Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

Background: mIHF belongs to a subfamily of proteins, distinct from E. coli IHF. Results: Functionally important amino acids of mIHF and the mechanism(s) underlying DNA binding, DNA bending, and site-specific recombination are distinct from that of E. coli IHF. Conclusion: mIHF functions could contribute beyond nucleoid compaction. Significance: Because mIHF is essential for growth, the molecular mechanisms identified here can be exploited in drug screening efforts. The annotated whole-genome sequence of Mycobacterium tuberculosis revealed that Rv1388 (Mtihf) is likely to encode for a putative 20-kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or the organization of the mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg-170, Arg-171, and Arg-173, which might be involved in DNA binding, and a conserved proline (Pro-150) in the tight turn. The phenotypic sensitivity of Escherichia coli ihfA and ihfB strains to UV and methyl methanesulfonate could be complemented with the wild-type Mtihf but not its alleles bearing mutations in the DNA-binding residues. Protein-DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, binds with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHF. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes DNA compaction into nucleoid-like or higher order filamentous structures. We therefore propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins.

Path Following Using Trajectory Shaping Guidance

Unmanned vehicle path following by pursuing a virtual target moving along the path is considered. Limitations for pure pursuit guidance are analyzed while following the virtual target on curved paths. Trajectory shaping guidance is proposed as an alternate guidance scheme for a general curvature path. It is proven that under certain tenable assumptions trajectory shaping guidance yields an identical path as that of the virtual target. By linear analysis it is shown that the convergence to the path for trajectory shaping guidance is twice as fast as pure pursuit. Simulations highlight significant improvement in position errors by using trajectory shaping guidance. Comparative simulation studies comply with analytic findings and present better performance as compared with pure pursuit and a nonlinear guidance methodology from the literature. Experimental validation supports the analytic and simulations studies as the guidance laws are implemented on a radio-controlled car in a laboratory environment.

Membrane-based deformable mirror: intrinsic aberrations and alignment issues

A deformable mirror (DM) is an important component of an adaptive optics system. It is known that an on-axis spherical/parabolic optical component, placed at an angle to the incident beam introduces defocus as well as astigmatism in the image plane. Although the former can be compensated by changing the focal plane position, the latter cannot be removed by mere optical realignment. Since the DM is to be used to compensate a turbulence-induced curvature term in addition to other aberrations, it is necessary to determine the aberrations induced by such (curved DM surface) an optical element when placed at an angle (other than 0 deg) of incidence in the optical path. To this effect, we estimate to a first order the aberrations introduced by a DM as a function of the incidence angle and deformation of the DM surface. We record images using a simple setup in which the incident beam is reflected by a 37 channel micro-machined membrane deformable mirror for various angles of incidence. It is observed that astigmatism is a dominant aberration, which was determined by measuring the difference between the tangential and sagittal focal planes. We justify our results on the basis of theoretical simulations and discuss the feasibility of using such a system for adaptive optics considering a trade-off between wavefront correction and astigmatism due to deformation. (C) 2015 Optical Society of America

HCN channels enhance spike phase coherence and regulate the phase of spikes and LFPs in the theta-frequency range

What are the implications for the existence of subthreshold ion channels, their localization profiles, and plasticity on local field potentials (LFPs)? Here, we assessed the role of hyperpolarization-activated cyclic-nucleotide-gated (HCN) channels in altering hippocampal theta-frequency LFPs and the associated spike phase. We presented spatiotemporally randomized, balanced theta-modulated excitatory and inhibitory inputs to somatically aligned, morphologically realistic pyramidal neuron models spread across a cylindrical neuropil. We computed LFPs from seven electrode sites and found that the insertion of an experimentally constrained HCN-conductance gradient into these neurons introduced a location- dependent lead in the LFP phase without significantly altering its amplitude. Further, neurons fired action potentials at a specific theta phase of the LFP, and the insertion of HCN channels introduced large lags in this spike phase and a striking enhancement in neuronal spike-phase coherence. Importantly, graded changes in either HCN conductance or its half-maximal activation voltage resulted in graded changes in LFP and spike phases. Our conclusions on the impact of HCN channels on LFPs and spike phase were invariant to changes in neuropil size, to morphological heterogeneity, to excitatory or inhibitory synaptic scaling, and to shifts in the onset phase of inhibitory inputs. Finally, we selectively abolished the inductive lead in the impedance phase introduced by HCN channels without altering neuronal excitability and found that this inductive phase lead contributed significantly to changes in LFP and spike phase. Our results uncover specific roles for HCN channels and their plasticity in phase-coding schemas and in the formation and dynamic reconfiguration of neuronal cell assemblies.

Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

The annotated whole-genome sequence of Mycobacterium tuberculosis indicated that Rv1388 (Mtihf) likely encodes a putative 20 kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or organization of mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF-duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg170, Arg171, and Arg173, which might be involved in DNA binding, and a conserved proline (P150) in the tight turn. The phenotypic sensitivity of Escherichia coli Delta ihfA and Delta ihfB strains to UV and methylmethanesulfonate could be complemented with the wild-type Mtihf, but not its alleles bearing mutations in the DNA-binding residues. Protein DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, bind with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHF alpha beta. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes compaction of DNA into nucleoid-like or higher-order filamentous structures. We hence propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins.

Phase-field elasticity model based on mechanical jump conditions

Computational models based on the phase-field method typically operate on a mesoscopic length scale and resolve structural changes of the material and furthermore provide valuable information about microstructure and mechanical property relations. An accurate calculation of the stresses and mechanical energy at the transition region is therefore indispensable. We derive a quantitative phase-field elasticity model based on force balance and Hadamard jump conditions at the interface. Comparing the simulated stress profiles calculated with Voigt/Taylor (Annalen der Physik 274(12):573, 1889), Reuss/Sachs (Z Angew Math Mech 9:49, 1929) and the proposed model with the theoretically predicted stress fields in a plate with a round inclusion under hydrostatic tension, we show the quantitative characteristics of the model. In order to validate the elastic contribution to the driving force for phase transition, we demonstrate the absence of excess energy, calculated by Durga et al. (Model Simul Mater Sci Eng 21(5):055018, 2013), in a one-dimensional equilibrium condition of serial and parallel material chains. To validate the driving force for systems with curved transition regions, we relate simulations to the Gibbs-Thompson equilibrium condition

Photoresponse of double-stacked graphene to Infrared radiation

We report the photoresponse of stacked graphene layers towards infrared radiation. Graphene is stacked in two configurations, namely, crossed and parallel layers. Raman analysis demonstrated a strong interaction among the stacked graphene layers. Graphene in the crossed configuration exhibited the presence of both negative and positive conductivities; however, other configurations of graphene exhibited positive conductivity only. The presence of negative photoconductivity is proposed to be due to oxygen or oxygen-related functional group absorbents that are trapped in between two monolayers of graphene and act as scattering centers for free carriers. An interesting trend is reported in differential conductivity when stacked layers are compared with multilayers and parallel-stacked graphene layers.

Integrating AlGaN/GaN high electron mobility transistor with Si: A comparative study of integration schemes

AlGaN/GaN high electron mobility transistor stacks deposited on a single growth platform are used to compare the most common transition, AlN to GaN, schemes used for integrating GaN with Si. The efficiency of these transitions based on linearly graded, step graded, interlayer, and superlattice schemes on dislocation density reduction, stress management, surface roughness, and eventually mobility of the 2D-gas are evaluated. In a 500 nm GaN probe layer deposited, all of these transitions result in total transmission electron microscopy measured dislocations densities of 1 to 3 x 10(9)/cm(2) and <1 nm surface roughness. The 2-D electron gas channels formed at an AlGaN-1 nm AlN/GaN interface deposited on this GaN probe layer all have mobilities of 1600-1900 cm(2)/V s at a carrier concentration of 0.7-0.9 x 10(13)/cm(2). Compressive stress and changes in composition in GaN rich regions of the AlN-GaN transition are the most effective at reducing dislocation density. Amongst all the transitions studied the step graded transition is the one that helps to implement this feature of GaN integration in the simplest and most consistent manner. (C) 2015 AIP Publishing LLC.

