Related papers: Magnetic Polymer Models for Epigenomic Organisatio…
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fibre is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors…
Magnetic polymers are examples of composite soft materials in which the competition between the large configurational entropy of the soft substrate (polymer) and the magnetic interaction may give rise to rich equilibrium phase diagrams as…
Chromatin is known to be organized into multiple domains of varying sizes and compaction. While these domains are often imagined as static structures, they are highly dynamic and show cell-to-cell variability. Since processes such as gene…
The three-dimensional organisation of chromosomes can be probed using methods such as Capture-C. However it is unclear how such population level data relates to the organisation within a single cell, and the mechanisms leading to the…
It is widely believed that the folding of the chromosome in the nucleus has a major effect on genetic expression. For example co-regulated genes in several species have been shown to colocalize in space despite being far away on the DNA…
Epigenetic cell memory, the inheritance of gene expression patterns across subsequent cell divisions, is a critical property of multi-cellular organisms. In recent work [10], a subset of the authors observed in a simulation study how the…
The fundamental biological processes of development of tissues and organs in multicellular organisms is governed by various signaling molecules, which are called morphogens. It is known that spatial and temporal variations in concentration…
The cell nucleus is increasingly recognized as a mechanosensitive organelle whose mesoscale mechanical heterogeneity (100 nm 10 um) is inseparable from genome regulation yet remains weakly integrated into systems biology and omics…
The mechanism through which cells determine their fate is intimately related to the spreading of certain biochemical (so-called epigenetic) marks along their genome. The mechanisms behind mark spreading and maintenance are not yet fully…
Heterogeneous distribution of passive and active domains in the chromosome plays a crucial role for its dynamic organization within the cell nucleus. Motivated by that here we investigate the steady-state conformation and dynamics of a…
During development, cell fates are determined through a combination of intracellular transcriptional regulations and extracellular signaling. As a result, spatial patterns of different cell types arise. We investigate the decision between…
Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. The Waddington landscape posits that gene circuits in a cell form a potential landscape of different cell types, wherein cells follow attractors of…
A mathematical model of genome degradation is proposed that takes into account a variable rate of mutation and increasing number of cells in a developing human organism. The model explains known properties of cancer development, in…
DNA supercoils are generated in genome regulation processes such as transcription and replication, and provide mechanical feedback to such processes. Under tension, DNA supercoil can present a coexistence state of plectonemic (P) and…
We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…
The architecture of the eukaryotic genome is characterized by a high degree of spatial organization. Chromosomes occupy preferred territories correlated to their state of activity and, yet, displace their genes to interact with remote sites…
Templated copolymerization, in which information stored in the sequence of a heteropolymer template is copied into another polymer product, is the mechanism behind all known methods of genetic information transfer. A key aspect of templated…
Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
How do mammalian cells that share the same genome exist in notably distinct phenotypes, exhibiting differences in morphology, gene expression patterns, and epigenetic chromatin statuses? Furthermore how do cells of different phenotypes…
Cellular differentiation is governed by gene regulatory networks, the high-dimensional stochastic biochemical systems that determine the transcriptional landscape and mediate cellular responses to signals and perturbations. Although…