Re-analysis of cryoEM data on HCV IRES bound to 40S subunit of human ribosome integrated with recent structural information suggests new contact regions between ribosomal proteins and HCV RNA

In this study, we combine available high resolution structural information on eukaryotic ribosomes with low resolution cryo-EM data on the Hepatitis C Viral RNA (IRES) human ribosome complex. Aided further by the prediction of RNA-protein interactions and restrained docking studies, we gain insights on their interaction at the residue level. We identified the components involved at the major and minor contact regions, and propose that there are energetically favorable local interactions between 40S ribosomal proteins and IRES domains. Domain II of the IRES interacts with ribosomal proteins S5 and S25 while the pseudoknot and the downstream domain IV region bind to ribosomal proteins S26, S28 and S5. We also provide support using UV cross-linking studies to validate our proposition of interaction between the S5 and IRES domains II and IV. We found that domain IIIe makes contact with the ribosomal protein S3a (S1e). Our model also suggests that the ribosomal protein S27 interacts with domain IIIc while S7 has a weak contact with a single base RNA bulge between junction IIIabc and IIId. The interacting residues are highly conserved among mammalian homologs while IRES RNA bases involved in contact do not show strict conservation. IRES RNA binding sites for S25 and S3a show the best conservation among related viral IRESs. The new contacts identified between ribosomal proteins and RNA are consistent with previous independent studies on RNA-binding properties of ribosomal proteins reported in literature, though information at the residue level is not available in previous studies.

Large deformation dynamic finite element analysis of delaminated composite plates using contact-impact conditions

A new C-0 composite plate finite element based on Reddy's third order theory is used for large deformation dynamic analysis of delaminated composite plates. The inter-laminar contact is modeled with an augmented Lagrangian approach. Numerical results show that the widely used ``unconditionally stable'' beta-Newmark method presents instability problems in the transient simulation of delaminated composite plate structures with large deformation. To overcome this instability issue, an energy and momentum conserving composite implicit time integration scheme presented by Bathe and Baig is used. It is found that a proper selection of the penalty parameter is very crucial in the contact simulation. (C) 2014 Elsevier Ltd. All rights reserved.

Transitory second-order reciprocal connection for two surfaces in point contact

This paper investigates the instantaneous spatial higher pair to lower pair substitute-connection which is kinematically equivalent up to acceleration analysis for two smooth surfaces in point contact. The existing first-order equivalent substitute-connection consisting of a Hooke's joint (U-joint) and a spherical joint (S-joint) connected by an additional link is extended up to second-order. A two step procedure is chalked out for achieving this equivalence. First, the existing method is employed for velocity equivalence. In the second step, the two centers of substitution are obtained as a conjugate relationship involving the principal normal curvatures of the surfaces at the contact point and the screw coordinates of the instantaneous screw axis (ISA) of the first-order relative motion. Unlike the classical planar replacement, this particular substitution cannot be done by merely examining the profiles of the contacting surfaces. An illustrative example of a three-link direct-contact mechanism is presented. (C) 2014 Elsevier Ltd. All rights reserved.

Sphere to ring morphological transformation in drying nanofluid droplets in a contact-free environment

Understanding the transients of buckling in drying colloidal suspensions is pivotal for producing new functional microstructures with tunable morphologies. Here, we report first observations and elucidate the buckling instability induced morphological transition (sphere to ring structure) in an acoustically levitated, heated nanosuspension droplet using dynamic energy balance. Droplet deformation featuring the formation of symmetric cavities is initiated by capillary pressure that is two to three orders of magnitude greater than the acoustic radiation pressure, thus indicating that the standing pressure field has no influence on the buckling front kinetics. With an increase in heat flux, the growth rate of surface cavities and their post-buckled volume increase while the buckling time period reduces, thereby altering the buckling pathway and resulting in distinct precipitate structures. However, irrespective of the heating rate, the volumetric droplet deformation exhibits a linear time dependence and the droplet vaporization is observed to deviate from the classical D-2-law.

Fracture in metallic glasses: mechanics and mechanisms

Significant progress in understanding the mechanical behavior of metallic glasses (MGs) was made over the past decade, particularly on mechanisms of plastic deformation. However, recent research thrust has been on exploring the mechanics and physics of fracture. MGs can be very brittle with K-Ic values similar to silicate glasses and ceramics or very tough with K-Ic akin to high toughness crystalline metals. Even the tough MGs can become brittle with structural relaxation following annealing at temperatures close to glass transition temperature (T-g). Detailed experimental studies coupled with complementary numerical simulations of the recent past have provided insights on the micromechanisms of failure as well as nature of crack tip fields, and established the governing fracture criteria for ductile and brittle glasses. In this paper, the above advances are reviewed and outstanding issues in the context of fracture of amorphous alloys that need to be resolved are identified.

