Techniques for realistic visualization of fluids: A survey

Visualization of fluids has wide applications in science, engineering and entertainment. Various methodologies Of visualizing fluids have evolved which emphasize on capturing different aspects of the fluids accurately. In this survey the existing methods for realistic visualization of fluids are reviewed. The approaches are classified based on the key concept they rely on for fluid modeling. This classification allows for easy selection of the method to be adopted for visualization given an application. It also enables identification of alternative techniques for fluid modeling.

Reconstructing Solid Model from 2D Scanned Images of Biological Organs for Finite Element Simulation

This work presents a methodology to reconstruct 3D biological organs from image sequences or other scan data using readily available free softwares with the final goal of using the organs (3D solids) for finite element analysis. The methodology deals with issues such as segmentation, conversion to polygonal surface meshes, and finally conversion of these meshes to 3D solids. The user is able to control the detail or the level of complexity of the solid constructed. The methodology is illustrated using 3D reconstruction of a porcine liver as an example. Finally, the reconstructed liver is imported into the commercial software ANSYS, and together with a cyst inside the liver, a nonlinear analysis performed. The results confirm that the methodology can be used for obtaining 3D geometry of biological organs. The results also demonstrate that the geometry obtained by following this methodology can be used for the nonlinear finite element analysis of organs. The methodology (or the procedure) would be of use in surgery planning and surgery simulation since both of these extensively use finite elements for numerical simulations and it is better if these simulations are carried out on patient specific organ geometries. Instead of following the present methodology, it would cost a lot to buy a commercial software which can reconstruct 3D biological organs from scanned image sequences.

Haptic Feedback for Injecting Biological Cells using Miniature Compliant Mechanisms

We present a real-time haptics-aided injection technique for biological cells using miniature compliant mechanisms. Our system consists of a haptic robot operated by a human hand, an XYZ stage for micro-positioning, a camera for image capture, and a polydimethylsiloxane (PDMS) miniature compliant device that serves the dual purpose of an injecting tool and a force-sensor. In contrast to existing haptics-based micromanipulation techniques where an external force sensor is used, we use visually captured displacements of the compliant mechanism to compute the applied and reaction forces. The human hand can feel the magnified manipulation force through the haptic device in real-time while the motion of the human hand is replicated on the mechanism side. The images are captured using a camera at the rate of 30 frames per second for extracting the displacement data. This is used to compute the forces at the rate of 30 Hz. The force computed in this manner is sent at the rate of 1000 Hz to ensure stable haptic interaction. The haptic cell-manipulation system was tested by injecting into a zebrafish egg cell after validating the technique at a size larger than that of the cell.

Synthesis, biological studies of linear and branched arabinofuranoside-containing glycolipids and their interaction with surfactant protein A

Oligoarabinofuranoside-containing glycolipids relevant to mycobacterial cell wall components were synthesized in order to understand the functional roles of such glycolipids. A series of linear tetra-, hexa-, octa-and a branched heptasaccharide oligoarabinofuranosides, with 1 -> 2 and 1 -> 5 a-linkages between the furanoside residues, were synthesized by chemical methods from readily available monomer building blocks. Upon the synthesis of glycolipids, constituted with a double alkyl chain-substituted sn-glycerol core and oligosaccharide fragments, biological studies were performed to identify the effect of synthetic glycolipids on the biofilm formation and sliding motilities of Mycobacterium smegmatis. Synthetic glycolipids and arabinofuranosides displayed an inhibitory effect on the growth profile, but mostly on the biofilm formation and maturation. Similarly, synthetic compounds also influenced the sliding motility of the bacteria. Further, biophysical studies were undertaken, so as to identify the interactions of the glycolipids with a pulmonary surfactant protein, namely surfactant protein A (SP-A), with the aid of the surface plasmon resonance technique. Specificities of each glycolipid interacting with SP-A were thus evaluated. From this study, glycolipids were found to exhibit higher apparent association constants than the corresponding oligosaccharide portion alone, without the double alkyl group-substituted glycerol core.

The biological and structural characterization of Mycobacterium tuberculosis UvrA provides novel insights into its mechanism of action

Mycobacterium tuberculosis is an extremely well adapted intracellular human pathogen that is exposed to multiple DNA damaging chemical assaults originating from the host defence mechanisms. As a consequence, this bacterium is thought to possess highly efficient DNA repair machineries, the nucleotide excision repair (NER) system amongst these. Although NER is of central importance to DNA repair in M. tuberculosis, our understanding of the processes in this species is limited. The conserved UvrABC endonuclease represents the multi-enzymatic core in bacterial NER, where the UvrA ATPase provides the DNA lesion-sensing function. The herein reported genetic analysis demonstrates that M. tuberculosis UvrA is important for the repair of nitrosative and oxidative DNA damage. Moreover, our biochemical and structural characterization of recombinant M. tuberculosis UvrA contributes new insights into its mechanism of action. In particular, the structural investigation reveals an unprecedented conformation of the UvrB-binding domain that we propose to be of functional relevance. Taken together, our data suggest UvrA as a potential target for the development of novel anti-tubercular agents and provide a biochemical framework for the identification of small-molecule inhibitors interfering with the NER activity in M. tuberculosis.

