Related papers: Directed Motion and Spatial Coherence in the Cell …
An active loop-extrusion mechanism is regarded as the main out--of--equilibrium mechanism responsible for the structuring of megabase-sized domains in chromosomes. We developed a model to study the dynamics of the chromosome fibre by…
We study the spontaneous ''sliding'' of histone spools (nucleosomes) along DNA as a result of thermally activated single base pair twist defects. To this end we map the system onto a suitably extended Frenkel-Kontorova model. Combining…
The origin of biological motion can be traced back to the function of molecular motor proteins. Cytoplasmic dynein and kinesin transport organelles within our cells moving along a polymeric filament, the microtubule. The motion of the…
Cell alignment often forms nematic order, which can lead to anomalous collective cell flow due to the so-called active force. Although it is appreciated that cell migration is driven by traction force, a quantitative evaluation of the…
The chromosome is a key player of cell physiology, and its dynamics provides valuable information about its physical organization. In both prokaryotes and eukaryotes, the short-time motion of chromosomal loci has been described as a Rouse…
Molecular center-of-mass motion is taken into account in the theory of coherent control of nuclear spin isomers of molecules. It is shown that infrared radiation resonant to the molecular rovibrational transition can substantially enrich…
Genome organization in eukaryotes during interphase stems from the delicate balance between non-random correlations present in the DNA polynucleotide linear sequence and the physico/chemical reactions which shape continuously the form and…
We employ the diffusing transcription factors model for numerical simulation of chromatin topology conformations and transcriptional processes of human chromatin. Simulations of a short chromatin filament reveal different possible pathways…
We propose a unified mechanism that reproduces the sequence of dynamical transitions observed during somitogenesis, the process of body segmentation during embryonic development, that is invariant across all vertebrate species. This is…
Embryonic development involves pattern formation characterized by the emergence of spatially localized domains characterized by distinct cell fates resulting from differential gene expression. The boundaries demarcating these domains are…
Using benzene sandwiched between two Au leads as a model system, we investigate from first principles the change in molecular conductance caused by different atomic structures around the metal-molecule contact. Our motivation is the…
The H-NS chromosome-organizing protein in E. coli can stabilize genomic DNA loops, and form oligomeric structures connected to repression of gene expression. Motivated by the link between chromosome organization, protein binding and gene…
During eukaryotic cell division, a microtubule-based structure called the spindle exerts forces on chromosomes, thereby organizing and segregating them Extensive work demonstrates that the forces acting parallel to the spindle axis,…
The biological function of proteins is encoded in their structure and expressed through the mediation of their dynamics. Local fluctuations are known to initiate biologically relevant pathways as they cooperatively enhance the dynamics in…
Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibriums measured in vitro with purified DNA and protein components. Recently, a new field of applications…
Ultrafast optical techniques allow to study ultrafast molecular dynamics involving both nuclear and electronic motion.To support interpretation, theoretical approaches are needed that can describe both the nuclear and electron…
Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of how genomes are folded is…
The actin cortex is a thin layer of actin, myosin, and actin binding proteins that underlies the membrane of most animal cells. It is highly dynamic and can undergo remodelling on time-scales of tens of seconds thanks to protein turnover…
We propose a model for the formation of chromatin loops based on the diffusive sliding of a DNA-bound factor which can dimerise to form a molecular slip-link. Our slip-links mimic the behaviour of cohesin-like molecules, which, along with…
Suspensions of swimming micro-organisms provide examples of coordinated active dynamics. That has stimulated the study of a phenomenological theory combining synchronization and polar order in active matter. Here, we consider another…