A Procedure for the 3D Reconstruction of Biological Organs from 2D Image Sequences

In this work, a procedure is presented for the reconstruction of biological organs from image sequences obtained through CT-scan. Although commercial software, which can accomplish this task, are readily available, the procedure presented here needs only free software. The procedure has been applied to reconstruct a liver from the scan data available in literature. 3D biological organs obtained this way can be used for the finite element analysis of biological organs and this has been demonstrated by carrying out an FE analysis on the reconstructed liver.

The 2D Coulomb gas on a 1D lattice

The statistical mechanics of a two-dimensional Coulomb gas confined to one dimension is studied, wherein hard core particles move on a ring. Exact self-duality is shown for a version of the sine-Gordon model arising in this context, thereby locating the transition temperature exactly. We present asymptotically exact results for the correlations in the model and characterize the low- and high-temperature phases. Numerical simulations provide support to these renormalization group calculations. Connections with other interesting problems, such as the quantum Brownian motion of a panicle in a periodic potential and impurity problems, are pointed out.

Half-sandwich (eta(6)-arene)ruthenium(II) chiral Schiff base complexes: Analysis of the diastereomeric mixtures in solution by 2D-NMR spectroscopy

2D NMR spectroscopy has been used to determine the metal configuration in solution of three complexes, viz. [(eta(6)-p-cymene)Ru(L*)Cl] (1) and [(eta(6)-p-cymene)Ru(L*)(L')] (ClO4) (L' = H2O, 2; PPh3, 3), where L* is the anion of (S)-(1-phenylethyl)salicylaldimine. The complexes exist in two diastereomeric forms in solution. Both the (R-Ru,S-C)- and (S-Ru,S-C)-diastereomers display the presence of attractive, CH/pi interaction involving the phenyl group attached to the chiral carbon and the cymene ring hydrogens. This interaction restricts the rotation of the C*-N single bond and, as a result, two structural types with either the hydrogen atom attached to the chiral carbon (C*) or the methyl group attached to C* in close proximity of the cymene ring protons get stabilized. Using 2D NMR spectroscopy as a tool, the spatial interaction involving these protons are studied in order to obtain the metal configuration(s) of the diastereomeric complexes in solution. This technique has enabled us to determine the metal configuration as (R-Ru,S-C) for the major isomers of 1-3 in solution.

Role of length scales on microwave thawing dynamics in 2D cylinders

Microwave (MW) thawing of 2D frozen cylinders exposed to uniform plane waves from one face, is modeled using the effective heat capacity formulation with the MW power obtained from the electric field equations. Computations are illustrated for tylose (23% methyl cellulose gel) which melts over a range of temperatures giving rise to a mushy zone. Within the mushy region the dielectric properties are functions of the liquid volume fraction. The resulting coupled, time dependent non-linear equations are solved using the Galerkin finite element method with a fixed mesh. Our method efficiently captures the multiple connected thawed domains that arise due to the penetration of MWs in the sample. For a cylinder of diameter D, the two length scales that control the thawing dynamics are D/D-p and D/lambda(m), where D-p and lambda(m) are the penetration depth and wavelength of radiation in the sample respectively. For D/D-p, D/lambda(m) much less than 1 power absorption is uniform and thawing occurs almost simultaneously across the sample (Regime I). For D/D-p much greater than 1 thawing is seen to occur from the incident face, since the power decays exponentially into the sample (Regime III). At intermediate values, 0.2 < D/D-p, D/lambda(m) < 2.0 (Regime II) thawing occurs from the unexposed face at smaller diameters, from both faces at intermediate diameters and from the exposed and central regions at larger diameters. Average power absorption during thawing indicates a monotonic rise in Regime I and a monotonic decrease in Regime III. Local maxima in the average power observed for samples in Regime II are due to internal resonances within the sample. Thawing time increases monotonically with sample diameter and temperature gradients in the sample generally increase from Regime I to Regime III. (C) 2002 Elsevier Science Ltd. All rights reserved.

