NON-COERCIVE RICCI FLOW INVARIANT CURVATURE CONES

This note is a study of nonnegativity conditions on curvature preserved by the Ricci flow. We focus on a specific class of curvature conditions which we call non-coercive: These are the conditions for which nonnegative curvature and vanishing scalar curvature does not imply flatness. We show, in dimensions greater than 4, that if a Ricci flow invariant nonnegativity condition is satisfied by all Einstein curvature operators with nonnegative scalar curvature, then this condition is just the nonnegativity of scalar curvature. As a corollary, we obtain that a Ricci flow invariant curvature condition, which is stronger than a nonnegative scalar curvature, cannot be strictly satisfied by curvature operators (other than multiples of the identity) of compact Einstein symmetric spaces. We also investigate conditions which are satisfied by all conformally flat manifolds with nonnegative scalar curvature.

MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature

Background: Aligning similar molecular structures is an important step in the process of bio-molecular structure and function analysis. Molecular surfaces are simple representations of molecular structure that are easily constructed from various forms of molecular data such as 3D atomic coordinates (PDB) and Electron Microscopy (EM) data. Methods: We present a Multi-Scale Morse-Smale Molecular-Surface Alignment tool, MS3ALIGN, which aligns molecular surfaces based on significant protrusions on the molecular surface. The input is a pair of molecular surfaces represented as triangle meshes. A key advantage of MS3ALIGN is computational efficiency that is achieved because it processes only a few carefully chosen protrusions on the molecular surface. Furthermore, the alignments are partial in nature and therefore allows for inexact surfaces to be aligned. Results: The method is evaluated in four settings. First, we establish performance using known alignments with varying overlap and noise values. Second, we compare the method with SurfComp, an existing surface alignment method. We show that we are able to determine alignments reported by SurfComp, as well as report relevant alignments not found by SurfComp. Third, we validate the ability of MS3ALIGN to determine alignments in the case of structurally dissimilar binding sites. Fourth, we demonstrate the ability of MS3ALIGN to align iso-surfaces derived from cryo-electron microscopy scans. Conclusions: We have presented an algorithm that aligns Molecular Surfaces based on the topology of surface curvature. Awebserver and standalone software implementation of the algorithm available at http://vgl.serc.iisc.ernet. in/ms3align.

Positive isotropic curvature and self-duality in dimension 4

We study a positivity condition for the curvature of oriented Riemannian 4-manifolds: the half-PIC condition. It is a slight weakening of the positive isotropic curvature (PIC) condition introduced by M. Micallef and J. Moore. We observe that the half-PIC condition is preserved by the Ricci flow and satisfies a maximality property among all Ricci flow invariant positivity conditions on the curvature of oriented 4-manifolds. We also study some geometric and topological aspects of half-PIC manifolds.

Smooth Path Planning for Passages with Heading and Curvature Discontinuities

The problem of continuous curvature path planning for passages is considered. This problem arises when an autonomous vehicle traverses between prescribed boundaries such as corridors, tunnels, channels, etc. Passage boundaries with curvature and heading discontinuities pose challenges for generating smooth paths passing through them. Continuous curvature half-S shaped paths derived from the Four Parameter Logistic Curve family are proposed as a prospective path planning solution. Analytic conditions are derived for generating continuous curvature paths confined within the passage boundaries. Zero end curvature highlights the scalability of the proposed solution and its compatibility with other path planners in terms of larger path planning domains. Various scenarios with curvature and heading discontinuities are considered presenting viability of the proposed solution.

Curvature Management in Buffer Layer for Device Quality GaN Growth on Si (111)

An efficient buffer layer scheme has been designed to address the issue of curvature management during metalorganic chemical vapour deposition growth of GaN on Si (111) substrate. This is necessary to prevent cracking of the grown layer during post-growth cooling down from growth temperature to room temperature and to achieve an allowable bow (<40 m) in the wafer for carrying out lithographic processes. To meet both these ends simultaneously, the stress evolution in the buffer layers was observed carefully. The reduction in precursor flow during the buffer layer growth provided better control over curvature evolution in the growing buffer layers. This has enabled the growth of a suitable high electron mobility transistor (HEMT) stack on 2'' Si (111) substrate of 300 m thickness with a bow as low as 11.4 m, having a two-dimensional electron gas (2DEG) of mobility, carrier concentration, and sheet resistance values 1510 cm(2)/V-s, 0.96 x 10(13)/cm(2), and 444 /, respectively. Another variation of similar technique resulted in a bow of 23.4 m with 2DEG mobility, carrier concentration, and sheet resistance values 1960 cm(2)/V-s, 0.98 x 10(13)/cm(2), and 325 /, respectively.

