DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins

Depth measures the extent of atom/residue burial within a protein. It correlates with properties such as protein stability, hydrogen exchange rate, protein-protein interaction hot spots, post-translational modification sites and sequence variability. Our server, DEPTH, accurately computes depth and solvent-accessible surface area (SASA) values. We show that depth can be used to predict small molecule ligand binding cavities in proteins. Often, some of the residues lining a ligand binding cavity are both deep and solvent exposed. Using the depth-SASA pair values for a residue, its likelihood to form part of a small molecule binding cavity is estimated. The parameters of the method were calibrated over a training set of 900 high-resolution X-ray crystal structures of single-domain proteins bound to small molecules (molecular weight < 1.5 KDa). The prediction accuracy of DEPTH is comparable to that of other geometry-based prediction methods including LIGSITE, SURFNET and Pocket-Finder (all with Matthew's correlation coefficient of similar to 0.4) over a testing set of 225 single and multi-chain protein structures. Users have the option of tuning several parameters to detect cavities of different sizes, for example, geometrically flat binding sites. The input to the server is a protein 3D structure in PDB format. The users have the option of tuning the values of four parameters associated with the computation of residue depth and the prediction of binding cavities. The computed depths, SASA and binding cavity predictions are displayed in 2D plots and mapped onto 3D representations of the protein structure using Jmol. Links are provided to download the outputs. Our server is useful for all structural analysis based on residue depth and SASA, such as guiding site-directed mutagenesis experiments and small molecule docking exercises, in the context of protein functional annotation and drug discovery.

Shock tunnel study of spiked aerodynamic bodies flying at hypersonic Mach numbers

A three-component accelerometer balance system is used to study the drag reduction effect of an aerodisc on large angle blunt cones flying at hypersonic Mach numbers. Measurements in a hypersonic shock tunnel at a freestream Mach number of 5.75 indicate more than 50% reduction in the drag coefficient for a 120degrees apex angle blunt cone with a forward facing aerospike having a flat faced aerodisc at moderate angles of attack. Enhancement of drag has been observed for higher angles of attack due to the impingement of the flow separation shock on the windward side of the cone. The flowfields around the large angle blunt cone with aerospike assembly flying at hypersonic Mach numbers are also simulated numerically using a commercial CFD code. The pressure and density levels on the model surface, which is under the aerodynamic shadow of the flat disc tipped spike, are found very low and a drag reduction of 64.34% has been deduced numerically.

Stability of fluid flow past a membrane

The stability of fluid flow past a membrane of infinitesimal thickness is analysed in the limit of zero Reynolds number using linear and weakly nonlinear analyses. The system consists of two Newtonian fluids of thickness R* and H R*, separated by an infinitesimally thick membrane, which is flat in the unperturbed state. The dynamics of the membrane is described by its normal displacement from the flat state, as well as a surface displacement field which provides the displacement of material points from their steady-state positions due to the tangential stress exerted by the fluid flow. The surface stress in the membrane (force per unit length) contains an elastic component proportional to the strain along the surface of the membrane, and a viscous component proportional to the strain rate. The linear analysis reveals that the fluctuations become unstable in the long-wave (alpha --> 0) limit when the non-dimensional strain rate in the fluid exceeds a critical value Lambda(t), and this critical value increases proportional to alpha(2) in this limit. Here, alpha is the dimensionless wavenumber of the perturbations scaled by the inverse of the fluid thickness R*(-1), and the dimensionless strain rate is given by Lambda(t) = ((gamma) over dot* R*eta*/Gamma*), where eta* is the fluid viscosity, Gamma* is the tension of the membrane and (gamma) over dot* is the strain rate in the fluid. The weakly nonlinear stability analysis shows that perturbations are supercritically stable in the alpha --> 0 limit.

Symmetry-breaking transitions in equilibrium shapes of coherent precipitates: Effect of elastic anisotropy and inhomogeneity

We examine the symmetry-breaking transitions in equilibrium shapes of coherent precipitates in two-dimensional (2-D) systems under a plane-strain condition with the principal misfit strain components epsilon(xx)*. and epsilon(yy)*. For systems with cubic elastic moduli, we first show all the shape transitions associated with different values of t = epsilon(yy)*/epsilon(xx)*. We also characterize each of these transitions, by studying its dependence on elastic anisotropy and inhomogeneity. For systems with dilatational misfit (t = 1) and those with pure shear misfit (t = -1), the transition is from an equiaxed shape to an elongated shape, resulting in a break in rotational symmetry. For systems with nondilatational misfit (-1 < t < 1; t not equal 0), the transition involves a break in mirror symmetries normal to the x- and y-axes. The transition is continuous in all cases, except when 0 < t < 1. For systems which allow an invariant line (-1 less than or equal to t < 0), the critical size increases with an increase in the particle stiffness. However, for systems which do not allow an invariant line (0 < t less than or equal to 1), the critical size first decreases, reaches a minimum, and then starts increasing with increasing particle stiffness; moreover, the transition is also forbidden when the particle stiffness is greater than a critical value.

