Molecule dynamics simulation was used on HPT(2,3,6,7,10,11-hexa-n-pentyloxytriphenylene), which is a discotic Liquid crystal. From analyzing the energy and displacement varying with the temperature, the phase transiti...Molecule dynamics simulation was used on HPT(2,3,6,7,10,11-hexa-n-pentyloxytriphenylene), which is a discotic Liquid crystal. From analyzing the energy and displacement varying with the temperature, the phase transition temperature of PM6MPP can be predicted. The deviations of T-g, T-m and T-i due to the MD time scale are small enough that it should be possibly used to predict the material properties especially when more powerful computers are available.展开更多
Intrinsically disordered proteins(IDPs)and their regions(IDRs)play crucial roles in cellular func-tions despite their lack of stable three-dimensional structures.In this study,we investigate the interac-tions between ...Intrinsically disordered proteins(IDPs)and their regions(IDRs)play crucial roles in cellular func-tions despite their lack of stable three-dimensional structures.In this study,we investigate the interac-tions between the C-terminal do-main of protein 4.1G(4.1G CTD)and the nuclear mitotic apparatus protein(NuMA)under varying pH and salt ion conditions to under-stand the regulatory mechanisms affecting their binding.4.1G CTD and NuMA bind effec-tively under neutral and alkaline conditions,but their interaction is disrupted under acidic conditions(pH 3.6).The protonation of positively charged residues at the C-terminal of 4.1G CTD under acidic conditions leads to increased electrostatic repulsion,weakening the overall binding free energy.Secondary structure analysis shows that specific regions of 4.1G CTD re-main stable under both pH conditions,but the C-terminal region(aa 990−1000)and the N-terminal region of NuMA(aa 1800−1810)exhibit significant reductions in secondary struc-ture probability under acidic conditions.Contact map analysis and solvent-accessible surface area analysis further support these findings by showing a reduced contact probability be-tween these regions under pH 3.6.These results provide a comprehensive understanding of how pH and ionic strength regulate the binding dynamics of 4.1G CTD and NuMA,emphasiz-ing the regulatory role of electrostatic interactions.展开更多
A new compound with the stone cheinical composition as Li3AlB2O6 but with a different x-ray powder diffraction pattern as reported before was synthesized and studied experimentally by M. He, Chen X Let al （J. Solid S...A new compound with the stone cheinical composition as Li3AlB2O6 but with a different x-ray powder diffraction pattern as reported before was synthesized and studied experimentally by M. He, Chen X Let al （J. Solid State Chem. 163, 369 （2002））, but there lacks first principles study on the structure of it. Using conjugant gradient （CG） molecule dynamics （MD） simulation with a full relaxation of the atomic positions and of the shape and size of the cell, the structure of Li3AlB2O6 is studied from first principles. For the density functional, the local density approximation （LDA） and the generalized gradient approximation （GGA） forms are used respectively. Both the LDA and GGA results support the experimental structure of M. He et al. The result of MD simulation using GGA agrees with the experimental result much better. The energy bands are also studied, the band gap given by LDA and GGA are 5.65 eV, 5.34eV, respectively.展开更多
Polymers exhibit extended structures at high temperatures or in good solvents and collapsed configurations at low temperatures or in poor solvents. This fundamental property is crucial to the design of materials, and ...Polymers exhibit extended structures at high temperatures or in good solvents and collapsed configurations at low temperatures or in poor solvents. This fundamental property is crucial to the design of materials, and indeed has been extensively studied in recent years. In this paper, the collapse of polyethylene rings on an attractive surface was investigated by using molecular dynamics simulations. It is found that the collapse of ring chains on the attractive surface is of distinct difference from their free counterparts, where the collapse becomes more continuous and a one-stage instead of two-stage collapse can be identified by the specific heat. Some hairpin-like crystal structures are found at low temperatures, which are induced by the adsorption interaction of polymer-surface. For a given chain length, the results were further compared with those of the adsorbed linear chains. Due to the topological constraint of ring chains, the number of hairpin structures is clearly less than that of the linear chains. These numerical simulations may provide some new insights into the folding of ring polymers under adsorption interactions.展开更多
文摘Molecule dynamics simulation was used on HPT(2,3,6,7,10,11-hexa-n-pentyloxytriphenylene), which is a discotic Liquid crystal. From analyzing the energy and displacement varying with the temperature, the phase transition temperature of PM6MPP can be predicted. The deviations of T-g, T-m and T-i due to the MD time scale are small enough that it should be possibly used to predict the material properties especially when more powerful computers are available.
