On the solution of bivariate population balance equations for aggregation: X-discretization of space for expansion and contraction of computational domain

A new structured discretization of 2D space, named X-discretization, is proposed to solve bivariate population balance equations using the framework of minimal internal consistency of discretization of Chakraborty and Kumar [2007, A new framework for solution of multidimensional population balance equations. Chem. Eng. Sci. 62, 4112-4125] for breakup and aggregation of particles. The 2D space of particle constituents (internal attributes) is discretized into bins by using arbitrarily spaced constant composition radial lines and constant mass lines of slope -1. The quadrilaterals are triangulated by using straight lines pointing towards the mean composition line. The monotonicity of the new discretization makes is quite easy to implement, like a rectangular grid but with significantly reduced numerical dispersion. We use the new discretization of space to automate the expansion and contraction of the computational domain for the aggregation process, corresponding to the formation of larger particles and the disappearance of smaller particles by adding and removing the constant mass lines at the boundaries. The results show that the predictions of particle size distribution on fixed X-grid are in better agreement with the analytical solution than those obtained with the earlier techniques. The simulations carried out with expansion and/or contraction of the computational domain as population evolves show that the proposed strategy of evolving the computational domain with the aggregation process brings down the computational effort quite substantially; larger the extent of evolution, greater is the reduction in computational effort. (C) 2011 Elsevier Ltd. All rights reserved.

On the solution of bivariate population balance equations for aggregation: Pivotwise expansion of solution domain

The solution of a bivariate population balance equation (PBE) for aggregation of particles necessitates a large 2-d domain to be covered. A correspondingly large number of discretized equations for particle populations on pivots (representative sizes for bins) are solved, although at the end only a relatively small number of pivots are found to participate in the evolution process. In the present work, we initiate solution of the governing PBE on a small set of pivots that can represent the initial size distribution. New pivots are added to expand the computational domain in directions in which the evolving size distribution advances. A self-sufficient set of rules is developed to automate the addition of pivots, taken from an underlying X-grid formed by intersection of the lines of constant composition and constant particle mass. In order to test the robustness of the rule-set, simulations carried out with pivotwise expansion of X-grid are compared with those obtained using sufficiently large fixed X-grids for a number of composition independent and composition dependent aggregation kernels and initial conditions. The two techniques lead to identical predictions, with the former requiring only a fraction of the computational effort. The rule-set automatically reduces aggregation of particles of same composition to a 1-d problem. A midway change in the direction of expansion of domain, effected by the addition of particles of different mean composition, is captured correctly by the rule-set. The evolving shape of a computational domain carries with it the signature of the aggregation process, which can be insightful in complex and time dependent aggregation conditions. (c) 2012 Elsevier Ltd. All rights reserved.

The relationship between classification of multi-domain proteins using an alignment-free approach and their functions: a case study with immunoglobulins

Establishing functional relationships between multi-domain protein sequences is a non-trivial task. Traditionally, delineating functional assignment and relationships of proteins requires domain assignments as a prerequisite. This process is sensitive to alignment quality and domain definitions. In multi-domain proteins due to multiple reasons, the quality of alignments is poor. We report the correspondence between the classification of proteins represented as full-length gene products and their functions. Our approach differs fundamentally from traditional methods in not performing the classification at the level of domains. Our method is based on an alignment free local matching scores (LMS) computation at the amino-acid sequence level followed by hierarchical clustering. As there are no gold standards for full-length protein sequence classification, we resorted to Gene Ontology and domain-architecture based similarity measures to assess our classification. The final clusters obtained using LMS show high functional and domain architectural similarities. Comparison of the current method with alignment based approaches at both domain and full-length protein showed superiority of the LMS scores. Using this method we have recreated objective relationships among different protein kinase sub-families and also classified immunoglobulin containing proteins where sub-family definitions do not exist currently. This method can be applied to any set of protein sequences and hence will be instrumental in analysis of large numbers of full-length protein sequences.

