Photofragment image analysis using the Onion-Peeling Algorithm

With the growing popularity of the velocity map imaging technique, a need for the analysis of photoion and photoelectron images arose. Here, a computer program is presented that allows for the analysis of cylindrically symmetric images. It permits the inversion of the projection of the 3D charged particle distribution using the Onion Peeling Algorithm. Further analysis includes the determination of radial and angular distributions, from which velocity distributions and spatial anisotropy parameters are obtained. Identification and quantification of the different photolysis channels is therefore straightforward. In addition, the program features geometry correction, centering, and multi-Gaussian fitting routines, as well as a user-friendly graphical interface and the possibility of generating synthetic images using either the fitted or user-defined parameters.

Program summary

Title of program: Glass OnionCatalogue identifier: ADRYProgram Summary URL:http://cpc.cs.qub.ac.uk/summaries/ADRYProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandLicensing provisions: noneComputer: IBM PCOperating system under which the program has been tested: Windows 98, Windows 2000, Windows NTProgramming language used: Delphi 4.0Memory required to execute with typical data: 18 MwordsNo. of bits in a word: 32No. of bytes in distributed program, including test data, etc.: 9 911 434Distribution format: zip fileKeywords: Photofragment image, onion peeling, anisotropy parametersNature of physical problem: Information about velocity and angular distributions of photofragments is the basis on which the analysis of the photolysis process resides. Reconstructing the three-dimensional distribution from the photofragment image is the first step, further processing involving angular and radial integration of the inverted image to obtain velocity and angular distributions. Provisions have to be made to correct for slight distortions of the image, and to verify the accuracy of the analysis process.Method of solution: The “Onion Peeling” algorithm described by Helm [Rev. Sci. Instrum. 67 (6) (1996)] is used to perform the image reconstruction. Angular integration with a subsequent multi-Gaussian fit supplies information about the velocity distribution of the photofragments, whereas radial integration with subsequent expansion of the angular distributions over Legendre Polynomials gives the spatial anisotropy parameters. Fitting algorithms have been developed to centre the image and to correct for image distortion.Restrictions on the complexity of the problem: The maximum image size (1280×1280) and resolution (16 bit) are restricted by available memory and can be changed in the source code. Initial centre coordinates within 5 pixels may be required for the correction and the centering algorithm to converge. Peaks on the velocity profile separated by less then the peak width may not be deconvolved. In the charged particle image reconstruction, it is assumed that the kinetic energy released in the dissociation process is small compared to the energy acquired in the electric field. For the fitting parameters to be physically meaningful, cylindrical symmetry of the image has to be assumed but the actual inversion algorithm is stable to distortions of such symmetry in experimental images.Typical running time: The analysis procedure can be divided into three parts: inversion, fitting, and geometry correction. The inversion time grows approx. as R³, where R is the radius of the region of interest: for R=200 pixels it is less than a minute, for R=400 pixels less then 6 min on a 400 MHz IBM personal computer. The time for the velocity fitting procedure to converge depends strongly on the number of peaks in the velocity profile and the convergence criterion. It ranges between less then a second for simple curves and a few minutes for profiles with up to twenty peaks. The time taken for the image correction scales as R² and depends on the curve profile. It is on the order of a few minutes for images with R=500 pixels.Unusual features of the program: Our centering and image correction algorithm is based on Fourier analysis of the radial distribution to insure the sharpest velocity profile and is insensitive to an uneven intensity distribution. There exists an angular averaging option to stabilize the inversion algorithm and not to loose the resolution at the same time.     

Nanostructured artificial nacre

Finding a synthetic pathway to artificial analogs of nacre and bones represents a fundamental milestone in the development of composite materials. The ordered brick-and-mortar arrangement of organic and inorganic layers is believed to be the most essential strength- and toughness-determining structural feature of nacre. It has also been found that the ionic crosslinking of tightly folded macromolecules is equally important. Here, we demonstrate that both structural features can be reproduced by sequential deposition of polyelectrolytes and clays. This simple process results in a nanoscale version of nacre with alternating organic and inorganic layers. The macromolecular folding effect reveals itself in the unique saw-tooth pattern of differential stretching curves attributed to the gradual breakage of ionic crosslinks in polyelectrolyte chains. The tensile strength of the prepared multilayers approached that of nacre, whereas their ultimate Young modulus was similar to that of lamellar bones. Structural and functional resemblance makes clay- polyelectrolyte multilayers a close replica of natural biocomposites. Their nanoscale nature enables elucidation of molecular processes occurring under stress.     

