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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



Single-molecule spectroscopy of interfacial electron transfer.  


It is widely appreciated that single-molecule spectroscopy (SMS) can be used to measure properties of individual molecules which would normally be obscured in an ensemble-averaged measurement. In this report we show how SMS can be used to measure photoinduced interfacial electron transfer (IET) and back electron transfer rates in a prototypical chromophore-bridge-electrode nonadiabatic electron transfer system. N-(1-hexylheptyl)-N'-(12-carboxylicdodecyl)perylene-3,4,9,10-tetracarboxylbisimide was synthesized and incorporated into mixed self-assembled monolayers (SAMs) on an ITO (tin-doped indium oxide, a p-type semiconductor) electrode. Single-molecule fluorescence time trajectories from this system reveals "blinks", momentary losses in fluorescence (>20 ms to seconds in duration), which are attributed to discrete electron transfer events: electron injection from the perylene chromophore into the conduction band of the ITO leads to the loss of fluorescence, and charge recombination (back electron transfer) leads to the return of fluorescence. Such blinks are not observed when an electrode is not present. The fluorescence trajectories were analyzed to obtain the forward and back electron rates; the measured rates are found to lie in the millisecond to second regime. Different rates are observed for different molecules, but the lifetime distributions for the forward or back electron transfer for any given molecule are well fit by single exponential kinetics. The methodology used is applicable to a wide variety of systems and can be used to study the effects of distance, orientation, linker, environment, etc. on electron transfer rates. The results and methodology have implications for molecular electronics, where understanding and controlling the range of possible behaviors inherent to molecular systems will likely be as important as understanding the individual behavior of any given molecule. PMID:14531709

Holman, Michael W; Liu, Ruchuan; Adams, David M



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.

Tsutsui, Makusu; Taniguchi, Masateru



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



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



Molecular electronics with single molecules in solid-state devices  

Microsoft Academic Search

The ultimate aim of molecular electronics is to understand and master single-molecule devices. Based on the latest results on electron transport in single molecules in solid-state devices, we focus here on new insights into the influence of metal electrodes on the energy spectrum of the molecule, and on how the electron transport properties of the molecule depend on the strength

Kasper Moth-Poulsen; Thomas Bjørnholm



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


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



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



New Measurement Techniques and Their Applications in Single Molecule Electronics  

NASA Astrophysics Data System (ADS)

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

Guo, Shaoyin


Electron transport in single molecules: from benzene to graphene.  


Electron movement within and between molecules--that is, electron transfer--is important in many chemical, electrochemical, and biological processes. Recent advances, particularly in scanning electrochemical microscopy (SECM), scanning-tunneling microscopy (STM), and atomic force microscopy (AFM), permit the study of electron movement within single molecules. In this Account, we describe electron transport at the single-molecule level. We begin by examining the distinction between electron transport (from semiconductor physics) and electron transfer (a more general term referring to electron movement between donor and acceptor). The relation between these phenomena allows us to apply our understanding of single-molecule electron transport between electrodes to a broad range of other electron transfer processes. Electron transport is most efficient when the electron transmission probability via a molecule reaches 100%; the corresponding conductance is then 2e(2)/h (e is the charge of the electron and h is the Planck constant). This ideal conduction has been observed in a single metal atom and a string of metal atoms connected between two electrodes. However, the conductance of a molecule connected to two electrodes is often orders of magnitude less than the ideal and strongly depends on both the intrinsic properties of the molecule and its local environment. Molecular length, means of coupling to the electrodes, the presence of conjugated double bonds, and the inclusion of possible redox centers (for example, ferrocene) within the molecular wire have a pronounced effect on the conductance. This complex behavior is responsible for diverse chemical and biological phenomena and is potentially useful for device applications. Polycyclic aromatic hydrocarbons (PAHs) afford unique insight into electron transport in single molecules. The simplest one, benzene, has a conductance much less than 2e(2)/h due to its large LUMO-HOMO gap. At the other end of the spectrum, graphene sheets and carbon nanotubes--consisting of infinite numbers of aromatic rings--have small or even zero energy gaps between the conduction and valence bands. Between these two limits are intermediate molecules with rich properties, such as perylene derivatives made of seven aromatic rings; the properties of these types of molecules have yet to be fully explored. Studying PAHs is important not only in answering fundamental questions about electron transport but also in the ongoing quest for molecular-scale electronic devices. This line of research also helps bridge the gap between electron transfer phenomena in small redox molecules and electron transport properties in nanostructures. PMID:19253984

Chen, F; Tao, N J



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


Statistics of single molecule rotation driven by electrons  

NASA Astrophysics Data System (ADS)

In stark contrast to nature, current manmade devices, with the exception of liquid crystals, make no use of nanoscale molecular motion. In order for molecules to be used as components in molecular machines, methods are required to couple individual molecules to external energy sources and to selectively excite motion in a given direction. Recently a new, stable and robust system of molecular rotors consisting of thioether molecules bound to metal surfaces has offered a method with which to study the rotation of individual molecules as a function of temperature, molecular chemistry, proximity of neighboring molecules, and surface structure [1,2]. Arrhenius plots for the rotation of dibutyl sulfide yielded a rotational barrier of 1.2 kJ per mol. While these results reveal that small amounts of thermal energy are capable of inducing rotation, thermodynamics dictates that thermal energy alone cannot be used to perform useful work in the absence of a temperature gradient. Electrical excitation of individual thioether molecular rotors is performed using with electrons from a scanning tunneling microscope tip. Experimental data for the electrically excited motion of asymmetric thioether molecules is presented and the statistics of and mechanism for directed motion is discussed [1,2]. [4pt] [1] ``A Quantitative Single-Molecule Study of Thioether Molecular Rotors'' A. E. Baber et al. ACS Nano 2008, 2, 2385-2391[0pt] [2] Experimental Demonstration of a Single-Molecule Electric Motor H. L. Tierney et al. - Nature Nanotechnology 2011, 6, 625-629

Sykes, Charles



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

PubMed Central

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

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



High Frequency Electron Paramagnetic Resonance Studies of Single Molecule Magnets  

NASA Astrophysics Data System (ADS)

Single crystal samples of different single-molecule magnets (SMMs) were studied by High Frequency Electron Paramagnetic Resonance (HFEPR) in order to characterize their magnetic properties. Multiple studies have been conducted to determine the spin Hamiltonian parameters for different systems, including various Mn and Ni based SMMs. The use of single crystals allows studies in multiple orientations: when the sample's easy axis of magnetization is aligned parallel (perpendicular) to the external field, the axial (transverse) anisotropy parameters can be determined. Variable temperature studies allow the determination of the sign of the axial anisotropy parameters, as well as the energy difference between the ground state and excited states. Multiple orientation studies in a Zn system that is lightly doped with Ni allow determination of the anisotropy parameters for a single Ni^+2 ion. These results can then be compared to those for the tetranuclear nickel complex consisting of 4 Ni^+2 ions, enabling an explanation for the fast magnetic quantum tunneling in this system. Finally, analysis of absorption peak linewidths enables characterization of the disorder in SMMs. All of these studies have contributed to a better understanding of the magnetic quantum tunneling behavior in these materials.

Datta, Saiti



Carbon tips for all-carbon single-molecule electronics.  


We present here an exhaustive ab initio study of the use of carbon-based tips as electrodes in single-molecule junctions. Motivated by recent experiments, we show that carbon tips can be combined with other carbon nanostructures, such as graphene, to form all-carbon molecular junctions with molecules like benzene or C60. Our results show that the use of carbon tips can lead to relatively conductive molecular junctions. However, contrary to junctions formed with standard metals, the conductance traces recorded during the formation of the all-carbon single-molecule junctions do not exhibit clear conductance plateaus, which can be attributed to the inability of the hydrogenated carbon tips to form chemical bonds with the organic molecules. Additionally, we explore here the use of carbon tips for scanning tunneling microscopy and show that they are well suited for obtaining sample images with atomic resolution. PMID:24838986

Dappe, Y J; González, C; Cuevas, J C



Carbon tips for all-carbon single-molecule electronics  

NASA Astrophysics Data System (ADS)

We present here an exhaustive ab initio study of the use of carbon-based tips as electrodes in single-molecule junctions. Motivated by recent experiments, we show that carbon tips can be combined with other carbon nanostructures, such as graphene, to form all-carbon molecular junctions with molecules like benzene or C60. Our results show that the use of carbon tips can lead to relatively conductive molecular junctions. However, contrary to junctions formed with standard metals, the conductance traces recorded during the formation of the all-carbon single-molecule junctions do not exhibit clear conductance plateaus, which can be attributed to the inability of the hydrogenated carbon tips to form chemical bonds with the organic molecules. Additionally, we explore here the use of carbon tips for scanning tunneling microscopy and show that they are well suited for obtaining sample images with atomic resolution.

Dappe, Y. J.; González, C.; Cuevas, J. C.



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.

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



Electron Induced Ortho-Meta Isomerization of Single Molecules  

NASA Astrophysics Data System (ADS)

A scanning tunneling microscope operating at 5 K is used to induce the isomerization of single chloronitrobenzene molecules on Cu(111) and verify the reaction. The threshold voltage of (227±7)mV for this reaction is explained based on electron-induced vibrational heating. We propose that the isomerization is initiated by simultaneous excitation of two vibrational molecular modes via inelastically tunneling electrons. This excitation results in a shift of the distribution probability of chlorine and hydrogen positions, which facilitates their mutual exchange.

Simic-Milosevic, V.; Mehlhorn, M.; Rieder, K.-H.; Meyer, J.; Morgenstern, K.



Electron-vibration interaction in multichannel single-molecule junctions.  


The effect of electron-vibration interaction in atomic-scale junctions with a single conduction channel was widely investigated both theoretically and experimentally. However, the more general case of junctions with several conduction channels has received very little attention. Here we study electron-vibration interaction in multichannel molecular junctions, formed by introduction of either benzene or carbon dioxide between platinum electrodes. By combining shot noise and differential conductance measurements, we analyze the effect of vibration activation on conductance in view of the distribution of conduction channels. Based on the shift of vibration energy while the junction is stretched, we identify vibration modes with transverse and longitudinal symmetry. The detection of different vibration modes is ascribed to efficient vibration coupling to different conduction channels according to symmetry considerations. While most of our observations can be explained in view of the theoretical models for a single conduction channel, the appearance of conductance enhancement, induced by electron-vibration interaction, at high conductance values indicates either unexpected high electron-vibration coupling or interchannel scattering. PMID:24252112

Ben-Zvi, Regev; Vardimon, Ran; Yelin, Tamar; Tal, Oren



Design and control of electron transport properties of single molecules  

PubMed Central

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

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



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


pi-conjugated polymers find a range of applications in electronic devices. These materials are generally highly disordered in terms of chain length and chain conformation, besides being influenced by a variety of chemical and physical defects. Although this characteristic can be of benefit in certain device applications, disorder severely complicates materials analysis. Accurate analytical techniques are, however, crucial to optimising synthetic procedures and assessing overall material purity. Fortunately, single-molecule spectroscopic techniques have emerged as an unlikely but uniquely powerful approach to unraveling intrinsic material properties from the bottom up. Building on the success of such techniques in the life sciences, single-molecule spectroscopy is finding increasing applicability in materials science, effectively enabling the dissection of the bulk down to the level of the individual molecular constituent. This article reviews recent progress in single molecule spectroscopy of conjugated polymers as used in organic electronics. PMID:20496402

Lupton, John M



Controlling Electronic States and Transport Properties at the Level of Single Molecules  

NASA Astrophysics Data System (ADS)

Since molecular electronics has been rapidly growing as a promising alternative of conventional electronics towards the ultimate miniaturization of electronic devices through the bottom-up strategy, it has become a long-term desire to understand and control the transport properties at the level of single molecules. In this presentation we show that one may modify the electronic states of single molecules, and thus control their transport properties through designing and fabrication of functional molecules or manipulating molecules with scanning tunneling microscopy. We demonstrated that the rectifying effect of single molecules can be realized by designing donor-barrier-acceptor architecture of Pyridine-?-C60 molecules to achieve the Aviram-Ratner rectifier through azafullerene C59N molecules The effect of the negative differential resistances can be realized by appropriately matching the molecular oribital symmetries between a cobalt phthalocyanine (CoPc) molecule and a Ni electrode. The electronic states and transport properties of single molecules, such as CoPc and melamine molecules, can be altered through manipulation or modifying molecular structures, leading to functionalized molecular devices.

Wang, Bing



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)



The role of molecule–electrode contact in single-molecule electronics  

NASA Astrophysics Data System (ADS)

Creating complex electronic systems from individual molecular components is one of the most formidable challenges in nanotechnology today. To achieve this goal it is necessary not only to design the functionality of the molecular system to create devices, but also to control the interface between bulk contacts and molecular systems. In this brief perspective we discuss the role of molecule–electrode contact in single-molecule systems. This contact is responsible for making the system mechanically stable enough to perform measurements, and can also have profound impacts on both the contact resistance and the energy level alignment in the system. We will discuss a variety of different linker groups that have been explored, note the advantages and disadvantages of various contact chemistries, and discuss new methodologies used for understanding the impact that the molecule–electrode contact has on the energetics of single-molecule devices.

Hihath, Joshua; Tao, Nongjian



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

PubMed Central

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

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



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.


Theoretical descriptions of electron transport through single molecules: Developing design tools for molecular electronic devices  

NASA Astrophysics Data System (ADS)

There are vast numbers of organic compounds that could be considered for use in molecular electronics. Hence there is a need for efficient and economical screening tools. Here we develop theoretical methods to describe electron transport through individual molecules, the ultimate goal of which is to establish design tools for molecular electronic devices. To successfully screen a compound for its use as a device component requires a proper representation of the quantum mechanics of electron transmission. In this work we report the development of tools for the description of electron transmission that are: Charge self-consistent, valid in the presence of a finite applied potential field and (in some cases) explicitly time-dependent. In addition, the tools can be extended to any molecular system, including biosystems, because they are free of restrictive parameterizations. Two approaches are explored: (1) correlation of substituent parameter values (sigma), (commonly found in organic chemistry textbooks) to properties associated with electron transport, (2) explicit tracking of the time evolution of the wave function of a nonstationary electron. In (1) we demonstrate that the a correlate strongly with features of the charge migration process, establishing them as useful indicators of electronic properties. In (2) we employ a time-dependent description of electron transport through molecular junctions. To date, the great majority of theoretical treatments of electron transport in molecular junctions have been of the time-independent variety. Time dependence, however, is critical to such properties as switching speeds in binary computer components and alternating current conductance, so we explored methods based on time-dependent quantum mechanics. A molecular junction is modeled as a single molecule sandwiched between two clusters of close-packed metal atoms or other donor and acceptor groups. The time dependence of electron transport is investigated by initially localizing an electron on the donor and following the time development of the corresponding non-stationary wavefunction of the time-independent Hamiltonian. We demonstrate that the time-dependent treatment of electron transport predicts physically intuitive results, while providing insights not available from time-independent methods.

Carroll, Natalie R.


Electronic measurements of single-molecule catalysis by cAMP-dependent protein kinase A.  


Single-molecule studies of enzymes open a window into their dynamics and kinetics. A single molecule of the catalytic domain of cAMP-dependent protein kinase A (PKA) was attached to a single-walled carbon nanotube device for long-duration monitoring. The electronic recording clearly resolves substrate binding, ATP binding, and cooperative formation of PKA's catalytically functional, ternary complex. Using recordings of a single PKA molecule extending over 10 min and tens of thousands of binding events, we determine the full transition probability matrix and conversion rates governing formation of the apo, intermediate, and closed enzyme configurations. We also observe kinetic rates varying over 2 orders of magnitude from one second to another. Anti-correlation of the on and off rates for PKA binding to the peptide substrate, but not ATP, demonstrates that regulation of enzyme activity results from altering the stability of the PKA-substrate complex, not its binding to ATP. The results depict a highly dynamic enzyme offering dramatic possibilities for regulated activity, an attribute useful for an enzyme with crucial roles in cell signaling. PMID:23631749

Sims, Patrick C; Moody, Issa S; Choi, Yongki; Dong, Chengjun; Iftikhar, Mariam; Corso, Brad L; Gul, O Tolga; Collins, Philip G; Weiss, Gregory A



Label-free "digital detection" of single-molecule DNA hybridization with a single electron transistor.  


Here we present a novel assay that eliminates fluorescent labels and enables "digital detection" of single-molecule DNA hybridization in complex matrixes with greatly simplified protocols. Electronic coupling of the binding state of a single oligonucleotide to the quantum dot (QD) of a single electron transistor (SET) affords direct observation of binding events in real-time via "molecular gating". The change of electrostatic charge associated with the molecular capture is used in lieu of a gate electrode to modulate the SET conductivity. Target oligos containing base mismatches do not elicit SET response under 0.1X SSC at room temperature nor do changes in ionic strength or pH. Furthermore, hybridization is detected even in optically inaccessible matrixes such as serum or quanidinium thiocyanate lysis buffer. PMID:16939245

Brousseau, Louis C



In situ superexchange electron transfer through a single molecule: A rectifying effect  

PubMed Central

An increasingly comprehensive body of literature is being devoted to single-molecule bridge-mediated electronic nanojunctions, prompted by their prospective applications in molecular electronics and single-molecule analysis. These junctions may operate in gas phase or electrolyte solution (in situ). For biomolecules, the latter is much closer to their native environment. Convenient target molecules are aromatic molecules, peptides, oligonucleotides, transition metal complexes, and, broadly, molecules with repetitive units, for which the conducting orbitals are energetically well below electronic levels of the solvent. A key feature for these junctions is rectification in the current–voltage relation. A common view is that asymmetric molecules or asymmetric links to the electrodes are needed to acquire rectification. However, as we show here, this requirement could be different in situ, where a structurally symmetric system can provide rectification because of the Debye screening of the electric field in the nanogap if the screening length is smaller than the bridge length. The Galvani potentials of each electrode can be varied independently and lead to a transistor effect. We explore this behavior for the superexchange mechanism of electron transport, appropriate for a wide class of molecules. We also include the effect of conformational fluctuations on the lowest unoccupied molecular orbital (LUMO) energy levels; that gives rise to non-Arrhenius temperature dependence of the conductance, affected by the molecule length. Our study offers an analytical formula for the current–voltage characteristics that demonstrates all these features. A detailed physical interpretation of the results is given with a discussion of reported experimental data.

Kornyshev, Alexei A.; Kuznetsov, Alexander M.; Ulstrup, Jens



Resolving Single Molecule Lysozyme Dynamics with a Carbon Nanotube Electronic Circuit  

NASA Astrophysics Data System (ADS)

High resolution, real-time monitoring of a single lysozyme molecule is demonstrated by fabricating nanoscale electronic devices based on single-walled carbon nanotubes (SWCNT). In this sensor platform, a biomolecule of interest is attached to a single SWCNT device. The electrical conductance transduces chemical events with single molecule sensitivity and 10 microsecond resolution. In this work, enzymatic turnover by lysozyme is investigated, because the mechanistic details for its processivity and dynamics remain incompletely understood. Stochastically distributed binding events between a lysozyme and its binding substrate, peptidoglycan, are monitored via the sensor conductance. Furthermore, the magnitude and repetition rate of these events varies with pH and the presence of inhibitors or denaturation agents. Changes in the conductance signal are analyzed in terms of lysozyme's internal hinge motion, binding events, and enzymatic processing.

Choi, Yongki; Moody, Issa S.; Perez, Israel; Sheps, Tatyana; Weiss, Gregory A.; Collins, Philip G.



Electric control of a {Fe4} single-molecule magnet in a single-electron transistor  

NASA Astrophysics Data System (ADS)

Using first-principles methods, we study theoretically the properties of an individual {Fe4} single-molecule magnet (SMM) attached to metallic leads in a single-electron transistor geometry. We show that the conductive leads do not affect the spin ordering and magnetic anisotropy of the neutral SMM. On the other hand, the leads have a strong effect on the anisotropy of the charged states of the molecule, which are probed in Coulomb blockade transport. Furthermore, we demonstrate that an external electric potential, modeling a gate electrode, can be used to manipulate the magnetic properties of the system. For a charged molecule, by localizing the extra charge with the gate voltage closer to the magnetic core, the anisotropy magnitude and spin ordering converges to the values found for the isolated {Fe4} SMM. We compare these findings with the results of recent quantum transport experiments in three-terminal devices.

Nossa, J. F.; Islam, M. F.; Canali, C. M.; Pederson, M. R.



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

NASA Astrophysics Data System (ADS)

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.; Bryce, Martin R.; Frampton, Harry; Chappell, David



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

NASA Astrophysics Data System (ADS)

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

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



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.



Spin dynamics in single-molecule magnets combining surface acoustic waves and high frequency electron paramagnetic resonance  

NASA Astrophysics Data System (ADS)

We report a new experimental technique that integrates high frequency surface acoustic waves (SAWs) with high frequency electron paramagnetic resonance (HFEPR) spectroscopy in order to measure spin dynamics on fast time scales in single-molecule magnets. After driving the system out of equilibrium by triggering magnetic avalanches, or simply by heating with short SAW pulses, the evolution of the spin populations within fixed energy levels is measured using HFEPR spectroscopy.

Hill, Stephen; Lawrence, Jonathan; Macia, Ferran; Hernandez, Joan Manel; Tejada, Javier; Santos, Paulo; Lampropoulos, Christos; Christou, George



Spin dynamics in single-molecule magnets combining surface acoustic waves and high-frequency electron paramagnetic resonance  

NASA Astrophysics Data System (ADS)

We report an experimental technique that integrates high-frequency surface acoustic waves (SAWs) with high-frequency electron paramagnetic resonance (HFEPR) spectroscopy in order to measure spin dynamics on fast time scales in single-molecule magnets. After the system is driven out of equilibrium by triggering magnetic avalanches, or simply by heating with short SAW pulses, the evolution of the spin populations within fixed energy levels is measured using HFEPR spectroscopy.

Macià, F.; Lawrence, J.; Hill, S.; Hernandez, J. M.; Tejada, J.; Santos, P. V.; Lampropoulos, C.; Christou, G.



LeRoy Apker Award Talk: Electronics at the Nanoscale: Graphene, Carbon Nanotubes, and Single-Molecule Devices  

Microsoft Academic Search

Low-dimensional nanostructures are emerging as model systems for fundamental studies of quantum transport, as well as promising candidates for novel post-silicon electronic devices incorporating quantum size effects. Key examples of these include few-layer graphene, carbon nanotubes, polymer nanofibers, and even single molecules. In this talk, I will summarize my work combining experimental and computational tools to study, control, and apply

Sujit Datta



Comprehensive high frequency electron paramagnetic resonance studies of single molecule magnets  

NASA Astrophysics Data System (ADS)

This dissertation presents research on a number of single molecule magnet (SMM) compounds conducted using high frequency, low temperature magnetic resonance spectroscopy of single crystals. By developing a new technique that incorporated other devices such as a piezoelectric transducer or Hall magnetometer with our high frequency microwaves, we were able to collect unique measurements on SMMs. This class of materials, which possess a negative, axial anisotropy barrier, exhibit unique magnetic properties such as quantum tunneling of a large magnetic moment vector. There are a number of spin Hamiltonians used to model these systems, the most common one being the giant spin approximation. Work done on two nickel systems with identical symmetry and microenvironments indicates that this model can contain terms that lack any physical significance. In this case, one must turn to a coupled single ion approach to model the system. This provides information on the nature of the exchange interactions between the constituent ions of the molecule. Additional studies on two similar cobalt systems show that, for these compounds, one must use a coupled single ion approach since the assumptions of the giant spin model are no longer valid. Finally, we conducted a collection of studies on the most famous SMM, Mn12Ac. Three different techniques were used to study magnetization dynamics in this system: stand-alone HFEPR in two different magnetization relaxation regimes, HFEPR combined with magnetometry, and HFEPR combined with surface acoustic waves. All of this research gives insight into the relaxation mechanisms in Mn12Ac.

Lawrence, Jonathan D.


Electronic structure of a Mn6 (S=4) single molecule magnet grafted on Au(111)  

NASA Astrophysics Data System (ADS)

Single molecule magnets (SMMs) form a new class of magnetic materials consisting of identical nanoscale particles that can show magnetization in the absence of a magnetic field. We have experimentally and theoretically investigated the low-spin (S=4) member of the Mn6 SMM family, properly functionalized with two 3-thiophenecarboxylate (3tpc) ligands in order to graft it on to a Au(111) surface. We report the theoretical density of states calculated within the local density approximation (LDA) scheme accounting for the on-site Coulomb repulsion (LDA+U) for U values ranging from 0to8eV . On the experimental side, by exploiting resonant photoemission at the Mn2p edge, we were able to single out the Mn3d derived states in the valence band energy region for a submonolayer distribution of Mn6-3tpc deposited on Au(111). From the comparison between the experimentally derived 3d density of states and the theoretical one, we found that the best agreement occurs for a U value of 4eV . From the binding energy of Mn2p3/2 core line, measured in situ, we also derived a value for the 2p-3d correlation energy of about 5eV —in agreement with previous determination.

Del Pennino, U.; Corradini, V.; Biagi, R.; de Renzi, V.; Moro, F.; Boukhvalov, D. W.; Panaccione, G.; Hochstrasser, M.; Carbone, C.; Milios, C. J.; Brechin, E. K.



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

NASA Astrophysics Data System (ADS)

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

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



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

NASA Astrophysics Data System (ADS)

The low temperature spin dynamics of the single-molecule magnet [Mn12O12(CH3COOH)16(H2O)4]. 2CH3COOH.4H2O, were studied using High Frequency Electron Paramagnetic Resonance (HFEPR) in order to demonstrate magnetic quantum tunneling between resonant spin projection states. We prepare the spins such that they populate only one side of the axial potential energy barrier and, using a magnetic field, we cause tunneling of the magnetic moment between resonant spin projection states. We then use HFEPR to monitor the populations on each side of the potential energy barrier. We show that, in addition to measuring the ensemble average of the relaxation, these HFEPR experiments demonstrate that one can separately monitor the relaxation from different parts of the inhomogeneous distribution of spin environments. This technique, therefore, provides an alternative method for performing hole-digging experiments for measuring spin relaxation dynamics.

Lawrence, Jon; Kim, Sung-Su; Hill, Steve; Murugesu, Muralee; Christou, George



Mediating Electronic Switching of Single Molecules by Varying the Interaction Strength of the Host Environment  

NASA Astrophysics Data System (ADS)

We have studied conjugated phenylene ethynylene oligomers inserted into amide-containing alkanethiolate self-assembled monolayers (SAMs) using scanning tunneling microscopy. The inserted molecules are implicated as molecular electronic device candidates and have shown interesting functionality as switches and wires. We investigate the stochastic switching of these conjugated molecules. Our previous work has shown that the local environment of these molecular switches mediates their switching when they are inserted into n-alkanethiolate matrices. In the present work, we investigate the switching of these molecules inserted in hydrogen-bonding, amide-containing alkanethiolate SAM matrices. The hydrogen bonded networks can affect the switching rates and properties of the inserted molecules by the additional stability imparted by the host matrix.

Lewis, Penelope A.; Weiss, Paul S.; Inman, Christina E.; Hutchison, James E.; Tour, James M.



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


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

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



Significant enhancement of energy barriers in dinuclear dysprosium single-molecule magnets through electron-withdrawing effects.  


The effect of electron-withdrawing ligands on the energy barriers of Single-Molecule Magnets (SMMs) is investigated. By introducing highly electron-withdrawing atoms on targeted ligands, the energy barrier was significantly enhanced. The structural and magnetic properties of five novel SMMs based on a dinuclear {Dy2} phenoxo-bridged motif are explored and compared with a previously studied {Dy2} SMM (1). All complexes share the formula [Dy2(valdien)2(L)2]·solvent, where H2valdien = N1,N3-bis(3-methoxysalicylidene) diethylenetriamine, the terminal ligand L = NO3(-) (1), CH3COO(-) (2), ClCH2COO(-) (3), Cl2CHCOO(-) (4), CH3COCHCOCH3(-) (5), CF3COCHCOCF3(-) (6), and solvent = 0.5 MeOH (4), 2 CH2Cl2 (5). Systematic increase of the barrier was observed for all complexes with the most drastic increase seen in 6 when the acac ligand of 5 was fluorinated resulting in a 7-fold enhancement of the anisotropic barrier. Ab initio calculations reveal more axial g tensors as well as higher energy first excited Kramers doublets in 4 and 6 leading to higher energy barriers for those complexes. PMID:23964606

Habib, Fatemah; Brunet, Gabriel; Vieru, Veacheslav; Korobkov, Ilia; Chibotaru, Liviu F; Murugesu, Muralee



Yeast cytochrome c integrated with electronic elements: a nanoscopic and spectroscopic study down to single-molecule level  

NASA Astrophysics Data System (ADS)

Various aspects of redox protein integration with nano-electronic elements are addressed by a multi-technique investigation of different yeast cytochrome c (YCC)-based hybrid systems. Three different immobilization strategies on gold via organic linkers are explored, involving either covalent bonding or electrostatic interaction. Specifically, Au surfaces are chemically modified by self-assembled monolayers (SAMs) exposing thiol-reactive groups, or by acid-oxidized single-wall carbon nanotubes (SWNTs). Atomic force microscopy and scanning tunnelling microscopy are employed to characterize the morphology and the electronic properties of single YCC molecules adsorbed on the modified gold surfaces. In each hybrid system, the protein molecules are stably assembled, in a native configuration. A standing-up arrangement of YCC on SAMs is suggested, together with an enhancement of the molecular conduction, as compared to YCC directly assembled on gold. The electrostatic interaction with functionalized SWNTs allows several YCC adsorption geometries, with a preferential high-spin haem configuration, as outlined by Raman spectroscopy. Moreover, the conduction properties of YCC, explored in different YCC nanojunctions by conductive atomic force microscopy, indicate the effectiveness of electrical conduction through the molecule and its dependence on the electrode material. The joint employment of several techniques confirms the key role of a well-designed immobilization strategy, for optimizing biorecognition capabilities and electrical coupling with conductive substrates at the single-molecule level, as a starting point for advanced applications in nano-biotechnology.

