Coarse Dynamics for Coarse Modeling: An Example From Population Biology

Coarse Dynamics for Coarse Modeling: An Example From Population Biology

Networks have become a popular way to concisely represent complex nonlinear systems where the interactions and parameters are imprecisely known. One challenge is how best to describe the associated dynamics, which can exhibit complicated behavior sensitive to small changes in parameters. A recently developed computational approach that we refer to as a database for dynamics provides a robust an...

Coarse-Grained Modeling of Protein Unfolding Dynamics

We present a new dynamic elastic network model (DENM) that describes the unfolding process of a force-loaded protein. The protein interaction network and its potentials are constructed based on information of its native-state structure obtained from the Protein Data Bank, with network nodes positioned at the Cα coordinates of the protein backbone. Specifically, to mimic the unfolding process, i...

Macromolecule Dynamics: from a Coarse Grain Approach to Continuum Modeling

Macromolecule Dynamics: from a Coarse Grain Approach to Continuum Modeling

Macroscopic dynamics through coarse-graining: a solvable example.

The recently derived fluctuation-dissipation formula [A. N. Gorban et al., Phys. Rev. E 63, 066124 (2001)] is illustrated by the explicit computation for McKean's kinetic model [H. P. McKean, J. Math. Phys. 8, 547 (1967)]. It is demonstrated that the result is identical, on the one hand, to the sum of the Chapman-Enskog expansion, and, on the other hand, to the exact solution of the invariance ...

Coarse Grained Molecular Dynamics