WorldWideScience

Sample records for absolute single-molecule entropies

  1. Counting numbers of synaptic proteins: absolute quantification and single molecule imaging techniques.

    Patrizio, Angela; Specht, Christian G

    2016-10-01

    The ability to count molecules is essential to elucidating cellular mechanisms, as these often depend on the absolute numbers and concentrations of molecules within specific compartments. Such is the case at chemical synapses, where the transmission of information from presynaptic to postsynaptic terminals requires complex interactions between small sets of molecules. Be it the subunit stoichiometry specifying neurotransmitter receptor properties, the copy numbers of scaffold proteins setting the limit of receptor accumulation at synapses, or protein packing densities shaping the molecular organization and plasticity of the postsynaptic density, all of these depend on exact quantities of components. A variety of proteomic, electrophysiological, and quantitative imaging techniques have yielded insights into the molecular composition of synaptic complexes. In this review, we compare the different quantitative approaches and consider the potential of single molecule imaging techniques for the quantification of synaptic components. We also discuss specific neurobiological data to contextualize the obtained numbers and to explain how they aid our understanding of synaptic structure and function. PMID:27335891

  2. On determining absolute entropy without quantum theory or the third law of thermodynamics

    Steane, Andrew M.

    2016-04-01

    We employ classical thermodynamics to gain information about absolute entropy, without recourse to statistical methods, quantum mechanics or the third law of thermodynamics. The Gibbs–Duhem equation yields various simple methods to determine the absolute entropy of a fluid. We also study the entropy of an ideal gas and the ionization of a plasma in thermal equilibrium. A single measurement of the degree of ionization can be used to determine an unknown constant in the entropy equation, and thus determine the absolute entropy of a gas. It follows from all these examples that the value of entropy at absolute zero temperature does not need to be assigned by postulate, but can be deduced empirically.

  3. Extracting Models in Single Molecule Experiments

    Presse, Steve

    2013-03-01

    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.

  4. Single molecules and nanotechnology

    Vogel, Horst

    2007-01-01

    This book focuses on recent advances in the rapidly evolving field of single molecule research. These advances are of importance for the investigation of biopolymers and cellular biochemical reactions, and are essential to the development of quantitative biology. Written by leading experts in the field, the articles cover a broad range of topics, including: quantum photonics of organic dyes and inorganic nanoparticles their use in detecting properties of single molecules the monitoring of single molecule (enzymatic) reactions single protein (un)folding in nanometer-sized confined volumes the dynamics of molecular interactions in biological cells The book is written for advanced students and scientists who wish to survey the concepts, techniques and results of single molecule research and assess them for their own scientific activities.

  5. Towards single molecule switches.

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

    2015-05-21

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

  6. Watching single molecules dance

    Mehta, Amit Dinesh

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

  7. Cold spots in quantum systems far from equilibrium: Local entropies and temperatures near absolute zero

    Shastry, Abhay; Stafford, Charles A.

    2015-12-01

    We consider a question motivated by the third law of thermodynamics: Can there be a local temperature arbitrarily close to absolute zero in a nonequilibrium quantum system? We consider nanoscale quantum conductors with the source reservoir held at finite temperature and the drain held at or near absolute zero, a problem outside the scope of linear response theory. We obtain local temperatures close to absolute zero when electrons originating from the finite temperature reservoir undergo destructive quantum interference. The local temperature is computed by numerically solving a nonlinear system of equations describing equilibration of a scanning thermoelectric probe with the system, and we obtain excellent agreement with analytic results derived using the Sommerfeld expansion. A local entropy for a nonequilibrium quantum system is introduced and used as a metric quantifying the departure from local equilibrium. It is shown that the local entropy of the system tends to zero when the probe temperature tends to zero, consistent with the third law of thermodynamics.

  8. Lanthanide single molecule magnets

    Tang, Jinkui

    2015-01-01

    This book begins by providing basic information on single-molecule magnets (SMMs), covering the magnetism of lanthanide, the characterization and relaxation dynamics of SMMs, and advanced means of studying lanthanide SMMs. It then systematically introduces lanthanide SMMs ranging from mononuclear and dinuclear to polynuclear complexes, classifying them and highlighting those SMMs with high barrier and blocking temperatures – an approach that provides some very valuable indicators for the structural features needed to optimize the contribution of an Ising type spin to a molecular magnet. The final chapter presents some of the newest developments in the lanthanide SMM field, such as the design of multifunctional and stimuli-responsive magnetic materials as well as the anchoring and organization of the SMMs on surfaces. In addition, the crystal structure and magnetic data are clearly presented with a wealth of illustrations in each chapter, helping newcomers and experts alike to better grasp ongoing trends and...

  9. Lanthanide single molecule magnets

    Tang, Jinkui; Zhang, Peng [Chinese Academy of Sciences, Changchun (China). Changchun Inst. of Applied Chemistry

    2015-10-01

    This book begins by providing basic information on single-molecule magnets (SMMs), covering the magnetism of lanthanide, the characterization and relaxation dynamics of SMMs and advanced means of studying lanthanide SMMs. It then systematically introduces lanthanide SMMs ranging from mononuclear and dinuclear to polynuclear complexes, classifying them and highlighting those SMMs with high barrier and blocking temperatures - an approach that provides some very valuable indicators for the structural features needed to optimize the contribution of an Ising type spin to a molecular magnet. The final chapter presents some of the newest developments in the lanthanide SMM field, such as the design of multifunctional and stimuli-responsive magnetic materials as well as the anchoring and organization of the SMMs on surfaces. In addition, the crystal structure and magnetic data are clearly presented with a wealth of illustrations in each chapter, helping newcomers and experts alike to better grasp ongoing trends and explore new directions.

  10. Single Molecule Mechanochemistry

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

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

  11. Topological Research on Standard Absolute Entropies,S(○)298, for Binary Inorganic Compounds

    2008-01-01

    For predicting the standard entropy of a binary inorganic compound, two novel connectivity indexes mQ,mG and their converse indexes mQ',mG' based on adjacency matrix of molecular graphs and ionic parameters gi, qi were pro-posed. The qi and gi are defined as qi=(1.1+Zi1.1)/(1.7+ni), gi:(1.4d-Zi)/(0.9+ri+ri-1), where Zi, ni, ri are the charge numbers, the outer electronic shell primary quantum numbers, and the radii of ionic I respectively. The good Quantitative Structure-Property Relationship (QSPR) models for the standard entropies of binary inorganic com-pound can be constructed from 0Q,0Q',1G, and 1G', by using a multivariate linear regression (MLR) method and an artificial neural network (NN) method. The correlation coefficient r, the standard error s, and the average absolute deviation of the MLR model and the NN model are 0.9905, 8.29 J·K-1,mol-1 and 6.48 J·K-1·mol-1, and 0.9960,5.37 J·K-1·mol-1 and 3.90 J·K-1·mol-1, respectively, for 371 binary inorganic compounds (training set). The cross-validation by using the leave-one-out method demonstrates that the MLR model is highly reliable from the point of view of statistics. The correlation coefficients, standard deviations and average absolute deviations of pre-dicted values of the standard entropies of other 185 binary inorganic compounds (test set) are 0.9897, 8.64 J·K-1·mol-1 and 6.84 J·K-1·mol-1, and 0.9957, 5.63 J·K-1·mol-1 and 4.18 J·K-1·mol-1 for the MLR model and the Nnmodel, respectively. The results show that the current method is more effective than literature methods for estimat-ing the standard entropy of a binary inorganic compound. Both MLR and NN methods can provide acceptable mod-els for the prediction of the standard entropies of binary inorganic compounds. The NN model for the standard en-tropies appears to be more reliable than the MLR model.

  12. Elucidating the Energetics of Entropically Driven Protein–Ligand Association: Calculations of Absolute Binding Free Energy and Entropy

    Deng, Nan-jie; Zhang, Peng; Cieplak, Piotr; Lai, Luhua

    2014-01-01

    The binding of proteins and ligands is generally associated with the loss of translational, rotational, and conformational entropy. In many cases, however, the net entropy change due to binding is positive. To develop a deeper understanding of the energetics of entropically driven protein–ligand binding, we calculated the absolute binding free energies and binding entropies for two HIV-1 protease inhibitors Nelfinavir and Amprenavir using the double-decoupling method with molecular dynamics simulations in explicit solvent. For both ligands, the calculated absolute binding free energies are in general agreement with experiments. The statistical error in the computed ΔG(bind) due to convergence problem is estimated to be ≥2 kcal/mol. The decomposition of free energies indicates that, although the binding of Nelfinavir is driven by nonpolar interaction, Amprenavir binding benefits from both nonpolar and electrostatic interactions. The calculated absolute binding entropies show that (1) Nelfinavir binding is driven by large entropy change and (2) the entropy of Amprenavir binding is much less favorable compared with that of Nelfinavir. Both results are consistent with experiments. To obtain qualitative insights into the entropic effects, we decomposed the absolute binding entropy into different contributions based on the temperature dependence of free energies along different legs of the thermodynamic pathway. The results suggest that the favorable entropic contribution to binding is dominated by the ligand desolvation entropy. The entropy gain due to solvent release from binding site appears to be more than offset by the reduction of rotational and vibrational entropies upon binding. PMID:21899337

  13. Elucidating the energetics of entropically driven protein-ligand association: calculations of absolute binding free energy and entropy.

    Deng, Nan-jie; Zhang, Peng; Cieplak, Piotr; Lai, Luhua

    2011-10-20

    The binding of proteins and ligands is generally associated with the loss of translational, rotational, and conformational entropy. In many cases, however, the net entropy change due to binding is positive. To develop a deeper understanding of the energetics of entropically driven protein-ligand binding, we calculated the absolute binding free energies and binding entropies for two HIV-1 protease inhibitors Nelfinavir and Amprenavir using the double-decoupling method with molecular dynamics simulations in explicit solvent. For both ligands, the calculated absolute binding free energies are in general agreement with experiments. The statistical error in the computed ΔG(bind) due to convergence problem is estimated to be ≥2 kcal/mol. The decomposition of free energies indicates that, although the binding of Nelfinavir is driven by nonpolar interaction, Amprenavir binding benefits from both nonpolar and electrostatic interactions. The calculated absolute binding entropies show that (1) Nelfinavir binding is driven by large entropy change and (2) the entropy of Amprenavir binding is much less favorable compared with that of Nelfinavir. Both results are consistent with experiments. To obtain qualitative insights into the entropic effects, we decomposed the absolute binding entropy into different contributions based on the temperature dependence of free energies along different legs of the thermodynamic pathway. The results suggest that the favorable entropic contribution to binding is dominated by the ligand desolvation entropy. The entropy gain due to solvent release from binding site appears to be more than offset by the reduction of rotational and vibrational entropies upon binding. PMID:21899337

  14. Single-Molecule DNA Analysis

    Efcavitch, J. William; Thompson, John F.

    2010-07-01

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

  15. Single-molecule magnet engineering

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

    2014-01-01

    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...

  16. QSPR study of standard absolute entropies for gaseous organic compounds using novel molecular connectivity indexes and Ring parameter

    Highlights: ► Variable atomic valence connectivity index δ′i, Ring parameter H, and variable molecular connectivity index mχ′k were proposed. ► A good four-parameter model can be constructed from H and mχ′k by using the best subsets regression analysis method. ► The MLR method can provide an accurate model for the prediction of the standard absolute entropies of gaseous organic compounds. - Abstract: For predicting the standard absolute entropies of gaseous organic compounds, variable molecular connectivity index mχ′k and Ring parameter H, based on adjacency matrix of molecular graphs, variable atomic valence connectivity index δ′i, and the numbers of chains (cycles) atomic of molecule niR, were proposed. The optimal values of parameters c, a, mi, and y included in the definition of δ′i, and mχ′k can be found by optimization method. When c = 0.91, a = 1.3, and y = 0.22, a good four-parameter model can be constructed from H and mχ′k by using the best subsets regression analysis method for the standard absolute entropies of gaseous organic compounds. The results show that the MLR method can provide an accurate model for the prediction of the standard absolute entropies of gaseous organic compounds.

  17. Efficient single molecule detection and single molecule photochemistry

    Affleck, R.L.; Ambrose, W.P.; Goodwin, P.M. [Los Alamos National Lab., NM (United States)] [and others

    1996-12-31

    Single molecule detection efficiencies greater than 90% in flowing sample streams can be attained by confining the sample to the center of the excitation laser beam and photobleaching the reagent stream immediately before it enters the detection flow cell. Photolysis of single molecules of B-Phycoerythrin dissolved in aqueous solution is observed as an abrupt cessation of the fluorescence from these molecules as they flow through {approximately}40 pl probe volume. An analysis of the survival times of individual molecules in the laser beams yields the photodestruction quantum yield of the molecule. Photon pair correlation measurements of the fluorescence detected from single B-PE molecules demonstrate that the molecule fluoresces from only one bilin chromophore at a time.

  18. A simplified confinement method for calculating absolute free energies and free energy and entropy differences.

    Ovchinnikov, Victor; Cecchini, Marco; Karplus, Martin

    2013-01-24

    A simple and robust formulation of the path-independent confinement method for the calculation of free energies is presented. The simplified confinement method (SCM) does not require matrix diagonalization or switching off the molecular force field, and has a simple convergence criterion. The method can be readily implemented in molecular dynamics programs with minimal or no code modifications. Because the confinement method is a special case of thermodynamic integration, it is trivially parallel over the integration variable. The accuracy of the method is demonstrated using a model diatomic molecule, for which exact results can be computed analytically. The method is then applied to the alanine dipeptide in vacuum, and to the α-helix ↔ β-sheet transition in a 16-residue peptide modeled in implicit solvent. The SCM requires less effort for the calculation of free energy differences than previous formulations because it does not require computing normal modes. The SCM has a diminished advantage for determining absolute free energy values, because it requires decreasing the MD integration step to obtain accurate results. An approximate confinement procedure is introduced, which can be used to estimate directly the configurational entropy difference between two macrostates, without the need for additional computation of the difference in the free energy or enthalpy. The approximation has convergence properties similar to those of the standard confinement method for the calculation of free energies. The use of the approximation requires about 5 times less wall-clock simulation time than that needed to compute enthalpy differences to similar precision from an MD trajectory. For the biomolecular systems considered in this study, the errors in the entropy approximation are under 10%. Practical applications of the methods to proteins are currently limited to implicit solvent simulations. PMID:23268557

  19. Single-molecule studies using magnetic traps.

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

    2012-01-01

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

  20. Electrochemical detection of single molecules.

    Fan, F R; Bard, A J

    1995-02-10

    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 approximately 15 nanometers and a conductive substrate. A scanning electrochemical microscope was used to adjust the tip-substrate distance ( approximately 10 nanometers), and the oxidation of [(trimethylammonio)methyl] ferrocene (Cp(2)FeTMA(+)) to Cp(2)FeTMA(2+) was carried out. The response was stochastic, and anodic current peaks were observed as the molecule moved into and out of the electrode-substrate gap. Similar experiments were performed with a solution containing two redox species, ferrocene carboxylate (Cp(2)FeCOO(-)) and Os(bpy)(3)(2+) (bpy is 2,2'-bipyridyl). PMID:17813918

  1. Single Molecule Studies of Chromatin

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

    2006-02-06

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

  2. Single-molecule stochastic resonance

    Hayashi, K; Manosas, M; Huguet, J M; Ritort, F; 10.1103/PhysRevX.2.031012

    2012-01-01

    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 noise. Here we carry out the first experimental study of SR in single DNA hairpins which exhibit cooperatively folding/unfolding transitions under the action of an applied oscillating mechanical force with optical tweezers. By varying the frequency of the force oscillation, we investigated the folding/unfolding kinetics of DNA hairpins in a periodically driven bistable free-energy potential. We measured 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 the signal-to-noise ratio (SNR) of the spectral density of measured fluctuations in molecular extension of the DNA hairpins is a good quantifier of the SR. The frequency dependence of the SNR exhibits a peak at a frequency value given by the resonance match...

  3. Making "Operations" inside a Single Molecule

    2005-01-01

    @@ Free and delicate manipulation of single molecules has long been expected by scientists so as to realize specific functions. In the 1990s, the laboratory led by Prof. Wison Ho from the University of California was successful in inducing chemical reactions at the single molecule level with scanning tunneling microscopy (STM), revealing the extensive potentials of "single molecule operation." However, until recently, researchers have failed to utilize the reaction to give rise to special physical properties.

  4. Single-molecule pulling: phenomenology and interpretation

    Franco, Ignacio; Schatz, George C

    2012-01-01

    Single-molecule pulling techniques have emerged as versatile tools for probing the noncovalent forces holding together the secondary and tertiary structure of macromolecules. They also constitute a way to study at the single-molecule level processes that are familiar from our macroscopic thermodynamic experience. In this Chapter, we summarize the essential phenomenology that is typically observed during single-molecule pulling, provide a general statistical mechanical framework for the interpretation of the equilibrium force spectroscopy and illustrate how to simulate single-molecule pulling experiments using molecular dynamics.

  5. Chemical principles of single-molecule electronics

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

    2016-03-01

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

  6. Adaptive anisotropic kernels for nonparametric estimation of absolute configurational entropies in high-dimensional configuration spaces.

    Hensen, Ulf; Grubmüller, Helmut; Lange, Oliver F

    2009-07-01

    The quasiharmonic approximation is the most widely used estimate for the configurational entropy of macromolecules from configurational ensembles generated from atomistic simulations. This method, however, rests on two assumptions that severely limit its applicability, (i) that a principal component analysis yields sufficiently uncorrelated modes and (ii) that configurational densities can be well approximated by Gaussian functions. In this paper we introduce a nonparametric density estimation method which rests on adaptive anisotropic kernels. It is shown that this method provides accurate configurational entropies for up to 45 dimensions thus improving on the quasiharmonic approximation. When embedded in the minimally coupled subspace framework, large macromolecules of biological interest become accessible, as demonstrated for the 67-residue coldshock protein. PMID:19658735

  7. Handbook of single-molecule electronics

    Moth-Poulsen, Kasper

    2015-01-01

    Single-molecule electronics has evolved as a vibrant research field during the last two decades. The vision is to be able to create electronic components at the highest level of miniaturization-the single molecule. This book compiles and details cutting-edge research with contributions from chemists, physicists, theoreticians, and engineers. It covers all aspects of single-molecule electronics, from the theory through experimental realizations and the chemical synthesis of molecular components to the implementation of molecular components in future integrated circuits. This book describes in d

  8. Molecular junctions: Single-molecule contacts exposed

    Nichols, Richard J.; Higgins, Simon J.

    2015-05-01

    Using a scanning tunnelling microscopy-based method it is now possible to get an atomistic-level description of the most probable binding and contact configuration for single-molecule electrical junctions.

  9. Broadband single-molecule excitation spectroscopy

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

    2016-01-01

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

  10. Single Molecule Applications of Quantum Dots

    Rasmussen, Thomas Elmelund; Jauffred, Liselotte; Brewer, Jonathan R.;

    2013-01-01

    tracking single lipids in lipid bilayers, 4) two-photon fluorescence correlation spectroscopy of QDs and 5) optical trapping and excitation of single QDs. In all of these applications, the focus is on the single particle sensitivity level of QDs. The high applicability of QDs in live cell imaging...... experiments held together with the prospects in localization microscopy and single molecule manipulation experiments gave QDs a promising future in single molecule research....

  11. Single-molecule recognition imaging microscopy

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

    2004-01-01

    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 gener...

  12. Single-molecule dynamics at variable temperatures

    Zondervan, Rob

    2006-01-01

    Single-molecule optics has evolved from a specialized variety of optical spectroscopy at low temperatures into a versatile tool to address questions in physics, chemistry, biology, and materials science. In this thesis, the potential of single-molecule (and ensemble) optical microscopy at variable temperatures is demonstrated: Electron transfer has been identified as a crucial step in the photodynamics of organic fluorophores, and long-term memory effects have been discovered in the relaxatio...

  13. Sample preparation for single molecule localization microscopy.

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

    2013-11-21

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

  14. Single-Molecule Studies in Live Cells

    Yu, Ji

    2016-05-01

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

  15. Single Molecule Biophysics Experiments and Theory

    Komatsuzaki, Tamiki; Takahashi, Satoshi; Yang, Haw; Silbey, Robert J; Rice, Stuart A; Dinner, Aaron R

    2011-01-01

    Discover the experimental and theoretical developments in optical single-molecule spectroscopy that are changing the ways we think about molecules and atoms The Advances in Chemical Physics series provides the chemical physics field with a forum for critical, authoritative evaluations of advances in every area of the discipline. This latest volume explores the advent of optical single-molecule spectroscopy, and how atomic force microscopy has empowered novel experiments on individual biomolecules, opening up new frontiers in molecular and cell biology and leading to new theoretical approaches

  16. Methods for calculating the absolute entropy and free energy of biological systems based on ideas from polymer physics.

    Meirovitch, Hagai

    2010-01-01

    The commonly used simulation techniques, Metropolis Monte Carlo (MC) and molecular dynamics (MD) are of a dynamical type which enables one to sample system configurations i correctly with the Boltzmann probability, P(i)(B), while the value of P(i)(B) is not provided directly; therefore, it is difficult to obtain the absolute entropy, S approximately -ln P(i)(B), and the Helmholtz free energy, F. With a different simulation approach developed in polymer physics, a chain is grown step-by-step with transition probabilities (TPs), and thus their product is the value of the construction probability; therefore, the entropy is known. Because all exact simulation methods are equivalent, i.e. they lead to the same averages and fluctuations of physical properties, one can treat an MC or MD sample as if its members have rather been generated step-by-step. Thus, each configuration i of the sample can be reconstructed (from nothing) by calculating the TPs with which it could have been constructed. This idea applies also to bulk systems such as fluids or magnets. This approach has led earlier to the "local states" (LS) and the "hypothetical scanning" (HS) methods, which are approximate in nature. A recent development is the hypothetical scanning Monte Carlo (HSMC) (or molecular dynamics, HSMD) method which is based on stochastic TPs where all interactions are taken into account. In this respect, HSMC(D) can be viewed as exact and the only approximation involved is due to insufficient MC(MD) sampling for calculating the TPs. The validity of HSMC has been established by applying it first to liquid argon, TIP3P water, self-avoiding walks (SAW), and polyglycine models, where the results for F were found to agree with those obtained by other methods. Subsequently, HSMD was applied to mobile loops of the enzymes porcine pancreatic alpha-amylase and acetylcholinesterase in explicit water, where the difference in F between the bound and free states of the loop was calculated. Currently

  17. Single Molecule Analysis Research Tool (SMART: an integrated approach for analyzing single molecule data.

    Max Greenfeld

    Full Text Available Single molecule studies have expanded rapidly over the past decade and have the ability to provide an unprecedented level of understanding of biological systems. A common challenge upon introduction of novel, data-rich approaches is the management, processing, and analysis of the complex data sets that are generated. We provide a standardized approach for analyzing these data in the freely available software package SMART: Single Molecule Analysis Research Tool. SMART provides a format for organizing and easily accessing single molecule data, a general hidden Markov modeling algorithm for fitting an array of possible models specified by the user, a standardized data structure and graphical user interfaces to streamline the analysis and visualization of data. This approach guides experimental design, facilitating acquisition of the maximal information from single molecule experiments. SMART also provides a standardized format to allow dissemination of single molecule data and transparency in the analysis of reported data.

  18. Single molecule fluorescence detection on functionalized surfaces

    Full text: The immobilization of organic molecules on surfaces is important for various applications in nanolithography and also essential in novel detectors for matter wave interferometry. We use fluorescence imaging up to the single molecule level to study the suppression of long-range surface diffusion of ZnTPP on pyridine functionalized surfaces. (author)

  19. Handbook of Single-Molecule Biophysics

    Hinterdorfer, Peter

    2009-01-01

    The last decade has seen the development of a number of novel biophysical methods that allow the manipulation and study of individual biomolecules. The ability to monitor biological processes at this fundamental level of sensitivity has given rise to an improved understanding of the underlying molecular mechanisms. Through the removal of ensemble averaging, distributions and fluctuations of molecular properties can be characterized, transient intermediates identified, and catalytic mechanisms elucidated. By applying forces on biomolecules while monitoring their activity, important information can be obtained on how proteins couple function to structure. The Handbook of Single-Molecule Biophysics provides an introduction to these techniques and presents an extensive discussion of the new biological insights obtained from them. Coverage includes: Experimental techniques to monitor and manipulate individual biomolecules The use of single-molecule techniques in super-resolution and functional imaging Single-molec...

  20. The symmetry of single-molecule conduction.

    Solomon, Gemma C; Gagliardi, Alessio; Pecchia, Alessandro; Frauenheim, Thomas; Di Carlo, Aldo; Reimers, Jeffrey R; Hush, Noel S

    2006-11-14

    We introduce the conductance point group which defines the symmetry of single-molecule conduction within the nonequilibrium Green's function formalism. It is shown, either rigorously or to within a very good approximation, to correspond to a molecular-conductance point group defined purely in terms of the properties of the conducting molecule. This enables single-molecule conductivity to be described in terms of key qualitative chemical descriptors that are independent of the nature of the molecule-conductor interfaces. We apply this to demonstrate how symmetry controls the conduction through 1,4-benzenedithiol chemisorbed to gold electrodes as an example system, listing also the molecular-conductance point groups for a range of molecules commonly used in molecular electronics research. PMID:17115774

  1. Artifacts in single-molecule localization microscopy.

    Burgert, Anne; Letschert, Sebastian; Doose, Sören; Sauer, Markus

    2015-08-01

    Single-molecule localization microscopy provides subdiffraction resolution images with virtually molecular resolution. Through the availability of commercial instruments and open-source reconstruction software, achieving super resolution is now public domain. However, despite its conceptual simplicity, localization microscopy remains prone to user errors. Using direct stochastic optical reconstruction microscopy, we investigate the impact of irradiation intensity, label density and photoswitching behavior on the distribution of membrane proteins in reconstructed super-resolution images. We demonstrate that high emitter densities in combination with inappropriate photoswitching rates give rise to the appearance of artificial membrane clusters. Especially, two-dimensional imaging of intrinsically three-dimensional membrane structures like microvilli, filopodia, overlapping membranes and vesicles with high local emitter densities is prone to generate artifacts. To judge the quality and reliability of super-resolution images, the single-molecule movies recorded to reconstruct the images have to be carefully investigated especially when investigating membrane organization and cluster analysis. PMID:26138928

  2. Single Molecule Data Analysis: An Introduction

    Tavakoli, Meysam; Li, Chun-Biu; Komatsuzaki, Tamiki; Pressé, Steve

    2016-01-01

    We review methods of data analysis for biophysical data with a special emphasis on single molecule applications. Our review is intended for anyone, from student to established researcher. For someone just getting started, we focus on exposing the logic, strength and limitations of each method and cite, as appropriate, the relevant literature for implementation details. We review traditional frequentist and Bayesian parametric approaches to data analysis and subsequently extend our discussion to recent non-parametric and information theoretic methods.

  3. Single-Molecule Imaging of Cellular Signaling

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

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

  4. Biomedical applications of single molecule detection

    Kelso, D. M.

    1997-05-01

    The search for increased sensitivity of bio-analytical techniques has recently shifted from signal generation to detection. While enzyme amplifiers and chemiluminescent reporters developed by chemists over the last two decades gradually moved detection limits to the attomol level, it has taken engineers only a few years to reach single- molecule sensitivity with the development of new instrumentation. A number of different approaches have successfully achieved single-molecule fluorescence detection including confocal and near-field scanning optical microscopy, photon-counting cameras, fluorescence- correlation and time-gated spectroscopy. They detect labels immobilized on substrates, diffusing in solution and flowing in electro-osmotic and hydrodynamically focused streams. Biotechnology has created numerous application s for single- molecule detection. In research labs, it can dramatically increase the rate of DNA sequencing, screen libraries for products of directed evolution, and characterize compounds in drug discovery programs. In medical diagnostics, ultra- sensitive detection technologies can be used for genetic screening, detection of infectious diseases, or multi- analyte profiles. It can be applied to immunoassays as well as DNA or RNA hybridization assays.

  5. Single molecule microscopy and spectroscopy: concluding remarks.

    van Hulst, Niek F

    2015-01-01

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

  6. Single-molecule electrophoresis. Final report

    Castro, A.; Shera, E.B.

    1996-05-22

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

  7. Electric field breakdown in single molecule junctions.

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

    2015-04-22

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

  8. Electromechanical Properties of Single Molecule Devices

    Bruot, Christopher

    Understanding the interplay between the electrical and mechanical properties of single molecules is of fundamental importance for molecular electronics. The sensitivity of charge transport to mechanical fluctuations is a key problem in developing long lasting molecular devices. Furthermore, harnessing this response to mechanical perturbation, molecular devices which can be mechanically gated can be developed. This thesis demonstrates three examples of the unique electromechanical properties of single molecules. First, the electromechanical properties of 1,4-benzenedithiol molecular junctions are investigate. Counterintuitively, the conductance of this molecule is found to increase by more than an order of magnitude when stretched. This conductance increase is found to be reversible when the molecular junction is compressed. The current-voltage, conductance-voltage and inelastic electron tunneling spectroscopy characteristics are used to attribute the conductance increase to a strain-induced shift in the frontier molecular orbital relative to the electrode Fermi level, leading to resonant enhancement in the conductance. Next, the effect of stretching-induced structural changes on charge transport in DNA molecules is studied. The conductance of single DNA molecules with lengths varying from 6 to 26 base pairs is measured and found to follow a hopping transport mechanism. The conductance of DNA molecules is highly sensitive to mechanical stretching, showing an abrupt decrease in conductance at surprisingly short stretching distances, with weak dependence on DNA length. This abrupt conductance decrease is attributed to force-induced breaking of hydrogen bonds in the base pairs at the end of the DNA sequence. Finally, the effect of small mechanical modulation of the base separation on DNA conductance is investigated. The sensitivity of conductance to mechanical modulation is studied for molecules of different sequence and length. Sequences with purine-purine stacking

  9. From single molecule to single tubules

    Guo, Chin-Lin

    2012-02-01

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

  10. Solving absolute value equation based on maximum entropy Newton- SOR algorithm%极大熵Newton-SOR迭代算法求解绝对值方程

    邓永坤

    2012-01-01

    主要研究绝对值方程Ax+B|z|=b的求解问题.首先通过利用极大熵理论将该绝对值方程转化为光滑方程组,建立求解该形式绝对值问题的Newton-SOR方法,并对算法的收敛性进行分析和证明;最后通过数值试验对算法的有效性进行测试.%This paper is concerned with the absolute value equation Ax + B | x | = b. First, using the maximum entropy function, and absolute value equations problem could be transformed into the approximation unconstrained differentiable problem, then using the Newton -SOR method to solve this problem. Theoretic analysis shows that the proposed method is effective. Numerical results indicate that the method is feasible and effective to absolute value equations problem.

  11. Collective effects in Single Molecule Magnets

    Subedi, Pradeep

    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

  12. Electrochemical Single-Molecule Transistors with Optimized Gate Coupling

    Osorio, Henrry M.; Catarelli, Samantha; Cea, Pilar;

    2015-01-01

    Electrochemical gating at the single molecule level of viologen molecular bridges in ionic liquids is examined. Contrary to previous data recorded in aqueous electrolytes, a clear and sharp peak in the single molecule conductance versus electrochemical potential data is obtained in ionic liquids....

  13. Single-molecule binding experiments on long time scales

    Elenko, Mark P.; Szostak, Jack W.; van Oijen, Antoine M.

    2010-01-01

    We describe an approach for performing single-molecule binding experiments on time scales from hours to days, allowing for the observation of slower kinetics than have been previously investigated by single-molecule techniques. Total internal reflection fluorescence microscopy is used to image the b

  14. Rotation of a single molecule within a supramolecular bearing

    Gimzewski, J.K.; Joachim, C.; Schlittler, R.R.;

    1998-01-01

    Experimental visualization and verification of a single-molecule rotor operating within a supramolecular bearing is reported. Using a scanning tunneling microscope, single molecules were observed to exist in one of two spatially defined states Laterally separated by 0.26 nanometers. One was...

  15. Single-Molecule FRET Study of DNA G-Quadruplex

    2002-01-01

    The DNA G-quadruplex formed by the human telomeric sequence is a potential target for novel anticancer drugs. We have investigated an intramolecular DNA G-quadruplex using single-molecule fluorescence resonance energy transfer and shown that individual folded quadruplexes can be identified. The mean proximity ratio measured at the single-molecule level was consistent with ensemble measurement.

  16. DNA analysis by single molecule stretching in nanofluidic biochips

    Abad, E.; Juarros, A.; Retolaza, A.;

    2011-01-01

    Imprint Lithography (NIL) technology combined with a conventional anodic bonding of the silicon base and Pyrex cover. Using this chip, we have performed single molecule imaging on a bench-top fluorescent microscope system. Lambda phage DNA was used as a model sample to characterize the chip. Single molecules of λ...

  17. Stability of the Free and Bound Microstates of a Mobile Loop of α-Amylase Obtained from the Absolute Entropy and Free Energy.

    Cheluvaraja, Srinath; Meirovitch, Hagai

    2008-01-01

    The hypothetical scanning molecular dynamics (HSMD) method is a relatively new technique for calculating the absolute entropy, S, and free energy, F, from a given sample generated by any simulation procedure. Thus, each sample conformation, i, is reconstructed by calculating transition probabilities that their product leads to the probability of i, hence to the entropy. HSMD is an exact method where all interactions are considered, and the only approximation is due to insufficient sampling. In previous studies HSMD (and HS Monte Carlo - HSMC) has been applied very successfully to liquid argon, TIP3P water, self-avoiding walks, and peptides in a α-helix, extended, and hairpin microstates. In this paper HSMD is developed further as applied to the flexible 7-residue surface loop, 304-310 (Gly-His-Gly-Ala-Gly-Gly-Ser) of the enzyme porcine pancreatic α-amylase. We are mainly interested in entropy and free energy differences ΔS = Sfree - Sbound (and ΔF=Ffree-Fbound) between the free and bound microstates of the loop, which are obtained from two separate MD samples of these microstates without the need to carry out thermodynamic integration. As for peptides, we find that relatively large systematic errors in Sfree and Sbound (and Ffree and Fbound) are cancelled in ΔS (ΔF) which is thus obtained efficiently with high accuracy, i.e., with a statistical error of 0.1-0.2 kcal/mol (T=300 K) using the AMBER force field and AMBER with the implicit solvation GB/SA. We provide theoretical arguments in support of this cancellation, discuss in detail the problems involved in the computational definition of a microstate in conformational space, suggest potential ways for enhancing efficiency further, and describe the next development where explicit water will replace implicit solvation. PMID:26619992

  18. An optical nanofiber-based interface for single molecules

    Skoff, Sarah M; Schauffert, Hardy; Rauschenbeutel, Arno

    2016-01-01

    Optical interfaces for quantum emitters are a prerequisite for implementing quantum networks. Here, we couple single molecules to the guided modes of an optical nanofiber. The molecules are embedded within a crystal that provides photostability and due to its inhomogeneous environment, a means to spectrally address single molecules. Single molecules are excited and detected solely via the nanofiber interface without the requirement of additional optical access. In this way, we realize a fully fiber-integrated system that is scalable and may become a versatile constituent for quantum hybrid systems.

  19. Massively parallel single-molecule manipulation using centrifugal force

    Halvorsen, Ken

    2009-01-01

    Precise manipulation of single molecules has already led to remarkable insights in physics, chemistry, biology and medicine. However, widespread adoption of single-molecule techniques has been impeded by equipment cost and the laborious nature of making measurements one molecule at a time. We have solved these issues with a new approach: massively parallel single-molecule force measurements using centrifugal force. This approach is realized in a novel instrument that we call the Centrifuge Force Microscope (CFM), in which objects in an orbiting sample are subjected to a calibration-free, macroscopically uniform force-field while their micro-to-nanoscopic motions are observed. We demonstrate high-throughput single-molecule force spectroscopy with this technique by performing thousands of rupture experiments in parallel, characterizing force-dependent unbinding kinetics of an antibody-antigen pair in minutes rather than days. Additionally, we verify the force accuracy of the instrument by measuring the well-est...

  20. Single Molecule Imaging in Living Cell with Optical Method

    2003-01-01

    Significance, difficult, international developing actuality and our completed works for single molecules imaging in living cell with optical method are described respectively. Additionally we give out some suggestions for the technology development further.

  1. Computer systems for annotation of single molecule fragments

    Schwartz, David Charles; Severin, Jessica

    2016-07-19

    There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

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

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

    2009-06-01

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

  3. Single Molecule Spectroscopy in Chemistry, Physics and Biology Nobel Symposium

    Gräslund, Astrid; Widengren, Jerker

    2010-01-01

    Written by the leading experts in the field, this book describes the development and current state-of-the-art in single molecule spectroscopy. The application of this technique, which started 1989, in physics, chemistry and biosciences is displayed.

  4. Single Molecule Scanning of DNA Radiation Oxidative Damage Project

    National Aeronautics and Space Administration — This proposal will develop an assay to map genomic DNA, at the single molecule level and in a nanodevice, for oxidative DNA damage arising from radiation exposure;...

  5. Electronic-vibrational coupling in single-molecule devices

    Aji, Vivek; Moore, J. E.; Varma, C. M.

    2003-01-01

    Experiments studying vibrational effects on electronic transport through single molecules have observed several seemingly inconsistent behaviors, ranging from up to 30 harmonics of a vibrational frequency in one experiment, to an absence of higher-harmonic peaks in another. We study the different manifestations of electronic-vibrational coupling in inelastic and elastic electron transport through single molecules. For the case of inelastic transport, higher harmonics are shown to be damped by...

  6. The electroluminescence and scanning tunneling microscopy of single molecules

    Buker, John William

    2009-01-01

    The scanning tunneling microscopy (STM) of single molecules has become a prominent experimental method in the field of molecular electronics. It has been found that in STM experiments, when an electric current flows through a single molecule, the molecule may luminesce. This electroluminescence, in conjunction with traditional STM data, provides a potentially important additional degree of freedom for understanding nanoscale systems. This thesis describes exploratory theoretical work on the n...

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

    Biteen, Julie S; Moerner, W. E.

    2010-01-01

    Single-molecule imaging enables biophysical measurements devoid of ensemble averaging, gives enhanced spatial resolution beyond the diffraction limit, and permits superresolution reconstructions. Here, single-molecule and superresolution imaging are applied to the study of proteins in live Caulobacter crescentus cells to illustrate the power of these methods in bacterial imaging. Based on these techniques, the diffusion coefficient and dynamics of the histidine protein kinase PleC, the locali...

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

    2007-01-01

    Precise, controllable single-molecule force spectroscopy studies of RNA and RNA-dependent processes have recently shed new light on the dynamics and pathways of RNA folding and RNA-enzyme interactions. A crucial component of this research is the design and assembly of an appropriate RNA construct. Such a construct is typically subject to several criteria. First, single-molecule force spectroscopy techniques often require an RNA construct that is longer than the RNA molecules used for bulk bio...

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

    Tao, Nongjian

    2012-04-01

    This special section of Journal of Physics: Condensed Matter (JPCM) is dedicated to Professor Stuart M Lindsay on the occasion of his 60th birthday and in recognition of his outstanding contributions to multiple research areas, including light scattering spectroscopy, scanning probe microscopy, biophysics, solid-liquid interfaces and molecular and nanoelectronics. It contains a collection of 14 papers in some of these areas, including a feature article by Lindsay. Each paper was subject to the normal rigorous review process of JPCM. In Lindsay's paper, he discusses the next generations of hybrid chemical-CMOS devices for low cost and personalized medical diagnosis. The discussion leads to several papers on nanotechnology for biomedical applications. Kawaguchi et al report on the detection of single pollen allergen particles using electrode embedded microchannels. Stern et al describe a structural study of three-dimensional DNA-nanoparticle assemblies. Hihath et al measure the conductance of methylated DNA, and discuss the possibility of electrical detection DNA methylation. Portillo et al study the electrostatic effects on the aggregation of prion proteins and peptides with atomic force microscopy. In an effort to understand the interactions between nanostructures and cells, Lamprecht et al report on the mapping of the intracellular distribution of carbon nanotubes with a confocal Raman imaging technique, and Wang et al focus on the intracellular delivery of gold nanoparticles using fluorescence microscopy. Park and Kristic provide theoretical analysis of micro- and nano-traps and their biological applications. This section also features several papers on the fundamentals of electron transport in single atomic wires and molecular junctions. The papers by Xu et al and by Wandlowksi et al describe new methods to measure conductance and forces in single molecule junctions and metallic atomic wires. Scullion et al report on the conductance of molecules with similar

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

    Denton, M.B.

    1992-07-29

    A technique for the detection of single fluorescent chromophores in a flowing stream is under development. This capability is an integral facet of a rapid DNA sequencing scheme currently being developed by Los Alamos National Laboratory. In previous investigations, the detection sensitivity was limited by the background Raman emission from the water solvent. A detection scheme based on a novel mode of operating a Charge-Coupled Device (CCD) is being developed which should greatly enhance the discrimination between fluorescence from a single molecule and the background Raman scattering from the solvent. Register shifts between rows in the CCD are synchronized with the sample flow velocity so that fluorescence from a single molecule is collected in a single moving charge packet occupying an area approaching that of a single pixel while the background is spread evenly among a large number of pixels. Feasibility calculations indicate that single molecule detection should be achieved with an excellent signal-to-noise ratio.

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

    Malý, Pavel; van Grondelle, Rienk; Mančal, Tomáš

    2015-01-01

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

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

    Huisman, Eek; Kamenetska, Masha; Venkataraman, Latha

    2011-03-01

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

  13. Single-Molecule Total Internal Reflection Fluorescence Microscopy.

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

    2016-01-01

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

  14. Single-Molecule Experiments in Vitro and in Silico

    Sotomayor, Marcos; Schulten, Klaus

    2007-05-01

    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.

  15. STM Studies of Isolated Mn12-Ph Single Molecule Magnets

    Reaves, Kelley; Kim, Kyongwan; Iwaya, Katsuya; Hitosugi, Taro; Zhao, Hanhua; Dunbar, Kim R.; Katzgraber, Helmut G.; Teizer, Winfried

    2012-01-01

    We study Mn12O12(C6H5COO)16(H2O)4 (Mn12-Ph) single-molecule magnets on highly ordered pyrolytic graphite (HOPG) using low temperature scanning tunneling microscopy (LT-STM) experiments. We report Mn12-Ph in isolation, resembling single molecules with metallic core atoms and organic outer ligands. The local tunneling current observed within the molecular structure shows a strong bias voltage dependency, which is distinct from that of the HOPG surface. Further, evidence of internal inhomogeneit...

  16. Molecular electronics with single molecules in solid-state devices.

    Moth-Poulsen, Kasper; Bjørnholm, Thomas

    2009-09-01

    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 of the electronic coupling between it and the electrodes. A variety of phenomena are observed depending on whether this coupling is weak, intermediate or strong. PMID:19734925

  17. Novel approaches for single molecule activation and detection

    Benfenati, Fabio; Torre, Vincent

    2014-01-01

    How can we obtain tools able to process and exchange information at the molecular scale In order to do this, it is necessary to activate and detect single molecules under controlled conditions. This book focuses on the generation of biologically-inspired molecular devices. These devices are based on the developments of new photonic tools able to activate and stimulate single molecule machines. Additionally, new light sensitive molecules can be selectively activated by photonic tools. These technological innovations will provide a way to control activation of single light-sensitive molecules, a

  18. Molecular electronics with single molecules in solid-state devices

    Moth-Poulsen, Kasper; Bjørnholm, Thomas

    2009-01-01

    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 how the electron transport properties of the molecule depend on the strength of the electronic coupling between it and the electrodes. A variety of phenomena are observed depending on whether this coupling is weak, intermediate or strong....

  19. Single Molecule 3D Orientation in Time and Space

    Börner, Richard; Ehrlich, Nicky; Hohlbein, Johannes; Hübner, Christian G.

    2016-01-01

    Interactions between single molecules profoundly depend on their mutual three-dimensional orientation. Recently, we demonstrated a technique that allows for orientation determination of single dipole emitters using a polarization-resolved distribution of fluorescence into several detection channe

  20. Single-Molecule Electronic Measurements with Metal Electrodes

    Lindsay, Stuart

    2005-01-01

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

  1. Atomic-Scale Control of Electron Transport through Single Molecules

    Wang, Y. F.; Kroger, J.; Berndt, R.;

    2010-01-01

    Tin-phthalocyanine molecules adsorbed on Ag(111) were contacted with the tip of a cryogenic scanning tunneling microscope. Orders-of-magnitude variations of the single-molecule junction conductance were achieved by controllably dehydrogenating the molecule and by modifying the atomic structure of...

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

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

    2015-05-13

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

  3. A single molecule DNA flow stretching microscope for undergraduates

    Williams, Kelly; Grafe, Brendan; Burke, Kathryn M.; Tanner, Nathan; van Oijen, Antoine M.; Loparo, Joseph; Price, Allen C.

