Matej Praprotnik: Molecular Simulation of Biophysical Systems
Vir: Ponedeljkov fizikalni kolokvij
Molecular Simulation of Biophysical Systems
Kemijski inštitut, Ljubljana
We present our recent multiscale biomolecular simulations, in which solvent molecules change their resolution back and forth between atomistic and coarse-grained representations according to their positions in the system. First, we discuss coupling of atomistic and coarse-grained models of salt solution using a 1-to-1 molecular mapping, i.e., one coarse-grained bead represents one water molecule. This salt solution model is applied in a multiscale simulation of a DNA molecule in 1 M NaCl salt solution environment. The region of high resolution moves together with the DNA center-of-mass so that the DNA itself is always modeled at high resolution. We show that the multiscale simulations yield a stable DNA-solution system, with statistical properties similar to those produced by the conventional all-atom molecular dynamics simulation. In order to make use of coarse-grained molecular models that are compatible with the MARTINI force field one has to resort to a supramolecular mapping, in particular to a 4-to-1 mapping, where four water molecules are represented with one coarse-grained bead. Here, we use our fine-grained salt solution model for the proximal solvent around the DNA molecule, whereas the distal solvent is modeled by the MARTINI model. Next, we perform a multiscale simulation of dense DNA arrays by enclosing a set of $16$ atomistically resolved DNA molecules within a semi-permeable membrane, allowing the passage of water and salt ions, and thus mimicking the behavior of DNA arrays subjected to external osmotic stress in a bathing solution of monovalent salt and multivalent counterions. By varying the DNA density, the local packing symmetry, and the counterion type, we are able to analyze the osmotic equation of state together with the full structural characterization of the DNA subphase, the counterion distribution and the solvent structural order in terms of its different order parameters and consequently identify the most important contribution to the DNA-DNA interactions at high DNA densities. Finally, we present our open boundary molecular dynamics method to conduct molecular simulations of open systems that can exchange mass, momentum, and energy with the environment. Our multiscale approaches pave the way for efficient biomolecular simulations, which require a large solvent reservoir to avoid boundary effects.
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