How does a flexible chain of active particles swell?

Kaiser, Andreas; Babel, Sonja; Hagen, Borge ten; Ferber, Christian von; Löwen, Hartmut

doi:10.1063/1.4916134

Cited by 113 publications

(164 citation statements)

References 76 publications

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“…The global conformational properties of FG repeats simulated with the TIP4P-D model are in better agreement with previous experimental observations than those from the TIP4P-Ew simulations. Specifically, in the TIP4P-Ew simulations, the FG repeats formed a relatively compact disordered ensemble with (i) a Flory exponent ν = 0.35 characterizing the power dependence of the radius of gyration (R g ) on chain length (48) (Fig. 2B) (according to Flory's theory of polymers, a value of 0.33-0.40 is typical for polymers in poor solvent such as globular proteins or premolten globules; ref.…”

Section: Resultsmentioning

confidence: 99%

Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex

Raveh

Karp

Sparks

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

131

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Nucleocytoplasmic transport is mediated by the interaction of transport factors (TFs) with disordered phenylalanine-glycine (FG) repeats that fill the central channel of the nuclear pore complex (NPC). However, the mechanism by which TFs rapidly diffuse through multiple FG repeats without compromising NPC selectivity is not yet fully understood. In this study, we build on our recent NMR investigations showing that FG repeats are highly dynamic, flexible, and rapidly exchanging among TF interaction sites. We use unbiased long timescale all-atom simulations on the Anton supercomputer, combined with extensive enhanced sampling simulations and NMR experiments, to characterize the thermodynamic and kinetic properties of FG repeats and their interaction with a model transport factor. Both the simulations and experimental data indicate that FG repeats are highly dynamic random coils, lack intrachain interactions, and exhibit significant entropically driven resistance to spatial confinement. We show that the FG motifs reversibly slide in and out of multiple TF interaction sites, transitioning rapidly between a strongly interacting state and a weakly interacting state, rather than undergoing a much slower transition between strongly interacting and completely noninteracting (unbound) states. In the weakly interacting state, FG motifs can be more easily displaced by other competing FG motifs, providing a simple mechanism for rapid exchange of TF/FG motif contacts during transport. This slide-and-exchange mechanism highlights the direct role of the disorder within FG repeats in nucleocytoplasmic transport, and resolves the apparent conflict between the selectivity and speed of transport.nuclear pore | molecular dynamics | nucleoporins | transport factors | NMR T he nuclear pore complex (NPC) regulates macromolecular transport between the nucleus and the cytoplasm in all eukaryotic cells (1, 2). The NPC allows for passive diffusion of small molecules including sugars, ions, and water, while simultaneously imposing size-dependent exclusion of macromolecules without nuclear transport factor (TF) binding sites, generating unique nuclear and cytoplasmic compartments (3, 4). Larger macromolecules can bypass the selectivity barrier of the NPC by interacting with TFs that shuttle cargo through the central channel of the pore. In pathological conditions, including many cancers and viral infections, the NPC is hijacked and used to transport undesired particles, or it is modified to attenuate the cellular responses to disease onset (5, 6).TFs traverse the NPC by selective and reversible association with disordered phenylalanine-glycine (FG) repeat domains of the FG nucleoporin proteins (FG Nups), which line the surface of the NPC (7-14). Each FG repeat domain consists of 5-50 FG repeats. In turn, each FG repeat consists of a single FG motif of various sequence flavors, such as the FSFG and GLFG motifs, and 10-30 spacer residues that separate consecutive FG motifs (15, 16). The spacer residues are strongly hydrophilic (17) and rich ...

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Section: Resultsmentioning

confidence: 99%

Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex

Raveh

Karp

Sparks

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

131

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“…Furthermore, non-spherical agents have been examined. Especially, elongated shapes as rodlike 17,39,40 or dumbbell swimmers 41,42 and even longer chains of active particles 43 were considered. Here, the type of active propulsion seems to play an important role 44 .…”

Section: Introductionmentioning

confidence: 99%

Phase behavior of active Brownian disks, spheres, and dimers

Siebert¹,

Letz²,

Speck³

et al. 2017

Soft Matter

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In this paper we provide high precision estimates of the phase diagram of active Brownian particles. We extract coexisting densities from simulations of phase separated states in an elongated box (slab geometry) which minimizes finite-size effects and allows for precise determination of points on the binodal lines. Using this method, we study the influence of both shape and dimensionality on the two-phase region. Active spheres and dumbbells of active particles are compared to the known phase diagram of active Brownian disks. In the case of dimers, both correlated and uncorrelated propulsion of the two beads are studied. The influence of correlation is discussed through a simple mapping.

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“…A variant of our model also currently under investigation are "active colloidal polymers" [107,108,[123][124][125]. In this case, many colloidal particles are linked to a linear chain.…”

Section: Resultsmentioning

confidence: 99%

“…On the one hand, the chain can be made of passive colloidal particles placed into a background of self-propelling microswimmers [123][124][125]. On the other hand, the chain itself could be composed of self-propelling Janus particles [107,108]. Naturally, also combinations of the two cases, or chains that are only partially active, can be studied in analogy to our simplified finitely-sized model microswimmers.…”

Section: Resultsmentioning

confidence: 99%

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Getting drowned in a swirl: Deformable bead-spring model microswimmers in external flow fields

2016

Self Cite

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Deformability is a central feature of many types of microswimmers, e.g. for artificially generated self-propelled droplets. Here, we analyze deformable bead-spring microswimmers in an externally imposed solvent flow field as simple theoretical model systems. We focus on their behavior in a circular swirl flow in two spatial dimensions. Linear (straight) two-bead swimmers are found to circle around the swirl with a slight drift to the outside with increasing activity. In contrast to that, we observe for triangular three-bead or square-like four-bead swimmers a tendency of being drawn into the swirl and finally getting drowned, although a radial inward component is absent in the flow field. During one cycle around the swirl, the self-propulsion direction of an active triangular or square-like swimmer remains almost constant, while their orbits become deformed exhibiting an "egg-like" shape. Over time, the swirl flow induces slight net rotations of these swimmer types, which leads to net rotations of the egg-shaped orbits. Interestingly, in certain cases, the orbital rotation changes sense when the swimmer approaches the flow singularity. Our predictions can be verified in real-space experiments on artificial microswimmers.

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How does a flexible chain of active particles swell?

Cited by 113 publications

References 76 publications

Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex

Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex

Phase behavior of active Brownian disks, spheres, and dimers

Getting drowned in a swirl: Deformable bead-spring model microswimmers in external flow fields

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