    2011-01-01

    The design of a simple, safe, and inexpensive single molecule flow stretching instrument is presented. The instrument uses a low cost upright microscope coupled to a webcam for imaging single DNA molecules that are tethered in an easy to construct microfluidic flow cell. The system requires no speci

  4. Single Molecule Study of Cellulase Hydrolysis of Crystalline Cellulose

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

    2009-12-01

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

  5. Visualizing Single-molecule DNA Replication with Fluorescence Microscopy

    Tanner, Nathan A.; Loparo, Joseph J.; Oijen, Antoine M. van

    2009-01-01

    We describe a simple fluorescence microscopy-based real-time method for observing DNA replication at the single-molecule level. A circular, forked DNA template is attached to a functionalized glass coverslip and replicated extensively after introduction of replication proteins and nucleotides. The g

  6. Single molecule binding dynamics measured with atomic force microscopy

    We present a new method to analyse simultaneous Topography and RECognition Atomic Force Microscopy data such that it becomes possible to measure single molecule binding rates of surface bound proteins. We have validated this method on a model system comprising a S-layer surface modified with Strep-tagII for binding sites and strep-tactin bound to an Atomic Force Microscope tip through a flexible Poly-Ethylene-Glycol linker. At larger distances, the binding rate is limited by the linker, which limits the diffusion of the strep-tactin molecule, but at lateral distances below 3 nm, the binding rate is solely determined by the intrinsic molecular characteristics and the surface geometry and chemistry of the system. In this regime, Kon as determined from single molecule TREC data is in agreement with Kon determined using traditional biochemical methods. - Highlights: • We discuss the importance of studying single molecule binding rates for surface bound proteins. • We show measurements of single molecule binding rates on a model system using AFM. • We discuss the influence of various components on the measured binding rates

  7. Electronic transport in benzodifuran single-molecule transistors

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

    2015-04-01

    Benzodifuran (BDF) single-molecule transistors have been fabricated in electromigration break junctions for electronic measurements. The inelastic electron tunneling spectrum validates that the BDF molecule is the pathway of charge transport. The gating effect is analyzed in the framework of a single-level tunneling model combined with transition voltage spectroscopy (TVS). The analysis reveals that the highest occupied molecular orbital (HOMO) of the thiol-terminated BDF molecule dominates the charge transport through Au-BDF-Au junctions. Moreover, the energy shift of the HOMO caused by the gate voltage is the main reason for conductance modulation. In contrast, the electronic coupling between the BDF molecule and the gold electrodes, which significantly affects the low-bias junction conductance, is only influenced slightly by the applied gate voltage. These findings will help in the design of future molecular electronic devices.Benzodifuran (BDF) single-molecule transistors have been fabricated in electromigration break junctions for electronic measurements. The inelastic electron tunneling spectrum validates that the BDF molecule is the pathway of charge transport. The gating effect is analyzed in the framework of a single-level tunneling model combined with transition voltage spectroscopy (TVS). The analysis reveals that the highest occupied molecular orbital (HOMO) of the thiol-terminated BDF molecule dominates the charge transport through Au-BDF-Au junctions. Moreover, the energy shift of the HOMO caused by the gate voltage is the main reason for conductance modulation. In contrast, the electronic coupling between the BDF molecule and the gold electrodes, which significantly affects the low-bias junction conductance, is only influenced slightly by the applied gate voltage. These findings will help in the design of future molecular electronic devices. Electronic supplementary information (ESI) available: The fabrication procedure for BDF single-molecule

  8. A gate-tunable single-molecule diode

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

    2016-04-01

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

  9. From nanofabrication to self-fabrication--tailored chemistry for control of single molecule electronic devices

    Moth-Poulsen, Kasper; Bjørnholm, Thomas

    2010-01-01

    Single molecule electronics is a field of research focused on the use of single molecules as electronics components. During the past 15 years the field has concentrated on development of test beds for measurements on single molecules. Bottom-up approaches to single molecule devices are emerging a...

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

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

    2015-01-01

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

  11. Incoherent x-ray scattering in single molecule imaging

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

    2014-01-01

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

  12. Single molecule imaging with longer x-ray laser pulses

    Martin, Andrew V; Caleman, Carl; Quiney, Harry M

    2015-01-01

    In serial femtosecond crystallography, x-ray laser pulses do not need to outrun all radiation damage processes because Bragg diffraction exceeds the damage-induced background scattering for longer pulses ($\\sim$ 50--100 fs). This is due to a "self-gating pulse" effect whereby damage terminates Bragg diffraction prior to the pulse completing its passage through the sample, as if that diffraction were produced by a shorter pulse of equal fluence. We show here that a similar gating effect applies to single molecule diffraction with respect to spatially uncorrelated damage processes like ionization and ion diffusion. The effect is clearly seen in calculations of the diffraction contrast, by calculating the diffraction of average structure separately to the diffraction from statistical fluctuations of the structure due to damage ("damage noise"). Our results suggest that sub-nanometer single molecule imaging with longer pulses, like those produced at currently operating facilities, should not yet be ruled out. The...

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

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

    2015-01-01

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

  14. Electronic Single Molecule Identification of Carbohydrate Isomers by Recognition Tunneling

    Im, JongOne; Liu, Hao; Zhao, Yanan; Sen, Suman; Biswas, Sudipta; Ashcroft, Brian; Borges, Chad; Wang, Xu; Lindsay, Stuart; Zhang, Peiming

    2016-01-01

    Glycans play a central role as mediators in most biological processes, but their structures are complicated by isomerism. Epimers and anomers, regioisomers, and branched sequences contribute to a structural variability that dwarfs those of nucleic acids and proteins, challenging even the most sophisticated analytical tools, such as NMR and mass spectrometry. Here, we introduce an electron tunneling technique that is label-free and can identify carbohydrates at the single-molecule level, offering significant benefits over existing technology. It is capable of analyzing sub-picomole quantities of sample, counting the number of individual molecules in each subset in a population of coexisting isomers, and is quantitative over more than four orders of magnitude of concentration. It resolves epimers not well separated by ion-mobility and can be implemented on a silicon chip. It also provides a readout mechanism for direct single-molecule sequencing of linear oligosaccharides.

  15. Single Molecule Study of Photoconversion and Spectral Heterogeneities of Fluorophores

    Liao, Zhiyu

    of conformational changes and dynamics. The photophysical properties of organic dyes directly determine the quality of the experiments. So the better understanding of the photophysical properties of organic dyes, the better we are able to design the experiments and interpret the data, especially in single molecule...... to understand the mechanisms of photobleaching behaviors of organic dyes, terrylene diimide (TDI) and amino-trioxatriangulenium dye (A3-TOTA+). Photobleaching is usually seen as permanent loss of fluorescence. In this work, we show that organic fluorophores can be converted into another chemical compound after...... 104 single molecule measurements. A simple and practical method is introduced to study the characteristics of the photoproducts at the ensemble level. Control experiments reveal that the reaction leading to photobleaching is oxygen related, but the composition of the photoproducts remains inconclusive...

  16. Directly measuring single molecule heterogeneity using force spectroscopy

    Hinczewski, Michael; Thirumalai, D

    2016-01-01

    One of the most intriguing results of single molecule experiments on proteins and nucleic acids is the discovery of functional heterogeneity: the observation that complex cellular machines exhibit multiple, biologically active conformations. The structural differences between these conformations may be subtle, but each distinct state can be remarkably long-lived, with random interconversions between states occurring only at macroscopic timescales, fractions of a second or longer. Though we now have proof of functional heterogeneity in a handful of systems---enzymes, motors, adhesion complexes---identifying and measuring it remains a formidable challenge. Here we show that evidence of this phenomenon is more widespread than previously known, encoded in data collected from some of the most well-established single molecule techniques: AFM or optical tweezer pulling experiments. We present a theoretical procedure for analyzing distributions of rupture/unfolding forces recorded at different pulling speeds. This re...

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

    Hybertsen M. S.

    2013-04-11

    By exploiting selective link chemistry, formation of single molecule junctions with reproducible conductance has become established. Systematic studies reveal the structure-conductance relationships for diverse molecules. I will draw on experiments from my collaborators at Columbia University, atomic-scale calculations and theory to describe progress in two areas. First, I will describe a novel route to form single molecule junctions, based on SnMe3 terminated molecules, in which gold directly bonds to carbon in the molecule backbone resulting in near ideal contact resistance [1]. Second, comparison of the conductance of junctions formed with molecular species containing either one backbone or two backbones in parallel allows demonstration of the role of quantum interference in the conductance superposition law at the molecular scale [2].

  18. Light sheet microscopy for single molecule tracking in living tissue.

    Jörg Gerhard Ritter

    Full Text Available 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 microm 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.

  19. Identifying Transport Behavior of Single-Molecule Trajectories

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

    2014-01-01

    Models of biological diffusion-reaction systems require accurate classification of the underlying diffusive dynamics (e.g., Fickian, subdiffusive, or superdiffusive). We use a renormalization group operator to identify the anomalous (non-Fickian) diffusion behavior from a short trajectory of a single molecule. The method provides quantitative information about the underlying stochastic process, including its anomalous scaling exponent. The classification algorithm is first validated on simula...

  20. Adsorption Geometry Determination of Single Molecules by Atomic Force Microscopy

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

    2013-01-01

    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 degrees. The method was applied to five pi-conjugated molecules, including three molecules from the olympicene family, adsorbed on Cu(111). For the olympicenes, we found th...

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

    Huckabay, Heath A; Dunn, Robert C

    2011-03-15

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

  2. n and p type character of single molecule diodes

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

    2015-01-01

    Looking for single molecule electronic devices, we have investigated the charge transport properties of individual tetra-phenylporphyrin molecules on different substrates by ultrahigh-vacuum scanning tunneling microscopy and spectroscopy and by first-principles calculations. The tetra-phenylporphyrins with a Co atom (Co-TPP) or 2 hydrogens (H2-TPP) in the central macrocycle when deposited on Cu3Au(100) substrates showed a diode-like behavior with p and n type character, respectively. After re...

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

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

    2010-01-01

    Single molecule force spectroscopy is a powerful method that uses the mechanical properties of DNA to explore DNA interactions. Here we describe how DNA stretching experiments quantitatively characterize the DNA binding of small molecules and proteins. Small molecules exhibit diverse DNA binding modes, including binding into the major and minor grooves and intercalation between base pairs of double-stranded DNA (dsDNA). Histones bind and package dsDNA, while other nuclear proteins such as hig...

  4. Controlling single-molecule junction conductance by molecular interactions

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

    2015-01-01

    For the rational design of single-molecular electronic devices, it is essential to understand environmental effects on the electronic properties of a working molecule. Here we investigate the impact of molecular interactions on the single-molecule conductance by accurately positioning individual molecules on the electrode. To achieve reproducible and precise conductivity measurements, we utilize relatively weak π-bonding between a phenoxy molecule and a STM-tip to form and cleave one contact ...

  5. Electric Field Controlled Magnetic Anisotropy in a Single Molecule

    Zyazin, Alexander S.; Berg, Johan W. G. van den; Osorio, Edgar A; Van Der Zant, Herre S J; Konstantinidis, Nikolaos P.; Leijnse, Martin; Wegewijs, Maarten R; May, Falk; Hofstetter, Walter; Danieli, Chiara; Cornia, Andrea

    2010-01-01

    We have measured quantum transport through an individual Fe$_4$ single-molecule magnet embedded in a three-terminal device geometry. The characteristic zero-field splittings of adjacent charge states and their magnetic field evolution are observed in inelastic tunneling spectroscopy. We demonstrate that the molecule retains its magnetic properties, and moreover, that the magnetic anisotropy is significantly enhanced by reversible electron addition / subtraction controlled with the gate voltag...

  6. Control of Single Molecule Fluorescence Dynamics by Stimulated Emission Depletion

    Marsh, R J; Osborne, M A; Bain, A. J.

    2003-01-01

    The feasibility of manipulating the single molecule absorption-emission cycle using picosecond stimulated emission depletion (STED) is investigated using a stochastic computer simulation. In the simulation the molecule is subjected to repeated excitation and depletion events using time delayed pairs of excitation (PUMP) and depletion (DUMP) pulses derived from a high repetition rate pulsed laser system. The model is used to demonstrate that a significant and even substantial reduction in the ...

  7. Single Molecule Spectroscopy for Studying Conformational Dynamics of Short Oligonucleotides

    Lin, Ron Reuven

    2012-01-01

    Understanding biology at the molecular level has been driving technological advances in biological and medical science for many years. Methods for probing molecular systems are often dependent on sampling the concerted actions of large assemblies of molecules rather than for studying individual molecules operating in isolation. Most methods used in experimental biology are largely insensitive to the activity of a single molecule. Over the past twenty five years, advances in a variety of di...

  8. Single molecule detection and fluorescence correlation spectroscopy on surfaces

    Hassler, Kai; Lasser, Theo

    2008-01-01

    In this thesis a new approach for single molecule detection and analysis is explored. This approach is based on the combination of two well established methods, fluorescence correlation spectroscopy (FCS) and total internal reflection fluorescence microscopy (TIRFM). In contrast to most existing fluorescence spectroscopy techniques, the subject of primary interest in FCS is not the fluorescence intensity itself but the random intensity fluctuation around the mean value. Intensity fluctuations...

  9. Single molecule detection and fluorescence correlation spectroscopy on surfaces

    Hassler, Kai

    2006-01-01

    In this thesis a new approach for single molecule detection and analysis is explored. This approach is based on the combination of two well established methods, fluorescence correlation spectroscopy (FCS) and total internal reflection fluorescence microscopy (TIRFM). In contrast to most existing fluorescence spectroscopy techniques, the subject of primary interest in FCS is not the fluorescence intensity itself but the random intensity fluctuation around the mean value. Intensity fluctuations...

  10. Potential of nanotechnologies for single molecule probing of individual cells

    Klepárník, Karel; Přikryl, Jan; Voráčová, Ivona; Hezinová, Věra; Lišková, Marcela; Foret, František

    Berlin : PicoQuant GmbH, 2010. s. 83. ISBN N. [International Workshop on "Single Molecule Spectroscopy and Ultrasensitive Analysis in the Life Sciences" /16./. 15.09.2010-17.09.2010, Berlin] R&D Projects: GA ČR GA203/08/1680 Institutional research plan: CEZ:AV0Z40310501 Keywords : nanotechnologies * quantum dots * fluorescent probes Subject RIV: CB - Analytical Chemistry, Separation

  11. Single-Molecule Fluorescence Quantification with a Photobleached Internal Standard

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

    2012-01-01

    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 ...

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

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

    2015-10-20

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

  13. Viruses and Tetraspanins: Lessons from Single Molecule Approaches

    Selma Dahmane

    2014-05-01

    Full Text Available 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.

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

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

    2016-01-01

    We derive approximate equations of motion for excited state dynamics of a multilevel open quantum system weakly interacting with light to describe fluorescence-detected single molecule spectra. Based on the Frenkel exciton theory, we construct a model for the chlorophyll part of the LHCII complex of higher plants and its interaction with previously proposed excitation quencher in the form of the lutein molecule Lut 1. The resulting description is valid over a broad range of timescales relevant for single molecule spectroscopy, i.e. from ps to minutes. Validity of these equations is demonstrated by comparing simulations of ensemble and single-molecule spectra of monomeric LHCII with experiments. Using a conformational change of the LHCII protein as a switching mechanism, the intensity and spectral time traces of individual LHCII complexes are simulated, and the experimental statistical distributions are reproduced. Based on our model, it is shown that with reasonable assumptions about its interaction with chlorophylls, Lut 1 can act as an efficient fluorescence quencher in LHCII. PMID:27189196

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

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

    2010-11-01

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

  16. A Single-Molecule Switch and Memory Element

    The mechanically controllable break-junction technique enables us to investigate charge-carrier transport through an individually contacted and addressed molecule. Using a statistical measurement and analysis approach, we acquire simultaneously current-voltage curves during the repeated formation and breaking of a molecular junction. Thereby, a reversible and controllable switching between two distinct conductive states of a single-molecule system was investigated. Voltage pulses are used to switch from a low to a high conductive ''on'' state, and, furthermore, to reset the switch again to the ''off'' state. On this single-molecule level, collective phenomena can be excluded and therefore the observed switching mechanism has a truly molecular origin. Both conductive states are stable and accessible via non-destructive reading. Combined with the ability to reset the switch, this opens the way to employ this single-molecule as a memory element which is demonstrated by repeated write-read-erase-read cycles with non-destructive read-outs

  17. Vibrationally coupled electron transport through single-molecule junctions

    Haertle, Rainer

    2012-04-26

    Single-molecule junctions are among the smallest electric circuits. They consist of a molecule that is bound to a left and a right electrode. With such a molecular nanocontact, the flow of electrical currents through a single molecule can be studied and controlled. Experiments on single-molecule junctions show that a single molecule carries electrical currents that can even be in the microampere regime. Thereby, a number of transport phenomena have been observed, such as, for example, diode- or transistor-like behavior, negative differential resistance and conductance switching. An objective of this field, which is commonly referred to as molecular electronics, is to relate these transport phenomena to the properties of the molecule in the contact. To this end, theoretical model calculations are employed, which facilitate an understanding of the underlying transport processes and mechanisms. Thereby, one has to take into account that molecules are flexible structures, which respond to a change of their charge state by a profound reorganization of their geometrical structure or may even dissociate. It is thus important to understand the interrelation between the vibrational degrees of freedom of a singlemolecule junction and the electrical current flowing through the contact. In this thesis, we investigate vibrational effects in electron transport through singlemolecule junctions. For these studies, we calculate and analyze transport characteristics of both generic and first-principles based model systems of a molecular contact. To this end, we employ a master equation and a nonequilibrium Green's function approach. Both methods are suitable to describe this nonequilibrium transport problem and treat the interactions of the tunneling electrons on the molecular bridge non-perturbatively. This is particularly important with respect to the vibrational degrees of freedom, which may strongly interact with the tunneling electrons. We show in detail that the resulting

  18. Simple test system for single molecule recognition force microscopy

    We have established an easy-to-use test system for detecting receptor-ligand interactions on the single molecule level using atomic force microscopy (AFM). For this, avidin-biotin, probably the best characterized receptor-ligand pair, was chosen. AFM sensors were prepared containing tethered biotin molecules at sufficiently low surface concentrations appropriate for single molecule studies. A biotin tether, consisting of a 6 nm poly(ethylene glycol) (PEG) chain and a functional succinimide group at the other end, was newly synthesized and covalently coupled to amine-functionalized AFM tips. In particular, PEG800 diamine was glutarylated, the mono-adduct NH2-PEG-COOH was isolated by ion exchange chromatography and reacted with biotin succinimidylester to give biotin-PEG-COOH which was then activated as N-hydroxysuccinimide (NHS) ester to give the biotin-PEG-NHS conjugate which was coupled to the aminofunctionalized AFM tip. The motional freedom provided by PEG allows for free rotation of the biotin molecule on the AFM sensor and for specific binding to avidin which had been adsorbed to mica surfaces via electrostatic interactions. Specific avidin-biotin recognition events were discriminated from nonspecific tip-mica adhesion by their typical unbinding force (∼40 pN at 1.4 nN/s loading rate), unbinding length (<13 nm), the characteristic nonlinear force-distance relation of the PEG linker, and by specific block with excess of free d-biotin. The convenience of the test system allowed to evaluate, and compare, different methods and conditions of tip aminofunctionalization with respect to specific binding and nonspecific adhesion. It is concluded that this system is well suited as calibration or start-up kit for single molecule recognition force microscopy

  19. The statistics of single molecule detection: An overview

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

    1995-12-31

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

  20. Electron transport in single molecules: from benzene to graphene.

    Chen, F; Tao, N J

    2009-03-17

    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

  1. Hybrid photodetector for single-molecule spectroscopy and microscopy

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

    2008-02-01

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

  2. Single Molecule Studies on Dynamics in Liquid Crystals

    Daniela Täuber

    2013-09-01

    Full Text Available 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.

  3. Spin coherence in a Mn3 single-molecule magnet

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

  4. Electronic Single Molecule Measurements with the Scanning Tunneling Microscope

    Im, Jong One

    Richard Feynman said "There's plenty of room at the bottom". This inspired the techniques to improve the single molecule measurements. Since the first single molecule study was in 1961, it has been developed in various field and evolved into powerful tools to understand chemical and biological property of molecules. This thesis demonstrates electronic single molecule measurement with Scanning Tunneling Microscopy (STM) and two of applications of STM; Break Junction (BJ) and Recognition Tunneling (RT). First, the two series of carotenoid molecules with four different substituents were investigated to show how substituents relate to the conductance and molecular structure. The measured conductance by STM-BJ shows that Nitrogen induces molecular twist of phenyl distal substituents and conductivity increasing rather than Carbon. Also, the conductivity is adjustable by replacing the sort of residues at phenyl substituents. Next, amino acids and peptides were identified through STM-RT. The distribution of the intuitive features (such as amplitude or width) are mostly overlapped and gives only a little bit higher separation probability than random separation. By generating some features in frequency and cepstrum domain, the classification accuracy was dramatically increased. Because of large data size and many features, supporting vector machine (machine learning algorithm for big data) was used to identify the analyte from a data pool of all analytes RT data. The STM-RT opens a possibility of molecular sequencing in single molecule level. Similarly, carbohydrates were studied by STM-RT. Carbohydrates are difficult to read the sequence, due to their huge number of possible isomeric configurations. This study shows that STM-RT can identify not only isomers of mono-saccharides and disaccharides, but also various mono-saccharides from a data pool of eleven analytes. In addition, the binding affinity between recognition molecule and analyte was investigated by comparing with

  5. Characterizing 3D RNA structure by single molecule FRET.

    Stephenson, James D; Kenyon, Julia C; Symmons, Martyn F; Lever, Andrew M L

    2016-07-01

    The importance of elucidating the three dimensional structures of RNA molecules is becoming increasingly clear. However, traditional protein structural techniques such as NMR and X-ray crystallography have several important drawbacks when probing long RNA molecules. Single molecule Förster resonance energy transfer (smFRET) has emerged as a useful alternative as it allows native sequences to be probed in physiological conditions and allows multiple conformations to be probed simultaneously. This review serves to describe the method of generating a three dimensional RNA structure from smFRET data from the biochemical probing of the secondary structure to the computational refinement of the final model. PMID:26853327

  6. Single Molecule Fluorescence Measurements of Ribosomal Translocation Dynamics

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

    2011-01-01

    We employ single-molecule fluorescence resonance energy transfer (smFRET) to study structural dynamics over the first two elongation cycles of protein synthesis, using ribosomes containing either Cy3-labeled ribosomal protein L11 and A- or P-site Cy5-labeled tRNA or Cy3 and Cy5 labeled tRNAs. Pre-translocation (PRE) complexes demonstrate fluctuations between classical and hybrid forms, with concerted motions of tRNAs away from L11 and from each other when classical complex converts to hybrid ...

  7. Single particle tracking and single molecule energy transfer

    Bräuchle, Christoph; Michaelis, Jens

    2009-01-01

    Closing a gap in the literature, this handbook gathers all the information on single particle tracking and single molecule energy transfer. It covers all aspects of this hot and modern topic, from detecting virus entry to membrane diffusion, and from protein folding using spFRET to coupled dye systems, as well recent achievements in the field. Throughout, the first-class editors and top international authors present content of the highest quality, making this a must-have for physical chemists, spectroscopists, molecular physicists and biochemists.

  8. Charge Transport in Single Molecule Junctions of Spirobifluorene Scaffold

    Hromadová, Magdaléna; Kolivoška, Viliam; Sokolová, Romana; Šebera, Jakub; Mészáros, G.; Valášek, M.; Mayor, C.

    Ústí nad Labem: Best servis, 2016 - (Navrátil, T.; Fojta, M.; Schwarzová, K.), s. 78-80 ISBN 978-80-905221-4-5. [Moderní elektrochemické metody /36./. Jetřichovice (CZ), 23.05.2016-27.05.2016] R&D Projects: GA ČR(CZ) GA14-05180S Grant ostatní: AV ČR(CZ) MTA-16-02 Institutional support: RVO:61388955 Keywords : single molecule conductance * spirobifluorene * break junction Subject RIV: CG - Electrochemistry

  9. Kondo effect in single-molecule spintronic devices

    We study the Kondo effect in a quantum dot or a single molecule coupled to ferromagnetic leads. Spin-dependent quantum charge fluctuations in the dot induce the lifting of the spin degeneracy of the dot. It leads to the dot's level spin splitting observed in the nonequilibrium transport as a splitting of a zero-bias anomaly in the differential conductance. We discuss basic properties of this effect and its temperature dependence using numerical renormalization group technique. Recent experimental results fit well to our theoretical consideration

  10. High contrast single molecule tracking in the pericellular coat

    Scrimgeour, Jan; McLane, Louis T.; Curtis, Jennifer E.

    2014-03-01

    The pericellular coat is a robust, hydrated, polymer brush-like structure that can extend several micrometers into the extracellular space around living cells. By controlling access to the cell surface, acting as a filter and storage reservoir for proteins, and actively controlling tissue-immune system interactions, the cell coat performs many important functions at scales ranging from the single cell to whole tissues. The cell coat consists of a malleable backbone - the large polysaccharide hyaluronic acid (HA) - with its structure, material properties, and ultimately its bio-functionality tuned by a diverse set of HA binding proteins. These proteins add charge, cross-links and growth factor-like ligands to the coat To probe the dynamic behavior of this soft biomaterial we have used high contrast single molecule imaging, based on highly inclined laser illumination, to observe individual fluorescently labeled HA binding proteins within the cell coat. Our work focuses on the cell coat of living chondrocyte (cartilage) cells, and in particular the effect of the large, highly charged, protein aggrecan on the properties of the coat. Through single molecule imaging we observe that aggrecan is tightly tethered to HA, and plays an important role in cell coat extension and stiffening.

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

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

    2014-01-01

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

  12. Common fluorescent proteins for single-molecule localization microscopy

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

    2015-07-01

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

  13. Single-molecule chemistry studied using the protein pore -α-hemolysin

    Choi, L.-S., Mach, T.; Bayley, Hagan

    2012-01-01

    Single-molecule detection has provided insights into how molecules behave. Without the averaging effect of ensemble measurements, the stochastic behaviour of single molecules can be observed and intermediate steps in multistep transformations can be clearly detected. The single-molecule reactants range from small molecules (e.g. propene) to proteins of several tens of kDa (e.g. myosin). One single-molecule detection technique is single-channel electrical recording. This approach is based on t...

  14. Single Molecule Spectroscopy on Photosynthetic Pigment-Protein Complexes

    Jelezko, F; Schuler, S; Thews, E; Tietz, C; Wechsler, A; Wrachtrup, J

    2001-01-01

    Single molecule spectroscopy was applied to unravel the energy transfer pathway in photosynthetic pigment-protein complexes. Detailed analysis of excitation and fluorescence emission spectra has been made for peripheral plant antenna LHC II and Photosystem I from cyanobacterium Synechococcus elongatus. Optical transitions of individual pigments were resolved under nonselective excitation of antenna chlorophylls. High-resolution fluorescence spectroscopy of individual plant antenna LHC II indicates that at low temperatures, the excitation energy is localized on the red-most Chl a pool absorbing at 680 nm. More than one pigment molecule is responsible for the fluorescence emission of the LHC II trimer. The spectral lines of single Chl a molecules absorbing at 675 nm are broadened because of the Foerster energy transfer towards the red-most pigments. Low-temperature spectroscopy on single PS I trimers indicates that two subgroups of pigments, which are present in the red antenna pool, differ by the strength of t...

  15. Single-molecule chemical reactions on DNA origami

    Voigt, Niels Vinther; Tørring, Thomas; Rotaru, Alexandru;

    2010-01-01

    as templates for building materials with new functional properties. Relatively large nanocomponents such as nanoparticles and biomolecules can also be integrated into DNA nanostructures and imaged. Here, we show that chemical reactions with single molecules can be performed and imaged at a local...... position on a DNA origami scaffold by atomic force microscopy. The high yields and chemoselectivities of successive cleavage and bond-forming reactions observed in these experiments demonstrate the feasibility of post-assembly chemical modification of DNA nanostructures and their potential use as locally......DNA nanotechnology and particularly DNA origami, in which long, single-stranded DNA molecules are folded into predetermined shapes, can be used to form complex self-assembled nanostructures. Although DNA itself has limited chemical, optical or electronic functionality, DNA nanostructures can serve...

  16. Polarization-dependent single-molecule spectroscopy on photosystem I

    Skandary, S.; Konrad, A.; Hussels, M.; Meixner, A. J.; Brecht, M.

    2015-08-01

    Single-molecule spectroscopy (SMS) at low temperature was used to study the spectral properties, heterogeneities and spectral dynamics of the chlorophyll a (Chl a) molecules responsible for the fluorescence emission of photosystem I (PS I). The fluorescence spectra of single PS I complexes are dominated by several red-shifted Chl a molecules categorized into red pools called C708 and C719. By polarization dependent measurements we demonstrate spectrally separate emissions corresponding to C708 and C719 in single PS I monomers and trimers. Moreover, we compared the results of SMS polarization dependent between monomeric and trimeric PS I complexes and give an estimation for the orientation between these red pools. As a consequence, we get new insight into the energy transfer towards and between the red Chl a molecules in PS I complexes.

  17. Single molecule DNA detection with an atomic vapor notch filter

    Uhland, Denis; Rendler, Torsten; Widmann, Matthias; Lee, Sang-Yun [University of Stuttgart and Stuttgart Research Center of Photonic Engineering (SCoPE) and IQST, 3rd Physics Institute, Stuttgart (Germany); Wrachtrup, Joerg; Gerhardt, Ilja [University of Stuttgart and Stuttgart Research Center of Photonic Engineering (SCoPE) and IQST, 3rd Physics Institute, Stuttgart (Germany); Max Planck Institute for Solid State Research, Stuttgart (Germany)

    2015-12-01

    The detection of single molecules has facilitated many advances in life- and material-science. Commonly the fluorescence of dye molecules is detected, which are attached to a non-fluorescent structure under study. For fluorescence microscopy one desires to maximize the detection efficiency together with an efficient suppression of undesired laser leakage. Here we present the use of the narrow-band filtering properties of hot atomic sodium vapor to selectively filter the excitation light from the red-shifted fluorescence of dye labeled single-stranded DNA molecules. A statistical analysis proves an enhancement in detection efficiency of more than 15% in a confocal and in a wide-field configuration. (orig.)

  18. n and p type character of single molecule diodes

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

    2015-02-01

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

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

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

    2015-10-01

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

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

    Reisner, Walter; Larsen, Niels Bent; Silahtaroglu, Asli;

    2010-01-01

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

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

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

    2016-02-01

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

  2. Single-Molecule Electrochemical Gating in Ionic Liquids

    Kay, Nicola J.; Higgins, Simon J.; Jeppesen, Jan O.;

    2012-01-01

    The single-molecular conductance of a redox active molecular bridge has been studied in an electrochemical single-molecule transistor configuration in a room-temperature ionic liquid (RTIL). The redox active pyrrolo-tetrathiafulvalene (pTTF) moiety was attached to gold contacts at both ends through...... −(CH2)6S– groups, and gating of the redox state was achieved with the electrochemical potential. The water-free, room-temperature, ionic liquid environment enabled both the monocationic and the previously inaccessible dicationic redox states of the pTTF moiety to be studied in the in situ scanning...... relaxation. Using this view, reorganization energies of ∼1.2 eV have been estimated for both the first and second redox transitions for the pTTF bridge in the 1-butyl-3-methylimidazolium trifluoromethanesulfonate (BMIOTf) ionic liquid environment. By contrast, in aqueous environments, a much smaller...

  3. Theory of electron transport through single molecules of polyaniline

    Lee, Myeong H [Department of Physics, Arizona State University, Tempe, AZ 85287-1504 (United States); Speyer, Gil [Fulton High Performance Computing Center, Arizona State University, Tempe, AZ 85287-1504 (United States); Sankey, Otto F [Department of Physics, Arizona State University, Tempe, AZ 85287-1504 (United States)

    2007-05-30

    We present theoretical results for the electron transport properties of the organic molecule polyaniline, especially leucoemeraldine (LEB), the fully reduced form. The electron tunnelling characteristics of these chain-like molecules are described by their complex band-structure. We explore how the bandgap and tunnelling decay parameter {beta} depend on the oxidation state of the molecule and on the torsion angle between rings. It is found that the metal Fermi level lies near the HOMO for gold contacts with a single leucoemeraldine molecule, which results in non-linear I-V characteristics. The conductance of a hepta-aniline (LEB) oligomer is obtained from a first-principles I-V curve and compared with the recent experimental results. We examine the effect of stretching of the molecule on its conductance to explain the discrepancy between the theoretical simulations and single-molecule conductance measurement experiment.

  4. Few-photon coherent nonlinear optics with a single molecule

    Maser, Andreas; Utikal, Tobias; Götzinger, Stephan; Sandoghdar, Vahid

    2015-01-01

    The pioneering experiments of linear spectroscopy were performed using flames in the 1800s, but nonlinear optical measurements had to wait until lasers became available in the twentieth century. Because the nonlinear cross section of materials is very small, usually macroscopic bulk samples and pulsed lasers are used. Numerous efforts have explored coherent nonlinear signal generation from individual nanoparticles or small atomic ensembles with millions of atoms. Experiments on a single semiconductor quantum dot have also been reported, albeit with a very small yield. Here, we report on coherent nonlinear spectroscopy of a single molecule under continuous-wave single-pass illumination, where efficient photon-molecule coupling in a tight focus allows switching of a laser beam by less than a handful of pump photons nearly resonant with the sharp molecular transition. Aside from their fundamental importance, our results emphasize the potential of organic molecules for applications such as quantum information pro...

  5. A Single-Molecule Hershey-Chase Experiment

    Van Valen, David; Chen, Yi-Ju; Tuson, Hannah; Wiggins, Paul; Phillips, Rob

    2012-01-01

    Ever since Hershey and Chase used phages to establish DNA as the carrier of genetic information in 1952, the precise mechanisms of phage DNA translocation have been a mystery. While bulk measurements have set a time scale for in vivo DNA translocation during bacteriophage infection, measurements of DNA ejection by single bacteriophages have only been made in vitro. Here, we present direct visualization of single bacteriophages infecting individual Escherichia coli cells. For bacteriophage lambda, we establish a mean ejection time of roughly 5 minutes with significant cell-to-cell variability, including pausing events. In contrast, corresponding in vitro single-molecule ejections take only 10 seconds to reach completion and do not exhibit significant variability. Our data reveal that the velocity of ejection for two different genome lengths collapses onto a single curve. This suggests that in vivo ejections are controlled by the amount of DNA ejected, in contrast with in vitro DNA ejections, which are governed...

  6. Synergizing superresolution optical fluctuation imaging with single molecule localization microscopy

    Schidorsky, Shachar; Razvag, Yair; Golan, Yonatan; Weiss, Shimon; Sherman, Eilon

    2016-01-01

    Single molecule localization microscopy (SMLM) techniques enable imaging biological samples well beyond the diffraction limit of light, but they vary significantly in their spatial and temporal resolutions. High-order statistical analysis of temporal fluctuations as in superresolution optical fluctuation imaging (SOFI) also enable imaging beyond diffraction limit, but usually at a lower resolution as compared to SMLM. Since the same data format is acquired for both methods, their algorithms can be applied to the same data set, and thus may be combined synergistically to improve overall imaging performance. Here, we find that SOFI converges much faster than SMLM, provides additive information to SMLM, and can efficiently reject background. We then show how SOFI-assisted SMLM imaging can improve SMLM image reconstruction by rejecting common sources of background, especially under low signal-to-background conditions. The performance of our approach was evaluated using a realistic simulation of fluorescence imagi...

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

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

    2015-05-13

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

  8. Enhancing Single Molecule Imaging in Optofluidics and Microfluidics

    Andreas E. Vasdekis

    2011-08-01

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

  9. Single-molecule fluorescence studies on DNA looping.

    Jeong, Jiyoun; Le, Tung T; Kim, Harold D

    2016-08-01

    Structure and dynamics of DNA impact how the genetic code is processed and maintained. In addition to its biological importance, DNA has been utilized as building blocks of various nanomachines and nanostructures. Thus, understanding the physical properties of DNA is of fundamental importance to basic sciences and engineering applications. DNA can undergo various physical changes. Among them, DNA looping is unique in that it can bring two distal sites together, and thus can be used to mediate interactions over long distances. In this paper, we introduce a FRET-based experimental tool to study DNA looping at the single molecule level. We explain the connection between experimental measurables and a theoretical concept known as the J factor with the intent of raising awareness of subtle theoretical details that should be considered when drawing conclusions. We also explore DNA looping-assisted protein diffusion mechanism called intersegmental transfer using protein induced fluorescence enhancement (PIFE). We present some preliminary results and future outlooks. PMID:27064000

  10. Single-molecule manipulation and chemistry with the STM

    We review recent theoretical work on the manipulation of single molecules with scanning probes, in particular the scanning tunnelling microscope (STM). The aim of theories and simulations is to account for the processes, ideally at a quantitative level, that permit the controlled manipulation of matter at the atomic scale in adsorbed molecular systems. In order to achieve this, simulations rely on total energy and electronic structure calculations where a trade-off is made between the size of the system and the accuracy of the calculation. This first stage of the calculation yields the basic quantities used for the second stage: the evaluation of the coupled electron-nuclear dynamics. This second stage is a formidable task and many approximations are involved. In this review, we will present some of the customary approximations regarding the theoretical study of mechanical and inelastic manipulations. Mechanical manipulations use the interaction between the acting probe (usually a metallic tip) and the targeted adsorbate. We review recent results in the field of adsorbate mechanical manipulations and explain how manipulations can be effected by using the interaction between the probe's tip and certain molecular groups of complex chemisorbed molecular systems. On the other hand, inelastic manipulations use the tunnelling current to convey energy with sub-aangstroem precision. This current can excite localized vibrations that can induce measurable variations of the tunnelling conductance, hence providing a means of detecting single-molecule vibrations. This current can also inject energy in a few reaction coordinates. Recently, the possibility of vibrational selective manipulations of NH3/Cu(100) has been experimentally demonstrated. The theory presented here addresses the actual pathways accessed when the molecule is excited by the tunnelling current from an STM

  11. Easy Absolute Values? Absolutely

    Taylor, Sharon E.; Mittag, Kathleen Cage

    2015-01-01

    The authors teach a problem-solving course for preservice middle-grades education majors that includes concepts dealing with absolute-value computations, equations, and inequalities. Many of these students like mathematics and plan to teach it, so they are adept at symbolic manipulations. Getting them to think differently about a concept that they…

  12. Single Molecule Screening of Disease DNA Without Amplification

    Ji-Young Lee

    2006-12-12

    The potential of single molecule detection as an analysis tool in biological and medical fields is well recognized today. This fast evolving technique will provide fundamental sensitivity to pick up individual pathogen molecules, and therefore contribute to a more accurate diagnosis and a better chance for a complete cure. Many studies are being carried out to successfully apply this technique in real screening fields. In this dissertation, several attempts are shown that have been made to test and refine the application of the single molecule technique as a clinical screening method. A basic applicability was tested with a 100% target content sample, using electrophoretic mobility and multiple colors as identification tools. Both electrophoretic and spectral information of individual molecule were collected within a second, while the molecule travels along the flow in a capillary. Insertion of a transmission grating made the recording of the whole spectrum of a dye-stained molecule possible without adding complicated instrumental components. Collecting two kinds of information simultaneously and combining them allowed more thorough identification, up to 98.8% accuracy. Probing mRNA molecules with fluorescently labeled cDNA via hybridization was also carried out. The spectral differences among target, probe, and hybrid were interpreted in terms of dispersion distances after transmission grating, and used for the identification of each molecule. The probes were designed to have the least background when they are free, but have strong fluorescence after hybridization via fluorescence resonance energy transfer. The mRNA-cDNA hybrids were further imaged in whole blood, plasma, and saliva, to test how far a crude preparation can be tolerated. Imaging was possible with up to 50% of clear bio-matrix contents, suggesting a simple lysis and dilution would be sufficient for imaging for some cells. Real pathogen DNA of human papillomavirus (HPV) type-I6 in human genomic DNA

  13. Photoinduced nuclear spin conversion of methyl groups of single molecules

    A methyl group is an outstanding quantum system due to its special symmetry properties. The threefold rotation around one of its bond is isomorphic to the group of even permutations of the remaining protons, a property which imposes severe quantum restrictions on the system, for instance a strict correlation of rotational states with nuclear spin states. The resulting long lifetimes of the rotational tunneling states of the methyl group can be exploited for applying certain high resolution optical techniques, like hole burning or single molecule spectroscopy to optically switch the methyl group from one tunneling state to another therebye changing the nuclear spin of the protons. One goal of the thesis was to perform this switching in single methyl groups. To this end the methyl group was attached to a chromophoric system, in the present case terrylene, which is well suited for single molecule spectroscopy as well as for hole burning. Experiments were performed with the bare terrylene molecule in a hexadecane lattice which served as a reference system, with alphamethyl terrylene and betamethyl terrylene, both embedded in hexadecane, too. A single molecular probe is a highly sensitive detector for dynamic lattice instabilities. Already the bare terrylene probe showed a wealth of interesting local dynamic effects of the hexadecane lattice which could be well acounted for by the assumption of two nearly degenerate sites with rather different optical and thermal properties, all of which could be determined in a quantitative fashion. As to the methylated terrylene systems, the experiments verified that for betamethyl terrylene it is indeed possible to measure rotational tunneling events in single methyl groups. However, the spectral patterns obtained was much more complicated than expected pointing to the presence of three spectroscopically different methyl groups. In order to achieve a definite assignement, molecular mechanics simulations of the terrylene probes in the

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

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

    2015-04-01

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

  15. Light-Induced Switching of Tunable Single-Molecule Junctions

    Sendler, Torsten

    2015-04-16

    A major goal of molecular electronics is the development and implementation of devices such as single-molecular switches. Here, measurements are presented that show the controlled in situ switching of diarylethene molecules from their nonconductive to conductive state in contact to gold nanoelectrodes via controlled light irradiation. Both the conductance and the quantum yield for switching of these molecules are within a range making the molecules suitable for actual devices. The conductance of the molecular junctions in the opened and closed states is characterized and the molecular level E 0, which dominates the current transport in the closed state, and its level broadening Γ are identified. The obtained results show a clear light-induced ring forming isomerization of the single-molecule junctions. Electron withdrawing side-groups lead to a reduction of conductance, but do not influence the efficiency of the switching mechanism. Quantum chemical calculations of the light-induced switching processes correlate these observations with the fundamentally different low-lying electronic states of the opened and closed forms and their comparably small modification by electron-withdrawing substituents. This full characterization of a molecular switch operated in a molecular junction is an important step toward the development of real molecular electronics devices.

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

    Adak, Olgun; Venkataraman, Latha

    2014-03-01

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

  17. Experimental techniques for single cell and single molecule biomechanics

    Lim, C.T. [Nano Biomechanics Laboratory, Division of Bioengineering and Department of Mechanical Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117576 (Singapore)]. E-mail: ctlim@nus.edu.sg; Zhou, E.H. [Nano Biomechanics Laboratory, Division of Bioengineering and Department of Mechanical Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117576 (Singapore); Li, A. [Nano Biomechanics Laboratory, Division of Bioengineering and Department of Mechanical Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117576 (Singapore); Vedula, S.R.K. [Nano Biomechanics Laboratory, Division of Bioengineering and Department of Mechanical Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117576 (Singapore); Fu, H.X. [Nano Biomechanics Laboratory, Division of Bioengineering and Department of Mechanical Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117576 (Singapore)

    2006-09-15

    Stresses and strains that act on the human body can arise either from external physical forces or internal physiological environmental conditions. These biophysical interactions can occur not only at the musculoskeletal but also cellular and molecular levels and can determine the health and function of the human body. Here, we seek to investigate the structure-property-function relationship of cells and biomolecules so as to understand their important physiological functions as well as establish possible connections to human diseases. With the recent advancements in cell and molecular biology, biophysics and nanotechnology, several innovative and state-of-the-art experimental techniques and equipment have been developed to probe the structural and mechanical properties of biostructures from the micro- down to picoscale. Some of these experimental techniques include the optical or laser trap method, micropipette aspiration, step-pressure technique, atomic force microscopy and molecular force spectroscopy. In this article, we will review the basic principles and usage of these techniques to conduct single cell and single molecule biomechanics research.

  18. Mapping the Transmission Functions of Single-Molecule Junctions.

    Capozzi, Brian; Low, Jonathan Z; Xia, Jianlong; Liu, Zhen-Fei; Neaton, Jeffrey B; Campos, Luis M; Venkataraman, Latha

    2016-06-01

    Charge transport phenomena in single-molecule junctions are often dominated by tunneling, with a transmission function dictating the probability that electrons or holes tunnel through the junction. Here, we present a new and simple technique for measuring the transmission functions of molecular junctions in the coherent tunneling limit, over an energy range of 1.5 eV around the Fermi energy. We create molecular junctions in an ionic environment with electrodes having different exposed areas, which results in the formation of electric double layers of dissimilar density on the two electrodes. This allows us to electrostatically shift the molecular resonance relative to the junction Fermi levels in a manner that depends on the sign of the applied bias, enabling us to map out the junction's transmission function and determine the dominant orbital for charge transport in the molecular junction. We demonstrate this technique using two groups of molecules: one group having molecular resonance energies relatively far from EF and one group having molecular resonance energies within the accessible bias window. Our results compare well with previous electrochemical gating data and with transmission functions computed from first principles. Furthermore, with the second group of molecules, we are able to examine the behavior of a molecular junction as a resonance shifts into the bias window. This work provides a new, experimentally simple route for exploring the fundamentals of charge transport at the nanoscale. PMID:27186894

  19. Gating a single-molecule transistor with individual atoms

    Martínez-Blanco, Jesús; Nacci, Christophe; Erwin, Steven C.; Kanisawa, Kiyoshi; Locane, Elina; Thomas, Mark; von Oppen, Felix; Brouwer, Piet W.; Fölsch, Stefan

    2015-08-01

    Transistors, regardless of their size, rely on electrical gates to control the conductance between source and drain contacts. In atomic-scale transistors, this conductance is sensitive to single electrons hopping via individual orbitals. Single-electron transport in molecular transistors has been previously studied using top-down approaches to gating, such as lithography and break junctions. But atomically precise control of the gate--which is crucial to transistor action at the smallest size scales--is not possible with these approaches. Here, we used individual charged atoms, manipulated by a scanning tunnelling microscope, to create the electrical gates for a single-molecule transistor. This degree of control allowed us to tune the molecule into the regime of sequential single-electron tunnelling, albeit with a conductance gap more than one order of magnitude larger than observed previously. This unexpected behaviour arises from the existence of two different orientational conformations of the molecule, depending on its charge state. Our results show that strong coupling between these charge and conformational degrees of freedom leads to new behaviour beyond the established picture of single-electron transport in atomic-scale transistors.

  20. Multiplexed single-molecule measurements with magnetic tweezers

    We present a method for performing multiple single-molecule manipulation experiments in parallel with magnetic tweezers. We use a microscope with a low magnification, and thus a wide field of view, to visualize multiple DNA-tethered paramagnetic beads and apply an optimized image analysis routine to track the three-dimensional position of each bead simultaneously in real time. Force is applied to each bead using an externally applied magnetic field. Since variations in the field parameters are negligible across the field of view, nearly identical manipulation of all visible beads is possible. However, we find that the error in the position measurement is inversely proportional to the microscope's magnification. To mitigate the increased error caused by demagnification, we have developed a strategy based on tracking multiple fixed beads. Our system is capable of simultaneously manipulating and tracking up to 34 DNA-tethered beads at 60 Hz with ∼1.5 nm resolution and with ∼10% variation in applied force.

