FRASS: the web-server for RNA structural comparison

<p>Abstract</p> <p>Background</p> <p>The impressive increase of novel RNA structures, during the past few years, demands automated methods for structure comparison. While many algorithms handle only small motifs, few techniques, developed in recent years, (ARTS, DIAL, SARA, SARSA, and LaJolla) are available for the structural comparison of large and intact RNA molecules.</p> <p>Results</p> <p>The FRASS web-server represents a RNA chain with its Gauss integrals and allows one to compare structures of RNA chains and to find similar entries in a database derived from the Protein Data Bank. We observed that FRASS scores correlate well with the ARTS and LaJolla similarity scores. Moreover, the-web server can also reproduce satisfactorily the DARTS classification of RNA 3D structures and the classification of the SCOR functions that was obtained by the SARA method.</p> <p>Conclusions</p> <p>The FRASS web-server can be easily used to detect relationships among RNA molecules and to scan efficiently the rapidly enlarging structural databases.</p

Computation of protein geometry and its applications: Packing and function prediction

This chapter discusses geometric models of biomolecules and geometric constructs, including the union of ball model, the weigthed Voronoi diagram, the weighted Delaunay triangulation, and the alpha shapes. These geometric constructs enable fast and analytical computaton of shapes of biomoleculres (including features such as voids and pockets) and metric properties (such as area and volume). The algorithms of Delaunay triangulation, computation of voids and pockets, as well volume/area computation are also described. In addition, applications in packing analysis of protein structures and protein function prediction are also discussed.Comment: 32 pages, 9 figure

Wettability alteration in carbonates: the effect of water-soluble carboxylic acids in crude oil

"Reprinted (adapted) with permission from Fathi, S J., Austad, T., Strand S., Puntervold, T. (2010) Wettability alteration in carbonates: the effect of water-soluble carboxylic acids in crude oil. Energy & Fuels 24(5), pp. 2974–2979. Copyright (2010) American Chemical Society. The article forms part of Jafar Fathi's PhD thesis: Water-based enhanced oil recovery (EOR) in carbonate reservoirs : initial wetting condition and wettability alteration by "Smart Water", Stavanger : University of StavangerAcidic components in crude oil influence the wetting condition through their effect on electrostatic interactions with the mineral surfaces. In this paper, we have extracted water-soluble acids from a crude oil with a high acid number (AN) to study the effect of these acidic materials on the wetting condition. The AN for the original oil was 1.8 mg of KOH/g, while the AN for the oil depleted in water-soluble acids was 1.5 mg of KOH/g. Two crude oils have been studied by a chromatographic wettability test and spontaneous imbibition using seawater as imbibing fluid to determine the differences in the wetting condition and oil recovery. In a spontaneous imbibition process at 110 °C, both the imbibition rate and ultimate recovery were higher in the cores saturated with the oil depleted in water-soluble acids. The difference in the imbibition rate and also ultimate recovery indicates that the carboxylic material from the oil depleted in water-soluble acids can be displaced easily compared to the original oil. The difference in wetting properties was also confirmed by chromatographic wettability tests. The water wetness appeared to be lower for the original oil compared to that for the treated oil. These crude oils were also investigated with respect to interfacial intension. Even though the strength of the bonding of carboxylic material onto the calcite surface is mostly dictated by the carboxylic group, the organic structure of the carboxylic material will have an influence on the wettability alteration process as well

Effect of water-extractable carboxylic acids in crude oil on wettability in carbonates

Reprinted (adapted) with permission from Fathi, S J., Austad, T., Strand S. (2011) Effect of water-extractable carboxylic acids in crude oil on wettability in carbonates. Energy & Fuels 25(6), pp. 2587–2592. Copyright (2011) American Chemical Society. The article forms part of the Jafar Fathi's PhD thesis : Fathi, J. (2011) Water-Based Enhanced Oil Recovery (EOR) by "Smart Water" in Carbonate Reservoirs. University of Stavanger.The acidic components of the crude oil have a profound effect on the initial wetting conditions and possible wettability alteration by seawater in carbonates. In this work, three types of crude oils with different concentrations of water-extractable acidic components were prepared from a base oil: (1) a reference oil, RES-40 [acid number (AN) = 1.90 mg of KOH/g and base number (BN) = 0.51 mg of KOH/g], (2) a treated oil depleted in water-extractable acidic components, termed treated oil (TO) (AN = 1.50 mg of KOH/g and BN = 0.53 mg of KOH/g), and (3) a crude oil containing only water-extractable acidic components, termed EWS-oil (AN = 1.90 mg of KOH/g and BN < 0.01 mg of KOH/g). Outcrop chalk cores were used as the porous medium, and the difference in oil displacement efficiency and wettability was compared. The spontaneous imbibition (SI) process was performed in two steps: first imbibing with formation water without any wettability modification and then with seawater, which acted as a wettability modifier. The oil recovery decreased as the content of water-extractable acidic material in the crude oil increased, for both formation water and seawater as imbibing fluids. The difference in wetting properties was also confirmed by chromatographic wettability analysis. The water wetness appeared to be lower for the cores saturated with the crude oil containing only water-extractable acids. It was concluded that water-extractable carboxylic acids present in crude oil have a great impact on the stability of the water film between the carbonate surface and the oil and seawater was less efficient as a wettability modifier when the extractable acids were adsorbed onto the carbonate surface. Observations from both SI and chromatographic wettability tests emphasize the importance of acid structures or acid types present in the crude oil compared to the acid concentrations

Mathematical problems for Moineau pumps

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Mathematical problems for Moineau pumps

No abstract