Spatial B-jump at sudden channel enlargements with abrupt drop

An analytical and experimental study of the hydraulic jump in stilling basins with abrupt drop and sudden enlargement, called the spatial B-jump here, is carried out for finding the sequent depth ratio and resulting energy dissipation. The spatial B-jump studied has its toe downstream of the expansion section, and the stream lines at the toe are characterized by downward curvature. An expression is obtained for the sequent depth ratio based on the momentum equation with suitable assumptions for the extra pressure force term because of the abrupt drop in the bed and sudden enlargement in the basin width. Predictions compare favorably with experiments. It is shown that the spatial B-jump needs less tailwater depth, thereby enhancing the stability of the jump when compared either with spatial jump, which forms in sudden expanding channels, or with B-jump, which forms in a channel with an abrupt drop in bed. It is also shown that there is a significant increase in relative energy loss for the spatial B-jump compared to either the spatial jump or B-jump alone.

Structural and Sequence Characteristics of Long alpha Helices in Globular Proteins

Elucidation of the detailed structural features and sequence requirements for iv helices of various lengths could be very important in understanding secondary structure formation in proteins and, hence. in the protein folding mechanism. An algorithm to characterize the geometry of an alpha helix from its C-alpha coordinates has been developed and used to analyze the structures of long cu helices (number of residues greater than or equal to 25) found in globular proteins, the crystal structure coordinates of which are available from the Brookhaven Protein Data Bank, Ail long a helices can be unambiguously characterized as belonging to one of three classes: linear, curved, or kinked, with a majority being curved. Analysis of the sequences of these helices reveals that the long alpha helices have unique sequence characteristics that distinguish them from the short alpha helices in globular proteins, The distribution and statistical propensities of individual amino acids to occur in long alpha heices are different from those found in short alpha helices, with amino acids having longer side chains and/or having a greater number of functional groups occurring more frequently in these helices, The sequences of the long alpha helices can be correlated with their gross structural features, i.e., whether they are curved, linear, or kinked, and in case of the curved helices, with their curvature.

Improved assessment of aerosol absorption using OMI-MODIS joint retrieval

The Ozone Monitoring Instrument (OMI) aboard EOS-Aura and the Moderate Resolution Imaging Spectroradiometer (MODIS) onboard EOS-Aqua fly in formation as part of the A-train. Though OMI retrieves aerosol optical depth (AOD) and aerosol absorption, it must assume aerosol layer height. The MODIS cannot retrieve aerosol absorption, but MODIS aerosol retrieval is not sensitive to aerosol layer height and with its smaller pixel size is less affected by subpixel clouds. Here we demonstrate an approach that uses MODIS-retrieved AOD to constrain the OMI retrieval, freeing OMI from making an a priori estimate of aerosol height and allowing a more direct retrieval of aerosol absorption. To predict near-UV optical depths using MODIS data we rely on the spectral curvature of the MODIS-retrieved visible and near-IR spectral AODs. Application of an OMI-MODIS joint retrieval over the north tropical Atlantic shows good agreement between OMI and MODIS-predicted AODs in the UV, which implies that the aerosol height assumed in the OMI-standard algorithm is probably correct. In contrast, over the Arabian Sea, MODIS-predicted AOD deviated from the OMI-standard retrieval, but combined OMI-MODIS retrievals substantially improved information on aerosol layer height (on the basis of validation against airborne lidar measurements). This implies an improvement in the aerosol absorption retrieval, but lack of UV absorption measurements prevents a true validation. Our study demonstrates the potential of multisatellite analysis of A-train data to improve the accuracy of retrieved aerosol products and suggests that a combined OMI-MODIS-CALIPSO retrieval has large potential to further improve assessments of aerosol absorption.

