arXiv subjects

John C. Crocker

Publications and source records attributed to John C. Crocker.

9 recordsLinked to original sources

arXiv2025

Slow Relaxation and Landscape-Driven Dynamics in Viscous Ripening Foams

Foams and dense emulsions display complex mechanical behavior, including intermittent rearrangement dynamics, power-law rheology, and slow recovery after perturbation. These effects have long been considered evidence for glassy physics in these and other materials having similar mechanics, such as the cytoskeleton. Here we study such anomalous mechanics in a simulated wet foam driven by ripening and find behavior that has a different physical origin than that in glasses. Rather, the dynamics is due to a balance of forces from the system's self-similar potential energy landscape and viscous stress. At the lowest viscosities, bubbles move intermittently, with the system shifting abruptly between shallow potential energy minima. For higher viscosities, in contrast, the bubbles move continuously and the system follows a tortuous, fractal path through high-dimensional configuration space, at higher mean energy than the lower viscosity case. The long-time dynamics and power-law rheology are the direct consequence of the potential energy landscape's self-similar geometry. Lastly, we find that the slow recovery of perturbed foams is due to the foam being kinetically rather than energetically trapped in high-energy portions of the energy landscape. Overall, viscous ripening foams follow a biased energy minimization pathway that explores regions of the energy landscape that are qualitatively different (flatter and smoother) than those corresponding to well-annealed glasses.

cond-mat.soft↗

arXiv2024

Building rigid networks with prestress and selective pruning

Biopolymer networks from the intracellular to tissue scale display high rigidity and tensile stress while having coordinations well below the normal threshold for mechanical rigidity. The elastic filaments in these networks are often severed by enzymes in a tension-inhibited manner. The effects of such pruning on the mechanics of prestressed networks have not been studied. We show that networks pruned by a tension-inhibited method remain rigid at much lower coordinations than randomly pruned ones. These findings suggest a possible reason for the repeated evolution of tension-inhibited filament-severing proteins.

cond-mat.soft↗

arXiv2024

Lévy distributed fluctuations in the living cell cortex

The actomyosin cortex is an active material that provides animal cells with a strong but flexible exterior, whose mechanics, including non-Gaussian fluctuations and occasional large displacements or cytoquakes, have defied explanation. We study the active fluctuations of the cortex using nanoscale tracking of arrays of flexible microposts adhered to multiple cultured cell types. When the confounding effects of static heterogeneity and tracking error are removed, the fluctuations are found to be heavy-tailed and well-described by a truncated Lévy alpha-stable distribution over a wide range of timescales, in multiple cell types. The largest random displacements closely resemble the earlier-reported cytoquakes, but notably, we find these cytoquakes are not due to earthquake-like cooperative rearrangement of many cytoskeletal elements. Rather, they are indistinguishable from chance large excursions of a super-diffusive random process driven by heavy-tailed noise. The non-cooperative microscopic events driving these fluctuations need not be larger than the expected elastic energy of single tensed cortical actin filaments, and the implied distribution of microscopic event energies will need to be accounted for by future models of the cytoskeleton.

physics.bio-ph↗

arXiv2024

Microstructural features governing fracture of a two-dimensional amorphous solid identified by machine learning

Brittle fracturing of materials is common in natural and industrial processes over a variety of length scales. Knowledge of individual particle dynamics is vital to obtain deeper insight into the atomistic processes governing crack propagation in such materials, yet it is challenging to obtain these details in experiments. We propose an experimental approach where isotropic dilational strain is applied to a densely packed monolayer of attractive colloidal microspheres, resulting in fracture. Using brightfield microscopy and particle tracking, we examine the microstructural evolution of the monolayer during fracturing. Furthermore, using a quantified representation of the microstructure in combination with a machine learning algorithm, we calculate the likelihood of regions of the monolayer to be on a crack line, which we term Weakness. From this analysis, we identify the most important contributions to crack propagation and find that local density is more important than orientational order. Our methodology and results provide a basis for further research on microscopic processes during the fracturing process.

