the first time the properties of a new class of spintronic nano-devices in which the electrical resistance of a non-magnetic quantum dot contacted by non-magnetic electrodes is controlled by transition metal-based single molecule nanomagnets (SMMs) bound to the dot. Although the SMMs do not lie directly in the current path in these devices, we show that the relative orientation of their magnetic moments can strongly influence on the electric current passing through the device. If the magnetic moment of one of the SMMs is reversed by the application of a magnetic field, we predict a large change in the resistance of the dot, i.e., a strong spin valve effect. The mechanism is resonant conduction via molecular orbitals extending over the entire system. The spin valve is activated by a gate that tunes the transport resonances through the Fermi energy. Detailed results will be presented for the case of Mn12 SMMs bound to a gold quantum dot. This work was supported by CIFAR and NSERC.

  12. Imaging of single-molecule translocation through nuclear pore complexes

    PubMed Central

    Yang, Weidong; Gelles, Jeff; Musser, Siegfried M.

    2004-01-01

    Nuclear pore complexes (NPCs) mediate bidirectional transport of proteins, RNAs, and ribonucleoprotein complexes across the double-membrane nuclear envelope. In vitro studies with purified transport cofactors have revealed a general scheme of cofactor-dependent transport energetically driven by the G protein Ran. However, the size and complexity of NPCs have made it difficult to clearly define the loci and kinetics of the cofactor–NPC interactions required for transport. We now report the use of single-molecule fluorescence microscopy to directly monitor a model protein substrate undergoing transport through NPCs in permeabilized cells. This substrate, NLS-2xGFP, interacts with NPCs for an average of 10 ± 1 ms during transport. However, because the maximum nuclear accumulation rate of NLS-2xGFP was measured to be at least ≈103 molecules per NPC per s, NPCs must be capable of transporting at least ≈10 substrate molecules simultaneously. Molecular tracking reveals that substrate molecules spend most of their transit time randomly moving in the central pore of the NPC and that the rate-limiting step is escape from the central pore. PMID:15306682

  13. 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.

  14. 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.

  15. 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.

  16. 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

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

    NASA Astrophysics Data System (ADS)

    Ebenstein, Yuval; Gassman, Natalie; Weiss, Shimon

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

  18. A Theoretical Justification for Single Molecule Peptide Sequencing

    PubMed Central

    Swaminathan, Jagannath; Boulgakov, Alexander A.; Marcotte, Edward M.

    2015-01-01

    The proteomes of cells, tissues, and organisms reflect active cellular processes and change continuously in response to intracellular and extracellular cues. Deep, quantitative profiling of the proteome, especially if combined with mRNA and metabolite measurements, should provide an unprecedented view of cell state, better revealing functions and interactions of cell components. Molecular diagnostics and biomarker discovery should benefit particularly from the accurate quantification of proteomes, since complex diseases like cancer change protein abundances and modifications. Currently, shotgun mass spectrometry is the primary technology for high-throughput protein identification and quantification; while powerful, it lacks high sensitivity and coverage. We draw parallels with next-generation DNA sequencing and propose a strategy, termed fluorosequencing, for sequencing peptides in a complex protein sample at the level of single molecules. In the proposed approach, millions of individual fluorescently labeled peptides are visualized in parallel, monitoring changing patterns of fluorescence intensity as N-terminal amino acids are sequentially removed, and using the resulting fluorescence signatures (fluorosequences) to uniquely identify individual peptides. We introduce a theoretical foundation for fluorosequencing and, by using Monte Carlo computer simulations, we explore its feasibility, anticipate the most likely experimental errors, quantify their potential impact, and discuss the broad potential utility offered by a high-throughput peptide sequencing technology. PMID:25714988

  19. Single molecule detection of direct, homologous, DNA/DNA pairing

    PubMed Central

    Danilowicz, C.; Lee, C. H.; Kim, K.; Hatch, K.; Coljee, V. W.; Kleckner, N.; Prentiss, M.

    2009-01-01

    Using a parallel single molecule magnetic tweezers assay we demonstrate homologous pairing of two double-stranded (ds) DNA molecules in the absence of proteins, divalent metal ions, crowding agents, or free DNA ends. Pairing is accurate and rapid under physiological conditions of temperature and monovalent salt, even at DNA molecule concentrations orders of magnitude below those found in vivo, and in the presence of a large excess of nonspecific competitor DNA. Crowding agents further increase the reaction rate. Pairing is readily detected between regions of homology of 5 kb or more. Detected pairs are stable against thermal forces and shear forces up to 10 pN. These results strongly suggest that direct recognition of homology between chemically intact B-DNA molecules should be possible in vivo. The robustness of the observed signal raises the possibility that pairing might even be the “default” option, limited to desired situations by specific features. Protein-independent homologous pairing of intact dsDNA has been predicted theoretically, but further studies are needed to determine whether existing theories fit sequence length, temperature, and salt dependencies described here. PMID:19903884

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

    PubMed

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

    2015-03-11

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

  1. 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

  2. Single-molecule Force Spectroscopy of Intercellular Adhesion in Cancer

    NASA Astrophysics Data System (ADS)

    Wirtz, Denis

    2009-03-01

    The progression of several human cancers correlates with the loss of a-catenin from E-cadherin-rich intercellular junctions and loss of adhesion. However, the potential role of a-catenin in directly modulating the adhesive function of individual E-cadherin molecules in human cancer is unknown. Here we use single-molecule force spectroscopy to probe the tensile strength, lifetime, and interaction energy between live human parental breast cancer cells lacking a-catenin and these cells where a-catenin is re-expressed. We find that the tensile strength and lifetime of single E-cadherin bonds between parental cells are significantly lower over a wide range of loading rates. Statistical analysis of the force-displacement spectra reveals that single cadherin bonds between cancer cells feature an exceedingly low energy barrier against tensile forces and low molecular rigidity. These results suggest that the loss of a-catenin drastically reduces the adhesive force between individual cadherin pairs on adjoining cells, explain the global loss of cell adhesion in human breast cancer cells and show that the forced expression of a-catenin in cancer cells can restore both higher intercellular avidity and intermolecular E-cadherin affinity.

  3. Flexible single molecule simulation of reaction-diffusion processes

    NASA Astrophysics Data System (ADS)

    Hellander, Stefan; Lötstedt, Per

    2011-05-01

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

  4. 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 β-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.

  5. Single Molecule Fluorescence Measurements of Ribosomal Translocation Dynamics

    PubMed Central

    Chen, Chunlai; Stevens, Benjamin; Kaur, Jaskarin; Cabral, Diana; Liu, Hanqing; Wang, Yuhong; Zhang, Haibo; Rosenblum, Gabriel; Smilansky, Zeev; Goldman, Yale E.; Cooperman, Barry S.

    2011-01-01

    We employ single-molecule fluorescence resonance energy transfer (smFRET) to study structural dynamics over the first two elongation cycles of protein synthesis, using ribosomes containing either Cy3-labeled ribosomal protein L11 and A- or P-site Cy5-labeled tRNA or Cy3 and Cy5 labeled tRNAs. Pre-translocation (PRE) complexes demonstrate fluctuations between classical and hybrid forms, with concerted motions of tRNAs away from L11 and from each other when classical complex converts to hybrid complex. EF-G·GTP binding to both hybrid and classical PRE complexes halts these fluctuations prior to catalyzing translocation to form the post-translocation (POST) complex. EF-G dependent translocation from the classical PRE complex proceeds via transient formation of a short-lived hybrid intermediate. A-site binding of either EF-G to the PRE complex or of aminoacyl-tRNA·EF-Tu ternary complex to the POST complex markedly suppresses ribosome conformational lability. PMID:21549313

  6. Single-molecule fluorescence measurements of ribosomal translocation dynamics.

    PubMed

    Chen, Chunlai; Stevens, Benjamin; Kaur, Jaskarin; Cabral, Diana; Liu, Hanqing; Wang, Yuhong; Zhang, Haibo; Rosenblum, Gabriel; Smilansky, Zeev; Goldman, Yale E; Cooperman, Barry S

    2011-05-01

    We employ single-molecule fluorescence resonance energy transfer (smFRET) to study structural dynamics over the first two elongation cycles of protein synthesis, using ribosomes containing either Cy3-labeled ribosomal protein L11 and A- or P-site Cy5-labeled tRNA or Cy3- and Cy5-labeled tRNAs. Pretranslocation (PRE) complexes demonstrate fluctuations between classical and hybrid forms, with concerted motions of tRNAs away from L11 and from each other when classical complex converts to hybrid complex. EF-G⋅GTP binding to both hybrid and classical PRE complexes halts these fluctuations prior to catalyzing translocation to form the posttranslocation (POST) complex. EF-G dependent translocation from the classical PRE complex proceeds via transient formation of a short-lived hybrid intermediate. A-site binding of either EF-G to the PRE complex or of aminoacyl-tRNA⋅EF-Tu ternary complex to the POST complex markedly suppresses ribosome conformational lability. PMID:21549313

  7. 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.

