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.

Role of the Ribosomal P-Site Elements of m(2)G966, m(5)C967, and the S9 C-Terminal Tail in Maintenance of the Reading Frame during Translational Elongation in Escherichia coli

The ribosomal P-site hosts the peptidyl-tRNAs during translation elongation. Which P-site elements support these tRNA species to maintain codon-anticodon interactions has remained unclear. We investigated the effects of P-site features of methylations of G966, C967, and the conserved C-terminal tail sequence of Ser, Lys, and Arg (SKR) of the S9 ribosomal protein in maintenance of the translational reading frame of an mRNA. We generated Escherichia coli strains deleted for the SKR sequence in S9 ribosomal protein, RsmB (which methylates C967), and RsmD (which methylates G966) and used them to translate LacZ from its +1 and -1 out-of-frame constructs. We show that the S9 SKR tail prevents both the +1 and -1 frameshifts and plays a general role in holding the P-site tRNA/peptidyl-tRNA in place. In contrast, the G966 and C967 methylations did not make a direct contribution to the maintenance of the translational frame of an mRNA. However, deletion of rsmB in the S9 Delta 3 background caused significantly increased -1 frameshifting at 37 degrees C. Interestingly, the effects of the deficiency of C967 methylation were annulled when the E. coli strain was grown at 30 degrees C, supporting its context-dependent role.

A Guided Wave approach for the detection of damage in a structure having elements with periodic damage

A wave propagation based approach for the detection of damage in components of structures having periodic damage has been proposed. Periodic damage pattern may arise in a structure due to periodicity in geometry and in loading. The method exploits the Block-Floquet band formation mechanism, a feature specific to structures with periodicity, to identify propagation bands (pass bands) and attenuation bands (stop bands) at different frequency ranges. The presence of damage modifies the wave propagation behaviour forming these bands. With proper positioning of sensors a damage force indicator (DFI) method can be used to locate the defect at an accuracy level of sensor to sensor distance. A wide range of transducer frequency may be used to obtain further information about the shape and size of the damage. The methodology is demonstrated using a few 1-D structures with different kinds of periodicity and damage. For this purpose, dynamic stiffness matrix is formed for the periodic elements to obtain the dispersion relationship using frequency domain spectral element and spectral super element method. The sensitivity of the damage force indicator for different types of periodic damages is also analysed.

Codes for solving three dimensional linear elastostatic problems using constant boundary elements while ignoring body forces

Three codes, that can solve three dimensional linear elastostatic problems using constant boundary elements while ignoring body forces, are provided here. The file 'bemconst.m' contains a MATLAB code for solving three dimensional linear elastostatic problems using constant boundary elements while ignoring body forces. The file 'bemconst.f90' is a Fortran translation of the MATLAB code contained in the file 'bemconst.m'. The file 'bemconstp.f90' is a parallelized version of the Fortran code contained in the file 'bemconst.f90'. The file 'inbem96.txt' is the input file for the Fortran codes contained in the files 'bemconst.f90' and 'bemconstp.f90'. Author hereby declares that the present codes are the original works of the author. Further, author hereby declares that any of the present codes, in full or in part, is not a translation or a copy of any of the existing codes written by someone else. Author's institution (Indian Institute of Science) has informed the author in writing that the institution is not interested in claiming any copyright on the present codes. Author is hereby distributing the present codes under the MIT License; full text of the license is included in each of the files that contain the codes.

Upper bound solution for pullout capacity of vertical anchors in sand using finite elements and limit analysis

The horizontal pullout capacity of vertical anchors embedded in sand has been determined by using an upper bound theorem of the limit analysis in combination with finite elements. The numerical results are presented in nondimensional form to determine the pullout resistance for various combinations of embedment ratio of the anchor (H/B), internal friction angle (ϕ) of sand, and the anchor-soil interface friction angle (δ). The pullout resistance increases with increases in the values of embedment ratio, friction angle of sand and anchor-soil interface friction angle. As compared to earlier reported solutions in literature, the present solution provides a better upper bound on the ultimate collapse load.

