Singular value decomposition based computationally efficient algorithm for rapid dynamic near-infrared diffuse optical tomography

Purpose: A computationally efficient algorithm (linear iterative type) based on singular value decomposition (SVD) of the Jacobian has been developed that can be used in rapid dynamic near-infrared (NIR) diffuse optical tomography. Methods: Numerical and experimental studies have been conducted to prove the computational efficacy of this SVD-based algorithm over conventional optical image reconstruction algorithms. Results: These studies indicate that the performance of linear iterative algorithms in terms of contrast recovery (quantitation of optical images) is better compared to nonlinear iterative (conventional) algorithms, provided the initial guess is close to the actual solution. The nonlinear algorithms can provide better quality images compared to the linear iterative type algorithms. Moreover, the analytical and numerical equivalence of the SVD-based algorithm to linear iterative algorithms was also established as a part of this work. It is also demonstrated that the SVD-based image reconstruction typically requires O(NN2) operations per iteration, as contrasted with linear and nonlinear iterative methods that, respectively, requir O(NN3) and O(NN6) operations, with ``NN'' being the number of unknown parameters in the optical image reconstruction procedure. Conclusions: This SVD-based computationally efficient algorithm can make the integration of image reconstruction procedure with the data acquisition feasible, in turn making the rapid dynamic NIR tomography viable in the clinic to continuously monitor hemodynamic changes in the tissue pathophysiology.

Off-axis field approximations for ion traps with apertures

In recent work (Int. J. Mass Spec., vol. 282, pp. 112–122) we have considered the effect of apertures on the fields inside rf traps at points on the trap axis. We now complement and complete that work by considering off-axis fields in axially symmetric (referred to as “3D”) and in two dimensional (“2D”) ion traps whose electrodes have apertures, i.e., holes in 3D and slits in 2D. Our approximation has two parts. The first, EnoAperture, is the field obtained numerically for the trap under study with apertures artificially closed. We have used the boundary element method (BEM) for obtaining this field. The second part, EdueToAperture, is an analytical expression for the field contribution of the aperture. In EdueToAperture, aperture size is a free parameter. A key element in our approximation is the electrostatic field near an infinite thin plate with an aperture, and with different constant-valued far field intensities on either side. Compact expressions for this field can be found using separation of variables, wherein the choice of coordinate system is crucial. This field is, in turn, used four times within our trap-specific approximation. The off-axis field expressions for the 3D geometries were tested on the quadrupole ion trap (QIT) and the cylindrical ion trap (CIT), and the corresponding expressions for the 2D geometries were tested on the linear ion trap (LIT) and the rectilinear ion trap (RIT). For each geometry, we have considered apertures which are 10%, 30%, and 50% of the trap dimension. We have found that our analytical correction term EdueToAperture, though based on a classical small-aperture approximation, gives good results even for relatively large apertures.

Phase diagram of the system Ca-Ti-O at 1200 K

Phase relations in the system Ca-Ti-O have been established by equilibration of several samples at 1200 K for prolonged periods and identification of phases in quenched samples by optical and scanning electron microscopy, XRD and EDS. Samples representing 20 compositions in the ternary system were analyzed. There was negligible solid solubility of Ca in the phases along the binary Ti-O, and of Ti in CaO. Four ternary oxides were identified: CaTiO3, Ca4Ti3O10 and Ca3Ti2O7 containing tetravalent titanium, and CaTi2O4 containing trivalent titanium. Tie-lines link calcium titanite (CaTi2O4) with the three calcium titanates (CaTiO3, Ca4Ti3O10 and Ca3Ti2O7), CaO, oxygen excess TiO1+delta and stoichiometric TiO. Tie-lines connect CaTiO3 with TiO2-x, Magneli phases TinO2n-1 (28 >= n >= 4), Ti3O5, Ti2O3 and TiO1+delta. CaO was found to coexist with TiO, and Ti-O solid solutions alpha and beta. The phase diagram is useful for understanding the mechanisms and kinetics of direct calciothermic reduction of TiO2 to metal and electrochemical reduction of TiO2 using graphite anode and molten CaCl2 electrolyte.

