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Register a new userInter-filament Attractions Narrow the Length Distribution of Actin Filaments
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We show that the exponential length distribution that is typical of actin filaments under physiological conditions dramatically narrows in the presence of (i) crosslinker proteins (ii) polyvalent counterions or (iii) depletion mediated attractions. A simple theoretical model shows that in equilibrium, short-range attractions enhance the tendency of filaments to align parallel to each other, eventually leading to an increase in the average filament length and a decrease in the relative width of the distribution of filament lengths.
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In eukaryotic genes the protein coding sequence is split into several fragments, the exons, separated by non-coding DNA stretches, the introns. Prokaryotes do not have introns in their genome. We report the calculations of stability domains of actin genes for various organisms in the animal, plant and fungi kingdoms. Actin genes have been chosen because they have been highly conserved during evolution. In these genes all introns were removed so as to mimic ancient genes at the time of the early eukaryotic development, i.e. before introns insertion. Common stability boundaries are found in evolutionary distant organisms, which implies that these boundaries date from the early origin of eukaryotes. In general boundaries correspond with introns positions of vertebrates and other animals actins, but not much for plants and fungi. The sharpest boundary is found in a locus where fungi, algae and animals have introns in positions separated by one nucleotide only, which identifies a hot-spot for insertion. These results suggest that some introns may have been incorporated into the genomes through a thermodynamic driven mechanism, in agreement with previous observations on human genes. They also suggest a different mechanism for introns insertion in plants and animals.
We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics simulations. Compliant, DNA-like filaments are found to undergo a continuous crossover from two distinct surface-ordered quadrupolar states, both characterized by tetrahedral patterns of topological defects, to either longitudinal or latitudinal bipolar structures with increasing polymer concentrations. These transitions, along with the intermediary arrangements that they involve, may be attributed to the combination of an orientational wetting phenomenon with subtle density- and contour-length-dependent variations in the elastic anisotropies of the corresponding liquid crystal phases. Conversely, the organization of rigid, microtubule-like polymers evidences a progressive breakdown of continuum elasticity theory as chain dimensions become comparable to the equilibrium radius of the encapsulating membrane. In this case, we observe a gradual shift from prolate, tactoid-like morphologies to oblate, erythrocyte-like structures with increasing contour lengths, which is shown to arise from the interplay between nematic ordering, polymer and membrane buckling. We further provide numerical evidence of a number of yet-unidentified, self-organized states in such confined systems of stiff achiral filaments, including spontaneous spiral smectic assemblies, faceted polyhedral and twisted bundle-like arrangements. Our results are quantified through the introduction of several order parameters and an unsupervised learning scheme for the localization of surface topological defects, and are in excellent agreement with field-theoretical predictions as well as classical elastic theories of thin rods and spherical shells.
Using analytical techniques and Langevin dynamics simulations, we investigate the dynamics of polymer translocation through a nanochannel embedded in two dimensions under an applied external field. We examine the translocation time for various ratio of the channel length $L$ to the polymer length $N$. For short channels $Lll N$, the translocation time $tau sim N^{1+ u}$ under weak driving force $F$, while $tausim F^{-1}L$ for long channels $Lgg N$, independent of the chain length $N$. Moreover, we observe a minimum of translocation time as a function of $L/N$ for different driving forces and channel widths. These results are interpreted by the waiting time of a single segment.
We theoretically study thermally activated elementary dynamical processes that precede full structural relaxation in ultra-dense particle liquids interacting via strong short range attractive forces. Our approach is based on a microscopic theory formulated at the particle trajectory level built on the dynamic free energy concept and an explicit treatment of how attractions control physical bonding. Mean time scales for bond breaking, the early stage of cage escape, and a fixed non-Fickian displacement are analyzed in the repulsive glass, bonded repulsive (attractive) glass, fluid, and dense gel regimes. The theory predicts a strong length-scale-dependent growth of these time scales with attractive force strength at fixed packing fraction, a much weaker slowing down with density at fixed attraction strength, and a strong decoupling of the shorter bond breaking time with the other two time scales that are controlled mainly by perturbed steric caging. All results are in good accord with simulations, and additional testable predictions are made. The classic statistical mechanical projection approximation of replacing all bare attractive and repulsive forces with a single effective force determined by pair structure incurs major errors for describing processes associated with thermally activated escape from transiently localized states.
In this Letter, we study the collective behaviour of a large number of self-propelled microswimmers immersed in a fluid. Using unprecedently large-scale lattice Boltzmann simulations, we reproduce the transition to bacterial turbulence. We show that, even well below the transition, swimmers move in a correlated fashion that cannot be described by a mean-field approach. We develop a novel kinetic theory that captures these correlations and is non-perturbative in the swimmer density. To provide an experimentally accessible measure of correlations, we calculate the diffusivity of passive tracers and reveal its non-trivial density dependence. The theory is in quantitative agreement with the lattice Boltzmann simulations and captures the asymmetry between pusher and puller swimmers below the transition to turbulence.
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