A MatLAB Based Virtual Phantom for 2D Electrical Impedance Tomography (MatVP2DEIT): Studying the Medical Electrical Impedance Tomography Reconstruction in Computer

Electrical Impedance Tomography (EIT) is a computerized medical imaging technique which reconstructs the electrical impedance images of a domain under test from the boundary voltage-current data measured by an EIT electronic instrumentation using an image reconstruction algorithm. Being a computed tomography technique, EIT injects a constant current to the patient's body through the surface electrodes surrounding the domain to be imaged (Omega) and tries to calculate the spatial distribution of electrical conductivity or resistivity of the closed conducting domain using the potentials developed at the domain boundary (partial derivative Omega). Practical phantoms are essentially required to study, test and calibrate a medical EIT system for certifying the system before applying it on patients for diagnostic imaging. Therefore, the EIT phantoms are essentially required to generate boundary data for studying and assessing the instrumentation and inverse solvers a in EIT. For proper assessment of an inverse solver of a 2D EIT system, a perfect 2D practical phantom is required. As the practical phantoms are the assemblies of the objects with 3D geometries, the developing of a practical 2D-phantom is a great challenge and therefore, the boundary data generated from the practical phantoms with 3D geometry are found inappropriate for assessing a 2D inverse solver. Furthermore, the boundary data errors contributed by the instrumentation are also difficult to separate from the errors developed by the 3D phantoms. Hence, the errorless boundary data are found essential to assess the inverse solver in 2D EIT. In this direction, a MatLAB-based Virtual Phantom for 2D EIT (MatVP2DEIT) is developed to generate accurate boundary data for assessing the 2D-EIT inverse solvers and the image reconstruction accuracy. MatVP2DEIT is a MatLAB-based computer program which simulates a phantom in computer and generates the boundary potential data as the outputs by using the combinations of different phantom parameters as the inputs to the program. Phantom diameter, inhomogeneity geometry (shape, size and position), number of inhomogeneities, applied current magnitude, background resistivity, inhomogeneity resistivity all are set as the phantom variables which are provided as the input parameters to the MatVP2DEIT for simulating different phantom configurations. A constant current injection is simulated at the phantom boundary with different current injection protocols and boundary potential data are calculated. Boundary data sets are generated with different phantom configurations obtained with the different combinations of the phantom variables and the resistivity images are reconstructed using EIDORS. Boundary data of the virtual phantoms, containing inhomogeneities with complex geometries, are also generated for different current injection patterns using MatVP2DEIT and the resistivity imaging is studied. The effect of regularization method on the image reconstruction is also studied with the data generated by MatVP2DEIT. Resistivity images are evaluated by studying the resistivity parameters and contrast parameters estimated from the elemental resistivity profiles of the reconstructed phantom domain. Results show that the MatVP2DEIT generates accurate boundary data for different types of single or multiple objects which are efficient and accurate enough to reconstruct the resistivity images in EIDORS. The spatial resolution studies show that, the resistivity imaging conducted with the boundary data generated by MatVP2DEIT with 2048 elements, can reconstruct two circular inhomogeneities placed with a minimum distance (boundary to boundary) of 2 mm. It is also observed that, in MatVP2DEIT with 2048 elements, the boundary data generated for a phantom with a circular inhomogeneity of a diameter less than 7% of that of the phantom domain can produce resistivity images in EIDORS with a 1968 element mesh. Results also show that the MatVP2DEIT accurately generates the boundary data for neighbouring, opposite reference and trigonometric current patterns which are very suitable for resistivity reconstruction studies. MatVP2DEIT generated data are also found suitable for studying the effect of the different regularization methods on reconstruction process. Comparing the reconstructed image with an original geometry made in MatVP2DEIT, it would be easier to study the resistivity imaging procedures as well as the inverse solver performance. Using the proposed MatVP2DEIT software with modified domains, the cross sectional anatomy of a number of body parts can be simulated in PC and the impedance image reconstruction of human anatomy can be studied.

REDUCING COMPUTATIONAL EFFORT IN SOLVING GEOMECHANICS PROBLEMS WITH UPPER BOUND FINITE ELEMENTS LIMIT ANALYSIS AND LINEAR OPTIMIZATION

This paper presents a simple technique for reducing the computational effort while solving any geotechnical stability problem by using the upper bound finite element limit analysis and linear optimization. In the proposed method, the problem domain is discretized into a number of different regions in which a particular order (number of sides) of the polygon is chosen to linearize the Mohr-Coulomb yield criterion. A greater order of the polygon needs to be selected only in that region wherein the rate of the plastic strains becomes higher. The computational effort required to solve the problem with this implementation reduces considerably. By using the proposed method, the bearing capacity has been computed for smooth and rough strip footings and the results are found to be quite satisfactory.

