NON-GLYCINE RESIDUES IN THE DISALLOWED REGIONS OF THE RAMACHANDRAN MAP AND THEIR NEIGHBORHOOD PREFERENCES

The allowed and the ``disallowed'' regions in the celebrated Ramachandran map (phi-psi] map) was elegantly deduced by Ramachandran, Ramakrishnan and Sasisekharan even before the protein crystal structures became available. This powerful map was derived based on rigid geometry of the peptide group and later several investigations on protein crystal structures reported the occurrence of a small fraction of the phi-psi] torsion angles in the disallowed region. The question is what factors make these residues adopt disallowed conformations? Is it driven by the necessity to maintain the overall topology or is it associated with function or is it just that the disallowed conformations are extreme limits of the allowed conformations? Today, with the availability of a large number of high resolution crystal structures, we have revisited this problem. Apart from validating some of the earlier findings such as residue propensities, preferred location in the secondary structure, we have explored their spatial neighborhood preferences using the protein structure network PSN] approach developed in our lab. Finally, the structural and functional implications of the disallowed conformations are examined.

PROPENSITIES OF AMINO ACID RESIDUES IN PROTEINS FOR DIFFERENT REGIONS OF THE RAMACHANDRAN MAP

Using a dataset of 1164 crystal structures of largely non-homologous proteins defined at a resolution of 1.5 angstrom or better, we have investigated the (phi,psi) preferences of 20 residue types by considering the residues which occur in loops. Propensities of residue types to occur in the loops with (phi,psi) values in the aa region of the Ramachandran map has a poor correlation coefficient of 0.48 to the Chou-Fasman propensities of the residue types to occur in the a-helical segments. However the correlation coefficient between propensities of residues in loops to adopt beta conformations and those in beta-sheet is much higher (0.95). These observations suggest that a-helix formation is well influenced by the local amino acid sequence while intrinsic preference of residue types for beta-sheet plays a major role in the formation of beta-sheet. The main chain polar groups of residues in loops, that can affect the (phi,psi) values, can be involved in intra-molecular hydrogen bonding. Therefore we investigated further by considering subset of residues in loops with low (0 to 2) number of intra-molecular hydrogen bonds per residue involving main chain polar atoms. For this subset, the correlation coefficients between propensities for alpha-helix and alpha(R) region and between beta-sheet and beta-region are 0.26 and 0.64 respectively. This reiterates higher intrinsic tendency of beta-region favouring residues to adopt beta-sheet than alpha(R) region favouring residues to adopt alpha-helical structure.

An extended finite element model coupled with level set method for stable pitting corrosion

Mass balance between metal and electrolytic solution, separated by a moving interface, in stable pit growth results in a set of governing equations which are solved for concentration field and interface position (pit boundary evolution), which requires only three inputs, namely the solid metal concentration, saturation concentration of the dissolved metal ions and diffusion coefficient. A combined eXtended Finite Element Model (XFEM) and level set method is developed in this paper. The extended finite element model handles the jump discontinuity in the metal concentrations at the interface, by using discontinuous-derivative enrichment formulation for concentration discontinuity at the interface. This eliminates the requirement of using front conforming mesh and re-meshing after each time step as in conventional finite element method. A numerical technique known as level set method tracks the position of the moving interface and updates it over time. Numerical analysis for pitting corrosion of stainless steel 304 is presented. The above proposed method is validated by comparing the numerical results with experimental results, exact solutions and some other approximate solutions.

An extended finite-element model coupled with level set method for analysis of growth of corrosion pits in metallic structures

Mass balance between metal and electrolytic solution, separated by a moving interface, in stable pit growth results in a set of governing equations which are solved for concentration field and interface position (pit boundary evolution). The interface experiences a jump discontinuity in metal concentration. The extended finite-element model (XFEM) handles this jump discontinuity by using discontinuous-derivative enrichment formulation, eliminating the requirement of using front conforming mesh and re-meshing after each time step as in the conventional finite-element method. However, prior interface location is required so as to solve the governing equations for concentration field for which a numerical technique, the level set method, is used for tracking the interface explicitly and updating it over time. The level set method is chosen as it is independent of shape and location of the interface. Thus, a combined XFEM and level set method is developed in this paper. Numerical analysis for pitting corrosion of stainless steel 304 is presented. The above proposed model is validated by comparing the numerical results with experimental results, exact solutions and some other approximate solutions. An empirical model for pitting potential is also derived based on the finite-element results. Studies show that pitting profile depends on factors such as ion concentration, solution pH and temperature to a large extent. Studying the individual and combined effects of these factors on pitting potential is worth knowing, as pitting potential directly influences corrosion rate.

