Multi-physics self-consistent modeling in nanotechnological applications: quantum dots and quantum-well lasers

This paper reports a self-consistent Poisson-Schr¨odinger scheme including the effects of the piezoelectricity, the spontaneous polarization and the charge density on the electronic states and the quasi-Fermi level energy in wurtzite type semiconductor heterojunction and quantum-laser.

Time-Resolved Resonance Raman Spectroscopy: Exploring Reactive Intermediates

The study of reaction mechanisms involves systematic investigations of the correlation between structure, reactivity, and time. The challenge is to be able to observe the chemical changes undergone by reactants as they change into products via one or several intermediates such as electronic excited states (singlet and triplet), radicals, radical ions, carbocations, carbanions, carbenes, nitrenes, nitrinium ions, etc. The vast array of intermediates and timescales means there is no single ``do-it-all'' technique. The simultaneous advances in contemporary time-resolved Raman spectroscopic techniques and computational methods have done much towards visualizing molecular fingerprint snapshots of the reactive intermediates in the microsecond to femtosecond time domain. Raman spectroscopy and its sensitive counterpart resonance Raman spectroscopy have been well proven as means for determining molecular structure, chemical bonding, reactivity, and dynamics of short-lived intermediates in solution phase and are advantageous in comparison to commonly used time-resolved absorption and emission spectroscopy. Today time-resolved Raman spectroscopy is a mature technique; its development owes much to the advent of pulsed tunable lasers, highly efficient spectrometers, and high speed, highly sensitive multichannel detectors able to collect a complete spectrum. This review article will provide a brief chronological development of the experimental setup and demonstrate how experimentalists have conquered numerous challenges to obtain background-free (removing fluorescence), intense, and highly spectrally resolved Raman spectra in the nanosecond to microsecond (ns-mu s) and picosecond (ps) time domains and, perhaps surprisingly, laid the foundations for new techniques such as spatially offset Raman spectroscopy.

Structural Annotation of Mycobacterium tuberculosis Proteome

Of the similar to 4000 ORFs identified through the genome sequence of Mycobacterium tuberculosis (TB) H37Rv, experimentally determined structures are available for 312. Since knowledge of protein structures is essential to obtain a high-resolution understanding of the underlying biology, we seek to obtain a structural annotation for the genome, using computational methods. Structural models were obtained and validated for similar to 2877 ORFs, covering similar to 70% of the genome. Functional annotation of each protein was based on fold-based functional assignments and a novel binding site based ligand association. New algorithms for binding site detection and genome scale binding site comparison at the structural level, recently reported from the laboratory, were utilized. Besides these, the annotation covers detection of various sequence and sub-structural motifs and quaternary structure predictions based on the corresponding templates. The study provides an opportunity to obtain a global perspective of the fold distribution in the genome. The annotation indicates that cellular metabolism can be achieved with only 219 folds. New insights about the folds that predominate in the genome, as well as the fold-combinations that make up multi-domain proteins are also obtained. 1728 binding pockets have been associated with ligands through binding site identification and sub-structure similarity analyses. The resource (http://proline.physics.iisc.ernet.in/Tbstructuralannotation), being one of the first to be based on structure-derived functional annotations at a genome scale, is expected to be useful for better understanding of TB and for application in drug discovery. The reported annotation pipeline is fairly generic and can be applied to other genomes as well.

On numerical prediction of the acoustic source characteristics of an engine exhaust system

The contemporary methods for source characterization rely mainly on experiments. These methods produce inaccurate results in the low‐frequency band, where the characteristics are all the more important. Moreover, the experimental methods cannot be used at the design stage. Hence, a numerical technique to obtain the source characteristics is desirable. In this paper, the pressure‐time history and the mass‐flux‐time history obtained by means of the time‐domain analysis have been used, along with the two‐load method to compute the source characteristics. Two new computational methods for obtaining the source characteristics have been described. These are much simpler, and computationally more economical than the complete time‐domain simulation, which makes use of the method of characteristics.

Distinctive contributions of the ribosomal P-site elements m(2)G966, m(5)C967 and the C-terminal tail of the S9 protein in the fidelity of initiation of translation in Escherichia coli

