The vibrational spectroscopy and dynamics of weakly bound neutral complexes

A growing number of binary and tertiary van der Waals and hydrogen-bonded complexes are being studied by means of near-infrared laser spectroscopy. Studies of this type have generated a wealth of detailed structural and dynamical information that provides exacting tests of the corresponding theoretical methods. An additional incentive for the investigation of such clusters arises from the fact that they may be considered as intermediates between the gas and condensed phases of matter. As a result, these systems represent a fertile meeting ground for researchers from both fields and can often be studied with a variety of methods.     

Single-molecule torsional pendulum

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

Near-field coherent spectroscopy and microscopy of a quantum dot system

We combined coherent nonlinear optical spectroscopy with nano-electron volt energy resolution and low-temperature near-field microscopy with subwavelength resolution (相似文献   

Single-molecule optomechanical cycle

Light-powered molecular machines are conjectured to be essential constituents of future nanoscale devices. As a model for such systems, we have synthesized a polymer of bistable photosensitive azobenzenes. Individual polymers were investigated by single-molecule force spectroscopy in combination with optical excitation in total internal reflection. We were able to optically lengthen and contract individual polymers by switching the azo groups between their trans and cis configurations. The polymer was found to contract against an external force acting along the polymer backbone, thus delivering mechanical work. As a proof of principle, the polymer was operated in a periodic mode, demonstrating for the first time optomechanical energy conversion in a single-molecule device.     

Single-molecule cut-and-paste surface assembly

We introduce a method for the bottom-up assembly of biomolecular structures that combines the precision of the atomic force microscope (AFM) with the selectivity of DNA hybridization. Functional units coupled to DNA oligomers were picked up from a depot area by means of a complementary DNA strand bound to an AFM tip. These units were transferred to and deposited on a target area to create basic geometrical structures, assembled from units with different functions. Each of these cut-and-paste events was characterized by single-molecule force spectroscopy and single-molecule fluorescence microscopy. Transport and deposition of more than 5000 units were achieved, with less than 10% loss in transfer efficiency.     

Single-molecule experiments in vitro and in silico

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.     

Single-molecule measurement of protein folding kinetics

In order to investigate the behavior of single molecules under conditions far from equilibrium, we have coupled a microfabricated laminar-flow mixer to a confocal optical system. This combination enables time-resolved measurement of F?rster resonance energy transfer after an abrupt change in solution conditions. Observations of a small protein show the evolution of the intramolecular distance distribution as folding progresses. This technique can expose subpopulations, such as unfolded protein under conditions favoring the native structure, that would be obscured in equilibrium experiments.     

Near-field optics: microscopy, spectroscopy, and surface modification beyond the diffraction limit

The near-field optical interaction between a sharp probe and a sample of interest can be exploited to image, spectroscopically probe, or modify surfaces at a resolution (down to approximately 12 nm) inaccessible by traditional far-field techniques. Many of the attractive features of conventional optics are retained, including noninvasiveness, reliability, and low cost. In addition, most optical contrast mechanisms can be extended to the near-field regime, resulting in a technique of considerable versatility. This versatility is demonstrated by several examples, such as the imaging of nanometric-scale features in mammalian tissue sections and the creation of ultrasmall, magneto-optic domains having implications for highdensity data storage. Although the technique may find uses in many diverse fields, two of the most exciting possibilities are localized optical spectroscopy of semiconductors and the fluorescence imaging of living cells.     

Single-molecule DNA sequencing of a viral genome

The full promise of human genomics will be realized only when the genomes of thousands of individuals can be sequenced for comparative analysis. A reference sequence enables the use of short read length. We report an amplification-free method for determining the nucleotide sequence of more than 280,000 individual DNA molecules simultaneously. A DNA polymerase adds labeled nucleotides to surface-immobilized primer-template duplexes in stepwise fashion, and the asynchronous growth of individual DNA molecules was monitored by fluorescence imaging. Read lengths of >25 bases and equivalent phred software program quality scores approaching 30 were achieved. We used this method to sequence the M13 virus to an average depth of >150x and with 100% coverage; thus, we resequenced the M13 genome with high-sensitivity mutation detection. This demonstrates a strategy for high-throughput low-cost resequencing.     

