A Numerical Scheme for Three-Dimensional Front Propagation and Control of Jordan Mode

As an example of a front propagation, we study the propagation of a three-dimensional nonlinear wavefront into a polytropic gas in a uniform state and at rest. The successive positions and geometry of the wavefront are obtained by solving the conservation form of equations of a weakly nonlinear ray theory. The proposed set of equations forms a weakly hyperbolic system of seven conservation laws with an additional vector constraint, each of whose components is a divergence-free condition. This constraint is an involution for the system of conservation laws, and it is termed a geometric solenoidal constraint. The analysis of a Cauchy problem for the linearized system shows that when this constraint is satisfied initially, the solution does not exhibit any Jordan mode. For the numerical simulation of the conservation laws we employ a high resolution central scheme. The second order accuracy of the scheme is achieved by using MUSCL-type reconstructions and Runge-Kutta time discretizations. A constrained transport-type technique is used to enforce the geometric solenoidal constraint. The results of several numerical experiments are presented, which confirm the efficiency and robustness of the proposed numerical method and the control of the Jordan mode.

Sequence-Structure Similarity: Do Sequentially Identical Peptide Fragments have Similar Three-Dimensional Structures?

The rapidly growing structure databases enhance the probability of finding identical sequences sharing structural similarity. Structure prediction methods are being used extensively to abridge the gap between known protein sequences and the solved structures which is essential to understand its specific biochemical and cellular functions. In this work, we plan to study the ambiguity between sequence-structure relationships and examine if sequentially identical peptide fragments adopt similar three-dimensional structures. Fragments of varying lengths (five to ten residues) were used to observe the behavior of sequence and its three-dimensional structures. The STAMP program was used to superpose the three-dimensional structures and the two parameters (Sequence Structure Similarity Score (Sc) and Root Mean Square Deviation value) were employed to classify them into three categories: similar, intermediate and dissimilar structures. Furthermore, the same approach was carried out on all the three-dimensional protein structures solved in the two organisms, Mycobacterium tuberculosis and Plasmodium falciparum to validate our results.

Conversion between electromagnetically induced transparency and absorption in a three-level lambda system

We show that it is possible to change from a subnatural electromagnetically induced transparency (EIT) feature to a subnatural electromagnetically induced absorption (EIA) feature in a (degenerate) three-level. system. The change is effected by turning on a second control beam counter-propagating with respect to the first beam. We observe this change in the D-2 line of Rb in a room temperature vapor cell. The observations are supported by density-matrix analysis of the complete sublevel structure including the effect of Doppler averaging, but can be understood qualitatively as arising due to the formation of N-type systems with the two control beams. Since many of the applications of EIT and EIA rely on the anomalous dispersion near the resonances, this introduces a new ability to control the sign of the dispersion. Copyright (C) EPLA, 2012

Practical fully three-dimensional reconstruction algorithms for diffuse optical tomography

We have developed an efficient fully three-dimensional (3D) reconstruction algorithm for diffuse optical tomography (DOT). The 3D DOT, a severely ill-posed problem, is tackled through a pseudodynamic (PD) approach wherein an ordinary differential equation representing the evolution of the solution on pseudotime is integrated that bypasses an explicit inversion of the associated, ill-conditioned system matrix. One of the most computationally expensive parts of the iterative DOT algorithm, the reevaluation of the Jacobian in each of the iterations, is avoided by using the adjoint-Broyden update formula to provide low rank updates to the Jacobian. In addition, wherever feasible, we have also made the algorithm efficient by integrating along the quadratic path provided by the perturbation equation containing the Hessian. These algorithms are then proven by reconstruction, using simulated and experimental data and verifying the PD results with those from the popular Gauss-Newton scheme. The major findings of this work are as follows: (i) the PD reconstructions are comparatively artifact free, providing superior absorption coefficient maps in terms of quantitative accuracy and contrast recovery; (ii) the scaling of computation time with the dimension of the measurement set is much less steep with the Jacobian update formula in place than without it; and (iii) an increase in the data dimension, even though it renders the reconstruction problem less ill conditioned and thus provides relatively artifact-free reconstructions, does not necessarily provide better contrast property recovery. For the latter, one should also take care to uniformly distribute the measurement points, avoiding regions close to the source so that the relative strength of the derivatives for measurements away from the source does not become insignificant. (c) 2012 Optical Society of America

Stabilization of O-Mn-O clusters (Mn-5) in three dimensionally extended MOF structures: synthesis, structure and properties

Four new three-dimensional Mn2+ ion-containing compounds have been prepared by employing a hydrothermal reaction between Mn(CH3COO)(2)center dot 4H(2)O, sulfodibenzoic acid (H(2)SDBA), imidazole, alkali hydroxide and water at 220 degrees C for 1 day. The compounds have Mn-5 (1-4) clusters connected by SDBA, forming the three-dimensional structure. A time and temperature dependent study on the synthesis mixture revealed the formation of a one-dimensional compound, Mn(SDBA)(H2O)(2), at lower temperatures (T <= 180 degrees C). The stabilization of the fcu related topology in the compounds is noteworthy. Magnetic studies indicate strong anti-ferromagnetic interactions between the Mn2+ ions within the clusters in the temperature range 75-300 K. The rare participation of a sulfonyl group in the bonding is important and can pave way for the design of new structures.

