Fluids of semiflexible ring polymers: effective potentials and clustering
We present a computational investigation of the structural properties of a fluid of semiflexible
ring polymers. Stiffness is introduced by implementing intramolecular barriers. Because of …
ring polymers. Stiffness is introduced by implementing intramolecular barriers. Because of …
The Rabl configuration limits topological entanglement of chromosomes in budding yeast
The three dimensional organization of genomes remains mostly unknown due to their high
degree of condensation. Biophysical studies predict that condensation promotes the …
degree of condensation. Biophysical studies predict that condensation promotes the …
New biologically motivated knot table
R Brasher, RG Scharein… - Biochemical Society …, 2013 - portlandpress.com
The knot nomenclature in common use, summarized in Rolfsen's knot table [Rolfsen (1990)
Knots and Links, American Mathematical Society], was not originally designed to distinguish …
Knots and Links, American Mathematical Society], was not originally designed to distinguish …
The symplectic geometry of closed equilateral random walks in 3-space
J Cantarella, C Shonkwiler - 2016 - projecteuclid.org
A closed equilateral random walk in 3-space is a selection of unit length vectors giving the
steps of the walk conditioned on the assumption that the sum of the vectors is zero. The …
steps of the walk conditioned on the assumption that the sum of the vectors is zero. The …
Orientation of DNA minicircles balances density and topological complexity in kinetoplast DNA
Kinetoplast DNA (kDNA), a unique mitochondrial structure common to trypanosomatid
parasites, contains thousands of DNA minicircles that are densely packed and can be …
parasites, contains thousands of DNA minicircles that are densely packed and can be …
Probability theory of random polygons from the quaternionic viewpoint
J Cantarella, T Deguchi… - Communications on Pure …, 2014 - Wiley Online Library
We build a new probability measure on closed space and plane polygons. The key
construction is a map, given by Hausmann and Knutson, using the Hopf map on quaternions …
construction is a map, given by Hausmann and Knutson, using the Hopf map on quaternions …
On the mean and variance of the writhe of random polygons
We here address two problems concerning the writhe of random polygons. First, we study
the behavior of the mean writhe as a function length. Second, we study the variance of the …
the behavior of the mean writhe as a function length. Second, we study the variance of the …
A fast direct sampling algorithm for equilateral closed polygons
Sampling equilateral closed polygons is of interest in the statistical study of ring polymers.
Over the past 30 years, previous authors have proposed a variety of simple Markov chain …
Over the past 30 years, previous authors have proposed a variety of simple Markov chain …
Generating equilateral random polygons in confinement
Y Diao, C Ernst, A Montemayor… - Journal of Physics A …, 2011 - iopscience.iop.org
One challenging problem in biology is to understand the mechanism of DNA packing in a
confined volume such as a cell. It is known that confined circular DNA is often knotted and …
confined volume such as a cell. It is known that confined circular DNA is often knotted and …
Generating equilateral random polygons in confinement III
Y Diao, C Ernst, A Montemayor… - Journal of Physics A …, 2012 - iopscience.iop.org
In this paper we continue our earlier studies (Diao et al 2011 J. Phys. A: Math. Theor. 44
405202, Diao et al J. Phys. A: Math. Theor. 45 275203) on the generation methods of …
405202, Diao et al J. Phys. A: Math. Theor. 45 275203) on the generation methods of …