97 research outputs found
The two-angle model and the phase diagram for Chromatin
We have studied the phase diagram for chromatin within the framework of the
two-angle model. Rather than improving existing models with finer details our
main focus of the work is getting mathematically rigorous results on the
structure, especially on the excluded volume effects and the effects on the
energy due to the long-range forces and their screening. Thus we present a
phase diagram for the allowed conformations and the Coulomb energies
Fluctuating semiflexible polymer ribbon constrained to a ring
Twist stiffness and an asymmetric bending stiffness of a polymer or a polymer
bundle is captured by the elastic ribbon model. We investigate the effects a
ring geometry induces to a thermally fluctuating ribbon, finding bend-bend
coupling in addition to twist-bend coupling. Furthermore, due to the geometric
constraint the polymer's effective bending stiffness increases. A new parameter
for experimental investigations of polymer bundles is proposed: the mean square
diameter of a ribbonlike ring, which is determined analytically in the
semiflexible limit. Monte Carlo simulations are performed which affirm the
model's prediction up to high flexibility.Comment: 6 pages, 3 figures, Version as published in Eur. Phys. J.
On the Limits of Analogy Between Self-Avoidance and Topology-Driven Swelling of Polymer Loops
The work addresses the analogy between trivial knotting and excluded volume
in looped polymer chains of moderate length, , where the effects of
knotting are small. A simple expression for the swelling seen in trivially
knotted loops is described and shown to agree with simulation data. Contrast
between this expression and the well known expression for excluded volume
polymers leads to a graphical mapping of excluded volume to trivial knots,
which may be useful for understanding where the analogy between the two
physical forms is valid. The work also includes description of a new method for
the computational generation of polymer loops via conditional probability.
Although computationally intensive, this method generates loops without
statistical bias, and thus is preferable to other loop generation routines in
the region .Comment: 10 pages, 5 figures, supplementary tex file and datafil
On the Dominance of Trivial Knots among SAPs on a Cubic Lattice
The knotting probability is defined by the probability with which an -step
self-avoiding polygon (SAP) with a fixed type of knot appears in the
configuration space. We evaluate these probabilities for some knot types on a
simple cubic lattice. For the trivial knot, we find that the knotting
probability decays much slower for the SAP on the cubic lattice than for
continuum models of the SAP as a function of . In particular the
characteristic length of the trivial knot that corresponds to a `half-life' of
the knotting probability is estimated to be on the cubic
lattice.Comment: LaTeX2e, 21 pages, 8 figur
Critical exponents for random knots
The size of a zero thickness (no excluded volume) polymer ring is shown to
scale with chain length in the same way as the size of the excluded volume
(self-avoiding) linear polymer, as , where . The
consequences of that fact are examined, including sizes of trivial and
non-trivial knots.Comment: 4 pages, 0 figure
Topological entropy of a stiff ring polymer and its connection to DNA knots
We discuss the entropy of a circular polymer under a topological constraint.
We call it the {\it topological entropy} of the polymer, in short. A ring
polymer does not change its topology (knot type) under any thermal
fluctuations. Through numerical simulations using some knot invariants, we show
that the topological entropy of a stiff ring polymer with a fixed knot is
described by a scaling formula as a function of the thickness and length of the
circular chain. The result is consistent with the viewpoint that for stiff
polymers such as DNAs, the length and diameter of the chains should play a
central role in their statistical and dynamical properties. Furthermore, we
show that the new formula extends a known theoretical formula for DNA knots.Comment: 14pages,11figure
Gyration radius of a circular polymer under a topological constraint with excluded volume
It is nontrivial whether the average size of a ring polymer should become
smaller or larger under a topological constraint.
Making use of some knot invariants, we evaluate numerically the mean square
radius of gyration for ring polymers having a fixed knot type, where the ring
polymers are given by self-avoiding polygons consisting of freely-jointed hard
cylinders. We obtain plots of the gyration radius versus the number of
polygonal nodes for the trivial, trefoil and figure-eight knots. We discuss
possible asymptotic behaviors of the gyration radius under the topological
constraint. In the asymptotic limit, the size of a ring polymer with a given
knot is larger than that of no topological constraint when the polymer is thin,
and the effective expansion becomes weak when the polymer is thick enough.Comment: 12pages,3figure
Dependence of the endpoint energy of X-ray radiation on the preliminary temperature change during the pyroelectric source operation in the pulsed mode
This paper presents the results of the study of the dependence of the endpoint energy of X-ray radiation on the preliminary change in the temperature of the lithium tantalate (LiTaO3) single crystal, which is a source of a strong electric field of the pyroelectric effect under vacuum condition
A discrete geometric approach for simulating the dynamics of thin viscous threads
We present a numerical model for the dynamics of thin viscous threads based
on a discrete, Lagrangian formulation of the smooth equations. The model makes
use of a condensed set of coordinates, called the centerline/spin
representation: the kinematical constraints linking the centerline's tangent to
the orientation of the material frame is used to eliminate two out of three
degrees of freedom associated with rotations. Based on a description of twist
inspired from discrete differential geometry and from variational principles,
we build a full-fledged discrete viscous thread model, which includes in
particular a discrete representation of the internal viscous stress.
Consistency of the discrete model with the classical, smooth equations is
established formally in the limit of a vanishing discretization length. The
discrete models lends itself naturally to numerical implementation. Our
numerical method is validated against reference solutions for steady coiling.
The method makes it possible to simulate the unsteady behavior of thin viscous
jets in a robust and efficient way, including the combined effects of inertia,
stretching, bending, twisting, large rotations and surface tension
Abundance of unknots in various models of polymer loops
A veritable zoo of different knots is seen in the ensemble of looped polymer
chains, whether created computationally or observed in vitro. At short loop
lengths, the spectrum of knots is dominated by the trivial knot (unknot). The
fractional abundance of this topological state in the ensemble of all
conformations of the loop of segments follows a decaying exponential form,
, where marks the crossover from a mostly unknotted
(ie topologically simple) to a mostly knotted (ie topologically complex)
ensemble. In the present work we use computational simulation to look closer
into the variation of for a variety of polymer models. Among models
examined, is smallest (about 240) for the model with all segments of the
same length, it is somewhat larger (305) for Gaussian distributed segments, and
can be very large (up to many thousands) when the segment length distribution
has a fat power law tail.Comment: 13 pages, 6 color figure
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