A MATLAB Code for Three Dimensional Linear Elastostatics using Constant Boundary Elements

Present work presents a code written in the very simple programming language MATLAB, for three dimensional linear elastostatics, using constant boundary elements. The code, in full or in part, is not a translation or a copy of any of the existing codes. Present paper explains how the code is written, and lists all the formulae used. Code is verified by using the code to solve a simple problem which has the well known approximate analytical solution. Of course, present work does not make any contribution to research on boundary elements, in terms of theory. But the work is justified by the fact that, to the best of author’s knowledge, as of now, one cannot find an open access MATLAB code for three dimensional linear elastostatics using constant boundary elements. Author hopes this paper to be of help to beginners who wish to understand how a simple but complete boundary element code works, so that they can build upon and modify the present open access code to solve complex engineering problems quickly and easily. The code is available online for open access (as supplementary file for the present paper), and may be downloaded from the website for the present journal.

Extracting Three Dimensional Surface Model of Human Kidney from the Visible Human Data Set using Free Software

Three dimensional digital model of a representative human kidney is needed for a surgical simulator that is capable of simulating a laparoscopic surgery involving kidney. Buying a three dimensional computer model of a representative human kidney, or reconstructing a human kidney from an image sequence using commercial software, both involve (sometimes significant amount of) money. In this paper, author has shown that one can obtain a three dimensional surface model of human kidney by making use of images from the Visible Human Data Set and a few free software packages (ImageJ, ITK-SNAP, and MeshLab in particular). Images from the Visible Human Data Set, and the software packages used here, both do not cost anything. Hence, the practice of extracting the geometry of a representative human kidney for free, as illustrated in the present work, could be a free alternative to the use of expensive commercial software or to the purchase of a digital model.

Simultaneous refolding and purification of recombinant proteins by macro-(affinity ligand) facilitated three-phase partitioning

A strategy called macro-(affinity ligand) facilitated three-phase partitioning (MLFTPP) is described for refolding of a diverse set of recombinant proteins starting from the solubilized inclusion bodies. It essentially consists of: (i) binding of the protein with a suitable smart polymer and (ii) precipitating the polymer-protein complex as an interfacial layer by mixing in a suitable amount of ammonium sulfate and t-butanol. Smart polymers are stimuli-responsive polymers that become insoluble on the application of a suitable stimulus (e.g., a change in the temperature, pH, or concentration of a chemical species such as Ca 2+ or K +). The MLFTPP process required approximately 10min, and the refolded proteins were found to be homogeneous on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The folded proteins were characterized by fluorescence emission spectroscopy, circular dichroism spectroscopy, biological activity, melting temperature, and surface hydrophobicity measurements by 8-anilino-1-naphthalenesulfonate fluorescence. Two refolded antibody fragments were also characterized by measuring K D by Biacore by using immobilized HIV-1 gp120. The data demonstrate that MLFTPP is a rapid and convenient procedure for refolding a variety of proteins from inclusion bodies at high concentration. Although establishing the generic nature of the approach would require wider trials by different groups, its success with the diverse kinds of proteins tried so far appears to be promising.

Adam-Gibbs Relation for Glass-Forming Liquids in Two, Three, and Four Dimensions

The Adam-Gibbs relation between relaxation times and the configurational entropy has been tested extensively for glass formers using experimental data and computer simulation results. Although the form of the relation contains no dependence on the spatial dimensionality in the original formulation, subsequent derivations of the Adam-Gibbs relation allow for such a possibility. We test the Adam-Gibbs relation in two, three, and four spatial dimensions using computer simulations of model glass formers. We find that the relation is valid in three and four dimensions. But in two dimensions, the relation does not hold, and interestingly, no single alternate relation describes the results for the different model systems we study.

Porous Three Dimensional Arrays of Plasmonic Nanoparticles

Plasmonic interactions in a well-defined array of metallic nanoparticles can lead to interesting optical effects, such as local electric field enhancement and shifts in the extinction spectra, which are of interest in diverse technological applications, including those pertaining to biochemical sensing and photonic circuitry. Here, we report on a single-step wafer scale fabrication of a three-dimensional array of metallic nanoparticles whose sizes and separations can be easily controlled to be anywhere between fifty to a few hundred nanometers, allowing the optical response of the system to be tailored with great control in the visible region of the spectrum. The substrates, apart from having a large surface area, are inherently porous and therefore suitable for optical sensing applications, such as surface enhanced Raman scattering, containing a high density of spots with enhanced local electric fields arising from plasmonic couplings.