  8. 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

  9. Magnetic Quantum Tunneling and Symmetry in Single Molecule Magnets

    NASA Astrophysics Data System (ADS)

    Kent, Andrew D.

    2003-03-01

    We have studied the symmetry of magnetic quantum tunneling (MQT) in single molecule magnets (SMMs) using a micro-Hall effect magnetometer and high field vector superconducting magnet system. In the most widely studied SMM, Mn12-acetate, an average crystal 4-fold symmetry in the magnetic response is shown to be due to local molecular environments of 2-fold symmetry that are rotated by 90 degrees with respect to one another. We attribute this to ligand disorder that leads to local rhombic distortions, a model first proposed by Cornia et al. based on x-ray diffraction data [1]. We have magnetically distilled a Mn12-acetate crystal to study a subset of these lower (2-fold) site symmetry molecules and present evidence for a spin-parity effect consistent with a local 2-fold symmetry [2]. These results highlight the importance of subtle changes in molecule environment in modulating magnetic anisotropy and MQT. [1] Cornia et al. Phys. Rev. Lett. 89, 257201 (2002) [2] E. del Barco, A. D. Kent, E. Rumberger, D. H. Hendrickson, G. Christou, submitted for publication (2002) and Europhys. Lett. 60, 768 (2002)

  10. 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.

  11. 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

  12. Thermopower distribution of single molecule junctions with different interaction types

    NASA Astrophysics Data System (ADS)

    Kim, Taekyeong

    2015-11-01

    The thermopower (S) distribution in single-molecule junctions with different interaction types were investigated by using a scanning tunneling microscope break-junction (STM-BJ) technique. We used 4,4'-bipyridine (BPy) and 1,2-bis(4-pyridyl)ethylene (BPyE) molecules, each having the Van der Waals (vdW) interaction between a pyridine ring and a Au atom and a donor-acceptor (DA) interaction between a nitrogen(N) atom and a Au atom, depending on the different binding geometries formed with the Au electrodes. From the full width at half maximum (FWHM) in the distribution of S, we found that S had a smaller variation for the vdW interaction compared to the DA interaction, due to the high binding stability of vdW interaction. Furthermore, we measured the molecular bonding forces which are in the range of 1.5 nN - 1.8 nN for the vdW interaction and 0.8 nN for the DA interaction. This confirms that the bonding is stronger for the vdW interaction than for the DA interaction, which is consistent with the experimental results for the S distributions as well as those for the molecular bonding stabilities.

  13. Single-molecule analysis of the full transcription cycle

    NASA Astrophysics Data System (ADS)

    Strick, Terence

    2005-03-01

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

  14. 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.

  15. Single-molecule detection of near-infrared phthalocyanine dyes

    NASA Astrophysics Data System (ADS)

    Li, You; Canfield, Brian; Davis, Lloyd

    2009-03-01

    The major advantage associated with near-IR monitoring is the fact that few compounds show intrinsic fluorescence in this region of the spectrum. Phthalocyanine dyes provide excellent photostability and hence are an attractive candidate for fluorescence bioassay applications. However, because of their small Stokes shifts, non-standard methods are needed for separation of fluorescence from scattered laser light. We have developed a custom confocal microscope that uses a low-cost laser diode operating at 665.8 nm for sample excitation and an angle-tuned Raman notch filter to block scattered laser radiation and provide high-throughput of fluorescence. Also, a diffraction grating is used to isolate the laser excitation wavelength from the block broadband luminescence of the laser. We have used the system to observe photon bursts from single molecules of zinc phthalocyanine fluorophores in an ethanol solution. The autocorrelation function of the photon trace provides a measure of the signal-to-noise ratio. We also discuss ongoing experiments to characterize the limits of detection of near-infrared fluorophores in aqueous solution using the microscope.

  16. 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

  17. Complementary Metal-Oxide-Semiconductor Integrated Carbon Nanotube Arrays: Toward Wide-Bandwidth Single-Molecule Sensing Systems.

    PubMed

    Warren, Steven B; Vernick, Sefi; Romano, Ethan; Shepard, Kenneth L

    2016-04-13

    There is strong interest in realizing genomic molecular diagnostic platforms that are label-free, electronic, and single-molecule. One attractive transducer for such efforts is the single-molecule field-effect transistor (smFET), capable of detecting a single electronic charge and realized with a point-functionalized exposed-gate one-dimensional carbon nanotube field-effect device. In this work, smFETs are integrated directly onto a custom complementary metal-oxide-semiconductor chip, which results in an array of up to 6000 devices delivering a measurement bandwidth of 1 MHz. In a first exploitation of these high-bandwidth measurement capabilities, point functionalization through electrochemical oxidation of the devices is observed with microsecond temporal resolution, which reveals complex reaction pathways with resolvable scattering signatures. High-rate random telegraph noise is detected in certain oxidized devices, further illustrating the measurement capabilities of the platform. PMID:26999579

  18. Bayesian orientation estimate and structure information from sparse single-molecule x-ray diffraction images.

    PubMed

    Walczak, Michał; Grubmüller, Helmut

    2014-08-01

    We developed a Bayesian method to extract macromolecular structure information from sparse single-molecule x-ray free-electron laser diffraction images. The method addresses two possible scenarios. First, using a "seed" structural model, the molecular orientation is determined for each of the provided diffraction images, which are then averaged in three-dimensional reciprocal space. Subsequently, the real space electron density is determined using a relaxed averaged alternating reflections algorithm. In the second approach, the probability that the "seed" model fits to the given set of diffraction images as a whole is determined and used to distinguish between proposed structures. We show that for a given x-ray intensity, unexpectedly, the achievable resolution increases with molecular mass such that structure determination should be more challenging for small molecules than for larger ones. For a sufficiently large number of recorded photons (>200) per diffraction image an M^{1/6} scaling is seen. Using synthetic diffraction data for a small glutathione molecule as a challenging test case, successful determination of electron density was demonstrated for 20000 diffraction patterns with random orientations and an average of 82 elastically scattered and recorded photons per image, also in the presence of up to 50% background noise. The second scenario is exemplified and assessed for three biomolecules of different sizes. In all cases, determining the probability of a structure given set of diffraction patterns allowed successful discrimination between different conformations of the test molecules. A structure model of the glutathione tripeptide was refined in a Monte Carlo simulation from a random starting conformation. Further, effective distinguishing between three differently arranged immunoglobulin domains of a titin molecule and also different states of a ribosome in a tRNA translocation process was demonstrated. These results show that the proposed method is robust and enables structure determination from sparse and noisy x-ray diffraction images of single molecules spanning a wide range of molecular masses. PMID:25215765

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

    PubMed Central

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

    2014-01-01

    Recent developments on various lab-on-a-chip techniques allow miniaturized and integrated devices to perform on-chip single-molecule studies. Fluidic-based platforms that utilize the unique microscale fluidic behavior are capable of conducting single-molecule experiments with high sensitivities and throughputs, while biomolecular systems can be studied on-chip using techniques such as DNA curtains, magnetic tweezers, and solid-state nanopores. The advances of these on-chip single-molecule techniques lead to next-generation lab-on-a-chip devices such as DNA transistors, and single-molecule real-time (SMRT) technology for rapid and low-cost whole genome DNA sequencing. In this Focus article, we will discuss some recent successes on developing lab-on-a-chip techniques for single-molecule studies and expound our thoughts on the near future of on-chip single-molecule studies. PMID:23670195

  20. High-Throughput Single-Molecule Studies of Protein-DNA Interactions

    PubMed Central

    Robison, Aaron D.; Finkelstein, Ilya J.

