title: Analysis of the conformational dependence of mass-metric tensor determinants in serial polymers with constraints.
abstract: It is well known that mass-metric tensor determinants det(G(s)) influence the equilibrium statistics and the rates of conformational transitions for polymers with constrained bond lengths and bond angles. It is now standard practice to include a Fixman-style compensating potential of the form U(c)(q(s)) proportional, variant(-k(B)T/2)ln[det(G(s))] as part of algorithms for torsional space molecular dynamics. This elegant strategy helps eliminate unwarranted biases that arise due to the imposition of holonomic constraints. However, the precise nature and extent of variation of det(G(s)) and hence ln[det(G(s))] with chain conformation and chain length has never been quantified. This type of analysis is crucial for understanding the nature of the conformational bias that the introduction of a Fixman potential aims to eliminate. Additionally, a detailed analysis of the conformational dependence of det(G(s)) will help resolve ambiguities regarding suggestions for incorporating terms related to det(G(s)) in the design of move sets in torsional space Monte Carlo simulations. In this work, we present results from a systematic study of the variation of det(G(s)) for a serial polymer with fixed bond lengths and bond angles as a function of chain conformation and chain length. This analysis requires an algorithm designed for rapid computation of det(G(s)) which simultaneously allows for a physical/geometric interpretation of the conformational dependence of det(G(s)). Consequently, we provide a detailed discussion of our adaptation of an O(n) algorithm from the robotics literature, which leads to simple recursion relations for direct evaluation of det(G(s)). Our analysis of the conformational dependence of det(G(s)) yields the following insights. (1) det(G(s)) is maximized for spatial conformers and minimized for planar conformations. (2) Previous work suggests that it is logical to expect that the conformational dependence of det(G(s)) becomes more pronounced with increase in chain length. Confirming this expectation, we provide systematic quantification of the nature of this dependency and show that the difference in det(G(s)) between spatial and planar conformers, i.e., between the maxima and minima of det(G(s)) grows systematically with chain length. Finally, we provide a brief discussion of implications of our analysis for the design of move sets in Monte Carlo simulations.
authors.affiliation: Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA.
authors.forename: Alexandru
authors.initials: A
authors.lastname: Patriciu
authors.forename: Gregory S
authors.initials: GS
authors.lastname: Chirikjian
authors.forename: Rohit V
authors.initials: RV
authors.lastname: Pappu