arXiv subjects

Simon Weir

Publications and source records attributed to Simon Weir.

5 recordsLinked to original sources

arXiv2023

Topological Linking Determines Elasticity in Limited Valence Networks

Understanding the relationship between the microscopic structure and topology of a material and its macroscopic properties is a fundamental challenge across a wide range of systems. Here, we investigate the viscoelasticity of DNA nanostar hydrogels - a model system for physical networks with limited valence - by coupling rheology measurements, confocal imaging and molecular dynamics simulations. We discover that these networks display a large degree of interpenetration and that loops within the network are topologically linked, forming a percolating network-within-network structure. Below overlapping concentration, the fraction of branching points and the pore size determine the high-frequency elasticity of these physical gels. At higher concentrations, we discover that this elastic response is dictated by the abundance of topological links between looped motifs in the gel. Our findings highlight the emergence of "topological elasticity" as a previously overlooked mechanism in generic network-forming liquids and gels and inform the design of topologically-controllable material behaviours.

cond-mat.soft↗

arXiv2023

Effects of Monovalent and Divalent Cations on the Rheology of Entangled DNA

In this paper we investigate the effects of varying cation valency and concentration on the rheology of entangled lambda DNA solutions. We show that monovalent cations moderately increase the viscoelasticty of the solutions mainly by stabilising linear condensation of lambda DNA ``monomers'' via hybridisation of their sticky ends. On the contrary, divalent cations have a far more complex and dramatic effect on the rheology of the solution and we observe evidence of inter-molecular DNA-DNA bridging by Mg2+. We argue that these results may be interesting in the context of dense solutions of single and double stranded DNA, e.g. in vivo or in biotechnology applications such as DNA origami and DNA hydrogels.

cond-mat.soft↗

arXiv2022

Runaway Transition in Irreversible Polymer Condensation with Cyclisation

The process of polymer condensation, i.e. the formation of bonds between reactive end-groups, is ubiquitous in both industry and biology. Here we study generic systems undergoing polymer condensation in competition with cyclisation. Using a generalised Smoluchowski theory, molecular dynamics simulations and experiments using DNA and T4 ligase, we find that this system displays a transition, from a regime with finite-length chains at infinite time and dominated by rings to one dominated by linear polymers that grow in time. Finally, we show that fluids prepared close to the transition may have profoundly different compositions and rheology at large condensation times.

cond-mat.soft↗

arXiv2022

Fluidification of entanglements by a DNA bending protein

In spite of the nanoscale and single-molecule insights into how nucleoid associated proteins (NAPs) interact with DNA, their role in modulating the mesoscale viscoelasticity of the entangled genome in vivo has been overlooked so far. By combining microrheology and molecular dynamics simulation we find that the important NAP called Integration Host Factor (IHF) lowers the viscosity of entangled $\lambda$DNA 20-fold at physiological concentrations and stoichiometries. We argue that IHF may act as a "genomic fluidiser", reducing the effective viscosity of the nucleoid $\sim$200-fold. Our results suggest a previously unappreciated key role of IHF in regulating DNA dynamics and re-organisation in vivo

cond-mat.soft↗

arXiv2021

Topological digestion drives time-varying rheology of entangled DNA fluids

Understanding and controlling the rheology of polymeric complex fluids that are pushed out-of-equilibrium is a fundamental problem in both industry and biology. For example, to package, repair, and replicate DNA, cells use enzymes to constantly manipulate DNA topology, length, and structure. Inspired by this, here we engineer and study DNA-based complex fluids that undergo enzymatically-driven topological and architectural alterations via restriction endonuclease (RE) reactions. We show that these systems display time-dependent rheological properties that depend on the concentrations and properties of the comprising DNA and REs. Through time-resolved microrheology experiments and Brownian Dynamics simulations, we show that conversion of supercoiled to linear DNA topology leads to a monotonic increase in viscosity. On the other hand, the viscosity of entangled linear DNA undergoing fragmentation displays a universal decrease that we rationalize using living polymer theory. Finally, to showcase the tunability of these behaviours, we design a DNA fluid that exhibits a time-dependent increase, followed by a temporally-gated decrease, of its viscosity. Our results present a class of polymeric fluids that leverage naturally occurring enzymes to drive diverse time-varying rheology by performing architectural alterations to the constituents.

cond-mat.soft↗