Zobrazeno 1 - 10
of 200
pro vyhledávání: '"Michieletto D"'
Autor:
Brackley, C. A., Michieletto, D., Mouvet, F., Johnson, J., Kelly, S., Cook, P. R., Marenduzzo, D.
Publikováno v:
Nucleus 7, 453 (2016)
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 bioinformatic data (e.g., chromatin state, histone modification, GC content). In
Externí odkaz:
http://arxiv.org/abs/2010.07135
Publikováno v:
Soft Matter 15, 5995 (2019)
We present a generic coarse-grained model to describe molecular motors acting on polymer substrates, mimicking, for example, RNA polymerase on DNA or kinesin on microtubules. The polymer is modeled as a connected chain of beads; motors are represente
Externí odkaz:
http://arxiv.org/abs/2010.06424
Autor:
Brackley, C. A., Johnson, J., Michieletto, D., Morozov, A. N., Nicodemi, M., Cook, P. R., Marenduzzo, D.
Publikováno v:
Nucleus 9, 95 (2018)
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 arrangement of the CTCF binding motifs that stabilize loops, and extrusion is t
Externí odkaz:
http://arxiv.org/abs/2010.02548
Publikováno v:
Phys. Rev. Lett. 124, 198101 (2020)
Vital biological processes such as genome repair require fast and efficient binding of selected proteins to specific target sites on DNA. Here we propose an active target search mechanism based on "chromophoresis", the dynamics of DNA-binding protein
Externí odkaz:
http://arxiv.org/abs/1908.06671
We study the effect of transcription on the kinetics of DNA supercoiling in 3D by means of Brownian dynamics simulations of a single nucleotide resolution coarse-grained model for double stranded DNA. By accounting for the action of a transcribing RN
Externí odkaz:
http://arxiv.org/abs/1906.03287
Publikováno v:
Phys. Rev. Lett. 119, 197801 (2017)
Understanding how topological constraints affect the dynamics of polymers in solution is at the basis of any polymer theory and it is particularly needed for melts of rings. These polymers fold as crumpled and space-filling objects and, yet, they dis
Externí odkaz:
http://arxiv.org/abs/1703.09688
Publikováno v:
Phys. Rev. Lett. 119, 118002 (2017)
There is a long-standing experimental observation that the melting of topologically constrained DNA, such as circular-closed plasmids, is less abrupt than that of linear molecules. This finding points to an intriguing role of topology in the physics
Externí odkaz:
http://arxiv.org/abs/1703.08367
Autor:
Brackley, C. A., Johnson, J., Michieletto, D., Morozov, A. N., Nicodemi, M., Cook, P. R., Marenduzzo, D.
Publikováno v:
Phys. Rev. Lett. 119, 138101 (2017)
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 the CTCF pr
Externí odkaz:
http://arxiv.org/abs/1612.07256
The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single nucleotide
Externí odkaz:
http://arxiv.org/abs/1608.03722
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To shed light
Externí odkaz:
http://arxiv.org/abs/1607.06640