Frustration in Optical Lattices of Interacting Bosons

The realization of optical lattices of cold atoms has opened up the possibility of engineering interacting lattice systems of bosons and fermions, stimulating a frenzy of research over the last decade. More recently, experimental techniques have been developed to apply synthetic gauge fields to these optical lattices. As a result, it has become possible to study quantum Hall physics and the effects of frustration in lattices of cold atoms. In this article we describe the combined effect of frustration and interactions on the superfluidity of bosons. By focussing on a frustrated ladder of interacting bosons, we show that the effect of frustration is for ``chiral'' order to develop, which manifests itself as an alternating pattern of circulating supercurrents. Remarkably, this order persists even when superfluidity is lost and the system enters a Mott phase giving rise to a novel chiral Mott insulator. We describe the combined physics of frustration and interactions by studying a fully frustrated one dimensional model of interacting bosons. The model is studied using mean-field theory, a direct quantum simulation and a higher dimensional classical theory in order to offer a full description of the different quantum phases contained in it and transitions between the different phases. In addition, we provide physical descriptions of the chiral Mott insulator as a vortex-anitvortex super solid and indirect excitonic condensate in addition to obtaining a variational wavefunction for it. We also briefly describe the chiral Mott states arising in other microscopic models.

A spectral multiscale method for wave propagation analysis: Atomistic-continuum coupled simulation

In this paper, we present a new multiscale method which is capable of coupling atomistic and continuum domains for high frequency wave propagation analysis. The problem of non-physical wave reflection, which occurs due to the change in system description across the interface between two scales, can be satisfactorily overcome by the proposed method. We propose an efficient spectral domain decomposition of the total fine scale displacement along with a potent macroscale equation in the Laplace domain to eliminate the spurious interfacial reflection. We use Laplace transform based spectral finite element method to model the macroscale, which provides the optimum approximations for required dynamic responses of the outer atoms of the simulated microscale region very accurately. This new method shows excellent agreement between the proposed multiscale model and the full molecular dynamics (MD) results. Numerical experiments of wave propagation in a 1D harmonic lattice, a 1D lattice with Lennard-Jones potential, a 2D square Bravais lattice, and a 2D triangular lattice with microcrack demonstrate the accuracy and the robustness of the method. In addition, under certain conditions, this method can simulate complex dynamics of crystalline solids involving different spatial and/or temporal scales with sufficient accuracy and efficiency. (C) 2014 Elsevier B.V. All rights reserved.

Hot deformation behavior of Ni-Fe-Ga-based ferromagnetic shape memory alloy - A study using processing map

Ni-Fe-Ga-based alloys form a new class of ferromagnetic shape memory alloys (FSMAs) that show considerable formability because of the presence of a disordered fcc gamma-phase. The current study explores the deformation processing of this alloy using an off-stoichiometric Ni55Fe59Ga26 alloy that contains the ductile gamma-phase. The hot deformation behavior of this alloy has been characterized on the basis of its flow stress variation obtained by isothermal constant true strain rate compression tests in the 1123-1323 K temperature range and strain rate range of 10(-3)-10 s(-1) and using a combination of constitutive modeling and processing map. The dynamic recrystallization (DRX) regime for thermomechanical processing has been identified for this Heusler alloy on the basis of the processing maps and the deformed microstructures. This alloy also shows evidence of dynamic strain-aging (DSA) effect which has not been reported so far for any Heusler FSMAs. Similar effect is also noticed in a Ni-Mn-Ga-based Heusler alloy which is devoid of any gamma-phase. (C) 2014 Elsevier Ltd. All rights reserved.

Long range emission enhancement and anisotropy in coupled quantum dots induced by aligned gold nanoantenna

Quantum dot arrays have been projected as the material of choice for next generation displays and photodetectors. Extensive ongoing research aims at improving optical and electrical efficiencies of such devices. We report experimental results on non-local long range emission intensity enhancement and anisotropy in quantum dot assemblies induced by isolated and partially aligned gold nanoantennas. Spatially resolved photoluminescence clearly demonstrate that the effect is maximum, when the longitudinal surface plasmon resonance of the nanoantenna is resonant with the emission maxima of the quantum dots. We estimated the decay length of this enhancement to be similar to 2.6 mu m, which is considerably larger than the range of near field interaction of metal nanoantenna. Numerical simulations qualitatively capture the near field behavior of the nanorods but fail to match the experimentally observed non-local effects. We have suggested how strong interactions of quantum dots in the close packed assemblies, mediated by the nanoantennas, could lead to such observed behavior. (C) 2014 AIP Publishing LLC.