基金supported by the National Natural Science Foundation of China(No.22073018,No.22377015).
文摘Intrinsically disordered proteins(IDPs)and their regions(IDRs)play crucial roles in cellular func-tions despite their lack of stable three-dimensional structures.In this study,we investigate the interac-tions between the C-terminal do-main of protein 4.1G(4.1G CTD)and the nuclear mitotic apparatus protein(NuMA)under varying pH and salt ion conditions to under-stand the regulatory mechanisms affecting their binding.4.1G CTD and NuMA bind effec-tively under neutral and alkaline conditions,but their interaction is disrupted under acidic conditions(pH 3.6).The protonation of positively charged residues at the C-terminal of 4.1G CTD under acidic conditions leads to increased electrostatic repulsion,weakening the overall binding free energy.Secondary structure analysis shows that specific regions of 4.1G CTD re-main stable under both pH conditions,but the C-terminal region(aa 990−1000)and the N-terminal region of NuMA(aa 1800−1810)exhibit significant reductions in secondary struc-ture probability under acidic conditions.Contact map analysis and solvent-accessible surface area analysis further support these findings by showing a reduced contact probability be-tween these regions under pH 3.6.These results provide a comprehensive understanding of how pH and ionic strength regulate the binding dynamics of 4.1G CTD and NuMA,emphasiz-ing the regulatory role of electrostatic interactions.
基金Project supported by the National Natural Science Foundation of China and CAEP （Grant No NSAF.10376021）.
文摘A new compound with the stone cheinical composition as Li3AlB2O6 but with a different x-ray powder diffraction pattern as reported before was synthesized and studied experimentally by M. He, Chen X Let al （J. Solid State Chem. 163, 369 （2002））, but there lacks first principles study on the structure of it. Using conjugant gradient （CG） molecule dynamics （MD） simulation with a full relaxation of the atomic positions and of the shape and size of the cell, the structure of Li3AlB2O6 is studied from first principles. For the density functional, the local density approximation （LDA） and the generalized gradient approximation （GGA） forms are used respectively. Both the LDA and GGA results support the experimental structure of M. He et al. The result of MD simulation using GGA agrees with the experimental result much better. The energy bands are also studied, the band gap given by LDA and GGA are 5.65 eV, 5.34eV, respectively.
基金financially supported by the National Natural Science Foundation of China(Nos.21204093,21174154,20874110)
文摘Polymers exhibit extended structures at high temperatures or in good solvents and collapsed configurations at low temperatures or in poor solvents. This fundamental property is crucial to the design of materials, and indeed has been extensively studied in recent years. In this paper, the collapse of polyethylene rings on an attractive surface was investigated by using molecular dynamics simulations. It is found that the collapse of ring chains on the attractive surface is of distinct difference from their free counterparts, where the collapse becomes more continuous and a one-stage instead of two-stage collapse can be identified by the specific heat. Some hairpin-like crystal structures are found at low temperatures, which are induced by the adsorption interaction of polymer-surface. For a given chain length, the results were further compared with those of the adsorbed linear chains. Due to the topological constraint of ring chains, the number of hairpin structures is clearly less than that of the linear chains. These numerical simulations may provide some new insights into the folding of ring polymers under adsorption interactions.