    2014-01-01

    Fluorescence and force-based single-molecule studies of protein-nucleic acid interactions continue to shed critical insights into many aspects of DNA and RNA processing. As single-molecule assays are inherently low-throughput, obtaining statistically relevant datasets remains a major challenge. Additionally, most fluorescence-based single-molecule particle-tracking assays are limited to observing fluorescent proteins that are in the low-nanomolar range, as spurious background signals predominate at higher fluorophore concentrations. These technical limitations have traditionally limited the types of questions that could be addressed via single-molecule methods. In this review, we describe new approaches for high-throughput and high-concentration single-molecule biochemical studies. We conclude with a discussion of outstanding challenges for the single-molecule biologist and how these challenges can be tackled to further approach the biochemical complexity of the cell. PMID:24859086

  1. Single molecule enzyme-linked immunosorbent assays: theoretical considerations.

    PubMed

    Chang, Lei; Rissin, David M; Fournier, David R; Piech, Tomasz; Patel, Purvish P; Wilson, David H; Duffy, David C

    2012-04-30

    We have developed a highly sensitive immunoassay-called digital ELISA-that is based on the detection of single enzyme-linked immunocomplexes on beads that are sealed in arrays of femtoliter wells. Digital ELISA was designed to be highly efficient in the capturing of target proteins, labeling of these proteins, and their detection in single molecule arrays (SiMoA); in essence, the goal of the assay is to "capture every molecule, detect every molecule". Here we provide the theoretical basis for the design of this assay derived from simple equations based on bimolecular interactions. Using these equations and knowledge of the concentrations of reagents, the times of interactions, and the on- and off-rates of the molecular interactions for each step of the assay, it is possible to predict the number of immunocomplexes that are formed and detected by SiMoA. The unique ability of SiMoA to count single immunocomplexes and determine an average number of enzymes per bead (AEB), makes it possible to directly compare the number of molecules detected experimentally to those predicted by theory. These predictions compare favorably to experimental data generated for a digital ELISA for prostate specific antigen (PSA). The digital ELISA process is efficient across a range of antibody affinities (K(D)~10(-11) -10(-9) M), and antibodies with high on-rates (k(on)>10(5) M(-1) s(-1)) are predicted to perform best. The high efficiency of digital ELISA and sensitivity of SiMoA to enzyme label also makes it possible to reduce the concentration of labeling reagent, reduce backgrounds, and increasing the specificity of the approach. Strategies for dealing with the dissociation of antibody complexes over time that can affect the signals in an assay are also described. PMID:22370429

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

    SciTech Connect

    Terentjevs, Aleksandrs; Steele, Mary P.; Blumenfeld, Michael L.; Ilyas, Nahid; Kelly, Leah L.; Fabiano, Eduardo; Monti, Oliver L.A.; Della Sala, Fabio

    2011-11-03

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

  3. Imaging interfacial electrical transport in graphene-MoS2 heterostructures with electron-beam-induced-currents

    NASA Astrophysics Data System (ADS)

    White, E. R.; Kerelsky, Alexander; Hubbard, William A.; Dhall, Rohan; Cronin, Stephen B.; Mecklenburg, Matthew; Regan, B. C.

    2015-11-01

    Heterostructure devices with specific and extraordinary properties can be fabricated by stacking two-dimensional crystals. Cleanliness at the inter-crystal interfaces within a heterostructure is crucial for maximizing device performance. However, because these interfaces are buried, characterizing their impact on device function is challenging. Here, we show that electron-beam induced current (EBIC) mapping can be used to image interfacial contamination and to characterize the quality of buried heterostructure interfaces with nanometer-scale spatial resolution. We applied EBIC and photocurrent imaging to map photo-sensitive graphene-MoS2 heterostructures. The EBIC maps, together with concurrently acquired scanning transmission electron microscopy images, reveal how a device's photocurrent collection efficiency is adversely affected by nanoscale debris invisible to optical-resolution photocurrent mapping.

  4. Imaging interfacial electrical transport in graphene–MoS{sub 2} heterostructures with electron-beam-induced-currents

    SciTech Connect

    White, E. R. Kerelsky, Alexander; Hubbard, William A.; Regan, B. C.; Dhall, Rohan; Cronin, Stephen B.; Mecklenburg, Matthew

    2015-11-30

    Heterostructure devices with specific and extraordinary properties can be fabricated by stacking two-dimensional crystals. Cleanliness at the inter-crystal interfaces within a heterostructure is crucial for maximizing device performance. However, because these interfaces are buried, characterizing their impact on device function is challenging. Here, we show that electron-beam induced current (EBIC) mapping can be used to image interfacial contamination and to characterize the quality of buried heterostructure interfaces with nanometer-scale spatial resolution. We applied EBIC and photocurrent imaging to map photo-sensitive graphene-MoS{sub 2} heterostructures. The EBIC maps, together with concurrently acquired scanning transmission electron microscopy images, reveal how a device's photocurrent collection efficiency is adversely affected by nanoscale debris invisible to optical-resolution photocurrent mapping.

  5. 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

  6. Orientation detection of a single molecule using pupil filter with electrically controllable polarization pattern

    NASA Astrophysics Data System (ADS)

    Hashimoto, Mamoru; Yoshiki, Keisuke; Kurihara, Makoto; Hashimoto, Nobuyuki; Araki, Tsutomu

    2015-12-01

    We have developed a system for measuring the orientation of single molecules using a conventional wide-field fluorescence microscope with a polarization filter consisting of a polarizer and a compact polarization mode converter. The polarization filter electrically controls the pattern of polarization filtering. Since the polarization of the fluorescence from a single molecule highly depends on the angle between the observation direction and the molecular direction, polarization pattern filtering at the pupil plane of the objective lens allows the orientation of a single molecule to be visualized. Using this system, we demonstrated the orientation detection of single molecules.

  7. 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

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

    NASA Astrophysics Data System (ADS)

    Raza, H.

    2008-11-01

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

  9. Isotope-Resolved and Charge-Sensitive Force Imaging Using Scanned Single Molecules

    NASA Astrophysics Data System (ADS)

    Sun, Yan; Rastawicki, Dominik; Liu, Yang; Mar, Warren; Manoharan, Hari; Miglio, Anna; Melinte, Sorin; Charlier, Jean-Christophe; Rignanese, Gian-Marco; He, Lianhua; Liu, Fang; Zhou, Aihui

    Originally conceived as surface imaging instruments, the scanning tunnelling microscope (STM) and the atomic force microscope (AFM) were recently used to probe molecular chemical bonds with exquisite sensitivity. Remarkably, molecule-functionalized scanning tips can also provide direct access to the inelastic electron tunneling spectrum (IETS) of the terminal molecule. Here we report atomic manipulation experiments addressing carbon monoxide (CO) isotopes at low temperatures. The unique and quantifiable dependence of the CO vibrational modes offers insight into tip-controlled force and charge sensing of surface adsorbates, subsurface defects, and quantum nanostructures. The specific behavior of the monitored vibrational modes originates from the interplay of interaction forces between the top electrode--a scanned tip functionalized with a single molecule--and the atomic scale force field surrounding the target atomically-assembled nanostructure. We also present density functional theory (DFT) computations that have been performed in order to scrutinize and visualize the vibrational spectroscopic fingerprints and local force fields.

  10. Photo-activation of Single Molecule Magnet Behavior in a Manganese-based Complex

    PubMed Central

    Fetoh, Ahmed; Cosquer, Goulven; Morimoto, Masakazu; Irie, Masahiro; El-Gammal, Ola; El-Reash, Gaber Abu; Breedlove, Brian K.; Yamashita, Masahiro

    2016-01-01

    A major roadblock to fully realizing molecular electronic devices is the ability to control the properties of each molecule in the device. Herein we report the control of the magnetic properties of single-molecule magnets (SMMs), which can be used in memory devices, by using a photo-isomerizable diarthylenthene ligand. Photo-isomerization of the diarylethene ligand bridging two manganese salen complexes with visible light caused a significant change in the SMM behavior due to opening of the six-membered ring of diarylethene ligand, accompanied by reorganization of the entire molecule. The ring-opening activated the frequency-dependent magnetization of the complex. Our results are a major step towards the realization of molecular memory devices composed of SMMs because the SMM behaviour can be turned on and off simply by irradiating the molecule. PMID:27026506

  11. 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.

