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brownian dynamics simulation of the cross-talking effect among modified histones on conformations of nucleosomes

Chinese Physics B 2010年第4期19卷 461-468页

作者：段兆文李伟谢平窦硕星王鹏业 Key Laboratory of Soft Matter Physics Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of Sciences

Using brownian dynamics simulation, we studied the effect of histone modifications On conformations of an array of nucleosomes in a segment of chromatin. The simulation demonstrated that the segment of chromatin shows the dynamic behaviour that its conformation can switch between a state with nearly all of the histones being wrapped by DNA and a state with nearly all of the histones being unwrapped by DNA, thus involving the ＂cross-talking＂ interactions among the histones. Each state can stay for a sufficiently long time. These conformational states are essential for gene expression or gene silence. The simulation also shows that these conformational states can be inherited by the daughter DNAs during DNA replication, giving a theoretical explanation of the epigenetic phenomenon.

关键词： nucleosome histone modification DNA brownian dynamics

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Conformation of an Amphiphilic Comb-like Copolymer in a Selective Solvent

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Chinese Journal of Polymer Science 2023年第9期41卷 1386-1391,I0006页

作者： Peng Hao Xing-Hong Mai Qiao-Yue Chen Ming-Ming Ding Xinjiang Laboratory of Phase Transitions and Microstructures in Condensed Matter Physics College of Physical Science and TechnologyYili Normal UniversityYining835000China School of Chemical Engineering and Light Industry Guangdong University of TechnologyGuangzhou510006China

We study the conformation of an amphiphilic comb-like copolymer in a selective solvent by using brownian dynamics simulations.Our results demonstrate that,there is an optimal total degree of polymerization to form spherical micelles.Only when the total degree of polymerization is less than the optimal total degree of polymerization,a unimolecular spherical micelle can be formed,otherwise,the spherical micelle will be transformed into a cylindrical micelle.When the total degree of polymerization is less than the optimal total degree of polymerization,the radius of gyration and the stretching factor meet an exponential relationship,where the power exponent decreases with the increase of the length of hydrophilic side chains.The fundamental principles uncovered here afford insights for the optimization of molecular design of amphiphilic comb-like copolymers in various applications.

关键词： Comb-like copolymer Conformation Selective solvent brownian dynamics

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Dynamical Demixing of a Binary Mixture Under Sedimentation

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Communications in Computational Physics 2023年第1期33卷 1-21页

作者： Andre S.Nunes Rodrigo C.V.Coelho Vasco C.Braz Margarida M.Telo da Gama Nuno A.M.Araujo Centro de F´ısica Te´orica e Computacional Faculdade de CiˆenciasUniversidade de LisboaP-1749-016 LisboaPortugal Departamento de F´ısica Faculdade de CienciasUniversidade de LisboaP-1749-016 LisboaPortugal Electric Ant Lab Science Park 1061098 XGAmsterdamThe Netherlands

We investigate the sedimentation dynamics of a binary mixture,the species of which differ by their Stokes coefficients but are identical otherwise.We analyze the sedimentation dynamics and the morphology of the final deposits using brownian dynamics simulations for mixtures with a range of sedimentation velocities of both species.In addition,we use the lattice Boltzmann method to study hydrodynamic effects.We found a threshold in the difference of the sedimentation velocities above which the species in the final deposit are segregated.The degree of segregation increases with the difference in the Stokes coefficients or the sedimentation velocities above the threshold.We propose a simple analytical model that captures the main features of the simulated deposits.

关键词： Sedimentation brownian dynamics lattice Boltzmann method

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Phoretic self-assembly of active colloidal molecules

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Chinese Physics B 2021年第5期30卷 57-62页

作者：雷李杰王硕张昕源赖文杰吴晋宇高永祥 Institute for Advanced Study Shenzhen UniversityShenzhen 518060China Institute of Microscale Optoelectronics Shenzhen UniversityShenzhen 518060China

We simulate the self-assembly of active colloidal molecules from binary mixtures of spherical particles using a brownian dynamics algorithm.These particles interact via phoretic interactions,which are determined by two independently tunable parameters,surface activity and surface mobility.In systems composed of equal-size particles,we observe the formation of colloidal molecules with well-defined coordination numbers and spatial arrangement,which also display distinct dynamic functions,such as resting,translating,and rotating.By changing the size ratio to 2:1 between the two species,we further observe the formation of colloidal molecules with new structures arising from breaking the size symmetry.By tuning the mutual interactions between the smaller species via their surface mobility,we are able to control their spacing as well as the coordination number of the colloidal molecules.This study highlights the importance of tuning surface parameters and size asymmetry in controlling the structure and the active dynamics of colloidal molecules.

