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1

Intermittent Single-Molecule Interfacial Electron Transfer Dynamics  

SciTech Connect

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.

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

2004-08-04

2

Intermittent Single-molecule Interfacial Electron Transfer Dynamics in Dye-TiO2 Nanoparticle systems  

NASA Astrophysics Data System (ADS)

Photosensitized interfacial electron transfer dynamics of single molecules of Coumarin 343 (C343) and Cresyl Violet (CV+) acetate dyes adsorbed at TiO2 nanoparticle (NP)-polymer and TiO2 NP-electrolyte interfaces are studied using single-molecule photon-stamping fluorescence spectroscopy. Fluorescence intensity trajectories of individual dye molecules adsorbed at a TiO2 NP-polymer interface in air showed intermittent 'on' and 'off' (blinking) fluorescence in sub-second to second time scales, which are well distinguished from blinking due to intersystem crossing to dark triplet state. Autocorrelation analyses of the intensity trajectories showed non-exponential fluctuation dynamics for the single molecules, and the average rates are of 5 s-1 for both the C343-TiO2 and CV+-TiO2 systems. We attribute the fluorescence intensity fluctuation to the intermittency of the single-molecule interfacial electron transfer reactivity and dynamics.

Biju, Vasudevanpillai; Micic, Miodrag; Hu, Dehong; Lu, H. Peter

2004-03-01

3

Single Molecule Electronics and Devices  

PubMed Central

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

Tsutsui, Makusu; Taniguchi, Masateru

2012-01-01

4

Single Molecule Electron Paramagnetic Resonance  

NASA Astrophysics Data System (ADS)

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.

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

2013-03-01

5

Single Molecule Spectroscopy of Electron Transfer  

SciTech Connect

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.

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

2009-10-20

6

Methods and applications in single molecule electronics  

NASA Astrophysics Data System (ADS)

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.

Hihath, Joshua

7

Single-molecule junctions beyond electronic transport  

NASA Astrophysics Data System (ADS)

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.

Aradhya, Sriharsha V.; Venkataraman, Latha

2013-06-01

8

Medium Effects in Single Molecule Electronics  

NASA Astrophysics Data System (ADS)

We use STM-based techniques for measuring the electrical properties of metal|molecule|metal junctions. For a family of molecules HS(CH2)6-Ar-(CH2)6SH (Ar = substituted benzene), we found that the single molecule conductances varied significantly with substituent, being higher for electron-donating substituents [1]. Later, we studied the effect of increasing conjugation on this system by examining oligothiophenes HS(CH2)6-[C4H4S]x-(CH2)6SH (x = 1, 2, 3, 5). We found that the conductances of junctions involving these molecules depended upon the medium in which the measurements were made. In fact, for x = 3, the conductance was two orders of magnitude higher in the presence of water than in anhydrous conditions [2]. This presentation will outline these studies, together with the results of transport calculations that rationalise these unusual findings, and will set the results in the context of existing literature on medium effects in single molecule conductance determinations. In collaboration with Edmund Leary and Richard Nichols, University of Liverpool; Colin Lambert, Iain Grace, and Chris Finch, University of Lancaster; and Wolfgang Haiss, University of Liverpool.

Higgins, Simon

2010-03-01

9

Single-molecule electron transfer reactions in nanomaterials  

SciTech Connect

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

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

2009-07-26

10

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

PubMed Central

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

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

2014-01-01

11

Electron transfer-based single molecule fluorescence as a probe for nano-environment dynamics.  

PubMed

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

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

2014-01-01

12

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

PubMed

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

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

2014-02-18

13

Single-Molecule Electronic Measurements with Metal Electrodes  

ERIC Educational Resources Information Center

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.

Lindsay, Stuart

2005-01-01

14

Tuning Fullerene Electronic Properties: From Single Molecules to Extended Monolayers  

NASA Astrophysics Data System (ADS)

Fullerenes provide powerful building blocks for creating nanostructures with unique electronic properties due to their flexible electronic structure. This behavior arises through a combination of molecular energy levels, intramolecular Coulomb forces, electron-phonon coupling, and local charging. When molecules are placed at an interface, substrate charge transfer and screening effects also play an important role. We have used cryogenic scanning tunneling spectroscopy to examine the interplay of these factors in determining molecular electronic structure from the single molecule regime all the way up to the full monolayer regime. We find that it is possible to reversibly change the charge state of individual fullerenes through single-atom doping, and we have examined how molecular electronic structure is influenced by extended monolayer formation and surface screening effects. We observe strong variations in local molecular electronic structure due to charge doping, and in local electron-phonon coupling due to fullerene composition.

Crommie, Michael

2005-03-01

15

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

E-print Network

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

Upadhyayula, Srigokul

2013-01-01

16

Contact and Length Dependent Effects in Single-Molecule Electronics  

NASA Astrophysics Data System (ADS)

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

Hines, Thomas

17

Inelastic electron tunneling spectroscopy on single-molecule magnets  

NASA Astrophysics Data System (ADS)

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

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

2002-03-01

18

Electronic transport properties of functional single molecule junctions  

NASA Astrophysics Data System (ADS)

We report experimental studies of single molecule conductance using two techniques: statistical measurements with repeatedly-formed breakjunctions in ambient conditions and low-temperature measurements with electromigrated breakjunctions. In each case, we chose molecules with specific functions. With statistical measurements, we measured the nonconducting open and conducting closed forms of dithienylethene, a photochromic (optically switchable) molecule. These molecules were synthesized with pyridine endgroups to achieve relatively well-defined and stable contacts to Au electrodes. For the closed isomer, we find a conductance of (3.3 ±0.5) G0, while that of the open isomer is below the noise floor of our measurement. We can therefore set a lower limit of 30 for the on/off ratio of this molecule. We are currently investigating the use of electromigrated graphene nano-constrictions and breakjunctions for spin-polarized single molecule conductance measurements and plan to present initial results for this technique.

Tam, E. S.; Abruna, H. D.; Ralph, D. C.

2012-02-01

19

Atomic-scale control of electron transport through single molecules.  

PubMed

Tin-phthalocyanine molecules adsorbed on Ag(111) were contacted with the tip of a cryogenic scanning tunneling microscope. Orders-of-magnitude variations of the single-molecule junction conductance were achieved by controllably dehydrogenating the molecule and by modifying the atomic structure of the surface electrode. Nonequilibrium Green's function calculations reproduce the trend of the conductance and visualize the current flow through the junction, which is guided through molecule-electrode chemical bonds. PMID:20482125

Wang, Y F; Kröger, J; Berndt, R; Vázquez, H; Brandbyge, M; Paulsson, M

2010-04-30

20

Simulation of Single Molecule Inelastic Electron Tunneling Signals in Paraphenylene-Vinylene Oligomers and Distyrylbenzene[2.2]paracyclophanes  

E-print Network

,21-25 and single-molecule adsorbates in scanning tunneling microscopy (STM) where the inelasticSimulation of Single Molecule Inelastic Electron Tunneling Signals in Paraphenylene to the measurement of electronic transport through single molecules have engendered a diverse array of experimental

Mukamel, Shaul

21

Electronic Barcoding of a Viral Gene at the Single-Molecule Level  

PubMed Central

A new single-molecule approach for rapid and purely electronic discrimination among similar genes is presented. Combining solid-state nanopores and ?-modified synthetic peptide nucleic acid (?PNA) probes, we accurately barcode genes by counting the number of probes attached to each gene, and measuring their relative spacing. We illustrate our method by sensing individual genes from two highly similar human immunodeficiency virus (HIV) subtypes, demonstrating feasibility of a novel, single-molecule diagnostic platform for rapid pathogen classification. PMID:22352964

Singer, Alon; Rapireddy, Srinivas; Ly, Danith H.; Meller, Amit

2013-01-01

22

Break junction under electrochemical gating: testbed for single-molecule electronics.  

PubMed

Molecular electronics aims to construct functional molecular devices at the single-molecule scale. One of the major challenges is to construct a single-molecule junction and to further manipulate the charge transport through the molecular junction. Break junction techniques, including STM break junctions and mechanically controllable break junctions are considered as testbed to investigate and control the charge transport on a single-molecule scale. Moreover, additional electrochemical gating provides a unique opportunity to manipulate the energy alignment and molecular redox processes for a single-molecule junction. In this review, we start from the technical aspects of the break junction technique, then discuss the molecular structure-conductance correlation derived from break junction studies, and, finally, emphasize electrochemical gating as a promising method for the functional molecular devices. PMID:25560965

Huang, Cancan; Rudnev, Alexander V; Hong, Wenjing; Wandlowski, Thomas

2015-02-10

23

REVIEWS OF TOPICAL PROBLEMS Electron-vibration interaction in tunneling processes through single molecules  

NASA Astrophysics Data System (ADS)

It is shown how effective Hamiltonians are constructed in the framework of the adiabatic approach to the electron-vibration interaction in electron tunneling through single molecules. Methods for calculating tunneling characteristics are discussed and possible features resulting from the electron-vibration coupling are described. The intensity of vibrations excited by a tunneling current in various systems is examined.

Arseev, Petr I.; Maslova, N. S.

2011-02-01

24

Protein Conformational Dynamics Probed by Single-Molecule Electron Transfer  

Microsoft Academic Search

Electron transfer is used as a probe for angstrom-scale structural changes in single protein molecules. In a flavin reductase, the fluorescence of flavin is quenched by a nearby tyrosine residue by means of photo-induced electron transfer. By probing the fluorescence lifetime of the single flavin on a photon-by-photon basis, we were able to observe the variation of flavin-tyrosine distance over

Haw Yang; Guobin Luo; Pallop Karnchanaphanurach; Tai-Man Louie; Ivan Rech; Sergio Cova; Luying Xun; X. Sunney Xie

2003-01-01

25

Vibrational Nonequilibrium Effects in the Conductance of Single Molecules with Multiple Electronic States  

NASA Astrophysics Data System (ADS)

Vibrational nonequilibrium effects in charge transport through single-molecule junctions are investigated. Focusing on molecular bridges with multiple electronic states, it is shown that electronic-vibrational coupling triggers a variety of vibronic emission and absorption processes, which influence the conductance properties and mechanical stability of single-molecule junctions profoundly. Employing a master equation and a nonequilibrium Green’s function approach, these processes are analyzed in detail for a generic model of a molecular junction and for benzenedibutanethiolate bound to gold electrodes.

Härtle, R.; Benesch, C.; Thoss, M.

2009-04-01

26

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

SciTech Connect

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.

Wu, S. W.; Ho, W. [Department of Physics and Astronomy and Department of Chemistry, University of California, Irvine, California 92697-4575 (United States)

2010-08-15

27

Electron-vibron coupling effects on electron transport via a single-molecule magnet  

NASA Astrophysics Data System (ADS)

We investigate how the electron-vibron coupling influences electron transport via an anisotropic magnetic molecule, such as a single-molecule magnet (SMM) Fe4, by using a model Hamiltonian with parameter values obtained from density-functional theory (DFT). The magnetic anisotropy parameters, vibrational energies, and electron-vibron coupling strengths of the Fe4 are computed using DFT. A giant spin model is applied to the Fe4 with only two charge states, specifically a neutral state with a total spin S =5 and a singly charged state with S =9 /2 , which is consistent with our DFT result and experiments on Fe4 single-molecule transistors. In sequential electron tunneling, we find that the magnetic anisotropy gives rise to new features in the conductance peaks arising from vibrational excitations. In particular, the peak height shows a strong, unusual dependence on the direction as well as magnitude of applied B field. The magnetic anisotropy also introduces vibrational satellite peaks whose position and height are modified with the direction and magnitude of applied B field. Furthermore, when multiple vibrational modes with considerable electron-vibron coupling have energies close to one another, a low-bias current is suppressed, independently of gate voltage and applied B field, although that is not the case for a single mode with a similar electron-vibron coupling. In the former case, the conductance peaks reveal a stronger B -field dependence than in the latter case. The new features appear because the magnetic anisotropy barrier is of the same order of magnitude as the energies of vibrational modes with significant electron-vibron coupling. Our findings clearly show the interesting interplay between magnetic anisotropy and electron-vibron coupling in electron transport via the Fe4. Similar behavior can be observed in transport via other anisotropic magnetic molecules.

McCaskey, Alexander; Yamamoto, Yoh; Warnock, Michael; Burzurí, Enrique; van der Zant, Herre S. J.; Park, Kyungwha

2015-03-01

28

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

SciTech Connect

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.

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

2011-03-11

29

Single-molecule imaging with x-ray free-electron lasers: dream or reality?  

PubMed

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. PMID:21469805

Fratalocchi, A; Ruocco, G

2011-03-11

30

Single Molecules  

NSDL National Science Digital Library

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

31

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

SciTech Connect

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.

Sotthewes, Kai; Heimbuch, René, E-mail: r.heimbuch@utwente.nl; Kumar, Avijit; Zandvliet, Harold J. W. [Physics of Interfaces and Nanomaterials, MESA Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500AE Enschede (Netherlands); Geskin, Victor [Service de Chimie des Materiaux Nouveaux, University of Mons, Mons (Belgium)

2014-01-01

32

Electronic spectrum and orbital filling in a single-molecule junction  

NASA Astrophysics Data System (ADS)

We study single-electron tunneling in three-terminal devices in which a single molecule bridges the gap between source and drain electrode. The molecular devices are made by electromigration and at low temperatures excitations appear in the stability diagram. For the OPV-5 molecule more than fifteen different excitations are visible, of which twelve match RAMAN spectra and the remaining ones are due to vibratrions of the molecule attached to gold electrodes at energies below 10 meV. Similar to carbon nanotubes, the observation of a singlet-triplet transition allow us to determine the orbital filling and spin configuration of the molecule.

Osorio, Edgar A.; O'Neill, Kevin; Wegewijs, Maarten; Stuhr-Hansen, Nicolai; Paaske, Jens; Bjornholm, Thomas; van der Zant, Herre

2008-03-01

33

Current noise in single-molecule junctions induced by electronic-vibrational coupling  

NASA Astrophysics Data System (ADS)

The influence of multiple vibrational modes on current fluctuations in electron transport through single-molecule junctions is investigated. Our analysis is based on a generic model of a molecular junction, which comprises a single electronic state on the molecular bridge coupled to multiple vibrational modes and fermionic leads, and employs a master equation approach. The results reveal that in molecular junctions with multiple vibrational modes, already weak to moderate electronic-vibrational coupling may result in high noise levels, especially at the onset of resonant transport, in accordance with the experimental findings of Secker et al. [Phys. Rev. Lett. 106, 136807 (2011), 10.1103/PhysRevLett.106.136807]. The underlying mechanisms are analyzed in some detail.

Schinabeck, C.; Härtle, R.; Weber, H. B.; Thoss, M.

2014-08-01

34

All-Optical Sensing of a Single-Molecule Electron Spin  

NASA Astrophysics Data System (ADS)

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

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

2014-11-01

35

Measurement and control of detailed electronic properties in a single molecule break junction.  

PubMed

The lack of detailed experimental controls has been one of the major obstacles hindering progress in molecular electronics. While large fluctuations have been occurring in the experimental data, specific details, related mechanisms, and data analysis techniques are in high demand to promote our physical understanding at the single-molecule level. A series of modulations we recently developed, based on traditional scanning probe microscopy break junctions (SPMBJs), have helped to discover significant properties in detail which are hidden in the contact interfaces of a single-molecule break junction (SMBJ). For example, in the past we have shown that the correlated force and conductance changes under the saw tooth modulation and stretch-hold mode of PZT movement revealed inherent differences in the contact geometries of a molecular junction. In this paper, using a bias-modulated SPMBJ and utilizing emerging data analysis techniques, we report on the measurement of the altered alignment of the HOMO of benzene molecules with changing the anchoring group which coupled the molecule to metal electrodes. Further calculations based on Landauer fitting and transition voltage spectroscopy (TVS) demonstrated the effects of modulated bias on the location of the frontier molecular orbitals. Understanding the alignment of the molecular orbitals with the Fermi level of the electrodes is essential for understanding the behaviour of SMBJs and for the future design of more complex devices. With these modulations and analysis techniques, fruitful information has been found about the nature of the metal-molecule junction, providing us insightful clues towards the next step for in-depth study. PMID:25485840

Wang, Kun; Hamill, Joseph; Zhou, Jianfeng; Guo, Cunlan; Xu, Bingqian

2014-01-01

36

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

SciTech Connect

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.

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

2014-02-07

37

Clay nanoparticle-supported single-molecule fluorescence spectroelectrochemistry.  

PubMed

Here we report that clay nanoparticles allow formation of a modified transparent electrode, spontaneous adsorption of fluorescent redox molecules on the clay layer, and thus the subsequent observation of single-molecule fluorescence spectroelectrochemistry. We can trace single-molecule fluorescence spectroelectrochemistry by probing the fluorescence intensity change of individually immobilized single redox molecules modulated via cyclic voltammetric potential scanning. This work opens a new approach to explore interfacial electron transfer mechanisms of redox reactions. PMID:19140768

Lei, Chenghong; Hu, Dehong; Ackerman, Eric

2009-02-01

38

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

PubMed Central

A biomimetic long-range electron transfer (ET) system consisting of the blue copper protein azurin, a tunneling barrier bridge, and a gold single-crystal electrode was designed on the basis of molecular wiring self-assembly principles. This system is sufficiently stable and sensitive in a quasi-biological environment, suitable for detailed observations of long-range protein interfacial ET at the nanoscale and single-molecule levels. Because azurin is located at clearly identifiable fixed sites in well controlled orientation, the ET configuration parallels biological ET. The ET is nonadiabatic, and the rate constants display tunneling features with distance-decay factors of 0.83 and 0.91 Ŗ1 in H2O and D2O, respectively. Redox-gated tunneling resonance is observed in situ at the single-molecule level by using electrochemical scanning tunneling microscopy, exhibiting an asymmetric dependence on the redox potential. Maximum resonance appears around the equilibrium redox potential of azurin with an on/off current ratio of ?9. Simulation analyses, based on a two-step interfacial ET model for the scanning tunneling microscopy redox process, were performed and provide quantitative information for rational understanding of the ET mechanism. PMID:16260751

Chi, Qijin; Farver, Ole; Ulstrup, Jens

2005-01-01

39

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

NASA Astrophysics Data System (ADS)

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.

Barhoum, Moussa

40

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

PubMed Central

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

2011-01-01

41

Nanographenes as active components of single-molecule electronics and how a scanning tunneling microscope puts them to work.  

PubMed

Single-molecule electronics, that is, realizing novel electronic functionalities from single (or very few) molecules, holds promise for application in various technologies, including signal processing and sensing. Nanographenes, which are extended polycyclic aromatic hydrocarbons (PAHs), are highly attractive subjects for studies of single-molecule electronics because the electronic properties of their flat conjugated systems can be varied dramatically through synthetic modification of their sizes and topologies. Single nanographenes provide high tunneling currents when adsorbed flat onto conducting substrates, such as graphite. Because of their chemical inertness, nanographenes interact only weakly with these substrates, thereby preventing the need for special epitaxial structure matching. Instead, self-assembly at the interface between a conducting solid, such as the basal plane of graphite, and a nanographene solution generally leads to highly ordered monolayers. Scanning tunneling spectroscopy (STS) allows the current-voltage characteristics to be measured through a single molecule positioned between two electrodes; the key to the success of STS is the ability to position the scanning tunneling microscopy (STM) tip freely with respect to the molecule in all dimensions, that is, both parallel and perpendicular to the surface. In this Account, we report the properties of nanographenes having sizes ranging from 0.7 to 3.1 nm and exhibiting various symmetry, periphery, and substitution types. The size of the aromatic system and the nature of its perimeter are two essential features affecting its HOMO-LUMO gap and charge carrier mobility in the condensed phase. Moreover, the extended pi area of larger substituted PAHs improves the degree of self-ordering, another key requirement for high-performance electronic devices. Self-assembly at the interface between an organic solution and the basal plane of graphite allows deposition of single molecules within the well-defined environment of a molecular monolayer. We have used STM and STS to investigate both the structures and electronic properties of these single molecules in situ. Indeed, we have observed key electronic functions, rectification and current control through single molecules, within a prototypical chemical field-effect transistor at ambient temperature. The combination of nanographenes and STM/STS, with the PAHs self-assembled in oriented molecular mono- or bilayers at the interface between an organic solution and the basal plane of graphite and contacted by the STM tip, is a simple, reliable, and versatile system for developing the fundamental concepts of molecular electronics. Our future targets include fast reversible molecular switches and complex molecular electronic devices coupled together from several single-molecule systems. PMID:18410086

Müllen, Klaus; Rabe, Jürgen P

2008-04-01

42

Wiring up Single Molecules  

NSDL National Science Digital Library

In recent years, circuit design has advanced to achieve extremely small feature sizes -- literally tens of millions of transistors can be integrated in a single chip. This progress has given rise to molecular electronics, the notion of creating electronic devices with single molecules as circuit elements. In this paper, the authors "discuss transistors, where electrons flow through discrete quantum states of a single molecule." Fabrication considerations are outlined, and the current-voltage responses of several such transistors that were fabricated by the authors are shown. The paper concludes by looking ahead to future possibilities of chemically-tailored transistors that could be designed with specific properties.

43

Functionality in single-molecule devices: Model calculations and applications of the inelastic electron tunneling signal in molecular junctions  

NASA Astrophysics Data System (ADS)

We analyze how functionality could be obtained within single-molecule devices by using a combination of non-equilibrium Green's functions and ab initio calculations to study the inelastic transport properties of single-molecule junctions. First, we apply a full non-equilibrium Green's function technique to a model system with electron-vibration coupling. We show that the features in the inelastic electron tunneling spectra (IETS) of the molecular junctions are virtually independent of the nature of the molecule-lead contacts. Since the contacts are not easily reproducible from one device to another, this is a very useful property. The IETS signal is much more robust versus modifications at the contacts and hence can be used to build functional nanodevices. Second, we consider a realistic model of a organic conjugated molecule. We use ab initio calculations to study how the vibronic properties of the molecule can be controlled by an external electric field which acts as a gate voltage. The control, through the gate voltage, of the vibron frequencies and (more importantly) of the electron-vibron coupling enables the construction of functionality: nonlinear amplification and/or switching is obtained from the IETS signal within a single-molecule device.

Dash, L. K.; Ness, H.; Verstraete, M. J.; Godby, R. W.

2012-02-01

44

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

E-print Network

. We confirm single-molecule resolution using optical fluorescence and atomic force microscopy to coarXiv:1311.1801v1[cond-mat.mes-hall]7Nov2013 All-optical sensing of a single-molecule electron spin crystal, which we use to detect single paramagnetic molecules covalently attached to the diamond surface

Walsworth, Ronald L.

45

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

PubMed

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

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

2014-12-01

46

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

Microsoft Academic Search

Surface structures controlled at the nanometer and single-molecule levels, with functions crucially determined by interfacial electron transfer (ET) are broadly reported in recent years, with different kinds of electrochemically controlled nanoscale\\/single molecule systems. One is the broad class of metallic and semiconductor-based nanoparticles, nano-arrays, nanotubes, and nanopits. Others are based on self-assembled molecular monolayers. The latter extend to bioelectrochemical systems

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

2005-01-01

47

Single molecule logical devices.  

PubMed

After almost 40 years of development, molecular electronics has given birth to many exciting ideas that range from molecular wires to molecular qubit-based quantum computers. This chapter reviews our efforts to answer a simple question: how smart can a single molecule be? In our case a molecule able to perform a simple Boolean function is a child prodigy. Following the Aviram and Ratner approach, these molecules are inserted between several conducting electrodes. The electronic conduction of the resulting molecular junction is extremely sensitive to the chemical nature of the molecule. Therefore designing this latter correctly allows the implementation of a given function inside the molecular junction. Throughout the chapter different approaches are reviewed, from hybrid devices to quantum molecular logic gates. We particularly stress that one can implement an entire logic circuit in a single molecule, using either classical-like intramolecular connections, or a deformation of the molecular orbitals induced by a conformational change of the molecule. These approaches are radically different from the hybrid-device approach, where several molecules are connected together to build the circuit. PMID:21826604

Renaud, Nicolas; Hliwa, Mohamed; Joachim, Christian

2012-01-01

48

Single molecule junctions, where a molecule with its perfect chemical reproducibility and versatility is the active part of an electronic device,  

E-print Network

Single molecule junctions, where a molecule with its perfect chemical reproducibility characteristics of nanojunctions both in the single electron transistor and the scanning tunneling microscopy (STM of modern electronics. Quantum dot molecules (QDM) represent a top-down one. A QDM is composed of two

Schubart, Christoph

49

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

NASA Astrophysics Data System (ADS)

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

Kastlunger, Georg; Stadler, Robert

2015-03-01

50

Observing magnetic anisotropy in electronic transport through individual single-molecule magnets  

NASA Astrophysics Data System (ADS)

We review different electron transport methods to probe the magnetic properties, such as the magnetic anisotropy, of an individual Fe4 SMM. The different approaches comprise first and higher order transport through the molecule. Gate spectroscopy, focusing on the charge degeneracy-point, is presented as a robust technique to quantify the longitudinal magnetic anisotropy of the SMM in different redox states. We provide statistics showing the robustness and reproducibility of the different methods. In addition, conductance measurements typically show high-energy excited states well beyond the ground spin multiplet of SMM. Some of these excitations have their origin in excited spin multiplets, others in vibrational modes of the molecule. The interplay between vibrations, charge and spin may yield a new approach for spin control.

Burzurí, E.; Gaudenzi, R.; van der Zant, H. S. J.

2015-03-01

51

Observing magnetic anisotropy in electronic transport through individual single-molecule magnets.  

PubMed

We review different electron transport methods to probe the magnetic properties, such as the magnetic anisotropy, of an individual Fe4 SMM. The different approaches comprise first and higher order transport through the molecule. Gate spectroscopy, focusing on the charge degeneracy-point, is presented as a robust technique to quantify the longitudinal magnetic anisotropy of the SMM in different redox states. We provide statistics showing the robustness and reproducibility of the different methods. In addition, conductance measurements typically show high-energy excited states well beyond the ground spin multiplet of SMM. Some of these excitations have their origin in excited spin multiplets, others in vibrational modes of the molecule. The interplay between vibrations, charge and spin may yield a new approach for spin control. PMID:25721135

Burzurí, E; Gaudenzi, R; van der Zant, H S J

2015-03-25

52

Single molecule laser spectroscopy.  

PubMed

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. PMID:25156641

Atta, Diaa; Okasha, Ali

2015-01-25

53

Single molecule laser spectroscopy  

NASA Astrophysics Data System (ADS)

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.

Atta, Diaa; Okasha, Ali

2015-01-01

54

Movies of molecular motions and reactions: the single-molecule, real-time transmission electron microscope imaging technique.  

