Related papers: How molecular knots can pass through each other
Semiflexible polymer models are widely used as a paradigm to understand structural phases in biomolecules including folding of proteins. Since stable knots are not so common in real proteins, the existence of stable knots in semiflexible…
The transport of DNA polymers through nanoscale pores is central to many biological processes, from bacterial gene exchange to viral infection. In single-molecule nanopore sensing, the detection of nucleic acid and protein analytes relies…
An analysis of extensive simulations of interacting self-avoiding polygons on cubic lattice shows that the frequencies of different knots realized in a random, collapsed polymer ring decrease as a negative power of the ranking order, and…
A system of neutral atoms trapped in an optical lattice and dispersively coupled to the field of an optical cavity can realize a variation of the Bose-Hubbard model with infinite-range interactions. This model exhibits a first order quantum…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
The advent of solid state nanodevices allows for interrogating the physico-chemical properties of a polyelectrolyte chain by electrophoretically driving it through a nanopore. Salient dynamical aspects of the translocation process have been…
We consider how beads can diffuse along a chain that wraps them, without becoming displaced from the chain; our proposed mechanism is analogous to the reptation of "stored length" in more familiar situations of polymer dynamics. The problem…
We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic…
In all theoretical treatments of electron transport through single molecules between two metal electrodes, a clear distinction has to be made between a coherent transport regime with a strong coupling throughout the junction and a Coulomb…
We consider the motion of semiflexible polymers in double-well potentials. We calculate shape, energy, and effective diffusion constant of kink excitations, and in particular their dependence on the bending rigidity of the semiflexible…
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…
We consider the diffusive motion of a localized knot along a linear polymer chain. In particular, we derive the mean diffusion time of the knot before it escapes from the chain once it gets close to one of the chain ends. Self-reptation of…
Knotted molecules occur naturally and are designed by scientists to gain special biological and material properties. Understanding and utilizing knotting require efficient methods to recognize and generate knotted structures, which are…
Molecular nanostructures may constitute the fabric of future quantum technologies, if their degrees of freedom can be fully harnessed. Ideally one might use nuclear spins as low-decoherence qubits and optical excitations for fast…
The motion of polymers with inhomogeneous structure through nanopores is discussed theoretically. Specifically, we consider the translocation dynamics of polymers consisting of double-stranded and single-stranded blocks. Since only the…
Topological entanglements are abundant, and often detrimental, in polymeric systems in biology and materials science. Here we theoretically investigate the topological simplification of knots by diffusing slip-links (SLs), which may…
Recent experiments demonstrated that knots in single DNA strands can be formed by hydrodynamic compression in a nanochannel. In this letter, we further elucidate the underlying molecular mechanisms by carrying out a compression experiment…
This paper details a series of experiments in searching for minimal energy configurations for knots and links using the computer program KnotPlot. The most interesting phenomena found in these experiments is the dependence of the…
The transport of polymers with folded configurations across membrane pores is investigated theoretically by analyzing simple discrete stochastic models. The translocation dynamics is viewed as a sequence of two events: motion of the folded…
The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also abound in viral DNA packaged inside bacteriophages. RNA molecules, on the…