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Polymers are a primary building block in many biomaterials, often interacting with anisotropic backgrounds. While previous studies have considered polymer dynamics within nematic solvents, rarely are the the effects of anisotropic viscosity and polymer elongation differentiated. Here, we study polymers embedded in nematic liquid crystals with isotropic viscosity via numerical simulations, to explicitly investigate the effect of nematicity on macromolecular conformation and how conformation alone can produce anisotropic dynamics. We employ a hybrid technique that captures nematic orientation, thermal fluctuations and hydrodynamic interactions. The coupling of the polymer backbone to the nematic field elongates the polymer, producing anisotropic diffusion even in nematic solvents with isotropic viscosity. For intermediate coupling, the competition between background anisotropy and macrmolecular entropy leads to hairpins - sudden kinks along the backbone of the polymer. Experiments of DNA embedded in a solution of rod-like fd viruses qualitatively support the role of hairpins in establishing characteristic conformational features that govern polymer dynamics. Hairpin diffusion along the backbone exponentially slows as coupling increases. Better understanding two-way coupling between polymers and their surroundings could allow the creation of more biomimetic composite materials., Comment: 13 pages, 7 figures, 2 appendices

A growing self-avoiding walk (GSAW) is a walk on a graph that is directed, does not visit the same vertex twice, and has a trapped endpoint. We show that the generating function enumerating GSAWs on a half-infinite strip of finite height is rational, and we give a procedure to construct a combinatorial finite state machine that allows one to compute this generating function. We then modify this procedure to compute generating functions for GSAWs under two probabilistic models. We perform Monte Carlo simulations to estimate the expected length and displacement for GSAWs on the quarter plane, half plane, full plane, and half-infinite strips of bounded height for which we cannot compute the generating function. Finally, we prove that the generating functions for Greek key tours (GSAWs on a finite grid that visit every vertex) on a half-infinite strip of fixed height are also rational, allowing us to resolve several conjectures.

Motivated by the observation of positive Gaussian curvature in kinetoplast DNA networks, we consider the effect of linking chirality in square lattice molecular chainmail networks using Langevin dynamics simulations and constrained gradient optimization. Linking chirality here refers to ordering of over-under versus under-over linkages between a loop and its neighbors. We consider fully alternating linking, maximally non-alternating, and partially non-alternating linking chiralities. We find that in simulations of polymer chainmail networks, the linking chirality dictates the sign of the Gaussian curvature of the final state of the chainmail membranes. Alternating networks have positive Gaussian curvature, similar to what is observed in kinetoplast DNA networks. Maximally non-alternating networks form isotropic membranes with negative Gaussian curvature. Partially non-alternating networks form flat diamond-shaped sheets which undergo a thermal folding transition when sufficiently large, similar to the crumpling transition in tethered membranes. We further investigate this topology-curvature relationship on geometric grounds by considering the tightest possible configurations and the constraints that must be satisfied to achieve them., Comment: 18 pages, 12 figures

We develop a minimal system to study the stochastic formation of Borromean links within topologically entangled networks without requiring the use of knot invariants. Borromean linkages may form in entangled solutions of open polymer chains or in Olympic gel systems such as kinetoplast DNA, but it is challenging to investigate this due to the difficulty of computing three-body link invariants. Here, we investigate randomly oriented rectangles densely packed within a volume, and evaluate them for Hopf linking and Borromean link formation. We show that dense packings of rectangles can form Borromean triplets and larger clusters, and that in high enough density the combination of Hopf and Borromean linking can create a percolating hypergraph through the network. We present data for the percolation threshold of Borromean hypergraphs, and discuss implications for the existence of Borromean connectivity within kinetoplast DNA., Comment: 6 pages, 4 figures

