Genetic algorithm in ab initio protein structure prediction using low resolution model : a review

Proteins are sequences of amino acids bound into a linear chain that adopt a specific folded three-dimensional (3D) shape. This specific folded shape enables proteins to perform specific tasks. The protein structure prediction (PSP) by ab initio or de novo approach is promising amongst various available computational methods and can help to unravel the important relationship between sequence and its corresponding structure. This article presents the ab initio protein structure prediction as a conformational search problem in low resolution model using genetic algorithm. As a review, the essence of twin removal, intelligence in coding, the development and application of domain specific heuristics garnered from the properties of the resulting model and the protein core formation concept discussed are all highly relevant in attempting to secure the best solution

Short range versus long range structure in Cu In,Ga Se2, Cu In,Ga 3Se5, and Cu In,Ga 5Se8

The Cu poor phases Cu In,Ga 3Se5 and Cu In,Ga 5Se8 play an important role both for understanding the Cu In,Ga Se material system and for growing high efficiency Cu In,Ga Se2 thin film solar cells. Using extended X ray absorption fine structure spectroscopy, we have studied the element specific short range structure of Cu In,Ga Se2, Cu In,Ga 3Se5, and Cu In,Ga 5Se8 alloys spanning the entire compositional range. The materials feature different local atomic arrangements and the element specific average bond lengths remain nearly constant despite significant changes of the lattice constants with increasing In to Ga ratio and decreasing Cu content. In particular, the average bond lengths of Cu Se and Ga Se are almost identical while the average In Se bond length is significantly longer in all three phases. The distance between lattice sites with mixed site occupation therefore corresponds to the weighted average of different element specific bond lengths rather than to the individual bond lengths themselves. Furthermore, the increasing number of vacancies with decreasing Cu content lead to both a significant unit cell contraction and a slight bond length expansion. The crystallographic long range structure and the element specific short range structure thus describe different structural aspects that are certainly interrelated but obviously not identica