The main objective of this paper is to develop a multiscale method for the static analysis of a nano-system, based on a combination of molecular mechanics and MLPG methods. The tangent-stiffness formulations are given for this multiscale method, as well as a pure molecular mechanics method. This method is also shown to naturally link the continuum local balance equation with molecular mechanics...

Hamiltonian Lie-Poisson structures of the three-wave equations associated with the Lie algebras 5u(3) and 5u(2, 1) are derived and shown to be compatible. Poisson reduction is performed using the method of invariants and geometric phases associated with the reconstruction are calculated. These results can be applied to applications of nonlinear-waves in, for instance, nonlinear optics. Some of ...

The automatic three-dimensional mesh generation system for molecular geometries developed in our laboratory is used to solve the Poisson]Boltzmann equation numerically using a finite element method. For a number of different systems, the results are found to be in good agreement with those obtained in finite difference calculations using the DelPhi program as well as with those from boundary el...

A general discussion of Hamiltonian and action principle formulations for fliud and plasma models is given. A procedure, based on Hamilton's principle of mechanics but adapted for continua, for the construction of action principles for fliud and kinetic models is given. The transformation from action principles in terms of the Lagrangian variable description to the Eulerian variable description...

Here, we systematically investigated how the force fields and the partial charge models for ligands affect the ranking performance of the binding free energies predicted by the Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) approaches. A total of 46 small molecules targeted to five different protein receptors were emp...

Tubulin is the target for many small-molecule natural compounds, which alter microtubules dynamics, and lead to cell cycle arrest and apoptosis. One of these compounds is colchicine, a plant alkaloid produced by Colchicum autumnale. While C. autumnale produces a potent cytotoxin, colchicine, and expresses its target protein, it is immune to colchicine's cytotoxic action and the mechanism of thi...