Knots in open strands such as ropes, fibers, and polymers, cannot typically be described in the language of knot theory, which characterizes only closed curves in space. Simulations of open knotted polymer chains, often parameterized to DNA, typically perform a closure operation and calculate the Alexander polynomial to assign a knot topology. This is limited in scenarios where the topology is less well-defined, for example when the chain is in the process of untying or is strongly confined. Here, we use a discretized version of the Second Vassiliev Invariant for open chains to analyze Langevin Dynamics simulations of untying and strongly confined polymer chains. We demonstrate that the Vassiliev parameter can accurately and efficiently characterize the knotted state of polymers, providing additional information not captured by a single-closure Alexander calculation. We discuss its relative strengths and weaknesses compared to standard techniques, and argue that it is a useful and powerful tool for analyzing polymer knot simulations., Comment: 14 pages, 8 figures

We use graph theory simulations and single molecule experiments to investigate percolation properties of kinetoplasts, the topologically linked mitochondrial DNA from trypanosome parasites. The edges of some kinetoplast networks contain a fiber of redundantly catenated DNA loops, but previous investigations of kinetoplast topology did not take this into account. Our graph simulations track the size of connected components in lattices as nodes are removed, analogous to the removal of minicircles from kinetoplasts. We find that when the edge loop is taken into account, the largest component after the network de-percolates is a remnant of the edge loop, before it undergoes a second percolation transition and breaks apart. This implies that stochastically removing minicircles from kinetoplast DNA would isolate large polycatenanes, which is observed in experiments that use photonicking to stochastically destroy kinetoplasts from Crithidia fasciculata. Our results imply kinetoplasts may be used as a source of linear polycatenanes for future experiments.

The ropelength of a knot is the minimum length required to tie it. Computational upper bounds have previously been computed for every prime knot with up to 11 crossings. Here, we present ropelength measurements for the 2176 knots with 12 crossings, of which 1288 are alternating and 888 are non-alternating. We report on the distribution of ropelengths within and between crossing numbers, as well as the space writhe of the tight knot configurations. It was previously established that tight alternating knots have a ``quantized'' space writhe close to a multiple of 4/7. Our data supports this for 12-crossing alternating knots and we find that non-alternating knots also show evidence of writhe quantization, falling near integer or half-integer multiples of 4/3, depending on the parity of the crossing number. Finally, we examine correlations between geometric properties and topological invariants of tight knots, finding that the ropelength is positively correlated with hyperbolic volume and its correlates, and that the space writhe is positively correlated with the Rasmussen s invariant., Comment: 6 figures, 10 pages, data files at https://doi.org/10.7910/DVN/6AXP61 Second version fixes typos in equations and references

A growing self-avoiding walk (GSAW) is a stochastic process that starts from the origin on a lattice and grows by occupying an unoccupied adjacent lattice site at random. A sufficiently long GSAW will reach a state in which all adjacent sites are already occupied by the walk and become trapped, terminating the process. It is known empirically from simulations that on a square lattice, this occurs after a mean of 71 steps. In Part I of a two-part series of manuscripts, we consider simplified lattice geometries only two sites high ("ladders") and derive generating functions for the probability distribution of GSAW trapping. We prove that a self-trapping walk on a square ladder will become trapped after a mean of 17 steps, while on a triangular ladder trapping will occur after a mean of 941/48 (~19.6 steps). We discuss additional implications of our results for understanding trapping in the "infinite" GSAW., Comment: 35 pages, 9 figures

Inspired by experiments on topologically linked DNA networks, we consider the connectivity of Borromean networks, in which no two rings share a pairwise-link, but groups of three rings form inseparable triplets. Specifically, we focus on square lattices at which each node is embedded a loop which forms a Borromean link with pairs of its nearest neighbors. By mapping the Borromean link network onto a lattice representation, we investigate the percolation threshold of these networks, (the fraction of occupied nodes required for a giant component), as well as the dissolution properties: the spectrum of topological links that would be released if the network were dissolved to varying degrees. We find that the percolation threshold of the Borromean square lattice occurs when approximately 60.75\% of nodes are occupied, slightly higher than the 59.27\% typical of a square lattice. Compared to the dissolution of Hopf-linked networks, a dissolved Borromean network will yield more isolated loops, and fewer isolated triplets per single loop. Our simulation results may be used to predict experiments from Borromean structures produced by synthetic chemistry., Comment: 9 pages, 7 figures