PubMed

"The truth is, the Science of Nature has been already too long made only a work of the Brain and the Fancy: It is now high time that it should return to the plainness and soundness of Observations on material and obvious things," proudly declared Robert Hooke in his highly successful picture book of microscopic and telescopic images, "Micrographia" in 1665. Hooke's statement has remained true in chemistry, where a considerable work of the brain and the fancy is still necessary. Single-molecule, real-time transmission electron microscope (SMRT-TEM) imaging at an atomic resolution now allows us to learn about molecules simply by watching movies of them. Like any dream come true, the new analytical technique challenged the old common sense of the communities, and offers new research opportunities that are unavailable by conventional methods. With its capacity to visualize the motions and the reactions of individual molecules and molecular clusters, the SMRT-TEM technique will become an indispensable tool in molecular science and the engineering of natural and synthetic substances, as well as in science education. PMID:23280645

Nakamura, Eiichi

2013-01-01

55

Interfacial electronic traps in surface controlled transistors  

Microsoft Academic Search

Carrier recombination at interfacial electronic traps under a surface controlling gate electrode is analyzed using the Shockley-Reed-Hall steady-state recombination kinetics to provide a theoretical basis for quantifying the direct-current current-voltage (DCIV) method for monitoring and diagnosis of MOS transistor reliability, design, and manufacturing processes. Analytical expressions for DCIV lineshape, linewidth, peak gate-voltage and peak amplitude are derived for the determination

Jin Cai; Chih-Tang Sah

2000-01-01

56

Towards single molecule DNA sequencing  

NASA Astrophysics Data System (ADS)

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

Liu, Hao

57

Structural and electronic properties of ultrathin tin-phthalocyanine films on Ag(111) at the single-molecule level.  

PubMed

Heads or tails? The evolution of structural and electronic properties of tin-phthalocyanine films has been analyzed for sub-monolayer to multilayer coverage using low-temperature scanning tunneling microscopy. Two molecular conformations are observed: randomly dispersed for the first layer, and islands with a single conformation in subsequent layers. PMID:19130515

Wang, Yongfeng; Kröger, Jörg; Berndt, Richard; Hofer, Werner

2009-01-01

58

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

SciTech Connect

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.

Brito Silva, C. A. Jr.; Granhen, E. R. [Pos-Graduacao em Engenharia Eletrica, Universidade Federal do Para, 66075-900 Belem, PA (Brazil); Silva, S. J. S. da; Leal, J. F. P. [Pos-Graduacao em Fisica, Universidade Federal do Para, 66075-110 Belem, PA (Brazil); Del Nero, J. [Departamento de Fisica, Universidade Federal do Para, 66075-110 Belem, PA (Brazil); Divisao de Metrologia de Materiais, Instituto Nacional de Metrologia, Normalizacao e Qualidade Industrial, 25250-020 Duque de Caxias, RJ (Brazil); Instituto de Fisica, Universidade Federal do Rio de Janeiro, 21941-972 Rio de Janeiro, RJ (Brazil); Pinheiro, F. A. [Instituto de Fisica, Universidade Federal do Rio de Janeiro, 21941-972 Rio de Janeiro, RJ (Brazil)

2010-08-15

59

Theory of plasmon enhanced interfacial electron transfer.  

PubMed

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 10(5) 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. PMID:25764984

Wang, Luxia; May, Volkhard

2015-04-10

60

Theory of plasmon enhanced interfacial electron transfer  

NASA Astrophysics Data System (ADS)

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.

Wang, Luxia; May, Volkhard

2015-04-01

61

Single Molecule Recordings of Lysozyme Activity  

PubMed Central

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

Choi, Yongki; Weiss, Gregory A.

2013-01-01

62

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

PubMed

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

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

2009-01-28

63

Cyanide-bridged [Fe8M6] clusters displaying single-molecule magnetism (M=Ni) and electron-transfer-coupled spin transitions (M=Co).  

PubMed

Cyanide-bridged metal complexes of [Fe(8)M(6)(?-CN)(14)(CN)(10)(tp)(8)(HL)(10)(CH(3)CN)(2)][PF(6)](4)?n?CH(3)CN?m?H(2)O (HL=3-(2-pyridyl)-5-[4-(diphenylamino)phenyl]-1H-pyrazole), tp(-) =hydrotris(pyrazolylborate), 1: M=Ni with n=11 and m=7, and 2: M=Co with n=14 and m=5) were prepared. Complexes 1 and 2 are isomorphous, and crystallized in the monoclinic space group P2(1)/n. They have tetradecanuclear cores composed of eight low-spin (LS) Fe(III) and six high-spin (HS) M(II) ions (M=Ni and Co), all of which are bridged by cyanide ions, to form a crown-like core structure. Magnetic susceptibility measurements revealed that intramolecular ferro- and antiferromagnetic interactions are operative in 1 and in a fresh sample of 2, respectively. Ac magnetic susceptibility measurements of 1 showed frequency-dependent in- and out-of-phase signals, characteristic of single-molecule magnetism (SMM), while desolvated samples of 2 showed thermal- and photoinduced intramolecular electron-transfer-coupled spin transition (ETCST) between the [(LS-Fe(II))(3) (LS-Fe(III))(5)(HS-Co(II))(3)(LS-Co(III))(3)] and the [(LS-Fe(III))(8)(HS-Co(II))(6)] states. PMID:21830241

Mitsumoto, Kiyotaka; Oshiro, Emiko; Nishikawa, Hiroyuki; Shiga, Takuya; Yamamura, Yasuhisa; Saito, Kazuya; Oshio, Hiroki

2011-08-22

64

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

PubMed

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

Rodriguez, Jorge H; Ziegler, Christopher J

2015-01-01

65

Stereoelectronic switching in single-molecule junctions  

NASA Astrophysics Data System (ADS)

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

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

2015-03-01

66

Fluorescence Microscopy of Single Molecules  

ERIC Educational Resources Information Center

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.

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

2004-01-01

67

Rigid adamantane tripod linkage for well-defined conductance of a single-molecule junction.  

PubMed

We present a systematic analysis of molecular level alignments and electron transport characteristics based on the non-equilibrium Green's function (NEGF) approach combined with density functional theory (DFT) for phenyl dithiol (PDT) derivatives with two different linkages, simple thiol (ST) and tripod-shaped adamantane trithiol (ATT). The substantial adamantane-metal bonds afford a rigid contact structure and well-defined conductance of a single-molecule junction irrespective of interfacial phenomena, which accordingly allows us to utilize the intrinsic nature of the molecule for designing molecular devices with prescribed transport characteristics. We suggest a feasible application of the ATT linkage embedded single-molecule junction to a molecular transistor based on the practical feature of the ATT linkage, which is the unsusceptible behavior of transmission under the applied bias voltage. The present result may serve as an important reference point for designing molecular devices with prescribed transport properties. PMID:20694223

Lee, Sang Uck; Mizuseki, Hiroshi; Kawazoe, Yoshiyuki

2010-10-01

68

Structure and DNA-binding properties of the Bacillus subtilis SpoIIIE DNA translocase revealed by single-molecule and electron microscopies  

PubMed Central

SpoIIIE/FtsK are a family of ring-shaped, membrane-anchored, ATP-fuelled motors required to segregate DNA across bacterial membranes. This process is directional and requires that SpoIIIE/FtsK recognize highly skewed octameric sequences (SRS/KOPS for SpoIIIE/FtsK) distributed along the chromosome. Two models have been proposed to explain the mechanism by which SpoIIIE/FtsK interact with DNA. The loading model proposes that SpoIIIE/FtsK oligomerize exclusively on SpoIIIE recognition sequence/orienting polar sequences (SRS/KOPS) to accomplish directional DNA translocation, whereas the target search and activation mechanism proposes that pre-assembled SpoIIIE/FtsK hexamers bind to non-specific DNA, reach SRS/KOPS by diffusion/3d hopping and activate at SRS/KOPS. Here, we employ single-molecule total internal reflection imaging, atomic force and electron microscopies and ensemble biochemical methods to test these predictions and obtain further insight into the SpoIIIE–DNA mechanism of interaction. First, we find that SpoIIIE binds DNA as a homo-hexamer with neither ATP binding nor hydrolysis affecting the binding mechanism or affinity. Second, we show that hexameric SpoIIIE directly binds to double-stranded DNA without requiring the presence of SRS or free DNA ends. Finally, we find that SpoIIIE hexamers can show open and closed conformations in solution, with open-ring conformations most likely resembling a state poised to load to non-specific, double-stranded DNA. These results suggest how SpoIIIE and related ring-shaped motors may be split open to bind topologically closed DNA. PMID:24297254

Cattoni, Diego I.; Thakur, Shreyasi; Godefroy, Cedric; Le Gall, Antoine; Lai-Kee-Him, Josephine; Milhiet, Pierre-Emmanuel; Bron, Patrick; Nöllmann, Marcelo

2014-01-01

69

Manipulating transport through a single-molecule junction  

SciTech Connect

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.

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

2013-12-07

70

Single molecule Studies of DNA Mismatch Repair  

PubMed Central

DNA mismatch repair involves is a widely conserved set of proteins that is essential to limit genetic drift in all organisms. The same system of proteins plays key roles in many cancer related cellular transactions in humans. Although the basic process has been reconstituted in vitro using purified components, many fundamental aspects of DNA mismatch repair remain hidden due in part to the complexity and transient nature of the interactions between the mismatch repair proteins and DNA substrates. Single molecule methods offer the capability to uncover these transient but complex interactions and allow novel insights into mechanisms that underlie DNA mismatch repair. In this review, we discuss applications of single molecule methodology including electron microscopy, atomic force microscopy, particle tracking, FRET, and optical trapping to studies of DNA mismatch repair. These studies have led to formulation of mechanistic models of how proteins identify single base mismatches in the vast background of matched DNA and signal for their repair. PMID:24746644

Erie, Dorothy A.; Weninger, Keith R.

2015-01-01

71

Diamond based single molecule magnetic resonance spectroscopy  

E-print Network

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

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

2012-12-07

72

Fluorophores for single molecule microscopy  

Microsoft Academic Search

The fluorescence photoncount distributions, photobleaching characteristics, and saturation intensities of the commonly used fluorescence tags tetramethylrhodamine and phycoerythrin were measured on the level of individual molecules. Although, the fluorescence properties of phycoerythrin seem to be superior in view of single molecule detection, the increased photostability of tetramethylrhodamine coupled both, to a lipid or an antibody, makes it the molecule of

G. J. Schütz; H. J. Gruber; H. Schindler; Th. Schmidt

1997-01-01

73

Large Mn25 single-molecule magnet with spin S = 51/2: magnetic and high-frequency electron paramagnetic resonance spectroscopic characterization of a giant spin state.  

PubMed

The synthesis and structural, spectroscopic, and magnetic characterization of a Mn25 coordination cluster with a large ground-state spin of S = 51/2 are reported. Reaction of MnCl2 with pyridine-2,6-dimethanol (pdmH2) and NaN3 in MeCN/MeOH gives the mixed valence cluster [Mn25O18(OH)2(N3)12(pdm)6(pdmH)6]Cl2 (1; 6Mn(II), 18Mn(III), Mn(IV)), which has a barrel-like cage structure. Variable temperature direct current (dc) magnetic susceptibility data were collected in the 1.8-300 K temperature range in a 0.1 T field. Variable-temperature and -field magnetization (M) data were collected in the 1.8-4.0 K and 0.1-7 T ranges and fit by matrix diagonalization assuming only the ground state is occupied at these temperatures. The fit parameters were S = 51/2, D = -0.020(2) cm(-1), and g = 1.87(3), where D is the axial zero-field splitting parameter. Alternating current (ac) susceptibility measurements in the 1.8-8.0 K range and a 3.5 G ac field oscillating at frequencies in the 50-1500 Hz range revealed a frequency-dependent out-of-phase (chi(M)'') signal below 3 K, suggesting 1 to be a single-molecule magnet (SMM). This was confirmed by magnetization vs dc field sweeps, which exhibited hysteresis loops but with no clear steps characteristic of resonant quantum tunneling of magnetization (QTM). However, magnetization decay data below 1 K were collected and used to construct an Arrhenius plot, and the fit of the thermally activated region above approximately 0.5 K gave U(eff)/k = 12 K, where U(eff) is the effective relaxation barrier. The g value and the magnitude and sign of the D value were independently confirmed by detailed high-frequency electron paramagnetic resonance (HFEPR) spectroscopy on polycrystalline samples. The combined studies confirm both the high ground-state spin S = 51/2 of complex 1 and that it is a SMM that, in addition, exhibits QTM. PMID:18788733

Murugesu, Muralee; Takahashi, Susumu; Wilson, Anthony; Abboud, Khalil A; Wernsdorfer, Wolfgang; Hill, Stephen; Christou, George

2008-10-20

74

Interfacial slippage of inorganic electronic materials on plastic substrates  

Microsoft Academic Search

The stretchable and flexible electronics with the structure of inorganic films on plastic substrate has recently attracted an increasing interest. Interfacial failure inevitably occurs when the structure is subject to repeated bending or stretching in application. An analysis is presented in this letter on the slipping failure mechanism for the interface between inorganic film and plastic substrate. The critical radius

Longchao Dai; Xue Feng; Bin Liu; Daining Fang

2010-01-01

75

Single-Molecule Enzymatic Dynamics  

Microsoft Academic Search

Enzymatic turnovers of single cholesterol oxidase molecules are observed in real time by monitoring the emission from the enzyme's fluorescent active site, flavin adenine dinucleotide (FAD). Although chemical kinetics, the Michaelis-Menten mechanism in particular, holds as a good approximation, statistical analyses of single-molecule trajectories reveal fluctuations in the rate of the activation step in the Michaelis-Menten mechanism. There exists a

H. Peter Lu; Luying Xun; Xiaoliang Xie

1998-01-01

76

Energy Transfer in Single-Molecule Photonic Wires  

Microsoft Academic Search

The ultimate goal in device miniaturisation aims at the incor- poration of single molecules as building blocks for the con- struction of molecule-based electronic, mechanical and optical devices. Molecular electronics, for instance, is emerging as a field that will conjecturally resolve the quest to scale electron- ics beyond the limit of \\

Gabriel Sanchez Mosteiro; Jacob P. Hoogenboom; Erik M. H. P. van Dijk; Niek. F. van Hulst

2005-01-01

77

Multiple events on single molecules: Unbiased estimation in single-molecule biophysics  

E-print Network

Multiple events on single molecules: Unbiased estimation in single-molecule biophysics Daniel A, Princeton, NJ, December 6, 2005 (received for review June 24, 2005) Most analyses of single-molecule of a motor protein acting on a single molecule must not exceed the total molecule length. We have developed

Dekker, Nynke

78

Single-molecule mechanics of mussel adhesion  

NASA Astrophysics Data System (ADS)

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

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

2006-08-01

79

Localization Accuracy in Single-Molecule Microscopy  

Microsoft Academic Search

One of the most basic questions in single-molecule microscopy concerns the accuracy with which the location of a single molecule can be determined. Using the Fisher information matrix it is shown that the limit of the localization accuracy for a single molecule is given by ?em\\/2?na?At, where ?em, na, ?, A, and t denote the emission wavelength of the single

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

2004-01-01

80

Nanometer Resolution Imaging by SIngle Molecule Switching  

SciTech Connect

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

Hu, Dehong; Orr, Galya

2010-04-02

81

Interfacial and thin film chemistry in electron device fabrication  

NASA Astrophysics Data System (ADS)

The fourth year's progress on the Columbia URI program on Interfacial and Thin-Film Chemistry in Electron Device Fabrication is reported. Progress has been made in three broad areas: Molecular Beam Epitaxy (MBE) Growth and Devices, Laser Surface Interactions, and Fundamentals of Processing Gas/Surface Interactions. Examples of specific results include the first study of laser-assisted Cl2 etching of copper, many new tunnelling and optical devices in layered semiconductors; a new 2-phase 2 deg charge coupled device (CCD); seminal studies of the Si-YBaCuO system; and the first observation of thin film growth by photoelectron injection.

Flynn, G.; Osgood, R.; Auston, D.; Fossum, E.; Turro, N.

1990-11-01

82

Single molecule spectroscopy of tetrahedral oligophenylenevinylene molecules  

E-print Network

Single molecule spectroscopy of tetrahedral oligophenylenevinylene molecules Melissa A. Summers form 17 July 2002 Abstract We probe the fluorescence from single molecules of a new class of tetrahedral oligo(phenylenevinylene) (OPV) molecules. Our results show that the tetrahedral molecules contain

Buratto, Steve

83

Single-molecule studies of DNA mechanics  

Microsoft Academic Search

During the past decade, physical techniques such as optical tweezers and atomic force microscopy were used to study the mechanical properties of DNA at the single-molecule level. Knowledge of DNA’s stretching and twisting properties now permits these single-molecule techniques to be used in the study of biological processes such as DNA replication and transcription.

Carlos Bustamante; Steven B Smith; Jan Liphardt; Doug Smith

2000-01-01

84

RICE UNIVERSITY Transport in Single Molecule Transistors  

E-print Network

RICE UNIVERSITY Transport in Single Molecule Transistors by Lam H. Yu A Thesis Submitted in Partial Houston, Texas January, 2006 #12;Abstract Transport in Single Molecule Transistors by Lam H. Yu molecule transistors (SMTs), nanometer-scale transistors in which charge transport occurs through

Natelson, Douglas

85

Single-molecule recognition imaging microscopy  

Microsoft Academic Search

Atomic force microscopy is a powerful and widely used imaging technique that can visualize single molecules and follow processes at the single-molecule level both in air and in solution. For maximum usefulness in biological applications, atomic force microscopy needs to be able to identify specific types of molecules in an image, much as fluorescent tags do for optical microscopy. The

C. Stroh; H. Wang; R. Bash; B. Ashcroft; J. Nelson; H. Gruber; D. Lohr; S. M. Lindsay; P. Hinterdorfer

2004-01-01

86

Single-molecule spectroscopy and microscopy  

Microsoft Academic Search

Advances in detector sensitivity and improvements in instrument design have recently provided scientists with tools to probe single molecules with light, and monitor their photophysical properties with exquisite sensitivity and spatial as well as temporal resolution. Spectroscopic and temporal information is used to explore molecular structure, conformational dynamics, local environment and intermolecular interactions of individual species. High-resolution single-molecule microscopy allows

Xavier Michalet; Shimon Weiss

2002-01-01

87

Mechanically Activated Molecular Switch through Single-Molecule Pulling  

SciTech Connect

We investigate a prototypical single-molecule switch marrying force spectroscopy and molecular electronics far from the thermodynamic limit. We use molecular dynamics to simulate a conducting atomic force microscope mechanically manipulating a molecule bound to a surface between a folded state and an unfolded state while monitoring the conductance. Both the complexity and the unique phenomenology of single-molecule experiments are evident in this system. As the molecule unfolds/refolds, the average conductance reversibly changes over 3 orders of magnitude; however, throughout the simulation the transmission fluctuates considerably, illustrating the need for statistical sampling in these systems. We predict that emergent single-molecule signatures will still be evident with conductance blinking, correlated with force blinking, being observable in a region of dynamic bistability. Finally, we illustrate some of the structure?function relationships in this system, mapping the dominant interactions in the molecule for mediating charge transport throughout the pulling simulation.

Franco, Ignacio; George, Christopher B.; Solomon, G. C.; Schatz, George C.; Ratner, Mark A.

2011-01-01

88

Single Molecule Analysis Research Tool (SMART): An Integrated Approach for Analyzing Single Molecule Data  

E-print Network

Single Molecule Analysis Research Tool (SMART): An Integrated Approach for Analyzing Single Molecule Data Max Greenfeld1,2. , Dmitri S. Pavlichin3. , Hideo Mabuchi4 *, Daniel Herschlag1,2 * 1, Stanford University, Stanford, California, United States of America Abstract Single molecule studies have

Herschlag, Dan

89

Single-molecule transistor fabrication by self-aligned lithography and in situ molecular assembly  

E-print Network

Single-molecule transistor fabrication by self-aligned lithography and in situ molecular assembly J of single-molecule transistors by self-aligned lithography and in situ molecular assembly. Ultrathin metal electronics is the realization of electronic switches comprising individual molecules as the key functional

Hone, James

90

Investigations on interfacial dynamics with ultrafast electron diffraction  

NASA Astrophysics Data System (ADS)

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.

Murdick, Ryan A.

91

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)

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.

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

2013-08-01

92

Single molecule junction conductance and binding geometry  

NASA Astrophysics Data System (ADS)

This Thesis addresses the fundamental problem of controlling transport through a metal-organic interface by studying electronic and mechanical properties of single organic molecule-metal junctions. Using a Scanning Tunneling Microscope (STM) we image, probe energy-level alignment and perform STM-based break junction (BJ) measurements on molecules bound to a gold surface. Using Scanning Tunneling Microscope-based break-junction (STM-BJ) techniques, we explore the effect of binding geometry on single-molecule conductance by varying the structure of the molecules, metal-molecule binding chemistry and by applying sub-nanometer manipulation control to the junction. These experiments are performed both in ambient conditions and in ultra high vacuum (UHV) at cryogenic temperatures. First, using STM imaging and scanning tunneling spectroscopy (STS) measurements we explore binding configurations and electronic properties of an amine-terminated benzene derivative on gold. We find that details of metal-molecule binding affect energy-level alignment at the interface. Next, using the STM-BJ technique, we form and rupture metal-molecule-metal junctions ˜104 times to obtain conductance-vs-extension curves and extract most likely conductance values for each molecule. With these measurements, we demonstrated that the control of junction conductance is possible through a choice of metal-molecule binding chemistry and sub-nanometer positioning. First, we show that molecules terminated with amines, sulfides and phosphines bind selectively on gold and therefore demonstrate constant conductance levels even as the junction is elongated and the metal-molecule attachment point is modified. Such well-defined conductance is also obtained with paracyclophane molecules which bind to gold directly through the pi system. Next, we are able to create metal-molecule-metal junctions with more than one reproducible conductance signatures that can be accessed by changing junction geometry. In the case of pyridine-linked molecules, conductance can be reliably switched between two distinct conductance states using sub-nanometer mechanical manipulation. Using a methyl sulfide linker attached to an oligoene backbone, we are able to create a 3-nm-long molecular potentiometer, whose resistance can be tuned exponentially with Angstom-scale modulations in metal-molecule configuration. These experiments points to a new paradigm for attaining reproducible electrical characteristics of metal-organic devices which involves controlling linker-metal chemistry rather than fabricating identically structured metal-molecule interfaces. By choosing a linker group which is either insensitive to or responds reproducibly to changes in metal-molecule configuration, one can design single molecule devices with functionality more complex than a simple resistor. These ambient temperature experiments were combined with UHV conductance measurements performed in a commercial STM on amine-terminated benzene derivatives which conduct through a non-resonant tunneling mechanism, at temperatures varying from 5 to 300 Kelvin. Our results indicate that while amine-gold binding remains selective irrespective of environment, conductance is not temperature independent, in contrast to what is expected for a tunneling mechanism. Furthermore, using temperature-dependent measurements in ambient conditions we find that HOMO-conducting amines and LUMO-conducting pyridines show opposite dependence of conductance on temperature. These results indicate that energy-level alignment between the molecule and the electrodes changes as a result of varying electrode structure at different temperatures. We find that temperature can serve as a knob with which to tune transport properties of single molecule-metal junctions.

Kamenetska, Maria

93

Single Molecule Probes of Lipid Membrane Structure  

E-print Network

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

Livanec, Philip W.

2009-12-14

94

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

E-print Network

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

Scherer, Norbert F.

95

Indistinguishable Photons from a Single Molecule  

E-print Network

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.

A. Kiraz; M. Ehrl; Th. Hellerer; O. E. Mustecaplioglu; C. Brauchle; A. Zumbusch

2005-05-05

96

Development of a single molecule optical probe  

Microsoft Academic Search

Advances in sensitive optical measurement schemes have led to the detection and the physical and chemical characterization of individual molecules. We are attempting to exploit the advances in single molecule detection by preparing single molecule probes based on near-field optical nanoprobes. A single carbocyanine dye C18 (DiI) molecule is immobilized on a near-field optical fiber probe. The single DiI molecule

Weihong Tan; Xinwen Wang

1998-01-01

97

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

PubMed

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

Madsen, J R; Akabani, G

2014-05-01

98

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

NASA Astrophysics Data System (ADS)

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.

Madsen, J. R.; Akabani, G.

2014-05-01

99

Extending Moore's law through molecular electronics and high-k gate oxides: Interfacial phenomena  

NASA Astrophysics Data System (ADS)

Molecular electronics offer the promise of continued scaling of devices to smaller dimensions. To integrate molecular devices into conventional electronics, the molecules must be bound to a substrate. While much work has been done toward the understanding of conduction and switching mechanisms in single molecules, the interface between molecule and substrate is much less understood. This work focuses on the interface of small aromatic molecules on Si (111)-7x7 surfaces. Most molecular electronics systems are based on organic molecules with large pi-conjugated systems. This work focuses on three smaller molecules with similar structures: phenylacetylene, styrene and biphenyl-bisacetylene. X-ray and UV photoelectron spectroscopy (XPS, UPS), scanning tunneling microscopy (STM) and density functional theory (DFT) calculations have been used to probe the molecule/silicon interface. Chemical attachment of the three molecules on the Si surface was verified using the three techniques. Comparison of the valence structure as measured by UPS with the theoretical density of states calculated by DFT demonstrated the binding geometry of the molecules. Phenylacetylene and biphenyl-bisacetylene were found to bind in a "[2+2] cycloaddition" mode, binding at the terminal acetylene in both cases. Styrene, though, was found to bind in a [4+2] mode; binding at the terminal C of the vinyl group, as well as a member of the phenyl ring. This binding mode breaks the aromaticity of the phenyl molecule and the pi-conjugation length does not extend to the surface. Alignment between highest occupied molecular orbital (HOMO) and silicon valence band, as well as work function measurements were also provided by UPS. These measurements showed a small barrier between silicon valence band and molecular HOMO for all three molecules. However, from the work function measurements an interfacial dipole was found for the phenylacetylene molecules, but not for the styrene. It is hypothesized that charge transfer occurs in the phenylacetylene cases as the pi-system extends to the surface, allowing an efficient route for charge transfer; this does not hold for styrene. This work demonstrates the role of the chemical bond in charge transfer at the molecule/silicon interface.

