title: Algorithmic generation of freely jointed hard sphere chains and properties of their inertial tensors.
abstract: A statistical algorithm, capable of generating a large number of freely jointed hard sphere chains, is presented. This is the first of a series of algorithms being developed to model unfolded proteins by different modes of hard sphere chains. The aim of these studies is to systematically investigate the effects of different factors, such as atomic radii, bond angles, torsion angles, chain length, etc., on the conformation of unfolded proteins and other random polymers. As continuous models, various types of hard sphere chains enable one to isolate the aforementioned factors one at a time for investigation and thus are advantageous over discrete lattice models. In particular, the freely jointed hard sphere chain model allows one to evaluate the excluded volume effect. As a first step in this endeavor, the average determinant D(N, r) and the average trace T(N, r) of the inertial tensor A of the random chains were calculated at various sphere radii r and chain lengths N. It is found that both the average determinant D(N, r) and the average trace T(N, r) scale linearly with chain length N after logarithmic transformation. However, the critical exponent of D(N, r) increases with r faster than that of T(N, r) as a result of the non-commutativity between the det operator and the average operator < >. The significance of the algorithm and the results obtained on understanding random polypeptide chains are discussed.
authors.affiliation: Department of Mathematics and Statistics, Wright State University, Dayton, Ohio 45435, USA. wwang@math.wright.edu
authors.forename: W
authors.initials: W
authors.lastname: Wang
authors.forename: Y B
authors.initials: YB
authors.lastname: Yu
mesh_terms: D000465:Algorithms; D008433:Mathematics; D008962:Models, Theoretical; D011487:Protein Conformation; D017510:Protein Folding