Student Poster Abstracts | Boulder School for Condensed Matter and Materials Physics (2024)

Student Poster Abstracts | Boulder School for Condensed Matter and Materials Physics (1)
Vidyesh Rao Anisetti
Email
Syracuse University

On physical processes that work like learning algorithms

Adaptive behavior is widespread in both living and non-living systems, manifesting in diverse ways from the directional growth of sunflowers in response to sunlight, to directed aging of materials. In our work we explain such adaptive behaviour through the lens of “learning” —as exemplified in neural networks. We show that there exists simple physical processes in nature that could work like learning algorithms.

No poster image available as this presentation involves work yet to be published.

Student Poster Abstracts | Boulder School for Condensed Matter and Materials Physics (2)
Anna Barth
Email
Cornell University

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.

Student Poster Abstracts | Boulder School for Condensed Matter and Materials Physics (4)
Quirine Braat
Email
Eindhoven University of Technology

Formation of motile cell clusters in heterogeneous model tumors: the role of cell-cell alignment

The formation of migrating cell clusters plays an important role in many biophysical processes, including cancer metastasis. In this work, we investigate how a potential cell-cell alignment mechanism affects the formation of motile cell clusters in the bulk of a heterogeneous tumor. We model the tumor as a two-dimensional heterogeneous confluent layer with both motile and non-motile cells using the Cellular Potts formalism. Our results indicate that the degree of clustering is governed by two distinct processes: the formation of clusters due to the presence of cell-cell alignment interactions among motile cells, and the suppression of clustering due to the presence of the dynamic cellular environment (comprised of the non-motile cells).

Student Poster Abstracts | Boulder School for Condensed Matter and Materials Physics (6)
Tejas Dethe
Email
Princeton University

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.

Student Poster Abstracts | Boulder School for Condensed Matter and Materials Physics (8)
Carlo Giorgetti
Email
University of Rome, La Sapienza

Red light-green light with bacteria: Time response in active turbulence

Dense bacterial suspensions exhibit collective behavior similar to inertial turbulence, even though the cells swim at an effective zero Reynolds number. Using light-driven bacteria, we study the onset of turbulence as a function of waiting time in dark, non-motile conditions. We find that “awakening” occurs on a characteristic time scale that is set by the waiting time. Furthermore, we show that the reawakened turbulent pattern can be strongly correlated with the past flow prior to light removal. This memory is only found for densities above a critical value, which is greater than that required for the onset of turbulence.

Student Poster Abstracts | Boulder School for Condensed Matter and Materials Physics (10)
Uday Ram Gubbala
Email
Institute of Science and Technology Austria

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 (hom*ogeneous 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.

Student Poster Abstracts | Boulder School for Condensed Matter and Materials Physics (12)
Jacob Hass
Email
University of Oregon

Extremes in Diffusive Systems Measure Statistics of the Environment

We consider many-particle diffusion in one spatial dimension modeled as Random Walks in a Random Environment (RWRE). A shared short-range space-time random environment determines the jump distributions that drive the motion of the particles. We determine universal power-laws for the environment’s contribution to the variance of the extreme first passage time and extreme location. We show that the prefactors rely upon a single extreme diffusion coefficient that is equal to the ensemble variance of the local drift imposed on particles by the random environment. This coefficient should be contrasted with the Einstein diffusion coefficient, which determines the prefactor in the power-law describing the variance of a single diffusing particle and is equal to the jump variance in the ensemble averaged random environment. Thus a measurement of the behavior of extremes in many-particle diffusion yields an otherwise difficult to measure statistical property of the fluctuations of the generally hidden environment in which that diffusion occurs. We verify our theory and the universal behavior numerically over many RWRE models and system sizes.

Student Poster Abstracts | Boulder School for Condensed Matter and Materials Physics (14)
Binghan Liu
Email
Virginia Tech

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.

Student Poster Abstracts | Boulder School for Condensed Matter and Materials Physics (15)
Joey McTiernan
Email
University of California, Merced

The Assembly and Budding of SARS-CoV-2

Upon the accumulation of viral structural proteins along the ER-Golgi intermediate compartment (ERGIC), SARS-CoV-2 assembles and buds off, driven by the interactions between these proteins, RNA and the ERGIC membrane. The membrane or M protein is thought to recruit other structural proteins, leading to the formation of protein aggregates and the subsequent induction of membrane curvature, prompting the onset of virion formation. However, the direct impact M protein has on the membrane and how this leads to assembly is unclear. Here, we combine all atom molecular dynamics (MD) simulations of an individual M protein with a mesoscopic continuum model describing the coupled evolution of membrane shape and M protein density to quantify viral assembly and budding. From our MD simulations, we identify the M protein’s ability to thin the membrane and induce curvature dependent on its conformation. By incorporating these properties into our continuum model and then comparing with atomic force microscopy measurements of protein aggregate formation, we estimate the membrane mediated M-M protein interaction and make predictions for the onset of assembly and budding under physiological conditions. This work provides a better understanding of how the interactions and dynamics of M protein lead to viral assembly and budding, supplying insights into alternative methods for preventing viral replication and implications for other enveloped viruses.

