70 research outputs found
Probing the entanglement and locating knots in ring polymers: a comparative study of different arc closure schemes
The interplay between the topological and geometrical properties of a polymer
ring can be clarified by establishing the entanglement trapped in any portion
(arc) of the ring. The task requires to close the open arcs into a ring, and
the resulting topological state may depend on the specific closure scheme that
is followed. To understand the impact of this ambiguity in contexts of
practical interest, such as knot localization in a ring with non trivial
topology, we apply various closure schemes to model ring polymers. The rings
have the same length and topological state (a trefoil knot) but have different
degree of compactness. The comparison suggests that a novel method, termed the
minimally-interfering closure, can be profitably used to characterize the arc
entanglement in a robust and computationally-efficient way. This closure method
is finally applied to the knot localization problem which is tackled using two
different localization schemes based on top-down or bottom-up searches.Comment: 9 pages, 7 figures. Submitted to Progress of Theoretical Physic
Equilibrium and kinetic properties of knotted ring polymers: a computational approach
We provide hereafter a summary of the Thesis organization. Chapter 1 contains a short
introduction to the mathematical theory of knots. Starting from the mathematical
definition of knotting, we introduce the fundamental concepts and knot properties used
throughout this Thesis.
In chapter 2 we tackle the problem of measuring the degree of localization of a knot.
This is in general a very challenging task, involving the assignment of a topological state
to open arcs of the ring. To assign a topological state to an open arc, one must first close it
into a ring whose topological state can be assessed using the tools introduced in chapter 1.
Consequently, the resulting topological state may depend on the specific closure scheme
that is followed. To reduce this ambiguity we introduce a novel closure scheme, the
minimally-interfering closure. We prove the robustness of the minimally-interfering
closure by comparing its results against several standard closure schemes.
We further show that the identified knotted portion depends also on the search
algorithm adopted to find it. The knot search algorithms adopted in literature can be
divided in two general categories: bottom-up searches and top-down searches. We show
that bottom-up and knot-down searches give in general different results for the length of
a knot, the difference increasing with increasing length of the polymer rings. We suggest
that this systematic difference can explain the discrepancies between previous numerical
results on the scaling behaviour of the knot length with increasing length of polymer
rings in good solvent.
In chapter 3 we investigate the mutual entanglement between multiple prime knots
tied on the same ring. Knots like these, which can be decomposed into simpler ones, are
called composite knots and dominate the knot spectrum of sufficiently long polymers [131].
Since prime knots are expected to localize to point-like decorations for asymptotically
large chain lengths, it is expected that composite knots should factorize into separate
prime components [101, 82, 43, 11]. Therefore the asymptotic properties of composite
knots should merely depend on the number of prime components (factor knots) by which
they are formed [101, 82, 43, 11] and the properties of the single prime components should be largely independent from the presence of other knots on the ring. We show that this
factorization into separate prime components is only partial for composite knots which
are dominant in an equilibrium population of Freely Jointed Rings. As a consequence
the properties of those prime knots which are found as separate along the chain depend
on the number of knots tied on it. We further show that these results can be explained
using a transparent one-dimensional model in which prime knots are substituted with
paraknots.
Chapters 4, 5 and 6 are dedicated to investigate the interplay between topological
entanglement and geometrical entanglement produced either by surrounding rings in a
dense solution or spherical confinement.
In chapter 4 we investigate the equilibrium and kinetic properties of solutions of
model ring polymers, modulating the interplay of inter- and intra-chain entanglement by
varying both solution density (from infinite dilution up to 40% volume occupancy) and
ring topology (by considering unknotted and trefoil-knotted chains). The equilibrium
metric properties of rings with either topology are found to be only weakly affected
by the increase of solution density. Even at the highest density, the average ring size,
shape anisotropy and length of the knotted region differ at most by 40% from those
of isolated rings. Conversely, kinetics are strongly affected by the degree of inter-chain
entanglement: for both unknots and trefoils the characteristic times of ring size relaxation,
reorientation and diffusion change by one order of magnitude across the considered range
of concentrations. Yet, significant topology-dependent differences in kinetics are observed
only for very dilute solutions (much below the ring overlap threshold). For knotted rings,
the slowest kinetic process is found to correspond to the diffusion of the knotted region
along the ring backbone.
In chapter 5 we study the interplay of geometrical and topological entanglement in
semiflexible knotted polymer rings under spherical confinement. We first characterize
how the top-down knot length lk depends on the ring contour length, Lc and the radius of
the confining sphere, Rc. In the no- and strong-confinement cases we observe weak knot
localization and complete knot delocalization, respectively. We show that the complex
interplay of lk, Lc and Rc that seamlessly bridges these two limits can be encompassed
by a simple scaling argument based on deflection theory. We then move to study the
behaviour of the bottom-up knot length lsk under the same conditions and observe
that it follows a qualitatively different behaviour from lk, decreasing upon increasing
confinement. The behaviour of lsk is rationalized using the same argument based on deflection theory. The qualitative difference between the two knot lengths highlights a
multiscale character of the entanglement emerging upon increasing confinement.
