1,725,862 research outputs found
Pore translocation of knotted DNA rings
Full text linkWe use an accurate coarse-grained model for DNA and stochastic molecular dynamics simulations to study the pore translocation of 10-kbp–long DNA rings that are knotted. By monitoring various topological and physical observables we find that there is not one, as previously assumed, but rather two qualitatively different modes of knot translocation. For both modes the pore obstruction caused by knot passage has a brief duration and typically occurs at a late translocation stage. Both effects are well in agreement with experiments and can be rationalized with a transparent model based on the concurrent tensioning and sliding of the translocating knotted chains. We also observed that the duration of the pore obstruction event is more controlled by the knot translocation velocity than the knot size. These features should advance the interpretation and design of future experiments aimed at probing the spontaneous knotting of biopolymers
How to fold intricately: using theory and experiments to unravel the properties of knotted proteins
Full text linkOver the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native state. Here, we review such developments by paying particular attention to the complementarity of experimental and computational studies. Key open issues that could be tackled with either or both approaches are finally pointed out
Dynamics of supercoiled DNA with complex knots: Large-scale rearrangements and persistent multi-strand interlocking
Full text linkKnots and supercoiling are both introduced in bacterial plasmids by catalytic processes involving DNA strand passages. While the effects on plasmid organization has been extensively studied for knotting and supercoiling taken separately, much less is known about their concurrent action. Here, we use molecular dynamics simulations and oxDNA, an accurate mesoscopic DNA model, to study the kinetic and metric changes introduced by complex (five-crossing) knots and supercoiling in 2 kbp-long DNA rings. We find several unexpected results. First, the conformational ensemble is dominated by two distinct states, differing in branchedness and knot size. Secondly, fluctuations between these states are as fast as the metric relaxation of unknotted rings. In spite of this, certain boundaries of knotted and plectonemically-wound regions can persist over much longer timescales. These pinned regions involve multiple strands that are interlocked by the cooperative action of topological and supercoiling constraints. Their long-lived character may be relevant for the simplifying action of topoisomerases
Knotting dynamics of DNA chains of different length confined in nanochannels
No full textLangevin dynamics simulations are used to characterize the typical mechanisms governing the spontaneous tying, untying and the dynamical evolution of knots in coarse-grained models of DNA chains confined in nanochannels. In particular we focus on how these mechanisms depend on the chain contour length, Lc, at a fixed channel width D = 56 nm corresponding to the onset of the Odijk scaling regime where chain backfoldings and hence knots are disfavoured but not suppressed altogether. We find that the lifetime of knots grows significantly with Lc, while that of unknots varies to a lesser extent. The underlying kinetic mechanisms are clarified by analysing the evolution of the knot position along the chain. At the considered confinement, in fact, knots are typically tied by local backfoldings of the chain termini where they are eventually untied after a stochastic motion along the chain. Consequently, the lifetime of unknots is mostly controlled by backfoldings events at the chain ends, which is largely independent of Lc. The lifetime of knots, instead, increases significantly with Lc because knots can, on average, travel farther along the chain before being untied. The observed interplay of knots and unknots lifetimes underpins the growth of the equilibrium knotting probability of longer and longer chains at fixed channel confinement
Electric-Field-Driven Trapping of Polyelectrolytes in Needle-like Backfolded States
No full textPolyelectrolytes with strong counterion couplings are compact at low electric fields but switch to elongated forms at high ones. As yet, little is known from both nanomanipulation experiments and theory about the transition mechanisms between compact and extended states. Here, we systematically address this out-of-equilibrium conversion using molecular dynamics simulations of coarse-grained polyelectrolyte chains of 1000 and 1500 monomers in a salt buffer of about 20 000 and 80 000 charged particles, respectively. We find that compact-to-elongated transitions are smooth and fast in only half of the trajectories. In the other half, the elongation is jammed halfway by the formation of backfolded, needle-like states. These states, which have not been envisioned before, have lifetimes that are orders of magnitude larger than the chain's relaxation time and ought to be detectable with current single-molecule experimental setups
Nonequilibrium Thermodynamics of DNA Nanopore Unzipping
Full text linkUsing theory and simulations, we carried out a first systematic characterization of DNA unzipping via nanopore translocation. Starting from partially unzipped states, we found three dynamical regimes depending on the applied force f: (i) heterogeneous DNA retraction and rezipping (f<17 pN), (ii) normal (17 pN<60 pN), and (iii) anomalous (f>60 pN) drift-diffusive behavior. We show that the normal drift-diffusion regime can be effectively modeled as a one-dimensional stochastic process in a tilted periodic potential. We use the theory of stochastic processes to recover the potential from nonequilibrium unzipping trajectories and show that it corresponds to the free-energy landscape for single-base-pair unzipping. Applying this general approach to other single-molecule systems with periodic potentials ought to yield detailed free-energy landscapes from out-of-equilibrium trajectories
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Entropy production of active Brownian particles going from liquid to hexatic and solid phases
No full textDue to its inherent intertwinement with irreversibility, entropy production is a prime observable to monitor in systems of active particles. In this numerical study, entropy production in the liquid, hexatic and solid phases of a two-dimensional system of active Brownian particles is examined at both average and fluctuation level. The trends of averages as functions of density show no singularity and marked changes in their derivatives at the hexatic-solid transition. Distributions show instead peculiar tail structures interpreted by looking at microscopic configurations. Particles in regions of low local order generate tail values according to different dynamical mechanisms: they move towards empty regions or bounce back and forth into close neighbours. The tail structures are reproduced by a simple single-particle model including an intermittent harmonic potential
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