Valipuram S. Manoranjan

Macropore transport of bromide as influenced by soil structure differences

Macropore transport of chemicals in soil often causes unexpected contamination of groundwater. The effect of soil structure on the functions of various sized macropores was assessed, investigating transport of nonreactive bromide (Br) under matric heads of 0, � 2, � 5 and � 10 cm using undisturbed soil columns from A, Bw and E horizons of a Thatuna silt loam soil (fine-silty, mixed, mesic Xeric Argialbolls). The experimental breakthrough curves (BTC) for Br were described with a two-region physical nonequilibrium model. Greatest macroporosity occurred in the A horizon and lowest in the E horizon. The measured pore water velocity m under saturated conditions ranged from 18.92 cm day � 1 in the E horizon to 64.28 cm day � 1 in the A horizon. While the greatest dispersivity k occurred in the Bw horizon due to medium subangular blocky and prizmatic aggregates, the lowest dispersivity occurred in the E horizon due to its low macroporosity and massive structure. The fitted mobile water partitioning coefficient b ranged from 0.30 in the A horizon under 0 cm matric head to 0.93 in the E horizon under 0 cm matric head. The calculated values of rate of diffusive mass exchange a decreased with decreasing matric head in A and Bw horizons, and slightly increased and then decreased in the E horizon. The difference among each of the values of the parameters m, b, a and k for the A, Bw and E horizons was greatest under saturated conditions. However, gradually decreasing matric head until about � 3 cm decreased the difference among the values for a particular parameter for different horizons, sharply. The difference remained fairly unchanged with further decreases in the matric head, suggesting that most of the variability in macropore transport of bromide for these horizons caused by pores with radii larger than about 0.5 mm. In A and Bw horizons, there was a sudden change in soil solution movement between � 2 and � 5 cm matric head, indicating that macropore flow generally occurred at matric heads greater than

Reactomes of porcine alveolar macrophages infected with porcine reproductive and respiratory syndrome virus.

Porcine reproductive and respiratory syndrome (PRRS) has devastated pig industries worldwide for many years. It is caused by a small RNA virus (PRRSV), which targets almost exclusively pig monocytes or macrophages. In the present study, five SAGE (serial analysis of gene expression) libraries derived from 0 hour mock-infected and 6, 12, 16 and 24 hours PRRSV-infected porcine alveolar macrophages (PAMs) produced a total 643,255 sequenced tags with 91,807 unique tags. Differentially expressed (DE) tags were then detected using the Bayesian framework followed by gene/mRNA assignment, arbitrary selection and manual annotation, which determined 699 DE genes for reactome analysis. The DAVID, KEGG and REACTOME databases assigned 573 of the DE genes into six biological systems, 60 functional categories and 504 pathways. The six systems are: cellular processes, genetic information processing, environmental information processing, metabolism, organismal systems and human diseases as defined by KEGG with modification. Self-organizing map (SOM) analysis further grouped these 699 DE genes into ten clusters, reflecting their expression trends along these five time points. Based on the number one functional category in each system, cell growth and death, transcription processes, signal transductions, energy metabolism, immune system and infectious diseases formed the major reactomes of PAMs responding to PRRSV infection. Our investigation also focused on dominant pathways that had at least 20 DE genes identified, multi-pathway genes that were involved in 10 or more pathways and exclusively-expressed genes that were included in one system. Overall, our present study reported a large set of DE genes, compiled a comprehensive coverage of pathways, and revealed system-based reactomes of PAMs infected with PRRSV. We believe that our reactome data provides new insight into molecular mechanisms involved in host genetic complexity of antiviral activities against PRRSV and lays a strong foundation for vaccine development to control PRRS incidence in pigs.

