Showing 1–2 of 2 results for author: Vu, G T

A minimal G$\bar{\textrm{o}}$-model for rebuilding whole genome structures from haploid single-cell Hi-C data

Authors: S. Wettermann, M. Brems, J. T. Siebert, G. T. Vu, T. J. Stevens, P. Virnau

Abstract: We present a minimal computational model, which allows very fast, on-the-fly construction of three dimensional haploid interphase genomes from single cell Hi-C contact maps using the HOOMD-blue molecular dynamics package on graphics processing units. Chromosomes are represented by a string of connected beads, each of which corresponds to 100,000 base pairs, and contacts are mediated via a structur… ▽ More We present a minimal computational model, which allows very fast, on-the-fly construction of three dimensional haploid interphase genomes from single cell Hi-C contact maps using the HOOMD-blue molecular dynamics package on graphics processing units. Chromosomes are represented by a string of connected beads, each of which corresponds to 100,000 base pairs, and contacts are mediated via a structure-based harmonic potential. We suggest and test two minimization protocols which consistently fold into conformationally similar low energy states. The latter are similar to previously published structures but are calculated in a fraction of the time. We find evidence that mere fulfillment of contact maps is insufficient to create experimentally relevant structures. Particularly, an excluded volume term is required in our model to induce the formation of chromosome territories. We also observe empirically that contact maps do not capture the chirality of the underlying structures. Depending on starting configurations and protocol details, one of two mirror images emerges. Finally, we analyze the occurrence of knots in a particular chromosome. The same knot appears in (almost) all structures irrespective of minimization protocols or even details of underlying potentials providing further evidence for the existence of knots in interphase chromatin. △ Less

Submitted 26 July, 2019; v1 submitted 8 April, 2019; originally announced April 2019.

Comments: 18 pages, 7 figures. The updated submission contains additional explanations (for example) to the Go model and why we use this in the context of chromatin, we address the stopping criterion. References have been added as a result to an email received pointing us to publications we had not read before

Curvature as a guiding field for patterns in thin block copolymer films

Authors: Giang Thi Vu, Anabella A. Abate, Leopoldo R. Gómez, Aldo D. Pezzutti, Richard A. Register, Daniel A. Vega, Friederike Schmid

Abstract: Experimental data on thin films of cylinder-forming block copolymers (BC) -- free-standing BC membranes as well as supported BC films -- strongly suggest that the local orientation of the BC patterns is coupled to the geometry in which the patterns are embedded. We analyze this phenomenon using general symmetry considerations and numerical self-consistent field studies of curved BC films in cylind… ▽ More Experimental data on thin films of cylinder-forming block copolymers (BC) -- free-standing BC membranes as well as supported BC films -- strongly suggest that the local orientation of the BC patterns is coupled to the geometry in which the patterns are embedded. We analyze this phenomenon using general symmetry considerations and numerical self-consistent field studies of curved BC films in cylindrical geometry. The stability of the films against curvature-induced dewetting is also analyzed. In good agreement with experiments, we find that the BC cylinders tend to align along the direction of curvature at high curvatures. At low curvatures, we identify a transition from perpendicular to parallel alignment in supported films, which is absent in free standing membranes. Hence both experiments and theory show that curvature can be used to manipulate and align BC patterns. △ Less

Submitted 2 August, 2018; v1 submitted 27 February, 2018; originally announced February 2018.

Journal ref: Phys. Rev. Lett. 121, 087801 (2018)