Assignment of the C-13 NMR spectrum by correlation to dipolar coupled proton-pairs and estimation of order parameters of a thiophene based liquid crystal

Materials with widely varying molecular topologies and exhibiting liquid crystalline properties have attracted considerable attention in recent years. C-13 NMR spectroscopy is a convenient method for studying such novel systems. In this approach the assignment of the spectrum is the first step which is a non-trivial problem. Towards this end, we propose here a method that enables the carbon skeleton of the different sub-units of the molecule to be traced unambiguously. The proposed method uses a heteronuclear correlation experiment to detect pairs of nearby carbons with attached protons in the liquid crystalline core through correlation of the carbon chemical shifts to the double-quantum coherences of protons generated through the dipolar coupling between them. Supplemented by experiments that identify non-protonated carbons, the method leads to a complete assignment of the spectrum. We initially apply this method for assigning the C-13 spectrum of the liquid crystal 4-n-pentyl-4'-cyanobiphenyl oriented in the magnetic field. We then utilize the method to assign the aromatic carbon signals of a thiophene based liquid crystal thereby enabling the local order-parameters of the molecule to be estimated and the mutual orientation of the different sub-units to be obtained.

A strongly coupled anisotropic fluid from dilaton driven holography

We consider a system consisting of 5 dimensional gravity with a negative cosmological constant coupled to a massless scalar, the dilaton. We construct a black brane solution which arises when the dilaton satisfies linearly varying boundary conditions in the asymptotically AdS(5) region. The geometry of this black brane breaks rotational symmetry while preserving translational invariance and corresponds to an anisotropic phase of the system. Close to extremality, where the anisotropy is big compared to the temperature, some components of the viscosity tensor become parametrically small compared to the entropy density. We study the quasi normal modes in considerable detail and find no instability close to extremality. We also obtain the equations for fluid mechanics for an anisotropic driven system in general, working upto first order in the derivative expansion for the stress tensor, and identify additional transport coefficients which appear in the constitutive relation. For the fluid of interest we find that the parametrically small viscosity can result in a very small force of friction, when the fluid is enclosed between appropriately oriented parallel plates moving with a relative velocity.

Development of a global inundation map at high spatial resolution from topographic downscaling of coarse-scale remote sensing data

Large-scale estimates of the area of terrestrial surface waters have greatly improved over time, in particular through the development of multi-satellite methodologies, but the generally coarse spatial resolution (tens of kms) of global observations is still inadequate for many ecological applications. The goal of this study is to introduce a new, globally applicable downscaling method and to demonstrate its applicability to derive fine resolution results from coarse global inundation estimates. The downscaling procedure predicts the location of surface water cover with an inundation probability map that was generated by bagged derision trees using globally available topographic and hydrographic information from the SRTM-derived HydroSHEDS database and trained on the wetland extent of the GLC2000 global land cover map. We applied the downscaling technique to the Global Inundation Extent from Multi-Satellites (GIEMS) dataset to produce a new high-resolution inundation map at a pixel size of 15 arc-seconds, termed GIEMS-D15. GIEMS-D15 represents three states of land surface inundation extents: mean annual minimum (total area, 6.5 x 10(6) km(2)), mean annual maximum (12.1 x 10(6) km(2)), and long-term maximum (173 x 10(6) km(2)); the latter depicts the largest surface water area of any global map to date. While the accuracy of GIEMS-D15 reflects distribution errors introduced by the downscaling process as well as errors from the original satellite estimates, overall accuracy is good yet spatially variable. A comparison against regional wetland cover maps generated by independent observations shows that the results adequately represent large floodplains and wetlands. GIEMS-D15 offers a higher resolution delineation of inundated areas than previously available for the assessment of global freshwater resources and the study of large floodplain and wetland ecosystems. The technique of applying inundation probabilities also allows for coupling with coarse-scale hydro-climatological model simulations. (C) 2014 Elsevier Inc All rights reserved.