Melting of an Anchored Bilayer: Molecular Dynamics Simulations of the Structural Transition in (CnH2n+1NH3)(2)PbI4 (n=12, 14, 16, 18)

The thermally driven Structural phase transition in the organic-inorganic hybrid perovskite (CnH2n+1NH3)(2)PbI4 has been investigated using molecular dynamics (MD) simulations. This system consists of positively charged alkyl-amine chains anchored to a rigid negatively charged PbI4 sheet with the chains organized as bilayers with a herringbone arrangement. Atomistic simulations were performed using ail isothermal-isobaric ensemble over a wide temperature range from 65 to 665 K for different alkyl chain lengths, n = 12, 14, 16, and 18. The simulations are able to reproduce the essential Features of the experimental observations of this system, including the existence of a transition, the linear variation of the transition temperature with alkyl chain length, and the expansion of the bilayer thickness at the transition. By use of the distance fluctuation Criteria, it is Shown that the transition is associated With a Melting of the alkyl chains of the anchored bilayer. Ail analysis of the conformation of the alkyl chains shows increased disorder in the form of gauche defects above due melting transition. Simulations also show that the melting transition is characterized by the complete disappearance of all-trans alkyl chains in the anchored bilayer, in agreement with experimental observations. A conformationally disordered chain has a larger effective cross-sectional area, and above due transition a uniformly tilted arrangement of the anchored chains call no longer be Sustained. At the melt the angular distribution of the orientation of the chains are 110 longer uniform; the chains are splayed allowing for increased space for individual chains of the anchored bilayer. This is reflected in a sharp rise in the ratio of the mean head-to-head to tail-to-tail distance of the chains of the bilayer at the transition resulting in in expansion of the bilayer thickness. The present MD simulations provide a simple explanation as to how changes in conformation of individual alkyl-chains gives rise to the observed increase in the interlayer lattice spacing of (CnH2n+1NH3)(2)PbI4 at the melting transition.

Multiple conformational states in crystals and in solution in alpha gamma hybrid peptides. Fragility of the C-12 helix in short sequences

The conformational properties of foldamers generated from alpha gamma hybrid peptide sequences have been probed in the model sequence Boc-Aib-Gpn-Aib-Gpn-NHMe. The choice of alpha-aminoisobutyryl (Aib) and gabapentin (Gpn) residues greatly restricts sterically accessible coil formational space. This model sequence was anticipated to be a short segment of the alpha gamma C-12 helix, stabilized by three successive 4 -> 1 hydrogen bonds, corresponding to a backbone-expanded analogue of the alpha polypeptide 3(10)-helix. Unexpectedly, three distinct crystalline polymorphs were characterized in the solid state by X-ray diffraction. In one form, two successive C-12 hydrogen bonds were obtained at the N-terminus, while a novel C-17 hydrogen-bonded gamma alpha gamma turn was observed at the C-terminus. In the other two polymorphs, isolated C-9 and C-7 hydrogen-bonded turns were observed at Gpn (2) and Gpn (4). Isolated C-12 and C-9 turns were also crystallographically established in the peptides Boc-Aib-Gpn-Aib-OMe and Boc-Gpn-Aib-NHMe, respectively. Selective line broadening of NH resonances and the observation of medium range NH(i)<-> NH(i+2) NOEs established the presence of conformational heterogeneity for the tetrapeptide in CDCl3 solution. The NMR results are consistent with the limited population of the continuous C-12 helix conformation. Lengthening of the (alpha gamma)(n) sequences in the nonapeptides Boc-Aib-Gpn-Aib-Gpn-Aib-Gpn-Aib-Gpn-Xxx (Xxx = Aib, Leu) resulted in the observation of all of the sequential NOEs characteristic of an alpha gamma C-12 helix. These results establish that conformational fragility is manifested in short hybrid alpha gamma sequences despite the choice of conformationally constrained residues, while stable helices are formed on chain extension.