Theoretical Insights to Niobium-Doped Monolayer MoS2-Gold Contact

We report a first principles study of the electronic properties for a contact formed between Nb-doped monolayer MoS2 and gold for different doping concentrations. We first focus on the shift of energy levels in band structure and the density of states with respect to the Fermi level for a geometrically optimized 5 x 5 MoS2 supercell for both pristine and Nb-doped structures. The doping is achieved by substituting Mo atoms with Nb atoms at random positions. It is observed that for an experimentally reported sheet hole doping concentration of (rho(2D)) 1.8 x 10(14) cm(-2), the pristine MoS2 converts to degenerate p-type semiconductor. Next, we interface this supercell with six layers of < 111 > cleaved surface of gold to investigate the contact nature of MoS2-Au system. By careful examination of projected band structure, projected density of states, effective potential and charge density difference, we demonstrate that the Schottky barrier nature observed for pure MoS2-Au contact can be converted from n-type to p-type by efficient Nb doping.

MODELING AND SIMULATION OF A THREE-WHEELED MOBILE ROBOT ON UNEVEN TERRAINS WITH TWO-DEGREE-OF-FREEDOM SUSPENSION MECHANISMS

A wheeled mobile robot (WMR) will move on an uneven terrain without slip if its torus-shaped wheels tilt in a lateral direction. An independent two degree-of-freedom (DOF) suspension is required to maintain contact with uneven terrain and for lateral tilting. This article deals with the modeling and simulation of a three-wheeled mobile robot with torus-shaped wheels and four novel two-DOF suspension mechanism concepts. Simulations are performed on an uneven terrain for three representative pathsa straight line, a circular, and an S'-shaped path. Simulations show that a novel concept using double four-bar mechanism performs better than the other three concepts.

Damage mechanisms in stainless steel and chromium carbide coatings under controlled environment fretting conditions

Fretting is of a serious concern in many industrial components, specifically, in nuclear industry for the safe and reliable operation of various component and/or system. Under fretting condition small amplitude oscillations induce surface degradation in the form of surface cracks and/or surface wear. Comprehensive experimental studies have been carried out simulating different fretting regimes under ambient and vacuum (10(-9) MPa) conditions and, temperature up to 400 degrees C. Studies have been carried out with stainless steel spheres on stainless steel flats, and stainless steel spheres against chromium carbide, with 25% nickel chrome binder coatings. Mechanical responses are correlated with the damage observed. It has been observed that adhesion plays a vital role in material degradation process, and its effectiveness depends on mechanical variables such as normal load, interfacial tangential displacement, characteristics of the contacting bodies and most importantly on the environment conditions. Material degradation mechanism for ductile materials involved severe plastic deformation, which results in the initiation or nucleation of cracks. Ratcheting has been observed as the governing damage mode for crack nucleation under cyclic tangential loading condition. Further, propagation of the cracks has been observed under fatigue and their orientation has been observed to be governed by the contact conditions prevailing at the contact interface. Coated surfaces show damage in the form of brittle fracture and spalling of the coatings. Existence of stick slip has been observed under high normal load and low displacement amplitude. It has also been observed that adhesion at the contact interface and instantaneous cohesive strength of the contacting bodies dictates the occurrence of material transfer. The paper discusses the mechanics and mechanisms involved in fretting damage under controlled environment conditions. (C) 2015 Elsevier B.V. All rights reserved.

Estimation of mechanical properties of single wall carbon nanotubes using molecular mechanics approach

Molecular mechanics based finite element analysis is adopted in the current work to evaluate the mechanical properties of Zigzag, Armchair and Chiral Single wall Carbon Nanotubes (SWCNT) of different diameters and chiralities. Three different types of atomic bonds, that is Carbon Carbon covalent bond and two types of Carbon Carbon van der Waals bonds are considered in the carbon nanotube system. The stiffness values of these bonds are calculated using the molecular potentials, namely Morse potential function and Lennard-Jones interaction potential function respectively and these stiffness's are assigned to spring elements in the finite element model of the CNT. The geometry of CNT is built using a macro that is developed for the finite element analysis software. The finite element model of the CNT is constructed, appropriate boundary conditions are applied and the behavior of mechanical properties of CNT is studied.