dOpenCL: Towards uniform programming of distributed heterogeneous multi-/many-core systems

Modern computer systems become increasingly distributed and heterogeneous by comprising multi-core CPUs, GPUs, and other accelerators. Current programming approaches for such systems usually require the application developer to use a combination of several programming models (e.g., MPI with OpenCL or CUDA) in order to exploit the system’s full performance potential. In this paper, we present dOpenCL (distributed OpenCL)—a uniform approach to programming distributed heterogeneous systems with accelerators. dOpenCL allows the user to run unmodified existing OpenCL applications in a heterogeneous distributed environment. We describe the challenges of implementing the OpenCL programming model for distributed systems, as well as its extension for running multiple applications concurrently. Using several example applications, we compare the performance of dOpenCL with MPI + OpenCL and standard OpenCL implementations.     

Learning communicative actions of conflicting human agents

One of the main problems to be solved while assisting inter-human conflict resolution is how to reuse the previous experience with similar agents. A machine learning technique for handling scenarios of interaction between conflicting human agents is proposed. Scenarios are represented by directed graphs with labelled vertices (for communicative actions) and arcs (for temporal and causal relationships between these actions and their parameters). For illustrative purposes, classification of a scenario is computed by comparing partial matching of its graph with graphs of positive and negative examples. Nearest Neighbour learning is followed by the JSM-based learning which minimised the number of false negatives and takes advantage of a more accurate way of matching sequences of communicative actions. Developed scenario representation and comparative analysis techniques are applied to the classification of textual customer complaints. It is shown that analysing the structure of communicative actions without context information is frequently sufficient to estimate complaint validity. Therefore, being domain-independent, proposed machine learning technique is a good compliment to a wide range of customer relation management applications where formal treatment of inter-human interactions is required in a decision-support mode.     

Electromagnetic wave scattering from the sea surface in the presence of wind wave patterns

The study is concerned with electromagnetic wave (EM) scattering by a random sea surface in the presence of coherent wave patterns. The coherent patterns are understood in a broad sense as the existence of certain dynamical coupling between linear Fourier components of the water wave field. We show that the presence of weakly nonlinear wave patterns can significantly change the EM scattering compared to the case of a completely random wave field. Generalizing the Random Phase Approximation (RPA) we suggest a new paradigm for EM scattering by a random sea surface.

The specific analysis carried out in the paper synthesizes the small perturbation method for EM scattering and a weakly nonlinear approach for wind wave dynamics. By investigating, in detail, two examples of a random sea surface composed of either Stokes waves or horse-shoe (‘crescent-shaped’) patterns the mechanism of the pattern effect on scattering is revealed. Each Fourier harmonic of the scattered EM field is found to be a sum of contributions due to different combinations of wave field harmonics. Among these ‘partial scatterings’ there are phase-dependent ones and, therefore, the intensity of the resulting EM harmonic is sensitive to the phase relations between the wind wave harmonics. The effect can be interpreted as interference of partial scatterings due to the co-existence of several phase-related periodic scattering grids. A straightforward generalization of these results enables us to obtain, for a given wind wave field and an incident EM field, an a priori estimate of whether the effects due to the patterns are significant and the commonly used RPA is inapplicable. When the RPA is inapplicable, we suggest its natural generalization by re-defining the statistical ensemble for water surface. First, EM scattering by an ‘elementary’ constituent pattern should be considered. Each such scattering is affected by the interference because the harmonics comprising the pattern are dynamically linked. Then, ensemble averaging, which takes into account the distribution of the pattern parameters (based on the assumption that the phases between the patterns are random), should be carried out. It is shown that, generally, this interference does not vanish for any statistical ensemble due to dynamical coupling between water wave harmonics. The suggested RPA generalization takes into account weak non-Gaussianity of water wave field m contrast to the traditional RPA which ignores it.     

