Understanding Topological Defects in Fluidized Dry Active Nematics

Soft Matter ◽  
2022 ◽  
Author(s):  
Bryce Palmer ◽  
Sheng Chen ◽  
Patrick Govan ◽  
Wen Yan ◽  
Tong Gao

Dense assemblies of self-propelling rods (SPRs) may exhibit fascinating collective behaviors and anomalous physical properties that are far away from equilibrium. Using large-scale Brownian dynamics simulations, we investigate the dynamics...

2016 ◽  
Author(s):  
C. A. Brackley ◽  
B. Liebchen ◽  
D. Michieletto ◽  
F. Mouvet ◽  
P. R. Cook ◽  
...  

AbstractFluorescence microscopy reveals that the contents of many (membrane-free) nuclear “bodies” exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To shed light on this, we perform large-scale Brownian dynamics simulations of a chromatin fiber interacting with an ensemble of (multivalent) DNA-binding proteins; these proteins switch between two states – active (binding) and inactive (non-binding). This system provides a model for any DNA-binding protein that can be modified post-translationally to change its affinity for DNA (e.g., like the phosphorylation of a transcription factor). Due to this out-of-equilibrium process, proteins spontaneously assemble into clusters of self-limiting size, as individual proteins in a cluster exchange with the soluble pool with kinetics like those seen in photo-bleaching experiments. This behavior contrasts sharply with that exhibited by “equilibrium”, or non-switching, proteins that exist only in the binding state; when these bind to DNA non-specifically, they form clusters that grow indefinitely in size. Our results point to post-translational modification of chromatin-bridging proteins as a generic mechanism driving the self-assembly of highly dynamic, non-equilibrium, protein clusters with the properties of nuclear bodies. Such active modification also reshapes intra-chromatin contacts to give networks resembling those seen in topologically-associating domains, as switching markedly favors local (short-range) contacts over distant ones.


2018 ◽  
Author(s):  
C. A. Brackley ◽  
J. Johnson ◽  
D. Michieletto ◽  
D. Marenduzzo

AbstractWe use Brownian dynamics simulations to study the formation of chromatin loops through diffusive sliding of molecular slip links, mimicking the behaviour of cohesin-like molecules. We recently proposed that diffusive sliding is sufficient to explain the extrusion of chromatin loops of hundreds of kilo-base-pairs (kbp), which may then be stabilised by interactions between cohesin and CTCF proteins. Here we show that the elasticity of the chromatin fibre strongly affects this dynamical process, and find that diffusive loop extrusion is more efficient on stiffer chromatin regions. Efficiency is also enhanced if cohesin loading sites are close to regions where CTCF is bound. In light of the heterogeneous physical properties of eukaryotic chromatin, we suggest that our results should be relevant to the looping and organisation of interphase chromosomes in vivo.


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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