cond-mat.soft↗

arXiv2023

Experimental observations of fractal landscape dynamics in a dense emulsion

Many soft and biological materials display so-called 'soft glassy' dynamics; their constituents undergo anomalous random motions and complex cooperative rearrangements. A recent simulation model of one soft glassy material, a coarsening foam, suggested that the random motions of its bubbles are due to the system configuration moving over a fractal energy landscape in high-dimensional space. Here we show that the salient geometrical features of such high-dimensional fractal landscapes can be explored and reliably quantified, using empirical trajectory data from many degrees of freedom, in a model-free manner. For a mayonnaise-like dense emulsion, analysis of the observed trajectories of oil droplets quantitatively reproduces the high-dimensional fractal geometry of the configuration path and its associated energy minima generated using a computational model. That geometry in turn drives the droplets' complex random motion observed in real space. Our results indicate that experimental studies can elucidate whether the similar dynamics in different soft and biological materials may also be due to fractal landscape dynamics.

cond-mat.soft↗

arXiv2022

Exploring canyons in glassy energy landscapes using metadynamics

The complex physics of glass forming systems is controlled by the structure of the low energy portions of their potential energy landscapes. Here, we report that a modified metadynamics algorithm efficiently explores and samples low energy regions of such high-dimensional landscapes. In the energy landscape for a model foam, our algorithm finds and descends meandering `canyons' in the landscape, which contain dense clusters of energy minima along their floors. Similar canyon structures in the energy landscapes of two model glass formers -- hard sphere fluids and the Kob-Andersen glass -- allow us to reach high densities and low energies, respectively. In the hard sphere system, fluid configurations are found to form continuous regions that cover the canyon floors up to densities well above the jamming transition. For the Kob-Andersen glass former, our technique samples low energy states with modest computational effort, with the lowest energies found approaching the predicted Kauzmann limit.

cond-mat.soft↗

arXiv2021

Probing lipid membrane bending mechanics using gold nanorod tracking

Lipid bilayer membranes undergo rapid bending undulations with wavelengths from tens of nanometers to tens of microns due to thermal fluctuations. Here, we probe such undulations and the membranes' mechanics by measuring the time-varying orientation of single gold nanorods (GNRs) adhered to the membrane, using high-speed dark field microscopy. In a lipid vesicle, such measurements allow the determination of the membrane's viscosity, bending rigidity and tension as well as the friction coefficient for sliding of the monolayers over one another. The in-plane rotation of the GNR is hindered by undulations in a membrane tension dependent manner, consistent with simulations. The motion of single GNRs adhered to the plasma membrane of living cultured cells similarly reveals that membrane's complex physics and coupling to the cell's actomyosin cortex.

cond-mat.soft↗

arXiv2006

Short and long range correlated motion observed in colloidal glasses and liquids

We use a confocal microscope to examine the motion of individual particles in a dense colloidal suspension. Close to the glass transition, particle motion is strongly spatially correlated. The correlations decay exponentially with particle separation, yielding a dynamic length scale of O(2-3 sigma) (in terms of particle diameter sigma). This length scale grows modestly as the glass transition is approached. Further, the correlated motion exhibits a strong spatial dependence on the pair correlation function g(r). Motion within glassy samples is weakly correlated, but with a larger spatial scale for this correlation.

cond-mat.dis-nn↗

arXiv2006

Power-law rheology and mechano-sensing in a cytoskeleton model with forced protein unfolding

We describe a model of cytoskeletal mechanics based on the force-induced conformational change of protein cross-links in a stressed polymer network. Slow deformation of simulated networks containing cross-links that undergo repeated, serial domain unfolding leads to an unusual state--with many cross-links accumulating near the critical force for further unfolding. Thermal activation of these links gives rise to power-law rheology resembling the previously unexplained mechanical response of living cells. Moreover, we hypothesize that such protein cross-links function as biochemical mechano-sensors of cytoskeletal deformation.

physics.bio-ph↗