Automatic ultrastructure segmentation of reconstructed cryoEM maps of icosahedral viruses.

We present an automatic algorithm to segment all the local and global asymmetric units of a three-dimensional density map of icosahedral viruses. This approach is readily applicable to the structural analysis of a broad range of virus structures that are reconstructed using cryo-electron microscopy (cryo-EM) technique. Our algorithm includes three major steps operating on the three dimensional density map: the detection of critical points of the volumetric density function, the detection of global and local symmetry axes, and, finally, the boundary segmentation of all the asymmetric units. We demonstrate the efficacy of our algorithm and report our results on several experimental volumetric datasets, consisting of both reconstructed cryo-EM molecular density maps taken from the European Bioinformatics Institute archive, as well our own synthetically generated (blurred) maps calculated from X-ray resolution molecular structural data taken from the Protein Data Bank.     

Modelling and kinetic aspects of a BTEX contaminated air-treating biofilter

In this study, the overall performance of a biofilter was evaluated in terms of its elimination capacity by using 3-D mesh techniques. The overall results indicate that the agreement between experimental data and model predictions is excellent for benzene, toluene, ethylbenzene and o-xylene (BTEX). In this study, the maximum removal rate (r _max) values for BTEX were 0.0117, 0.0126, 0.0081 and 0.0146 g m^–3 h^–1, and the half-saturation constant (K_S ) values were calculated to be 0.269, 0.297, 0.156 and 0.394 g m^–3, respectively. For this system, the coefficients of determination (r ²) of BTEX compounds were greater than 0.97. The BTEX concentration profiles along the depth were also determined using a convection–diffusion reactor (CDR) model. The sums of squares of the errors (SSEs) of BTEX were 0.0078, 0.0059, 0.0129 and 0.0269, respectively, with r ² values greater than 0.99 for all four compounds at low concentrations.     

ADSORPTIVE TREATMENT OF CYANIDE-BEARING WASTEWATER: A PROSPECT FOR SUGAR INDUSTRY WASTE

The biosorption of cyanide ions from aqueous solution by bagasse was studied in a batch adsorption system with pH, contact time, cyanide ion concentration, metal ion concentration, and adsorbent dosage as variables. XRD, FT-IR spectroscopy, CHN, proximate, ultimate, and TG/DTG thermal analyses were used for the characterization of bagasse. The biosorption capacities and rates of biosorption of cyanide ions onto bagasse were evaluated. The Langmuir and Freundlich adsorption models were applied to describe the isotherms and isotherm constants. Biosorption isothermal data were interpreted by the Langmuir model followed by the Freundlich model with maximum adsorption capacity of 98% of cyanide ion on bagasse. The kinetic experimental data were properly correlated with the first- and second-order kinetic model.     

Kinetics of the removal of mono-chlorobenzene vapour from waste gases using a trickle bed air biofilter

The performance of a trickle bed air biofilter (TBAB) in the removal of mono-chlorobenzene (MCB) was evaluated in concentrations varying from 0.133 to 7.187 g m(-3) and at empty bed residence time (EBRT) varying from 37.7 to 188.52 s. More than 90% removal efficiency in the trickle bed air biofilter was achieved for the inlet MCB concentration up to 1.069 g m(-3) and EBRT less than 94.26 s. The trickle bed air biofilter was constructed with coal packing material, inoculated with a mixed consortium of activated sludge obtained from sewage treatment plant. The continuous performance of the removal of MCB in the trickle bed air biofilter was monitored for various gas concentrations, gas flow rates, and empty bed residence time. The experiment was conducted for a period of 75 days. The trickle bed air biofilter degrading MCB with an average elimination capacity of 80 g m(-3) h(-1) was obtained. The effect of starvation was also studied. After starvation period of 8 days, the degradation was low but recovered within a short period of time. Using macrokinetic determination method, the Michaelis-Menten kinetic constant K(m) and maximum reaction rate, r(max) evaluated as 0.121 g m(-3) s(-1) and 7.45 g m(-3), respectively.     

Approximating the Generalized Voronoi Diagram of Closely Spaced Objects

We present an algorithm to compute an approximation of the generalized Voronoi diagram (GVD) on arbitrary collections of 2D or 3D geometric objects. In particular, we focus on datasets with closely spaced objects; GVD approximation is expensive and sometimes intractable on these datasets using previous algorithms. With our approach, the GVD can be computed using commodity hardware even on datasets with many, extremely tightly packed objects. Our approach is to subdivide the space with an octree that is represented with an adjacency structure. We then use a novel adaptive distance transform to compute the distance function on octree vertices. The computed distance field is sampled more densely in areas of close object spacing, enabling robust and parallelizable GVD surface generation. We demonstrate our method on a variety of data and show example applications of the GVD in 2D and 3D.     