  12. Photo-activation of Single Molecule Magnet Behavior in a Manganese-based Complex

    NASA Astrophysics Data System (ADS)

    Fetoh, Ahmed; Cosquer, Goulven; Morimoto, Masakazu; Irie, Masahiro; El-Gammal, Ola; El-Reash, Gaber Abu; Breedlove, Brian K.; Yamashita, Masahiro

    2016-03-01

    A major roadblock to fully realizing molecular electronic devices is the ability to control the properties of each molecule in the device. Herein we report the control of the magnetic properties of single-molecule magnets (SMMs), which can be used in memory devices, by using a photo-isomerizable diarthylenthene ligand. Photo-isomerization of the diarylethene ligand bridging two manganese salen complexes with visible light caused a significant change in the SMM behavior due to opening of the six-membered ring of diarylethene ligand, accompanied by reorganization of the entire molecule. The ring-opening activated the frequency-dependent magnetization of the complex. Our results are a major step towards the realization of molecular memory devices composed of SMMs because the SMM behaviour can be turned on and off simply by irradiating the molecule.

  13. 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.

  14. STM Study of the Adsorption of Single-Molecule Magnet Fe4 on Bi(111) Surface

    NASA Astrophysics Data System (ADS)

    Luo, Yuan; Luo, Lan; Sun, Kai; Tao, Min-Long; Wang, Jun-Zhong

    2015-07-01

    Single-molecule magnets (SMMs) have unique magnetic properties such as quantum tunneling of magnetization and quantum coherent oscillation, which have potential applications in quantum computation and information storage. In this paper, using the tip-deposition method, we have grafted individual Fe4 molecules onto the semi-metallic Bi(111) surface. Low temperature scanning tunneling microscope (LT-STM) was used to characterize the molecular morphology and electronic structures. It was found that individual Fe4 molecules reveal a triangle shape, which is consistent with the molecular structure of Fe4. Scanning tunneling spectroscopy (STS) analysis indicated that the HOMO-LUMO gap is 0.49 eV. These studies provide direct information about the adsorption of individual SMMs on semi-metal surfaces.

  15. 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

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

    PubMed

    Antunes, Maria A; Coutinho, Joana T; Santos, Isabel C; Maralo, Joaquim; Almeida, Manuel; Baldov, Jos J; Pereira, Laura C J; Gaita-Ario, 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

  17. Tuning the Thermoelectric Properties of a Single-Molecule Junction by Mechanical Stretching

    NASA Astrophysics Data System (ADS)

    Pontes, Renato; Torres, Alberto; da Silva, Antonio J. R.; Fazzio, Adalberto

    2015-03-01

    We theoretically investigate, as a function of the stretching, the behaviour of the thermoelectric properties - Seebeck coefficient (S), the electronic heat conductance (κel) and the figure of merit (ZT) - of a molecule-based junction composed by benzene-1,4-dithiol 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, goes to 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. The authors thank the Brazilian funding agencies CNPq, CAPES and FAPESP. We also thank CENAPAD-SP for the computational facilities.

  18. 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.

  19. Single molecule studies of DNA packaging by bacteriophages

    NASA Astrophysics Data System (ADS)

    Fuller, Derek Nathan

    The DNA packaging dynamics of bacteriophages φ29, gamma, and T4 were studied at the single molecule level using a dual trap optical tweezers. Also, a method for producing long DNA molecules by PCR for optical tweezers studies of protein DNA interactions is presented and thoroughly characterized. This DNA preparation technique provided DNA samples for the φ29 and T4 studies. In the studies of φ29, the role of charge was investigated by varying the ionic conditions of the packaging buffer. Ionic conditions in which the DNA charge was highly screened due to divalent and trivalent cations showed the lowest resistance to packaging of the DNA to high density. This confirmed the importance of counterions in shielding the DNA interstrand repulsion when packaged to high density. While the ionic nature of the packaging buffer had a strong effect on packaging velocities, there was no clear trend between the counterion-screened charge of the DNA and the maximum packaging velocity. The packaging studies of lambda and T4 served as systems for comparative studies with φ29. Each system showed similarities to the φ29 system and unique differences. Both the lambda and T4 packaging motors were capable of generating forces in excess of 50 pN and showed remarkably high processivity, similar to φ29. However, dynamic structural transitions were observed with lambda that are not observed with φ29. The packaging of the lambda genome showed capsid expansion at approximately 30 percent of the genome packaged and capsid rupture at 90 percent of the genome packaged in the absence of capsid stabilizing protein gpD. Unique to the T4 packaging motor, packaging dynamics showed a remarkable amount of variability in velocities. This variability was seen both within individual packaging phages and from one phage to the next. This is possibly due to different conformational states of the packaging machinery. Additionally, lambda and T4 had average packaging velocities under minimal load of 600 bp/s and 700 bp/s, respectively, as compared to 140 bp/s for φ29.

  20. 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

  1. Single Molecule Study of DNA Organization and Recombination

    NASA Astrophysics Data System (ADS)

    Xiao, Botao

    We have studied five projects related to DNA organization and recombination using mainly single molecule force-spectroscopy and statistical tools. First, HU is one of the most abundant DNA-organizing proteins in bacterial chromosomes and participates in gene regulation. We report experiments that study the dependence of DNA condensation by HU on force, salt and HU concentration. A first important result is that at physiological salt levels, HU only bends DNA, resolving a previous paradox of why a chromosome-compacting protein should have a DNA-stiffening function. A second major result is quantitative demonstration of strong dependencies of HU-DNA dissociation on both salt concentration and force. Second, we have used a thermodynamic Maxwell relation to count proteins driven off large DNAs by tension, an effect important to understanding DNA organization. Our results compare well with estimates of numbers of proteins HU and Fis in previous studies. We have also shown that a semi-flexible polymer model describes our HU experimental data well. The force-dependent binding suggests mechano-chemical mechanisms for gene regulation. Third, the elusive role of protein H1 in chromatin has been clarified with purified H1 and Xenopus extracts. We find that H1 compacts DNA by both bending and looping. Addition of H1 enhances chromatin formation and maintains the plasticity of the chromatin. Fourth, the topology and mechanics of DNA twisting are critical to DNA organization and recombination. We have systematically measured DNA extension as a function of linking number density from 0.08 to -2 with holding forces from 0.2 to 2.4 pN. Unlike previous proposals, the DNA extension decreases with negative linking number. Finally, DNA recombination is a dynamic process starting from enzyme-DNA binding. We report that the Int-DBD domain of lambda integrase binds to DNA without compaction at low Int-DBD concentration. High concentration of Int-DBD loops DNA below a threshold force, which depends on salt concentration. We also report experiments with the recombinase Hin mutant H107Y. The synapse formation is demonstrated with single DNA containing two hix sites. We further show preliminary data for cleavage and subunit rotation from a braiding assay. These direct observations elucidate the recombination mechanism.

  2. 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.

  3. 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 (τTraditional = 2.2 × 10-9 s and τNHALD = 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.

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

    SciTech Connect

    Alexandrov, Vitali Y.; Rosso, Kevin M.

    2015-01-01

    Goethite (α-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.

  5. Electronic Transport properties of SET and REST states of interfacial phase-change memory

    NASA Astrophysics Data System (ADS)

    Nakamura, Hisao; Tominaga, Junji; Asai, Yoshihiro; Rungger, Ivan; Narayan, Awadhesh; Sanvito, Stefano

    2015-03-01

    The phase change memory (PCM) is one of most promising nonvolatile information storage technologies. Recently, the superlattice structure of GeTe/Sb2Te3 is proposed as PCM to reduce the restive switching energy. This PCM is called interfacial PCM (iPCM) and it is considered that SET and RESET states are realized only by the flip-flop transition of Ge atoms in crystal phase because of small loss of entropy. Furthermore, the GeTe is sandwiched by Sb2Te3 topological insulator. In this study, we performed the first principles electric transport calculations including spin-orbit interactions. We presents the mechanism of resistive switch by the transition of Ge atoms as well as the volume change effect and the role of spin-orbit interaction to resistance ration of SET and RESE states.