Student Poster Abstracts | Boulder School for Condensed Matter and Materials Physics (17)
Billie Meadowcroft
Email
University College London

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.

Student Poster Abstracts | Boulder School for Condensed Matter and Materials Physics (19)
Aniruddh Murali
Email
University of Southern Denmark

Liquid Crystal Order of Cells near Corners

Anisotropically shaped cells tend to self-align, giving rise to domains of nematic ordering while experiencing splay and bend, and forming topological defects akin to those observed in 2D nematic liquid crystals. To elucidate the physical properties of this unique liquid crystal, the research explores the behavior of monolayers of cells in proximity to corners and sharp edges. Through in-vitro experiments, a distinct correlation between wedge angle and the nature of deformation in cell monolayers becomes apparent. Smaller wedge angles predominantly trigger splay deformation, whereas larger angles induce bend deformation. Notably, the angle at which splay and bend deformations are equally likely is determined by the ratio between splay and bend elastic constants and becomes thus an indirect measurement of the elastic anisotropy of the system. Furthermore, the splay and bend deformations under confinement are influenced by the adhesion strength of the cells with the substrate. This investigation offers valuable insights into the intricate interplay among cellular morphology, confining geometry, and adhesion properties, shedding light on the mechanics of cellular self-alignment and deformation.

Student Poster Abstracts | Boulder School for Condensed Matter and Materials Physics (21)
Raghavendra Nimiwal
Email
Columbia University

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.

Student Poster Abstracts | Boulder School for Condensed Matter and Materials Physics (22)
Toshi Parmar
Email
University of California, Santa Barbara

Modelling A Growing Active Nematic That Collectively Senses an Anisotropic Substrate

Apolar elongated cells growing on an aligned liquid crystal elastomer collectively sense the substrate orientation. As cells grow and divide along their long axis, they create locally aligned domains of high density separated by low density disordered regions. The ordered domains then grow in size and align with the substrate. At high densities cells jam and growth ceases. The jamming density depends on the order: Highly aligned cells jam at higher densities. The degree of order of the final state depends on the initial seeding density, with smaller seeding densities leading to more aligned monolayers. While the mechanism of sensing the substrate orientation is not known, adding a focal adhesion kinase inhibitor, which disrupts cell-substrate adhesion, leads to the loss of collective directional sensing. We model this system as an overdamped compressible active nematic with growing density. The initial cell aggregation is driven by a Cahn-Hilliard like free-energy and the coupling of density gradients to the orientational dynamics. We incorporate the interaction with the substrate via two possible mechanisms: as an external field biasing the direction of the nematic, and as anisotropic friction experienced by cells. We first show that arresting rearrangements and growth by making rotational viscosity and growth-rate density dependent reproduces the dependence of final order on seeding density. We next show that activity, anisotropic friction, flow-alignment, and alignment of Q-tensor to density gradients all act in concert to engender substrate-sensing at the collective level. We qualitatively reproduce the swirling and laning patterns seen in experiments and plan on exploring the relative importance of friction anisotropy, activity, and density-gradient alignment.

Student Poster Abstracts | Boulder School for Condensed Matter and Materials Physics (24)
Yury Polyachenko
Email
Princeton University

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.

Student Poster Abstracts | Boulder School for Condensed Matter and Materials Physics (26)
Jairo M. Rojas
Email
University of Illinois, Urbana-Champaign

Beyond 2D Tissue Mechanics: A 3D Continuum Shell Theory for Epithelial Cells

Two-dimensional (2D) models for confluent tissues correlate the mechanical state of monolayers to morphological indicators, such as the shape of their cellular components. However, this approach proves inadequate for in-vitro cultured MDCK epithelia. Confocal microscopy reveals significant and systematic variations of cross-sectional cell shape along the apical-basal axis, contradicting 2D theory even when averaged. Therefore, we model the shape of the cell boundary in three dimensions using elastic shell theory with appropriate boundary conditions directly related to the cellular actin distribution, particularly the fiber bundles at the basal side. The analytical solutions align with our experimental observations and allow realistic modeling of actin-related cell mechanics based on observable biological effects. This 3D continuum shell model serves as a rich platform for deriving effective morphological indicators aimed at diagnosing tissue mechanics and health.