Biodesulfurization of dibenzothiophene using recombinant Pseudomonas strain

BACKGROUND: The sulfur content in crude oil available from various sources ranges from 0.03 to values as high as 8.0 wt%. These high quantities of sulfur must be removed before the crude oil is processed because combustion of this oil would result in severe environmental pollution, such as acid rain. Due to high utility and operating costs, the conventional hydrodesulfurization process (HDS) is considered to be uneconomic. The biotechnological option, biodesulfurization (BDS) seems an attractive low cost, environmentally benign technology. RESULTS: This paper reports the development of a recombinant strain of bacteria designed by introducing desulfurizing, dsz genes containing plasmid pSAD 225‐32, which was isolated from Rhodococcus erythropolis IGTS8 into a gram negative solvent‐tolerant bacterium, Pseudomonas putida (MTCC 1194). This recombinant bacterium can desulfurize the dibenzothiophene (DBT) in the sulfur selective 4S‐pathway. It has been observed that for the same concentration of DBT, the recombinant strain's growth rate is greater than that of the parent strain. Increasing the concentration of DBT resulted in an increase of lag phase as well as decreased growth rate, which shows that the bacteria is following substrate inhibition type kinetics. This genetically modified bacterium can desulfurize 73.1% of 1.2 mmol L^?1 DBT (dissolved in ethanol) in 67 h of cultivation time using growing cells. CONCLUSIONS: It is concluded that further research in this area of biodesulfurization using genetically modified organisms may remove the bottlenecks presently in the way of commercialization of the BDS process. Copyright © 2007 Society of Chemical Industry     

An automatic 3D mesh generation method for domains with multiple materials

This paper describes an automatic and efficient approach to construct unstructured tetrahedral and hexahedral meshes for a composite domain made up of heterogeneous materials. The boundaries of these material regions form non-manifold surfaces. In earlier papers, we developed an octree-based isocontouring method to construct unstructured 3D meshes for a single material (homogeneous) domain with manifold boundary. In this paper, we introduce the notion of a material change edge and use it to identify the interface between two or several different materials. A novel method to calculate the minimizer point for a cell shared by more than two materials is provided, which forms a non-manifold node on the boundary. We then mesh all the material regions simultaneously and automatically while conforming to their boundaries directly from volumetric data. Both material change edges and interior edges are analyzed to construct tetrahedral meshes, and interior grid points are analyzed for proper hexahedral mesh construction. Finally, edge-contraction and smoothing methods are used to improve the quality of tetrahedral meshes, and a combination of pillowing, geometric flow and optimization techniques is used for hexahedral mesh quality improvement. The shrink set of pillowing schemes is defined automatically as the boundary of each material region. Several application results of our multi-material mesh generation method are also provided.     

Multiwalled CNTs for Cr(VI) removal from industrial wastewater: An advanced study on adsorption,kinetics, thermodynamics for the comparison between the embedded and non‐embedded carboxyl group

The adsorption capabilities of multiwalled carbon nanotubes (MWCNTs) with and without the embedded carboxyl group for the removal of parts per million levels of hexavalent chromium were examined as a function of several parameters, namely contact time, pH of initial solution, initial concentration of Cr(VI), adsorbent dosage as well as temperature of solution. Adsorption isotherms have been utilized to explain the adsorption mechanism. Ion exchange, intra‐particle diffusion, and electrostatic interactions are found to be the fundamental mechanisms describing the adsorption of Cr(VI). The maximum adsorption capacities of Cr(VI) ion by raw MWCNTs and functionalized MWCNTs were found to be 84.75 and 78.13 mg · g^?1, respectively, as calculated by the Langmuir adsorption isotherm model. This is with regard to the electron‐rich atoms inside the functional group which repels the negatively charged dichromate ions. Kinetic studies were performed, and the data was found in good agreement with the pseudo‐second‐order.     

SIMD Optimization of Linear Expressions for Programmable Graphics Hardware

The increased programmability of graphics hardware allows efficient graphical processing unit (GPU) implementations of a wide range of general computations on commodity PCs. An important factor in such implementations is how to fully exploit the SIMD computing capacities offered by modern graphics processors. Linear expressions in the form of , where A is a matrix, and and are vectors, constitute one of the most basic operations in many scientific computations. In this paper, we propose a SIMD code optimization technique that enables efficient shader codes to be generated for evaluating linear expressions. It is shown that performance can be improved considerably by efficiently packing arithmetic operations into four‐wide SIMD instructions through reordering of the operations in linear expressions. We demonstrate that the presented technique can be used effectively for programming both vertex and pixel shaders for a variety of mathematical applications, including integrating differential equations and solving a sparse linear system of equations using iterative methods.