Theory of wavelet-based coarse-graining hierarchies for molecular dynamics

Coarse-graining RNA nanostructures for molecular dynamics simulations.

A series of coarse-grained models have been developed for study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural information. Such a treatment allows us to reach, for systems of thousands of nucleotides, a time scale of microseconds (i.e. by three orders of magnitude longer than ...

Systematic coarse-graining of nanoparticle interactions in molecular dynamics simulation.

A recently developed multiscale coarse-graining procedure [Izvekov, S.; Voth, G. A. J. Phys. Chem. B 2005, 109, 2469] is extended to derive coarse-grained models for nanoparticles. The methodology is applied to C(60) and to carbonaceous nanoparticles produced in combustion environments. The coarse-graining of the interparticle force field is accomplished applying a force-matching procedure to d...

Shape-Based Coarse Graining

Internal coarse-graining of molecular systems.

Modelers of molecular signaling networks must cope with the combinatorial explosion of protein states generated by posttranslational modifications and complex formation. Rule-based models provide a powerful alternative to approaches that require explicit enumeration of all possible molecular species of a system. Such models consist of formal rules stipulating the (partial) contexts wherein spec...

Coarse graining and control theory model reduction

We explain a method, inspired by control theory model reduction and interpolation theory, that rigorously establishes the types of coarse graining that are appropriate for systems with quadratic, generalized Hamiltonians. For such systems, general conditions are given that establish when local coarse grainings should be valid. Interestingly, our analysis provides a reduction method that is vali...