Single-molecule detection sensitivity using planar integrated optics on a chip

We present a fully planar integrated optical approach to single-molecule detection based on microfabricated planar networks of intersecting solid and liquid-core waveguides. We study fluorescence from dye molecules in liquid-core antiresonant reflecting optical waveguides, and demonstrate subpicoliter excitation volumes, parallel excitation through multiple pump waveguides, and single-molecule detection sensitivity. Integrated silicon photonics combined with single-molecule detection in solution create a compact, robust, and sensitive platform that has applications in numerous fields ranging from atomic physics to the life sciences.     

Surprises in the phase diagram of an anderson impurity model for a single C60(n-) molecule

We find by Wilson numerical renormalization group and conformal field theory that a three-orbital Anderson impurity model for a C60(n-) molecule has a very rich phase diagram which includes non-Fermi-liquid stable and unstable fixed points with interesting properties, most notably high sensitivity to doping n. We discuss the implications of our results to the conductance behavior of C60-based single-molecule transistor devices.     

Magnetic dipolar ordering and quantum phase transition in an Fe8 molecular magnet

We show that a crystal of mesoscopic Fe(8) single-molecule magnets is an experimental realization of the quantum Ising model in a transverse field, with dipolar interactions. Quantum annealing has enabled us to explore the quantum and classical phase transitions between the paramagnetic and ferromagnetic phases, at thermodynamical equilibrium. The phase diagram and critical exponents that we obtain agree with expectations for the mean-field universality class.     

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.     

Single-molecule spectroscopy of radical pairs,a theoretical treatment and experimental considerations

ABSTRACT

In this work, we propose to extend the scope of single-molecule spectroscopy to spin chemistry investigations of single radical pairs. A consistent theory of single-molecule spectroscopy on single radical pairs is proposed, which allows one to show that bunching phenomena are affected by singlet–triplet interconversion in radical pairs, which is, in turn, affected by local and external magnetic fields. A detailed study on the feasibility of such experiments with single flavin adenine dinucleotide, FAD, molecules is presented. We conclude that the observation of magnetic field effects on single FAD molecules is feasible but experimentally challenging for measurements on integrated fluorescence intensity and fluorescence event statistics.     

Denaturation transition of stretched DNA

We generalize the Poland-Scheraga model to consider DNA denaturation in the presence of an external stretching force. We demonstrate the existence of a force-induced DNA denaturation transition and obtain the temperature-force phase diagram. The transition is determined by the loop exponent c, for which we find the new value c = 4 nu-1/2 such that the transition is second order with c = 1.85 < 2 in d = 3. We show that a finite stretching force F destabilizes DNA, corresponding to a lower melting temperature T(F), in agreement with single-molecule DNA stretching experiments.     

Dynamic force spectroscopy of protein-DNA interactions by unzipping DNA

We demonstrate the first site-specific single-molecule characterization of the prominent activation barrier for the disruption of a protein-DNA binding complex. We achieved this new capability by combining dynamic force spectroscopy with unzipping force analysis of protein association and used the combination to investigate restriction enzyme binding to specific DNA sites. Analysis revealed lifetimes and interaction distances for three protein-DNA interactions. This new method is able to distinguish protein-DNA binding complexes on a site-specific, single-molecule basis.     

Photon antibunching in the fluorescence of a single dye molecule embedded in a thin polymer film

We used scanning confocal microscopy to study the fluorescence from a single terrylene molecule embedded in a thin polymer film of polymethyl methacrylate, at room temperature, with a high signal-to-background ratio. The photon-pair correlation function g((2))(tau) exhibits perfect photon antibunching at tau = 0 and a limit of 1.3, compatible with bunching associated with the molecular triplet state. Application of this molecular system to a triggered single-photon source based on single-molecule fluorescence is investigated.     