An automatic algorithm for mixed mode crack growth rate based on drop potential method

A new automatic algorithm for the assessment of mixed mode crack growth rate characteristics is presented based on the concept of an equivalent crack. The residual ligament size approach is introduced to implementation this algorithm for identifying the crack tip position on a curved path with respect to the drop potential signal. The automatic algorithm accounting for the curvilinear crack trajectory and employing an electrical potential difference was calibrated with respect to the optical measurements for the growing crack under cyclic mixed mode loading conditions. The effectiveness of the proposed algorithm is confirmed by fatigue tests performed on ST3 steel compact tension-shear specimens in the full range of mode mixities from pure mode Ito pure mode II. (C) 2015 Elsevier Ltd. All rights reserved.

Stability analysis of thick piezoelectric metal based FGM plate using first order and higher order shear deformation theory

This paper presents the stability analysis of functionally graded plate integrated with piezoelectric actuator and sensor at the top and bottom face, subjected to electrical and mechanical loading. The finite element formulation is based on first order and higher order shear deformation theory, degenerated shell element, von-Karman hypothesis and piezoelectric effect. The equation for static analysis is derived by using the minimum energy principle and solutions for critical buckling load is obtained by solving eigenvalue problem. The material properties of the functionally graded plate are assumed to be graded along the thickness direction according to simple power law function. Two types of boundary conditions are used, such as SSSS (simply supported) and CSCS (simply supported along two opposite side perpendicular to the direction of compression and clamped along the other two sides). Sensor voltage is calculated using present analysis for various power law indices and FG (functionally graded) material gradations. The stability analysis of piezoelectric FG plate is carried out to present the effects of power law index, material variations, applied mechanical pressure and piezo effect on buckling and stability characteristics of FG plate.

In-plane elastic responses of circular cell honeycombs and bundled circular tubes in a diamond array structure

Assemblages of circular tubes and circular honeycombs in close packed arrangement are presently both competing and complementing regular honeycomb structures (HCS). The intrinsic isotropy of bundled tubes/rings in hexagonal arrays restricts their use to applications with isotopic need. With the aim of extending the utility of tubes/rings assemblages to anisotropic needs, this paper explores the prospects of bundled tubes and circular honeycombs in a general diamond array structure (DAS) to cater these needs. To this end, effective transverse Young's moduli and Poisson's ratio for thick/thin DAS are obtained theoretically. Analysis frameworks including thin ring theory (TRT), curved beam theory (CBT) and elasticity formulations are tested and corroborated by FEA employing contact elements. Results indicate that TRT and CBT are reasonable for thin tubes and honeycombs. Nevertheless, TRT yields compact formulae to study the anisotropy ratio, moduli spectrum and sensitivity of the assemblage as a function of thicknesses and array structure. These formulae supplement designers as a guide to tailor the structures. On the other hand, elasticity formulation can estimate over a larger range including very thick tubes/rings. In addition, this formulation offers to estimate refined transverse strengths of assemblages. (C) 2015 Elsevier Ltd. All rights reserved.

