Integrated microanalytical technology enabling rapid and automated protein identification

Protein identification through peptide mass mapping by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has become a standard technique, used in many laboratories around the world. The traditional methodology often includes long incubations (6-24 h) and extensive manual steps. In an effort to address this, an integrated microanalytical platform has been developed for automated identification of proteins. The silicon micromachined analytical tools, i.e., the microchip immobilized enzyme reactor (mu-chip IMER), the piezoelectric microdispenser, and the high-density nanovial target plates, are the cornerstones in the system. The mu-chip IMER provides on-line enzymatic digestion of protein samples (1 microL) within 1-3 min, and the microdispenser enables subsequent on-line picoliter sample preparation in a high-density format. Interfaced to automated MALDI-TOF MS, these tools compose a highly efficient platform that can analyze 100 protein samples in 3.5 h. Kinetic studies on the microreactors are reported as well as the operation of this microanalytical platform for protein identification, wherein lysozyme, myoglobin, ribonuclease A, and cytochrome c have been identified with a high sequence coverage (50-100%).     

Fabrication and simulation of diffractive optical elements with superimposed antireflection subwavelength gratings

With the aim of reducing surface reflections and increasing the diffraction efficiency we investigated the superposition of subwavelength phase gratings onto blazed phase gratings. With direct-write electron-beam lithography bare blazed gratings and blazed gratings carrying subwavelength gratings were fabricated and their optical performances compared. For TE polarization the subwavelength-carrying gratings showed a maximum diffraction efficiency of 90.6%, whereas the corresponding maximum value for the bare grating was 86.3%. The experiment was simulated with rigorous diffraction theory.     

Off-plane computer-generated waveguide hologram

We present the theory, design, fabrication and evaluation of off-plane computer-generated waveguide holograms (OP-CGWHs). The hologram structure is composed of an array of rectangular elements each containing a waveguide grating coupler. The function of the rectangular elements is twofold: outcoupling the guided optical wave, and introducing phase shift. The phase shift of each rectangular element can be determined by controlling the dislocation of the grating grooves along the guided wave propagation direction. In addition, the phase pattern of the OP-CGWH can be designed using many existing algorithms for computer-generated holograms (CGH), such as the iterative Fourier transform algorithm (IFTA). A design example is presented for a waveguide array generator, which outcouples a Gaussian-like incident guided wave and simultaneously produces an array of spots in free space. Such an OP-CGWH device, based on an AlGaAs-GaAs waveguide, was fabricated using electron-beam lithography and reactive ion beam etching. Experimental results are presented that demonstrate the effectiveness of the proposed idea. The uniformity error and the power efficiency of the fabricated OP-CGWH array generator were measured to be approximately 8% and 30%, respectively     

Incoupling waveguide holograms for simultaneous focusing into multiple arbitrary positions

A design method is presented that enables the realization of a novel type of incoupling waveguide hologram (IWGH) that simultaneously focuses the incoupled light to any desired positions in the waveguide. IWGH's, or grating couplers, are gratinglike structures etched into the waveguide surface. They couple the light incident from free space into the waveguide. The grating lines can be dislocated with respect to each other to provide phase modulation of the incoupled light. By use of this phase modulation, novel beam splitting and focusing functions can be built into the IWGH's. The new design algorithm is based on a model that assumes a simple relation between the incident light wave and the locally excited guided wave. This model is used to obtain an efficient formulation of the optimization problem. Four different IWGH's were designed and fabricated in InP for light at 1550-nm wavelength. Experiments confirm that these IWGH's are capable of incoupling the incident wave and simultaneously splitting and focusing the guided wave into multiple positions in the waveguide at different distances from the IWGH.     

