Coarse-Grained Molecular Dynamics Study based on TorchMD

The coarse grained(CG)model implements the molecular dynamics simulation by simplifying atom properties and interaction between them.Despite losing certain detailed information,the CG model is still the first-thought option to study the large molecule in long time scale with less computing resource.The deep learning model mainly mimics the human studying process to handle the network input as the image to achieve a good classification and regression result.In this work,the TorchMD,a MD framework combining the CG model and deep learning model,is applied to study the protein folding process.In 3D collective variable(CV)space,the modified find density peaks algorithm is applied to cluster the conformations from the TorchMD CG simulation.The center conformation in different states is searched.And the boundary conformations between clusters are assigned.The string algorithm is applied to study the path between two states,which are compared with the end conformations from all atoms simulations.The result shows that the main phenomenon of protein folding with TorchMD CG model is the same as the all-atom simulations,but with a less simulating time scale.The workflow in this work provides another option to study the protein folding and other relative processes with the deep learning CG model.

Spatio-temporal Pattern and Spatial Heterogeneity of Ecotones Based on Land Use Types of Southeastern Da Hinggan Mountains in China

Ecotones have received great attention due to its critical function in energy flux, species harbor, global carbon sequestration, and land-atmosphere interaction. This study investigated land use pattern and spatial heterogeneity of the ecotones among agricultural land, forest land, and grassland of the southeastern Da Hinggan Mountains in the northeastern China. The change of these delineated ecotones under different slopes and aridity conditions was analyzed by two landscape indices, edge density(ED) and core area percentage of landscape(CPL), to explore the inter-linkage between spatial structure of ecotones and socioeconomic development and land management. Specifically, the ecotones such as agriculture-forest(AF) ecotone, forest-grassland(FG) ecotone, and agriculture-forestgrassland(AFG) ecotone moved from the arid southeast to the humid northwest. The flat area with small slope is more edge-fragmented than the steep area since the ED decreases as the slope increases. The AF ecotone mostly found in the humid region is moving to more humid areas while the agriculture-grassland(AG) ecotone mostly found in the dry region is moving towards the drier region.

OxLDL－induced Cytotoxicity and Its Inhibition by API_（0134） in Cultured Porcine Aortic Endothelial Cells

Protective effects of API0134 on endotheliai cells (EC) damaged by oxidatively modified low density lipoprotein (oxLDL) were studied. The results showed that the content of endothelia (ET) and malondialdehyde (MDA) in the media of porcine aortic EC incubated with oxLDL were increased and the cGMP was decreased significantly, and the activity of superoxide dismutase (SOD) was inhibited. The effect of cytotoxicity of oxLDL can be eliminated by API0134.These results suggest that API0134 may protect EC against damages elicited by oxLDL.

Effect of algal flocculation on dissolved organic matters using cationic starch modified soils

Modified soils（MSs） are being increasingly used as geo-engineering materials for the sedimentation removal of cyanobacterial blooms. Cationic starch（CS） has been tested as an effective soil modifier, but little is known about its potential impacts on the treated water.This study investigated dissolved organic matters in the bloom water after algal removal using cationic starch modified soils（CS-MSs）. Results showed that the dissolved organic carbon（DOC） could be decreased by CS-MS flocculation and the use of higher charge density CS yielded a greater DOC reduction. When CS with the charge density of 0.052, 0.102 and0.293 meq/g were used, DOC was decreased from 3.4 to 3.0, 2.3 and 1.7 mg/L, respectively.The excitation–emission matrix fluorescence spectroscopy and UV254 analysis indicated that CS-MS exhibits an ability to remove some soluble organics, which contributed to the DOC reduction. However, the use of low charge density CS posed a potential risk of DOC increase due to the high CS loading for effective algal removal. When CS with the charge density of 0.044 meq/g was used, DOC was increased from 3.4 to 3.9 mg/L. This study suggested, when CS-MS is used for cyanobacterial bloom removal, the content of dissolved organic matters in the treated water can be controlled by optimizing the charge density of CS. For the settled organic matters, other measures（e.g., capping treatments using oxygen loaded materials） should be jointly applied after algal flocculation.