Thermal degradation processes in polysulfide copolymers investigated by direct pyrolysis mass spectrometry and flash pyrolysis-gas chromatography/mass spectrometry

This is the first report on the analysis of random block polysulfide copolymers containing different amounts of repeating units in the copolymer backbone, which has been studied by direct pyrolysis mass spectrometry (DPMS) and by pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS). The homopolymers such as poly(ethylene sulfide) (PES), poly(styrene sulfide) (PSS), and two random copolymers, viz., poly(ethylene sulfide(x)-co-styrene sulfide(y)) [copolymer I (x = y = 0.5) and copolymer II (x = 0.74, y = 0.26)] were investigated by both DPMS and Py-GC/MS (except copolymer II) techniques. In the case of copolymer I, the thermal degradation products of SE1, SE2, S-2, and S2E (S = styrene sulfide, E = ethylene sulfide) were detected in DPMS, whereas the formation of SE1 and SE2 were observed by Py-GC/MS technique. However, for copolymer II, SE3 was also found along with SE1, SE2, S-2, and S2E in DPMS. The formation of additional product (SE3) observed in copolymer II could be due to an increase in the block length formed during copolymerization. Further, a comparative study on thermal degradation of PES, poly(ethylene disulfide) (PEDS), and poly(ethylene tetrasulfide) (PETS) were investigated by Py-GC/MS. The pyrolysis products detected by both DPMS and Py-GC/MS indicates that the thermal decomposition of these polymers yield cyclic sulfides through an intramolecular exchange or by backbiting processes. The linear products with thiol and vinyl groups were also observed by Py-GC/MS along with the cyclic products via carbon hydrogen transfer reaction.

Reconstructing Solid Model from 2D Scanned Images of Biological Organs for Finite Element Simulation

This work presents a methodology to reconstruct 3D biological organs from image sequences or other scan data using readily available free softwares with the final goal of using the organs (3D solids) for finite element analysis. The methodology deals with issues such as segmentation, conversion to polygonal surface meshes, and finally conversion of these meshes to 3D solids. The user is able to control the detail or the level of complexity of the solid constructed. The methodology is illustrated using 3D reconstruction of a porcine liver as an example. Finally, the reconstructed liver is imported into the commercial software ANSYS, and together with a cyst inside the liver, a nonlinear analysis performed. The results confirm that the methodology can be used for obtaining 3D geometry of biological organs. The results also demonstrate that the geometry obtained by following this methodology can be used for the nonlinear finite element analysis of organs. The methodology (or the procedure) would be of use in surgery planning and surgery simulation since both of these extensively use finite elements for numerical simulations and it is better if these simulations are carried out on patient specific organ geometries. Instead of following the present methodology, it would cost a lot to buy a commercial software which can reconstruct 3D biological organs from scanned image sequences.

Scalable processes for fabricating non-volatile memory devices using self-assembled 2D arrays of gold nanoparticles as charge storage nodes

We propose robust and scalable processes for the fabrication of floating gate devices using ordered arrays of 7 nm size gold nanoparticles as charge storage nodes. The proposed strategy can be readily adapted for fabricating next generation (sub-20 nm node) non-volatile memory devices.

Coordination-driven self-assembly of 2D-metallamacrocycles using a shape-selective Pt(2)(II)-organometallic 90 degrees acceptor: design, synthesis and sensing study

