کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
760202 896510 2009 20 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
Dynamical models of molecular chains and efficient integration algorithms
موضوعات مرتبط
مهندسی و علوم پایه سایر رشته های مهندسی مهندسی مکانیک
پیش نمایش صفحه اول مقاله
Dynamical models of molecular chains and efficient integration algorithms
چکیده انگلیسی

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.

ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Communications in Nonlinear Science and Numerical Simulation - Volume 14, Issue 2, February 2009, Pages 593–612
نویسندگان
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