Single polymer dynamics for molecular rheology

Abstract

Single polymer dynamics offers a powerful approach to study molecular-level interactions and dynamic microstructure in materials. Direct visualization of single chain dynamics has uncovered new ideas regarding the rheology and non-equilibrium dynamics of macromolecules, including the importance of molecular individualism, dynamic heterogeneity, and molecular sub-populations that govern macroscale behavior. In recent years, the field of single polymer dynamics has been extended to increasingly complex materials, including architecturally complex polymers such as combs, bottlebrushes, and ring polymers and entangled solutions of long chain polymers in flow. Single molecule visualization, complemented by modeling and simulation techniques such asBrownian dynamics and Monte Carlo methods, allow for unparalleled access to the molecular-scale dynamics of polymeric materials. In this review, recent progress in the field of single polymer dynamics is examined by highlighting major developments and new physics to emerge from these techniques. The molecular properties of DNA as a model polymer are examined, including the role of flexibility, excluded volume interactions, and hydrodynamic interactions in governing behavior. Recent developments in studying polymer dynamics in time-dependent flows, new chemistries and new molecular topologies, and the role of intermolecular interactions in concentrated solutions are considered. Moreover, cutting-edge methods in simulation techniques are further reviewed as an ideal complementary method to single polymer experiments. Future work aimed at extending the field of single polymer dynamics to new materials promises to uncover original and unexpected information regarding the flow dynamics of polymeric systems.

DiTe2: Calculating the diffusion tensor for flexible molecules

“…based transformation described in eqs. (10) and (11). Being q k = d k , θ k , or ϕ k , that is, one of the internal coordinates that specify the position of atom k in the Z-Matrix, then for atoms 1, 3, and 4 (recall that the center of the reference frame is in atom 2) one has ∂ 2 ∂q k e x 1 ¼ δ k,2 δ q, d ∂S 2 ∂d 2 e 0 ðA1Þ…”

“…Evaluating dissipative properties of molecules is a task that is becoming essential in computational chemistry, especially in molecular dynamics (MD) simulations of macromolecules and ensembles of macromolecules. [1][2][3][4][5][6][7][8][9][10] Coarse-graining (CG) techniques prefer, when possible, to treat the medium implicitly as a thermal bath that contributes to the energetics in a mean field fashion and to the dynamics by imposing fluctuation-dissipation to the momenta associated with the coordinates of the relevant part of the system, which is described explicitly. Under these assumptions, the time evolution of the relevant coordinates is stochastic and in the diffusive regime (which is a reasonable assumption for most molecules in room temperature solvents), the dynamics is Brownian, and described by a diffusion tensor.…”

Pore‐Scale Flow Characterization of Polymer Solutions in Microfluidic Porous Media

“…[95,[99][100][101][102] For example, single molecules of DNA can be trapped at the stagnation point in a microfluidic cross-slot channel, enabling the dynamics of elongation to be monitored as the extensional flow is varied. [103,104] Additionally, the DNA can be embedded within a background polymer solution, acting as a probe of the polymer conformations in the more concentrated solution. [105,106] In general, a polymer chain's equilibrium elongation increases monotonically with Wi e , transitioning gradually from a more coiled state at Wi e = 0 to a more stretched state at higher Wi e ≳ 0.5.…”

Internal friction can be measured with the Jarzynski equality

“…Though the dumbbell model offers much qualitative insight into the behavior of polymeric molecules, 31 bead-spring-chain models with multiple springs, are needed to quantitatively describe experimental features such as the viscoelastic properties of polymer solutions 33 and the dynamics of single molecules. 50 Indeed the effect of internal friction on the rheology and dynamics of polymers has been studied with bead-spring-chain models, in which a dashpot with a common value of the damping coefficient is included in parallel with each of the connecting springs. 32,51,52 It would be interesting to explore the connection between the internal friction coefficient estimated from the average dissipated work (in the limit of zero solvent viscosity) from such a model, and the damping coefficient of each dashpot in the model.…”