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We demonstrate the use of multiscale polymer modelling to quantitatively predict DNA linear dichroism (LD) in shear flow. LD is the difference in absorption of light polarised along two perpendicular axes, and has long been applied to study biopolymer structure and drug-biopolymer interactions. As LD is orientation-dependent, the sample must be aligned in order to measure a signal. Shear flow via a Couette cell can generate the required orientation, however it is challenging to separate the LD due to changes in polymer conformation from specific interactions, e.g. drug-biopolymer. In this study, we have applied a combination of Brownian dynamics and equilibrium Monte Carlo simulations to accurately predict polymer alignment, and hence flow LD, at modest computational cost. As the optical and conformational contributions to the LD can be explicitly separated, our findings allow for enhanced quantitative interpretation of LD spectra through the use of an in-silico model to capture conformational changes. Our model requires no fitting and only five input parameters, the DNA contour length, persistence length, optical factor, solvent quality, and relaxation time, all of which have been well characterized in prior literature. The method is sufficiently general to apply to a wide range of biopolymers beyond DNA, and our findings could help guide the search for new pharmaceutical drug targets via flow LD., Comment: 10 pages, 4 figures, includes supplementary information, to appear in Biophysical Journal

The static and dynamic properties of dendrimers in semidilute solutions of linear chains of comparable size are investigated using Brownian dynamics simulations. The radius of gyration and diffusivity of a wide variety of low generation dendrimers and linear chains in solution follow universal scaling laws independent of their topology. Analysis of the shape functions and internal density of dendrimers shows that they are more spherical than linear chains and have a dense core. At intermediate times, dendrimers become subdiffusive, with an exponent higher than that previously reported for nanoparticles in semidilute polymer solutions. The long-time diffusivity of dendrimers does not follow theoretical predictions for nanoparticles. We propose a new scaling law for the long-time diffusion coefficients of dendrimers which accounts for the fact that, unlike nanoparticles, dendrimers shrink with an increase in background solution concentration. Analysis of the properties of a special case of a higher functionality dendrimer shows a transition from polymer-like to nanoparticle-like behaviour., Comment: 17 pages, 12 figures, includes supplementary information

Solutions of polymer chains are modelled using non-equilibrium Brownian dynamics simulations, with physically associative beads which form reversible crosslinks to establish a system-spanning physical gel network. Rheological properties such as the zero-shear-rate viscosity and relaxation modulus are investigated systematically as functions of polymer concentration and the binding energy between associative sites. It is shown that a system-spanning network can form regardless of binding energy at sufficiently high concentration. However, the contribution to the stress sustained by this physical network can decay faster than other relaxation processes, even single chain relaxations. If the polymer relaxation time scales overlap with short-lived associations, the mechanical response of a gel becomes ``evanescent'', decaying before it can be rheologically observed, even though the network is instantaneously mechanically rigid. In our simulations, the concentration of elastically active chains and the dynamic modulii are computed independently. This makes it possible to combine structural and rheological information to identify the concentration at which the sol-gel transition occurs as a function of binding energy. Further, it is shown that the competition of scales between the sticker dissociation time and the single-polymer relaxation time determines if the gel is in the evanescent regime., Comment: 25 pages, 13 figures, includes supplementary information, to appear in Macromolecules

Although the non-equilibrium behaviour of polymer solutions is generally well understood, particularly in extensional flow, there remain several unanswered questions for dilute solutions in simple shear flow, and full quantitative agreement with experiments has not been achieved. For example, experimental viscosity data exhibit qualitative differences in shear-thinning exponents, shear rate for onset of shear-thinning and high-shear Newtonian plateaus depending on polymer semiflexibility, contour length and solvent quality. While polymer models are able to incorporate all of these effects through various spring force laws, bending potentials, excluded volume (EV) potentials, and hydrodynamic interaction (HI), the inclusion of each piece of physics has not been systematically matched to experimentally observed behaviour. Furthermore, attempts to develop multiscale models (in the sense of representing an arbitrarily small or large polymer chain) which can make quantitative predictions are hindered by the lack of ability to fully match the results of bead-rod models, often used to represent a polymer chain at the Kuhn step level, with bead-spring models, which take into account the entropic elasticity.In light of these difficulties, this work aims to develop a general model based on the so-called FENE-Fraenkel spring, originally formulated by Larson and coworkers [J. Chem. Phys. 124 (2006), 10.1063/1.2161210], which can span the range from rigid rod to traditional entropic spring, as well as include a bending potential, EV and HI. As we show, this model can reproduce, and smoothly move between, a wide range of previously observed polymer solution rheology in shear flow., Comment: To appear in the Journal of Rheology. 30 pages, 28 figures