Delfino, I.; Bonanni, B.; Andolfi, L.; Baldacchini, C.; Bizzarri, A. R.; Cannistraro, S.



Single molecule magnets: High frequency electron paramagnetic resonance study of two isomeric forms of an Mn12 molecule  

NASA Astrophysics Data System (ADS)

Different crystallographic forms of the single molecule magnet [Mn12O12(O2CR)16(H2O)4] (complex 1) with a given R substituent have been isolated. The two different isomeric forms of the p-methylbenzoate complex crystallize as [Mn12O12(O2CC6H4-p-Me)16(H2O)4].(HO2CC6H4-p-Me) (complex 2) and [Mn12O12(O2CC6H4-p-Me)16(H2O)4].3H2O (complex 3). In complex 2, one MnIII ion has an abnormal Jahn-Teller distortion axis oriented at an oxide ion, and thus 2 and 3 are Jahn-Teller isomers. This reduces the symmetry of the core of complex 2 compared with that of complex 3. Complex 2 likely has a larger tunneling matrix element and this explains why this complex shows an out-of-phase ac peak (?M'') in the signal in the 2-3 K region, whereas complex 3 has its ?M'' peak in the 4-7 K range, i.e., the rate of tunneling of magnetization is greater in complex 2 than complex 3. High frequency electron paramagnetic resonance (HFEPR) experiments were performed on both isomers. Computed simulations of the experimental HFEPR data yield spin Hamiltonian parameters for both complexes.

Aubin, S. M. J.; Sun, Z.; Rumberger, E. M.; Hendrickson, D. N.; Christou, G.



Single-molecule fluorescence spectroscopy studies of photo-induced electron transfer between CdSe/ZnS quantum dots and fullerene  

NASA Astrophysics Data System (ADS)

Photo-induced electron transfer in CdSe/ZnS semiconductor quantum dot-fullerene conjugates was investigated by single molecule fluorescence spectroscopy. The average rate for photoinduced electron transfer is estimated around 108s-1. Quenching by electron transfer is observed in the "on" state and it manifests both as reduced fluorescence intensity and as shortening in fluorescence lifetime. As a result, the electron transfer changes the on/off dynamics of the fluorescence intensity of individual quantum dots.

Xu, Zhihua; Cotlet, Mircea



Understanding the electronic structure, optical, and vibrational properties of the Fe8 Br8 single-molecule magnet  

NASA Astrophysics Data System (ADS)

We present the results of our all-electron density functional calculation on the electronic structure and optical properties of [Fe8O2(OH)12(C6H15N3)6Br6]2+ , the functional building block of the [(C6H15N3)6Fe8(?3-O)2(?2-OH)12]Br7(H2O)Br.8H2O single-molecule magnet. The calculated results are compared with the experimentally measured optical spectrum, and the primary features of the excitations are assigned. Excellent agreement is obtained. The calculated spin minority gap is 0.23eV , the spin majority gap is 0.54eV , and the spin majority to minority gap is 0.15eV . Notably, the low-energy spin minority gap is not a dipole-allowed excitation. Experimentally, we find that [(C6H15N3)6Fe8(?3-O)2(?2-OH)12]Br7(H2O)Br.8H2O is a semiconductor, with a dipole-allowed optical gap of approximately 0.6eV (peak position at ˜0.9eV ) and an additional optically observable electronic excitation centered at 0.4eV . The latter feature is weak and broad, with superimposed ( C?H , N?H , and O?H ) vibrational structure. We suggest that the 0.4eV peak in the optical conductivity may be attributable to the spin majority highest occupied molecular orbital to spin minority lowest unoccupied molecular orbital excitation, activated by inclusion of spin-orbit coupling, which mixes states of different symmetry and spin. Overall, we find that the low-energy excitations are dominated by Fed?Fed interionic excitations and that the dipole-allowed excitations involve antiferromagnetically coupled pairs of Fe ions. At higher energy, the features are primarily due to Op?Fed charge transfer transitions. A discussion of the vibrational properties is also included along with an analysis of how the electronic structure results support reduced moments on the minority spin Fe ions.

Baruah, Tunna; Kortus, Jens; Pederson, Mark R.; Weso?owski, Roman; Haraldsen, Jason T.; Musfeldt, Janice L.; North, J. Micah; Zipse, David; Dalal, Naresh S.



Tight-binding model of Mn12 single-molecule magnets: Electronic and magnetic structure and transport properties  

NASA Astrophysics Data System (ADS)

We describe and analyze a tight-binding model of single-molecule magnets (SMMs) that captures both the spin and spatial aspects of the SMM electronic structure. The model generalizes extended Hückel theory to include the effects of spin polarization and spin-orbit coupling. For neutral and negatively charged Mn12 SMMs with acetate or benzoate ligands, the model yields the total SMM spin, the spins of the individual Mn ions, the magnetic easy axis orientation, the size of the magnetic anisotropy barrier, and the size of the highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO-LUMO) gap consistent with experiment. For neutral molecules, the predicted spins and spatial locations of the HOMO are consistent with the results of density functional calculations. For the total spin and location of the LUMO, density functional theory based calculations yield varied results, while the present model yields results consistent with experiments on negatively charged molecules. For Mn12 SMMs with thiolate- and methylsulphide-terminated benzoate ligands (Mn12-Ph-Th), we find the HOMO to be located on the magnetic core of the molecule, but (unlike for the Mn12 SMMs that have previously been studied theoretically) we predict the LUMO and near-LUMO orbitals of Mn12-Ph-Th to be located on ligands. Therefore, we predict that for these Mn12 SMMs, resonant and off-resonant coherent transport via near-LUMO orbitals, not subject to Coulomb blockade, should occur. We propose that this effect can be used to identify specific experimentally realized SMM transistors in which the easy axis and magnetic moment are approximately parallel to the direction of the current flow. We also predict effective spin filtering by these SMMs to occur at low bias whether the transport is mediated by the HOMO that is on the magnetic core of the SMM or by near-LUMO orbitals located on the nominally nonmagnetic ligands.

Rostamzadeh Renani, Fatemeh; Kirczenow, George



Sub-nanoscale, single-molecule, magnetic electronic switching from externally perturbed spin states in iron (III)-based complexes  

NASA Astrophysics Data System (ADS)

Both the temperature and pressure dependent spin state transition behaviour of two Fe(III) complexes will be exemplified. Such compounds are considered attractive as potential molecular switch devices for low power, low weight, high density nanomemory arrays in computer applications, or as sensors. Spin state configurations are readily investigated by 57Fe Mössbauer spectroscopy in the range 300-4 K, or at high pressures up to 20 GPa in diamond anvil cells. An iron coordination compound with the chemical formula {[FeIIIL2] [ClO4]}2·EtOH, where L- is a uni-negative ligand, HL is N-(pyridin-2-ylmethyl)salicylideneamine and EtOH is ethanol, is in the high spin (HS), 6A1g, state at room temperature. The onset of low spin (LS) population occurs at {\\sim }240 K and this increases monotonically as the temperature is lowered to 100 K. At 70 K the sample is predominantly in the LS state although a remnant {\\sim }12{%} HS population persists to the lowest recorded temperature of {\\sim }15 K. Thermodynamic parameters associated with the energy barrier between the two spin states are deduced from the temperature dependence of the equilibrium constant K. Pressure induced spin switching from the high moment HS state to the low moment LS electronic state in a haem-porphyrin [FeIII(TPP)(NCS)] will also be shown. Spin pairing onset occurs at a moderate pressure of {\\sim }5 GPa. HS and LS isomers exist in equilibrium up to {\\sim }12 GPa at room temperature. The sample is fully LS populated at P>12 GPa. Temperature and pressure dependent spin-spin relaxation is used to account for the pressure evolution of the (asymmetric) quadrupole split resonance profile. Density functional theory calculations, in conjunction with crystallographic data, are used to consider the structural response to such a spin state variation, perhaps suggesting the possibility of a mechanically operated single-molecule magnetic switch.

Hearne, G. R.; Munro, O.; Pearson, N.; Shongwe, M.



Nanophotonics and Single Molecules  

Microsoft Academic Search

Single emitting molecules are currently providing a new window into nanoscale systems ranging from biology to materials science.\\u000a The amount of information that can be extracted from each single molecule depends upon the specific photophysical properties\\u000a of the fluorophore and how these properties are affected by the nearby environment. For this reason, it is necessary to develop\\u000a single-molecule emitters with

W. E. Moerner; P. James Schuck; David P. Fromm; Anika Kinkhabwala; Samuel J. Lord; Stefanie Y. Nishimura; Katherine A. Willets; Arvind Sundaramurthy; Gordon Kino; Meng He; Zhikuan Lu; Robert J. Twieg


Frequency dependence of the quadratic electron-phonon coupling constant in a polymer glass: Direct measurement by single-molecule spectroscopy  

Microsoft Academic Search

The frequency dependence of the quadratic coupling constant between the electron system of the chromophores and the quasilocal vibrational modes of the matrix, B(omega0) , and its distribution was measured in a disordered system via single-molecule spectroscopy. A correlation between B and omega0 was found which does not follow a power law. The analysis of this result allows us to

Andrei V. Naumov; Yury G. Vainer; Lothar Kador



Ultrafast Interfacial Proton-Coupled Electron Transfer  

SciTech Connect

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

Petek, Hrvoje; Zhao, Jin



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


Solvational Barriers to Interfacial Electron Transfer: Minimization via Valence Delocalization.  

National Technical Information Service (NTIS)

Standard rate constants (k (sub s)) for interfacial electron transfer (ET) have been obtained for several redox couples featuring very small internal activation barriers. To render these ordinarily fast rates measurable, we have employed low-defect-densit...

J. T. Hupp X. L. Zhang



Interfacial and Thin Film Chemistry in Electron Device Fabrication.  

National Technical Information Service (NTIS)

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...

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



Interfacial and Thin Film Chemistry in Electron Device Fabrication.  

National Technical Information Service (NTIS)

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: MBE Growth and Devices, Laser Surface Interactions, and Fundamentals of ...

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



Nanochannel Based Single Molecule Recycling  

PubMed Central

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

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



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



Fluorescence Excitation of Single Molecules.  

National Technical Information Service (NTIS)

A few years ago, many people would have deemed the optical observation of single molecules nearly impossible. Yet, new experiments at room and at liquid helium temperatures have started to remove this psychological barrier. Several applications to trace d...

M. Orrit J. Bernard



Interfacial trapping for hot electron injection in silicon  

NASA Astrophysics Data System (ADS)

We have evidenced a new interfacial trapping phenomenon for hot electron injection in silicon by studying magnetic tunnel transistors (MTTs) with a MgO tunneling barrier emitter and a Cu/Si Shottky barrier collector. Transport measurements on hot electrons indicate that an interfacial charge trapping and a backscattering-induced collector current limitation take place with the MTT spin-valve base both in parallel and antiparallel states when the temperature is lower than 25 K, which results in a rapid decrease of the magnetocurrent ratio from ~2000% at 25 K to 800% at 17 K. The binding energy of the trapped electron is estimated to be about 1.7 meV, which is also found to increase with the magnetic field. A simple analytic model considering the interfacial electron trapping and releasing is proposed to explain the experimental results.

Lu, Y.; Lacour, D.; Lengaigne, G.; Le Gall, S.; Suire, S.; Montaigne, F.; Hehn, M.



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

SciTech Connect

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

Harrison, Ian



Correlated Single Quantum Dot Blinking and Interfacial Electron Transfer Dynamics  

PubMed Central

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

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



Correlated Single Quantum Dot Blinking and Interfacial Electron Transfer Dynamics.  


The electron transfer (ET) dynamics from core/multi-shell (CdSe/CdS(3ML)ZnCdS(2ML)ZnS(2ML)) quantum dots (QDs) to adsorbed Fluorescein (F27) molecules have been studied by single particle spectroscopy to probe the relationship between single QD interfacial electron transfer and blinking dynamics. Electron transfer from the QD to F27 and the subsequent recombination were directly observed by ensemble-averaged transient absorption spectroscopy. Single QD-F27 complexes show correlated fluctuation of fluorescence intensity and lifetime, similar to those observed in free QDs. With increasing ET rate (controlled by F27-to-QD ratio), the lifetime of on states decreases and relative contribution of off states increases. It was shown that ET is active for QDs in on states, the excited state lifetime of which reflects the ET rate, whereas in the off state QD excitons decay by Auger relaxation and ET is not a competitive quenching pathway. Thus, the blinking dynamics of single QDs modulate their interfacial ET activity. Furthermore, interfacial ET provides an additional pathway for generating off states, leading to correlated single QD interfacial ET and blinking dynamics in QD-acceptor complexes. Because blinking is a general phenomenon of single QDs, it appears that the correlated interfacial ET and blinking and the resulting intermittent ET activity are general phenomena for single QDs. PMID:21915369

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



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


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



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)



Single-Molecule Enzymatic Dynamics  

SciTech Connect

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 memory effect: an enzymatic turnover is not independent of its previous turnovers. This non-Markovian behavior, otherwise hidden in ensemble-averaged measurements, is attributed to slow fluctuations of protein conformations. Static heterogeneity and dynamical variation of reaction rates, essentially indistinguishable in ensemble-averaged experiments, can now be determined separately by the real-time single-molecule approach.

Lu, H. Peter; Xun, Luying; Xie, Xiaoliang



Single-Molecule Anisotropy Imaging  

Microsoft Academic Search

A novel method, single-molecule anisotropy imaging, has been employed to simultaneously study lateral and rotational diffusion of fluorescence-labeled lipids on supported phospholipid membranes. In a fluid membrane composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, in which the rotational diffusion time is on the order of the excited-state lifetime of the fluorophore rhodamine, a rotational diffusion constant, Drot=7×107rad2\\/s, was determined. The lateral diffusion constant, measured

G. S. Harms; M. Sonnleitner; G. J. Schütz; H. J. Gruber; Th. Schmidt



Electrochemical Detection of Single Molecules  

Microsoft Academic Search

The electrochemical behavior of a single molecule can be observed by trapping a small volume of a dilute solution of the electroactive species between an ultramicroelectrode tip with a diameter of ~15 nanometers and a conductive substrate. A scanning electrochemical microscope was used to adjust the tip-substrate distance (~10 nanometers), and the oxidation of [(trimethylammonio)methyl] ferrocene (Cp_2FeTMA^+) to Cp_2FeTMA2+ was

Fu-Ren F. Fan; Allen J. Bard



Franck-Condon blockade in a single-molecule transistor.  


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

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



Single Molecules as Nanophotonic Probes and Sources  

Microsoft Academic Search

Optical spectroscopy of single molecules in condensed phases provides a tool to sense local nanoenvironments that complements and extends conventional bulk ensemble-averaged measurements. Since typical single-molecule fluorophores are on the order of a few nm in size, detecting the state of the single molecule allows exploration of several features of the interaction of the molecule with its immediate neighbors in

W. E. Moerner



Single-molecule torsional pendulum.  


We have built a torsional pendulum based on an individual single-walled carbon nanotube, which is used as a torsional spring and mechanical support for the moving part. The moving part can be rotated by an electric field, resulting in large but fully elastic torsional deformations of the nanotube. As a result of the extremely small restoring force associated with the torsional deformation of a single molecule, unusually large oscillations are excited by the thermal energy of the pendulum. By diffraction analysis, we are able to determine the handedness of the molecule in our device. Mechanical devices with molecular-scale components are potential building blocks for nanoelectromechanical systems and may also serve as sensors or actuators. PMID:16141068

Meyer, Jannik C; Paillet, Matthieu; Roth, Siegmar



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.



Single-molecule mechanics of mussel adhesion  

PubMed Central

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.

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



Single-molecule imaging by optical absorption  

NASA Astrophysics Data System (ADS)

To date, optical studies of single molecules at room temperature have relied on the use of materials with high fluorescence quantum yield combined with efficient spectral rejection of background light. To extend single-molecule studies to a much larger pallet of substances that absorb but do not fluoresce, scientists have explored the photothermal effect, interferometry, direct attenuation and stimulated emission. Indeed, very recently, three groups have succeeded in achieving single-molecule sensitivity in absorption. Here, we apply modulation-free transmission measurements known from absorption spectrometers to image single molecules under ambient conditions both in the emissive and strongly quenched states. We arrive at quantitative values for the absorption cross-section of single molecules at different wavelengths and thereby set the ground for single-molecule absorption spectroscopy. Our work has important implications for research ranging from absorption and infrared spectroscopy to sensing of unlabelled proteins at the single-molecule level.

Celebrano, Michele; Kukura, Philipp; Renn, Alois; Sandoghdar, Vahid



Single-Molecule Stochastic Resonance  

NASA Astrophysics Data System (ADS)

Stochastic resonance (SR) is a well-known phenomenon in dynamical systems. It consists of the amplification and optimization of the response of a system assisted by stochastic (random or probabilistic) noise. Here we carry out the first experimental study of SR in single DNA hairpins which exhibit cooperatively transitions from folded to unfolded configurations under the action of an oscillating mechanical force applied with optical tweezers. By varying the frequency of the force oscillation, we investigate the folding and unfolding kinetics of DNA hairpins in a periodically driven bistable free-energy potential. We measure several SR quantifiers under varied conditions of the experimental setup such as trap stiffness and length of the molecular handles used for single-molecule manipulation. We find that a good quantifier of the SR is the signal-to-noise ratio (SNR) of the spectral density of measured fluctuations in molecular extension of the DNA hairpins. The frequency dependence of the SNR exhibits a peak at a frequency value given by the resonance-matching condition. Finally, we carry out experiments on short hairpins that show how SR might be useful for enhancing the detection of conformational molecular transitions of low SNR.

Hayashi, K.; de Lorenzo, S.; Manosas, M.; Huguet, J. M.; Ritort, F.



Distributed response analysis of conductive behavior in single molecules  

PubMed Central

The ab initio computational approach of distributed response analysis is used to quantify how electrons move across conjugated molecules in an electric field, in analogy to conduction. The method promises to be valuable for characterizing the conductive behavior of single molecules in electronic devices.

in het Panhuis, Marc; Munn, Robert W.; Popelier, Paul L. A.; Coleman, Jonathan N.; Foley, Brian; Blau, Werner J.



Memristive properties of single-molecule magnets  

NASA Astrophysics Data System (ADS)

Single-molecule magnets weakly coupled to two ferromagnetic leads act as memory devices in electronic circuits—their response depends on history, not just on the instantaneous applied voltage. We show that magnetic anisotropy introduces a wide separation of time scales between fast and slow relaxation processes in the system, which leads to a pronounced memory dependence in a wide intermediate time regime. We study the response to a harmonically varying bias voltage from slow to rapid driving within a master-equation approach. The system is not purely memristive but shows a partially capacitive response on short time scales. In the intermediate time regime, the molecular spin can be used as the state variable in a two-terminal molecular memory device.

Timm, Carsten; Di Ventra, Massimiliano



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.


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



Extracting Models in Single Molecule Experiments  

NASA Astrophysics Data System (ADS)

Single molecule experiments can now monitor the journey of a protein from its assembly near a ribosome to its proteolytic demise. Ideally all single molecule data should be self-explanatory. However data originating from single molecule experiments is particularly challenging to interpret on account of fluctuations and noise at such small scales. Realistically, basic understanding comes from models carefully extracted from the noisy data. Statistical mechanics, and maximum entropy in particular, provide a powerful framework for accomplishing this task in a principled fashion. Here I will discuss our work in extracting conformational memory from single molecule force spectroscopy experiments on large biomolecules. One clear advantage of this method is that we let the data tend towards the correct model, we do not fit the data. I will show that the dynamical model of the single molecule dynamics which emerges from this analysis is often more textured and complex than could otherwise come from fitting the data to a pre-conceived model.

Presse, Steve



Interfacial Electron Transfer into Functionalized Crystalline Polyoxotitanate Nanoclusters  

PubMed Central

Interfacial electron transfer (IET) between a chromophore and a semi-conductor nanoparticle is one of the key processes in a dye sensitized solar cell. Theoretical simulations of the electron transfer in polyoxotitanate nanoclusters Ti17O24(OPri)20 (Ti17) functionalized with four para-nitrophenyl acetylacetone (NPA-H) adsorbates, of which the atomic structure has been fully established by X-ray diffraction measurements, are presented. Complementary experimental information showing IET has been obtained by EPR spectroscopy. Evolution of the time-dependent photoexcited electron during the initial 5 fs after instantaneous excitation to the NPA LUMO+1 has been evaluated. Evidence for delocalization of the excitation over multiple chromophoresafter excitation to the NPA LUMO+2 state on a 15 fs timescale is also obtained. While chromophores are generally considered electronically isolated with respect to neighboring sensitizers, our calculations show that this is not necessarily the case. The present work is the most comprehensive study to date of a sensitized semiconductor nanoparticle in which the structure of the surface and the mode of molecular adsorption are precisely defined.

Snoeberger, Robert C.; Young, Karin J.; Tang, Jiji; Allen, Laura J.



Single-molecule transport in three-terminal devices  

NASA Astrophysics Data System (ADS)

Transport through single molecules has been studied using different test beds. In this paper we focus on three-terminal devices in which a molecule bridges the gap between two gold electrodes and a third electrode—the gate—is able to modulate the conduction properties of the junction. Depending on the electronic coupling, ?, between the molecule and the gold electrodes, different transport regimes can be distinguished. We show measurements on junctions incorporating different single-molecule systems which demonstrate the distinction between these regimes, as well as the experimental limitations in controlling the exact value of ?.

Osorio, E. A.; Bjørnholm, T.; Lehn, J.-M.; Ruben, M.; van der Zant, H. S. J.



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



Electronic structures of interfacial states formed at polymeric semiconductor heterojunctions  

NASA Astrophysics Data System (ADS)

Heterojunctions between organic semiconductors are central to the operation of light-emitting and photovoltaic diodes, providing respectively for electron-hole capture and separation. However, relatively little is known about the character of electronic excitations stable at the heterojunction. We have developed molecular models to study such interfacial excited electronic excitations that form at the heterojunction between model polymer donor and polymer acceptor systems: poly(9,9-dioctylfluorene-co-bis-N,N-(4-butylphenyl)-bis-N,N-phenyl-1,4-phenylenediamine) (PFB) with poly(9,9-dioctylfluorene-co-benzothiadiazole) (F8BT), and poly(9,9-dioctylfluorene-co-N-(4-butylphenyl)diphenylamine) (TFB) with F8BT. We find that for stable ground-state geometries the excited state has a strong charge-transfer character. Furthermore, when partly covalent, modelled radiative lifetimes (~10-7s) and off-chain axis polarization (30?) match observed `exciplex' emission. Additionally for the PFB:F8BT blend, geometries with fully ionic character are also found, thus accounting for the low electroluminescence efficiency of this system.

Huang, Ya-Shih; Westenhoff, Sebastian; Avilov, Igor; Sreearunothai, Paiboon; Hodgkiss, Justin M.; Deleener, Caroline; Friend, Richard H.; Beljonne, David



Single molecule studies of homologous recombination†  

PubMed Central

Single molecule methods offer an unprecedented opportunity to examine complex macromolecular reactions that are obfuscated by ensemble averaging. The application of single molecule techniques to study DNA processing enzymes has revealed new mechanistic details that are unobtainable from bulk biochemical studies. Homologous DNA recombination is a multi-step pathway that is facilitated by numerous enzymes that must precisely and rapidly manipulate diverse DNA substrates to repair potentially lethal breaks in the DNA duplex. In this review, we present an overview of single molecule assays that have been developed to study key aspects of homologous recombination and discuss the unique information gleaned from these experiments.

Finkelstein, Ilya J.; Greene, Eric C.



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.



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


Wavelet analysis for single molecule localization microscopy.  


Localization of single molecules in microscopy images is a key step in quantitative single particle data analysis. Among them, single molecule based super-resolution optical microscopy techniques require high localization accuracy as well as computation of large data sets in the order of 10(5) single molecule detections to reconstruct a single image. We hereby present an algorithm based on image wavelet segmentation and single particle centroid determination, and compare its performance with the commonly used gaussian fitting of the point spread function. We performed realistic simulations at different signal-to-noise ratios and particle densities and show that the calculation time using the wavelet approach can be more than one order of magnitude faster than that of gaussian fitting without a significant degradation of the localization accuracy, from 1 nm to 4 nm in our range of study. We propose a simulation-based estimate of the resolution of an experimental single molecule acquisition. PMID:22330449

Izeddin, I; Boulanger, J; Racine, V; Specht, C G; Kechkar, A; Nair, D; Triller, A; Choquet, D; Dahan, M; Sibarita, J B



Convex Lens-Induced Confinement for Imaging Single Molecules  

PubMed Central

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

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



Single-molecule recognition imaging microscopy.  


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 results presented here demonstrate that the highly specific antibody-antigen interaction can be used to generate single-molecule maps of specific types of molecules in a compositionally complex sample while simultaneously carrying out high-resolution topographic imaging. Because it can identify specific components, the technique can be used to map composition over an image and to detect compositional changes occurring during a process. PMID:15314231

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



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.

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



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

SciTech Connect

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

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



Single molecule analysis by biological nanopore sensors.  


Nanopore sensors provide a highly innovative technique for a rapid and label-free single molecule analysis, which holds a great potential in routing applications. Biological nanopores have been used as ultra-sensitive sensors over a wide range of single molecule analysis including DNA sequencing, disease diagnosis, drug screening, environment monitoring and the construction of molecule machines. This mini review will focus on the current strategies for the identification and characterization of an individual analyte, especially based on our recent achievements in biological nanopore biosensors. PMID:24991734

Ying, Yi-Lun; Cao, Chan; Long, Yi-Tao



The art of catching and probing single molecules.  


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



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



Photoluminescent Mn4 single-molecule magnet.  


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



Interaction of Single Molecules With Metallic Nanoparticles  

Microsoft Academic Search

We theoretically investigate the interaction between a single molecule and a metallic nanoparticle (MNP). We develop a general quantum mechanical description for the calculation of the enhancement of radiative and nonradiative decay channels for a molecule situated in the near-field regime of the MNP. Using a boundary element method approach, we compute the scattering rates for several nanoparticle shapes. We

Ulrich Hohenester; Andreas Truegler



Flexibility of phenylene oligomers revealed by single molecule spectroscopy.  


The rigidity of a p-phenylene oligomer (p-terphenyl) has been investigated by single molecule confocal fluorescence microscopy. Two different rylene diimide dyes attached to the terminal positions of the oligomer allowed for wavelength selective excitation of the two chromophores. In combination with polarization modulation the spatial orientation of the transition dipoles of both end groups could be determined independently. We have analyzed 597 single molecules in two different polymer hosts, polymethylmethacrylate and Zeonex. On average we find a 22 degrees deviation from the linear gas phase geometry (T = 0 K), indicating a rather high flexibility of the p-phenylene oligomer independent of the matrix. To substantiate our experimental results, we have performed quantum chemical calculations at the density functional theory level for the molecular geometry and the electronic excitations. Our findings are in agreement with former experiments on the persistence length of poly(p-phenylenes). PMID:17042646

Fückel, Burkhard; Hinze, Gerald; Diezemann, Gregor; Nolde, Fabian; Müllen, Klaus; Gauss, Jürgen; Basché, Thomas



Flexibility of phenylene oligomers revealed by single molecule spectroscopy  

NASA Astrophysics Data System (ADS)

The rigidity of a p-phenylene oligomer (p-terphenyl) has been investigated by single molecule confocal fluorescence microscopy. Two different rylene diimide dyes attached to the terminal positions of the oligomer allowed for wavelength selective excitation of the two chromophores. In combination with polarization modulation the spatial orientation of the transition dipoles of both end groups could be determined independently. We have analyzed 597 single molecules in two different polymer hosts, polymethylmethacrylate and Zeonex®. On average we find a 22° deviation from the linear gas phase geometry (T=0 K), indicating a rather high flexibility of the p-phenylene oligomer independent of the matrix. To substantiate our experimental results, we have performed quantum chemical calculations at the density functional theory level for the molecular geometry and the electronic excitations. Our findings are in agreement with former experiments on the persistence length of poly(p-phenylenes).

Fückel, Burkhard; Hinze, Gerald; Diezemann, Gregor; Nolde, Fabian; Müllen, Klaus; Gauss, Jürgen; Basché, Thomas



Strongly enhanced field-dependent single-molecule electroluminescence.  


