Related papers: Three-Dimensional Loop Extrusion
We study a model for the denaturation transition of DNA in which the molecules are considered as composed of a sequence of alternating bound segments and denaturated loops. We take into account the excluded-volume interactions between…
Cell crawling requires the generation of intracellular forces by the cytoskeleton and their transmission to an extracellular substrate through specific adhesion molecules. Crawling cells show many features of excitable systems, such as…
In order to interpret recent experimental studies of the dependence of conductance of ds-DNA as the DNA is pulled from the 3'end1-3'end2 ends, which find a sharp conductance jump for a very short (4.5 %) stretching length, we carried out…
We combine matrix-product state (MPS) and Mean-Field (MF) methods to model the real-time evolution of a three-dimensional (3D) extended Hubbard system formed from one-dimensional (1D) chains arrayed in parallel with weak coupling in-between…
Using Monte Carlo simulations, we study the dynamic transitions in the unzipping of an adsorbed homogeneous polymer on a surface (or wall). We consider three different types of surfaces. One end of the polymer is always kept anchored, and…
The oxygen O2p_sigma and copper Cu4s and Cu3d_x^2-y^2 orbitals are involved in a simple LCAO model for determination of the conduction band and the oxygen-oxygen hopping is considered as a small parameter with respect to the transition…
In this talk, we discuss the phenomenology of radiative 3-loop seesaw models. The 3-loop suppression allows the new particles to have masses at the TeV scale, along with relatively large Yukawa couplings, while retaining consistency with…
DNA loop formation is one of several mechanisms used by organisms to regulate genes. The free energy of forming a loop is an important factor in determining whether the associated gene is switched on or off. In this paper we use an elastic…
We discuss the effects of convective overshooting in the PMS evolution of intermediate mass stars, by analysing in detail the early evolution towards the main sequence of a 2 M_sun stellar model. These effects can be extremely important in…
Computational elucidation of membrane protein (MP) structures is challenging partially due to lack of sufficient solved structures for homology modeling. Here we describe a high-throughput deep transfer learning method that first predicts…
The normal/superconducting phase boundary Tc has been calculated for mesoscopic loops, as a function of an applied perpendicular magnetic field H. While for thin-wire loops and filled disks the Tc(H) curves are well known, the intermediate…
Entropic repulsion between DNA ring polymers under confinement is the key mechanism governing the spatial segregation of bacterial chromosomes, although it remains incompletely understood how proteins aid the process of entropic…
We combine confocal imaging, microfluidics and image analysis to record 3D-images of cells in flow. This enables us to recover the full 3D representation of several hundred living cells per minute. Whereas 3D confocal imaging has thus far…
The model of facilitated diffusion describes how DNA-binding proteins, such as transcription factors (TFs), find their chromosomal targets by combining 3D diffusion through the cytoplasm and 1D sliding along nonspecific DNA sequences. The…
Superdiffusion is an anomalous transport behavior. Recently, a new mechanism, termed the ``nodal mechanism," has been proposed to induce superdiffusion in quantum models. However, existing realizations of the nodal mechanism have so far…
DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve…
We use Brownian dynamics simulations and analytical theory to compare two prominent types of single molecule transitions. One is the adsorption transition of a loop (a chain with two ends bound to an attractive substrate) driven by an…
We present a computer simulation study of the compact self-avoiding loops as regards their length and topological state. We use a Hamiltonian closed path on the cubic-shaped segment of a 3D cubic lattice as a model of a compact polymer. The…
Macroscopic properties of heterogeneous media are frequently modelled by regular lattice models, which are based on a relatively small basic cluster of lattice sites. Here, we extend one of such models to any cluster's size kxk. We also…
Three-Dimensional Gaussian Splatting (3DGS) has shown substantial promise in the field of computer vision, but remains unexplored in the field of magnetic resonance imaging (MRI). This study explores its potential for the reconstruction of…