Search for: All records

ABSTRACT The crowded bacterial cytoplasm is comprised of biomolecules that span several orders of magnitude in size and electrical charge. This complexity has been proposed as the source of the rich spatial organization and apparent anomalous diffusion of intracellular components, although this has not been tested directly. Here, we use biplane microscopy to track the 3D motion of self-assembled bacterial Genetically Encoded Multimeric nanoparticles (bGEMs) with tunable size (20 to 50 nm) and charge (−2160 to +1800 e) in liveEscherichia colicells. To probe intermolecular details at spatial and temporal resolutions beyond experimental limits, we also developed a colloidal whole-cell model that explicitly represents the size and charge of cytoplasmic macromolecules and the porous structure of the bacterial nucleoid. Combining these techniques, we show that bGEMs spatially segregate by size, with small 20-nm particles enriched inside the nucleoid, and larger and/or positively charged particles excluded from this region. Localization is driven by entropic and electrostatic forces arising from cytoplasmic polydispersity, nucleoid structure, geometrical confinement, and interactions with other biomolecules including ribosomes and DNA. We observe that at the timescales of traditional single molecule tracking experiments, motion appears sub-diffusive for all particle sizes and charges. However, using computer simulations with higher temporal resolution, we find that the apparent anomalous exponents are governed by the region of the cell in which bGEMs are located. Molecular motion does not display anomalous diffusion on short time scales and the apparent sub-diffusion arises from geometrical confinement within the nucleoid and by the cell boundary. 

Modulating the interaction potential between colloids suspended in a fluid can trigger equilibrium phase transitions as well as the formation of non-equilibrium “arrested states,” such as gels and glasses. Faithful representation of such interactions is essential for using simulation to interrogate the microscopic details of non-equilibrium behavior and for extrapolating observations to new regions of phase space that are difficult to explore in experiments. Although the extended law of corresponding states predicts equilibrium phases for systems with short-ranged interactions, it proves inadequate for equilibrium predictions of systems with longer-ranged interactions and for predicting non-equilibrium phenomena in systems with either short- or long-ranged interactions. These shortcomings highlight the need for new approaches to represent and disambiguate interaction potentials that replicate both equilibrium and non-equilibrium phase behavior. In this work, we use experiments and simulations to study a system with long-ranged thermoresponsive colloidal interactions and explore whether a resolution to this challenge can be found in regions of the phase diagram where temporal effects influence material state. We demonstrate that the conditions for non-equilibrium arrest by colloidal gelation are sensitive to both the shape of the interaction potential and the thermal quench rate. We exploit this sensitivity to propose a kinetics-based algorithm to extract distinct arrest conditions for candidate potentials that accurately selects between potentials that differ in shape but share the same predicted equilibrium structure. The algorithm selects the candidate that best matches the non-equilibrium behavior between simulation and experiments. Because non-equilibrium behavior in simulation is encoded entirely by the interparticle potential, the results are agnostic to the particular mechanism(s) by which arrest occurs, and so we expect our method to apply to a range of arrested states, including gels and glasses. Beyond its utility in constructing models, the method reveals that each potential has a quantitatively distinct arrest line, providing insight into how the shape of longer-ranged potentials influences the conditions for colloidal gelation. 

Correction for ‘Phase mechanics of colloidal gels: osmotic pressure drives non-equilibrium phase separation’ by Lilian C. Johnson et al. , Soft Matter , 2021, 17 , 3784–3797, DOI: 10.1039/D0SM02180F. 

Although dense colloidal gels with interparticle bonds of order several kT are typically described as resulting from an arrest of phase separation, they continue to coarsen with age, owing to the dynamics of their temporary bonds. Here, k is Boltzmann's constant and T is the absolute temperature. Computational studies of gel aging reveal particle-scale dynamics reminiscent of condensation that suggests very slow but ongoing phase separation. Subsequent studies of delayed yield reveal structural changes consistent with re-initiation of phase separation. In the present study we interrogate the idea that mechanical yield is connected to a release from phase arrest. We study aging and yield of moderately concentrated to dense reversible colloidal gels and focus on two macroscopic hallmarks of phase separation: increases in surface-area to volume ratio that accompanies condensation, and minimization of free energy. The interplay between externally imposed fields, Brownian motion, and interparticle forces during aging or yield, changes the distribution of bond lengths throughout the gel, altering macroscopic potential energy. The gradient of the microscopic potential (the interparticle force) gives a natural connection of potential energy to stress. We find that the free energy decreases with age, but this slows down as bonds get held stretched by glassy frustration. External perturbations break just enough bonds to liberate negative osmotic pressure, which we show drives a cascade of bond relaxation and rapid reduction of the potential energy, consistent with renewed phase separation. Overall, we show that mechanical yield of reversible colloidal gels releases kinetic arrest and can be viewed as non-equilibrium phase separation.