An Amino Acid Substitution Matrix for Protein Conformation Identification

Amino acid substitution matrices play an essential role in protein sequence alignment, a fundamental task in bioinformatics. Most widely used matrices, such as PAM matrices derived from homologous sequences and BLOSUM matrices derived from aligned segments of PROSITE, did not integrate conformation information in their construction. There are a few structure-based matrices, which are derived from limited data of structure alignment. Using databases PDB_SELECT and DSSP, we create a database of sequence-conformation blocks which explicitly represent sequence-structure relationship. Members in a block are identical in conformation and are highly similar in sequence. From this block database, we derive a conformation-specific amino acid substitution matrix CBSM60. The matrix shows an improved performance in conformational segment search and homolog detection.

Flow Stress of Biomorphous Metal-Matrix Composites

For metal-matrix composites (MMCs), interfacial debonding between the ductile matrix and the reinforcing hard inclusions is an important failure mode. A fundamental approach to improving the properties of MMCs is to optimize their microstructure to achieve maximum strength and toughness. Here, we investigate the flow stress of a MMC with a nanoscale microstructure similar to that of bone. Such a 'biomorphous' MMC would be made of staggered hard and slender nanoparticles embedded in a ductile matrix. We show that the large aspect ratio and the nanometer size of inclusions in the biomorphous MMC lead to significantly improved properties with increased tolerance of interfacial damage. In this case, the partially debonded inclusions continue to carry mechanical load transferred via longitudinal shearing of the matrix material between neighboring inclusions. The larger the inclusion aspect ratio, the larger is the flow stress and work hardening rate for the composite. Increasing the volume concentration of inclusion also makes the biomorphous MMC more tolerant of interfacial damage.

Material response and failure mechanism of unidirectional metal matrix composites under impulsive shear loading

The material response and failure mechanism of unidirectional metal matrix composite under impulsive shear loading are investigated in this paper. Both experimental and analytical studies were performed. The shear strength of unidirectional C-f/A356.0 composite and A356.0 aluminum alloy at high strain rate were measured with a modified split Hopkinson torsional bar technique. The results indicated that the carbon fibers did not improve the shear strength of aluminum matrix if the fiber orientation aligned with the shear loading axis. The microscopic inspection of the fractured surface showed a multi-scale zigzag feature which implied a complicated shear failure mechanism in the composite. In addition to testing, the micromechanical stress field in the composite was analyzed by the generalized Eshelby equivalent method (GEEM). The influence of cracking in matrix on the micromechanical stress field was investigated as well. The results showed that the stress distribution in the composite is quite nonhomogeneous and very high shear stress concentrations are found in some regions in the matrix. The high shear stress concentration in the matrix induces tensile cracking at 45 degrees to the shear direction. This in turn aggravates the stress concentration at the fiber/matrix interface and finally leads to a catastrophic failure in the composite. From the correlation between the analysis and experimental results, the shear failure mechanism of unidirectional C-f/A356.0 composite can be elucidated qualitatively.