Effect of vitamins A and K on colon lysosomes

1. 1. Colon lysosome were separated by differential centrifugation and lysosomes with three different densities, probably arising from the three layers of colon, were found. 2. 2. Hypervitaminosis A resulted in a significant increase in prothrombin time which was restored to normal on vitamin K1 (20) supplementation. 3. 3. There was no appreciable change in the liver storage of vitamin A between hypervitaminotic rats receiving vitamin A and those rats receiving vitamin K1 (20) in addition to excess vitamin A. 4. 4. The colon lysosomes were unstable in hypervitaminosis A, showing an increased free activity of lysosomal enzymes like β-glucuronidase, acid phosphatase and arylsulphatase. This increase of free activity of lysoso3al enzymes in hypervitaminosis A could be prevented by oral supplementation of vitamin K1 (20). 5. 5. In "mild" vitamin A deficiency the release of arylsulphatase was significantly retarded, whereas the decreased free acid phosphatase activity was not significant. 6. 6. "Severe" vitamin A deficiency resulted in a significantly increased free activity of arylsulphatase and acid phosphatase, thus showing the instability of the lysosomal particles in this condition. 7. 7. Addition of vitamin K1 (20) to the incubation medium in vitro could prevent the vitamin A-induced release of arylsulphatase from liver lysosomes, whereas α-tocopherol was inactive. 8. 8. Retinol and retinoic acid were nearly twice as active as ethanol in the release of arylsulphatase from lysosomes in vitro, whereas 5,6-monoepoxyretinoic acid was inactive. 9. 9. The role of vitamins A and K on the lysosomal membrane structure is discussed.

Non-linear couette flow with heat transfer using the B-G-K model

In recent years a large number of investigators have devoted their efforts to the study of flow and heat transfer in rarefied gases, using the BGK [1] model or the Boltzmann kinetic equation. The velocity moment method which is based on an expansion of the distribution function as a series of orthogonal polynomials in velocity space, has been applied to the linearized problem of shear flow and heat transfer by Mott-Smith [2] and Wang Chang and Uhlenbeck [3]. Gross, Jackson and Ziering [4] have improved greatly upon this technique by expressing the distribution function in terms of half-range functions and it is this feature which leads to the rapid convergence of the method. The full-range moments method [4] has been modified by Bhatnagar [5] and then applied to plane Couette flow using the B-G-K model. Bhatnagar and Srivastava [6] have also studied the heat transfer in plane Couette flow using the linearized B-G-K equation. On the other hand, the half-range moments method has been applied by Gross and Ziering [7] to heat transfer between parallel plates using Boltzmann equation for hard sphere molecules and by Ziering [83 to shear and heat flow using Maxwell molecular model. Along different lines, a moment method has been applied by Lees and Liu [9] to heat transfer in Couette flow using Maxwell's transfer equation rather than the Boltzmann equation for distribution function. An iteration method has been developed by Willis [10] to apply it to non-linear heat transfer problems using the B-G-K model, with the zeroth iteration being taken as the solution of the collisionless kinetic equation. Krook [11] has also used the moment method to formulate the equivalent continuum equations and has pointed out that if the effects of molecular collisions are described by the B-G-K model, exact numerical solutions of many rarefied gas-dynamic problems can be obtained. Recently, these numerical solutions have been obtained by Anderson [12] for the non-linear heat transfer in Couette flow,

Elimination of common mode voltage and fifth and seventh harmonics in a multilevel inverter fed IM drive using 12-sided polygonal voltage spacephasor

A multilevel inverter with 12-sided polygonal voltage space vector structure is proposed in this paper. The present scheme provides elimination of common mode voltage variation and 5(th) and 7(th) order harmonics in the entire operating range of the drive. The proposed multi level structure is achieved by cascading only the conventional two-level inverters with asymmetrical DC link voltages. The bandwidths problems associated with conventional hexagonal voltage space vector structure current controllers, due to the presence of 5(th) and 7(th) harmonics, in the over modulation region, is absent in the present 12-sided structure. So a linear voltage control up to 12-step operation is possible, from the present twelve sided scheme, with less current control complexity. An open-end winding structure is used for the induction motor drive.

Quantitative structural refinement of mn K edge XANES in LaMnO3 and CaMnO3 perovskites

The special magnetotransport properties of hole doped manganese perovskites originate from a complex interplay among structural, magnetic and electronic degree of freedom. In this picture the local atomic structure around Mn ions plays a special role and this is the reason why short range order techniques like X-ray absorption spectroscopy (XAS) have been deeply exploited for studying these compounds. The analysis of near edge region features (XANES) of XAS spectra can provide very fine details of the local structure around Mn, complementary to the EXAFS, so contributing to the full understanding of the peculiar physical properties of these materials. Nevertheless the XANES analysis is complicated by the large amount of structural and electronic details involved making difficult the quantitative interpretation.This work exploits the recently developed MXAN code to achieve a full structural refinement of the Mn K edge XANES of LaMnO3 and CaMnO3 compounds; they are the end compounds of the doped manganite series LaxCa1-xMnO3, in which the Mn ions are present only in one charge state as Mn3+ and Mn4+ respectively. The good agreement between the results derived from the analysis of near edge and extended region of the XAS spectra demonstrates that a quantitative picture of the local structure call be obtained from structural refinement of Mn K edge XANES data in these crystalline compounds. The XANES analysis offers, in addition.. the possibility to directly achieve information on the topology of local atomic structure around the absorber not directly achievable from EXAFS.

