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.

Theoretical foundation of Zisman's empirical equation for wetting of liquids on solid surfaces

Theories of wetting of liquids on solid surfaces under the condition that van der Waals force is dominant are briefly reviewed. We show theoretically that Zisman's empirical equation for wetting of liquids on solid surfaces is a linear approximation of the Young-van der Waals equation in the wetting region, and we express the two parameters in Zisman's empirical equation in terms of the dielectric polarizabilities of the solid and liquids. The materials contained in this paper are suitable for physics teaching of wetting phenomena for undergraduate, graduate, general physicist, etc.

Effects of convection and solid wall on the diffusion in microscale convection flows

The diffusive transport properties in microscale convection flows are studied by using the direct simulation Monte Carlo method. The effective diffusion coefficient D is computed from the mean square displacements of simulated molecules based on the Einstein diffusion equation D = x2 t /2t. Two typical convection flows, namely, thermal creep convection and Rayleigh– Bénard convection, are investigated. The thermal creep convection in our simulation is in the noncontinuum regime, with the characteristic scale of the vortex varying from 1 to 100 molecular mean free paths. The diffusion is shown to be enhanced only when the vortex scale exceeds a certain critical value, while the diffusion is reduced when the vortex scale is less than the critical value. The reason for phenomenon of diffusion reduction in the noncontinuum regime is that the reduction effect due to solid wall is dominant while the enhancement effect due to convection is negligible. A molecule will lose its memory of macroscopic velocity when it collides with the walls, and thus molecules are hard to diffuse away if they are confined between very close walls. The Rayleigh– Bénard convection in our simulation is in the continuum regime, with the characteristic length of 1000 molecular mean free paths. Under such condition, the effect of solid wall on diffusion is negligible. The diffusion enhancement due to convection is shown to scale as the square root of the Péclet number in the steady convection regime, which is in agreement with previous theoretical and experimental results. In the oscillation convection regime, the diffusion is more strongly enhanced because the molecules can easily advect from one roll to its neighbor due to an oscillation mechanism. © 2010 American Institute of Physics. doi:10.1063/1.3528310

Slow highly charged ion O4+ induced electron emission from clean solid surfaces

The. total electron emission yields following the interaction of slow highly charged ions (SHCI) O4+ with different material surfaces (W, Au, Si and SiO2) have been measured. It is found that the electron emission yield gamma increases proportionally with the projectile velocity v ranging from 5.36 x 10(5)m/s to 10.7 x 10(5)m/s. The total emission yield is dependent on the target materials, and it turns out to follow the relationship gamma(Au) > gamma(Si)> gamma(W). The result shows that the electron emission yields are mainly determined by the electron stopping power of the target when the projectile potential energy is taken as a constant, which is in good agreement with the former studies