Application of molecular dynamics simulation in self-assembly

Abstract During the past few years, numerous studies have been done in self-assembly. Among most of these studies, Molecular Dynamic Simulation is widely used to construct the experiment model. This work firstly introduced three practical applications of MD simulation in self-assembly. Then, two main kinds of simulation are discussed including all-atom simulation and coarse-grained simulation, together with the way of thoughts before the simulation start. It is found that researchers always start with the whole analysis of the substances that need to be studied. It helps to confirm the appropriate model that can apply in the simulation naturally. Besides, depended on the principles that need to be studied, the way of establishing the simulation system varies, ranging from separation experiment in both types of simulation to the change of essential parameters. Furthermore, the adoption of L-J potential in MD simulation proves to be a wise option on account of its convenient and simple model. It is remarkable that, considering some small details like the differences between implicit and explicit solution, classical Martini force field is replaced by Dry Martini force field.

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Molecular dynamics simulation of reversible electroporation with Martini force field

BioMedical Engineering OnLine ◽

10.1186/s12938-019-0743-1 ◽

2019 ◽

Vol 18 (1) ◽

Cited By ~ 1

Author(s):

Cheng Zhou ◽

Kefu Liu

Keyword(s):

Force Field ◽

Self Assembly ◽

Time Scale ◽

Membrane Integrity ◽

Basic Mechanism ◽

Dynamics Simulation ◽

Coarse Grained ◽

Phospholipid Membrane ◽

Martini Force Field ◽

Reversible Electroporation

Abstract Background After the discovery of membrane-reversible electroporation decades ago, the procedure has been used extensively in biology, biotechnology and medicine. The research on the basic mechanism has increasingly attracted attention. Although most research has focused on models that consider all atomic and molecular interactions and much atomic-level information can be obtained, the huge computational demand limits the models to simulations of only a few nanometers on the spatial scale and a few nanoseconds on the time scale. In order to more comprehensively study the reversible electroporation mechanism of phospholipid membrane on the nanoscale and at longer time intervals of up to 100 ns, we developed a dipalmitoylphosphatidylcholine (DPPC) phospholipid membrane model with the coarse-grained Martini force field. The model was tested by separately examining the morphology of the phospholipid membrane, the hydrophilic channel size, the distribution of the voltage potential on both sides of the membrane, and the movement of water molecules and ions during electroporation. Results The results showed that the process went through several stages: (1) the formation of the pore with defects originating on the surface. (2) The maintenance of the pore. The defects expanded to large pores and the size remains unchanged for several nanoseconds. (3) Pore healing stage due to self-assembly. Phospholipid membrane shrunk and the pore size decreased until completely closed. The pores were not circular in cross-section for most of the time and the potential difference across the membrane decreased dramatically after the pores formed, with almost no restoration of membrane integrity even when the pores started to close. Conclusions The mechanism of the reversible electroporation process on the nanoscale level, including defects, expansion, stability, and pore closing stages on a longer time scale of up to 100 ns was demonstrated more comprehensively with the coarse-grained Martini force field, which took both the necessary molecular information and the calculation efficiency into account.

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