Related papers: Three-Dimensional Loop Extrusion
Structural-Maintenance-of-Chromosome (SMC) complexes such as condensins organise the folding of chromosomes. However, their role in modulating the entanglement of DNA and chromatin is not fully understood. To address this question, we…
We propose Squeeze3D, a novel framework that leverages implicit prior knowledge learnt by existing pre-trained 3D generative models to compress 3D data at extremely high compression ratios. Our approach bridges the latent spaces between a…
Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages,…
We study percolation problems of overlapping objects where the underlying geometry is such that in D-dimensions, a subset of the directions has a lattice structure, while the remaining directions have a continuum structure. The resulting…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on…
Recent advances in the understanding of the melting behavior of double-stranded DNA with statistical mechanics methods lead to improved estimates of the weight factors for the dissociation events of the chains, in particular for interior…
We study the infrared structure of the Standard Model (SM) restricted to the first generation of fermions, including the full SM gauge group, up to three-loop order, and determine the resulting cusp and collinear anomalous dimensions for…
Molecular conformation generation, a critical aspect of computational chemistry, involves producing the three-dimensional conformer geometry for a given molecule. Generating molecular conformation via diffusion requires learning to reverse…
Many fundamental biological processes are regulated by protein-DNA complexes called {\it synaptosomes}, which possess multiple interaction sites. Despite the critical importance of synaptosomes, the mechanisms of their formation remain not…
In a recent letter, a simple method was proposed to generate solvable models that predict the critical properties of statistical systems in hyperspherical geometries. To that end, it was shown how to reduce a random walk in $D$ dimensions…
We study the elastic behaviour of a supercoiled DNA molecule. The simplest model is that of a rod like chain, involving two elastic constants, the bending and the twist rigidities. We show that this model is singular and needs a small…
We study the effect of transcription on the kinetics of DNA supercoiling in 3D by means of Brownian dynamics simulations of a single nucleotide resolution coarse-grained model for double stranded DNA. By accounting for the action of a…
Reviewing work done in collaboration with Jennifer Hodgdon, we derive the most general crack growth law allowed by symmetry for mixed-mode three-dimensional fracture. We do so using the system developed in condensed matter physics to derive…
Protein-DNA complexes with loops play a fundamental role in a wide variety of cellular processes, ranging from the regulation of DNA transcription to telomere maintenance. As ubiquitous as they are, their precise in vivo properties and…
Various subsets of self-avoiding walks naturally appear when investigating existing methods designed to predict the 3D conformation of a protein of interest. Two such subsets, namely the folded and the unfoldable self-avoiding walks, are…
Context: We integrate the 2D MHD ideal equations of a straight slab to simulate observational results associated with fundamental sausage trapped modes. Aims: Starting from a non-equilibrium state with a dense chromospheric layer, we…
The mechanism and driving forces of chromosome segregation in the bacterial cell cycle of E. coli is one of the least understood events in its life cycle. Using principles of entropic repulsion between polymer loops confined in a cylinder,…
In this work, we describe a method for large-scale 3D cell-tracking through a segmentation selection approach. The proposed method is effective at tracking cells across large microscopy datasets on two fronts: (i) It can solve problems…
We study pairs of interacting self-avoiding walks on the 3d simple cubic lattice. They have a common origin and are allowed to overlap only at the same monomer position along the chain. The latter overlaps are indeed favored by an energetic…