Finally, in chapter 6 we adopt a complementary approach, using topological analysis
(the properties of the knot spectrum) to infer the physical properties of packaged
bacteriophage genome. With their m long dsDNA genome packaged inside capsids
whose diameter are in the 50 80 nm range, bacteriophages bring the highest level of
compactification and arguably the simplest example of genome organization in living
organisms [31, 40]. Cryo-em studies showed that DNA in bacteriophages epsilon-15 and
phi-29 is neatly ordered in concentric shells close to the capsid wall, while an increasing
level of disorder was measured when moving away from the capsid internal surface. On
the other hand the detected spectrum of knots formed by DNA that is circularised
inside the P4 viral capsid showed that DNA tends to be knotted with high probability,
with a knot spectrum characterized by complex knots and biased towards torus knots
and against achiral ones. Existing coarse-grain DNA models, while being capable of
reproducing the salient physical aspects of free, unconstrained DNA, are not able to
reproduce the experimentally observed features of packaged viral DNA. We show, using
stochastic simulation techniques, that both the shell ordering and the knot spectrum
can be reproduced quantitatively if one accounts for the preference of contacting DNA
strands to juxtapose at a small twist angle, as in cholesteric liquid crystals
Multiscale entanglement in ring polymers under spherical confinement
The interplay of geometrical and topological entanglement in semiflexible
knotted polymer rings confined inside a spherical cavity is investigated using
advanced numerical methods. By using stringent and robust algorithms for
locating knots, we characterize how the knot length lk depends on the ring
contour length, Lc and the radius of the confining sphere, Rc . In the no- and
strong- confinement cases we observe weak knot localization and complete knot
delocalization, respectively. We show that the complex interplay of lk, Lc and
Rc that seamlessly bridges these two limits can be encompassed by a simple
scaling argument based on deflection theory. The same argument is used to
rationalize the multiscale character of the entanglement that emerges with
increasing confinement.Comment: 9 pages 9 figure
Viral RNA as a branched polymer
Myriad viruses use positive-strand RNA molecules as their genomes. Far from
being only a repository of genetic material, viral RNA performs numerous other
functions mediated by its physical structure and chemical properties. In this
chapter, we focus on its structure and discuss how long RNA molecules can be
treated as branched polymers through planar graphs. We describe the major
results that can be obtained by this approach, in particular the observation
that viral RNA genomes have a characteristic compactness that sets them aside
from similar random RNAs. We also discuss how different parameters used in the
current RNA folding software influence the resulting structures and how they
can be related to experimentally observable quantities. Finally, we show how
the connection to branched polymers can be extended to take advantage of known
results from polymer physics and can be further moulded to include additional
interactions, such as excluded volume or electrostatics.Comment: 24 pages, 9 figure
Dynamic and Facilitated Binding of Topoisomerase Accelerates Topological Relaxation
: How type 2 Topoisomerase (TopoII) proteins relax and simplify the topology of DNA molecules is one of the most intriguing open questions in genome and DNA biophysics. Most of the existing models neglect the dynamics of TopoII which is expected of proteins searching their targets via facilitated diffusion. Here, we show that dynamic binding of TopoII speeds up the topological relaxation of knotted substrates by enhancing the search of the knotted arc. Intriguingly, this in turn implies that the timescale of topological relaxation is virtually independent of the substrate length. We then discover that considering binding biases due to facilitated diffusion on looped substrates steers the sampling of the topological space closer to the boundaries between different topoisomers yielding an optimally fast topological relaxation. We discuss our findings in the context of topological simplification in vitro and in vivo
Dynamic and Facilitated Binding of Topoisomerase Accelerates Topological Relaxation
How type 2 Topoisomerase (TopoII) proteins relax and simplify the topology of
DNA molecules is one of the most intriguing open questions in biophysics. Most
of the existing models neglect the dynamics of TopoII which is characteristics
for proteins searching their targets via facilitated diffusion. Here, we show
that dynamic binding of TopoII speeds up the topological relaxation of knotted
substrates by enhancing the search of the knotted arc. Intriguingly, this in
turn implies that the timescale of topological relaxation is virtually
independent of the substrate length. We then discover that considering binding
biases due to facilitated diffusion on looped substrates steers the sampling of
the topological space closer to the boundaries between different topoisomers
yielding an optimally fast topological relaxation. We discuss our findings in
the context of topological simplification in vitro and in vivo
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