Prediction of nonlocal scaling parameter for armchair and zigzag single-walled carbon nanotubes based on molecular structural mechanics, nonlocal elasticity and wave propagation

Atomic vibration in the Carbon Nanotubes (CNTs) gives rise to non-local interactions. In this paper, an expression for the non-local scaling parameter is derived as a function of the geometric and electronic properties of the rolled graphene sheet in single-walled CNTs. A self-consistent method is developed for the linearization of the problem of ultrasonic wave propagation in CNTs. We show that (i) the general three-dimensional elastic problem leads to a single non-local scaling parameter (e(0)), (ii) e(0) is almost constant irrespective of chirality of CNT in the case of longitudinal wave propagation, (iii) e(0) is a linear function of diameter of CNT for the case of torsional mode of wave propagation, (iv) e(0) in the case of coupled longitudinal-torsional modes of wave propagation, is a function which exponentially converges to that of axial mode at large diameters and to torsional mode at smaller diameters. These results are valid in the long-wavelength limit. (C) 2011 Elsevier Ltd. All rights reserved.

Prediction of protein-protein interactions between human host and a pathogen and its application to three pathogenic bacteria

Molecular understanding of disease processes can be accelerated if all interactions between the host and pathogen are known. The unavailability of experimental methods for large-scale detection of interactions across host and pathogen organisms hinders this process. Here we apply a simple method to predict protein-protein interactions across a host and pathogen organisms. We use homology detection approaches against the protein-protein interaction databases. DIP and iPfam in order to predict interacting proteins in a host-pathogen pair. In the present work, we first applied this approach to the test cases involving the pairs phage T4 - Escherichia coli and phage lambda - E. coli and show that previously known interactions could be recognized using our approach. We further apply this approach to predict interactions between human and three pathogens E. coli, Salmonella enterica typhimurium and Yersinia pestis. We identified several novel interactions involving proteins of host or pathogen that could be thought of as highly relevant to the disease process. Serendipitously, many interactions involve hypothetical proteins of yet unknown function. Hypothetical proteins are predicted from computational analysis of genome sequences with no laboratory analysis on their functions yet available. The predicted interactions involving such proteins could provide hints to their functions. (C) 2011 Elsevier B.V. All rights reserved.

Prediction of separation factor in foam separation of proteins

A phenomenological model has been developed for predicting separation factors obtained in concentrating protein solutions using batch-foam columns. The model considers the adsorption of surface active proteins onto the air-water interface of bubbles, and drainage of liquid from the foam, which are the two predominant processes responsible for separation in foam columns. The model has been verified with data collected on casein and bovine serum albumin (BSA) solutions, for which adsorption isotherms are available in the literature. It has been found that an increase in liquid pool height above the gas distributor and the time allowed for drainage result in a better separation. Further, taller foam columns yield poorer separation at constant time of drainage. The model successfully predicts the observed results. (C) 1997 Elsevier Science Ltd.

Prediction of the senses of helical amphiphilic assemblies from effective intermolecular pair potential: Studies on chiral monolayers and bilayers

It is well-known that the senses (or the handedness) of the helical assemblies formed from compressed monolayers and bilayers of chiral amphiphiles are highly specific about the chirality of the monomers concerned. We present here a molecular approach that can successfully predict the senses of such helical morphologies. The present approach is based on a reduced tractable description in terms of an effective pair potential (EPP) which depends on the distance of separation and the relative orientations of the two amphiphiles. This approach explicitly considers the pairwise intermolecular interactions between the groups attached to the chiral centers of the two neighboring amphiphiles. It is found that for a pair of the same kind of enantiomers the minimum energy configuration favors a twist angle between molecules and that this twist from neighbor to neighbor gives rise to the helicity of the aggregate. From the known twist angles at the minimum energy configuration the successive arrangement of an array of molecules can be predicted. Therefore, the sense of the helicity can be predicted from the molecular interactions. The predicted senses of the helical structures are in complete agreement with all known experimental results.

