Atoms and molecules are the focus of the computer simulation technique known as molecular dynamics.
Molecular dynamics is the name of a computer simulation technique used to observe how particles move. To do this, a computer tests the interaction of molecules and atoms over a certain period of time.
Using numerical procedures, algorithms from information theory and computer science , as well as principles and conjectures from chemistry , physics and mathematics , this resource provides relevant information regarding the gradual evolution of a system that may be biological, chemical or physical.
Molecular dynamics , a methodology conceived within theoretical physics that has been expanded to become useful in materials science and biophysics , is not exact because there is a margin of error even when trying to work with the best possible approximation. It should be noted that the simulated behavior is not one hundred percent faithful to reality, but rather offers a representative overview of a certain behavior in a phase space .
Principles and characteristics of molecular dynamics
When it comes to understanding what molecular dynamics is, what its characteristics are, what principles it is based on and how it is carried out, it is essential to learn about multiple expressions and concepts.
It is essential to master the concepts of force fields (such as, from the perspective of classical physics , the gravitational field and the electromagnetic field , for example) and intermolecular forces (referring to the interactions that occur between molecules, such as dipole-dipole attractions and dispersion or Van der Waals forces , to cite two references).
It is also necessary to know and be able to solve Newton's equations of motion in order to calculate the forces that occur between atoms . The same is true for time integration algorithms , a set of which the so-called Verlet algorithm is a part: to take advantage of molecular dynamics, this type of resource must also be incorporated.
Through the technique called molecular dynamics, it is possible to simulate the movement of DNA, considering its interactions and folding.
Applications
The field of application of molecular dynamics is very diverse, as will be seen from the data that we will share below.
As has been shown in practice, this computational method is effective for carrying out tests and making findings related to the protein field, specifically around protein-ligand interaction and protein folding .
Materials science experts, meanwhile, use molecular dynamics techniques when working with porous materials or when working in the field of nanotechnology .
It is also useful for studying chemical reactions and collecting information on the properties of gases or liquids. Work related to membrane dynamics and drug design , to name a few, benefits from the methodology of molecular dynamics .
The combination of this technique and artificial intelligence is also paving the way for a revolutionary era that, although still requires testing and development, promises results of enormous scientific relevance. An example of this is the design of a dual agonist of a receptor identified as GIP/GLP-1 that is emerging as an effective solution in the treatment of pathologies such as obesity and type 2 diabetes .
Requirements for molecular dynamics simulation
To carry out a molecular dynamics simulation, it is necessary to prepare the systems taking into account, among other things, the thermodynamic ensembles . The isothermal-isobaric ensemble (NPT) and the canonical ensemble (NVT) cannot be overlooked.
Practical and theoretical training must also consider the teaching and application of the thermostatization technique and the methodology aimed at analyzing and interpreting the results of each simulation .
Likewise, it is necessary to train in the use of molecular dynamics software (GROMACS, AMBER, NAMD) and have tools to visualize the simulations.
Molecular dynamics generates enormous benefits for the evolution of scientific research and technological developments, which is why it is used in numerous disciplines.
Advances and studies
Although there are still limitations and challenges to overcome through research and experimentation, studies and advances in molecular dynamics continue to grow worldwide.
Some time ago, to detail a relevant case on an international scale, a group of researchers from Barcelona announced the creation of a free and open access database focused on molecular dynamics simulations that are very useful for learning more about viral proteins linked to COVID-19 .
It is a modern and innovative development, its promoters pointed out, capable of being compatible with current simulations and that even allows working with systems of considerable size and long trajectories.
On the other hand, the use of molecular dynamics simulations to describe, at an atomic scale, the phenomenon of permeability without the need to previously synthesize compounds has become more important. Specifically, this technique has been considered in a work on predicting the level of permeability observable in small compounds taking into account the blood-brain barrier.