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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. 

The actomyosin cytoskeleton enables cells to resist deformation, crawl, change their shape and sense their surroundings. Despite decades of study, how its molecular constituents can assemble together to form a network with the observed mechanics of cells remains poorly understood. Recently, it has been shown that the actomyosin cortex of quiescent cells can undergo frequent, abrupt reconfigurations and displacements, called cytoquakes. Notably, such fluctuations are not predicted by current physical models of actomyosin networks, and their prevalence across cell types and mechanical environments has not previously been studied. Using micropost array detectors, we have performed high-resolution measurements of the dynamic mechanical fluctuations of cells’ actomyosin cortex and stress fiber networks. This reveals cortical dynamics dominated by cytoquakes—intermittent events with a fat-tailed distribution of displacements, sometimes spanning microposts separated by 4 μm, in all cell types studied. These included 3T3 fibroblasts, where cytoquakes persisted over substrate stiffnesses spanning the tissue-relevant range of 4.3 kPa–17 kPa, and primary neonatal rat cardiac fibroblasts and myofibroblasts, human embryonic kidney cells and human bone osteosarcoma epithelial (U2OS) cells, where cytoquakes were observed on substrates in the same stiffness range. Overall, these findings suggest that the cortex self-organizes into a marginally stable mechanical state whose physics may contribute to cell mechanical properties, active behavior and mechanosensing.

 

The dynamics of the cellular actomyosin cytoskeleton are crucial to many aspects of cellular function. Here, we describe techniques that employ active micropost array detectors (AMPADs) to measure cytoskeletal rheology and mechanical force fluctuations. The AMPADS are arrays of flexible poly(dimethylsiloxane) (PDMS) microposts with magnetic nanowires embedded in a subset of microposts to enable actuation of those posts via an externally applied magnetic field. Techniques are described to track the magnetic microposts’ motion with nanometer precision at up to 100 video frames per second to measure the local cellular rheology at well‐defined positions. Application of these high‐precision tracking techniques to the full array of microposts in contact with a cell also enables mapping of the cytoskeletal mechanical fluctuation dynamics with high spatial and temporal resolution. This article describes (1) the fabrication of magnetic micropost arrays, (2) measurement protocols for both local rheology and cytoskeletal force fluctuation mapping, and (3) special‐purpose software routines to reduce and analyze these data. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.

Basic Protocol 1: Fabrication of magnetic micropost arrays

Basic Protocol 2: Data acquisition for cellular force fluctuations on non‐magnetic micropost arrays

Basic Protocol 3: Data acquisition for local cellular rheology measurements with magnetic microposts

Basic Protocol 4: Data reduction: determining microposts’ motion

Basic Protocol 5: Data analysis: determining local rheology from magnetic microposts

Basic Protocol 6: Data analysis for force fluctuation measurements

Support Protocol 1: Fabrication of magnetic Ni nanowires by electrodeposition

Support Protocol 2: Configuring Streampix for magnetic rheology measurements

 

Displacive transformations in colloidal crystals may offer a pathway for increasing the diversity of accessible configurations without the need to engineer particle shape or interaction complexity. To date, binary crystals composed of spherically symmetric particles at specific size ratios have been formed that exhibit floppiness and facile routes for transformation into more rigid structures that are otherwise not accessible by direct nucleation and growth. There is evidence that such transformations, at least at the micrometer scale, are kinetically influenced by concomitant solvent motion that effectively induces hydrodynamic correlations between particles. Here, we study quantitatively the impact of such interactions on the transformation of binary bcc-CsCl analog crystals into close-packed configurations. We first employ principal-component analysis to stratify the explorations of a bcc-CsCl crystallite into orthogonal directions according to displacement. We then compute diffusion coefficients along the different directions using several dynamical models and find that hydrodynamic correlations, depending on their range, can either enhance or dampen collective particle motions. These two distinct effects work synergistically to bias crystallite deformations toward a subset of the available outcomes.