Interaction of water molecules in non-identical protein structures

The interaction of the protein atoms with the surrounding water oxygen atoms has been computed for 392 protein chains from 369 protein structures belonging to 90% non-homologous high resolution (<= 1.5 angstrom) protein Structures with a crystallographic R-factor <= 20%. The percentage composition of the polar atoms is found to be 36.3%. An average of 82.55% of water oxygen atoms are found to be in the primary hydration shell and 15.12% in the secondary hydration shell. The average Percentage of interactions of water oxygen atoms with the polar atoms of the main chain and side chain are 54% and 46%. respectively. The interaction of the acidic residues, aspartate and glutamate, with the water oxygen atoms is more when compared to that of the other residues.

Approximate multipole coefficients of RF ion traps as functions of aperture size

In this study we present approximate analytical expressions for estimating the variation in multipole expansion coefficients as a function of the size of the apertures in the electrodes in axially symmetric (3D) and two-dimensional (2D) ion trap ion traps. Following the approach adopted in our earlier studies which focused on the role of apertures to fields within the traps, here too, the analytical expression we develop is a sum of two terms, A(n,noAperiure), the multipole expansion coefficient for a trap with no apertures and A(n,dueToAperture), the multipole expansion coefficient contributed by the aperture. A(n,noAperture) has been obtained numerically and A(n,dueToAperture) is obtained from the n th derivative of the potential within the trap. The expressions derived have been tested on two 3D geometries and two 2D geometries. These include the quadrupole ion trap (QIT) and the cylindrical ion trap (CIT) for 3D geometries and the linear ion trap (LIT) and the rectilinear ion trap (RIT) for the 2D geometries. Multipole expansion coefficients A(2) to A(12), estimated by our analytical expressions, were compared with the values obtained numerically (using the boundary element method) for aperture sizes varying up to 50% of the trap dimension. In all the plots presented, it is observed that our analytical expression for the variation of multipole expansion coefficients versus aperture size closely follows the trend of the numerical evaluations for the range of aperture sizes considered. The maximum relative percentage errors, which provide an estimate of the deviation of our values from those obtained numerically for each multipole expansion coefficient, are seen to be largely in the range of 10-15%. The leading multipole expansion coefficient, A(2), however, is seen to be estimated very well by our expressions, with most values being within 1% of the numerically determined values, with larger deviations seen for the QIT and the LIT for large aperture sizes. (C) 2010 Elsevier B.V. All rights reserved.

Metabolome based reaction graphs of M.tuberculosis and M.leprae: A comparative network analysis

Background. Several types of networks, such as transcriptional, metabolic or protein-protein interaction networks of various organisms have been constructed, that have provided a variety of insights into metabolism and regulation. Here, we seek to exploit the reaction-based networks of three organisms for comparative genomics. We use concepts from spectral graph theory to systematically determine how differences in basic metabolism of organisms are reflected at the systems level and in the overall topological structures of their metabolic networks. Methodology/Principal Findings. Metabolome-based reaction networks of Mycobacterium tuberculosis, Mycobacterium leprae and Escherichia coli have been constructed based on the KEGG LIGAND database, followed by graph spectral analysis of the network to identify hubs as well as the sub-clustering of reactions. The shortest and alternate paths in the reaction networks have also been examined. Sub-cluster profiling demonstrates that reactions of the mycolic acid pathway in mycobacteria form a tightly connected sub-cluster. Identification of hubs reveals reactions involving glutamate to be central to mycobacterial metabolism, and pyruvate to be at the centre of the E. coli metabolome. The analysis of shortest paths between reactions has revealed several paths that are shorter than well established pathways. Conclusions. We conclude that severe downsizing of the leprae genome has not significantly altered the global structure of its reaction network but has reduced the total number of alternate paths between its reactions while keeping the shortest paths between them intact. The hubs in the mycobacterial networks that are absent in the human metabolome can be explored as potential drug targets. This work demonstrates the usefulness of constructing metabolome based networks of organisms and the feasibility of their analyses through graph spectral methods. The insights obtained from such studies provide a broad overview of the similarities and differences between organisms, taking comparative genomics studies to a higher dimension.