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

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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Brownian dynamics simulations of one-patch inverse patchy particles

Physical Chemistry Chemical Physics ◽

10.1039/c9cp04247d ◽

2019 ◽

Vol 21 (42) ◽

pp. 23447-23458 ◽

Cited By ~ 3

Author(s):

Manuella Cerbelaud ◽

Khaoula Lebdioua ◽

Công Tâm Tran ◽

Benoît Crespin ◽

Anne Aimable ◽

...

Keyword(s):

Self Assembly ◽

Brownian Dynamics ◽

The Self ◽

Patchy Particles ◽

Dynamics Simulations ◽

Brownian Dynamics Simulations

92 bead colloids are used to study the self-assembly of large surface anistropic particles.

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Ephemeral protein binding to DNA shapes stable nuclear bodies and chromatin domains

10.1101/065664 ◽

2016 ◽

Author(s):

C. A. Brackley ◽

B. Liebchen ◽

D. Michieletto ◽

F. Mouvet ◽

P. R. Cook ◽

...

Keyword(s):

Dna Binding ◽

Self Assembly ◽

Brownian Dynamics ◽

Large Scale ◽

Nuclear Bodies ◽

Underlying Structure ◽

Post Translational Modification ◽

Equilibrium Process ◽

Dynamics Simulations ◽

Brownian Dynamics Simulations

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.

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MESOSCALE COMPUTER SIMULATIONS OF POLYMER-TETHERED ORGANIC/INORGANIC NANOCUBE SELF-ASSEMBLY

International Journal of Modern Physics C ◽

10.1142/s0129183109014503 ◽

2009 ◽

Vol 20 (09) ◽

pp. 1443-1456 ◽

Cited By ~ 3

Author(s):

ELAINE R. CHAN ◽

LIN C. HO ◽

SHARON C. GLOTZER

Keyword(s):

Self Assembly ◽

Brownian Dynamics ◽

Surrounding Medium ◽

Structural Features ◽

Minimal Models ◽

Flexible Coil ◽

Dynamics Simulations ◽

Brownian Dynamics Simulations ◽

Oligomeric Silsesquioxane

A molecular simulation study of the mesoscale self-assembly of tethered nanoparticles having a cubic geometry is presented. Minimal models of the tethered nanocubes are developed to represent a polyhedral oligomeric silsesquioxane (POSS) molecule with polymeric substituents. The models incorporate some of the essential structural features and interaction specificity of POSS molecules, and facilitate access to the long length and timescales pertinent to the assembly process while foregoing atomistic detail. The types of self-assembled nanostructures formed by the tethered nanocubes in solution are explored via Brownian dynamics simulations using these minimal models. The influence of various parameters, including the conditions of the surrounding medium, the molecular weight and chemical composition of the tether functionalities, and the number of tethers on the nanocube, on the formation of specific structures is demonstrated. The role of cubic nanoparticle geometry on self-assembly is also assessed by comparing the types of structures formed by tethered nanocubes and by their flexible coil triblock copolymer and tethered nanosphere counterparts. Morphological phase diagrams are proposed to describe the behavior of the tethered nanocubes.

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Self-assembly of amphiphilic truncated cones to form hollow nanovesicles

RSC Advances ◽

10.1039/c8ra01100a ◽

2018 ◽

Vol 8 (24) ◽

pp. 13526-13536

Author(s):

Yali Wang ◽

Xuehao He

Keyword(s):

Capsid Protein ◽

Self Assembly ◽

Brownian Dynamics ◽

The Self ◽

Truncated Cone ◽

Anisotropic Interactions ◽

Dynamics Simulations ◽

Brownian Dynamics Simulations ◽

Protein Shell

To mimic the unique properties of capsid (protein shell of a virus), we performed Brownian dynamics simulations of the self-assembly of amphiphilic truncated cone particles with anisotropic interactions.

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Non-equilibrium chromosome looping via molecular slip-links

10.1101/095992 ◽

2016 ◽

Cited By ~ 1

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.

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Self-assembly of actin monomers into long filaments: Brownian dynamics simulations

The Journal of Chemical Physics ◽

10.1063/1.3159003 ◽

2009 ◽

Vol 131 (1) ◽

pp. 015102 ◽

Cited By ~ 13

Author(s):

Kunkun Guo ◽

Julian Shillcock ◽

Reinhard Lipowsky

Keyword(s):

Self Assembly ◽

Brownian Dynamics ◽

Dynamics Simulations ◽

Brownian Dynamics Simulations

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Self-Assembly of Single-Polymer-Tethered Nanoparticle Amphiphiles upon Varying Tail Length

Nanomaterials ◽

10.3390/nano10112108 ◽

2020 ◽

Vol 10 (11) ◽

pp. 2108

Author(s):

Qingxiao Li ◽

You-Liang Zhu ◽

Xinhui Zhang ◽

Kaidong Xu ◽

Jina Wang ◽

...

Keyword(s):

Self Assembly ◽

Brownian Dynamics ◽

Tail Length ◽

Selective Solvent ◽

Hydrophobic Polymer ◽

System Temperature ◽

The Rich ◽

Dynamics Simulations ◽

Phase Behaviors ◽

Brownian Dynamics Simulations

We systematically investigated the roles of tail length on the self-assembly of shape amphiphiles composed of a hydrophobic polymer chain (tail) and a hydrophilic nanoparticle in selective solvent using Brownian dynamics simulations. The shape amphiphiles exhibited a variety of self-assembled aggregate morphologies which can be tuned by changing tail length (n) in combination with amphiphile concentration (φ) and system temperature (T*). Specifically, at high φ with T*=1.4, the morphology varied following the sequence “spheres → cylinders → vesicles” upon increasing n, agreeing well with experimental observations. At low φ with T*=1.4 or at high φ with T*=1.2, the morphology sequence becomes “spheres or spheres and cylinders mixture → cylinders → vesicles → spheres” upon increasing n, which has not been found experimentally. Two morphological phase diagrams depending on n and φ were constructed for T*=1.4 and 1.2, respectively. The rich phase behaviors on varying tail length could provide the feasible routes to fabricate target aggregate morphologies in various applications, especially for the vesicles with tunable thickness of membranes that are crucial in drug and gene delivery.

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