Weiland, Conan

100

Interfacial and thin film chemistry in electron device fabrication  

NASA Astrophysics Data System (ADS)

Progress on the Columbia URI program on 'Interfacial and Thin Film Chemistry in Electron Device Fabrication' is reported for the 1986-1991 period. Three broad areas of research included MBE Growth and Devices, Laser Surface Interactions, and Fundamentals of Processing Gas/Surface Interactions. Research in the area of MBE Growth and Devices included Heterostructures Grown by Molecular Beam Epitaxy by Professor Wen Wang and Interface Chemical Modification of Metal on Superconductor-Semiconductor Systems by Professor Ed Yang. Research in the area of Laser Surface Interactions included Laser-Surface Interactions and In Situ Diagnostics of Surface Chemistry During Electronic Processing by Professor Richard Osgood, Jr.; In Situ Optical Diagnostics of Semiconductors Prepared by Laser Chemical Processing and Other Novel Methods by Professor Irving Herman; and Ultrafast Optoelectronic Measurements of Surfaces and Interfaces by Professor David Auston. Research in Fundamentals of Processing Gas/Surface Interactions included Quantum State-Resolved Studies of Gas/Surface Chemical Reactions by Professor George Flynn and Photochemical and Photophysical Probes of Interfaces by Professor Nicholas Turro. Research results of Columbia's Principal Investigators supported by ONR/URI were published in nearly 200 scholarly articles which are listed in this report.

Auston, D.; Flynn, G.; Herman, I.; Osgood, R.; Turro, N.

1992-01-01

101

Multitime correlation functions for single molecule kinetics with fluctuating bottlenecks  

E-print Network

and microscopy of processes involving single molecules and quantum dots in condensed phase environments.1Multitime correlation functions for single molecule kinetics with fluctuating bottlenecks Valeri December 2001 Stochastic trajectories in single molecule kinetics coupled to several Gaussian Markovian

Mukamel, Shaul

102

Single Molecule Spectroscopy for Studying Conformational Dynamics of Short Oligonucleotides  

E-print Network

SPADs for single molecule microscopy. In particular, we showapplications in single molecule fluorescence microscopy. Wemicroscopy at room temperatures, paving the way for more recent advances which have expanded the single molecule

Lin, Ron Reuven

2012-01-01

103

Optimal Statistical Methods for Analysis of Single-Molecule Data  

E-print Network

single-molecule fluorescence spectro- scopoy and microscopy.fluorescence microscopy of single molecules. J. Phys. Chem.single molecules studied by spectrally-resolved fluorescence lifetime imaging microscopy (

Watkins, Lucas

2009-01-01

104

Incoherent x-ray scattering in single molecule imaging  

E-print Network

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

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

2014-01-01

105

The art of catching and probing single molecules.  

PubMed

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

Zandvliet, Harold J W

2012-01-01

106

Density Functional Theory with Dissipation: Transport through Single Molecules  

SciTech Connect

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.

Kieron Burke

2012-04-30

107

Protein folding at single-molecule resolution  

PubMed Central

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

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

2011-01-01

108

Single molecule nanometry for biological physics  

PubMed Central

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

Kim, Hajin; Ha, Taekjip

2013-01-01

109

Life at the Single Molecule Level  

SciTech Connect

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.

Xie, Xiaoliang Sunny (Harvard) [Harvard

2011-03-04

110

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

PubMed

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 ?-? 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 ?-? stacking interaction offer conceptual advances in single-molecule multichannel conductance, and are perfect models for conductance studies in biological systems, organic thin films, and ?-stacked columnar aggregates. PMID:25694026

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

111

Photoluminescent Mn4 single-molecule magnet.  

PubMed

The synthesis of [Mn(4)(anca)(4)(Hmdea)(2)(mdea)(2)].2CHCl(3) (1) is reported along with room temperature fluorescence, UV-vis, and NMR spectra. Direct current magnetization versus field data reveal a S = 8 ground state. Quantized steps in temperature- and field-dependent magnetization versus field hysteresis loops confirm single-molecule magnet behavior. PMID:18947226

Beedle, Christopher C; Stephenson, Casey J; Heroux, Katie J; Wernsdorfer, Wolfgang; Hendrickson, David N

2008-12-01

112

Longitudinal Field Modes Probed by Single Molecules  

Microsoft Academic Search

We demonstrate that a strong longitudinal, nonpropagating field is generated at the focus of a radially polarized beam mode. This field is localized in space and its energy density exceeds the energy density of the transverse field by more than a factor of 2. Single molecules with fixed absorption dipole moments are used to probe the longitudinal field. Vice versa,

L. Novotny; M. R. Beversluis; K. S. Youngworth; T. G. Brown

2001-01-01

113

Single-Molecule Fluorescence Resonance Energy Transfer  

Microsoft Academic Search

Fluorescent resonance energy transfer (FRET) is a powerful technique for studying conformational distribution and dynamics of biological molecules. Some conformational changes are difficult to synchronize or too rare to detect using ensemble FRET. FRET, detected at the single-molecule level, opens up new opportunities to probe the detailed kinetics of structural changes without the need for synchronization. Here, we discuss practical

Taekjip Ha

2001-01-01

114

Towards single-molecule nanomechanical mass spectrometry  

E-print Network

Towards single-molecule nanomechanical mass spectrometry A. K. Naik1 , M. S. Hanay1 , W. K. Hiebert1,2 , X. L. Feng1 and M. L. Roukes1 * Mass spectrometry provides rapid and quantitative species in real time. Here, we report the first demonstration of mass spectrometry based on single

Roukes, Michael L.

115

Towards single molecule detection using photoacoustic microscopy  

NASA Astrophysics Data System (ADS)

Recently, a number of optical imaging modalities have achieved single molecule sensitivity, including photothermal imaging, stimulated emission microscopy, ground state depletion microscopy, and transmission microscopy. These optical techniques are based on optical absorption contrast, extending single-molecule detection to non-fluorescent chromophores. Photoacoustics is a hybrid technique that utilizes optical excitation and ultrasonic detection, allowing it to scale both the optical and acoustic regimes with 100% sensitivity to optical absorption. However, the sensitivity of photoacoustics is limited by thermal noise, inherent in the medium itself in the form of acoustic black body radiation. In this paper, we investigate the molecular sensitivity of photoacoustics in the context of the thermal noise limit. We show that single molecule sensitivity is achievable theoretically at room temperature for molecules with sufficiently fast relaxation times. Hurdles to achieve single molecule sensitivity in practice include development of detection schemes that work at short working distance, <100 microns, high frequency, <100 MHz, and low loss, <10 dB.

Winkler, Amy M.; Maslov, Konstantin; Wang, Lihong V.

2013-03-01

116

Single Molecule Detection in Life Sciences  

Microsoft Academic Search

In recent years, the development of single molecule detection (SMD) techniques has opened up a new era of life science. The dynamic properties of biomolecules and the unique operations of molecular machines, which were hidden in averaged ensemble measurements, have been unveiled. The SMD techniques have rapidly been expanding to include a wide range of life science. The experiments on

Yoshiharu Ishii; Toshio Yanagida

2000-01-01

117

Single molecule microscopy using focal plane illumination  

Microsoft Academic Search

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

Jörg Ritter; Werner Wendler; Ulrich Kubitscheck

118

Microfabricated Substrates for Studying Single Molecule Mechanics  

E-print Network

Microfabricated Substrates for Studying Single Molecule Mechanics P R O J E C T L E A D E R : James enable the simultaneous use of Total Internal Reflection Fluorescence (TIRF) microscopy and force tweezer force measurements by allowing the use of TIRF microscopy to observe molecular motion while

119

Single-Molecule Studies of Gene Expression  

E-print Network

R N A h a i r p i n Translation Handle (RNA•DNA) Ribosomeand translation. During transcription, RNA polymerase moves along a DNADNA) 5? B Biotin Streptavidin Micropipette Figure 3.1: Experimental geometry for the single-molecule translation

Hodges, Hamilton Courtney

2009-01-01

120

Interfacial shear stress, peeling stress, and die cracking stress in trilayer electronic assemblies  

Microsoft Academic Search

Interfacial shear stress, peeling stress, and die cracking stress due to thermal and elastic mismatch in layered electronic assemblies are one of the major causes of the mechanical failure of electronic packages. A simple but rather accurate method is developed to estimate these thermal stresses for packages with different layer lengths. For layered electronics with thin adhesives, analytical expressions are

Kang Ping Wang; Yonggang Young Huang; Abhijit Chandra; Kai Xiong Hu

2000-01-01

121

Application of Recognition Tunneling in Single Molecule Identification  

NASA Astrophysics Data System (ADS)

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.

Zhao, Yanan

122

Enzymatic single-molecule kinetic isotope effects.  

PubMed

Ensemble-based measurements of kinetic isotope effects (KIEs) have advanced physical understanding of enzyme-catalyzed reactions, but controversies remain. KIEs are used as reporters of rate-limiting H-transfer steps, quantum mechanical tunnelling, dynamics and multiple reactive states. Single molecule (SM) enzymatic KIEs could provide new information on the physical basis of enzyme catalysis. Here, single pair fluorescence energy transfer (spFRET) was used to measure SM enzymatic KIEs on the H-transfer catalyzed by the enzyme pentaerythritol tetranitrate reductase. We evaluated a range of methods for extracting the SM KIE from single molecule spFRET time traces. The SM KIE enabled separation of contributions from nonenzymatic protein and fluorophore processes and H-transfer reactions. Our work demonstrates SM KIE analysis as a new method for deconvolving reaction chemistry from intrinsic dynamics. PMID:23402437

Pudney, Christopher R; Lane, Richard S K; Fielding, Alistair J; Magennis, Steven W; Hay, Sam; Scrutton, Nigel S

2013-03-13

123

Single molecule transcription profiling with AFM*  

PubMed Central

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

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

2009-01-01

124

Automated imaging system for single molecules  

DOEpatents

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.

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

2012-09-18

125

Single-Molecule Spectroscopy Using Microfluidic Platforms  

Microsoft Academic Search

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

Samuel Kim; Richard N. Zare

2010-01-01

126

Single-Molecule Biomechanics with Optical Methods  

Microsoft Academic Search

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

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

1999-01-01

127

Cavity optomechanical transduction sensing of single molecules  

E-print Network

We report narrow linewidth optomechanical oscillation of a silica microsphere immersed in a buffer solution. Through a novel optomechanical transduction sensing approach, single 10-nm-radius silica beads and Bovine serum albumin (BSA) protein molecules with a molecular weight of 66 kDalton were detected. This approach predicts the detection of 3.9 kDalton single molecules at a signal-to-noise ration above unity.

Yu, Wenyan; Lin, Qiang; Lu, and Tao

2015-01-01

128

Lanthanide single molecule magnets: progress and perspective.  

PubMed

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

Zhang, Peng; Zhang, Li; Tang, Jinkui

2015-03-01

129

Trapping and manipulating single molecules of DNA  

NASA Astrophysics Data System (ADS)

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.

Shon, Min Ju

130

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

NASA Astrophysics Data System (ADS)

This special section of Journal of Physics: Condensed Matter (JPCM) is dedicated to Professor Stuart M Lindsay on the occasion of his 60th birthday and in recognition of his outstanding contributions to multiple research areas, including light scattering spectroscopy, scanning probe microscopy, biophysics, solid-liquid interfaces and molecular and nanoelectronics. It contains a collection of 14 papers in some of these areas, including a feature article by Lindsay. Each paper was subject to the normal rigorous review process of JPCM. In Lindsay's paper, he discusses the next generations of hybrid chemical-CMOS devices for low cost and personalized medical diagnosis. The discussion leads to several papers on nanotechnology for biomedical applications. Kawaguchi et al report on the detection of single pollen allergen particles using electrode embedded microchannels. Stern et al describe a structural study of three-dimensional DNA-nanoparticle assemblies. Hihath et al measure the conductance of methylated DNA, and discuss the possibility of electrical detection DNA methylation. Portillo et al study the electrostatic effects on the aggregation of prion proteins and peptides with atomic force microscopy. In an effort to understand the interactions between nanostructures and cells, Lamprecht et al report on the mapping of the intracellular distribution of carbon nanotubes with a confocal Raman imaging technique, and Wang et al focus on the intracellular delivery of gold nanoparticles using fluorescence microscopy. Park and Kristic provide theoretical analysis of micro- and nano-traps and their biological applications. This section also features several papers on the fundamentals of electron transport in single atomic wires and molecular junctions. The papers by Xu et al and by Wandlowksi et al describe new methods to measure conductance and forces in single molecule junctions and metallic atomic wires. Scullion et al report on the conductance of molecules with similar lengths but different energy barrier profiles in order to elucidate electron transport in the molecular junctions. Kiguchi and Murakoshi study metallic atomic wires under electrochemical potential control. Asai reports on a theoretical study of rectification in substituted atomic wires. Finally, Weiss et al report on a new method to pattern and functionalize oxide-free germanium surfaces with self-assembled organic monolayers, which provides interfaces between inorganic semiconductors and organic molecules. Nanoelectronics, sensors and single molecule biophysics contents Biochemistry and semiconductor electronics—the next big hit for silicon?Stuart Lindsay Electrical detection of single pollen allergen particles using electrode-embedded microchannelsChihiro Kawaguchi, Tetsuya Noda, Makusu Tsutsui, Masateru Taniguchi, Satoyuki Kawano and Tomoji Kawai Quasi 3D imaging of DNA-gold nanoparticle tetrahedral structuresAvigail Stern, Dvir Rotem, Inna Popov and Danny Porath Effects of cytosine methylation on DNA charge transportJoshua Hihath, Shaoyin Guo, Peiming Zhang and Nongjian Tao Effect of electrostatics on aggregation of prion protein Sup35 peptideAlexander M Portillo, Alexey V Krasnoslobodtsev and Yuri L Lyubchenko Mapping the intracellular distribution of carbon nanotubes after targeted delivery to carcinoma cells using confocal Raman imaging as a label-free techniqueC Lamprecht, N Gierlinger, E Heister, B Unterauer, B Plochberger, M Brameshuber, P Hinterdorfer, S Hild and A Ebner Caveolae-mediated endocytosis of biocompatible gold nanoparticles in living Hela cellsXian Hao, Jiazhen Wu, Yuping Shan, Mingjun Cai, Xin Shang, Junguang Jiang and Hongda Wang Stability of an aqueous quadrupole micro-trapJae Hyun Park and Predrag S Krsti? Electron transport properties of single molecular junctions under mechanical modulationsJianfeng Zhou, Cunlan Guo and Bingqian Xu An approach to measure electromechanical properties of atomic and molecular junctionsIlya V Pobelov, Gábor Mészáros, Koji Yoshida, Artem Mishchenko, Murat Gulcur, Martin R Bryce and Thomas Wandlowski S

Tao, Nongjian

2012-04-01

131

Theoretical investigation on single-molecule chiroptical spectroscopy  

SciTech Connect

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.

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

2013-12-10

132

Correlations in Single Molecule Photon Statistics: Renewal Indicator Jianshu Cao  

E-print Network

Correlations in Single Molecule Photon Statistics: Renewal Indicator Jianshu Cao Department be revealed through single molecule photon statistical analysis. The standard Poisson indicator defined the transfer matrix method to demonstrate the difference between the two indicators. The relationship between

Cao, Jianshu

133

Cold Molecular Ions:. Single Molecule Studies  

NASA Astrophysics Data System (ADS)

Single molecular ions can be sympathetically cooled to a temperature in the mK-range and become spatially localized within a few ?m3 through the Coulomb interaction with laser-cooled atomic ions, and hence be an excellent starting point for a variety of single molecule studies. By applying a rather simple, non-destructive technique for the identification of the individual molecular ions relying on an in situ mass measurement of the molecules, studies of the photofragmentation of singly-charged aniline ions (C6H7N+) as well as investigations of isotope effects in reactions of Mg+ ions with HD molecules have been carried out.

Drewsen, M.

2009-03-01

134

Single-molecule electrophoresis. Final report  

SciTech Connect

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.

Castro, A.; Shera, E.B.

1996-05-22

135

Large negative differential conductance in single-molecule break junctions  

NASA Astrophysics Data System (ADS)

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

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

2014-10-01

136

Large negative differential conductance in single-molecule break junctions.  

PubMed

Molecular electronics aims at exploiting the internal structure and electronic orbitals of molecules to construct functional building blocks. To date, however, the overwhelming majority of experimentally realized single-molecule junctions can be described as single quantum dots, where transport is mainly determined by the alignment of the molecular orbital levels with respect to the Fermi energies of the electrodes and the electronic coupling with those electrodes. Particularly appealing exceptions include molecules in which two moieties are twisted with respect to each other and molecules in which quantum interference effects are possible. Here, we report the experimental observation of pronounced negative differential conductance in the current-voltage characteristics of a single molecule in break junctions. The molecule of interest consists of two conjugated arms, connected by a non-conjugated segment, resulting in two coupled sites. A voltage applied across the molecule pulls the energy of the sites apart, suppressing resonant transport through the molecule and causing the current to decrease. A generic theoretical model based on a two-site molecular orbital structure captures the experimental findings well, as confirmed by density functional theory with non-equilibrium Green's functions calculations that include the effect of the bias. Our results point towards a conductance mechanism mediated by the intrinsic molecular orbitals alignment of the molecule. PMID:25173832

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

2014-10-01

137

Optical Studies of Single Molecules at Room Temperature  

Microsoft Academic Search

Recent developments in optical studies of single molecules at room temperature are reviewed, with an emphasis on the underlying principles and the potential of single-molecule experiments. Examples of single-molecule studies are given, including photophysics and photochemistry pertinent to single-molecule measurements, spectral fluctuations, Raman spectroscopy, diffusional motions, conformational dynamics, fluorescence resonant energy transfer, exciton dynamics, and enzymatic turnovers. These studies illustrate

Xiaoliang Xie; Jay K. Trautman

1998-01-01

138

Single-molecule surface- and tip-enhanced raman spectroscopy  

Microsoft Academic Search

A review is given on single-molecule surface- and tip-enhanced Raman spectroscopy (SERS and TERS). It sketches the historical development along different routes toward huge near-field enhancements, the basis of single-molecule enhanced Raman spectroscopy; from SNOM to apertureless SNOM to tip-enhanced Raman spectroscopy (TERS) and microscopy; from SERS to single-molecule SERS to single-molecule TERS. The claim of extremely high enhancement factors

Bruno Pettinger

2010-01-01

139

Single-Molecule Dynamics and Mechanisms of Metalloregulators and Metallochaperones  

E-print Network

Single-Molecule Dynamics and Mechanisms of Metalloregulators and Metallochaperones Peng Chen in using single-molecule fluorescence imaging techniques to identify the mechanisms of metal homeostaticR-family metalloregulators and copper chaperones can fulfill their functions. This work also summarizes other related single-molecule

Chen, Peng

140

Monitoring Single-Molecule Reactivity on a Carbon Nanotube  

E-print Network

Monitoring Single-Molecule Reactivity on a Carbon Nanotube Brett R. Goldsmith, John G. Coroneus interacting with its immediate environment. The conductance of the nanotube device directly transduces single-molecule's potential for complementing optical methods in single-molecule research. Compared to conventional

Weiss, Gregory A.

141

Future of Biomedical Sciences: Single Molecule Microscopy Nils G. Walter  

E-print Network

Future of Biomedical Sciences: Single Molecule Microscopy Nils G. Walter Department of Chemistry by single molecule microscopy, since most molecules (at least all biopolymers) in a cell are present in very Conference on ``Frontiers in Live Cell Imaging'', heralded the breakout of single molecule microscopies from

Walter, Nils G.

142

Lucky Imaging: Improved Localization Accuracy for Single Molecule Imaging  

E-print Network

, to improve resolution in single molecule fluo- rescence microscopy. We show that by selectively discarding of fluorescently labeled linker for activation of T cells. INTRODUCTION Single molecule fluorescence microscopy has determination microscopy (SPDM) (16), single molecule high resolution imaging with photobleach- ing (SHRImP) (17

Wallace, Mark

143

Single-Molecule Manipulation DOI: 10.1002/anie.200604546  

E-print Network

. Single-molecule force microscopy and fluorescence spec- troscopy reveal individual molecular properties the biophysical techniques capable of probing single-molecule properties, optical-tweezers force microscopy this technique, we describe the first combination of optical-tweezers force microscopy with the single-molecule

Lang, Matthew

144

Masters projects in: Single-molecule tracking of protein  

E-print Network

components, such as tRNAs In vitro single-molecule fluorescence microscopy using TIRF techniques In vivoMasters projects in: Single-molecule tracking of protein synthesis in live E. coli cells Ribosome-ray crystallography; and more recently single-molecule fluorescence based in vitro techniques probing structure

Uppsala Universitet

145

Fluorescence Detection of Single Molecules Applicable to Small Volume Assays  

E-print Network

. Single Molecule Detection on Surfaces 3.1. Far-Field Microscopy 3.2. Near-Field Microscopy 4. Conclusion1 Fluorescence Detection of Single Molecules Applicable to Small Volume Assays Jörg Enderlein, W Alamos, New Mexico 87545, USA Table of contents 1. Introduction 2. Single Molecule Detection in Fluids 3

Enderlein, Jörg

146

Nanometer-localized multiple single-molecule fluorescence microscopy  

E-print Network

Nanometer-localized multiple single-molecule fluorescence microscopy Xiaohui Qu* , David Wu demonstrates nanometer-localized multiple single-molecule (NALMS) fluorescence microscopy by using both to five single molecules within a diffrac- tion-limited area. NALMS microscopy will greatly facilitate

La Rosa, Andres H.

147

Quantitative Characterization of Filament Dynamics by Single-Molecule Lifetime  

E-print Network

. Single-Molecule Lifetime Measurements A. Extract and Sample Preparation B. Microscopy C. Data AnalysisCHAPTER 29 Quantitative Characterization of Filament Dynamics by Single-Molecule Lifetime Dynamics C. Connecting to Other Types of Measurements IV. Results and Conclusion References Abstract Single-molecule

Needleman, Daniel

148

Hidden Markov Modelling of Single Molecule FRET Trajectories  

E-print Network

The development of single-molecule fluorescence energy transfer (FRET) microscopy has provided ground Single-molecule fluorescence resonance energy transfer (FRET) microscopy has proved to be a powerful toolHidden Markov Modelling of Single Molecule FRET Trajectories Life Sciences Interface DTC Short

Goldschmidt, Christina

149

Single Molecule Microscopy and Hole-Burning Spectroscopy : Tools for  

E-print Network

Single Molecule Microscopy and Hole-Burning Spectroscopy : Tools for the Study of Biological.1 Motivation and Outline of Presentation 1.2 Summary and Main Results 1.2.1 Single Molecule Microscopy 1.2.1 Hole-Burning Spectroscopy 1.3 References Chapter 2 Single Molecule Microscopy 2.1Characterization

Schmidt, Thomas

150

Nanometer-localized multiple single-molecule fluorescence microscopy  

Microsoft Academic Search

Fitting the image of a single molecule to the point spread function of an optical system greatly improves the precision with which single molecules can be located. Centroid localization with nanometer precision has been achieved when a sufficient number of photons are collected. However, if multiple single molecules reside within a diffraction-limited spot, this localization approach does not work. This

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

2004-01-01

151

Upping fluorescence Paving the way for single-molecule medical  

E-print Network

single molecule imaging, using confocal microscopy, some of the molecules disappear on subsequentUpping fluorescence ­ Paving the way for single-molecule medical sensors The presence to the information content of single molecule fluorescence measurement[2]. Ideally, a single fluorophore should last

Strathclyde, University of

152

A Bayesian method for single molecule, fluorescence burst analysis  

E-print Network

. Renn, and U. P. Wild, "Multiparameter microscopy and spectroscopy for single- molecule analytics," AnalA Bayesian method for single molecule, fluorescence burst analysis P. R. Barber,1,2,* S. M. Ameer lifetime (BIFL) experiment, identification of fluorescent bursts from single molecules above background

Coolen, ACC "Ton"

153

Dual objective fluorescence microscopy for single molecule imaging applications  

Microsoft Academic Search

Fluorescence microscopy is an invaluable tool for studying biological processes in cells. In the recent past there has been significant interest in imaging cellular processes at the single molecule level. Single molecule experiments remove ensemble averaging effects and provide information that is typically not accessible through bulk experiments. One of the major requirements in single molecule imaging applications is that

Sripad Ram; Prashant Prabhat; E. Sally Ward; Raimund J. Ober

2009-01-01

154

Toward Single-Molecule Nanomechanical Mass Spectrometry  

NASA Astrophysics Data System (ADS)

Mass spectrometry (MS) has become a preeminent methodology of proteomics since it provides rapid and quantitative identification of protein species with relatively low sample consumption. Yet with the trend toward biological analysis at increasingly smaller scales, ultimately down to the volume of an individual cell, MS with few-to-single molecule resolution will be required. We report the first realization of MS based on single-biological-molecule detection with nanoelectromechanical systems (NEMS). NEMS provide unparalleled mass resolution, now sufficient for detection of individual molecular species in real time. However, high sensitivity is only one of several components required for MS. We demonstrate a first complete prototype NEMS-MS system for single-molecule mass spectrometry providing proof-of-principle for this new technique. Nanoparticles and protein species are introduced by electrospray injection from the fluid phase in ambient conditions into vacuum and subsequently delivered to the NEMS detector by hexapole ion optics . Mass measurements are then recorded in real-time as analytes adsorb, one-by-one, onto a phase-locked, ultrahigh frequency (UHF) NEMS resonator. These first NEMS-MS spectra, obtained with modest resolution from only several hundred mass adsorption events, presage the future capabilities of this methodology. We outline the substantial improvements feasible in near term, through recent advances and technological avenues that are unique to NEMS-MS.

Roukes, Michael

2009-03-01

155

Electric field breakdown in single molecule junctions.  

PubMed

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

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

2015-04-22

156

Single-Molecule STM Studies on Atomically-Flat Nanoparticles  

NASA Astrophysics Data System (ADS)

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.

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

157

Kinetic parameters of association and dissociation between single molecules measured by single-molecule force spectroscopy  

Microsoft Academic Search

This presentation is focused on development of experimental scanning probe microscopy (SPM) approaches to quantify kinetic parameters of association and dissociation between receptor--ligand pairs. The potential of mean force (pmf) between interacting molecules is quantified by single molecule force spectroscopy (SMFS) approach. In SMFS molecules are allowed to interact and form molecular bond. Consequent measurements of rupture forces are used

Boris Akhremitchev

2009-01-01

158

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

E-print Network

Characterization of interfacial reactions in magnetite tunnel junctions with transmission electron of Physics. DOI: 10.1063/1.1688535 I. INTRODUCTION Half metallic magnetite (Fe3O4) has been thought to be one is also discussed. II. EXPERIMENT Thin films were deposited onto Si or oxidized Si wafers by either rf

Laughlin, David E.

159

Actinide-based single-molecule magnets.  

