Modulating internal transition kinetics of responsive macromolecules by collective crowding

Abstract

Packing and crowding are used in biology as mechanisms to (self-)regulate internal molecular or cellular processes based on collective signaling. Here, we study how the transition kinetics of an internal “switch” of responsive macromolecules is modified collectively by their spatial packing. We employ Brownian dynamics simulations of a model of Responsive Colloids, in which an explicit internal degree of freedom—here, the particle size—moving in a bimodal energy landscape self-consistently responds to the density fluctuations of the crowded environment. We demonstrate that populations and transition times for the two-state switching kinetics can be tuned over one order of magnitude by “self-crowding.” An exponential scaling law derived from a combination of Kramers’ and liquid state perturbation theory is in very good agreement with the simulations.

Perspective: New directions in dynamical density functional theory

“…Such a theory would fit in the currently empty spot at the top right of figure 1. A further interesting idea, suggested in [289], would be to combine PFT with RDDFT (see section 3) in order to model far-from-equilibrium effects in chemical reactions.…”

Liquid structure of bistable responsive macromolecules using mean-field density-functional theory

“…25 Moreover, using a bimodal parent landscape of the colloidal size, the influence of crowding on the internal switching kinetics was examined using BD simulations. 26 However, the explicit effects of particle softness and hardness on particle's mean size, polydispersity, packing fraction and other structural bulk properties have not been systematically considered. In addition, it would be desirable to have complementary theoretical tools than BD simulations to study the structure and thermodynamics of larger systems in equilibrium and nonequilibrium more efficiently.…”

“…RC polydispersity, δ = ∆σ 1/2 / σ , as a function of ρ * 0 ε for different values of the particle softness: τ/σ 0 = 0.02, 0.05, 0.1 and 0.2. Lines with solid symbols correspond to the bimodal distribution (Eq 26). and lines with open symbols to the unimodal Gaussian distribution (Eq.…”