Zobrazeno 1 - 10
of 99
pro vyhledávání: '"Brackley, C. A."'
Understanding the interactions between viruses and surfaces or interfaces is important, as they provide the principles underpinning the cleaning and disinfection of contaminated surfaces. Yet, the physics of such interactions is currently poorly unde
Externí odkaz:
http://arxiv.org/abs/2010.12530
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
Autor:
Brackley, C. A.
There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to be able t
Externí odkaz:
http://arxiv.org/abs/1912.03188
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
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the compressional el
Externí odkaz:
http://arxiv.org/abs/1703.06067
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