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

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

    2015-03-11

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

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

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

    2014-11-12

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

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

    Kim, Taekyeong

    2015-11-01

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

  4. Computing magnetic anisotropy constants of single molecule magnets

    S Ramasesha; Shaon Sahoo; Rajamani Raghunathan; Diptiman Sen

    2009-09-01

    We present here a theoretical approach to compute the molecular magnetic anisotropy parameters, and for single molecule magnets in any given spin eigenstate of exchange spin Hamiltonian. We first describe a hybrid constant -valence bond (VB) technique of solving spin Hamiltonians employing full spatial and spin symmetry adaptation and we illustrate this technique by solving the exchange Hamiltonian of the Cu6Fe8 system. Treating the anisotropy Hamiltonian as perturbation, we compute the and values for various eigenstates of the exchange Hamiltonian. Since, the dipolar contribution to the magnetic anisotropy is negligibly small, we calculate the molecular anisotropy from the single-ion anisotropies of the metal centers. We have studied the variation of and by rotating the single-ion anisotropies in the case of Mn12Ac and Fe8 SMMs in ground and few low-lying excited states of the exchange Hamiltonian. In both the systems, we find that the molecular anisotropy changes drastically when the single-ion anisotropies are rotated. While in Mn12Ac SMM values depend strongly on the spin of the eigenstate, it is almost independent of the spin of the eigenstate in Fe8 SMM. We also find that the value is almost insensitive to the orientation of the anisotropy of the core Mn(IV) ions. The dependence of on the energy gap between the ground and the excited states in both the systems has also been studied by using different sets of exchange constants.

  5. A single molecule investigation of the photostability of quantum dots.

    Eva Christensen Arnspang

    Full Text Available 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 β-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 β-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.

  6. Experimental techniques for single cell and single molecule biomechanics

    Stresses and strains that act on the human body can arise either from external physical forces or internal physiological environmental conditions. These biophysical interactions can occur not only at the musculoskeletal but also cellular and molecular levels and can determine the health and function of the human body. Here, we seek to investigate the structure-property-function relationship of cells and biomolecules so as to understand their important physiological functions as well as establish possible connections to human diseases. With the recent advancements in cell and molecular biology, biophysics and nanotechnology, several innovative and state-of-the-art experimental techniques and equipment have been developed to probe the structural and mechanical properties of biostructures from the micro- down to picoscale. Some of these experimental techniques include the optical or laser trap method, micropipette aspiration, step-pressure technique, atomic force microscopy and molecular force spectroscopy. In this article, we will review the basic principles and usage of these techniques to conduct single cell and single molecule biomechanics research

  7. A theoretical justification for single molecule peptide sequencing.

    Jagannath Swaminathan

    2015-02-01

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

  8. Single Molecule Fluorescence Measurements of Ribosomal Translocation Dynamics

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

    2011-01-01

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

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

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

    2011-05-01

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

  10. Single-molecule dissection of stacking forces in DNA.

    Kilchherr, Fabian; Wachauf, Christian; Pelz, Benjamin; Rief, Matthias; Zacharias, Martin; Dietz, Hendrik

    2016-09-01

    We directly measured at the single-molecule level the forces and lifetimes of DNA base-pair stacking interactions for all stack sequence combinations. Our experimental approach combined dual-beam optical tweezers with DNA origami components to allow positioning of blunt-end DNA helices so that the weak stacking force could be isolated. Base-pair stack arrays that lacked a covalent backbone connection spontaneously dissociated at average rates ranging from 0.02 to 500 per second, depending on the sequence combination and stack array size. Forces in the range from 2 to 8 piconewtons that act along the helical direction only mildly accelerated the stochastic unstacking process. The free-energy increments per stack that we estimate from the measured forward and backward kinetic rates ranged from -0.8 to -3.4 kilocalories per mole, depending on the sequence combination. Our data contributes to understanding the mechanics of DNA processing in biology, and it is helpful for designing the kinetics of DNA-based nanoscale devices according to user specifications. PMID:27609897

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

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

    2010-02-01

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

  12. Single molecule microscopy on Store-Operated Calcium channels

    Store-Operated Calcium Entry is essential for many signaling processes in non-excitable cells. The best studied Store-Operated Calcium current is the Calcium-Release-Activated-Calcium (CRAC) current in T-cells and mast cells, with Orai1 representing the essential pore forming subunit. Functional CRAC channels in store-depleted cells are composed of four Orai1 subunits. However, the stoichiometric composition in resting cells is still discussed controversially: both a tetrameric and a dimeric stoichiometry of resting-state Orai1 have been reported for immobilized or immobile Orai1 proteins. The aim of this thesis was to design a more versatile approach that allows reliable determination of the subunit stoichiometry of mobile Orai1 channels. The motive for this approach is that mobile sub-fractions of the entire Orai1 population provide the cleanest pool of data, devoid of contributions e.g. from immobile Orai1 clusters or Orai1-loaded vesicles attached to the plasma membrane. Moreover, resting-state Orai1 is predominantly mobile, and mobility appears critical for the lateral redistribution which occurs upon store depletion. The method per se is based on single molecule fluorescence microscopy and brightness analysis. Orai1 proteins were fused to a monomeric variant of Green Fluorescent Protein (mGFP) and over-expressed in a human cell line (T24). The 1:1 labeling stoichiometry allows using the brightness of individual Orai1-mGFP channels as a direct measure of the pore stoichiometry. Due to over-expression a potential mixing with endogenous Orai1 can be neglected. However, over-expression of Orai1-mGFP results in channel densities that are too high to allow for resolving single channels using diffraction limited optical microscopy. In order to overcome this challenge, I developed an experimental strategy that allows reduction of the density of actively fluorescent Orai1-mGFP channels without altering the labeling stoichiometry. In order to reduce the surface density

  13. Efficient unfolding pattern recognition in single molecule force spectroscopy data

    Labudde Dirk

    2011-06-01

    Full Text Available Abstract Background Single-molecule force spectroscopy (SMFS is a technique that measures the force necessary to unfold a protein. SMFS experiments generate Force-Distance (F-D curves. A statistical analysis of a set of F-D curves reveals different unfolding pathways. Information on protein structure, conformation, functional states, and inter- and intra-molecular interactions can be derived. Results In the present work, we propose a pattern recognition algorithm and apply our algorithm to datasets from SMFS experiments on the membrane protein bacterioRhodopsin (bR. We discuss the unfolding pathways found in bR, which are characterised by main peaks and side peaks. A main peak is the result of the pairwise unfolding of the transmembrane helices. In contrast, a side peak is an unfolding event in the alpha-helix or other secondary structural element. The algorithm is capable of detecting side peaks along with main peaks. Therefore, we can detect the individual unfolding pathway as the sequence of events labeled with their occurrences and co-occurrences special to bR's unfolding pathway. We find that side peaks do not co-occur with one another in curves as frequently as main peaks do, which may imply a synergistic effect occurring between helices. While main peaks co-occur as pairs in at least 50% of curves, the side peaks co-occur with one another in less than 10% of curves. Moreover, the algorithm runtime scales well as the dataset size increases. Conclusions Our algorithm satisfies the requirements of an automated methodology that combines high accuracy with efficiency in analyzing SMFS datasets. The algorithm tackles the force spectroscopy analysis bottleneck leading to more consistent and reproducible results.

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

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

    2012-05-01

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

  15. Single-molecule Electronics: Cooling Individual Vibrational Modes by the Tunneling Current

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

    2015-01-01

    Electronic devices composed of single molecules constitute the ultimate limit in the continued downscaling of electronic components. A key challenge for single-molecule electronics is to control the temperature of these junctions. Controlling heating and cooling effects in individual vibrational modes, can in principle, be utilized to increase stability of single-molecule junctions under bias, to pump energy into particular vibrational modes to perform current-induced reactions or to increase...

  16. Structural and electronic properties of single molecules and organic layers on surfaces

    Sotthewes, Kai

    2016-01-01

    Single molecules and organic layers on well-defined solid surfaces have attracted tremendous attention owing to their interesting physical and chemical properties. The ultimate utility of single molecules or self-assembled monolayers (SAMs) for potential applications is critically dependent on the structural, electronic and dynamic properties. Therefore is it important to study the structural and electronic properties as well as the dynamic processes of single molecules and organic layers on ...

  17. Single-molecule interfacial electron transfer dynamics manipulated by external electric current

    Zhang, Guofeng; Chen, Ruiyun; Gao, Yan; Wang, Xiaobo; Jia, Suotang

    2011-01-01

    Interfacial electron transfer (IET) dynamics in 1,1'-dioctadecyl-3, 3, 3', 3'-tetramethylindodicarbocyanine (DiD) dye molecules / indium tin oxide (ITO) film system have been probed at the ensemble and single-molecule level by recording the change of fluorescence emission intensity. By comparing the difference of the external electric current (EEC) dependence of lifetime and intensity for enambles and single molecules, it is shown that the single-molecule probe can effcienly demonstrate the IET dynamics. The backward electron transfer and electron transfer of ground state induce the single molecules fluorescence quenching when an EEC is applied to ITO film.

  18. Monitoring Conformational Dynamics with Single-Molecule Fluorescence Energy Transfer: Applications in Nucleosome Remodeling

    Deindl, Sebastian; Zhuang, Xiaowei

    2016-01-01

    Due to its ability to track distance changes within individual molecules or molecular complexes on the nanometer scale and in real time, single-molecule fluorescence resonance energy transfer (single-molecule FRET) is a powerful tool to tackle a wide range of important biological questions. Using our recently developed single-molecule FRET assay to monitor nucleosome translocation as an illustrative example, we describe here in detail how to set up, carry out, and analyze single-molecule FRET experiments that provide time-dependent information on biomolecular processes. PMID:22929765

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

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

    2015-12-01

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

  20. Theoretical analysis of single molecule spectroscopy lineshapes of conjugated polymers

    Devi, Murali

    Conjugated Polymers(CPs) exhibit a wide range of highly tunable optical properties. Quantitative and detailed understanding of the nature of excitons responsible for such a rich optical behavior has significant implications for better utilization of CPs for more efficient plastic solar cells and other novel optoelectronic devices. In general, samples of CPs are plagued with substantial inhomogeneous broadening due to various sources of disorder. Single molecule emission spectroscopy (SMES) offers a unique opportunity to investigate the energetics and dynamics of excitons and their interactions with phonon modes. The major subject of the present thesis is to analyze and understand room temperature SMES lineshapes for a particular CP, called poly(2,5-di-(2'-ethylhexyloxy)-1,4-phenylenevinylene) (DEH-PPV). A minimal quantum mechanical model of a two-level system coupled to a Brownian oscillator bath is utilized. The main objective is to identify the set of model parameters best fitting a SMES lineshape for each of about 200 samples of DEH-PPV, from which new insight into the nature of exciton-bath coupling can be gained. This project also entails developing a reliable computational methodology for quantum mechanical modeling of spectral lineshapes in general. Well-known optimization techniques such as gradient descent, genetic algorithms, and heuristic searches have been tested, employing an L2 measure between theoretical and experimental lineshapes for guiding the optimization. However, all of these tend to result in theoretical lineshapes qualitatively different from experimental ones. This is attributed to the ruggedness of the parameter space and inadequateness of the L2 measure. On the other hand, when the dynamic reduction of the original parameter space to a 2-parameter space through feature searching and visualization of the search space paths using directed acyclic graphs(DAGs), the qualitative nature of the fitting improved significantly. For a more

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

    Nelson, A J; Hess, S T

    2014-04-01

    Resolution describes the smallest details within a sample that can be recovered by a microscope lens system. For optical microscopes detecting visible light, diffraction limits the resolution to ∼200-250 nm. In contrast, localization measures the position of an isolated object using its image. Single fluorescent molecules can be localized with an uncertainty of a few tens of nanometres, and in some cases less than one nanometre. Superresolution fluorescence localization microscopy (SRFLM) images and localizes fluorescent molecules in a sample. By controlling the visibility of the fluorescent molecules with light, it is possible to cause a sparse subset of the tags to fluoresce and be spatially separated from each other. A movie is acquired with a camera, capturing images of many sets of visible fluorescent tags over a period of time. The movie is then analysed by a computer whereby all of the single molecules are independently measured, and their positions are recorded. When the coordinates of a sufficient number of molecules are collected, an image can be rendered by plotting the coordinates of the localized molecules. The spatial resolution of these rendered images can be better than 20 nm, roughly an order of magnitude better than the diffraction limited resolution. The invention of SRFLM has led to an explosion of related techniques. Through the use of specialized optics, the fluorescent signal can be split into multiple detection channels. These channels can capture additional information such as colour (emission wavelength), orientation and three-dimensional position of the detected molecules. Measurement of the colour of the detected fluorescence can allow researchers to distinguish multiple types of fluorescent tags and to study the interaction between multiple molecules of interest. Three-dimensional imaging and determination of molecular orientations offer insight into structural organization of the sample. SRFLM is compatible with living samples and

  2. Single molecule studies of DNA packaging by bacteriophages

    Fuller, Derek Nathan

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

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

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

    2009-06-04

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

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

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

    2012-01-01

    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 spectroscop...

  5. Injection molded nanofluidic chips: Fabrication method and functional tests using single-molecule DNA experiments

    Utko, Pawel; Persson, Karl Fredrik; Kristensen, Anders;

    2011-01-01

    We demonstrate that fabrication of nanofluidic systems can be greatly simplified by injection molding of polymers. We functionally test our devices by single-molecule DNA experiments in nanochannels.......We demonstrate that fabrication of nanofluidic systems can be greatly simplified by injection molding of polymers. We functionally test our devices by single-molecule DNA experiments in nanochannels....

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

    Zhang, Jingdong; Chi, Qijin; Albrecht, Tim;

    2005-01-01

    Surface structures controlled at the nanometer and single-molecule levels, with functions crucially determined by interfacial electron transfer (ET) are broadly reported in recent years, with different kinds of electrochemically controlled nanoscale/single molecule systems. One is the broad class...

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

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

    2012-01-01

    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 d

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

    Glaser, Thorsten

    2011-01-01

    Since the discovery that Mn(12)OAc acts as a single-molecule magnet (SMM), an increasing number of transition metal complexes have been demonstrated to behave as SMMs. The signature of a SMM is a slow relaxation of the magnetization at low temperatures accompanied by a magnetic hysteresis. The origin of SMM behaviour is the existence of an appreciable thermal barrier U for spin-reversal called magnetic anisotropy barrier which is related to the combination of a large total spin ground state (S(t)) and an easy-axis magnetic anisotropy. The extensive research on Mn(12)OAc and other SMMs has established more prerequisites for a rational development of new SMMs besides the high-spin ground state and the magnetic anisotropy: the symmetry should be at least C(3) to minimize the quantum tunneling of the magnetization through the anisotropy barrier but lower than cubic to avoid the cancellation of the local anisotropies upon projection onto the spin ground state. Based on these prerequisites, we have designed the ligand triplesalen which combines the phloroglucinol bridging unit for high spin ground states by the spin-polarization mechanism with a salen-like ligand environment for single-site magnetic anisotropies by a strong tetragonal ligand field. The C(3) symmetric, trinuclear complexes of the triplesalen ligand (talen(t-Bu(2)))(6-) exhibit a strong ligand folding resulting in an overall bowl-shaped molecular structure. This ligand folding preorganizes the axial coordination sites of the metal salen subunits for the complementary binding of three facial nitrogen atoms of a hexacyanometallate unit. This leads to a high driving force for the formation of heptanuclear complexes [M(t)(6)M(c)](n+) by the assembly of three molecular building blocks. Attractive van der Waals interactions of the tert-butyl phenyl units of two triplesalen trinuclear building blocks increase the driving force. In this respect, we have been able to synthesize the isostructural series [Mn(III)(6

  9. An Organolanthanide Building Block Approach to Single-Molecule Magnets.

    Harriman, Katie L M; Murugesu, Muralee

    2016-06-21

    Single-molecule magnets (SMMs) are highly sought after for their potential application in high-density information storage, spintronics, and quantum computing. SMMs exhibit slow relaxation of the magnetization of purely molecular origin, thus making them excellent candidates towards the aforementioned applications. In recent years, significant focus has been placed on the rare earth elements due to their large intrinsic magnetic anisotropy arising from the near degeneracy of the 4f orbitals. Traditionally, coordination chemistry has been utilized to fabricate lanthanide-based SMMs; however, heteroatomic donor atoms such as oxygen and nitrogen have limited orbital overlap with the shielded 4f orbitals. Thus, control over the anisotropic axis and induction of f-f interactions are limited, meaning that the performance of these systems can only extend so far. To this end, we have placed considerable attention on the development of novel SMMs whose donor atoms are conjugated hydrocarbons, thereby allowing us to perturb the crystal field of lanthanide ions through the use of an electronic π-cloud. This approach allows for fine tuning of the anisotropic axis of the molecule, allowing this method the potential to elicit SMMs capable of reaching much larger values for the two vital performance measurements of an SMM, the energy barrier to spin reversal (Ueff), and the blocking temperature of the magnetization (TB). In this Account, we describe our efforts to exploit the inherent anisotropy of the late 4f elements; namely, Dy(III) and Er(III), through the use of cyclooctatetraenyl (COT) metallocenes. With respect to the Er(III) derivatives, we have seen record breaking success, reaching blocking temperatures as high as 14 K with frozen solution magnetometry. These results represent the first example of such a high TB being observed for a system with only a single spin center, formally known as a single-ion magnet (SIM). Our continued interrelationship between theoretical

  10. Dependence of tunneling current through a single molecule of phenylene oligomers on the molecular length.

    Wakamatsu, Satoshi; Fujii, Shintaro; Akiba, Uichi; Fujihira, Masamichi

    2003-01-01

    The electrical properties of single phenylene oligomers were studied in terms of the dependence of the tunneling current on the length of the oligomers using self-assembling techniques and scanning tunneling microscopy (STM). It is important to isolate single molecules in an insulating matrix for the measurement of the conductivity of the single molecule. We demonstrate here a novel self-assembled monolayer (SAM) matrix appropriate for isolation of the single molecules. A bicyclo[2.2.2]octane derivative was used for a SAM matrix, in which the single molecules were inserted at molecular lattice defects. The isolated single molecules of phenylene oligomers inserted in the SAM matrix were observed as protrusions in STM topography using a constant current mode. We measured the topographic heights of the molecular protrusions using STM and estimated the decay constant, beta, of the tunneling current through the single phenylene oligomers using a bilayer tunnel junction model. PMID:12801653

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

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

    2015-03-27

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

  12. Optical tweezers absolute calibration

    Dutra, R S; Neto, P A Maia; Nussenzveig, H M

    2014-01-01

    Optical tweezers are highly versatile laser traps for neutral microparticles, with fundamental applications in physics and in single molecule cell biology. Force measurements are performed by converting the stiffness response to displacement of trapped transparent microspheres, employed as force transducers. Usually, calibration is indirect, by comparison with fluid drag forces. This can lead to discrepancies by sizable factors. Progress achieved in a program aiming at absolute calibration, conducted over the past fifteen years, is briefly reviewed. Here we overcome its last major obstacle, a theoretical overestimation of the peak stiffness, within the most employed range for applications, and we perform experimental validation. The discrepancy is traced to the effect of primary aberrations of the optical system, which are now included in the theory. All required experimental parameters are readily accessible. Astigmatism, the dominant effect, is measured by analyzing reflected images of the focused laser spo...

  13. Investigation of photobleaching and saturation of single molecules by fluorophore recrossing events

    A method for investigation of photobleaching and saturation of single molecules by fluorophore recrossing events in a laser beam is described. The diffraction-limited probe volumes encountered in single-molecule detection (SMD) produce high excitation irradiance, which can decrease available signal. The single molecules of several dyes were detected and the data was used to extract interpeak times above a defined threshold value. The interpeak times revealed the number of fluorophore recrossing events. The number of molecules detected that were within 2 ms of each other represented a molecular recrossing for this work. Calcein, fluorescein and R-phycoerythrin were analyzed and the saturation irradiance and photobleaching effects were determined as a function of irradiance. This approach is simple and it serves as a method of optimizing experimental conditions for single-molecule detection

  14. Investigation of photobleaching and saturation of single molecules by fluorophore recrossing events

    Burrows, Sean M.; Reif, Randall D. [Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061 (United States); Pappas, Dimitri [Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061 (United States)], E-mail: d.pappas@ttu.edu

    2007-08-15

    A method for investigation of photobleaching and saturation of single molecules by fluorophore recrossing events in a laser beam is described. The diffraction-limited probe volumes encountered in single-molecule detection (SMD) produce high excitation irradiance, which can decrease available signal. The single molecules of several dyes were detected and the data was used to extract interpeak times above a defined threshold value. The interpeak times revealed the number of fluorophore recrossing events. The number of molecules detected that were within 2 ms of each other represented a molecular recrossing for this work. Calcein, fluorescein and R-phycoerythrin were analyzed and the saturation irradiance and photobleaching effects were determined as a function of irradiance. This approach is simple and it serves as a method of optimizing experimental conditions for single-molecule detection.

  15. Single-molecule detection using continuous wave excitation of two-photon fluorescence

    Hou, Ximiao; Cheng, Wei

    2011-08-01

    Two-photon fluorescence (TPF) is one of the most important discoveries for biological imaging. Although a cw laser is known to excite TPF, its application in TPF imaging has been very limited due to the perceived low efficiency of excitation. Here we directly excited fluorophores with an IR cw laser used for optical trapping and achieved single-molecule fluorescence sensitivity: discrete stepwise photobleaching of enhanced green fluorescent proteins was observed. The single-molecule fluorescence intensity analysis and on-time distribution strongly indicate that a cw laser can generate TPF detectable at the single-molecule level, and thus opens the door to single-molecule TPF imaging using cw lasers.

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

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

    2015-02-21

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

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

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

    2016-05-01

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

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

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

    2016-03-01

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

  19. Nanopore Detector based analysis of single-molecule conformational kinetics and binding interactions

    Winters-Hilt Stephen

    2006-01-01

    Abstract Background A Nanopore Detector provides a means to transduce single molecule events into observable channel current changes. Nanopore-based detection can report directly, or indirectly, on single molecule kinetics. The nanopore-based detector can directly measure molecular characteristics in terms of the blockade properties of individual molecules – this is possible due to the kinetic information that is embedded in the blockade measurements, where the adsorption-desorption history o...

  20. Image Analysis of Defocused Single-molecule Images for Three-dimensional Molecule Orientation Studies

    Patra, D; Gregor, I.; Enderlein, J.

    2004-01-01

    An efficient algorithm for pattern matching has been developed based on least-squares analysis of fitting a discrete set of master patterns against measured images. This algorithm has been applied to determine three-dimensional molecule orientations in defocused single-molecule images. The developed algorithm exploits the excellent agreement between electrodynamic calculations of single-molecule emission and experimentally measured images. The procedure is found to be reliable and simple and ...

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

    Surface structures controlled at the nanometer and single-molecule levels, with functions crucially determined by interfacial electron transfer (ET) are broadly reported in recent years, with different kinds of electrochemically controlled nanoscale/single molecule systems. One is the broad class of metallic and semiconductor-based nanoparticles, nano-arrays, nanotubes, and nanopits. Others are based on self-assembled molecular monolayers. The latter extend to bioelectrochemical systems with redox metalloproteins and DNA-based molecules as targets. We overview here some recent achievements in areas of interfacial electrochemical ET systems, mapped to the nanoscale and single-molecule levels. Focus is on both experimental and theoretical studies in our group. Systems addressed are organized monolayers of redox active transition metal complexes, and metalloproteins and metalloenzymes on single-crystal Au(1 1 1)-electrode surfaces. These systems have been investigated by voltammetry, spectroscopy, microcantilever technology, and scanning probe microscopy. A class of Os-complexes has shown suitable as targets for electrochemical in situ scanning tunnelling microscopy (STM), with close to single-molecule scanning tunnelling spectroscopic (STS) features. Mapping of redox metalloproteins from the three major classes, i.e. blue copper proteins, heme proteins, and iron-sulfur proteins, at the monolayer and single-molecule levels have also been achieved. In situ STM and spectroscopy of redox molecules and biomolecules have been supported by new theoretical frames, which extend established theory of interfacial electrochemical ET. The electrochemical nanoscale and single-molecule systems discussed are compared with other recent nanoscale and single-molecule systems with conspicuous device-like properties, particularly unimolecular rectifiers and single-molecule transistors. Both of these show analogies to electrochemical in situ STM features of redox molecules and

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

    Sherif, Siya; Rubio-Bollinger, G.; Pinilla-Cienfuegos, E.; Coronado, E.; Cuevas, J. C.; Agrait, Nicolas

    2015-01-01

    We demonstrate large rectification ratios (> 100) in single-molecule junctions based on a metal-oxide cluster (polyoxometalate), using a scanning tunneling microscope (STM) both at ambient conditions and at low temperature. These rectification ratios are the largest ever observed in a single-molecule junction, and in addition these junctions sustain current densities larger than 10^5 A/cm^2. By following the variation of the I-V characteristics with tip-molecule separation we demonstrate unam...

  3. DNA origami as a tool for single-molecule fluorescence studies

    Stein, Ingo

    2012-01-01

    Single-molecule fluorescence studies have become a routine practice in laboratories worldwide. As an experimental tool, especially fluorescence resonance energy transfer (FRET) has helped to unravel conformational changes and interactions of biomolecules. With the DNA origami method a new technique to create nanoscale shapes with DNA as a building material was recently introduced. As shown in this work, DNA nanotechnology can be readily combined with single-molecule FRET experiments, opening ...

  4. Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins

    Nettels, D; Muller-Spath, S.; Kuster, F.; Hofmann, H.; Haenni, D.; Ruegger, S.; Reymond, L.; Hoffmann, A.; Kubelka, J.; Heinz, B.; Gast, K.; Best, R. B.; Schuler, B

    2009-01-01

    We used single-molecule FRET in combination with other biophysical methods and molecular simulations to investigate the effect of temperature on the dimensions of unfolded proteins. With single-molecule FRET, this question can be addressed even under near-native conditions, where most molecules are folded, allowing us to probe a wide range of denaturant concentrations and temperatures. We find a compaction of the unfolded state of a small cold shock protein with increasing temperature in both...

  5. Bi-Analyte Surface Enhanced Raman Scattering for unambiguous evidence of single molecule detection

    Le Ru, E C; Meyer, M

    2005-01-01

    A method is proposed to pin down an unambiguous proof for single molecule surface enhanced Raman spectroscopy (SERS). The simultaneous use of two analyte molecules enables a clear confirmation of the single (or few) molecule nature of the signals. This method eliminates most of the uncertainties associated with low dye concentrations in previous experiments. It further shows that single-molecule signals are very common in SERS, both in liquids and on dry substrates.

  6. Photonic Methods to Enhance Fluorescence Correlation Spectroscopy and Single Molecule Fluorescence Detection

    Hervé Rigneault; Jérome Wenger

    2010-01-01

    Recent advances in nanophotonics open the way for promising applications towards efficient single molecule fluorescence analysis. In this review, we discuss how photonic methods bring innovative solutions for two essential questions: how to detect a single molecule in a highly concentrated solution, and how to enhance the faint optical signal emitted per molecule? The focus is set primarily on the widely used technique of fluorescence correlation spectroscopy (FCS), yet the discussion can be ...

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

    Professor William Moerner

    2010-07-09

    The 2010 Gordon Conference on Single-Molecule Approaches to Biology focuses on cutting-edge research in single-molecule science. Tremendous technical developments have made it possible to detect, identify, track, and manipulate single biomolecules in an ambient environment or even in a live cell. Single-molecule approaches have changed the way many biological problems are addressed, and new knowledge derived from these approaches continues to emerge. The ability of single-molecule approaches to avoid ensemble averaging and to capture transient intermediates and heterogeneous behavior renders them particularly powerful in elucidating mechanisms of biomolecular machines: what they do, how they work individually, how they work together, and finally, how they work inside live cells. The burgeoning use of single-molecule methods to elucidate biological problems is a highly multidisciplinary pursuit, involving both force- and fluorescence-based methods, the most up-to-date advances in microscopy, innovative biological and chemical approaches, and nanotechnology tools. This conference seeks to bring together top experts in molecular and cell biology with innovators in the measurement and manipulation of single molecules, and will provide opportunities for junior scientists and graduate students to present their work in poster format and to exchange ideas with leaders in the field. A number of excellent poster presenters will be selected for short oral talks. Topics as diverse as single-molecule sequencing, DNA/RNA/protein interactions, folding machines, cellular biophysics, synthetic biology and bioengineering, force spectroscopy, new method developments, superresolution imaging in cells, and novel probes for single-molecule imaging will be on the program. Additionally, the collegial atmosphere of this Conference, with programmed discussion sessions as well as opportunities for informal gatherings in the afternoons and evenings in the beauty of the Il Ciocco site in

  8. Single-molecule investigations of the stringent response machinery in living bacterial cells

    English, Brian P.; Hauryliuk, Vasili; Sanamrad, Arash; Tankov, Stoyan; Dekker, Nynke H.; Elf, Johan

    2011-01-01

    The RelA-mediated stringent response is at the heart of bacterial adaptation to starvation and stress, playing a major role in the bacterial cell cycle and virulence. RelA integrates several environmental cues and synthesizes the alarmone ppGpp, which globally reprograms transcription, translation, and replication. We have developed and implemented novel single-molecule tracking methodology to characterize the intracellular catalytic cycle of RelA. Our single-molecule experiments show that Re...

  9. Single-molecule Michaelis-Menten kinetics: Effect of substrate fluctuations

    In this work we have simulated a stochastic model of single-molecule enzymatic kinetics and applied several statistics to find whether substrate fluctuations can cause significant deviations from the standard single-molecule Michaelis-Menten kinetics. We have found that substrate fluctuations can be detected under favorable conditions (i.e. for fast irreversible binding) when long turnover time trajectories are analyzed. However, for reversible and/or slow intrinsic binding substrate fluctuations may be difficult to observe experimentally

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

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

    2015-09-01

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

  11. Metal-Catalyzed Chemical Reaction of Single Molecules Directly Probed by Vibrational Spectroscopy.

    Choi, Han-Kyu; Park, Won-Hwa; Park, Chan-Gyu; Shin, Hyun-Hang; Lee, Kang Sup; Kim, Zee Hwan

    2016-04-01

    The study of heterogeneous catalytic reactions remains a major challenge because it involves a complex network of reaction steps with various intermediates. If the vibrational spectra of individual molecules could be monitored in real time, one could characterize the structures of the intermediates and the time scales of reaction steps without ensemble averaging. Surface-enhanced Raman scattering (SERS) spectroscopy does provide vibrational spectra with single-molecule sensitivity, but typical single-molecule SERS signals exhibit spatial heterogeneities and temporal fluctuations, making them difficult to be used in single-molecule kinetics studies. Here we show that SERS can monitor the single-molecule catalytic reactions in real time. The surface-immobilized reactants placed at the junctions of well-defined nanoparticle-thin film structures produce time-resolved SERS spectra with discrete, step-transitions of photoproducts. We interpret that such SERS-steps correspond to the reaction events of individual molecules occurring at the SERS hotspot. The analyses of the yield, dynamics, and the magnitude of such SERS steps, along with the associated spectral characteristics, fully support our claim. In addition, a model that is based on plasmonic field enhancement and surface photochemistry reproduces the key features of experimental observation. Overall, the result demonstrates that it is possible, under well-controlled conditions, to differentiate the chemical and physical processes contributing to the single-molecule SERS signals, and thus shows the use of single-molecule SERS as a tool for studying the metal-catalyzed organic reactions. PMID:26964567

  12. Multi-period Mean-absolute Deviation Fuzzy Portfolio Selection Model with Entropy Constraints%具有熵约束的多阶段均值-绝对偏差模糊投资组合决策

    张鹏; 张卫国; 曾玉婷

    2016-01-01

    文章运用可能性绝对偏差和比例熵分别度量风险和分散化程度,提出了具有风险控制和线性交易成本的终期财富最大化的多阶段模糊投资组合模型。运用可能理论,将该模型转化为显示的非线性动态优化问题。由于投资过程存在交易成本,上述模型为具有路径依赖性的动态优化问题。文章提出了前向动态规划方法求解。最后,通过实证研究比较了不同熵的取值投资组合最优投资比例和最终财富的变化。%This paper considers a multi-period fuzzy portfolio selection problem maximizing the terminal wealth imposed by risk control, in which risk of assets and the divergence measure of portfolio are, respectively, meas-ured by fuzzy absolute deviation and proportion entropy.Based on the theories of possibility theory, the proposed model is transformed into a crisp nonlinear programming problem.Because of the transaction costs, the multi-period portfolio selection is a dynamic optimization problem with path dependence.Furthermore, a forward dynamic programming method is designed to obtain the optimal portfolio strategy.Finally, an example is given to illustrate the behavior of the proposed model and the designed algorithm.

  13. Multicolour single molecule imaging in cells with near infra-red dyes.

    Christopher J Tynan

    Full Text Available BACKGROUND: The autofluorescence background of biological samples impedes the detection of single molecules when imaging. The most common method of reducing the background is to use evanescent field excitation, which is incompatible with imaging beyond the surface of biological samples. An alternative would be to use probes that can be excited in the near infra-red region of the spectrum, where autofluorescence is low. Such probes could also increase the number of labels that can be imaged in multicolour single molecule microscopes. Despite being widely used in ensemble imaging, there is a currently a shortage of information available for selecting appropriate commercial near infra-red dyes for single molecule work. It is therefore important to characterise available near infra-red dyes relevant to multicolour single molecule imaging. METHODOLOGY/PRINCIPAL FINDINGS: A range of commercially available near infra-red dyes compatible with multi-colour imaging was screened to find the brightest and most photostable candidates. Image series of immobilised samples of the brightest dyes (Alexa 700, IRDye 700DX, Alexa 790 and IRDye 800CW were analysed to obtain the mean intensity of single dye molecules, their photobleaching rates and long period blinking kinetics. Using the optimum dye pair, we have demonstrated for the first time widefield, multi-colour, near infra-red single molecule imaging using a supercontinuum light source in MCF-7 cells. CONCLUSIONS/SIGNIFICANCE: We have demonstrated that near infra-red dyes can be used to avoid autofluorescence background in samples where restricting the illumination volume of visible light fails or is inappropriate. We have also shown that supercontinuum sources are suited to single molecule multicolour imaging throughout the 470-1000 nm range. Our measurements of near infra-red dye properties will enable others to select optimal dyes for single molecule imaging.

  14. Single-molecule interfacial electron transfer in donor-bridge-nanoparticle acceptor complexes.

    Jin, Shengye; Snoeberger, Robert C; Issac, Abey; Stockwell, David; Batista, Victor S; Lian, Tianquan

    2010-11-18

    Photoinduced interfacial electron transfer (IET) in sulforhodamine B (SRhB)-aminosilane-Tin oxide (SnO(2)) nanoparticle donor-bridge-acceptor complexes has been studied on a single molecule and ensemble average level. On both SnO(2) and ZrO(2), the sum of single molecule fluorescence decays agree with the ensemble average results, suggesting complete sampling of molecules under single molecule conditions. Shorter fluorescence lifetime on SnO(2) than on ZrO(2) is observed and attributed to IET from SRhB to SnO(2). Single molecule lifetimes fluctuate with time and vary among different molecules, suggesting both static and dynamic IET heterogeneity in this system. Computational modeling of the complexes shows a distribution of molecular conformation, leading to a distribution of electronic coupling strengths and ET rates. It is likely that the conversion between these conformations led to the fluctuation of ET rate and fluorescence lifetime on the single molecule level. PMID:20225886

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

    Moerner, W. E. William E.

    2015-10-01

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

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

    Rombach-Riegraf, Verena; Oswald, Peter; Bienert, Roland; Petersen, Jan [Albert-Ludwigs-Universitaet Freiburg, Institut fuer Physikalische Chemie, Albertstrasse 23a, 79104 Freiburg (Germany); Domingo, M.P. [Instituto de Carboquimica (CSIC), Miguel Luesma 4, 50018 Zaragoza (Spain); Pardo, Julian [Grupo Apoptosis, Inmunidad y Cancer, Departamento Bioquimica y Biologia Molecular y Celular, Fac. Ciencias, Universidad de Zaragoza, Zaragoza (Spain); Fundacion Aragon I-D (ARAID), Gobierno de Aragon, Zaragoza (Spain); Immune Effector Cells Group, Aragon Health Research Institute (IIS Aragon), Biomedical Research Centre of Aragon (CIBA) Fundacion Aragon I-D - ARAID, Gobierno de Aragon, Zaragoza (Spain); Graeber, P. [Albert-Ludwigs-Universitaet Freiburg, Institut fuer Physikalische Chemie, Albertstrasse 23a, 79104 Freiburg (Germany); Galvez, E.M., E-mail: eva@icb.csic.es [Instituto de Carboquimica (CSIC), Miguel Luesma 4, 50018 Zaragoza (Spain); Immune Effector Cells Group, Aragon Health Research Institute (IIS Aragon), Biomedical Research Centre of Aragon (CIBA) Fundacion Aragon I-D - ARAID, Gobierno de Aragon, Zaragoza (Spain)

    2013-01-04

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

  17. Bekenstein Entropy is String Entropy

    Halyo, Edi

    2009-01-01

    We argue that Bekenstein entropy can be interpreted as the entropy of an effective string with a rescaled tension. Using the AdS/CFT correspondence we show that the Bekenstein entropy on the boundary CFT is given by the entropy of a string at the stretched horizon of the AdS black hole in the bulk. The gravitationally redshifted tension and energy of the string match those required to reproduce Bekenstein entropy.

  18. Single molecule detection using charge-coupled device array technology. Technical progress report

    Denton, M.B.

    1992-07-29

    A technique for the detection of single fluorescent chromophores in a flowing stream is under development. This capability is an integral facet of a rapid DNA sequencing scheme currently being developed by Los Alamos National Laboratory. In previous investigations, the detection sensitivity was limited by the background Raman emission from the water solvent. A detection scheme based on a novel mode of operating a Charge-Coupled Device (CCD) is being developed which should greatly enhance the discrimination between fluorescence from a single molecule and the background Raman scattering from the solvent. Register shifts between rows in the CCD are synchronized with the sample flow velocity so that fluorescence from a single molecule is collected in a single moving charge packet occupying an area approaching that of a single pixel while the background is spread evenly among a large number of pixels. Feasibility calculations indicate that single molecule detection should be achieved with an excellent signal-to-noise ratio.

  19. Single-molecule three-color FRET with both negligible spectral overlap and long observation time.

    Sanghwa Lee

    Full Text Available Full understanding of complex biological interactions frequently requires multi-color detection capability in doing single-molecule fluorescence resonance energy transfer (FRET experiments. Existing single-molecule three-color FRET techniques, however, suffer from severe photobleaching of Alexa 488, or its alternative dyes, and have been limitedly used for kinetics studies. In this work, we developed a single-molecule three-color FRET technique based on the Cy3-Cy5-Cy7 dye trio, thus providing enhanced observation time and improved data quality. Because the absorption spectra of three fluorophores are well separated, real-time monitoring of three FRET efficiencies was possible by incorporating the alternating laser excitation (ALEX technique both in confocal microscopy and in total-internal-reflection fluorescence (TIRF microscopy.

  20. Plasmonic nanopore-based platforms for single-molecule Raman scattering

    Deng, Liang; Wang, Yixin; Liu, Chen; Hu, Dora Juan Juan; Shum, Perry Ping; Su, Lei

    2016-08-01

    We propose and demonstrate a novel plasmonic nanopore platform based on a bowtie-nanopore structure, for single-molecule sensing. In this nano-structure, nano-bowties are integrated with solid-state nanopores to provide localized surface plasmon resonances for signal enhancement. We design and optimize the nano-structure by tuning both the bowtie gap and the bowtie angle, and investigate their influences on field enhancement, thereby achieving single-molecule sensitivity. In addition, we study the field enhancement by introducing an engineered photonic nano-cavity. This further strengthens the electric enhancement. An overall Raman enhancement factor of 2×108 is achieved in our simulation. This is believed to be sufficient for single-molecule sensing. The proposed bowtie-nanopore structure can be multiplexed on a single substrate for simultaneous multi-channel detection, paving the way for demanding applications such as DNA sequencing.

  1. Nanopore sensing at ultra-low concentrations using single-molecule dielectrophoretic trapping

    Freedman, Kevin J.; Otto, Lauren M.; Ivanov, Aleksandar P.; Barik, Avijit; Oh, Sang-Hyun; Edel, Joshua B.

    2016-01-01

    Single-molecule techniques are being developed with the exciting prospect of revolutionizing the healthcare industry by generating vast amounts of genetic and proteomic data. One exceptionally promising route is in the use of nanopore sensors. However, a well-known complexity is that detection and capture is predominantly diffusion limited. This problem is compounded when taking into account the capture volume of a nanopore, typically 108-1010 times smaller than the sample volume. To rectify this disproportionate ratio, we demonstrate a simple, yet powerful, method based on coupling single-molecule dielectrophoretic trapping to nanopore sensing. We show that DNA can be captured from a controllable, but typically much larger, volume and concentrated at the tip of a metallic nanopore. This enables the detection of single molecules at concentrations as low as 5 fM, which is approximately a 103 reduction in the limit of detection compared with existing methods, while still maintaining efficient throughput.

  2. Orbital-selective single molecule excitation and spectroscopy based on plasmon-exciton coupling

    Imada, Hiroshi; Imai-Imada, Miyabi; Kawahara, Shota; Kimura, Kensuke; Kim, Yousoo

    2016-01-01

    The electronic excitation of molecules triggers diverse phenomena such as luminescence and photovoltaic effects, which are the bases of various energy-converting devices. Understanding and control of the excitations at the single-molecule level are long standing targets, however, they have been hampered by the limited spatial resolution in optical probing techniques. Here we investigate the electronic excitation of a single molecule with sub-molecular precision using a localised plasmon at the tip apex of a scanning tunnelling microscope (STM) as an excitation probe. Coherent energy transfer between the plasmon and molecular excitons is discovered when the plasmon is located in the proximity of isolated molecules, which is corroborated by a theoretical analysis. The polarised plasmonic field enables selective excitation of an electronic transition between anisotropic frontier molecular orbitals. Our findings have established the foundation of a novel single-molecule spectroscopy with STM, providing an integra...

  3. Shedding light on protein folding, structural and functional dynamics by single molecule studies

    Bavishi, Krutika; Hatzakis, Nikos

    2014-01-01

    in non-synchronized ensemble measurements. Single molecule studies have thus provided novel insights about how the dynamic sampling of the free energy landscape dictates all aspects of protein behavior; from its folding to function. Here we will survey some of the state of the art contributions in...... deciphering mechanisms that underlie protein folding, structural and functional dynamics by single molecule fluorescence microscopy techniques. We will discuss a few selected examples highlighting the power of the emerging techniques and finally discuss the future improvements and directions.......The advent of advanced single molecule measurements unveiled a great wealth of dynamic information revolutionizing our understanding of protein dynamics and behavior in ways unattainable by conventional bulk assays. Equipped with the ability to record distribution of behaviors rather than the mean...

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

    Lambert, C J

    2015-02-21

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

  5. Structure from Fleeting Illumination of Faint Spinning Objects in Flight with Application to Single Molecules

    Fung, Russell; Saldin, Dilano K; Ourmazd, Abbas

    2008-01-01

    There are many instances when the structure of a weakly-scattering spinning object in flight must be determined to high resolution. Examples range from comets to nanoparticles and single molecules. The latter two instances are the subject of intense current interest. Substantial progress has recently been made in illuminating spinning single particles in flight with powerful X-ray bursts to determine their structure with the ultimate goal of determining the structure of single molecules. However, proposals to reconstruct the molecular structure from diffraction "snapshots" of unknown orientation require ~1000x more signal than available from next-generation sources. Using a new approach, we demonstrate the recovery of the structure of a weakly scattering macromolecule at the anticipated next-generation X-ray source intensities. Our work closes a critical gap in determining the structure of single molecules and nanoparticles by X-ray methods, and opens the way to reconstructing the structure of spinning, or ra...

  6. Biophysical Insights from Temperature-Dependent Single-Molecule Förster Resonance Energy Transfer

    Holmstrom, Erik D.; Nesbitt, David J.

    2016-05-01

    Single-molecule fluorescence microscopy techniques can be used in combination with micrometer length-scale temperature control and Förster resonance energy transfer (FRET) in order to gain detailed information about fundamental biophysical phenomena. In particular, this combination of techniques has helped foster the development of remarkable quantitative tools for studying both time- and temperature-dependent structural kinetics of biopolymers. Over the past decade, multiple research efforts have successfully incorporated precise spatial and temporal control of temperature into single-molecule FRET (smFRET)-based experiments, which have uncovered critical thermodynamic information on a wide range of biological systems such as conformational dynamics of nucleic acids. This review provides an overview of various temperature-dependent smFRET approaches from our laboratory and others, highlighting efforts in which such methods have been successfully applied to studies of single-molecule nucleic acid folding.

  7. Single-molecule conductance with nitrile and amino contacts with Ag or Cu electrodes

    The single-molecule conductance of 1,4-dicyanobenzene (DCB), 1,4-benzenediamine (BDA) and 4,4'-biphenyldicarbonitrile (BPDC) with Ag and/or Cu electrodes is measured by electrochemical jump-to-contact STM-break junction. All single-molecule junctions present three sets of conductance values revealing different contact geometries. We observe that the single-molecule conductance of Ag-BDA-Ag junction is larger that of Ag-DCB-Ag junction, and DCB with Ag contacts are more conductive than that with Cu ones. This is related to a different electronic coupling between the molecules and the electrodes. Tunneling decay constants of 1.70 and 1.68 per phenyl group were found for Ag and Cu electrodes, respectively. The present study therefore shows that nitrile and amino groups can also be used as effective anchors for other metals than gold

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

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

    2016-03-01

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

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

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

    2016-03-01

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

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

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

    2016-03-21

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

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

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

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

    Ruiyun Chen

    2014-02-01

    Full Text Available 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.

  13. Coherent Interaction of Light and Single Molecules in a Dielectric Nanoguide

    Faez, Sanli; Haakh, Harald R; Götzinger, Stephan; Sandoghdar, Vahid

    2014-01-01

    We present a new scheme for performing optical spectroscopy on single molecules. A glass capillary with a diameter of 600 nm filled with an organic crystal tightly guides the excitation light and provides a maximum spontaneous emission coupling factor ($\\beta$) of 18% for the dye molecules doped in the organic crystal. Combination of extinction, fluorescence excitation and resonance fluorescence spectroscopy with microscopy provides high-resolution spatio-spectral access to a very large number of single molecules in a linear geometry. We discuss strategies for exploring a range of quantum optical phenomena, including coherent cooperative interactions in a mesoscopic ensemble of molecules mediated by a single mode of propagating photons.