PubMed

Actinide single-molecule magnetism has experienced steady growth over the last five years since the first discovery of slow magnetic relaxation in the mononuclear complex U(Ph(2)BPz(2))(3). Given their large spin-orbit coupling and the radial extension of the 5f orbitals, the actinides are well-suited for the design of both mononuclear and exchange-coupled molecules, and indeed at least one new system has emerged every year. By some measures, the actinides are already demonstrating promise for one day exceeding the performance characteristics of transition metal and lanthanide complexes. However, much further work is needed to understand the nature of the slow relaxation in mononuclear actinide complexes, as well as the influence of magnetic exchange on slow relaxation in multinuclear species. This perspective seeks to summarize the successes in the field and to address some of the many open questions in this up and coming area of research. PMID:25352033

Meihaus, Katie R; Long, Jeffrey R

2015-02-14

160

Presence and spatial distribution of interfacial electronic states in LaMnO3-SrMnO3 superlattices  

Microsoft Academic Search

We report direct evidence of interfacial states at the onset of OK edge confined to a spatial distance of 1 unit-cell full-width at half maximum at the sharp interfaces between epitaxial films of LaMnO3 and SrMnO3 from electron energy-loss spectroscopy (EELS) measurements. The interfacial states are sensitive to interface sharpness; at rough interfaces with interfacial steps of 1-2 unit cells

A. B. Shah; Q. M. Ramasse; S. J. May; Jerald Kavich; J. G. Wen; X. Zhai; J. N. Eckstein; J. Freeland; A. Bhattacharya; J. M. Zuo

2010-01-01

161

Presence and spatial distribution of interfacial electronic states in LaMnO3-SrMnO3 superlattices  

NASA Astrophysics Data System (ADS)

We report direct evidence of interfacial states at the onset of OK edge confined to a spatial distance of 1 unit-cell full-width at half maximum at the sharp interfaces between epitaxial films of LaMnO3 and SrMnO3 from electron energy-loss spectroscopy (EELS) measurements. The interfacial states are sensitive to interface sharpness; at rough interfaces with interfacial steps of 1-2 unit cells in height, experimental data shows a reduction, or suppression, of the interfacial states. The EELS measurements were performed using a fine electron probe obtained by electron lens aberration correction. By scanning the electron probe across the interface, we are able to map the spatial distribution of the interfacial states across interfaces at high resolution.

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

2010-09-01

162

Single Molecule Lifetime Studies of Small Clusters of Semiconductor Nanocrystals  

NASA Astrophysics Data System (ADS)

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

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

2009-10-01

163

Scanning transmission electron microscopy investigations of interfacial layers in HfO2 gate stacks  

NASA Astrophysics Data System (ADS)

Electron energy-loss spectroscopy combined with high-angle annular dark-field (HAADF) imaging in scanning transmission electron microscopy was used to investigate the chemistry of interfacial layers in HfO2 gate stacks capped with polycrystalline Si gate electrodes. To interpret the energy-loss near-edge fine structure (ELNES) obtained from the interfacial layers, reference spectra were obtained from single crystal hafnium silicate (HfSiO4), monoclinic HfO2 powder, and amorphous SiO2. No bulk-like silicate bonding could be detected in the ELNES of Si L2,3 and O K edges recorded from layers at the Si substrate interface. Compared to bulk SiO2, the interfacial ELNES showed additional features that were caused by overlap of signals from Si, HfO2, and SiO2, despite a relatively small electron probe size of ˜3Å. HAADF showed that interfacial roughness caused the projected thickness of nominally pure SiO2 (within the detection limit of the method) to be as small as ˜5Å in many locations.

Agustin, Melody P.; Bersuker, Gennadi; Foran, Brendan; Boatner, Lynn A.; Stemmer, Susanne

2006-07-01

164

Turning a Single Molecule into an Electric Motor  

NASA Astrophysics Data System (ADS)

Significant progress has been made in the construction of molecular motors powered by light and by chemical reactions, but electrically-driven motors have only just been demonstrated [1,2] after many theoretical proposals. Studying the rotation of molecules bound to surfaces offers the advantage that a single layer can be assembled, monitored and manipulated using the tools of surface science. Thioether molecules constitute a simple, robust system with which to study molecular rotation as a function of temperature, electron energy, applied fields, and proximity of neighboring molecules. A butyl methyl sulphide (BuSMe) molecule adsorbed on a copper surface can be operated as a single-molecule electric motor. Electrons from a scanning tunneling microscope are used to drive directional motion of the BuSMe 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 the molecule and the tip of the microscope (which serves as the electrode), which illustrates the importance of the symmetry of the metal contacts in atomic-scale electrical devices. [1] Experimental Demonstration of a Single-Molecule Electric Motor H. L. Tierney, C. J. Murphy, A. D. Jewell, A. E. Baber, E. V. Iski, H. Y. Khodaverdian, A. F. McGuire, Nikolai Klebanov and E. C. H. Sykes - Nature Nanotechnology 2011, 6, 625-629 [2] Electrically driven directional motion of a four-wheeled molecule on a metal surface Kudernac, T., Ruangsupapichat, N., Parschau, M., Macia, B., Katsonis, N., Harutyunyan, S. R., Ernst, K.-H., Feringa, B. L. - Nature 2011, 479, 208--211

Sykes, Charles

2013-03-01

165

Single molecule pulling with large time steps  

NASA Astrophysics Data System (ADS)

Recently, we presented a generalization of the Jarzynski nonequilibrium work theorem for phase space mappings. The formalism shows that one can determine free energy differences from approximate trajectories obtained from molecular dynamics simulations in which very large time steps are used. In this work we test the method by simulating the force-induced unfolding of a deca-alanine helix in vacuum. The excellent agreement between results obtained with a small, conservative time step of 0.5fs and results obtained with a time step of 3.2fs (i.e., close to the stability limit) indicates that the large-time-step approach is practical for such complex biomolecules. We further adapt the method of Hummer and Szabo for the simulation of single molecule force spectroscopy experiments to the large-time-step method. While trajectories generated with large steps are approximate and may be unphysical—in the simulations presented here we observe a violation of the equipartition theorem—the computed free energies are exact in principle. In terms of efficiency, the optimum time step for the unfolding simulations lies in the range 1-3fs .

Oberhofer, Harald; Dellago, Christoph; Boresch, Stefan

2007-06-01

166

n and p type character of single molecule diodes  

PubMed Central

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

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

2015-01-01

167

n and p type character of single molecule diodes.  

PubMed

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

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

2015-01-01

168

n and p type character of single molecule diodes  

NASA Astrophysics Data System (ADS)

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.

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

2015-02-01

169

Tunneling spectroscopy of organic monolayers and single molecules.  

PubMed

Basic concepts in tunneling spectroscopy applied to molecular systems are presented. Junctions of the form M-A-M, M-I-A-M, and M-I-A-I'-M, where A is an active molecular layer, are considered. Inelastic electron tunneling spectroscopy (IETS) is found to be readily applied to all the above device types. It can provide both vibrational and electron spectroscopic data about the molecules comprising the A layer. In IETS there are no strong selection rules (although there are preferences) so that transitions that are normally IR, Raman, or even photon-forbidden can be observed. In the electronic transition domain, spin and Laporte forbidden transitions may be observed. Both vibrational and electronic IETS can be acquired from single molecules. The negative aspect of this seemingly ideal spectroscopic method is the thermal line width of about 5 k(B)T. This limits the useful measurement of vibrational IETS to temperatures below about 10 K. In the case of most electronic transitions where the intrinsic linewidth is much broader, useful experiments above 100 K are possible. One further limitation of electronic IETS is that it is generally limited to transitions with energy less than about 20,000 cm(-1). IETS can be identified by peaks in d(2) I/dV (2) vs bias voltage plots that occur at the same position (but not necessarily same intensity) in either bias polarity.Elastic tunneling spectroscopy is discussed in the context of processes involving molecular ionization and electron affinity states, a technique we call orbital mediated tunneling spectroscopy, or OMTS. OMTS can be applied readily to M-I-A-M and M-I-A-I'-M systems, but application to M-A-M junctions is problematic. Spectra can be obtained from single molecules. Ionization state results correlate well with UPS spectra obtained from the same systems in the same environment. Both ionization and affinity levels measured by OMTS can usually be correlated with one electron oxidation and reduction potentials for the molecular species in solution. OMTS can be identified by peaks in dI/dV vs bias voltage plots that do not occur at the same position in either bias polarity. Because of the intrinsic width of the ionization and affinity transitions, OMTS can be applied at temperatures above 500 K.This is not a comprehensive review of more than 20 years of research and there are many excellent papers that are not cited here. An absence of a citation is not a reflection on the quality of the work. PMID:21710381

Hipps, K W

2012-01-01

170

Interfacial Electron Transfer and Transient Photoconductivity Studied with Terahertz Spectroscopy  

NASA Astrophysics Data System (ADS)

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

Milot, Rebecca Lee

171

Transport and interfacial transfer of electrons in dye-sensitized nanocrystalline solar cells  

Microsoft Academic Search

Current understanding of the mechanisms of electron transport and interfacial transfer in the dye-sensitized nanocrystalline solar cell is reviewed, and thermodynamic and kinetic aspects of the cell are related to cell performance. The current voltage characteristics of the I3?\\/I? redox couple on platinum and on bare as well as TiO2-coated tin oxide |glass substrates has been studied using thin layer

L. M Peter; N. W Duffy; R. L Wang; K. G. U Wijayantha

2002-01-01

172

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

SciTech Connect

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.

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

1998-04-01

173

Microarray analysis at single molecule resolution  

PubMed Central

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

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

2010-01-01

174

'Single molecule': theory and experiments, an introduction  

PubMed Central

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

2013-01-01

175

Effect of interactions and degeneracy on transmission through a single molecule  

NASA Astrophysics Data System (ADS)

Electron transmission through a single-molecule junction in the Coulomb blockade regime is analyzed in the isolated resonance approximation for molecules with degenerate HOMO and/or LUMO orbitals. Electron-electron interactions are included in a capacitive charging model derived from pi-electron effective field theory. For the case of a buckyball junction with Pt electrodes, we find that the number of transmission channels is limited by the five-fold degenerate HOMO resonance.

Stefferson, Michael; Hudson, Jarred; Stafford, Charles

2011-10-01

176

Single Molecule Tip Enhanced Raman Spectroscopy NSF Grant # 1121262  

E-print Network

MRSEC Single Molecule Tip Enhanced Raman Spectroscopy NSF Grant # 1121262 Matthew D. Sonntag1, it can "see" one single molecule at a time, this was carried out by studying the vibrational signature fingerprint that allows molecule identification. J. Phys. Chem. C, 2012, 116 (1), pp 478­483 · R6G-d4 · R6G-d0

Shahriar, Selim

177

A Single-Molecule Study of RNA Catalysis and Folding  

E-print Network

A Single-Molecule Study of RNA Catalysis and Folding Xiaowei Zhuang,1 * Laura E. Bartley,2 * Hazen microscopy, we studied the catalysis by and folding of individual Tetrahymena thermophila ribozyme molecules and undocks from the ribozyme core was observed directly in single-molecule time trajectories, allowing

Herschlag, Dan

178

Combined single-molecule force and fluorescence measurements for biology  

E-print Network

Minireview Combined single-molecule force and fluorescence measurements for biology Mark I Wallace as a collection of interacting cells, so can a cell be considered as a collection of individual molecules, a view, some of which allow cellular processes to be examined at the level of a single molecule. In particular

Wallace, Mark

179

Sorting Single Molecules: Application to Diagnostics and Evolutionary Biotechnology  

Microsoft Academic Search

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

Manfred Eigen; Rudolf Rigler

1994-01-01

180

Single-Molecule Magnetic Tweezers Studies of Type IB Topoisomerases  

E-print Network

.2). Above the flow cell, a pair of permanent magnets or an electromagnet is suspended on a motorized stageChapter 7 Single-Molecule Magnetic Tweezers Studies of Type IB Topoisomerases Jan Lipfert, Daniel A the application of single-molecule force spectroscopy techniques to the study of topoisomerases. Magnetic tweezers

Dekker, Nynke

181

Single molecule microscopy: peak-frequency trajectories and linewidth distribution  

Microsoft Academic Search

Fluorescence microscopy has been adapted to cryogenic temperatures and combined with efficient image processing and analysis to observe many single molecules in parallel. The capabilities of this setup are demonstrated with the parallel recording of peak-frequency trajectories for 62 terrylene-molecules in n-hexadecane and with the measurement of 918 single molecule linewidths for terrylene in dodecane in 200 s.

Hermann Bach; Elizabeth A. Donley; Markus Traber; Alois Renn; Urs P. Wild

1998-01-01

182

Statistical Analysis of Single-Molecule AFM Force Spectroscopy Curves  

E-print Network

Statistical Analysis of Single-Molecule AFM Force Spectroscopy Curves Alexei Valiaev1,2 , Stefan-extension curves obtained from single-molecule force spectroscopy (SMFS) measurements. We apply this methodology: Statistical Analysis of AFM Curves Keywords: atomic force microscopy, freely-jointed chain, worm-like chain

Schmidler, Scott

183

Methods of single-molecule fluorescence spectroscopy and microscopy  

Microsoft Academic Search

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

W. E. Moerner; David P. Fromm

2003-01-01

184

Nils G. Walter Department of Chemistry, Single Molecule Analysis Group  

E-print Network

2011 . 0 10:0-1:00 Nils G. Walter Department of Chemistry, Single Molecule Analysis Group Scientists Watching Action Movies: Real-Time Single Molecule Fluorescence Imaging of Natural and Engineered-assemble into structures of complex architecture and functionality. Fluorescence microscopy offers a non-invasive tool

Takada, Shoji

185

Single-molecule Fluorescence Spectroelectrochemistry of Cresyl Violet  

SciTech Connect

We coupled scanning fluorescence microscopy with a potentiostat via a three-electrode electrochemical cell to enable single-molecule fluorescence spectroelectrochemistry of cresyl violet in aqueous solution, where the single-molecule fluorescence intensity of cresyl violet is modulated synchronously with the cyclic voltammetric potential scanning.

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

2008-11-21

186

Force and Velocity Measured for Single Molecules of RNA  

E-print Network

- force microscopy techniques capable of de- tecting movement by single molecules (2­4), and transcriptionForce and Velocity Measured for Single Molecules of RNA Polymerase Michelle D. Wang,* Mark J, the synthesis of an RNA copy of the template DNA. Each RNA molecule is synthesized in its entirety by a single

Block, Steven

187

Statistical Analysis of Single-Molecule AFM Force Spectroscopy Curves  

E-print Network

Statistical Analysis of Single-Molecule AFM Force Spectroscopy Curves Alexei Valiaev1 , Stefan from single-molecule force spectroscopy (SMFS) measurements. We apply this methodology to force. Running title: Statistical Analysis of AFM Curves Keywords: atomic force microscopy, freely-jointed chain

Schmidler, Scott

188

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

E-print Network

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

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

2008-11-02

189

Conductance measurement of pyridyl-based single molecule junctions with Cu and Au contacts  

NASA Astrophysics Data System (ADS)

We studied the conductance of pyridyl-based single molecule junctions with Cu contacts by using an electrochemical jump-to-contact scanning tunneling microscopy break junction (ECSTM-BJ) approach. The single molecule junctions of 4,4?-bipyridine (BPY), 1,2-di(pyridin-4-yl)ethene (BPY-EE) and 1,2-di(pyridin-4-yl)ethane (BPY-EA) bridged with Cu clusters show three sets of conductance values. These values are smaller than the conductance values of single molecule junctions with Au electrodes measured by the traditional scanning tunneling microscopy break junction in acidic or neutral solutions, which can be attributed to the different electronic coupling efficiencies between molecules and electrodes. The consistent conductance of pyridyl-based molecules in acidic and neutral solutions may show that the protonated pyridyl group contacts to the electrode through the deprotonated form.

Zhou, Xiao-Yi; Peng, Zheng-Lian; Sun, Yan-Yan; Wang, Li-Na; Niu, Zhen-Jiang; Zhou, Xiao-Shun

2013-11-01

190

Analyzing Single-Molecule Time Series via Nonparametric Bayesian Inference.  

PubMed

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

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

2015-02-01

191

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

E-print Network

Single Molecule Electrochemistry Fu-Ren F. Fan, Juhyoun Kwak, and Allen J. Bard*, Contribution from sheath, small numbers of molecules (1-10) can be trapped between the tip and a substrate. Repeated electron transfers of an electroactive molecule as it shuttles by diffusion between tip and substrate

Kwak, Juhyoun

192

Single-molecule electrochemistry: present status and outlook.  

PubMed

The development of methods for detecting and manipulating matter at the level of individual macromolecules represents one of the key scientific advancements of recent decades. These techniques allow us to get information that is largely unobtainable otherwise, such as the magnitudes of microscopic forces, mechanistic details of catalytic processes, macromolecular population heterogeneities, and time-resolved, step-by-step observation of complex kinetics. Methods based on optical, mechanical, and ionic-conductance signal transduction are particularly developed. However, there is scope for new approaches that can broaden the range of molecular systems that we can study at this ultimate level of sensitivity and for developing new analytical methods relying on single-molecule detection. Approaches based on purely electrical detection are particularly appealing in the latter context, since they can be easily combined with microelectronics or fluidic devices on a single microchip to create large parallel assays at relatively low cost. A form of electrical signal transduction that has so far remained relatively underdeveloped at the single-molecule level is the direct detection of the charge transferred in electrochemical processes. The reason for this is simple: only a few electrons are transferred per molecule in a typical faradaic reaction, a heterogeneous charge-transfer reaction that occurs at the electrode's surface. Detecting this tiny amount of charge is impossible using conventional electrochemical instrumentation. A workaround is to use redox cycling, in which the charge transferred is amplified by repeatedly reducing and oxidizing analyte molecules as they randomly diffuse between a pair of electrodes. For this process to be sufficiently efficient, the electrodes must be positioned within less than 100 nm of each other, and the analyte must remain between the electrodes long enough for the measurement to take place. Early efforts focused on tip-based nanoelectrodes, descended from scanning electrochemical microscopy, to create suitable geometries. However, it has been challenging to apply these technologies broadly. In this Account, we describe our alternative approach based on electrodes embedded in microfabricated nanochannels, so-called nanogap transducers. Microfabrication techniques grant a high level of reproducibility and control over the geometry of the devices, permitting systematic development and characterization. We have employed these devices to demonstrate single-molecule sensitivity. This method shows good agreement with theoretical analysis based on the Brownian motion of discrete molecules, but only once the finite time resolution of the experimental apparatus is taken into account. These results highlight both the random nature of single-molecule signals and the complications that it can introduce in data interpretation. We conclude this Account with a discussion on how scientists can overcome this limitation in the future to create a new experimental platform that can be generally useful for both fundamental studies and analytical applications. PMID:23270398

Lemay, Serge G; Kang, Shuo; Mathwig, Klaus; Singh, Pradyumna S

2013-02-19

193

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

NASA Astrophysics Data System (ADS)

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.

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

2015-03-01

194

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

PubMed Central

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

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

2015-01-01

195

Breaking the concentration limit of optical single-molecule detection.  

PubMed

Over the last decade, single-molecule detection has been successfully utilized in the life sciences and materials science. Yet, single-molecule measurements only yield meaningful results when working in a suitable, narrow concentration range. On the one hand, diffraction limits the minimal size of the observation volume in optical single-molecule measurements and consequently a sample must be adequately diluted so that only one molecule resides within the observation volume. On the other hand, at ultra-low concentrations relevant for sensing, the detection volume has to be increased in order to detect molecules in a reasonable timespan. This in turn results in the loss of an optimal signal-to-noise ratio necessary for single-molecule detection. This review discusses the requirements for effective single-molecule fluorescence applications, reflects on the motivation for the extension of the dynamic concentration range of single-molecule measurements and reviews various approaches that have been introduced recently to solve these issues. For the high-concentration limit, we identify four promising strategies including molecular confinement, optical observation volume reduction, temporal separation of signals and well-conceived experimental designs that specifically circumvent the high concentration limit. The low concentration limit is addressed by increasing the measurement speed, parallelization, signal amplification and preconcentration. The further development of these ideas will expand our possibilities to interrogate research questions with the clarity and precision provided only by the single-molecule approach. PMID:24019005

Holzmeister, Phil; Acuna, Guillermo P; Grohmann, Dina; Tinnefeld, Philip

2014-02-21

196

Microscopy beyond the diffraction limit using actively controlled single molecules  

PubMed Central

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

MOERNER, W.E.

2013-01-01

197

Single Molecule Detection and Imaging in Single Living Cells  

NASA Astrophysics Data System (ADS)

Direct observation of single molecules and single molecular events inside living cells could dramatically improve our understanding of basic cellular processes (e.g., signal transduction and gene transcription) as well as improving our knowledge on the intracellular transport and fate of therapeutic agents (e.g., antisense RNA and gene therapy vectors). This talk will focus on using single-molecule fluorescence and luminescent quantum dots to examine the dynamics and spatial distribution of RNA and proteins inside living cells and on the surface membrane surface. These single-molecule studies yield a detailed description of molecular events and cellular structures under physiological conditions.

Nie, Shuming

2002-03-01

198

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

SciTech Connect

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.

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

2009-01-01

199

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

PubMed Central

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

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

2012-01-01

200

Exploring the mechanome with optical tweezers and single molecule fluorescence  

E-print Network

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

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

2008-01-01

201

Modeling and analysis of single-molecule experiments  

E-print Network

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

Witkoskie, James B

2005-01-01

202

Understanding Enzyme Activity Using Single Molecule Tracking (Poster)  

SciTech Connect

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.

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

2009-06-01

203

Single molecule directivity enhanced Raman scattering using nanoantennas.  

PubMed

Single molecule detection by directivity enhanced Raman scattering is demonstrated using nanoantennas. Bianalyte Raman scattering is used to confirm the detection of single molecules of Rhodamine 6G and Nile Blue A in aqueous solution. Calculations show that Raman enhancement factors of 10(13) can be achieved by combined optimization of the local field enhancement (hotspot with 10(11) enhancement) and antenna directionality (with 10(2) enhancement). PMID:22515915

Ahmed, Aftab; Gordon, Reuven

2012-05-01

204

Simple test system for single molecule recognition force microscopy  

Microsoft Academic Search

We have established an easy-to-use test system for detecting receptor–ligand interactions on the single molecule level using atomic force microscopy (AFM). For this, avidin–biotin, probably the best characterized receptor–ligand pair, was chosen. AFM sensors were prepared containing tethered biotin molecules at sufficiently low surface concentrations appropriate for single molecule studies. A biotin tether, consisting of a 6nm poly(ethylene glycol) (PEG)

Christian K. Riener; Cordula M. Stroh; Andreas Ebner; Christian Klampfl; Alex A. Gall; Christoph Romanin; Yuri L. Lyubchenko; Peter Hinterdorfer; Hermann J. Gruber

2003-01-01

205

Massively Parallel Single-Molecule Manipulation Using Centrifugal Force  

PubMed Central

Abstract 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

Halvorsen, Ken; Wong, Wesley P.

2010-01-01

206

Single Molecule Conductance Measurement of Photochromic Molecules and Carotenoids  

NASA Astrophysics Data System (ADS)

We report data for the single molecule conductance of (a) photochromic molecules in the `open' and `closed' forms and (b) carotenoid polyenes. The photochromic molecules we studied switch between an open state (that absorbs in the UV to become closed) and a closed state (that absorbs in the visible to become open) through light-induced isomerization. The molecular resistance is 526±90 M? in the open form and 4±1 M? in the closed form when attached to gold break junction electrodes via thiol linkages. Carotenoid polyenes play an essential role as `molecular wires' in photosynthesis. We measured the electrical conductance of a series of carotenoids with 5, 7, 9 and 11 double-single bond pairs. The electronic decay constant, ?, is determined to be 0.224±0.036å-1 in close agreement with the value obtained from first principles simulations (0.217±0.01 å-1). The absolute values of the molecular conductance are within a factor three of those calculated from first-principles.

He, Jin; Terazono, Yuichi; Lindsay, Stuart

2005-03-01

207

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

PubMed

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 concerning protein dynamics and localization, including single particle tracking and immunohistochemistry, and finish by examining the prospects of upcoming applications, such as correlative light and electron microscopy and super-resolution. Advances in single molecule imaging, including multi-color and three-dimensional QD tracking, have provided new insights into the mechanisms of cell signaling and protein trafficking. New forms of QD tracking in vivo have allowed the observation of biological processes at molecular level resolution in the physiological context of the whole animal. Further methodological development of multiplexed QD-based immunohistochemistry assays should enable 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

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

2015-04-01

208

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

PubMed

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

Hihath, Joshua; Bruot, Christopher; Nakamura, Hisao; Asai, Yoshihiro; Díez-Pérez, Ismael; Lee, Youngu; Yu, Luping; Tao, Nongjian

2011-10-25

209

Nanoscale Methods for Single-Molecule Electrochemistry  

NASA Astrophysics Data System (ADS)

The development of experiments capable of probing individual molecules has led to major breakthroughs in fields ranging from molecular electronics to biophysics, allowing direct tests of knowledge derived from macroscopic measurements and enabling new assays that probe population heterogeneities and internal molecular dynamics. Although still somewhat in their infancy, such methods are also being developed for probing molecular systems in solution using electrochemical transduction mechanisms. Here we outline the present status of this emerging field, concentrating in particular on optical methods, metal-molecule-metal junctions, and electrochemical nanofluidic devices.

Mathwig, Klaus; Aartsma, Thijs J.; Canters, Gerard W.; Lemay, Serge G.

2014-06-01

210

Observing single molecule chemical reactions on metal nanoparticles.  

SciTech Connect

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

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

2001-01-01

211

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

PubMed Central

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

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

212

Radio Frequency Scanning Tunneling Spectroscopy for Single-Molecule Spin Resonance  

NASA Astrophysics Data System (ADS)

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

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

2014-09-01

213

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

PubMed

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

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

2014-09-26

214

Fisher information for EMCCD imaging with application to single molecule microscopy  

Microsoft Academic Search

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

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

2010-01-01

215

Extending Single-Molecule Microscopy Using Optical Fourier Processing  

PubMed Central

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

2015-01-01

216

Probing Cellular Protein Complexes via Single Molecule Pull-down  

PubMed Central

Proteins perform most cellular functions in macromolecular complexes. The same protein often participates in different complexes to exhibit diverse functionality. Current ensemble approaches of identifying cellular protein interactions cannot reveal physiological permutations of these interactions. Here, we describe a single molecule pull-down (SiMPull) assay that combines the principles of conventional pull-down assay with single molecule fluorescence microscopy and enables direct visualization of individual cellular protein complexes. SiMPull can reveal how many proteins and of which kinds are present in the in vivo complex, as we show using protein kinase A. We then demonstrate a wide applicability to various signaling proteins found in cytosol, membrane, and cellular organelles, and to endogenous protein complexes from animal tissue extracts. The pulled down proteins are functional and are used, without further processing, for single molecule biochemical studies. SiMPull should provide a rapid, sensitive and robust platform for analyzing protein assemblies in biological pathways. PMID:21614075

Jain, Ankur; Liu, Ruijie; Ramani, Biswarathan; Arauz, Edwin; Ishitsuka, Yuji; Ragunathan, Kaushik; Park, Jeehae; Chen, Jie; Xiang, Yang K.; Ha, Taekjip

2011-01-01

217

Analytical tools for single-molecule fluorescence imaging in cellulo  

E-print Network

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

Leake, Mark

2015-01-01

218

Single molecule detection using charge-coupled device array technology  

SciTech Connect

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.

