Related papers: Epigenetic state encodes locus-specific chromatin …
The formation of condensates is now considered as a major organization principle of eukaryotic cells. Several studies have recently shown that the properties of these condensates are affected by enzymatic reactions. We propose here a simple…
Previous studies of the flexibilities of ancestral proteins suggests that proteins evolve their function by altering their native state ensemble. Here we propose a more direct method of visualizing this by measuring the changes in the…
Transposable elements (TEs) constitute a significant portion of eukaryotic genomes, yet their role in chromatin organization remains poorly understood. This study investigates the distribution patterns of TEs around chromatin ligation…
Phase separation into compositionally and physically distinct domains is ubiquitous in (non)living matter ranging from alloys and emulsions to biomolecular condensates in cells. The organization of these domains can be controlled, for…
Conducting Polymer Dendrites (CPD) can engrave sophisticated patterns of electrical interconnects in their morphology with low-voltage spikes and few resources: they may unlock in operando manufacturing functionalities for electronics using…
The state of chromatin in individual cells is directly related to the state of the whole organism and may be used for assessment of the state of the whole organism. Many hereditary diseases are connected with chromatin rearrangements.…
Nucleosome organization in eukaryotic genomes has a deep impact on gene function. Although progress has been recently made in the identification of various concurring factors influencing nucleosome positioning, it is still unclear whether…
A lattice of elastic rods organized in a parallelepiped geometry can be axially loaded up to an arbitrary amount without distortion and then be subject to incremental displacements. Using quasi-static homogenization theory, this lattice can…
A large offspring number diploid biparental multilocus population model of Moran type is our object of study. At each timestep, a pair of diploid individuals drawn uniformly at random contribute offspring to the population. The number of…
Organic semiconductors exhibit properties of individual molecules and extended crystals simultaneously. The strongly bound excitons they host are typically described in the molecular limit, but excitons can delocalize over many molecules,…
Understanding the organization of matter under the long-range electrostatic force is a fundamental problem in multiple fields. In this work, based on the electrically charged tethered membrane model, we reveal regular structures underlying…
Inspired by active shape morphing in developing tissues and biomaterials, we investigate two generic mechanochemical models where the deformations of a thin elastic sheet are driven by, and in turn affect, the concentration gradients of a…
We explore the interaction between two genetic incompatibilities (underdominant loci in diploid organisms) in a population occupying a one-dimensional space. We derive a system of partial differential equations describing the dynamics of…
We explore how inherent flexibility of a protein molecule influences the mechanism controlling the kinetics of allosteric transitions using a variational model inspired from work in protein folding. The striking differences in the predicted…
Epigenetic Tracking is a mathematical model of biological cells, originally conceived to study embryonic development. Computer simulations proved the capacity of the model to generate complex 3-dimensional cellular structures, and the…
Classical cellular automata represent a class of explicit discrete spacetime lattice models in which complex large-scale phenomena emerge from simple deterministic rules. With the goal to uncover different physically distinct classes of…
We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…
Cell mechanical functions like locomotion, contraction and division are controlled by the cytoskeleton, a dynamic biopolymer network whose mechanical properties remain poorly understood. We perform single-cell uniaxial stretching…
By means of a minimal physical model, we investigate the interplay of two phase transitions at play in chromatin organization: (1) liquid-liquid phase separation (LLPS) within the fluid solvating chromatin, resulting in the formation of…
Genetic interactions can strongly influence the fitness effects of individual mutations, yet the impact of these epistatic interactions on evolutionary dynamics remains poorly understood. Here we investigate the evolutionary role of…