Single-molecule lysozyme dynamics monitored by an electronic circuit

Tethering a single lysozyme molecule to a carbon nanotube field-effect transistor produced a stable, high-bandwidth transducer for protein motion. Electronic monitoring during 10-minute periods extended well beyond the limitations of fluorescence techniques to uncover dynamic disorder within a single molecule and establish lysozyme as a processive enzyme. On average, 100 chemical bonds are processively hydrolyzed, at 15-hertz rates, before lysozyme returns to its nonproductive, 330-hertz hinge motion. Statistical analysis differentiated single-step hinge closure from enzyme opening, which requires two steps. Seven independent time scales governing lysozyme's activity were observed. The pH dependence of lysozyme activity arises not from changes to its processive kinetics but rather from increasing time spent in either nonproductive rapid motions or an inactive, closed conformation.     

Single-molecule kinetics of lambda exonuclease reveal base dependence and dynamic disorder

We used a multiplexed approach based on flow-stretched DNA to monitor the enzymatic digestion of lambda-phage DNA by individual bacteriophage lambda exonuclease molecules. Statistical analyses of multiple single-molecule trajectories observed simultaneously reveal that the catalytic rate is dependent on the local base content of the substrate DNA. By relating single-molecule kinetics to the free energies of hydrogen bonding and base stacking, we establish that the melting of a base from the DNA is the rate-limiting step in the catalytic cycle. The catalytic rate also exhibits large fluctuations independent of the sequence, which we attribute to conformational changes of the enzyme-DNA complex.     

Single-molecule fluorescence experiments determine protein folding transition path times

The transition path is the tiny fraction of an equilibrium molecular trajectory when a transition occurs as the free-energy barrier between two states is crossed. It is a single-molecule property that contains all the mechanistic information on how a process occurs. As a step toward observing transition paths in protein folding, we 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 F?rster resonance energy transfer experiments. Whereas the folding rate coefficients differ by a factor of 10,000, the transition-path times differ by a factor of less than 5, which shows that a fast- and a slow-folding protein take almost the same time to fold when folding actually happens. A very simple model based on energy landscape theory can explain this result.     

Single-molecule speckle analysis of actin filament turnover in lamellipodia

Lamellipodia are thin, veil-like extensions at the edge of cells that contain a dynamic array of actin filaments. We describe an approach for analyzing spatial regulation of actin polymerization and depolymerization in vivo in which we tracked single molecules of actin fused to the green fluorescent protein. Polymerization and the lifetime of actin filaments in lamellipodia were measured with high spatial precision. Basal polymerization and depolymerization occurred throughout lamellipodia with largely constant kinetics, and polymerization was promoted within one micron of the lamellipodium tip. Most of the actin filaments in the lamellipodium were generated by polymerization away from the tip.     

Optical pumping and vibrational cooling of molecules

The methods producing cold molecules from cold atoms tend to leave molecular ensembles with substantial residual internal energy. For instance, cesium molecules initially formed via photoassociation of cold cesium atoms are in several vibrational levels nu of the electronic ground state. We applied a broadband femtosecond laser that redistributes the vibrational population in the ground state via a few electronic excitation/spontaneous emission cycles. The laser pulses are shaped to remove the excitation frequency band of the nu = 0 level, preventing re-excitation from that state. We observed a fast and efficient accumulation ( approximately 70% of the initially detected molecules) in the lowest vibrational level, nu = 0, of the singlet electronic state. The validity of this incoherent depopulation pumping method is very general and opens exciting prospects for laser cooling and manipulation of molecules.     

Atomic-scale desorption through electronic and vibrational excitation mechanisms

The scanning tunneling microscope has been used to desorb hydrogen from hydrogen-terminated silicon (100) surfaces. As a result of control of the dose of incident electrons, a countable number of desorption sites can be created and the yield and cross section are thereby obtained. Two distinct desorption mechanisms are observed: (i) direct electronic excitation of the Si-H bond by field-emitted electrons and (ii) an atomic resolution mechanism that involves multiple-vibrational excitation by tunneling electrons at low applied voltages. This vibrational heating effect offers significant potential for controlling surface reactions involving adsorbed individual atoms and molecules.