Student Poster Abstracts | Boulder School for Condensed Matter and Materials Physics (27)
Sreeja Sasidharan
Email
Lehigh University

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.

Student Poster Abstracts | Boulder School for Condensed Matter and Materials Physics (29)
Luca Scharrer
Email
University of Chicago

Nonequilibrium Pattern Formation in Flocking

Flocking systems as describable by the Toner-Tu equations display two hom*ogeneous steady-states: disordered and ordered (flocking). In a finite 1-D system below a critical size, one of these two phases is always linearly stable; as the system size is increased above some critical length, both phases become unstable to the formation of system-spanning density- and magnetization-waves. Inspired by recent works showing that coupled fields with nonreciprocal interactions can display novel spatiotemporally dynamic phases, we attempt to understand the formation of these flocking band patterns in this context by focusing on the nonreciprocal coupling present between the density and magnetization fields.

Student Poster Abstracts | Boulder School for Condensed Matter and Materials Physics (31)
Rushikesh Shinde
Email
Université Paris Cité

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.

Student Poster Abstracts | Boulder School for Condensed Matter and Materials Physics (33)
Dor Shohat
Email
Tel Aviv University

Crumpled thin sheets – a tabletop journey through nonequilibrium glassy dynamics

Understanding the unusual but seemingly universal dynamics of disordered systems trapped far from equilibrium remains a major challenge in condensed matter physics. Yet, they are not very hard to observe. Take, for example, a thin plastic sheet and crumple it into a ball. It might not be immediately evident, but this seemingly mundane object exhibits many of the hallmark behaviors shared by complex non-equilibrium and disordered systems. These include slow relaxations and creep, intermittent mechanical responses, emission of broadly distributed crackling noise and a range of memory effects.

The macroscopic tabletop nature of crumpled sheets allows us to measure and correlate observables at all scales – from changes in the local structure to global mechanical response. We find that the effective degrees are freedom are localized, bistable elements, similarly to many amorphous solids. We then leverage unique experimental accessibility to build to bottom-up understanding of complex macroscopic phenomena. Under cyclic strain, the bistable elements to emergent memory effects and a programmable stiffness. Under constant loading, their slow yet correlated activation gives rise to logarithmic creep and a beautiful example of Self-Organized Criticality. We identify the minimal underlying principles for these phenomena such that our insights can be exported to disordered systems on all scales, from supercooled liquids to earthquake dynamics.

Student Poster Abstracts | Boulder School for Condensed Matter and Materials Physics (35)
Sasiri Juliana Vargas Urbano
Email
University of Delaware

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.

Student Poster Abstracts | Boulder School for Condensed Matter and Materials Physics (37)
Kaarthik Varma
Email
Cornell University

Critical Phenomena in Biomolecular Condensates: Structure and Dynamics

The study of biomolecular condensates in a cell has become increasingly important due to its implications in health physiology and disease. Phase separation has become a popular framework to study them. Any system which shows phase separation can be characterized by an underlying phase diagram, with tie lines. What implications does location on the phase diagram have on the properties of the biomolecular condensates? To address this question, we focus on a fascinating point on the phase diagram – the critical point and seek to enumerate all the interesting effects related to proximity to the critical point. We start with a very simple model system for biomolecular condensates – mixture of protein (BSA) in polymer (PEG) whose phase diagram is well known to us. We measure the supramolecular structure and material properties of the protein mixtures near the critical point. We compare to scaling theories and discuss implications for the dynamics of condensates.

Student Poster Abstracts | Boulder School for Condensed Matter and Materials Physics (39)
Xiuyang Xia
Email
Ludwig-Maximilians-Universität München

Linker-mediated designed self-assembly and superselectivity

Using multiple weak bindings to form effectively strong interactions, namely multivalent interactions, constitutes the cornerstone of various biological processes. Compared to conventional multivalent bindings, indirect linker-mediated bridging provides new axes for regulating interactions by adjusting both the density and specificity of linkers. In this context, linkers are defined as small, dual-ended molecules capable of transiently and reversibly binding to receptors and ligands on host and guest structures, respectively. This creates bridges that connect these entities. The specificity of the linkers also enables in situ programmability, allowing for the precise “stitching” together of building blocks in synthetic multicomponent systems by introducing specific linkers.

I will present our recent work on the linker-mediated designed assembly of DNA-coated colloids and the superselectivity observed in linker-mediated multivalent nanoparticle adsorption. I will discuss the intriguing entropy-induced phase behaviors resulting from both valence-limited and multivalent natures. Additionally, I will highlight the potential application of the designed precise fabrication on nanoscale, as well as the design of new sensors to detect biomarkers.

Student Poster Abstracts
 | Boulder School for Condensed Matter and Materials Physics (2024)

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