Prediction of reaeration rates in square, stirred tanks

Experiments were conducted on the oxygen transfer coefficient, k(L)a(20), through surface aeration in geometrically similar square tanks, with a rotor of diameter D fitted with six flat blades. An optimal geometric similarity of various linear dimensions, which produced maximum k(L)a(20) for any rotational speed of rotor N by an earlier study, was maintained. A simulation equation uniquely correlating k = k(L)a(20)(nu/g(2))(1/3) (nu and g are kinematic viscosity of water and gravitational constant, respectively), and a parameter governing the theoretical power per unit volume, X = (ND2)-D-3/(g(4/3)nu(1/3)), is developed. Such a simulation equation can be used to predict maximum k for any N in any size of such geometrically similar square tanks. An example illustrating the application of results is presented. Also, it has been established that neither the Reynolds criterion nor the Froude criterion is singularly valid to simulate either k or K = k(L)a(20)/N, simultaneously in all the sizes of tanks, even through they are geometrically similar. Occurrence of "scale effects" due to the Reynolds and the Froude laws of similitude on both k and K are also evaluated.

DNA Free Energy-Based Promoter Prediction and Comparative Analysis of Arabidopsis and Rice Genomes

The cis-regulatory regions on DNA serve as binding sites for proteins such as transcription factors and RNA polymerase. The combinatorial interaction of these proteins plays a crucial role in transcription initiation, which is an important point of control in the regulation of gene expression. We present here an analysis of the performance of an in silico method for predicting cis-regulatory regions in the plant genomes of Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) on the basis of free energy of DNA melting. For protein-coding genes, we achieve recall and precision of 96% and 42% for Arabidopsis and 97% and 31% for rice, respectively. For noncoding RNA genes, the program gives recall and precision of 94% and 75% for Arabidopsis and 95% and 90% for rice, respectively. Moreover, 96% of the false-positive predictions were located in noncoding regions of primary transcripts, out of which 20% were found in the first intron alone, indicating possible regulatory roles. The predictions for orthologous genes from the two genomes showed a good correlation with respect to prediction scores and promoter organization. Comparison of our results with an existing program for promoter prediction in plant genomes indicates that our method shows improved prediction capability.

An investigation into the feasibility of fetal lung maturity prediction using statistical textural features

Fetal lung and liver tissues were examined by ultrasound in 240 subjects during 24 to 38 weeks of gestational age in order to investigate the feasibility of predicting the maturity of the lung from the textural features of sonograms. A region of interest of 64 X 64 pixels is used for extracting textural features. Since the histological properties of the liver are claimed to remain constant with respect to gestational age, features obtained from the lung region are compared with those from liver. Though the mean values of some of the features show a specific trend with respect to gestation age, the variance is too high to guarantee definite prediction of the gestational age. Thus, we restricted our purview to an investigation into the feasibility of fetal lung maturity prediction using statistical textural features. Out of 64 features extracted, those features that are correlated with gestation age and less computationally intensive are selected. The results of our study show that the sonographic features hold some promise in determining whether the fetal lung is mature or immature.

Stress-Strain Prediction of Jointed Rocks using Artificial Neural Networks

The applicability of Artificial Neural Networks for predicting the stress-strain response of jointed rocks at varied confining pressures, strength properties and joint properties (frequency, orientation and strength of joints) has been studied in the present paper. The database is formed from the triaxial compression tests on different jointed rocks with different confining pressures and different joint properties reported by various researchers. This input data covers a wide range of rock strengths, varying from very soft to very hard. The network was trained using a 3 layered network with feed forward back propagation algorithm. About 85% of the data was used for training and remaining15% for testing the predicting capabilities of the network. Results from the analyses were very encouraging and demonstrated that the neural network approach is efficient in capturing the complex stress-strain behaviour of jointed rocks. A single neural network is demonstrated to be capable of predicting the stress-strain response of different rocks, whose intact strength vary from 11.32 MPa to 123 MPa and spacing of joints vary from 10 cm to 100 cm for confining pressures ranging from 0 to 13.8 MPa.