搜索

x

留言板

尊敬的读者、作者、审稿人, 关于本刊的投稿、审稿、编辑和出版的任何问题, 您可以本页添加留言。我们将尽快给您答复。谢谢您的支持!

姓名
邮箱
手机号码
标题
留言内容
验证码

打结高分子链穿孔行为的研究

温晓会 章林溪

引用本文:
Citation:

打结高分子链穿孔行为的研究

温晓会, 章林溪

A knotted polymer chain passing through a pore

Wen Xiao-Hui, Zhang Lin-Xi
PDF
导出引用
  • 以三叶草型结(即31结)为例,采用分子动力学(MD)方法,研究打结高分子链在外场力作用下穿越微孔的动力学过程.模拟发现,在拉动打结高分子链的过程中,结的大小呈涨落变化,直至最后散结.定性讨论了结的存在对高分子链穿孔速率的影响.在外场力作用下,打结高分子链平均穿孔时间(τ)与链长(N)满足标度关系τ~N α,其中标度系数α随外场力f增大而增大.对于短链,外场力越大,平均穿孔时间越短
    A knotted polymer chain passing through a pore is investigated by molecule dynamics method. In this paper, we take 31 knot as an example. It is found that, during the process of translocation, the size of the knot fluctuates until the knot is unknotted. In addition, the effect of the knot on the translocation velocity of the knotted chain is also discussed. For the given external force, the average translocation time τ satisfies the scaling relation:τ~N α, and the scaling exponent α increases with the external force f. For short knotted polymer chains, the average translocation time τ decreases when the external force f increases. However, for very long knotted polymer chains, the average translocation time τ increases when the external force f increases. In the meantime, the position of knot in a knotted polymer chain also affects the average translocation time τ strongly. The closer the knot approaches the first translocated monomer, the longer the average translocation time. This investigation can provide some insights into the translocation of knotted polymer chains (especially knotted DNA) through the nanopore, and help us understand the translocation behavior of biomacromolecules.
    • 基金项目: 国家自然科学基金(批准号:20574052,20774066,20974081,20934004)资助的课题.
    [1]

    Mansfield M L 1994 Macromolecules 27 5924

    [2]

    Lua R, Borovinskiy A L, Grosberg A Y 2004 Polymer 45 717

    [3]

    Virnau P, Kantor Y, Kardar M 2005 J. Am. Chem. Soc. 127 15102

    [4]

    Matthews R, Louis A A, Yeomans J M 2009 Phys. Rev. Lett. 102 088101

    [5]

    Murzin A G, Brenner S E, Hubbard T, Chothia C 1995 J. Mol. Biol. 247 536

    [6]

    Wang X H, Shen Y, Zhang L X 2009 Chin. Phys. B 18 1684

    [7]

    Atiyah M F 1990 The Geometry and Physics of Knots (Cambridge: Cambridge University Press) p291

    [8]

    Katritch V, Bednar J, Michoud D, Scharein R G, Dubochet J, Stasiak A 1996 Nature 384 142

    [9]

    Katritch V, Olson W K, Pieranski P, Dubochet J, Stasiak A 1997 Nature 388 148

    [10]

    Virnau P, Mirny L A, Kardar M 2006 PLoS Comput. Biol. 2 1074

    [11]

    Han J, Turner S W, Craighead H G 1999 Phys. Rev. Lett. 83 1688

    [12]

    Turner S W P, Cabodi M, Craighead H G 2002 Phys. Rev. Lett. 88 128103

    [13]

    Grigoriev S M, Muro C, Dejean L M, Campo M L, Martinez-Caballero S, Kinnally K W 2004 Int. Rev. Cytol. 238 227

    [14]

    Szabo I, Bathori G, Tombola F, Brini M, Coppola A, Zoratti M 1997 J. Biol. Chem. 272 25275

    [15]

    Hanss B, Leal-Pinto E, Bruggeman L A, Copeland T D, Klotman P E 1998 Proc. Natl. Acad. Sci. U.S.A. 95 1921

    [16]

    Tseng Y L, Liu J J, Hong R L 2002 Mol. Pharmacol. 62 864

    [17]

    Kasianowicz J J, Brandin E, Branton D, Deamer D 1996 Proc. Natl. Acad. Sci. U.S.A. 93 13770

    [18]

    Meller A, Nivon L, Brandin E, Golovchenko J, Branton D 2000 Proc. Natl. Acad. Sci. U.S.A. 97 1079

    [19]

    Jiang S C, Zhang L X, Xia A G, Chen H P, Cheng J 2010 Chin. Phys. B 19 018106

    [20]

    Ali I, Marenduzzo D, Yeomans J M 2006 Phys. Rev. Lett. 96 208102

    [21]

    Ali I, Marenduzzo D, Yeomans J M 2008 Biophys. J. 94 4159

    [22]

    Li Y L, Luo C L 2002 Acta Phys. Sin. 51 2589 (in Chinese) [李延龄、罗成林 2002 物理学报 51 2589]