  14. Alternating Laser Excitation for Solution-Based Single-Molecule FRET.

    Kapanidis, Achillefs; Majumdar, Devdoot; Heilemann, Mike; Nir, Eyal; Weiss, Shimon

    2015-11-01

    Single-molecule fluorescence resonance energy transfer (smFRET) has been widely applied to the study of fluorescently labeled biomolecules on surfaces and in solution. Sorting single molecules based on fluorescent dye stoichiometry provides one with further layers of information and also enables "filtering" of unwanted molecules from the analysis. We accomplish this sorting by using alternating laser excitation (ALEX) in combination with smFRET measurements; here we describe the implementation of these methodologies for the study of biomolecules in solution. PMID:26527772

  15. Single molecule experiments challenge the strict wave-particle dualism of light.

    Greulich, Karl Otto

    2010-01-01

    Single molecule techniques improve our understanding of the photon and light. If the single photon double slit experiment is performed at the "single photon limit" of a multi-atom light source, faint light pulses with more than one photon hamper the interpretation. Single molecules, quantum dots or defect centres in crystals should be used as light source. "Single photon detectors" do not meet their promise-only "photon number resolving single photon detectors" do so. Particularly, the accumulation time argument, the only safe basis for the postulate of a strictly particle like photon, has so far not yet been verified. PMID:20162017

  16. Single Molecule Experiments Challenge the Strict Wave-Particle Dualism of Light

    Karl Otto Greulich

    2010-01-01

    Full Text Available Single molecule techniques improve our understanding of the photon and light. If the single photon double slit experiment is performed at the “single photon limit” of a multi-atom light source, faint light pulses with more than one photon hamper the interpretation. Single molecules, quantum dots or defect centres in crystals should be used as light source. “Single photon detectors” do not meet their promise―only “photon number resolving single photon detectors” do so. Particularly, the accumulation time argument, the only safe basis for the postulate of a strictly particle like photon, has so far not yet been verified.

  17. Electric Field Induced Fluorescence Modulation of Single Molecules in PMMA Based on Electron Transfer

    Suotang Jia

    2012-09-01

    Full Text Available We present a method to modulate the fluorescence of non-polar single squaraine-derived rotaxanes molecules embedded in a polar poly(methyl methacrylate (PMMA matrix under an external electric field. The electron transfer between single molecules and the electron acceptors in a PMMA matrix contributes to the diverse responses of fluorescence intensities to the electric field. The observed instantaneous and non-instantaneous electric field dependence of single-molecule fluorescence reflects the redistribution of electron acceptors in PMMA induced by electronic polarization and orientation polarization of polar polymer chains in an electric field.

  18. Intersystem Crossing Mechanisms and Single Molecule Fluorescence: Terrylene in Anthracene Crystals

    Single molecule spectroscopy requires molecules with low triplet yields and/or short triplet lifetimes. The intersystem crossing (ISC) rate may be dramatically enhanced by the host matrix. Comparing the fluorescence intensity of single terrylene molecules in para-terphenyl, naphthalene, and anthracene crystals, we found a reduction of the saturation intensity by three orders of magnitude in the latter case. The fluorescence autocorrelation function indicates that the bottleneck state is the terrylene triplet. We propose a ping-pong mechanism between host and guest. This intermolecular ISC mechanism, which can open whenever the host triplet lies lower than the guest singlet, was overlooked in previous single molecule investigations

  19. Time, absolute.

    Mughal, Muhammad Aurang Zeb

    2009-01-01

    The concept of absolute time is a hypothetical model from the laws of classical physics postulated by Isaac Newton in the Principia in 1687. Although the Newtonian model of absolute time has since been opposed and rejected in light of more recent scholarship, it still provides a way to study science with reference to time and understand the phenomena of time within the scientific tradition. According to this model, it is assumed that time runs at the same rate for all the observers in the uni...

  20. The Relation between Structure and Quantum Interference in Single Molecule Junctions

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

    2010-01-01

    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 guideli...... wires....

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

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

    2016-05-24

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

  2. Ninth international conference on hole burning, single molecule and related spectroscopies: science and applications (HBSM 2006)

    This conference was organized around 9 sessions: -) single molecule, -) quantum optics, -) hole-burning materials and mechanisms, -) single nano-particle spectroscopy, -) dephasing and spectral diffusion, -) microwave photonics, -) biological systems, -) rare earth doped materials, -) novel laser sources. This document gathers only the slides of the presentations

  3. Theoretical Investigation of a Single Molecule Device:Geometrical Configurations and Electronic Properties

    YUAN Zhe; SU Chang-Rong; ZHANG Shi-Zhong; LI Jia-Ming

    2004-01-01

    @@ Using the first-principle molecular dynamics simulations, we have studied the molecular geometrical configurations as well as the corresponding electronic structures of a single molecule device assembled by the mechanically controllable break junction technique with variations of the electrode distance. There are some very interesting features varying with the electrode distance.

  4. Shedding Light on Protein Folding, Structural and Functional Dynamics by Single Molecule Studies

    Krutika Bavishi

    2014-11-01

    Full Text Available The advent of advanced single molecule measurements unveiled a great wealth of dynamic information revolutionizing our understanding of protein dynamics and behavior in ways unattainable by conventional bulk assays. Equipped with the ability to record distribution of behaviors rather than the mean property of a population, single molecule measurements offer observation and quantification of the abundance, lifetime and function of multiple protein states. They also permit the direct observation of the transient and rarely populated intermediates in the energy landscape that are typically averaged out in non-synchronized ensemble measurements. Single molecule studies have thus provided novel insights about how the dynamic sampling of the free energy landscape dictates all aspects of protein behavior; from its folding to function. Here we will survey some of the state of the art contributions in deciphering mechanisms that underlie protein folding, structural and functional dynamics by single molecule fluorescence microscopy techniques. We will discuss a few selected examples highlighting the power of the emerging techniques and finally discuss the future improvements and directions.

  5. Combination of Micro-fluidic Chip with Fluorescence Correlation Spectroscopy for Single Molecule Detection

    2006-01-01

    A single molecule detection technique was developed by the combination of a single channel poly (dimethylsiloxane)/glass micro-fluidic chip and fluorescence correlation spectroscopy (FCS). This method was successfully used to determine the proportion of two model components in the mixture containing fluorescein and the rhodamine-green succinimidyl ester.

  6. Inelastic X-ray scattering in single molecule imaging with free-electron lasers

    Imaging of the structure of bio-macromolecules with atomic resolution is essential to comprehend their function. Because many proteins do not form crystals, it would be enormously beneficial to be able to image single molecules. Free-electron lasers (FEL) offer an ideal tool to image nanocrystals and single-molecules with atomic resolution. The structural information is contained in the elastic X-ray scattering signal. However, in contrast to crystallography, in single molecule imaging there are no Bragg reflections, which means the elastic scattering is not enhanced. Because the usual scattering detectors cannot distinguish between elastically or inelastically scattered photons, the quality of the signal is attenuated by inelastic scattering. Here, we present a study of inelastic x-ray scattering under typical single molecule imaging conditions. We show the scattering spectrum as well as elastic and inelastic scattering probabilities, using the example of a carbon atom. Furthermore, we include the radiation damage caused by the highly intense FEL X-ray pulse by solving a rate equation model. In this way we obtain the elastic and inelastic scattering patterns of a carbon atom for different pulse durations and fluences.

  7. A wireless centrifuge force microscope (CFM) enables multiplexed single-molecule experiments in a commercial centrifuge.

    Hoang, Tony; Patel, Dhruv S; Halvorsen, Ken

    2016-08-01

    The centrifuge force microscope (CFM) was recently introduced as a platform for massively parallel single-molecule manipulation and analysis. Here we developed a low-cost and self-contained CFM module that works directly within a commercial centrifuge, greatly improving accessibility and ease of use. Our instrument incorporates research grade video microscopy, a power source, a computer, and wireless transmission capability to simultaneously monitor many individually tethered microspheres. We validated the instrument by performing single-molecule force shearing of short DNA duplexes. For a 7 bp duplex, we observed over 1000 dissociation events due to force dependent shearing from 2 pN to 12 pN with dissociation times in the range of 10-100 s. We extended the measurement to a 10 bp duplex, applying a 12 pN force clamp and directly observing single-molecule dissociation over an 85 min experiment. Our new CFM module facilitates simple and inexpensive experiments that dramatically improve access to single-molecule analysis. PMID:27587129

  8. Visualizing repetitive diffusion activity of double-strand RNA binding proteins by single molecule fluorescence assays.

    Koh, Hye Ran; Wang, Xinlei; Myong, Sua

    2016-08-01

    TRBP, one of double strand RNA binding proteins (dsRBPs), is an essential cofactor of Dicer in the RNA interference pathway. Previously we reported that TRBP exhibits repetitive diffusion activity on double strand (ds)RNA in an ATP independent manner. In the TRBP-Dicer complex, the diffusion mobility of TRBP facilitates Dicer-mediated RNA cleavage. Such repetitive diffusion of dsRBPs on a nucleic acid at the nanometer scale can be appropriately captured by several single molecule detection techniques. Here, we provide a step-by-step guide to four different single molecule fluorescence assays by which the diffusion activity of dsRBPs on dsRNA can be detected. One color assay, termed protein induced fluorescence enhancement enables detection of unlabeled protein binding and diffusion on a singly labeled RNA. Two-color Fluorescence Resonance Energy Transfer (FRET) in which labeled dsRBPs is applied to labeled RNA, allows for probing the motion of protein along the RNA axis. Three color FRET reports on the diffusion movement of dsRBPs from one to the other end of RNA. The single molecule pull down assay provides an opportunity to collect dsRBPs from mammalian cells and examine the protein-RNA interaction at single molecule platform. PMID:27012177

  9. Quantifying and optimizing single-molecule switching nanoscopy at high speeds.

    Yu Lin

    Full Text Available Single-molecule switching nanoscopy overcomes the diffraction limit of light by stochastically switching single fluorescent molecules on and off, and then localizing their positions individually. Recent advances in this technique have greatly accelerated the data acquisition speed and improved the temporal resolution of super-resolution imaging. However, it has not been quantified whether this speed increase comes at the cost of compromised image quality. The spatial and temporal resolution depends on many factors, among which laser intensity and camera speed are the two most critical parameters. Here we quantitatively compare the image quality achieved when imaging Alexa Fluor 647-immunolabeled microtubules over an extended range of laser intensities and camera speeds using three criteria - localization precision, density of localized molecules, and resolution of reconstructed images based on Fourier Ring Correlation. We found that, with optimized parameters, single-molecule switching nanoscopy at high speeds can achieve the same image quality as imaging at conventional speeds in a 5-25 times shorter time period. Furthermore, we measured the photoswitching kinetics of Alexa Fluor 647 from single-molecule experiments, and, based on this kinetic data, we developed algorithms to simulate single-molecule switching nanoscopy images. We used this software tool to demonstrate how laser intensity and camera speed affect the density of active fluorophores and influence the achievable resolution. Our study provides guidelines for choosing appropriate laser intensities for imaging Alexa Fluor 647 at different speeds and a quantification protocol for future evaluations of other probes and imaging parameters.

  10. Ninth international conference on hole burning, single molecule and related spectroscopies: science and applications (HBSM 2006)

    NONE

    2006-07-01

    This conference was organized around 9 sessions: -) single molecule, -) quantum optics, -) hole-burning materials and mechanisms, -) single nano-particle spectroscopy, -) dephasing and spectral diffusion, -) microwave photonics, -) biological systems, -) rare earth doped materials, -) novel laser sources. This document gathers only the slides of the presentations.

  11. Spectral multitude and spectral dynamics reflect changing conjugation length in single molecules of oligophenylenevinylenes

    Kobayashi, Hiroyuki

    2012-01-01

    Single-molecule study of phenylenevinylene oligomers revealed distinct spectral forms due to different conjugation lengths which are determined by torsional defects. Large spectral jumps between different spectral forms were ascribed to torsional flips of a single phenylene ring. These spectral changes reflect the dynamic nature of electron delocalization in oligophenylenevinylenes and enable estimation of the phenylene torsional barriers. © 2012 The Owner Societies.

  12. Spectroscopic and transport measurements of single molecules in solution using an electrokinetic trap

    Wang, Quan; Moerner, W. E.

    2014-03-01

    In aqueous solution, diffusion generally limits the observation window of a nano-meter sized single molecule to milliseconds and prevents quantitative determination of spectroscopic and transport properties molecule-by-molecule. The anti-Brownian electrokinetic (ABEL) trap is a feedback-based microfluidic device that enables prolonged (multiseconds) observation of single molecules in solution. The amount of information that can be extracted from each molecule in solution is thus boosted by three orders of magnitude. We describe recent advances in extending the ABEL trap to conduct both spectroscopic and transport measurements of single trapped molecules. First, by combining the trap with multi-parameter fluorescence detection, synchronized dynamics in different observables can be visualized in solution. We use single molecules of Atto 633 as an example and show that this popular label switches between different emissive states under common imaging conditions. Next, we show how transport properties of trapped single molecules can be extracted in addition to spectroscopic readouts. Due to their direct sensitivity to molecular size and charge, measured transport coefficients can be used to distinguish different molecular species and trace biomolecular interactions in solution. We demonstrate this new paradigm by monitoring DNA hybridization/melting in real-time.

  13. Single-molecule FRET and linear dichroism studies of DNA breathing and helicase binding at replication fork junctions

    Phelps, Carey; Lee, Wonbae; Jose, Davis; von Hippel, Peter H.; Marcus, Andrew H.

    2013-01-01

    Unique single-molecule fluorescence techniques were used to monitor DNA “breathing” at and near the junctions of model DNA replication forks on biologically relevant microsecond-to-millisecond time scales. Experiments performed in the absence and presence of helicase complexes addressed the role of these fluctuations in helicase function during DNA replication. These studies simultaneously monitored single-molecule Förster resonance energy transfer and single-molecule fluorescence linear dich...

  14. Spatial and temporal superresolution concepts to study plasma membrane organization by single molecule fluorescence techniques

    Fluorescence microscopy techniques are currently among the most important experimental tools to study cellular processes. Ultra-sensitive detection devices nowadays allow for measuring even individual farnesylacetate labeled target molecules with nanometer spatial accuracy and millisecond time resolution. The emergence of single molecule fluorescence techniques especially contributed to the field of membrane biology and provided basic knowledge on structural and dynamic features of the cellular plasma membrane. However, we are still confronted with a rather fragmentary understanding of the complex architecture and functional interrelations of membrane constituents. In this thesis new concepts in one- and dual-color single molecule fluorescence techniques are presented that allow for addressing organization principles and interaction dynamics in the live cell plasma membrane. Two complementary experimental strategies are described which differ in their detection principle: single molecule fluorescence imaging and fluorescence correlation spectroscopy. The presented methods are discussed in terms of their implementation, accuracy, quantitative and statistical data analysis, as well as live cell applications. State-of-the-art dual color single molecule imaging is introduced as the most direct experimental approach to study interaction dynamics between differently labeled target molecules. New analytical estimates for robust data analysis are presented that facilitate quantitative recording and identification of co localizations in dual color single molecule images. A novel dual color illumination scheme is further described that profoundly extends the current range and sensitivity of conventional dual color single molecule experiments. The method enables working at high surface densities of fluorescent molecules - a feature typically incommensurable with single molecule imaging - and is especially suited for the detection of rare interactions by tracking co localized

  15. Absolute beginners

    Costa, Carlos Casimiro da; Costa, Jacinta Casimiro da

    2012-01-01

    Tomorrow, I m recovering my Thursday child as an absolute beginner , Transporting you to the essential touch of surface skin and space, Only for you, i do not regret, looking for education in a materia set. My love is your love , my materiality is you making things, The legacy of our ethnography, craftsmen s old and disappear, make me strong hard feelings, Recovering experiences and knowledge sprinkled in powder of stone, wood and metal ( ) reflecting in your dirty face the ...

  16. Single-molecule FRET studies on alpha-synuclein oligomerization of Parkinson’s disease genetically related mutants

    Tosatto, Laura; Horrocks, Mathew H.; Dear, Alexander J.; Knowles, Tuomas P. J.; Dalla Serra, Mauro; Cremades, Nunilo; Dobson, Christopher M.; Klenerman, David

    2015-11-01

    Oligomers of alpha-synuclein are toxic to cells and have been proposed to play a key role in the etiopathogenesis of Parkinson’s disease. As certain missense mutations in the gene encoding for alpha-synuclein induce early-onset forms of the disease, it has been suggested that these variants might have an inherent tendency to produce high concentrations of oligomers during aggregation, although a direct experimental evidence for this is still missing. We used single-molecule Förster Resonance Energy Transfer to visualize directly the protein self-assembly process by wild-type alpha-synuclein and A53T, A30P and E46K mutants and to compare the structural properties of the ensemble of oligomers generated. We found that the kinetics of oligomer formation correlates with the natural tendency of each variant to acquire beta-sheet structure. Moreover, A53T and A30P showed significant differences in the averaged FRET efficiency of one of the two types of oligomers formed compared to the wild-type oligomers, indicating possible structural variety among the ensemble of species generated. Importantly, we found similar concentrations of oligomers during the lag-phase of the aggregation of wild-type and mutated alpha-synuclein, suggesting that the properties of the ensemble of oligomers generated during self-assembly might be more relevant than their absolute concentration for triggering neurodegeneration.

  17. Photochemistry and fluorescence emission dynamics of single molecules in solution: B-phycoerythrin

    Wu, M.; Goodwin, P.M.; Ambrose, W.P.; Keller, R.A. [Los Alamos National Lab., NM (United States)

    1996-10-24

    We report the first detailed studies of the photochemistry of single molecules in aqueous solution. Photolysis of single B-phycoerythrin (B-PE) molecules, a highly fluorescent phycobiliprotein containing 34 bilin chromophores, is observed as an abrupt cessation of the fluorescence emission from individual molecules as they flow through a =40 pL probe volume. These measurements demonstrate that B-PE is photolyzed in a single photochemical step. The observation of abrupt photobleaching of single molecules could not be made in a bulk measurement because the signal would be averaged over many molecules to yield a continuous decay. Photon pair correlation measurements of the fluorescence detected from single B-PE molecules demonstrate that the molecule behaves as a single quantum system, not as a collection of 34 independent chromophores. 45 refs., 5 figs.

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

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

    2014-05-01

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

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

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

    2011-10-25

    Designing, controlling, and understanding rectification behavior in molecular-scale devices has been a goal of the molecular electronics community for many years. Here we study the transport behavior of a single molecule diode, and its nonrectifying, symmetric counterpart at low temperatures, and at both low and high biases to help elucidate the electron-phonon interactions and transport mechanisms in the rectifying system. We find that the onset of current rectification occurs at low biases, indicating a significant change in the elastic transport pathway. However, the peaks in the inelastic electron tunneling (IET) spectrum are antisymmetric about zero bias and show no significant changes in energy or intensity in the forward or reverse bias directions, indicating that despite the change in the elastic transmission probability there is little impact on the inelastic pathway. These results agree with first principles calculations performed to evaluate the IETS, which also allow us to identify which modes are active in the single molecule junction. PMID:21932824

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

    Xie, Sunney; Choi, Paul; Cai, Long

    2009-03-01

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

  1. Poisson indicator and Fano factor for probing dynamic disorder in single-molecule enzyme inhibition kinetics.

    Chaudhury, Srabanti

    2014-09-01

    We consider a generic stochastic model to describe the kinetics of single-molecule enzyme inhibition reactions in which the turnover events correspond to conversion of substrate into a product by a single enzyme molecule in the presence of an inhibitor. We observe that slow fluctuations between the active and inhibited state of the enzyme or the enzyme substrate complex can induce dynamic disorder, which is manifested in the measurement of the Poisson indicator and the Fano factor as functions of substrate concentrations for different inhibition reactions. For a single enzyme molecule inhibited by the product, we derive a single-molecule Michaelis-Menten equation for the reaction rate, which shows a dependence on the substrate concentration similar to the ensemble enzymatic catalysis rate as obtained from bulk experimental results. The measurement of Fano factor is shown to be able to discriminate reactions following different inhibition mechanisms and also extract kinetic rates. PMID:25122511

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

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

    2015-07-01

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

  3. Single-molecule diffusion and conformational dynamics by spatial integration of temporal fluctuations

    Bayoumi, Maged Fouad

    2014-10-06

    Single-molecule localization and tracking has been used to translate spatiotemporal information of individual molecules to map their diffusion behaviours. However, accurate analysis of diffusion behaviours and including other parameters, such as the conformation and size of molecules, remain as limitations to the method. Here, we report a method that addresses the limitations of existing single-molecular localization methods. The method is based on temporal tracking of the cumulative area occupied by molecules. These temporal fluctuations are tied to molecular size, rates of diffusion and conformational changes. By analysing fluorescent nanospheres and double-stranded DNA molecules of different lengths and topological forms, we demonstrate that our cumulative-area method surpasses the conventional single-molecule localization method in terms of the accuracy of determined diffusion coefficients. Furthermore, the cumulative-area method provides conformational relaxation times of structurally flexible chains along with diffusion coefficients, which together are relevant to work in a wide spectrum of scientific fields.

  4. Single molecule fluorescence fluctuations of the cyanine dyes linked covalently to DNA

    AUMILER; Damir

    2009-01-01

    The intersystem crossing and isomerization dynamics of free-Cy3,Cy3-ssDNA,free-Cy5 and Cy5-ssDNA are obtained through simple analysis of rapid on/off blinking from single molecule fluorescence intensity time-traces and the fluorescence correlation spectroscopy(FCS).The on-and off-times observed in fluorescence time traces of single cyanine dyes are due to the formation of the triplet state and isomerization,where both the interaction with DNA and long central polymethine chain of cyanine dyes increase the barriers of isomerization,leading to long off-time.The results indicate that the single molecule fluorescence fluctuation together with the resulting second autocorrelation analysis are powerful methods for determining the triplet state and isomerization dynamics,which could be the simple techniques and complementary to other spectroscopic techniques,such as fluorescence decay measurement and laser flash photolysis to study the photophysical processes of complex molecules.

  5. Chemical structure imaging of a single molecule by atomic force microscopy at room temperature

    Iwata, Kota; Yamazaki, Shiro; Mutombo, Pingo; Hapala, Prokop; Ondráček, Martin; Jelínek, Pavel; Sugimoto, Yoshiaki

    2015-07-01

    Atomic force microscopy is capable of resolving the chemical structure of a single molecule on a surface. In previous research, such high resolution has only been obtained at low temperatures. Here we demonstrate that the chemical structure of a single molecule can be clearly revealed even at room temperature. 3,4,9,10-perylene tetracarboxylic dianhydride, which is strongly adsorbed onto a corner-hole site of a Si(111)-(7 × 7) surface in a bridge-like configuration is used for demonstration. Force spectroscopy combined with first-principle calculations clarifies that chemical structures can be resolved independent of tip reactivity. We show that the submolecular contrast over a central part of the molecule is achieved in the repulsive regime due to differences in the attractive van der Waals interaction and the Pauli repulsive interaction between different sites of the molecule.

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

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

    2015-07-24

    We demonstrate large rectification ratios (> 100) in single-molecule junctions based on a metal-oxide cluster (polyoxometalate), using a scanning tunneling microscope (STM) both at ambient conditions and at low temperature. These rectification ratios are the largest ever observed in a single-molecule junction, and in addition these junctions sustain current densities larger than 10(5) A cm(-2). By following the variation of the I-V characteristics with tip-molecule separation we demonstrate unambiguously that rectification is due to asymmetric coupling to the electrodes of a molecule with an asymmetric level structure. This mechanism can be implemented in other type of molecular junctions using both organic and inorganic molecules and provides a simple strategy for the rational design of molecular diodes. PMID:26133791

  7. Radio-frequency excitation of single molecules by scanning tunnelling microscopy

    We have upgraded a low-temperature scanning tunnelling microscope (STM) with a radio-frequency (RF) modulation system to extend STM spectroscopy to the range of low energy excitations (<1 meV). We studied single molecules of a stable hydrocarbon π-radical weakly physisorbed on Au(111). At 5 K thermal excitation of the adsorbed molecules is inhibited due to the lack of short-wavelength phonons of the substrate. We demonstrate resonant excitation of mechanical modes of single molecules by RF tunnelling at 115 MHz, which induces structural changes in the molecule ranging from controlled diffusion and modification of bond angles to bond breaking as the ultimate climax (resonance catastrophe). Our results pave the way towards RF-STM-based spectroscopy and controlled manipulation of molecular nanostructures on a surface. (paper)

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

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

  9. pyFRET: A Python Library for Single Molecule Fluorescence Data Analysis

    Murphy, Rebecca R; Klenerman, David

    2014-01-01

    Single molecule F\\"orster resonance energy transfer (smFRET) is a powerful experimental technique for studying the properties of individual biological molecules in solution. However, as adoption of smFRET techniques becomes more widespread, the lack of available software, whether open source or commercial, for data analysis, is becoming a significant issue. Here, we present pyFRET, an open source Python package for the analysis of data from single-molecule fluorescence experiments from freely diffusing biomolecules. The package provides methods for the complete analysis of a smFRET dataset, from burst selection and denoising, through data visualisation and model fitting. We provide support for both continuous excitation and alternating laser excitation (ALEX) data analysis. pyFRET is available as a package downloadable from the Python Package Index (PyPI) under the open source three-clause BSD licence, together with links to extensive documentation and tutorials, including example usage and test data. Additio...

  10. Interferometric scattering microscopy and its combination with single-molecule fluorescence imaging.

    Ortega Arroyo, Jaime; Cole, Daniel; Kukura, Philipp

    2016-04-01

    Interferometric scattering microscopy (iSCAT) is a light scattering-based imaging modality that offers a unique combination of imaging speed and precision for tracking nanoscopic labels and enables label-free optical sensing down to the single-molecule level. In contrast to fluorescence, iSCAT does not suffer from limitations associated with dye photochemistry and photophysics, or the requirement for fluorescent labeling. Here we present a protocol for constructing an iSCAT microscope from commercially available optical components and demonstrate its compatibility with simultaneously operating single-molecule, objective-type, total internal reflection fluorescence microscopy. Given an intermediate level of experience with optics and microscopy, for instance graduate-level familiarity with laser beam steering and optical components, this protocol can be completed in a time frame of 2 weeks. PMID:26938114

  11. Single-molecule spectroscopy of protein conformational dynamics in live eukaryotic cells.

    König, Iwo; Zarrine-Afsar, Arash; Aznauryan, Mikayel; Soranno, Andrea; Wunderlich, Bengt; Dingfelder, Fabian; Stüber, Jakob C; Plückthun, Andreas; Nettels, Daniel; Schuler, Benjamin

    2015-08-01

    Single-molecule methods have become widely used for quantifying the conformational heterogeneity and structural dynamics of biomolecules in vitro. Their application in vivo, however, has remained challenging owing to shortcomings in the design and reproducible delivery of labeled molecules, the range of applicable analysis methods, and suboptimal cell culture conditions. By addressing these limitations in an integrated approach, we demonstrate the feasibility of probing protein dynamics from milliseconds down to the nanosecond regime in live eukaryotic cells with confocal single-molecule Förster resonance energy transfer (FRET) spectroscopy. We illustrate the versatility of the approach by determining the dimensions and submicrosecond chain dynamics of an intrinsically disordered protein; by detecting even subtle changes in the temperature dependence of protein stability, including in-cell cold denaturation; and by quantifying the folding dynamics of a small protein. The methodology opens possibilities for assessing the effect of the cellular environment on biomolecular conformation, dynamics and function. PMID:26147918

  12. Single-molecule chemistry and physics explored by low-temperature scanning probe microscopy.

    Swart, Ingmar; Gross, Leo; Liljeroth, Peter

    2011-08-28

    It is well known that scanning probe techniques such as scanning tunnelling microscopy (STM) and atomic force microscopy (AFM) routinely offer atomic scale information on the geometric and the electronic structure of solids. Recent developments in STM and especially in non-contact AFM have allowed imaging and spectroscopy of individual molecules on surfaces with unprecedented spatial resolution, which makes it possible to study chemistry and physics at the single molecule level. In this feature article, we first review the physical concepts underlying image contrast in STM and AFM. We then focus on the key experimental considerations and use selected examples to demonstrate the capabilities of modern day low-temperature scanning probe microscopy in providing chemical insight at the single molecule level. PMID:21584325

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

    Morrison, Greg; Hyeon, Changbong; Hinczewski, Michael; Thirumalai, D.

    2011-04-01

    We establish a framework for assessing whether the transition state location of a biopolymer, which can be inferred from single molecule pulling experiments, corresponds to the ensemble of structures that have equal probability of reaching either the folded or unfolded states (Pfold=0.5). Using results for the forced unfolding of a RNA hairpin, an exactly soluble model, and an analytic theory, we show that Pfold is solely determined by s, an experimentally measurable molecular tensegrity parameter, which is a ratio of the tensile force and a compaction force that stabilizes the folded state. Applications to folding landscapes of DNA hairpins and a leucine zipper with two barriers provide a structural interpretation of single molecule experimental data. Our theory can be used to assess whether molecular extension is a good reaction coordinate using measured free energy profiles.

  14. Effect of the ac field on a single-molecule magnet bridged between conducting leads

    We study quantum spin-rotation effects for a single-molecule magnet bridged between two conducting leads in the ac and dc magnetic fields. The Landau-Zener dynamics induced by the magnetic field generates mechanical torque, making the molecule to oscillate. This mechanical motion of the molecule exhibits unique features that can be detected by measuring the electronic tunneling current through the molecule. - Highlights: → Magnetic molecules (MM) have been proposed as ultimate units of magnetic memory. → Several experiments were performed to measure electric current through a single molecule. → We study mechanical vibrations of a MM bridged between two leads in the presence of ac and dc fields. → Through quantum spin-rotation coupling such fields generate mechanical motion of the molecule. → The twist of the molecule can be detected by measuring the tunneling current through the molecule.

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

    Chen, Lipeng; Zhao, Yang, E-mail: YZhao@ntu.edu.sg [Division of Materials Science, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798 (Singapore); Gelin, Maxim F.; Domcke, Wolfgang [Department of Chemistry, Technische Universität München, Garching D-85747 (Germany)

    2015-04-28

    We develop a first principles theoretical description of femtosecond double-pump single-molecule signals of molecular aggregates. We incorporate all singly excited electronic states and vibrational modes with significant exciton-phonon coupling into a system Hamiltonian and treat the ensuing system dynamics within the Davydov D{sub 1} Ansatz. The remaining intra- and inter-molecular vibrational modes are treated as a heat bath and their effect is accounted for through lineshape functions. We apply our theory to simulate single-molecule signals of the light harvesting complex II. The calculated signals exhibit pronounced oscillations of mixed electron-vibrational (vibronic) origin. Their periods decrease with decreasing exciton-phonon coupling.

  16. Electron transfer behaviour of biological macromolecules towards the single-molecule level

    Zhang, Jingdong; Grubb, Mikala; Hansen, Allan Glargaard; Kuznetsov, A.M.; Boisen, Anja; Wackerbarth, Hainer; Ulstrup, Jens

    2003-01-01

    single-molecule levels.We discuss here these advances with reference to two specific redox metalloproteins, the blue single-copper protein Pseudomonas aeruginosa azurin and the single-haem protein Saccharomyces cerevisiae yeast cytochrome c, and a short oligonucleotide. Both proteins can be immobilized...... on Au(111) by chemisorption via exposed sulfur-containing residues. Voltammetric, interfacial capacitance, x-ray photoelectron spectroscopy and microcantilever sensor data, together with in situ STM with single-molecule resolution, all point to a coherent view of monolayer organization with protein...... electron transfer (ET) function retained. In situ STM can also address the microscopic mechanisms for electron tunnelling through the biomolecules and offers novel notions such as coherent multi-ET between the substrate and tip via the molecular redox levels. This differs in important respects from...

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

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

    2016-06-01

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

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

    Fratalocchi, Andrea

    2011-03-09

    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.

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

    Yoshida, Kenji; Shibata, Kenji; Hirakawa, Kazuhiko

    2015-09-01

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

  20. Wafer-scale metasurface for total power absorption, local field enhancement and single molecule Raman spectroscopy

    Dongxing Wang; Wenqi Zhu; Michael D Best; Camden, Jon P.; Kenneth B. Crozier

    2013-01-01

    The ability to detect molecules at low concentrations is highly desired for applications that range from basic science to healthcare. Considerable interest also exists for ultrathin materials with high optical absorption, e.g. for microbolometers and thermal emitters. Metal nanostructures present opportunities to achieve both purposes. Metal nanoparticles can generate gigantic field enhancements, sufficient for the Raman spectroscopy of single molecules. Thin layers containing metal nanostruc...

  1. Amine-Linked Single Molecule Circuits: Systematic Trends Across Molecular Families

    Hybertsen, Mark S.; Venkataraman, Latha; Klare, Jennifer E.; Whalley, Adam C.; Steigerwald, Michael L.; Nuckolls, Colin

    2008-01-01

    A comprehensive review is presented of single molecule junction conductance measurements across families of molecules measured while breaking a gold point contact in a solution of molecules with amine end groups. A theoretical framework unifies the picture for the amine-gold link bonding and the tunnel coupling through the junction using Density Functional Theory based calculations. The reproducible electrical characteristics and utility for many molecules is shown to result from the selectiv...

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

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

    2014-01-01

    The human proteome has millions of protein variants due to alternative RNA splicing and post-translational modifications, and variants that are related to diseases are frequently present in minute concentrations. For DNA and RNA, low concentrations can be amplified using the polymerase chain reaction, but there is no such reaction for proteins. Therefore, the development of single molecule protein sequencing is a critical step in the search for protein biomarkers. Here we show that single ami...

  3. Time-dependent spin and transport properties of a single molecule magnet in a tunnel junction

    Hammar, H.; J. Fransson

    2016-01-01

    In single molecule magnets, the exchange between a localized spin moment and the electronic background provides a suitable laboratory for studies of dynamical aspects of both the local spin and transport properties. Here we address the time-evolution of a localized spin moment coupled to an electronic level in a molecular quantum dot embedded in a tunnel junction between metallic leads. The interactions between the localized spin moment and the electronic level generates an effective interact...

  4. Super and Sub-Poissonian photon statistics for single molecule spectroscopy

    He, Yong; Barkai, Eli

    2004-01-01

    We investigate the distribution of the number of photons emitted by a single molecule undergoing a spectral diffusion process and interacting with a continuous wave laser field. The spectral diffusion is modeled based on a stochastic approach, in the spirit of the Anderson-Kubo line shape theory. Using a generating function formalism we solve the generalized optical Bloch equations, and obtain an exact analytical formula for the line shape and Mandel's Q parameter. The line shape exhibits wel...

  5. Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy.

    Hofmann H.; Soranno A; Borgia A; Gast K; Nettels D; Schuler B.

    2012-01-01

    The dimensions of unfolded and intrinsically disordered proteins are highly dependent on their amino acid composition and solution conditions, especially salt and denaturant concentration. However, the quantitative implications of this behavior have remained unclear, largely because the effective theta-state, the central reference point for the underlying polymer collapse transition, has eluded experimental determination. Here, we used single-molecule fluorescence spectroscopy and two-focus c...

  6. Single molecule analysis reveals three phases of DNA degradation by an exonuclease

    Lee, Gwangrog; Yoo, Jungmin; Leslie, Benjamin J.; Ha, Taekjip

    2011-01-01

    λ exonuclease degrades one strand of duplex DNA in the 5’-3’ direction to generate a 3’ overhang required for recombination. Its ability to hydrolyze thousands of nucleotides processively is attributed to its ring structure and most studies have focused on the processive phase. Here, we use single molecule FRET to reveal three phases of λ exonuclease reactions: initiation, distributive and processive phases. The distributive phase occurs at early reactions where the 3’ overhang is too short f...

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

    Schwartz, Jerrod J.; Quake, Stephen R

    2009-01-01

    Although DNA replication is often imagined as a regular and continuous process, the DNA polymerase enzyme is a complicated machine and can pause upon encountering physical and chemical barriers. We used single molecule measurements to make a detailed characterization of this behavior as a function of the template's secondary structure and the sequence context. Strand displacement replication through a DNA hairpin by single DNA polymerase molecules was measured in real time with near single ba...

  8. Folding and ligand recognition of the TPP riboswitch aptamer at single-molecule resolution

    Haller, Andrea; Altman, Roger B.; Soulière, Marie F.; Blanchard, Scott C; Micura, Ronald

    2013-01-01

    Thiamine pyrophosphate (TPP)-sensitive mRNA domains are the most prevalent riboswitches known. Despite intensive investigation, the complex ligand recognition and concomitant folding processes in the TPP riboswitch that culminate in the regulation of gene expression remain elusive. Here, we used single-molecule fluorescence resonance energy transfer imaging to probe the folding landscape of the TPP aptamer domain in the absence and presence of magnesium and TPP. To do so, distinct labeling pa...

  9. Control led sequential dehydrogenation of single molecules by scanning tunneling microscopy

    Sanvito, Stefano

    2010-01-01

    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 H 2 dissociation as well as the intermediate state, in which only one H atom is separated from the ...

  10. Two-photon Induced Hot Electron Transfer to a Single Molecule in a Scanning Tunneling Microscope

    Wu, Shiwei; Ho, Wilson

    2010-01-01

    The junction of a scanning tunneling microscope (STM) operating in the tunneling regime was irradiated with femtosecond laser pulses. A photo-excited hot electron in the STM tip resonantly tunnels into an excited state of a single molecule on the surface, converting it from the neutral to the anion. The electron transfer rate depends quadratically on the incident laser power, suggesting a two-photon excitation process. This nonlinear optical process is further confirmed by the polarization me...

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

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

    2012-01-01

    The electron transfer properties of proteins are normally measured as molecularly averaged ensembles. Through these and related measurements, proteins are widely regarded as macroscopically insulating materials. Using scanning tunnelling microscopy (STM), we present new measurements of the conductance through single-molecules of the electron transfer protein cytochrome b562 in its native conformation, under pseudo-physiological conditions. This is achieved by thiol (SH) linker pairs at opposi...

  12. Action spectroscopy for single-molecule motion induced by vibrational excitation with a scanning tunneling microscope

    Ueba, H.; Persson, B.N.J.

    2007-01-01

    We propose an action spectroscopy for single-molecule motion induced by vibrational excitation with a scanning tunneling microscope (STM). Calculations of the inelastic tunneling current for excitation of the C-O stretch mode of the CO molecule on metal surfaces are combined with a theory which describes how the energy in the vibrational mode is transferred to a reaction coordinate mode to overcome the activation barrier. The calculated rate for CO hopping on Pd (110) as a function of the bia...

  13. Understanding the electroluminescence emitted by single molecules in scanning tunneling microscopy experiments

    Buker, John; Kirczenow, George

    2008-01-01

    We explore theoretically the electroluminescence of single molecules. We adopt a local-electrode framework that is appropriate for scanning tunneling microscopy (STM) experiments where electroluminescence originates from individual molecules of moderate size on complex substrates: Couplings between the STM tip and molecule and between the molecule and multiple substrate sites are treated on the same footing, as local electrodes contacting the molecule. Electron flow is modelled with the Lippm...

  14. Hierarchically-coupled hidden Markov models for learning kinetic rates from single-molecule data

    van de Meent, Jan-Willem; Bronson, Jonathan E.; Wood, Frank; Gonzalez Jr., Ruben L.; Wiggins, Chris H.

    2013-01-01

    We address the problem of analyzing sets of noisy time-varying signals that all report on the same process but confound straightforward analyses due to complex inter-signal heterogeneities and measurement artifacts. In particular we consider single-molecule experiments which indirectly measure the distinct steps in a biomolecular process via observations of noisy time-dependent signals such as a fluorescence intensity or bead position. Straightforward hidden Markov model (HMM) analyses attemp...

  15. Transcription initiation by human RNA polymerase II visualized at single-molecule resolution

    Revyakin, Andrey; Zhang, Zhengjian; Coleman, Robert A.; Li, Yan; Inouye, Carla; Lucas, Julian K.; Park, Sang-Ryul; Chu, Steven; Tjian, Robert

    2012-01-01

    RNA polymerase II (Pol II) transcription is an immensely complex process that involves a myriad of regulatory factors and elements. In a technical tour de force, Tjian and colleagues now define an in vitro reconstituted Pol II system to detect and quantify Pol II transcription at single-molecule resolution using fluorescence video-microscopy. The study provides valuable insight into transcription reinitiation and, significantly, paves the way for a new era of opportunities in investigating th...

  16. DYNAMIC SINGLE-MOLECULE FORCE SPECTROSCOPY OF RHODOPSIN IN NATIVE MEMBRANES

    Park, Paul S.-H.; Müller, Daniel J.

    2015-01-01

    Membrane proteins are an important class of proteins in biology and therapeutics. Understanding the dynamic nature of the molecular interactions that stabilize membrane protein structure is critical to dissect the mechanism of action and dysfunction of these proteins. Single-molecule force spectroscopy (SMFS) and dynamic SMFS (DFS) are emerging nanotechniques that allow the study of membrane proteins under the physiologically relevant conditions of a lipid bilayer and buffer conditions. These...

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

    Dudko, Olga K.; Mathé, Jérôme; Szabo, Attila; Meller, Amit; Hummer, Gerhard

    2007-01-01

    Single-molecule force experiments provide powerful new tools to explore biomolecular interactions. Here, we describe a systematic procedure for extracting kinetic information from force-spectroscopy experiments, and apply it to nanopore unzipping of individual DNA hairpins. Two types of measurements are considered: unzipping at constant voltage, and unzipping at constant voltage-ramp speeds. We perform a global maximum-likelihood analysis of the experimental data at low-to-intermediate ramp s...

  18. Electric control of a $\\{Fe_4\\}$ single-molecule magnet in a single-electron transistor

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

    2013-01-01

    Using first-principles methods we study theoretically the properties of an individual $\\{Fe_4\\}$ 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 e...

  19. Effect of disorder on ultrafast exciton dynamics probed by single molecule spectroscopy

    Hernando, Jordi; van Dijk; Jacob P. Hoogenboom; Garcia-Lopez, Juan José; David N. Reinhoudt; Crego-Calama, Mercedes; Garcia-Parajo, Maria F.; Hulst, van, N.F.

    2006-01-01

    We present a single-molecule study unraveling the effect of static disorder on the vibrational-assisted ultrafast exciton dynamics in multichromophoric systems. For every single complex, we probe the initial exciton relaxation process by an ultrafast pump-probe approach and the coupling to vibrational modes by emission spectra, while fluorescence lifetime analysis measures the amount of static disorder. Exploiting the wide range of disorder found from complex to complex, we demonstrate that s...

  20. Single-molecule imaging of DNA curtains reveals intrinsic energy landscapes for nucleosome deposition

    Visnapuu, Mari-Liis; Greene, Eric C.

    2009-01-01

    Here we use single-molecule imaging to determine coarse-grained intrinsic energy landscapes for nucleosome deposition on model DNA substrates. Our results reveal distributions that are correlated with recent in silico predictions, reinforcing the hypothesis that DNA contains some intrinsic positioning information. We also show that cis-regulatory sequences in human DNA coincide with peaks in the intrinsic landscape, whereas valleys correspond to non-regulatory regions, and we present evidence...

  1. Spin-coupled double-quantum-dot behavior inside a single-molecule transistor

    Bernand-Mantel, A.; Seldenthuis, J. S.; Beukman, A.; van der Zant, H. S. J.; Meded, V.; Chandrasekhar, R; Fink, K.; Ruben, M; Evers, F.

    2010-01-01

    We report on the observation of Kondo and split Kondo peaks in single-molecule transistors containing a single spin transition molecule with a Fe2+ ion. Coulomb blockade characteristics reveal a double quantum dot behavior in a parallel configuration, making our system a molecular equivalent to a semiconducting double-quantum-dot system. As the gate voltage is increased the charging of the second dot by an additional electron induces a splitting of the Kondo peak. We discuss possible origins ...

  2. Toward single-molecule detection with sensors based on propagating surface plasmons

    Kvasnička, Pavel; Chadt, Karel; Vala, Milan; Bocková, Markéta; Homola, Jiří

    2012-01-01

    Roč. 37, č. 2 (2012), s. 163-165. ISSN 0146-9592 R&D Projects: GA AV ČR KAN200670701; GA MŠk OC09058; GA MŠk(CZ) LH11102 Institutional research plan: CEZ:AV0Z20670512 Keywords : optical biosenzor * single molecule * surface plasmon microscopy Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 3.385, year: 2012

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

    Sobhy, M. A.

    2011-11-07

    Single-molecule fluorescence imaging is at the forefront of tools applied to study biomolecular dynamics both in vitro and in vivo. The ability of the single-molecule fluorescence microscope to conduct simultaneous multi-color excitation and detection is a key experimental feature that is under continuous development. In this paper, we describe in detail the design and the construction of a sophisticated and versatile multi-color excitation and emission fluorescence instrument for studying biomolecular dynamics at the single-molecule level. The setup is novel, economical and compact, where two inverted microscopes share a laser combiner module with six individual laser sources that extend from 400 to 640 nm. Nonetheless, each microscope can independently and in a flexible manner select the combinations, sequences, and intensities of the excitation wavelengths. This high flexibility is achieved by the replacement of conventional mechanical shutters with acousto-optic tunable filter (AOTF). The use of AOTF provides major advancement by controlling the intensities, duration, and selection of up to eight different wavelengths with microsecond alternation time in a transparent and easy manner for the end user. To our knowledge this is the first time AOTF is applied to wide-field total internal reflection fluorescence (TIRF) microscopy even though it has been commonly used in multi-wavelength confocal microscopy. The laser outputs from the combiner module are coupled to the microscopes by two sets of four single-mode optic fibers in order to allow for the optimization of the TIRF angle for each wavelength independently. The emission is split into two or four spectral channels to allow for the simultaneous detection of up to four different fluorophores of wide selection and using many possible excitation and photoactivation schemes. We demonstrate the performance of this new setup by conducting two-color alternating excitation single-molecule fluorescence resonance energy

  4. In silico single-molecule manipulation of DNA with rigid body dynamics.

    Pascal Carrivain; Maria Barbi; Jean-Marc Victor

    2014-01-01

    We develop a new powerful method to reproduce in silico single-molecule manipulation experiments. We demonstrate that flexible polymers such as DNA can be simulated using rigid body dynamics thanks to an original implementation of Langevin dynamics in an open source library called Open Dynamics Engine. We moreover implement a global thermostat which accelerates the simulation sampling by two orders of magnitude. We reproduce force-extension as well as rotation-extension curves of reference ex...