Recapitulating tumour microenvironment in chitosan-gelatin three-dimensional scaffolds: an improved in vitro tumour model

Owing to the reduced co-relationship between conventional flat Petri dish culture (two-dimensional) and the tumour microenvironment, there has been a shift towards three-dimensional culture systems that show an improved analogy to the same. In this work, an extracellular matrix (ECM)-mimicking three-dimensional scaffold based on chitosan and gelatin was fabricated and explored for its potential as a tumour model for lung cancer. It was demonstrated that the chitosan-gelatin (CG) scaffolds supported the formation of tumoroids that were similar to tumours grown in vivo for factors involved in tumour-cell-ECM interaction, invasion and metastasis, and response to anti-cancer drugs. On the other hand, the two-dimensional Petri dish surfaces did not demonstrate gene-expression profiles similar to tumours grown in vivo. Further, the three-dimensional CG scaffolds supported the formation of tumoroids, using other types of cancer cells such as breast, cervix and bone, indicating a possible wider potential for in vitro tumoroid generation. Overall, the results demonstrated that CG scaffolds can be an improved in vitro tool to study cancer progression and drug screening for solid tumours.

Demonstrating the Usefulness of CAELinux for Computer Aided Engineering using an Example of the Three Dimensional Reconstruction of a Pig Liver

CAELinux is a Linux distribution which is bundled with free software packages related to Computer Aided Engineering (CAE). The free software packages include software that can build a three dimensional solid model, programs that can mesh a geometry, software for carrying out Finite Element Analysis (FEA), programs that can carry out image processing etc. Present work has two goals: 1) To give a brief description of CAELinux 2) To demonstrate that CAELinux could be useful for Computer Aided Engineering, using an example of the three dimensional reconstruction of a pig liver from a stack of CT-scan images. One can note that instead of using CAELinux, using commercial software for reconstructing the liver would cost a lot of money. One can also note that CAELinux is a free and open source operating system and all software packages that are included in the operating system are also free. Hence one can conclude that CAELinux could be a very useful tool in application areas like surgical simulation which require three dimensional reconstructions of biological organs. Also, one can see that CAELinux could be a very useful tool for Computer Aided Engineering, in general.

Multilevel dodecagonal space-vector generation for induction motor drives by cascading three-level and two-level inverters

This study proposes an inverter circuit topology capable of generating multilevel dodecagonal (12-sided polygon) voltage space vectors by the cascaded connection of two-level and three-level inverters. By the proper selection of DC-link voltages and resultant switching states for the inverters, voltage space vectors whose tips lie on three concentric dodecagons, are obtained. A rectifier circuit for the inverter is also proposed, which significantly improves the power factor. The topology offers advantages such as the complete elimination of the fifth and seventh harmonics in phase voltages and an extension of the linear modulation range. In this study, a simple method for the calculation of pulse width modulation timing was presented along with extensive simulation and experimental results in order to validate the proposed concept.

NMR Analysis of Cross Strand Aromatic Interactions in an 8 Residue Hairpin and a 14 Residue Three Stranded beta-Sheet Peptide

Cross strand aromatic interactions between a facing pair of phenylalanine residues in antiparallel beta-sheet structures have been probed using two structurally defined model peptides. The octapeptide Boc-(LFVPPLFV)-P-D-P-L-OMe (peptide 1) favors the beta-hairpin conformation nucleated by the type II' beta-turn formed by the (D)Pro-(L)Pro segment, placing Phe2 and Phe7 side chains in proximity. Two centrally positioned (D)Pro-(L)Pro segments facilitate the three stranded beta-sheet formation in the 14 residue peptide Boc-LFV(D)P(L)PLFVA(D)P(L)PLFV-OMe (peptide 2) in which the Phe2/Phe7 orientations are similar to that in the octapeptide. The anticipated folded conformations of peptides 1 and 2 are established by the delineation of intramolecularly hydrogen bonded NH groups and by the observation of specific cross strand NOEs. The observation of ring current shifted aromatic protons is a diagnostic of close approach of the Phe2 and Phe7 side chains. Specific assignment of aromatic proton resonances using HSQC and HSQC-TOCSY methods allow an analysis of interproton NOEs between the spatially proximate aromatic rings. This approach facilitates specific assignments in systems containing multiple aromatic rings in spectra at natural abundance. Evidence is presented for a dynamic process which invokes a correlated conformational change about the C-alpha-C-beta(chi(1)) bond for the pair of interacting Phe residues. NMR results suggest that aromatic ring orientations observed in crystals are maintained in solution. Anomalous temperature dependence of ring current induced proton chemical shifts suggests that solvophobic effects may facilitate aromatic ring clustering in apolar solvents.

Sum rules and three point functions

Sum rules constraining the R-current spectral densities are derived holographically for the case of D3-branes, M2-branes and M5-branes all at finite chemical potentials. In each of the cases the sum rule relates a certain integral of the spectral density over the frequency to terms which depend both on long distance physics, hydrodynamics and short distance physics of the theory. The terms which which depend on the short distance physics result from the presence of certain chiral primaries in the OPE of two it-currents which are turned on at finite chemical potential. Since these sum rules contain information of the OPE they provide an alternate method to obtain the structure constants of the two R-currents and the chiral primary. As a consistency check we show that the 3 point function derived from the sum rule precisely matches with that obtained using Witten diagrams.