    [23]

    Zhang X R, Shen Z G, Chen J F, Wang W C 2003 Acta Phys. Sin. 52 163 (in Chinese) [张现仁、沈志刚、陈建峰、汪文川 2003 物理学报 52 163]

    [24]

    Xie Y J, Shi Q W, Wang X P, Zhu P P, Yang H Y, Zhang X Y 2004 Acta Phys. Sin. 53 2796 (in Chinese) [谢永军、石勤伟、王晓平、朱平平、杨海洋、张兴元 2004 物理学报 53 2796]

    [25]

    Luo K F, Ala-Nissila T, Ying S C, Bhattacharya A 2008 Phys. Rev. Lett. 100 058101

    [26]

    Jiang S C, Zhang L X, Xia A G, Chen H P 2009 Acta Phys. Sin. 59 4337 (in Chinese) [江绍钏、章林溪、夏阿根、陈宏平 2010 物理学报 59 4337]

    [27]

    Luo K F, Ala-Nissila Nissila T A, Ying S C, Bhattacharya A 2007 Phys. Rev. Lett. 99 148102

  • [1]

    Mansfield M L 1994 Macromolecules 27 5924

    [2]

    Lua R, Borovinskiy A L, Grosberg A Y 2004 Polymer 45 717

    [3]

    Virnau P, Kantor Y, Kardar M 2005 J. Am. Chem. Soc. 127 15102

    [4]

    Matthews R, Louis A A, Yeomans J M 2009 Phys. Rev. Lett. 102 088101

    [5]

    Murzin A G, Brenner S E, Hubbard T, Chothia C 1995 J. Mol. Biol. 247 536

    [6]

    Wang X H, Shen Y, Zhang L X 2009 Chin. Phys. B 18 1684

    [7]

    Atiyah M F 1990 The Geometry and Physics of Knots (Cambridge: Cambridge University Press) p291

    [8]

    Katritch V, Bednar J, Michoud D, Scharein R G, Dubochet J, Stasiak A 1996 Nature 384 142

    [9]

    Katritch V, Olson W K, Pieranski P, Dubochet J, Stasiak A 1997 Nature 388 148

    [10]

    Virnau P, Mirny L A, Kardar M 2006 PLoS Comput. Biol. 2 1074

    [11]

    Han J, Turner S W, Craighead H G 1999 Phys. Rev. Lett. 83 1688

    [12]

    Turner S W P, Cabodi M, Craighead H G 2002 Phys. Rev. Lett. 88 128103

    [13]

    Grigoriev S M, Muro C, Dejean L M, Campo M L, Martinez-Caballero S, Kinnally K W 2004 Int. Rev. Cytol. 238 227

    [14]

    Szabo I, Bathori G, Tombola F, Brini M, Coppola A, Zoratti M 1997 J. Biol. Chem. 272 25275

    [15]

    Hanss B, Leal-Pinto E, Bruggeman L A, Copeland T D, Klotman P E 1998 Proc. Natl. Acad. Sci. U.S.A. 95 1921

    [16]

    Tseng Y L, Liu J J, Hong R L 2002 Mol. Pharmacol. 62 864

    [17]

    Kasianowicz J J, Brandin E, Branton D, Deamer D 1996 Proc. Natl. Acad. Sci. U.S.A. 93 13770

    [18]

    Meller A, Nivon L, Brandin E, Golovchenko J, Branton D 2000 Proc. Natl. Acad. Sci. U.S.A. 97 1079

    [19]

    Jiang S C, Zhang L X, Xia A G, Chen H P, Cheng J 2010 Chin. Phys. B 19 018106

    [20]

    Ali I, Marenduzzo D, Yeomans J M 2006 Phys. Rev. Lett. 96 208102

    [21]

    Ali I, Marenduzzo D, Yeomans J M 2008 Biophys. J. 94 4159

    [22]

    Li Y L, Luo C L 2002 Acta Phys. Sin. 51 2589 (in Chinese) [李延龄、罗成林 2002 物理学报 51 2589]

    [23]

    Zhang X R, Shen Z G, Chen J F, Wang W C 2003 Acta Phys. Sin. 52 163 (in Chinese) [张现仁、沈志刚、陈建峰、汪文川 2003 物理学报 52 163]

    [24]

    Xie Y J, Shi Q W, Wang X P, Zhu P P, Yang H Y, Zhang X Y 2004 Acta Phys. Sin. 53 2796 (in Chinese) [谢永军、石勤伟、王晓平、朱平平、杨海洋、张兴元 2004 物理学报 53 2796]

    [25]

    Luo K F, Ala-Nissila T, Ying S C, Bhattacharya A 2008 Phys. Rev. Lett. 100 058101

    [26]

    Jiang S C, Zhang L X, Xia A G, Chen H P 2009 Acta Phys. Sin. 59 4337 (in Chinese) [江绍钏、章林溪、夏阿根、陈宏平 2010 物理学报 59 4337]

    [27]

