2 research outputs found
Implementation and performance analysis of bridging Monte Carlo moves for off-lattice single chain polymers in globular states
Bridging algorithms are global Monte Carlo moves which allow for an efficient
sampling of single polymer chains. In this manuscript we discuss the adaptation
of three bridging algorithms from lattice to continuum models, and give details
on the corrections to the acceptance rules which are required to fulfill
detailed balance. For the first time we are able to compare the efficiency of
the moves by analyzing the occurrence of knots in globular states. For a
flexible homopolymer chain of length N=1000, independent configurations can be
generated up to two orders of magnitude faster than with slithering snake
moves.Comment: 12 pages, 5 figures, preprint submitted to computer physics
communication
The fractal globule as a model of chromatin architecture in the cell
The fractal globule is a compact polymer state that emerges during polymer condensation as a result of topological constraints which prevent one region of the chain from passing across another one. This long-lived intermediate state was introduced in 1988 (Grosberg et al. 1988) and has not been observed in experiments or simulations until recently (Lieberman-Aiden et al. 2009). Recent characterization of human chromatin using a novel chromosome conformational capture technique brought the fractal globule into the spotlight as a structural model of human chromosome on the scale of up to 10Â Mb (Lieberman-Aiden et al. 2009). Here, we present the concept of the fractal globule, comparing it to other states of a polymer and focusing on its properties relevant for the biophysics of chromatin. We then discuss properties of the fractal globule that make it an attractive model for chromatin organization inside a cell. Next, we connect the fractal globule to recent studies that emphasize topological constraints as a primary factor driving formation of chromosomal territories. We discuss how theoretical predictions, made on the basis of the fractal globule model, can be tested experimentally. Finally, we discuss whether fractal globule architecture can be relevant for chromatin packing in other organisms such as yeast and bacteria