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

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



Diamond-based single-molecule magnetic resonance spectroscopy  

NASA Astrophysics Data System (ADS)

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. In this paper, we demonstrate theoretically that a single nitrogen-vacancy 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 would find applications in single-molecule spectroscopy in chemistry and biology, for example in determining the protein structure or in monitoring macromolecular motions, and can thus provide a tool to help unravel the microscopic mechanisms underlying bio-molecular function.

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



Automated imaging system for single molecules  


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



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.

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



Superresolution Imaging using Single-Molecule Localization  

PubMed Central

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

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



Single molecule photophysics near metallic nanostructures  

NASA Astrophysics Data System (ADS)

Metal-enhanced fluorescence (MEF) is useful in single molecule detection (SMD) by increasing the photostability, brightness and increase in radiative decay rates of fluorophores. We have investigated MEF from an individual fluorophore tethered to a single silver nanoparticle and also a single fluorophore between a silver dimer. The fluorescence lifetime results revealed a near-field interaction mechanism of fluorophore with the metal particle. Finite-difference time-domain (FDTD) calculations were employed to study the distribution of electric field near the metal monomer and dimer. The coupling effect of metal particles on the fluorescence enhancement was studied. We have also investigated the photophysics of FRET near metal nanoparticles and our preliminary results suggest an enhanced FRET efficiency in the presence of a metal nanoparticle. In total, our results demonstrate improved detectability at the single molecule level for a variety of fluorophores and quantum dots in proximity to the silver nanoparticles due to the near-field metal-fluorophore interactions.

Zhang, Jian; Fu, Yi; Ray, Krishanu; Chowdhury, Mustafa H.; Szmacinski, Henryk; Nowaczyk, Kazimierz; Lakowicz, Joseph R.



Single Molecule Detection of Nanomechanical Motion  

NASA Astrophysics Data System (ADS)

We investigate theoretically how single molecule spectroscopy techniques can be used to perform fast and high resolution displacement detection and manipulation of nanomechanical oscillators, such as singly clamped carbon nanotubes. We analyze the possibility of real time displacement detection by the luminescence signal and of displacement fluctuations by the degree of second order coherence. Estimates of the electromechanical coupling constant indicate that intriguing regimes of strong backaction between the two-level system of a molecule and the oscillator can be realized.

Puller, Vadim; Lounis, Brahim; Pistolesi, Fabio



Increased throughput single molecule detection of DNA  

Microsoft Academic Search

In this work, we present research in using confocal optical techniques with femtolitre focal volumes and obtain very high signal-to-noise and signal-to-background ratios for single molecule detection (SMD). We were able to achieve improved signal strength by using highly fluorescent quantum dots and nanopatterned substrates to obtain plasmon induced resonant fluorescence enhancement. A method to simultaneously using multiple excitation spots

Rajan Gurjar; Madhavi Seetamraju; Noah Kolodziejski; Richard Myers; Christopher Staples; James Christian; Michael R. Squillante; Gerald Entine



Prospects for Single Molecule Information Devices  

Microsoft Academic Search

Present information technologies use semiconductor devices and magnetic\\/optical discs, however, they are all foreseen to face fundamental limitations within a decade. Therefore, superseding devices are required for the next paradigm of high performance information technologies. This paper describes prospects for single molecule devices suitable for future information technologies. Possible four milestones for realizing the Peta(1015)\\/Exa(1018)-floating operations per second (FLOPS) personal

Yasuo Wada



Periodic acceptor excitation spectroscopy of single molecules  

Microsoft Academic Search

Alternating-laser excitation (ALEX) spectroscopy has recently been added to the single-molecule spectroscopy toolkit. ALEX\\u000a monitors interaction and stoichiometry of biomolecules, reports on biomolecular structure by measuring accurate Förster resonance\\u000a energy transfer (FRET) efficiencies, and allows sorting of subpopulations on the basis of stoichiometry and FRET. Here, we\\u000a demonstrate that a simple combination of one continuous-wave donor-excitation laser and one directly

Sören Doose; Mike Heilemann; Xavier Michalet; Shimon Weiss; Achillefs N. Kapanidis



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



Single-molecule nanometry for biological physics.  


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 ms time resolution, as well as how these new tools are providing fundamental insights into 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 the 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



Graphical models for inferring single molecule dynamics  

PubMed Central

Background The recent explosion of experimental techniques in single molecule biophysics has generated a variety of novel time series data requiring equally novel computational tools for analysis and inference. This article describes in general terms how graphical modeling may be used to learn from biophysical time series data using the variational Bayesian expectation maximization algorithm (VBEM). The discussion is illustrated by the example of single-molecule fluorescence resonance energy transfer (smFRET) versus time data, where the smFRET time series is modeled as a hidden Markov model (HMM) with Gaussian observables. A detailed description of smFRET is provided as well. Results The VBEM algorithm returns the model’s evidence and an approximating posterior parameter distribution given the data. The former provides a metric for model selection via maximum evidence (ME), and the latter a description of the model’s parameters learned from the data. ME/VBEM provide several advantages over the more commonly used approach of maximum likelihood (ML) optimized by the expectation maximization (EM) algorithm, the most important being a natural form of model selection and a well-posed (non-divergent) optimization problem. Conclusions The results demonstrate the utility of graphical modeling for inference of dynamic processes in single molecule biophysics.



Single-molecule nanometry for biological physics  

NASA Astrophysics Data System (ADS)

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 ms time resolution, as well as how these new tools are providing fundamental insights into 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 the 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.

Kim, Hajin; Ha, Taekjip



Probing single molecules in single living cells.  


Single-molecule detection in single living cells has been achieved by using confocal fluorescence microscopy and externally tagged probe molecules. The intracellular background fluorescence is substantially higher than that in aqueous buffer, but this background is continuous and stable and does not significantly interfere with the measurement of single-molecule photon bursts. As a result, single-molecule data have been obtained on three types of fluorescent probes at spatially resolved locations (e.g., cytoplasm and nucleus) inside human HeLa cells. First, the iron transport protein transferrin labeled with tetramethylrhodamine undergoes rapid receptor-mediated endocytosis, and single transferrin molecules are detected inside living cells. Second, the cationic dye rhodamine 6G (R6G) enters cultured cells by a potential-driven process, and single R6G molecules are observed as intense photon bursts when they move in and out of the intracellular laser beam. Third, we report results on synthetic oligonucleotides that are tagged with a fluorescent dye and are taken up by living cells via a passive, nonendocytic pathway. PMID:11101238

Byassee, T A; Chan, W C; Nie, S



Single-molecule sensing electrode embedded in-plane nanopore  

NASA Astrophysics Data System (ADS)

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

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



Silicon nanowire based single-molecule SERS sensor  

NASA Astrophysics Data System (ADS)

One-dimensional nanowire (NW) optical sensors have attracted great attention as promising nanoscale tools for applications such as probing inside living cells. However, achieving single molecule detection on NW sensors remains an interesting and unsolved problem. In the present paper, we investigate single-molecule detection (SMD) on a single SiNW based surface-enhanced Raman scattering (SERS) sensor, fabricated by controllably depositing silver nanoparticles on a SiNW (AgNP-SiNW). Both Raman spectral blinking and bi-analyte approaches are performed in aqueous solution to investigate SMD on individual SiNW SERS sensors. The results extend the functions of the SiNW sensor to SMD and provide insight into the molecule level illustration on the sensing mechanism of the nanowire sensor.One-dimensional nanowire (NW) optical sensors have attracted great attention as promising nanoscale tools for applications such as probing inside living cells. However, achieving single molecule detection on NW sensors remains an interesting and unsolved problem. In the present paper, we investigate single-molecule detection (SMD) on a single SiNW based surface-enhanced Raman scattering (SERS) sensor, fabricated by controllably depositing silver nanoparticles on a SiNW (AgNP-SiNW). Both Raman spectral blinking and bi-analyte approaches are performed in aqueous solution to investigate SMD on individual SiNW SERS sensors. The results extend the functions of the SiNW sensor to SMD and provide insight into the molecule level illustration on the sensing mechanism of the nanowire sensor. Electronic supplementary information (ESI) available: Additional information on the experimental details, quantitative evaluation of the enhancement factor, and stability of the sensor. See DOI: 10.1039/c3nr01879b

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



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

SciTech Connect

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

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



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



Single-molecule magnets: two-electron reduced version of a Mn12 complex and environmental influences on the magnetization relaxation of (PPh4)(2)[Mn(12)O(12)(O(2)CCHCl2)(16)(H2O)4].  


The complex [Mn(12)O(12)(O(2)CCHCl(2))(16)(H(2)O)(4)] (2) in MeCN exhibits three quasi-reversible one-electron reduction processes at significantly higher potentials than [Mn(12)O(12)(O(2)CMe)(16)(H(2)O)(4)] (1). This has allowed the two-electron reduced version of 2 to be generated and isolated. Reaction of 2 with one and two equivalents of PPh(4)I led to isolation of (PPh(4))[Mn(12)O(12)(O(2)CCHCl(2))(16)(H(2)O)(4)] (3) and (PPh(4))(2)[Mn(12)O(12)(O(2)CCHCl(2))(16)(H(2)O)(4)] (4), respectively. The latter represents a new isolated oxidation level of the Mn(12) family of single-molecule magnets (SMMs). Crystallization from CH(2)Cl(2)/hexanes yields a mixture of two crystal forms, 4.4CH(2)Cl(2).H(2)O (4a) and 4.6CH(2)Cl(2) (4b), both of which have been structurally characterized as triclinic and monoclinic, respectively. The molecular structures are very similar, with the added electrons localized on former Mn(III) ions to give a trapped-valence 2Mn(II), 6Mn(III), 4Mn(IV) oxidation state description. Dried solid analyzed as unsolvated 4. (1)H NMR spectral data in CD(2)Cl(2) confirm that 4 retains its solid-state structure in solution. Bulk DC magnetization data for dried 4 in the 1.80-4.00 K and 10-70 kG ranges were fit to give S = 10, D = -0.275 cm(-1), g = 2.00 and |D|/g = 0.14 cm(-1), where D is the axial zero-field splitting (anisotropy) parameter. Complexes 4a and 4b give resolvable frequency-dependent out-of-phase (chi(M)'') signals in AC susceptibility studies resulting from the magnetization relaxation of SMMs. Relaxation rate vs T data to 1.8 K obtained from the chi(M)'' vs temperature studies were supplemented with rate vs T data measured to lower temperatures via magnetization vs time decay data, and these were fit to the Arrhenius equation to give the effective barrier to relaxation (U(eff)). The U(eff) values are 18.5 and 30.3 K for 4a and 4b, respectively. A similar analysis for dried 4 using AC data gave U(eff) = 32 K. Magnetization vs DC field sweeps on single crystals of 4a and 4b gave hysteresis loops containing steps due to quantum tunneling of magnetization (QTM). The step separations yielded |D|/g values of 0.087 and 0.14 cm(-1) for 4a and 4b, respectively, suggesting that the differences in U(eff) are primarily caused by changes to D. The combined work demonstrates the sensitivity of the magnetic properties of these new [Mn(12)](2-) SMMs to subtle differences in their environment as determined by the precise packing, solvent molecules, and overall crystal symmetry (space group) and represents an important caveat to workers in the field. PMID:12643720

Soler, Monica; Wernsdorfer, Wolfgang; Abboud, Khalil A; Huffman, John C; Davidson, Ernest R; Hendrickson, David N; Christou, George



Periodic acceptor excitation spectroscopy of single molecules  

PubMed Central

Alternating-laser excitation (ALEX) spectroscopy has recently been added to the single-molecule spectroscopy toolkit. ALEX monitors interaction and stoichiometry of biomolecules, reports on biomolecular structure by measuring accurate Förster resonance energy transfer (FRET) efficiencies, and allows sorting of subpopulations on the basis of stoichiometry and FRET. Here, we demonstrate that a simple combination of one continuous-wave donor-excitation laser and one directly modulated acceptor-excitation laser (Periodic Acceptor eXcitation) is sufficient to recapitulate the capabilities of ALEX while minimizing the cost and complexity associated with use of modulation techniques.

Doose, Soren; Heilemann, Mike; Michalet, Xavier; Weiss, Shimon



Modeling transport through single-molecule junctions  

Microsoft Academic Search

Non-equilibrium Green's functions (NEGF) formalism combined with extended Hckel (EHT) and charging model are used to study\\u000a electrical conduction through single-molecule junctions. The analyzed molecular complex is composed of the asymmetric 1,4-Bis((2?-para-mercaptophenyl)-ethinyl)-2-acetyl-amino-5-nitrobenzene molecule symmetrically coupled to two gold electrodes. Owing to this\\u000a model, the accurate values of the current flowing through such junctions can be obtained by utilizing basic fundamentals

Kamil Walczak; Sergey Edward Lyshevski



Chemistry of Single Molecules at Surfaces  

NASA Astrophysics Data System (ADS)

Vibrational excitation of single molecules at surfaces will open an ultimate way of the reaction control in nano-meter scale. Direct excitation along the reaction coordinate coupled with the multiple excitations will lead to molecule-to-molecule chemistry. For the indirect process, anharmonic coupling between the excited vibrational state and the reaction coordinate plays an important role. Action spectrum for cic-2-butene on Pd(110) exhibits low frequency vibrational modes are excited by inelastic tunneling but are not clearly visible in STM-IETS.

Kawai, Maki; Komeda, T.; Kim, Y.; Sainoo, Y.



Single Molecule Dynamics Studied by Polarization Modulation  

SciTech Connect

We observed and made unambiguous distinctions between abrupt photophysical events of single molecules: a rotational jump of a single dipole, a transition to a dark state (reversible and irreversible photobleaching), and a spectral jump. The study was performed in the far field by modulating the excitation polarization and monitoring the fluorescence in time. This technique also allowed us to measure the in-plane dipole orientation of stationary single molecular dipoles with subdegree accuracy and to resolve desorption and readsorption of fluorophores from and onto a glass surface. In one case, clear evidence was obtained for rapid rotation of the dipole after a desorption process. {copyright} {ital 1996 The American Physical Society.}

Ha, T.; Enderle, T.; Chemla, S. [Physics Department, University of California at Berkeley, Berkeley, California 94720 (United States)] [Physics Department, University of California at Berkeley, Berkeley, California 94720 (United States); [Molecular Design Institute, Materials Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720 (United States); Selvin, R. [Life Science Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720 (United States)] [Life Science Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720 (United States); Weiss, S. [Molecular Design Institute, Materials Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720 (United States)] [Molecular Design Institute, Materials Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720 (United States)



Hybrid photodetector for single-molecule spectroscopy and microscopy  

PubMed Central

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

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



Quantum design rules for single molecule logic gates.  


Recent publications have demonstrated how to implement a NOR logic gate with a single molecule using its interaction with two surface atoms as logical inputs [W. Soe et al., ACS Nano, 2011, 5, 1436]. We demonstrate here how this NOR logic gate belongs to the general family of quantum logic gates where the Boolean truth table results from a full control of the quantum trajectory of the electron transfer process through the molecule by very local and classical inputs practiced on the molecule. A new molecule OR gate is proposed for the logical inputs to be also single metal atoms, one per logical input. PMID:21792457

Renaud, N; Hliwa, M; Joachim, C



Single-molecule chemical denaturation of riboswitches  

PubMed Central

To date, single-molecule RNA science has been developed almost exclusively around the effect of metal ions as folding promoters and stabilizers of the RNA structure. Here, we introduce a novel strategy that combines single-molecule Förster resonance energy transfer (FRET) and chemical denaturation to observe and manipulate RNA dynamics. We demonstrate that the competing interplay between metal ions and denaturant agents provides a platform to extract information that otherwise will remain hidden with current methods. Using the adenine-sensing riboswitch aptamer as a model, we provide strong evidence for a rate-limiting folding step of the aptamer domain being modulated through ligand binding, a feature that is important for regulation of the controlled gene. In the absence of ligand, the rate-determining step is dominated by the formation of long-range key tertiary contacts between peripheral stem-loop elements. In contrast, when the adenine ligand interacts with partially folded messenger RNAs, the aptamer requires specifically bound Mg2+ ions, as those observed in the crystal structure, to progress further towards the native form. Moreover, despite that the ligand-free and ligand-bound states are indistinguishable by FRET, their different stability against urea-induced denaturation allowed us to discriminate them, even when they coexist within a single FRET trajectory; a feature not accessible by existing methods.

Dalgarno, Paul A.; Bordello, Jorge; Morris, Rhodri; St-Pierre, Patrick; Dube, Audrey; Samuel, Ifor D. W.; Lafontaine, Daniel A.; Penedo, J. Carlos



Gene expression analysis using single molecule detection  

PubMed Central

Recent developments of single molecule detection techniques and in particular the introduction of fluorescence correlation spectroscopy (FCS) led to a number of important applications in biological research. We present a unique approach for the gene expression analysis using dual-color cross-correlation. The expression assay is based on gene-specific hybridization of two dye-labeled DNA probes to a selected target gene. The counting of the dual-labeled molecules within the solution allows the quantification of the expressed gene copies in absolute numbers. As detection and analysis by FCS can be performed at the level of single molecules, there is no need for any type of amplification. We describe the gene expression assay and present data demonstrating the capacity of this novel technology. In order to prove the gene specificity, we performed experiments with gene-depleted total cDNA. The biological application was demonstrated by quantifying selected high, medium and low abundant genes in cDNA prepared from HL-60 cells.

Korn, Kerstin; Gardellin, Paola; Liao, Bohao; Amacker, Mario; Bergstrom, ?sa; Bjorkman, Henrik; Camacho, Agnes; Dorhofer, Sabine; Dorre, Klaus; Enstrom, Johanna; Ericson, Thomas; Favez, Tatiana; Gosch, Michael; Honegger, Adrian; Jaccoud, Sandra; Lapczyna, Markus; Litborn, Erik; Thyberg, Per; Winter, Holger; Rigler, Rudolf



Single Molecule Studies of Nucleocytoplasmic Transport  

PubMed Central

Molecular traffic between the cytoplasm and the nucleoplasm of eukaryotic cells is mediated by nuclear pore complexes (NPCs). Hundreds, if not thousands, of molecules interact with and transit through each NPC every second. The pore is blocked by a permeability barrier, which consists of a network of intrinsically unfolded polypeptides containing thousands of phenylalanine-glycine (FG) repeat motifs. This FG-network rejects larger molecules and admits smaller molecules or cargos bound to nuclear transport receptors (NTRs). For a cargo transport complex, minimally consisting of a cargo molecule plus an NTR, access to the permeability barrier is provided by interactions between the NTR and the FG repeat motifs. Numerous models have been postulated to explain the controlled accessibility and the transport characteristics of the FG-network, but the amorphous, flexible nature of this structure has hindered characterization. A relatively recent development is the ability to monitor the real-time movement of single molecules through individual NPCs via single molecule fluorescence (SMF) microscopy. A major advantage of this approach is that it can be used to continuously monitor a series of specific molecular interactions in an active pore with millisecond time resolution, which therefore allows one to distinguish between kinetic and thermodynamic control. Novel insights and prospects for the future are outlined in this review.

Tu, Li-Chun; Musser, Siegfried M.



Direct spectroscopic observation of quantum jumps of a single molecule  

NASA Astrophysics Data System (ADS)

BOHR'S notion of quantum jumps between electronic states of an excited atom has now been demonstrated experimentally for single ions confined in radio-frequency traps and interacting with a driving laser field1-3. In these experiments the fluorescence of a strongly allowed transition was shown to cease abruptly when the ion jumped into a metastable state which was coupled to the common electronic ground state by a weak radiative transition. But attempts to monitor quantum jumps of single molecules have been hampered by the fact that the lifetime of the metastable triplet state was too short in relation to the photon detection rate. By using a system with favourable photophysical parameters-terrylene doped into p-terphenyl crystals4-we have now been able to observe directly quantum jumps between electronic states of single terrylene molecules. In contrast to single atoms, here the quantum jumps occur as non-radiative transitions between states of different multiplicity, and are manifested as interruptions of the fluorescence signal. These results demonstrate how single-molecule spectros-copy can reveal truly quantum-mechanical effects in large polyatomic molecules.

Basché, Th.; Kummer, S.; Bräuchle, C.



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

Microsoft Academic Search

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

Michael Strano



Current status of single-molecule spectroscopy: Theoretical aspects  

Microsoft Academic Search

We survey the current status of single-molecule spectroscopy in the view point of theoretical aspects. After an explanation of basic concepts in single-molecule spectroscopy, we focus on the following topics: (1) line shape phenomena in disordered media, (2) photon counting statistics for time-dependent fluctuations in single-molecule spectroscopy, (3) fluorescence intensity fluctuations for nonergodic systems, (4) time-resolved single-molecule fluorescence for conformational

Younjoon Jung; Eli Barkai; Robert J. Silbey



Synthesis of single-molecule nanocars.  


The drive to miniaturize devices has led to a variety of molecular machines inspired by macroscopic counterparts such as molecular motors, switches, shuttles, turnstiles, barrows, elevators, and nanovehicles. Such nanomachines are designed for controlled mechanical motion and the transport of nanocargo. As researchers miniaturize devices, they can consider two complementary approaches: (1) the "top-down" approach, which reduces the size of macroscopic objects to reach an equivalent microscopic entity using photolithography and related techniques and (2) the "bottom-up" approach, which builds functional microscopic or nanoscopic entities from molecular building blocks. The top-down approach, extensively used by the semiconductor industry, is nearing its scaling limits. On the other hand, the bottom-up approach takes advantage of the self-assembly of smaller molecules into larger networks by exploiting typically weak molecular interactions. But self-assembly alone will not permit complex assembly. Using nanomachines, we hope to eventually consider complex, enzyme-like directed assembly. With that ultimate goal, we are currently exploring the control of nanomachines that would provide a basis for the future bottom-up construction of complex systems. This Account describes the synthesis of a class of molecular machines that resemble macroscopic vehicles. We designed these so-called nanocars for study at the single-molecule level by scanning probe microscopy (SPM). The vehicles have a chassis connected to wheel-terminated axles and convert energy inputs such as heat, electric fields, or light into controlled motion on a surface, ultimately leading to transport of nanocargo. At first, we used C(60) fullerenes as wheels, which allowed the demonstration of a directional rolling mechanism of a nanocar on a gold surface by STM. However, because of the low solubility of the fullerene nanocars and the incompatibility of fullerenes with photochemical processes, we developed new p-carborane- and ruthenium-based wheels with greater solubility in organic solvents. Although fullerene wheels must be attached in the final synthetic step, p-carborane- and ruthenium-based wheels do not inhibit organometallic coupling reactions, which allows a more convergent synthesis of molecular machines. We also prepared functional nanotrucks for the transport of atoms and molecules, as well as self-assembling nanocars and nanotrains. Although engineering challenges such as movement over long distance and non-atomically flat surfaces remain, the greatest current research challenge is imaging. The detailed study of nanocars requires complementary single molecule imaging techniques such as STM, AFM, TEM, or single-molecule fluorescence microscopy. Further developments in engineering and synthesis could lead to enzyme-like manipulation and assembly of atoms and small molecules in nonbiological environments. PMID:19245268

Vives, Guillaume; Tour, James M



Single molecule detection for in vitro diagnostics  

NASA Astrophysics Data System (ADS)

In this paper we present a novel highly sensitive detection system for diagnostic applications. The system is designed to meet the needs of medical diagnostics for reliable measurements of pathogens and biomarkers in the low concentration regime. It consists of a confocal detection unit, micro-structured sampling cells, and a "Virtual lab" analysis software. The detection unit works with laser induced fluorescence and is designed to provide accurate and highly sensitive measurement at the single molecule level. Various sampling cells are micro-structured in glass, silicon or polymers to enable measurements under flow and nonflow conditions. Sampling volume is below one microliter. The "Virtual lab" software analyzes the light intensity online according to the patent pending "Accurate Stochastic Fluorescence Spectroscopy" (ASFS) developed by FluIT Biosystems GmbH. Tools for simulation and experiment optimization are included as well. Experimental results for various applications with relevance for in vitro diagnostics will be presented.

Kirner, Thomas; Ackermann, Jörg; Mathis, Harald P.; Greiner, Benjamin; Tonn, Thomas; Tschachojan, David; Kukoc-Zivojnov, Natasa; Giehring, Sebastian



Single molecule diffusion in critical lipid bilayers  

NASA Astrophysics Data System (ADS)

Time-dependent single molecule diffusion coefficients are discussed for a fluorescent probe molecule in lipid mixtures near a miscibility critical point. The calculations take advantage of the theoretical wave vector dependent composition diffusion coefficients obtained by Inaura and Fujitani [J. Phys. Soc. Jpn. 77, 114603 (2008)]. It is suggested that the diffusion of the probe molecule reflects in part the time-dependent composition diffusion near a critical point. The calculations show a striking biphasic time-dependent diffusion that switches from a faster diffusion at short times to a slower diffusion at a time approximately equal to ??2/D where ? is the correlation length and D is the composition diffusion coefficient at the switch time. This biphasic diffusion should be readily detectable experimentally.

McConnell, Harden



High throughput single molecule detection for monitoring biochemical reactions  

PubMed Central

The design, performance and application of a novel optical system for high throughput single molecule detection (SMD) configured in a continuous flow format using microfluidics is reported. The system consisted of a microfabricated polymer-based multi-channel fluidic network situated within the optical path of a laser source (?ex = 660 nm) with photon transduction accomplished using an electron-multiplying charge coupled device (EMCCD) operated in a frame transfer mode that allowed tracking single molecules as they passed through a large field-of-view (FoV) illumination zone. The microfluidic device consisted of 30 microchannels possessing dimensions of 30 ?m (width) × 20 ?m (depth) with a 25 mm pitch. Individual molecules were electrokinetically driven through the fluidic network and excited within the wide-field illumination area with the resulting fluorescence collected via an objective and imaged onto the EMCCD camera. The detection system demonstrated sufficient sensitivity to detect single DNA molecules labeled with a fluorescent tag (AlexaFluor 660) identified through their characteristic emission wavelength and the burst of photons produced during their transit through the excitation volume. In its present configuration and fluidic architecture, the sample processing throughput was ?4.02 × 105 molecules s?1, but could be increased dramatically through the use of narrower channels and a smaller pitch. The system was further evaluated using a single molecule-based fluorescence quenching assay for measuring the population differences between duplexed and single-stranded DNA molecules as a function of temperature for determining the duplex melting temperature, Tm.

Okagbare, Paul I.; Soper, Steven A.



Single molecule measurements and biological motors.  


Recent technological advances in lasers and optical detectors have enabled a variety of new, single molecule technologies to be developed. Using intense and highly collimated laser light sources in addition to super-sensitive cameras, the fluorescence of single fluorophores can now be imaged in aqueous solution. Also, laser optical tweezers have enabled the piconewton forces produced by pair of interacting biomolecules to be measured directly. However, for a researcher new to the field to begin to use such techniques in their own research might seem a daunting prospect. Most of the equipment that is in use is custom-built. However, most of the equipment is essence fairly simple and the aim of this article is to provide an entry point to the field for a newcomer. It focuses mainly on those practical aspects which are not particularly well covered in the literature, and aims to provide an overview of the field as a whole with references and web links to more detailed sources elsewhere. Indeed, the opportunity to publish an article such as this on the Internet affords many new opportunities (and more space!) for presenting scientific ideas and information. For example, we have illustrated the nature of optical trap data with an interactive Java simulation; provided links to relevant web sites and technical documents, and included a large number of colour figures and plots. Our group's research focuses on molecular motors, and the bias of this article reflects this. It turns out that molecular motors have been a paradigm (or prototype) for single molecule research and the field has seen a rapid development in the techniques. It is hoped that the methods described here will be broadly applicable to other biological systems. PMID:16136326

Knight, Alex E; Mashanov, Gregory; Molloy, Justin E



Vibrationally induced decoherence in single-molecule junctions  

NASA Astrophysics Data System (ADS)

We investigate the interplay of quantum interference effects and electronic-vibrational coupling in electron transport through single-molecule junctions, employing a nonequilibrium Green's function approach. Our findings show that inelastic processes lead, in general, to a quenching of quantum interference effects. This quenching is more pronounced for increasing bias voltages and levels of vibrational excitation. As a result of this vibrationally induced decoherence, vibrational signatures in the transport characteristics of a molecular contact may strongly deviate from a simple Franck-Condon picture. This includes signatures in both the resonant and the nonresonant transport regimes. Moreover, it is shown that local cooling by electron-hole pair creation processes can influence the transport characteristics profoundly, giving rise to a significant temperature dependence of the electrical current.

Härtle, R.; Butzin, M.; Thoss, M.



Bringing single-molecule spectroscopy to macromolecular protein complexes  

PubMed Central

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

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



Scanning tunneling microscopy and spectroscopy of single molecules and nanocrystals in double-barrier tunnel junctions  

Microsoft Academic Search

Electron transport in single molecules and nanocrystals was studied in the regime of weak electronic coupling to the electrodes. To decouple the electronic states of the adsorbates from the metal substrate, they were adsorbed on thin insulating layers, such as oxide or alkali halide, grown or deposited on the metal substrate. The presence of the two tunneling barriers allows observation

Gareguin R. Mikaelian



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



Single-molecule fluorescence quenching near small nanoparticles  

NASA Astrophysics Data System (ADS)

We study theoretically radiative and nonradiative decay of a single molecule near small gold nanoparticle. The local field enhancement leads to an increased radiative decay rate while the energy transfer from molecule to optically-inactive electronic states in nanoparticle results in a decrease in fluorescence quantum efficiency for small molecule-nanoparticle distances. We performed a DFT-TDLDA calculation of both the enhancement and the quenching for small nanometer-sized gold nanoparticles. We found that in a close proximity to the surface, the non-radiative decay rate is dominated by generation of electron-hole pairs out of the Fermi sea resulting in a significantly lower quantum efficiency as compared to that obtained from electromagnetic calculations. For large distances, the efficiency is maximal for molecule polarized normal to the surface, whereas for small distances it is maximal for parallel orientation.

