Related papers: Simulating topological domains in human chromosome…
We study band modulations and topological transitions in a one-dimensional periodic bead-on-string chain. Using an exact transfer-matrix formulation of the wave equation with periodically modulated mass density, combined with numerical…
Surviving in a diverse environment requires corresponding organism responses. At the cellular level, such adjustment relies on the transcription factors (TFs) which must rapidly find their target sequences amidst a vast amount of…
Topological phases protected by symmetry can occur in gapped and---surprisingly---in critical systems. We consider non-interacting fermions in one dimension with spinless time-reversal symmetry. It is known that the phases are classified by…
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…
One of the most important tasks in understanding the complex spatial organization of the genome consists in extracting information about this spatial organization, the function and structure of chromatin topological domains from existing…
Semiflexible polymers in poor solvents exhibit a rich variety of collapsed morphologies, including globules, toroids, and rodlike bundles, arising from the competition between attractive interactions and chain stiffness. Computer…
The chromatin folding and the spatial arrangement of chromosomes in the cell play a crucial role in DNA replication and genes expression. An improper chromatin folding could lead to malfunctions and, over time, diseases. For eukaryotes,…
We study 3D chaotic dynamics through an analysis of transport in a granular flow in a half-full spherical tumbler rotated sequentially about two orthogonal axes (a bi-axial "blinking" tumbler). The flow is essentially quasi-2D in any…
Cortical folding exhibits substantial inter-individual variability while preserving stable anatomical landmarks that enable fine-scale characterization of cortical organization. Among these, the three-hinge gyrus (3HG) serves as a key…
The spatial organization of the DNA in the cell nucleus plays an important role for gene regulation, DNA replication, and genomic integrity. Through the development of chromosome conformation capture experiments (such as 3C, 4C, Hi-C) it is…
The day we understand the time evolution of subcellular elements at a level of detail comparable to physical systems governed by Newton's laws of motion seems far away. Even so, quantitative approaches to cellular dynamics add to our…
Identifying molecular signatures from complex disease patients with underlying symptomatic similarities is a significant challenge in the analysis of high dimensional multi-omics data. Topological data analysis (TDA) provides a way of…
The extent of coupling between the folding of a protein and its binding to a substrate varies from protein to protein. Some proteins have highly structured native states in solution, while others are natively disordered and only fold fully…
As protein folding is a NP-complete problem, artificial intelligence tools like neural networks and genetic algorithms are used to attempt to predict the 3D shape of an amino acids sequence. Underlying these attempts, it is supposed that…
Foundation models (FMs) such as CLIP and SAM have recently shown great promise in image segmentation tasks, yet their adaptation to 3D medical imaging-particularly for pathology detection and segmentation-remains underexplored. A critical…
Timely up- or down-regulation of gene expression is crucial for cellular differentiation and function. While gene upregulation via transcriptional activators has been extensively investigated, gene silencing remains understudied, especially…
We evaluate, by means of molecular dynamics simulations employing a realistic DNA coarse-grained model, the phase behaviour and the structural and dynamic properties of tetravalent DNA nanostars, i.e. nanoconstructs completely made of DNA.…
We employ molecular dynamics simulations to explore how internal flexibility affects phase transitions in soft-matter systems composed of dimers interacting via a core-softened potential with two characteristic length scales. Monomers are…
Results of numerical 3D simulations of propagation of acoustic waves inside the Sun are presented. A linear 3D code which utilizes realistic OPAL equation of state was developed by authors. Modified convectively stable standard solar model…
We propose a driving protocol which allows to use quantum dot arrays as quantum simulators for 1D topological phases. We show that by driving the system out of equilibrium, one can imprint bond-order in the lattice (producing structures…