Related papers: Three-Dimensional Loop Extrusion
A simple model of DNA based on two interacting polymers has been used to study the unzipping of a double stranded DNA subjected to a periodic force. We propose a dynamical transition, where without changing the physiological condition, it…
QCD evolution equations in minimal subtraction schemes have a hidden symmetry: One can construct three operators that commute with the evolution kernel and form an $SL(2)$ algebra, i.e. they satisfy (exactly) the $SL(2)$ commutation…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behavior of a short RNA or a single stranded DNA molecule that forms hairpin structure and calculate the properties…
We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal…
We introduce a model for stochastic transport on a one-dimensional substrate with particles assuming different conformations during their stepping cycles. These conformations correspond to different footprints on the substrate: in order to…
Magnetic tweezers are used to study the mechanical response under torsion of single nucleosome arrays reconstituted on tandem repeats of 5S positioning sequences. Regular arrays are extremely resilient and can reversibly accommodate a large…
The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments…
Complex DNA topological structures, including polymer loops, are frequently observed in biological processes when protein molecules simultaneously bind to several distant sites on DNA. However, the molecular mechanisms of formation of these…
The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of…
Many researchers have been encouraged to describe the dynamics of chromosomal loci in chromatin using the classical Rouse model of polymer dynamics by the agreement between the measured mean square displacement (MSD) versus time of…
The mechanism of threshold elongation (overstretching) of DNA macromolecules under the action of external force is studied within the framework of phenomenological approach. When considering the task it is taken into account that…
There is no settled universal 3D representation for geometry with many alternatives such as point clouds, meshes, implicit functions, and voxels to name a few. In this work, we present a new, compelling alternative for representing shapes…
We calculate the equation of state of DNA under tension for the case that the DNA features loops. Such loops occur transiently during DNA condensation in the presence of multivalent ions or sliding cationic protein linkers. The…
We investigate, via Monte Carlo simulations, the phase structure of a system of closed, nonintersecting but otherwise non-interacting, loops in 3 Euclidean dimensions. The loops correspond to closed trajectories of massive particles and we…
We study the impact of DNA coiling on the search rate of proteins moving along the DNA contour interspersed by three-dimensional (3D) bulk excursions. When the DNA is coiled proteins performing short 3D hops along a DNA segment can be…
In the present manuscript, we formulate a 3D mathematical model describing the capture of a contaminant in an adsorption column. The novelty of our approach involves the description of mass transfer by adsorption via a nonlinear evolution…
We consider a model of loop-erased random walks on the finite pre-Sierpinski gasket which permits rigorous analysis. We prove the existence of the scaling limit and show that the path of the limiting process is almost surely self-avoiding,…
We derive the single molecule equation of state (force-extension relation) for DNA molecules bearing sliding loops and deflection defects. Analytical results are obtained in the large force limit by employing an analogy with instantons in…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
We construct two exactly soluble lattice spin models that demonstrate the importance of three-loop braiding statistics for the classification of 3D gapped quantum phases. The two models are superficially similar: both are gapped and both…