  5. Interrogating Biology with Force: Single Molecule High-Resolution Measurements with Optical Tweezers

    Capitanio, Marco; Pavone, Francesco S.

    2013-01-01

    Single molecule force spectroscopy methods, such as optical and magnetic tweezers and atomic force microscopy, have opened up the possibility to study biological processes regulated by force, dynamics of structural conformations of proteins and nucleic acids, and load-dependent kinetics of molecular interactions. Among the various tools available today, optical tweezers have recently seen great progress in terms of spatial resolution, which now allows the measurement of atomic-scale conformat...

  6. Tight Binding Model of Mn12 Single Molecule Magnets: Electronic and Magnetic Structure and Transport Properties

    Renani, Fatemeh Rostamzadeh; Kirczenow, George

    2012-01-01

    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 Huckel 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 anisotrop...

  7. Theory of the electronic and magnetic structure and transport properties of single molecule magnets

    Rostamzadeh Renani, Fatemeh

    2013-01-01

    Developing electronic components at the molecular scale is the ultimate goal in molecular electronics. Because of their large magnetic anisotropy barriers and associated stable magnetic moments, single molecule magnets (SMMs) bring a new dimension to this field and also raise the possibility of molecular magnetic information storage and quantum computation. Therefore the transport properties of transistors based on individual SMMs are attracting considerable experimental and theoretical inter...

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

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

    2008-01-01

    Nanopores hold great promise as single-molecule analytical devices and biophysical model systems because the ionic current blockades they produce contain information about the identity, concentration, structure, and dynamics of target molecules. The porin MspA of Mycobacterium smegmatis has remarkable stability against environmental stresses and can be rationally modified based on its crystal structure. Further, MspA has a short and narrow channel constriction that is promising for DNA sequen...

  9. Single-Molecule Conductance in a Series of Extended Viologen Molecules

    Kolivoška, Viliam; Valášek, Michal; Gál, Miroslav; Sokolová, Romana; Kocábová, Jana; Pospíšil, Lubomír; Mészáros, G.; Hromadová, Magdaléna

    2013-01-01

    Roč. 4, č. 4 (2013), s. 589-595. ISSN 1948-7185 R&D Projects: GA ČR GA203/09/0705; GA AV ČR IAA400400802; GA MŠk(CZ) MEB041006 Institutional support: RVO:61388955 ; RVO:61388963 Keywords : single molecule conductance * extended viologens * electron transfer Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 6.687, year: 2013

  10. Influence of quantum dot labels on single molecule movement in the plasma membrane

    Clausen, Mathias P.; Lagerholm, B. Christoffer

    2011-01-01

    Single particle tracking results are very dependent on the probe that is used. In this study we have investigated the influence that functionalized quantum dots (QDs) have on the recorded movement in single molecule tracking experiments of plasma membrane species in live cells. Potential issues in...... simultaneous investigations of different plasma membrane species in order to discriminate the effect of the label from differences in movement of the target molecules....

  11. An Undecanuclear Ferrimagnetic Cu9Dy2 Single Molecule Magnet Achieved through Ligand Fine-Tuning.

    Kühne, Irina A; Kostakis, George E; Anson, Christopher E; Powell, Annie K

    2016-05-01

    We describe the concept of increasing the nuclearity of a previously reported high-spin Cu5Gd2 core using a "fine-tuning" ligand approach. Thus, two Cu9Ln2 coordination clusters, with Ln = Dy (1) and Gd (2), were synthesized with the Gd compound having a ground spin state of (17)/2 and the Dy analogue showing single-molecule-magnet behavior in zero field. PMID:27096219

  12. Accounting for Limited Detection Efficiency and Localization Precision in Cluster Analysis in Single Molecule Localization Microscopy

    Shivanandan, Arun; Unnikrishnan, Jayakrishnan; RADENOVIC, Aleksandra

    2015-01-01

    Single Molecule Localization Microscopy techniques like PhotoActivated Localization Microscopy, with their sub-diffraction limit spatial resolution, have been popularly used to characterize the spatial organization of membrane proteins, by means of quantitative cluster analysis. However, such quantitative studies remain challenged by the techniques' inherent sources of errors such as a limited detection efficiency of less than 60%, due to incomplete photo-conversion, and a limited localizatio...

  13. Basis Entropy

    Chen, Xing

    2016-01-01

    Projective measurement can increase the entropy of a state $\\rho$, the increased entropy is not only up to the basis of projective measurement, but also has something to do with the properties of the state itself. In this paper we define this increased entropy as basis entropy. And then we discuss the usefulness of this new concept by showing its application in explaining the success probability of Grover's algorithm and the existence of quantum discord. And as shown in the paper, this new co...

  14. Massively parallel haplotyping on microscopic beads for the high-throughput phase analysis of single molecules.

    Boulanger, Jérôme; Muresan, Leila; Tiemann-Boege, Irene

    2012-01-01

    In spite of the many advances in haplotyping methods, it is still very difficult to characterize rare haplotypes in tissues and different environmental samples or to accurately assess the haplotype diversity in large mixtures. This would require a haplotyping method capable of analyzing the phase of single molecules with an unprecedented throughput. Here we describe such a haplotyping method capable of analyzing in parallel hundreds of thousands single molecules in one experiment. In this method, multiple PCR reactions amplify different polymorphic regions of a single DNA molecule on a magnetic bead compartmentalized in an emulsion drop. The allelic states of the amplified polymorphisms are identified with fluorescently labeled probes that are then decoded from images taken of the arrayed beads by a microscope. This method can evaluate the phase of up to 3 polymorphisms separated by up to 5 kilobases in hundreds of thousands single molecules. We tested the sensitivity of the method by measuring the number of mutant haplotypes synthesized by four different commercially available enzymes: Phusion, Platinum Taq, Titanium Taq, and Phire. The digital nature of the method makes it highly sensitive to detecting haplotype ratios of less than 1:10,000. We also accurately quantified chimera formation during the exponential phase of PCR by different DNA polymerases. PMID:22558329

  15. Wafer-scale metasurface for total power absorption, local field enhancement and single molecule Raman spectroscopy

    Wang, Dongxing; Zhu, Wenqi; Best, Michael D.; Camden, Jon P.; Crozier, Kenneth B.

    2013-01-01

    The ability to detect molecules at low concentrations is highly desired for applications that range from basic science to healthcare. Considerable interest also exists for ultrathin materials with high optical absorption, e.g. for microbolometers and thermal emitters. Metal nanostructures present opportunities to achieve both purposes. Metal nanoparticles can generate gigantic field enhancements, sufficient for the Raman spectroscopy of single molecules. Thin layers containing metal nanostructures (“metasurfaces”) can achieve near-total power absorption at visible and near-infrared wavelengths. Thus far, however, both aims (i.e. single molecule Raman and total power absorption) have only been achieved using metal nanostructures produced by techniques (high resolution lithography or colloidal synthesis) that are complex and/or difficult to implement over large areas. Here, we demonstrate a metasurface that achieves the near-perfect absorption of visible-wavelength light and enables the Raman spectroscopy of single molecules. Our metasurface is fabricated using thin film depositions, and is of unprecedented (wafer-scale) extent. PMID:24091825

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

    Kai Sotthewes

    2014-01-01

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

  17. Monitoring Nanoscale Deformations in a Drawn Polymer Melt with Single-Molecule Fluorescence Polarization Microscopy.

    Krause, Stefan; Neumann, Martin; Fröbe, Melanie; Magerle, Robert; von Borczyskowski, Christian

    2016-02-23

    Elongating a polymer melt causes polymer segments to align and polymer coils to deform along the drawing direction. Despite the importance of this molecular response for understanding the viscoelastic properties and relaxation behavior of polymeric materials, studies on the single-molecule level are rare and were not performed in real time. Here we use single-molecule fluorescence polarization microscopy for monitoring the position and orientation of single fluorescent perylene diimide molecules embedded in a free-standing thin film of a polymethyl acrylate (PMA) melt with a time resolution of 500 ms during the film drawing and the subsequent stress relaxation period. The orientation distribution of the perylene diimide molecules is quantitatively described with a model of rod-like objects embedded in a uniaxially elongated matrix. The orientation of the fluorescent probe molecules is directly coupled to the local deformation of the PMA melt, which we derive from the distances between individual dye molecules. In turn, the fluorescence polarization monitors the shape deformation of the polymer coils on a length scale of 5 nm. During stress relaxation, the coil shape relaxes four times more slowly than the mechanical stress. This shows that stress relaxation involves processes on length scales smaller than a polymer coil. Our work demonstrates how optical spectroscopy and microscopy can be used to study the coupling of individual fluorescent probe molecules to their embedding polymeric matrix and to an external mechanical stimulus on the single-molecule level. PMID:26831762

  18. Solution-Based Single-Molecule FRET Studies of K(+) Channel Gating in a Lipid Bilayer.

    Sadler, Emma E; Kapanidis, Achillefs N; Tucker, Stephen J

    2016-06-21

    Ion channels are dynamic multimeric proteins that often undergo multiple unsynchronized structural movements as they switch between their open and closed states. Such structural changes are difficult to measure within the context of a native lipid bilayer and have often been monitored via macroscopic changes in Förster resonance energy transfer (FRET) between probes attached to different parts of the protein. However, the resolution of this approach is limited by ensemble averaging of structurally heterogeneous subpopulations. These problems can be overcome by measurement of FRET in single molecules, but this presents many challenges, in particular the ability to control labeling of subunits within a multimeric protein with acceptor and donor fluorophores, as well as the requirement to image large numbers of individual molecules in a membrane environment. To address these challenges, we randomly labeled tetrameric KirBac1.1 potassium channels, reconstituted them into lipid nanodiscs, and performed single-molecule FRET confocal microscopy with alternating-laser excitation as the channels diffused in solution. These solution-based single-molecule FRET measurements of a multimeric ion channel in a lipid bilayer have allowed us to probe the structural changes that occur upon channel activation and inhibition. Our results provide direct evidence of the twist-to-shrink movement of the helix bundle crossing during channel gating and demonstrate how this method might be applied to real-time structural studies of ion channel gating. PMID:27332124

  19. Single-molecule imaging of BMP4 dimerization on human periodontal ligament cells.

    Mi, H-W; Lee, M-C; Chiang, Y-C; Chow, L-P; Lin, C-P

    2011-11-01

    We expressed bone morphogenetic protein 4 (BMP4) fused with enhanced green fluorescent protein (BMP4-EGFP) in the secretory pathways of producer cells. Fluorescent EGFP was acquired only after we interrupted the transport of BMP4-EGFP by culturing cells at a lower temperature (20°C), and the dynamics of BMP4-EGFP could be monitored by single-molecule microscopy. Western blotting analysis confirmed that exposure to low temperature helped the integrated formation of BMP4-EGFP fusion proteins. In this study, for the first time, we could image the fluorescently labeled BMP4 molecules localized on the plasma membrane of living hPDL cells. The one-step photobleaching with EGFP and the "blinking" behavior of quantum dots suggest that the fluorescent spots represent the events of single BMP4 molecules. Single-molecule tracking showed that the BMP receptors (BMPR) dimerize after BMP4 stimulation, or that a complex of one BMP4 molecule and a pre-formed BMPR dimer develops first, followed by the binding of the second BMP4 molecule. Furthermore, BMP4-EGFP enhanced the osteogenic differentiation of hPDL cells via signal transduction involving BMP receptors. This single-molecule imaging technique might be a valuable tool for the future development of BMP4 gene therapy and regenerative medicine mediated by hPDLs. PMID:21841042

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

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

    2015-07-28

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

  1. Quantification of dye-mediated photodamage during single-molecule DNA imaging.

    Tycon, Michael A; Dial, Catherine F; Faison, Keia; Melvin, Whitney; Fecko, Christopher J

    2012-07-01

    Single-molecule fluorescence imaging of DNA-binding proteins has enabled detailed investigations of their interactions. However, the intercalating dyes used to visually locate DNA molecules have the undesirable effect of photochemically damaging the DNA through radical intermediaries. Unfortunately, this damage occurs as single-strand breaks (SSBs), which are visually undetectable but can heavily influence protein behavior. We investigated the formation of SSBs on DNA molecules by the dye YOYO-1 using complementary single-molecule imaging and gel electrophoresis-based damage assays. The single-molecule assay imaged hydrodynamically elongated lambda DNA, enabling the real-time detection of double-strand breaks (DSBs). The gel assay, which used supercoiled plasmid DNA, was sensitive to both SSBs and DSBs. This enabled the quantification of SSBs that precede DSB formation. Using the parameters determined from the gel damage assay, we applied a model of stochastic DNA damage to the time-resolved DNA breakage data, extracting the rates of single-strand breakage at two dye staining ratios and measuring the damage reduction from the radical scavengers ascorbic acid and β-mercaptoethanol. These results enable the estimation of the number of SSBs that occur during imaging and are scalable over a wide range of laser intensities used in fluorescence microscopy. PMID:22484041

  2. Measuring ultrafast protein folding rates from photon-by-photon analysis of single molecule fluorescence trajectories

    Chung, Hoi Sung, E-mail: chunghoi@niddk.nih.gov [Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520 (United States); Cellmer, Troy; Louis, John M. [Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520 (United States); Eaton, William A., E-mail: eaton@helix.nih.gov [Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520 (United States)

    2013-08-30

    Highlights: ► Photon trajectories were measured for an ultrafast folding protein using single molecule FRET. ► Folding rates were obtained from a photon-by-photon analysis using a maximum likelihood method. ► Incorporating acceptor blinking into the analysis improved the accuracy of the extracted rates. ► The rates agree with the results from both the correlation analysis and ensemble laser temperature-jump. - Abstract: Folding and unfolding rates for the ultrafast folding villin subdomain were determined from a photon-by-photon analysis of fluorescence trajectories in single molecule FRET experiments. One of the obstacles to measuring fast kinetics in single molecule fluorescence experiments is blinking of the fluorophores on a timescale that is not well separated from the process of interest. By incorporating acceptor blinking into a two-state kinetics model, we show that it is possible to extract accurate rate coefficients on the microsecond time scale for folding and unfolding using the maximum likelihood method of Gopich and Szabo. This method yields the most likely parameters of a given model that can reproduce the observed photon trajectories. The extracted parameters agree with both the decay rate of the donor–acceptor cross correlation function and the results of ensemble equilibrium and kinetic experiments using nanosecond laser temperature jump.

  3. Single-molecule spectroscopic study of enhanced intrinsic phycoerythrin fluorescence on silver nanostructured surfaces.

    Ray, Krishanu; Chowdhury, Mustafa H; Lakowicz, Joseph R

    2008-09-15

    In this paper, we report on steady-state and time-resolved single-molecule fluorescence measurements performed on a phycobiliprotein, R-phycoerythrin (RPE), assembled on silver nanostructures. Single-molecule measurements clearly show that RPE molecules display a 10-fold increase in fluorescence intensity, with a 7-fold decrease in lifetime when they are assembled on silver nanostructured surfaces, as compared to control glass slides. The emission spectrum of individual RPE molecules also displays a significant fluorescence enhancement on silver nanostructures as compared to glass. From intensity and lifetime histograms, it is clear that the intensities as well as lifetimes of individual RPE molecules on silver nanostructures are more heterogeneously distributed than that on glass. This single-molecule study provides further insight on the heterogeneity in the fluorescence intensity and lifetimes of the RPE molecules on both glass and SiFs surfaces, which is otherwise not possible to observe using ensemble measurements. Finite-difference time-domain calculations have been performed to study the enhanced near-fields induced around silver nanoparticles by a radiating excited-state fluorophore, and the effect of such enhanced fields on the fluorescence enhancement observed is discussed. PMID:18690697

  4. Nonlinear reconstruction of single-molecule free-energy surfaces from univariate time series

    Wang, Jiang; Ferguson, Andrew L.

    2016-03-01

    The stable conformations and dynamical fluctuations of polymers and macromolecules are governed by the underlying single-molecule free energy surface. By integrating ideas from dynamical systems theory with nonlinear manifold learning, we have recovered single-molecule free energy surfaces from univariate time series in a single coarse-grained system observable. Using Takens' Delay Embedding Theorem, we expand the univariate time series into a high dimensional space in which the dynamics are equivalent to those of the molecular motions in real space. We then apply the diffusion map nonlinear manifold learning algorithm to extract a low-dimensional representation of the free energy surface that is diffeomorphic to that computed from a complete knowledge of all system degrees of freedom. We validate our approach in molecular dynamics simulations of a C24H50 n -alkane chain to demonstrate that the two-dimensional free energy surface extracted from the atomistic simulation trajectory is - subject to spatial and temporal symmetries - geometrically and topologically equivalent to that recovered from a knowledge of only the head-to-tail distance of the chain. Our approach lays the foundations to extract empirical single-molecule free energy surfaces directly from experimental measurements.

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

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

    2008-12-30

    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 approximately 20 higher interaction rates, required only half as much voltage to observe interaction, and allowed ssDNA to reside in the vestibule approximately 100 times longer than the first mutant. Our results introduce MspA as a nanopore for nucleic acid analysis and highlight its potential as an engineerable platform for single-molecule detection and characterization applications. PMID:19098105

  6. Single-Molecule Investigation of Initiation Dynamics of an Organometallic Catalyst.

    Ng, James D; Upadhyay, Sunil P; Marquard, Angela N; Lupo, Katherine M; Hinton, Daniel A; Padilla, Nicolas A; Bates, Desiree M; Goldsmith, Randall H

    2016-03-23

    The action of molecular catalysts comprises multiple microscopic kinetic steps whose nature is of central importance in determining catalyst activity and selectivity. Single-molecule microscopy enables the direct examination of these steps, including elucidation of molecule-to-molecule variability. Such molecular diversity is particularly important for the behavior of molecular catalysts supported at surfaces. We present the first combined investigation of the initiation dynamics of an operational palladium cross-coupling catalyst at the bulk and single-molecule levels, including under turnover conditions. Base-initiated kinetics reveal highly heterogeneous behavior indicative of diverse catalyst population. Unexpectedly, this distribution becomes more heterogeneous at increasing base concentration. We model this behavior with a two-step saturation mechanism and identify specific microscopic steps where chemical variability must exist in order to yield observed behavior. Critically, we reveal how structural diversity at a surface translates into heterogeneity in catalyst behavior, while demonstrating how single-molecule experiments can contribute to understanding of molecular catalysts. PMID:26944030

  7. Nanoengineering a single-molecule mechanical switch using DNA self-assembly

    The ability to manipulate and observe single biological molecules has led to both fundamental scientific discoveries and new methods in nanoscale engineering. A common challenge in many single-molecule experiments is reliably linking molecules to surfaces, and identifying their interactions. We have met this challenge by nanoengineering a novel DNA-based linker that behaves as a force-activated switch, providing a molecular signature that can eliminate errant data arising from non-specific and multiple interactions. By integrating a receptor and ligand into a single piece of DNA using DNA self-assembly, a single tether can be positively identified by force–extension behavior, and receptor–ligand unbinding easily identified by a sudden increase in tether length. Additionally, under proper conditions the exact same pair of molecules can be repeatedly bound and unbound. Our approach is simple, versatile and modular, and can be easily implemented using standard commercial reagents and laboratory equipment. In addition to improving the reliability and accuracy of force measurements, this single-molecule mechanical switch paves the way for high-throughput serial measurements, single-molecule on-rate studies, and investigations of population heterogeneity.

  8. Nanoengineering a single-molecule mechanical switch using DNA self-assembly

    Halvorsen, Ken; Schaak, Diane; Wong, Wesley P.

    2011-12-01

    The ability to manipulate and observe single biological molecules has led to both fundamental scientific discoveries and new methods in nanoscale engineering. A common challenge in many single-molecule experiments is reliably linking molecules to surfaces, and identifying their interactions. We have met this challenge by nanoengineering a novel DNA-based linker that behaves as a force-activated switch, providing a molecular signature that can eliminate errant data arising from non-specific and multiple interactions. By integrating a receptor and ligand into a single piece of DNA using DNA self-assembly, a single tether can be positively identified by force-extension behavior, and receptor-ligand unbinding easily identified by a sudden increase in tether length. Additionally, under proper conditions the exact same pair of molecules can be repeatedly bound and unbound. Our approach is simple, versatile and modular, and can be easily implemented using standard commercial reagents and laboratory equipment. In addition to improving the reliability and accuracy of force measurements, this single-molecule mechanical switch paves the way for high-throughput serial measurements, single-molecule on-rate studies, and investigations of population heterogeneity.

  9. Single-molecule kinetics under force: probing protein folding and enzymatic activity with optical tweezers

    Wong, Wesley

    2010-03-01

    Weak non-covalent bonds between and within single molecules govern many aspects of biological structure and function (e.g. DNA base-paring, receptor-ligand binding, protein folding, etc.) In living systems, these interactions are often subject to mechanical forces, which can greatly alter their kinetics and activity. My group develops and applies novel single-molecule manipulation techniques to explore and quantify these force-dependent kinetics. Using optical tweezers, we have quantified the force-dependent unfolding and refolding kinetics of different proteins, including the cytoskeletal protein spectrin in collaboration with E. Evans's group [1], and the A2 domain of the von Willebrand factor blood clotting protein in collaboration with T. Springer's group [2]. Furthermore, we have studied the kinetics of the ADAMTS13 enzyme acting on a single A2 domain, and have shown that physiolgical forces in the circulation can act as a cofactor for enzymatic cleavage, regulating hemostatic activity [2]. References: 1. E. Evans, K. Halvorsen, K. Kinoshita, and W.P. Wong, Handbook of Single Molecule Biophysics, P. Hinterdorfer, ed., Springer (2009). 2. X. Zhang, K. Halvorsen, C.-Z. Zhang, W.P. Wong, and T.A. Springer, Science 324 (5932), 1330-1334 (2009).

  10. Measuring ultrafast protein folding rates from photon-by-photon analysis of single molecule fluorescence trajectories

    Highlights: ► Photon trajectories were measured for an ultrafast folding protein using single molecule FRET. ► Folding rates were obtained from a photon-by-photon analysis using a maximum likelihood method. ► Incorporating acceptor blinking into the analysis improved the accuracy of the extracted rates. ► The rates agree with the results from both the correlation analysis and ensemble laser temperature-jump. - Abstract: Folding and unfolding rates for the ultrafast folding villin subdomain were determined from a photon-by-photon analysis of fluorescence trajectories in single molecule FRET experiments. One of the obstacles to measuring fast kinetics in single molecule fluorescence experiments is blinking of the fluorophores on a timescale that is not well separated from the process of interest. By incorporating acceptor blinking into a two-state kinetics model, we show that it is possible to extract accurate rate coefficients on the microsecond time scale for folding and unfolding using the maximum likelihood method of Gopich and Szabo. This method yields the most likely parameters of a given model that can reproduce the observed photon trajectories. The extracted parameters agree with both the decay rate of the donor–acceptor cross correlation function and the results of ensemble equilibrium and kinetic experiments using nanosecond laser temperature jump

  11. Magnetic Relaxation Study on Single Crystals of Ni4 Single-Molecule Magnets

    LI Yan-Rong; LIU Hai-Qing; LIU Ying; SU Shao-Kui; WANG Yun-Ping

    2009-01-01

    The ac susceptibility of single crystals of Nia single-molecule magnets is measured by a compensation measurement setup. The magnetic relaxation time calculated from the peak of the out-phase component of the susceptibility fits the Arrhenius law well and gives an effective spin-flipping energy barrier of Ueff = 7.2 K. This value is far below the classical activation energy barrier of U = 14 K, whereas it is close to the energy gap between the Sz = ±4 and Sz = ±3 doublets, which indicates that quantum tunneling between the Sz = 3 and Sz = -3 states plays a key role in the magnetic relaxation. Therefore the relaxation process combines thermal activation and quantum tunneling. Also we deduce that the blocking temperature of Ni4 single-molecule magnets is lower than 0.3 K by extrapolating the relaxation time plot, which ensures that this single-molecule magnet material enters a long-range magnetic ordered state instead of a spin glass state at 0.91 K.

  12. Fabrication of Low Noise Borosilicate Glass Nanopores for Single Molecule Sensing

    Bafna, Jayesh A.; Soni, Gautam V.

    2016-01-01

    We show low-cost fabrication and characterization of borosilicate glass nanopores for single molecule sensing. Nanopores with diameters of ~100 nm were fabricated in borosilicate glass capillaries using laser assisted glass puller. We further achieve controlled reduction and nanometer-size control in pore diameter by sculpting them under constant electron beam exposure. We successfully fabricate pore diameters down to 6 nm. We next show electrical characterization and low-noise behavior of these borosilicate nanopores and compare their taper geometries. We show, for the first time, a comprehensive characterization of glass nanopore conductance across six-orders of magnitude (1M-1μM) of salt conditions, highlighting the role of buffer conditions. Finally, we demonstrate single molecule sensing capabilities of these devices with real-time translocation experiments of individual λ-DNA molecules. We observe distinct current blockage signatures of linear as well as folded DNA molecules as they undergo voltage-driven translocation through the glass nanopores. We find increased signal to noise for single molecule detection for higher trans-nanopore driving voltages. We propose these nanopores will expand the realm of applications for nanopore platform. PMID:27285088

  13. Absolute Summ

    Phillips, Alfred, Jr.

    Summ means the entirety of the multiverse. It seems clear, from the inflation theories of A. Guth and others, that the creation of many universes is plausible. We argue that Absolute cosmological ideas, not unlike those of I. Newton, may be consistent with dynamic multiverse creations. As suggested in W. Heisenberg's uncertainty principle, and with the Anthropic Principle defended by S. Hawking, et al., human consciousness, buttressed by findings of neuroscience, may have to be considered in our models. Predictability, as A. Einstein realized with Invariants and General Relativity, may be required for new ideas to be part of physics. We present here a two postulate model geared to an Absolute Summ. The seedbed of this work is part of Akhnaton's philosophy (see S. Freud, Moses and Monotheism). Most important, however, is that the structure of human consciousness, manifest in Kenya's Rift Valley 200,000 years ago as Homo sapiens, who were the culmination of the six million year co-creation process of Hominins and Nature in Africa, allows us to do the physics that we do. .

  14. STM/STS analysis of molecular chains consisting of Mn{sub 6}Cr single molecule magnets and single molecules on highly ordered pyrolytic graphite (HOPG)

    Gryzia, Aaron; Brechling, Armin; Hachmann, Wiebke; Sacher, Marc D.; Heinzmann, Ulrich [Molecular and Surface Physics, Bielefeld University (Germany); Heidemeier, Maik; Glaser, Thorsten [Anorganic Chemistry I, Bielefeld University (Germany)

    2008-07-01

    We report on the preparation and characterization of Mn{sub 6}Cr-Single Molecule Magnets on a HOPG(0001) surface. The Mn{sub 6}Cr-molecules show 1D molecular arrangements with many interesting features, such as the occurrence of discrete kink angles in the molecular chains of 30 deg., only two different molecular orientations, the orientation of the chains along the main crystal axis of HOPG and much larger molecule-molecule distances than expected from the van der Waals radii of the molecules. By STS we characterized Mn{sub 6}Cr, thus gaining information on the electronic levels of the molecule and the shift of the levels whether it is part of a chain or not. One of our goals is to obtain data about the exact orientation of the molecule in respect to the surface; thus we can make a statement for the physical interaction why the molecules are assembling in chains. First results of these measurements are presented.

  15. Electron transfer behaviour of biological macromolecules towards the single-molecule level

    Redox metalloproteins immobilized on metallic surfaces in contact with aqueous biological media are important in many areas of pure and applied sciences. Redox metalloprotein films are currently being addressed by new approaches where biotechnology including modified and synthetic proteins is combined with state-of-the-art physical electrochemistry with emphasis on single-crystal, atomically planar electrode surfaces, in situ scanning tunnelling microscopy (STM) and other surface techniques. These approaches have brought bioelectrochemistry important steps forward towards the nanoscale and single-molecule levels. We discuss here these advances with reference to two specific redox metalloproteins, the blue single-copper protein Pseudomonas aeruginosa azurin and the single-haem protein Saccharomyces cerevisiae yeast cytochrome c, and a short oligonucleotide. Both proteins can be immobilized on Au(111) by chemisorption via exposed sulfur-containing residues. Voltammetric, interfacial capacitance, x-ray photoelectron spectroscopy and microcantilever sensor data, together with in situ STM with single-molecule resolution, all point to a coherent view of monolayer organization with protein electron transfer (ET) function retained. In situ STM can also address the microscopic mechanisms for electron tunnelling through the biomolecules and offers novel notions such as coherent multi-ET between the substrate and tip via the molecular redox levels. This differs in important respects from electrochemical ET at a single metal/electrolyte interface. Similar data for a short oligonucleotide immobilized on Au(111) show that oligonucleotides can be characterized with comparable detail, with novel perspectives for addressing DNA electronic conduction mechanisms and for biological screening towards the single-molecule level

  16. A thin permeable-membrane device for single-molecule manipulation

    Park, Chang-Young; Jacobson, David R.; Nguyen, Dan T.; Willardson, Sam; Saleh, Omar A.

    2016-01-01

    Single-molecule manipulation instruments have unparalleled abilities to interrogate the structure and elasticity of single biomolecules. Key insights are derived by measuring the system response in varying solution conditions; yet, typical solution control strategies require imposing a direct fluid flow on the measured biomolecule that perturbs the high-sensitivity measurement and/or removes interacting molecules by advection. An alternate approach is to fabricate devices that permit solution changes by diffusion of the introduced species through permeable membranes, rather than by direct solution flow through the sensing region. Prior implementations of permeable-membrane devices are relatively thick, disallowing their use in apparatus that require the simultaneous close approach of external instrumentation from two sides, as occurs in single-molecule manipulation devices like the magnetic tweezer. Here, we describe the construction and use of a thin microfluidic device appropriate for single-molecule studies. We create a flow cell of only ˜500 μm total thickness by sandwiching glass coverslips around a thin plastic gasket and then create permeable walls between laterally separated channels in situ through photo-induced cross-linking of poly(ethylene glycol) diacrylate hydrogels. We show that these membranes permit passage of ions and small molecules (thus permitting solution equilibration in the absence of direct flow), but the membranes block the passage of larger biomolecules (thus retaining precious samples). Finally, we demonstrate the suitability of the device for high-resolution magnetic-tweezer experiments by measuring the salt-dependent folding of a single RNA hairpin under force.

  17. Fluorescence spectroscopy of single molecules at room temperature and its applications

    Ha, Taekjip

    1996-12-01

    We performed fluorescence spectroscopy of single and pairs of dye molecules on a surface at room temperature. Near field scanning optical microscope (NSOM) and far field scanning optical microscope with multi-color excitation/detection capability were built. The instrument is capable of optical imaging with 100nm resolution and has the sensitivity necessary for single molecule detection. A variety of dynamic events which cannot be observed from an ensemble of molecules is revealed when the molecules are probed one at a time. They include (1) spectral jumps correlated with dark states, (2) individually resolved quantum jumps to and from the meta-stable triplet state, (3) rotational jumps due to desorption/readsorption events of single molecules on the surface. For these studies, a computer controlled optical system which automatically and rapidly locates and performs spectroscopic measurements on single molecules was developed. We also studied the interaction between closely spaced pairs of molecules. In particular, fluorescence resonance energy transfer between a single resonant pair of donor and acceptor molecules was measured. Photodestruction dynamics of the donor or acceptor were used to determine the presence and efficiency of energy transfer Dual molecule spectroscopy was extended to a non-resonant pair of molecules to obtain high resolution differential distance information. By combining NSOM and dual color scheme, we studied the co-localization of parasite proteins and host proteins on a human red blood cell membrane infected with malaria. These dual-molecule techniques can be used to measure distances, relative orientations, and changes in distances/orientations of biological macromolecules with very good spatial, angular and temporal resolutions, hence opening new capabilities in the study of such systems.

  18. Structural and dynamic views of the CRISPR-Cas system at the single-molecule level.

    Lee, Seung Hwan; Bae, Sangsu

    2016-04-01

    The CRISPR-Cas system has emerged as a fascinating and important genome editing tool. It is now widely used in biology, biotechnology, and biomedical research in both academic and industrial settings. To improve the specificity and efficiency of Cas nucleases and to extend the applications of these systems for other areas of research, an understanding of their precise working mechanisms is crucial. In this review, we summarize current studies on the molecular structures and dynamic functions of type I and type II Cas nucleases, with a focus on target DNA searching and cleavage processes as revealed by single-molecule observations. [BMB Reports 2016; 49(4): 201-207]. PMID:26923305

  19. Fast, DNA-sequence independent translocation by FtsK in a single-molecule experiment

    Saleh, Omar A; Pérals, Corine; Barre, François-Xavier; Allemand, Jean-François

    2004-01-01

    Escherichia coli FtsK is an essential cell division protein, which is thought to pump chromosomal DNA through the closing septum in an oriented manner by following DNA sequence polarity. Here, we perform single-molecule measurements of translocation by FtsK50C, a derivative that functions as a DNA translocase in vitro. FtsK50C translocation follows Michaelis–Menten kinetics, with a maximum speed of ∼6.7 kbp/s. We present results on the effect of applied force on the speed, distance translocat...

  20. Applying Semiconductor Technologies and Metrology Tools to Biomedical Research: Manipulation and Detection of Single Molecules

    Berlin, Andrew A.; Sundararajan, Narayan; Koo, Tae-Woong

    2005-09-01

    Intel's Precision Biology research effort is working to combine Intel's expertise in nanotechnology with aspects of biology and medicine to create highly sensitive instrumentation for biomolecular analysis. The ability to manipulate, detect, and identify biological molecules at ultra-low concentrations is important for applications ranging from whole-genome DNA sequencing to protein-based early disease detection. In this paper we describe our work to develop a molecular labeling system based on Surface-Enhanced Raman Spectroscopy (SERS), to enable highly sensitive protein detection. We also present a set of microfluidic and spectroscopic techniques that our team has developed for transporting and identifying single molecules in solution.

  1. Bias voltage induced resistance switching effect in single-molecule magnets’ tunneling junction

    An electric-pulse-induced reversible resistance change effect in a molecular magnetic tunneling junction, consisting of a single-molecule magnet (SMM) sandwiched in one nonmagnetic and one ferromagnetic electrode, is theoretically investigated. By applying a time-varying bias voltage, the SMM's spin orientation can be manipulated with large bias voltage pulses. Moreover, the different magnetic configuration at high-resistance/low-resistance states can be ‘read out’ by utilizing relative low bias voltage. This device scheme can be implemented with current technologies (Khajetoorians et al 2013 Science 339 55) and has potential application in molecular spintronics and high-density nonvolatile memory devices. (paper)

  2. A single molecule switch based on two Pd nanocrystals linked by a conjugated dithiol

    Ved Varun Agrawal; Reji Thomas; G U Kulkarni; C N R Rao

    2005-11-01

    Tunneling spectroscopy measurements have been carried out on a single molecule device formed by two Pd nanocrystals (dia. ∼ 5 nm) electronically coupled by a conducting molecule, dimercaptodiphenylacetylene. The – data, obtained by positioning the tip over a nanocrystal electrode, exhibit negative differential resistance (NDR) on a background M-I-M characteristics. The NDR feature occurs at ∼ 0.67 V at 300 K and shifts to a higher bias of 1.93 V at 90 K. When the tip is held in the middle region of the device, a Coulomb blockade region is observed (± ∼ 0.3 V).

  3. A single-molecule study of polycrystalline microstructure by fluorescence polarization spectroscopy

    The structure of n-hexadecane polycrystalline matrices is examined with single molecule fluorescence spectroscopy at a temperature of 1.7 K. Some single chromophores exhibit spectral dynamics during experiments: their resonances either jump between two frequencies or split into two components. By means of polarization measurements, we investigate the molecular spectra in order to distinguish between the case of two spatially unresolved molecules and the case of chromophore - two level system (TLS) pair. For closely spaced molecules two-dimensional Gaussian function fitting is applied to extract the spatial coordinates of the molecules. For TLS-chromophore systems, parameters of the TLSs are estimated

  4. Tuning the spin dynamics of single molecule magnets via dipolar interactions

    Hofmann, A.; Salman, Z.

    2014-12-01

    We present calculations of the dipolar field distribution acting on a single molecule magnet due to its neighbours in thin films. The calculations are presented for different packing/configuration scenarios, with different easy axis orientations. The potential for controlling the molecular spin dynamics by tuning the molecule-substrate interaction and its competition with intra-molecular interactions is discussed. We argue that by altering the configuration of the molecular moments, and thus their dipolar interactions, one can enhance or slow down their spin dynamics.

  5. Mechanical force-induced DNA damage during AFM single-molecule manipulation

    Many environmental factors can cause DNA damage, such as radiation, heat, oxygen free radical, etc., which can induce mutation during DNA replication. Meanwhile, DNA molecules are subjected to various mechanical forces in numerous biological processes. However, it is unknown whether the mechanical force would induce DNA damage and introduce mutation during DNA replication, With the combination of single-molecule manipulation based on atomic force microscopy (AFM), single molecular polymerase chain reaction (SM-PCR) and Sanger's sequencing, we investigated the effect of mechanical force on DNA. The results show that mechanical force can cause DNA damage and induce DNA mutation during amplification. (authors)

  6. Stepwise Quenching of Exciton Fluorescence in Carbon Nanotubes by Single Molecule Reactions

    Cognet, Laurent; Rocha, John-David R; Doyle, Condell D; Tour, James M; Weisman, R Bruce

    2007-01-01

    Single-molecule chemical reactions with individual single-walled carbon nanotubes were observed through near-infrared photoluminescence microscopy. The emission intensity within distinct submicrometer segments of single nanotubes changes in discrete steps after exposure to acid, base, or diazonium reactants. The steps are uncorrelated in space and time, and reflect the quenching of mobile excitons at localized sites of reversible or irreversible chemical attack. Analysis of step amplitudes reveals an exciton diffusional range of about 90 nanometers, independent of nanotube structure. Each exciton visits approximately 104 atomic sites during its lifetime, providing highly efficient sensing of local chemical and physical perturbations.

  7. Single-Molecule Electrochemical Transistor Utilizing a Nickel-Pyridyl Spinterface

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

    2015-01-01

    Using a scanning tunnelling microscope break-junction technique, we produce 4,4′-bipyridine (44BP) single-molecule junctions with Ni and Au contacts. Electrochemical control is used to prevent Ni oxidation and to modulate the conductance of the devices via nonredox gating—the first time this has been shown using non-Au contacts. Remarkably the conductance and gain of the resulting Ni-44BP-Ni electrochemical transistors is significantly higher than analogous Au-based devices. Ab-initio calcula...

  8. Molecular tips for scanning tunneling microscopy: intermolecular electron tunneling for single-molecule recognition and electronics.

    Nishino, Tomoaki

    2014-01-01

    This paper reviews the development of molecular tips for scanning tunneling microscopy (STM). Molecular tips offer many advantages: first is their ability to perform chemically selective imaging because of chemical interactions between the sample and the molecular tip, thus improving a major drawback of conventional STM. Rational design of the molecular tip allows sophisticated chemical recognition; e.g., chiral recognition and selective visualization of atomic defects in carbon nanotubes. Another advantage is that they provide a unique method to quantify electron transfer between single molecules. Understanding such electron transfer is mandatory for the realization of molecular electronics. PMID:24420248

  9. Theoretical and Experimental Exploration of the Structures and Electronic States of Single Molecules

    HOU Jianguo; YANG Jinlong; WANG Haiqian; WANG Bing; ZHU Qingshi

    2007-01-01

    @@ The scanning tunnel microscopy/spectroscopy(STM/STS) is a powerful technique in probing the surface structures and the electronic states on a single molecular scale. Although a scanning tunneling microscope has a high spatial resolution in a topographic image, the image just reflects the spatial distribution of the electronic states, instead of the geometric structure of single molecules. Moreover, some additional factors,like the influence of the substrate and the STM tip, may also affect an STM image. So, it is still a challenge to determine the molecular conformation, molecular orientation, and intramolecular structure and electronic states on a single molecular scale.

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

    Darancet, Pierre; Doak, Peter; Neaton, Jeffrey

    2010-03-01

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

  11. Dzyaloshinskii-Moriya interaction in transport through single-molecule transistors.

    Herzog, S; Wegewijs, M R

    2010-07-01

    The Dzyaloshinskii-Moriya interaction is shown to result in a canting of spins in a single-molecule transistor. We predict nonlinear transport signatures of this effect induced by spin-orbit coupling for the generic case of a molecular dimer. The conductance is calculated using a master equation and is found to exhibit a non-trivial dependence on the magnitude and direction of an external magnetic field. We show how three-terminal transport measurements allow for a determination of the coupling vector characterizing the Dzyaloshinskii-Moriya interaction. In particular, we show how its orientation, defining the intramolecular spin chirality, can be probed with ferromagnetic electrodes. PMID:20571197

  12. Interaction of spin and vibrations in transport through single-molecule magnets

    Falk May

    2011-10-01

    Full Text Available We study electron transport through a single-molecule magnet (SMM and the interplay of its anisotropic spin with quantized vibrational distortions of the molecule. Based on numerical renormalization group calculations we show that, despite the longitudinal anisotropy barrier and small transverse anisotropy, vibrational fluctuations can induce quantum spin-tunneling (QST and a QST-Kondo effect. The interplay of spin scattering, QST and molecular vibrations can strongly enhance the Kondo effect and induce an anomalous magnetic field dependence of vibrational Kondo side-bands.

  13. Coherent (photon) vs incoherent (current) detection of multidimensional optical signals from single molecules in open junctions

    Agarwalla, Bijay Kumar; Hua, Weijie; Zhang, Yu; Mukamel, Shaul [Department of Chemistry, University of California, Irvine, California 92697 (United States); Harbola, Upendra [Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012 (India)

    2015-06-07

    The nonlinear optical response of a current-carrying single molecule coupled to two metal leads and driven by a sequence of impulsive optical pulses with controllable phases and time delays is calculated. Coherent (stimulated, heterodyne) detection of photons and incoherent detection of the optically induced current are compared. Using a diagrammatic Liouville space superoperator formalism, the signals are recast in terms of molecular correlation functions which are then expanded in the many-body molecular states. Two dimensional signals in benzene-1,4-dithiol molecule show cross peaks involving charged states. The correlation between optical and charge current signal is also observed.

  14. Time-dependent study of single-molecule SERS signal from yeast cytochrome c

    Delfino, Ines; Bizzarri, Anna Rita; Cannistraro, Salvatore

    2006-08-01

    A study of cytochrome c from Saccharomyces cerevisiae adsorbed on silver colloids at very low concentration is carried out by surface-enhanced Raman scattering. Spectra acquired at different times exhibit dramatic fluctuations in both line frequency and intensity indicating that single molecule detection is approached. The intensity fluctuations are investigated by means of a second order time correlation analysis. Such an approach has allowed us to put into evidence the presence of two distinct dynamical phenomena. The results are discussed in connection with diffusion processes to which the protein undergoes with respect to the surface of the Ag nanoclusters and with a modulation of the enhancement of the Raman signal.

  15. Switching of a Quantum Dot Spin Valve by Single Molecule Magnets

    Renani, Fatemeh Rostamzadeh; Kirczenow, George

    2013-01-01

    We explore theoretically the spin transport in nanostructures consisting of a gold quantum dot bridging nonmagnetic electrodes and two Mn12-Ph single molecule magnets (SMMs) that are thiol-bonded to the dot but are not in direct contact with the electrodes. We find that reversal of the magnetic moment of either SMM by the application of a magnetic field leads to a large change in the resistance of the dot, i.e., a strong spin valve effect. We show that this phenomenon arises from a novel phys...

  16. A Trigonal Prismatic Mononuclear Cobalt(II) Complex Showing Single-Molecule Magnet Behavior.

    Novikov, Valentin V; Pavlov, Alexander A; Nelyubina, Yulia V; Boulon, Marie-Emmanuelle; Varzatskii, Oleg A; Voloshin, Yan Z; Winpenny, Richard E P

    2015-08-12

    Single-molecule magnets (SMMs) with one transition-metal ion often rely on unusual geometry as a source of magnetically anisotropic ground state. Here we report a cobalt(II) cage complex with a trigonal prism geometry showing single ion magnet behavior with very high Orbach relaxation barrier of 152 cm(-1). This, to our knowledge, is the largest reported relaxation barrier for a cobalt-based mononuclear SMM. The trigonal prismatic coordination provided by the macrocyclic ligand gives intrinsically more stable molecular species than previously reported SMMs, thus making this type of cage complexes more amendable to possible functionalization that will boost their magnetic anisotropy even further. PMID:26199996

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

    Atomic Force Microscopy (AFM) allows for a highly sensitive detection of spectroscopic signals. This has been first demonstrated for NMR of a single molecule and recently extended to stimulated Raman in the optical regime. We theoretically investigate the use of optical forces to detect time and frequency domain nonlinear optical signals. We show that, with proper phase matching, the AFM-detected signals closely resemble coherent heterodyne-detected signals. Applications are made to AFM-detected and heterodyne-detected vibrational resonances in Coherent Anti-Stokes Raman Spectroscopy (χ(3)) and sum or difference frequency generation (χ(2))

  18. Single-Molecule Electronics with Cross- Conjugated Molecules: Quantum Interference, IETS and Non-Equilibrium "Temperatures"

    Jørgensen, Jacob Lykkebo

    , which is characterised by destructive quantum interference. The molecules are cross-conjugated, which means that the two parts of the molecules are conjugated to a third part, but not to each other. This gives rise to an anti-resonance in the trans- mission. In the low bias and low temperature regime......, the electrons can tunnel in- elastically from the left to the right electrode. This is the process behind inelastic electron tunnelling spectroscopy (IETS), which is a single-molecule spectroscopic method, where the vibrational ngerprint of a molecule is di- rectly observed by the tunnelling current...

  19. Theory of single-molecule experiments in the overstretching force regime

    Manca, Fabio; Palla, Pier Luca; Cleri, Fabrizio; Colombo, Luciano

    2012-01-01

    We present a statistical mechanics analysis of the finite-size elasticity of biopolymers, consisting of domains which can exhibit transitions between more than one stable state at large applied force. The constant-force (Gibbs) and constant-displacement (Helmholtz) formulations of single molecule stretching experiments are shown to converge in the thermodynamic limit. Monte Carlo simulations of continuous three dimensional polymers of variable length are carried out, based on this formulation. We demonstrate that the experimental force-extension curves for short and long chain polymers are described by a unique universal model, despite the differences in chemistry and rate-dependence of transition forces.