Matching sender and receiver: poikilothermy and frequency tuning in a tree cricket

Animals communicate in non-ideal and noisy conditions. The primary method they use to improve communication efficiency is sender-receiver matching: the receiver's sensory mechanism filters the impinging signal based on the expected signal. In the context of acoustic communication in crickets, such a match is made in the frequency domain. The males broadcast a mate attraction signal, the calling song, in a narrow frequency band centred on the carrier frequency (CF), and the females are most sensitive to sound close to this frequency. In tree crickets, however, the CF changes with temperature. The mechanisms used by female tree crickets to accommodate this change in CF were investigated at the behavioural and biomechanical level. At the behavioural level, female tree crickets were broadly tuned and responded equally to CFs produced within the naturally occurring range of temperatures (18 to 27 degrees C). To allow such a broad response, however, the transduction mechanisms that convert sound into mechanical and then neural signals must also have a broad response. The tympana of the female tree crickets exhibited a frequency response that was even broader than suggested by the behaviour. Their tympana vibrate with equal amplitude to frequencies spanning nearly an order of magnitude. Such a flat frequency response is unusual in biological systems and cannot be modelled as a simple mechanical system. This feature of the tree cricket auditory system not only has interesting implications for mate choice and species isolation but may also prove exciting for bio-mimetic applications such as the design of miniature low frequency microphones.

Thermal instability in a three-dimensional rigid container with prescribed heat flux at lower boundary

The Bénard–Marangoni convection is studied in a three-dimensional container with thermally insulated lateral walls and prescribed heat flux at lower boundary. The upper surface of the incompressible, viscous fluid is assumed to be flat with temperature dependent surface tension. A Galerkin–Tau method with odd and even trial functions satisfying all the essential boundary conditions except the natural boundary conditions at the free surface has been used to solve the problem. The critical Marangoni and Rayleigh numbers are determined for the onset of steady convection as a function of aspect ratios x0 and y0 for the cases of Bénard–Marangoni, pure Marangoni and pure Bénard convections. It is observed that critical parameters are decreasing with an increase in aspect ratios. The flow structures corresponding to the values of the critical parameters are presented in all the cases. It is observed that the critical parameters are higher for case with heat flux prescribed than those corresponding to the case with prescribed temperature. The critical Marangoni number for pure Marangoni convection is higher than critical Rayleigh number corresponding to pure Bénard convection for a given aspect ratio whereas the reverse was observed for two-dimensional infinite layer.

Some properties of boundary layer flow during the transition from laminar to turbulent motion

Transition in the boundary layer on a flat plate is examined from the point of view of intermittent production of turbulent spots. On the hypothesis of localized laminar breakdown, for which there is some expermental evidence, Emmons’ probability calculations can be extended to explain the observed statistical similarity of transition regions. Application of these ideas allows detailed calculations of the boundary layer parameters including mean velocity profiles and skin friction during transition. The mean velocity profiles belong to a universal one-parameter family with the intermittency factor as the parameter. From an examination of experimental data the probable existence of a relation between the transition Reynolds number and the rate of production of the turbulent spots is deduced. A simple new technique for the measurement of the intermittency factor by a Pitot tube is reported.

Effect of Post-Metallization Hydrogen Annealing on C-V Characteristic of Zirconia Grown Using Atomic Layer Deposition

Substantial amount of fixed charge present in most of the alternative gate dielectrics gives rise to large shifts in the flat-band voltage (VFB) and charge trapping and de-trapping causes hysterectic changes on voltage cycling. Both phenomena affect stable and reliable transistor operation. In this paper we have studied for the first time the effect of post-metallization hydrogen annealing on the C-V curve of MOS capacitors employing zirconia, one of the most promising gate dielectric. Samples were annealed in hydrogen ambient for up to 30 minutes at different temperatures ranging from room temperature to 400°C. C-V measurements were done after annealing at each temperature and the hysteresis width was calculated from the C-V curves. A minimum hysteresis width of ∼35 mV was observed on annealing the sample at 200°C confirming the excellent suitability of this dielectric

Lubricant Degradation and Related Wear of a Steel Pin in Lubricated Sliding Against a Steel Disc

