Ultrafast Raman loss spectroscopy (URLS): instrumentation and principle

In this paper, we report on the concept and the design principle of ultrafast Raman loss spectroscopy (URLS) as a structure-elucidating tool. URLS is an analogue of stimulated Raman scattering (SRS) but more sensitive than SRS with better signal-to-noise ratio. It involves the interaction of two laser sources, namely, a picosecond (ps) Raman pump pulse and a white-light (WL) continuum, with a sample, leading to the generation of loss signals on the higher energy (blue) side with respect to the wavelength of the Raman pump unlike the gain signal observed on the lower energy (red) side in SRS. These loss signals are at least 1.5 times more intense than the SRS signals. An experimental study providing an insight into the origin of this extra intensity in URLS as compared to SRS is reported. Furthermore, the very requirement of the experimental protocol for the signal detection to be on the higher energy side by design eliminates the interference from fluorescence, which appears on the red side. Unlike CARS, URLS signals are not precluded by the non-resonant background and, being a self-phase-matched process, URLS is experimentally easier. Copyright (C) 2011 John Wiley & Sons, Ltd.

Continuum theory of edge states of topological insulators: variational principle and boundary conditions

We develop a continuum theory to model low energy excitations of a generic four-band time reversal invariant electronic system with boundaries. We propose a variational energy functional for the wavefunctions which allows us to derive natural boundary conditions valid for such systems. Our formulation is particularly suited for developing a continuum theory of the protected edge/surface excitations of topological insulators both in two and three dimensions. By a detailed comparison of our analytical formulation with tight binding calculations of ribbons of topological insulators modelled by the Bernevig-Hughes-Zhang (BHZ) Hamiltonian, we show that the continuum theory with a natural boundary condition provides an appropriate description of the low energy physics.

A Modified Fluorimetric Method for Determination of Hydrogen Peroxide Using Homovanillic Acid Oxidation Principle

Hydrogen peroxide (H2O2) level in biological samples is used as an important index in various studies. Quantification of H2O2 level in tissue fractions in presence of H2O2 metabolizing enzymes may always provide an incorrect result. A modification is proposed for the spectrofluorimetric determination of H2O2 in homovanillic acid (HVA) oxidation method. The modification was included to precipitate biological samples with cold trichloroacetic acid (TCA, 5% w/v) followed by its neutralization with K2HPO4 before the fluorimetric estimation of H2O2 is performed. TCA was used to precipitate the protein portions contained in the tissue fractions. After employing the above modification, it was observed that H2O2 content in tissue samples was >= 2 fold higher than the content observed in unmodified method. Minimum 2 h incubation of samples in reaction mixture was required for completion of the reaction. The stability of the HVA dimer as reaction product was found to be > 12 h. The method was validated by using known concentrations of H2O2 and catalase enzyme that quenches H2O2 as substrate. This method can be used efficiently to determine more accurate tissue H2O2 level without using internal standard and multiple samples can be processed at a time with additional low cost reagents such as TCA and K2HPO4.

Super-Resolution Reconstruction in Frequency-Domain Optical-Coherence Tomography Using the Finite-Rate-of-Innovation Principle

The standard approach to signal reconstruction in frequency-domain optical-coherence tomography (FDOCT) is to apply the inverse Fourier transform to the measurements. This technique offers limited resolution (due to Heisenberg's uncertainty principle). We propose a new super-resolution reconstruction method based on a parametric representation. We consider multilayer specimens, wherein each layer has a constant refractive index and show that the backscattered signal from such a specimen fits accurately in to the framework of finite-rate-of-innovation (FRI) signal model and is represented by a finite number of free parameters. We deploy the high-resolution Prony method and show that high-quality, super-resolved reconstruction is possible with fewer measurements (about one-fourth of the number required for the standard Fourier technique). To further improve robustness to noise in practical scenarios, we take advantage of an iterated singular-value decomposition algorithm (Cadzow denoiser). We present results of Monte Carlo analyses, and assess statistical efficiency of the reconstruction techniques by comparing their performance against the Cramer-Rao bound. Reconstruction results on experimental data obtained from technical as well as biological specimens show a distinct improvement in resolution and signal-to-reconstruction noise offered by the proposed method in comparison with the standard approach.

De novo inference of protein function from coarse-grained dynamics

Inference of molecular function of proteins is the fundamental task in the quest for understanding cellular processes. The task is getting increasingly difficult with thousands of new proteins discovered each day. The difficulty arises primarily due to lack of high-throughput experimental technique for assessing protein molecular function, a lacunae that computational approaches are trying hard to fill. The latter too faces a major bottleneck in absence of clear evidence based on evolutionary information. Here we propose a de novo approach to annotate protein molecular function through structural dynamics match for a pair of segments from two dissimilar proteins, which may share even <10% sequence identity. To screen these matches, corresponding 1 mu s coarse-grained (CG) molecular dynamics trajectories were used to compute normalized root-mean-square-fluctuation graphs and select mobile segments, which were, thereafter, matched for all pairs using unweighted three-dimensional autocorrelation vectors. Our in-house custom-built forcefield (FF), extensively validated against dynamics information obtained from experimental nuclear magnetic resonance data, was specifically used to generate the CG dynamics trajectories. The test for correspondence of dynamics-signature of protein segments and function revealed 87% true positive rate and 93.5% true negative rate, on a dataset of 60 experimentally validated proteins, including moonlighting proteins and those with novel functional motifs. A random test against 315 unique fold/function proteins for a negative test gave >99% true recall. A blind prediction on a novel protein appears consistent with additional evidences retrieved therein. This is the first proof-of-principle of generalized use of structural dynamics for inferring protein molecular function leveraging our custom-made CG FF, useful to all. (C) 2014 Wiley Periodicals, Inc.

