Student Poster Abstracts

Universal scaling of shear thickening suspensions under acoustic perturbation

Nearly all dense suspensions undergo dramatic and abrupt thickening transitions in their flow behavior when sheared at high stresses. Such transitions occur when suspended particles come into frictional contact with each other to form structures that resist the flow. These frictional contacts can be disrupted with acoustic perturbations, thereby lowering the suspension’s viscosity. Acoustic perturbations offer a convenient way to control the suspension’s shear thickening behavior in real time, as the suspension responds to the perturbation nearly instantaneously. Here, we fold these acoustic perturbations into a universal scaling framework for shear thickening, in which the viscosity is described by a crossover scaling function from the frictionless jamming point to a frictional shear jamming critical point. We test this theory on sheared suspensions with acoustic perturbations and find experimentally that the data for all shear stresses, volume fractions, and acoustic powers can be collapsed onto a single universal curve. Within this framework, a scaling parameter that is a function of stress, volume fraction and acoustic power determines the proximity of the system to the frictional shear jamming critical point and ultimately the viscosity. Our results demonstrate the broad applicability of the scaling framework, its utility for experimentally manipulating the system, and open the door to importing the vast theoretical machinery developed to understand equilibrium critical phenomena to elucidate fundamental physical aspects of the non-equilibrium shear thickening transition.

Pattern Formation for Tunable Functionality in Soft Matter

Pattern formation as a result of spontaneous symmetry breaking, not only can mediate biological function but also be harnessed to create novel materials. Our work focuses on two different systems – elastic phononic crystals and phase-separating flows – to elucidate how patterns arising in soft matter can be used to create functional materials.

Elastic phononic crystals are soft, deformable metamaterials that have periodic modulations in their material properties, which are used to control the propagation of acoustic waves for applications such as filtering and wave-guiding. The wave propagation properties of phononic crystals, represented via band diagrams, are not only affected by material properties, but also by the symmetry properties of the crystal. These properties can influence the formation of directional as well as complete band gaps. We have developed a group representation-based framework to explain the effects of unit cell symmetries in the band diagram for undeformed elastic phononic crystals. We are now extending the group theoretic framework to account for symmetry-breaking bifurcated patterns in deformable crystals caused by buckling. This generalized symmetry-based analysis can be used to formulate rational design rules for acoustic metamaterials as well as to study generalized problems in soft matter physics via group-theoretic considerations.

Phase-separating flows, on the other hand, can lead to patterns based on nonequilibrium thermodynamics. These patterns can be used to create multilayered multicomponent droplets, as has been shown by previous researchers in Oil-Water-Ethanol systems. We study the problem of phase separation caused by the selective diffusion of one component (ethanol) out of a ternary mixture, making the mixture unstable to perturbations that lead to spinodal decomposition. In a simplified 1D Flory-Huggins type model with Cahn-Hilliard kinetics, we see the emergence of a concentration-dependent interaction parameter that guides which spatial regions of the ternary mixture have the potential to undergo phase separation. We are now characterizing the properties of an associated phase separating front, by exploring the front velocity and spectral properties of the patterns created. Our analysis can then be used to study phase separation in microchannel co-flow systems, which can help design material fibers or droplets by controlling the underlying pattern-forming phase separation processes.