Asymmetric Berry-phase interference patterns in a single-molecule magnet

A Mn(4) single-molecule magnet displays asymmetric Berry-phase interference patterns in the transverse-field (H(T)) dependence of the magnetization tunneling probability when a longitudinal field (H(L)) is present, contrary to symmetric patterns observed for H(L)=0. Reversal of H(L) results in a reflection of the transverse-field asymmetry about H(T)=0, as expected on the basis of the time-reversal invariance of the spin-orbit Hamiltonian which is responsible for the tunneling oscillations. A fascinating motion of Berry-phase minima within the transverse-field magnitude-direction phase space results from a competition between noncollinear magnetoanisotropy tensors at the two distinct Mn sites.     

Single-molecule surface- and tip-enhanced raman spectroscopy

A review is given on single-molecule surface- and tip-enhanced Raman spectroscopy (SERS and TERS). It sketches the historical development along different routes toward huge near-field enhancements, the basis of single-molecule enhanced Raman spectroscopy; from SNOM to apertureless SNOM to tip-enhanced Raman spectroscopy (TERS) and microscopy; from SERS to single-molecule SERS to single-molecule TERS. The claim of extremely high enhancement factors of 10¹⁴ in single-molecule SERS is critically discussed, in particular in the view of recent experimental and theoretical results that limits the electromagnetic enhancement to ? 10¹¹. In the field of TERS only very few reports on single-molecule TERS exist: single-molecule TERS on dyes and on a protein (cytochrome c). In the latter case, TERS ‘sees’ even subunits of this protein, either amino-acids or the heme, depending on the orientation of the protein relative to the tip. The former case concerns the dye brilliant cresyl blue adsorbed either on a Au surface under ambient conditions or on a Au(111) surface in ultra high vacuum. These results indicate that significant progress is to be expected for TERS in general and for single-molecule TERS in particular.     

Evidence for a single hydrogen molecule connected by an atomic chain

Stable, single-molecule conducting-bridge configurations are typically identified from peak structures in a conductance histogram. In previous work on Pt with H2 at cryogenic temperatures it has been shown that a peak near 1G0 identifies a single-molecule Pt-H2-Pt bridge. The histogram shows an additional structure with lower conductance that has not been identified. Here, we show that it is likely due to a hydrogen decorated Pt chain in contact with the H2 molecular bridge.     

Underwound DNA under tension: structure, elasticity, and sequence-dependent behaviors

DNA melting under torsion plays an important role in a wide variety of cellular processes. In the present Letter, we have investigated DNA melting at the single-molecule level using an angular optical trap. By directly measuring force, extension, torque, and angle of DNA, we determined the structural and elastic parameters of torsionally melted DNA. Our data reveal that under moderate forces, the melted DNA assumes a left-handed structure as opposed to an open bubble conformation and is highly torsionally compliant. We have also discovered that at low forces melted DNA properties are highly dependent on DNA sequence. These results provide a more comprehensive picture of the global DNA force-torque phase diagram.     

Fast, flexible algorithm for calculating photon correlations

We introduce a new algorithm for computing correlations of photon arrival time data acquired in single-molecule fluorescence spectroscopy and fluorescence correlation spectroscopy (FCS). The algorithm is based on rewriting the correlation as a counting operation on photon pairs and can be used with arbitrary bin widths and spacing. The flexibility of the algorithm is demonstrated by use of FCS simulations and single-molecule photon antibunching experiments. Execution speed is comparable to the commonly used multiple-tau correlation technique. Wide bin spacings are possible that allow for real-time software calculation of correlations, even for high count rates.     

Single-molecule detection of biomolecules by surface-enhanced coherent anti-Stokes Raman scattering

We report on the applicability of combining surface-enhanced Raman scattering (SERS) with coherent anti-Stokes Raman scattering for high-sensitivity detection of biological molecules. We found that this combination of techniques provides more than 3 orders of signal enhancement compared with SERS and permits monitoring of biological molecules such as deoxyguanosine monophosphate (dGMP) and deoxyadenosine monophosphate at the single-molecule level. This combined technique also improved detection sensitivity for angiotensin peptide. As this is believed to be the first report of detection of dGMP at the single-molecule level, we suggest that this approach can serve as a new tool for biological studies.     