Identification of explosives with two-dimensional ultraviolet resonance Raman spectroscopy

The first two-dimensional (2D) resonance Raman spectra of TNT, RDX, HMX, and PETN are measured with an instrument that sequentially and rapidly switches between laser wavelengths, illuminating these explosives with forty wavelengths between 210 nm and 280 nm. Two-dimensional spectra reflect variations in resonance Raman scatter with illumination wavelength, adding information not available from single or few one-dimensional spectra, thereby increasing the number of variables available for use in identification, which is especially useful in environments with contaminants and interferents. We have recently shown that 2D resonance Raman spectra can identify bacteria. Thus, a single device that identifies the presence of explosives, bacteria, and other chemicals in complex backgrounds may be feasible.     

Ferroelectric Materials: Probing Local and Global Ferroelectric Phase Stability and Polarization Switching in Ordered Macroporous PZT (Adv. Funct. Mater. 5/2011)

We describe the characterization, ferroelectric phase stability and polarization switching in strain‐free assemblies of PbZr_0.3Ti_0.7O₃ (PZT) nanostructures. The 3‐dimensionally ordered macroporous structures present uniquely large areas and volumes of PZT where the microstructure is spatially modulated and the composition is homogeneous. Variable temperature powder X‐ray diffraction (XRD) studies show that the global structure is crystalline and tetragonal at room temperature and undergoes a reversible tetragonal to cubic phase transition on heating/cooling. The measured phase‐transition temperature is 50–60 °C lower than bulk PZT of the same composition. The local ferroelectric properties were assessed using piezoresponse force spectroscopy that reveal an enhanced piezoresponse from the nanostructured films and demonstrate that the switching polarization can be spatially mapped across these structures. An enhanced piezoresponse is observed in the nanostructured films which we attribute to the formation of strain free films, thus for the first time we are able to assess the effects of crystallite‐size independently of internal stress. Corresponding polarization distributions have been calculated for the bulk and nanostructured materials using a direct variational method and Landau‐Ginzburg‐Devonshire (LGD) theory. By correlating local and global characterization techniques we have for the first time unambiguously demonstrated the formation of tetragonal and ferroelectric PZT in large volume nanostructured architectures. With the wide range of materials available that can be formed into such controlled architectures we conclude that this study opens a pathway for the effective studies of nanoscale ferroelectrics in uniquely large volumes.     

BF<Subscript>3</Subscript>OEt<Subscript>2</Subscript>-coinitiated cationic polymerization of cyclopentadiene in the presence of water at room temperature

The cationic polymerization of cyclopentadiene (CPD) with 1-(4-methoxyphenyl)ethanol (1)/BF₃OEt₂ initiating system in CH₂Cl₂:CH₃CN 4:1 (v/v) mixture at room temperature and in the presence of water ([H₂O]/[BF₃OEt₂] up to 8) is reported. The number-average molecular weights of obtained polymers increased in direct proportion to monomer conversion or initial monomer concentration (M _n ≤ 4,000 g mol⁻¹) in agreement with calculated values, and were inversely proportional to initiator concentration. Polymer MWDs were relatively narrow (M _w/M _n = 1.4–1.7) up to 60% of monomer conversion. It was also shown that regioselectivity of CPD polymerization with 1/BF₃OEt₂ initiating system did not depend significantly on water, monomer, or initiator concentration (1,4-structures content was nearly 60% in all cases).     

Gene Expression Analyses Support Fallopian Tube Epithelium as the Cell of Origin of Epithelial Ovarian Cancer

Folate receptor alpha (FOLR1/FRA) is reported to be overexpressed in epithelial ovarian cancers (EOC), especially the serous histotype. Further, while dysregulation of the folate-dependent 1-carbon cycle has been implicated in tumorogenesis, little is known relative to the potential mechanism of action of FOLR1 expression in these processes. We therefore investigated the expression of FOLR1, other folate receptors, and genes within the 1-carbon cycle in samples of EOC, normal ovary and fallopian tube on a custom TaqMan Low Density Array. Also included on this array were known markers of EOC such as MSLN, MUC16 and HE4. While few differences were observed in the expression profiles of genes in the 1-carbon cycle, genes previously considered to be overexpressed in EOC (e.g., FOLR1, MSLN, MUC16 and HE4) showed significantly increased expression when comparing EOC to normal ovary. However, when the comparator was changed to normal fallopian tube, these differences were abolished, supporting the hypothesis that EOC derives from fallopian fimbriae and, further, that markers previously considered to be upregulated or overexpressed in EOC are most likely not of ovarian origin, but fallopian in derivation. Our findings therefore support the hypothesis that the cell of origin of EOC is tubal epithelium.