An exact solution of coarse-grained polymer models with fluctuating internal friction and hydrodynamic interactions has not been proposed so far due to a one-to-all coupling between the connector vector velocities that precludes the formulation of the governing stochastic differential equations. A methodology for the removal of this coupling is presented, and the governing stochastic differential equations, obtained by attaching a kinetic interpretation to the Fokker-Planck equation for the system, are integrated numerically using Brownian dynamics simulations. The proposed computational route eliminates the calculation of the divergence of the diffusion tensor which appears in models with internal friction, and is about an order of magnitude faster than the recursion-based algorithm for the decoupling of connector-vector velocities previously developed [J. Rheol., 65, 903 (2021)] for the solution of freely draining models with internal friction. The effects of the interplay of various combinations of finite extensibility, internal friction and hydrodynamic interactions on the steady-shear-viscosity is examined. While finite extensibility leads solely to shear-thinning, both internal friction and hydrodynamic interactions result in shear-thinning followed by shear-thickening. The shear-thickening induced by internal friction effects are more pronounced than that due to hydrodynamic interactions., Comment: Comments: To appear in the Journal of Rheology, 20 pages, 9 figures, includes Supplemental Material

Due to their unique topology of having no chain ends, dilute solutions of ring polymers exhibit behaviour distinct from their linear chain counterparts. The universality of their static and dynamic properties, as a function of solvent quality $z$ in the thermal crossover regime between $\theta$ and athermal solvents, is studied here using Brownian dynamics simulations. The universal ratio $U_{\text{RD}}$ of the radius of gyration $R_g$ to the hydrodynamic radius $R_H$ is determined, and a comparative study of the swelling ratio $\alpha_g$ of the radius of gyration, the swelling ratio $\alpha_H$ of the hydrodynamic radius, and the swelling ratio $\alpha_X$ of the mean polymer stretch $X$ along the $x$-axis, for linear and ring polymers, is carried out. The ratio $U_{\text{RD}}$ for dilute ring polymer solutions is found to converge asymptotically to a constant value as $z \to \infty$, which is a major difference from the behaviour of solutions of linear chains, where no such asymptotic limit exists. Additionally, the ratio of the mean stretch along the $x$-axis to the hydrodynamic radius, $(X/R_H)$, is found to be independent of $z$ for polymeric rings, unlike in the case for linear polymers. These results indicate a fundamental difference in the scaling of static and dynamic properties of rings and linear chains in the thermal crossover regime., Comment: 20 pages, 14 figures. To appear in the Special Issue of the Journal of Rheology on Ring Polymers

The Rouse model with internal friction (RIF), a widely used theoretical framework to interpret the effects of internal friction on conformational transitions in biomolecules, is shown to be an approximate treatment that is based on preaveraging internal friction. By comparison with Brownian dynamics simulations of an exact coarse-grained model that incorporates fluctuations in internal friction, the accuracy of the preaveraged model predictions is examined both at and away from equilibrium. While the two models predict intrachain autocorrelations that approach each other for long enough chain segments, they differ in their predictions for shorter segments. Furthermore, the two models differ qualitatively in their predictions for the chain extension and viscosity in shear flow, which is taken to represent a prototypical out-of-equilibrium condition., Comment: 24 pages, 10 figures

Chromatin is known to be organized into multiple domains of varying sizes and compaction. While these domains are often imagined as static structures, they are highly dynamic and show cell-to-cell variability. Since processes such as gene regulation and DNA replication occur in the context of these domains, it is important to understand their organization, fluctuation and dynamics. To simulate chromatin domains, one requires knowledge of interaction strengths among chromatin segments. Here, we derive interaction strength parameters from experimentally known contact maps and use them to predict chromatin organization and dynamics. Taking two domains on the human chromosome as examples, we investigate its 3D organization, size/shape fluctuations, and dynamics of different segments within a domain, accounting for hydrodynamic effects. Considering different cell types, we quantify changes in interaction strengths and chromatin shape fluctuations in different epigenetic states. Perturbing the interaction strengths systematically, we further investigate how epigenetic-like changes can alter the spatio-temporal nature of the domains. Our results show that heterogeneous weak interactions are crucial in determining the organization of the domains. Computing effective stiffness and relaxation times, we investigate how perturbations in interactions affect the solid-like and liquid-like nature of chromatin domains. Quantifying dynamics of chromatin segments within a domain, we show how the competition between polymer entropy and interaction energy influence the timescales of loop formation and maintenance of stable loops., Comment: 19 pages, 8 figures, supplementary material included, to appear in Biophysical Journal

A coarse-grained bead-spring-dashpot chain model with the dashpots representing the presence of internal friction, is solved exactly numerically, for the case of chains with more than two beads. Using a decoupling procedure to remove the explicit coupling of a bead's velocity with that of its nearest neighbors, the governing set of stochastic differential equations are solved with Brownian dynamics simulations to obtain material functions in oscillatory and steady simple shear flow. Simulation results for the real and imaginary components of the complex viscosity have been compared with the results of previously derived semi-analytical approximations, and the difference in the predictions are seen to diminish with an increase in the number of beads in the chain. The inclusion of internal friction results in a non-monotonous variation of the viscosity with shear rate, with the occurrence of continuous shear-thickening following an initial shear-thinning regime. The onset of shear-thickening in the first normal stress coefficient is pushed to lower shear rates with an increase in the internal friction parameter., Comment: 24 pages, 10 figures, includes supplementary information