Phase behaviour of pure and mixed patchy colloids — Theory and simulation

“…To study the BIA in more detail, here we use Langevin dynamics simulations of a simple polymer model, with proteins represented by "patchy particles" [ The latter are rigid bodies made up from spheres (a "central" bead surrounded by "patch" beads), similar to the patchy particles models common in the soft matter physics literature [15][16][17][18]. We use a common bead-and-spring polymer model [19], which could represent DNA or chromatin-we use a persistence length close to that of the latter.…”

Section: Modelmentioning

confidence: 99%

Polymer compaction and bridging-induced clustering of protein-inspired patchy particles

Brackley

2020

J. Phys.: Condens. Matter

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There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to be able to compact DNA in vitro, and many others have been observed in foci or puncta when fluorescently labelled and imaged in vivo. In this work we study, using coarse-grained Langevin dynamics simulations, the compaction of polymers by simple model proteins and a phenomenon known as the "bridging-induced attraction". The latter is a mechanism observed in previous simulations [Brackley et al., Proc. Natl. Acad. Sci. USA 110 (2013)], where proteins modelled as spheres form clusters via their multivalent interactions with a polymer, even in the absence of any explicit protein-protein attractive interactions. Here we extend this concept to consider more detailed model proteins, represented as simple "patchy particles" interacting with a semi-flexible bead-and-spring polymer. We find that both the compacting ability and the effect of the bridging-induced attraction depend on the valence of the model proteins. These effects also depend on the shape of the protein, which determines its ability to form bridges.

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“…Its predictions are often in close qualitative and quantitative agreement with exact simulations of patchy particle models. 10,12,[14][15][16][17]26 Formally, TPT is derived from a graph-theoretic expansion and a partial re-summation centered around a few key physical assumptions: [51][52][53][54] (1) each patch on a particle can only bond with one other patch, (2) bond formation is statistically uncorrelated between patches on a particle, and (3) bonding occurs in a tree-like structure (i.e., closed loops are not permitted). As a result of these assumptions, TPT has a relatively simple closed-form expression for the free energy, rendering thermodynamic stability and equilibrium phase coexistence calculations computationally inexpensive.…”

Section: Theorymentioning

confidence: 99%

Structure and phase behavior of polymer-linked colloidal gels

Howard

Jadrich

Lindquist

et al. 2019

The Journal of Chemical Physics

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Low-density "equilibrium" gels that consist of a percolated, kinetically arrested network of colloidal particles and are resilient to aging can be fabricated by restricting the number of effective bonds that form between the colloids. Valence-restricted patchy particles have long served as one archetypal example of such materials, but equilibrium gels can also be realized through a synthetically simpler and scalable strategy that introduces a secondary linker, such as a small ditopic molecule, to mediate the bonds between the colloids. Here, we consider the case where the ditopic linker molecules are low-molecular-weight polymers and demonstrate using a model colloid-polymer mixture how macroscopic properties such as the phase behavior as well as the microstructure of the gel can be designed through the polymer molecular weight and concentration. The low-density window for equilibrium gel formation is favorably expanded using longer linkers, while necessarily increasing the spacing between all colloids. However, we show that blends of linkers with different sizes enable wider variation in microstructure for a given target phase behavior. Our computational study suggests a robust and tunable strategy for the experimental realization of equilibrium colloidal gels.

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Phase behaviour of pure and mixed patchy colloids — Theory and simulation

Cited by 43 publications

References 98 publications

Colloidal molecules and patchy particles: complementary concepts, synthesis and self-assembly

Colloidal molecules and patchy particles: complementary concepts, synthesis and self-assembly

Polymer compaction and bridging-induced clustering of protein-inspired patchy particles

Structure and phase behavior of polymer-linked colloidal gels

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