Molecular Dynamics - Areas of Application

Areas of Application

There is a significant difference between the focus and methods used by chemists and physicists, and this is reflected in differences in the jargon used by the different fields. In chemistry and biophysics, the interaction between the particles is either described by a "force field" (classical MD), a quantum chemical model, or a mix between the two. These terms are not used in physics, where the interactions are usually described by the name of the theory or approximation being used and called the potential energy, or just the "potential".

Beginning in theoretical physics, the method of MD gained popularity in materials science and since the 1970s also in biochemistry and biophysics. In chemistry, MD serves as an important tool in protein structure determination and refinement using experimental tools such as X-ray crystallography and NMR. It has also been applied with limited success as a method of refining protein structure predictions. In physics, MD is used to examine the dynamics of atomic-level phenomena that cannot be observed directly, such as thin film growth and ion-subplantation. It is also used to examine the physical properties of nanotechnological devices that have not or cannot yet be created.

In applied mathematics and theoretical physics, molecular dynamics is a part of the research realm of dynamical systems, ergodic theory, Atomic, molecular, and optical physics and statistical mechanics in general. The concepts of energy conservation and molecular entropy come from thermodynamics. Some techniques to calculate conformational entropy such as principal components analysis come from information theory. Mathematical techniques such as the transfer operator become applicable when MD is seen as a Markov chain. Also, there is a large community of mathematicians working on volume preserving, symplectic integrators for more computationally efficient MD simulations.

MD can also be seen as a special case of the discrete element method (DEM) in which the particles have spherical shape (e.g. with the size of their van der Waals radii.) Some authors in the DEM community employ the term MD rather loosely, even when their simulations do not model actual molecules.