Biological and materials properties of various cholesterol based systems

Liposomes composed of cationic lipids have become very popular gene delivery vehicles. A great deal of research is being pursued to make efficient vectors by varying their molecular architecture. Cholesterol being ubiquitous component in most of the animal cell membranes is increasingly being used as a hydrophobic segment of synthetic cationic lipids. In this review we describe various cholesterol based cationic lipids and focus on the effect of modifying various structural segments like linker and the head group of the cationic lipids on gene transfection efficiency with a special emphasis on the importance of ether linkage between cholesteryl backbone and the polar head group. Interaction of cationic cholesteryl lipids with dipalmitylphosphatidycholine membranes is also discussed here. Apart from cholesterol being an attractive scaffold in the drug/gene delivery vehicles, certain cholesteryl derivatives have also been shown to be attractive room temperature liquid-crystalline materials.

Injection-molded high-density polyethylene-hydroxyapatite-aluminum oxide hybrid composites for hard-tissue replacement: Mechanical, biological, and protein adsorption behavior

In this article, we report the mechanical and biocompatibility properties of injection-molded high-density polyethylene (HDPE) composites reinforced with 40 wt % ceramic filler [hydroxyapatite (HA) and/or Al2O3] and 2 wt % titanate as a coupling agent. The mechanical property measurements revealed that a combination of a maximum tensile strength of 18.7 MPa and a maximum tensile modulus of about 855 MPa could be achieved with the injection-molded HDPE20 wt % HA20 wt % Al2O3 composites. For the same composite composition, the maximum compression strength was determined to be 71.6 MPa and the compression modulus was about 660 MPa. The fractrography study revealed the uniform distribution of ceramic fillers in the semicrystalline HDPE matrix. The cytocompatibility study with osteoblast-like SaOS2 cells confirmed extensive cell adhesion and proliferation on the injection-molded HDPE20 wt % HA20 wt % Al2O3 composites. The cell viability analysis with the 3(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay revealed a statistically significant difference between the injection-molded HDPE20 wt % HA20 wt % Al2O3 composites and sintered HA for various culture durations of upto 7 days. The difference in cytocompatibility properties among the biocomposites is explained in terms of the difference in the protein absorption behavior. (C) 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012

From anomalies in neat liquid to structure, dynamics and function in the biological world

Water brings its remarkable thermodynamic and dynamic anomalies in the pure liquid state to biological world where water molecules face a multitude of additional interactions that frustrate its hydrogen bond network. Yet the water molecules participate and control enormous number of biological processes in manners which are yet to be understood at a molecular level. We discuss thermodynamics, structure, dynamics and properties of water around proteins and DNA, along with those in reverse micelles. We discuss the roles of water in enzyme kinetics, in drug-DNA intercalation and in kinetic-proof reading ( the theory of lack of errors in biosynthesis). We also discuss how water may play an important role in the natural selection of biomolecules. (C) 2011 Elsevier B. V. All rights reserved.

Uncertainty visualization using HDR volume rendering

In this paper, we explore a novel idea of using high dynamic range (HDR) technology for uncertainty visualization. We focus on scalar volumetric data sets where every data point is associated with scalar uncertainty. We design a transfer function that maps each data point to a color in HDR space. The luminance component of the color is exploited to capture uncertainty. We modify existing tone mapping techniques and suitably integrate them with volume ray casting to obtain a low dynamic range (LDR) image. The resulting image is displayed on a conventional 8-bits-per-channel display device. The usage of HDR mapping reveals fine details in uncertainty distribution and enables the users to interactively study the data in the context of corresponding uncertainty information. We demonstrate the utility of our method and evaluate the results using data sets from ocean modeling.

Synthesis, spectroscopic properties and biological evaluation of transition metal complexes of salicylhydrazone of anthranilhydrazide: X-ray crystal structure of copper complex

The transition metal complexes of salicylhydrazone of anthranilhydrazide (H2L) were synthesised. The structures of metal complexes were characterized by various spectroscopic [IR, NMR, UV-Vis, EPR], thermal and other physicochemical methods. The single-crystal X-ray diffraction study of [Cu(HL)Cl]center dot H2O reveal its orthorhombic system with space group P2(1)2(1)2 and Z=4. The copper center has a distorted square planar geometry with ONO and Cl as the donor atoms. The ligand and its metal chelates have been screened for their antimicrobial and anti-tubercular activities using serial dilution method. Metal complexes in general have exhibited better antibacterial and antifungal activity than the free ligand and in few cases better than the standard used. Among the bacterial strains used, the complexes are highly potent against Gram-positive strains compared to Gram-negative. Anti-tubercular activity exhibited by the Co(II) complex is comparable with the standard used. (C) 2011 Elsevier B. V. All rights reserved.

Flow visualization in turbulent free convection over horizontal smooth and grooved surfaces

The present paper discusses the flow visualization for turbulent free convection in a tank of water with the bottom surface being a smooth or a grooved surface and the top of the water surface exposed to ambient. The grooved surface is of parallel 90 degrees V-grooves with groove height of 10 mm and groove width of 20 mm. The experiment is carried out with aspect ratio (AR) of 2.9 and Rayleigh number (Ra) in the range, 1.3 x 10(7) - 4 x 10(7). Here AR is the aspect ratio (= width of fluid layer/height of fluid layer). Heat flux at the bottom surface is from electrical heating. From the pH-dye visualization, interesting flow structures are observed and these structures are analyzed with the help of plumes dynamics and temperature variations with time. (C) 2011 Elsevier Ltd. All rights reserved.