Pure rotational coherent anti-Stokes Raman spectroscopy in mixtures of CO and N2

We present a model for quantitative measurements in binary mixtures of nitrogen and carbon monoxide by the use of dual-broadband rotational coherent anti-Stokes Raman spectroscopy. The model has been compared with experimental rotational coherent anti-Stokes Raman scattering spectra recorded within the temperature range of 294-702 K. Temperatures and concentrations were evaluated by spectral fits using libraries of theoretically calculated spectra. The relative error of the temperature measurements was 1-2%, and the absolute error of the CO concentration measurements was <0.5% for temperatures < or =600 K. For higher temperatures, the gas composition was not chemically stable, and we observed a conversion of CO to CO2. The influence of important spectroscopic parameters such as the anisotropic polarizability and Raman line-broadening coefficients are discussed in terms of concentration measurements. In particular, it is shown that the CO concentration measurement was more accurate if N2-CO and CO-N2 line-broadening coefficients were included in the calculation. The applicability of the model for quantitative flame measurements is demonstrated by measuring CO concentrations in ethylene/air flames.     

On Duality between Quantum Maps and Quantum States

We investigate the space of quantum operations, as well as the larger space of maps which are positive, but not completely positive. A constructive criterion for decomposability is presented. A certain class of unistochastic operations, determined by unitary matrices of extended dimensionality, is defined and analyzed. Using the concept of the dynamical matrix and the Jamiokowski isomorphism we explore the relation between the set of quantum operations (dynamics) and the set of density matrices acting on an extended Hilbert space (kinematics). An analogous relation is established between the classical maps and an extended space of the discrete probability distributions.     

Developing control logic using aspect-oriented programming and sequence planning

A fundamental functionality of a Programmable Logic Controller (PLC) is to control and execute a set of operations. But a large part of the program code is more involved in supporting the user with concerns like alarm, HMI, communication, safety and manual control. Code related to these supporting concerns is often tangled with operation execution code, the core concerns, which makes it hard to reuse.This paper describes a method to reuse code and functionality when developing PLC programs and code libraries. The method proposes that core concerns are planned with a software tool called Sequence Planner, and the supporting concerns are integrated into the core concerns with a tool based on aspect-oriented programming.     

An experiment on creating scenario profiles for software change

Scenario profiles are used increasingly often for the assessment of quality attributes during the architectural design of software systems. However, the definition of scenario profiles is subjective and no data is available on the effects of individuals on scenario profiles. In this paper we present the design, analysis and results of a controlled experiment on the effect of individuals on scenario profiles, so that others can replicate the experiments on other projects and people. Both scenario profiles created by individuals and by groups are studied. The findings from the experiment showed that groups with prepared members proved to be the best method for creating scenario profiles. Unprepared groups did not perform better than individuals when creating scenario profiles. This revised version was published online in June 2006 with corrections to the Cover Date.     

Multi-criteria Decision Analysis (MCDA) for Integrated Water Resources Management (IWRM) in the Lake Poopo Basin, Bolivia

Integrated Water Resources Management (IWRM) is a relatively new approach in Bolivia. However, it is now generally accepted that this approach needs to be established in order to find sustainable solutions for development and is actively promoted by the Water Ministry, especially in environmentally fragile regions, such as the Lake Poopo basin. The Lake Poopo basin is one of the poorest regions in the Bolivian Altiplano. It is confronted with severe water scarcity during the dry season, leading to low water quality, a high water-poverty index and low values of the watershed sustainability index. Furthermore, salinization and environmental degradation of soil and water are forcing people to migrate to urban areas. These are some of the factors underlying an ever-increasing complexity in integrated water resources management in the region. This paper proposes and develops a Multi-criteria Decision Analysis (MCDA) in the Lake Poopo basin, based on economic, social and environmental criteria in an uncertain decision environment in order to support stakeholders in managing their water resources. Saaty’s analytical hierarchy process (AHP) theory is applied here to solve the MCDA and to identify the alternatives using the highest expected utility value. The paper identifies the best solutions for existing conflicts, while promoting interaction with stakeholders and instruments in order to reach a sustainable strategy for water resources management in this water-scarce region.