Pustovit, V. N.; Shahbazyan, T. V.



Tracking Nanocars Using Single Molecule Spectroscopy  

NASA Astrophysics Data System (ADS)

Nanocars belong to an exciting new class of molecules known as molecular machines. They consist of four fullerene or carborane wheels attached to a chassis consisting of a stiff aromatic backbone. The nanocars are designed to roll over a solid surface making them potential candidates for nano-cargo transporters. Here, we present our results on tracking of nanocars by single molecule fluorescence spectroscopy. By attaching the fluorescent tag tetramethylrhodamin isothiocyanate to the nanocars, we were able to visualize and track individual nanocars using confocal sample scanning microscopy. Fluorescence images were analyzed for directional movement as opposed to random diffusion or stage drift. We had to overcome 2 major problems in our image analysis: 1) fluorescence photo-blinking and 2) photo-bleaching. We developed routines that are capable of tracking individual fluorescent molecules while accounting for photo-blinking and photo-bleaching. The ability to track individual nanocars is checked independently by simulations. Our method is not limited to tracking of nanocars however, and can be extended to follow individual molecules in biological or mechanical systems as well.

Link, Stephan; Khatua, Saumyakanti; Claytor, Kevin; Guerrero, Jason; Tour, James



Single-molecule magnets ``without'' intermolecular interactions  

NASA Astrophysics Data System (ADS)

Intermolecular magnetic interactions (dipole-dipole and exchange) affect strongly the magnetic relaxation of crystals of single-molecule magnets (SMMs), especially at low temperature, where quantum tunneling of the magnetization (QTM) dominates. This leads to complex many-body problems [l]. Measurements on magnetically diluted samples are desirable to clearly sort out the behaviour of magnetically-isolated SMMs and to reveal, by comparison, the effect of intermolecular interactions. Here, we diluted a Fe4 SMM into a diamagnetic crystal lattice, affording arrays of independent and iso-oriented magnetic units. We found that the resonant tunnel transitions are much sharper, the tunneling efficiency changes significantly, and two-body QTM transitions disappear. These changes have been rationalized on the basis of a dipolar shuffling mechanism and of transverse dipolar fields, whose effect has been analyzed using a multispin model. Our findings directly prove the impact of intermolecular magnetic couplings on the SMM behaviour and disclose the magnetic response of truly-isolated giant spins in a diamagnetic crystalline environment.[4pt] [1] W. Wernsdorfer, at al, PRL 82, 3903 (1999); PRL 89, 197201 (2002); Nature 416, 406 (2002); IS Tupitsyn, PCE Stamp, NV Prokof'ev, PRB 69, 132406 (2004).

Wernsdorfer, W.; Vergnani, L.; Rodriguez-Douton, M. J.; Cornia, A.; Neugebauer, P.; Barra, A. L.; Sorace, L.; Sessoli, R.



High-sensitivity single molecule fluorescence detection using scanning single-molecule counting  

NASA Astrophysics Data System (ADS)

A new, simple technique for single molecule fluorescence detection has been developed and detection limit of less than 100 aM fluorophores has been demonstrated. The technique, similarly to Fluorescence Correlation Spectroscopy (FCS) and other related techniques, uses confocal optics, but differs in that it detects individual molecules crossing the inside of a scanning confocal volume without using statistical techniques as applied in FCS or similar methods. The scanning speed of the confocal volume is higher than the Brownian motion speed of the molecules. Thus, the time evolution of the light intensity data reflects the confocal volume intensity profile, which clearly shows the crossing of single molecules. The estimated total scanning volume enables the concentration or the density of molecules to be obtained. In addition, information related to the rotational and translational diffusion of the molecule was obtained for the purpose of identifying different molecules. It was shown that utilizing the plural characteristic properties of molecules passing through a confocal volume makes possible the discrimination of different molecules. The proposed technique is based on the simple principle of counting molecules one by one using a scanning confocal volume, and is hereafter referred to as Scanning Single-Molecule Counting (SSMC).

Yamaguchi, Mitsushiro; Tanabe, Tetsuya; Nakata, Hidetaka; Hanashi, Takuya; Nishikawa, Kazutaka; Hori, Kunio; Kondo, Seiji



Multiple events on single molecules: unbiased estimation in single-molecule biophysics.  


Most analyses of single-molecule experiments consist of binning experimental outcomes into a histogram and finding the parameters that optimize the fit of this histogram to a given data model. Here we show that such an approach can introduce biases in the estimation of the parameters, thus great care must be taken in the estimation of model parameters from the experimental data. The bias can be particularly large when the observations themselves are not statistically independent and are subjected to global constraints, as, for example, when the iterated steps of a motor protein acting on a single molecule must not exceed the total molecule length. We have developed a maximum-likelihood analysis, respecting the experimental constraints, which allows for a robust and unbiased estimation of the parameters, even when the bias well exceeds 100%. We demonstrate the potential of the method for a number of single-molecule experiments, focusing on the removal of DNA supercoils by topoisomerase IB, and validate the method by numerical simulation of the experiment. PMID:16439482

Koster, Daniel A; Wiggins, Chris H; Dekker, Nynke H



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.



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



Single-Molecule Fluorescence Studies of RNA: A Decade's Progress  

PubMed Central

Over the past decade, single-molecule fluorescence studies have elucidated the structure-function relationship of RNA molecules. The real-time observation of individual RNAs by single-molecule fluorescence has unveiled the dynamic behavior of complex RNA systems in unprecedented detail, revealing the presence of transient intermediate states and their kinetic pathways. This review provides an overview of how single-molecule fluorescence has been used to explore the dynamics of RNA folding and catalysis.

Karunatilaka, Krishanthi S.; Rueda, David



'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'.



Microarray analysis at single-molecule resolution.  


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 of 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 2-20 microm and quantifies the abundance of target molecules by determining average pixel intensities, a novel high-resolution approach 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. First, it consists of a single-molecule detection step, based on undecimated wavelet transforms, and second, 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 micrometer 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 is 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



Magnetization barrier reduction in Mn12 single-molecule magnets  

NASA Astrophysics Data System (ADS)

High-frequency electron paramagnetic resonance (HFEPR) and AC susceptibility data will be presented for a new high-symmetry Mn12-Ac complex, [Mn12O12(OAc)16(MeOH)4]. MeOH, in which the acetic acid solvent is replaced by a single methanol. The results are compared with those of several other Mn12 single-molecule magnets (SMMs), including Mn12-Ac.2CH3COOH. AC susceptibility studies indicate that Mn12-Ac.MeOH has a relatively large effective barrier, Ueff ˜ 74 K, in comparison to Mn12-Ac.2CH3COOH. Meanwhile, EPR studies suggest more-or-less identical zero-field-splitting parameters for the two complexes. Based on these findings, we discuss the factors that can lead to reductions in Ueff in various Mn12 SMMs.

Redler, Gage; Koo, Changhyun; Datta, Saiti; Lampropoulos, Christos; Stamatatos, Theocharis C.; Christou, George; Hill, Stephen



Tunneling spectroscopy of organic monolayers and single molecules.  


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



Collective effects in Single Molecule Magnets  

NASA Astrophysics Data System (ADS)

Single molecule magnets (SMMs), such as Mn12-acetate, are composed of transition metal ions and consists of identical molecules with large ground-state spin (S = 10) and a strong uniaxial anisotropy (65 K). Below about 3 K, Mn12-acetate exhibits magnetic hysteresis with steps at specific values of longitudinal magnetic field due to resonant quantum tunneling between spin up and down projections along the easy axis. The intermolecular exchange interactions between spins on molecules are quite small and spins are considered to be independent and non-interacting. However, the molecules do interact with each other both through magnetic dipolar interactions and through the lattice (e.g. phonons). I have investigated collective effects in SMMs due to these intermolecular interactions. In the thesis I will present experiments that explored magnetic ordering due to magnetic dipole interactions in Mn12-acetate and Mn12-acetate-MeOH. I will also present exper- iments on the onset of magnetic de agration in Mn12-acetate due to a thermal instability. The magnetic ordering studies involved investigating the effect of transverse fields on the susceptibility of single crystals of Mn12-acetate and Mn12-acetate- MeOH. Transverse fields increase quantum spin uctuations that suppress long- range order. However, the suppression of the Curie temperature by transverse fields in Mn12-acetate is far more rapid than predicted by the Transverse-Field Ising Ferromagnetic Model (TFIFM) and instead agrees with the predictions of the Random-Field Ising Ferromagnet Model. It appears that solvent disorder in Mn12-acetate gives rise to a distribution of random-fields that further suppress long-range order. Subsequent studies on Mn12-acetate-MeOH, with the same spin and similar lattice constants but without solvent disorder as Mn12-acetate, agrees with the TFIFM. The magnetic de agration studies involved studying the instability that leads to the ignition of magnetic deflagration in a thermally driven Mn 12-acetate crystal. When spins prepared in a metastable state reverse, Zeeman energy is released that diffuses away. In some circumstances, the heat released cannot be compensated by thermal diffusion, resulting in an instability that gives rise to a front of rapidly reversing spins traveling through the crystal. We observed a sharp crossover from relaxation driven by heat diffusion to a self-sustained reversal front that propagates at a constant subsonic speed.

Subedi, Pradeep


Photoinduced interfacial electron transfer within a mesoporous transparent conducting oxide film.  


Interfacial electron transfer to and from conductive Sn-doped In2O3 (ITO) nanoparticles (NPs) in mesoporous thin films has been investigated by transient absorption measurements using surface-bound [Ru(II)(bpy)2(dcb)](2+) (bpy is 2,2'-bipyridyl and dcb is 4,4'-(COOH)2-2,2'-bipyridyl). Metal-to-ligand charge transfer excitation in 0.1 M LiClO4 MeCN results in efficient electron injection into the ITO NPs on the picosecond time scale followed by back electron transfer on the nanosecond time scale. Rates of back electron transfer are dependent on thermal annealing conditions with the rate constant increasing from 1.8 × 10(8) s(-1) for oxidizing annealing conditions to 8.0 × 10(8) s(-1) for reducing conditions, presumably due to an enhanced electron concentration in the latter. PMID:24460093

Farnum, Byron H; Morseth, Zachary A; Lapides, Alexander M; Rieth, Adam J; Hoertz, Paul G; Brennaman, M Kyle; Papanikolas, John M; Meyer, Thomas J



Detection of Single Molecules using Two-Photon Excitation  

Microsoft Academic Search

We have developed a technique which enables us to detect single molecules in solution and on surfaces using two-photon excitation. A major experimental difficulty in observing single molecules (single chromophore) fluorescence is a low signal to background ratio. In one-photon excitation, fluorescence excitation (Raman and Rayleigh) overlaps with the fluorescence emission spectrum. Time gating techniques are often needed to reduce

Tim Ragan; Peter T. C. So; Keith Berland; Weiming Yu; Nienhaus Uli; Enrico Gratton



TOPICAL REVIEW: Single-molecule fluorescence spectroscopy of biomolecular folding  

Microsoft Academic Search

Single-molecule fluorescence spectroscopy is emerging as an important tool for studying biomolecular folding dynamics. Its usefulness stems from its ability to directly map heterogeneities in folding pathways and to provide information about the energy landscape of proteins and ribonucleic acid (RNA) molecules. Single-molecule fluorescence techniques relevant for folding studies, including methods for trapping and immobilizing molecules, are described and compared

Gilad Haran



iBioSeminar: Single Molecule Manipulation in Biochemistry  

NSDL National Science Digital Library

Dr. Bustamante begins his talk by explaining why one would wish to study biochemical reactions at the level of single molecules. He explains that many processes within the cell are carried out by very few molecules. By studying single molecules, it is possible to obtain details about the mechanism of a reaction that cannot be ascertained by studying a population of molecules.

Carlos Bustamante (University of California, Berkeley and Howard Hughes Medical Institute;)



Intensity enhancement and spectral fluctuations in single molecule Raman spectroscopy  

Microsoft Academic Search

The discovery that giant field enhancements make it possible to record vibrational spectra of single molecules on textured metal surfaces [1] has captured the imagination of many spectroscopists and could form the basis for many enticing potential applications. We will discuss studies that correlate various silver surface preparations with our ability to observe single molecule Raman spectra of molecules adsorbed

Lewis Rothberg



Microfluidics for biological measurements with single-molecule resolution.  


Single-molecule approaches in biology have been critical in studies ranging from the examination of physical properties of biological macromolecules to the extraction of genetic information from DNA. The variation intrinsic to many biological processes necessitates measurements with single-molecule resolution in order to accurately recapitulate population distributions. Microfluidic technology has proven to be useful in the facilitation and even enhancement of single-molecule studies because of the precise liquid handling, small volume manipulation, and high throughput capabilities of microfluidic devices. In this review we survey the microfluidic "toolbox" available to the single-molecule specialist and summarize some recent biological applications of single-molecule detection on chip. PMID:24484883

Streets, Aaron M; Huang, Yanyi



Interfacial Electron Transfer in TiO2 Surfaces Sensitized with Ru(II)-Polypyridine Complexes  

NASA Astrophysics Data System (ADS)

Studies of interfacial electron transfer (IET) in TiO2 surfaces functionalized with (1) pyridine-4-phosphonic acid, (2) [Ru(tpy)(tpy(PO3H2))]2+, and (3) [Ru(tpy)(bpy)(H2O)-Ru(tpy)(tpy(PO3H2))]4+ (tpy = 2,2':6,2''-terpyridine; bpy = 2,2'-bipyridine) are reported. We characterize the electronic excitations, electron injection time scales, and interfacial electron transfer (IET) mechanisms through phosphonate anchoring groups. These are promising alternatives to the classic carboxylates of conventional dye-sensitized solar cells since they bind more strongly to TiO2 surfaces and form stable covalent bonds that are unaffected by humidity. Density functional theory calculations and quantum dynamics simulations of IET indicate that electron injection in 1-TiO2 can be up to 1 order of magnitude faster when 1 is attached to TiO2 in a bidentate mode (? ˜ 60 fs) than when attached in a monodentate motif (? ˜ 460 fs). The IET time scale also depends strongly on the properties of the sensitizer as well as on the nature of the electronic excitation initially localized in the adsorbate molecule. We show that IET triggered by the visible light excitation of 2-TiO2 takes 1-10 ps when 2 is attached in a bidentate mode, a time comparable to the lifetime of the excited electronic state. IET due to visible-light photoexcitation of 3-TiO2 is slower, since the resulting electronic excitation remains localized in the tpy-tpy bridge that is weakly coupled to the electronic states of the conduction band of TiO2. These results are particularly valuable to elucidate the possible origin of IET efficiency drops during photoconversion in solar cells based on Ru(II)-polypyridine complexes covalently attached to TiO2 thin films with phosphonate linkers.

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



Dissecting single-molecule signal transduction in carbon nanotube circuits with protein engineering  

PubMed Central

Single molecule experimental methods have provided new insights into biomolecular function, dynamic disorder, and transient states that are all invisible to conventional measurements. A novel, non-fluorescent single molecule technique involves attaching single molecules to single-walled carbon nanotube field-effective transistors (SWNT FETs). These ultrasensitive electronic devices provide long-duration, label-free monitoring of biomolecules and their dynamic motions. However, generalization of the SWNT FET technique first requires design rules that can predict the success and applicability of these devices. Here, we report on the transduction mechanism linking enzymatic processivity to electrical signal generation by a SWNT FET. The interaction between SWNT FETs and the enzyme lysozyme was systematically dissected using eight different lysozyme variants synthesized by protein engineering. The data prove that effective signal generation can be accomplished using a single charged amino acid, when appropriately located, providing a foundation to widely apply SWNT FET sensitivity to other biomolecular systems.

Choi, Yongki; Olsen, Tivoli J.; Sims, Patrick C.; Moody, Issa S.; Corso, Brad L.; Dang, Mytrang N.; Weiss, Gregory A.; Collins, Philip G.



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


The recent advent in single-molecule imaging and manipulation methods has made a significant impact on the understanding of molecular mechanisms underlying many essential cellular processes. Single-molecule techniques such as electron microscopy and DNA fiber assays have been employed to study the duplication of genome in eukaryotes. Here, we describe a single-molecule assay that allows replication of DNA attached to the functionalized surface of a microfluidic flow cell in a soluble Xenopus leavis egg extract replication system and subsequent visualization of replication products via fluorescence microscopy. We also explain a method for detection of replication proteins, through fluorescently labeled antibodies, on partially replicated DNA immobilized at both ends to the surface. PMID:22503776

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



Breaking the concentration limit of optical single-molecule detection.  


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



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.

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



Manipulating NiFe/AlOx interfacial chemistry for the spin-polarized electrons transport  

NASA Astrophysics Data System (ADS)

Through vacuum annealing, interfacial chemical composition of sputter-deposited AlOx/NiFe/AlOx can be controlled for electron transport manipulation. Chemical status change at the NiFe/AlOx interface was quantified by X-ray photoelectron spectroscopy and correlated to the structure and electron transport properties of the heterostructure. It is found that elemental Al existed in the insulting AlOx after annealing at intermediate temperature can improve the AlOx/NiFe interface and thus favor the electronic transport. Annealing at higher temperature will result in native AlOx formation and degrade transport properties due to the NiFe/AlOx interfaces deterioration caused by significant difference in thermal expansion coefficients of the two materials.

Zhao, Chong-Jun; Sun, Li; Ding, Lei; Li, Jian-Wei; Zhang, Jing-Yan; Cao, Yi; Yu, Guang-Hua



Strong interfacial dipole formation with thermal evaporation of lithium cobalt oxide for efficient electron injections  

NASA Astrophysics Data System (ADS)

We investigated the electronic structures at the interface of Al/lithium cobalt oxide (LiCoO2)/tris(8-hydoxyquinoline) aluminum (Alq3) to elucidate the origin of the electron injection enhancement with the insertion of the LiCoO2 layer in organic light-emitting devices using in situ photoelectron spectroscopy experiments. We discovered that LiCoO2 was decomposed into lithium oxide (Li2O) by thermal evaporation, and only Li2O was deposited on the desired substrate. Li2O forms a strong interfacial dipole, which reduces the surface potential on Alq3 due to its extremely low work function. As a result, the electron injection barrier was dramatically decreased by the Li2O layer. Furthermore, there is no strong chemical interaction at the interface of Al/Li2O/Alq3; hence, this would contribute to extend the device lifetime.

Lee, Hyunbok; Park, Soohyung; Lee, Jeihyun; Lee, Younjoo; Shin, Dongguen; Jeong, Kwangho; Yi, Yeonjin



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.




Single-molecule detection: applications to ultrasensitive biochemical analysis  

NASA Astrophysics Data System (ADS)

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

Castro, Alonso; Shera, E. Brooks



Single-molecule measurements of DNA topology and topoisomerases.  


Topological properties of DNA influence its mechanical and biochemical interactions. Genomic DNA is maintained in a state of topological homeostasis by topoisomerases and is subjected to mechanical stress arising from replication and segregation. Despite their fundamental roles, the effects of topology and force have been difficult to ascertain. Developments in single-molecule manipulation techniques have enabled precise control and measurement of the topology of individual DNA molecules under tension. This minireview provides an overview of these single-molecule techniques and illustrates their unique capabilities through a number of specific examples of single-molecule measurements of DNA topology and topoisomerase activity. PMID:20382732

Neuman, Keir C



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


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

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



Real-time single-molecule imaging of quantum interference.  


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

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



Biophysical Variables Which Are Available from Single-Molecule Optical Studies  

NASA Astrophysics Data System (ADS)

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

Moerner, W. E.



Nanodevices based on plasmonics for few\\/single molecule detection  

Microsoft Academic Search

Different plasmonic based devices are fabricated using novel micro and nanofabrication techniques for single molecule detection: Self-similar Ag-nanosphere based plasmonic devices, device comprising tapered nanolens and photonic crystal cavity and, finally, Si micropillars based superhydrobhobic surface.

Enzo Di Fabrizio



Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy  

Microsoft Academic Search

Dynamic structural changes of macromolecules undergoing biochemical reactions can be studied using novel single molecule spectroscopy tools. Recent advances in applying such distance and orientation molecular rulers to biological systems are reviewed, and future prospects and challenges are discussed.

Shimon Weiss



Monitoring multiple distances within a single molecule using switchable FRET  

Microsoft Academic Search

The analysis of structure and dynamics of biomolecules is important for understanding their function. Toward this aim, we introduce a method called 'switchable FRET', which combines single-molecule fluorescence resonance energy transfer (FRET) with reversible photoswitching of fluorophores. Typically, single-molecule FRET is measured within a single donor-acceptor pair and reports on only one distance. Although multipair FRET approaches that monitor multiple

Stephan Uphoff; Seamus J Holden; Ludovic Le Reste; Javier Periz; Sebastian van de Linde; Mike Heilemann; Achillefs N Kapanidis



Single-molecule probes in organic field-effect transistors  

Microsoft Academic Search

The goal of this thesis is to study charge transport phenomena in organic materials. This is done optically by means of single-molecule\\u000aspectroscopy in a field-effect transistor based on a molecular crystal.\\u000a\\u000aWe present (in Chapter 2) a fundamental requirement for single-molecule\\u000aspectroscopy concerning the energy levels of the guest molecule with\\u000arespect to the ones of the host molecule.

Aurélien Armel Louis Nicolet



Single Molecule Detection and Imaging in Single Living Cells  

Microsoft Academic Search

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

Shuming Nie



Charge Transport in Azobenzene-Based Single-Molecule Junctions  

NASA Astrophysics Data System (ADS)

The azobenzene class of molecules has become an archetype of molecular photoswitch research, due to their simple structure and the significant difference of the electronic system between their cis and trans isomers. However, a detailed understanding of the charge transport for the two isomers, when embedded in a junction with electrodes is still lacking. In order to clarify this issue, we investigate charge transport properties through single Azobenzene-ThioMethyl (AzoTM) molecules in a mechanically controlled break junction (MCBJ) system at 4.2 K. Single-molecule conductance, I-V characteristics, and IETS spectra of molecular junctions are measured and compared with first-principles transport calculations. Our studies elucidate the origin of a slightly higher conductance of junctions with cis isomer and demonstrate that IETS spectra of cis and trans forms show distinct vibrational fingerprints that can be used for identifying the isomer.[1] 1. Y. Kim, A. Garcia-Lekue, D. Sysoiev, T. Frederiksen, U. Groth, E. Scheer, Phys. Rev. Lett. (accepted).

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



Vibrational properties of single-molecule magnet Fe4  

NASA Astrophysics Data System (ADS)

A single-molecule magnet (SMM) Fe4 consists of four Fe ions interacting through O anions via antiferromagnetic superexchange coupling, with the total ground-state spin of S=5. The SMM Fe4 has a magnetic anisotropy energy of 16 K, and its ground-state spin multiplet is well separated from the first excited spin multiplet. A recent experimental effort demonstrated that SMMs Fe4 can be deposited on various substrates with magnetic cores intact and that individual Fe4 molecules can be bridged between electrodes. SMMs Fe4 deposited on substrates or in contact with electrodes revealed interesting magnetic and transport properties. Electronic and spin degrees of freedom of SMM Fe4 may be coupled to vibrational degrees of freedom. Such coupling can affect various properties of SMM Fe4. Here we present our calculation of vibrational spectra (Raman and infrared) of SMM Fe4 using density-functional theory (DFT) within simple harmonic oscillator approximation. We identify normal modes and compare our calculated result with available experimental data.

Warnock, Michael; Park, Kyungwha; Yamamoto, Yoh



Looking for higher anisotropy barriers in single-molecule magnets  

NASA Astrophysics Data System (ADS)

We report single-crystal high-frequency electron paramagnetic resonance (HFEPR) studies of a series of recently discovered Mn6^III single-molecule magnets (SMMs) with large barriers to magnetization reversal. All of the complexes consist of Mn3^III triangles with a ferromagnetic interaction between them. Recent studies have shown that the exchange interactions within the triangular Mn3^III units can be switched from antiferromagnetic to ferromagnetic,^1 resulting in a switching of the spin from S = 4 to 12 for many of the Mn6 complexes. This strategy to ``increase S'' has resulted in the highest magnetic energy barrier and blocking temperature for any known SMM to date. Extensive frequency, temperature and field-orientation dependent HFEPR measurements were performed to determine the magnetic anisotropy parameters for each complex. These studies have contributed to important new insights concerning strategies for designing SMMs with high blocking temperatures, particularly for complexes containing manganese in its +3 oxidation state. ^1 T. C. Stamatatos et al., J. Am. Chem. Soc. 129, 12505-12511, 2007.

Datta, Saiti; Milios, Constantinos; Brechin, Euan; Hill, Stephen



Frustrated Rotations in Single-Molecule Junctions  

SciTech Connect

We compare the conductance of 1,4-bis(methylthio)benzene with that of 2,3,6,7-tetrahydrobenzo[1,2-b:4,5-b{prime}]dithiophene and the conductance of 1,4-bis(methylseleno)benzene with that of 2,3,6,7-tetrahydrobenzo[1,2-b:4,5-b{prime}]diselenophene and show explicitly that the orientation of an Au-S or Au-Se bond relative to the aromatic {pi} system controls electron transport through conjugated molecules. Specifically, we have found that the conduction pathway connects the Au electrodes to the aromatic {pi}-system via the chalcogen p lone pairs, and greater overlaps among these components lead to higher conductivity through the molecular junction.

Park,Y.S.; Hybertsen,M.; Widawsky, J.R.; Kamenetska, M.; Steigerwald, M.L.; Nuckolls, C.; Venkataraman, L.



Frustrated rotations in single-molecule junctions.  


We compare the conductance of 1,4-bis(methylthio)benzene with that of 2,3,6,7-tetrahydrobenzo[1,2-b:4,5-b']dithiophene and the conductance of 1,4-bis(methylseleno)benzene with that of 2,3,6,7-tetrahydrobenzo[1,2-b:4,5-b']diselenophene and show explicitly that the orientation of an Au-S or Au-Se bond relative to the aromatic pi system controls electron transport through conjugated molecules. Specifically, we have found that the conduction pathway connects the Au electrodes to the aromatic pi-system via the chalcogen p lone pairs, and greater overlaps among these components lead to higher conductivity through the molecular junction. PMID:19722660

Park, Young S; Widawsky, Jonathan R; Kamenetska, Maria; Steigerwald, Michael L; Hybertsen, Mark S; Nuckolls, Colin; Venkataraman, Latha



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

Microsoft Academic Search

Single molecule studies on CdSe quantum dots functionalized with oligo-phenylene vinylene ligands (CdSe-OPV) provide evidence of strong electronic communication that facilitate charge and energy transport between the OPV ligands and the CdSe quantum dot core. This electronic interaction greatly modify, the photoluminescence properties of both bulk and single CdSe-OPV nanostructure thin film samples. Size-correlated wide-field fluorescence imaging show that blinking

Michael Yemoh Odoi



Molecular wires in single-molecule junctions: charge transport and vibrational excitations.  


We investigate the effect of vibrations on the electronic transport through single-molecule junctions, using the mechanically controlled break junction technique. The molecules under investigation are oligoyne chains with appropriate end groups, which represent both an ideally linear electrical wire and an ideal molecular vibrating string. Vibronic features can be detected as satellites to the electronic transitions, which are assigned to longitudinal modes of the string by comparison with density functional theory data. PMID:20521299

Ballmann, Stefan; Hieringer, Wolfgang; Secker, Daniel; Zheng, Qinglin; Gladysz, John A; Görling, Andreas; Weber, Heiko B



Double point contact single molecule absorption spectroscopy  

NASA Astrophysics Data System (ADS)

Our primary objective with the presentation of this thesis is to utilize superconducting transport through microscopic objects to both excite and analyze the vibrational degrees of freedom of various molecules of a biological nature. The technique stems from a Josephson junction's ability to generate radiation that falls in the terahertz gap (? 10 THz) and consequently can be used to excite vibrational modes of simple and complex molecules. Analysis of the change in IV characteristics coupled with the differential conductance dIdV allows determination of both the absorption spectra and the vibrational modes of biological molecules. Presented here are both the theoretical foundations of superconductivity relevant to our experimental technique and the fabrication process of our samples. Comparisons between our technique and that of other absorption spectroscopy techniques are included as a means of providing a reference upon which to judge the merits of our novel procedure. This technique is meant to improve not only our understanding of the vibrational degrees of freedom of useful biological molecules, but also these molecule's structural, electronic and mechanical properties.