  6. Single-molecule detection and radiation control in solutions at high concentrations via a heterogeneous optical slot antenna

    NASA Astrophysics Data System (ADS)

    Zhao, Chenglong; Liu, Yongmin; Yang, Jing; Zhang, Jiasen

    2014-07-01

    We designed a heterogeneous optical slot antenna (OSA) that is capable of detecting single molecules in solutions at high concentrations, where most biological processes occur. A heterogeneous OSA consists of a rectangular nanoslot fabricated on heterogeneous metallic films formed by sequential deposition of gold and aluminum on a glass substrate. The rectangular nanoslot gives rise to large field and fluorescence enhancement for single molecules. The near-field intensity inside a heterogeneous OSA is 170 times larger than that inside an aluminum zero-mode waveguide (ZMW), and the fluorescence emission rate of a molecule inside the heterogeneous OSA is about 70 times higher than that of the molecule in free space. Our proposed heterogeneous optical antenna enables excellent balance between performance and cost. The design takes into account the practical experimental conditions so that the parameters chosen in the simulation are well within the reach of current nano-fabrication technologies. Our results can be used as a direct guidance for designing high-performance, low-cost plasmonic nanodevices for the study of bio-molecule and enzyme dynamics at the single-molecule level.We designed a heterogeneous optical slot antenna (OSA) that is capable of detecting single molecules in solutions at high concentrations, where most biological processes occur. A heterogeneous OSA consists of a rectangular nanoslot fabricated on heterogeneous metallic films formed by sequential deposition of gold and aluminum on a glass substrate. The rectangular nanoslot gives rise to large field and fluorescence enhancement for single molecules. The near-field intensity inside a heterogeneous OSA is 170 times larger than that inside an aluminum zero-mode waveguide (ZMW), and the fluorescence emission rate of a molecule inside the heterogeneous OSA is about 70 times higher than that of the molecule in free space. Our proposed heterogeneous optical antenna enables excellent balance between performance and cost. The design takes into account the practical experimental conditions so that the parameters chosen in the simulation are well within the reach of current nano-fabrication technologies. Our results can be used as a direct guidance for designing high-performance, low-cost plasmonic nanodevices for the study of bio-molecule and enzyme dynamics at the single-molecule level. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr01407c

  7. Enhanced Electron Extraction Capability of Polymer Solar Cells via Employing Electrostatically Self-Assembled Molecule on Cathode Interfacial Layer.

    PubMed

    Li, Zhiqi; Zhang, Xinyuan; Liu, Chunyu; Zhang, Zhihui; Li, Jinfeng; Shen, Liang; Guo, Wenbin; Ruan, Shengping

    2016-03-30

    In this paper, high-performance inverted polymer solar cells (PSCs) with a modified cathode buffer layer, titanium dioxide:polyethylenimine (TiO2:PEI), are demonstrated. The TiO2-O-PEI transport layer was fabricated by electrostatically self-assembled monolayers (ESAM) of PEI molecules. Protonated amine functional groups of PEI can combine protons (H(+)) hydrolyzing from its aqueous solution. Also, PEI could produce ESAM on the surface of hydroxylated TiO2 because of its cationic characteristics. The incorporation of the TiO2-O-PEI layer enhances the photocurrent and power conversion efficiency (PCE) due to the improved interfacial electron transport and extraction of the TiO2-O-PEI surface and the increased light absorption of the active layer. The enhanced PCE, low-cost materials, and solution process of TiO2-O-PEI buffer layers provide a promising method for highly efficient PSCs. PMID:26955888

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

    DOEpatents

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

    2009-12-29

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

  9. How accurately can a single molecule be localized in three dimensions using a fluorescence microscope?

    PubMed Central

    Ram, Sripad; Ward, E. Sally; Ober, Raimund J.

    2010-01-01

    Single molecule fluorescence microscopy is a relatively novel technique that is used, for example, to study the behavior of individual biomolecules in cells. Since a single molecule can move in all three dimensions in a cellular environment, the three dimensional tracking of single molecules can provide valuable insights into cellular processes. It is therefore of importance to know the accuracy with which the location of a single molecule can be determined with a fluorescence microscope. We study this performance limit of a fluorescence microscope from a statistical point of view by deriving the Fisher information matrix for the estimation problem of the location of the single molecule. In this way we obtain a lower bound on the standard deviation of any reasonable (unbiased) estimation method of the location parameters. This lower bound provides a fundamental limit on the accuracy with which a single molecule can be localized using a fluorescence microscope and is given in terms of such quantities as the photon detection rate of the single molecule, the acquisition time, the numerical aperture of the objective lens etc. We also present results that show how factors such as noise sources, detector size and pixelation deteriorate the fundamental limit of the localization accuracy. The present results can be used to evaluate and optimize experimental setups in order to carry out three dimensional single molecule tracking experiments and provide guidelines for experimental design. PMID:20448826

  10. 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

  11. Observing lysozyme's closing and opening motions by high-resolution single-molecule enzymology.

    PubMed

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

    2015-06-19

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

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

    NASA Astrophysics Data System (ADS)

    Takahashi, Susumu

    2009-03-01

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

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

    PubMed

    Krzemiński, Łukasz; Ndamba, Lionel; Canters, Gerard W; Aartsma, Thijs J; Evans, Stephen D; Jeuken, Lars J C

    2011-09-28

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

  14. Rational design of single-molecule magnets: a supramolecular approach.

    PubMed

    Glaser, Thorsten

    2011-01-01

    Since the discovery that Mn(12)OAc acts as a single-molecule magnet (SMM), an increasing number of transition metal complexes have been demonstrated to behave as SMMs. The signature of a SMM is a slow relaxation of the magnetization at low temperatures accompanied by a magnetic hysteresis. The origin of SMM behaviour is the existence of an appreciable thermal barrier U for spin-reversal called magnetic anisotropy barrier which is related to the combination of a large total spin ground state (S(t)) and an easy-axis magnetic anisotropy. The extensive research on Mn(12)OAc and other SMMs has established more prerequisites for a rational development of new SMMs besides the high-spin ground state and the magnetic anisotropy: the symmetry should be at least C(3) to minimize the quantum tunneling of the magnetization through the anisotropy barrier but lower than cubic to avoid the cancellation of the local anisotropies upon projection onto the spin ground state. Based on these prerequisites, we have designed the ligand triplesalen which combines the phloroglucinol bridging unit for high spin ground states by the spin-polarization mechanism with a salen-like ligand environment for single-site magnetic anisotropies by a strong tetragonal ligand field. The C(3) symmetric, trinuclear complexes of the triplesalen ligand (talen(t-Bu(2)))(6-) exhibit a strong ligand folding resulting in an overall bowl-shaped molecular structure. This ligand folding preorganizes the axial coordination sites of the metal salen subunits for the complementary binding of three facial nitrogen atoms of a hexacyanometallate unit. This leads to a high driving force for the formation of heptanuclear complexes [M(t)(6)M(c)](n+) by the assembly of three molecular building blocks. Attractive van der Waals interactions of the tert-butyl phenyl units of two triplesalen trinuclear building blocks increase the driving force. In this respect, we have been able to synthesize the isostructural series [Mn(III)(6)Cr(III)](3+), [Mn(III)(6)Fe(III)](3+), and [Mn(III)(6)Co(III)](3+) with [Mn(III)(6)Cr(III)](3+) being a SMM. A detailed analysis and comparison of the magnetic properties of the three heptanuclear complexes and the tetranuclear half-unit [Mn(III)(3)Cr(III)](3+) provides significant insight for further optimization of the SMM properties. The modular assembly of the heptanuclear complexes from three molecular building blocks allows the fine-tuning of the molecular and steric properties of each building block without losing the driving force for the formation of the heptanuclear complexes. This possibility of rational improvements of our isostructural series is the main advantage of our supramolecular approach. PMID:20862425

  15. 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.

  16. 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.

  17. 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

  18. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

    Iron(II) phthalocyanine (FePc) molecule causes novel Kondo effects derived from the unique electronic structure of multi-spins and multi-orbitals when attached to Au(111). Two unpaired electrons in the dz2 and the degenerate d? orbitals are screened stepwise, resulting in spin and spin+orbital Kondo effects, respectively. We investigated the impact on the Kondo effects of the coordination of CO and NO molecules to the Fe2+ ion as chemical stimuli by using scanning tunneling microscopy (STM) and density functional theory calculations. The impacts of the two diatomic molecules are different from each other as a result of the different electronic configurations. The coordination of CO converts the spin state from triplet to singlet, and then the Kondo effects completely disappear. In contrast, an unpaired electron survives in the molecular orbital composed of Fe dz2 and NO 5? and 2?* orbitals for the coordination of NO, causing a sharp Kondo resonance. The isotropic magnetic response of the peak indicates the origin is the spin Kondo effect. The diatomic molecules attached to the Fe2+ ion were easily detached by applying a pulsed voltage at the STM junction. These results demonstrate that the single molecule chemistry enables us to switch and control the spin and the many-body quantum states reversibly.

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

    SciTech Connect

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

    2014-08-07

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

  1. Solid phase single-molecule counting of antibody binding to supported protein layers surface with low nonspecific adsorption.