Synthesis of a series of two-dimensional metallamacrocycles via coordination-driven self-assembly of a shape-selective Pt(2)(II)-molecular building unit incorporating carbazole-ethynyl functionality is described. An equimolar (1 : 1) combination of a Pt(2)(II)-organometallic 90 degrees acceptor, 1, with rigid linear ditopic donors (L(a) and L(b)) afforded [4 + 4] self-assembled octanuclear molecular squares, 2 and 3, in quantitative yields, respectively [L(a) = 4,4'-bipyridine; L(b) = trans-1,2-bis(4-pyridyl)ethylene]. Conversely, a similar treatment of 1 with an amide-based unsymmetrical flexible ditopic donor, L(c), resulted in the formation of a [2 + 2] self-sorted molecular rhomboid (4a) as a single product [L(c) = N-(4-pyridyl)isonicotinamide]. Despite the possibility of several linkage isomeric macrocycles (rhomboid, triangle and square) due to the different connectivity of L(c), the formation of a single and symmetrical molecular rhomboid (4a) as the only product is an interesting observation. All the self-assembled macrocycles (2, 3 and 4a) were fully characterized by multinuclear NMR ((1)H and (31)P) and ESI-MS analysis. Further structural insights about the size and shape of the macrocycles were obtained through energy minimization using density functional theory (DFT) calculations. Decoration of the starting carbazole building unit with Pt-ethynyl functionality enriches the assemblies to be more p-electron rich and luminescent in nature. Macrocycles 2 and 3 could sense the presence of electron deficient nitroaromatics in solution by quenching of the initial intensity upon gradual addition of picric acid (PA). They exhibited the largest quenching response with high selectivity for nitroaromatics compared to several other electron deficient aromatics tested.

Evaluation of 2D image reconstruction using fan-beam FBP algorithm with no backprojection weight from WLP completed truncated projection data

This paper presents the image reconstruction using the fan-beam filtered backprojection (FBP) algorithm with no backprojection weight from windowed linear prediction (WLP) completed truncated projection data. The image reconstruction from truncated projections aims to reconstruct the object accurately from the available limited projection data. Due to the incomplete projection data, the reconstructed image contains truncation artifacts which extends into the region of interest (ROI) making the reconstructed image unsuitable for further use. Data completion techniques have been shown to be effective in such situations. We use windowed linear prediction technique for projection completion and then use the fan-beam FBP algorithm with no backprojection weight for the 2-D image reconstruction. We evaluate the quality of the reconstructed image using fan-beam FBP algorithm with no backprojection weight after WLP completion.

Parallel Computation of 2D Morse-Smale Complexes

The Morse-Smale complex is a useful topological data structure for the analysis and visualization of scalar data. This paper describes an algorithm that processes all mesh elements of the domain in parallel to compute the Morse-Smale complex of large two-dimensional data sets at interactive speeds. We employ a reformulation of the Morse-Smale complex using Forman's Discrete Morse Theory and achieve scalability by computing the discrete gradient using local accesses only. We also introduce a novel approach to merge gradient paths that ensures accurate geometry of the computed complex. We demonstrate that our algorithm performs well on both multicore environments and on massively parallel architectures such as the GPU.

Reversible Formation of a Planar Chiral Ferrocenylboroxine and Its Supramolecular Structure

The boronic acid (pS)-1,2-NpFcB(OH)(2) (1) was obtained by treatment of the lithiated species (pS)-1,2-NpFcLi with B(O(i)Pr)(3), followed by acidic workup; subsequent dehydration gave the enantiomerically pure boroxine [(pS)-1,2-NpFcBO](3) (2) in 49% isolated yield. Multinuclear and 2D NMR spectroscopies, single-crystal X-ray diffraction, and elemental analysis served to confirm the structure of 2. In the solid-state structure, all three of the naphthyl groups point in one direction and all of the ferrocenyl moieties are placed on the opposite face of the boroxine ring, which is also the preferred conformation in solution according to a (1)H, (1)H-NOESY experiment. Cyclic voltammetry revealed three separate reversible oxidation events, which suggests significant communication between the ferrocenyl moieties. These redox processes experience a cathodic shift upon addition of 4-dimethylaminopyridine (DMAP) as a Lewis base. The six-membered ring is opened upon treatment with hot CHCl(3)/MeOH to form the methoxy species (pS)-1,2-NpFcB(OH)(OMe) (3), which can be converted back to the cycle 2 by dissolution in wet CHCl(3), followed by column chromatography on silica gel.

