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1. A first proof of knot localization for polymers in a nanochannel

   https://doi.org/10.1088/1751-8121/ad6c01  

   Beaton, Nicholas R; Ishihara, Kai; Atapour, Mahshid; Eng, Jeremy W; Vazquez, Mariel; Shimokawa, Koya; Soteros, Christine E (August 2024, Journal of Physics A: Mathematical and Theoretical)

   Abstract Based on polymer scaling theory and numerical evidence, Orlandini, Tesi, Janse van Rensburg and Whittington conjectured in 1996 that the limiting entropy of knot-typeKlattice polygons is the same as that for unknot polygons, and that the entropic critical exponent increases by one for each prime knot in the knot decomposition ofK. This Knot Entropy (KE) conjecture is consistent with the idea that for unconfined polymers, knots occur in a localized way (the knotted part is relatively small compared to polymer length). For full confinement (to a sphere or box), numerical evidence suggests that knots are much less localized. Numerical evidence for nanochannel or tube confinement is mixed, depending on how the size of a knot is measured. Here we outline the proof that the KE conjecture holds for polygons in the $\mathrm{\infty }\times 2\times 1$lattice tube and show that knotting is localized when a connected-sum measure of knot size is used. Similar results are established for linked polygons. This is the first model for which the knot entropy conjecture has been proved. 

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2. The distribution of knots in the Petaluma model

   https://doi.org/10.2140/agt.2018.18.3647  

   Even-Zohar, C; Hass, J; Linial, N; Nowik, T (October 2018, Algebraic geometric topology)

   The representation of knots by petal diagrams (Adams et al 2012) naturally defines a sequence of distributions on the set of knots. We establish some basic properties of this randomized knot model. We prove that in the random n–petal model the probability of obtaining every specific knot type decays to zero as n, the number of petals, grows. In addition we improve the bounds relating the crossing number and the petal number of a knot. This implies that the n–petal model represents at least exponentially many distinct knots. Past approaches to showing, in some random models, that individual knot types occur with vanishing probability rely on the prevalence of localized connect summands as the complexity of the knot increases. However, this phenomenon is not clear in other models, including petal diagrams, random grid diagrams and uniform random polygons. Thus we provide a new approach to investigate this question. 

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3. The second Vassiliev measure of uniform random walks and polygons in confined space

   https://doi.org/10.1088/1751-8121/ac4abf  

   Smith, Philip; Panagiotou, Eleni (February 2022, Journal of Physics A: Mathematical and Theoretical)

   Abstract Biopolymers, like chromatin, are often confined in small volumes. Confinement has a great effect on polymer conformations, including polymer entanglement. Polymer chains and other filamentous structures can be represented by polygonal curves in three-space. In this manuscript, we examine the topological complexity of polygonal chains in three-space and in confinement as a function of their length. We model polygonal chains by equilateral random walks in three-space and by uniform random walks (URWs) in confinement. For the topological characterization, we use the second Vassiliev measure. This is an integer topological invariant for polygons and a continuous functions over the real numbers, as a function of the chain coordinates for open polygonal chains. For URWs in confined space, we prove that the average value of the Vassiliev measure in the space of configurations increases as O ( n 2 ) with the length of the walks or polygons. We verify this result numerically and our numerical results also show that the mean value of the second Vassiliev measure of equilateral random walks in three-space increases as O ( n ). These results reveal the rate at which knotting of open curves and not simply entanglement are affected by confinement. 

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4. Hydrodynamics of a single filament moving in a fluid spherical membrane

   Shi, W.; Moradi, M.; Nazockdast, E. (January 2022, ArXivorg)

   Dynamic organization of the cytoskeletal filaments and rod-like proteins in the cell membrane and other biological interfaces occurs in many cellular processes. Previous modeling studies have considered the dynamics of a single rod on fluid planar membranes. We extend these studies to the more physiologically relevant case of a single filament moving in a spherical membrane. Specifically, we use a slender-body formulation to compute the translational and rotational resistance of a single filament of length L moving in a membrane of radius R and 2D viscosity ηm, and surrounded on its interior and exterior with Newtonian fluids of viscosities η− and η+. We first discuss the case where the filament's curvature is at its minimum κ=1/R. We show that the boundedness of spherical geometry gives rise to flow confinement effects that increase in strength with increasing the ratio of filament's length to membrane radius L/R. These confinement flows only result in a mild increase in filament's resistance along its axis, ξ∥, and its rotational resistance, ξΩ. As a result, our predictions of ξ∥ and ξΩ can be quantitatively mapped to the results on a planar membrane. In contrast, we find that the drag in perpendicular direction, ξ⊥, increases superlinearly with the filament's length, when L/R>1 and ultimately ξ⊥→∞ as L/R→π. Next, we consider the effect of the filament's curvature, κ, on its parallel motion, while fixing the membrane's radius. We show that the flow around the filament becomes increasingly more asymmetric with increasing its curvature. These flow asymmetries induce a net torque on the filament, coupling its parallel and rotational dynamics. This coupling becomes stronger with increasing L/R and κ. 

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5. Active Condensation of Filaments Under Spatial Confinement

   https://doi.org/10.3389/fphy.2022.897255  

   Ansari, Saad; Yan, Wen; Lamson, Adam Ray; Shelley, Michael J.; Glaser, Matthew A.; Betterton, Meredith D. (June 2022, Frontiers in Physics)

   Living systems exhibit self-organization, a phenomenon that enables organisms to perform functions essential for life. The interior of living cells is a crowded environment in which the self-assembly of cytoskeletal networks is spatially constrained by membranes and organelles. Cytoskeletal filaments undergo active condensation in the presence of crosslinking motor proteins. In past studies, confinement has been shown to alter the morphology of active condensates. Here, we perform simulations to explore systems of filaments and crosslinking motors in a variety of confining geometries. We simulate spatial confinement imposed by hard spherical, cylindrical, and planar boundaries. These systems exhibit non-equilibrium condensation behavior where crosslinking motors condense a fraction of the overall filament population, leading to coexistence of vapor and condensed states. We find that the confinement lengthscale modifies the dynamics and condensate morphology. With end-pausing crosslinking motors, filaments self-organize into half asters and fully-symmetric asters under spherical confinement, polarity-sorted bilayers and bottle-brush-like states under cylindrical confinement, and flattened asters under planar confinement. The number of crosslinking motors controls the size and shape of condensates, with flattened asters becoming hollow and ring-like for larger motor number. End pausing plays a key role affecting condensate morphology: systems with end-pausing motors evolve into aster-like condensates while those with non-end-pausing crosslinking motor proteins evolve into disordered clusters and polarity-sorted bundles. 

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