Manipulations of atoms and molecules by scanning probe microscopyk

Scanning probe microscopy (SPM), including scanning tunneling microscopy (STM) and atomic force microscopy (AFM), has become a powerful tool in building nanoscale structures required by modern industry. In this article, the use of SPM for the manipulation of atoms and molecules for patterning nanostructures for opt-electronic and biomedical applications is reviewed. The principles and procedures of manipulation using STM and AFM-based technologies are presented with an emphasis on their ability to create a wide variety of nanostructures for different applications. The interaction among the atoms/molecules, surface, and tip are discussed. The approaches for positioning the atom/molecule from and to the desired locations and for precisely controlling its movement are elaborated for each specific manipulation technique. As an AFM-based technique, the dip-pen nanolithography is also included. Finally, concluding remarks on technological improvement and future research is provided.

Downhill kinetics of biomolecular interface binding: Globally connected scenario

We study the kinetics of the biomolecular binding process at the interface using energy landscape theory. The global kinetic connectivity case is considered for a downhill funneled energy landscape. By solving the kinetic master equation, the kinetic time for binding is obtained and shown to have a U-shape curve-dependence on the temperature. The kinetic minimum of the binding time monotonically decreases when the ratio of the underlying energy gap between native state and average non-native states versus the roughness or the fluctuations of the landscape increases. At intermediate temperatures,fluctuations measured by the higher moments of the binding time lead to non-Poissonian, non-exponential kinetics. At both high and very low temperatures, the kinetics is nearly Poissonian and exponential.

The complex kinetics of protein folding in wide temperature ranges

The complex protein folding kinetics in wide temperature ranges is studied through diffusive dynamics on the underlying energy landscape. The well-known kinetic chevron rollover behavior is recovered from the mean first passage time, with the U-shape dependence on temperature. The fastest folding temperature T-0 is found to be smaller than the folding transition temperature T-f. We found that the fluctuations of the kinetics through the distribution of first passage time show rather universal behavior, from high-temperature exponential Poissonian kinetics to the relatively low-temperature highly nonexponential kinetics. The transition temperature is at T-k and T-0, T-k, T-f. In certain low-temperature regimes, a power law behavior at long time emerges. At very low temperatures ( lower than trapping transition temperature T< T-0/(4&SIM;6)), the kinetics is an exponential Poissonian process again.

Dominant kinetic paths on biomolecular binding-folding energy landscape

The identification of kinetic pathways is a central issue in understanding the nature of flexible binding. A new approach is proposed here to study the dynamics of this binding-folding process through the establishment of a path integral framework on the underlying energy landscape. The dominant kinetic paths of binding and folding can be determined and quantified. In this case, the corresponding kinetic paths of binding are shown to be intimately correlated with those of folding and the dynamics becomes quite cooperative. The kinetic time can be obtained through the contributions from the dominant paths and has a U-shape dependence on temperature.

Effects of chain flexibility on polymer conformation in dilute solution studied by lattice Monte Carlo simulation

Effects of chain flexibility on the conformation of homopolymers in good solvents have been investigated by Monte Carlo simulation. Bond angle constraint coupled with persistence length of polymer chains has been introduced in the modified eight-site bond fluctuation simulation model. The study about the effects of chain flexibility on polymer sizes reveals that the orientation of polymer chains under confinement is driven by the loss of conformation entropy. The conformation of polymer chains undergoing a gradual change from spherical iso-diametric ellipsoid to rodlike iso-diametric ellipsoid with the decrease of polymer chain flexibility in a wide region has been clearly illustrated from several aspects. Furthermore, a comparison of the freely jointed chain (FJC) model and the wormlike chain (WLC) model has also been made to describe the polymer sizes in terms of chain flexibility and quasi-quantitative boundary toward the suitability of the models.

Surface-enhanced Raman scattering studies on aggregated silver nanoplates in aqueous solution

Four different sizes of citrate-protected silver nanoplates with the corresponding in-plane dipole resonance band at 530, 619, 778, and 858 nm, respectively, are synthesized for surface-enhanced Raman scattering (SERS) study. Their aggregation behaviors are monitored by use of UV-vis spectroscopy. During the aggregation process, a marked red shift of the in-plane dipole resonance of silver nanoplates is observed, whereas other resonance modes of them only have small alterations in the site or intensity. Aggregated silver nanoplates can serve as active SERS substrates with an enhancement factor of about 4.5 x 10(5) using 2-aminothiophenol as a probing molecule. The SERS performance of silver nanoplates is even superior to the commonly used Lee-Meisel silver colloid, making them very attractive for SERS applications.

First-passage time distribution and non-Markovian diffusion dynamics of protein folding

We study the kinetics of protein folding via statistical energy landscape theory. We concentrate on the local-connectivity case, where the configurational changes can only occur among neighboring states, with the folding progress described in terms of an order parameter given by the fraction of native conformations. The non-Markovian diffusion dynamics is analyzed in detail and an expression for the mean first-passage time (MFPT) from non-native unfolded states to native folded state is obtained. It was found that the MFPT has a V-shaped dependence on the temperature. We also find that the MFPT is shortened as one increases the gap between the energy of the native and average non-native folded states relative to the fluctuations of the energy landscape. The second- and higher-order moments are studied to infer the first-passage time distribution. At high temperature, the distribution becomes close to a Poisson distribution, while at low temperatures the distribution becomes a Levy-type distribution with power-law tails, indicating a nonself-averaging intermittent behavior of folding dynamics. We note the likely relevance of this result to single-molecule dynamics experiments, where a power law (Levy) distribution of the relaxation time of the underlined protein energy landscape is observed.