  20. Single-molecule assay reveals strand switching and enhanced processivity of UvrD

    Dessinges, Marie-Noëlle; Lionnet, Timothée; Xi, Xu Guang; Bensimon, David; Croquette, Vincent

    2004-01-01

    DNA helicases are enzymes capable of unwinding double-stranded DNA (dsDNA) to provide the single-stranded DNA template required in many biological processes. Among these, UvrD, an essential DNA repair enzyme, has been shown to unwind dsDNA while moving 3′-5′ on one strand. Here, we use a single-molecule manipulation technique to monitor real-time changes in extension of a single, stretched, nicked dsDNA substrate as it is unwound by a single enzyme. This technique offers a means for measuring...

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

    Shin, Yongdae; Davis, Joseph H.; Brau, Ricardo R.; Martin, Andreas; Kenniston, Jon A.; Baker, Tania A.; Sauer, Robert T.; Lang, Matthew J.

    2009-01-01

    ClpXP is an ATP-fueled molecular machine that unfolds and degrades target proteins. ClpX, an AAA+ enzyme, recognizes specific proteins, and then uses cycles of ATP hydrolysis to denature any native structure and to translocate the unfolded polypeptide into ClpP for degradation. Here, we develop and apply single-molecule fluorescence assays to probe the kinetics of protein denaturation and degradation by ClpXP. These assays employ a single-chain variant of the ClpX hexamer, linked via a single...

  2. Linker-dependent Junction Formation Probability in Single-Molecule Junctions

    Yoo, Pil Sun; Kim, Taekyeong [HankukUniversity of Foreign Studies, Yongin (Korea, Republic of)

    2015-01-15

    We compare the junction formation probabilities of single-molecule junctions with different linker molecules by using a scanning tunneling microscope-based break-junction technique. We found that the junction formation probability varies as SH > SMe > NH2 for the benzene backbone molecule with different types of anchoring groups, through quantitative statistical analysis. These results are attributed to different bonding forces according to the linker groups formed with Au atoms in the electrodes, which is consistent with previous works. Our work allows a better understanding of the contact chemistry in the metal.molecule junction for future molecular electronic devices.

  3. Refractive index fluctuations in solids: nanoprobing by means of single-molecule spectroscopy

    Anikushina, T A; Gorshelev, A A; Naumov, A V

    2015-01-01

    We suggest a novel approach for probing of local fluctuations of the refractive index $n$ in solids by means of single-molecule (SM) spectroscopy. It is based on the dependence $T_1(n)$ of the effective radiative lifetime $T_1$ of dye centres in solids on $n$ due to the local field effects. Detection of SM zero-phonon lines at ultra-low temperatures gives the values of SM natural spectral linewidth (which is inverse proportional to $T_1$) and makes it possible to reveal the distribution of the local $n$ values in solids. Here we demonstrate this possibility on the example of amorphous polyethylene and polycrystalline naphthalene doped with terrylene.

  4. Structural and dynamic views of the CRISPR-Cas system at the single-molecule level

    Lee, Seung Hwan; Bae, Sangsu

    2016-01-01

    The CRISPR-Cas system has emerged as a fascinating and important genome editing tool. It is now widely used in biology, biotechnology, and biomedical research in both academic and industrial settings. To improve the specificity and efficiency of Cas nucleases and to extend the applications of these systems for other areas of research, an understanding of their precise working mechanisms is crucial. In this review, we summarize current studies on the molecular structures and dynamic functions of type I and type II Cas nucleases, with a focus on target DNA searching and cleavage processes as revealed by single-molecule observations. [BMB Reports 2016; 49(4): 201-207] PMID:26923305

  5. Attached molecular motor in a trapped single molecule assay as a bidimensional Brownian multistable system.

    Marcucci, L; Yanagida, T

    2013-06-01

    To elucidate the physical properties of the force generation mechanism in molecular motors, we have obtained an analytical solution of the bidimensional Fokker-Plank equation which describes a common setup used in single molecule experiments. As a first application of this general result, we have shown that the size of the trapping system affects the dwell time of a multistable particle linearly. A quantitative application to skeletal actomyosin complex, using direct observation of force generation dynamics in the literature, shows that the size of the trapping system used was important for increasing the dwell time of the myosin head stable states to an observable time scale. PMID:23848719

  6. Volume Entropy

    Astuti, Valerio; Christodoulou, Marios; Rovelli, Carlo

    2016-01-01

    Building on a technical result by Brunnemann and Rideout on the spectrum of the Volume operator in Loop Quantum Gravity, we show that the dimension of the space of the quadrivalent states --with finite-volume individual nodes-- describing a region with total volume smaller than $V$, has \\emph{finite} dimension, bounded by $V \\log V$. This allows us to introduce the notion of "volume entropy": the von Neumann entropy associated to the measurement of volume.

  7. The physics of pulling polyproteins: a review of single molecule force spectroscopy using the AFM to study protein unfolding

    Hughes, Megan L.; Dougan, Lorna

    2016-07-01

    One of the most exciting developments in the field of biological physics in recent years is the ability to manipulate single molecules and probe their properties and function. Since its emergence over two decades ago, single molecule force spectroscopy has become a powerful tool to explore the response of biological molecules, including proteins, DNA, RNA and their complexes, to the application of an applied force. The force versus extension response of molecules can provide valuable insight into its mechanical stability, as well as details of the underlying energy landscape. In this review we will introduce the technique of single molecule force spectroscopy using the atomic force microscope (AFM), with particular focus on its application to study proteins. We will review the models which have been developed and employed to extract information from single molecule force spectroscopy experiments. Finally, we will end with a discussion of future directions in this field.

  8. Bacteriochlorophyll Aggregates Self-Assembled on Functionalized Gold Nanorod Cores as Mimics of Photosynthetic Chlorosomal Antennae: A Single Molecule Study

    Furumaki, S.; Vácha, František; Hirata, S.; Vácha, M.

    2014-01-01

    Roč. 8, č. 3 (2014), s. 2176-2182. ISSN 1936-0851 Institutional support: RVO:60077344 Keywords : Single molecule spectroscopy * molecular aggregate * bacteriochlorophyll * chromosome Subject RIV: BO - Biophysics Impact factor: 12.881, year: 2014

  9. Single molecule narrowfield microscopy of protein-DNA binding dynamics in glucose signal transduction of live yeast cells

    Wollman, Adam J M

    2016-01-01

    Single-molecule narrowfield microscopy is a versatile tool to investigate a diverse range of protein dynamics in live cells and has been extensively used in bacteria. Here, we describe how these methods can be extended to larger eukaryotic, yeast cells, which contain sub-cellular compartments. We describe how to obtain single-molecule microscopy data but also how to analyse these data to track and obtain the stoichiometry of molecular complexes diffusing in the cell. We chose glucose mediated signal transduction of live yeast cells as the system to demonstrate these single-molecule techniques as transcriptional regulation is fundamentally a single molecule problem - a single repressor protein binding a single binding site in the genome can dramatically alter behaviour at the whole cell and population level.

  10. Max Delbruck Prize in Biological Physics Lecture: Single-molecule protein folding and transition paths

    Eaton, William

    2012-02-01

    The transition path is the tiny fraction of an equilibrium molecular trajectory when a transition occurs by crossing the free energy barrier between two states. It is a uniquely single-molecule property, and has not yet been observed experimentally for any system in the condensed phase. The importance of the transition path in protein folding is that it contains all of the mechanistic information on how a protein folds. As a major step toward observing transition paths, we have determined the average transition-path time for a fast and a slow-folding protein from a photon-by-photon analysis of fluorescence trajectories in single-molecule FRET experiments. While the folding rate coefficients differ by 10,000-fold, surprisingly, the transition-path times differ by less than 5-fold, showing that a successful barrier crossing event takes almost the same time for a fast- and a slow-folding protein, i.e. almost the same time to fold when it actually happens.

  11. Single-Molecule Imaging of DNAs with Sticky Ends at Water/Fused Silica Interface

    Slavica Isailovic

    2005-12-17

    Total internal reflection fluorescence microscopy (TIRFM) was used to study intermolecular interactions of DNAs with unpaired (sticky) ends of different lengths at water/fused silica interface at the single-molecule level. Evanescent field residence time, linear velocity and adsorption/desorption frequency were measured in a microchannel for individual DNA molecules from T7, Lambda, and PSP3 phages at various pH values. The longest residence times and the highest adsorption/desorption frequencies at the constant flow at pH 5.5 were found for PSP3 DNA, followed by lower values for Lambda DNA, and the lowest values for T7 DNA. Since T7, Lambda, and PSP3 DNA molecules contain none, twelve and nineteen unpaired bases, respectively, it was concluded that the affinity of DNAs for the surface increases with the length of the sticky ends. This confirms that hydrophobic and hydrogen-bonding interactions between sticky ends and fused-silica surface are driving forces for DNA adsorption at the fused-silica surface. Described single-molecule methodology and results therein can be valuable for investigation of interactions in liquid chromatography, as well as for design of DNA hybridization sensors and drug delivery systems.

  12. Plasmofluidic single-molecule surface-enhanced Raman scattering from dynamic assembly of plasmonic nanoparticles

    Patra, Partha Pratim; Chikkaraddy, Rohit; Tripathi, Ravi P. N.; Dasgupta, Arindam; Kumar, G. V. Pavan

    2014-07-01

    Single-molecule surface-enhanced Raman scattering (SM-SERS) is one of the vital applications of plasmonic nanoparticles. The SM-SERS sensitivity critically depends on plasmonic hot-spots created at the vicinity of such nanoparticles. In conventional fluid-phase SM-SERS experiments, plasmonic hot-spots are facilitated by chemical aggregation of nanoparticles. Such aggregation is usually irreversible, and hence, nanoparticles cannot be re-dispersed in the fluid for further use. Here, we show how to combine SM-SERS with plasmon polariton-assisted, reversible assembly of plasmonic nanoparticles at an unstructured metal-fluid interface. One of the unique features of our method is that we use a single evanescent-wave optical excitation for nanoparticle assembly, manipulation and SM-SERS measurements. Furthermore, by utilizing dual excitation of plasmons at metal-fluid interface, we create interacting assemblies of metal nanoparticles, which may be further harnessed in dynamic lithography of dispersed nanostructures. Our work will have implications in realizing optically addressable, plasmofluidic, single-molecule detection platforms.

  13. Virtual reality visual feedback for hand-controlled scanning probe microscopy manipulation of single molecules.

    Leinen, Philipp; Green, Matthew F B; Esat, Taner; Wagner, Christian; Tautz, F Stefan; Temirov, Ruslan

    2015-01-01

    Controlled manipulation of single molecules is an important step towards the fabrication of single molecule devices and nanoscale molecular machines. Currently, scanning probe microscopy (SPM) is the only technique that facilitates direct imaging and manipulations of nanometer-sized molecular compounds on surfaces. The technique of hand-controlled manipulation (HCM) introduced recently in Beilstein J. Nanotechnol. 2014, 5, 1926-1932 simplifies the identification of successful manipulation protocols in situations when the interaction pattern of the manipulated molecule with its environment is not fully known. Here we present a further technical development that substantially improves the effectiveness of HCM. By adding Oculus Rift virtual reality goggles to our HCM set-up we provide the experimentalist with 3D visual feedback that displays the currently executed trajectory and the position of the SPM tip during manipulation in real time, while simultaneously plotting the experimentally measured frequency shift (Δf) of the non-contact atomic force microscope (NC-AFM) tuning fork sensor as well as the magnitude of the electric current (I) flowing between the tip and the surface. The advantages of the set-up are demonstrated by applying it to the model problem of the extraction of an individual PTCDA molecule from its hydrogen-bonded monolayer grown on Ag(111) surface. PMID:26665087

  14. A general approach to break the concentration barrier in single-molecule imaging

    Loveland, Anna B.

    2012-09-09

    Single-molecule fluorescence imaging is often incompatible with physiological protein concentrations, as fluorescence background overwhelms an individual molecule\\'s signal. We solve this problem with a new imaging approach called PhADE (PhotoActivation, Diffusion and Excitation). A protein of interest is fused to a photoactivatable protein (mKikGR) and introduced to its surface-immobilized substrate. After photoactivation of mKikGR near the surface, rapid diffusion of the unbound mKikGR fusion out of the detection volume eliminates background fluorescence, whereupon the bound molecules are imaged. We labeled the eukaryotic DNA replication protein flap endonuclease 1 with mKikGR and added it to replication-competent Xenopus laevis egg extracts. PhADE imaging of high concentrations of the fusion construct revealed its dynamics and micrometer-scale movements on individual, replicating DNA molecules. Because PhADE imaging is in principle compatible with any photoactivatable fluorophore, it should have broad applicability in revealing single-molecule dynamics and stoichiometry of macromolecular protein complexes at previously inaccessible fluorophore concentrations. © 2012 Nature America, Inc. All rights reserved.

  15. Drift correction for single-molecule imaging by molecular constraint field, a distance minimum metric

    The recent developments of far-field optical microscopy (single molecule imaging techniques) have overcome the diffraction barrier of light and improve image resolution by a factor of ten compared with conventional light microscopy. These techniques utilize the stochastic switching of probe molecules to overcome the diffraction limit and determine the precise localizations of molecules, which often requires a long image acquisition time. However, long acquisition times increase the risk of sample drift. In the case of high resolution microscopy, sample drift would decrease the image resolution. In this paper, we propose a novel metric based on the distance between molecules to solve the drift correction. The proposed metric directly uses the position information of molecules to estimate the frame drift. We also designed an algorithm to implement the metric for the general application of drift correction. There are two advantages of our method: First, because our method does not require space binning of positions of molecules but directly operates on the positions, it is more natural for single molecule imaging techniques. Second, our method can estimate drift with a small number of positions in each temporal bin, which may extend its potential application. The effectiveness of our method has been demonstrated by both simulated data and experiments on single molecular images

  16. Excitonic Coupling in Linear and Trefoil Trimer Perylenediimide Molecules Probed by Single-Molecule Spectroscopy

    Yoo, Hyejin

    2012-10-25

    Perylenediimide (PDI) molecules are promising building blocks for photophysical studies of electronic interactions within multichromophore arrays. Such PDI arrays are important materials for fabrication of molecular nanodevices such as organic light-emitting diodes, organic semiconductors, and biosensors because of their high photostability, chemical and physical inertness, electron affinity, and high tinctorial strength over the entire visible spectrum. In this work, PDIs have been organized into linear (L3) and trefoil (T3) trimer molecules and investigated by single-molecule fluorescence microscopy to probe the relationship between molecular structures and interchromophoric electronic interactions. We found a broad distribution of coupling strengths in both L3 and T3 and hence strong/weak coupling between PDI units by monitoring spectral peak shifts in single-molecule fluorescence spectra upon sequential photobleaching of each constituent chromophore. In addition, we used a wide-field defocused imaging technique to resolve heterogeneities in molecular structures of L3 and T3 embedded in a PMMA polymer matrix. A systematic comparison between the two sets of experimental results allowed us to infer the correlation between intermolecular interactions and molecular structures. Our results show control of the PDI intermolecular interactions using suitable multichromophoric structures. © 2012 American Chemical Society.

  17. Virtual reality visual feedback for hand-controlled scanning probe microscopy manipulation of single molecules

    Philipp Leinen

    2015-11-01

    Full Text Available Controlled manipulation of single molecules is an important step towards the fabrication of single molecule devices and nanoscale molecular machines. Currently, scanning probe microscopy (SPM is the only technique that facilitates direct imaging and manipulations of nanometer-sized molecular compounds on surfaces. The technique of hand-controlled manipulation (HCM introduced recently in Beilstein J. Nanotechnol. 2014, 5, 1926–1932 simplifies the identification of successful manipulation protocols in situations when the interaction pattern of the manipulated molecule with its environment is not fully known. Here we present a further technical development that substantially improves the effectiveness of HCM. By adding Oculus Rift virtual reality goggles to our HCM set-up we provide the experimentalist with 3D visual feedback that displays the currently executed trajectory and the position of the SPM tip during manipulation in real time, while simultaneously plotting the experimentally measured frequency shift (Δf of the non-contact atomic force microscope (NC-AFM tuning fork sensor as well as the magnitude of the electric current (I flowing between the tip and the surface. The advantages of the set-up are demonstrated by applying it to the model problem of the extraction of an individual PTCDA molecule from its hydrogen-bonded monolayer grown on Ag(111 surface.

  18. Tuning Charge and Correlation Effects for a Single Molecule on a Graphene Device

    Tsai, Hsin-Zon; Wickenburg, Sebastian; Lu, Jiong; Lischner, Johannes; Omrani, Arash A.; Riss, Alexander; Karrasch, Christoph; Jung, Han Sae; Khajeh, Ramin; Wong, Dillon; Watanabe, Kenji; Taniguchi, Takashi; Zettl, Alex; Louie, Steven G.; Crommie, Michael F.

    Controlling electronic devices down to the single molecule level is a grand challenge of nanotechnology. Single-molecules have been integrated into devices capable of tuning electronic response, but a drawback for these systems is that their microscopic structure remains unknown due to inability to image molecules in the junction region. Here we present a combined STM and nc-AFM study demonstrating gate-tunable control of the charge state of individual F4TCNQ molecules at the surface of a graphene field effect transistor. This is different from previous studies in that the Fermi level of the substrate was continuously tuned across the molecular orbital energy level. Using STS we have determined the resulting energy level evolution of the LUMO, its associated vibronic modes, and the graphene Dirac point (ED). We show that the energy difference between ED and the LUMO increases as EF is moved away from ED due to electron-electron interactions that renormalize the molecular quasiparticle energy. This is attributed to gate-tunable image-charge screening in graphene and corroborated by ab initio calculations.

  19. Feedback-controlled electro-kinetic traps for single-molecule spectroscopy

    Manoj Kumbakhar; Dirk Hähnel; Ingo Gregor; Jörg Enderlein

    2014-01-01

    A principal limitation of single-molecule spectroscopy in solution is the diffusionlimited residence time of a given molecule within the detection volume. A common solution to this problem is to immobilize molecules of interest on a passivated glass surface for extending the observation time to obtain reliable data statistics. However, surface tethering of molecules often introduces artifacts, particularly when studying the structural dynamics of biomolecules. To circumvent this limitation, we investigated alternative ways to extend single-molecule observation times in solution without surface immobilization. Among various possibilities, the so-called anti-Brownian electro-kinetic trap (or ABEL trap) seems best suited to achieve this goal. The essential part of this trap is a feedback-controlled electro-kinetic steering of a molecule’s position in reaction to its diffusive Brownian motion which is monitored by fluorescence, thus keeping the molecule within a sub-micron sized detection volume. Fluorescence trace recordings of over thousands of milliseconds duration on individual dye molecules within an ABEL trap have been reported. In this short review, we shall briefly discuss the principle and some results of ABEL trapping of individual molecules with possible extensions to future works.

  20. Characterisation of the effects of optical aberrations in single molecule techniques.

    Coles, Benjamin C; Webb, Stephen E D; Schwartz, Noah; Rolfe, Daniel J; Martin-Fernandez, Marisa; Lo Schiavo, Valentina

    2016-05-01

    Optical aberrations degrade image quality in fluorescence microscopy, including for single-molecule based techniques. These depend on post-processing to localize individual molecules in an image series. Using simulated data, we show the impact of optical aberrations on localization success, accuracy and precision. The peak intensity and the proportion of successful localizations strongly reduces when the aberration strength is greater than 1.0 rad RMS, while the precision of each of those localisations is halved. The number of false-positive localisations exceeded 10% of the number of true-positive localisations at an aberration strength of only ~0.6 rad RMS when using the ThunderSTORM package, but at greater than 1.0 rad RMS with the Radial Symmetry package. In the presence of coma, the localization error reaches 100 nm at ~0.6 rad RMS of aberration strength. The impact of noise and of astigmatism for axial resolution are also considered. Understanding the effect of aberrations is crucial when deciding whether the addition of adaptive optics to a single-molecule microscope could significantly increase the information obtainable from an image series. PMID:27231619

  1. Stepwise growth of surface-grafted DNA nanotubes visualized at the single-molecule level

    Hariri, Amani A.; Hamblin, Graham D.; Gidi, Yasser; Sleiman, Hanadi F.; Cosa, Gonzalo

    2015-04-01

    DNA nanotubes offer a high aspect ratio and rigidity, attractive attributes for the controlled assembly of hierarchically complex linear arrays. It is highly desirable to control the positioning of rungs along the backbone of the nanotubes, minimize the polydispersity in their manufacture and reduce the building costs. We report here a solid-phase synthesis methodology in which, through a cyclic scheme starting from a ‘foundation rung’ specifically bound to the surface, distinct rungs can be incorporated in a predetermined manner. Each rung is orthogonally addressable. Using fluorescently tagged rungs, single-molecule fluorescence studies demonstrated the robustness and structural fidelity of the constructs and confirmed the incorporation of the rungs in quantitative yield (>95%) at each step of the cycle. Prototype structures that consisted of up to 20 repeat units, about 450 nm in contour length, were constructed. Combined, the solid-phase synthesis strategy described and its visualization through single-molecule spectroscopy show good promise for the production of custom-made DNA nanotubes.

  2. Biocompatible fluorescent silicon nanocrystals for single-molecule tracking and fluorescence imaging.

    Nishimura, Hirohito; Ritchie, Ken; Kasai, Rinshi S; Goto, Miki; Morone, Nobuhiro; Sugimura, Hiroyuki; Tanaka, Koichiro; Sase, Ichiro; Yoshimura, Akihiko; Nakano, Yoshitaro; Fujiwara, Takahiro K; Kusumi, Akihiro

    2013-09-16

    Fluorescence microscopy is used extensively in cell-biological and biomedical research, but it is often plagued by three major problems with the presently available fluorescent probes: photobleaching, blinking, and large size. We have addressed these problems, with special attention to single-molecule imaging, by developing biocompatible, red-emitting silicon nanocrystals (SiNCs) with a 4.1-nm hydrodynamic diameter. Methods for producing SiNCs by simple chemical etching, for hydrophilically coating them, and for conjugating them to biomolecules precisely at a 1:1 ratio have been developed. Single SiNCs neither blinked nor photobleached during a 300-min overall period observed at video rate. Single receptor molecules in the plasma membrane of living cells (using transferrin receptor) were imaged for ≥10 times longer than with other probes, making it possible for the first time to observe the internalization process of receptor molecules at the single-molecule level. Spatial variations of molecular diffusivity in the scale of 1-2 µm, i.e., a higher level of domain mosaicism in the plasma membrane, were revealed. PMID:24043702

  3. Single-molecule study on polymer diffusion in a melt state: Effect of chain topology

    Habuchi, Satoshi

    2013-08-06

    We report a new methodology for studying diffusion of individual polymer chains in a melt state, with special emphasis on the effect of chain topology. A perylene diimide fluorophore was incorporated into the linear and cyclic poly(THF)s, and real-time diffusion behavior of individual chains in a melt of linear poly(THF) was measured by means of a single-molecule fluorescence imaging technique. The combination of mean squared displacement (MSD) and cumulative distribution function (CDF) analysis demonstrated the broad distribution of diffusion coefficient of both the linear and cyclic polymer chains in the melt state. This indicates the presence of spatiotemporal heterogeneity of the polymer diffusion which occurs at much larger time and length scales than those expected from the current polymer physics theory. We further demonstrated that the cyclic chains showed marginally slower diffusion in comparison with the linear counterparts, to suggest the effective suppression of the translocation through the threading-entanglement with the linear matrix chains. This coincides with the higher activation energy for the diffusion of the cyclic chains than of the linear chains. These results suggest that the single-molecule imaging technique provides a powerful tool to analyze complicated polymer dynamics and contributes to the molecular level understanding of the chain interaction. © 2013 American Chemical Society.

  4. Single molecule simulations in complex geometries with embedded dynamic one-dimensional structures

    Hellander, Stefan

    2013-01-01

    Stochastic models of reaction-diffusion systems are important for the study of biochemical reaction networks where species are present in low copy numbers or if reactions are highly diffusion limited. In living cells many such systems include reactions and transport on one-dimensional structures, such as DNA and microtubules. The cytoskeleton is a dynamic structure where individual fibers move, grow and shrink. In this paper we present a simulation algorithm that combines single molecule simulations in three-dimensional space with single molecule simulations on one-dimensional structures of arbitrary shape. Molecules diffuse and react with each other in space, they associate to and dissociate from one-dimensional structures as well as diffuse and react with each other on the one-dimensional structure. A general curve embedded in space can be approximated by a piecewise linear curve to arbitrary accuracy. The resulting algorithm is hence very flexible. Molecules bound to a curve can move by pure diffusion or v...

  5. Single molecule DNA interaction kinetics of retroviral nucleic acid chaperone proteins

    Williams, Mark

    2010-03-01

    Retroviral nucleocapsid (NC) proteins are essential for several viral replication processes including specific genomic RNA packaging and reverse transcription. The nucleic acid chaperone activity of NC facilitates the latter process. In this study, we use single molecule biophysical methods to quantify the DNA interactions of wild type and mutant human immunodeficiency virus type 1 (HIV-1) NC and Gag and human T-cell leukemia virus type 1 (HTLV-1) NC. We find that the nucleic acid interaction properties of these proteins differ significantly, with HIV-1 NC showing rapid protein binding kinetics, significant duplex destabilization, and strong DNA aggregation, all properties that are critical components of nucleic acid chaperone activity. In contrast, HTLV-1 NC exhibits significant destabilization activity but extremely slow DNA interaction kinetics and poor aggregating capability, which explains why HTLV-1 NC is a poor nucleic acid chaperone. To understand these results, we developed a new single molecule method for quantifying protein dissociation kinetics, and applied this method to probe the DNA interactions of wild type and mutant HIV-1 and HTLV-1 NC. We find that mutations to aromatic and charged residues strongly alter the proteins' nucleic acid interaction kinetics. Finally, in contrast to HIV-1 NC, HIV-1 Gag, the nucleic acid packaging protein that contains NC as a domain, exhibits relatively slow binding kinetics, which may negatively impact its ability to act as a nucleic acid chaperone.

  6. Electron diffraction of CBr4 in superfluid helium droplets: A step towards single molecule diffraction

    He, Yunteng; Zhang, Jie; Kong, Wei

    2016-07-01

    We demonstrate the practicality of electron diffraction of single molecules inside superfluid helium droplets using CBr4 as a testing case. By reducing the background from pure undoped droplets via multiple doping, with small corrections for dimers and trimers, clearly resolved diffraction rings of CBr4 similar to those of gas phase molecules can be observed. The experimental data from CBr4 doped droplets are in agreement with both theoretical calculations and with experimental results of gaseous species. The abundance of monomers and clusters in the droplet beam also qualitatively agrees with the Poisson statistics. Possible extensions of this approach to macromolecular ions will also be discussed. This result marks the first step in building a molecular goniometer using superfluid helium droplet cooling and field induced orientation. The superior cooling effect of helium droplets is ideal for field induced orientation, but the diffraction background from helium is a concern. This work addresses this background issue and identifies a possible solution. Accumulation of diffraction images only becomes meaningful when all images are produced from molecules oriented in the same direction, and hence a molecular goniometer is a crucial technology for serial diffraction of single molecules.

  7. Group transfer theory of single molecule imaging experiments in the F-ATPase biomolecular motor

    Volkan-Kacso, Sandor; Marcus, Rudolph

    I describe a chemo-mechanical theory to treat single molecule imaging and ``stalling'' experiments on the F-ATPase enzyme. This enzyme is an effective stepping biomolecular rotary motor with a rotor shaft and a stator ring. Using group transfer theoretical approach the proposed structure-based theory couples the binding transition of nucleotides in the stator subunits and the physics of torsional elasticity in the rotor. The twisting of the elastic rotor domain acts as a perturbation upon the driving potential, the Gibbs free energy. In the theory, without the use of adjustastable parameters, we predict the rate and equilibrium constant dependence of steps such as ATP binding and phosphate release as a function of manipulated rotor angle. Then we compare these predictions to available data from stalling experiments. Besides treating experiments, the theory can provide guides for atomistic simulations, which could calculate the reorganization parameter and the torsional spring constant. The framework is generic and I discuss its application to other single molecule experiments, such as controlled rotation and other biomolecular motors, including motor-DNA complexes and linear motors.[PNAS, Early Edition, Oct. 19, 2015, doi: 10.1073/pnas.1518489112

  8. Investigation of saturation and photobleaching of allophycocyanin by single-molecule recrossing events.

    Tian, Yu; Pappas, Dimitri

    2010-03-01

    Phycobiliprotein fluorescent labels are playing an increasingly important role in bioanalysis. They are also being used more and more frequently as light-harvesting materials for energy research. It is therefore critical to study the working conditions of these fluorescent dyes. Allophycocyanin (APC) belongs to a group of phycobiliproteins and features red excitation and emission, making it both a useful fluorophore and light-harvesting material. Saturation irradiance and photobleaching of APC were studied by single-molecule detection in this work. The mean fluorescence intensity at different laser powers was calculated from extracted single-molecule fluorescence peaks. By interpolating the figure of the mean fluorescence intensity as a function of excitation power, the experimental saturation irradiance can be extracted. By comparing the experimental with the calculated saturation irradiance, it can be demonstrated that the triplet state for APC was formed at higher excitation irradiance. The technique of molecular recrossing events was applied to investigate the photobleaching of APC. Normalized recrossing events confirmed that photobleaching occurred at high excitation power. This work provided the optimizing experimental conditions for APC both as a fluorophore and as a light-harvesting molecule. PMID:20223069

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

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

    2016-03-01

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

  10. Single-molecule studies of DNA transcription using atomic force microscopy

    Atomic force microscopy (AFM) can detect single biomacromolecules with a high signal-to-noise ratio on atomically flat biocompatible support surfaces, such as mica. Contrast arises from the innate forces and therefore AFM does not require imaging contrast agents, leading to sample preparation that is relatively straightforward. The ability of AFM to operate in hydrated environments, including humid air and aqueous buffers, allows structure and function of biological and biomolecular systems to be retained. These traits of the AFM are ensuring that it is being increasingly used to study deoxyribonucleic acid (DNA) structure and DNA–protein interactions down to the secondary structure level. This report focuses in particular on reviewing the applications of AFM to the study of DNA transcription in reductionist single-molecule bottom-up approaches. The technique has allowed new insights into the interactions between ribonucleic acid (RNA) polymerase to be gained and enabled quantification of some aspects of the transcription process, such as promoter location, DNA wrapping and elongation. More recently, the trend is towards studying the interactions of more than one enzyme operating on a single DNA template. These methods begin to reveal the mechanics of gene expression at the single-molecule level and will enable us to gain greater understanding of how the genome is transcribed and translated into the proteome. (topical review)

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

    Boghossian, Ardemis A; Zhang, Jingqing; Le Floch-Yin, François T; Ulissi, Zachary W; Bojo, Peter; Han, Jae-Hee; Kim, Jong-Ho; Arkalgud, Jyoti R; Reuel, Nigel F; Braatz, Richard D; Strano, Michael S

    2011-08-28

    Recent advances in nanotechnology have produced the first sensor transducers capable of resolving the adsorption and desorption of single molecules. Examples include near infrared fluorescent single-walled carbon nanotubes that report single-molecule binding via stochastic quenching. A central question for the theory of such sensors is how to analyze stochastic adsorption events and extract the local concentration or flux of the analyte near the sensor. In this work, we compare algorithms of varying complexity for accomplishing this by first constructing a kinetic Monte Carlo model of molecular binding and unbinding to the sensor substrate and simulating the dynamics over wide ranges of forward and reverse rate constants. Methods involving single-site probability calculations, first and second moment analysis, and birth-and-death population modeling are compared for their accuracy in reconstructing model parameters in the presence and absence of noise over a large dynamic range. Overall, birth-and-death population modeling was the most robust in recovering the forward rate constants, with the first and second order moment analysis very efficient when the forward rate is large (>10(-3) s(-1)). The precision decreases with increasing noise, which we show masks the existence of underlying states. Precision is also diminished with very large forward rate constants, since the sensor surface quickly and persistently saturates. PMID:21895176

  12. Chitosan-coated anisotropic silver nanoparticles as a SERS substrate for single-molecule detection

    Surface-enhanced Raman spectroscopy (SERS) is a technique that has become widely used for identifying and providing structural information about molecular species in low concentration. There is an ongoing interest in finding optimum particle size, shape and spatial distribution for optimizing the SERS substrates and pushing the sensitivity toward the single-molecule detection limit. This work reports the design of a novel, biocompatible SERS substrate based on small clusters of anisotropic silver nanoparticles embedded in a film of chitosan biopolymer. The SERS efficiency of the biocompatible film is assessed by employing Raman imaging and spectroscopy of adenine, a significant biological molecule. By combining atomic force microscopy with SERS imaging we find that the chitosan matrix enables the formation of small clusters of silver nanoparticles, with junctions and gaps that greatly enhance the Raman intensities of the adsorbed molecules. The study demonstrates that chitosan-coated anisotropic silver nanoparticle clusters are sensitive enough to be implemented as effective plasmonic substrates for SERS detection of nonresonant analytes at the single-molecule level. (paper)

  13. A comparison of single molecule and amplification based sequencing of cancer transcriptomes.

    Lee T Sam

    Full Text Available The second wave of next generation sequencing technologies, referred to as single-molecule sequencing (SMS, carries the promise of profiling samples directly without employing polymerase chain reaction steps used by amplification-based sequencing (AS methods. To examine the merits of both technologies, we examine mRNA sequencing results from single-molecule and amplification-based sequencing in a set of human cancer cell lines and tissues. We observe a characteristic coverage bias towards high abundance transcripts in amplification-based sequencing. A larger fraction of AS reads cover highly expressed genes, such as those associated with translational processes and housekeeping genes, resulting in relatively lower coverage of genes at low and mid-level abundance. In contrast, the coverage of high abundance transcripts plateaus off using SMS. Consequently, SMS is able to sequence lower- abundance transcripts more thoroughly, including some that are undetected by AS methods; however, these include many more mapping artifacts. A better understanding of the technical and analytical factors introducing platform specific biases in high throughput transcriptome sequencing applications will be critical in cross platform meta-analytic studies.

  14. Light sheet microscopy for tracking single molecules on the apical surface of living cells.

    Li, Yu; Hu, Ying; Cang, Hu

    2013-12-12

    Single particle tracking is a powerful tool to study single molecule dynamics in living biological samples. However, current tracking techniques, which are based mainly on epifluorescence, confocal, or TIRF microscopy, have difficulties in tracking single molecules on the apical surface of a cell. We present here a three-dimensional (3D) single particle tracking technique that is based on prism coupled light-sheet microscopy (PCLSM). This novel design provides a signal-to-noise ratio comparable to confocal microscopy while it has the capability of illuminating at arbitrary depth. We demonstrate tracking of single EGF molcules on the apical surface of live cell membranes from their binding to EGF receptors until they are internalized or photobleached. We found that EGF exhibits multiple diffusion behaviors on live A549 cell membranes. At room temperature, the average diffusion coefficient of EGF on A549 cells was measured to be 0.13 μm(2)/s. Depletion of cellular cholesterol with methyl-β-cyclodextrin leads to a broader distribution of diffusion coefficients and an increase of the average diffusion coefficient at room temperature. This light-sheet based 3D single particle tracking technique solves the technique difficulty of tracking single particles on apical membranes and is able to document the whole "lifetime" of a particle from binding till photobleaching or internalization. PMID:23895420

  15. Plasmonics and single-molecule detection in evaporated silver-island films

    Moula, G.; Aroca, R.F. [Materials and Surface Science Group, University of Windsor, Ontario (Canada); Rodriguez-Oliveros, R.; Sanchez-Gil, J.A. [Instituto de Estructura de la Materia, Consejo Superior de Investigaciones Cientificas, Serrano 121, 28006 Madrid (Spain); Albella, P. [Centro de Fisica de Materiales (CSIC-UPV/EHU) and Donostia International Physics Center (DIPC), 20018 Donostia, San Sebastian (Spain)

    2012-11-15

    The plasmonic origin of surface-enhanced Raman scattering (SERS) leads to the concept of hotspots and plasmon coupling that can be realized in the interstitial regions, or on specially engineered, silver and gold nanostructures. It is also possible to achieve spatial locations of high local field or hotspots on silver-island films (SIF) allowing single-molecule detection (SMD). When a single monomolecular layer coating the SIFs contains dye molecules dispersed in it, single-molecule impurities, (with an average of one hundred dye molecules in 1 {mu}m{sup 2}, which is the field of view of the micro-Raman system), SMD is observed as a rare statistical event. Here, the SMD results for silver-island films are presented, with the same nominal mass thickness, but differing in the localized surface plasmon resonance that is a function of the temperature of substrate during deposition. A blue-shifted plasmon can be seen as a decrease in plasmon coupling for deposition at higher temperature. A simple two-particle model for localized plasmon resonance coupling calculations, including the shape and substrate effects seems to explain the trend of observations. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  16. Single-Molecule Imaging Reveals Topology Dependent Mutual Relaxation of Polymer Chains

    Abadi, Maram

    2015-08-24

    The motion and relaxation of linear and cyclic polymers under entangled conditions are investigated by means of a newly developed single-molecule tracking technique, cumulative-area (CA) tracking. CA tracking enables simultaneous quantitative characterization of the diffusion mode, diffusion rate, and relaxation time that have been impossible with a widely used conventional single-molecule localization and tracking method, by analyzing cumulative areas occupied by the moving molecule. Using the novel approach, we investigate the motion and relaxation of entangled cyclic polymers, which have been an important but poorly understood question. Fluorescently labeled 42 kbp linear or cyclic tracer dsDNAs in concentrated solutions of unlabeled linear or cyclic DNAs are used as model systems. We show that CA tracking can explicitly distinguish topology-dependent diffusion mode, rate, and relaxation time, demonstrating that the method provides an invaluable tool for characterizing topological interaction between the entangled chains. We further demonstrate that the current models proposed for the entanglement between cyclic polymers which are based on cyclic chains moving through an array of fixed obstacles cannot correctly describe the motion of the cyclic chain under the entangled conditions. Our results rather suggest the mutual relaxation of the cyclic chains, which underscore the necessity of developing a new model to describe the motion of cyclic polymer under the entangled conditions based on the mutual interaction of the chains.

  17. Effects of bonding type and interface geometry on coherent transport through the single-molecule magnet Mn12

    Park, Kyungwha; Barraza-Lopez, Salvador; García-Suárez, Víctor M.; Ferrer, Jaime

    2010-01-01

    We examine theoretically coherent electron transport through the single-molecule magnet Mn-12, bridged between Au(111) electrodes, using the nonequilibrium Green's function method and the density-functional theory. We analyze the effects of bonding type, molecular orientation, and geometry relaxation on the electronic properties and charge and spin transport across the single-molecule junction. We consider nine interface geometries leading to five bonding mechanisms and two molecular orientat...

  18. Structure-property relationships in redox-gated single molecule junctions - A comparison of pyrrolo-tetrathiafulvalene and viologen redox groups

    Leary, E.; Higgins, S.J.; van Zalinge, H.; Haiss, W.; Nichols, Richard John; Nygaard, Sune; Jeppesen, Jan Oskar; Ulstrup, Jens

    2008-01-01

    We demonstrate that the electrical 'switching" behavior of single molecules connected between two electrode contacts can be controlled by altering their structure and electrochemical characteristics. The electrical properties of gold vertical bar molecule vertical bar gold single molecule junctio...

  19. Universal entropy relations: entropy formulae and entropy bound

    Liu, Hang; Meng, Xin-he; Xu, Wei; Zhu, Bin

    2016-01-01

    We survey the applications of universal entropy relations in black holes with multi-horizons. In sharp distinction to conventional entropy product, the entropy relationship here not only improve our understanding of black hole entropy but was introduced as an elegant technique trick for handling various entropy bounds and sum. Despite the primarily technique role, entropy relations have provided considerable insight into several different types of gravity, including massive gravity, Einstein-...

  20. Single-molecule analysis of DNA cross-links using nanopore technology

    Wolna, Anna H.

    The alpha-hemolysin (alpha-HL) protein ion channel is a potential next-generation sequencing platform that has been extensively used to study nucleic acids at a single-molecule level. After applying a potential across a lipid bilayer, the imbedded alpha-HL allows monitoring of the duration and current levels of DNA translocation and immobilization. Because this method does not require DNA amplification prior to sequencing, all the DNA damage present in the cell at any given time will be present during the sequencing experiment. The goal of this research is to determine if these damage sites give distinguishable current levels beyond those observed for the canonical nucleobases. Because DNA cross-links are one of the most prevalent types of DNA damage occurring in vivo, the blockage current levels were determined for thymine-dimers, guanine(C8)-thymine(N3) cross-links and platinum adducts. All of these cross-links give a different blockage current level compared to the undamaged strands when immobilized in the ion channel, and they all can easily translocate across the alpha-HL channel. Additionally, the alpha-HL nanopore technique presents a unique opportunity to study the effects of DNA cross-links, such as thymine-dimers, on the secondary structure of DNA G-quadruplexes folded from the human telomere sequence. Using this single-molecule nanopore technique we can detect subtle structural differences that cannot be easily addressed using conventional methods. The human telomere plays crucial roles in maintaining genome stability. In the presence of suitable cations, the repetitive 5'-TTAGGG human telomere sequence can fold into G-quadruplexes that adopt the hybrid fold in vivo. The telomere sequence is hypersensitive to UV-induced thymine-dimer (T=T) formation, and yet the presence of thymine dimers does not cause telomere shortening. The potential structural disruption and thermodynamic stability of the T=T-containing natural telomere sequences were studied to

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

    Pan, Shanlin [Univ. of Alabama, Tuscaloosa, AL (United States)

    2014-11-16

    Our research under support of this DOE grant is focused on applied and fundamental aspects of model organic solar cell systems. Major accomplishments are: 1) we developed a spectroelectorchemistry technique of single molecule single nanoparticle method to study charge transfer between conjugated polymers and semiconductor at the single molecule level. The fluorescence of individual fluorescent polymers at semiconductor surfaces was shown to exhibit blinking behavior compared to molecules on glass substrates. Single molecule fluorescence excitation anisotropy measurements showed the conformation of the polymer molecules did not differ appreciably between glass and semiconductor substrates. The similarities in molecular conformation suggest that the observed differences in blinking activity are due to charge transfer between fluorescent polymer and semiconductor, which provides additional pathways between states of high and low fluorescence quantum efficiency. Similar spectroelectrochemistry work has been done for small organic dyes for understand their charge transfer dynamics on various substrates and electrochemical environments; 2) We developed a method of transferring semiconductor nanoparticles (NPs) and graphene oxide (GO) nanosheets into organic solvent for a potential electron acceptor in bulk heterojunction organic solar cells which employed polymer semiconductor as the electron donor. Electron transfer from the polymer semiconductor to semiconductor and GO in solutions and thin films was established through fluorescence spectroscopy and electroluminescence measurements. Solar cells containing these materials were constructed and evaluated using transient absorption spectroscopy and dynamic fluorescence techniques to understand the charge carrier generation and recombination events; 3) We invented a spectroelectorchemistry technique using light scattering and electroluminescence for rapid size determination and studying electrochemistry of single NPs in an

  2. Bayesian Decision Tree for the Classification of the Mode of Motion in Single-Molecule Trajectories

    Türkcan, Silvan

    2015-01-01

    Membrane proteins move in heterogeneous environments with spatially (sometimes temporally) varying friction and with biochemical interactions with various partners. It is important to reliably distinguish different modes of motion to improve our knowledge of the membrane architecture and to understand the nature of interactions between membrane proteins and their environments. Here, we present an analysis technique for single molecule tracking (SMT) trajectories that can determine the preferred model of motion that best matches observed trajectories. Information theory criteria, such as the Bayesian information criterion (BIC), the Akaike information criterion (AIC), and modified AIC (AICc), are used to select the preferred model. The considered group of models includes free Brownian motion, and confined motion in 2nd or 4th order potentials. We determine the best information criteria for classifying trajectories. We tested its limits through simulations matching large sets of experimental conditions and buil...

  3. Interfacial electrochemical electron transfer in biology – Towards the level of the single molecule

    Zhang, Jingdong; Chi, Qijin; Hansen, Allan Glargaard;

    2012-01-01

    Physical electrochemistry has undergone a remarkable evolution over the last few decades, integrating advanced techniques and theory from solid state and surface physics. Single-crystal electrode surfaces have been a core notion, opening for scanning tunnelling microscopy directly in aqueous...... electrolyte (in situ STM). Interfacial electrochemistry of metalloproteins is presently going through a similar transition. Electrochemical surfaces with thiol-based promoter molecular monolayers (SAMs) as biomolecular electrochemical environments and the biomolecules themselves have been mapped with...... unprecedented resolution, opening a new area of single-molecule bioelectrochemistry. We consider first in situ STM of small redox molecules, followed by in situ STM of thiol-based SAMs as molecular views of bioelectrochemical environments. We then address electron transfer metalloproteins, and multi...

  4. Stable metal-organic frameworks containing single-molecule traps for enzyme encapsulation

    Feng, Dawei; Liu, Tian-Fu; Su, Jie; Bosch, Mathieu; Wei, Zhangwen; Wan, Wei; Yuan, Daqiang; Chen, Ying-Pin; Wang, Xuan; Wang, Kecheng; Lian, Xizhen; Gu, Zhi-Yuan; Park, Jihye; Zou, Xiaodong; Zhou, Hong-Cai

    2015-01-01

    Enzymatic catalytic processes possess great potential in chemical manufacturing, including pharmaceuticals, fuel production and food processing. However, the engineering of enzymes is severely hampered due to their low operational stability and difficulty of reuse. Here, we develop a series of stable metal-organic frameworks with rationally designed ultra-large mesoporous cages as single-molecule traps (SMTs) for enzyme encapsulation. With a high concentration of mesoporous cages as SMTs, PCN-333(Al) encapsulates three enzymes with record-high loadings and recyclability. Immobilized enzymes that most likely undergo single-enzyme encapsulation (SEE) show smaller Km than free enzymes while maintaining comparable catalytic efficiency. Under harsh conditions, the enzyme in SEE exhibits better performance than free enzyme, showing the effectiveness of SEE in preventing enzyme aggregation or denaturation. With extraordinarily large pore size and excellent chemical stability, PCN-333 may be of interest not only for enzyme encapsulation, but also for entrapment of other nanoscaled functional moieties.

