Statistics and dynamics of plectonemes in braided structures

Braids composed by two intertwined filaments naturally arise in biological systems, such as during DNA replication [1] and in amyloid fibrils [2]. Interestingly, braids subject to a pulling force display a phase transition [3]: when the linking number between the two strands exceeds a critical number, the braid, initially straight, writhes in 3D forming structures known as plectonemes. Nowadays, single molecule experiments can easily investigate the physics behind such a transition and plectonemes diffusion along the braided structure [4].

In the last few years, we developed a polymer model which, combined with a stochastic field theory, allows to visualise plectonemes as structures interacting through phenomena typical of liquid-gas systems [5]. Moreover, a further application of the polymer model has allowed investigation into site-selection mechanisms of retroviruses into DNA braids revealing spatio-temporal correlations between consecutive integration events [6].

In this talk I will summarise our main results providing insights about polymer braids, their applications and possible future research areas.

[1] A. Mariezcurrena and F. Uhlmann. Genes & Development 31, 2151 (2017).

[2] C. Ionescu-Zanetti, R. Khurana, J. R. Gillespie, J. S. Petrick, L. C. Trabachino, L. J. Minert, S. A. Carter, and A. L. Fink. Proceedings of the National Academy of Sciences 96, 13175 (1999).

[3] G. Charvin, A. Vologodskii, D. Bensimon, and V. Croquette. Biophysical Journal 88, 4124 (2005).

[4] M. T. J. van Loenhout, M. V. de Grunt, and C. Dekker. Science 338, 94 (2012).

[5] G. Forte, M. Caraglio, D. Marenduzzo, and E. Orlandini. Physical Review E 99, 052503 (2019).

[6] G. Forte, D. Michieletto, D. Marenduzzo, and E. Orlandini. Journal of the Royal Society Interface 18, 20210229 (2021).

Nov 28, 2022 Leave a Comment

Buckling instabilities in chaining bacterial colonies

Bacteria in the natural environment frequently grow as structured communities known as bacterial biofilms. The morphology of the colony is an emergent property, driven in part by the growth and activity of the constituents. Here, we are interested in the effect of pole-pole adhesion between constituents on the resulting colony dynamics and properties, in an effort to understand more about colonies of chaining bacteria such as \textit{Bacillus subtilis}. In this work, we investigate a 2D discrete element simulation of a growing bacterial colony composed of non-motile rod-shaped bacteria where daughter cells are able to `chain’ together with springs. We find that despite the simplicity of the model, the emergent dynamics and morphology of the colony are drastically altered. At small chain lengths, the classic mosaic of micro-domains is recovered where the colony is isotropic on large length-scales but locally is heterogeneous and composed of domains of aligned cells. As we increase the chain length, there is a crossover to a regime where the colony is able to collectively buckle, characterised by an oscillatory-type morphology and a peak in observable properties e.g. colony aspect ratio, density, micro-domain area etc.. Continuing to increase the chain length gives rise to the possibility of individual chains buckling due to active stresses within the chain overcoming the restoring elastic force of the links, leading to a winding, ribbon-like appearance of the colony and a collapse in the observable properties.

Nov 21, 2022 Leave a Comment

Supercritical Fluids – Not Quite So Indistinguishable

While the gaseous and solid states of matter are relatively well understood, and clearly distinguished by their lack of or presence of long-range order, a complete characterisation of the liquid state is still being debated. Generally, liquids have been thought of by analogy to gases, as an extreme case of non-ideal gases. The problem with this approach is that one can compress a fluid to reach densities comparable to those of the solid, which cannot be tackled by analogy to gases. Midway through the last century, Yakov Frenkel proposed a ‘Kinetic Theory of Liquids’, where he aimed to describe liquids by analogy to solids, leading to a more realistic but also significantly conceptually denser theory than traditional gas analogies. Due to the latter fact his theory was largely ignored by researchers without a particular interest in very high densities, i.e. the canonical liquids community. However, in 2012, a crossover was proposed to occur in supercritical and near-supercritical fluids (Brazhkin, PRL) between a non-rigid ‘gas’-like state and a rigid ‘liquid’-like state. This crossover, called a ‘Frenkel line’, was originally characterised by the onset of oscillations in the velocity autocorrelation function of fluids as density is increased. In this talk I will present our efforts concerning this topic, first finding a structural marker associated with the Frenkel line crossover, identifying correlated changes in the evolution of the nearest neighbour coordination number and diffusion constant and the use of a machine-learned interatomic forcefield positing this crossover to originate at the triple point and formulate an analytic criterion for it. I will talk about how a fluid state crossover can be coherently identified in both traditional fluids (Krypton, Nitrogen) as well as colloidal/micellar systems, and discuss whether this is related to the Frenkel line, the recently found ‘c’-transition (Brazhkin, PRE 2021) or if we can even call a continuous crossover a ‘line’.

Nov 14, 2022 Leave a Comment

Novel binary hydrides synthesized under high pressure

Metal hydrides are important materials for hydrogen and energy storage. High pressure is an effective tool for the synthesis of new hydrides, because it dramatically increases the Gibbs free energy of molecular H2, thus increasing its reactivity. With the discovery of superconductivity in H3S with a critical temperature of 203K at 150GPa considerable efforts of the high-pressure community were concentrated on the search of novel hydrogen-rich materials under high pressure. In this talk I will give a short overview of the ongoing progress, with a focus on the Zr-H, Ta-H, Gd-H, Rb-H and Cs-H systems.

Nov 7, 2022 Leave a Comment