    Luo K F, Ala-Nissila Nissila T A, Ying S C, Bhattacharya A 2007 Phys. Rev. Lett. 99 148102

  • [1] 王超, 周艳丽, 吴凡, 陈英才. 高分子链在分子刷表面吸附的Monte Carlo模拟. 物理学报, 2020, 69(16): 168201. doi: 10.7498/aps.69.20200411
    [2] 孙立望, 李洪, 汪鹏君, 高和蓓, 罗孟波. 利用神经网络识别高分子链在表面的吸附相变. 物理学报, 2019, 68(20): 200701. doi: 10.7498/aps.68.20190643
    [3] 王超, 陈英才, 周艳丽, 罗孟波. 两嵌段高分子链在周期管道内扩散的Monte Carlo模拟. 物理学报, 2017, 66(1): 018201. doi: 10.7498/aps.66.018201
    [4] 蒋滢, 陈征宇. 蠕虫状链模型在高分子物理研究中的应用. 物理学报, 2016, 65(17): 178201. doi: 10.7498/aps.65.178201
    [5] 华昀峰, 张冬, 章林溪. 半刚性高分子链螺旋结构诱导纳米棒的有序结构. 物理学报, 2015, 64(8): 088201. doi: 10.7498/aps.64.088201
    [6] 黄德财, 陈伟中, 杨安娜, 孙敏, 胡凤兰, 赵敏. 孤立波在一维复合颗粒链中传播特性的模拟研究. 物理学报, 2014, 63(15): 154502. doi: 10.7498/aps.63.154502
    [7] 刘娜娜, 孙建林, 夏垒, 曾颖峰. 缓蚀剂在铜表面吸附行为的研究. 物理学报, 2013, 62(20): 203102. doi: 10.7498/aps.62.203102
    [8] 郭龙婷, 孙继忠, 黄艳, 刘升光, 王德真. 低能氢粒子沿不同角度轰击钨(001)表面的反射概率及入射深度分布的分子动力学研究. 物理学报, 2013, 62(22): 227901. doi: 10.7498/aps.62.227901
    [9] 仝焕平, 章林溪. 受限于圆柱体内半刚性高分子链的螺旋结构转变. 物理学报, 2012, 61(5): 058701. doi: 10.7498/aps.61.058701
    [10] 张治海, 孙继忠, 刘升光, 王德真. 载能氢原子与石墨(001)面碰撞过程中的能量传递行为的分子动力学研究. 物理学报, 2012, 61(4): 047901. doi: 10.7498/aps.61.047901
    [11] 孙继忠, 张治海, 刘升光, 王德真. 载能氢同位素原子与石墨(001)面碰撞的分子动力学研究. 物理学报, 2012, 61(5): 055201. doi: 10.7498/aps.61.055201
    [12] 李守阳, 孙继忠, 张治海, 刘升光, 王德真. 单空位缺陷对载能氢原子与石墨层间碰撞的能量交换的影响的分子动力学研究. 物理学报, 2011, 60(5): 057901. doi: 10.7498/aps.60.057901
    [13] 余波, 应阳君, 许海波. 中子半影成像的两种非线性重建方法研究. 物理学报, 2010, 59(8): 5351-5357. doi: 10.7498/aps.59.5351
    [14] 韩同伟, 贺鹏飞. 石墨烯弛豫性能的分子动力学模拟. 物理学报, 2010, 59(5): 3408-3413. doi: 10.7498/aps.59.3408
    [15] 朱亚波, 鲍振, 蔡存金, 杨玉杰. 模拟研究碳纳米管的热稳定性质. 物理学报, 2009, 58(11): 7833-7837. doi: 10.7498/aps.58.7833
    [16] 王 禹, 章林溪. 外力诱导吸附高分子单链的拉伸分子动力学研究. 物理学报, 2008, 57(5): 3281-3286. doi: 10.7498/aps.57.3281
    [17] 张晋鲁, 蒋建国, 蒋新革, 黄以能. 线性高分子体系中高分子链间排除体积效应的模型化. 物理学报, 2007, 56(9): 5088-5092. doi: 10.7498/aps.56.5088
    [18] 袁剑辉, 程玉民. 单壁碳纳米管杨氏模量的掺杂效应. 物理学报, 2007, 56(8): 4810-4816. doi: 10.7498/aps.56.4810
    [19] 李宝兴, 叶美英, 褚巧燕, 俞 健. 玻璃微流控芯片表面改性的微观机理研究. 物理学报, 2007, 56(6): 3446-3452. doi: 10.7498/aps.56.3446
    [20] 吴长勤, 张国平, 裘慧明. 高分子链中的光学非线性基本态. 物理学报, 1995, 44(1): 64-71. doi: 10.7498/aps.44.64
计量
  • 文章访问数:  7406
  • PDF下载量:  649
  • 被引次数: 0
出版历程
  • 收稿日期:  2009-11-16
  • 修回日期:  2010-04-23
  • 刊出日期:  2010-05-05

/

返回文章
返回