Related papers: Three-Dimensional Loop Extrusion
The geometrization of electrodynamics is obtained by performing the complex extension of the covariant derivative operator to include the Cartan torsion vector and applying this derivative to the Ginzburg-Landau equation of superfluids and…
We note that a tridiagonal matrix representation of the algebra of the partially asymmetric exclusion process (PASEP) lends itself to interpretation as the transfer matrix for weighted Motzkin lattice paths. A continued fraction…
We study the three-dimensional persistent random walk with drift. Then we develop a thermodynamic model that is based on this random walk without assuming the Boltzmann-Gibbs form for the equilibrium distribution. The simplicity of the…
The correlations between the sequence of monomers in a polymer and its three-dimensional structure is a grand challenge in polymer science and biology. The properties and functions of macromolecules depend on their 3D shape that has…
DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional…
Subsystem symmetry has emerged as a powerful organizing principle for unconventional quantum phases of matter, most prominently fracton topological orders. Here, we focus on a special subclass of such symmetries, known as higher-form…
Cell layers eliminate unwanted cells through the extrusion process, which underlines healthy versus flawed tissue behaviors. Although several biochemical pathways have been identified, the underlying mechanical basis including the forces…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behaviour of a single stranded short DNA molecule that form hairpin structure. Using exact enumeration method we…
We have developed a generalized semi-analytic approach for efficiently computing cyclization and looping $J$ factors of DNA under arbitrary binding constraints. Many biological systems involving DNA-protein interactions impose precise…
We introduce a two-species exclusion model to describe the key features of the conflict between the RNA polymerase (RNAP) motor traffic, engaged in the transcription of a segment of DNA, concomitant with the progress of two DNA replication…
We present micro-rheological measurments of the drag force on colloids pulled through a solution of lambda-DNA (used here as a monodisperse model polymer) with an optical tweezer. The experiments show a violation of the Stokes-Einstein…
We review our current understanding on the outer envelope structures of massive stars based on three dimensional (3D) radiation hydrodynamic simulations. We briefly summarize the fundamental issues to construct hydrostatic one dimensional…
In a recent paper, Michael J. Saxton proposes to interpret as anomalous diffusion the occurrence of apparent transient sub-diffusive regimes in mean-squared displacements (MSD) plots, calculated from experimental trajectories of molecules…
In many important cellular processes, including mRNA translation, gene transcription, phosphotransfer, and intracellular transport, biological "particles" move along some kind of "tracks". The motion of these particles can be modeled as a…
High-resolution 3D medical image generation remains challenging because fully volumetric models are computationally expensive, while efficient 2D slice generators often fail to preserve anatomical consistency across the third dimension. We…
The determination of the folding mechanisms of proteins is critical to understand the topological change that can propagate Alzheimer and Creutzfeld-Jakobs diseases, among others. The computational community has paid considerable attention…
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with…
This paper focuses on the probability that a portion of DNA closes on itself through thermal fluctuations. We investigate the dependence of this probability upon the size r of a protein bridge and/or the presence of a kink at half DNA…
We analyze maximum entropy random graph ensembles with constrained degrees, drawn from arbitrary degree distributions, and a tuneable number of 3-loops (triangles). We find that such ensembles generally exhibit two transitions, a clustering…
The scaling properties of DNA knots of different complexities were studied by atomic force microscope. Following two different protocols DNA knots are adsorbed onto a mica surface in regimes of (i) strong binding, that induces a kinetic…