Analysis Of Curved Laminated Beams Of Bimodulus Composite-Materials

Composite materials exhibiting different moduli in tension and in compression, commonly called as bimodular composites are being used in many engineering fields. A finite element analysis is carried out for small deflection static behavior of laminated curved beams of bi modulus materials for both solid and hollow circular cross-sections using an iterative procedure. The finite element has 16 d.o.f. and uses the displacement field in terms of first order Hermite in terpolation polynomials. The neutral surface, i.e. the locus of points having zero axial strain is found to vary drastically depending on the loading, lay up schemes and radius of curvature. As il lustrations, plots of the cross-sections of the ruled neutral-surface are presented for some of the investigated cases. Using this element a few problems of curved laminated beams of bimodulus materials are solved for both solid and hollow circular cross-sections.

Forced convection along a longitudinal cylinder embedded in a saturated porous medium

The thermal boundary layer along an isothermal cylinder in a porous 3edium is studied numerically by a finite difference scheme and also using the method of extended perturbation series. The series in terms of the transverse curvature parameter ξ extended to seven terms and is subsequently improved by applying the Shanks transformation twice and thrice, respectively. Results for heat transfer characteristics are found in very good agreement.

Anisotropic gaussian beams

Anisotropic gaussian beams are obtained as exact solutions to the parabolic wave equation. These beams have a quadratic phase front whose principal radii of curvature are non-degenerate everywhere. It is shown that, for the lowest order beams, there exists a plane normal to the beam axis where the intensity distribution is rotationally symmetric about the beam axis. A possible application of these beams as normal modes of laser cavities with astigmatic mirrors is noted.

Structural Polymorphism of the Nucleosomal DNA and Implications for Protein Binding

A nucleosome forms a basic unit of the chromosome structure. A biologically relevant question is how much of the nucleosomal conformational space is accessible to protein-free DNA, and what proportion of the nucleosomal conformations are induced by bound histones. To investigate this, we have analysed high resolution xray crystal structure datasets of DNA in protein-free as well as protein-bound forms, and compared the dinucleotide step parameters for the two datasets with those for high resolution nucleosome structures. Our analysis shows that most of the dinucleotide step parameter values for the nucleosome structures lie within the range accessible to protein-free DNA, indirectly indicating that the histone core plays more of a stabilizing role. The nucleosome structures are observed to assume smooth and nearly planar curvature, implying that ‘normal’ B-DNA like parameters can give rise to a curved geometry at the gross structural level. Different nucleosome

Continuation of limit cycles near saddle homoclinic points using splines in phase space

We present a new algorithm for continuation of limit cycles of autonomous systems as a system parameter is varied. The algorithm works in phase space with an ordered set of points on the limit cycle, along with spline interpolation. Currently popular algorithms in bifurcation analysis packages compute time-domain approximations of limit cycles using either shooting or collocation. The present approach seems useful for continuation near saddle homoclinic points, where it encounters a corner while time-domain methods essentially encounter a discontinuity (a relatively short period of rapid variation). Other phase space-based algorithms use rescaled arclength in place of time, but subsequently resemble the time-domain methods. Compared to these, we introduce additional freedom through a variable stretching of arclength based on local curvature, through the use of an auxiliary index-based variable. Several numerical examples are presented. Comparisons with results from the popular package, MATCONT, are favorable close to saddle homoclinic points.

Motion of a viscous fluid with suspended particles in a curved tube

In this paper we have discussed the motion of a viscous fluid with suspended particles through a curved tube of small curvature ratio. The system is treated as two separate interacting continua. Solutions for axial and secondary velocities are obtained in the form of asymptotic expansions in powers of Dean Number. The streamline pattern for the particulate phase reveals many interesting features. The influence of the particulate continium on the fluid is described by the parameter τ which depends on the density ratio of the two continua. The concentration distribution of the particles in a given cross section is determined. It is noticed that the particles move closer to the wall for certain values of the concentration and the density ratio.

Stresses around two equal circular elastic inclusions in a pressurised cylindrical shell

The stress problem of two equal circular elastic inclusions in a pressurised cylindrical shell has been solved by using single inclusion solutions together with Graf’s addition theorem. The effect of the inter-inclusion distance on the interface stresses in the shell as well as in the inclusion is studied. The results obtained for small values of curvature parameter fi @*=(a*/8Rt) [12(1-v*)]“*, a, R, t being inclusion radius and shell radius and thickness) when compared with the flat-plate results show good agreement. The results obtained in non-dimensional form are presented graphically.