High-Temperature Deformation Processing Map Approach for Obtaining the Desired Microstructure in a Multi-component (Ni-Ti-Cu-Fe) Alloy

An equiatomic NiTiCuFe multi-component alloy with simple body-centered cubic (bcc) and face-centered cubic solid-solution phases in the microstructure was processed by vacuum induction melting furnace under dynamic Ar atmosphere. High-temperature uniaxial compression experiments were conducted on it in the temperature range of 1073 K to 1303 K (800 degrees C to 1030 degrees C) and strain rate range of 10(-3) to 10(-1) s(-1). The data generated were analyzed with the aid of the dynamic materials model through which power dissipation efficiency and instability maps were generated so as to identify the governing deformation mechanisms that are operative in different temperature-strain rate regimes with the aid of complementary microstructural analysis of the deformed specimens. Results indicate that the stable domain for the high temperature deformation of the multi-component alloy occurs in the temperature range of 1173 K to 1303 K (900 degrees C to 1030 degrees C) and (epsilon) over dot range of 10(-3) to 10(-1.2) s(-1), and the deformation is unstable at T = 1073 K to 1153 K (800 degrees C to 880 degrees C) and (epsilon) over dot = 10(-3) to 10(-1.4) s(-1) as well as T = 1223 K to 1293 K (950 degrees C to 1020 degrees C) and (epsilon) over dot = 10(-1.4) to 10(-1) s(-1), with adiabatic shear banding, localized plastic flow, or cracking being the unstable mechanisms. A constitutive equation that describes the flow stress of NiTiCuFe multi-component alloy as a function of strain rate and deformation temperature was also determined. (C) The Minerals, Metals & Materials Society and ASM International 2015

Hybrid Elements for Modelling Squeeze Film Effects Coupled with Structural Interactions in Vibratory MEMS Devices

We present a hybrid finite element based methodology to solve the coupled fluid structure problem of squeeze film effects in vibratory MEMS devices, such as gyroscopes, RF switches, and 2D resonators. The aforementioned devices often have a thin plate like structure vibrating normally to a fixed substrate, and are generally not perfectly vacuum packed. This results in a thin air film being trapped between the vibrating plate and the fixed substrate which behaves like a squeeze film offering both stiffness and damping. For accurate modelling of such devices the squeeze film effects must be incorporated. Extensive literature is available on squeeze film modelling, however only a few studies address the coupled fluid elasticity problem. The majority of the studies that account for the plate elasticity coupled with the fluid equation, either use approximate mode shapes for the plate or use iterative solution strategies. In an earlier work we presented a single step coupled methodology using only one type of displacement based element to solve the coupled problem. The displacement based finite element models suffer from locking issues when it comes to modelling very thin structures with the lateral dimensions much larger than the plate thickness as is typical in MEMS devices with squeeze film effects. In this work we present another coupled formulation where we have used hybrid elements to model the structural domain. The numerical results show a huge improvement in convergence and accuracy with coarse hybrid mesh as compared to displacement based formulations. We further compare our numerical results with experimental data from literature and find them to be in good accordance.

Inductively coupled reactive ion etching studies on sputtered yttria stabilized zirconia thin films in SF6, Cl-2, and BCl3 chemistries

Downscaling of yttria stabilized zirconia (YSZ) based electrochemical devices and gate oxide layers requires successful pattern transfer on YSZ thin films. Among a number of techniques available to transfer patterns to a material, reactive ion etching has the capability to offer high resolution, easily controllable, tunable anisotropic/isotropic pattern transfer for batch processing. This work reports inductively coupled reactive ion etching studies on sputtered YSZ thin films in fluorine and chlorine based plasmas and their etch chemistry analyses using x-ray photoelectron spectroscopy. Etching in SF6 plasma gives an etch rate of 7 nm/min chiefly through physical etching process. For same process parameters, in Cl-2 and BCl3 plasmas, YSZ etch rate is 17 nm/min and 45 nm/min, respectively. Increased etch rate in BCl3 plasma is attributed to its oxygen scavenging property synergetic with other chemical and physical etch pathways. BCl3 etched YSZ films show residue-free and smooth surface. The surface atomic concentration ratio of Zr/Y in BCl3 etched films is closer to as-annealed YSZ thin films. On the other hand, Cl-2 etched films show surface yttrium enrichment. Selectivity ratio of YSZ over silicon (Si), silicon dioxide (SiO2) and silicon nitride (Si3N4) are 1:2.7, 1:1, and 1:0.75, respectively, in BCl3 plasma. YSZ etch rate increases to 53 nm/min when nonoxygen supplying carrier wafer like Si3N4 is used. (C) 2015 American Vacuum Society.

Giant actuation in bulk carbon nanotubes under coupled electric and magnetic fields

We report an enhanced actuation in bulk carbon nanotubes (CNTs) under coupled electric and magnetic fields, which is much higher than that evaluated in the presence of individual fields. Coupled electric and magnetic fields induce a directional actuation demonstrating a transformation from polarity independent to dependent actuation behavior of CNTs. Both qualitative and quantitative analyses are performed to understand this transformation in the bulk CNTs. Moreover, actuations along radial and axial directions of CNTs have also demonstrated a similar directional behavior.