In-plane effective shear modulus of generalized circular honeycomb structures and bundled tubes in a diamond array structure

Use of circular hexagonal honeycomb structures and tube assemblies in energy absorption systems has attracted a large number of literature on their characterization under crushing and impact loads. Notwithstanding these, effective shear moduli (G*) required for complete transverse elastic characterization and in analyses of hierarchical structures have received scant attention. In an attempt to fill this void, the present study undertakes to evaluate G* of a generalized circular honeycomb structures and tube assemblies in a diamond array structure (DAS) with no restriction on their thickness. These structures present a potential to realize a spectrum of moduli with minimal modifications, a point of relevance for manufactures and designers. To evaluate G* in this paper, models based on technical theories - thin ring theory and curved beam theory - and rigorous theory of elasticity are investigated and corroborated with FEA employing contact elements. Technical theories which give a good match for thin HCS offer compact expressions for moduli which can be harvested to study sensitivity of moduli on topology. On the other hand, elasticity model offers a very good match over a large range of thickness along with exact analysis of stresses by employing computationally efficient expressions. (C) 2015 Elsevier Ltd. All rights reserved.

Quantitative In Situ Analysis of Deformation in Sliding Metals: Effect of Initial Strain State

Using in situ, high-speed imaging of a hard wedge sliding against pure aluminum, and image analysis by particle image velocimetry, the deformation field in sliding is mapped at high resolution. This model system is representative of asperity contacts on engineered surfaces and die-workpiece contacts in deformation and machining processes. It is shown that large, uniform plastic strains of 1-5 can be imposed at the Al surface, up to depths of 500 mu m, under suitable sliding conditions. The spatial strain and strain rate distributions are significantly influenced by the initial deformation state of the Al, e.g., extent of work hardening, and sliding incidence angle. Uniform straining occurs only under conditions of steady laminar flow in the metal. Large pre-strains and higher sliding angles promote breakdown in laminar flow due to surface fold formation or flow localization in the form of shear bands, thus imposing limits on uniform straining by sliding. Avoidance of unsteady sliding conditions, and selection of parameters like sliding angle, thus provides a way to control the deformation field. Key characteristics of the sliding deformation such as strain and strain rate, laminar flow, folding and prow formation are well predicted by finite element simulation. The deformation field provides a quantitative basis for interpreting wear particle formation. Implications for engineering functionally graded surfaces, sliding wear and ductile failure in metals are discussed.

Fracture Testing at Small-Length Scales: From Plasticity in Si to Brittleness in Pt

The field of micro-/nano-mechanics of materials has been driven, on the one hand by the development of ever smaller structures in devices, and, on the other, by the need to map property variations in large systems that are microstructurally graded. Observations of `smaller is stronger' have also brought in questions of accompanying fracture property changes in the materials. In the wake of scattered articles on micro-scale fracture testing of various material classes, this review attempts to provide a holistic picture of the current state of the art. In the process, various reliable micro-scale geometries are shown, challenges with respect to instrumentation to probe ever smaller length scales are discussed and examples from recent literature are put together to exhibit the expanse of unusual fracture response of materials, from ductility in Si to brittleness in Pt. Outstanding issues related to fracture mechanics of small structures are critically examined for plausible solutions.

A peridynamic theory for linear elastic shells

A state-based peridynamic formulation for linear elastic shells is presented. The emphasis is on introducing, possibly for the first time, a general surface based peridynamic model to represent the deformation characteristics of structures that have one geometric dimension much smaller than the other two. A new notion of curved bonds is exploited to cater for force transfer between the peridynamic particles describing the shell. Starting with the three dimensional force and deformation states, appropriate surface based force, moment and several deformation states are arrived at. Upon application on the curved bonds, such states yield the necessary force and deformation vectors governing the motion of the shell. By incorporating a shear correction factor, the formulation also accommodates analysis of shells that have higher thickness. In order to attain this, a consistent second order approximation to the complementary energy density is considered and incorporated in peridynamics via constitutive correspondence. Unlike the uncoupled constitution for thin shells, a consequence of a first order approximation, constitutive relations for thick shells are fully coupled in that surface wryness influences the in-plane stress resultants and surface strain the moments. Our proposal on the peridynamic shell theory is numerically assessed against simulations on static deformation of spherical and cylindrical shells, that of flat plates and quasi-static fracture propagation in a cylindrical shell. (C) 2016 Elsevier Ltd. All rights reserved.