关键词： brownian dynamics diffusiophoresis active colloidal molecule self-assembly

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Effect of Hydrodynamic Interaction on Flow-induced Polymer Translocation Through a Nanotube

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Chemical Research in Chinese Universities 2015年第4期31卷 658-663页

作者： DING Mingming DUAN Xiaozheng LU Yuyuan SHI Tongfei State Key Laboratory of Polymer Physics and Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun 130022 P R. China

We investigated the effect of hydrodynamic interaction（HI） on flow-induced polymer translocation through a nanotube by brownian dynamics simulations. Whether there is HI in the simulation system is separately controlled by using different diffusion tensors. It is found that HI has no effect on critical velocity flux for long po- lymer chains due to the competition between more drag force and the hindrance of chain stretching from HI, however, HI broadens the transition interval. In addition, for flow-induced polymer translocation with HI, the critical velocity flux firstly slowly decreases with the increase of chain length and then becomes identical to that of it without HI, that is, the critical velocity flux is independent of chain length. At the same time, HI also accelerates the translocation process and makes the relative variation amplitude of single bead translocation time smaller. In fact, HI can enhance the intrachain cooperativity to make the whole chain obtain more drag force from fluid field and hinder chain stret- ching, both of which play an important role in translocation process.

关键词： Polymer translocation Hydrodynamic interaction brownian dynamics Critical velocity flux Transloca-tion time

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启动剪切下缠结高分子流体应力过冲的本质

启动剪切下缠结高分子流体应力过冲的本质

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2014年全国高分子材料科学与工程研讨会

作者：卢宇源安立佳王十庆王振纲中国科学院长春应用化学研究所高分子物理与化学国家重点实验室 University of Akron California Institute of Technology

＜正＞表征外场下缠结高分子流体的链构型和缠结及阐释其动力学演化是最近10年来国际非线性流变学研究的焦点。粒子示踪测速仪观测的很多重要非线性流变学现象不能基于现有单链平均场下的管子模型阐释。我们利用布朗动力学模拟与理论分... 详细信息

＜正＞表征外场下缠结高分子流体的链构型和缠结及阐释其动力学演化是最近10年来国际非线性流变学研究的焦点。粒子示踪测速仪观测的很多重要非线性流变学现象不能基于现有单链平均场下的管子模型阐释。我们利用布朗动力学模拟与理论分析,针对缠结高分子流体的非线性流变学行为开展了深入的研究。我们的工作指出,在剪切速率高于1/τd且低于1/τd的启动形变下,（1）高分子链不仅发生了取向,而且显著地被拉伸了,这说明高分子链的运动不服从R0use动力学;（2）缠结的高分子链确实发生了解缠结,且在启动形变初期,被拉伸的"缠

关键词： Stress Overshoot Startup Shear entanglements brownian dynamics

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非平衡粒子浴下的brush-like链行为

非平衡粒子浴下的brush-like链行为

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中国化学会2017全国高分子学术论文报告会

作者：田文得苏州大学

研究非平衡态的brush行为是高分子物理中有趣且前沿的课题。该文中,我们构建了一个胶体链组成的brush结构,研究其在非平衡粒子浴中的结构和动力学性质。我们采用具有活性物质特点的粒子,构建远离平衡态的粒子浴,关注brush-like链的结构... 详细信息

研究非平衡态的brush行为是高分子物理中有趣且前沿的课题。该文中,我们构建了一个胶体链组成的brush结构,研究其在非平衡粒子浴中的结构和动力学性质。我们采用具有活性物质特点的粒子,构建远离平衡态的粒子浴,关注brush-like链的结构和动力学行为。为更好的体现非平衡特性,我们构建简单的两维体现进行研究。我们发现随着驱动力增加,粒子会进入并聚集在brush chain的周围,粒子的分布出现纵向和横向的不均匀性。在比较大的驱动力下,brush链形成bundle结构,且bundle结构进行左右周期性摆动。对brush高度统计分析可见,brush链被拉伸且被推倒。倾斜度随着驱动力的增加而增大。此外,我们还发现在非平衡粒子浴中,brush链的Rg和平均高度h和链长N成很好的现象关系。进一步,我们分析了chain形成bundle并beating的物理机制。

关键词： brush-like chain non-equilibrium bath brownian dynamics beating

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