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.

Viscosity scaling in concentrated dispersions and its impact on colloidal aggregation

2015 ◽  
Vol 17 (37) ◽  
pp. 24392-24402 ◽  
Author(s):  
Lucrèce Nicoud ◽  
Marco Lattuada ◽  
Stefano Lazzari ◽  
Massimo Morbidelli
Keyword(s):  
Brownian Dynamics ◽  
Colloidal Aggregation ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations ◽  
Concentrated Dispersions

Viscosity scaling in concentrated dispersions is identified using Brownian dynamics simulations, and its impact on colloidal aggregation is quantified.

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.

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