Multiresolution molecular mechanics: Implementation and efficiency

The Molecular Mechanics Model of Carbon Allotropes

Carbon can form numerous allotropes because of its valency. Graphene, carbon nanotubes,capped carbon nanotubes, buckyballs, and nanocones are well-known polymorphs of carbon.Remarkable mechanical properties of these carbon atoms have made them the subject of intenseresearch. Several studies have been conducted on carbon nanotubes or graphene. In the presentstudy, the molecular mechanics method ...

Multiresolution Molecular Shapes

We introduce a multiresolution representation scheme for variable levels of detail of molecular shapes (shapes synthesized as sets of balls). In particular, we consider in our model the exact boundary computation of the the basic union of balls for CPK model and solvent accessible surface as well as the more complex rolling ball solvent contact surface and molecular skin. Our decimation/refinem...

Molecular multiresolution surfaces

The surface of a molecule determines much of its chemical and physical property, and is of great interest and importance. In this Letter, we introduce the concept of molecular multiresolution surfaces as a new paradigm of multiscale biological modeling. Molecular multiresolution surfaces contain not only a family of molecular surfaces, corresponding to different probe radii, but also the solven...

Efficient Implementation of Multiresolution Triangle Strips

Molecular mechanics and electrostatic effects.

Continuum solvent models predict a quadratic charge dependence (linear response) of the free energy of a system of charged solutes. The relation between this prediction and the structure of the solvation shell around the solutes is discussed. Studies of the derivative of the free energy with respect to the charges for different reference states are shown to be a convenient way of testing the li...