Dynamical models of molecular chains and efficient integration algorithms

• Published in: Communications in nonlinear science & numerical simulation Vol. 14; no. 2; pp. 593 - 612
• Main Authors: Bazzani, Armando, Benedetti, Carlo, Rambaldi, Sandro, Rossi, Luca, Turchetti, Giorgio
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01.02.2009
• Subjects: Algorithms; Biological; Computer simulation; Flipping rule; Hard springs; Mathematical models; Molecular chains; Nonlinear dynamics; Rigid-body dynamics; Rigidity constraints; Runge-Kutta method; Runge–Kutta; Thermal baths; Runge–Kutta; 45.40.−f; Rigidity constraints; Flipping rule; 07.05.Tp; Hard springs; 02.60.Lj; 36.20.Fz; Molecular chains
• ISSN: 1007-5704; 1878-7274
• DOI: 10.1016/j.cnsns.2007.10.003

Chains of point masses and chains of rigid bodies are used to model biological polymers. To investigate their dynamics we propose a method which allows an efficient realization of the constraints jointly with a simple and accurate integration of the free rigid body motion. The method is quite effective to evolute the geodesic flow of a rigid body chain and the global performance depends on the computational complexity of the algorithms used to compute the interaction forces. Our approach is suitable to describe a chain of rigid bodies immersed in a thermal bath. In the method we propose, the constraints are realized by hard springs whose elastic constant is set to maximize the energy dissipation rate of a Runge–Kutta integrator scheme. Moreover the use of local Lagrangian coordinates is introduced using the possibility of a continuous change of chart, such that the distance from the coordinate singularities is the highest possible. For a chain of point masses the numerical results are checked with another method where the constraints are exactly realized by means of Lagrangian coordinates. When the chain is subject to regular interactions potentials plus a thermal bath the exact and approximate constraints realization provide comparable results.