Coordination-Driven Self-Assembly of 2D-Metallamacrocycles Using a New Carbazole-Based Dipyridyl Donor: Synthesis, Characterization, and C-60 Binding Study

A new carbazole-based 90 degrees dipyridyl donor 3,6-di(4-pyridylethynyl)carbazole (L) containing carbazole-ethynyl functionality is synthesized in reasonable yield using the Sonagashira coupling reaction. Multinuclear NMR, electrospray ionization-mass spectrometry (ESI-MS), including single crystal X-ray diffraction analysis characterized this 90 degrees building unit. The stoichiometry combination of L with several Pd(II)/Pt(II)-based 90 degrees acceptors (1a-1d) yielded 2 + 2] self-assembled metallacycles (2a-2d) under mild conditions in quantitative yields 1a = cis-(dppf)Pd(OTf)(2); 1b = cis-(dppf)Pt(OTf)(2); 1c = cis-(tmen)Pd(NO3)(2); 1d = 3,6-bis{trans-Pt(C C) (PEt3)(2)(NO3))carbazole]. All these macrocycles were characterized by various spectroscopic techniques, and the molecular structure of 2a was unambiguously determined by single crystal X-ray diffraction analysis. Incorporation of ethynyl functionality to the carbazole backbone causes the resulted macrocycles (2a-2d) to be pi-electron rich and thereby exhibit strong emission characteristics. The macrocycle 2a has a large internal concave aromatic surface. The fluorescence quenching study suggests that 2a forms a similar to 1:1 complex with C-60 with a high association constant of K-sv = 1.0 X 10(5) M-1.

Combining adiabatic and Hartmann-Hahn cross-polarization for sensitivity enhancement in solid state separated local field 2D-NMR experiments of partially ordered systems

In this Letter, we examine magnetization in double- and zero-quantum reservoirs of an ensemble of spin-1/2 nuclei and describe their role in determining the sensitivity of a class of separated local field NMR experiments based on Hartmann-Hahn cross-polarization. We observe that for the liquid crystal system studied, a large dilute spin-polarization, obtained initially by the use of adiabatic cross-polarization, can enhance the sensitivity of the above experiment. The signal enhancement factors, however, are found to vary and depend on the local dynamics. The experimental results have been utilized to obtain the local order-parameters of the system. (C) 2012 Elsevier B. V. All rights reserved.

Realization of thermally durable close-packed 2D gold nanoparticle arrays using self-assembly and plasma etching

Realization of thermally and chemically durable, ordered gold nanostructures using bottom-up self-assembly techniques are essential for applications in a wide range of areas including catalysis, energy generation, and sensing. Herein, we describe a modular process for realizing uniform arrays of gold nanoparticles, with interparticle spacings of 2 nm and above, by using RF plasma etching to remove ligands from self-assembled arrays of ligand-coated gold nanoparticles. Both nanoscale imaging and macroscale spectroscopic characterization techniques were used to determine the optimal conditions for plasma etching, namely RF power, operating pressure, duration of treatment, and type of gas. We then studied the effect of nanoparticle size, interparticle spacing, and type of substrate on the thermal durability of plasma-treated and untreated nanoparticle arrays. Plasma-treated arrays showed enhanced chemical and thermal durability, on account of the removal of ligands. To illustrate the application potential of the developed process, robust SERS (surface-enhanced Raman scattering) substrates were formed using plasma-treated arrays of silver-coated gold nanoparticles that had a silicon wafer or photopaper as the underlying support. The measured value of the average SERS enhancement factor (2 x 10(5)) was quantitatively reproducible on both silicon and paper substrates. The silicon substrates gave quantitatively reproducible results even after thermal annealing. The paper-based SERS substrate was also used to swab and detect probe molecules deposited on a solid surface.