Network physics of attractive colloidal gels: Resilience, rigidity, and phase diagram.

Colloidal gels exhibit solid-like behavior at vanishingly small fractions of solids, owing to ramified space-spanning networks that form due to particle-particle interactions. These networks give the gel its rigidity, and with stronger attractions the elasticity grows as well. The emergence of rigidity can be described through a mean field approach; nonetheless, fundamental understanding of how rigidity varies in gels of different attractions is lacking. Moreover, recovering an accurate gelation phase diagram based on the system's variables has been an extremely challenging task. Understanding the nature of colloidal clusters, and how rigidity emerges from their connections is key to controlling and designing gels with desirable properties. Here, we employ network analysis tools to interrogate and characterize the colloidal structures. We construct a particle-level network, having all the spatial coordinates of colloids with different attraction levels, and also identify polydisperse rigid fractal clusters using a Gaussian mixture model, to form a coarse-grained cluster network that distinctly shows main physical features of the colloidal gels. A simple mass-spring model then is used to recover quantitatively the elasticity of colloidal gels from these cluster networks. Interrogating the resilience of these gel networks shows that the elasticity of a gel (a dynamic property) is directly correlated to its cluster network's resilience (a static measure). Finally, we use the resilience investigations to devise [and experimentally validate] a fully resolved phase diagram for colloidal gelation, with a clear solid-liquid phase boundary using a single volume fraction of particles well beyond this phase boundary.

Topological origins of yielding in short-ranged weakly attractive colloidal gels.

Yielding of the particulate network in colloidal gels under applied deformation is accompanied by various microstructural changes, including rearrangement, bond rupture, anisotropy, and reformation of secondary structures. While much work has been done to understand the physical underpinnings of yielding in colloidal gels, its topological origins remain poorly understood. Here, employing a series of tools from network science, we characterize the bonds using their orientation and network centrality. We find that bonds with higher centralities in the network are ruptured the most at all applied deformation rates. This suggests that a network analysis of the particulate structure can be used to predict the failure points in colloidal gels a priori.

Structure and Dynamics of Force Clusters and Networks in Shear Thickening Suspensions.

Dense suspensions can exhibit shear thickening in response to large deformation. A consensus has emerged over the past few years on the formation of force networks, that span the entire system size, that lead to increased resistance to motion. Nonetheless, the characteristics of these networks are to a large extent poorly understood. Here, force networks formed in continuous and discontinuous shear thickening dense suspensions (CST and DST, respectively) are studied. We first show the evolution of the network formation and its topological heterogeneities as the applied stress increases. Subsequently, we identify force communities and coarse grain the suspension into a cluster network, and show that cluster-level dynamics are responsible for stark differences between the CST and DST behavior. Our results suggest that the force clusters formed in the DST regime are considerably more constrained in their motion, while CST clusters are loosely connected to their surrounding clusters.

Jamming Distance Dictates Colloidal Shear Thickening.

We report experimental and computational observations of dynamic contact networks for colloidal suspensions undergoing shear thickening. The dense suspensions are comprised of sterically stabilized poly(methyl methacrylate) colloids that are spherically symmetric and have varied surface roughness. Confocal rheometry and dissipative particle dynamics simulations show that the shear thickening strength ß scales exponentially with the scaled deficit contact number and the scaled jamming distance. Rough colloids, which experience additional rotational constraints, require an average of 1.5-2 fewer particle contacts as compared to smooth colloids, in order to generate the same ß. This is because the surface roughness enhances geometric friction in such a way that the rough colloids do not experience a large change in the free volume near the jamming point. The available free volume for colloids of different roughness is related to the deficiency from the maximum number of nearest neighbors at jamming under shear. Our results further suggest that the force per contact is different for particles with different morphologies.

Predicting yielding in attractive colloidal gels.

One of the defining characteristics of soft glassy materials is their ability to exhibit a yield stress, which can result in an overall elasto-visco-plastic mechanics. To design soft materials with specific properties, it is essential to gain a comprehensive understanding of the topological and structural failure points that occur during yielding. However, predicting these failure points, which lead to yielding, is challenging due to the dynamic nature of structure development and its cooccurrence with other complicated processes, such as local rearrangements and anisotropy. In this study, we employ a series of tools from network science to investigate colloidal gels as a model for soft glassy materials during yielding. Our findings reveal that edge betweenness centrality can be utilized as a universal predictor for yielding across various state variables, including the volume fraction of solids, the strength, and the range of attraction between colloids.

Semi-quantitative detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct long-read sequencing.

Here, we develop and apply a semi-quantitative method for the high-confidence identification of pseudouridylated sites on mammalian mRNAs via direct long-read nanopore sequencing. A comparative analysis of a modification-free transcriptome reveals that the depth of coverage and specific k-mer sequences are critical parameters for accurate basecalling. By adjusting these parameters for high-confidence U-to-C basecalling errors, we identify many known sites of pseudouridylation and uncover previously unreported uridine-modified sites, many of which fall in k-mers that are known targets of pseudouridine synthases. Identified sites are validated using 1000-mer synthetic RNA controls bearing a single pseudouridine in the center position, demonstrating systematic under-calling using our approach. We identify mRNAs with up to 7 unique modification sites. Our workflow allows direct detection of low-, medium-, and high-occupancy pseudouridine modifications on native RNA molecules from nanopore sequencing data and multiple modifications on the same strand.

Life and death of colloidal bonds control the rate-dependent rheology of gels.

Colloidal gels exhibit rich rheological responses under flowing conditions. A clear understanding of the coupling between the kinetics of the formation/rupture of colloidal bonds and the rheological response of attractive gels is lacking. In particular, for gels under different flow regimes, the correlation between the complex rheological response, the bond kinetics, microscopic forces, and an overall micromechanistic view is missing in previous works. Here, we report the bond dynamics in short-range attractive particles, microscopically measured stresses on individual particles and the spatiotemporal evolution of the colloidal structures in different flow regimes. The interplay between interparticle attraction and hydrodynamic stresses is found to be the key to unraveling the physical underpinnings of colloidal gel rheology. Attractive stresses, mostly originating from older bonds dominate the response at low Mason number (the ratio of shearing to attractive forces) while hydrodynamic stresses tend to control the rheology at higher Mason numbers, mostly arising from short-lived bonds. Finally, we present visual mapping of particle bond numbers, their life times and their borne stresses under different flow regimes.