Publications (7)
Non-equilibrium chromosome looping via molecular slip-links
C. A. Brackley, J. Johnson, D. Michieletto +4
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…
Modelling the 3D spatiotemporal organisation of chromatin replication
G. Forte, S. Buonomo, P. R. Cook +3
We propose a polymer model for the dynamics of chromatin replication in three dimensional space. Our simulations indicate that both immobile and tracking replisomes may self-assemb…
Depletion effects and loop formation in self-avoiding polymers
N. M. Toan, D. Marenduzzo, P. R. Cook +1
Langevin dynamics is employed to study the looping kinetics of self-avoiding polymers both in ideal and crowded solutions. A rich kinetics results from the competition of two crowd…
Binding of bivalent transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and domains
C. A. Brackley, J. Johnson, S. Kelly +2
Biophysicists are modeling conformations of interphase chromosomes, often basing the strengths of interactions between segments distant on the genetic map on contact frequencies de…
Simulating topological domains in human chromosomes with a fitting-free model
C. A. Brackley, D. Michieletto, F. Mouvet +4
We discuss a polymer model for the 3D organization of human chromosomes. A chromosome is represented by a string of beads, with each bead being "colored" according to 1D bioinforma…
Extrusion without a motor: a new take on the loop extrusion model of genome organization
C. A. Brackley, J. Johnson, D. Michieletto +4
Chromatin loop extrusion is a popular model for the formation of CTCF loops and topological domains. Recent HiC data have revealed a strong bias in favour of a particular arrangeme…