Howard, John Brooks


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


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

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



Interfacial electron transfer of Shewanella putrefaciens enhanced by nanoflaky nickel oxide array in microbial fuel cells  

NASA Astrophysics Data System (ADS)

A uniform nanoflaky nickel oxide (NiO) array is constructed on carbon cloth via optimized conditions, and further employed as an anode in Shewanella putrefaciens (S. putrefaciens) microbial fuel cells (MFCs). Results indicate that the NiO nanoflakes/carbon cloth anode significantly improves the MFC performance in comparison to the unmodified carbon cloth, delivering about three times higher power density. This attributes to an enhanced interfacial electron transfer rate between bacteria cell and nanoflaky NiO array-modified carbon fiber and improved adhesion of bacteria cells on the modified carbon fiber for more active reaction centers. Considering the facile synthesis process, low cost and long discharging lifetime, this NiO/carbon cloth anode could be very promising to be applied for high performance, large scale MFCs.

Qiao, Yan; Wu, Xiao-Shuai; Li, Chang Ming



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.



Towards physiological complexity with in vitro single-molecule biophysics  

PubMed Central

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

Duzdevich, Daniel; Greene, Eric C.



Single-Molecule Protein Conformational Dynamics in Cell Signaling  

SciTech Connect

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




Influence of the carbon fiber surface properties on interfacial adhesion in carbon fiber–acrylate composites cured by electron beam  

Microsoft Academic Search

Two different commercial references of oxidized carbon fibers were used to investigate the influence of different oxidation surface treatments on the interfacial adhesion with an acrylate resin cured by electron beam. For each type of fiber, a characterization of the topography and the chemistry of the surface was done. The 90° flexural strength of unidirectional composites was measured in order

F. Vautard; P. Fioux; L. Vidal; J. Schultz; M. Nardin; B. Defoort



Transchip: Single Molecule Detection of Transcriptional Elongation Complexes  

PubMed Central

A new single molecule system – Transchip – was developed for analysis of transcription products at their genomic origins. The bacteriophage T7 RNA polymerase and its promoters were used in a model system, and resultant RNAs were imaged and detected at their positions along single template DNA molecules. This system, Transchip, has drawn from critical aspects of Optical Mapping, a single molecule system that enables the construction of high resolution, ordered restriction maps of whole genomes from single DNA molecules. Through statistical analysis of hundreds of single molecule template/transcript complexes, Transchip enables analysis of the locations and strength of promoters, the direction and processivity of transcription reactions and termination of transcription. These novel results suggest that the new system may serve as a high-throughput platform to investigate transcriptional events on a large, genome-wide scale.

Wu, Tian; Schwartz, David C.



Single-Molecule Experiments in Vitro and in Silico  

NASA Astrophysics Data System (ADS)

Single-molecule force experiments in vitro enable the characterization of the mechanical response of biological matter at the nanometer scale. However, they do not reveal the molecular mechanisms underlying mechanical function. These can only be readily studied through molecular dynamics simulations of atomic structural models: “in silico” (by computer analysis) single-molecule experiments. Steered molecular dynamics simulations, in which external forces are used to explore the response and function of macromolecules, have become a powerful tool complementing and guiding in vitro single-molecule experiments. The insights provided by in silico experiments are illustrated here through a review of recent research in three areas of protein mechanics: elasticity of the muscle protein titin and the extracellular matrix protein fibronectin; linker-mediated elasticity of the cytoskeleton protein spectrin; and elasticity of ankyrin repeats, a protein module found ubiquitously in cells but with an as-yet unclear function.

Sotomayor, Marcos; Schulten, Klaus



The importance of surfaces in single-molecule bioscience  

PubMed Central

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

Visnapuu, Mari-Liis; Duzdevich, Daniel



Temperature dependent single molecule rotational dynamics in PMA.  


Temperature dependent measurements of the rotational diffusion of single dye molecules in the polymer poly(methyl acrylate) (PMA) are presented and compared to shear viscosity data and numerical simulations of the rotational diffusion process. It is found that single molecule rotational diffusion very accurately follows the Debye-Stokes-Einstein predictions for the shear viscosity without any additional parameter. We employ a simple model of dynamic changes of the rotational speed of a single molecule. This dynamic heterogeneity model is based on a Gaussian distribution of activation energies in a VFTH (Vogel-Fulcher-Tammann-Hesse) type temperature dependence of the polymer viscosity. The simulations explain all experimental details concerning the stretched exponential single molecule relaxation dynamics and the related distributions. They also reveal that the observed distributions are related to the intrinsic physical properties of the polymer but do not in general reflect the instantaneous spread of local viscous properties. PMID:21183981

Adhikari, Subhasis; Selmke, Markus; Cichos, Frank



Single-molecule assays for investigating protein misfolding and aggregation.  


Protein misfolding and aggregation are relevant to many fields. Recently, their investigation has experienced a revival as a central topic in the research of numerous human diseases, including Parkinson's and Alzheimer's. Much has been learned from ensemble biochemical approaches, but the inherently heterogeneous nature of the underlying processes has obscured many important details. Single-molecule techniques offer unique capabilities to study heterogeneous systems, while providing high temporal and structural resolution to characterize them. In this Perspective, we give an overview of the single-molecule assays that have been applied to protein misfolding and aggregation, which are mainly based on fluorescence and force spectroscopy. We describe some of the technical challenges involved in studying aggregation at the single-molecule level and discuss what has been learned about aggregation mechanisms from the different approaches. PMID:23612887

Hoffmann, Armin; Neupane, Krishna; Woodside, Michael T



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.




Tracking single molecules at work in living cells.  


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

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



Simultaneous time and frequency resolved fluorescence microscopy of single molecules.  

SciTech Connect

Single molecule fluorophores were studied for the first time with a new confocal fluorescence microscope that allows the wavelength and emission time to be simultaneously measured with single molecule sensitivity. In this apparatus, the photons collected from the sample are imaged through a dispersive optical system onto a time and position sensitive detector. This detector records the wavelength and emission time of each detected photon relative to an excitation laser pulse. A histogram of many events for any selected spatial region or time interval can generate a full fluorescence spectrum and correlated decay plot for the given selection. At the single molecule level, this approach makes entirely new types of temporal and spectral correlation spectroscopy of possible. This report presents the results of simultaneous time- and frequency-resolved fluorescence measurements of single rhodamine 6G (R6G), tetramethylrhodamine (TMR), and Cy3 embedded in thin films of polymethylmethacrylate (PMMA).

Hayden, Carl C.; Gradinaru, Claudiu C.; Chandler, David W.; Luong, A. Khai



Single-molecule fluorescence spectroscopy in (bio)catalysis  

PubMed Central

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

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



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.



Extending single-molecule microscopy using optical fourier processing.  


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

Backer, Adam S; Moerner, W E



Single molecule processivity and dynamics of cAMP-dependent protein kinase (PKA)  

NASA Astrophysics Data System (ADS)

Using single-walled carbon nanotube (SWNT) transistors, we monitored the processivity and dynamics of single molecules of cAMP-dependent protein kinase (PKA). As PKA enzymatically phosphorylates its peptide substrate, it generates an electronic signal in the transistor that can be monitored continuously and with 20 ?s resolution. The electronic recording directly resolves substrate binding, ATP binding, and cooperative formation of PKA's catalytically functional, ternary complex. Statistical analysis of many events determines on- and off-rates for each of these events, as well as the full transistion probability matrix between them. Long duration monitoring further revealed minute-to-minute rate variability for a single molecule, and different mechanistic statistics for ATP binding than for substrate. The results depict a highly dynamic enzyme offering dramatic possibilities for regulated activity, an attribute that is useful for an enzyme that plays crucial roles in cell signaling.

Sims, Patrick C.; Choi, Yongki; Dong, Chengjun; Moody, Issa S.; Iftikhar, Mariam; Tolga Gul, O.; Weiss, Gregory A.; Collins, Philip G.



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

SciTech Connect

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

Iancu, Violeta



Interlaced Optical Force-Fluorescence Measurements for Single Molecule Biophysics  

Microsoft Academic Search

Combining optical tweezers with single molecule fluorescence offers a powerful technique to study the biophysical properties of single proteins and molecules. However, such integration into a combined, coincident arrangement has been severely limited by the dramatic reduction in fluorescence longevity of common dyes under simultaneous exposure to trapping and fluorescence excitation beams. We present a novel approach to overcome this

Ricardo R. Brau; Peter B. Tarsa; Jorge M. Ferrer; Peter Lee; Matthew J. Lang



Interlaced Optical Force-Fluorescence Measurements for Single Molecule Biophysics  

PubMed Central

Combining optical tweezers with single molecule fluorescence offers a powerful technique to study the biophysical properties of single proteins and molecules. However, such integration into a combined, coincident arrangement has been severely limited by the dramatic reduction in fluorescence longevity of common dyes under simultaneous exposure to trapping and fluorescence excitation beams. We present a novel approach to overcome this problem by alternately modulating the optical trap and excitation beams to prevent simultaneous exposure of the fluorescent dye. We demonstrate the dramatic reduction of trap-induced photobleaching effects on the common single molecule fluorescence dye Cy3, which is highly susceptible to this destructive pathway. The extension in characteristic fluorophore longevity, a 20-fold improvement when compared to simultaneous exposure to both beams, prolongs the fluorescence emission to several tens of seconds in a combined, coincident arrangement. Furthermore, we show that this scheme, interlaced optical force-fluorescence, does not compromise the trap stiffness or single molecule fluorescence sensitivity at sufficiently high modulation frequencies. Such improvement permits the simultaneous measurement of the mechanical state of a system with optical tweezers and the localization of molecular changes with single molecule fluorescence, as demonstrated by mechanically unzipping a 15-basepair DNA segment labeled with Cy3.

Brau, Ricardo R.; Tarsa, Peter B.; Ferrer, Jorge M.; Lee, Peter; Lang, Matthew J.



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); Xavier Michalet (Lawrence Berkeley National Laboratory;Materials Sciences and Biophysical Sciences Divisions); Shimon Weiss (Lawrence Berkeley National Laboratory;Materials Sciences and Biophysical Sciences Divisions)



Combined single-molecule force and fluorescence measurements for biology  

Microsoft Academic Search

ABSTRACT: Recent advances in single-molecule techniques allow the application of force to an individual biomolecule whilst simultaneously monitoring its response using fluorescent probes. The effects of applied mechanical load on single-enzyme turnovers, biomolecular interactions and conformational changes can now be studied with nanometer precision and millisecond time resolution.

Mark I Wallace; Justin E Molloy; David R Trentham



Modeling single molecule detection probabilities in microdroplets. Final report  

SciTech Connect

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

Hill, S.C.



Single-molecule photophysics, from cryogenic to ambient conditions.  


We review recent progress in characterizing and understanding the photophysics of single molecules in condensed matter, mostly at cryogenic temperatures. We discuss the central role of the triplet state in limiting the number of useful host-guest systems, notably a new channel, intermolecular intersystem crossing. Another important limitation to the use of single molecules is their photo-reactivity, leading to blinking of the fluorescence signal, and eventually to its loss by photo-bleaching. These processes are at the heart of modern super-resolution schemes. We then examine some of the new host-guest systems recently discovered following these general principles, and the mechanisms of spectral diffusion and dephasing that they have revealed. When charges are injected into organic conductors, they get trapped and influence single molecules via the local fields they create in the material, and via their coupling to localized vibrations. Understanding these processes is necessary for better control of spectral diffusion and dephasing of single molecules. We finally conclude by giving some outlook on future directions of this fascinating field. PMID:24190080

Kozankiewicz, Boles?aw; Orrit, Michel



The dynamics of single-molecule DNA in flow  

Microsoft Academic Search

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

Eric S. G. Shaqfeh



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.

Qian, Hong; Kou, S. C.



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



A plutonium-based single-molecule magnet.  


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



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.



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



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

PubMed Central

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

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



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


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

PubMed Central

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

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



Carbon nanotube nanoelectromechanical systems as magnetometers for single-molecule magnets.  


Due to outstanding mechanical and electronic properties, carbon nanotube nanoelectromechanical systems (NEMS) were recently proposed as ultrasensitive magnetometers for single-molecule magnets (SMM). In this article, we describe a noninvasive grafting of a SMM on a carbon nanotube NEMS, which conserves both the mechanical properties of the carbon nanotube NEMS and the magnetic properties of the SMM. We will demonstrate that the nonlinearity of a carbon nanotube's mechanical motion can be used to probe the reversal of a molecular spin, associated with a bis(phthalocyaninato)terbium(III) single-molecule magnet, providing an experimental evidence for the detection of a single spin by a mechanical degree of freedom on a molecular level. PMID:23802618

Ganzhorn, Marc; Klyatskaya, Svetlana; Ruben, Mario; Wernsdorfer, Wolfgang



Vibronic excitation of single molecules: a new technique for studying low-temperature dynamics.  


Herein, we present vibronic excitation and detection of purely electronic zero-phonon lines (ZPL) of single molecules as a new tool for investigating dynamics at cryogenic temperatures. Applications of this technique to study crystalline and amorphous matrix materials are presented. In the crystalline environment, spectrally stable ZPLs are observed at moderate excitation powers. By contrast, investigations at higher excitation intensities reveal the opening of local degrees of freedom and spectral jumps, which we interpret as the observation of elementary steps in the melting of a crystal. We compare these results to spectral single-molecule trajectories recorded in a polymer. The way in which much more complicated spectral features can be analysed is shown. Surprisingly, pronounced spectral shifts on a previously not accessible large energy scale are observed, which are hard to reconcile with the standard two-level model system used to describe low-temperature dynamics in disordered systems. PMID:15884077

Kiraz, Alper; Ehrl, Moritz; Hellriegel, Christian; Bräuchle, Christoph; Zumbusch, Andreas



Unfolding dynamics of cytochrome c revealed by single-molecule and ensemble-averaged spectroscopy.  


Denaturant-induced conformational change of yeast iso-1-cytochrome c (Cytc) has been comprehensively investigated in the single-molecule and bulk phases. By fluorescence-quenching experiments with dye-labelled heme-protein (Alexa 488-labelled Cytc, Cytc-A488), we clearly show that the fluorescence quenching observed from folded Cytc-A488 is due mainly to photoinduced electron transfer (PET) between electron-donating amino acids such as tryptophan and the dye attached to the protein. In addition, the unfolding process of Cytc-A488 observed in the single-molecule and bulk phases can be explained well in terms of a three-state model: Cytc unfolds through an intermediate with a native-like compactness. By quantitative analysis of fluorescence correlation spectroscopy (FCS) data, we were able to observe a relaxation time of ?1.5 ?s corresponding to segmental motion and fast folding dynamics of 55 ?s in the unfolded state of Cytc. The results presented here also suggest that a combination of single-molecule and ensemble-averaged spectroscopy is necessary to provide convincing and comprehensive assignments of protein kinetics. PMID:21305089

Choi, Jungkweon; Kim, Sooyeon; Tachikawa, Takashi; Fujitsuka, Mamoru; Majima, Tetsuro



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.



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.



Magnetic relaxation in cyanide based single molecule magnets  

NASA Astrophysics Data System (ADS)

The present contribution is aimed at the elaboration of the model of magnetic relaxation in the cyano-bridged pentanuclear Mn(III) 2Mn(II) 3 cluster that belongs to a new family of single molecule magnets (SMM) containing ions with unquenched orbital angular momenta. We proceed from the energy pattern of the cluster formed by the trigonal component of the crystal field acting on the ground-state cubic terms 4T1(t24) of the Mn(III)-ions, spin-orbital interaction and Heisenberg exchange between Mn(II) and Mn(III) ions. The ground state of the cluster possesses the total angular momentum projection ? MJ? = 15/2, while the energies of the excited states increase with decreasing ? MJ? values, thus giving rise to a barrier for the reversal of magnetization. The monophonon transitions between the states ? MJ> and ? MJ ± 1>, ? MJ ± 2> induced by electron-vibrational interaction are shown to be allowed. The rates of all possible transitions between the states with 1/2 < ? MJ? < 15/2 are calculated in the temperature range 0.1 K < T < 3 K. With the purpose of calculation of the temperature dependence of the relaxation time of magnetization we solve the set of master equations for the populations n(t) of the ? MJ> states of the Mn(III) 2Mn(II) 3 clusters. The relaxation time is shown to diminish from 10 12s to 10 s with decrease in temperature from 1 K to 3 K for the cluster [Mn(III)(CN) 6] 2[Mn(II)(tmphen) 2] 3 (tmphen = 3,4,7,8-tetramethyl-1,10-phenanthroline) with the trigonal crystal field parameter ? = -251 cm -1. The obtained values of the relaxation time are in qualitative agreement with the temperature dependence of the ac susceptibilities observed for this SMM. In order to reveal the possibility of enhancing the relaxation time of magnetization in the family of clusters Mn(III) 2Mn(II) 3 we vary the trigonal crystal field parameter ? ??( ? < 0) and demonstrate that increase in ? ?? leads to a considerable growth of the relaxation time.

Klokishner, S. I.; Ostrovsky, S. M.; Palii, A. V.; Dunbar, K.



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.

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



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.



Monitoring multiple distances within a single molecule using switchable FRET.  


The analysis of structure and dynamics of biomolecules is important for understanding their function. Toward this aim, we introduce a method called 'switchable FRET', which combines single-molecule fluorescence resonance energy transfer (FRET) with reversible photoswitching of fluorophores. Typically, single-molecule FRET is measured within a single donor-acceptor pair and reports on only one distance. Although multipair FRET approaches that monitor multiple distances have been developed, they are technically challenging and difficult to extend, mainly because of their reliance on spectrally distinct acceptors. In contrast, switchable FRET sequentially probes FRET between a single donor and spectrally identical photoswitchable acceptors, dramatically reducing the experimental and analytical complexity and enabling direct monitoring of multiple distances. Our experiments on DNA molecules, a protein-DNA complex and dynamic Holliday junctions demonstrate the potential of switchable FRET for studying dynamic, multicomponent biomolecules. PMID:20818380

Uphoff, Stephan; Holden, Seamus J; Le Reste, Ludovic; Periz, Javier; van de Linde, Sebastian; Heilemann, Mike; Kapanidis, Achillefs N



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.

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



Photophysical processes in single molecule organic fluorescent probes.  


The use of organic fluorescent probes in biochemical and biophysical applications of single molecule spectroscopy and fluorescence microscopy techniques continues to increase. As single molecule measurements become more quantitative and new developments in super-resolution imaging allow researchers to image biological materials with unprecedented resolution, it is becoming increasingly important to understand how the properties of the probes influence the signals measured in these experiments. In this review, we focus on the photochemical and photophysical processes of organic fluorophores that affect the properties of fluorescence emission. This includes photobleaching, quenching, and the formation of non-emissive (dark) states that result in fluorescence blinking in a variety of timescales. These processes, if overlooked, can result in an erroneous interpretation of the data. Understanding their physical origins, on the other hand, allows researchers to design experiments and interpret results so that the maximum amount of information about the system of interest can be extracted from fluorescence signals. PMID:24141280

Stennett, Elana M S; Ciuba, Monika A; Levitus, Marcia



Silicon nanowire based single-molecule SERS sensor.  


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

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



High-Resolution, Single-Molecule Measurements of Biomolecular Motion  

PubMed Central

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

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



Light Sheet Microscopy for Single Molecule Tracking in Living Tissue  

PubMed Central

Single molecule observation in cells and tissue allows the analysis of physiological processes with molecular detail, but it still represents a major methodological challenge. Here we introduce a microscopic technique that combines light sheet optical sectioning microscopy and ultra sensitive high-speed imaging. By this approach it is possible to observe single fluorescent biomolecules in solution, living cells and even tissue with an unprecedented speed and signal-to-noise ratio deep within the sample. Thereby we could directly observe and track small and large tracer molecules in aqueous solution. Furthermore, we demonstrated the feasibility to visualize the dynamics of single tracer molecules and native messenger ribonucleoprotein particles (mRNPs) in salivary gland cell nuclei of Chironomus tentans larvae up to 200 µm within the specimen with an excellent signal quality. Thus single molecule light sheet based fluorescence microscopy allows analyzing molecular diffusion and interactions in complex biological systems.

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



Multicolor single molecule tracking of stochastically active synthetic dyes.  


Single particle tracking can reveal dynamic information at the scale of single molecules in living cells but thus far has been limited either in the range of potential protein targets or in the quality and number of tracks attainable. We demonstrate a new approach to single molecule tracking by using the blinking properties of synthetic dyes targeted to proteins of interest with genetically encoded tags to generate high-density tracks while maintaining flexibility in protein labeling. We track membrane proteins using different combinations of dyes and show that the concept can be extended to three-color imaging. Moreover, we show that this technique is not limited to the membrane by performing live tracking of proteins in intracellular compartments. PMID:22519662

Benke, Alexander; Olivier, Nicolas; Gunzenhäuser, Julia; Manley, Suliana



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.



Single-Molecule Fluorescence Spectroscopy and Microscopy of Biomolecular Motors  

NASA Astrophysics Data System (ADS)

The methods of single-molecule fluorescence spectroscopy and microscopy have been recently utilized to explore the mechanism of action of several members of the kinesin and myosin biomolecular motor protein families. Whereas ensemble averaging is removed in single-molecule studies, heterogeneity in the behavior of individual motors can be directly observed, without synchronization. Observation of translocation by individual copies of motor proteins allows analysis of step size, rate, pausing, and other statistical properties of the process. Polarization microscopy as a function of nucleotide state has been particularly useful in revealing new and highly rotationally mobile forms of particular motors. These experiments complement X-ray and biochemical studies and provide a detailed view into the local dynamical behavior of motor proteins.

Peterman, Erwin J. G.; Sosa, Hernando; Moerner, W. E.



TOPICAL REVIEW: Single-molecule fluorescence spectroscopy of biomolecular folding  

NASA Astrophysics Data System (ADS)

Single-molecule fluorescence spectroscopy is emerging as an important tool for studying biomolecular folding dynamics. Its usefulness stems from its ability to directly map heterogeneities in folding pathways and to provide information about the energy landscape of proteins and ribonucleic acid (RNA) molecules. Single-molecule fluorescence techniques relevant for folding studies, including methods for trapping and immobilizing molecules, are described and compared in this review. Some emphasis is placed on fluorescence resonance energy transfer, which is particularly useful for studying conformational dynamics of biomolecules. Studies on protein and RNA folding using this methodology are reviewed and set in the more general context of folding science. Finally, some of the interesting future prospects in this field are delineated.

Haran, Gilad



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.

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




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



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.

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



Probing DNA clamps with single-molecule force spectroscopy  

PubMed Central

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

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



Single-molecule magnetic tweezers studies of type IB topoisomerases.  


The past few years have seen the application of single-molecule force spectroscopy techniques to the study of topoisomerases. Magnetic tweezers are particularly suited to the study of topoisomerases due to their unique ability to exert precise and straightforward control of the supercoiled state of DNA. Here, we illustrate in a stepwise fashion how the dynamic properties of type IB topoisomerases can be monitored using this technique. PMID:19763943

Lipfert, Jan; Koster, Daniel A; Vilfan, Igor D; Hage, Susanne; Dekker, Nynke H



Single-molecule spectroscopy of semiconductor nanocrystals on plasmonic nanostructures  

NASA Astrophysics Data System (ADS)

In the past several years we have demonstrated the metal-enhanced fluorescence (MEF) and the significant changes in the photophysical properties of fluorophores in the presence of metallic nanostructures and nanoparticles using ensemble spectroscopic studies. Here, in the present study, we explored the new insights of these interactions using single-molecule fluorescence spectroscopy. The single molecule study is expected to provide more information, especially on the heterogeneity in the fluorescence enhancement and decrease in lifetimes associated with fluorophore-metal interactions, which is otherwise not possible to observe using ensemble measurements. For the present study, we considered using CdTe nanocrystals (QDots) prepared using modified Weller method as the fluorophores under investigation. QDots having few nanometer sizes, tunable absorption and fluorescence spectral properties, and high photo-stabilities are of important class of fluorescent probes. Because of these unique features Qdots are widely used as probes in various fields, including biological labeling and imaging. These CdTe nanocrystals show characteristic spectral features in solution and on the solid substrate. The CdTe nanocrystals dispersed in PVA and spin-casted on SiFs surface show ~5-fold increase in fluorescence intensity and ~3-fold decrease in lifetimes compared to on glass substrate. The data obtained using ensemble and single molecule spectroscopy are complimentary to each other. Additionally as anticipated we have seen increased heterogeneity in the plasmon induced fluorescence modulations. Moreover single molecule spectroscopic study revealed significant reduction in blinking of CdTe nanocrystals on plasmonic nanostructures. Subsequently, we present these important findings on metal-fluorophore interactions of CdTe nanocrystals (QDots) on plasmonic nanostructures.

Ray, Krishanu; Badugu, Ramachandram; Lakowicz, Joseph R.



Advanced multifocus confocal laser scanning microscope for single molecule studies  

NASA Astrophysics Data System (ADS)

A new multi-focus multi-confocal set-up for performing fluorescence spectroscopy of single molecules in solution is presented. The ultimate goal of the set-up is to track individual molecules during diffusion in solution, when all standard methods of trapping such as optical tweezers or dielectrophoretic traps fail. We present here a detailed description of the experimental setup and show first experimental results.

Dertinger, Thomas; Koberling, Felix; Benda, Ales; Erdmann, Rainer; Hof, Martin; Enderlein, Joerg



Single-Molecule Choreography between Telomere Proteins and G Quadruplexes.  


Telomeric DNA binds proteins to protect chromosome ends, but it also adopts G quadruplex (GQ) structures. Two new studies by Hwang and colleagues (in this issue of Structure) and Ray and colleagues (published elsewhere) use single molecule imaging to reveal how GQs affect the binding of different telomere associated proteins. The data suggest that GQs play important roles in regulating accessibility of telomeres. PMID:24918337

Hopfner, Karl-Peter



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



High-throughput single-molecule optofluidic analysis  

PubMed Central

We describe a high-throughput, automated single-molecule measurement system, equipped with microfluidics. the microfluidic mixing device has integrated valves and pumps to accurately accomplish titration of biomolecules with picoliter resolution. We demonstrate that the approach enabled rapid sampling of biomolecule conformational landscape and of enzymatic activity, in the form of transcription by Escherichia coli RNA polymerase, as a function of the chemical environment.

Kim, Soohong; Streets, Aaron M; Lin, Ron R; Quake, Stephen R; Weiss, Shimon; Majumdar, Devdoot S



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


Mechanical Single Molecule Investigations of SNARE Protein Interactions  

NASA Astrophysics Data System (ADS)

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

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



Viruses and Tetraspanins: Lessons from Single Molecule Approaches  

PubMed Central

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

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



Single-molecule studies of actin assembly and disassembly factors.  


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



Single molecule conformational memory extraction: p5ab RNA hairpin.  


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

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



Field Regulation of Single Molecule Conductivity by a Charged Atom  

NASA Astrophysics Data System (ADS)

A new concept for a single molecule transistor is demonstrated [1]. A single chargeable atom adjacent to a molecule shifts molecular energy levels into alignment with electrode levels, thereby gating current through the molecule. Seemingly paradoxically, the silicon substrate to which the molecule is covalently attached provides 2, not 1, effective contacts to the molecule. This is achieved because the single charged silicon atom is at a substantially different potential than the remainder of the substrate. Charge localization at one dangling bond is ensured by covalently capping all other surface atoms. Dopant level control and local Fermi level control can change the charge state of that atom. The same configuration is shown to be an effective transducer to an electrical signal of a single molecule detection event. Because the charged atom induced shifting results in conductivity changes of substantial magnitude, these effects are easily observed at room temperature. [1] Paul G. Piva1,Gino A. DiLabio, Jason L. Pitters, Janik Zikovsky, Moh'd Rezeq, Stanislav Dogel, Werner A. Hofer & Robert A. Wolkow, Field regulation of single-molecule conductivity by a charged surface atom, NATURE 435, 658-661 (2005)

Wolkow, Robert



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.

Hamadani, Kambiz M.; Weiss, Shimon



Viruses and tetraspanins: lessons from single molecule approaches.  


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

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



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.

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



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



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.

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



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.

Rech, Ivan; Maccagnani, Piera; Ghioni, Massimo



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.

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.



Manipulation of a single molecule ground state by means of gold atom contacts  

NASA Astrophysics Data System (ADS)

Single gold adatoms were manipulated on a Au(1 1 1) surface with the tip of a scanning tunnelling microscope to contact selected peripheral ? bonds of a single Coronene molecule. Tunnelling electron spectroscopy and differential conductance mapping of the Au-Coronene complexes show how Coronene's electronic ground state is shifted down in energy as the function of the number of interacting Au atoms, demonstrating that a Coronene molecule can function like a single molecule counter. The number of interacting atoms can be counted by simply following the linear energy downshift of Coronene's ground state.

Manzano, C.; Soe, W. H.; Hliwa, M.; Grisolia, M.; Wong, H. S.; Joachim, C.



A comparative study on the deposition of Mn12 single molecule magnets on the Au(111) surface.  


