Amino acid interaction preferences in helical membrane proteins

Membrane proteins are involved in a number of important biological functions. Yet, they are poorly understood from the structure and folding point of view. The external environment being drastically different from that of globular proteins, the intra-protein interactions in membrane proteins are also expected to be different. Hence, statistical potentials representing the features of inter-residue interactions based exclusively on the structures of membrane proteins are much needed. Currently, a reasonable number of structures are available, making it possible to undertake such an analysis on membrane proteins. In this study we have examined the inter-residue interaction propensities of amino acids in the membrane spanning regions of the alpha-helical membrane (HM) proteins. Recently we have shown that valuable information can be obtained on globular proteins by the evaluation of the pair-wise interactions of amino acids by classifying them into different structural environments, based on factors such as the secondary structure or the number of contacts that a residue can make. Here we have explored the possible ways of classifying the intra-protein environment of HM proteins and have developed scoring functions based on different classification schemes. On evaluation of different schemes, we find that the scheme which classifies amino acids to different intra-contact environment is the most promising one. Based on this classification scheme, we also redefine the hydrophobicity scale of amino acids in HM proteins.

Characterization of vesicles from ion-paired gemini surfactants by small angle neutron scattering

Detailed small angle neutron scattering ( SANS) studies were carried out with the aqueous vesicular (unilamellar) suspension of dimeric ion-paired lipids (2a-2c) for spacer lengths corresponding to n-values of 2, 6 and 10 and monomeric ion-paired lipid (3) below and above the phase transition temperature of each amphiphile. The vesicular structure strongly depends on the spacer chain length. The mean vesicle size is smallest for the lipid with a short spacer, n = 3 and it increases with the increase in the spacer chain length. The bilayer thickness also decreases with the increase in the spacer chain length. The size polydispersity increases with the increase in the spacer chain length (n-value).

Turbulent free convection above a heated plate inclined at a small angle to the horizontal Journal

An investigation has been made of the structure of the motion above a heated plate inclined at a small angle (about 10°) to the horizontal. The turbulence is considered in terms of the similarities to and differences from the motion above an exactly horizontal surface. One effect of inclination is, of course, that there is also a mean motion. Accurate data on the mean temperature field and the intensity of the temperature fluctuations have been obtained with platinum resistance thermometers, the signals being processed electronically. More approximate information on the velocity field has been obtained with quartz fibre anemometers. These results have been supplemented qualitatively by simultaneous observations of the temperature and velocity fluctuations and also by smoke experiments. The principal features of the flow inferred from these observations are as follows. The heat transfer and the mean temperature field are not much altered by the inclination, though small, not very systematic, variations may result from the complexities of the velocity field. This supports the view that the mean temperature field is largely governed by the large-scale motions. The temperature fluctuations show a systematic variation with distance from the lower edge and resemble those above a horizontal plate when this distance is large. The largescale motions of the turbulence start close to the lower edge, but the smaller eddies do not attain full intensity until the air has moved some distance up the plate. The mean velocity receives a sizable contribution from a ‘through-flow’ between the side-walls. Superimposed on this are developments that show that the momentum transfer processes are complex and certainly not capable of representation by any simple theory such as an eddy viscosity. On the lower part of the plate there is surprisingly large acceleration, but further up the mixing action of the small eddies has a decelerating effect.

On a Novel Geometric Representation of Rotation

This paper presents a novel method of representing rotation and its application to representing the ranges of motion of coupled joints in the human body, using planar maps. The present work focuses on the viability of this representation for situations that relied on maps on a unit sphere. Maps on a unit sphere have been used in diverse applications such as Gauss map, visibility maps, axis-angle and Euler-angle representations of rotation etc. Computations on a spherical surface are difficult and computationally expensive; all the above applications suffer from problems associated with singularities at the poles. There are methods to represent the ranges of motion of such joints using two-dimensional spherical polygons. The present work proposes to use multiple planar domain “cube” instead of a single spherical domain, to achieve the above objective. The parameterization on the planar domains is easy to obtain and convert to spherical coordinates. Further, there is no localized and extreme distortion of the parameter space and it gives robustness to the computations. The representation has been compared with the spherical representation in terms of computational ease and issues related to singularities. Methods have been proposed to represent joint range of motion and coupled degrees of freedom for various joints in digital human models (such as shoulder, wrist and fingers). A novel method has been proposed to represent twist in addition to the existing swing-swivel representation.