    PubMed

    Jiang, Dafeng; Zhang, Qianqian; Shen, Xibo; Wang, Lei; Jiang, Wei

    2010-08-15

    On the basis of the supported protein layers (SPLs) substrate, the study presented an ultrasensitive and highly specific platform for single-molecule fluorescence detection of antibody using quantum dots (QDs) as probes. To construct the SPLs surface platform for antibody immobilization, bovine serum albumin (BSA), anti-BSA, and protein G were firstly attached to carboxyl-terminated substrate surfaces by turns. Then nonspecific adsorption of single antibody molecules on SPLs surfaces was investigated. Through the irreversible interaction between streptavidin and biotin, streptavidin-QD conjugates were employed to conjugate with biotinylated antibody, producing QD-antibody conjugates for generating fluorescent signals in fluorescent imaging. Epi-fluorescence microscopy equipped with an electron multiplying charge-coupled device was chosen as the tool for single-molecule fluorescence detection here. The concentration of antibody is quantified based on the direct counting of individual fluorescent spots, one by one. The generated fluorescent signals increased with the increasing concentration of immobilized antibody and were found to be proportional to antibody concentrations. The better brightness and photostability of QDs, and slower increase in the number of counted molecules make a large linear dynamic range of 1.0x10(-14) to 3.0x10(-12)mol L(-1) between the number of single molecules and antibody concentrations, which is comparable to the previously reported surface-based SMD analysis. PMID:20678659

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

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

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

  3. 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.

  4. "Butterfly effect" in CuO/graphene composite nanosheets: a small interfacial adjustment triggers big changes in electronic structure and Li-ion storage performance.

    PubMed

    Zhang, Xiaoting; Zhou, Jisheng; Song, Huaihe; Chen, Xiaohong; Fedoseeva, Yu V; Okotrub, A V; Bulusheva, L G

    2014-10-01

    Generally speaking, excellent electrochemical performance of metal oxide/graphene nanosheets (GNSs) composite is attributed to the interfacial interaction (or "synergistic effect") between constituents. However, there are no any direct observations on how the electronic structure is changed and how the properties of Li-ion storage are affected by adjusting the interfacial interaction, despite of limited investigations on the possible nature of binding between GNSs and metal oxide. In this paper, CuO nanosheets/GNSs composites with a little Cu2O (ca. 4 wt %) were utilized as an interesting model to illustrate directly the changes of interfacial nature as well as its deep influence on the electronic structure and Li-ion storage performance of composite. The interfacial adjustment was successfully fulfilled by removal of Cu2O in the composite by NH3·H2O. Formation of Cu-O-C bonds on interfaces both between CuO and GNSs, and Cu2O and GNSs in the original CuO/GNSs composites was detected. The small interfacial alteration by removal of the little Cu2O results in the obvious changes in electronic structure, such as weakening of covalent Cu-O-C interfacial interaction and recovery of π bonds in graphene, and simultaneously leads to variations in electrochemical performance of composites, including a 21% increase of reversible capacity, degradation of cyclic stability and rate-performance, and obvious increase of charge-transfer resistance, which can be called a "butterfly effect" in graphene-based metal oxide composites. These interesting phenomena could be helpful to design not only the high-performance graphene/metal oxide anode materials but also various advanced graphene-based composites used in the other fields such as sensors, catalysis, fuel cells, solar cells, etc. PMID:25226227

  5. Comparative study on the interfacial electron transfer of zinc porphyrins with meso-π-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-π-extension on the redox behaviors and interfacial electron transfer kinetics. The meso-π-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

  6. Spectroscopy and Structure of Diamondoid-Fullerene Hybrid Molecules at the Single-Molecule Level

    NASA Astrophysics Data System (ADS)

    Randel, Jason C.; Ndabashimiye, Georges; Manoharan, Hari C.

    2011-03-01

    Diamondoids---a nanometer-scale form of carbon sharing the sp 3 bonding structure of bulk diamond---are promising new electronic and mechanical device elements and have recently become accessible to experiments. While new fields of research have also sprouted from carbon's sp 2 forms (such as graphene, fullerenes, and carbon nanotubes), materials representing the intersection of sp 2 and sp 3 bonding structures are an exciting new arena for nanoscale science and technology. In this study, we investigate hybrid molecules fusing sp 2 and sp 3 allotropes of carbon (in the form of C60 fullerenes and molecular diamondoids, respectively) into one well-defined system. We use low-temperature scanning tunneling microscopy to characterize monolayers and single molecules with sub-molecular resolution. We show the degree to which the electronic properties of the hybrid molecules differ from their single-allotrope components, and highlight the intriguing electronic features that emerge which have no analog in either of the separate molecular constituents. We thank S. Melinte for aiding measurements, and J. E. P. Dahl, R. M. Carlson, and P. R. Schreiner for materials and synthesis. We acknowledge support from DOE and the Chevron Corporation.

  7. 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

  8. 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.

  9. 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.

  10. Versatile electron-collecting interfacial layer by in situ growth of silver nanoparticles in nonconjugated polyelectrolyte aqueous solution for polymer solar cells.

    PubMed

    Yuan, Kai; Chen, Lie; Chen, Yiwang

    2014-10-01

    Novel PEIE-Ag composites by in situ growth of silver nanoparticles in poly(ethylenimine)-ethoxylated (PEIE) aqueous solution are explored as an efficient interfacial layer for improving inverted polymer solar cells (PSCs) performance. The hybrid PEIE-Ag interfacial material is simple to fabricate only via ultraviolet irradiation with good water-solubility and unique film formation. The generated Ag nanoparticles can anchor in the PEIE polymer chains to form a conductive continuous interpenetrating network structure. Combining of the advantages of PEIE and Ag nanoparticles, the PEIE-Ag shows enhanced charge transport, electron selective and collection, and improved light-harvesting, mainly due to the surface plasmon resonance effect, better energy alignment induced by the formation of ideal dipole layer, as well as the improved conductivity. These distinguished interfacial properties result in the power conversion efficiency of inverted PSCs based on poly[4,8-bis(2-ethyl-hexyl-thiophene-5-yl)-benzo[1,2-b:4,5-b]dithiophene-2,6-diyl]-alt-[2-(2-ethyl-hexanoyl)-thieno[3,4-b]thiophen-4,6-diyl] (PBDTTT-C-T) and [6,6]-phenyl C71-butyric acid methyl ester (PC71BM) photoactive layer substantially improved up to 7.66% from 6.11%. Moreover, the device performance is insensitively dependent on the thickness of the PEIE-Ag interfacial layer, broadening the thicknesses selection window for interfacial materials. These results demonstrate that PEIE-Ag is a potential interfacial material compatible with roll-to-roll techniques and suitable for printed electronic devices. PMID:25207753

  11. Metal/dielectric thermal interfacial transport considering cross-interface electron-phonon coupling: Theory, two-temperature molecular dynamics, and thermal circuit

    NASA Astrophysics Data System (ADS)

    Lu, Zexi; Wang, Yan; Ruan, Xiulin

    2016-02-01

    The standard two-temperature equations for electron-phonon coupled thermal transport across metal/nonmetal interfaces are modified to include the possible coupling between metal electrons with substrate phonons. The previous two-temperature molecular dynamics (TT-MD) approach is then extended to solve these equations numerically at the atomic scale, and the method is demonstrated using Cu/Si interface as an example. A key parameter in TT-MD is the nonlocal coupling distance of metal electrons and nonmetal phonons, and here we use two different approximations. The first is based on Overhauser's "joint-modes" concept, while we use an interfacial reconstruction region as the length scale of joint region rather than the phonon mean-free path as in Overhauser's original model. In this region, the metal electrons can couple to the joint phonon modes. The second approximation is the "phonon wavelength" concept where electrons couple to phonons nonlocally within the range of one phonon wavelength. Compared with the original TT-MD, including the cross-interface electron-phonon coupling can slightly reduce the total thermal boundary resistance. Whether the electron-phonon coupling within the metal block is nonlocal or not does not make an obvious difference in the heat transfer process. Based on the temperature profiles from TT-MD, we construct a new mixed series-parallel thermal circuit. We show that such a thermal circuit is essential for understanding metal/nonmetal interfacial transport, while calculating a single resistance without solving temperature profiles as done in most previous studies is generally incomplete. As a comparison, the simple series circuit that neglects the cross-interface electron-phonon coupling could overestimate the interfacial resistance, while the simple parallel circuit in the original Overhauser's model underestimates the total interfacial resistance.

