학교 과제로 한 molecular simulation, 특히 biomolecular simulation 에 대한 내용입니다.
1. Table of contents
2. Abstract 2
1. About Molecular Simulation
3. Simulation cells
4. Simulation Algorithms
5. Biomolecular simulations
Molecular docking simulation
1. Computerized Drug Design
2. Modeling DNA Structure via molecular simulation
Filling carbon nanotubes with DNA
1. Non-equilibrium molecular dynamics
2. Continuum-level simulation and the material point method
3. Dynamic feedback between MD and MPM
1) NEMD simulation
2) MPM simulation
Molecular simulation is a general term for the use of computer models to describe chemical systems at an atomic level of detail. In a molecular simulation, a chemical system is described using the individual positions and orientations of every atom or molecule. Different methods can be used to obtain both thermodynamic and kinetic properties of the system. A molecular simulation specifies a collection of atoms and molecules in a simulation cell, interacting through a potential, and evolving according to some simulation algorithm.
Biomolecular simulation is using molecular simulations for the compounds such as complexes of protein and ligand, to find the details of the mechanisms at atomic or molecular levels.
I introduced two applications of biomolecular simulations. Computer Drug Design employs 3D molecular graphics, which can be defined as the generation, manipulation, calculation, and prediction of realistic chemical structures and associated physicochemical and biological properties. So new drugs can be rapidly created and tested for binding and toxicity in the computer environment at relatively low cost.
Molecular Dynamics (MD) computer simulation is a powerful computational approach to the study of macromolecular structure and fast motions. An accurate dynamical model obtained from MD can provide a general theoretical basis for understanding the intrinsic natures
And lastly, I introduced a new theory, which combines two different size quantities, microscopic-level molecular dynamics simulations coupled to corresponding macro-scale continuum-level simulations.
1. Becker, Oren M (2001) Computational biochemistry and biophysics M. Dekker
2. Leontis, Neocles B Molecular modeling of nucleic acids American Chemical Society
3. Gelb Research Group, Washington University