In lubricated sliding contacts, components wear out and the lubricating oil ages with time. The present work explores the interactive influence between lubricant aging and component wear. The flat face of a steel pin is slid against a rotating steel disk under near isothermal conditions while the contact is immersed in a reservoir of lubricant (hexadecane). The chemical changes in the oil with time are measured by vibrational spectroscopy and gas chromatography. The corresponding chemistry of the pin surface is recorded using X-ray photoelectron spectroscopy while the morphology of the worn pins; surface and subsurface, are observed using a combination of focused ion beam milling and scanning electron 5 microscopy. When compared to thermal auto-oxidation of the lubricant alone, steel on steel friction and wear are found to accentuate the decomposition of oil and to reduce the beneficial impact of antioxidants. The catalytic action of nascent iron, an outcome of pin wear and disk wear, is shown to contribute to this detrimental effect. Over long periods of sliding, the decomposition products of lubricant aging on their own, as well as in conjunction with their products of reaction with iron, generate a thick tribofilm that is highly protective in terms of friction and wear.

Measurement of Heat Transfer Rate on Backward-Facing Steps at Hypersonic Mach Number

Two backward-facing models with step heights of 2 and 3 mm are used to measure the convective surface heat transfer rates by using platinum thin-film gauges, deposited on Macor inserts. Heat transfer rates have been theoretically calculated along the flat plate portion of a model using the Eckert reference temperature method. The experimentally determined surface heat transfer rate distributions are compared with theoretical and numerical estimations. Experimental heat flux distribution over a flat plate model showed good agreement with the reference temperature method at stagnation enthalpy range of 0.8-2 MJ/kg. Theoretical analysis has been used for downstream of a backward-facing step using Gai's nondimensional analysis. It has been found from the present study that approximately 10 and 8 step heights are required for the flow to reattach for 2 and 3 mm step height backward-facing step models, respectively, at a nominal Mach number of 7.6.

Comparative Analysis of Pilot-Assisted Distributed Cophasing Approaches in Wireless Sensor Networks

This paper compares and analyzes the performance of distributed cophasing techniques for uplink transmission over wireless sensor networks. We focus on a time-division duplexing approach, and exploit the channel reciprocity to reduce the channel feedback requirement. We consider periodic broadcast of known pilot symbols by the fusion center (FC), and maximum likelihood estimation of the channel by the sensor nodes for the subsequent uplink cophasing transmission. We assume carrier and phase synchronization across the participating nodes for analytical tractability. We study binary signaling over frequency-flat fading channels, and quantify the system performance such as the expected gains in the received signal-to-noise ratio (SNR) and the average probability of error at the FC, as a function of the number of sensor nodes and the pilot overhead. Our results show that a modest amount of accumulated pilot SNR is sufficient to realize a large fraction of the maximum possible beamforming gain. We also investigate the performance gains obtained by censoring transmission at the sensors based on the estimated channel state, and the benefits obtained by using maximum ratio transmission (MRT) and truncated channel inversion (TCI) at the sensors in addition to cophasing transmission. Simulation results corroborate the theoretical expressions and show the relative performance benefits offered by the various schemes.

Precoder Designs for MIMO Broadcast Channels with Imperfect CSI

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Seismic Microzonation: Principles,Practices and Experiments

This paper presents an overview of the seismic microzonation and the grade/level based study along with methods used for estimating hazard. The principles of seismic microzonation along with some current practices are discussed. Summary of seismic microzonation experiments carried out in India is presented. A detailed work of seismic microzonation of Bangalore has been presented as a case study. In this case study, a seismotectonic map for microzonation area has been developed covering 350 km radius around Bangalore, India using seismicity and seismotectonic parameters of the region. For seismic microzonation Bangalore Mahanagar Palike (BMP) area of 220 km2 has been selected as the study area. Seismic hazard analysis has been carried out using deterministic as well as probabilistic approaches. Synthetic ground motion at 653 locations, recurrence relation and peak ground acceleration maps at rock level have been generated. A detailed site characterization has been carried out using borehole with standard penetration test (SPT) ―N‖ values and geophysical data. The base map and 3-dimensional sub surface borehole model has been generated for study area using geographical information system (GIS). Multichannel analysis of surface wave (MASW)method has been used to generate one-dimensional shear wave velocity profile at 58 locations and two- dimensional profile at 20 locations. These shear wave velocities are used to estimate equivalent shear wave velocity in the study area at every 5m intervals up to a depth of 30m. Because of wider variation in the rock depth, equivalent shear for the soil overburden thickness alone has been estimated and mapped using ArcGIS 9.2. Based on equivalent shear wave velocity of soil overburden thickness, the study area is classified as ―site class D‖. Site response study has been carried out using geotechnical properties and synthetic ground motions with program SHAKE2000.The soil in the study area is classified as soil with moderate amplification potential. Site response results obtained using standard penetration test (SPT) ―N‖ values and shear wave velocity are compared, it is found that the results based on shear wave velocity is lower than the results based on SPT ―N‖ values. Further, predominant frequency of soil column has been estimated based on ambient noise survey measurements using instruments of L4-3D short period sensors equipped with Reftek 24 bit digital acquisition systems. Predominant frequency obtained from site response study is compared with ambient noise survey. In general, predominant frequencies in the study area vary from 3Hz to 12Hz. Due to flat terrain in the study area, the induced effect of land slide possibility is considered to be remote. However, induced effect of liquefaction hazard has been estimated and mapped. Finally, by integrating the above hazard parameters two hazard index maps have been developed using Analytic Hierarchy Process (AHP) on GIS platform. One map is based on deterministic hazard analysis and other map is based on probabilistic hazard analysis. Finally, a general guideline is proposed by bringing out the advantages and disadvantages of different approaches.

