Single-Chain Nanoparticles under Homogeneous Shear Flow

Shear flow as a tool to distinguish microscopic activities of molecular machines in a chromatin loop

Several types of molecular machines move along biopolymers like chromatin. However, the details about the microscopic activity of these machines and how to distinguish their modes of action are not well understood. We propose that the activity of such machines can be classified by studying looped chromatin under shear flow. Our simulations show that a chromatin-like polymer with two types of activities-constant (type-I) or local curvature-dependent tangential forces (type-II)-exhibits very different behavior under shear flow. We show that one can distinguish both activities by measuring the nature of a globule-to-extended coil transition, tank treading, and tumbling dynamics.

Supercoiled ring polymers under shear flow

We apply monomer-resolved computer simulations of supercoiled ring polymers under shear, taking full account of the hydrodynamic interactions, accompanied, in parallel, by simulations in which these are switched off. The combination of bending and torsional rigidities inherent in these polymers, in conjunction with hydrodynamics, has a profound impact on their flow properties. In contrast to their flexible counterparts, which dramatically deform and inflate under shear [Liebetreu et al., Commun. Mater. 2020, 1, 4], supercoiled rings undergo only weak changes in their overall shape and they display both a reduced propensity to tumbling (at fixed Weissenberg number) and a much stronger orientational resistance with respect to their flexible counterparts. In the presence of hydrodynamic interactions, the coupling of the polymer to solvent flow is capable of bringing about a topological transformation of writhe to twist at strong shear upon conservation of the overall linking number.

Real-time temperature measurement in stochastic rotation dynamics

Many physical and chemical processes involve energy change with rates that depend sensitively on local temperature. Important examples include heterogeneously catalyzed reactions and activated desorption. Because of the multiscale nature of such systems, it is desirable to connect the macroscopic world of continuous hydrodynamic and temperature fields to mesoscopic particle-based simulations with discrete particle events. In this work we show how to achieve real-time measurement of the local temperature in stochastic rotation dynamics (SRD), a mesoscale method particularly well suited for problems involving hydrodynamic flows with thermal fluctuations. We employ ensemble averaging to achieve local temperature measurement in dynamically changing environments. After validation by heat diffusion between two isothermal plates, heating of walls by a hot strip, and by temperature programed desorption, we apply the method to a case of a model flow reactor with temperature-sensitive heterogeneously catalyzed reactions on solid spherical catalysts. In this model, adsorption, chemical reactions, and desorption are explicitly tracked on the catalyst surface. This work opens the door for future projects where SRD is used to couple hydrodynamic flows and thermal fluctuations to solids with complex temperature-dependent surface mechanisms.

Crowded solutions of single-chain nanoparticles under shear flow

Single-chain nanoparticles (SCNPs) are ultrasoft objects obtained through purely intramolecular cross-linking of single polymer chains. By means of computer simulations with implemented hydrodynamic interactions, we investigate for the first time the effect of the shear flow on the structural and dynamic properties of SCNPs in semidilute and concentrated solutions. We characterize the dependence of several conformational and dynamic observables on the shear rate and the concentration, obtaining a set of power-law scaling laws. The concentration has a very different effect on the shear rate dependence of the former observables in SCNPs than in simple linear chains. Whereas for the latter the scaling behaviour is marginally dependent on the concentration, two clearly different scaling regimes are found for the SCNPs below and above the overlap concentration. At fixed shear rate SCNPs and linear chains also respond very differently to crowding. Whereas, at moderate and high Weissenberg numbers the linear chains swell, the SCNPs exhibit a complex non-monotonic behaviour. We suggest that these findings are inherently related to the topological interactions preventing concatenation of the SCNPs, which lead to less interpenetration than for linear chains, and to the limitation to stretching imposed by the permanent cross-links in the SCNPs, which itself limits the ways to spatially arrange in the shear flow.

Mesoscale modelling of polymer aggregate digestion

We use mesoscale simulations to gain insight into the digestion of biopolymers by studying the break-up dynamics of polymer aggregates (boluses) bound by physical cross-links. We investigate aggregate evolution, establishing that the linking bead fraction and the interaction energy are the main parameters controlling stability with respect to diffusion. We show via a simplified model that chemical breakdown of the constituent molecules causes aggregates that would otherwise be stable to disperse. We further investigate breakdown of biopolymer aggregates in the presence of fluid flow. Shear flow in the absence of chemical breakdown induces three different regimes depending on the flow Weissenberg number ( W i ). i) At W i ≪ 1 , shear flow has a negligible effect on the aggregates. ii) At W i ∼ 1 , the aggregates behave approximately as solid bodies and move and rotate with the flow. iii) At W i ≫ 1 , the energy input due to shear overcomes the attractive cross-linking interactions and the boluses are broken up. Finally, we study bolus evolution under the combined action of shear flow and chemical breakdown, demonstrating a synergistic effect between the two at high reaction rates.