Sven Lammers

Sven in Geneva

Department of Chemistry
Klingelbergstr. 80
4056 Basel

phone: +41 61 207 3810

Research Interests

My main interest is the application of physical and chemical theories  to biological phenoma. So in this sense I work right on the interface between life and natural sciences. In particular the application of molecular dynamics simulations can give some important insights to processes which take place in living organisms.
Proton transfer in ammonia

Proton transfer plays an important role in many enzymatic reactions. These processes are  fundamental to life, without them living organisms could not survive. To study the dynamics of these reactions in detail it is therefore necessary to develop theoritical methods to investigate them on the molecular level. The illustration to the left shows such a proton transfer in a simplified way. The potential energy curve in this case would look similiar to the red line in the plot shown in the figure. A transfer would rarely occur in this situation because the proton has to overcome the potential barrier, only tunneling would allow the proton to cross the barrier. Dynamics therefore plays an important role here. If the ammonia molecules move closer together the potential energy curve  would look more like the blue line in figure. A crossing would take place much easier now.

To describe the dynamics it is necessary to compute the potential energy at the all possible geometrical configurations. The derivative of this potential energy delivers the forces acting on the particles. 
If the energy is to be calculated by quantum mechanical methods then several hours would be needed to generate a molecular dynamics simulation. But if a force field could be used to propagate the particles then the some results could be obtained only in minutes of computational time. The task now is to develop an analytical function which describes the the properties of the potential energy surface correctly.
In the potential energy surface plot shown below such has been used to calculate  the contour lines of equal energies not only for the linear proton transfer but also for different geometries by rotation in plane of one ammonia molecule around the other .

contour plot