Geochemical behaviour of dissolved trace elements in a monsoon-dominated tropical river basin, Southwestern India

The study presents a 3-year time series data on dissolved trace elements and rare earth elements (REEs) in a monsoon-dominated river basin, the Nethravati River in tropical Southwestern India. The river basin lies on the metamorphic transition boundary which separates the Peninsular Gneiss and Southern Granulitic province belonging to Archean and Tertiary-Quaternary period (Western Dharwar Craton). The basin lithology is mainly composed of granite gneiss, charnockite and metasediment. This study highlights the importance of time series data for better estimation of metal fluxes and to understand the geochemical behaviour of metals in a river basin. The dissolved trace elements show seasonality in the river water metal concentrations forming two distinct groups of metals. First group is composed of heavy metals and minor elements that show higher concentrations during dry season and lesser concentrations during the monsoon season. Second group is composed of metals belonging to lanthanides and actinides with higher concentration in the monsoon and lower concentrations during the dry season. Although the metal concentration of both the groups appears to be controlled by the discharge, there are important biogeochemical processes affecting their concentration. This includes redox reactions (for Fe, Mn, As, Mo, Ba and Ce) and pH-mediated adsorption/desorption reactions (for Ni, Co, Cr, Cu and REEs). The abundance of Fe and Mn oxyhydroxides as a result of redox processes could be driving the geochemical redistribution of metals in the river water. There is a Ce anomaly (Ce/Ce*) at different time periods, both negative and positive, in case of dissolved phase, whereas there is positive anomaly in the particulate and bed sediments. The Ce anomaly correlates with the variations in the dissolved oxygen indicating the redistribution of Ce between particulate and dissolved phase under acidic to neutral pH and lower concentrations of dissolved organic carbon. Unlike other tropical and major world rivers, the effect of organic complexation on metal variability is negligible in the Nethravati River water.

Solving Axisymmetric Stability Problems by Using Upper Bound Finite Elements, Limit Analysis, and Linear Optimization

A numerical formulation has been proposed for solving an axisymmetric stability problem in geomechanics with upper bound limit analysis, finite elements, and linear optimization. The Drucker-Prager yield criterion is linearized by simulating a sphere with a circumscribed truncated icosahedron. The analysis considers only the velocities and plastic multiplier rates, not the stresses, as the basic unknowns. The formulation is simple to implement, and it has been employed for finding the collapse loads of a circular footing placed over the surface of a cohesive-frictional material. The formulation can be used to solve any general axisymmetric geomechanics stability problem.

Novel Rearrangements in the Staphylococcal Cassette Chromosome Mec Type V Elements of Indian ST772 and ST672 Methicillin Resistant Staphylococcus aureus Strains

Staphylococcus aureus is a commensal gram positive bacteria which causes severe and non severe infections in humans and livestock. In India, ST772 is a dominant and ST672 is an emerging clone of Staphylococcus aureus. Both cause serious human diseases, and carry type V SCCmec elements. The objective of this study was to characterize SCCmec type V elements of ST772 and ST672 because the usual PCR methods did not amplify all primers specific to the type. Whole genome sequencing analysis of seven ST772 and one ST672 S. aureus isolates revealed that the SCCmec elements of six of the ST772 isolates were the smallest of the extant type V elements and in addition have several other novel features. Only one ST772 isolate and the ST672 isolate carried bigger SCCmec cassettes which were composites carrying multiple ccrC genes. These cassettes had some similarities to type V SCCmec element from M013 isolate (ST59) from Taiwan in certain aspects. SCCmec elements of all Indian isolates had an inversion of the mec complex, similar to the bovine SCCmec type X. This study reveals that six out of seven ST772 S. aureus isolates have a novel type V (5C2) SCCmec element while one each of ST772 and ST672 isolates have a composite SCCmec type V element (5C2&5) formed by the integration of type V SCCmec into a MSSA carrying a SCC element, in addition to the mec gene complex inversions and extensive recombinations.

Synthesis, properties and applications of graphene doped with boron, nitrogen and other elements

Chemical doping of graphene becomes necessary to create a band gap which is useful for various applications. Furthermore, chemical doping of elements like boron and nitrogen in graphene gives rise to useful properties. Since chemically doped graphene is both of academic and technical importance, we have prepared this article on the present status of various aspects of this important class of materials. In doing so, we have covered the recent literature on this subject citing all the major references. Some of the aspects that we have covered are the synthesis of chemically doped graphene followed by properties and applications. The applications discussed relate to gas adsorption, lithium batteries, supercapacitors, oxygen reduction reaction, field emission and photochemical water splitting. Characterization of chemically doped graphene also included. We believe that the article will be useful to all those interested in graphene and related materials and provides the present status of the subject. (C) 2014 Elsevier Ltd. All rights reserved.

