Exploring the most stable aptamer/target molecule complex by the stochastic tunnelling-basin hopping-discrete molecular dynamics method.

The stochastic tunnelling-basin hopping-discrete molecular dynamics (STUN-BH-DMD) method was applied to the search for the most stable biomolecular complexes in water by using the MARTINI coarse-grained (CG) model. The epithelial cell adhesion molecule (EpCAM, PDB code: 4MZV) was used as an EpCAM adaptor for an EpA (AptEpA) benchmark target molecule. The effects of two adsorption positions on the EpCAM were analysed, and it is found that the AptEpA adsorption configuration located within the EpCAM pocket-like structure is more stable and the energy barrier is lower due to the interaction with water. By the root mean square deviation (RMSD), the configuration of EpCAM in water is more conservative when the AptEpA binds to EpCAM by attaching to the pocket space of the EpCAM dimer. For AptEpA, the root mean square fluctuation (RMSF) analysis result indicates Nucleobase 1 and Nucleobase 2 display higher flexibility during the CGMD simulation. Finally, from the binding energy contour maps and histogram plots of EpCAM and each AptEpA nucleobase, it is clear that the binding energy adsorbed to the pocket-like structure is more continuous than that energy not adsorbed to the pocket-like structure. This study has proposed a new numerical process for applying the STUN-BH-DMD with the CG model, which can reduce computational details and directly find a more stable AptEpA/EpCAM complex in water.

The Mechanical Behaviors of Polyethylene/Silver Nanoparticle Composites: an Insight from Molecular Dynamics study.

This research uses molecular dynamics simulation (MD) to study the mechanical properties of pristine polyethylene (PE) and its composites which include silver nanoparticles (PE/AgNPs) at two AgNP weight fractions of 1.05 wt% and 3.10 wt%. The stress-strain distribution of the tensile process shows that the embedded AgNPs can significantly improve the Young's modulus and tensile strength of the pristine PE, due to improvements in the local density and strength of the PE near the AgNP surface in the range of 12 Å. Regarding the effect of temperature on the mechanical properties of pristine PE and PE/AgNP composites, the Young's modulus and the strength of the pristine PE and PE/AgNP composites decreased significantly at 350 K and 450 K, respectively, consistent with predicted melting temperature of pristine PE, which lies at around 360 K. At such temperatures as these, PE material has stronger ductility and a higher mobility of AgNPs in the PE matrix than those at 300 K. With the increase of tensile strain, AgNPs tend to be close, and the fracture of PE leads to a similarity between both the Young's modulus and ultimate strength found for the pristine PE and those found for the PE/AgNP composites at 350 K and 450 K, respectively.