THE RESPONSES OF Microcystis TO SEDIMENT ENVIRONMENTS AND THE ASSESSMENT FOR ITS OVERWINTERING - A SIMULATION STUDY IN A NOVEL DEVICE

A novel multi-cell device made of organic glass was designed to study morphological and physiological characteristics of Microcystis population trapped in simulated sediment conditions. Changes of colonial morphology and antioxidant activities of the population were observed and measured over the range of 31-day incubation. During the incubation, the antioxidant enzyme activities fluctuated significantly in sediment environments. The activities of catalase (CAT), glutathione peroxidase (GPx) and malondialdehyde (NIDA) reached the highest on the 11(th) day, 6(th) day and 6(th) day. respectively, and then dropped down remarkably in the following days. The ratios of Fv/Fm and the maximal electron transfer rate (ETRm) declined during the initial days (1 similar to 11(th) day), but rebounded on the 16(th) day, which were consistent with the variations of total protein. In the end of incubation. gas vacuoles were hard]), observed and the gelatinous sheath was partly disappeared in the population of Microcystis. Nevertheless, the remaining populations. upon transferred to culture medium, were able to grow though experiencing a longer lag phase of nine days. The results indicated that the sediment environments were able to cause negative effects on M. aeruginosa cells. The cells, however, responded to against the possible damage afterwards. It is thus proposed the acute responses in the population during the early stage of sedimentation could be of importance in aiding the long-term survivor of Microcystis and recruitment in lake sediments. The present study also demonstrated the utility of the device in simulating the sediment environments for further investigation.

QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by “GAMESS”, and the rest atoms are treated as MM part calculated by “TINKER”. The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with theQMpart with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(1 0 0) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the imidazole rings are attached to the substrate more tightly than other bases in this peptide.

Molecular Dynamics Simulation of Barnacle Cement

Barnacle cement is an underwater adhesive that is used for permanent settlement. Its main components are insoluble protein complexes that have not been fully studied. In present article, we chose two proteins of barnacle cement for study, 36-KD protein and Mrcp-100K protein. In order to investigate the characteristic of above two proteins, we introduced the method of molecular modeling. And the simulation package GROMACS was used to simulate the behavior of these proteins. In this article, before the simulations, we introduce some theories to predict the time scale for polymer relaxation. During the simulation, we mainly focus on two properties of these two proteins: structural stability and adhesive force to substrate. First, we simulate the structural stability of two proteins in water, and then the stability of 36-KD protein in seawater environment is investigated.We find that the stability varies in the different environments. Next, to study adhesive ability of two proteins, we simulate the process of peeling the two proteins from the substrate (graphite). Then, we analyze the main reasons of these results. We find that hydrogen bonds in proteins play an important role in the protein stability. In the process of the peeling, we use Lennard–Jones 12-6 potential to calculate the van der Waals interactions between proteins and substrate.

QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by "GAMESS", and the rest atoms are treated as MM part calculated by "TINKER". The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with the QM part with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(100) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the in-tidazole rings are attached to the substrate more tightly than other bases in this peptide.

Molecular Dynamics Simulation of Barnacle Cement

Barnacle cement is an underwater adhesive that is used for permanent settlement. Its main components are insoluble protein complexes that have not been fully studied. In present article, we chose two proteins of barnacle cement for study, 36-KD protein and Mrcp-100K protein. In order to investigate the characteristic of above two proteins, we introduced the method of molecular modeling. And the simulation package GROMACS was used to simulate the behavior of these proteins. In this article, before the simulations, we introduce some theories to predict the time scale for polymer relaxation. During the simulation, we mainly focus on two properties of these two proteins: structural stability and adhesive force to substrate. First, we simulate the structural stability of two proteins in water, and then the stability of 36-KD protein in seawater environment is investigated. We find that the stability varies in the different environments. Next, to study adhesive ability of two proteins, we simulate the process of peeling the two proteins from the substrate (graphite). Then, we analyze the main reasons of these results. We find that hydrogen bonds in proteins play an important role in the protein stability. In the process of the peeling, we use Lennard-Jones 12-6 potential to calculate the van der Waals interactions between proteins and substrate.

simulation and interaction of fluid dynamics

In the fluid simulation, the fluids and their surroundings may greatly change properties such as shape and temperature simultaneously, and different surroundings would characterize different interactions, which would change the shape and motion of the fluids in different ways. On the other hand, interactions among fluid mixtures of different kinds would generate more comprehensive behavior. To investigate the interaction behavior in physically based simulation of fluids, it is of importance to build physically correct models to represent the varying interactions between fluids and the environments, as well as interactions among the mixtures. In this paper, we will make a simple review of the interactions, and focus on those most interesting to us, and model them with various physical solutions. In particular, more detail will be given on the simulation of miscible and immiscible binary mixtures. In some of the methods, it is advantageous to be taken with the graphics processing unit (GPU) to achieve real-time computation for middle-scale simulation.

Carbon-13 nuclear magnetic resonance spectrum simulation of pyridines and quinolines

Artificial neural network (ANN) and multiple linear regression (MLR) were used for the simulation of C-13 NMR chemical shifts of 118 central carbon atoms in 18 pyridines and quinolines. The electronic and geometric features were calculated to describe the environments of the central carbon atom. The results provided by ANN method were better than that achieved by MLR.

Study on corrosion of steels in marine environment by corrosion simulation device

Three kinds of steels were studied using electrically connected hanging specimen in the corrosion simulation device and offshore long scale hanging specimen. The experimental results obtained by the two methods show that the device can better reflect the offshore corrosion environment. A Ni-Cu-P steel specimen was studied through analysis of the specimen's corrosion products and corrosion types. The surface of the samples before and after the removal of the rust layer produced by these two methods were observed and compared after some experiments. The microstructure of the corrosion products under different marine environments were analyzed and compared through IR. It indicated good correlation between the electrically connected hanging specimen method and the long scale hanging specimen method.

Study on corrosion simulation device for marine structural steel

A corrosion simulation device was studied using offshore long scale hanging specimens. An Ni-Cu-P steel specimen was studied by analysing its corrosion products and corrosion types. The appearance of the samples and the surface of the metallic substrate after the removal of the rust layer produced by these two methods were observed and compared after 470 days of exposure. The phase structure of the corrosion products under different marine environments were analysed and compared. It further indicated good correlation between the electrically connected hanging specimen method and the long scale hanging specimen method.