scholarly journals Brownian Dynamics Simulations of a Self-Avoiding Chain Model of a Chromosome in a Spherical Confinement

2014 ◽  
Vol 106 (2) ◽  
pp. 79a
Author(s):  
Young-Gui Yoon ◽  
Changbong Hyeon
Polymers ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 260 ◽  
Author(s):  
Jizeng Wang ◽  
Kai Li

We investigated the statistical behaviors of semiflexible polymer chains, which were simultaneously subjected to force stretching and rectangular tube confinement. Based on the wormlike chain model and Odijk deflection theory, we derived a new deflection length, by using which new compact formulas were obtained for the confinement free energy and force–confinement–extension relations. These newly derived formulas were justified by numerical solutions of the eigenvalue problem associated with the Fokker–Planck governing equation and extensive Brownian dynamics simulations based on the so-called generalized bead-rod (GBR) model. We found that, compared to classical deflection theory, these new formulas were valid for a much more extended range of the confinement size/persistence length ratio and had no adjustable fitting parameters for sufficiently long semiflexible chains in the whole deflection regime.


Author(s):  
Jizeng Wang ◽  
Kai Li

We quantitatively investigated the statistical behaviors of semiflexible polymer chains, which are simultaneously subjected to force stretching and rectangular tube confinement. Based on the wormlike chain model and Odijk deflection theory, we derived a new deflection length, by which new compact formulas are obtained for the confinement free energy and force-confinement-extension relation. These newly derived formulas have been justified by numerical solutions of an eigenvalue problem associated with the Fokker-Planck governing equation and extensive Brownian dynamics simulations based on the so-called Generalized Bead-Rod (GBR) model. We found that, comparing to the classical deflection theory, these new formulas are valid for a much extended range of the confinement-size /persistence-length ratio, and have no adjustable fitting parameters for sufficient long semiflexible chains in the whole deflection regime.


Author(s):  
Konstantinos Manikas ◽  
Markus Hütter ◽  
Patrick D. Anderson

AbstractThe effect of time-dependent external fields on the structures formed by particles with induced dipoles dispersed in a viscous fluid is investigated by means of Brownian Dynamics simulations. The physical effects accounted for are thermal fluctuations, dipole-dipole and excluded volume interactions. The emerging structures are characterised in terms of particle clusters (orientation, size, anisotropy and percolation) and network structure. The strength of the external field is increased in one direction and then kept constant for a certain amount of time, with the structure formation being influenced by the slope of the field-strength increase. This effect can be partially rationalized by inhomogeneous time re-scaling with respect to the field strength, however, the presence of thermal fluctuations makes the scaling at low field strength inappropriate. After the re-scaling, one can observe that the lower the slope of the field increase, the more network-like and the thicker the structure is. In the second part of the study the field is also rotated instantaneously by a certain angle, and the effect of this transition on the structure is studied. For small rotation angles ($$\theta \le 20^{{\circ }}$$ θ ≤ 20 ∘ ) the clusters rotate but stay largely intact, while for large rotation angles ($$\theta \ge 80^{{\circ }}$$ θ ≥ 80 ∘ ) the structure disintegrates and then reforms, due to the nature of the interactions (parallel dipoles with perpendicular inter-particle vector repel each other). For intermediate angles ($$20<\theta <80^{{\circ }}$$ 20 < θ < 80 ∘ ), it seems that, during rotation, the structure is altered towards a more network-like state, as a result of cluster fusion (larger clusters). The details provided in this paper concern an electric field, however, all results can be projected into the case of a magnetic field and paramagnetic particles.


2021 ◽  
Author(s):  
Dillip Kumar Mohapatra ◽  
Philip James Camp ◽  
John Philip

We probe the influence of particle size polydispersity on field-induced structures and structural transitions in magnetic fluids (ferrofluids) using phase contrast optical microscopy, light scattering and Brownian dynamics simulations. Three...


Author(s):  
Oliver Henrich ◽  
Fabian Weysser ◽  
Michael E. Cates ◽  
Matthias Fuchs

Brownian dynamics simulations of bidisperse hard discs moving in two dimensions in a given steady and homogeneous shear flow are presented close to and above the glass transition density. The stationary structure functions and stresses of shear-melted glass are compared quantitatively to parameter-free numerical calculations of monodisperse hard discs using mode coupling theory within the integration through transients framework. Theory qualitatively explains the properties of the yielding glass but quantitatively overestimates the shear-driven stresses and structural anisotropies.


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