Different approaches to the deposition of Mn(12) single molecule magnets on the Au(111) surface and their characterization by a broad variety of techniques are investigated with respect to their suitability for a profound corroboration of the integrity of the Mn(12) core. In this context, the most recent improvements in the experimental approaches are presented and the latest results on the electronic properties of Mn(12) are linked to each other. The results confirm the high instability of Mn(12) single molecule magnets on surfaces and reveal the need for an amendment of the requirements to define the structural integrity of Mn(12) molecules on surfaces. PMID:18185866

Voss, Sönke; Burgert, Michael; Fonin, Mikhail; Groth, Ulrich; Rüdiger, Ulrich



First-principles quantum transport modeling of thermoelectricity in single-molecule nanojunctions with graphene nanoribbon electrodes  

Microsoft Academic Search

We overview nonequilibrium Green function combined with density functional theory (NEGF-DFT) modeling of independent electron and phonon transport in nanojunctions with applications focused on a new class of thermoelectric devices where a single molecule is attached to two metallic zigzag graphene nanoribbons (ZGNRs) via highly transparent contacts. Such contacts make possible injection of evanescent wavefunctions from ZGNRs, so that their

Branislav K. Nikolic; Kamal K. Saha; Troels Markussen; Kristian S. Thygesen



Interfacial electronic structure of gold nanoparticles on Si(100): alloying versus quantum size effects.  


Gold nanoparticles (Au NPs) were prepared on a native-oxide-covered Si(100) substrate by sputter-deposition followed by thermal annealing. The size of Au NPs could be controlled in the range of 8-48 nm by varying the sputter-deposition time and post-annealing temperature. The interparticle separation was found to be directly related to the size of Au NPs, with smaller separations for particles of smaller size. The surface morphology, crystal structure, and interfacial composition of the chemical states of these supported Au NPs were studied as a function of their average size by using scanning electron microscopy, glancing-incidence X-ray diffraction, and depth-profiling X-ray photoelectron spectroscopy (XPS), respectively. The new Au 4f7/2 peak found at 1.1-1.2 eV higher in binding energy than that for the metallic Au feature (at 84.0 eV) can be attributed to the formation of Au silicide at the interface between Au NPs and the Si substrate. Depth-profiling XPS experiments revealed no discernible change in the binding energies of the Au silicide and metallic Au 4f features with increasing Ar+ sputtering time, indicating that the Au-to-silicide interface is abrupt. Furthermore, the shift in the Au 5d5/2 valence band to a higher binding energy and the reduction of the Au 5d spin-orbit splitting with increasing Ar+ sputtering time also support the formation of Au silicide. No clear evidence for the quantum size effect was observed for the supported NPs. The finite density of state at the Fermi level and the fixed Au 4f7/2 peak position clearly indicate the metallic nature of the Au silicide at the Au-Si interface. PMID:19518081

Sohn, Youngku; Pradhan, Debabrata; Radi, Abdullah; Leung, K T



In situ high-resolution transmission electron microscopy study of interfacial reactions of Cu thin films on amorphous silicon  

NASA Astrophysics Data System (ADS)

Interfacial reactions of Cu with amorphous silicon (a-Si) in the Cu/a-Si/glass system are studied by in situ high-resolution transmission electron microscopy at 550 °C. Various Cu silicides, such as ?-Cu3Si, Cu15Si4, and Cu5Si, and Cu particles are observed. The formation of the Cu particles can be attributed to a heating effect from electron beam irradiation. Around the Cu silicides, crystallization of a-Si occurs. Around the Cu particles, however, crystallization does not occur. Crystallization appears to be enhanced by Cu dissolved in a-Si.

Lee, Sung Bo; Choi, Duck-Kyun; Phillipp, Fritz; Jeon, Kyung-Sook; Kim, Chang Kyung



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.



Single Molecule Energetics of F1-ATPase Motor  

PubMed Central

Motor proteins are essential in life processes because they convert the free energy of ATP hydrolysis to mechanical work. However, the fundamental question on how they work when different amounts of free energy are released after ATP hydrolysis remains unanswered. To answer this question, it is essential to clarify how the stepping motion of a motor protein reflects the concentrations of ATP, ADP, and Pi in its individual actions at a single molecule level. The F1 portion of ATP synthase, also called F1-ATPase, is a rotary molecular motor in which the central ?-subunit rotates against the ?3?3 cylinder. The motor exhibits clear step motion at low ATP concentrations. The rotary action of this motor is processive and generates a high torque. These features are ideal for exploring the relationship between free energy input and mechanical work output, but there is a serious problem in that this motor is severely inhibited by ADP. In this study, we overcame this problem of ADP inhibition by introducing several mutations while retaining high enzymatic activity. Using a probe of attached beads, stepping rotation against viscous load was examined at a wide range of free energy values by changing the ADP concentration. The results showed that the apparent work of each individual step motion was not affected by the free energy of ATP hydrolysis, but the frequency of each individual step motion depended on the free energy. This is the first study that examined the stepping motion of a molecular motor at a single molecule level with simultaneous systematic control of ?GATP. The results imply that microscopically defined work at a single molecule level cannot be directly compared with macroscopically defined free energy input.

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



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


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



Single-molecule studies of kinesin family motor proteins  

NASA Astrophysics Data System (ADS)

Kinesin family motor proteins drive many essential cellular processes, including cargo transport and mitotic spindle assembly and regulation. They accomplish these tasks by converting the chemical energy released from the hydrolysis of adenosine triphosphate (ATP) directly into mechanical motion along microtubules in cells. Optical traps allow us to track and apply force to individual motor proteins, and have already revealed many details of the movement of conventional kinesin, although the precise mechanism by which chemical energy is converted into mechanical motion is unclear. Other kinesin family members remain largely uncharacterized. This dissertation details the use of a novel optical-trapping assay to study Eg5, a Kinesin-5 family member involved in both spindle assembly and pole separation during mitosis. We demonstrate that individual Eg5 dimers are relatively slow and force-insensitive motors that take about 8 steps, on average, before detaching from the microtubule. Key differences in processivity and force-response between Eg5 and conventional kinesin suggest ways in which the two motors might have evolved to perform very different tasks in cells. This dissertation also details efforts to unravel how chemical energy is converted into mechanical motion by simultaneously measuring mechanical transitions (with an optical trap) and nucleotide binding and release (with single-molecule fluorescence) for individual conventional kinesin motors. We constructed a combined instrument, demonstrated its capabilities by unzipping fluorescently-labeled DNA duplexes, and used this instrument to record the motion of individual conventional kinesin motors powered by the hydrolysis of fluorescent nucleotides. Preliminary data reveal the challenges inherent in such measurements and guide proposals for future experimental approaches. Finally, this dissertation includes several chapters intended to serve as practical guides to understanding, constructing, and maintaining optical traps and single-molecule fluorescence microscopes, as well as implementing novel surface chemistry treatments for the development of new single-molecule assay geometries.

Fordyce, Polly


A functional single-molecule binding assay via force spectroscopy  

PubMed Central

Protein–ligand interactions, including protein–protein interactions, are ubiquitously essential in biological processes and also have important applications in biotechnology. A wide range of methodologies have been developed for quantitative analysis of protein–ligand interactions. However, most of them do not report direct functional/structural consequence of ligand binding. Instead they only detect the change of physical properties, such as fluorescence and refractive index, because of the colocalization of protein and ligand, and are susceptible to false positives. Thus, important information about the functional state of protein–ligand complexes cannot be obtained directly. Here we report a functional single-molecule binding assay that uses force spectroscopy to directly probe the functional consequence of ligand binding and report the functional state of protein–ligand complexes. As a proof of principle, we used protein G and the Fc fragment of IgG as a model system in this study. Binding of Fc to protein G does not induce major structural changes in protein G but results in significant enhancement of its mechanical stability. Using mechanical stability of protein G as an intrinsic functional reporter, we directly distinguished and quantified Fc-bound and Fc-free forms of protein G on a single-molecule basis and accurately determined their dissociation constant. This single-molecule functional binding assay is label-free, nearly background-free, and can detect functional heterogeneity, if any, among protein–ligand interactions. This methodology opens up avenues for studying protein–ligand interactions in a functional context, and we anticipate that it will find broad application in diverse protein–ligand systems.

Cao, Yi; Balamurali, M. M.; Sharma, Deepak; Li, Hongbin



Analytical tools for single-molecule fluorescence imaging in cellulo.  


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

Leake, M C



DNA replication at the single-molecule level.  


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

Stratmann, S A; van Oijen, A M



Single-molecule chemistry of metal phthalocyanine on noble metal surfaces.  


To develop new functional materials and nanoscale electronics, researchers would like to accurately describe and precisely control the quantum state of a single molecule on a surface. Scanning tunneling microscopy (STM), combined with first-principles simulations, provides a powerful technique for acquiring this level of understanding. Traditionally, metal phthalocyanine (MPc) molecules, composed of a metal atom surrounded by a ligand ring, have been used as dyes and pigments. Recently, MPc molecules have shown great promise as components of light-emitting diodes, field-effect transistors, photovoltaic cells, and single-molecule devices. In this Account, we describe recent research on the characterization and control of adsorption and electronic states of a single MPc molecule on noble metal surfaces. In general, the electronic and magnetic properties of a MPc molecule largely depend on the type of metal ion within the phthalocyanine ligand and the type of surface on which the molecule is adsorbed. However, with the STM technique, we can use on-site molecular "surgery" to manipulate the structure and the properties of the molecule. For example, STM can induce a dehydrogenation reaction of the MPc, which allows us to control the Kondo effect, which describes the spin polarization of the molecule and its interaction with the complex environment. A specially designed STM tip can allow researchers to detect certain molecule-surface hybrid states that are not accessible by other techniques. By matching the local orbital symmetry of the STM tip and the molecule, we can generate the negative differential resistance effect in the formed molecular junction. This orbital symmetry based mechanism is extremely robust and does not critically depend on the geometry of the STM tip. In summary, this simple model system, a MPc molecule absorbed on a noble metal surface, demonstrates the power of STM for quantum characterization and manipulation of single molecules, highlighting the potential of this technique in a variety of applications. PMID:20359193

Li, Zhenyu; Li, Bin; Yang, Jinlong; Hou, Jian Guo



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

NASA Astrophysics Data System (ADS)

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

Xu, Mingsheng


Pentanuclear dysprosium hydroxy cluster showing single-molecule-magnet behavior.  


A pentanuclear dysprosium hydroxy cluster of composition [Dy 5(mu 4-OH)(mu 3-OH) 4(mu-eta (2)-Ph 2acac) 4(eta (2)-Ph 2acac) 6] ( 1; Ph 2acac = dibenzoylmethanide) was prepared starting from [DyCl 3.6H 2O] and dibenzoylmethane. Both static (dc) and dynamic (ac) magnetic properties of 1 have been studied. Below 3 K, the appearance of slow relaxation of the magnetization typical for single-molecule magnets is seen, even if no hysteresis effects on the M vs H data are observed above 1.8 K. PMID:18582033

Gamer, Michael T; Lan, Yanhua; Roesky, Peter W; Powell, Annie K; Clérac, Rodolphe



Optical methods for single molecule detection and analysis.  


As analytical chemists, the highest resolution measurement one can make is at the single molecule level; it just does not get any better than that. To determine the concentration of a molecule in solution, the best way is to count the number of molecules in a given volume. As long as the volume contains a statistically large enough number of molecules and is above the Poisson noise limit, molecular counting is the most accurate way to make a measurement. Molecular counting is the method of the future and is beginning to be performed today. PMID:23215010

Walt, David R



Tunneling anisotropic magnetoresistance in single-molecule magnet junctions  

NASA Astrophysics Data System (ADS)

We theoretically investigate quantum transport through single-molecule magnet (SMM) junctions with ferromagnetic and normal-metal leads in the sequential regime. The current obtained by means of the rate-equation gives rise to the tunneling anisotropic magnetoresistance (TAMR), which varies with the angle between the magnetization direction of ferromagnetic lead and the easy axis of SMM. The angular dependence of TAMR can serve as a probe to determine experimentally the easy axis of SMM. Moreover, it is demonstrated that both the magnitude and the sign of TAMR are tunable by the bias voltage, suggesting a new spin-valve device with only one magnetic electrode in molecular spintronics.

Xie, Haiqing; Wang, Qiang; Jiao, Hujun; Liang, J.-Q.



The statistics of single molecule detection: An overview  

SciTech Connect

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

Enderlein, J.; Robbins, D.L.; Ambrose, W.P. [and others



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



Magnetic characterization of a Mn6 Single-molecule Magnet  

NASA Astrophysics Data System (ADS)

Single Molecule magnets (SMMs) are excellent candidates for the exploration of fundamental quantum effects at the nanoscale, as well as for potential applications in emerging technologies, such as quantum computation. Of particular interest are Mn6 SMMs, one of which has the highest effective energy barrier to magnetization reversal reported so far in the literature. We have performed Hall-effect magnetometry on single crystals of a new kind of Mn6 at cryogenic temperatures (>230mK). We will discuss the dependence of the hysteresis loops on the temperature and different sweep rates of the applied magnetic field. The high saturation fields observed in this SMM will be discussed.

Singh, Simranjeet; Del Barco, Enrique; Ali, Mahammad



Single Molecules Studies Using Optical Trapping and Fluorescence Techniques  

NASA Astrophysics Data System (ADS)

Biological organisms must compactly store and yet efficiently read the huge amounts of genetic information contained in their DNA. In the cell nucleus, DNA is highly compact as compared to naked DNA. The primary packing unit, the nucleosome, consists of roughly two turns of DNA wrapped around a core histone octamer. The mechanical stability of nucleosomes determines the accessibility of DNA to the cellular machinery that must decode it. We will discuss our recent progress towards understanding the mechanical stability of nucleosomes using single-molecule studies. Co-author: Alla Shundrovsky, Cornell University

Wang, Michelle D.



Advances in magnetic tweezers for single molecule and cell biophysics.  


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

Kilinc, Devrim; Lee, Gil U



Adsorption Geometry Determination of Single Molecules by Atomic Force Microscopy  

NASA Astrophysics Data System (ADS)

We measured the adsorption geometry of single molecules with intramolecular resolution using noncontact atomic force microscopy with functionalized tips. The lateral adsorption position was determined with atomic resolution, adsorption height differences with a precision of 3 pm, and tilts of the molecular plane within 0.2°. The method was applied to five ?-conjugated molecules, including three molecules from the olympicene family, adsorbed on Cu(111). For the olympicenes, we found that the substitution of a single atom leads to strong variations of the adsorption height, as predicted by state-of-the-art density-functional theory, including van der Waals interactions with collective substrate response effects.

Schuler, Bruno; Liu, Wei; Tkatchenko, Alexandre; Moll, Nikolaj; Meyer, Gerhard; Mistry, Anish; Fox, David; Gross, Leo



Two methods of temperature control for single-molecule measurements.  


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

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



Single Molecule Studies on Dynamics in Liquid Crystals  

PubMed Central

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

Tauber, Daniela; von Borczyskowski, Christian



Hindered Rotational Diffusion and Rotational Jumps of Single Molecules  

SciTech Connect

We extended the sensitivity of fluorescence polarization anisotropy measurements to the single molecule level by studying the polarization response of single fluorophores rapidly rotating in liquid. Comparison with a simple model calculation allows us to obtain information on the hindered motion as well as on the rotational diffusion in the presence of specific molecular interactions. We also observed rotational jumps between surface-bound and unbound states and show that they are, similar to jumps to long dark states, photoactivated. {copyright} {ital 1998} {ital The American Physical Society}

Ha, T.; Glass, J.; Enderle, T.; Chemla, D.S.; Weiss, S. [Materials Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720 (United States)] [Materials Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720 (United States); Glass, J.; Chemla, D.S. [Department of Physics, University of California at Berkeley, Berkeley, California 94720 (United States)] [Department of Physics, University of California at Berkeley, Berkeley, California 94720 (United States)



Single-molecule photochemical reactions of Auger-ionized quantum dots  

PubMed Central

Photoinduced electron transfer in donor-acceptor systems composed of quantum dots (QDs) and electron donors or acceptors is a subject of considerable recent research interest due to the potential applications of such systems in both solar energy harvesting and degradation of organic pollutants. Herein, we employed single-molecule imaging and spectroscopy techniques for the detection of photochemical reactions between 1,4-diaminobutane (DAB) and CdSe/ZnS single QDs. We investigated the reactions by analyzing photoluminescence (PL) intensity and lifetime of QDs at ensemble and single-molecule levels. While DAB was applied to single QDs tethered on a cover slip or QDs dispersed in a solution, PL intensity of QD continuously decreased with a concomitant increase in the PL lifetime. Interestingly, these changes in the PL properties of QD were predominant under high-intensity photoactivation. We hypothesize that the above changes in the PL properties surface due to the transfer of an electron from DAB to Auger-ionized QD followed by elimination of a proton from DAB and the formation of a QD-DAB adduct. Thus, a continuous decrease in the PL intensity of QDs under high-intensity photoactivation is attributed to continuous photochemical reactions of DAB with single QDs and the formation of QD-(DAB)n adducts. We believe that detection and analysis of such photochemical reactions of single QDs with amines will be of considerable broad interest due to the significant impact of photoinduced electron transfer reactions in energy management and environmental remediation.

Hamada, Morihiko; Shibu, Edakkattuparambil Sidharth; Itoh, Tamitake; Kiran, Manikantan Syamala; Nakanishi, Shunsuke; Ishikawa, Mitsuru; Biju, Vasudevanpillai



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


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



TiO2-SnO2:F interfacial electronic structure investigated by soft x-ray absorption spectroscopy  

NASA Astrophysics Data System (ADS)

The electronic structure of the titanium dioxide (TiO2)-fluorine-doped tin dioxide (SnO2:F) interface is investigated by soft x-ray absorption spectroscopy using synchrotron radiation. The measurements probe the site- and symmetry-selected unoccupied density of states and reflect the interaction between an early transition-metal-oxide (d0) semiconductor and a post-transition-metal-oxide (d10) degenerate semiconductor. The distinct interfacial electronic structure of TiO2-SnO2:F is established by contrasting spectra with those for anatase and rutile TiO2, SnO2:F, and ZnO-SnO2:F and CdO-SnO2:F interfaces. Oxygen 1s absorption spectra, which relate to the O 2p partial density of states of the conduction band, indicate that the interface is associated with a reduction in Ti d-O p orbital hybridization and an alteration of the TiO2 crystal field. These observations are consistent with measured titanium 2p absorption spectra, which in addition provide evidence for distortion of long-range order around the cation site in the interfacial TiO2. The TiO2-SnO2:F interface is a functional component of a number of optoelectronic devices, perhaps most notably within the anode structure of solar cell architectures. In nonequilibrium conditions, such as those found in operating solar cells, interfacial electronic structure directly influences performance by modifying, for instance, the quasi-Fermi level electrons and the potential distribution at the transparent electrode.

Kronawitter, Coleman X.; Kapilashrami, Mukes; Bakke, Jonathan R.; Bent, Stacey F.; Chuang, Cheng-Hao; Pong, Way-Faung; Guo, Jinghua; Vayssieres, Lionel; Mao, Samuel S.



DCDHF Fluorophores for Single-Molecule Imaging in Cells**  

PubMed Central

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

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



Single-Molecule Electrical Random Resequencing of DNA and RNA  

NASA Astrophysics Data System (ADS)

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.

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



Ultra-stable organic fluorophores for single-molecule research.  


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



Single Molecule Studies of Energy Transfer in Semiconductor Nanocrystal Clusters  

NASA Astrophysics Data System (ADS)

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

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



Single molecule studies of the neuronal SNARE fusion machinery  

PubMed Central

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

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



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.

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



Ultrabright bowtie nanoaperture antenna probes studied by single molecule fluorescence.  


We report on a novel design for the fabrication of ultrabright bowtie nanoaperture antenna (BNA) probes to breach the intrinsic trade-off between power transmission and field confinement of circular nanoapertures as in near-field scanning optical microscopy (NSOM) or planar zero mode waveguides. The approach relies on the nanofabrication of BNAs at the apex of tapered optical fibers tuned to diameters close to their cutoff region, resulting in 10(3)× total improvement in throughput over conventional NSOM probes of similar confinement area. By using individual fluorescence molecules as optical nanosensors, we show for the first time nanoimaging of single molecules using BNA probes with an optical confinement of 80 nm, measured the 3D near-field emanating from these nanostructures and determined a ~6-fold enhancement on the single molecule signal. The broadband field enhancement, nanoscale confinement, and background free illumination provided by these nanostructures offer excellent perspectives as ultrabright optical nanosources for a full range of applications, including cellular nanoimaging, spectroscopy, and biosensing. PMID:23098104

Mivelle, Mathieu; van Zanten, Thomas S; Neumann, Lars; van Hulst, Niek F; Garcia-Parajo, Maria F



Probing Protein Channel Dynamics At The Single Molecule Level.  

NASA Astrophysics Data System (ADS)

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

Lee, M. Ann; Dunn, Robert C.



Single-molecule sequencing of an individual human genome  

PubMed Central

Recent advances in high-throughput DNA sequencing technologies have enabled order-of-magnitude improvements in both cost and throughput. Here we report the use of single-molecule methods to sequence an individual human genome. We aligned billions of 24- to 70-bp reads (32 bp average) to ~90% of the National Center for Biotechnology Information (NCBI) reference genome, with 28× average coverage. Our results were obtained on one sequencing instrument by a single operator with four data collection runs. Single-molecule sequencing enabled analysis of human genomic information without the need for cloning, amplification or ligation. We determined ~2.8 million single nucleotide polymorphisms (SNPs) with a false-positive rate of less than 1% as validated by Sanger sequencing and 99.8% concordance with SNP genotyping arrays. We identified 752 regions of copy number variation by analyzing coverage depth alone and validated 27 of these using digital PCR. This milestone should allow widespread application of genome sequencing to many aspects of genetics and human health, including personal genomics.

Pushkarev, Dmitry; Neff, Norma F; Quake, Stephen R



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.

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



Visualizing helicases unwinding DNA at the single molecule level  

PubMed Central

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

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



Localizing single molecules in three dimensions - a brief review  

PubMed Central

Single molecule tracking in three dimensions (3D) in a live cell environment holds the promise of revealing important new biological insights. However, conventional microscopy based imaging techniques are not well suited for fast 3D tracking of single molecules in cells. Previously we developed an imaging modality multifocal plane microscopy (MUM) to image fast intracellular dynamics in 3D in live cells. Recently, we have reported an algorithm, the MUM localization algorithm (MUMLA), for the 3D localization of point sources that are imaged using MUM. Here, we present a review of our results on MUM and MUMLA. We have validated MUMLA through simulated and experimental data and have shown that the 3D-position of quantum dots (QDs) can be determined with high spatial accuracy over a wide spatial range. We have calculated the Cramer-Rao lower bound for the problem of determining the 3D location of point sources from MUM and from conventional microscopes. Our analyses shows that MUM overcomes the poor depth discrimination of the conventional microscope, and thereby paves the way for high accuracy tracking of nanoparticles in a live cell environment. We have also shown that the performance of MUMLA comes consistently close to the Cramer-Rao lower bound.

Ram, Sripad; Prabhat, Prashant; Chao, Jerry; Abraham, Anish V.; Ward, E. Sally



High sensitivity optical microscope for single molecule spectroscopy studies  

NASA Astrophysics Data System (ADS)

We describe the setup and apply two algorithms for fast imaging in a sample raster scanning two photon microscope. Imaging can be performed at a rate of 1-100 lines per second with a closed loop piezo actuator, and the detection is performed via avalanche photodiodes. This allows to investigate single molecule emission with 50 ms time resolution. In a slow scanning algorithm we have implemented fluorescence fluctuation analysis by computing the photon counting histogram (PCH) on each pixel of the image. In a fast-scan acquistion method the image acquistion rate is 5 lines per second on a large field of view and high resolution(50 nm scanning step, 100×100 ?m2 field of view) and ?100 lines per second on smaller field of views with optically limited resolution (200 nm scanning step, 20×20 ?m2 field of view). This figure, which is lower than the typical value for normal confocal scanning imaging (?500 lines per second), allows nevertheless to perform imaging studies of extended samples in reasonable times for intracellular kinetics and interactions. With this setup and by means of the PCH analysis we are able to discriminate between local concentration and molecular brightness on extended samples also at the level of the single molecule.

Malengo, Gabriele; Milani, Roberto; Cannone, Fabio; Krol, Silke; Diaspro, Alberto; Chirico, Giuseppe



Progress in quantitative single-molecule localization microscopy.  


With the advent of single-molecule localization microscopy (SMLM) techniques, intracellular proteins can be imaged at unprecedented resolution with high specificity and contrast. These techniques can lead to a better understanding of cell functioning, as they allow, among other applications, counting the number of molecules of a protein specie in a single cell, studying the heterogeneity in protein spatial organization, and probing the spatial interactions between different protein species. However, the use of these techniques for accurate quantitative measurements requires corrections for multiple inherent sources of error, including: overcounting due to multiple localizations of a single fluorophore (i.e., photoblinking), undercounting caused by incomplete photoconversion, uncertainty in the localization of single molecules, sample drift during the long imaging time, and inaccurate image registration in the case of dual-color imaging. In this paper, we review recent efforts that address some of these sources of error in quantitative SMLM and give examples in the context of photoactivated localization microscopy (PALM). PMID:24748502

Deschout, H; Shivanandan, A; Annibale, P; Scarselli, M; Radenovic, A



Single-Molecule Fluorescence Quantification with a Photobleached Internal Standard  

PubMed Central

In cellular and molecular biology, fluorophores are employed to aid in tracking and quantifying molecules involved in cellular function. We previously developed a sensitive single-molecule quantification technique to count the number of proteins and the variation of the protein number over the population of individual sub-cellular organelles. However, environmental effects on the fluorescent intensity of fluorophores can make it difficult to accurately quantify proteins using these sensitive techniques. In this paper, we demonstrate the use of photobleaching to extract an accurate single-molecule calibration intensity distribution from the sample directly to avoid any differences in environment that may alter the count. Using this technique, we were able to show that goat anti-mouse IgG antibody labeled with Alexa Fluor 488, an environmentally insensitive fluorophore, exhibited an average fluorescence equivalent to 4.6 single fluorophores. SynaptopHluorin vesicles, which contain the environmentally sensitive green fluorescent protein, exhibited an average of 4.4 single green fluorescent proteins per vesicle.

Gadd, Jennifer C.; Fujimoto, Bryant S.; Bajjalieh, Sandra M.; Chiu, Daniel T.



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.

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



New assay for multiple single molecule enzyme kinetics  

NASA Astrophysics Data System (ADS)

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

Lee, Alan I.; Brody, James P.



Controlling Protein Conformations to Explore Unprecedented Material Properties by Single-Molecule Surgery.  

National Technical Information Service (NTIS)

The primary objective of our single-molecule material science project is to mechanically and optically control and regulate single-molecule protein conformations to explore unprecedented properties and capture such exclusive states in real-time at an extr...

H. P. Lu



Single-molecule imaging on living bacterial cell surface by high-speed AFM.  


Advances in microscopy have contributed to many biologic discoveries. Electron microscopic techniques such as cryo-electron tomography are remarkable tools for imaging the interiors of bacterial cells in the near-native state, whereas optical microscopic techniques such as fluorescence imaging are useful for following the dynamics of specific single molecules in living cells. Neither technique, however, can be used to visualize the structural dynamics of a single molecule at high resolution in living cells. In the present study, we used high-speed atomic force microscopy (HS-AFM) to image the molecular dynamics of living bacterial cell surfaces. HS-AFM visualizes the dynamic molecular processes of isolated proteins at sub-molecular resolution without the need for complicated sample preparation. In the present study, magnetotactic bacterial cells were anchored in liquid medium on substrate modified by poly-L-lysine and glutaraldehyde. High-resolution HS-AFM images of live cell surfaces showed that the bacterial outer membrane was covered with a net-like structure comprising holes and the hole rims framing them. Furthermore, HS-AFM captured the dynamic movement of the surface ultrastructure, showing that the holes in the net-like structure slowly diffused in the cell surface. Nano-dissection revealed that porin trimers constitute the net-like structure. Here, we report for the first time the direct observation of dynamic molecular architectures on a live cell surface using HS-AFM. PMID:22613761

Yamashita, Hayato; Taoka, Azuma; Uchihashi, Takayuki; Asano, Tomoya; Ando, Toshio; Fukumori, Yoshihiro



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

NASA Astrophysics Data System (ADS)

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 ?1-like and ?5-like symmetries.

Gangineni, R. B.; Bellouard, C.; Duluard, A.; Negulescu, B.; Baraduc, C.; Gaudin, G.; Tiusan, C.



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.



Single-molecule orientation measurements with a quadrated pupil  

NASA Astrophysics Data System (ADS)

We present a means of measuring the dipole orientation of a fluorescent, rotationally fixed single molecule (SM), using a specially designed phase mask, termed a "quadrated pupil," conjugate to the back focal plane of a conventional widefield microscope. In comparison to image-fitting techniques that infer orientation by matching simulations to defocused or excessively magnified images, the quadrated pupil approach is more robust to minor modeling discrepancies, defocus, and optical aberrations. Precision on the order of 1°-5° is achieved in proofof- concept experiments for both azimuthal (?) and polar (?) angles. Since the phase mask is implemented on a liquid-crystal spatial light modulator (SLM) that may be deactivated without any mechanical perturbation of the sample or imaging system, the technique may be readily integrated into conventional imaging studies.

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



Photochromism of diarylethene single molecules in polymer matrices.  


