1. Molecular Modeling? A molecular model of a chemical substance (or materials; DNA, NaCl, etc.) is to display (or represent) both the three-dimensional positions of the atoms and the bonds between them, that is, the molecular geometry and topology, with the aim of simplifying and presenting the essential, physical and chemical, properties.

2. Molecular Modeling? Computer-based molecular models also allow animations, molecular dynamics simulationsas well as quantum mechanical computations that are very important for understanding the molecular geometry and functions. Quantum mechanical calculations (solving the Schrodinger equation) allow to understand the geometry at equilibrium, their vibrations around equilibrium, molecular orbitals, electron distributions, electric dipole moments, electron transport, optical properties, and so on. Molecular dynamics simulations (solving the Newton equation) involves simulations of molecular geometry and topology changes with time (at finite temperatures) as a result of both intra- and inter-molecular interactions between atoms. bulk heterojunction solar cell