Reduced-order preconditioning for bidomain simulations

Simulations of the bidomain equations involve solving large, sparse, linear systems of the form Ax = b. Being an initial value problems, it is solved at every time step. Therefore, efficient solvers are essential to keep simulations tractable. Iterative solvers, especially the preconditioned conjugate gradient (PCG) method, are attractive since memory demands are minimized compared to direct methods, albeit at the cost of solution speed. However, a proper preconditioner can drastically speed up the solution process by reducing the number of iterations. In this paper, a novel preconditioner for the PCG method based on system order reduction using the Arnoldi method (A-PCG) is proposed. Large order systems, generated during cardiac bidomain simulations employing a finite element method formulation, are solved with the A-PCG method. Its performance is compared with incomplete LU (ILU) preconditioning. Results indicate that the A-PCG estimates an approximate solution considerably faster than the ILU, often within a single iteration. To reduce the computational demands in terms of memory and run time, the use of a cascaded preconditioner was suggested. The A-PCG was applied to quickly obtain an approximate solution, and subsequently a cheap iterative method such as successive overrelaxation (SOR) is applied to further refine the solution to arrive at a desired accuracy. The memory requirements are less than those of direct LU but more than ILU method. The proposed scheme is shown to yield significant speedups when solving time evolving systems.     

Exploiting charge-transfer complexation for selective measurement of gas-phase olefins with nanoparticle-coated chemiresistors

Charge-transfer-mediated olefin-selective sensing by use of chemiresistors (CR) coated with composite films of n-octanethiolate-monolayer-protected gold nanoparticles (C8-MPN) and each of several square-planar PtCl2(olefin)(pyridine) coordination complexes is described. Where the gas-phase olefin analyte differs from that initially coordinated to Pt, olefin substitution occurs and is accompanied by a persistent shift in the composite film resistance. Commensurate changes in film mass are also observed with a similarly coated thickness shear mode resonator. Regeneration is possible by exposure to the initially complexed olefin gas or vapor. If the olefin analyte is the same as that initially coordinated to Pt, then a reversible charge-transfer interaction occurs that is accompanied by a decrease in film resistance (increase in film mass), which recovers spontaneously after removal of the olefin from the atmosphere above the sensor. This behavior differs from that of MPN-coated CRs lacking such Pt complexes, which invariably yield resistance increases upon exposure to nonpolar vapors. Red shifts in the UV-vis absorbance spectra of the PtCl2(olefin)(pyridine) complexes in solution upon addition of free olefin support the hypothesis that Pt-olefin coordination in the composite films creates temporary low-resistance pathways that compete effectively with the concurrent increase in tunneling resistance associated with swelling-induced separation of C8-MPN cores. Structurally analogous non-olefins produce only increases in film resistance. Selective measurement of styrene, ethylene, 1-octene, and 1,3-butadiene is illustrated. Olefin detection limits are reduced as much as 23 000-fold by inclusion of the corresponding Pt complex in the CR interface film. Composite films suffer a gradual loss of selectivity from decomposition of the Pt-olefin complex, apparently facilitated by a Au-Pt charge transfer.     

Double-codified gold nanolabels for enhanced immunoanalysis

A novel double-codified nanolabel (DC-AuNP) based on gold nanoparticle (AuNP) modified with anti-human IgG peroxidase (HRP)-conjugated antibody is reported. It represents a simple assay that allows enhanced spectrophotometric and electrochemical detection of antigen human IgG as a model protein. The method takes advantage of two properties of the DC-AuNP label: first, the HRP label activity toward the OPD chromogen that can be related to the analyte concentration and measured spectrophotometrically; second, the intrinsic electrochemical properties of the gold nanoparticle labels that being proportional to the protein concentration can be directly quantified by stripping voltammetry. Beside these two main direct determinations of human IgG, a secondary indirect detection was also applicable to this system, exploiting the high molar absorptivity of gold colloids, by which, the color intensity of their solution was proportional to the concentration of the antigen used in the assay. Paramagnetic beads were used as supporting material to immobilize the sandwich-type immunocomplexes resulting in incubation and washing times shorter than those typically needed in classical ELISA tests by means of a rapid magnetic separation of the unbound components. A built-in magnet graphite-epoxy-composite electrode allowed a sensibly enhanced adsorption and electrochemical quantification of the specifically captured AuNPs. The used DC-AuNP label showed an excellent specificity/selectivity, as a matter of fact using a different antigen (goat IgG) a minimal nonspecific electrochemical or spectrophotometric signal was measured. The detection limits for this novel double-codified nanoparticle-based assay were 52 and 260 pg of human IgG/mL for the spectrophotometric (HRP-based) and electrochemical (AuNP-based) detections, respectively, much lower than those typically achieved by ELISA tests. The developed label and method is versatile, offers enhanced performances, and can be easily extended to other protein detection schemes as well as in DNA analysis.     

Model of vapor-induced resistivity changes in gold-thiolate monolayer-protected nanoparticle sensor films

An investigation of the modulation of charge transport through thin films of n-octanethiolate monolayer-protected gold nanoparticles (MPN) induced by the sorption of organic vapors is presented. A model is derived that allows predictions of MPN-coated chemiresistor (CR) responses from vapor-film partition coefficients, and analyte densities and dielectric constants. Calibrations with vapors of 28 compounds collected from an array of CRs and a parallel thickness-shear-mode resonator are used to verify assumptions inherent in the model and to assess its performance. Results afford insights into the nature of the vapor-MPN interactions, including systematic variations in apparent film swelling efficiencies, and show that the model can predict CR responses typically to within 24%. Using CRs of different dimensions, vapor sensitivities are found to be virtually independent of the MPN film volume over a range of 104 (device-area x MPN layer thickness). Sensitivities vary inversely with analyte vapor pressure similarly for the two sensor types, but the CR sensor affords significantly greater signal-to-noise ratios, yielding calculated detection limits in the low-part-per-billion concentration range for several of the analytes tested. The implications of these results for implementing MPN-coated CR arrays as detectors in microanalytical systems are considered.     