Denton, M.B.

1992-07-29

219

Evidence of natural isotopic distribution from single-molecule SERS  

E-print Network

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

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

2008-11-03

220

Detectors for single-molecule fluorescence imaging and spectroscopy  

PubMed Central

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

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

2010-01-01

221

Single-molecule fluorescence characterization in native environment  

PubMed Central

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

Ajtai, Katalin

2010-01-01

222

Probing plasma membrane dynamics at the single-molecule level.  

PubMed

The plant plasma membrane is highly dynamic and changes multiple aspects of its organization in response to environmental and internal factors. A detailed understanding of membrane dynamics in living plant cells has remained obscure because of the limited spatial resolution of conventional optical microscopy. Recently, several single-molecule imaging approaches have been developed and used to provide valuable insights into the fundamental biochemical and biophysical properties of the plant plasma membrane, including the organization of membrane microdomains and the dynamics of single-molecule diffusion. Here we review single-molecule imaging methods, including total internal reflection fluorescence microscopy (TIRFM), fluorescence correlation spectroscopy (FCS), and super-resolution microscopy, and examine their contributions to recent progress in understanding protein dynamics and membrane organization in living plant cells. PMID:23911558

Li, Xiaojuan; Luu, Doan-Trung; Maurel, Christophe; Lin, Jinxing

2013-11-01

223

Open-frame system for single-molecule microscopy  

NASA Astrophysics Data System (ADS)

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.

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

224

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

NASA Astrophysics Data System (ADS)

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

Dadosh, Tali

225

A multi-state single-molecule switch actuated by rotation of an encapsulated cluster within a fullerene cage  

NASA Astrophysics Data System (ADS)

We demonstrate a single-molecule switch based on tunneling electron-driven rotation of a triangular Sc3N cluster within an icosahedral C80 fullerene cage among three pairs of enantiomorphic configurations. Scanning tunneling microscopy imaging of switching within single molecules and electronic structure theory identify the conformational isomers and their isomerization pathways. Bias-dependent action spectra and modeling identify the antisymmetric stretch vibration of Sc3N cluster to be the gateway for energy transfer from the tunneling electrons to the cluster rotation. Hierarchical switching of conductivity through the internal cluster motion among multiple stationary states while maintaining a constant shape, is advantageous for the integration of endohedral fullerene-based single-molecule memory and logic devices into parallel molecular computing architectures.

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

2012-11-01

226

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

SciTech Connect

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

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

2012-11-12

227

Single-molecule magnet Mn12 on graphene  

NASA Astrophysics Data System (ADS)

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

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

2014-09-01

228

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

PubMed Central

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

Talaga, David S.

2009-01-01

229

Thermal deposition of intact tetrairon(III) single-molecule magnets in high-vacuum conditions.  

PubMed

A tetrairon(III) single-molecule magnet is deposited using a thermal evaporation technique in high vacuum. The chemical integrity is demonstrated by time-of-flight secondary ion mass spectrometry on a film deposited on Al foil, while superconducting quantum interference device magnetometry and alternating current susceptometry of a film deposited on a kapton substrate show magnetic properties identical to the pristine powder. High-frequency electron paramagnetic resonance spectra confirm the characteristic behavior for a system with S = 5 and a large Ising-type magnetic anisotropy. All these results indicate that the molecules are not damaged during the deposition procedure keeping intact the single-molecule magnet behavior. PMID:19283797

Margheriti, Ludovica; Mannini, Matteo; Sorace, Lorenzo; Gorini, Lapo; Gatteschi, Dante; Caneschi, Andrea; Chiappe, Daniele; Moroni, Riccardo; de Mongeot, Francesco Buatier; Cornia, Andrea; Piras, Federica M; Magnani, Agnese; Sessoli, Roberta

2009-06-01

230

Quantitative measurement of fluorescence brightness of single molecules  

NASA Astrophysics Data System (ADS)

Single-molecule fluorescence spectroscopy and imaging probe many characteristics of the fluorescence from individual molecules like relative intensity, polarization, lifetime and spectrum. However, such an important and fundamental parameter as absolute fluorescence intensity (or in other words fluorescence brightness), which is proportional to the absorption cross section and fluorescence quantum yield, has not yet been sufficiently exploited in the field. One reason for that is the difficulty of absolute fluorescence brightness measurements. In the present work a detailed description of fluorescence brightness measurements of single molecules is given. We discuss several important factors like the power density and polarization of excitation light, the substrates and the local environment. It is shown that the fluorescence brightness of a single molecule indeed can be measured with sufficient accuracy and used as a powerful parameter for characterization of materials at single molecule/particle level. The brightness of a single object can give similar information as the fluorescence quantum yield that is crucial for understanding the photophysical properties for individual multi-chromophoric systems in inhomogeneous environments.

Tian, Yuxi; Halle, Johannes; Wojdyr, Michal; Sahoo, Dibakar; Scheblykin, Ivan G.

2014-09-01

231

Single-Molecule Spectroscopy DOI: 10.1002/ange.201105388  

E-print Network

Single-Molecule Spectroscopy DOI: 10.1002/ange.201105388 Single-Particle and Ensemble Diffusivities,* and Christoph Bräuchle* Diffusion is the omnipresent, random motion of matter, such as atoms and molecules conditions the diffusivities of guest molecules inside a nanostructured porous glass using two conceptually

Ulm, Universität

232

Single-Molecule Circuits with Well-Defined Molecular Conductance  

E-print Network

Single-Molecule Circuits with Well-Defined Molecular Conductance Latha Venkataraman,*,,| Jennifer E-terminated molecules by breaking Au point contacts in a molecular solution at room temperature. We find that the variability of the observed conductance for the diamine molecule-Au junctions is much less than

Hone, James

233

CHEMICAL PHYSICS: Single-Molecule Spectroscopy Comes of Age  

NSDL National Science Digital Library

Access to the article is free, however registration and sign-in are required. In their Perspective, Kelley et al. report from a recent symposium on single-molecule spectroscopy. The symposium demonstrates that the field has matured and is now providing unprecedented insights in biology and materials science.

Anne Myers Kelley (Kansas State University; Department of Chemistry)

2001-06-01

234

ccsd00001150 Getting DNA twist rigidity from single molecule  

E-print Network

ccsd­00001150 (version 1) : 17 Feb 2004 Getting DNA twist rigidity from single molecule experiments to study the extension versus rotation diagrams of single supercoiled DNA molecules. We reproduce: elastic twisted rods, contact, numerical path following, biomechanics. At #12;rst the DNA molecule can

235

Single-Molecule Spectroscopy DOI: 10.1002/anie.201105388  

E-print Network

Single-Molecule Spectroscopy DOI: 10.1002/anie.201105388 Single-Particle and Ensemble Diffusivities,* and Christoph Bräuchle* Diffusion is the omnipresent, random motion of matter, such as atoms and molecules conditions the diffusivities of guest molecules inside a nanostructured porous glass using two conceptually

Ulm, Universität

236

Single-molecule analysis of DNA-protein complexes  

E-print Network

Single-molecule analysis of DNA-protein complexes using nanopores Breton Hornblower1,2, Amy Coombs1 molecules through a protein nanopore. Electrical force applied to individual ssDNA-exonuclease I complexes pulls the two molecules apart, while ion current probes the dissociation rate of the complex. Nanopore

Meller, Amit

237

Enhancement and Quenching of Single-Molecule Fluorescence  

Microsoft Academic Search

We present an experimental and theoretical study of the fluorescence rate of a single molecule as a function of its distance to a laser-irradiated gold nanoparticle. The local field enhancement leads to an increased excitation rate whereas nonradiative energy transfer to the particle leads to a decrease of the quantum yield (quenching). Because of these competing effects, previous experiments showed

Pascal Anger; Palash Bharadwaj; Lukas Novotny

2006-01-01

238

Ten years of tension: single-molecule DNA mechanics  

Microsoft Academic Search

The basic features of DNA were elucidated during the half-century following the discovery of the double helix. But it is only during the past decade that researchers have been able to manipulate single molecules of DNA to make direct measurements of its mechanical properties. These studies have illuminated the nature of interactions between DNA and proteins, the constraints within which

Carlos Bustamante; Zev Bryant; Steven B. Smith

2003-01-01

239

An RNA toolbox for single-molecule force spectroscopy studies  

PubMed Central

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

Vilfan, Igor D.; Kamping, Wiecher; van den Hout, Michiel; Candelli, Andrea; Hage, Susanne; Dekker, Nynke H.

2007-01-01

240

Single Molecule Study of Cellulase Hydrolysis of Crystalline Cellulose  

SciTech Connect

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.

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

2009-12-01

241

Rapid single-molecule imaging in cyclic olefin copolymer channels.  

PubMed

Rapid preparation of high quality capture surfaces is a major challenge for surface-based single-molecule protein binding assays. Here we introduce a simple method to activate microfluidic chambers made from cyclic olefin copolymer for single-molecule imaging with total internal reflection fluorescence microscopy. We describe a surface coating protocol and demonstrate single-molecule imaging in off-the-shelf microfluidic parts that can be activated for binding assays within a few minutes. As the first example, biotinylated protein directly captured on the neutravidin-coated surface was detected using fluorescently labeled antibody. We then showed detection of a fusion construct containing green fluorescence protein and verified its single fluorophore behavior by observing stepwise photobleaching events. Finally, a target protein was identified in the crude cell lysate using antibody-sandwich complex formation. In all experiments, controls were completed to ensure that nonspecific binding to the surface was minimal. Based on our results, we conclude that the simple surface preparation described in this paper enables single-molecule imaging assays without time-consuming coating procedures. Microsc. Res. Tech. 78:309-316, 2015. © 2015 Wiley Periodicals, Inc. PMID:25704038

Skinner, Joseph P; Tetin, Sergey Y

2015-04-01

242

Strong extinction of a laser beam by a single molecule  

E-print Network

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

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

2006-04-24

243

Single molecule Raman spectroscopy and local work function fluctuations  

E-print Network

Single molecule Raman spectroscopy provides information on individual molecules with vibrational-level resolution. The unique mechanisms leading to the huge Raman cross-section enhancement necessary for single molecule sensitivity are under intense investigation in several laboratories. We recently analyzed large spectral fluctuations in single molecule spectra of rhodamine 6G on silver surfaces (A. Weiss and G. Haran, J. Phys. Chem. B (2001), 105, 12348-12354). The appearance of the fluctuations in two particular vibrational bands, and their dependence on several parameters, suggested that they originate in a charge transfer interaction of an adsorbed molecule with the surface. We argued that the fluctuations are due to variations of the local work function at the position of the molecule. In the current paper the fluctuations are further analyzed in terms of the intensity ratio between a fluctuating and a quiescent band, and it is found that the distribution of this ratio is independent of laser power, unlike the correlation time of the fluctuations. We show that a simple model, based on the energetics of charge transfer, can be used to extract the local work function distribution from the intensity ratio distribution. In a second experiment, single molecule spectra are collected from colloids immersed in water and in glycerol and a threefold decrease in fluctuation rate is found in the more viscous fluid. This indicates that surface dynamics are indeed responsible for the fluctuations, involving the motion of the adsorbed molecule and possibly also that of surface silver atoms around it.

Gilad Haran

2004-08-02

244

Single-Molecule Devices DOI: 10.1002/ange.201308398  

E-print Network

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

Borguet, Eric

245

Single-Molecule Devices DOI: 10.1002/anie.201308398  

E-print Network

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

Borguet, Eric

246

Enzyme-Coated Carbon Nanotubes as Single-Molecule Biosensors  

E-print Network

Enzyme-Coated Carbon Nanotubes as Single-Molecule Biosensors Koen Besteman, Jeong-O Lee, Frank G. M. The enzyme-coated tube is found to act as a pH sensor with large and reversible changes in conductance upon

Dekker, Cees

247

Simultaneous single molecule atomic force and fluorescence lifetime imaging  

NASA Astrophysics Data System (ADS)

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

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

2010-02-01

248

Investigating single molecule adhesion by atomic force spectroscopy.  

PubMed

Atomic force spectroscopy is an ideal tool to study molecules at surfaces and interfaces. An experimental protocol to couple a large variety of single molecules covalently onto an AFM tip is presented. At the same time the AFM tip is passivated to prevent unspecific interactions between the tip and the substrate, which is a prerequisite to study single molecules attached to the AFM tip. Analyses to determine the adhesion force, the adhesion length, and the free energy of these molecules on solid surfaces and bio-interfaces are shortly presented and external references for further reading are provided. Example molecules are the poly(amino acid) polytyrosine, the graft polymer PI-g-PS and the phospholipid POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine). These molecules are desorbed from different surfaces like CH3-SAMs, hydrogen terminated diamond and supported lipid bilayers under various solvent conditions. Finally, the advantages of force spectroscopic single molecule experiments are discussed including means to decide if truly a single molecule has been studied in the experiment. PMID:25867282

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

2015-01-01

249

Statistics and Related Topics in Single-Molecule Biophysics  

PubMed Central

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

Qian, Hong; Kou, S. C.

2014-01-01

250

Light Sheet Microscopy for Single Molecule Tracking in Living Tissue  

Microsoft Academic Search

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

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

2010-01-01

251

Real-time single-molecule imaging of quantum interference  

E-print Network

Real-time single-molecule imaging of quantum interference Thomas Juffmann1 , Adriana Milic1,4 and molecules5­7 and, in contrast to classical physics, quantum interference can be observed when single-field fluorescence microscopy detected the position of each molecule with an accuracy of 10 nm and revealed the build

252

Dynamics of a GPCR studied with single-molecule microscopy  

Microsoft Academic Search

The behavior of single G-protein coupled receptor molecules were studied with single-molecule microscopy in the plasmamembrane during Dictyostelium discoideum chemotaxis. The mobility of the receptor was different in the anterior and posterior regions of living cells migrating towards the source of chemoattractant. This difference of mobility can account for an amplification of the extracellular signal, necessary for chemotaxis. It was

Sandra de Keijzer

2006-01-01

253

Partially Condensed DNA Conformations Observed by Single Molecule Fluorescence Microscopy  

Microsoft Academic Search

To detect partially condensed conformations of a double-stranded DNA molecule, single molecule fluorescence microscopy is performed here. The single DNA molecules are ethidium stained, 670 kilobase pair bacteriophage G genomes that are observed both during and after expulsion from capsids. Expulsion occurs in an agarose gel. Just after expulsion, the entire G DNA molecule typically has a partially condensed conformation

Philip Serwer; Shirley J. Hayes

2001-01-01

254

Molecular rearrangements observed by single-molecule microscopy  

Microsoft Academic Search

We have applied quantitative single-molecule photoluminescence microscopy for directly observing molecular rearrangements in a polymeric material subjected to tensile deformation. The system examined is a blend of fluorescent conjugated polymer molecules embedded in polyethylene, known to exhibit strong phase separation. Statistical analysis of the sizes of phase-separated domains reveals that during tensile deformation large domains of fluorescent molecules are transformed

W. Trabesinger; A. Renn; B. Hecht; U. P. Wild; A. Montali; P. Smith; Ch. Weder

2001-01-01

255

A plutonium-based single-molecule magnet.  

PubMed

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

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

2014-08-01

256

Modeling Single Molecule Fluorescence and Lasing. Final report  

SciTech Connect

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

Hill, Steven C.

1998-10-01

257

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

SciTech Connect

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.

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

2011-06-01

258

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

PubMed Central

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

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

2012-01-01

259

Hybrid photodetector for single-molecule spectroscopy and X. Michalet*a  

E-print Network

Hybrid photodetector for single-molecule spectroscopy and microscopy X. Michalet*a , Adrian Chengb photodetector, single-molecule, fluorescence, spectroscopy, microscopy, lifetime, afterpulsing, TCSPC, photocathode, FCS 1. INTRODUCTION 1.1 Single-molecule fluorescence spectroscopy and microscopy Single-molecule

Michalet, Xavier

260

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

E-print Network

Single-Molecule Microscopy Studies of Electric-Field Poling in Chromophore-Polymer Composite field are investigated using single-molecule confocal fluorescence microscopy. Single-molecule of polarization-sensitive single-molecule microscopy in elucidating the details of molecular reorientation during

Reid, Philip J.

261

The optics inside an automated single molecule array analyzer  

NASA Astrophysics Data System (ADS)

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.

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

262

Fluorescence-force spectroscopy at the single molecule level  

NASA Astrophysics Data System (ADS)

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.

Zhou, Ruobo

263

Effect of interfacial bond type on the electronic and structural properties of GaSb\\/InAs superlattices  

Microsoft Academic Search

We have investigated the effects of interfacial bond configuration on the electronic and structural properties of thin (001)GaSb\\/InAs superlattices by using state-of-the-art ab initio molecular dynamics techniques to calculate the electronic and structural properties of two twelve-atom model GaSb\\/InAs superlattices which have been constructed to contain only In-Sb (model 1) or Ga-As (model 2) interface bonds, respectively. We find the

L. A. Hemstreet; C. Y. Fong; J. S. Nelson

1993-01-01

264

Chapter 7 Single-Molecule Fluorescence Microscopy and its Applications to Single-Molecule Sequencing by Cyclic Synthesis  

Microsoft Academic Search

Single-molecule DNA sequencing (SMDS) had been proposed well before genomic research had advanced to the point where the DNA sequences of a few human individuals became available. Skepticism arose as to whether or not there was a need to replace methods that had been proven to be productive by a new technology. However, DNA information from thousands of individuals is

Benedict Hebert; Ido Braslavsky

2007-01-01

265

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

PubMed Central

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

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

266

A 48-pixel array of Single Photon Avalanche Diodes for multispot Single Molecule analysis.  

PubMed

In this paper we present an array of 48 Single Photon Avalanche Diodes (SPADs) specifically designed for multispot Single Molecule Analysis. The detectors have been arranged in a 12×4 square geometry with a pitch-to-diameter ratio of ten in order to minimize the collection of the light from non-conjugated excitation spots. In order to explore the trade-offs between the detectors' performance and the optical coupling with the experimental setup, SPADs with an active diameter of 25 and of 50µm have been manufactured. The use of a custom technology, specifically designed for the fabrication of the detectors, allowed us to combine a high photon detection efficiency (peak close to 50% at a wavelength of 550nm) with a low dark count rate compatible with true single molecule detection. In order to allow easy integration into the optical setup for parallel single-molecule analysis, the SPAD array has been incorporated in a compact module containing all the electronics needed for a proper operation of the detectors. PMID:24357913

Gulinatti, Angelo; Rech, Ivan; Maccagnani, Piera; Ghioni, Massimo

2013-02-01

267

A 48-pixel array of single photon avalanche diodes for multispot single molecule analysis  

NASA Astrophysics Data System (ADS)

In this paper we present an array of 48 Single Photon Avalanche Diodes (SPADs) specifically designed for multispot Single Molecule Analysis. The detectors have been arranged in a 12x4 square geometry with a pitch-to-diameter ratio of ten in order to minimize the collection of the light from non-conjugated excitation spots. In order to explore the tradeoffs between the detectors' performance and the optical coupling with the experimental setup, SPADs with an active diameter of 25 and of 50?m have been manufactured. The use of a custom technology, specifically designed for the fabrication of the detectors, allowed us to combine a high photon detection efficiency (peak close to 50% at a wavelength of 550nm) with a low dark count rate compatible with true single molecule detection. In order to allow easy integration into the optical setup for parallel single-molecule analysis, the SPAD array has been incorporated in a compact module containing all the electronics needed for a proper operation of the detectors.

Gulinatti, Angelo; Rech, Ivan; Maccagnani, Piera; Ghioni, Massimo

2013-01-01

268

Single-molecule DNA detection with an engineered MspA protein nanopore  

PubMed Central

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

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

2008-01-01

269

A 48-pixel array of Single Photon Avalanche Diodes for multispot Single Molecule analysis  

PubMed Central

In this paper we present an array of 48 Single Photon Avalanche Diodes (SPADs) specifically designed for multispot Single Molecule Analysis. The detectors have been arranged in a 12×4 square geometry with a pitch-to-diameter ratio of ten in order to minimize the collection of the light from non-conjugated excitation spots. In order to explore the trade-offs between the detectors’ performance and the optical coupling with the experimental setup, SPADs with an active diameter of 25 and of 50µm have been manufactured. The use of a custom technology, specifically designed for the fabrication of the detectors, allowed us to combine a high photon detection efficiency (peak close to 50% at a wavelength of 550nm) with a low dark count rate compatible with true single molecule detection. In order to allow easy integration into the optical setup for parallel single-molecule analysis, the SPAD array has been incorporated in a compact module containing all the electronics needed for a proper operation of the detectors. PMID:24357913

Rech, Ivan; Maccagnani, Piera; Ghioni, Massimo

2013-01-01

270

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

NASA Astrophysics Data System (ADS)

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

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

2013-03-01

271

Characterization of interfacially electronic structures of gold-magnetite heterostructures using X-ray absorption spectroscopy.  

PubMed

Gold-magnetite heterostructures are novel nanomaterials which can rapidly catalyze the reduction reaction of nitroaromatics. In this study, the interfacially structural and electronic properties of various morphologies of Au-Fe3O4 heterostructures were systematically investigated using X-ray absorbance spectroscopy (XAS) and X-ray photoelectron spectroscopy (XPS). The effect of change in electronic structure and charge transfer on electrochemically catalytic activity of Au-Fe3O4 heterostructures was further evaluated by oxygen reduction reaction (ORR). The shifts in binding energy of Au4f and Fe2p peaks in XPS spectra indicate the charge transfer between the Au and Fe3O4 nanoparticles. The increase in d-hole population of Au seeds after the conjugation with iron oxides follows the order flower-like Au-Fe3O4 (FLNPs)>dumbbell-like Au-Fe3O4 (DBNPs)>Au seeds. In addition, the Fe(2+) valence state increases in Au-Fe3O4 heterostructures, which provides evidence to support the hypothesis of charge transfer between Au and Fe3O4 nanoparticles. The theoretical simulation of Au L3-edge XAS further confirms the production of Au-Fe and Au-O bonds at the interface of Au/Fe3O4 and the epitaxial linkage relationship between Au and Fe3O4 nanoparticles. In addition, the electron deficient of Au seeds increases upon increasing Fe3O4 nanoparticles on a single Au seed, and subsequently decreases the catalytic activity of Au in the Au-Fe3O4 heterostructures. The catalytic activity of Au-Fe3O4 toward ORR follows the order Au seeds>Au-Fe3O4 DBNPs>Au-Fe3O4 FLNPs, which is positively correlated to the extent of electronic deficiency of Au in Au-Fe3O4 heterostructures. PMID:24407694

Lin, Fang-hsin; Doong, Ruey-an

2014-03-01

272

Single Molecule Junctions: Probing Contact Chemistry and Fundamental Circuit Laws  

SciTech Connect

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].

Hybertsen M. S.

2013-04-11

273

Single-Molecule Observation of Prokaryotic DNA Replication  

PubMed Central

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

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

2010-01-01

274

Three-dimensional Molecular Modeling with Single Molecule FRET  

PubMed Central

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

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

2011-01-01

275

Polymers and single molecule fluorescence spectroscopy, what can we learn?  

PubMed

This tutorial review summarizes the most important results and developments in the field of polymer science by means of single molecule fluorescence spectroscopy (SMFS) at ambient temperatures. A broad range of topics will be addressed and it will be discussed which single molecule methods are suitable to get the maximum amount of information about polymer structure, polymer dynamics and the photophysics of incorporated or embedded dye molecules. In particular, we will report on the use of polymer films for immobilization of molecules, the visualization of dynamics near the glass transition temperature Tg, the reptation of polymer chains, the conformation adopted by polymer chains and the in situ observation of the polymerization reaction itself. PMID:19169450

Wöll, Dominik; Braeken, Els; Deres, Ania; De Schryver, Frans C; Uji-i, Hiroshi; Hofkens, Johan

2009-02-01

276

Applications of optical trapping to single molecule DNA  

SciTech Connect

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.

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

1997-12-01

277

Tetraanionic biphenyl lanthanide complexes as single-molecule magnets.  

PubMed

Inverse sandwich biphenyl complexes [(NN(TBS))Ln]2(?-biphenyl)[K(solvent)]2 [NN(TBS) = 1,1'-fc(NSi(t)BuMe2)2; Ln = Gd, Dy, Er; solvent = Et2O, toluene; 18-crown-6], containing a quadruply reduced biphenyl ligand, were synthesized and their magnetic properties measured. One of the dysprosium biphenyl complexes was found to exhibit antiferromagnetic coupling and single-molecule-magnet behavior with Ueff of 34 K under zero applied field. The solvent coordinated to potassium affected drastically the nature of the magnetic interaction, with the other dysprosium complex showing ferromagnetic coupling. Ab initio calculations were performed to understand the nature of magnetic coupling between the two lanthanide ions bridged by the anionic arene ligand and the origin of single-molecule-magnet behavior. PMID:25695369

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

2015-03-01

278

Cylindrical channel plasmon resonance for single-molecule sensing  

NASA Astrophysics Data System (ADS)

Quasi-3D nanoplasmonic structures are investigated, and the interaction of cavity and surface plasmon modes in Au cylindrical channels is discussed. By fastidious choice of geometrical parameters, it is shown that localized surface plasmon resonances (LSPR) inside the channels are established and are highly sensitive to changes in the local dielectric environment. In this study, cylindrical channels are added to the surface of gold nanopillars whose geometry otherwise permits LSPR. The inclusion of the channels creates a plasmonic waveguide supporting whispering gallery mode (WGM) cylindrical channel plasmons, which result from the coupled hybridized field. FDTD simulations reveal the possibility of single-molecule sensitivity of these cylindrical channel nanopillars (CCNP) by demonstrating near-IR wavelength shifts in the detected reflectance from a modeled array of CCNPs in various dielectric environments. The reported sensitivity of this metamaterial provides a platform for SPR single-molecule studies and exhibits potential for label-free biological and chemical sensing.

Terranova, Brandon; Bellingham, Alyssa A.; Herbert, Sylvia; Fontecchio, Adam K.