  5. Time-, Frequency-, and Wavevector-Resolved X-Ray Diffraction from Single Molecules

    Bennett, Kochise; Zhang, Yu; Dorfman, Konstantin E; Mukamel, Shaul

    2014-01-01

    Using a quantum electrodynamic framework, we calculate the off-resonant scattering of a broad-band 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 ...

  6. Comparison of Techniques for Single-Molecule Conductance Measurements of Expanded Pyridinium Molecules

    Lachmanová, Štěpánka; Hromadová, Magdaléna; Sokolová, Romana; Kocábová, Jana; Gasior, Jindřich; Mészáros, G.; Lainé, P. P.

    Ústí nad Labem : Srsenová Lenka - Best Servis, 2015 - (Navrátil, T.; Fojta, M.; Schwarzová, K.), s. 124-127 ISBN 978-80-905221-3-8. [Moderní elektrochemické metody /35./. Jetřichovice (CZ), 18.05.2015-22.05.2015] R&D Projects: GA ČR(CZ) GA14-05180S Grant ostatní: Rada Programu interní porpory projektů mezinárodní spolupráce AV ČR M200401202; GA MŠk(CZ) 7AMB15FR027; GA AV(CZ) HU/2013/05 Institutional support: RVO:61388955 Keywords : Single-molecule conductance * Scanning Tunneling Microscopy Break Junction * Mechanically Controled Break Junction Subject RIV: CG - Electrochemistry

  7. Shot noise of the spin inelastic tunneling through a quantum dot with single molecule-magnet

    Chang Bo; Liang Jiu-Qing

    2011-01-01

    We have studied the quantum fluctuations of inelastic spin-electron scattering in quantum dot with an embedded biaxial single molecule-magnet and particularly investigated the zero-frequency shot noise and Fano factor in different magnetic fields. It is found that the shot noise and Fano factor exhibit a stepwise behaviour as bias increases in the presence of interaction between the electron and molecule-magnet for a weak magnetic field. As magnetic field becomes strong, a dip is displayed in the shot-noise-bias curve due to the suppression of inelastic shot noise caused by the quantum tunneling of magnetisation. Because of the spontaneous inelastic tunneling at zero bias, a small shot noise occurs, which results in the case of Fano factor F > 1. Moreover, our results show that the sweeping speed can also influence the shot noise and Fano factor obviously.

  8. Shot noise of the spin inelastic tunneling through a quantum dot with single molecule-magnet

    We have studied the quantum fluctuations of inelastic spin-electron scattering in quantum dot with an embedded biaxial single molecule-magnet and particularly investigated the zero-frequency shot noise and Fano factor in different magnetic fields. It is found that the shot noise and Fano factor exhibit a stepwise behaviour as bias increases in the presence of interaction between the electron and molecule-magnet for a weak magnetic field. As magnetic field becomes strong, a dip is displayed in the shot-noise-bias curve due to the suppression of inelastic shot noise caused by the quantum tunneling of magnetisation. Because of the spontaneous inelastic tunneling at zero bias, a small shot noise occurs, which results in the case of Fano factor F ≫ 1. Moreover, our results show that the sweeping speed can also influence the shot noise and Fano factor obviously. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  9. A single-molecule approach to explore binding, uptake and transport of cancer cell targeting nanotubes

    In the past decade carbon nanotubes (CNTs) have been widely studied as a potential drug-delivery system, especially with functionality for cellular targeting. Yet, little is known about the actual process of docking to cell receptors and transport dynamics after internalization. Here we performed single-particle studies of folic acid (FA) mediated CNT binding to human carcinoma cells and their transport inside the cytosol. In particular, we employed molecular recognition force spectroscopy, an atomic force microscopy based method, to visualize and quantify docking of FA functionalized CNTs to FA binding receptors in terms of binding probability and binding force. We then traced individual fluorescently labeled, FA functionalized CNTs after specific uptake, and created a dynamic ‘roadmap’ that clearly showed trajectories of directed diffusion and areas of nanotube confinement in the cytosol. Our results demonstrate the potential of a single-molecule approach for investigation of drug-delivery vehicles and their targeting capacity. (paper)

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

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

    2015-05-01

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

  11. Quantifying molecule-surface interactions using AFM-based single-molecule manipulation

    Tautz, F. S.; Wagner, C.; Temirov, R.; Fournier, N.; Green, M.; Esat, T.; Leinen, P.; Groetsch, A.; Ruiz, V. G.; Tkatchenko, A.; Li, C.; Muellen, K.; Rohlfing, M.

    2015-03-01

    Scanning probe microscopy plays an important role in the investigation of molecular adsorption. Promising, is the possibility to probe the molecule-surface interaction while tuning its strength through AFM tip-induced single-molecule manipulation. Here, we outline a strategy to achieve quantitative understanding of such manipulation experiments. The example of qPlus sensor based PTCDA molecule lifting experiments is used to demonstrate how different aspects of the molecule-surface interaction, namely the short-range adsorption potential, the asymptotic van der Waals potential, local chemical bonds which are the source of the surface corrugation, and molecule-molecule interactions can be measured with SPM and interpreted by the help of force-field simulations.

  12. Single Molecule Localization Microscopy of Mammalian Cell Nuclei on the Nanoscale.

    Szczurek, Aleksander; Xing, Jun; Birk, Udo J; Cremer, Christoph

    2016-01-01

    Nuclear texture analysis is a well-established method of cellular pathology. It is hampered, however, by the limits of conventional light microscopy (ca. 200 nm). These limits have been overcome by a variety of super-resolution approaches. An especially promising approach to chromatin texture analysis is single molecule localization microscopy (SMLM) as it provides the highest resolution using fluorescent based methods. At the present state of the art, using fixed whole cell samples and standard DNA dyes, a structural resolution of chromatin in the 50-100 nm range is obtained using SMLM. We highlight how the combination of localization microscopy with standard fluorophores opens the avenue to a plethora of studies including the spatial distribution of DNA and associated proteins in eukaryotic cell nuclei with the potential to elucidate the functional organization of chromatin. These views are based on our experience as well as on recently published research in this field. PMID:27446198

  13. Fluorescence imaging for bacterial cell biology: from localization to dynamics, from ensembles to single molecules.

    Yao, Zhizhong; Carballido-López, Rut

    2014-01-01

    Fluorescent proteins and developments in superresolution (nanoscopy) and single-molecule techniques bring high sensitivity, speed, and one order of magnitude gain in spatial resolution to live-cell imaging. These technologies have only recently been applied to prokaryotic cell biology, revealing the exquisite subcellular organization of bacterial cells. Here, we review the parallel evolution of fluorescence microscopy methods and their application to bacteria, mainly drawing examples from visualizing actin-like MreB proteins in the model bacterium Bacillus subtilis. We describe the basic principles of nanoscopy and conventional techniques and their advantages and limitations to help microbiologists choose the most suitable technique for their biological question. Looking ahead, multidimensional live-cell nanoscopy combined with computational image analysis tools, systems biology approaches, and mathematical modeling will provide movie-like, mechanistic, and quantitative description of molecular events in bacterial cells. PMID:25002084

  14. Energy transfer pathway probed by single-molecule pump-dump experiment

    Tao, Ming-Jie; Deng, Fu-Guo; Cheng, Yuan-Chung

    2015-01-01

    The structure of Fenna-Matthews-Olson (FMO) light-harvesting complex has long been recognized as containing seven bacteriochlorophyll (BChl) molecules. Recently, an additional BChl molecule was discovered in the crystal structure of the FMO complex, which may serve as a link between baseplate and the remaining seven molecules. Here, we investigate excitation energy transfer (EET) process by simulating single-molecule pump-dump experiment in the eight-molecules complex. We adopt the coherent modified Redfield theory and non-Markovian quantum jump method to simulate EET dynamics. This scheme provides a practical approach of detecting the realistic EET pathway in BChl complexes with currently available experimental technology. And it may assist optimizing design of artificial light-harvesting devices.

  15. Proposal for probing energy transfer pathway by single-molecule pump-dump experiment

    Tao, Ming-Jie; Ai, Qing; Deng, Fu-Guo; Cheng, Yuan-Chung

    2016-06-01

    The structure of Fenna-Matthews-Olson (FMO) light-harvesting complex had long been recognized as containing seven bacteriochlorophyll (BChl) molecules. Recently, an additional BChl molecule was discovered in the crystal structure of the FMO complex, which may serve as a link between baseplate and the remaining seven molecules. Here, we investigate excitation energy transfer (EET) process by simulating single-molecule pump-dump experiment in the eight-molecules complex. We adopt the coherent modified Redfield theory and non-Markovian quantum jump method to simulate EET dynamics. This scheme provides a practical approach of detecting the realistic EET pathway in BChl complexes with currently available experimental technology. And it may assist optimizing design of artificial light-harvesting devices.

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

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

    2015-03-01

    We theoretically investigate, as a function of the stretching, the behaviour of the thermoelectric properties - Seebeck coefficient (S), the electronic heat conductance (κel) and the figure of merit (ZT) - of a molecule-based junction composed by benzene-1,4-dithiol molecule (BDT) coupled to Au(111) surfaces at room temperature. We show that the thermoelectric properties of a single molecule junction can be tuned by mechanic stretching. The Seebeck coefficient is positive, indicating that it is dominated by the HOMO. Furthermore, it increases as the HOMO level, which is associated to the sulphur atom, goes to energies close to the Fermi energy. By modelling the transmission coefficient of the system as a single lorentzian peak, we propose a scheme to obtain the maximum ZT of any molecular junction. The authors thank the Brazilian funding agencies CNPq, CAPES and FAPESP. We also thank CENAPAD-SP for the computational facilities.

  17. A single-molecule approach to explore binding, uptake and transport of cancer cell targeting nanotubes

    Lamprecht, C.; Plochberger, B.; Ruprecht, V.; Wieser, S.; Rankl, C.; Heister, E.; Unterauer, B.; Brameshuber, M.; Danzberger, J.; Lukanov, P.; Flahaut, E.; Schütz, G.; Hinterdorfer, P.; Ebner, A.

    2014-03-01

    In the past decade carbon nanotubes (CNTs) have been widely studied as a potential drug-delivery system, especially with functionality for cellular targeting. Yet, little is known about the actual process of docking to cell receptors and transport dynamics after internalization. Here we performed single-particle studies of folic acid (FA) mediated CNT binding to human carcinoma cells and their transport inside the cytosol. In particular, we employed molecular recognition force spectroscopy, an atomic force microscopy based method, to visualize and quantify docking of FA functionalized CNTs to FA binding receptors in terms of binding probability and binding force. We then traced individual fluorescently labeled, FA functionalized CNTs after specific uptake, and created a dynamic ‘roadmap’ that clearly showed trajectories of directed diffusion and areas of nanotube confinement in the cytosol. Our results demonstrate the potential of a single-molecule approach for investigation of drug-delivery vehicles and their targeting capacity.

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

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

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

  19. Single-molecule magnet behavior in 2,2'-bipyrimidine-bridged dilanthanide complexes.

    Yu, Wen; Schramm, Frank; Pineda, Eufemio Moreno; Lan, Yanhua; Fuhr, Olaf; Chen, Jinjie; Isshiki, Hironari; Wernsdorfer, Wolfgang; Wulfhekel, Wulf; Ruben, Mario

    2016-01-01

    A series of 2,2'-bipyrimidine-bridged dinuclear lanthanide complexes with the general formula [Ln(tmhd)3]2bpm (tmhd = 2,2,6,6-tetramethyl-3,5-heptanedionate, bpm = 2,2'-bipyrimidine, Ln = Gd(III), 1; Tb(III), 2; Dy(III), 3; Ho(III), 4 and Er(III), 5) has been synthesized and characterized. Sublimation of [Tb(tmhd)3]2bpm onto a Au(111) surface leads to the formation of a homogeneous film with hexagonal pattern, which was studied by scanning tunneling microscopy (STM). The bulk magnetic properties of all complexes have been studied comprehensively. The dynamic magnetic behavior of the Dy(III) and Er(III) compounds clearly exhibits single molecule magnet (SMM) characteristics with an energy barrier of 97 and 25 K, respectively. Moreover, micro-SQUID measurements on single crystals confirm their SMM behavior with the presence of hysteresis loops. PMID:26925361

  20. A variable-temperature scanning tunneling microscope capable of single-molecule vibrational spectroscopy

    The design and performance of a variable-temperature scanning tunneling microscope (STM) is presented. The microscope operates from 8 to 350 K in ultrahigh vacuum. The thermally compensated STM is suspended by springs from the cold tip of a continuous flow cryostat and is completely surrounded by two radiation shields. The design allows for in situ dosing and irradiation of the sample as well as for the exchange of samples and STM tips. With the STM feedback loop off, the drift of the tip-sample spacing is approximately 0.001 Angstrom/min at 8 K. It is demonstrated that the STM is well-suited for the study of atomic-scale chemistry over a wide temperature range, for atomic-scale manipulation, and for single-molecule inelastic electron tunneling spectroscopy (IETS). copyright 1999 American Institute of Physics

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

    Della Pia, Eduardo Antonio; Chi, Qijin; Macdonald, J. Emyr;

    2012-01-01

    The electron transfer properties of proteins are normally measured as molecularly averaged ensembles. Through these and related measurements, proteins are widely regarded as macroscopically insulating materials. Using scanning tunnelling microscopy (STM), we present new measurements of the...... conductance through single-molecules of the electron transfer protein cytochrome b562 in its native conformation, under pseudo-physiological conditions. This is achieved by thiol (SH) linker pairs at opposite ends of the molecule through protein engineering, resulting in defined covalent contact between a...... gold surface and a platinum–iridium STM tip. Two different orientations of the linkers were examined: a long-axis configuration (SH-LA) and a short-axis configuration (SH-SA). In each case, the molecular conductance could be ‘gated’ through electrochemical control of the heme redox state. Reproducible...

  2. Direct measurement and modulation of single-molecule coordinative bonding forces in a transition metal complex

    Hao, Xian; Zhu, Nan; Gschneidtner, Tina;

    2013-01-01

    Coordination chemistry has been a consistently active branch of chemistry since Werner's seminal theory of coordination compounds inaugurated in 1893, with the central focus on transition metal complexes. However, control and measurement of metal-ligand interactions at the single-molecule level...... remain a daunting challenge. Here we demonstrate an interdisciplinary and systematic approach that enables measurement and modulation of the coordinative bonding forces in a transition metal complex. Terpyridine is derived with a thiol linker, facilitating covalent attachment of this ligand on both gold...... significant impact on the metal-ligand interactions. The present approach represents a major advancement in unravelling the nature of metal-ligand interactions and could have broad implications in coordination chemistry....

  3. Conformational equilibria in monomeric alpha-synuclein at the single molecule level

    Sandal, Massimo; Tessari, Isabella; Mammi, Stefano; Bergantino, Elisabetta; Musiani, Francesco; Brucale, Marco; Bubacco, Luigi; Samori', Bruno

    2007-01-01

    Natively unstructured proteins defy the classical "one sequence-one structure" paradigm of protein science. Monomers of these proteins in pathological conditions can aggregate in the cell, a process that underlies socially relevant neurodegenerative diseases such as Alzheimer and Parkinson. A full comprehension of the formation and structure of the so-called misfolded intermediates from which the aggregated states ensue is still lacking. We characterized the folding and the conformational diversity of alpha-synuclein (aSyn), a natively unstructured protein involved in Parkinson disease, by mechanically stretching single molecules of this protein and recording their mechanical properties. These experiments permitted us to directly observe directly and quantify three main classes of conformations that, under in vitro physiological conditions, exist simultaneously in the aSyn sample, including disordered and "beta-like" structures. We found that this class of "beta-like" structures is directly related to aSyn ag...

  4. Conformations and adsorption behavior of poly(allylamine hydrochloride)studied by single molecule force spectroscopy

    2008-01-01

    Poly(allylamine hydrochIoride)(PAH),which is frequently used in fabricating polyelectrolyte multilayer films,was studied by single molecule force spectroscopy(SMFS).Plenty of force-extension curves with a long plateau were obtained in water,indicating that train-like structure was predominant when PAH was adsorbed on the substrate.It was found that the peak-type force-extension curves of PAH in water were not able to be fitted by the modified freely-iointed chain model.Additionally,there was a flat region in the derivative of force-extension curves.Thus.it was inferred that PAH chain in water was in a special conformation and underwent a"conformationaI transition"under the stretching of an external force.This phenomenon did not appear in the SMFS experiment in 1 mol/L urea solution,which indicated that urea was able to break the speciaI conformation.

  5. Single-molecule spectromicroscopy: a route towards sub-wavelength refractometry.

    Anikushina, T A; Gladush, M G; Gorshelev, A A; Naumov, A V

    2015-01-01

    We suggest a novel approach for spatially resolved probing of local fluctuations of the refractive index n in solids by means of single-molecule (SM) spectroscopy. It is based on the dependence T1(n) of the effective radiative lifetime T1 of dye centres in solids on n due to the local-field effects. Detection of SM zero-phonon lines at low temperatures gives the values of the SM natural spectral linewidth (which is inversely proportional to T1) and makes it possible to reveal the distribution of the local n values in solids. Here we demonstrate this possibility on the example of amorphous polyethylene and polycrystalline naphthalene doped with terrylene. In particular, we show that the obtained distributions of lifetime limited spectral linewidths of terrylene molecules embedded into these matrices are due to the spatial fluctuations of the refractive index local values. PMID:26415096

  6. Topoisomerase I as a Biomarker: Detection of Activity at the Single Molecule Level

    Proszek, Joanna; Roy, Amit; Jakobsen, Ann-Katrine;

    2014-01-01

    hTopI have been reported to result in CPT resistance. Therefore, hTOPI gene copy number, mRNA level, protein amount, and enzyme activity have been studied to explain differences in cellular response to CPT. We show that Rolling Circle Enhanced Enzyme Activity Detection (REEAD), allowing measurement...... of hTopI cleavage-religation activity at the single molecule level, may be used to detect posttranslational enzymatic differences influencing CPT response. These differences cannot be detected by analysis of hTopI gene copy number, mRNA amount, or protein amount, and only become apparent upon...... measuring the activity of hTopI in the presence of CPT. Furthermore, we detected differences in the activity of the repair enzyme tyrosyl-DNA phosphodiesterase 1, which is involved in repair of hTopI-induced DNA damage. Since increased TDP1 activity can reduce cellular CPT sensitivity we suggest that a...

  7. Fluorescence lifetime fluctuations of single molecules probe local density fluctuations in disordered media: a bulk approach.

    Vallée, R A L; Tomczak, N; Vancso, G J; Kuipers, L; van Hulst, N F

    2005-03-15

    We investigated the nanometer scale mobility of polymers in the glassy state by monitoring the dynamics of embedded single fluorophores. Recently we reported on fluorescence lifetime fluctuations which reflect the segmental rearrangement dynamics of the polymer in the surroundings of the single molecule probe. Here we focus on the nature of these fluorescence lifetime fluctuations. First the potential role of quenching and molecular conformational changes is discussed. Next we concentrate on the influence of the radiative density of states on the spontaneous emission of individual dye molecules embedded in a polymer. To this end we present a theory connecting the effective-medium theory to a cell-hole model, originating from the Simha-Somcynsky free-volume theory. The relation between the derived distributions of free volume and fluorescence lifetime allows one to determine the number of segments involved in the local rearrangement directly from experimental data. Results for two different polymers as a function of temperature are presented. PMID:15836240

  8. Data mining for materials design: A computational study of single molecule magnet

    We develop a method that combines data mining and first principles calculation to guide the designing of distorted cubane Mn4+ Mn 33+ single molecule magnets. The essential idea of the method is a process consisting of sparse regressions and cross-validation for analyzing calculated data of the materials. The method allows us to demonstrate that the exchange coupling between Mn4+ and Mn3+ ions can be predicted from the electronegativities of constituent ligands and the structural features of the molecule by a linear regression model with high accuracy. The relations between the structural features and magnetic properties of the materials are quantitatively and consistently evaluated and presented by a graph. We also discuss the properties of the materials and guide the material design basing on the obtained results

  9. Spin-dependent negative differential conductance in transport through single-molecule magnets

    Luo Wei; Wang Rui-Qiang; Hu Liang-Bin; Yang Mou

    2013-01-01

    Transport properties are theoretically studied through an anisotropy single-molecule magnet symmetrically connected to two identical ferromagnetic leads.It is found that even though in parallel configuration of leads' magnetizations,the total current still greatly depends on the spin polarization of leads at certain particular bias region,and thus for large polarization a prominent negative differential conductance (NDC) emerges.This originates from the joint effect of single-direction transitions and spin polarization,which removes the symmetry between spin-up and spin-down transitions.The present mechanism of NDC is remarkably different from the previously reported mechanisms.To clarify the physics of the NDC,we further monitored the shot noise spectroscopy and found that the appearance of the NDC is accompanied by the rapid decrease of Fano factor.

  10. Diagnosing Heterogeneous Dynamics in Single Molecule/Particle Trajectories with Multiscale Wavelets

    Chen, Kejia; Guan, Juan; Granick, Steve

    2013-01-01

    We describe a simple automated method to extract and quantify transient heterogeneous dynamical changes from large datasets generated in single molecule/particle tracking experiments. Based on wavelet transform, the method transforms raw data to locally match dynamics of interest. This is accomplished using statistically adaptive universal thresholding, whose advantage is to avoid a single arbitrary threshold that might conceal individual variability across populations. How to implement this multiscale method is described, focusing on local confined diffusion separated by transient transport periods or hopping events, with 3 specific examples: in cell biology, biotechnology, and glassy colloid dynamics. This computationally-efficient method can run routinely on hundreds of millions of data points analyzed within an hour on a desktop personal computer.

  11. Probing conformational changes of gramicidin ion channels by single-molecule patch-clamp fluorescence microscopy

    Harms, Gregory S.; Orr, Galya; Montal, Mauricio; Thrall, Brian D.; Colson, Steve D.; Lu, H Peter

    2003-09-01

    Stochastic and inhomogeneous conformational changes often regulate the dynamics of ion channels. Such inhomogeneity makes it difficult, if not impossible; to be characterized not only by ensemble-averaged experiments by also by single-channel patch recording that does not specifically probe the associated conformational changes. Here, we report on our work using a new approach combining single-molecule fluorescence spectroscopy and single-channel patch recording to investigate conformational changes of individual gramicidin ion channels. We observed fluorescence self-quenching and single-pair fluorescence resonance energy transfer (spFRET) from dye-labeled gramicidin dimmers within the channel was open. We also observed that the efficiency of self-quenching and spFRETS is widely distributed when the channel is closed. Our results strongly suggest a hitherto undetectable correlation of multiple conformational states of the gramicidin channel associated with closed and open states under physiologically-related conditions.

  12. Data mining for materials design: A computational study of single molecule magnet

    Dam, Hieu Chi; Pham, Tien Lam; Ho, Tu Bao; Nguyen, Anh Tuan; Nguyen, Viet Cuong

    2014-01-01

    We develop a method that combines data mining and first principles calculation to guide the designing of distorted cubane Mn4 +Mn^{3+}_3 single molecule magnets. The essential idea of the method is a process consisting of sparse regressions and cross-validation for analyzing calculated data of the materials. The method allows us to demonstrate that the exchange coupling between Mn4 + and Mn3 + ions can be predicted from the electronegativities of constituent ligands and the structural features of the molecule by a linear regression model with high accuracy. The relations between the structural features and magnetic properties of the materials are quantitatively and consistently evaluated and presented by a graph. We also discuss the properties of the materials and guide the material design basing on the obtained results.

  13. In silico single-molecule manipulation of DNA with rigid body dynamics.

    Pascal Carrivain

    2014-02-01

    Full Text Available We develop a new powerful method to reproduce in silico single-molecule manipulation experiments. We demonstrate that flexible polymers such as DNA can be simulated using rigid body dynamics thanks to an original implementation of Langevin dynamics in an open source library called Open Dynamics Engine. We moreover implement a global thermostat which accelerates the simulation sampling by two orders of magnitude. We reproduce force-extension as well as rotation-extension curves of reference experimental studies. Finally, we extend the model to simulations where the control parameter is no longer the torsional strain but instead the torque, and predict the expected behavior for this case which is particularly challenging theoretically and experimentally.

  14. In silico single-molecule manipulation of DNA with rigid body dynamics.

    Carrivain, Pascal; Barbi, Maria; Victor, Jean-Marc

    2014-02-01

    We develop a new powerful method to reproduce in silico single-molecule manipulation experiments. We demonstrate that flexible polymers such as DNA can be simulated using rigid body dynamics thanks to an original implementation of Langevin dynamics in an open source library called Open Dynamics Engine. We moreover implement a global thermostat which accelerates the simulation sampling by two orders of magnitude. We reproduce force-extension as well as rotation-extension curves of reference experimental studies. Finally, we extend the model to simulations where the control parameter is no longer the torsional strain but instead the torque, and predict the expected behavior for this case which is particularly challenging theoretically and experimentally. PMID:24586127

  15. Multiple states of the Tyr318Leu mutant of dihydroorotate dehydrogenase revealed by single molecule kinetics

    Shi, J.; Palfey, B.A.; Dertouzos, J.;

    2004-01-01

    single enzyme molecules through the characteristic on-off fluorescence signal, which corresponds to flavin mononucleotide (FMN) interconverting between the oxidized and reduced states during turnover. Our single-molecule data provide evidence of a distinct static heterogeneity in the enzymatic activity......, with some molecules going through the on-off cycles 5-fold faster than others, however, there is no detectable dynamic disorder in DHOD turnover. When 0.1% reduced Triton X-100, a detergent that more closely simulates the natural membrane environment, is added, our data suggest the degree of static...... molecular heterogeneity is reduced. The observation of static heterogeneity suggests that the enzyme, which associates with the membrane in vivo, is present in distinct conformations that result in different catalytic efficiencies. The alternate conformations are most likely the result of the loss of van...

  16. Visualization of DNA Double-Strand Break Repair at the Single-Molecule Level

    Dynan, William S.; Li, Shuyi; Mernaugh, Raymond; Wragg, Stephanie; Takeda, Yoshihiko

    2003-03-27

    Exposure to low doses of ionizing radiation is universal. The signature injury from ionizing radiation exposure is induction of DNA double-strand breaks (DSBs). The first line of defense against DSBs is direct ligation of broken DNA ends via the nonhomologous end-joining pathway. Because even a relatively high environmental exposure induces only a few DSBs per cell, our current understanding of the response to this exposure is limited by the ability to measure DSB repair events reliably in situ at a single-molecule level. To address this need, we have taken advantage of biological amplification, measuring relocalization of proteins and detection of protein phosphorylation as a surrogate for detection of broken ends themselves. We describe the use of specific antibodies to investigate the kinetics and mechanism of repair of very small numbers of DSBs in human cells by the nonhomologous end-joining pathway.

  17. Biophysics of DNA-Protein Interactions From Single Molecules to Biological Systems

    Williams, Mark C

    2011-01-01

    This book presents a concise overview of current research on the biophysics of DNA-protein interactions. A wide range of new and classical methods are presented by authors investigating physical mechanisms by which proteins interact with DNA. For example, several chapters address the mechanisms by which proteins search for and recognize specific binding sites on DNA, a process critical for cellular function. Single molecule methods such as force spectroscopy as well as fluorescence imaging and tracking are described in these chapters as well as other parts of the book that address the dynamics of protein-DNA interactions. Other important topics include the mechanisms by which proteins engage DNA sequences and/or alter DNA structure. These simple but important model interactions are then placed in the broader biological context with discussion of larger protein-DNA complexes . Topics include replication forks, recombination complexes, DNA repair interactions, and ultimately, methods to understand the chromatin...

  18. Bayesian field theoretic reconstruction of bond potential and bond mobility in single molecule force spectroscopy

    Chang, Joshua C; Chou, Tom

    2015-01-01

    Quantifying the forces between and within macromolecules is a necessary first step in understanding the mechanics of molecular structure, protein folding, and enzyme function and performance. In such macromolecular settings, dynamic single-molecule force spectroscopy (DFS) has been used to distort bonds. The resulting responses, in the form of rupture forces, work applied, and trajectories of displacements, have been used to reconstruct bond potentials. Such approaches often rely on simple parameterizations of one-dimensional bond potentials, assumptions on equilibrium starting states, and/or large amounts of trajectory data. Parametric approaches typically fail at inferring complex-shaped bond potentials with multiple minima, while piecewise estimation may not guarantee smooth results with the appropriate behavior at large distances. Existing techniques, particularly those based on work theorems, also do not address spatial variations in the diffusivity that may arise from spatially inhomogeneous coupling to...

  19. A highly specific gold nanoprobe for live-cell single-molecule imaging

    Leduc, Cecile; Gautier, Jérémie; Soto-Ribeiro, Martinho; Wehrle-Haller, B; Gautreau, Alexis; Giannone, Gregory; Cognet, Laurent; Lounis, Brahim

    2013-01-01

    Single molecule tracking in live cells is the ultimate tool to study subcellular protein dynamics, but it is often limited by the probe size and photostability. Due to these issues, long-term tracking of proteins in confined and crowded environments, such as intracellular spaces, remains challenging. We have developed a novel optical probe consisting of 5-nm gold nanoparticles functionalized with a small fragment of camelid antibodies that recognize widely used GFPs with a very high affinity, which we call GFP-nanobodies. These small gold nanoparticles can be detected and tracked using photothermal imaging for arbitrarily long periods of time. Surface and intracellular GFP-proteins were effectively labeled even in very crowded environments such as adhesion sites and cytoskeletal structures both in vitro and in live cell cultures. These nanobody-coated gold nanoparticles are probes with unparalleled capabilities; small size, perfect photostability, high specificity, and versatility afforded by combination with...

  20. A general method to improve fluorophores for live-cell and single-molecule microscopy.

    Grimm, Jonathan B; English, Brian P; Chen, Jiji; Slaughter, Joel P; Zhang, Zhengjian; Revyakin, Andrey; Patel, Ronak; Macklin, John J; Normanno, Davide; Singer, Robert H; Lionnet, Timothée; Lavis, Luke D

    2015-03-01

    Specific labeling of biomolecules with bright fluorophores is the keystone of fluorescence microscopy. Genetically encoded self-labeling tag proteins can be coupled to synthetic dyes inside living cells, resulting in brighter reporters than fluorescent proteins. Intracellular labeling using these techniques requires cell-permeable fluorescent ligands, however, limiting utility to a small number of classic fluorophores. Here we describe a simple structural modification that improves the brightness and photostability of dyes while preserving spectral properties and cell permeability. Inspired by molecular modeling, we replaced the N,N-dimethylamino substituents in tetramethylrhodamine with four-membered azetidine rings. This addition of two carbon atoms doubles the quantum efficiency and improves the photon yield of the dye in applications ranging from in vitro single-molecule measurements to super-resolution imaging. The novel substitution is generalizable, yielding a palette of chemical dyes with improved quantum efficiencies that spans the UV and visible range. PMID:25599551

  1. Persistence of slow dynamics in Tb(OETAP)2 single molecule magnets embedded in conducting polymers

    Orlando, T.; Filibian, M.; Sanna, S.; Giménez-Agullo, N.; Sáenz de Pipaón, C.; Ballester, P.; Galán-Mascarós, J. R.; Carretta, P.

    2016-09-01

    The spin dynamics of Tb(OETAP)2 single ion magnets was investigated by means of muon spin relaxation (μSR) both in the bulk material as well as when the molecule is embedded into PEDOT:PSS polymer conductor. The spin fluctuation time is characterized by a high temperature activated trend, with an energy barrier around 320 K, and by a low temperature tunneling regime. When the single ion magnet is embedded into the polymer the energy barrier only slightly decreases and the fluctuation time remains of the same order of magnitude, even at low temperature. This finding shows that these single molecule magnets preserve their characteristics which, if combined with those of the conducting polymer, result in a hybrid material of potential interest for organic spintronics.

  2. Single-molecule fluorescence polarization study of conformational change in archaeal group II chaperonin.

    Ryo Iizuka

    Full Text Available Group II chaperonins found in archaea and in eukaryotic cytosol mediate protein folding without a GroES-like cofactor. The function of the cofactor is substituted by the helical protrusion at the tip of the apical domain, which forms a built-in lid on the central cavity. Although many studies on the change in lid conformation coupled to the binding and hydrolysis of nucleotides have been conducted, the molecular mechanism of lid closure remains poorly understood. Here, we performed a single-molecule polarization modulation to probe the rotation of the helical protrusion of a chaperonin from a hyperthermophilic archaeum, Thermococcus sp. strain KS-1. We detected approximately 35° rotation of the helical protrusion immediately after photorelease of ATP. The result suggests that the conformational change from the open lid to the closed lid state is responsible for the approximately 35° rotation of the helical protrusion.

  3. Structure of highly rigid ionic polymers from single molecules to membranes

    He, Lilin; Cornelius, Christopher J.

    2005-03-01

    The structure of ionic polymers in solutions and in their solid state is governed by the segregation to hydrophilic and hydrophobic regions. Very rigid backbones with persistence lengths much larger than the size of the monomer limit the segregation affecting the resulting structure and dynamics of the polymers. Using a newly synthesized para phenylene based sulfonated polymer with a potential to serve as a polymeric electrolytic membrane for fuel cell applications, we followed the structure of highly rigid ionic polymers from a single molecule to a water swollen membranes using small angle neutron scattering and AFM/TEM techniques. AFM and TEM images show that the dry membranes have domains with a diameter from 30 nm to 70nm. Small angle neutron scattering probes the smaller structure in the membranes from dry to swollen states. Fitting to Teubner-Strey model of SANS data indicates the bi-continuous phases were formed with water and ethanol despite the rigidity of the backbone.

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

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

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

  5. Applications of a single-molecule detection in early disease diagnosis and enzymatic reaction study

    Li, Jiangwei [Iowa State Univ., Ames, IA (United States)

    2008-01-01

    Various single-molecule techniques were utilized for ultra-sensitive early diagnosis of viral DNA and antigen and basic mechanism study of enzymatic reactions. DNA of human papilloma virus (HPV) served as the screening target in a flow system. Alexa Fluor 532 (AF532) labeled single-stranded DNA probes were hybridized to the target HPV-16 DNA in solution. The individual hybridized molecules were imaged with an intensified charge-coupled device (ICCD) in two ways. In the single-color mode, target molecules were detected via fluorescence from hybridized probes only. This system could detect HPV-16 DNA in the presence of human genomic DNA down to 0.7 copy/cell and had a linear dynamic range of over 6 orders of magnitude. In the dual-color mode, fluorescence resonance energy transfer (FRET) was employed to achieve zero false-positive count. We also showed that DNA extracts from Pap test specimens did not interfere with the system. A surface-based method was used to improve the throughput of the flow system. HPV-16 DNA was hybridized to probes on a glass surface and detected with a total internal reflection fluorescence (TIRF) microscope. In the single-probe mode, the whole genome and target DNA were fluorescently labeled before hybridization, and the detection limit is similar to the flow system. In the dual-probe mode, a second probe was introduced. The linear dynamic range covers 1.44-7000 copies/cell, which is typical of early infection to near-cancer stages. The dual-probe method was tested with a crudely prepared sample. Even with reduced hybridization efficiency caused by the interference of cellular materials, we were still able to differentiate infected cells from healthy cells. Detection and quantification of viral antigen with a novel single-molecule immunosorbent assay (SMISA) was achieved. Antigen from human immunodeficiency virus type 1(HIV-1) was chosen to be the target in this study. The target was sandwiched between a monoclonal capture antibody and a

  6. [Digital PCR compartmentalization I. Single-molecule detection of rare mutations].

    Perez-Toralla, Karla; Pekin, Deniz; Bartolo, Jean-François; Garlan, Fanny; Nizard, Philippe; Laurent-Puig, Pierre; Baret, Jean-Christophe; Taly, Valérie

    2015-01-01

    Polymerase chain reaction based techniques have been widely used in laboratory settings. Several applications in oncology, virology or prenatal diagnosis require highly sensitive detection methods, which cannot be achieved with conventional techniques. Digital PCR (dPCR) was developed from the association of PCR and limiting dilution procedures. It is based on the compartmentalization of DNA molecules in small volumes. Controlling the size and the content of each compartment is crucial to obtain a high sensitivity with a single molecule resolution. Microfluidics offers promising tools to isolate DNA fragments such as microdroplets, microchambers or microwells with volumes ranging from few picoliters to nanoliters. The review provides an overview of recent developments of microfluidics dPCR platforms and how this technology can influence the management of cancer patients. PMID:25658735

  7. Electron transfer and redox metalloenzyme catalysis at the single-molecule level

    Hansen, Allan Glargaard; Zhang, Jingdong; Christensen, Hans Erik Mølager;

    2004-01-01

    transfer (ET). Image interpretation requires, however, theoretical support, as STM represents both electronic and topographic features. Molecules with accessible redox levels offer other insight into electron tunneling mechanisms, addressed in detail for ET metalloproteins. We present here in situ STM...... concentrations where most of the enzyme is in the enzyme-substrate bound state. Molecular resolution for both cysteamine/Au(111) and AxCuNiR/cysteamine/ Au(111) electrode surfaces was achieved. The enzyme coverage is about 1.5 x 10(-13) Mol cm(-2), which is low compared with an ideal close-packed monolayer...... structures and larger assemblies are needed to disentangle enzyme mechanisms at the single-molecule level....

  8. Rotational relaxation time of polyelectrolyte xanthan chain via single molecule tracking method

    Lee, Jeong Yong; Jung, Hyun Wook; Hyun, Jae Chun

    2012-12-01

    Effect of solvent viscosity on the longest rotational relaxation time of xanthan molecule has been examined using a single molecule tracking method. Incorporating inverted epi-fluorescence microscope and chargedcoupled device (CCD) camera, various features of xanthan ( i.e., radius of gyration, orientation angle, etc.) were interpreted by image processing algorithm from the captured real xanthan images. From the best-fit of the autocorrelation function on the orientation angle, the longest rotational relaxation time was effectively determined. Rotational relaxation time increases with the medium solvent viscosity due to the slow movement of xanthan molecule. It is confirmed that there is a good agreement between experiments and Brownian dynamics simulations on the relaxation patterns of xanthan chain.

  9. Single-molecule imaging with longer X-ray laser pulses.

    Martin, Andrew V; Corso, Justine K; Caleman, Carl; Timneanu, Nicusor; Quiney, Harry M

    2015-11-01

    During the last five years, serial femtosecond crystallography using X-ray laser pulses has been developed into a powerful technique for determining the atomic structures of protein molecules from micrometre- and sub-micrometre-sized crystals. One of the key reasons for this success is the 'self-gating' pulse effect, whereby the X-ray laser pulses do not need to outrun all radiation damage processes. Instead, X-ray-induced damage terminates the Bragg diffraction prior to the pulse completing its passage through the sample, as if the Bragg diffraction were generated by a shorter pulse of equal intensity. As a result, serial femtosecond crystallography does not need to be performed with pulses as short as 5-10 fs, but can succeed for pulses 50-100 fs in duration. It is shown here that a similar gating effect applies to single-molecule diffraction with respect to spatially uncorrelated damage processes like ionization and ion diffusion. The effect is clearly seen in calculations of the diffraction contrast, by calculating the diffraction of the average structure separately to the diffraction from statistical fluctuations of the structure due to damage ('damage noise'). The results suggest that sub-nanometre single-molecule imaging with 30-50 fs pulses, like those produced at currently operating facilities, should not yet be ruled out. The theory presented opens up new experimental avenues to measure the impact of damage on single-particle diffraction, which is needed to test damage models and to identify optimal imaging conditions. PMID:26594374

  10. Unraveling the physics of nanofluidic phenomena at the single-molecule level

    Despite groundbreaking potential in a broad application space, several nanofluidic phenomena remain poorly understood. Toward advancing the understanding of fluid behavior under nanoscale confinement, we developed a novel, ideal platform for fundamental molecular transport studies, in which the fluidic channel is a single carbon nanotube (CNT). CNTs offer the advantage of simple chemistry and structure, which can be synthetically tuned with nanometer precision and accurately modeled. With combined experimental and computational approaches, we demonstrated that CNT pores with 1-5 nm diameters conduct giant ionic currents that follow an unusual sublinear electrolyte concentration dependence. The large magnitude of the ionic conductance appears to originate from a strong electro-osmotic flow in smooth CNT pores. First-principle simulations suggest that electro-osmotic flow arises from localized negative polarization charges on carbon atoms near a potassium (K+) ion and from the strong cation-graphitic wall interactions, which drive K+ ions much closer to the wall than chlorides (Cl-). Single-molecule translocation studies reveal that charged molecules may be distinguished from neutral species on the basis of the sign of the transient current change during their passage through the nanopore. Together with shedding light on a few controversial questions in the CNT nanofluidics area, these results may benefit LLNL's Security Mission by providing the foundation for the development of advanced single-molecule detection system for bio/chem/explosive analytes. In addition, these experimental and computational platforms can be applied to advance fundamental knowledge in other fields, from energy storage and membrane separation to superfluid physics.

  11. A perspective of the dynamic structure of the nucleus explored at the single-molecule level.

    Dange, Thomas; Joseph, Aviva; Grünwald, David

    2011-01-01

    Cellular life can be described as a dynamic equilibrium of a highly complex network of interacting molecules. For this reason, it is no longer sufficient to "only" know the identity of the participants in a cellular process, but questions such as where, when, and for how long also have to be addressed to understand the mechanism being investigated. Additionally, ensemble measurements may not sufficiently describe individual steps of molecular mobility, spatial-temporal resolution, kinetic parameters, and geographical mapping. It is vital to investigate where individual steps exactly occur to enhance our understanding of the living cell. The nucleus, home too many highly complex multi-order processes, such as replication, transcription, splicing, etc., provides a complicated, heterogeneous landscape. Its dynamics were studied to a new level of detail by fluorescence correlation spectroscopy (FCS). Single-molecule tracking, while still in its infancy in cell biology, is becoming a more and more attractive method to deduce key elements of this organelle. Here we discuss the potential of tracking single RNAs and proteins in the nucleus. Their dynamics, localization, and interaction rates will be vital to our understanding of cellular life. To demonstrate this, we provide a review of the HIV life cycle, which is an extremely elegant balance of nuclear and cytoplasmic functions and provides an opportunity to study mechanisms deeply integrated within the structure of the nucleus. In summary, we aim to present a specific, dynamic view of nuclear cellular life based on single molecule and FCS data and provide a prospective for the future. PMID:20842420

  12. A Cell Lysis and Protein Purification - Single Molecule Assay Devices for Evaluation of Genetically Engineered Proteins

    Nakyama, Tetsuya; Tabata, Kazuhito; Noji, Hiroyuki; Yokokawa, Ryuji

    We have developed two devices applicable to evaluate genetically engineered proteins in single molecule assay: on-chip cell lysis device, and protein purification - assay device. A motor protein, F1-ATPase expressed in E.coli, was focused in this report as a target protein. Cell lysis was simply performed by applying pulse voltage between Au electrodes patterned by photolithography, and its efficiency was determined by absorptiometry. The subsequent processes, purification and assay of extracted proteins, were demonstrated in order to detect F1-ATPase and to evaluate its activity. The specific bonding between his-tag in F1-ATPase and Ni-NTA coated on a glass surface was utilized for the purification process. After immobilization of F1-ATPase, avidin-coated microspheres and adenosine tri-phosphate (ATP) solution were infused sequentially to assay the protein. Microsphere rotation was realized by activity of F1-ATPase corresponding to ATP hydrolysis. Results show that the cell lysis device, at the optimum condition, extracts enough amount of protein for single molecule assay. Once cell lysate was injected to the purification - assay device, proteins were diffused in the lateral direction in a Y-shape microchannel. The gradient of protein concentratioin provides an optimal concentration for the assay i.e. the highest density of rotating beads. Density of rotating beads is also affected by the initial concentration of protein injected to the device. The optimum concentration was achieved by our cell lysis device not by the conventional method by ultrasonic wave. Rotation speed was analyzed for several microspheres assayed in the purification - assay device, and the results were compatible to that of conventional assay in which F1-ATPase was purified in bulk scale. In conclusion, we have demonstrated on-chip cell lysis and assay appropriate for the sequential analysis without any pretreatment. On-chip devices replacing conventional bioanalytical methods will be

  13. Unraveling the physics of nanofluidic phenomena at the single-molecule level

    Fornasiero, Francesco [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2015-10-13

    Despite groundbreaking potential in a broad application space, several nanofluidic phenomena remain poorly understood. Toward advancing the understanding of fluid behavior under nanoscale confinement, we developed a novel, ideal platform for fundamental molecular transport studies, in which the fluidic channel is a single carbon nanotube (CNT). CNTs offer the advantage of simple chemistry and structure, which can be synthetically tuned with nanometer precision and accurately modeled. With combined experimental and computational approaches, we demonstrated that CNT pores with 1-5 nm diameters conduct giant ionic currents that follow an unusual sublinear electrolyte concentration dependence. The large magnitude of the ionic conductance appears to originate from a strong electro-osmotic flow in smooth CNT pores. First-principle simulations suggest that electro-osmotic flow arises from localized negative polarization charges on carbon atoms near a potassium (K+) ion and from the strong cation-graphitic wall interactions, which drive K+ ions much closer to the wall than chlorides (Cl-). Single-molecule translocation studies reveal that charged molecules may be distinguished from neutral species on the basis of the sign of the transient current change during their passage through the nanopore. Together with shedding light on a few controversial questions in the CNT nanofluidics area, these results may benefit LLNL’s Security Mission by providing the foundation for the development of advanced single-molecule detection system for bio/chem/explosive analytes. In addition, these experimental and computational platforms can be applied to advance fundamental knowledge in other fields, from energy storage and membrane separation to superfluid physics.