Optimal Cell Migration in Heterogenous Environments

Collective cell migration is an important phenomenon in many biological processes, such as embryonic development, cancer metastasis, and tissue repair. One of the key features of this is the directionality and coordination of the multicellular movements through some biomechanical interactions that are not well understood yet. To understand the role of tissue dynamics (rigidity, interfacial tensions, and differential activity) on the migration of cellular clusters, we employed a 2D Self-propelled Voronoi model (cell motility is modelled via the active ornstein-uhlenbeck process) coupled with an additional interfacial tension controlling the heterotypic cell interactions to simulate a cell cluster migration in a confluent tissue. We find that a caged-to-migratory transition happens in monolayers (homogeneous in rigidity) for increasing cluster activity very similar to the activity-induced solid-fluid transition that is a universal feature of these confluent models. Interfacial tension, on the other hand, regulates the cluster integrity during the movement and invokes leader-follower like dynamics in mixed clusters of varying cell motilities. Both in the cases of pure motile cell clusters and mixed motile and non-motile cell clusters, we observe optimality in the Heterotypic Interfacial Tension (HIT) strengths for varying cluster sizes and motilities i.e low HIT strength isn’t enough for coherent migration and high HIT strength leads to a pinning-like effect at the interface between different cell types caging the cells from movement. To test the effectivity of this 2D Voronoi modelling framework, we focused on simulating cell clusters with several components (different activity levels and interfacial tensions with each other) to mimic the coherent ingression of cells with varying Nodal levels during zebrafish gastrulation. By introducing Nodal-dependant values for cell motility and differential heterotypic interfacial tensions (DHIT), we are able to correlate the experimental observation qualitatively to our model predictions, highlighting the importance of the interplay between cell adhesion and directed motility for efficient cluster migration.

Evaporation of Colloidal Suspensions of Aspherical Particles

Recent studies have shown that size-dependent stratification can occur in a rapidly drying suspension of a polydisperse mixture of spherical colloids. In this work we utilize molecular dynamics simulations based on an implicit solvent model to investigate the role of particle shape in such far-from-equilibrium processes. Rigid-body composite particles with various shapes, including spheres, hollow spheres, tetrahedra, cubes, rods, and disks, are prepared using Lennard-Jones beads. Our results reveal that under controlled environment where particles in different shapes have similar diffusivity, diffusiophoresis can be the dominate factor compared to surface effect. In a binary mixture of particles, diffusiophoresis can be used to induce stratification if particles in different shapes have significantly different surface area. For particles with similar surface area, there is no stratification regardless of their shapes even when their shapes differ strikingly (e.g., rods vs. disks). Our results thus indicate that when using solvent evaporation to assemble, separate, or stratify colloidal particles in different shape, diffusiohoresis can be an important factor to control the distribution of the particles in the drying film.

Membrane-less cell division

The simplest and most ancient form of reproduction, one of the most fundamental of life’s processes, is cell division. The classical view of cell division is that the cell duplicates its elements within the cytoplasm and organises these elements spatially into two halves. The cell membrane, which acts as a barrier between the inside of the cell and the external environment, then is pinched in the centre and cuts the cell into two. However, recent experiments show this classical view might not be the full picture. When zebrafish embryos are treated with Aurora B, the membranes between cells within the embryo fail to deform and divide cells. The new cellular compartments, however, are intact and there is little diffusion between them. In this work we explore the pattern-formation implied by such cellular compartments and discover it is set by spindle microtubules. We investigate the roles of microtubule polymerisation dynamics, microtubule-associated motors, diffusion timescales and pressure-induced flows in the creation and maintenance of membrane-less barriers between neighbouring cells.

Excluded volume and geometric effects on the dynamics of associating polymers

Polymer solutions with associating groups can form transient polymer networks and undergo reversible gelation, characterized by a significant slowdown in polymer dynamics. This study examines the effects of excluded volume and geometric constraints imposed by the relative size of the sticky groups, “stickers“, and non-sticky groups, “spacers“, on this slowdown. We demonstrate that smaller sticky groups induce a Vogel-Fulcher-Tammann like slowdown with variable activation energies. In contrast, when sticky groups are comparable in size to the spacers, an Arrhenius-type slowdown is observed. These findings provide insight into the molecular mechanisms governing polymer dynamics in associating networks.

