Translocation of closed polymers through a nanopore under an applied external field

The dynamic behaviours of the translocations of closed circular polymers and closed knotted polymers through a nanopore, under the driving of an applied field, are studied by three-dimensional Langevin dynamics simulations. The power-law scaling of the translocation time τ with the chain length N and the distribution of translocation time are investigated separately. For closed circular polymers, a crossover scaling of translocation time with chain length is found to be τ～ N α , with the exponent α varying from α = 0.71 for relatively short chains to α = 1.29 for longer chains under driving force F = 5. The scaling behaviour for longer chains is in good agreement with experimental results, in which the exponent α = 1.27 for the translocation of double-strand DNA. The distribution of translocation time D(τ) is close to a Gaussian function for duration time τ < τ p and follows a falling exponential function for duration time τ > τ p . For closed knotted polymers, the scaling exponent α is 1.27 for small field force (F = 5) and 1.38 for large field force (F = 10). The distribution of translocation time D(τ) remarkably features two peaks appearing in the case of large driving force. The interesting result of multiple peaks can conduce to the understanding of the influence of the number of strands of polymers in the pore at the same time on translocation dynamic process and scaling property.     

Structural statistical properties of knotted proteins

The composition and residue--residue interactions of knotted proteins, compared with those of other proteins, can provide considerable insight into the driver of the knots in proteins. In this paper, we calculate the probabilities of 20 amino acids in 273 knotted entries from the Protein Data Bank (PDB). The collection of 273 entries contains all knotted structures in the PDB, and it is not a subset. With an appropriate value of R_c, the numbers of all residue--residue contacts are counted in all 273 knotted structures. To make an accurate comparison, we count up to 9000 other entries from the PDB as well, and these entries spread over all sorts. In knotted structures, Leu occupies a maximal proportion of 9.62% among all 20 amino acids, and Leu, Phe, Trp, Gly, His, Gln, Asp, Lys and Pro may all play a more important role. Also, we analyse the effects of amino acid residues on the long-range contacts. We observe a larger average number of long-range contacts in the knotted structures than that in other ones, implying their important role in achieving the knots. Accordingly, the average number of short-range contacts becomes small when the structure becomes knotted because it depends mainly on the short-haul sequence of amino acids to form the short-range contact. In addition, the shape distribution of knotted proteins and the contrast with the other proteins are also presented. A comparison shows that the knots may make structures more globular because the average shape factor is 0.059 for the knotted proteins, which is only about 1/3 of the average shape factor for the other proteins.     

外力诱导吸附高分子单链的拉伸分子动力学研究

采用拉伸分子动力学方法研究聚乙烯单链在真空中从一个强吸附表面被拉伸的动力学过程. 当聚乙烯单链从中间1/3处被拉伸时,通过理想弹簧可测量其平均力〈f〉,发现在拉力与拉伸距离的曲线上出现了两个平台,这与实验结果非常一致,同时研究了在这个过程中链的形状变化情况,发现形状变化经历了四个阶段. 当聚乙烯单链的一端与吸附表面成一定倾斜角拉伸时,发现通过理想弹簧测量到的平均吸附力〈f〉与倾斜角θ在θ>20°的范围里总保持线性关系,并且其斜率随着拉伸速度的增加而增 关键词： 拉伸分子动力学 聚乙烯链 吸附现象     

(α/β)_8桶状蛋白质中紧密接触对的统计性质研究

在计算蛋白质分子中的氨基酸紧密接触对时采用以氨基酸的重心代替Cα 原子的新方法 ,通过计算(α/β) 8桶状蛋白质中的中程和远程紧密接触对的数目 ,研究了不同氨基酸在形成紧密接触对时所具有的不同能力以及在蛋白质结构稳定性中所起的不同作用 .发现在 (α β) 8桶状蛋白质中氨基酸形成的远程紧密接触对数目与它的Fauchere Pliska疏水性实验数值 (FPH)存在着非常好的线性关系 ,而对于氨基酸所形成的中程紧密接触对数目不存在这种关系 .同时还研究了 (α β) 8桶状蛋白质分子大小 ,发现其回转半径大小与表示远程接触对数目的远程次序值LRO存在着关系 .表明这一类 (α β) 8桶状蛋白质具有相似的结构 ,分子的远程接触对数目越多 ,分子越紧密 ,分子尺寸就越小 .同时还研究了不同氨基酸之间形成紧密接触对的能力 .     

