Zero-mode waveguides provide a powerful technology for studying single-molecule real-time dynamics of biological systems at physiological ligand concentrations. We customized a commercial zero-mode waveguide-based DNA sequencer for use as a versatile instrument for single-molecule fluorescence detection and showed that the system provides long fluorophore lifetimes with good signal to noise and low spectral cross-talk. We then used a ribosomal translation assay to show real-time fluidic delivery during data acquisition, showing it is possible to follow the conformation and composition of thousands of single biomolecules simultaneously through four spectral channels. This instrument allows high-throughput multiplexed dynamics of single-molecule biological processes over long timescales. The instrumentation presented here has broad applications to single-molecule studies of biological systems and is easily accessible to the biophysical community.D etermining the molecular details of the time evolution of complex multicomponent biological systems requires analysis at the single-molecule level because of their stochastic and heterogeneous nature. Ideally, such experiments would track simultaneously the composition of a biological system (bound ligands, factors, and cofactors) and the conformation of the individual molecules in real time. Single-molecule fluorescence methods, such as total internal reflection fluorescence (TIRF) microscopy, allow the observations of the compositional dynamics (through arrival of fluorescently labeled ligands, factors, or cofactors) and conformational dynamics (through FRET) of single-molecular species. However, these traditional singlemolecule methods are hindered by limitations in maximal fluorescent component concentrations (up to 50 nM) (1), limited simultaneous detection (two to three colors) (2-6), and low throughput (a few hundred molecules at most per experiment) (7). As such, the full potential of single-molecule fluorescence to investigate a range of biological problems under physiologically relevant conditions has not yet been harnessed.Zero-mode waveguides (ZMWs) are small metallic apertures patterned on glass substrates that overcome the concentration restrictions by optically limiting background excitation (8). Each ZMW consists of an ∼150-nm-diameter metallic aperture that restricts the excitation light to a zeptoliter volume, making possible experiments with near-physiological concentrations (up to 20 μM) of fluorescently labeled ligands (1). Previous advances in nanofabrication (9), surface chemistry (10), and detection instrumentation (11) have led to ZMW-based instrumentation capable of the direct observation of DNA polymerization (12), reverse transcription (13), processive myosin motion (14), and translation by the ribosome (15, 16) with multicolor single-molecule detection. However, this sophisticated technology has not been broadly available to the scientific community. Despite multiple efforts to develop ZMW instrumentation, the combined difficulties in fabrica...

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RDF (Resource Description Framework) and RDF Schema (collectively called RDF(S)) are the normative language to describe the Web resource information. How to construct RDF(S) from the existing data sources is becoming an important research issue. In particular, UML (Unified Modeling Language) is being widely applied to data modeling in many application domains, and how to construct RDF(S) from the existing UML models becomes an important issue to be solved in the context of Semantic Web. By comparing and analyzing the characteristics of UML and RDF(S), this paper proposes an approach for constructing RDF(S) from UML and implements a prototype construction tool. First, we give the formal definitions of UML and RDF(S). After that, a construction approach from UML to RDF(S) is proposed, a construction example is provided, and the analyses and discussions about the approach are done. Further, based on the proposed approach, a prototype construction tool is implemented, and the experiment shows that the approach and the tool are feasible.

A recently developed inverse scattering method based on the distorted-wave Born approximation (DWBA) that applies to objects embedded in known background media [Inverse Probl.19, 855 (2003);20, 1307 (2004)] is implemented for the special case of circularly symmetric scatterers embedded in circularly symmetric backgrounds. The newly developed scheme is applied in a computer-simulation study of optical diffraction tomography (ODT), and the results are compared and contrasted with reconstructions obtained using the filtered backpropagation algorithm (FBP algorithm). Unlike the DWBA-based inversion algorithm, the FBP algorithm does not take into account multiple scattering within the known background, and it is found that the newly implemented scheme yields reconstructions much superior to those obtained using the FBP algorithm. The research reported applies to a number of important applications that include ultrasound nondestructive evaluation testing of cylinders for defects as well as ODT.

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