Robust fluorescent photoswitching molecules, having perylene bisimide as the fluorescent unit and diarylethene as the switching unit, were prepared, and their photochromic reactions were measured at the single-molecule level in various polymer matrices. The histograms of the fluorescent on and off times were found to deviate from normal exponential distribution and showed a peak when the molecules are embedded in rigid polymer matrices, such as Zeonex or poly(methyl methacrylate) (PMMA). In soft polymer matrices, such as poly(n-buthyl methacrylate) (PnBMA), exponential distribution was observed for the on and off times. The abnormal distribution suggests that the quantum yields of the photoreactions are not constant and the molecules undergo the reactions after absorbing a certain number of photons. A multilocal minima model was proposed to explain the environmental effect. PMID:17432858

Fukaminato, Tuyoshi; Umemoto, Tohru; Iwata, Yasuhide; Yokojima, Satoshi; Yoneyama, Mitsuru; Nakamura, Shinichiro; Irie, Masahiro



Single molecule magnets: from thin films to nano-patterns.  


Single molecule magnets (SMM) are a class of molecules exhibiting magnetic properties similar to those observed in conventional bulk magnets, but of molecular origin. SMMs have been proposed as potential candidates for several technological applications that require highly controlled thin films and patterns. Here we present an overview of the most important approaches for thin film growth and micro(nano)-patterning of SMM, giving special attention to Mn(12) based molecules. We present both conventional approaches to thin film growth (Langmuir-Blodgett, chemical approach, dip and dry, laser evaporation), patterning (micro-contact printing, deposition on patterned surface, moulding of homogeneous films) and new methods specifically developed for SMM (lithographically controlled wetting, lithographically controlled de-mixing). PMID:18231680

Cavallini, Massimiliano; Facchini, Massimo; Albonetti, Cristiano; Biscarini, Fabio



Reconstructing folding energy landscapes by single-molecule force spectroscopy.  


Folding may be described conceptually in terms of trajectories over a landscape of free energies corresponding to different molecular configurations. In practice, energy landscapes can be difficult to measure. Single-molecule force spectroscopy (SMFS), whereby structural changes are monitored in molecules subjected to controlled forces, has emerged as a powerful tool for probing energy landscapes. We summarize methods for reconstructing landscapes from force spectroscopy measurements under both equilibrium and nonequilibrium conditions. Other complementary, but technically less demanding, methods provide a model-dependent characterization of key features of the landscape. Once reconstructed, energy landscapes can be used to study critical folding parameters, such as the characteristic transition times required for structural changes and the effective diffusion coefficient setting the timescale for motions over the landscape. We also discuss issues that complicate measurement and interpretation, including the possibility of multiple states or pathways and the effects of projecting multiple dimensions onto a single coordinate. PMID:24895850

Woodside, Michael T; Block, Steven M



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)



Eukaryotic transcriptional dynamics: from single molecules to cell populations  

PubMed Central

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

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



Chromatin remodeling: insights and intrigue from single-molecule studies  

PubMed Central

Chromatin remodelers are ATP-hydrolyzing machines specialized to restructure, mobilize or eject nucleosomes, allowing regulated exposure of DNA in chromatin. Recently, remodelers have been analyzed using single-molecule techniques in real time, revealing them to be complex DNA-pumping machines. The results both support and challenge aspects of current models of remodeling, supporting the idea that the remodeler translocates or pumps DNA loops into and around the nucleosome, while also challenging earlier concepts about loop formation, the character of the loop and how it propagates. Several complex behaviors were observed, such as reverse translocation and long translocation bursts of the remodeler, without appreciable DNA twist. This review presents and discusses revised models for nucleosome sliding and ejection that integrate this new information with the earlier biochemical studies.

Cairns, Bradley R



Single-molecule FRET with total internal reflection microscopy.  


Single-molecule (sm) fluorescence detection is a powerful method for studying biological events without time and population averaging. Förster (fluorescence) resonance energy transfer (FRET) is a spectroscopic technique in which the efficiency of energy transfer from donor to acceptor molecules is used to determine distances between molecules in the 30-80 Å range. Structural changes in biological molecules or relative motion between two interacting molecules can be detected by a change in FRET. This article focuses primarily on smFRET based on total internal reflection (TIR) microscopy. It begins with discussions of dye choice and labeling of nucleic acids and proteins. These are followed by information on surface preparation and data acquisition. Various methods of data analysis are then presented, as is information on setting up TIR microscopy, both the objective and the prism types. PMID:23209135

Joo, Chirlmin; Ha, Taekjip



Imaging and identifying impurities in single-molecule FRET studies.  


Single-molecule (sm) Förster (fluorescence) resonance energy transfer (FRET) is a spectroscopic technique in which the efficiency of energy transfer from donor to acceptor molecules is used to determine distances between molecules in the 30-80 Å range. Structural changes in biological molecules or relative motion between two interacting molecules can be detected by a change in FRET. To study the conformational changes of individual molecules over extended time periods, the molecules must be immobilized on a coated surface that allows highly specific tethering of DNA, RNA, or protein. Nevertheless, there are always some fluorescent impurities on the surface and, without experience in sm imaging, it is often difficult to distinguish molecules of interest from impurities. This protocol describes the use of an imaging buffer that enhances the photostability of cyanine dyes used for smFRET, with emphasis on distinguishing molecules of interest from impurities. PMID:23028079

Joo, Chirlmin; Ha, Taekjip



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


The alternating-laser excitation (ALEX) scheme continues to expand the possibilities of fluorescence-based assays to study biological entities and interactions. Especially the combination of ALEX and single-molecule Förster Resonance Energy Transfer (smFRET) has been very successful as ALEX enables the sorting of fluorescently labelled species based on the number and type of fluorophores present. ALEX also provides a convenient way of accessing the correction factors necessary for determining accurate molecular distances. Here, we provide a comprehensive overview of the concept and current applications of ALEX and we explicitly discuss how to obtain fully corrected distance information across the entire FRET range. We also present new ideas for applications of ALEX which will push the limits of smFRET-based experiments in terms of temporal and spatial resolution for the study of complex biological systems. PMID:24037326

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



Single-molecule imaging revealed dynamic GPCR dimerization.  


Single fluorescent-molecule video imaging and tracking in living cells are revolutionizing our understanding of molecular interactions in the plasma membrane and intracellular membrane systems. They have revealed that molecular interactions occur surprisingly dynamically on much shorter time scales (?1s) than those expected from the results by conventional techniques, such as pull-down assays (minutes to hours). Single-molecule imaging has unequivocally showed that G-protein-coupled receptors (GPCRs) undergo dynamic equilibrium between monomers and dimers, by enabling the determination of the 2D monomer-dimer equilibrium constant, the dimer dissociation rate constant (typically ?10s(-1)), and the formation rate constant. Within one second, GPCRs typically undergo several cycles of monomer and homo-dimer formation with different partners. PMID:24480089

Kasai, Rinshi S; Kusumi, Akihiro



Single-Molecule Encoders for Tracking Motor Proteins on DNA  

NASA Astrophysics Data System (ADS)

Devices such as inkjet printers and disk drives track position and velocity using optical encoders, which produce periodic signals precisely synchronized with linear or rotational motion. We have implemented this technique at the nanometer scale by labeling DNA with regularly spaced fluorescent dyes. The resulting molecular encoders can be used in several ways for high-resolution continuous tracking of individual motor proteins. These measurements do not require mechanical coupling to macroscopic instrumentation, are automatically calibrated by the underlying structure of DNA, and depend on signal periodicity rather than absolute level. I will describe the synthesis of single-molecule encoders, data from and modeling of experiments on a helicase and a DNA polymerase, and some ideas for future work.

Lipman, Everett A.



Ultrasensitive nucleic acid sequence detection by single-molecule electrophoresis  

SciTech Connect

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

Castro, A; Shera, E.B.



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


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

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



Visualizing Cyclic Peptide Hydration at the Single-Molecule Level  

NASA Astrophysics Data System (ADS)

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.

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



Single-molecule controlled emission in planar plasmonic cavities  

NASA Astrophysics Data System (ADS)

We study the fluorescence emission from single dye molecules in coplanar plasmonic cavities composed of a thin gold film surrounded by two in-plane surface plasmon Bragg mirrors. We first discuss the effect of the presence of Bragg mirrors on the radiation diagram of surface plasmon coupled emission. Then, we investigate the role of the planar cavity size by single-molecule fluorescence lifetime imaging. Experimental data are compared to numerical simulations of the decay rates calculated as a function of the molecule orientation and position within the cavity. The creation of new decay channels by coupling to the cavity modes is also discussed. We measure a plasmonic Purcell factor up to five, attributed to the enhancement of the radiative rate.

Derom, S.; Bouhelier, A.; Kumar, A.; Leray, A.; Weeber, J.-C.; Buil, S.; Quélin, X.; Hermier, J. P.; Francs, G. Colas des



Single-molecule magnet engineering: building-block approaches.  


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



Single-Molecule Detection in Micron-Sized Capillaries  

NASA Astrophysics Data System (ADS)

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

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



DNA-cisplatin interaction studied with single molecule stretching experiments.  


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



Simultaneous Determination of Conductance and Thermopower of Single Molecule Junctions  

NASA Astrophysics Data System (ADS)

We present a study of concurrent determination of conductance (G) and thermopower (S) of single-molecule junctions via direct measurement of electrical and thermoelectric currents. The junctions are created using the STM-based break-junction technique where a cold Au tip is repeatedly brought in and out of contact with a hot Au-on-mica substrate in an environment of the target molecule. We explore several amine-Au and pyridine-Au linked molecules that are predicted to conduct through either the highest occupied molecular orbital (HOMO) or the lowest unoccupied molecular orbital (LUMO), respectively. We find that the Seebeck coefficient is negative for pyridine-Au linked LUMO-conducting junctions and positive for amine-Au linked HOMO-conducting junctions. From histograms of thousands of junctions, we use the most probable Seebeck coefficient to determine a power factor, GS^2, for each junction studied, and find that GS^2 generally increases with G.

Widawsky, Jonathan; Darancet, Pierre; Neaton, Jeffrey; Venkataraman, Latha



What Do We Measure With Single-Molecule Force Spectroscopy?  

NASA Astrophysics Data System (ADS)

Single-molecule force spectroscopy is a powerful technique for studying detailed intra- and inter- molecular interactions by manipulating single biomolecules at the nanometer scale. Force is measured while one pulls on the molecules. However, relating the measured information to equilibrium thermodynamic properties is challenging. Jarzynksi's equality allows one to reconstruct the free energy surface as a function of molecular end-to-end distance^1,2. Using protein folding as an example, we studied the parameters that influence the unfolding process, such as pulling velocity, tempearture, and chemical denaturant concentration in the solution, to demonatrate that valuable equailibrium thermodynamic information can be obtained using this technique. 1. N. C. Harris, Y. Song, and C.-H. Kiang, Phys. Rev. Lett., 99 068101 (2007). 2.``Pulling Strings: Stretching Proteins Can Reveal How They Fold,'' Science News, 172 22 (2007).

Kiang, Ching-Hwa; Harris, Nolan; Botello, Eric; Chen, Wei-Hung



Controlled sequential dehydrogenation of single molecules by scanning tunneling microscopy  

NASA Astrophysics Data System (ADS)

Scanning tunneling microscopy (STM) is today the most powerful and versatile tool available for imaging and manipulating single molecules on surfaces. Here, we explore its ultimate limit by demonstrating the possibility of controlling sequential di-dehydrogenation of single Co-Salen molecules sublimated on Cu. In particular, we are able to explore the final products of the H2 dissociation as well as the intermediate state, in which only one H atom is separated from the molecule. This is achieved by low-temperature STM with the dissociation induced by either point spectroscopy or in the standard constant-current mode. Crucial for the interpretation of the data is our ability to perform state-of-the-art density-functional theory simulations of both topographic and spectroscopical STM images. This work demonstrates that STM combined with theory can give access to the atomic details of a chemical reaction even when the reaction products are completely unknown.

Baadji, Nadjib; Kuck, Stefan; Brede, Jens; Hoffmann, Germar; Wiesendanger, Roland; Sanvito, Stefano



Single-molecule paleoenzymology probes the chemistry of resurrected enzymes  

PubMed Central

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

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



Single-molecule analysis of Pseudomonas fluorescens footprints.  


Understanding the molecular mechanisms of bacterial adhesion and biofilm formation is an important topic in current microbiology and a key in nanomedicine for developing new antibacterial strategies. There is growing evidence that the production of extracellular polymeric substances at the cell-substrate interface plays a key role in strengthening bacterial adhesion. Yet, because these adhesive polymers are available in small amounts and are localized at interfaces, they are difficult to study using traditional techniques. Here, we use single-molecule atomic force microscopy (AFM) to functionally analyze the biophysical properties (distribution, adhesion, and extension) of bacterial footprints, that is, adhesive macromolecules left on substrate surfaces after removal of the attached cells. We focus on the large adhesin protein LapA from Pseudomonas fluorescens, which mediates cell attachment to a wide diversity of surfaces. Using AFM tips functionalized with specific antibodies, we demonstrate that adhesion of bacteria to hydrophobic substrates leads to the active accumulation of the LapA protein at the cell-substrate interface. We show that single LapA proteins left on the substrate after cell detachment localize into microscale domains corresponding to the bacterial size and exhibit multiple adhesion peaks reflecting the adhesion and extension of adsorbed LapA proteins. The mechanical behavior of LapA-based footprints makes them ideally suited to function as multipurpose bridging polymers, enabling P. fluorescens to attach to various surfaces. Our experiments show that single-molecule AFM offers promising prospects for characterizing the biophysics and dynamics of the cell-substrate interface in the context of bacterial adhesion, on a scale that was not accessible before. PMID:24456070

El-Kirat-Chatel, Sofiane; Boyd, Chelsea D; O'Toole, George A; Dufrêne, Yves F



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



The study of single anticancer peptides interacting with HeLa cell membranes by single molecule force spectroscopy  

NASA Astrophysics Data System (ADS)

To determine the effects of biophysical parameters (e.g. charge, hydrophobicity, helicity) of peptides on the mechanism of anticancer activity, we applied a single molecule technique--force spectroscopy based on atomic force microscope (AFM)--to study the interaction force at the single molecule level. The activity of the peptide and analogs against HeLa cells exhibited a strong correlation with the hydrophobicity of peptides. Our results indicated that the action mode between ?-helical peptides and cancer cells was largely hydrophobicity-dependent.To determine the effects of biophysical parameters (e.g. charge, hydrophobicity, helicity) of peptides on the mechanism of anticancer activity, we applied a single molecule technique--force spectroscopy based on atomic force microscope (AFM)--to study the interaction force at the single molecule level. The activity of the peptide and analogs against HeLa cells exhibited a strong correlation with the hydrophobicity of peptides. Our results indicated that the action mode between ?-helical peptides and cancer cells was largely hydrophobicity-dependent. Electronic supplementary information (ESI) available: Peptide design, biophysical properties, biological activities and experimental section. See DOI: 10.1039/c2nr11541g

Shan, Yuping; Huang, Jinfeng; Tan, Juanjuan; Gao, Gui; Liu, Shuheng; Wang, Hongda; Chen, Yuxin



Surface-junction effects on interfacial electron transfer between bis(terpyridine)iron(II) and hydrogen-terminated silicon(111) electrode.  


Interfacial electron transfer at bis(tpy)–iron(II) complexes (tpy=2,2’:6’,2’’-terpyridine) on Si(111) electrodes was investigated by using four types of surfaceanchor terpyridine ligands. Despite the greater distance, electron transfer between the bis(tpy)–iron(II) unit and the electrode is accelerated in surface-anchor ligands with an additional phenylene group. PMID:24677418

Maeda, Hiroaki; Sakamoto, Ryota; Nishihara, Hiroshi



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



Modification and characterization of fluorescent conjugated polymer nanoparticles for single molecule detection  

NASA Astrophysics Data System (ADS)

Single molecule tracking using fluorescent dye or nanoparticle labels has emerged as a useful technique for probing biomolecular processes. Considerable interest arises in the development of nanoparticle labels with brighter fluorescence in order to improve the spatial and temporal resolution of single molecule detection and to facilitate the application of single molecule detection methods to a wider range of intracellular processes. The McNeill laboratory recently reported that conjugated polymer nanoparticles exhibit fluorescence cross-sections roughly 10--100 times higher than other luminescent nanoparticles of similar size, excellent photostability (2.2x108 photons emitted per nanoparticle prior to photobleaching), and saturated emission rates roughly 100 times higher than that of the molecular dyes and more than 1000 times higher than that of colloidal semiconductor quantum dots. One purpose of this graduate research is the development of highly fluorescent, bioconjugated nanoparticle labels based on conjugated polymers for demanding fluorescence applications such as single molecule tracking in live cells. Three surface modification methods (conjugated polymer nanoparticles encapsulated with lipid silica agents, conjugated polymer nanoparticles encapsulated with tetraethyl orthosilicate(TEOS) and hybrid nanoparticles with thiol pendant groups by the Stober Method (3-mercaptopropyl trimethoxysilane (MPS))) have been developed to protect the conjugated polymer, passivate the nanoparticle surface, and provide a chemical handle for bioconjugation such as nanoparticle encapsulation with alkoxysilanes and Stober method. After encapsulation, the fluorescence quantum yield of silica-encapsulated nanoparticles is improved by 20% as compared to bare conjugated polymer nanoparticles, while the photostability is improved by a factor of 2, indicating that some protection of the polymer is provided by the encapsulating layer. Another purpose of my research is the manipulation of the photophysics and photochemistry of conjugated polymer nanoparticles based on developing a more complete understanding of the various processes that control or limit nanoparticle brightness and photostability. The results indicate that a combination of photophysical processes including electron transfer to molecular oxygen, energy transfer, and exciton diffusion result in saturation and photobleaching phenomena that currently limit brightness. This study provides the potential methods and strategies aimed at manipulating such processes or limiting their effect on fluorescence brightness. Finally, efficient intra-particle energy transfer has been demonstrated in dye-doped CP nanoparticles, which provides a new strategy for improving nanoparticle fluorescence brightness and photostability, obtaining nanoparticles with red emission to avoid autofluorescence in mammalian tissue, and for designing novel sensitive biosensors based on energy transfer to sensor dyes.

Zheng, Yueli


Single-molecule metal-induced energy transfer (smMIET): resolving nanometer distances at the single-molecule level.  


We present a new concept for measuring distance values of single molecules from a surface with nanometer accuracy using the energy transfer from the excited molecule to surface plasmons of a metal film. We measure the fluorescence lifetime of individual dye molecules deposited on a dielectric spacer as a function of a spacer thickness. By using our theoretical model, we convert the lifetime values into the axial distance of individual molecules. Similar to Förster resonance energy transfer (FRET), this allows emitters to be localized with nanometer accuracy, but in contrast to FRET the distance range at which efficient energy transfer takes place is an order of magnitude larger. Our technique can be potentially used as a tool for measuring intramolecular distances of biomolecules and complexes. PMID:24478241

Karedla, Narain; Chizhik, Alexey I; Gregor, Ingo; Chizhik, Anna M; Schulz, Olaf; Enderlein, Jörg



Heteroepitaxial metallo-phthalocyanine (MPc, M = cobalt, nickel, copper) thin films on gold: Atomic and interfacial electronic structures  

NASA Astrophysics Data System (ADS)

Organic semiconductors have become a hot topic for research within the past few years. This work describes research into a family of organic semiconductors known as metallo-phthalocyanine (MPc) in which the electronic and optical properties can be easily tuned by the systematic modification of the metal cations and ligands. More specifically, thin films of CoPc, NiPc, and CuPc have been evaporated onto a "5 x 20" reconstructed Au(001) substrate and have been investigated by employing low energy electron diffraction and ultraviolet photoelectron spectroscopy. Low energy electron diffraction reveals that thin films of CuPc and NiPc are highly ordered with a square unit cell aligned along the substrate <110> and <11¯0> axes. In addition, deposition of CuPc onto the Au(001) substrate when at room temperature and elevated temperatures reveal that the square unit cell is larger when the substrate is heated. On the other hand, CoPc thin films are not well ordered as evidenced by multiple rotationally equivalent square domains, which are separated by 16°. Even more interesting is that the contrast between NiPc and CoPc on Au(001) is further found in the interfacial electronic structure. Ultraviolet photoelectron spectroscopy studies of the interfacial layers of NiPc deposited on the reconstructed gold substrate indicate that NiPc physisorbs on the gold surface as verified by a uniform molecular orbital (MO) shift. However, similar studies of the interfacial layers of CoPc depict an interaction between the CoPc 13a1g MO and the Au surface suggesting a charge transfer between the two. In addition to the research into MPc thin films, this work also describes the development of a Low Energy Electron Diffraction Intensity versus Voltage (LEED-IV) system for the Laboratory for Surface Analysis and Modification. This development involved the merging of various hardware and software systems by means of LabVIEW environment. Characterization of the system performance was carried out through the use of a MoS2 sample with known LEED-IV characteristics. The results of the system characterization revealed that the fully operational and ready to be applied to other samples.

Ellis, Trinity S.



Large tunable image-charge effects in single-molecule junctions  

NASA Astrophysics Data System (ADS)

Metal/organic interfaces critically determine the characteristics of molecular electronic devices, because they influence the arrangement of the orbital levels that participate in charge transport. Studies on self-assembled monolayers show molecule-dependent energy-level shifts as well as transport-gap renormalization, two effects that suggest that electric-field polarization in the metal substrate induced by the formation of image charges plays a key role in the alignment of the molecular energy levels with respect to the metal's Fermi energy. Here, we provide direct experimental evidence for an electrode-induced gap renormalization in single-molecule junctions. We study charge transport through single porphyrin-type molecules using electrically gateable break junctions. In this set-up, the position of the occupied and unoccupied molecular energy levels can be followed in situ under simultaneous mechanical control. When increasing the electrode separation by just a few ångströms, we observe a substantial increase in the transport gap and level shifts as high as several hundreds of meV. Analysis of this large and tunable gap renormalization based on atomic charges obtained from density functional theory confirms and clarifies the dominant role of image-charge effects in single-molecule junctions.

Perrin, Mickael L.; Verzijl, Christopher J. O.; Martin, Christian A.; Shaikh, Ahson J.; Eelkema, Rienk; van Esch, Jan H.; van Ruitenbeek, Jan M.; Thijssen, Joseph M.; van der Zant, Herre S. J.; Duli?, Diana



Single Molecule Manipulation and Spectroscopy of Chlorophyll-a from Spinach  

NASA Astrophysics Data System (ADS)

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

Benson, Jessica-Jones



The relation between structure and quantum interference in single molecule junctions.  


Quantum interference (QI) of electron pathways has recently attracted increased interest as an enabling tool for single-molecule electronic devices. Although various molecular systems have been shown to exhibit QI effects and a number of methods have been proposed for its analysis, simple guidelines linking the molecular structure to QI effects in the phase-coherent transport regime have until now been lacking. In the present work we demonstrate that QI in aromatic molecules is intimately related to the topology of the molecule's ? system and establish a simple graphical scheme to predict the existence of QI-induced transmission antiresonances. The generality of the scheme, which is exact for a certain class of tight-binding models, is proved by a comparison to first-principles transport calculations for 10 different configurations of anthraquinone as well as a set of cross-conjugated molecular wires. PMID:20879779

Markussen, Troels; Stadler, Robert; Thygesen, Kristian S



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.

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



Compact Quantum Dots for Single-molecule Imaging  

PubMed Central

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

Smith, Andrew M.; Nie, Shuming



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


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



Single molecule vibrationally mediated chemistry. Towards state-specific strategies for molecular handling  

NASA Astrophysics Data System (ADS)

Tunnelling electrons may scatter inelastically with an adsorbate, releasing part of their energy through the excitation of molecular vibrations. The resolution of inelastic processes with a low temperature scanning tunnelling microscope (STM) provides a valuable tool to chemically characterize single adsorbates and their adsorption mechanisms. Here, we present a molecular scale picture of single molecule vibrational chemistry, as resolved by STM. To understand the way a reaction proceed it is needed knowledge about both the excitation and damping of a molecular vibration. The excitation is mediated by the specific coupling between electronic molecular resonances present at the Fermi level and vibrational states of the adsorbate. Thus, the two-dimensional mapping of the inelastic signal with an STM provides the spatial distribution of the adsorbate electronic states (near the Fermi level) which are predominantly coupled to the particular vibrational mode observed. The damping of the vibration follows a competition between different mechanisms, mediated via the creation of electron-hole pairs or via anharmonic coupling between vibrational states. This latter case give rise to effective energy transfer mechanisms which eventually may focus vibrational energy in a specific reaction coordinate. In this single-molecule work-bench, STM provides alternative tools to understand reactivity in the limit of low excitation rate, which demonstrate the existence of state-specific excitation strategies which may lead to selectivity in the product of a reaction. The author acknowledges his co-workers in the work presented here, H. Conrad, N. Lorente, H.-P. Rust, and Z. Song, as well as collaborations with J. Gómez Herrero, J.J. Jackiw, D. Sánchez-Portal and P.S. Weiss.

Pascual, J. I.



Microfluidic device for the electrokinetic manipulation of single molecules  

NASA Astrophysics Data System (ADS)

We are developing a microfluidic device for three-dimensional electrokinetic manipulation of single fluorescent molecules in solution. The device consists of electrode pairs deposited onto glass cover slips via UV microlithography and ionic sputtering. By positioning two such electrode pairs in a tetrahedral configuration separated by 100 microns and applying appropriate digitally-controlled voltages to each, the apparatus generates an electric field of selected directionality in the central bounded region. Proof of concept is demonstrated by controlling the motion of micron-size latex beads, visualized with an EM-CCD camera. By use of a double Mach-Zehnder interferometer configuration, 40 fs Ti:Sapphire laser pulses (repetition rate 76 MHz) are split into four temporally interleaved pulses (effective rate 304 MHz), which are then focused to the vertices of a tetrahedron (approximately one micron per side) within the central electrode region to generate two-photon-excited fluorescence from single molecules. The time stamp data from this four-focus probe, collected with a custom fast-timing single-photon avalanche diode, enables characterization of particle motion through fluorescence cross-correlation spectroscopy.

King, Jason; Davis, Lloyd; Canfield, Brian; Hofmeister, William; Sampson, Philip



Flexible single molecule simulation of reaction-diffusion processes  

SciTech Connect

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

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



Alternative Spliceosome Assembly Pathways Revealed by Single Molecule Fluorescence Microscopy  

PubMed Central

SUMMARY Removal of introns from nascent transcripts (pre-mRNAs) by the spliceosome is an essential step in eukaryotic gene expression. Previous studies have suggested that the earliest steps in spliceosome assembly in yeast are highly ordered, with stable recruitment of U1 snRNP to the 5' splice site necessarilypreceding recruitment of U2 snRNP to the branch site to form the “pre-spliceosome”. Using Colocalization Single Molecule Spectroscopy (CoSMoS) to follow initial spliceosome assembly on eight different S. cerevisiae pre-mRNAs, we here demonstrate that active yeast spliceosomes can form by both U1-first and U2-first pathways. Both assembly pathways yield prespliceosomes functionally equivalent for subsequent U5•U4/U6 tri-snRNP recruitment and for intron excision. Although fractional flux through the two pathways varies on different introns, both are operational on all introns studied. Thus, multiple pathways exist toassemble functional spliceosomes. These observations provide new insight into the mechanisms of cross-intron coordination of initial spliceosome assembly.

Shcherbakova, Inna; Hoskins, Aaron A.; Friedman, Larry J.; Serebrov, Victor; Correa, Ivan R.; Xu, Ming-Qun; Gelles, Jeff; Moore, Melissa J.



Coupling single-molecule magnets to quantum circuits  

NASA Astrophysics Data System (ADS)

In this work we study theoretically the coupling of single-molecule magnets (SMMs) to a variety of quantum circuits, including microwave resonators with and without constrictions and flux qubits. The main result of this study is that it is possible to achieve strong and ultrastrong coupling regimes between SMM crystals and the superconducting circuit, with strong hints that such a coupling could also be reached for individual molecules close to constrictions. Building on the resulting coupling strengths and the typical coherence times of these molecules (? ?s), we conclude that SMMs can be used for coherent storage and manipulation of quantum information, either in the context of quantum computing or in quantum simulations. Throughout the work we also discuss in detail the family of molecules that are most suitable for such operations, based not only on the coupling strength, but also on the typical energy gaps and the simplicity with which they can be tuned and oriented. Finally, we also discuss practical advantages of SMMs, such as the possibility to fabricate the SMMs ensembles on the chip through the deposition of small droplets.

Jenkins, Mark; Hümmer, Thomas; José Martínez-Pérez, María; García-Ripoll, Juanjo; Zueco, David; Luis, Fernando



Extracting conformational memory from single-molecule kinetic data.  


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

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



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



A Single Molecule Investigation of the Photostability of Quantum Dots  

PubMed Central

Quantum dots (QDs) are very attractive probes for multi-color fluorescence imaging in biological applications because of their immense brightness and reported extended photostability. We report here however that single QDs, suitable for biological applications, that are subject to continuous blue excitation from a conventional 100 W mercury arc lamp will undergo a continuous blue-switching of the emission wavelength eventually reaching a permanent dark, photobleached state. We further show that ?-mercaptoethanol has a dual stabilizing effect on the fluorescence emission of QDs: 1) by increasing the frequency of time that a QD is in its fluorescent state, and 2) by decreasing the photobleaching rate. The observed QD color spectral switching is especially detrimental for multi-color single molecule applications, as we regularly observe spectral blue-shifts of 50 nm, or more even after only ten seconds of illumination. However, of significant importance for biological applications, we find that even small, biologically compatible, concentrations (25 µM) of ?-mercaptoethanol has a significant stabilizing effect on the emission color of QDs, but that greater amounts are required to completely abolish the spectral blue shifting or to minimize the emission intermittency of QDs.

