scholarly journals Non-equilibrium chromosome looping via molecular slip-links

2016 ◽  
Author(s):  
C. A. Brackley ◽  
J. Johnson ◽  
D. Michieletto ◽  
A. N. Morozov ◽  
M. Nicodemi ◽  
...  
Keyword(s):  
Motor Activity ◽  
Osmotic Pressure ◽  
Brownian Dynamics ◽  
Ratchet Effect ◽  
Single Slip ◽  
Exactly Solvable ◽  
Set Up ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations ◽  
Non Equilibrium

AbstractWe propose a model for the formation of chromatin loops based on the diffusive sliding of a DNA-bound factor which can dimerise to form a molecular slip-link. Our slip-links mimic the behaviour of cohesin-like molecules, which, along with the CTCF protein, stabilize loops which organize the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable non-equilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favour of convergent CTCF-mediated chromosome loops observed experimentally. Importantly, our model does not require any underlying, and energetically costly, motor activity of cohesin. We also find that the diffusive motion of multiple slip-links along chromatin may be rectified by an intriguing ratchet effect that arises if slip-links bind to the chromatin at a preferred "loading site". This emergent collective behaviour is driven by a 1D osmotic pressure which is set up near the loading point, and favours the extrusion of loops which are much larger than the ones formed by single slip-links.

scholarly journals Dynamics of dissipative self-assembly of particles interacting through oscillatory forces

2016 ◽  
Vol 186 ◽  
pp. 399-418 ◽  
Author(s):  
M. Tagliazucchi ◽  
I. Szleifer
Keyword(s):  
Steady State ◽  
Self Assembly ◽  
Brownian Dynamics ◽  
Oscillation Period ◽  
Interparticle Forces ◽  
Dynamics Simulations ◽  
Oscillation Frequencies ◽  
Brownian Dynamics Simulations ◽  
Fast Oscillations ◽  
Non Equilibrium

Dissipative self-assembly is the formation of ordered structures far from equilibrium, which continuously uptake energy and dissipate it into the environment. Due to its dynamical nature, dissipative self-assembly can lead to new phenomena and possibilities of self-organization that are unavailable to equilibrium systems. Understanding the dynamics of dissipative self-assembly is required in order to direct the assembly to structures of interest. In the present work, Brownian dynamics simulations and analytical theory were used to study the dynamics of self-assembly of a mixture of particles coated with weak acids and bases under continuous oscillations of the pH. The pH of the system modulates the charge of the particles and, therefore, the interparticle forces oscillate in time. This system produces a variety of self-assembled structures, including colloidal molecules, fibers and different types of crystalline lattices. The most important conclusions of our study are: (i) in the limit of fast oscillations, the whole dynamics (and not only those at the non-equilibrium steady state) of a system of particles interacting through time-oscillating interparticle forces can be described by an effective potential that is the time average of the time-dependent potential over one oscillation period; (ii) the oscillation period is critical to determine the order of the system. In some cases the order is favored by very fast oscillations while in others small oscillation frequencies increase the order. In the latter case, it is shown that slow oscillations remove kinetic traps and, thus, allow the system to evolve towards the most stable non-equilibrium steady state.

scholarly journals Generic model for tunable colloidal aggregation in multidirectional fields

Soft Matter ◽  
2015 ◽  
Vol 11 (37) ◽  
pp. 7356-7366 ◽  
Author(s):  
Florian Kogler ◽  
Orlin D. Velev ◽  
Carol K. Hall ◽  
Sabine H. L. Klapp
Keyword(s):  
Brownian Dynamics ◽  
Colloidal Particles ◽  
Generic Model ◽  
External Fields ◽  
Colloidal Aggregation ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations ◽  
Non Equilibrium

Based on Brownian dynamics simulations we investigate the non-equilibrium aggregation of colloidal particles in external fields.

scholarly journals Structure evolution of suspensions under time-dependent electric or magnetic field

2021 ◽  
Author(s):  
Konstantinos Manikas ◽  
Markus Hütter ◽  
Patrick D. Anderson
Keyword(s):  
Magnetic Field ◽  
Field Strength ◽  
Brownian Dynamics ◽  
Thermal Fluctuations ◽  
Time Dependent ◽  
Structure Evolution ◽  
Strength Increase ◽  
Large Rotation ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations

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.

scholarly journals Influence of size polydispersity on magnetic field tunable structures in magnetic nanofluids containing superparamagnetic nanoparticles.

2021 ◽  
Author(s):  
Dillip Kumar Mohapatra ◽  
Philip James Camp ◽  
John Philip
Keyword(s):  
Magnetic Field ◽  
Particle Size ◽  
Light Scattering ◽  
Optical Microscopy ◽  
Brownian Dynamics ◽  
Phase Contrast ◽  
Superparamagnetic Nanoparticles ◽  
Magnetic Nanofluids ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations

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...

scholarly journals Hard discs under steady shear: comparison of Brownian dynamics simulations and mode coupling theory

2009 ◽  
Vol 367 (1909) ◽  
pp. 5033-5050 ◽  
Author(s):  
Oliver Henrich ◽  
Fabian Weysser ◽  
Michael E. Cates ◽  
Matthias Fuchs
Keyword(s):  
Brownian Dynamics ◽  
Mode Coupling ◽  
Transition Density ◽  
Two Dimensions ◽  
Coupling Theory ◽  
Mode Coupling Theory ◽  
Stationary Structure ◽  
Homogeneous Shear Flow ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations

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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