Coarse-Grained Molecular Dynamics Modeling of a Branched Polyetherimide

Coarse Grained Molecular Dynamics

Coarse-Grained Structural Modeling of Molecular Motors Using Multibody Dynamics.

Experimental and computational approaches are needed to uncover the mechanisms by which molecular motors convert chemical energy into mechanical work. In this article, we describe methods and software to generate structurally realistic models of molecular motor conformations compatible with experimental data from different sources. Coarse-grained models of molecular structures are constructed b...

Coarse-Grained Molecular Dynamics and Multiscale Modeling of NEMS Resonators

We review concurrent multiscale simulations of dynamic and temperature-dependent processes found in nanomechanical systems coupled to larger scale surroundings. We focus on the behavior of sub-micron MicroElectro-Mechanical Systems (MEMS), especially microresonators. These systems are often called NEMS, for Nano-Electro-Mechanical Systems. The coupling of length scales methodology we have devel...

Coarse-grained molecular dynamics simulations of biomolecules

Coarse-grained molecular dynamics (CGMD) simulations are increasingly being used to analyze the behaviors of biological systems. When appropriately used, CGMD can simulate the behaviors of molecular systems several hundred times faster than elaborate all-atom molecular dynamics simulations with similar accuracy. CGMD parameters for lipids, proteins, nucleic acids, and some artificial substances...

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...