Substitution Matrices of Residue Triplets Derived from Protein Blocks.

In protein sequence alignment, residue similarity is usually evaluated by substitution matrix, which scores all possible exchanges of one amino acid with another. Several matrices are widely used in sequence alignment, including PAM matrices derived from homologous sequence and BLOSUM matrices derived from aligned segments of BLOCKS. However, most matrices have not addressed the high-order residue-residue interactions that are vital to the bioproperties of protein.With consideration for the inherent correlation in residue triplet, we present a new scoring scheme for sequence alignment. Protein sequence is treated as overlapping and successive 3-residue segments. Two edge residues of a triplet are clustered into hydrophobic or polar categories, respectively. Protein sequence is then rewritten into triplet sequence with 2 · 20 · 2 = 80 alphabets. Using a traditional approach, we construct a new scoring scheme named TLESUMhp (TripLEt SUbstitution Matrices with hydropobic and polar information) for pairwise substitution of triplets, which characterizes the similarity of residue triplets. The applications of this matrix led to marked improvements in multiple sequence alignment and in searching structurally alike residue segments. The reason for the occurrence of the ‘‘twilight zone,’’ i.e., structure explosion of lowidentity sequences, is also discussed.

A study on water film in saturated sand

Water film can serve as a sliding surface and cause landslides on gentle slopes. The development of "water film" in saturated sand is analyzed numerically and theoretically based on a quasi-three-phase model. It is shown that stable water films initiate and grow if the choking state (where the fluid velocity decreases to near zero) remains steady in a liquefied sand column. Discontinuity can occur in pore water velocity, grain velocity and pore pressure after the initiation of a water film. However, the discontinuity and water film can disappear once the choking state is changed. The key to the formation of water film is the choking in the sand column caused by eroded fine grains.

Numerical investigation of particle velocity distributions in aeolian sand transport

Particle velocity distribution in a blowing sand cloud is a reflection of saltation movement of many particles. Numerical analysis is performed for particle velocity distribution with a discrete particle model. The probability distributions of resultant particle velocity in the impact-entrainment process, particle horizontal and vertical velocities at different heights and the vertical velocity of ascending particles are analyzed. The probability distributions of resultant impact and lift-off velocities of saltating particles can be expressed by a log-normal function, and that of impact angle comply with an exponential function. The probability distribution of particle horizontal and vertical velocities at different heights shows a typical single-peak pattern. In the lower part of saltation layer, the particle horizontal velocity distribution is positively skewed. Further analysis shows that the probability density function of the vertical velocity of ascending particles is similar to the right-hand part of a normal distribution function, and a general equation is acquired for the probability density function of non-dimensional vertical velocity of ascending particles which is independent of diameter of saltating particles, wind strength and height. These distributions in the present numerical analysis are consistent with reported experimental results. The present investigation is important for understanding the saltation state in wind-blown sand movement. (C) 2009 Elsevier B.V. All rights reserved.

Sand storms: CFD analysis of Reynolds stress and collision stress of particles near sand bed

Sand storm is a serious environmental threat to humans. Sand particles are transported by saltation and suspension, causing soil erosion in one place and deposition in another. In order to prevent and predict sand storms, the causes and the manners of particle motions must be studied in detail. In this paper a standard k-epsilon model is used for the gas phase simulation and the discrete element method (DEM) is used to predict the movements of particles using an in-house procedure. The data are summarized in an Eulerian-Eulerian regime after simulation to get the statistical particle Reynolds stress and particle collision stress. The results show that for the current case the Reynolds stress and the air shear stress predominate in the region 20-250 mm above the initial sand bed surface. However, in the region below 3 mm, the collision stress must be taken into account in predicting particle movement. (C) 2010 Chinese Society of Particuology and Institute of Process Engineering, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

CFD-DEM simulation of three-dimensional aeolian sand movement

A three-dimensional CFD-DEM model is proposed to investigate the aeolian sand movement. The results show that the mean particle horizontal velocity can be expressed by a power function of heights. The probability distribution of the impact and lift-off velocities of particles can be described by a log-normal function, and that of the impact and lift-off angles can be expressed by an exponential function. The probability distribution of particle horizontal velocity at different heights can be described as a lognormal function, while the probability distribution of longitudinal and vertical velocity can be described as a normal function. The comparison with previous two-dimensional calculations shows that the variations of mean particle horizontal velocity along the heights in two-dimensional and three-dimensional models are similar. However, the mean particle density of the two-dimensional model is larger than that in reality, which will result in the overestimation of sand transportation rate in the two-dimensional calculation. The study also shows that the predicted probability distributions of particle velocities are in good agreement with the experimental results.

Chemical composition and source characterization of spring aerosol over Horqin sand land in northeastern China

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Optical dating of Holocene sand dune activities in the Horqin sand-fields in inner Mongolia；China；using the SAR protocol

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