In this note, we attempt to find counterexamples to the conjecture that the ideal form of a knot, that which minimizes its contour length while respecting a no-overlap constraint, also minimizes the volume of the knot, as determined by its convex hull. We measure the convex hull volume of knots during the length annealing process, identifying local minima in the hull volume that arise due to buckling and symmetry breaking. We use T(p,2) torus knots as an illustrative example of a family of knots whose locally minimal-length embeddings are not necessarily ordered by volume. We identify several knots whose central curve has a convex hull volume that is not minimized in the ideal configuration, and find that $8_{19}$ has a non-ideal global minimum in its convex hull volume even when the thickness of its tube is taken into account., Comment: 8 pages, 5 figures, 3 supplemental videos

Recent experiments have elucidated the physical properties of kinetoplasts, which are chain-mail-like structures found in the mitochondria of trypanosome parasites formed from catenated DNA rings. Inspired by these studies, we use Monte Carlo simulations to examine the behavior of two-dimensional networks ("membranes") of linked rings. For simplicity, we consider only identical rings that are circular and rigid and that form networks with a regular linking structure. We find that the scaling of the eigenvalues of the shape tensor with membrane size are consistent with the behavior of the flat phase observed in self-avoiding covalent membranes. Increasing ring thickness tends to swell the membrane. Remarkably, unlike covalent membranes, the linked-ring membranes tend to form concave structures with an intrinsic curvature of entropic origin associated with local excluded-volume interactions. The degree of concavity increases with increasing ring thickness and is also affected by the type of linking network. The relevance of the properties of linked-ring model membranes to those observed in kinetoplasts is discussed., Comment: 11 pages, 11 figures

The ropelength of a knot is the minimum contour length of a tube of unit radius that traces out the knot in three dimensional space without self-overlap, colloquially the minimum amount of rope needed to tie a given knot. Theoretical upper and lower bounds have been established for the asymptotic relationship between crossing number and ropelength and stronger bounds have been conjectured, but numerical bounds have only been calculated exhaustively for knots and links with up to 11 crossings, which are not sufficiently complex to test these conjectures. Existing ropelength measurements also have not established the complexity required to reach asymptotic scaling with crossing number. Here, we investigate the ropelength of knots and links beyond the range of tested crossing numbers, past both the 11-crossing limit as well as the 16-crossing limit of the standard knot catalog. We investigate torus knots up to 1023 crossings, establishing a stronger upper bound for T(p,2) knots and links and demonstrating power-law scaling in T(p,p+1) below the proven limit. We investigate satellite knots up to 42 crossings to determine the effect of a systematic crossing-increasing operation on ropelength, finding that a satellite knot typically has thrice the ropelength of its companion. We find that ropelength is well described by a model of repeated Hopf links in which each component adopts a minimal convex hull around the cross-section of the others, and derive formulae that heuristically predict the crossing-ropelength relationship of knots and links without free parameters., Comment: 14 pages, 8 figures

The statistics of self-avoiding random walks have been used to model polymer physics for decades. A self-avoiding walk that grows one step at a time on a lattice will eventually trap itself, which occurs after an average of 71 steps on a square lattice. Here, we consider the effect of nearest-neighbor attractive interactions on the growing self-avoiding walk, and examine the effect that self-attraction has both on the statistics of trapping as well as on chain statistics through the transition between expanded and collapsed walks at the theta point. We find the trapping length increases exponentially with the nearest-neighbor contact energy, but that there is a local minimum in trapping length for weakly self-attractive walks. While it has been controversial whether growing self-avoiding walks have the same asymptotic behavior as traditional self-avoiding walks, we find that the theta point is not at the same location for growing self-avoiding walks, and that the persistence length converges much more rapidly to a smaller value., Comment: 9 pages, 8 figures + 2 in appendix

