Molekyledynamiksimuleringers rolle som værktøj i det biofysiske arbejde

Marietta Bækdal Gugerel, Josephine Bjergbæk Olsson, Kristian Jensen Pedersen & Stefan Profft

Student thesis: Termpaper


This project addresses the influence of computer simulations in the field of physical biology regarding medicaments. The project will try to debate general molecular dynamic simulations is a good tool in this field of work. Topics such as computer simulations, molecular dynamics simulations and Cytochrome P450 will be examined theoretically and with a scientific theory perspective. This project will discuss scientific theory perspectives such as the idealized com- puter simulation model and the importance of a guiding theory in context with both simula- tions and experiments. In the project, a simple simulation has been made regarding Hooke’s law and Newton’s second law of motion. The 5 most frequently used interactions in molecular dynamics simulations will be described theoretically and some of the approximations and alternatives such as the Morse potential. Molecular dynamics simulations, examining Cyto- chrome P450, can simulate whether or not a medicament will bind to the enzyme. The pur- pose of these simulations is to make sure that the medicament only binds to one specific sub- type of Cytochrome P450 since the family of Cytochrome P450 is only similar structurally and not functionally. It is discovered that there is no clear definition of what a simulation is, but the different definitions does not differ too severely. The idealized computer model is shown to be a good starting point for setting up a model, but it is not possible to follow the model completely in reality. Molecular dynamics simulations have benefitted physical biology in many ways, but it is important to remember that these simulations are model based and do not necessarily depict the reality. These simulations must be seen as a tool. It can either sup- port the experiment, theory or provide basis for a new theory or experiment. Simulations are to be seen as a new important tool that has brought change to the scientific view on models and theories. The combination of simulations and experiments have shown that it is no longer necessary to have a complete theory to study a topic of interest and that models can use sim- plifications to describe something more complex.

EducationsBasic - Bachelor Study Program in Natural Science, (Bachelor Programme) Basic
Publication date19 Jan 2014
SupervisorsJesper Schmidt Hansen


  • molekyledynamiksimulering
  • vekselvirkninger
  • computersimulation
  • Cytokrom P450