2014-02-01

279

STM CONTROL OF CHEMICAL REACTIONS: Single-Molecule Synthesis  

NASA Astrophysics Data System (ADS)

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

Hla, Saw-Wai; Rieder, Karl-Heinz

2003-10-01

280

Single-Molecule Studies of DNA Replisome Function  

PubMed Central

Fast and accurate replication of DNA is accomplished by the interactions of multiple proteins in the dynamic DNA replisome. The DNA replisome effectively coordinates the leading and lagging strand synthesis of DNA. These complex, yet elegantly organized, molecular machines have been studied extensively by kinetic and structural methods to provide an in-depth understanding of the mechanism of DNA replication. Owing to averaging of observables, unique dynamic information of the biochemical pathways and reactions are concealed in conventional ensemble methods. However, recent advances in the rapidly expanding field of single-molecule analyses to study single biomolecules offer opportunities to probe and understand the dynamic processes involved in large biomolecular complexes such as replisomes. This review will focus on the recent developments in the biochemistry and biophysics of DNA replication employing single-molecule techniques and the insights provided by these methods towards a better understanding of the intricate mechanisms of DNA replication. PMID:19665592

Perumal, Senthil K.; Yue, Hongjun; Hu, Zhenxin; Spiering, Michelle M.; Benkovic, Stephen J.

2010-01-01

281

Single Molecule DNA Detection with an Atomic Vapor Notch Filter  

E-print Network

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

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

2015-01-01

282

Single-molecule methods to study membrane receptor oligomerization.  

PubMed

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

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

2015-03-16

283

Single-molecule imaging in live bacteria cells  

PubMed Central

Bacteria, such as Escherichia coli and Caulobacter crescentus, are the most studied and perhaps best-understood organisms in biology. The advances in understanding of living systems gained from these organisms are immense. Application of single-molecule techniques in bacteria have presented unique difficulties owing to their small size and highly curved form. The aim of this review is to show advances made in single-molecule imaging in bacteria over the past 10 years, and to look to the future where the combination of implementing such high-precision techniques in well-characterized and controllable model systems such as E. coli could lead to a greater understanding of fundamental biological questions inaccessible through classic ensemble methods. PMID:23267188

Ritchie, Ken; Lill, Yoriko; Sood, Chetan; Lee, Hochan; Zhang, Shunyuan

2013-01-01

284

Semiconductor Quantum Rods as Single Molecule Fluorescent Biological Labels  

PubMed Central

In this paper, we report the development of rod shaped semiconductor nanocrystals (quantum rods) as fluorescent biological labels. Water soluble biocompatible quantum rods have been prepared by surface silanization and applied for non-specific cell tracking as well as specific cellular targeting. Quantum rods are brighter single molecule probes as compared to quantum dots. They have many potential applications as biological labels in situations where their properties offer advantages over quantum dots. PMID:17212460

Fu, Aihua; Gu, Weiwei; Boussert, Benjamin; Koski, Kristie; Gerion, Daniele; Manna, Liberato; Le Gros, Mark; Larabell, Carolyn; Alivisatos, A. Paul

2014-01-01

285

Single-Molecule Covalent Chemistry in a Protein Nanoreactor  

Microsoft Academic Search

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

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

286

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

Microsoft Academic Search

By exploiting the extremely large effective cross sections ( 10-17-10-16 cm2\\/molecule) available from surface-enhanced Raman scattering (SERS), we achieved the first observation of single molecule Raman scattering. Measured spectra of a single crystal violet molecule in aqueous colloidal silver solution using one second collection time and about 2×105 W\\/cm2 nonresonant near-infrared excitation show a clear ``fingerprint'' of its Raman features

Katrin Kneipp; Yang Wang; Harald Kneipp; Lev T. Perelman; Irving Itzkan; Ramachandra R. Dasari; Michael S. Feld

1997-01-01

287

Single-Molecule Analysis of Chemotactic Signaling in Dictyostelium Cells  

Microsoft Academic Search

Single-molecule imaging techniques were used to reveal the binding of individual cyclic adenosine 3',5'-monophosphate molecules to heterotrimeric guanine nucleotide-binding protein coupled receptors on the surface of living Dictyostelium discoideum cells. The binding sites were uniformly distributed and diffused rapidly in the plane of the membrane. The probabilities of individual association and dissociation events were greater for receptors at the anterior

Masahiro Ueda; Yasushi Sako; Toshiki Tanaka; Peter Devreotes; Toshio Yanagida

2001-01-01

288

A Single-Molecule Study of RNA Catalysis and Folding  

Microsoft Academic Search

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

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

2000-01-01

289

Diffusion of carbon nanotubes with single-molecule fluorescence microscopy  

Microsoft Academic Search

Single walled carbon nanotubes (SWNTs) are a promising gene and drug delivery system since their physical dimensions mimic nucleic acids. Towards this aim, the hydrophobicity of SWNTs was averted by coating with ribonucleic acid (RNA) polymer [poly(rU)] or bovine serum albumin (BSA) and the consequent diffusion of these synthetic-biomolecular hybrids was studied by single-molecule fluorescence microscopy. The diffusion coefficient for

Q. Lu; K. O. Freedman; R. Rao; G. Huang; J. Lee; L. L. Larcom; A. M. Rao; P. C. Ke

2004-01-01

290

Single-Molecule Microscopy and Force Spectroscopy of Membrane Proteins  

Microsoft Academic Search

Single-molecule atomic force microscopy (AFM) provides novel ways to characterize the structure-function relationship of native\\u000a membrane proteins. High-resolution AFM topographs allow observing the structure of single proteins at sub-nanometer resolution\\u000a as well as their conformational changes, oligomeric state, molecular dynamics and assembly. We will review these feasibilities\\u000a illustrating examples of membrane proteins in native and reconstituted membranes. Classification of individual

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

291

Single molecule microscopy in 3D cell cultures and tissues.  

PubMed

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

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

2014-12-15

292

Single-Molecule Covalent Chemistry in a Protein Nanoreactor  

NASA Astrophysics Data System (ADS)

Covalent chemistry can be observed at the single-molecule level by using engineered protein pores as "nanoreactors". By recording the ionic current driven through single engineered alpha-hemolysin (?HL) pores in a transmembrane potential, individual bond-making and bond-breaking steps that occur within the pore and perturb the current are monitored with sub-millisecond time-resolution. Recently, a variety of covalent reactions of small molecules have been observed by this approach including irreversible light-activated chemistry, multiple turnovers of reversible reactions, the turnover of normally irreversible reactions in a twocompartment system and a step-by- step polymerization. These single-molecule experiments are revealing information about fundamental chemical processes that cannot be extracted from ensemble measurements. Further, the approach can be used to examine the effects of the local environment on chemistry and catalysis, and to construct sensors for reactive molecules based on covalent chemistry rather than non-covalent binding interactions. Alternative approaches to small molecule covalent chemistry at the single-molecule level are described in the review, as well as the problems and present limitations of the nanoreactor approach.

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

293

Single-Molecule Nanosecond Anisotropy Dynamics of Tethered Protein Motions  

SciTech Connect

Confined and hindered protein motions are generally found in living cells, with tethered rotational motions of proteins or protein domains particularly associated with and relevant to the early events of molecular interactions in cell signaling at extra- and intracellular membrane surfaces. Ensemble-averaged time-resolved fluorescence anisotropy has been extensively applied to study the protein rotational and conformational motion dynamics under physiologically relevant conditions. However, the spatial and temporal inhomogeneities of the non-synchronizable stochastic protein rotational and conformational motions are extremely difficult for such ensemble-averaged measurements to characterize. Here, we report on a demonstration of the single-molecule nanosecond anisotropy and its application to studying the tethered protein motion of a T4 lysozyme on a biologically comparable surface under water. The rotational motions of the tethered proteins are confined in a half-sphere volume primarily defined by the linker and the surface. We have observed dynamic inhomogeneity of the rotational diffusion dynamics, i.e., diffusion rate fluctuation, due to interactions between the proteins and the surface. However, we also found that the long-time averages of the dynamically inhomogeneous diffusion rates of single molecules are essentially homogeneous amongst the single molecules examined.

Hu, Dehong; Lu, H Peter

2003-01-16

294

Toward single-molecule optical mapping of the epigenome.  

PubMed

The past 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 at the population level. The complex composition of the genome has made it an ideal system to study at 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 nanoscale and enhanced optical resolving power for analysis of genomic information. During the past few 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

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

2014-01-28

295

Single-molecule imaging of hyaluronan in human synovial fluid  

NASA Astrophysics Data System (ADS)

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.

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

2010-11-01

296

Towards Single-Molecule Optical Mapping of the Epigenome  

PubMed Central

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

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

297

Single molecule pull-down for studying protein interactions  

PubMed Central

This protocol describes a single molecule pull-down (SiMPull) assay for analyzing physiological protein complexes. The assay combines the conventional pull-down assay with single molecule total internal reflection fluorescence microscopy, and allows probing single macromolecular complexes directly from cell or tissue extracts. In this method, antibodies against the protein of interest are immobilized on a passivated microscope slide. When cell extracts are applied, the surface-tethered antibody captures the protein together with its physiological interaction partners. After washing away the unbound components, single molecule fluorescence microscopy is used to probe the pulled down proteins. Captured proteins are visualized through genetically encoded fluorescent protein tags or through antibody labeling. This ultra-sensitive assay requires at least 10-fold less reagents, is significantly faster and provides quantitative data compared to western blot analysis. Furthermore, SiMPull can distinguish between multiple association states of the same protein. SiMPull is generally applicable to proteins from a variety of cellular contexts and to endogenous proteins. Starting with the cell extracts and passivated slides, the assay requires 1.5 – 2.5 hours for data acquisition and analysis. PMID:22322217

Jain, Ankur; Liu, Ruijie; Xiang, Yang K.; Ha, Taekjip

2013-01-01

298

Nonequilibrium Single Molecule Protein Folding in a Coaxial Mixer  

PubMed Central

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

Hamadani, Kambiz M.; Weiss, Shimon

2008-01-01

299

Single-Molecule Studies of Actin Assembly and Disassembly Factors  

PubMed Central

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

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

2014-01-01

300

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

SciTech Connect

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.

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

301

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

SciTech Connect

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.

Lian, Tianquan

2014-04-22

302

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

NASA Astrophysics Data System (ADS)

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

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

2015-03-01

303

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

PubMed

To develop advanced materials for electronic devices, it is of utmost importance to design organic building blocks with tunable functionality and to study their properties at the molecular level. For organic electronic and photovoltaic applications, the ability to vary the nature of charge carriers and so create either electron donors or acceptors is critical. Here we demonstrate that charge carriers in single-molecule junctions can be tuned within a family of molecules that contain electron-deficient thiophene-1,1-dioxide (TDO) building blocks. Oligomers of TDO were designed to increase electron affinity and maintain delocalized frontier orbitals while significantly decreasing the transport gap. Through thermopower measurements we show that the dominant charge carriers change from holes to electrons as the number of TDO units is increased. This results in a unique system in which the charge carrier depends on the backbone length, and provides a new means to tune p- and n-type transport in organic materials. PMID:25698329

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

2015-03-01

304

High-k dielectric stack-ellipsometry and electron diffraction measurements of interfacial oxides  

NASA Astrophysics Data System (ADS)

With the silicon interface becoming increasingly scrutinized in high dielectric constant materials for SiO2 replacement, fine distinctions in the quality of silicon cleaning can have a large impact on MOS parameters. One of the cleaning schemes that have potential to replace the industry standard RCA clean with HF/H2O etch is a modified version of the Shiraki clean. The evolution of Si (100) surface cleaned by the modified Shiraki method has been investigated by a conventional, single-wave length ellipsometer. Using Low Energy Electron Diffraction (LEED), we have calibrated the ellipsometric measurement for the as-cleaned silicon surface. It was found that a lower baseline of 0.7˜0.9 nm from ellipsometric measurements could be established as equivalent to a clean, hydrogen passivated surface. To verify the effect of the interfacial oxide thickness on the dielectric constant of the high-k gate stack, thickness of the thin-oxide grown under high vacuum condition was measured and correlated with the dielectric constant of the HfO2 gate dielectric layer.

Choi, Kisik; Harris, Harlan R.; Nikishin, Sergey; Gangopadhyay, Shubhra; Temkin, Henryk

2003-09-01

305

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

PubMed

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

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

306

Scanning exciton microscopy and single-molecule resolution and detection  

NASA Astrophysics Data System (ADS)

Subwavelength light sources have been constructed with the aid of luminescent and exciton transporting materials. These EXCITOR (exciton transmitted optical radiation) sources produce evanescent luminescence and can be used as scanning, light emitting tips of nanometer dimensions. They can also be used as scanning exciton donor tips. The theoretical resolution limit of this kind of near-field optical microscopy is on the atomic or molecular scale. The detection limit is a single molecule, but in contrast to other single molecule detection methods, this single molecule could be identified spatially as well as spectrally. Experimental examples of such an EXCITOR tip consist of gold or aluminum coated glass micropipettes with active crystal tips (anthracene, tetracene, perylene, etc.). Design considerations involve optical, excitonic, photochemical and mechanical properties of the luminescent point source. As it is scanned over a sample, it senses a variety of perturbations such as quenching or external heavy atom effects. It can also actively excite a luminescent probe. The latter process can be non-radiative (e.g., Forster) or may involve absorption and re-emission of evanescent luminescence. Spatially coupled emission and absorption processes are of both theoretical and practical interest. They open a way for reducing by many orders of magnitude the number of photons required to excite a single, isolated chromophore. Molecular exiton microscopy allows extention of near-field microscopy beyond the 50 nm limit already achieved and, thus, permits a new frontier of resolution with light based on the limits of energy transfer measurements. In essence, then, the goal of this research is a spectrally sensitive light microscope that will have the capability to zoom non-destructively and in air from the limits of resolution of lens-based confocal light microscopy (200 nm) to molecular dimensions of 1 nm.

Kopelman, Raoul; Tan, Weihong; Lewis, Aaron; Lieberman, Klony S.

1991-07-01

307

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

PubMed

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

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

2009-06-22

308

Single molecule detection and underwater fluorescence imaging with cantilevered near-field fiber optic probes  

E-print Network

Tapping-mode near-field scanning optical microscopy (NSOM) employing a cantilevered fiber optic probe is utilized to image the fluorescence from single molecules and samples in aqueous environments. The single molecule fluorescenceimages demonstrate...

Talley, Chad E.; Lee, M. Annie; Dunn, Robert C.

1998-04-03

309

A distribution-based method to resolve single-molecule Förster resonance energy transfer observations  

E-print Network

We introduce a new approach to analyze single-molecule Förster resonance energy transfer (FRET) data. The method recognizes that FRET efficiencies assumed by traditional ensemble methods are unobservable for single molecules. ...

Backovi?, Mihailo; Price, E. Shane; Johnson, Carey K.; Ralston, John P.

2011-04-12

310

Single-molecule characterization and engineering of the surfaces of nucleic acid sensors  

E-print Network

Single-molecule kinetics and super-resolution microscopy byforce microscopy (EC-AFM) with single-molecule resolution.microscopy imag- ing would appear to be well suited to characterize single DNA molecules

Josephs, Eric Alan

2013-01-01

311

Single Molecule as a Local Acoustic Detector for Mechanical Oscillators  

NASA Astrophysics Data System (ADS)

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.

Tian, Yuxi; Navarro, Pedro; Orrit, Michel

2014-09-01

312

Recent developments in single-molecule DNA mechanics  

PubMed Central

Over the past two decades, measurements on individual stretched and twisted DNA molecules have helped define the basic elastic properties of the double helix and enabled real-time functional assays of DNA-associated molecular machines. Recently, new magnetic tweezers approaches for simultaneously measuring freely fluctuating twist and extension have begun to shed light on the structural dynamics of large nucleoprotein complexes. Related technical advances have facilitated direct measurements of DNA torque, contributing to a better understanding of abrupt structural transitions in mechanically stressed DNA. The new measurements have also been exploited in studies that hint at a developing synergistic relationship between single-molecule manipulation and structural DNA nanotechnology. PMID:22658779

Bryant, Zev; Oberstrass, Florian C.; Basu, Aakash

2013-01-01

313

Resonant Magnetization Tunneling in Single-Molecule Magnets  

Microsoft Academic Search

Data are presented for three different types of single-molecule magnets (SMM's): [Mn12O12(O2CR)16(H2O)4],[Cation][Mn12O12(O2CR)16(H2O)4], and the distorted cubane [Mn Mn 3O3X(O2CR)3L3] complexes. All three types of complexes exhibit slow magnetization relaxation at temperatures below 5 K. Each molecule can change the direction of its magnetization only slowly at these low temperatures. Manisfetations of this are seen in magnetization hysteresis loops and in

Sheila M. J. Aubin; Daniel Ruiz; Evan Rumberger; Ziming Sun; Belen Albela; Michael W. Wemple; Neil R. Dilley; Joan Ribas; M. Brian Maple; George Christou; David N. Hendrickson

1999-01-01

314

Detection of pathogenic DNA at the single-molecule level  

NASA Astrophysics Data System (ADS)

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

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

2011-03-01

315

Fluorescence image of a single molecule in a microsphere: model  

SciTech Connect

We model fluorescence images of single molecules in spherical dielectric microcavities. Molecules are treated as time-harmonic dipoles. Images are integrated over emission frequencies. Because of the strong refractive properties of the enclosing sphere, the fluorescence image depends on the refractive index of the sphere and the position, the orientation, and the emission frequency of the molecule. When the dipole{close_quote}s emission is at the frequency of a microsphere resonance, the brightest regions in the images appear to originate from outside the sphere for some dipole positions. This type of calculation should help in interpreting images of molecules in microspheres. {copyright} 1999 Optical Society of America

Hill, S.C. [Army Research Laboratory, 2800 Powder Mill Road, Adelphi, Maryland 20783 (United States); Nachman, P. [TRW Inc., One Space Park Drive, Redondo Beach, California 90278 (United States); Arnold, S. [Microparticle Photophysics Laboratory, Polytechnic University, Brooklyn, New York 11021 (United States); Ramsey, J.M.; Barnes, M.D. [Chemical and Analytical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6142 (United States)

1999-11-01

316

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

NASA Astrophysics Data System (ADS)

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.

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

2015-04-01

317

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

PubMed

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

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

2015-04-10

318

Theoretical Investigation of Aspects of Single-Molecule Fluorescence Detection in Microcapillaries  

E-print Network

­ water interfaces is so great as to prevent efficient single- molecule detection. Thus, one goalTheoretical Investigation of Aspects of Single-Molecule Fluorescence Detection in Microcapillaries of a theoretical investigation of two aspects of single-molecule detection by laser-induced fluorescence

Enderlein, Jörg

319

Single Molecule Measurements of Repressor Protein 1D Diffusion on DNA Y. M. Wang,1  

E-print Network

Single Molecule Measurements of Repressor Protein 1D Diffusion on DNA Y. M. Wang,1 Robert H. Austin 10 October 2005; published 27 July 2006) We used single-molecule imaging techniques and measured [10­14]. We used a single-molecule method approach to study LacI-DNA binding, and ob- served

Voigt, Chris

320

Single-molecule studies of complex systems: the replisome Antoine M. van Oijen  

E-print Network

Single-molecule studies of complex systems: the replisome Antoine M. van Oijen Received 30th August and reaction mechanisms. An important future goal is extending the applicability of single-molecule techniques will be used as an example to illustrate recent progress in the development of various single-molecule

321

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

E-print Network

Single-molecule analysis of DNA replication in Xenopus egg extracts Hasan Yardimci a , Anna B: Available online 6 April 2012 Communicated by Marcel Mechali Keywords: Single-molecule DNA replication Fluorescence microscopy a b s t r a c t The recent advent in single-molecule imaging and manipulation methods

322

Single-molecule dynamics of semiflexible Gaussian chains Shilong Yang, James B. Witkoskie, and Jianshu Caoa)  

E-print Network

Single-molecule dynamics of semiflexible Gaussian chains Shilong Yang, James B. Witkoskie to determine the statistics and correlations of single-molecule fluorescence resonant energy transfer FRET the intrachain dynamics at the single-molecule level. When measured with finite time resolution

Cao, Jianshu

323

Dissecting Contact Mechanics from Quantum Interference in Single-Molecule Junctions of Stilbene Derivatives  

E-print Network

insight into the structure-conductance relationship in single-molecule junctions because it providesDissecting Contact Mechanics from Quantum Interference in Single- Molecule Junctions of Stilbene lead to dramatic modulation and suppression of conductance in single-molecule junctions. Probing

Hone, James

324

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

E-print Network

DOI: 10.1002/ijch.201100102 Single-Molecule Studies of HIV-1 Protease Catalysis Enabled by Chemical. Spectroscopic studies of enzyme catalysis on a single-molecule level[2] provide an additional level of spatio peptide and protein synthesis for single-molecule studies of enzyme catalysis. Keywords: chemical protein

Myong, Sua

325

Single-Molecule Measurements of the Persistence Length of Double-Stranded RNA  

E-print Network

RNA using two different single-molecule techniques: magnetic tweezers and atomic force microscopy. We deduce single- molecule techniques, magnetic tweezers and atomic force microscopy (AFM), to measure itsSingle-Molecule Measurements of the Persistence Length of Double-Stranded RNA J. A. Abels, F

Dekker, Nynke

326

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

E-print Network

trapping - confocal fluorescence microscopy 1 J Introduction Single-molecule detection and single-moleculeCONCEPTS Optical Detection and Manipulation of Single Molecules in Room-Temperature Solutions on single enzymes, for example, have revealed very different catalytic rates for individual enzyme molecule

Zare, Richard N.

327

DOI: 10.1002/cbic.200800739 Observing Proteins as Single Molecules Encapsulated in  

E-print Network

-like environment. In typical single-molecule studies using confocal microscopy, a tightly focused laser beamDOI: 10.1002/cbic.200800739 Observing Proteins as Single Molecules Encapsulated in Surface vesicles[14,15] and polymeric vesicles[16,17] has been established. With respect to single-molecule studies

Enderlein, Jörg

328

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

Microsoft Academic Search

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

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

2005-01-01

329

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

E-print Network

,Anthony J Manzo & Mohamed A Sobhy Single-molecule microscopy has evolved into the ultimate microscopy. We also provide guidelines for choosing the right approach from the available single-molecule and single-molecule microscopy. In the 1980s so-called scanning probe and near-field microscopes were

Walter, Nils G.

330

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

E-print Network

polydispersion in reaction kinetics. Here we use single-molecule fluorescence microscopy to study twoSingle-Molecule Kinetics Reveals a Hidden Surface Reaction Intermediate in Single is further resolvable by single-turnover kinetics at the subparticle level. Detailed single-molecule kinetic

Chen, Peng

331

How Does a Single Pt Nanocatalyst Behave in Two Different Reactions? A Single-Molecule Study  

E-print Network

ABSTRACT: Using single-molecule microscopy of fluoro- genic reactions we studied Pt nanoparticle catalysis fluorescence microscopy,25-27 and electrochemical detection.28-31 Our group has used single- molecule-deacetylation reaction and the other a reductive N-deoxygenation reaction, using single- molecule microscopy

Chen, Peng

332

Orientation imaging of single molecules by wide-field epifluorescence microscopy  

E-print Network

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

Enderlein, Jörg

333

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

E-print Network

Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy Keir C Neuman1 & Attila Nagy2 Single-molecule force spectroscopy has emerged as a powerful tool and displacement generated by single molecules ranging from cells to proteins. Although there is an ever

Ritort, Felix

334

MAGNETIC QUANTUM TUNNELING AND RELATED PHENOMENA IN SINGLE MOLECULE MAGNETS Presentation  

E-print Network

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

del Barco, Enrique

335

Three-Pulse Photon Echo of Finite Numbers of Molecules: Single-Molecule Traces  

E-print Network

of single-molecule photon echo or equivalent types of measurements. In particular, the three-pulse photonThree-Pulse Photon Echo of Finite Numbers of Molecules: Single- Molecule Traces Hui Dong and Graham, 6227]. To avoid this drawback of ensemble measurements and evaluate single-molecule behavior, a quantum

Fleming, Graham R.

336

Computational micromechanics analysis of electron hopping and interfacial damage induced piezoresistive response in carbon nanotube-polymer nanocomposites  

NASA Astrophysics Data System (ADS)

Carbon nanotube (CNT)-polymer nanocomposites have been observed to exhibit an effective macroscale piezoresistive response, i.e., change in macroscale resistivity when subjected to applied deformation. The macroscale piezoresistive response of CNT-polymer nanocomposites leads to deformation/strain sensing capabilities. It is believed that the nanoscale phenomenon of electron hopping is the major driving force behind the observed macroscale piezoresistivity of such nanocomposites. Additionally, CNT-polymer nanocomposites provide damage sensing capabilities because of local changes in electron hopping pathways at the nanoscale because of initiation/evolution of damage. The primary focus of the current work is to explore the effect of interfacial separation and damage at the nanoscale CNT-polymer interface on the effective macroscale piezoresistive response. Interfacial separation and damage are allowed to evolve at the CNT-polymer interface through coupled electromechanical cohesive zones, within a finite element based computational micromechanics framework, resulting in electron hopping based current density across the separated CNT-polymer interface. The macroscale effective material properties and gauge factors are evaluated using micromechanics techniques based on electrostatic energy equivalence. The impact of the electron hopping mechanism, nanoscale interface separation and damage evolution on the effective nanocomposite electrostatic and piezoresistive response is studied in comparison with the perfectly bonded interface. The effective electrostatic/piezoresistive response for the perfectly bonded interface is obtained based on a computational micromechanics model developed in the authors’ earlier work. It is observed that the macroscale effective gauge factors are highly sensitive to strain induced formation/disruption of electron hopping pathways, interface separation and the initiation/evolution of interfacial damage.

Chaurasia, A. K.; Ren, X.; Seidel, G. D.

2014-07-01

337

Biophysical characterization of DNA binding from single molecule force measurements  

PubMed Central

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

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

2010-01-01

338

Single-molecule microscopy using tunable nanoscale confinement  

NASA Astrophysics Data System (ADS)

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

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

2013-09-01

339

Ultra-Stable Organic Fluorophores for Single-Molecule Research  

PubMed Central

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

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

2013-01-01

340

Single molecule study of a processivity clamp sliding on DNA  

SciTech Connect

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.

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

2007-07-05

341

Tunable magnetoresistance in an asymmetrically coupled single-molecule junction  

NASA Astrophysics Data System (ADS)

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.

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

2015-03-01

342

Studying the Nucleated Mammalian Cell Membrane by Single Molecule Approaches  

PubMed Central

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

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

2014-01-01

343

Single-Molecule Electrical Random Resequencing of DNA and RNA  

PubMed Central

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

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

2012-01-01

344

Biophysical characterization of DNA binding from single molecule force measurements  

NASA Astrophysics Data System (ADS)

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.