Seismic Microzonation of Bangalore - Preliminary Maps

This paper presents an overview of the seismic microzonation and the grade/level based study along with methods used for estimating hazard. The principles of seismic microzonation along with some current practices are discussed. Summary of seismic microzonation experiments carried out in India is presented. A detailed work of seismic microzonation of Bangalore has been presented as a case study. In this case study, a seismotectonic map for microzonation area has been developed covering 350 km radius around Bangalore, India using seismicity and seismotectonic parameters of the region. For seismic microzonation Bangalore Mahanagar Palike (BMP) area of 220 km2 has been selected as the study area. Seismic hazard analysis has been carried out using deterministic as well as probabilistic approaches. Synthetic ground motion at 653 locations, recurrence relation and peak ground acceleration maps at rock level have been generated. A detailed site characterization has been carried out using borehole with standard penetration test (SPT) ―N‖ values and geophysical data. The base map and 3-dimensional sub surface borehole model has been generated for study area using geographical information system (GIS). Multichannel analysis of surface wave (MASW)method has been used to generate one-dimensional shear wave velocity profile at 58 locations and two- dimensional profile at 20 locations. These shear wave velocities are used to estimate equivalent shear wave velocity in the study area at every 5m intervals up to a depth of 30m. Because of wider variation in the rock depth, equivalent shear for the soil overburden thickness alone has been estimated and mapped using ArcGIS 9.2. Based on equivalent shear wave velocity of soil overburden thickness, the study area is classified as ―site class D‖. Site response study has been carried out using geotechnical properties and synthetic ground motions with program SHAKE2000.The soil in the study area is classified as soil with moderate amplification potential. Site response results obtained using standard penetration test (SPT) ―N‖ values and shear wave velocity are compared, it is found that the results based on shear wave velocity is lower than the results based on SPT ―N‖ values. Further, predominant frequency of soil column has been estimated based on ambient noise survey measurements using instruments of L4-3D short period sensors equipped with Reftek 24 bit digital acquisition systems. Predominant frequency obtained from site response study is compared with ambient noise survey. In general, predominant frequencies in the study area vary from 3Hz to 12Hz. Due to flat terrain in the study area, the induced effect of land slide possibility is considered to be remote. However, induced effect of liquefaction hazard has been estimated and mapped. Finally, by integrating the above hazard parameters two hazard index maps have been developed using Analytic Hierarchy Process (AHP) on GIS platform. One map is based on deterministic hazard analysis and other map is based on probabilistic hazard analysis. Finally, a general guideline is proposed by bringing out the advantages and disadvantages of different approaches.

Topology Optimization of Micromachined Structures with the Manufacturing Constraints of KOH Etching of (110) Silicon

The focus of this paper is on designing useful compliant micro-mechanisms of high-aspect-ratio which can be microfabricated by the cost-effective wet etching of (110) orientation silicon (Si) wafers. Wet etching of (110) Si imposes constraints on the geometry of the realized mechanisms because it allows only etch-through in the form of slots parallel to the wafer's flat with a certain minimum length. In this paper, we incorporate this constraint in the topology optimization and obtain compliant designs that meet the specifications on the desired motion for given input forces. Using this design technique and wet etching, we show that we can realize high-aspect-ratio compliant micro-mechanisms. For a (110) Si wafer of 250 µm thickness, the minimum length of the etch opening to get a slot is found to be 866 µm. The minimum achievable width of the slot is limited by the resolution of the lithography process and this can be a very small value. This is studied by conducting trials with different mask layouts on a (110) Si wafer. These constraints are taken care of by using a suitable design parameterization rather than by imposing the constraints explicitly. Topology optimization, as is well known, gives designs using only the essential design specifications. In this work, we show that our technique also gives manufacturable mechanism designs along with lithography mask layouts. Some designs obtained are transferred to lithography masks and mechanisms are fabricated on (110) Si wafers.