On the superposition principle in interference experiments

The superposition principle is usually incorrectly applied in interference experiments. This has recently been investigated through numerics based on Finite Difference Time Domain (FDTD) methods as well as the Feynman path integral formalism. In the current work, we have derived an analytic formula for the Sorkin parameter which can be used to determine the deviation from the application of the principle. We have found excellent agreement between the analytic distribution and those that have been earlier estimated by numerical integration as well as resource intensive FDTD simulations. The analytic handle would be useful for comparing theory with future experiments. It is applicable both to physics based on classical wave equations as well as the non-relativistic Schrodinger equation.

A taxonomic mystery for more than 180 years: the identity and systematic position of Brachysaura minor (HARDWICKE & GRAY, 1827)

Brachysaura is a monotypic genus of agamid lizard found in the Indian subcontinent; the identity and systematic position of B. minor has been long debated, and it has at times been subsumed into Agama, Charasia and Laudakia, with some authors suggesting affinities to Calotes. We constructed nuclear and mitochondrial phylogenetic trees including Brachysaura and allied agamid genera to resolve its phylogenetic position. We also compared osteology and external morphology with the genera Agama, Calotes and Laudakia. Hemipenial morphology was compared with Calotes and some other agamids from South Asia. Both nuclear and mitochondrial phylogenies demonstrate that Brachysaura is nested within the widespread South and Southeast Asian genus Calotes, with which it also shares certain external morphological, osteological and hemipenial characters. Adaptations to ground dwelling in Brachysaura minor has resulted in unique modifications to its body plan, which is likely why generic allocation has been long confused. This study also highlights the need for an integrated systematic approach to resolve taxonomic ambiguity in Asian agamids.

Ellipse Fitting Using the Finite Rate of Innovation Sampling Principle

Standard approaches for ellipse fitting are based on the minimization of algebraic or geometric distance between the given data and a template ellipse. When the data are noisy and come from a partial ellipse, the state-of-the-art methods tend to produce biased ellipses. We rely on the sampling structure of the underlying signal and show that the x- and y-coordinate functions of an ellipse are finite-rate-of-innovation (FRI) signals, and that their parameters are estimable from partial data. We consider both uniform and nonuniform sampling scenarios in the presence of noise and show that the data can be modeled as a sum of random amplitude-modulated complex exponentials. A low-pass filter is used to suppress noise and approximate the data as a sum of weighted complex exponentials. The annihilating filter used in FRI approaches is applied to estimate the sampling interval in the closed form. We perform experiments on simulated and real data, and assess both objective and subjective performances in comparison with the state-of-the-art ellipse fitting methods. The proposed method produces ellipses with lesser bias. Furthermore, the mean-squared error is lesser by about 2 to 10 dB. We show the applications of ellipse fitting in iris images starting from partial edge contours, and to free-hand ellipses drawn on a touch-screen tablet.

Generic identity of Camptorrhiza indica (Colchicaceae) based on cytogenetics and molecular phylogenetics

The tribe Iphigenieae (Colchicaceace, Liliales) includes two genera, viz. Camptorrhiza and Iphigenia, which are distributed in Africa, India, and Australasia. Iphigenia is represented by 12 species, of which six occur in India while Camptorrhiza comprises one species each in Africa (C. strumosa) and India (C. indica). The genus Camptorrhiza possesses a knee-shaped tuber attached to the corms, filaments with a thick bulge in the middle and styles with single stigma. Iphigenia on the other hand lacks knee-shaped tuber, bears linear filaments and has styles with three stigmas. Camptorrhiza indica possesses ovoid corms, linear filaments and styles with a single stigma. These characters are intermediate between Iphigenia and Camptorrhiza and hence we studied the cytogenetics and phylogenetic placement of this species to ascertain its generic identity. Somatic chromosome count (2n = 22) and karyotypic features of C. indica are very similar to that of Iphigenia species. Molecular phylogenetic studies based on atpB-rbcL, rps16, trnL, and trnL-F regions showed that C. indica is nested within a lineage of Indian Iphigenia species. Thus, C. indica was reduced to a species of Iphigenia, i.e., I. ratnagirica. Camptorrhiza is now a monotypic genus restricted only to southern Africa. A key to the Indian Iphigenia species is provided. In addition, a new combination Wurmbea novae-zelandiae is proposed for Iphigenia novae-zelandiae.