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

2010-09-01

345

Tunable magnetoresistance in an asymmetrically coupled single-molecule junction.  

PubMed

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

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

2015-03-01

346

Watching Individual Proteins Acting on Single Molecules of DNA  

PubMed Central

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

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

2011-01-01

347

Single molecule mechanical probing of the SNARE protein interactions.  

PubMed

Exocytotic release of neurotransmitters is mediated by the ternary soluble N-ethyl maleimide-sensitive fusion protein attachment protein receptors (SNAREs) complex, comprised of syntaxin (Sx), synaptosome-associated protein of 25 kDa (SNAP25), and synaptobrevin 2 (Sb2). Since exocytosis involves the nonequilibrium process of association and dissociation of bonds between molecules of the SNARE complex, dynamic measurements at the single molecule level are necessary for a detailed understanding of these interactions. To address this issue, we used the atomic force microscope in force spectroscopy mode to show from single molecule investigations of the SNARE complex, that Sx1A and Sb2 are zippered throughout their entire SNARE domains without the involvement of SNAP25. When SNAP25B is present in the complex, it creates a local interaction at the 0 (ionic) layer by cuffing Sx1A and Sb2. Force loading rate studies indicate that the ternary complex interaction is more stable than the Sx1A-Sb2 interaction. PMID:16648158

Liu, W; Montana, Vedrana; Bai, Jihong; Chapman, Edwin R; Mohideen, U; Parpura, Vladimir

2006-07-15

348

Direct quantification of single-molecules of microRNA by total internal reflection fluorescence microscopy.  

PubMed

MicroRNAs (miRNAs) express differently in normal and cancerous tissues and thus are regarded as potent cancer biomarkers for early diagnosis. However, the short length and low abundance of miRNAs have brought challenges to the established detection assay in terms of sensitivity and selectivity. In this work, we present a novel miRNA detection assay in single-molecule level with total internal reflection fluorescence microscopy (TIRFM). It is a solution-based hybridization detection system that does not require pretreatment steps such as sample enrichment or signal amplification. The hsa-miR-21 (miR-21) is chosen as target miRNA for its significant elevated content in a variety of cancers as reported previously. Herein, probes of complementary single-stranded oligonucleotide were hybridized in solution to miR-21 and labeled with fluorescent dye YOYO-1. The fluorescent hybrids were imaged by an electron-multiplying charge-coupled device (EMCCD) coupled TIRFM system and quantified by single-molecule counting. This single molecule detection (SMD) assay shows a good correlation between the number of molecules detected and the factual concentration of miRNA. The detection assay is applied to quantify the miR-21 in extracted total RNA samples of cancerous MCF-7 cells, HepG2 cells, and normal HUVEC cells, respectively. The results agreed very well with those from the prevalent real-time polymerase chain reaction (qRT-PCR) analysis. This assay is of high potential for applications in miRNA expression profiling and early cancer diagnosis. PMID:20704380

Chan, Ho-Man; Chan, Lai-Sheung; Wong, Ricky Ngok-Shun; Li, Hung-Wing

2010-08-15

349

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

PubMed

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

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

2014-11-26

350

4.1.6 SINGLE MOLECULE RESONANT TUNNELING SPECTROSCOPY N. P. Guisinger, N. L. Yoder, M. C. Hersam, "Probing Charge Transport at the Single Molecule Level on  

E-print Network

20 4.1.6 SINGLE MOLECULE RESONANT TUNNELING SPECTROSCOPY N. P. Guisinger, N. L. Yoder, M. C. Hersam, "Probing Charge Transport at the Single Molecule Level on Silicon by Using Cryogenic Ultra-High Vacuum to image and probe individual organic molecules on silicon. At cryogenic temperatures, the precision

Shull, Kenneth R.

351

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

NASA Astrophysics Data System (ADS)

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).

Strano, Michael

2009-03-01

352

DNA-cisplatin interaction studied with single molecule stretching experiments.  

PubMed

By performing single molecule stretching experiments with optical tweezers, we have studied the changes in the mechanical properties of DNA-cisplatin complexes as a function of some variables of interest such as the drug diffusion time and concentration in the sample. We propose a model to explain the behavior of the persistence length as a function of the drug concentration, extracting the binding data from pure mechanical measurements. Such analysis has allowed us to show that cisplatin binds cooperatively to the DNA molecule. In addition, DNA compaction by the action of the drug was also observed under our experimental conditions by studying the kinetics of some mechanical properties such as the radius of gyration and the end-to-end distance, e.g. Crisafuli et al., Integr. Biol., 2011, xx, xxxx. PMID:22513758

Crisafuli, F A P; Cesconetto, E C; Ramos, E B; Rocha, M S

2012-05-01

353

X-ray induced demagnetization of single-molecule magnets  

SciTech Connect

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.

Dreiser, Jan, E-mail: jan.dreiser@epfl.ch [Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI (Switzerland); Institute of Condensed Matter Physics, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne (Switzerland); Westerström, Rasmus [Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI (Switzerland); Physik-Institut, Universität Zürich, 8057 Zürich (Switzerland); Department of Physics and Astronomy, Uppsala University, 751 20 Uppsala (Sweden); Piamonteze, Cinthia; Nolting, Frithjof [Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI (Switzerland); Rusponi, Stefano; Brune, Harald [Institute of Condensed Matter Physics, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne (Switzerland); Yang, Shangfeng [Hefei National Laboratory for Physical Sciences at Microscale, Department of Materials Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026 (China); Popov, Alexey; Dunsch, Lothar [Department of Electrochemistry and Conducting Polymers, Leibniz Institute of Solid State and Materials Research, 01069 Dresden (Germany); Greber, Thomas, E-mail: greber@physik.uzh.ch [Physik-Institut, Universität Zürich, 8057 Zürich (Switzerland)

2014-07-21

354

Single-molecule denaturation mapping of DNA in nanofluidic channels.  

PubMed

Here we explore the potential power of denaturation mapping as a single-molecule technique. By partially denaturing YOYO-1-labeled DNA in nanofluidic channels with a combination of formamide and local heating, we obtain a sequence-dependent "barcode" corresponding to a series of local dips and peaks in the intensity trace along the extended molecule. We demonstrate that this structure arises from the physics of local denaturation: statistical mechanical calculations of sequence-dependent melting probability can predict the barcode to be observed experimentally for a given sequence. Consequently, the technique is sensitive to sequence variation without requiring enzymatic labeling or a restriction step. This technique may serve as the basis for a new mapping technology ideally suited for investigating the long-range structure of entire genomes extracted from single cells. PMID:20616076

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

2010-07-27

355

Progress towards DNA sequencing at the single molecule level  

SciTech Connect

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.

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

1995-12-01

356

Enhancing Single Molecule Imaging in Optofluidics and Microfluidics  

PubMed Central

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

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

2011-01-01

357

Linear trinuclear cobalt(ii) single molecule magnet.  

PubMed

The introduction of NaBPh4 into a methanolic solution of CoCl2·6H2O and 2-[(pyridine-2-ylimine)-methyl]phenol (Hpymp) afforded {[Co(II)3(pymp)4(MeOH)2][BPh4]2}·2MeOH () with a centro-symmetrically linear trinuclear structure. Magnetic analysis of exhibited significant intracluster ferromagnetic exchange (2.4 cm(-1)) and slow relaxation of magnetization in both zero and non-zero static fields below 5 K, giving the first [Co(II)3] single molecule magnet with an effective energy barrier of 17.2(3) cm(-1) under a 500 Oe dc field. PMID:25562308

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

2015-01-28

358

Single-molecule magnet engineering: building-block approaches.  

PubMed

Tailoring the specific magnetic properties of any material relies on the topological control of the constituent metal ion building blocks. Although this general approach does not seem to be easily applied to traditional inorganic bulk magnets, coordination chemistry offers a unique tool to delicately tune, for instance, the properties of molecules that behave as "magnets", the so-called single-molecule magnets (SMMs). Although many interesting SMMs have been prepared by a more or less serendipitous approach, the assembly of predesigned, isolatable molecular entities into higher nuclearity complexes constitutes an elegant and fascinating strategy. This Feature article focuses on the use of building blocks or modules (both terms being used indiscriminately) to direct the structure, and therefore also the magnetic properties, of metal ion complexes exhibiting SMM behaviour. PMID:24626635

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

2014-05-01

359

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

SciTech Connect

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

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

1997-03-01

360

Single molecule thermodynamics of ATP synthesis by F1-ATPase  

NASA Astrophysics Data System (ADS)

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

Toyabe, Shoichi; Muneyuki, Eiro

2015-01-01

361

Visualizing Cyclic Peptide Hydration at the Single-Molecule Level  

PubMed Central

The role of water molecules in the selective transport of potassium ions across cell membranes is important. Experimental investigations of valinomycin–water interactions remain huge challenge due to the poor solubility of valinomycin in water. Herein, we removed this experimental obstacle by introducing gaseous water and valinomycin onto a Cu(111) surface to investigate the hydration of valinomycin. By combining scanning tunneling microscopy (STM) with density functional theory (DFT) calculations, we revealed that water could affect the adsorption structure of valinomycin. Hydrogen bond interactions occurred primarily at the carbonyl oxygen of valinomycin and resulted in the formation of valinomycin hydrates. The single-molecule perspective revealed in our investigation could provide new insight into the role of water on the conformation transition of valinomycin, which might provide a new molecular basis for the ion transport mechanism at the water/membrane interface. PMID:23955234

Chen, Yumin; Deng, Ke; Qiu, Xiaohui; Wang, Chen

2013-01-01

362

Single molecule desorption studies on immobilized nanoclay particle surfaces.  

PubMed

AFM-based single molecule force spectroscopy was performed on sheetlike inorganic particles of Na-montmorillonite to study the pH-dependent adsorption and desorption behavior of polyelectrolytes in aqueous solutions. Polyallylamine macromolecules were covalently attached on gold-coated AFM cantilevers. Heterogeneous surfaces were formed by immobilizing the nanoclay sheets on mica-stripped ultraflat Au(111) surfaces using aminothiol chemistry. Because of the constant surface charge of the particles over a wide pH range, polymer line charge density was the only parameter that affected the adsorption and desorption behavior when the ionic concentration was kept constant. Polarization modulation infrared-reflection absorption spectroscopy (PM-IRRAS) was performed on cast polyallylamine films to study the pH-dependent charge density of polyallylamine molecules. A good correlation was found between the line charge density and the adsorption characteristics of polyallylamine. PMID:20230055

Ozkaya, Berkem; Ozcan, Ozlem; Thissen, Peter; Grundmeier, Guido

2010-06-01

363

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

E-print Network

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

Shoichi Toyabe; Eiro Muneyuki

2015-01-16

364

Three dimensional single molecule localization using a phase retrieved pupilfunction  

PubMed Central

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

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

2013-01-01

365

Connecting Rare DNA Conformations and Surface Dynamics using Single-Molecule Resonance Energy Transfer  

PubMed Central

A mechanistic understanding of single-stranded DNA (ssDNA) behavior in the near-surface environment is critical to advancing DNA-directed self-assembled nanomaterials. A new approach is described that uses total internal reflection fluorescence microscopy to measure resonance energy transfer at the single-molecule level, providing a mechanistic understanding of the connection between molecular conformation and interfacial dynamics near amine-modified surfaces. Large numbers (>105) of ssDNA trajectories were observed, permitting dynamic correlation of molecular conformation with desorption and surface mobility. On the basis of dynamic behavior, molecules could be designated as members of the more common coiled population or a rare, weakly bound conformation. Molecules in the coiled state generally exhibited slow diffusion and conformational fluctuations that decreased with increasing average end-to-end distance. Lattice simulations of adsorbed self-avoiding polymers successfully predicted these trends. In contrast, the weakly bound conformation, observed in about 5% of molecules, had a large end-to-end distance but demonstrated conformational fluctuations that were much higher than predicted by simulations for adsorbed flexible chains. This conformation correlated positively with desorption events and led to fast diffusion, indicating weak surface associations. Understanding the role of the weakly bound conformation in DNA hybridization, and how solution conditions and surface properties may favor it, could lead to improved self-assembled nanomaterials. PMID:21942411

Kastantin, Mark; Schwartz, Daniel K.

2011-01-01

366

Single-molecule FRET measures bends and kinks in DNA.  

PubMed

We present advances in the use of single-molecule FRET measurements with flexibly linked dyes to derive full 3D structures of DNA constructs based on absolute distances. The resolution obtained by this single-molecule approach harbours the potential to study in detail also protein- or damage-induced DNA bending. If one is to generate a geometric structural model, distances between fixed positions are needed. These are usually not experimentally accessible because of unknown fluorophore-linker mobility effects that lead to a distribution of FRET efficiencies and distances. To solve this problem, we performed studies on DNA double-helices by systematically varying donor acceptor distances from 2 to 10 nm. Analysis of dye-dye quenching and fluorescence anisotropy measurements reveal slow positional and fast orientational fluorophore dynamics, that results in an isotropic average of the FRET efficiency. We use a nonlinear conversion function based on MD simulations that allows us to include this effect in the calculation of absolute FRET distances. To obtain unique structures, we performed a quantitative statistical analysis for the conformational search in full space based on triangulation, which uses the known helical nucleic acid features. Our higher accuracy allowed the detection of sequence-dependent DNA bending by 16 degrees . For DNA with bulged adenosines, we also quantified the kink angles introduced by the insertion of 1, 3 and 5 bases to be 32 degrees +/- 6 degrees , 56 degrees +/- 4 degrees and 73 +/- 2 degrees , respectively. Moreover, the rotation angles and shifts of the helices were calculated to describe the relative orientation of the two arms in detail. PMID:19020079

Wozniak, Anna K; Schröder, Gunnar F; Grubmüller, Helmut; Seidel, Claus A M; Oesterhelt, Filipp

2008-11-25

367

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

PubMed

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

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

2010-03-01

368

Coherent control of single molecules at room temperature.  

PubMed

The detection of individual molecules allows to unwrap the inhomogeneously broadened ensemble and reveal the spatial disorder and temporal dynamics of single entities. During 20 years of increasing sophistication this approach has provided valuable insights into biomolecular interactions, cellular processes, polymer dynamics, etc. Unfortunately the detection of fluorescence, i.e. incoherent spontaneous emission, has essentially kept the time resolution of the single molecule approach out of the range of ultrafast coherent processes. In parallel coherent control of quantum interferences has developed as a powerful method to study and actively steer ultrafast molecular interactions and energy conversion processes. However the degree of coherent control that can be reached in ensembles is restricted, due to the intrinsic inhomogeneity of the synchronized subset. Clearly the only way to overcome spatio-temporal disorder and achieve key control is by addressing individual units: coherent control of single molecules. Here we report the observation and manipulation of vibrational wave-packet interference in individual molecules at ambient conditions. We show that adapting the time and phase distribution of the optical excitation field to the dynamics of each molecule results in a superior degree of control compared to the ensemble approach. Phase reversal does invert the molecular response, confirming the control of quantum coherence. Time-phase maps show a rich diversity in excited state dynamics between different, yet chemically identical, molecules. The presented approach is promising for single-unit coherent control in multichromophoric systems. Especially the role of coherence in the energy transfer of single antenna complexes under physiological conditions is subject of great attention. Now the role of energy disorder and variation in coupling strength can be explored, beyond the inhomogeneously broadened ensemble. PMID:22452073

Brinks, Daan; Hildner, Richard; Stefani, Fernando D; van Hulst, Niek F

2011-01-01

369

Single-cell and single-molecule laser biotechnology  

NASA Astrophysics Data System (ADS)

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.

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

1996-01-01

370

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

PubMed

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

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

2014-02-01

371

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

PubMed Central

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

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

2012-01-01

372

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

NASA Astrophysics Data System (ADS)

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

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

2014-08-01

373

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

PubMed

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

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

374

Quantum tunneling of magnetization in lanthanide single-molecule magnets, bis(phthalocyaninato)terbium and bis(phthalocyaninato)-dysprosium anions  

Microsoft Academic Search

Magnetization versus field measurements were performed on single crystals of [(Pc)2TbIII0.02YIII0.98]^TBA+ and [(Pc)2DyIII0.02YIII0.98]^TBA+ (Pc: phthalocyaninato, TBA: tetrabutylammonium) at 0.04 K. The [(Pc)2TbIII] complex, the first lanthanide single-molecule magnet, exhibited clear staircase-like structures, which are assigned to resonant quantum tunneling between entangled states of the electron and nuclear spin systems.

Naoto Ishikawa; Miki Sugita; Wolfgang Wernsdorfer

2005-01-01

375

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

SciTech Connect

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.

Hopkins, Patrick E.

2011-10-01

376

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

SciTech Connect

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

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

2014-05-05

377

Single Molecule Screening of Disease DNA Without Amplification  

SciTech Connect

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.

Ji-Young Lee

2006-12-12

378

Single-molecule fluorescence imaging of DNA at a potential-controlled interface.  

PubMed

Many interfacial chemical phenomena are governed in part by electrostatic interactions between polyelectrolytes and charged surfaces; these phenomena can influence the performance of biosensors, adsorption of natural polyelectrolytes (humic substances) on soils, and production of polyelectrolyte multilayer films. In order to understand electrostatic interactions that govern these phenomena, we have investigated the behavior of a model polyelectrolyte, 15 kbp fluorescently labeled plasmid DNA, near a polarized indium tin oxide (ITO) electrode surface. The interfacial population of DNA was monitored in situ by imaging individual molecules through the transparent electrode using total-internal-reflection fluorescence microscopy. At applied potentials of +0.8 V versus Ag/AgCl, the DNA interfacial population near the ITO surface can be increased by 2 orders of magnitude relative to bulk solution. The DNA molecules attracted to the interface do not adsorb to ITO, but rather they remain mobile with a diffusion coefficient comparable to free solution. Ionic strength strongly influences the sensitivity of the interfacial population to applied potential, where the increase in the interfacial population over a +300 mV change in potential varies from 20% in 30 mM ionic strength to over 25-fold in 300 ?M electrolyte. The DNA accumulation with applied potential was interpreted using a simple Boltzmann model to predict average ion concentrations in the electrical double layer and the fraction of interfacial detection volume that is influenced by applied potential. A Gouy-Chapman model was also applied to the data to account for the dependence of the ion population on distance from the electrode surface, which indicates that the net charge on DNA responsible for interactions with the polarized surface is low, on the order of one excess electron. The results are consistent with a small fraction of the DNA plasmid being resident in the double-layer and with counterions screening much of the DNA excess charge. PMID:23741971

Peterson, Eric M; Harris, Joel M

2013-07-01

379

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

PubMed Central

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

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

2014-01-01

380

High-throughput single-molecule studies of protein-DNA interactions.  

PubMed

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

Robison, Aaron D; Finkelstein, Ilya J

2014-10-01

381

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

SciTech Connect

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.

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

2011-11-03

382

SINGLE MOLECULE APPROACHES TO BIOLOGY, 2010 GORDON RESEARCH CONFERENCE, JUNE 27JULY 2, 2010, ITALY  

Microsoft Academic Search

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

William Moerner

2010-01-01

383

Applications of single-molecule microscopy to problems in dyed composite materials  

Microsoft Academic Search

Recent progress in single-molecule spectroscopy of dyed composite materials is reviewed. In particular, single-molecule studies of dyed polymer films and dye inclusion crystals are described that seek to understand local guest-host interactions and environmental heterogeneity. Single-molecule orientational studies of chromophores in polymer films and mixed crystals are discussed with particular relevance to materials and device applications. Studies of single-molecular reorientational

Kristin L. Wustholz; Daniel R. B. Sluss; Bart Kahr; Philip J. Reid

2008-01-01

384

Applications of single-molecule microscopy to problems in dyed composite materials  

Microsoft Academic Search

Recent progress in single-molecule spectroscopy of dyed composite materials is reviewed. In particular, single-molecule studies of dyed polymer films and dye inclusion crystals are described that seek to understand local guest–host interactions and environmental heterogeneity. Single-molecule orientational studies of chromophores in polymer films and mixed crystals are discussed with particular relevance to materials and device applications. Studies of single-molecular reorientational

Kristin L. Wustholz; Daniel R. B. Sluss; Bart Kahr; Philip J. Reid

2008-01-01

385

Single-Molecule Mechanical Identification and Sequencing: Proof of Principle  

PubMed Central

High-throughput low-cost DNA sequencing has emerged as one of the challenges of the post-genomic era. Here we present the proof of concept for a new single-molecule platform that allows for DNA identification and sequencing. In contrast with most present methods, our scheme is not based on the detection of the fluorescence of incorporated nucleotides, but rather on the measurement of a DNA hairpin length. By cyclically modulating the force pulling on small magnetic beads tethered by a hairpin to a surface, one can unzip and rezip the molecule. In the presence of complementary oligonucleotides in solution, reziping may be transiently interrupted by the hybrids they form with the hairpin. By measuring the extension of the blocked hairpin, one can determine the position of the hybrid along the molecule with nearly single base precision. Our approach, well adapted to a high-throughput scheme, can be used to identify a DNA fragment of known sequence among a sample of various fragments and to sequence an unknown DNA fragment by hybridization or ligation. PMID:22406857

Ding, Fangyuan; Manosas, Maria; Spiering, Michelle M.; Benkovic, Stephen J.; Bensimon, David; Allemand, Jean-François; Croquette, Vincent

2012-01-01

386

Single Molecule Epigenetic Analysis in a Nanofluidic Channel  

PubMed Central

Epigenetic states are governed by DNA methylation and a host of modifications to histones bound with DNA. These states are essential for proper developmentally regulated gene expression and are perturbed in many diseases. There is great interest in identifying epigenetic mark placement genome-wide and understanding how these marks vary among cell types, with changes in environment or according to health and disease status. Current epigenomic analyses employ bisulfite sequencing and chromatin immunoprecipitation, but query only one type of epigenetic mark at a time, DNA methylation or histone modifications, and often require substantial input material. To overcome these limitations, we established a method using nanofluidics and multi-color fluorescence microscopy to detect DNA and histones in individual chromatin fragments at about 10 Mbp/min. We demonstrated its utility for epigenetic analysis by identifying DNA methylation on individual molecules. This technique will provide the unprecedented opportunity for genome-wide, simultaneous analysis of multiple epigenetic states on single molecules using femtogram quantities of material. PMID:20184350

Cipriany, Benjamin R.; Zhao, Ruqian; Murphy, Patrick J.; Levy, Stephen L.; Tan, Christine P.; Craighead, Harold G.; Soloway, Paul D.

2010-01-01

387

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

PubMed Central

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

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

2009-01-01

388

Single-molecule imaging in live cell using gold nanoparticles.  

PubMed

Optimal single particle tracking experiments in live cells requires small and photostable probes, which do not modify the behavior of the molecule of interest. Current fluorescence-based microscopy of single molecules and nanoparticles is often limited by bleaching and blinking or by the probe size. As an alternative, we present in this chapter the synthesis of a small and highly specific gold nanoprobe whose detection is based on its absorption properties. We first present a protocol to synthesize 5-nm-diameter gold nanoparticles and functionalize them with a nanobody, a single-domain antibody from camelid, targeting the widespread green fluorescent protein (GFP)-tagged proteins with a high affinity. Then we describe how to detect and track these individual gold nanoparticles in live cell using photothermal imaging microscopy. The combination of a probe with small size, perfect photostability, high specificity, and versatility through the vast existing library of GFP-proteins, with a highly sensitive detection technique enables long-term tracking of proteins with minimal hindrance in confined and crowded environments such as intracellular space. PMID:25640421

Leduc, Cécile; Si, Satyabrata; Gautier, Jérémie J; Gao, Zhenghong; Shibu, Edakkattuparambil S; Gautreau, Alexis; Giannone, Grégory; Cognet, Laurent; Lounis, Brahim

2015-01-01

389

DNA Y structure: a versatile, multidimensional single molecule assay.  

PubMed

Optical trapping is a powerful single molecule technique used to study dynamic biomolecular events, especially those involving DNA and DNA-binding proteins. Current implementations usually involve only one of stretching, unzipping, or twisting DNA along one dimension. To expand the capabilities of optical trapping for more complex measurements would require a multidimensional technique that combines all of these manipulations in a single experiment. Here, we report the development and utilization of such a novel optical trapping assay based on a three-branch DNA construct, termed a "Y structure". This multidimensional assay allows precise, real-time tracking of multiple configurational changes. When the Y structure template is unzipped under both force and torque, the force and extension of all three branches can be determined simultaneously. Moreover, the assay is readily compatible with fluorescence, as demonstrated by unzipping through a fluorescently labeled, paused transcription complex. This novel assay thus allows for the visualization and precision mapping of complex interactions of biomechanical events. PMID:25291441

Inman, James T; Smith, Benjamin Y; Hall, Michael A; Forties, Robert A; Jin, Jing; Sethna, James P; Wang, Michelle D

2014-11-12

390

Multiplex single-molecule interaction profiling of DNA barcoded proteins  

PubMed Central

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

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

2014-01-01

391

Noise characterization of metal-single molecule contacts  

NASA Astrophysics Data System (ADS)

Noise spectra of molecule-free and molecule-containing mechanically controllable break junctions were investigated. The molecule-free junctions revealed typical 1 /f noise characteristics. We studied three molecules as they bridged the electrodes: 11-mercaptoundecanoicacid, 1,8-octanedithiol, and 1,4-benzenedithiol, which possess different bonding strengths. For all of them, an additional Lorentzian-shape 1/f2 noise component was registered with a characteristic frequency when the electrodes were bridged by an individual molecule. Measurements of time-dependent voltage fluctuations for the molecule-containing junctions bring out two-current state fluctuations, which in the frequency domain correspond to the 1/f2 noise. Moreover, it is revealed that characteristic frequencies of these noise components are independent of molecule bonding strengths at the interface, but correlate with the molecule weights and current amplitudes in the lock-in state, in which the electrode gap is bridged by a single molecule. We attribute the noise monitored during charge transport through a molecular junction to the current induced molecular reconfigurations and suggest that the noise analysis can be used for characterization of metal-molecule coupling.

Xiang, D.; Sydoruk, V.; Vitusevich, S.; Petrychuk, M. V.; Offenhäusser, A.; Kochelap, V. A.; Belyaev, A. E.; Mayer, D.

2015-02-01

392

A single-molecule view of gene regulation in cancer  

NASA Astrophysics Data System (ADS)

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.

Larson, Daniel

2013-03-01

393

A single molecule study of cellulase hydrolysis of crystalline cellulose  

NASA Astrophysics Data System (ADS)

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

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

2010-02-01

394

Single molecule analysis of Trypanosoma brucei DNA replication dynamics.  