The accuracy of pairing of the anticodon of the initiator tRNA (tRNA(fMet)) and the initiation codon of an mRNA, in the ribosomal P-site, is crucial for determining the translational reading frame. However, a direct role of any ribosomal element(s) in scrutinizing this pairing is unknown. The P-site elements, m(2)G966 (methylated by RsmD), m(5)C967 (methylated by RsmB) and the C-terminal tail of the protein S9 lie in the vicinity of tRNA(fMet). We investigated the role of these elements in initiation from various codons, namely, AUG, GUG, UUG, CUG, AUA, AUU, AUC and ACG with tRNA(CAU)(fmet) (tRNA(fMet) with CAU anticodon); CAC and CAU with tRNA(GUG)(fme); UAG with tRNA(GAU)(fMet) using in vivo and computational methods. Although RsmB deficiency did not impact initiation from most codons, RsmD deficiency increased initiation from AUA, CAC and CAU (2- to 3.6-fold). Deletion of the S9 C-terminal tail resulted in poorer initiation from UUG, GUG and CUG, but in increased initiation from CAC, CAU and UAC codons (up to 4-fold). Also, the S9 tail suppressed initiation with tRNA(CAU)(fMet)lacking the 3GC base pairs in the anticodon stem. These observations suggest distinctive roles of 966/967 methylations and the S9 tail in initiation.

Intensity profile of light scattered from a rough surface

We present in this paper, approximate analytical expressions for the intensity of light scattered by a rough surface, whose elevation. xi(x,y) in the z-direction is a zero mean stationary Gaussian random variable. With (x,y) and (x',y') being two points on the surface, we have h. = 0 with a correlation, = sigma(2)g(r), where r = (x - x')(2) + ( y - y')(2)](1/2) is the distance between these two points. We consider g(r) = exp-r/l)(beta)] with 1 <= beta <= 2, showing that g(0) = 1 and g(r) -> 0 for r >> l. The intensity expression is sought to be expressed as f(v(xy)) = {1 + (c/2y)v(x)(2) + v(y)(2)]}(-y), where v(x) and v(y) are the wave vectors of scattering, as defined by the Beckmann notation. In the paper, we present expressions for c and y, in terms of sigma, l, and beta. The closed form expressions are verified to be true, for the cases beta = 1 and beta = 2, for which exact expressions are known. For other cases, i.e., beta not equal 1, 2 we present approximate expressions for the scattered intensity, in the range, v(xy) = (v(x)(2) + v(y)(2))(1/2) <= 6.0 and show that the relation for f(v(xy)), given above, expresses the scattered intensity quite accurately, thus providing a simple computational methods in situations of practical importance.

Exponential compact higher order scheme and their stability analysis for unsteady convection-diffusion equations

Exponential compact higher-order schemes have been developed for unsteady convection-diffusion equation (CDE). One of the developed scheme is sixth-order accurate which is conditionally stable for the Peclet number 0 <= Pe <= 2.8 and the other is fourth-order accurate which is unconditionally stable. Schemes for two-dimensional (2D) problems are made to use alternate direction implicit (ADI) algorithm. Example problems are solved and the numerical solutions are compared with the analytical solutions for each case.

Analysis of the conformations of septanoside sugars

Conformational analysis of unnatural seven-membered sugars, namely, septanoses and septanosides are discussed herein. The conformational properties of these sugars in the solid state, solution phase and computational methods are presented. The analyses reveal that conformations of septanosides are diverse and largely unpredictable, as compared furanosides and pyranosides.

Quadrature Domains in C-n

We prove two density theorems for quadrature domains in , . It is shown that quadrature domains are dense in the class of all product domains of the form , where is a smoothly bounded domain satisfying Bell's Condition R and is a smoothly bounded domain and also in the class of all smoothly bounded complete Hartogs domains in C-2.

A Reliable Residual Based A Posteriori Error Estimator for a Quadratic Finite Element Method for the Elliptic Obstacle Problem

A residual based a posteriori error estimator is derived for a quadratic finite element method (FEM) for the elliptic obstacle problem. The error estimator involves various residuals consisting of the data of the problem, discrete solution and a Lagrange multiplier related to the obstacle constraint. The choice of the discrete Lagrange multiplier yields an error estimator that is comparable with the error estimator in the case of linear FEM. Further, an a priori error estimate is derived to show that the discrete Lagrange multiplier converges at the same rate as that of the discrete solution of the obstacle problem. The numerical experiments of adaptive FEM show optimal order convergence. This demonstrates that the quadratic FEM for obstacle problem exhibits optimal performance.

Lower Bound Axisymmetric Limit Analysis Using Drucker-Prager Yield Cone and Simulation with Mohr-Coulomb Pyramid

This paper presents a lower bound limit analysis approach for solving an axisymmetric stability problem by using the Drucker-Prager (D-P) yield cone in conjunction with finite elements and nonlinear optimization. In principal stress space, the tip of the yield cone has been smoothened by applying the hyperbolic approximation. The nonlinear optimization has been performed by employing an interior point method based on the logarithmic barrier function. A new proposal has also been given to simulate the D-P yield cone with the Mohr-Coulomb hexagonal yield pyramid. For the sake of illustration, bearing capacity factors N-c, N-q and N-gamma have been computed, as a function of phi, both for smooth and rough circular foundations. The results obtained from the analysis compare quite well with the solutions reported from literature.