Statistical interior properties of globular proteins

The character of forming long-range contacts affects the three-dimensional structure of globular proteins deeply. As the different ability to form long-range contacts between 20 types of amino acids and 4 categories of globular proteins, the statistical properties are thoroughly discussed in this paper. Two parameters N_C and N_D are defined to confine the valid residues in detail. The relationship between hydrophobicity scales and valid residue percentage of each amino acid is given in the present work and the linear functions are shown in our statistical results. It is concluded that the hydrophobicity scale defined by chemical derivatives of the amino acids and nonpolar phase of large unilamellar vesicle membranes is the most effective technique to characterise the hydrophobic behavior of amino acid residues. Meanwhile, residue percentage P_i and sequential residue length L_i of a certain protein i are calculated under different conditions. The statistical results show that the average value of P_i as well as L_i of all-α proteins has a minimum among these 4 classes of globular proteins, indicating that all-α proteins are hardly capable of forming long-range contacts one by one along their linear amino acid sequences. All-β proteins have a higher tendency to construct long-range contacts along their primary sequences related to the secondary configurations, i.e. parallel and anti-parallel configurations of β sheets. The investigation of the interior properties of globular proteins give us the connection between the three-dimensional structure and its primary sequence data or secondary configurations, and help us to understand the structure of protein and its folding process well.     

聚亚甲基链的弹性形变研究

本文采用旋转异构态模型,对聚亚甲基链受到无相变的弹性形变后的热力学性质进行研究,计算出在不同形变时聚亚甲基链体系的自由能、内能等热力学函数,同时还分析了应力与弹性形变的关系以及内能对弹性形变的贡献。     

Cylindrical-confinement-induced phase behaviours of diblock copolymer melts

The phase behaviours of diblock copolymers under cylindrical confinement are studied in two-dimensional space by using the self-consistent field theory. Several phase parameters are adjusted to investigate the cylindrical-confinement-induced phase behaviours of diblock copolymers. A series of lamella-cylinder mixture phases, such as the mixture of broken-lamellae and cylinders and the mixture of square-lamellae and cylinders, are observed by varying the phase parameters, in which the behaviours of these mixture phases are discussed in the corresponding phase diagrams. Fur-thermore, the free energies of these mixture phases are investigated to illustrate their evolution processes. Our results are compared with the available observations from the experiments and simulations respectively, and they are in good agreement and provide an insight into the phase behaviours under cylindrical confinement.     

(α/β)8桶状蛋白质中紧密接触对的统计性质研究

在计算蛋白质分子中的氨基酸紧密接触对时采用以氨基酸的重心代替C^α原子的新方法，通过计算（α/β）8桶状蛋白质中的中程和远程紧密接触对的数目，研究了不同氨基酸在形成紧密接触对时所具有的不同能力以及在蛋白质结构稳定性中所起的不同作用．发现在（α/β）8桶状蛋白质中氨基酸形成的远程紧密接触对数目与它的Fauchere—Pliska疏水性实验数值(FPH)存在着非常好的线性关系，而对于氨基酸所形成的中程紧密接触对数目不存在这种关系．同时还研究了（α/β）8桶状蛋白质分子大小，发现其回转半径大小与表示远程接触对数目的远程次序值LRO存在着关系．表明这一类（α/β）8桶状蛋白质具有相似的结构，分子的远程接触对数目越多，分子越紧密，分子尺寸就越小．同时还研究了不同氨基酸之间形成紧密接触对的能力．     

Processes of DNA condensation induced by multivalent cations： Approximate annealing experiments and molecular dynamics simulations

The condensation of DNA induced by spermine is studied by atomic force microscopy （AFM） and molecular dynamics （MD） simulation in this paper. In our experiments, an equivalent amount of multivalent cations is added to the DNA solutions in different numbers of steps, and we find that the process of DNA condensation strongly depends on the speed of adding cations. That is, the slower the spermine cations are added, the slower the DNA aggregates. The MD and steered molecular dynamics （SMD） simulation results agree well with the experimental results, and the simulation data also show that the more steps of adding multivalent cations there are, the more compact the condensed DNA structure will be. This investigation can help us to control DNA condensation and understand the complicated structures of DNA--cation complexes.     

类蛋白质分子的二级结构对力学行为的影响

采用Kolinski等建立的类蛋白质分子的格点模型,研究了由典型的(HHPPHPP)x重复单元构成、含有α螺旋结构的类蛋白质分子链在拉伸过程中的构象性质和力学行为.发现不同强度的α螺旋相互作用会直接影响其拉伸过程.α螺旋相互作用强的类蛋白质分子链,具有更低的内能,更小的应力,在拉伸过程中更容易失去紧密接触对,同时也更容易被拉成“棒状”结构,但在整个拉伸过程中,α螺旋结构且能保持稳定;还发现类蛋白质分子的链长对拉伸也有影响,对较长的类蛋白质分子链,其内能更低,弹性力更小,自由能更大,紧密接触对的含量比例也更高,而“棒状化”程度较小.这些研究能够帮助我们加深对蛋白质分子的构象和弹性力学行为的理解.