Structure, interactions and evolutionary implications of a domain-swapped lectin dimer from Mycobacterium smegmatis

Crystal structure determination of the lectin domain of MSMEG_3662 from Mycobacterium smegmatis and its complexes with mannose and methyl-alpha-mannose, the first effort of its kind on a mycobacterial lectin, reveals a structure very similar to beta-prism II fold lectins from plant sources, but with extensive unprecedented domain swapping in dimer formation. The two subunits in a dimer often show small differences in structure, but the two domains, not always related by 2-fold symmetry, have the same structure. Each domain carries three sugar-binding sites, similar to those in plant lectins, one on each Greek key motif. The occurrence of beta-prism II fold lectins in bacteria, with characteristics similar to those from plants, indicates that this family of lectins is of ancient origin and had evolved into a mature system before bacteria and plants diverged. In plants, the number of binding sites per domain varies between one and three, whereas the number is two in the recently reported lectin domains from Pseudomonas putida and Pseudomonas aeruginosa. An analysis of the sequences of the lectins and the lectin domains shows that the level of sequence similarity among the three Greek keys in each domain has a correlation with the number of binding sites in it. Furthermore, sequence conservation among the lectins from different species is the highest for that Greek key which carries a binding site in all of them. Thus, it would appear that carbohydrate binding influences the course of the evolution of the lectin.

Optimum Parameter Selection in Sparse Reconstruction of Frequency-Domain Optical-Coherence Tomography Signals

For a multilayered specimen, the back-scattered signal in frequency-domain optical-coherence tomography (FDOCT) is expressible as a sum of cosines, each corresponding to a change of refractive index in the specimen. Each of the cosines represent a peak in the reconstructed tomogram. We consider a truncated cosine series representation of the signal, with the constraint that the coefficients in the basis expansion be sparse. An l(2) (sum of squared errors) data error is considered with an l(1) (summation of absolute values) constraint on the coefficients. The optimization problem is solved using Weiszfeld's iteratively reweighted least squares (IRLS) algorithm. On real FDOCT data, improved results are obtained over the standard reconstruction technique with lower levels of background measurement noise and artifacts due to a strong l(1) penalty. The previous sparse tomogram reconstruction techniques in the literature proposed collecting sparse samples, necessitating a change in the data capturing process conventionally used in FDOCT. The IRLS-based method proposed in this paper does not suffer from this drawback.

Semi-automatic generation of learning domain modules for technology supported learning systems

In a time when Technology Supported Learning Systems are being widely used, there is a lack of tools that allows their development in an automatic or semi-automatic way. Technology Supported Learning Systems require an appropriate Domain Module, ie. the pedagogical representation of the domain to be mastered, in order to be effective. However, content authoring is a time and effort consuming task, therefore, efforts in automatising the Domain Module acquisition are necessary.Traditionally, textbooks have been used as the main mechanism to maintain and transmit the knowledge of a certain subject or domain. Textbooks have been authored by domain experts who have organised the contents in a means that facilitate understanding and learning, considering pedagogical issues.Given that textbooks are appropriate sources of information, they can be used to facilitate the development of the Domain Module allowing the identification of the topics to be mastered and the pedagogical relationships among them, as well as the extraction of Learning Objects, ie. meaningful fragments of the textbook with educational purpose.Consequently, in this work DOM-Sortze, a framework for the semi-automatic construction of Domain Modules from electronic textbooks, has been developed. DOM-Sortze uses NLP techniques, heuristic reasoning and ontologies to fulfill its work. DOM-Sortze has been designed and developed with the aim of automatising the development of the Domain Module, regardless of the subject, promoting the knowledge reuse and facilitating the collaboration of the users during the process.

Trawling gear and towing power of the Nigerian inshore fishing trawlers

This paper deals with the relation between trawling gear and towing power of the Nigerian inshore fishing trawlers. Information on the size as well as weight variations of the existing otter boards as they relate to the horse power of the engine and length of warps in relation to fishing depth are given