Simulation of Macromolecules Immersed in Stretching Flow By Dissipative Particle Dynamics; Interpretation of Response Modes By Proper Orthogonal Decomposition

We employ Dissipative Particle Dynamics (DPD) to create a stretching flow in a domain with periodic boundary conditions. The flow features a stagnation point flow at the center of the simulation box. Test bodies, such as macromolecules, colloids, cells or vesicles, are initially placed at the stagnation point, and time records of their kinematics are recorded. Post processing is carried out with Proper Orthogonal Decomposition (POD), a tool commonly employed in the analysis of simulated turbulence, and adapted for particle systems (L. Grinberg, Proper orthogonal decomposition of atomistic flow simulations, Journal of Computational Physics 231 (2012), 5542).  In this work POD is employed to separate the basic modes of deformation of the test body from the thermal fluctuations. The probability distribution function (PDF) of the fluctuations in the vicinity of the stagnation point is obtained for both the stretching and compressing regions of the base flow. The method will be illustrated with the modes of an inextensible filament, modeled as a bead-spring chain, over the whole range of bending resistance.