Atomistic simulation

Primary investigator: Carsten Svaneborg University of Southern, Denmark (ongoing research)

I use NAMD to perform simulations of single and double stranded DNA at various conditions. By calculating the centres of mass of the nucleosides (green spheres), we can use the simulations to learn about the interaction potentials (potentials of mean force) that should be used in one bead per nucleoside coarse-grained DNA models. The video below is a 40 bp long poly-AT strand at T=300K.

PNA dynamics

Primary investigator: Pawell Weronski, Polish Academy of Sciences, Poland

We have used molecular dynamics simulations to study the self-assembly and stability of fatty acid and phosphor lipid assemblies (membranes and micelles) and their interactions with small peptide nucleic acid (PNA) molecules. Classical MD computer simulation is a powerful and suitable method for modeling the phenomena at the molecular level provided that quantum effects can be neglected and sufficient computational resources are available. This approach allows calculation the molecular system time evolution by considering forces (electrostatic, dispersion, and chemical bonds) acting on individual atoms and numerically solving Newton's equations of motion over short time steps, based on the system’s potential function. Most of the parameters for our systems have already been obtained from ab initio quantum chemistry computations or vibrational spectroscopy and are available in the standard MD packages such as CHARMM. Those that are not directly available can be approximated using the existing parameters for similar chemical structures. This is the case for the peptide nucleic acid (PNA) that we have used in our simulations as the information molecule. This lab-created analogue of DNA, in which the nucleic bases (adenine, guanine, thymine and cytosine) are attached to a pseudo-peptide backbone, is much less hydrophilic than the natural DNA nucleic acids and therefore is expected either in direct form or with modified backbones to be able to adsorb at the surfactant-water interface, which is a necessary condition for an appropriately coupled gene and container replication process for the minimal protocell

Related publications:

  1. Weronski P., Jiang Y., and Rasmussen S., Molecular Dynamics Study of Small PNA Molecules in Lipid-Water System, Biophysical Journal, Volume 92 May 2007
  2. Weronski P., Jiang Y., and Rasmussen, S. "Application of Molecular dynamics computer simulations in the design of a minimal self-replicating molecular machine", Complexity, vol. 13, pp. 10-17, 2008