  12. Non-fluorescent schemes for single-molecule detection, imaging and spectroscopy

    NASA Astrophysics Data System (ADS)

    Arroyo, Jaime Ortega; Kukura, Philipp

    2016-01-01

    For decades, optical studies of single molecules have relied on fluorescence detection. The availability of alternative approaches for single-molecule interrogation would greatly expand the range of addressable molecules beyond species that are highly emissive and photostable, thus offering new applications in fields other than molecular biophysics and imaging. Here, we discuss the range of recent developments in optical label-free detection and imaging schemes that offer single-molecule sensitivity, with an emphasis on plasmonically enhanced and scattering-based approaches. We highlight the advantages and challenges facing these emerging methodologies and briefly outline their potential future applications.

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

    PubMed Central

    Lenn, Tchern; Leake, Mark C.

    2012-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2007-06-01

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

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

    NASA Astrophysics Data System (ADS)

    Colyer, Ryan A.; Scalia, Giuseppe; Villa, Federica A.; Guerrieri, Fabrizio; Tisa, Simone; Zappa, Franco; Cova, Sergio; Weiss, Shimon; Michalet, Xavier

    2011-03-01

    Single-molecule spectroscopy is a powerful approach to measuring molecular properties such as size, brightness, conformation, and binding constants. Due to the low concentrations in the single-molecule regime, measurements with good statistical accuracy require long acquisition times. Previously we showed a factor of 8 improvement in acquisition speed using a custom-CMOS 8x1 SPAD array. Here we present preliminary results with a 64X improvement in throughput obtained using a liquid crystal on silicon spatial light modulator (LCOS-SLM) and a novel standard CMOS 1024 pixel SPAD array, opening the way to truly high-throughput single-molecule spectroscopy.

  16. Do-it-yourself guide: How to use the modern single molecule toolkit

    PubMed Central

    Walter, Nils G.; Huang, Cheng-Yen; Manzo, Anthony J.; Sobhy, Mohamed A.

    2008-01-01

    Single molecule microscopy has evolved into the ultimate-sensitivity toolkit to study systems from small molecules to living cells, with the prospect of revolutionizing the modern biosciences. Here we survey the current state-of-the-art in single molecule tools including fluorescence spectroscopy, tethered particle microscopy, optical and magnetic tweezers, and atomic force microscopy. Our review seeks to guide the biological scientist in choosing the right approach from the available single molecule toolkit for applications ranging as far as structural biology, enzymology, nanotechnology, and systems biology. PMID:18511916

  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. Surface Chemically Switchable Ultraviolet Luminescence from Interfacial Two-Dimensional Electron Gas.

    PubMed

    Islam, Mohammad A; Saldana-Greco, Diomedes; Gu, Zongquan; Wang, Fenggong; Breckenfeld, Eric; Lei, Qingyu; Xu, Ruijuan; Hawley, Christopher J; Xi, X X; Martin, Lane W; Rappe, Andrew M; Spanier, Jonathan E

    2016-01-13

    We report intense, narrow line-width, surface chemisorption-activated and reversible ultraviolet (UV) photoluminescence from radiative recombination of the two-dimensional electron gas (2DEG) with photoexcited holes at LaAlO3/SrTiO3. The switchable luminescence arises from an electron transfer-driven modification of the electronic structure via H-chemisorption onto the AlO2-terminated surface of LaAlO3, at least 2 nm away from the interface. The control of the onset of emission and its intensity are functionalities that go beyond the luminescence of compound semiconductor quantum wells. Connections between reversible chemisorption, fast electron transfer, and quantum-well luminescence suggest a new model for surface chemically reconfigurable solid-state UV optoelectronics and molecular sensing. PMID:26675987

  19. Tunnel-Current based Single-Molecule Detection Method of Biopolymer Identification

    NASA Astrophysics Data System (ADS)

    Ohshiro, Takahito; Tsutsui, Makusu; Yokota, Kazumichi; Taniguchi, Masateru; Bionanotechnology Team

    2015-03-01

    We have been proposed a tunneling-current based identification as a single-molecule biopolymer sequencing. This methodology is based on sequentially reading the tunneling-current across individual single-biopolymer in the sequence, resulting in a high-speed electrical discrimination of the individual nucleotides. In this study, we report on a read of nucleotide sequence by the transverse electron transport through nanogap-electrode. We measured the extent of the electron-tunneling by using nanofabricated, mechanically controllable break junction, and determined the conductance values for deoxyribo/ribo- nucleoside monophosphates. When the molecules passed between the nanoelectrodes separated by a sub-nanometer gap, the tunneling-current through the molecules was increased, relative to that in the absence of molecules. The current intensity is found to be closely related to the individual molecular energy level. We also applied this method to base-typing in oligonucleotides. Based on the electrical conductivity for single-nucleotides, we read the fragment of sample nucleotide passing through the sensing electrode. On the basis of a reconstruction of the read fragment sequences, we successfully determined a sample nucleotide sequence.

  20. 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.

  1. Molecular Quantum Spintronics: Supramolecular Spin Valves Based on Single-Molecule Magnets and Carbon Nanotubes

    PubMed Central

    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 TbPc2 (Pc = phthalocyanine) rare-earth based single-molecule magnets (SMMs). The drafting was achieved by tailoring supramolecular π-π 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 (TB ~ 1 K) of isolated TbPc2 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

  2. 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

  3. Thiophene-based Tripodal Anchor Units for Hole Transport in Single-Molecule Junctions with Gold Electrodes.

    PubMed

    Ie, Yutaka; Tanaka, Kazunari; Tashiro, Aya; Lee, See Kei; Testai, Henrique Rosa; Yamada, Ryo; Tada, Hirokazu; Aso, Yoshio

    2015-09-17

    Molecule-metal junctions are inevitable for the realization of single-molecule electronics. In this study, we developed new tripodal anchors with electron-rich aromatic rings to achieve robust contact with gold electrodes, an effective hybridization of the π orbital with gold electrodes (π channel), and hole transport through π-channel hybridization. Cyclic voltammetry and X-ray photoelectron spectroscopy measurements of the monolayers indicated that the thiophene-based tripodal molecule exhibits anchoring characteristics as expected. The electrical conductance of thiophene-anchored bistripodal molecules using the scanning tunneling microscope (STM)-based break junction technique confirmed the formation of molecular junctions. The Seebeck coefficient of this compound estimated from thermoelectric voltage measurements using a STM was determined to be a positive value, which indicates that the charge carriers are holes. On the contrary, the corresponding pyridine-anchored molecules showed electron transport. These results reveal the versatility of π-channel tripodal anchors for the control of charge-carrier type in single-molecule electronics. PMID:26722752

  4. A single molecule rectifier with strong push-pull coupling

    NASA Astrophysics Data System (ADS)

    Saraiva-Souza, Aldilene; Macedo de Souza, Fabricio; Aleixo, Vicente F. P.; Girão, Eduardo Costa; Filho, Josué Mendes; Meunier, Vincent; Sumpter, Bobby G.; Souza Filho, Antônio Gomes; Del Nero, Jordan

    2008-11-01

    We theoretically investigate the electronic charge transport in a molecular system composed of a donor group (dinitrobenzene) coupled to an acceptor group (dihydrophenazine) via a polyenic chain (unsaturated carbon bridge). Ab initio calculations based on the Hartree-Fock approximations are performed to investigate the distribution of electron states over the molecule in the presence of an external electric field. For small bridge lengths (n =0-3) we find a homogeneous distribution of the frontier molecular orbitals, while for n >3 a strong localization of the lowest unoccupied molecular orbital is found. The localized orbitals in between the donor and acceptor groups act as conduction channels when an external electric field is applied. We also calculate the rectification behavior of this system by evaluating the charge accumulated in the donor and acceptor groups as a function of the external electric field. Finally, we propose a phenomenological model based on nonequilibrium Green's function to rationalize the ab initio findings.

