Uses for Molecular Dynamics Simulation

Molecular dynamics uses approximations of known laws of physics to simulate the motion of atoms and macromolecules. The technique has been used to probe the function and action of many biological molecules, allowing researchers to test hypotheses to an unprecedented resolution. There are many types of molecular dynamics simulations, each designed to give a certain balance of accuracy and speed to answer very specific questions.

Molecular dynamics depends on the ergodic hypothesis, where it is assumed that the averages of statistical ensembles are the same as time averages. This justification is rooted deeply in statistical mechanics and allows researchers to run long simulations and make conclusions about the properties of a system based on this simulation.

MD simulation provides a unique opportunity for scientists. Because the system is entirely computational, any portion can be tweaked even if the result is unphysical. By this method, it is possible to test hypotheses and find mechanisms through any means imaginable. It also allows researchers to test individual particles, which is nearly impossible by experimental methods.

Molecular dynamics has found a great deal of use in the simulation of biological macromolecules. The motions of molecules can be used to predict protein folding, secondary structure, and large scale structural changes of molecules such as channels in biological membranes.

The first MD simulation involving macromolecules was a simulation of bovine pancreatic trypsin inhibitor. This protein is one of the best studied in terms of kinetics and folding and the simulation gave a greater understanding of protein motion and how it relates to a given protein’s function.

The most well-known example of molecular dynamics is through the work of Vija Pande at Stanford as part of the Folding@Home project. This project took advantage of idle computer time on hundreds of thousands of personal computers to perform a folding simulation of the villin headpiece. This simulation involved 20,000 atoms for a simulation time of 500 microseconds, a huge computational effort.

Since the 1970s, molecular dynamics has been used heavily in material science. These researchers use MD to examine the physical properties of specific environments or nano-technologies. Research scientists in crystallography and NMR utilize MD to refine their solved protein structures.

Our understanding of membrane proteins and lipid bilayers has been greatly furthered by work using molecular dynamics. Many coarse-grained methods have also found great success simulating these systems for far less computational expense than similarly sized systems. They have been used to simulate the motions of proteins embedded in the bilayer and to look for clues about the mechanisms of ion transport in membrane pores.