Finite element analysis of free vibration of the delaminated composite plate with variable kinematic multilayered plate elements

Composite laminates are prone to delamination. Implementation of delamination in the Carrera Unified Formulation frame work using nine noded quadrilateral MITC9 element is discussed in this article. MITC9 element is devoid of shear locking and membrane locking. Delaminated as well as healthy structure is analyzed for free mode vibration. The results from the present work are compared with the available experimental or/and research article or/and the three dimensional finite element simulations. The effect of different kinds and different percentages of area of delamination on the first three natural frequencies of the structure is discussed. The presence of open-mode delamination mode shape for large delaminations within the first three natural frequencies is discussed. Also, the switching of places between the second bending mode, with that of the first torsional mode frequency is discussed. Results obtained from different ordered theories are compared in the presence of delamination. Advantage of layerwise theories as compared to equivalent single layer theories for very large delaminations is stated. The effect of different kinds of delamination and their effect on the second bending and first torsional mode shape is discussed. (C) 2014 Elsevier Ltd. All rights reserved.

Mixed finite elements for electromagnetic analysis

The occurrence of spurious solutions is a well-known limitation of the standard nodal finite element method when applied to electromagnetic problems. The two commonly used remedies that are used to address this problem are (i) The addition of a penalty term with the penalty factor based on the local dielectric constant, and which reduces to a Helmholtz form on homogeneous domains (regularized formulation); (ii) A formulation based on a vector and a scalar potential. Both these strategies have some shortcomings. The penalty method does not completely get rid of the spurious modes, and both methods are incapable of predicting singular eigenvalues in non-convex domains. Some non-zero spurious eigenvalues are also predicted by these methods on non-convex domains. In this work, we develop mixed finite element formulations which predict the eigenfrequencies (including their multiplicities) accurately, even for nonconvex domains. The main feature of the proposed mixed finite element formulation is that no ad-hoc terms are added to the formulation as in the penalty formulation, and the improvement is achieved purely by an appropriate choice of finite element spaces for the different variables. We show that the formulation works even for inhomogeneous domains where `double noding' is used to enforce the appropriate continuity requirements at an interface. For two-dimensional problems, the shape of the domain can be arbitrary, while for the three-dimensional ones, with our current formulation, only regular domains (which can be nonconvex) can be modeled. Since eigenfrequencies are modeled accurately, these elements also yield accurate results for driven problems. (C) 2014 Elsevier Ltd. All rights reserved.

Beyond classical dynamic structural plasticity using mesh-free modelling techniques

The problem of modelling the transient response of an elastic-perfectly-plastic cantilever beam, carrying an impulsively loaded tip mass, is,often referred to as the Parkes cantilever problem 25]; The permanent deformation of a cantilever struck transversely at its tip, Proc. R. Soc. A., 288, pp. 462). This paradigm for classical modelling of projectile impact on structures is re-visited and updated using the mesh-free method, smoothed particle hydrodynamics (SPH). The purpose of this study is to investigate further the behaviour of cantilever beams subjected to projectile impact at its tip, by considering especially physically real effects such as plastic shearing close to the projectile, shear deformation, and the variation of the shear strain along the length and across the thickness of the beam. Finally, going beyond macroscopic structural plasticity, a strategy to incorporate physical discontinuity (due to crack formation) in SPH discretization is discussed and explored in the context of tip-severance of the cantilever beam. Consequently, the proposed scheme illustrates the potency for a more refined treatment of penetration mechanics, paramount in the exploration of structural response under ballistic loading. The objective is to contribute to formulating a computational modelling framework within which transient dynamic plasticity and even penetration/failure phenomena for a range of materials, structures and impact conditions can be explored ab initio, this being essential for arriving at suitable tools for the design of armour systems. (C) 2014 Elsevier Ltd. All rights reserved.

Optimal error estimate using mesh equidistribution technique for singularly perturbed system of reaction-diffusion boundary-value problems

In this article, we study the problem of determining an appropriate grading of meshes for a system of coupled singularly perturbed reaction-diffusion problems having diffusion parameters with different magnitudes. The central difference scheme is used to discretize the problem on adaptively generated mesh where the mesh equation is derived using an equidistribution principle. An a priori monitor function is obtained from the error estimate. A suitable a posteriori analogue of this monitor function is also derived for the mesh construction which will lead to an optimal second-order parameter uniform convergence. We present the results of numerical experiments for linear and semilinear reaction-diffusion systems to support the effectiveness of our preferred monitor function obtained from theoretical analysis. (C) 2014 Elsevier Inc. All rights reserved.