On designing a fuzzy control system using an optimization algorithm

Abstract Fuzzy logic in control systems is becoming increasingly popular as a method of handling non-linear control problems. The design of fuzzy systems is generally undertaken using a trial-and-error approach. A system so developed may be less than optimum and often this is the case for known examples of control systems. Currently, there is no procedure for optimization which is appropriate for every system. In this paper a method to design and to optimize a fuzzy control system is developed. The results of computer simulations of a system constructed using this technique are presented and discussed.

A systematic approach to obtaining fuzzy sets for control systems

The behavior of a control practitioner, who may be acting only on subjective or intuitive knowledge could be represented by one or more fuzzy subsets of the set (assumed to be finite) of all states of a controlled system. In this paper a systematic approach is proposed for determining the grades of membership of such fuzzy sets. These sets and the plant are then optimized against a performance index. The results of applying this method to a particular second order system are presented and then compared with those obtained by using a continuous deterministic model of the same plant. Implications for the design of controllers are then drawn. >

Exact Solution for Contaminant Transport with Kinetic Langmuir Sorption

We study a contaminant transport model with Langmuir sorption under nonequilibrium conditions and show that the aqueous phase concentration profile can be obtained exactly in the form of a traveling wave front. The methodology of finding the exact solution is outlined, and an illustrative example is presented.

Lead-Acid Battery Model Under Discharge With a Fast Splitting Method

A mathematical model of a valve-regulated lead-acid battery under discharge is presented as simplified from a standard electrodynamics model. This nonlinear reaction-diffusion model of a battery cell is solved using an operator splitting method to quickly and accurately simulate sulfuric acid concentration. This splitting method incorporates one-sided approximation schemes to preserve continuity over material interfaces encompassing discontinuous parameters. Numerical results are compared with measured data by calculating battery voltage from modeled acid concentration as derived from the Nernst equation.

Allostery through protein-induced DNA bubbles

Allostery through DNA is increasingly recognized as an important modulator of DNA functions. Here, we show that the coalescence of protein-induced DNA bubbles can mediate allosteric interactions that drive protein aggregation. We propose that such allostery may regulate DNAs flexibility and the assembly of the transcription machinery. Mitochondrial transcription factor A (TFAM), a dual-function protein involved in mitochondrial DNA (mtDNA) packaging and transcription initiation, is an ideal candidate to test such a hypothesis owing to its ability to locally unwind the double helix. Numerical simulations demonstrate that the coalescence of TFAM-induced bubbles can explain experimentally observed TFAM oligomerization. The resulting melted DNA segment, approximately 10 base pairs long, around the joints of the oligomers act as flexible hinges, which explains the efficiency of TFAM in compacting DNA. Since mitochondrial polymerase (mitoRNAP) is involved in melting the transcription bubble, TFAM may use the same allosteric interaction to both recruit mitoRNAP and initiate transcription.

A two-step Jacobi-type iterative method

Abstract In multigrid methods, it is preferred to employ smoothing techniques which are convergent. In practice, the standard Jacobi and Gauss-Seidel methods are the choices for “smoothers” However, it is known that if the spectral radius condition is violated, then convergence is not guaranteed for these methods. In this paper we develop a simple two-step Jacobi-type method which has better convergence properties and which can be employed as a convergent “smoother” wherever the standard iterative methods fail. We provide the convergence proofs and demonstrate the applicability of the method on a variety of problems.

Analysis of a population model with efficient resource utilization

Abstract In this paper we study a population model that incorporates the efficiency of resource utilization. We carry out a phase plane analysis of themodel and look at the solution behavior when the model is posed as an initial boundary value problem. The study involves using MATLAB and doing numerical simulations employing a finite difference scheme. The results are contrasted to the logistic population model.

Travelling wave solutions of a contaminant transport model with nonlinear sorption

We study a contaminant transport model with a cubic sorption isotherm. It is shown that aqueous concentration profiles can be obtained exactly in the form of homoclinic and heteroclinic waves. We describe the method of obtaining such exact solutions and present the solutions along with the corresponding phase plane portraits. This paper generalizes our earlier work [1].