Towards DNA transcription targeting

In order to perform useful biological functions, phase-separated biomolecular condensates comprising proteins and RNAs must assemble at specific locations within a living cell. However, the biophysical mechanisms by which such spatial control is achieved remain poorly understood. To address this question, we present an experimentally motivated coarse-grained model of a class of transcriptional condensates that are believed to play a role in initiating DNA transcription. Specifically, we consider transcriptional condensates composed of the bromodomain protein BRD4, which selectively associates with chromatin via specific interactions with acetylated histone tails. Through a combination of equilibrium and nonequilibrium molecular dynamics simulations, we elucidate how BRD4–chromatin interactions tune both the partitioning of chromatin into BRD4 condensates and the nucleation pathway by which BRD4 condensates assemble. We show that both the patterning of histone acetylation marks and the oligomerization state of BRD4 molecules govern the sensitivity and specificity of chromatin-seeded heterogeneous nucleation, whereas disruption of BRD4–chromatin interactions suppresses the chromatin-associated nucleation pathway. Our findings provide a molecularly detailed view of the biophysical mechanisms governing BRD4 condensate formation and suggest potential strategies for regulating transcription via spatiotemporal control of transcriptional condensate nucleation.

Hydrodynamic force on lipid-anchored proteins depends on protein shape

Flow in the surrounding fluid can transport lipid-anchored proteins laterally across lipid membranes. This transport can separate proteins according to their folded size and shape, since larger proteins experience higher force from shear flow. Here we present microfluidics-based measurements of protein transport across supported lipid bilayers. Our experiments use fluorescence microscopy to detect femtonewton-scale forces on the aqueous part of the protein with sufficient precision to distinguish between proteins with similar molecular weights but different shapes.

Flow localisation on Active Nematic Surfaces

During morphogenetic processes, active flows occur in the plane of curved tissues. Tissues often exhibit orientational order, and topological defects arise during tissue development. We have studied the behavior of a +1 defect in a film of active ordered fluid on a curved axi-symmetric surface. We find strikingly different physics compared with the flat-space variant of the problem. We focus in particular on the influence of extrinsic curvature in the elastic free energy, usually neglected in theories of ordered fluids on curved surfaces. We consider two biologically-relevant surfaces: a capped-tube-like rigid surface, similar to epithelial tubes; and a bump on an otherwise flat plane. In the first case, we find that the activity threshold for instability becomes independent of system size, and spontaneous rotational flows become localized. In the latter case, we find that an aster can be passively unstable towards a spiral state, and as a result, contractility-driven active flows are threshold-less and localized. High contractility extinguishes the flow and restores the aster. Surprisingly, for high enough saddle curvature, the spiral to aster transition shifts from continuous to discontinuous. Our study demonstrates how the influence of an external polar-ordering field can induce local spontaneous flows, offering novel approaches to controlling the behavior of active flows.

Homeocurvature adaptation of phospholipids underlies pressure-specialization of deep-sea invertebrates

The deep ocean is dark, cold, and pressurized — pressure increases by 1 bar for every 10 m depth. How does marine life adapt to this extreme environment? Given that lipid membranes are sensitive to both temperature and pressure (they are the most compressible biological material in a cell), one expects to find adaptations in the lipidomes of organisms that are specialized for life at high pressure. Here, we explore this question using the ctenophores as a model organism. Ctenophores make up a marine invertebrate phylum that is the oldest distinct lineage on the metazoan tree, and different species have adapted independently to many pressure and temperature regimes. Building on years of work by the Haddock lab collecting different ctenophore species from different marine environments, and on recent work by the Budin lab obtaining ctenophore lipidomes, we use MD simulations to study how ctenophore lipidomes adapt to maintain critical material properties within a narrow range. We find that depth strongly predicts plasmalogen abundance, with deep-adapted ctenophore lipidomes containing as much as 73 mol % phosphatidylethanolamine plasmalogen. Our simulations and analysis suggest that plasmalogen maintains membrane deformability at high pressure so that vital cellular functions (eg, endo- and exocytosis) can still be performed under deep-sea conditions. These results imply that in addition to other more widely appreciated membrane properties (such as fluidity), lipid intrinsic curvature is also subject to natural selection in the deep sea.