PubMed

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

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

395

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

PubMed Central

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

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

2012-01-01

396

Optical Microcavity: Sensing down to Single Molecules and Atoms  

PubMed Central

This review article discusses fundamentals of dielectric, low-loss, optical micro-resonator sensing, including figures of merit and a variety of microcavity designs, and future perspectives in microcavity-based optical sensing. Resonance frequency and quality (Q) factor are altered as a means of detecting a small system perturbation, resulting in realization of optical sensing of a small amount of sample materials, down to even single molecules. Sensitivity, Q factor, minimum detectable index change, noises (in sensor system components and microcavity system including environments), microcavity size, and mode volume are essential parameters to be considered for optical sensing applications. Whispering gallery mode, photonic crystal, and slot-type microcavities typically provide compact, high-quality optical resonance modes for optical sensing applications. Surface Bloch modes induced on photonic crystals are shown to be a promising candidate thanks to large field overlap with a sample and ultra-high-Q resonances. Quantum optics effects based on microcavity quantum electrodynamics (QED) would provide novel single-photo-level detection of even single atoms and molecules via detection of doublet vacuum Rabi splitting peaks in strong coupling. PMID:22319393

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

2011-01-01

397

Classification of dynamical diffusion states in single molecule tracking microscopy.  

PubMed

Single molecule tracking of membrane proteins by fluorescence microscopy is a promising method to investigate dynamic processes in live cells. Translating the trajectories of proteins to biological implications, such as protein interactions, requires the classification of protein motion within the trajectories. Spatial information of protein motion may reveal where the protein interacts with cellular structures, because binding of proteins to such structures often alters their diffusion speed. For dynamic diffusion systems, we provide an analytical framework to determine in which diffusion state a molecule is residing during the course of its trajectory. We compare different methods for the quantification of motion to utilize this framework for the classification of two diffusion states (two populations with different diffusion speed). We found that a gyration quantification method and a Bayesian statistics-based method are the most accurate in diffusion-state classification for realistic experimentally obtained datasets, of which the gyration method is much less computationally demanding. After classification of the diffusion, the lifetime of the states can be determined, and images of the diffusion states can be reconstructed at high resolution. Simulations validate these applications. We apply the classification and its applications to experimental data to demonstrate the potential of this approach to obtain further insights into the dynamics of cell membrane proteins. PMID:25099798

Bosch, Peter J; Kanger, Johannes S; Subramaniam, Vinod

2014-08-01

398

Single molecule analysis of Trypanosoma brucei DNA replication dynamics  

PubMed Central

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

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

399

Single Molecule Views of Protein Movement on Single Stranded DNA  

PubMed Central

The advent of new technologies allowing the study of single biological molecules continues to have a major impact on studies of interacting systems as well as enzyme reactions. These approaches (fluorescence, optical and magnetic “tweezers”), in combination with ensemble methods, have been particularly useful for mechanistic studies of protein-nucleic acid interactions and enzymes that function on nucleic acids. We review progress in the use of single molecule methods to observe and perturb the activities of proteins and enzymes that function on flexible single stranded DNA. These include single stranded (ss)DNA binding (SSB) proteins, recombinases (RecA/Rad51) and helicases/translocases that operate as motor proteins and play central roles in genome maintenance. We emphasize methods that have been used to detect and study the movement of these proteins (both ATP-dependent directional and random movement) along the ssDNA and the mechanistic and functional information that can result from detailed analysis of such movement. PMID:22404684

Ha, Taekjip; Kozlov, Alexander G.; Lohman, Timothy M.

2013-01-01

400

Whole-mount single molecule FISH method for zebrafish embryo  

PubMed Central

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

Oka, Yuma; Sato, Thomas N.

2015-01-01

401

Locked nucleic acid oligomers as handles for single molecule manipulation  

PubMed Central

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

Berezney, John P.; Saleh, Omar A.

2014-01-01

402

A Theoretical Justification for Single Molecule Peptide Sequencing  

PubMed Central

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

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

2015-01-01

403

Quantum interference in off-resonant transport through single molecules  

NASA Astrophysics Data System (ADS)

We provide a simple set of rules for predicting interference effects in off-resonant transport through single molecule junctions. These effects fall into two classes, showing, respectively, an odd or an even number of nodes in the linear conductance within a given molecular charge state, and we demonstrate how to decide the interference class directly from the contacting geometry. For neutral alternant hydrocarbons, we employ the Coulson-Rushbrooke-McLachlan pairing theorem to show that the interference class is decided simply by tunneling on and off the molecule from same or different sublattices. More generally, we investigate a range of smaller molecules by means of exact diagonalization combined with a perturbative treatment of the molecule-lead tunnel coupling. While these results generally agree well with GW calculations, they are shown to be at odds with simpler mean-field treatments. For molecules with spin-degenerate ground states, we show that for most junctions interference causes no transmission nodes, but we argue that it may lead to a nonstandard gate dependence of the zero-bias Kondo resonance.

Pedersen, Kim G. L.; Strange, Mikkel; Leijnse, Martin; Hedegârd, Per; Solomon, Gemma C.; Paaske, Jens

2014-09-01

404

Mechanical fatigue in repetitively stretched single molecules of titin.  

PubMed Central

Relaxed striated muscle cells exhibit mechanical fatigue when exposed to repeated stretch and release cycles. To understand the molecular basis of such mechanical fatigue, single molecules of the giant filamentous protein titin, which is the main determinant of sarcomeric elasticity, were repetitively stretched and released while their force response was characterized with optical tweezers. During repeated stretch-release cycles titin becomes mechanically worn out in a process we call molecular fatigue. The process is characterized by a progressive shift of the stretch-force curve toward increasing end-to-end lengths, indicating that repeated mechanical cycles increase titin's effective contour length. Molecular fatigue occurs only in a restricted force range (0-25 pN) during the initial part of the stretch half-cycle, whereas the rest of the force response is repeated from one mechanical cycle to the other. Protein-folding models fail to explain molecular fatigue on the basis of an incomplete refolding of titin's globular domains. Rather, the process apparently derives from the formation of labile nonspecific bonds cross-linking various sites along a pre-unfolded titin segment. Because titin's molecular fatigue occurs in a physiologically relevant force range, the process may play an important role in dynamically adjusting muscle's response to the recent history of mechanical perturbations. PMID:11159452

Kellermayer, M S; Smith, S B; Bustamante, C; Granzier, H L

2001-01-01

405

Temperature-cycle microscopy reveals single-molecule conformational heterogeneity.  

PubMed

Our previous temperature-cycle study reported FRET transitions between different states on FRET-labeled polyprolines [Yuan et al., PCCP, 2011, 13, 1762]. The conformational origin of such transitions, however, was left open. In this work, we apply temperature-cycle microscopy of single FRET-labeled polyproline and dsDNA molecules and compare their responses to resolve the conformational origin of different FRET states. We observe different steady-state FRET distributions and different temperature-cycle responses in the two samples. Our temperature-cycle results on single molecules resemble the results in steady-state measurements but reveal a dark state which could not be observed otherwise. By comparing the timescales and probabilities of different FRET states in temperature-cycle traces, we assign the conformational heterogeneity reflected by different FRET states to linker dynamics, dye-chain and dye-dye interactions. The dark state and low-FRET state are likely due to dye-dye interactions at short separations. PMID:25659944

Yuan, Haifeng; Gaiduk, Alexander; Siekierzycka, Joanna R; Fujiyoshi, Satoru; Matsushita, Michio; Nettels, Daniel; Schuler, Benjamin; Seidel, Claus A M; Orrit, Michel

2015-02-18

406

Whole-mount single molecule FISH method for zebrafish embryo.  

PubMed

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

Oka, Yuma; Sato, Thomas N

2015-01-01

407

A theoretical justification for single molecule peptide sequencing.  

PubMed

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

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

2015-02-01

408

Competition between Supercoils and Toroids in Single Molecule DNA Condensation  

PubMed Central

The condensation of free DNA into toroidal structures in the presence of multivalent ions and polypeptides is well known. Recent single molecule experiments have shown that condensation into toroids occurs even when the DNA molecule is subjected to tensile forces. Here we show that the combined tension and torsion of DNA in the presence of condensing agents dramatically modifies this picture by introducing supercoiled DNA as a competing structure in addition to toroids. We combine a fluctuating elastic rod model of DNA with phenomenological models for DNA interaction in the presence of condensing agents to compute the minimum energy configuration for given tension and end-rotations. We show that for each tension there is a critical number of end-rotations above which the supercoiled solution is preferred and below which toroids are the preferred state. Our results closely match recent extension rotation experiments on DNA in the presence of spermine and other condensing agents. Motivated by this, we construct a phase diagram for the preferred DNA states as a function of tension and applied end-rotations and identify a region where new experiments or simulations are needed to determine the preferred state. PMID:22828338

Argudo, David; Purohit, Prashant K.

2012-01-01

409

Single Molecule Analysis of Serotonin Transporter Regulation Using Quantum Dots  

NASA Astrophysics Data System (ADS)

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.

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

2011-03-01

410

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

DOEpatents

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.

Lee, James W.; Thundat, Thomas G.

2006-04-25

411

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

SciTech Connect

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.

Bennett, Kochise, E-mail: kcbennet@uci.edu; Biggs, Jason D.; Zhang, Yu; Dorfman, Konstantin E.; Mukamel, Shaul, E-mail: smukamel@uci.edu [University of California, Irvine, California 92697-2025 (United States)

2014-05-28

412

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

NASA Astrophysics Data System (ADS)

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.

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

2014-05-01

413

Electrochemical control of single-molecule conductance by Fermi-level tuning and conjugation switching.  

PubMed

Controlling charge transport through a single molecule connected to metallic electrodes remains one of the most fundamental challenges of nanoelectronics. Here we use electrochemical gating to reversibly tune the conductance of two different organic molecules, both containing anthraquinone (AQ) centers, over >1 order of magnitude. For electrode potentials outside the redox-active region, the effect of the gate is simply to shift the molecular energy levels relative to the metal Fermi level. At the redox potential, the conductance changes abruptly as the AQ unit is oxidized/reduced with an accompanying change in the conjugation pattern between linear and cross conjugation. The most significant change in conductance is observed when the electron pathway connecting the two electrodes is via the AQ unit. This is consistent with the expected occurrence of destructive quantum interference in that case. The experimental results are supported by an excellent agreement with ab initio transport calculations. PMID:25494539

Baghernejad, Masoud; Zhao, Xiaotao; Baruël Ørnsø, Kristian; Füeg, Michael; Moreno-García, Pavel; Rudnev, Alexander V; Kaliginedi, Veerabhadrarao; Vesztergom, Soma; Huang, Cancan; Hong, Wenjing; Broekmann, Peter; Wandlowski, Thomas; Thygesen, Kristian S; Bryce, Martin R

2014-12-31

414

Many-body transitions in a single molecule visualized by scanning tunnelling microscopy  

NASA Astrophysics Data System (ADS)

Many-body effects arise from the collective behaviour of large numbers of interacting particles, for example, electrons, and the properties of such a system cannot be understood considering only single or non-interacting particles. Despite the generality of the many-body picture, there are only a few examples of experimentally observing such effects in molecular systems. Measurements of the local density of states of single molecules by scanning tunnelling spectroscopy is usually interpreted in terms of single-particle molecular orbitals. Here, we show that the simple single-particle picture fails qualitatively to account for the resonances in the tunnelling spectra of different charge states of cobalt phthalocyanine molecules. Instead, these resonances can be understood as a series of many-body excitations of the different ground states of the molecule. Our theoretical approach opens an accessible route beyond the single-particle picture in quantifying many-body states in molecules.

Schulz, Fabian; Ijäs, Mari; Drost, Robert; Hämäläinen, Sampsa K.; Harju, Ari; Seitsonen, Ari P.; Liljeroth, Peter

2015-03-01

415

Single-Molecule Fluorescence Studies of Protein Folding and Conformational Xavier Michalet,* Shimon Weiss, and Marcus Jager*  

E-print Network

Single-Molecule Fluorescence Studies of Protein Folding and Conformational Dynamics Xavier Michalet Diagram 1788 2.2. Fluorescence Polarization 1788 2.3. FRET 1789 2.4. Single-Molecule ET 1789 3. Single-Molecule Data Acquisition and Analysis Methods 1790 3.1. Single-Molecule Fluorescence Experimental Setups 1790 3

Michalet, Xavier

416

Condensation of two-dimensional oxide-interfacial charges into one-dimensional electron chains by the misfit-dislocation strain field.  

PubMed

The success of semiconductor technology is largely ascribed to controlled impacts of strains and defects on the two-dimensional interfacial charges. Interfacial charges also appear in oxide heterojunctions such as LaAlO3/SrTiO3 and (Nd0.35Sr0.65)MnO3/SrTiO3. How the localized strain field of one-dimensional misfit dislocations, defects resulting from the intrinsic misfit strains, would affect the extended oxide-interfacial charges is intriguing and remains unresolved. Here we show the atomic-scale observation of one-dimensional electron chains formed in (Nd0.35Sr0.65)MnO3/SrTiO3 by the condensation of characteristic two-dimensional interfacial charges into the strain field of periodically arrayed misfit dislocations, using chemical mapping and quantification by scanning transmission electron microscopy. The strain-relaxed inter-dislocation regions are readily charge depleted, otherwise decorated by the pristine charges, and the corresponding total-energy calculations unravel the undocumented charge-reservoir role played by the dislocation-strain field. This two-dimensional-to-one-dimensional electronic condensation represents a novel electronic-inhomogeneity mechanism at oxide interfaces and could stimulate further studies of one-dimensional electron density in oxide heterostructures. PMID:24663109

Chang, C-P; Chu, M-W; Jeng, H T; Cheng, S-L; Lin, J G; Yang, J-R; Chen, C H

2014-01-01

417

Condensation of two-dimensional oxide-interfacial charges into one-dimensional electron chains by the misfit-dislocation strain field  

NASA Astrophysics Data System (ADS)

The success of semiconductor technology is largely ascribed to controlled impacts of strains and defects on the two-dimensional interfacial charges. Interfacial charges also appear in oxide heterojunctions such as LaAlO3/SrTiO3 and (Nd0.35Sr0.65)MnO3/SrTiO3. How the localized strain field of one-dimensional misfit dislocations, defects resulting from the intrinsic misfit strains, would affect the extended oxide-interfacial charges is intriguing and remains unresolved. Here we show the atomic-scale observation of one-dimensional electron chains formed in (Nd0.35Sr0.65)MnO3/SrTiO3 by the condensation of characteristic two-dimensional interfacial charges into the strain field of periodically arrayed misfit dislocations, using chemical mapping and quantification by scanning transmission electron microscopy. The strain-relaxed inter-dislocation regions are readily charge depleted, otherwise decorated by the pristine charges, and the corresponding total-energy calculations unravel the undocumented charge-reservoir role played by the dislocation-strain field. This two-dimensional-to-one-dimensional electronic condensation represents a novel electronic-inhomogeneity mechanism at oxide interfaces and could stimulate further studies of one-dimensional electron density in oxide heterostructures.

Chang, C.-P.; Chu, M.-W.; Jeng, H. T.; Cheng, S.-L.; Lin, J. G.; Yang, J.-R.; Chen, C. H.

2014-03-01

418

Partially condensed DNA conformations observed by single molecule fluorescence microscopy.  

PubMed Central

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

Serwer, P; Hayes, S J

2001-01-01

419

Single-molecule manipulation measurements of polymer/solution interactions  

NASA Astrophysics Data System (ADS)

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

Dittmore, Andrew N.

420

Single molecule fluorescence probes dynamics of barrier crossing  

PubMed Central

Kramers developed the theory on how chemical reaction rates are influenced by the viscosity of the medium1,2. At the viscosity of water, the kinetics of unimolecular reactions are described by diffusion of a Brownian particle over a free-energy barrier separating reactants and products. For reactions in solution this famous theory extended Eyring's transition state theory, and is widely applied in physics, chemistry, and biology, including reactions as complex as protein folding3,4. Because the diffusion coefficient of Kramers theory is determined by the dynamics in the sparsely-populated region of the barrier top, its properties have not been directly measured for any molecular system. Here we show that the Kramers diffusion coefficient and free energy barrier can be characterized by measuring the temperature- and viscosity-dependence of the transition path time for protein folding. The transition path is the small fraction of an equilibrium trajectory for a single molecule when the free-energy barrier separating two states is actually crossed (Fig. 1a). Its duration, the transition path time, can now be determined from photon trajectories for single protein molecules undergoing folding/unfolding transitions5. Our finding of a long transition path time with an unusually small solvent viscosity-dependence suggests that internal friction as well as solvent friction determine the Kramers diffusion coefficient for ?-helical proteins, as opposed to a breakdown of his theory that occurs for many small-molecule reactions2. It is noteworthy that the new and fundamental information concerning Kramers theory and the dynamics of barrier crossings obtained here come from experiments on a protein rather than a much simpler chemical or physical system. PMID:24153185

Chung, Hoi Sung; Eaton, William A.

2013-01-01

421

Single-molecule fluorescence probes dynamics of barrier crossing  

NASA Astrophysics Data System (ADS)

Kramers developed the theory on how chemical reaction rates are influenced by the viscosity of the medium. At the viscosity of water, the kinetics of unimolecular reactions are described by diffusion of a Brownian particle over a free-energy barrier separating reactants and products. For reactions in solution this famous theory extended Eyring's transition state theory, and is widely applied in physics, chemistry and biology, including to reactions as complex as protein folding. Because the diffusion coefficient of Kramers' theory is determined by the dynamics in the sparsely populated region of the barrier top, its properties have not been directly measured for any molecular system. Here we show that the Kramers diffusion coefficient and free-energy barrier can be characterized by measuring the temperature- and viscosity-dependence of the transition path time for protein folding. The transition path is the small fraction of an equilibrium trajectory for a single molecule when the free-energy barrier separating two states is actually crossed. Its duration, the transition path time, can now be determined from photon trajectories for single protein molecules undergoing folding/unfolding transitions. Our finding of a long transition path time with an unusually small solvent viscosity dependence suggests that internal friction as well as solvent friction determine the Kramers diffusion coefficient for ?-helical proteins, as opposed to a breakdown of his theory, which occurs for many small-molecule reactions. It is noteworthy that the new and fundamental information concerning Kramers' theory and the dynamics of barrier crossings obtained here come from experiments on a protein rather than a much simpler chemical or physical system.

Chung, Hoi Sung; Eaton, William A.

2013-10-01

422

LETTER doi:10.1038/nature13761 Multiplex single-molecule interaction profiling of  

E-print Network

LETTER doi:10.1038/nature13761 Multiplex single-molecule interaction profiling of DNA-seq) technology for parallel protein interaction profiling leveraging single-molecule advantages. DNA barcodes,2 In contrast with advances in massively parallel DNA sequencing1 , high-throughput protein analyses2

423

Image Analysis of Defocused Single-Molecule Images for Three-Dimensional Molecule Orientation Studies  

E-print Network

Image Analysis of Defocused Single-Molecule Images for Three-Dimensional Molecule Orientation-squares analysis of fitting a discrete set of master patterns against measured images. This algorithm has been applied to determine three- dimensional molecule orientations in defocused single-molecule images

Enderlein, Jörg

424

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

DOEpatents

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.

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

2009-12-29

425

Large single-molecule fluorescence enhancements produced by a bowtie nanoantenna  

E-print Network

Large single-molecule fluorescence enhancements produced by a bowtie nanoantenna Anika Kinkhabwala1 mismatch between light and nanoscale objects such as single molecules, it is important to be able to control light­molecule interactions1­4. Plasmonic nanoantennas create highly enhanced local fields when

Fan, Shanhui

426

Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures  

E-print Network

Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures, 2004 Here we present a technique called single-molecule high-resolution colocalization (SHREC molecules as probes, we are able to circumvent the Rayleigh criterion and measure distances much smaller

Spudich, James A.

427

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

E-print Network

Single-molecule studies of repressor­DNA interactions show long-range interactions Y. M. Wang performed single-molecule studies of GFP­LacI repressor proteins bound to bacteriophage DNA containing a 256 studies is to obtain information from single protein­DNA molecules, rather than ensembles of millions

428

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

E-print Network

Dynamics of Single-Molecule Rotations on Surfaces that Depend on Symmetry, Interactions Rotating surface-mounted molecules have attracted the attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule

429

Enhancing single-molecule photostability by optical feedback from quantum jump detection  

E-print Network

Enhancing single-molecule photostability by optical feedback from quantum jump detection V. Jacques; published online 20 November 2008 We report an optical technique that yields an enhancement of single-molecule of the molecule to the triplet state is optically detected. The resulting improvement in photostability

Murray, John D.

430

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

NSDL National Science Digital Library

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

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

2005-02-01

431

Full Counting Statistics of Strongly Non-Ohmic Transport through Single Molecules Jens Koch,1  

E-print Network

Full Counting Statistics of Strongly Non-Ohmic Transport through Single Molecules Jens Koch,1 M. E. Raikh,2 and Felix von Oppen1 1 Institut fu¨r Theoretische Physik, Freie Universita¨t Berlin, Arnimallee statistics of charge transport through single molecules, strongly coupled to a weakly damped vibrational mode

von Oppen, Felix

432

Probing the conductance superposition law in single-molecule circuits with parallel paths  

E-print Network

Probing the conductance superposition law in single-molecule circuits with parallel paths H.S. Hybertsen3 * According to Kirchhoff's circuit laws, the net conductance of two parallel components investigate the conductance superposition law for parallel components in single-molecule circuits

Venkataraman, Latha

433

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

E-print Network

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

Miekisz, Jacek

434

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

E-print Network

to characterize in ensemble-averaged measurements. The single-molecule approach enables studying the catalysis single-molecule Áuorescence studies of single Au-nanoparticle catalysis, focusing on the theoretical these questions, one needs to study nanoparticle catalysis at the single-particle level. Several research groups

Chen, Peng

435

Optical Recognition of Converted DNA Nucleotides for Single-Molecule DNA  

E-print Network

Optical Recognition of Converted DNA Nucleotides for Single-Molecule DNA Sequencing Using Nanopore ABSTRACT We demonstrate the feasibility of a nanopore based single-molecule DNA sequencing method, which conversion N anopore-based DNA sequencing is widely consid- ered to be a promising next generation sequencing

436

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

E-print Network

atomic force microscopy (AFM) imaging and single molecule force spectroscopy (SMFS) to study bProbing protein conformations at the oil droplet­water interface using single-molecule force-lactoglobulin (b-LG) molecules localized at the interface between oil droplets and water. To immobilize the oil

Dutcher, John

437

Single-molecule binding experiments on long time scales Mark P. Elenko,1  

E-print Network

of Physics. doi:10.1063/1.3473936 I. SINGLE-MOLECULE MICROSCOPY FOR BINDING Binding is arguably the most fluorescence TIRF microscopy5 to visualize receptor-ligand interactions at the single-molecule level. TIRFSingle-molecule binding experiments on long time scales Mark P. Elenko,1 Jack W. Szostak,2

Heller, Eric

438

Single molecule polarization microscopy for investigating real time structural dynamics of biological macromolecules  

Microsoft Academic Search

To quantitatively monitor structural dynamics of individual biomolecules in real time, a single-molecule polarization microscopy technique has been developed. This novel approach combines the single molecule sensitivity of total internal reflection fluorescence microscopy with orientation measurements by time-resolved fluorescence polarization. With this technique, functionally relevant conformational changes of individual biomolecules can be continuously detected at 10 ms time resolution or

Joseph N. Forkey; Margot E. Quinlan; J. E. T. Corrie; Y. E. Goldman

1999-01-01

439

A New Optical Method for Characterizing Single Molecule Interactions based on Dark Field Microscopy  

E-print Network

A New Optical Method for Characterizing Single Molecule Interactions based on Dark Field Microscopy of Technology, Lorentzweg 1, NL-2628 CJ Delft, The Netherlands ABSTRACT Single-molecule techniques continue tagged with gold nanobeads and observed under dark field microscopy to study single molecular

Rieger, Bernd

440

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

E-print Network

-internal-reflection fluorescence (TIRF) microscopy. Citation: Lee S, Lee J, Hohng S (2010) Single-Molecule Three-Color FRETSingle-Molecule Three-Color FRET with Both Negligible Spectral Overlap and Long Observation Time-color detection capability in doing single- molecule fluorescence resonance energy transfer (FRET) experiments

Hohng, Sung Chul

441

Accurate Single Molecule FRET Efficiency Determination for Surface Immobilized DNA Using Maximum Likelihood Calculated Lifetimes  

E-print Network

Accurate Single Molecule FRET Efficiency Determination for Surface Immobilized DNA Using MaximumVed: October 4, 2006; In Final Form: January 12, 2007 Single molecule fluorescent lifetime trajectories directly measured using time-tagged single-photon counting and scanning confocal microscopy. A modified

442

Appearing in Proc. SPIE Volume 5222 (in press, 2003). Novel fluorophores for single-molecule imaging  

E-print Network

have been performing optical spectroscopy and microscopy on single reporter molecules in liquid, glass of single-molecule spectroscopy and microscopy uses optical excitation to explore these interactions betweenAppearing in Proc. SPIE Volume 5222 (in press, 2003). Novel fluorophores for single-molecule

Ostroverkhova, Oksana

443

Tunneling Currents through a Single Molecule Isolated in a New Matrix  

Microsoft Academic Search

The electrical properties of single phenylene oligomers were studied in terms of the dependence of the tunneling current on the length of the oligomers using self-assembling techniques and scanning tunneling microscopy (STM). It is important to isolate single molecules in an insulating matrix for the measurement of the conductivity of the single molecule. We show a novel self-assembled monolayer (SAM)

S. Wakamatsu; S. Fujii; U. Akiba; M. Fujihira

2003-01-01

444

A correlation force spectrometer for single molecule measurements under tensile load  

E-print Network

.15­20 Comparing the dual trap technique with atomic force microscopy (AFM) single molecule forceA correlation force spectrometer for single molecule measurements under tensile load Milad Radiom,1-correlation measurements is less than one third of the value for single-cantilever force microscopy. The dynamics

Paul, Mark

445

Developing Single-Molecule TPM Experiments for Direct Observation of Successful RecA-Mediated Strand  

E-print Network

Developing Single-Molecule TPM Experiments for Direct Observation of Successful Rec particle motion (TPM) to investigate the fates of the invading and the outgoing strands during E. coli RecA-mediated pairing and strand exchange at the single-molecule level in the absence of force. TPM experiments measure

Cox, Michael M.

446

A single-molecule characterization of p53 search on DNA  

E-print Network

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

447

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

PubMed

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 ? 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

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

2014-10-01

448

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

NASA Astrophysics Data System (ADS)

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.

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

2014-08-01

449

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

NASA Astrophysics Data System (ADS)

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