We consider the relativistic generalization of the problem of the "least uncomfortable" linear trajectory from point A to point B. The traditional problem minimizes the time-integrated squared acceleration (termed the "discomfort"), and there is a universal solution for all distances and durations. This universality fails when the maximum speed of the trajectory becomes relativistic, and we consider the more general case of minimizing the squared proper acceleration over a proper time. The least uncomfortable relativistic trajectory has a rapidity that evolves like the motion of a particle in a hyperbolic sine potential, agreeing with the classical solution at low velocities. We consider the special case of a hypothetical trip to Alpha Centauri, and compare the minimal-discomfort trajectory to one with uniform Earth-like acceleration., Comment: 5 Pages, 3 figures. Comment on: Anderson, D., Mats Desaix, and R. Nyqvist. "The least uncomfortable journey from A to B." American Journal of Physics 84.9 (2016): 690-695

We use a nanofluidic system to investigate the emergence of thermally driven collective phenomena along a single polymer chain. In our approach, a single DNA molecule is confined in a nanofluidic slit etched with arrays of embedded nanocavities; the cavity lattice is designed so that a single chain occupies multiple cavities. Fluorescent video-microscopy data shows that waves of excess fluorescence propagate across the cavity-straddling molecule, corresponding to propagating fluctuations of contour overdensity in the cavities. The waves are quantified by examining the correlation in intensity fluctuations between neighbouring cavities. Correlations grow from an anti-correlated minimum to a correlated maximum before decaying, corresponding to a transfer of contour between neighbouring cavities at a fixed transfer time-scale. The observed dynamics can be modelled using Langevin dynamics simulations and a minimal lattice model of coupled diffusion. This study shows how confinement-based sculpting of the polymer equilibrium configuration, by renormalizing the physical system into a series of discrete cavity states, can lead to new types of dynamic collective phenomena., Comment: 10 pages, 5 figures, 2 supplementary movies Document updated to include URLs to movies

We explore the gravitational dynamics of falling through planetary interiors. Two trajectory classes are considered: a straight cord between two surface points, and the brachistochrone path that minimizes the falling time between two points. The times taken to fall along these paths, and the shapes of the brachistochrone paths, are examined for the Moon, Mars, Earth, Saturn, and the Sun, based on models of their interiors. A toy model of the internal structure, a power-law gravitational field, characterizes the dynamics with one parameter, the exponent of the power-law, with values from -2 for a point-mass to +1 for a uniform sphere. Smaller celestial bodies behave like a uniform sphere, while larger bodies begin to approximate point-masses, consistent with an effective exponent describing their interior gravity., Comment: 6 pages, 5 figures

How long does it take to fall down a tunnel through the center of the Earth to the other side? Assuming a uniformly dense Earth, it would take 42 minutes, but this assumption has not been validated. This paper examines the gravity tunnel without this restriction, using the internal structure of the Earth as ascertained by seismic data, and the dynamics are solved numerically. The time taken to fall along the diameter is found to be 38 rather than 42 minutes. The time taken to fall along a straight line between any two points is no longer independent of distance, but interpolates between 42 minutes for short trips and 38 minutes for long trips. The brachistochrone path (minimizing the fall time between any two points) is similar to the uniform density solution, but tends to reach a greater maximum depth and takes less time to traverse. Although the assumption of uniform density works well in many cases, the simpler assumption of a constant gravitational field serves as a better approximation to the true results., Comment: 8 pages, 7 figures

Cavitation and bubble dynamics are central concepts in engineering, the natural sciences, and the mathematics of fluid mechanics. Due to the nonlinear nature of their dynamics, the governing equations are not fully solvable. Here, the dynamics of a spherical bubble in an N-dimensional fluid are discussed in the hope that examining bubble behavior in N dimensions will add insight to their behavior in three dimensions. Several canonical results in bubble dynamics are re-derived, including the Rayleigh collapse time, the Rayleigh-Plesset equation, and the Minnaert frequency. Numerical simulations are used to examine the onset of nonlinear behavior. Overall, the dynamics of bubbles are faster at higher dimensions, with nonlinear behavior occurring at lower amplitudes. Several features are found to be unique to three dimensions, including the trend of nonlinear behaviour and apparent coincidences in timescales., Comment: 8 pages, 5 figures