Related papers: Simulating topological domains in human chromosome…
Understanding chromatin organization and dynamics is important since they crucially affect DNA functions. In this study, we investigate chromatin dynamics by statistically analyzing single-nucleosome movement in living human cells. Bi-modal…
We demonstrate that ultracold polyatomic symmetric top molecules, such as methyl fluoride, loaded into an optical lattice and subject to DC electric and microwave field dressing, can display topological order via a self-consistent analog of…
Semiflexible polymers in concentrated lyotropic solution are studied within a bead-spring model by molecular dynamics simulations, focusing on the emergence of a smectic A phase and its properties. We systematically vary the density of the…
The architecture of the eukaryotic genome is characterized by a high degree of spatial organization. Chromosomes occupy preferred territories correlated to their state of activity and, yet, displace their genes to interact with remote sites…
Based on a newly proposed spatial data model - spatial chromatic model (SCM), we developed a spatial coding scheme, called full-coded ordinary arranged chromatic diagram (full-OACD). Full-OACD is a type of spatial tessellation, where space…
Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…
A topological phase is a phase of matter which cannot be characterized by a local order parameter. It has been shown that gapped phases in 1D systems can be completely characterized using tools related to projective representations of the…
While the topological order in two dimensions has been studied extensively since the discover of the integer and fractional quantum Hall systems, topological states in 3 spatial dimensions are much less understood. In this paper, we propose…
We consider three different continuum polymer models, that all depend on a tunable parameter r that determines the strength of the excluded-volume interactions. In the first model chains are obtained by concatenating hard spherocylinders of…
Eukaryotic DNA is packaged into chromatin: one-dimensional arrays of nucleosomes separated by stretches of linker DNA are folded into 30-nm chromatin fibers which in turn form higher-order structures. Each nucleosome, the fundamental unit…
Polymer models are used to describe chromatin, which can be folded at different spatial scales by binding molecules. By folding, chromatin generates loops of various sizes. We present here a randomly cross-linked (RCL) polymer model, where…
Atomically thin 2-dimensional heterostructures are a promising, novel class of materials with groundbreaking properties. The possiblity of choosing the many constituent components and their proportions allows optimizing these materials to…
Faithful segregation of genetic material during cell division requires alignment of chromosomes between two spindle poles and attachment of their kinetochores to each of the poles. Failure of these complex dynamical processes leads to…
We study the self-organization of flexible planar trimer particles on a structureless surface. The molecules are made up of two mesogenic units linked by a spacer, all of which are modeled as hard needles of the same length. Each molecule…
The conformation space of a 20-residue antiparallel $\beta$-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, and the transitions between them are links. The…
There is now a certain consensus that Transcription Factors (TFs) reach their target sites, where they regulate gene transcription, via a mechanism dubbed facilitated diffusion (FD). In FD, the TF cycles between events of 3D-diffusion in…
Semiflexible polymers are widely used as a paradigm for understanding structural phases in biomolecules including folding of proteins. Here, we compare bead-spring and bead-stick variants of coarse-grained semiflexible polymer models that…
This paper discusses phase space structures encountered in the neighborhood of periodic orbits with high order multiplicity in a 3D autonomous Hamiltonian system with a potential of galactic type. We consider 4D spaces of section and we use…
Ultra-cold atoms in 1D bi-chromatic lattices constitute a surprisingly simple system for the study of topological insulators. We show that topological phase transitions constitute a general feature of bosons in 1D bi-chromatic lattices, and…
Modern biological techniques such as Hi-C permit to measure probabilities that different chromosomal regions are close in space. These probabilities can be visualised as matrices called contact maps. In this paper, we introduce a…