  5. Introducing Dimensionality to the Archetypical Mn12 Single-Molecule Magnet: a Family of [Mn12]n Chains.

    PubMed

    Corrales, Sergio A; Cain, John M; Uhlig, Kelley A; Mowson, Andrew M; Papatriantafyllopoulou, Constantina; Peprah, Marcus K; Ozarowski, Andrew; Tasiopoulos, Anastasios J; Christou, George; Meisel, Mark W; Lampropoulos, Christos

    2016-02-15

    The [Mn12O12(O2CR)16(L4)] family (R = various; L = terminal ligand) of clusters holds a special place in molecular magnetism; they are the most well-studied single-molecule magnets (SMMs). Targeted linkage of these SMMs has now been achieved for the first time. The resulting chain structures have been confirmed crystallographically, and the magnetic properties, up to 1.14 GPa, and high-field electron paramagnetic resonance spectra have been collected and analyzed. PMID:26844593

  6. First-principles study of a single-molecule magnet Mn12 monolayer on the graphene surface.

    NASA Astrophysics Data System (ADS)

    Li, Xiangguo; Cheng, Hai-Ping

    2014-03-01

    Electronic structures of single-molecule magnets Mn12 on graphene surfaces are studied using spin-polarized density-functional theory. Charge transfer between molecule and graphene, densities of states, and magnetization are fully analyzed. We also report effects of various ligands and strain. Our results suggest that graphene can be p-doped upon Mn12 adsorption, and the doping level is closely related to the choice of ligands in molecule. In addition, we find that the strain in graphene plays an important role in modulating the doping level. Acknowledgement: DOE/BES-DE-FG02-02ER45995; NERSC and UF/HPC.

  7. Ab initio calculations as a quantitative tool in the inelastic neutron scattering study of a single-molecule magnet analogue.

    PubMed

    Vonci, Michele; Giansiracusa, Marcus J; Gable, Robert W; Van den Heuvel, Willem; Latham, Kay; Moubaraki, Boujemaa; Murray, Keith S; Yu, Dehong; Mole, Richard A; Soncini, Alessandro; Boskovic, Colette

    2016-01-26

    Ab initio calculations carried out on the Tb analogue of the single-molecule magnet family Na9[Ln(W5O18)2] (Ln = Nd, Gd, Ho and Er) have allowed interpretation of the inelastic neutron scattering spectra. The combined experimental and theoretical approach sheds new light on the sensitivity of the electronic structure of the Tb(iii) ground and excited states to small structural distortions from axial symmetry, thus revealing the subtle relationship between molecular geometry and magnetic properties of the two isostructural species that comprise the sample. PMID:26690503

  8. Correction: 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

    2016-06-01

    Correction for 'Single-molecule magnet behaviour in polynuclear assembly of trivalent cerium ions with polyoxomolybdates' by A. Ben Khélifa, et al., Dalton Trans., 2015, 44, 16458-16464. PMID:27161299

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

    PubMed

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

    2016-01-01

    Single-molecule imaging has changed the way we understand many biological mechanisms, particularly in neurobiology, by shedding light on intricate molecular events down to the nanoscale. However, current single-molecule studies in neuroscience have been limited to cultured neurons or organotypic slices, leaving as an open question the existence of fast receptor diffusion in intact brain tissue. Here, for the first time, we targeted dopamine receptors in vivo with functionalized quantum dots and were able to perform single-molecule tracking in acute rat brain slices. We propose a novel delocalized and non-inflammatory way of delivering nanoparticles (NPs) in vivo to the brain, which allowed us to label and track genetically engineered surface dopamine receptors in neocortical neurons, revealing inherent behaviour and receptor activity regulations. We thus propose a NP-based platform for single-molecule studies in the living brain, opening new avenues of research in physiological and pathological animal models. PMID:26971573

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

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

    PubMed Central

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

    2016-01-01

    Single-molecule imaging has changed the way we understand many biological mechanisms, particularly in neurobiology, by shedding light on intricate molecular events down to the nanoscale. However, current single-molecule studies in neuroscience have been limited to cultured neurons or organotypic slices, leaving as an open question the existence of fast receptor diffusion in intact brain tissue. Here, for the first time, we targeted dopamine receptors in vivo with functionalized quantum dots and were able to perform single-molecule tracking in acute rat brain slices. We propose a novel delocalized and non-inflammatory way of delivering nanoparticles (NPs) in vivo to the brain, which allowed us to label and track genetically engineered surface dopamine receptors in neocortical neurons, revealing inherent behaviour and receptor activity regulations. We thus propose a NP-based platform for single-molecule studies in the living brain, opening new avenues of research in physiological and pathological animal models. PMID:26971573

  12. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    PubMed

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

    2016-05-14

    Single-molecule detection has become an indispensable technology in life science, and medical research. In order to get meaningful information on many biological processes, single-molecule analysis is required in micro-molar concentrations. At such high concentrations, it is very challenging to isolate a single molecule with conventional diffraction-limited optics. Recently, optical aperture nanoantennas (OANs) have emerged as a powerful tool to enhance the single-molecule detection under a physiological environment. The OANs, which consist of nano-scale apertures on a metallic film, have the following unique properties: (1) nanoscale light confinement; (2) enhanced fluorescence emission; (3) tunable radiation pattern; (4) reduced background noise; and (5) massive parallel detection. This review presents the fundamentals, recent developments and future perspectives in this emerging field. PMID:27120086

  15. 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.

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

    DOE PAGESBeta

    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 themore » 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.« less

  17. Interfacial electron transfer between the photoexcited porphyrin molecule and TiO2 nanoparticles: effect of catecholate binding.

    PubMed

    Ramakrishna, G; Verma, Sandeep; Jose, D Amilan; Kumar, D Krishna; Das, Amitava; Palit, Dipak K; Ghosh, Hirendra N

    2006-05-11

    Interfacial electron transfer (ET) dynamics of 5,10,15-trisphenyl-20-(3,4-dihydroxybenzene) porphyrin (TPP-cat) adsorbed on TiO2 nanoparticles has been studied by femtosecond transient absorption spectroscopy in the visible and near-IR region exciting at 400 and 800 nm. TPP-cat molecule forms a charge transfer (CT) complex with TiO2 nanoparticles through the catechol moiety with the formation of a five-membered ring. Optical absorption measurements have shown that the Q-band of TPP-cat interacts strongly with TiO2 due to chelation; however, the Soret band is affected very little. Optical absorption measurements indicate that the catechol moiety also interacts with TiO2 nanoparticles showing the characteristic band of pure catechol-TiO2 charge transfer (CT) in the visible region. Electron injection has been confirmed by monitoring the cation radical, instant bleach, and injected electron in the conduction band of TiO2 nanoparticles. Electron injection time has been measured to be < 100 fs and recombination kinetics has been best fitted with a multiexponential function, where the majority of the injected electrons come back to the parent cation radical with a time constant of approximately 800 fs for both excitation wavelengths. However, the reaction channel for the electron injection process has been found to be different for both wavelengths. Excitation at 800 nm, found to populate the CT state of the Q-band, and from the photoexcited CT state electron injection into the conduction band, takes place through diffusion. On the other hand, with excitation at 400 nm, a complicated reaction channel takes place. Excitation with 400 nm light excites both the CT band of Cat-TiO2 and also the Soret band of TPP-cat. We have discussed the reaction path in the TPP-cat/TiO2 system after exciting with both 400 and 800 nm laser light. We have also compared ET dynamics by exciting at both wavelengths. PMID:16671709

  18. 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.

  19. Hidden Markov analysis of trajectories in single-molecule experiments and the effects of missed events.

    PubMed

    Stigler, Johannes; Rief, Matthias

    2012-03-01

    The ever more complex fluctuation patterns discovered by single molecule experiments require statistical methods to analyze multi-state hopping traces of long lengths. Hidden Markov modeling is a statistical tool that offers the scalability to analyze even complex data and extract kinetic information. We give an introduction on how to implement hidden Markov modeling for the analysis of single molecule force spectroscopic traces, deal with missed events, and test the method on a calcium binding protein. PMID:22392881

  20. Single-molecule imaging of non-equilibrium molecular ensembles on the millisecond timescale.

    PubMed

    Juette, Manuel F; Terry, Daniel S; Wasserman, Michael R; Altman, Roger B; Zhou, Zhou; Zhao, Hong; Blanchard, Scott C

    2016-04-01

    Single-molecule fluorescence microscopy is uniquely suited for detecting transient molecular recognition events, yet achieving the time resolution and statistics needed to realize this potential has proven challenging. Here we present a single-molecule imaging and analysis platform using scientific complementary metal-oxide semiconductor (sCMOS) detectors that enables imaging of 15,000 individual molecules simultaneously at millisecond rates. This system enabled the detection of previously obscured processes relevant to the fidelity mechanism in protein synthesis. PMID:26878382