  14. Three-in-one enzyme assay based on single molecule detection in femtoliter arrays.

    Liebherr, Raphaela B; Hutterer, Albert; Mickert, Matthias J; Vogl, Franziska C; Beutner, Andrea; Lechner, Alfred; Hummel, Helmut; Gorris, Hans H

    2015-09-01

    Large arrays of femtoliter-sized chambers are important tools for single molecule research as well as bioanalytical applications. We have optimized the design and fabrication of two array types consisting of 250 × 250 (62 500) femtoliter chambers either by surface etching of fused silica slides or by polydimethylsiloxane (PDMS) molding. Highly diluted solutions of β-galactosidase were enclosed in such arrays to monitor the fluorogenic reactions of hundreds of individual enzyme molecules in parallel by wide-field fluorescence microscopy. An efficient mechanical sealing procedure was developed to prevent diffusion of the fluorescent reaction product out of the chambers. Different approaches for minimizing non-specific surface adsorption were explored. The signal acquisition was optimized to grant both a large field of view and an efficient signal acquisition from each femtoliter chamber. The optimized femtoliter array has enabled a three-in-one enzyme assay system: First, the concentration of active enzyme can be determined in a digital way by counting fluorescent chambers in the array. Second, the activity of the enzyme bulk solution is given by averaging many individual substrate turnover rates without the need for knowing the exact enzyme concentration. Third-unlike conventional enzyme assays-the distribution of individual substrate turnover rates yields insight into the conformational heterogeneity in an enzyme population. The substrate turnover rates of single β-galactosidase molecules were found to be broadly distributed and independent of the type of femtoliter array. In general, both types of femtoliter arrays are highly sensitive platforms for enzyme analysis at the single molecule level and yield consistent results. Graphical Abstract Isolation and analysis of individual enzyme molecules in large arrays of femtoliter-sized chambers. PMID:26253226

  15. Single-molecule imaging with longer X-ray laser pulses

    Andrew V. Martin

    2015-11-01

    Full Text Available During the last five years, serial femtosecond crystallography using X-ray laser pulses has been developed into a powerful technique for determining the atomic structures of protein molecules from micrometre- and sub-micrometre-sized crystals. One of the key reasons for this success is the `self-gating' pulse effect, whereby the X-ray laser pulses do not need to outrun all radiation damage processes. Instead, X-ray-induced damage terminates the Bragg diffraction prior to the pulse completing its passage through the sample, as if the Bragg diffraction were generated by a shorter pulse of equal intensity. As a result, serial femtosecond crystallography does not need to be performed with pulses as short as 5–10 fs, but can succeed for pulses 50–100 fs in duration. It is shown here that a similar gating effect applies to single-molecule diffraction with respect to spatially uncorrelated damage processes like ionization and ion diffusion. The effect is clearly seen in calculations of the diffraction contrast, by calculating the diffraction of the average structure separately to the diffraction from statistical fluctuations of the structure due to damage (`damage noise'. The results suggest that sub-nanometre single-molecule imaging with 30–50 fs pulses, like those produced at currently operating facilities, should not yet be ruled out. The theory presented opens up new experimental avenues to measure the impact of damage on single-particle diffraction, which is needed to test damage models and to identify optimal imaging conditions.

  16. Arithmetic of quantum entropy function

    Quantum entropy function is a proposal for computing the entropy associated with the horizon of a black hole in the extremal limit, and is related via AdS/CFT correspondence to the dimension of the Hilbert space in a dual quantum mechanics. We show that in N = 4 supersymmetric string theories, quantum entropy function formalism naturally explains the origin of the subtle differences between the microscopic degeneracies of quarter BPS dyons carrying different torsion, i.e. different arithmetical properties. These arise from additional saddle points in the path integral - whose existence depends on the arithmetical properties of the black hole charges - constructed as freely acting orbifolds of the original AdS2 x S2 near horizon geometry. During this analysis we demonstrate that the quantum entropy function is insensitive to the details of the infrared cutoff used in the computation, and the details of the boundary terms added to the action. We also discuss the role of the asymptotic symmetries of AdS2 in carrying out the path integral in the definition of quantum entropy function. Finally we show that even though quantum entropy function is expected to compute the absolute degeneracy in a given charge and angular momentum sector, it can also be used to compute the index. This can then be compared with the microscopic computation of the index.

  17. Entropy Maximization

    K B Athreya

    2009-09-01

    It is shown that (i) every probability density is the unique maximizer of relative entropy in an appropriate class and (ii) in the class of all pdf that satisfy $\\int fh_id_=_i$ for $i=1,2,\\ldots,\\ldots k$ the maximizer of entropy is an $f_0$ that is proportional to $\\exp(\\sum c_i h_i)$ for some choice of $c_i$. An extension of this to a continuum of constraints and many examples are presented.

  18. Geometric Entropy

    Das, Diptarka

    2010-01-01

    The laws of mechanics of stationary black holes bear a close resemblance with the laws of thermodynamics. This is not only a mathematical analogy but also a physical one that helps us answer deep questions related to the thermodynamic properties of the black holes. It turns out that we can define an entropy which is purely geometrical for black holes. In this thesis we explain Wald's formulation which identifies black hole entropy for an arbitrary covariant theory of gravity. We would like to know precisely what inputs go into arriving at Wald's formalism. This expression for the entropy clearly depends on the precise form of the action. The secondary theme of this thesis is to distinguish thermodynamic laws which are kinematic from those which are dynamical. We would like to see explicitly in the derivation of these laws, where exactly the form of action plays a role. In the beginning we motivate the definition of entropy using the Einstein-Hilbert Lagrangian. We encounter the Zeroth law, the Hawking radiati...

  19. Beyond experimental noise: Analyzing single-molecule data of heterogeneous systems. Comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb and S.K. Sarkar

    Meroz, Yasmine

    2015-06-01

    In the 1980s the world witnessed the advent of single-molecule experiments. The first atomic resolution characterization of a surface was reported by scanning tunneling microscope (STM) in 1982 [1], followed by atomic force microscope (AFM) in 1986 [2]. The first optical detection and spectroscopy of a single molecule in a solid took place in 1989 [3,4], in a time where essentially all chemical experiments were made on bulk, i.e. averaging over millions of copies of the same molecule.

  20. Carnot to Clausius: caloric to entropy

    This paper discusses how the Carnot engine led to the formulation of the second law of thermodynamics and entropy. The operation of the engine is analysed both in terms of heat as the caloric fluid and heat as a form of energy. A keystone of Carnot's thinking was the absolute conservation of caloric. Although the Carnot analysis was partly incorrect, Clausius showed that by reinterpreting Carnot's caloric as entropy he was able to formulate the second law

  1. Studying Chemical Reactions, One Bond at a Time, with Single Molecule AFM Techniques

    Fernandez, Julio M.

    2008-03-01

    The mechanisms by which mechanical forces regulate the kinetics of a chemical reaction are unknown. In my lecture I will demonstrate how we use single molecule force-clamp spectroscopy and protein engineering to study the effect of force on the kinetics of thiol/disulfide exchange. Reduction of disulfide bond via the thiol/disulfide exchange chemical reaction is crucial in regulating protein function and is of common occurrence in mechanically stressed proteins. While reduction is thought to proceed through a substitution nucleophilic bimolecular (SN2) reaction, the role of a mechanical force in modulating this chemical reaction is unknown. We apply a constant stretching force to single engineered disulfide bonds and measure their rate of reduction by dithiothreitol (DTT). We find that while the reduction rate is linearly dependent on the concentration of DTT, it is exponentially dependent on the applied force, increasing 10-fold over a 300 pN range. This result predicts that the disulfide bond lengthens by 0.34 å at the transition state of the thiol/disulfide exchange reaction. In addition to DTT, we also study the reduction of the engineered disulfide bond by the E. coli enzyme thioredoxin (Trx). Thioredoxins are enzymes that catalyze disulfide bond reduction in all organisms. As before, we apply a mechanical force in the range of 25-450 pN to the engineered disulfide bond substrate and monitor the reduction of these bonds by individual enzymes. In sharp contrast with the data obtained with DTT, we now observe two alternative forms of the catalytic reaction, the first requiring a reorientation of the substrate disulfide bond, causing a shortening of the substrate polypeptide by 0.76±0.07 å, and the second elongating the substrate disulfide bond by 0.21±0.01 å. These results support the view that the Trx active site regulates the geometry of the participating sulfur atoms, with sub-ångström precision, in order to achieve efficient catalysis. Single molecule

  2. Characterization of nanostructures in the live cell plasma membrane utilizing advanced single molecule fluorescence techniques

    Unrevealing the detailed structure of the cellular plasma membrane at a nanoscopic length scale is the key for understanding the regulation of various signaling pathways or interaction mechanism. Hypotheses postulate the existence of nanoscopic lipid platforms in the cell membrane which are termed lipid- or membrane rafts. Based on biochemical studies, rafts are believed to play a crucial role in many signaling processes. However, there is currently not much information on their size, shape, stability, surface density, composition and heterogeneity. In this thesis I present an ultra-sensitive fluorescence based method which allows for the first time the direct imaging of single mobile rafts in the live cell plasma membrane. The method senses rafts by their property to assemble a characteristic set of fluorescent marker-proteins or lipids on a time-scale of seconds. A special photobleaching protocol was developed and used to reduce the surface density of labeled mobile rafts down to the level of well-isolated diffraction-limited spots, without altering the single spot brightness. The statistical distribution of probe molecules per raft was determined by single molecule brightness analysis. For demonstration, I used the consensus markers Bodipy-GM1, a fluorescent lipid analogue, and glycosylphosphatidyl-inositol-anchored monomeric GFP. For both markers I found cholesterol-dependent association in the plasma membrane of living CHO and Jurkat T cells in the resting state, indicating the presence of mobile, stable rafts hosting these probes. I further characterized these structures by taking cell-to-cell variations under consideration. By comparing Bodipy-GM1 with mGFP-GPI homo-association upon temperature variation, two different states - a non-equilibrated and an equilibrated state - could be identified. I conclude that rafts are loaded non-randomly; the characteristic load is maintained during its lifetime in the plasma membrane of a non-activated cell. Beside these

  3. Plasmonic antennas and zero mode waveguides to enhance single molecule fluorescence detection and fluorescence correlation spectroscopy towards physiological concentrations

    Punj, Deep; Moparthi, Satish Babu; de Torres, Juan; Grigoriev, Victor; Rigneault, Hervé; Wenger, Jérôme

    2014-01-01

    Single-molecule approaches to biology offer a powerful new vision to elucidate the mechanisms that underpin the functioning of living cells. However, conventional optical single molecule spectroscopy techniques such as F\\"orster fluorescence resonance energy transfer (FRET) or fluorescence correlation spectroscopy (FCS) are limited by diffraction to the nanomolar concentration range, far below the physiological micromolar concentration range where most biological reaction occur. To breach the diffraction limit, zero mode waveguides and plasmonic antennas exploit the surface plasmon resonances to confine and enhance light down to the nanometre scale. The ability of plasmonics to achieve extreme light concentration unlocks an enormous potential to enhance fluorescence detection, FRET and FCS. Single molecule spectroscopy techniques greatly benefit from zero mode waveguides and plasmonic antennas to enter a new dimension of molecular concentration reaching physiological conditions. The application of nano-optics...

  4. Physical manipulation of single-molecule DNA using microbead and its application to analysis of DNA-protein interaction

    We carried out an individual DNA manipulation using an optical trapping for a microbead. This manipulation system is based on a fluorescent microscopy equipped with an IR laser. Both ends of linear DNA molecule were labeled with a biotin and a thiol group, respectively. Then the biotinylated end was attached to a microbead, and the other was immobilized on a thiol-linkable glass surface. We controlled the form of an individual DNA molecule by moving the focal point of IR laser, which trapped the microbead. In addition, we applied single-molecule approach to analyze DNA hydrolysis. We also used microchannel for single-molecule observation of DNA hydrolysis. The shortening of DNA in length caused by enzymatic hydrolysis was observed in real-time. The single-molecule DNA manipulation should contribute to elucidate detailed mechanisms of DNA-protein interactions

  5. Single-molecule detection of proteins with antigen-antibody interaction using resistive-pulse sensing of submicron latex particles

    Takakura, T.; Yanagi, I.; Goto, Y.; Ishige, Y.; Kohara, Y.

    2016-03-01

    We developed a resistive-pulse sensor with a solid-state pore and measured the latex agglutination of submicron particles induced by antigen-antibody interaction for single-molecule detection of proteins. We fabricated the pore based on numerical simulation to clearly distinguish between monomer and dimer latex particles. By measuring single dimers agglutinated in the single-molecule regime, we detected single human alpha-fetoprotein molecules. Adjusting the initial particle concentration improves the limit of detection (LOD) to 95 fmol/l. We established a theoretical model of the LOD by combining the reaction kinetics and the counting statistics to explain the effect of initial particle concentration on the LOD. The theoretical model shows how to improve the LOD quantitatively. The single-molecule detection studied here indicates the feasibility of implementing a highly sensitive immunoassay by a simple measurement method using resistive-pulse sensing.

  6. Stretching and immobilization of DNA for studies of protein–DNA interactions at the single-molecule level

    Dukkipati VenkatRam

    2007-01-01

    Full Text Available AbstractSingle-molecule studies of the interactions of DNA and proteins are important in a variety of biological or biotechnology processes ranging from the protein’s search for its DNA target site, DNA replication, transcription, or repair, and genome sequencing. A critical requirement for single-molecule studies is the stretching and immobilization of otherwise randomly coiled DNA molecules. Several methods for doing so have been developed over the last two decades, including the use of forces derived from light, magnetic and electric fields, and hydrodynamic flow. Here we review the immobilization and stretching mechanisms for several of these techniques along with examples of single-molecule DNA–protein interaction assays that can be performed with each of them.

  7. Single-Molecule Break Junctions Based on a Perylene-Diimide Cyano-Functionalized (PDI8-CN2) Derivative

    Frisenda, Riccardo; Parlato, Loredana; Barra, Mario; van der Zant, Herre S. J.; Cassinese, Antonio

    2015-07-01

    In this letter, we report the single-molecule conductance properties of a cyano-functionalized perylene-diimide derivative (PDI8-CN2) investigated with gold nano-electrodes. This molecule is of large interest for the fabrication of high-performance and air-stable n-type organic field-effect transistors. Low-bias experiments performed on mechanically controllable break junctions reveal the presence of two different values of the single-molecule conductance, which differ by about two orders of magnitudes. Up to date, this feature was never observed for other perylene-diimide compounds having alternative chemical moieties attached to the basic aromatic core. Theoretical calculations suggest that the highest single-molecule conductance value here observed, comprised between 10-2 and 10-3 G0, is related to a charge transport path directly linking the two cyano groups.

  8. Extracting physical chemistry from mechanics: a new approach to investigate DNA interactions with drugs and proteins in single molecule experiments

    Rocha, M S

    2015-01-01

    In this review we focus on the idea of establishing connections between the mechanical properties of DNAligand complexes and the physical chemistry of DNA-ligand interactions. This type of connection is interesting because it opens the possibility of performing a robust characterization of such interactions by using only one experimental technique: single molecule stretching. Furthermore, it also opens new possibilities in comparing results obtained by very different approaches, in special when comparing single molecule techniques to ensemble-averaging techniques. We start the manuscript reviewing important concepts of the DNA mechanics, from the basic mechanical properties to the Worm-Like Chain model. Next we review the basic concepts of the physical chemistry of DNA-ligand interactions, revisiting the most important models used to analyze the binding data and discussing their binding isotherms. Then, we discuss the basic features of the single molecule techniques most used to stretch the DNA-ligand complex...

  9. Energetic modeling and single-molecule verification of dynamic regulation on receptor complexes by actin corrals and lipid raft domains

    Lin, Chien Y.; Huang, Jung Y.; Lo, Leu-Wei

    2014-12-01

    We developed an energetic model by integrating the generalized Langevin equation with the Cahn-Hilliard equation to simulate the diffusive behaviors of receptor proteins in the plasma membrane of a living cell. Simulation results are presented to elaborate the confinement effects from actin corrals and protein-induced lipid domains. Single-molecule tracking data of epidermal growth factor receptors (EGFR) acquired on live HeLa cells agree with the simulation results and the mechanism that controls the diffusion of single-molecule receptors is clarified. We discovered that after ligand binding, EGFR molecules move into lipid nanodomains. The transition rates between different diffusion states of liganded EGFR molecules are regulated by the lipid domains. Our method successfully captures dynamic interactions of receptors at the single-molecule level and provides insight into the functional architecture of both the diffusing EGFR molecules and their local cellular environment.

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

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

    2015-10-01

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

  11. Seeing the vibrational breathing of a single molecule through time-resolved coherent anti-Stokes Raman scattering

    Yampolsky, Steven; Dey, Shirshendu; Hulkko, Eero; Banik, Mayukh; Potma, Eric O; Apkarian, Vartkess A

    2014-01-01

    The motion of chemical bonds within molecules can be observed in real time, in the form of vibrational wavepackets prepared and interrogated through ultrafast nonlinear spectroscopy. Such nonlinear optical measurements are commonly performed on large ensembles of molecules, and as such, are limited to the extent that ensemble coherence can be maintained. Here, we describe vibrational wavepacket motion on single molecules, recorded through time-resolved, surface-enhanced, coherent anti-Stokes Raman scattering. The required sensitivity to detect the motion of a single molecule, under ambient conditions, is achieved by equipping the molecule with a dipolar nano-antenna (a gold dumbbell). In contrast with measurements in ensembles, the vibrational coherence on a single molecule does not dephase. It develops phase fluctuations with characteristic statistics. We present the time evolution of discretely sampled statistical states, and highlight the unique information content in the characteristic, early-time probabi...

  12. Effects of ionizing radiation on cell-matrix interactions at the single molecule level

    Single molecule microscopy is a technology that allows for accurate assessment of the location and motion of single fluorescent molecules, even in the context of observations on living biological samples. In the present thesis, a flexible analysis tool for single molecule data as obtained in biological experiments was established. The development of a tool to faithfully detect and localize diffraction-limited images of individual fluorescent probes was necessary since data acquired under cell cultivation conditions that account for a three-dimensional microenvironment as experienced physiologically by cells in native tissue poses a challenge not faced ordinarily. After design, implementation, quantitative tests using simulations for comparisons and verification, and evaluation of the different steps of the analysis procedure including local background estimation, local noise estimation, de-noising approaches, detection, localization, and post-processing, analysis capabilities were utilized to evaluate the impact of x-ray irradiation on the plasma membrane architecture of U2OS human osteosarcoma cells as assessed by tracking individual fluorescent lipid-mimetic dye molecules diffusing in the outer membrane leaflet. It was shown that lateral diffusion in the plasma membrane is well described as two-phase anomalous subdiffusion and presence of 3D extracellular matrix leads to lower anomalous exponents of the fast fraction in comparison to monolayer cell culture. Interestingly, even high single-dose (25 Gy) treatments known to induce membrane-mediated apoptosis in tumor microvessel endothelium via membrane viscosity enhancing ceramide generation were not observed to alter membrane architecture in U2OS cells which can be related to amplifying, feedback-driven redox-signaling in the endothelium absent in U2OS. In summary, the sensitive and accurate framework developed in this thesis to assess minute changes of plasma membrane located dynamic processes did not uncover a

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

    White, Alexander James

    The last decade has seen incredible growth in the quality of experiments being done on single molecule junctions. Contemporary experimental measurements have expanded far beyond simple electron transport. Measurement of vibronic eects, quantum interference and decoherence eects, molecular optical response (Raman spectroscopy), and molecular spintronics are just some of the continuing areas of research in single molecule junctions. Experimental advancements demand advanced theoretical treatments, which can be used accurately within appropriate physical regimes, in order to understand measured phenomena and predict interesting directions for future study. In this dissertation we will study systems with strong intra-system interactions using a many-body states based approach. We will be focused on three related processes in molecular junctions: electron transport, electronic energy transfer, and molecular excitation. Inelastic electron transport in the regime of strong and nonlinear electron-vibration coupling within and outside of the Born-Oppenheimer regime will be investigated. To understand their appropriateness, we will compare simple semi-classical approximations in molecular redox junctions and electron-counting devices to fully quantum calculations based on many-body system states. The role of coherence and quantum interference in energy and electron transfer in molecular junctions is explored. Experiments that simultaneously measure surface enhanced Raman scattering and electron conduction have revealed a strong interaction between conducting electrons and molecular excitation. We investigate the role of the molecular response to a classical surface plasmon enhanced electric eld considering the back action of the oscillating molecular dipole. Raman scattering is quantum mechanical by nature and involves strong interaction between surface plasmons in the contacts and the molecular excitation. We develop a scheme for treating strong plasmon-molecular excitation

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

    Laurence, Ted Alfred

    2002-07-30

    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 introduced by interactions between molecules and surfaces. These methods are used to perform studies of the folding of Chymotrypsin Inhibitor 2, a small, single-domain protein, and of single-stranded DNA (ssDNA) homopolymers. Confocal microscopy is used in combination with sensitive detectors to detect bursts of photons from fluorescently labeled biomolecules as they diffuse through the focal volume. These bursts are analyzed to extract fluorescence resonance energy transfer (FRET) efficiency. Advances in data acquisition and analysis techniques that are providing a more complete picture of the accessible molecular information are discussed. Photon Arrival-time Interval Distribution (PAID) analysis is a new method for monitoring macromolecular interactions by fluorescence detection with simultaneous determination of coincidence, brightness, diffusion time, and occupancy (proportional to concentration) of fluorescently-labeled molecules undergoing diffusion in a confocal detection volume. This method is based on recording the time of arrival of all detected photons, and then plotting the two-dimensional histogram of photon pairs, where one axis is the time interval between each pair of photons 1 and 2, and the second axis is the number of other photons detected in the time interval between photons 1 and 2. PAID is related to Fluorescence Correlation Spectroscopy (FCS) by a collapse of this histogram onto the time interval axis. PAID extends auto- and cross-correlation FCS

  15. FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET.

    Ingargiola, Antonino; Lerner, Eitan; Chung, SangYoon; Weiss, Shimon; Michalet, Xavier

    2016-01-01

    Single-molecule Förster Resonance Energy Transfer (smFRET) allows probing intermolecular interactions and conformational changes in biomacromolecules, and represents an invaluable tool for studying cellular processes at the molecular scale. smFRET experiments can detect the distance between two fluorescent labels (donor and acceptor) in the 3-10 nm range. In the commonly employed confocal geometry, molecules are free to diffuse in solution. When a molecule traverses the excitation volume, it emits a burst of photons, which can be detected by single-photon avalanche diode (SPAD) detectors. The intensities of donor and acceptor fluorescence can then be related to the distance between the two fluorophores. While recent years have seen a growing number of contributions proposing improvements or new techniques in smFRET data analysis, rarely have those publications been accompanied by software implementation. In particular, despite the widespread application of smFRET, no complete software package for smFRET burst analysis is freely available to date. In this paper, we introduce FRETBursts, an open source software for analysis of freely-diffusing smFRET data. FRETBursts allows executing all the fundamental steps of smFRET bursts analysis using state-of-the-art as well as novel techniques, while providing an open, robust and well-documented implementation. Therefore, FRETBursts represents an ideal platform for comparison and development of new methods in burst analysis. We employ modern software engineering principles in order to minimize bugs and facilitate long-term maintainability. Furthermore, we place a strong focus on reproducibility by relying on Jupyter notebooks for FRETBursts execution. Notebooks are executable documents capturing all the steps of the analysis (including data files, input parameters, and results) and can be easily shared to replicate complete smFRET analyzes. Notebooks allow beginners to execute complex workflows and advanced users to

  16. Effects of ionizing radiation on cell-matrix interactions at the single molecule level

    Lauer, Florian

    2015-04-20

    Single molecule microscopy is a technology that allows for accurate assessment of the location and motion of single fluorescent molecules, even in the context of observations on living biological samples. In the present thesis, a flexible analysis tool for single molecule data as obtained in biological experiments was established. The development of a tool to faithfully detect and localize diffraction-limited images of individual fluorescent probes was necessary since data acquired under cell cultivation conditions that account for a three-dimensional microenvironment as experienced physiologically by cells in native tissue poses a challenge not faced ordinarily. After design, implementation, quantitative tests using simulations for comparisons and verification, and evaluation of the different steps of the analysis procedure including local background estimation, local noise estimation, de-noising approaches, detection, localization, and post-processing, analysis capabilities were utilized to evaluate the impact of x-ray irradiation on the plasma membrane architecture of U2OS human osteosarcoma cells as assessed by tracking individual fluorescent lipid-mimetic dye molecules diffusing in the outer membrane leaflet. It was shown that lateral diffusion in the plasma membrane is well described as two-phase anomalous subdiffusion and presence of 3D extracellular matrix leads to lower anomalous exponents of the fast fraction in comparison to monolayer cell culture. Interestingly, even high single-dose (25 Gy) treatments known to induce membrane-mediated apoptosis in tumor microvessel endothelium via membrane viscosity enhancing ceramide generation were not observed to alter membrane architecture in U2OS cells which can be related to amplifying, feedback-driven redox-signaling in the endothelium absent in U2OS. In summary, the sensitive and accurate framework developed in this thesis to assess minute changes of plasma membrane located dynamic processes did not uncover a

  17. DNA origami based Au-Ag-core-shell nanoparticle dimers with single-molecule SERS sensitivity

    Prinz, J.; Heck, C.; Ellerik, L.; Merk, V.; Bald, I.

    2016-03-01

    DNA origami nanostructures are a versatile tool to arrange metal nanostructures and other chemical entities with nanometer precision. In this way gold nanoparticle dimers with defined distance can be constructed, which can be exploited as novel substrates for surface enhanced Raman scattering (SERS). We have optimized the size, composition and arrangement of Au/Ag nanoparticles to create intense SERS hot spots, with Raman enhancement up to 1010, which is sufficient to detect single molecules by Raman scattering. This is demonstrated using single dye molecules (TAMRA and Cy3) placed into the center of the nanoparticle dimers. In conjunction with the DNA origami nanostructures novel SERS substrates are created, which can in the future be applied to the SERS analysis of more complex biomolecular targets, whose position and conformation within the SERS hot spot can be precisely controlled.DNA origami nanostructures are a versatile tool to arrange metal nanostructures and other chemical entities with nanometer precision. In this way gold nanoparticle dimers with defined distance can be constructed, which can be exploited as novel substrates for surface enhanced Raman scattering (SERS). We have optimized the size, composition and arrangement of Au/Ag nanoparticles to create intense SERS hot spots, with Raman enhancement up to 1010, which is sufficient to detect single molecules by Raman scattering. This is demonstrated using single dye molecules (TAMRA and Cy3) placed into the center of the nanoparticle dimers. In conjunction with the DNA origami nanostructures novel SERS substrates are created, which can in the future be applied to the SERS analysis of more complex biomolecular targets, whose position and conformation within the SERS hot spot can be precisely controlled. Electronic supplementary information (ESI) available: Additional information about materials and methods, designs of DNA origami templates, height profiles, additional SERS spectra, assignment of DNA

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

    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 introduced by interactions between molecules and surfaces. These methods are used to perform studies of the folding of Chymotrypsin Inhibitor 2, a small, single-domain protein, and of single-stranded DNA (ssDNA) homopolymers. Confocal microscopy is used in combination with sensitive detectors to detect bursts of photons from fluorescently labeled biomolecules as they diffuse through the focal volume. These bursts are analyzed to extract fluorescence resonance energy transfer (FRET) efficiency. Advances in data acquisition and analysis techniques that are providing a more complete picture of the accessible molecular information are discussed. Photon Arrival-time Interval Distribution (PAID) analysis is a new method for monitoring macromolecular interactions by fluorescence detection with simultaneous determination of coincidence, brightness, diffusion time, and occupancy (proportional to concentration) of fluorescently-labeled molecules undergoing diffusion in a confocal detection volume. This method is based on recording the time of arrival of all detected photons, and then plotting the two-dimensional histogram of photon pairs, where one axis is the time interval between each pair of photons 1 and 2, and the second axis is the number of other photons detected in the time interval between photons 1 and 2. PAID is related to Fluorescence Correlation Spectroscopy (FCS) by a collapse of this histogram onto the time interval axis. PAID extends auto- and cross-correlation FCS

  19. Bridging the gap between single molecule and ensemble methods for measuring lateral dynamics in the plasma membrane

    Christensen, Eva Arnspang; Schwartzentruber, J.; Clausen, M. P.;

    2013-01-01

    comparing the results for a biotinylated lipid labeled at high densities with Atto647N-strepatvidin (sAv) or sparse densities with sAv-QDs. In this latter case, we see that the recovered diffusion rate is two-fold greater for the same lipid and in the same cell-type when labeled with Atto647N-sAv as...... compared to sAv-QDs. This data demonstrates that kICS can be used for analysis of single molecule data and furthermore can bridge between samples with a labeling densities ranging from single molecule to ensemble level measurements....

  20. Formation of solid-state excitons in ultrathin crystalline films of PTCDA: From single molecules to molecular stacks

    We directly follow the evolution of the absorption spectrum from a single molecule to a dimer and further to a one-dimensional molecular stack: We determine the optical absorption properties of ordered monolayer to multilayer films of PTCDA (3,4,9,10-perylenetetracarboxylic dianhydride) on muscovite mica(0001) surfaces by in situ differential reflectance spectroscopy. The data clearly show the transition from the single molecule to a dimer spectrum, followed by the exciton delocalization to a molecular crystal exciton. The accompanying spectral shifts compare favorably with recent model concepts

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

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

    2013-03-01

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

  2. Single-Molecule Break Junctions Based on a Perylene-Diimide Cyano-Functionalized (PDI8-CN2) Derivative

    2015-01-01

    In this letter, we report the single-molecule conductance properties of a cyano-functionalized perylene-diimide derivative (PDI8-CN2) investigated with gold nano-electrodes. This molecule is of large interest for the fabrication of high-performance and air-stable n-type organic field-effect transistors. Low-bias experiments performed on mechanically controllable break junctions reveal the presence of two different values of the single-molecule conductance, which differ by about two orders of ...

  3. Note: A method to isolate and detect a large number of single molecules by microdroplet fluorescence spectroscopy

    Ng, K. C.; Heredia, K. H.; Kliewer, D.

    2012-03-01

    A laser induced fluorescence system, in combination with a glass-frit nebulizer and a photo-voltaic cell detector, is described for single molecule detection. The glass-frit nebulizer continuously generates a large number of droplets with an average droplet size of three micrometers in diameter. Rhodamine 6G molecules were detected at the 10-12 M level. Concentrations 10-12-10-10 M would provide mostly single molecules (0, 1, 2, 3, …) in the individual droplets, as determined by Poisson distribution.

  4. Optical mapping of a rice B AC clone using restriction endonuclease and imaging with fluorescent microscopy at single molecule level

    2002-01-01

    A method of constructing restriction map by optical mapping and single molecule fluorescent microscopy is described. DNA molecules were aligned and adsorbed on a glass coverslip surface by a mbdified "molecular combing"technique, and then the surface-immobilized DNAs were cleaved in situ with a restriction endonuclease. Individual DNA molecules digested by the endonuclease EcoR I were observable with fluorescent microscopy. Using optical mapping, a physical map of a rice bacterial artificial chromosome clone was constructed. This method will facilitate genomic mapping and tracing the dynamic process in real time at a single molecule level with fluorescence microscopy.

  5. In situ single molecule imaging of cell membranes: linking basic nanotechniques to cell biology, immunology and medicine

    Pi, Jiang; Jin, Hua; Yang, Fen; Chen, Zheng W.; Cai, Jiye

    2014-10-01

    The cell membrane, which consists of a viscous phospholipid bilayer, different kinds of proteins and various nano/micrometer-sized domains, plays a very important role in ensuring the stability of the intracellular environment and the order of cellular signal transductions. Exploring the precise cell membrane structure and detailed functions of the biomolecules in a cell membrane would be helpful to understand the underlying mechanisms involved in cell membrane signal transductions, which could further benefit research into cell biology, immunology and medicine. The detection of membrane biomolecules at the single molecule level can provide some subtle information about the molecular structure and the functions of the cell membrane. In particular, information obtained about the molecular mechanisms and other information at the single molecule level are significantly different from that detected from a large amount of biomolecules at the large-scale through traditional techniques, and can thus provide a novel perspective for the study of cell membrane structures and functions. However, the precise investigations of membrane biomolecules prompts researchers to explore cell membranes at the single molecule level by the use of in situ imaging methods, as the exact conformation and functions of biomolecules are highly controlled by the native cellular environment. Recently, the in situ single molecule imaging of cell membranes has attracted increasing attention from cell biologists and immunologists. The size of biomolecules and their clusters on the cell surface are set at the nanoscale, which makes it mandatory to use high- and super-resolution imaging techniques to realize the in situ single molecule imaging of cell membranes. In the past few decades, some amazing imaging techniques and instruments with super resolution have been widely developed for molecule imaging, which can also be further employed for the in situ single molecule imaging of cell membranes. In

  6. Pesin's Entropy Formula for Systems Between and

    Tian, Xueting

    2014-09-01

    In this article we give a new observation of Pesin's entropy formula, motivated from Mañé's proof of (Ergod Theory Dyn Sys 1:95-102, 1981). Let be a compact Riemann manifold and be a diffeomorphism on . If is an -invariant probability measure which is absolutely continuous relative to Lebesgue measure and nonuniformly-Hlder-continuous(see Definition 1.1), then we have Pesin's entropy formula, i.e., the metric entropy satisfies where are the Lyapunov exponents at with respect to Nonuniformly-H lder-continuous is a new notion from probabilistic perspective weaker than

  7. Homogenous adsorption of Mn{sub 6}Cr single-molecule-magnets on substrates

    Koop, Peter; Gryzia, Aaron; Helmstedt, Andreas; Hachmann, Wiebke; Brechling, Armin; Sacher, Marc; Heinzmann, Ulrich [Molecular and Surface Physics, Bielefeld University (Germany); Hoeke, Veronika; Glaser, Thorsten [Anorganic Chemistry I, Bielefeld University (Germany)

    2010-07-01

    Mn{sub 6}Cr is a single-molecule-magnet (SMM) consisting of two bowl-shaped compounds, each containing three Mn-atoms. These compounds are bound together by a Cr-complex. For charge neutrality, counterions have to be coupled to the SMM. Investigation of separated SMM, the molecule-substrate interaction and/or possible future applications e.g. data storage, requires preparation of monolayers or thin films. This preparation is done by solving Mn{sub 6}Cr in methanol, and dropping few {mu}l of the solution onto a 9 x 9 mm sized substrate. Depending on the choice of substrate Au, SiO{sub 2} (native Oxide, 50 nm Oxide), HOPG, Ru, Mn{sub 6}Cr concentration, the angle of the sample while being prepared and the amount of applied solution Mn{sub 6}Cr yields strongly varying kinds of assembly. On the one hand, clusters emerge in the solution just a moment before the solvent dries, depending on the concentration of Mn{sub 6}Cr in the solution. On the other hand the lateral distribution of the SMM is correlated with the droplet-size, the angle of the sample during preparation and the counterions, e.g. lactate anions cause Mn{sub 6}Cr to create membranes. The samples have been investigated by means of optical microscopy, SEM, surface profilometry and AFM.

  8. Complete architecture of the archaeal RNA polymerase open complex from single-molecule FRET and NPS

    Nagy, Julia; Grohmann, Dina; Cheung, Alan C. M.; Schulz, Sarah; Smollett, Katherine; Werner, Finn; Michaelis, Jens

    2015-01-01

    The molecular architecture of RNAP II-like transcription initiation complexes remains opaque due to its conformational flexibility and size. Here we report the three-dimensional architecture of the complete open complex (OC) composed of the promoter DNA, TATA box-binding protein (TBP), transcription factor B (TFB), transcription factor E (TFE) and the 12-subunit RNA polymerase (RNAP) from Methanocaldococcus jannaschii. By combining single-molecule Förster resonance energy transfer and the Bayesian parameter estimation-based Nano-Positioning System analysis, we model the entire archaeal OC, which elucidates the path of the non-template DNA (ntDNA) strand and interaction sites of the transcription factors with the RNAP. Compared with models of the eukaryotic OC, the TATA DNA region with TBP and TFB is positioned closer to the surface of the RNAP, likely providing the mechanism by which DNA melting can occur in a minimal factor configuration, without the dedicated translocase/helicase encoding factor TFIIH.

  9. A survey of the sorghum transcriptome using single-molecule long reads.

    Abdel-Ghany, Salah E; Hamilton, Michael; Jacobi, Jennifer L; Ngam, Peter; Devitt, Nicholas; Schilkey, Faye; Ben-Hur, Asa; Reddy, Anireddy S N

    2016-01-01

    Alternative splicing and alternative polyadenylation (APA) of pre-mRNAs greatly contribute to transcriptome diversity, coding capacity of a genome and gene regulatory mechanisms in eukaryotes. Second-generation sequencing technologies have been extensively used to analyse transcriptomes. However, a major limitation of short-read data is that it is difficult to accurately predict full-length splice isoforms. Here we sequenced the sorghum transcriptome using Pacific Biosciences single-molecule real-time long-read isoform sequencing and developed a pipeline called TAPIS (Transcriptome Analysis Pipeline for Isoform Sequencing) to identify full-length splice isoforms and APA sites. Our analysis reveals transcriptome-wide full-length isoforms at an unprecedented scale with over 11,000 novel splice isoforms. Additionally, we uncover APA of ∼11,000 expressed genes and more than 2,100 novel genes. These results greatly enhance sorghum gene annotations and aid in studying gene regulation in this important bioenergy crop. The TAPIS pipeline will serve as a useful tool to analyse Iso-Seq data from any organism. PMID:27339290

  10. Field-induced conductance switching by charge-state alternation in organometallic single-molecule junctions

    Schwarz, Florian; Kastlunger, Georg; Lissel, Franziska; Egler-Lucas, Carolina; Semenov, Sergey N.; Venkatesan, Koushik; Berke, Heinz; Stadler, Robert; Lörtscher, Emanuel

    2016-02-01

    Charge transport through single molecules can be influenced by the charge and spin states of redox-active metal centres placed in the transport pathway. These intrinsic properties are usually manipulated by varying the molecule's electrochemical and magnetic environment, a procedure that requires complex setups with multiple terminals. Here we show that oxidation and reduction of organometallic compounds containing either Fe, Ru or Mo centres can solely be triggered by the electric field applied to a two-terminal molecular junction. Whereas all compounds exhibit bias-dependent hysteresis, the Mo-containing compound additionally shows an abrupt voltage-induced conductance switching, yielding high-to-low current ratios exceeding 1,000 at bias voltages of less than 1.0 V. Density functional theory calculations identify a localized, redox-active molecular orbital that is weakly coupled to the electrodes and closely aligned with the Fermi energy of the leads because of the spin-polarized ground state unique to the Mo centre. This situation provides an additional slow and incoherent hopping channel for transport, triggering a transient charging effect in the entire molecule with a strong hysteresis and large high-to-low current ratios.

  11. Amine-linked single-molecule circuits: systematic trends across molecular families

    A comprehensive review is presented of single-molecule junction conductance measurements across families of molecules measured while breaking a gold point contact in a solution of molecules with amine end groups. A theoretical framework unifies the picture for the amine-gold link bonding and the tunnel coupling through the junction using density functional theory based calculations. The reproducible electrical characteristics and utility for many molecules is shown to result from the selective binding between the gold electrodes and amine link groups through a donor-acceptor bond to undercoordinated gold atoms. While the bond energy is modest, the maximum force sustained by the junction is comparable to, but less than, that required to break gold point contacts. The calculated tunnel coupling provides conductance trends for all 41 molecule measurements presented here, as well as insight into the variability of conductance due to the conformational changes within molecules with torsional degrees of freedom. The calculated trends agree to within a factor of 2 with the measured values for conductance ranging from 10-7G0 to 10-2G0, where G0 is the quantum of conductance (2e2/h)

  12. Amine-linked single-molecule circuits: systematic trends across molecular families.

    Hybertsen, Mark S; Venkataraman, Latha; Klare, Jennifer E; Whalley, Adam C; Steigerwald, Michael L; Nuckolls, Colin

    2008-09-17

    A comprehensive review is presented of single-molecule junction conductance measurements across families of molecules measured while breaking a gold point contact in a solution of molecules with amine end groups. A theoretical framework unifies the picture for the amine-gold link bonding and the tunnel coupling through the junction using density functional theory based calculations. The reproducible electrical characteristics and utility for many molecules is shown to result from the selective binding between the gold electrodes and amine link groups through a donor-acceptor bond to undercoordinated gold atoms. While the bond energy is modest, the maximum force sustained by the junction is comparable to, but less than, that required to break gold point contacts. The calculated tunnel coupling provides conductance trends for all 41 molecule measurements presented here, as well as insight into the variability of conductance due to the conformational changes within molecules with torsional degrees of freedom. The calculated trends agree to within a factor of 2 with the measured values for conductance ranging from 10(-7)G(0) to 10(-2)G(0), where G(0) is the quantum of conductance (2e(2)/h). PMID:21694422

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

    Franke, Katharina J; Pascual, Jose Ignacio

    2012-10-01

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

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

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

    2014-06-01

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

  15. Single molecule λ-DNA stretching studied by microfluidics and single particle tracking

    Wang, Jun; Lu, Chang

    2007-10-01

    DNA stretching has been an intensively studied topic due to its involvement in the cellular functions. In this work, we studied DNA stretching based on microfluidics and single particle tracking techniques. Microfluidics generates well-defined flow field within microscale channels and potentially allows the incorporation of chemical and biological assays with the single molecule experiments. Single DNA molecules were tethered to the channel bottom (glass) at one end and to fluorescent microbeads at the other end. The microscale flow exerted hydrodynamic force on the microbead with a magnitude dependent on the flow rate. The force-extension curves of the single DNA molecules were obtained by localizing the fluorescent microbead with nanometer precision at different flow rates. We were able to obtain DNA force-extension curves which fit the wormlike chain model very well. Furthermore, we also observed plateaus at low forces (15-30pN) in these curves when the hydrodynamic force was kept constant for a duration of 10s at each flow rate. One possible reason is that stretching force with long duration lowers the activation barrier for the conformational changes of a double-stranded DNA molecule. We expect that this approach will be useful for studying the force associated with biological events involving single DNA molecules in general.

  16. Chemical polyglycosylation and nanolitre detection enables single-molecule recapitulation of bacterial sugar export

    Kong, Lingbing; Almond, Andrew; Bayley, Hagan; Davis, Benjamin G.

    2016-05-01

    The outermost protective layer of both Gram-positive and Gram-negative bacteria is composed of bacterial capsular polysaccharides. Insights into the interactions between the capsular polysaccharide and its transporter and the mechanism of sugar export would not only increase our understanding of this key process, but would also help in the design of novel therapeutics to block capsular polysaccharide export. Here, we report a nanolitre detection system that makes use of the bilayer interface between two droplets, and we use this system to study single-molecule recapitulation of sugar export. A synthetic strategy of polyglycosylation based on tetrasaccharide monomers enables ready synthetic access to extended fragments of K30 oligosaccharides and polysaccharides. Examination of the interactions between the Escherichia coli sugar transporter Wza and very small amounts of fragments of the K30 capsular polysaccharide substrate reveal the translocation of smaller but not larger fragments. We also observe capture events that occur only on the intracellular side of Wza, which would complement coordinated feeding by adjunct biosynthetic machinery.

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

    Riccardo Frisenda

    2015-07-01

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

  18. Single-molecule measurement of the effective temperature in non-equilibrium steady states

    Dieterich, E.; Camunas-Soler, J.; Ribezzi-Crivellari, M.; Seifert, U.; Ritort, F.

    2015-11-01

    Temperature is a well-defined quantity for systems in equilibrium. For glassy systems, it has been extended to the non-equilibrium regime, showing up as an effective quantity in a modified version of the fluctuation-dissipation theorem. However, experimental evidence supporting this definition remains scarce. Here, we present the first direct experimental demonstration of the effective temperature by measuring correlations and responses in single molecules in non-equilibrium steady states generated under external random forces. We combine experiment, analytical theory and simulations for systems with different levels of complexity, ranging from a single bead in an optical trap to two-state and multiple-state DNA hairpins. From these data, we extract a unifying picture for the existence of an effective temperature based on the relative order of various timescales characterizing intrinsic relaxation and external driving. Our study thus introduces driven small systems as a fertile ground to address fundamental concepts in statistical physics, condensed-matter physics and biophysics.

  19. Super- and sub-Poissonian photon statistics for single molecule spectroscopy.

    He, Yong; Barkai, Eli

    2005-05-01

    We investigate the distribution of the number of photons emitted by a single molecule undergoing a spectral diffusion process and interacting with a continuous wave laser field. The spectral diffusion is modeled based on a stochastic approach, in the spirit of the Anderson-Kubo line shape theory. Using a generating function formalism we solve the generalized optical Bloch equations and obtain an exact analytical formula for the line shape and Mandel's Q parameter. The line shape exhibits well-known behaviors, including motional narrowing when the stochastic modulation is fast and power broadening. The Mandel parameter, describing the line shape fluctuations, exhibits a transition from a quantum sub-Poissonian behavior in the fast modulation limit to a classical super-Poissonian behavior found in the slow modulation limit. Our result is applicable for weak and strong laser fields, namely, for arbitrary Rabi frequency. We show how to choose the Rabi frequency in such a way so that the quantum sub-Poissonian nature of the emission process becomes strongest. A lower bound on Q is found and simple limiting behaviors are investigated. A nontrivial behavior is obtained in the intermediate modulation limit, when the time scales for spectral diffusion and the lifetime of the excited state become similar. A comparison is made between our results and previous ones derived, based on the semiclassical generalized Wiener-Khintchine formula. PMID:15918743

  20. Two-Photon Excitation of a Plasmonic Nanoswitch Monitored by Single-Molecule Fluorescence Microscopy.

    Impellizzeri, Stefania; Simoncelli, Sabrina; Hodgson, Gregory K; Lanterna, Anabel E; McTiernan, Christopher D; Raymo, Françisco M; Aramendia, Pedro F; Scaiano, Juan C

    2016-05-17

    Visible-light excitation of the surface plasmon band of silver nanoplates can effectively localize and concentrate the incident electromagnetic field enhancing the photochemical performance of organic molecules. Herein, the first single-molecule study of the plasmon-assisted isomerization of a photochrome-fluorophore dyad, designed to switch between a nonfluorescent and a fluorescent state in response to the photochromic transformation, is reported. The photochemistry of the switchable assembly, consisting of a photochromic benzooxazine chemically conjugated to a coumarin moiety, is examined in real time with total internal reflection fluorescence microscopy in the presence of silver nanoplates excited with a 633 nm laser. The metallic nanostructures significantly enhance the visible light-induced performance of the photoconversion, which normally requires ultraviolet excitation. The resulting ring-open isomer is strongly fluorescent and can also be excited at 633 nm. These stochastic emission events are used to monitor photochromic activation and show quadratic dependence on incident power. The utilization of a single laser wavelength for both photochromic activation and excitation effectively mimics a pseudo two-colours system. PMID:27060994