After transition in a soft-walled microchannel

In comparison to the flow in a rigid channel, there is a multifold reduction in the transition Reynolds number for the flow in a microchannel when one of the walls is made sufficiently soft, due to a dynamical instability induced by the fluid-wall coupling, as shown by Verma & Kumaran (J. Fluid Mech., vol. 727, 2013, pp. 407-455). The flow after transition is characterised using particle image velocimetry in the x-y plane, where x is the streamwise direction and y is the cross-stream coordinate along the small dimension of the channel of height 0.2-0.3 mm. The flow after transition is characterised by a mean velocity profile that is flatter at the centre and steeper at the walls in comparison to that for a laminar flow. The root mean square of the streamwise fluctuating velocity shows a characteristic sharp increase away from the wall and a maximum close to the wall, as observed in turbulent flows in rigid-walled channels. However, the profile is asymmetric, with a significantly higher maximum close to the soft wall in comparison to that close to the hard wall, and the Reynolds stress is found to be non-zero at the soft wall, indicating that there is a stress exerted by fluid velocity fluctuations on the wall. The maximum of the root mean square of the velocity fluctuations and the Reynolds stress (divided by the fluid density) in the soft-walled microchannel for Reynolds numbers in the range 250-400, when scaled by suitable powers of the maximum velocity, are comparable to those in a rigid channel at Reynolds numbers in the range 5000-20 000. The near-wall velocity profile shows no evidence of a viscous sublayer for (y upsilon(*)/nu) as low as two, but there is a logarithmic layer for (y upsilon(*)/nu) up to approximately 30, where the von Karman constants are very different from those for a rigid-walled channel. Here, upsilon(*) is the friction velocity, nu is the kinematic viscosity and y is the distance from the soft surface. The surface of the soft wall in contact with the fluid is marked with dye spots to monitor the deformation and motion along the fluid-wall interface. Low-frequency oscillations in the displacement of the surface are observed after transition in both the streamwise and spanwise directions, indicating that the velocity fluctuations are dynamically coupled to motion in the solid.

Simulations of impinging droplets with surfactant-dependent dynamic contact angle

An arbitrary Lagrangian-Eulerian (ALE) finite element scheme for computations of soluble surfactant droplet impingement on a horizontal surface is presented. The numerical scheme solves the time-dependent Navier-Stokes equations for the fluid flow, scalar convection-diffusion equation for the surfactant transport in the bulk phase, and simultaneously, surface evolution equations for the surfactants on the free surface and on the liquid-solid interface. The effects of surfactants on the flow dynamics are included into the model through the surface tension and surfactant-dependent dynamic contact angle. In particular, the dynamic contact angle (theta(d)) of the droplet is defined as a function of the surfactant concentration at the contact line and the equilibrium contact angle (theta(0)(e)) of the clean surface using the nonlinear equation of state for surface tension. Further, the surface forces are included into the model as surface divergence of the surface stress tensor that allows to incorporate the Marangoni effects without calculating the surface gradient of the surfactant concentration on the free surface. In addition to a mesh convergence study and validation of the numerical results with experiments, the effects of adsorption and desorption surfactant coefficients on the flow dynamics in wetting, partially wetting and non-wetting droplets are studied in detail. It is observed that the effects of surfactants are more in wetting droplets than in the non-wetting droplets. Further, the presence of surfactants at the contact line reduces the equilibrium contact angle further when theta(0)(e) is less than 90 degrees, and increases it further when theta(0)(e) is greater than 90 degrees. Nevertheless, the presence of surfactants has no effect on the contact angle when theta(0)(e) = 90 degrees. The numerical study clearly demonstrates that the surfactant-dependent contact angle has to be considered, in addition to the Marangoni effect, in order to study the flow dynamics and the equilibrium states of surfactant droplet impingement accurately. The proposed numerical scheme guarantees the conservation of fluid mass and of the surfactant mass accurately. (C) 2015 Elsevier Inc. All rights reserved.

Handling large variations in mechanics: Some applications

There is a need to use probability distributions with power-law decaying tails to describe the large variations exhibited by some of the physical phenomena. The Weierstrass Random Walk (WRW) shows promise for modeling such phenomena. The theory of anomalous diffusion is now well established. It has found number of applications in Physics, Chemistry and Biology. However, its applications are limited in structural mechanics in general, and structural engineering in particular. The aim of this paper is to present some mathematical preliminaries related to WRW that would help in possible applications. In the limiting case, it represents a diffusion process whose evolution is governed by a fractional partial differential equation. Three applications of superdiffusion processes in mechanics, illustrating their effectiveness in handling large variations, are presented.

Physical Insights on the Ambiguous Metal-Graphene Interface and Proposal for Improved Contact Resistance

The ambiguous behavior of metal-graphene interface has been addressed in this paper using density functional theory and nonequilibrium Green's function formalism. For the first time, the fundamental chemistry of metal-graphene interface, in particular role of sp-hybridized and sp(2)-hybridized carbon atoms, has been emphasized and discussed in detail in this paper. It was discovered that the sp-hybridized sites at the edge of a graphene monolayer contribute to 40% of current conduction when compared with sp(2)-hybridized atom sites in the graphene-metal overlap region. Moreover, we highlighted the insignificance of an additional metal layer, i.e., sandwiched contact, due to lacking sp-hybridized carbon sites. A fundamental way of defining the contact resistance, while keeping chemical bonding in mind, has been proposed. The bonding insight has been further used to propose the novel ways of interfacing metal with graphene, which results in a 40% reduction in contact resistance.