Lagerholm, B. Christoffer



Spin Anisotropy Effects in Dimer Single Molecule Magnets  

NASA Astrophysics Data System (ADS)

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

Efremov, Dmitri; Klemm, Richard



Single Molecule Electrical Sequencing of DNA and RNA  

NASA Astrophysics Data System (ADS)

Gating nanopore devices are composed of nanopores with embedded nanoelectrodes, and they are expected to be one of the core devices used to realize label-free, low-cost DNA sequencing, subsequently leading to 1000-genome sequencing technologies. The operating principle of these nanodevices is based on identifying single base molecules of single DNA passing through a nanopore using a tunneling current between nanoelectrodes. We successfully identified single base molecules of DNA and RNA using tunneling currents. To make gating nanopore devices fit for practical use, core technologies should be integrated on one device chip. One core technology is the identification of single DNA and RNA composed of many base molecules using tunneling currents. We have succeeded in the single-molecule electrical sequencing of DNA and RNA formed by 3 and 7 base molecules, respectively, using a hybrid method of identifying single base molecules via a tunnelling current and random sequencing. A method that controls the speed of a single DNA passing through a nanopore is one core technology that determines the speed and accuracy of sequencing. We successfully developed a method that controls the translocation speed of a single DNA by three orders of magnitude using a voltage between nanoelectrodes.

Taniguchi, Masateru



Bayesian Inference for Improved Single Molecule Fluorescence Tracking  

PubMed Central

Single molecule tracking is widely used to monitor the change in position of lipids and proteins in living cells. In many experiments in which molecules are tagged with a single or small number of fluorophores, the signal/noise ratio may be limiting, the number of molecules is not known, and fluorophore blinking and photobleaching can occur. All these factors make accurate tracking over long trajectories difficult and hence there is still a pressing need to develop better algorithms to extract the maximum information from a sequence of fluorescence images. We describe here a Bayesian-based inference approach, based on a trans-dimensional sequential Monte Carlo method that utilizes both the spatial and temporal information present in the image sequences. We show, using model data, where the real trajectory of the molecule is known, that our method allows accurate tracking of molecules over long trajectories even with low signal/noise ratio and in the presence of fluorescence blinking and photobleaching. The method is then applied to real experimental data.

Yoon, Ji Won; Bruckbauer, Andreas; Fitzgerald, William J.; Klenerman, David



Single-Molecule Fluorescence Spectroscopy using Phospholipid Bilayer Nanodiscs  

PubMed Central

Nanodiscs are a new class of model membranes that are being used to solubilize and study a range of integral membrane proteins and membrane-associated proteins. Unlike other model membranes, the Nanodisc bilayer is bounded by a scaffold protein coat that confers enhanced stability and a narrow particle size distribution. The bilayer diameter can be precisely controlled by changing the diameter of the protein coat. All these properties make Nanodiscs excellent model membranes for single molecule fluorescence applications. In this chapter, we describe our work using Nanodiscs to apply total internal reflection fluorescence microscopy (TIRFM), fluorescence correlation spectroscopy (FCS) and Förster resonance energy transfer (FRET) to study the integral membrane protein cytochrome P450 3A4 and the membrane-binding proteins islet amyloid popypeptide (IAPP) and ?-synuclein, respectively. The monodisperse size distribution of Nanodiscs enhances control over the oligomeric state of the membrane protein of interest, and also facilitates accurate solution-based measurements. Nanodiscs also comprise an excellent system to stably immobilize integral membrane proteins in a bilayer without covalent modification, enabling a range of surface-based experiments where accurate localization of the protein of interest is required.

Nath, Abhinav; Trexler, Adam J.; Koo, Peter; Miranker, Andrew D.; Atkins, William M.; Rhoades, Elizabeth



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.

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



Photothermal cantilever actuation for fast single-molecule force spectroscopy  

NASA Astrophysics Data System (ADS)

Photothermal cantilever excitation provides a fast and easy to implement means to control the deflection of standard atomic force microscopy cantilevers. Minute heat pulses yield deflections on the order of several tens of nanometers or when the deflection is kept constant, forces of several hundreds of piconewton can be applied. In our case these pulses resulted in less than 1 K temperature changes at the sample position. Here we present and characterize the implementation of photothermal actuation for single-molecule force-spectroscopy experiments. When molecules are stretched under force-clamp conditions, fast control cycles that re-establish the pulling force after the rupture of molecular domains are essential for detecting the complete unfolding pattern with high precision. By combining the fast response of photothermal cantilever excitation with a conventional piezoactuator, a fast force-clamp with high accuracy and large working distances is reached. Simple feedback mechanisms and standard cantilever geometries lead to step response times of less than 90 ?s, which is more than one order of magnitude faster than those of conventional force-clamp systems that are based only on piezo feedback. We demonstrate the fast and accurate performance of the setup by unfolding a protein construct consisting of one green fluorescent protein and eight surrounding immunoglobulin domains at constant force.

Stahl, Stefan W.; Puchner, Elias M.; Gaub, Hermann E.



Single molecule studies reveal new mechanisms for microtubule severing  

NASA Astrophysics Data System (ADS)

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

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



Single molecule imaging of protein molecules in nanopores.  


The interactions between single protein molecules and nanoporous polycarbonate membranes were investigated at the single molecule level. Entrapment of proteins was shown to be size selective and was dependent on the membrane pore diameter. A pore size that is only slightly larger than the maximum dimension of the proteins was inadequate for intrusion into the pores. For a given protein, the number of molecules found at a given depth decreased as the pore size decreased. In addition, as the depth increased, for a given size pore, the number of molecules decreased rapidly. The depth-dependent histograms nicely fit a one-dimensional diffusion model. However, a highly restricted motion was observed even when the pore diameter was 10 times the size of the protein, resulting in anomalously small diffusion coefficients. We also demonstrated the subtle differences in depth distribution among BSA and hemoglobin that have nearly the same molecular weight but slightly different molecular shapes. These results give unique insights into the detailed mechanism of size-exclusion chromatography and membrane filtration. PMID:20000771

Ma, Changbei; Yeung, Edward S



Simultaneous determination of conductance and thermopower of single molecule junctions.  


We report the first concurrent determination of conductance (G) and thermopower (S) of single-molecule junctions via direct measurement of electrical and thermoelectric currents using a scanning tunneling microscope-based break-junction technique. We explore several amine-Au and pyridine-Au linked molecules that are predicted to conduct through either the highest occupied molecular orbital (HOMO) or the lowest unoccupied molecular orbital (LUMO), respectively. We find that the Seebeck coefficient is negative for pyridine-Au linked LUMO-conducting junctions and positive for amine-Au linked HOMO-conducting junctions. Within the accessible temperature gradients (<30 K), we do not observe a strong dependence of the junction Seebeck coefficient on temperature. From histograms of thousands of junctions, we use the most probable Seebeck coefficient to determine a power factor, GS(2), for each junction studied, and find that GS(2) increases with G. Finally, we find that conductance and Seebeck coefficient values are in good quantitative agreement with our self-energy corrected density functional theory calculations. PMID:22128800

Widawsky, Jonathan R; Darancet, Pierre; Neaton, Jeffrey B; Venkataraman, Latha



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.

Argudo, David; Purohit, Prashant K.



Quantifying multiscale noise sources in single-molecule time series  

PubMed Central

When analyzing single-molecule data, a low-dimensional set of system observables typically serve as the observational data. We calibrate stochastic dynamical models from time series that record such observables (our focus throughout is on a molecule’s end-to-end distance). Numerical techniques for quantifying noise from multiple time scales in a single trajectory, including experimental instrument and inherent thermal noise, are demonstrated. The techniques are applied to study time series coming from both simulations and experiments associated with the nonequilibrium mechanical unfolding of titin’s I27 domain. The estimated models can be used for several purposes: (1) detect dynamical signatures of “rare events” by analyzing the effective diffusion and force as a function of the monitored observable; (2) quantify the influence that experimentally unobservable conformational degrees of freedom have on the dynamics of the monitored observable; (3) quantitatively compare the inherent thermal noise to other noise sources, e.g. instrument noise, variation induced by conformational heterogeneity, etc.; (4) simulate random quantities associated with repeated experiments; (5) apply pathwise (i.e. trajectory-wise) hypothesis tests to assess the goodness-of-fit of models and even detect conformational transitions in noisy signals. These items are all illustrated with several examples.

Calderon, Christopher P.; Harris, Nolan C.; Kiang, Ching-Hwa; Cox, Dennis D.



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.

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



Enhanced accuracy of single-molecule diffusion measurements with a photocleavable energy-transfer dyad.  


A photocleavable energy-transfer dyad was synthesized, characterized, and applied to single-molecule fluorescence microscopy. After photocleavage, a combination of independent two-color single-molecule tracking and analysis of single-molecule energy-transfer efficiencies allows the determination of the temporal evolution of the relative distances between both fragments from the nm to the ?m scale. This gives access to a broad range of diffusion coefficients. PMID:24222580

Dill, Maren; Baier, Moritz C; Mecking, Stefan; Wöll, Dominik



A New Theoretical Approach to Single-Molecule Fluorescence Optical Studies of RNA Dynamics  

Microsoft Academic Search

Single-molecule fluorescence spectroscopy in condensed phases has many important chemical and biological applications. The single-molecule fluorescence measurements contain information about conformational dynamics on a vast range of time scales. Based on the data analysis protocols methodology proposed by X. Sunney Xie, the theoretical study here mainly focuses on the single-molecule studies of single RNA with interconversions among different conformational states,

Xinghai Zhao; Guangcun Shan; Shuying Bao




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



Simultaneous Patch-Clamp Recording and Single-Molecule Imaging Study of Single-Molecule Ion Channel Dynamics  

NASA Astrophysics Data System (ADS)

By combining real-time single-molecule fluorescence imaging measurements with real-time single-channel current measurements in membranes of lipid bilayers or in living cells, we are now able to probe single ion-channel-protein conformational changes simultaneously correlated with single ion-channel current trajectories, providing an understanding at the molecular-level of the dynamics and mechanisms of ion-channel proteins. This technical innovation has been used to gain an understanding of how ion-channel activities are regulated by conformational change dynamics and assembly mechanisms of the dye-labeled gramicidin channels, which has revealed that the gramicidin channel activity is regulated by complex gramicidin dimer conformational changes. A new multiple-state model for gramicidin ion-channel dynamics, more complex than the classic two-state diffusion model, has been postulated based on our experimental results. The single-channel activity of recombinant NMDA receptors transiently expressed in a mammalian cell-line has been recorded when tetramethylrhodamine-labeled cysteine (TMR-cysteine) and glycine were introduced into the patch-pipette in cell-attached or inside-out patches. Correlated images of a single TMR-cysteine and single NMDA channel recordings have been investigated in real-time, which begins to shed light on the molecular-level understanding of the ligand-receptor interaction dynamics in NMDA receptors in living cells.

Harms, Greg; Orr, Galya; Thrall, Brian; Montal, Mauricio; Colson, Steve; Lu, H. Peter



Novel Labeling Schemes for Single-Molecule Nanoscopy  

PubMed Central

Single molecule localization-based superresolution microscopy methods, such as PALM or STORM, have been breakthrough techniques of the last years. Until now however, they require special fluorescent proteins to be cloned or high-affinity antibodies to be generated for specific labeling. On the other hand, many laboratories will have most of their constructs in GFP form and entire genomes are available as functional GFP-fusion proteins. Here, we report a method that makes all these constructs available for superresolution microscopy by targeting GFP with tiny, high-affinity antibodies coupled to blinking dyes. It thus combines the molecular specificity of genetic tagging with the high photon yield of organic dyes and minimal linkage error, as demonstrated on microtubules, living neurons and yeast cells. We show that in combination with GFP-libraries, virtually any known protein can immediately be used in superresolution microscopy and that high-throughput superresolution imaging using simplified labeling schemes is possible. The labeling density in superresolution microscopy based on photoactivatable fluorophores is limited by the fact that a small, but significant fraction is always in the bright state. To overcome this limitation we implemented binding-activated localization microscopy (BALM), which is based on the localization of individual binding events of fluorophores that show a fluorescence enhancement upon binding to their target structures. Using nucleic acid stains on double-stranded DNA we yielded a resolution of –14 nm (fwhm) and a spatial sampling of 1/nm in vitro and could visualize the organization of the bacterial chromosome in fixed Escherichia coli cells. In general, the principle of binding-activated localization microscopy can be extended to other dyes and targets such as protein structures.

Schoen, Ingmar; Kaplan, Charlotte; Platonova, Evgenia; Vogel, Viola; Ewers, Helge; Ries, Jonas



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.


Single Molecule Force Spectroscopy using Optical Traps and AFMs  

NASA Astrophysics Data System (ADS)

Force spectroscopy is an important single-molecule technique to study the energetics and dynamics of biological systems. Both optical traps and atomic force microscopes (AFMs) can measure the dynamics of individual molecules. My talk will focus on two intellectually distinct ways to improve these experiments: passive force clamps and an optically stabilized AFM. To increase measurement precision, feedback is used to maintain a constant force on a molecule - often called a force clamp. Precise yet rapid active feedback is limited by Brownian motion. This limited bandwidth leads to significant fluctuations in force that are particularly pronounced for the rapid, large changes in extension seen in nucleic acid structures (e.g. DNA hairpins, ribozymes, riboswitches). Here, we show that the dynamics determined in active force clamps are five-to-seven fold different than in a passive force clamp, which has a (˜30-fold faster control of force. Thus, the dynamics of biological molecules can be significantly altered by the mechanism of force feedback. In AFM-based force spectroscopy experiments, force versus extension curves are generated by retracting the tip using a PZT stage while measuring force via cantilever deflection. Extension is not stable over the long times due to drift in the AFM assembly (˜10 nm/min). We developed an ultrastable AFM by measuring and thereby stabilizing the tip in 3D using a laser scattered off the apex of a commercial AFM tip, not its back side. A second laser detected and thereby stabilized the sample. We next demonstrated simultaneous and independent measurement of extension and force. Preliminary studies of bacteriorhodopsin, a model membrane protein, highlight this instruments unique force- and position-clamp modes.

Perkins, Tom



Single Molecule Force Spectroscopy using Optical Traps and AFMs  

NASA Astrophysics Data System (ADS)

Force spectroscopy is an important single-molecule technique to study the energetics and dynamics of biological systems. Both optical traps and atomic force microscopes (AFMs) can measure the dynamics of individual molecules. My talk will focus on two intellectually distinct ways to improve these experiments: passive force clamps and an optically stabilized AFM. To increase measurement precision, feedback is used to maintain a constant force on a molecule -- often called a force clamp. Precise yet rapid active feedback is limited by Brownian motion. This limited bandwidth leads to significant fluctuations in force that are particularly pronounced for the rapid, large changes in extension seen in nucleic acid structures (e.g. DNA hairpins, ribozymes, riboswitches). Here, we show that the dynamics determined in active force clamps are five-to-seven fold different than in a passive force clamp, which has a ˜30-fold faster control of force. Thus, the dynamics of biological molecules can be significantly altered by the mechanism of force feedback. In AFM-based force spectroscopy experiments, force versus extension curves are generated by retracting the tip using a PZT stage while measuring force via cantilever deflection. Extension is inferred, not measured, and therefore convolved with drift in the AFM assembly (˜10 nm/min). We developed an ultrastable AFM by scattering a laser off the apex of a commercial AFM tip to measure and thereby stabilize the tip in 3D. A second laser stabilized the sample, leading to a 100-fold improvement in tip-sample stability compared to the previous state-of-the-art at ambient conditions (in air at room temperature). We next demonstrated simultaneous and independent measurement of extension and force in liquid. Preliminary studies of bacteriorhodopsin, a model membrane protein, highlight this instrument's unique force- and position-clamp modes.

Perkins, Thomas



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.

Chung, Hoi Sung; Eaton, William A.



Improved single molecule force spectroscopy using micromachined cantilevers.  


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

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



Novel Polymer Linkers for Single Molecule AFM Force Spectroscopy  

PubMed Central

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

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



Exciton self trapping in photosynthetic pigment-protein complexes studied by single-molecule spectroscopy.  


Evidence for the formation of self-trapped exciton states in photosynthetic antenna complexes is provided by comparing single-molecule fluorescence-excitation and emission spectra that have been recorded from the same individual LH2 complex from Rhodopseudomonas acidophila . While the excitation spectra showed the signatures for the B800 and B850 bands as observed previously, two distinctively different types of emission spectra were found. One group of antenna complexes shows spectra with a relatively narrow spectral profile with a clear signature of a zero-phonon line, whereas the other group of complexes displays spectra that consist only of a broad featureless band. Analysis of these data reveals clear correlations between the spectral position of the emission, the width of the spectral profile, and the associated electron-phonon coupling strength. PMID:22908848

Kunz, Ralf; Timpmann, Kõu; Southall, June; Cogdell, Richard J; Freiberg, Arvi; Köhler, Jürgen



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


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

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



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


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

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



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



Local magnetic properties of a monolayer of Mn12 single molecule magnets.  


The magnetic properties of a monolayer of Mn12 single molecule magnets grafted onto a silicon (Si) substrate have been investigated using depth-controlled beta-detected nuclear magnetic resonance. A low-energy beam of spin-polarized radioactive 8Li was used to probe the local static magnetic field distribution near the Mn12 monolayer in the Si substrate. The resonance line width varies strongly as a function of implantation depth as a result of the magnetic dipolar fields generated by the Mn12 electronic magnetic moments. The temperature dependence of the line width indicates that the magnetic properties of the Mn12 moments in this low-dimensional configuration differ from bulk Mn12. PMID:17488049

Salman, Z; Chow, K H; Miller, R I; Morello, A; Parolin, T J; Hossain, M D; Keeler, T A; Levy, C D P; MacFarlane, W A; Morris, G D; Saadaoui, H; Wang, D; Sessoli, R; Condorelli, G G; Kiefl, R F



Studies of protein folding and dynamics using single molecule fluorescence spectroscopy.  


Single molecule fluorescence spectroscopy is emerging as an extremely powerful and sensitive tool to study complex biological problems. Single molecule fluorescence measurements can extract useful information that is hidden in the ensemble averaged biophysical or biochemical studies by virtue of their wide range of spatial and temporal resolution capabilities. With these advantages, single molecule fluorescence spectroscopy enables us to monitor the conformational states and their dynamics in the form of statistical distribution or time trajectory of physical observables. This review illustrates how the single molecule fluorescence spectroscopy has been used to solve questions on the complexity and heterogeneity of protein folding and dynamics. PMID:24805942

Basak, Sujit; Chattopadhyay, Krishnananda



Total internal reflection fluorescence microscopy imaging-guided confocal single-molecule fluorescence spectroscopy  

PubMed Central

We have developed an integrated spectroscopy system combining total internal reflection fluorescence microscopy imaging with confocal single-molecule fluorescence spectroscopy for two-dimensional interfaces. This spectroscopy approach is capable of both multiple molecules simultaneously sampling and in situ confocal fluorescence dynamics analyses of individual molecules of interest. We have demonstrated the calibration with fluorescent microspheres, and carried out single-molecule spectroscopy measurements. This integrated single-molecule spectroscopy is powerful in studies of single molecule dynamics at interfaces of biological and chemical systems.

Zheng, Desheng; Kaldaras, Leonora; Lu, H. Peter



Understanding the Conductance of Single-Molecule Junctions from First Principles  

NASA Astrophysics Data System (ADS)

Discovering the anatomy of single-molecule junctions, in order to exploit their transport behavior, poses fundamental challenges to nanoscience. First-principles calculations based on density-functional theory (DFT) can, together with experiment, provide detailed atomic-scale insights into the transport properties, and their relation to junction structure and electronic properties. Here, a DFT scattering state approach [1] is used to explore the single-molecule conductance of two prototypical junctions as a function of junction geometry, in the context of recent experiments. First, the computed conductance of 15 distinct benzene-diamine-Au junctions is compared to a large robust experimental data set [2]. The amine-gold bonding is shown to be highly selective, but flexible, resulting in a conductance that is insensitive to other details of the junction structure. The range of computed conductance corresponds well to the narrow distribution in experiment, although the average calculated conductance is approximately 7 times larger. This discrepancy is attributed to the absence of many-electron corrections in the DFT molecular orbital energies; a simple physically-motivated estimate for the self-energy corrections results in a conductance that is much closer to experiment [3]. Second, similar first-principles techniques are applied to a range of bipyridine-Au junctions. The extent to which Au-pyridine link bonding is affected by the constraints of forming bipyridine-Au junctions is investigated. In some contrast to the amine case, the computed conductance shows a strong sensitivity to the tilt of the bipyridine rings relative to the Au surfaces. Experiments probing the conductance of bipyridine-Au junctions are discussed in the context of these findings. [1] H. J. Choi et al, Phys Rev B, 76, 155420 (2007) [2] L. Venkataraman et al, Nano Lett 6, 458 (2006) [3] S. Y. Quek et al, Nano Lett. 7, 3477 (2007)

Quek, Su Ying



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

SciTech Connect

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

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



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

NASA Astrophysics Data System (ADS)

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

Odoi, Michael Yemoh


Interfacial reactions between titanium and borate glass.  

National Technical Information Service (NTIS)

Interfacial reactions between melts of several borate glasses and titanium have been investigated by analytical scanning electron microscopy (SEM) and x-ray photoelectron spectroscopy (XPS). A thin titanium boride interfacial layer is detected by XPS afte...

R. K. Brow S. K. Saha J. I. Goldstein



The origin of transverse anisotropy in axially symmetric single molecule magnets.  


Single-crystal high-frequency electron paramagnetic resonance spectroscopy has been employed on a truly axial single molecule magnet of formula [Mn(12)O(12)(tBu-CH(2)CO(2))16(CH(3)OH)4].CH(3)OH to investigate the origin of the transverse magnetic anisotropy, a crucial parameter that rules the quantum tunneling of the magnetization. The crystal structure, including the absolute structure of the crystal used for EPR experiments, has been fully determined and found to belong to I4 tetragonal space group. The angular dependence of the resonance fields in the crystallographic ab plane shows the presence of high-order tetragonal anisotropy and strong dependence on the MS sublevels with the second-highest-field transition being angular independent. This was rationalized including competing fourth- and sixth-order transverse parameters in a giant spin Hamiltonian which describes the magnetic anisotropy in the ground S = 10 spin state of the cluster. To establish the origin of these anisotropy terms, the experimental results have been further analyzed using a simplified multispin Hamiltonian which takes into account the exchange interactions and the single ion magnetic anisotropy of the Mn(III) centers. It has been possible to establish magnetostructural correlations with spin Hamiltonian parameters up to the sixth order. Transverse anisotropy in axial single molecule magnets was found to originate from the multispin nature of the system and from the breakdown of the strong exchange approximation. The tilting of the single-ion easy axes of magnetization with respect to the 4-fold molecular axis of the cluster plays the major role in determining the transverse anisotropy. Counterintuitively, the projections of the single ion easy axes on the ab plane correspond to hard axes of magnetization. PMID:17685613

Barra, Anne-Laure; Caneschi, Andrea; Cornia, Andrea; Gatteschi, Dante; Gorini, Lapo; Heiniger, Leo-Philipp; Sessoli, Roberta; Sorace, Lorenzo



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

NASA Astrophysics Data System (ADS)

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

Takahashi, Susumu



Single molecule surface enhanced resonance Raman scattering (SERRS) of the enhanced green fluorescent protein (EGFP)  

Microsoft Academic Search

One of the most intriguing findings in single molecule spectroscopy (SMS) is the observation of Raman spectra of individual molecules, despite the small cross section of the transitions involved. The observation of the spectra can be explained by the surface enhanced Raman scattering (SERRS) effect. At the single-molecule level, the SERRS-spectra recorded as a function of time reveal inhomogeneous behaviour

Johan Hofkens; Frans C. De Schryver; Mircea Cotlet; Satoshi Habuchi



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); Kenneth D. Osborn (University of Kansas Department of Chemistry); Michael W. Allen (University of Kansas Department of Chemistry); Brian D. Slaughter (University of Kansas Department of Chemistry)



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


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) [Los Alamos, NM; Redondo, Antonio (Los Alamos, NM) [Los Alamos, NM; Olazabal, Virginia (Los Alamos, NM) [Los Alamos, NM; Hoffbauer, Mark A. (Los Alamos, NM) [Los Alamos, NM; Akhadov, Elshan A. (Los Alamos, NM) [Los Alamos, NM



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

Microsoft Academic Search

Single-molecule methods have the potential to provide information about conformational dynamics and molecular interactions that cannot be obtained by other methods. Removal of ensemble averaging provides several benefits, including the ability to detect heterogeneous populations and the ability to observe asynchronous reactions. Single-molecule diffusion methodologies using fluorescence resonance energy transfer (FRET) are developed to monitor conformational dynamics while minimizing perturbations

Ted Alfred



Zero-mode waveguides: Sub-wavelength nanostructures for single molecule studies at high concentrations  

Microsoft Academic Search

The study of single fluorescent molecules allows individual measurements which can reveal characteristics typically obscured by ensemble averages. Yet, single molecule spectroscopy through traditional optical techniques is hindered by the diffraction limit of light. This restricts the accessible concentrations for single molecule experiments to the nano- to picomolar range. Zero-mode waveguides (ZMWs), optical nanostructures fabricated in a thin aluminum film,

Jose M. Moran-Mirabal; Harold G. Craighead



Experimental and Computational Characterization of Biological Liquid Crystals: A Review of Single-Molecule Bioassays  

PubMed Central

Quantitative understanding of the mechanical behavior of biological liquid crystals such as proteins is essential for gaining insight into their biological functions, since some proteins perform notable mechanical functions. Recently, single-molecule experiments have allowed not only the quantitative characterization of the mechanical behavior of proteins such as protein unfolding mechanics, but also the exploration of the free energy landscape for protein folding. In this work, we have reviewed the current state-of-art in single-molecule bioassays that enable quantitative studies on protein unfolding mechanics and/or various molecular interactions. Specifically, single-molecule pulling experiments based on atomic force microscopy (AFM) have been overviewed. In addition, the computational simulations on single-molecule pulling experiments have been reviewed. We have also reviewed the AFM cantilever-based bioassay that provides insight into various molecular interactions. Our review highlights the AFM-based single-molecule bioassay for quantitative characterization of biological liquid crystals such as proteins.

Eom, Kilho; Yang, Jaemoon; Park, Jinsung; Yoon, Gwonchan; Soo Sohn, Young; Park, Shinsuk; Yoon, Dae Sung; Na, Sungsoo; Kwon, Taeyun



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


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

Glaser, Thorsten



Electronic Interfacial Effects in Epitaxial Heterostructures based on LaMnO3.  

NASA Astrophysics Data System (ADS)

Studies of chemically abrupt interfaces provide an ideal platform to study the effects of discontinuities and asymmetries of the electronic configuration on the transport and magnetic properties of complex oxides. In addition, the behavior of complex materials near interfaces plays the most crucial role not only in devices and nanostructures but also in complex structures in the form of composites and superlattices, including artificial multiferroics. Interfaces in the ABO3 perovskite system are particularly attractive because structurally similar oxides with fundamentally different physical properties can be integrated epitaxially. To explore the electronic effects at interfaces and to probe the physical properties that result from local electronic changes, we have synthesized structures containing LaMnO3 and insulating perovskites using pulsed laser deposition. The local electron energy loss spectroscopy (EELS) capability of a scanning transmission electron microscope (STEM) is used to probe the electronic configuration in the LaMnO3 films as a function of the distance from the interfaces. The results are compared to macroscopic measurements and theoretical predictions. Research sponsored by the U.S. Department of Energy under contract DE-AC05-00OR22725 with the Oak Ridge National Laboratory, managed by UT-Battelle, LLC.

Christen, Hans M.; Varela, M.; Lee, H. N.; Kim, D. H.; Chisholm, M. F.; Cantoni, C.; Petit, L.; Schulthess, T. C.; Lowndes, D. H.



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


The human proteome has millions of protein variants due to alternative RNA splicing and post-translational modifications, and variants that are related to diseases are frequently present in minute concentrations. For DNA and RNA, low concentrations can be amplified using the polymerase chain reaction, but there is no such reaction for proteins. Therefore, the development of single-molecule protein sequencing is a critical step in the search for protein biomarkers. Here, we show that single amino acids can be identified by trapping the molecules between two electrodes that are coated with a layer of recognition molecules, then measuring the electron tunnelling current across the junction. A given molecule can bind in more than one way in the junction, and we therefore use a machine-learning algorithm to distinguish between the sets of electronic 'fingerprints' associated with each binding motif. With this recognition tunnelling technique, we are able to identify D and L enantiomers, a methylated amino acid, isobaric isomers and short peptides. The results suggest that direct electronic sequencing of single proteins could be possible by sequentially measuring the products of processive exopeptidase digestion, or by using a molecular motor to pull proteins through a tunnel junction integrated with a nanopore. PMID:24705512

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