Characterization of a near-infrared laparoscopic hyperspectral imaging system for minimally invasive surgery

We developed and characterized a new imaging platform for minimally invasive surgical venues, specifically a system to help guide laparoscopic surgeons to visualize biliary anatomy. This platform is a novel combination of a near-infrared hyperspectral imaging system coupled with a conventional surgical laparoscope. Intraoperative tissues are illuminated by optical fibers arranged in a ring around a center-mounted relay lens collecting back-reflected light from tissues to the hyperspectral imaging system. The system consists of a focal plane array (FPA) and a liquid crystal tunable filter, which is continuously tunable in the near-infrared spectral range of 650-1100 nm with the capability of passing light with a mean bandwidth of 6.95 nm, and the FPA is a high-sensitivity back-illuminated, deep depleted charge-coupled device. Placing a standard resolution target 5.1 cm from the distal end of the laparoscope, a typical intraoperative working distance, produced a 7.6-cm-diameter field of view with an optimal spatial resolution of 0.24 mm. In addition, the system's spatial and spectral resolution and its wavelength tuning accuracy are characterized. The spectroscopic images are formatted into a three-dimensional hyperspectral image cube and processed using principle component analysis. The processed images provide contrast based on measured spectra associated with chemically different anatomical structures helping identify the main molecular chromophores inherent to each tissue. The principal component images were found to image swine gallbladder and biliary structures from surrounding tissues, in real time, during cholecystectomy surgery. Furthermore, it is shown that surgeons can interrogate selected image subregions for their molecular composition identifying biliary anatomy during surgery and before any invasive action is undertaken.     

Quantitative analysis of systematic errors originated from wall adsorption and sample plug lengths in affinity capillary electrophoresis using two-dimensional simulation

Two-dimensional (2D) simulation of capillary electrophoresis is developed to model affinity interaction and wall adsorption simultaneously. Finite difference schemes are used to evaluate the mass-transfer equation in cylindrical coordinates. A Langmuir second-order kinetic law is applied to regulate the wall adsorption and desorption processes. Contributions from the simulation parameters are investigated extensively, and parameters for accurate and efficient simulation are identified. With the 2D model, capillary zone electrophoresis and affinity capillary electrophoresis (ACE) in the presence of strong or weak wall adsorption are simulated to elucidate peak distortions. Finite sample injection length/amount and wall adsorption that lead to systematic errors in the estimated binding constants in ACE are quantified for the first time with both actual experiments and computer simulation. Methods for correcting the estimated binding constants are proposed to extend the usefulness of ACE.     

Single-molecule detection of surface-hybridized human papilloma virus DNA for quantitative clinical screening

We present an improved method to quantify viral DNA in human cells at the single- molecule level. Human papilloma virus (HPV)-16 DNA was hybridized to probes that were covalently bound to a glass surface and detected with a single-molecule imaging system. In the single-probe mode, the whole genome and target DNA were fluorescently labeled before hybridization. In the dual-probe mode, a second probe was introduced that has a fluorescently labeled 1-kb DNA strand connected to the 50-nt probe sequence. With the single-probe method, the detection limit was 0.7 copy/cell, which was similar to that reported in a flow system earlier. With the dual-probe method, the linear dynamic range covers 1.44-7000 copies/cell, which is typical of early infection to near-cancer stages. Both methods were applied to cell line samples with known HPV-16 infection, and the result showed a good match with the reported viral load. DNA from cervical cells, collected with the Pap smear sampling method, was spiked with HPV-16 DNA and submitted to this assay to show compatibility with conventional sampling methods. The dual-probe method was further tested with a crudely prepared sample. The cells were heat lyzed and spun down, and the supernatant was immediately submitted to hybridization. Even with reduced hybridization efficiency caused by the interference of cellular materials, we were still able to differentiate infected cells with 600 copies/cell from healthy cells.     

Hard target UV lidar measurements of isoprene mixing ratios and emission rates from eucalyptus trees

The application of UV lidar to measure isoprene concentrations for environmental studies has been investigated. With a hard target lidar system at 223 nm, isoprene mixing ratios above eucalyptus trees were measured with a sensitivity of about 1 ppbv. Results over a long timescale were compared with an existing model of isoprene emission for a wide range of temperature and sunlight values. Fast time dependent results yielded a leaf emission rate of 25 microg g(-1) hour(-1), consistent with emission from other eucalyptus species. Requirements for development of the system for range resolved isoprene number density measurements using atmospheric backscatter lidar are discussed.     

Evidence for organosulfates in secondary organic aerosol

Recent work has shown that particle-phase reactions contribute to the formation of secondary organic aerosol (SOA), with enhancements of SOA yields in the presence of acidic seed aerosol. In this study, the chemical composition of SOA from the photooxidations of alpha-pinene and isoprene, in the presence or absence of sulfate seed aerosol, is investigated through a series of controlled chamber experiments in two separate laboratories. By using electrospray ionization-mass spectrometry, sulfate esters in SOA produced in laboratory photooxidation experiments are identified for the first time. Sulfate esters are found to account for a larger fraction of the SOA mass when the acidity of seed aerosol is increased, a result consistent with aerosol acidity increasing SOA formation. Many of the isoprene and alpha-pinene sulfate esters identified in these chamber experiments are also found in ambient aerosol collected at several locations in the southeastern U.S. It is likely that this pathway is important for other biogenic terpenes, and may be important in the formation of humic-like substances (HULIS) in ambient aerosol.