Nuclear spin dynamics in the quantum regime of a single-molecule magnet

We show that the nuclear spin dynamics in the single-molecule magnet Mn12-ac below 1 K is governed by quantum tunneling fluctuations of the cluster spins, combined with intercluster nuclear spin diffusion. We also obtain the first experimental proof that-surprisingly-even deep in the quantum regime the nuclear spins remain in good thermal contact with the lattice phonons. We propose a simple model for how T-independent tunneling fluctuations can relax the nuclear polarization to the lattice that may serve as a framework for more sophisticated theories.     

单分子尺度的光量子态调控与单分子电致发光研究

分子尺度上的光电相互作用研究可以为发展未来信息和能源技术提供科学基础.扫描隧道显微镜不仅可以用来观察和操纵纳米世界中的原子和分子,而且其高度局域化的隧穿电流还可以被用来激发隧道结中的分子,使之发光,以研究局域场下的分子光电特性.本文综述了中国科学技术大学单分子光电研究组近期在锌酞菁分子电致发光方面取得的科学进展,包括：1）利用有效的电子脱耦合与纳腔等离激元调控技术,实现了隧穿电子激发下的单个锌酞菁分子的电致荧光,并通过发展相关的光子发射统计测量方法,表征了单个分子在隧穿电子激发下的电致荧光具有单光子发射特性;2）发展了具有亚纳米空间分辨的荧光光谱成像技术,实现了对酞菁分子间相干偶极相互作用特征的实空间观察;3）对分子与纳腔等离激元之间的相干耦合作用进行了亚纳米精度的操控,在单分子水平上观察到了法诺共振和兰姆位移效应.这些研究结果不仅为研发基于有机分子的电泵纳米光源与单光子光源等分子光电器件提供了新的思路,而且为在单分子尺度上研究分子光电特性、分子间能量转移以及场与物质之间的相互作用规律等提供了新的表征方法.     

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.     

Electron transport through single Mn12 molecular magnets

We report transport measurements through a single-molecule magnet, the Mn12 derivative [Mn12O12(O2C-C6H4-SAc)16(H2O)4], in a single-molecule transistor geometry. Thiol groups connect the molecule to gold electrodes that are fabricated by electromigration. Striking observations are regions of complete current suppression and excitations of negative differential conductance on the energy scale of the anisotropy barrier of the molecule. Transport calculations, taking into account the high-spin ground state and magnetic excitations of the molecule, reveal a blocking mechanism of the current involving nondegenerate spin multiplets.     

The Effect of Physical Form of DNA on ExonucleaseIII Activity Revealed by Single-molecule Observations

Single-molecule studies have revealed molecular behaviors usually hidden in the ensemble and time averaging of bulk experiments. Single-molecule measurement that can control physical form of individual DNA molecules is a powerful method to obtain new knowledge about correlation between DNA-tension and enzyme activity. Here we study the effect of physical form of DNA on exonucleaseIII (ExoIII) reaction. ExoIII has a double-stranded DNA specific 3′→5′ exonuclease activity and the digestion is distributive. We observed the ExoIII digestion of individual stretched DNA molecules from the free ends. The sequentially captured photographs demonstrated that the digested DNA molecule linearly shortened with the reaction time. We also carried out the single-molecule observation under random coiled form by pausing the buffer flow. The digestion rates obtained from both single-molecule experiments showed that the digestion rate under the stretched condition was two times higher than the random coiled condition. The correlation between physical form of DNA and digestion rate of ExoIII was clearly demonstrated by single-molecule observations.     

Fluorescence from Diffusing Single Molecules Illuminates Biomolecular Structure and Dynamics

This review provides an account of single-molecule fluorescence methodologies for freely diffusing molecules applied to a diverse array of biological problems pertaining to biomolecular folding and assembly. We describe the principles of confocal fluorescence microscopy to detect and analyze fluorescence bursts from diffusing single molecules. These methods including single-molecule fluorescence resonance energy transfer, coincidence, correlations and polarization offer a powerful means to uncover hidden information about conformational sub-populations and interconversion dynamics of biomolecular systems in a wide range of timescales. We offer several key examples to illustrate how these methodologies have been extremely useful in teasing out structural and dynamical aspects of many important biomolecular systems.