molecular dynamics simulation

摘要： Enhancing the stability of biomolecules is one of the hot topics in industry.In this study,we enhanced the stability of an important protein called LEPTIN.LEPTIN is a hormone secreted by fat cells playing an essential role in body weight and composition,and its deficiency can result in several disorders.The treatment of related LEPTIN dysfunctions is often available in the form of injection.To decrease the cost and the frequency of its applications can be achieved by increasing its lifetime through engineering LEPTIN.In this study,to engineer LEPTIN,we have introduced disulfide bonds.Disulfide By Design server was used to predict the suitable nominate pairs,which suggested three pairs of amino acids to be mutated to cysteine for disulfide bond formation.Additionally,to further evaluate the effect of combined mutations,we combined these three nominated pairs to produce three more mutants.In order to assess the effect of introduced mutations,molecular dynamic(MD)simulation was performed.The result suggests that Mutant-1 is more stable in comparison to wild-type and the other mutants.Moreover,docking results showed that the introduced mutation does not affect the receptor binding performance;therefore,it can be considered a suitable choice for future protein engineering.

摘要： To explore the mechanism of the wrinkle formation in graphene on transition metal substrate,a molecular dynamics(MD)simulation package that allows us to simulate systems of millions of atoms was developed.Via the MD simulation,we reveal the detailed kinetics of wrinkles formation on a Cu substrate under compressive strain,from nucleation to one-dimensional propagation and then the splitting of a large wrinkle to a few smaller ones,which is in good conformity with experimental observation.Further study reveals that both friction and the adhesion between graphene and Cu substrate are critical for the wrinkle formation and wrinkles can be easily formed with a lower frictional force and/or a smaller adhesion.Finally,we have shown that impurities in graphene or substrates can greatly facilitate the nucleation of wrinkles.The systematic exploration of the wrinkle formation in graphene on a substrate is expected to facilitate the experimental designs for the controllable synthesis of high-quality graphene.

摘要： The atomic configuration of chemical short-range order (CSRO) for the Zr-base metallic glasses was investigated by using nano-diffraction and high resolution transmission electronic microscopy (HRTEM) technology with a beam size of 0.5 nm. It is illustrated that the pattern of atomic configuration of CSRO might have various compound counterparts because of the chemical interaction of bonding atoms. Some atomic configuration of MCSRO is similar to the icosahedral structure with 10-fold symmetry of very weak spots. In deed, the nano-beam technology could clearly detect the evolution of atomic configuration in nanometer scale during the transformation from the metallic melt to the primary crystallization. The local atomic configuration of CSRO is also investigated by molecular dynamics simulation (MD) for the Zr2Ni compound in a wider temperature range. The CSRO in the melt could be pictorially demonstrated as distorted coordination polyhedron of the compound structure and/or the structure similar to cubo-octahedron analogs. The MD simulation illustrates that the atomic packing of long-range order disappears just above the melting point, but the chemical interaction of bonding atoms still exists that leads to form the various CSRO with the atomic configuration similar to stable or metastable unit cell of Zr2Ni compound. The icosahedral polyhedron became more abundance as the overheating temperature was raised.

摘要： TEM (Transmission Electron Microscope) observations show that corrosion process during stress corrosion cracking (SCC)enhances dislocation emission and motion; and microcrack of SCC initiates when the corrosion-enhanced dislocation emission and motion reaches a certain condition. The passive film or dealloyed layer formed during corrosion or SCC can induce a large tensile stress,which can assist the applied stress to enhance dislocation emission and motion, and then SCC occurs. Experiments show that the variation of SCC susceptibility of brass, α-Ti and stainless steel with the applied potential and pH value of the solution is consistent with that of the corrosion-induced additive stress. Molecular dynamics simulations show that a dealloyed layer can generate a tensile stress; and the corrosion (dealloyed layer)-induced tensile stress can assist the applied stress to enhance dislocation emission and crack propagation.