In situ electrochemical scanning tunnelling microscopy investigation of structure for horseradish peroxidase and its electrocatalytic property

Immobilization of protein molecules is a fundamental problem for scanning tunnelling microscopy (STM) measurements with high resolution. In this paper, an electrochemical method has been proved to be an effective way to fix native horseradish peroxidase (HRP) as well as inactivated HRP from electrolyte onto a highly oriented pyrolytic graphite (HOPG) surface. This preparation is suitable for both ex situ and in situ electrochemical STM (ECSTM) measurements. In situ STM has been successfully employed to observe totally different structures of HRP in three typical cases: (1) in situ ECSTM reveals an oval-shaped pattern for a single molecule in neutral buffer solution, which is in good agreement with the dimension determined as 6.2 x 4.3 x 1.2. nm(3) by ex situ STM for native HRP; (2) in situ ECSTM shows that the adsorbed HRP molecules on HOPG in a denatured environment exhibit swelling globes at the beginning and then change into a V-shaped pattern after 30 min; (3) in situ ECSTM reveals a black hole in every ellipsoidal sphere for inactivated HRP in strong alkali solution. The cyclic voltammetry results indicate that the adsorbed native HRP can directly catalyse the reduction of hydrogen peroxide, demonstrating that a direct electron transfer reduction occurred between the enzyme and HOPG electrode, whereas the corresponding cyclic voltammograms for denatured HRP and inactivated HRP adsorbed on HOPG electrodes indicate a lack of ability to catalyse H2O2 reduction, which confirms that the HRP molecules lost their biological activity. Obviously, electrochemical results powerfully support in situ STM observations.

Oligonucleotide ligation assay-based DNA chip for multiplex detection of single nucleotide polymorphism

An oligonucleotide ligation assay-based DNA chip has been developed to detect single nucleotide polymorphism. Synthesized nonamers, complementary to the flanking sequences of the mutation sites in target DNA, were immobilized onto glass slides through disulfide bonds on their 5' terminus. Allele-specific pentamers annealed adjacent to the nonamers on the complementary target DNA, containing 5'-phosphate groups and biotin labeled 3'-ends, were mixed with the target DNA in tube. Ligation reactions between nonamers and pentamers were carried out on chips in the presence of T4 DNA ligase. Ligation products were directly visualized on chips through enzyme-linked assay. The effect of G:T mismatch at different positions of pentamers on the ligation were evaluated. The results showed that any mismatch between pentamer and the target DNA could lead to the decrease of ligation, which can be detected easily. The established approach was further used for multiplex detection of mutations in rpoB gene of rifampin-resistant Mycobacterium tuberculosis clinical isolates. (C) 2003 Elsevier B.V. All rights reserved.

Transfer and detection of single electrons using metal-oxide-semiconductor field-effect transistors

A single-electron turnstile and electrometer circuit was fabricated on a silicon-on-insulator substrate. The turnstile, which is operated by opening and closing two metal-oxide-semiconductor field-effect transistors (MOSFETs) alternately, allows current quantization at 20 K due to single-electron transfer. Another MOSFET is placed at the drain side of the turnstile to form an electron storage island. Therefore, one-by-one electron entrance into the storage island from the turnstile can be detected as an abrupt change in the current of the electrometer, which is placed near the storage island and electrically coupled to it. The correspondence between the quantized current and the single-electron counting was confirmed.

Quantum trajectory analysis for electrical detection of single-electron spin resonance

A Monte Carlo simulation on the basis of quantum trajectory approach is carried out for the measurement dynamics of a single-electron spin resonance. The measured electron, which is confined in either a quantum dot or a defect trap, is tunnel coupled to a side reservoir and continuously monitored by a mesoscopic detector. The simulation not only recovers the observed telegraphic signal of detector current, but also predicts unique features in the output power spectrum which are associated with electron dynamics in different regimes.

Low potential detection of glutamate based on the electrocatalytic oxidation of NADH at thionine/single-walled carbon nanotubes composite modified electrode

A glutamate biosensor based on the electrocatalytic oxidation of reduced nicotinamide adenine dinucleotide (NADH), which was generated by the enzymatic reaction, was developed via employing a single-walled carbon nanotubes/thionine (Th-SWNTs) nanocomposite as a mediator and an enzyme immobilization matrix. The biosensor, which was fabricated by immobilizing glutamate dehydrogenase (GIDH) on the surface of Th-SWNTs, exhibited a rapid response (ca. 5 s), a low detection limit (0.1 mu M), a wide and useful linear range (0.5-400 mu M), high sensitivity (137.3 +/- 15.7) mu A mM(-1) cm(-2), higher biological affinity, as well as good stability and repeatability. In addition, the common interfering species, such as ascorbic acid, uric acid, and 4-acetamidophenol, did not cause any interference due to the use of a low operating potential (190 mV vs. NHE). The biosensor can be used to quantify the concentration of glutamate in the physiological level. The Th-SWNTs system represents a simple and effective approach to the integration of dehydrogenase and electrodes, which can provide analytical access to a large group of enzymes for wide range of bioelectrochemical applications including biosensors and biofuel cells.

Detection of Terahertz Photon by GaAs-Based Single Electron Transistor at Low Temperatures

A reproducible terahertz (THz) photocurrent was observed at low temperatures in a Schottky wrap gate single electron transistor with a normal-incident of a CH_3OH gas laser with the frequency 2. 54THz.The change of source-drain current induced by THz photons shows that a satellite peak is generated beside the resonance peak. THz photon energy can be characterized by the difference of gate voltage positions between the resonance peak and satellite peak. This indicates that the satellite peak exactly results from the THz photon-assisted tunneling. Both experimental results and theoretical analysis show that a narrow spacing of double barriers is more effective for the enhancement of THz response.