Nonlinear Model Predictive Spread Acceleration Guidance with Impact Angle Constraint for Stationary Targets

A new technique named as model predictive spread acceleration guidance (MPSAG) is proposed in this paper. It combines nonlinear model predictive control and spread acceleration guidance philosophies. This technique is then used to design a nonlinear suboptimal guidance law for a constant speed missile against stationary target with impact angle constraint. MPSAG technique can be applied to a class of nonlinear problems, which leads to a closed form solution of the lateral acceleration (latax) history update. Guidance command assumed is the lateral acceleration (latax), applied normal to the velocity vector. The new guidance law is validated by considering the nonlinear kinematics with both lag-free as well as first order autopilot delay. The simulation results show that the proposed technique is quite promising to come up with a nonlinear guidance law that leads to both very small miss distance as well as the desired impact angle.

Nonlinear Model Predictive Spread Acceleration Guidance with Impact Angle Constraint for Slow-moving Targets

A new technique named as model predictive spread acceleration guidance (MPSAG) is proposed in this paper. It combines nonlinear model predictive control and spread acceleration guidance philosophies. This technique is then used to design a nonlinear suboptimal guidance law for a constant speed missile against stationary target with impact angle constraint. MPSAG technique can be applied to a class of nonlinear problems, which leads to a closed form solution of the lateral acceleration (latax) history update. Guidance command assumed is the lateral acceleration (latax), applied normal to the velocity vector. The new guidance law is validated by considering the nonlinear kinematics with both lag-free as well as first order autopilot delay. The simulation results show that the proposed technique is quite promising to come up with a nonlinear guidance law that leads to both very small miss distance as well as the desired impact angle.

Dynamic contact angle beating from drops impacting onto solid surfaces exhibiting anisotropic wetting

This paper reports an experimental investigation of low Weber number water drops impacting onto solid surfaces exhibiting anisotropic wetting. The wetting anisotropy is created by patterning the solid surfaces with unidirectional parallel grooves. Temporal measurements of impacting drop parameters such as drop base contact diameter, apparent contact angle of drop, and drop height at the center are obtained from high-speed video recordings of drop impacts. The study shows that the impact of low Weber number water drops on the grooved surface exhibits beating phenomenon in the temporal variations of the dynamic contact angle anisotropy and drop height at the center of the impacting drop. It is observed that the beating phenomenon of impacting drop parameters is caused by the frequency difference between the dynamic contact angle oscillations of impacting drop liquid oriented perpendicular and parallel to the direction of grooves on the grooved surface. The primary trigger for the phenomenon is the existence of non-axisymmetric drop flow on the grooved surface featuring pinned and free motions of drop liquid in the directions perpendicular and parallel to the grooves, respectively. The beat frequency is almost independent of the impact drop Weber number. Further experimental measurements with solid surfaces of different groove textures show that the grooved surface with larger wetting anisotropy may be expected to show a dominant beating phenomenon. The phenomenon is gradually damped out with time and is fully unrecognizable at higher drop impact Weber numbers. (C) 2011 Elsevier B.V. All rights reserved.

Nonlinear Suboptimal Guidance with Impact Angle Constraint for Slow Moving Targets in 1-D Using MPSP

Using a recently developed method named as model predictive static programming (MPSP), a nonlinear suboptimal guidance law for a constant speed missile against a slow moving target with impact angle constraint is proposed. In this paper MPSP technique leads to a closed form solution of the latax history update for the given problem. Guidance command is the latax,which is normal to the missile velocity and the terminal constraints are miss distance and impact angle. The new guidance law is validated by considering the nonlinear kinematics with both lag-free and first order autopilot delay.

3D Image Reconstruction From Truncated Helical Cone Beam Projection Data - A Linear Prediction Approach

With the introduction of 2D flat-panel X-ray detectors, 3D image reconstruction using helical cone-beam tomography is fast replacing the conventional 2D reconstruction techniques. In 3D image reconstruction, the source orbit or scanning geometry should satisfy the data sufficiency or completeness condition for exact reconstruction. The helical scan geometry satisfies this condition and hence can give exact reconstruction. The theoretically exact helical cone-beam reconstruction algorithm proposed by Katsevich is a breakthrough and has attracted interest in the 3D reconstruction using helical cone-beam Computed Tomography.In many practical situations, the available projection data is incomplete. One such case is where the detector plane does not completely cover the full extent of the object being imaged in lateral direction resulting in truncated projections. This result in artifacts that mask small features near to the periphery of the ROI when reconstructed using the convolution back projection (CBP) method assuming that the projection data is complete. A number of techniques exist which deal with completion of missing data followed by the CBP reconstruction. In 2D, linear prediction (LP)extrapolation has been shown to be efficient for data completion, involving minimal assumptions on the nature of the data, producing smooth extensions of the missing projection data.In this paper, we propose to extend the LP approach for extrapolating helical cone beam truncated data. The projection on the multi row flat panel detectors has missing columns towards either ends in the lateral direction in truncated data situation. The available data from each detector row is modeled using a linear predictor. The available data is extrapolated and this completed projection data is backprojected using the Katsevich algorithm. Simulation results show the efficacy of the proposed method.