Rheology and Collective Behavior in Living Tissue

Recent experiments and simulations have indicated that confluent epithelial layers, where there are no gaps or overlaps between the cells, can transition from a soft fluid-like state to a solid-like state, with dynamics that share many features with glass transitions. While a coherent picture has begun to form connecting the microscopic mechanisms that drive this transition with macroscopic observables, much less is known of its consequences in biological processes. Do tissues tune themselves to a fluid state in order to promote collective motion? Has evolution made use of the ability of tissues to tune themselves between fluid and solid states in programming the complex steps leading from the embryo to the organism? Here we describe our recent e↵orts to answer such questions using continuum and mesoscopic models. Employing the biophysical vertex model, active cells in confluent tissue are described as polygons with shape-based energies. Recent work has shown that this class of models yields a solid-liquid transition of tissue with evidence of glassy dynamics near the transition line. Here, we extend one such model to include the influence of cell division and cell death. With careful numerical studies, we refute a recent claim that the presence of such division and death will always fluidify the tissue. In the second part of the thesis, we develop a novel hydrodynamic model of confluent motile tissues that couples a structural order parameter for tissue rigidity to cell polarization. Using this continuum model we identify a new mechanism for pattern formation in confluent tissues via rigidity sensing that we name “morphotaxis”. We find that a single “morphotactic” parameter controls whether a tissue will remain homogeneous or will develop patterns such as asters and bands

Correlating Cell Shape and Cellular Stress in Motile Confluent Tissues

Collective cell migration is a highly regulated process involved in wound healing, cancer metastasis and morphogenesis. Mechanical interactions among cells provide an important regulatory mechanism to coordinate such collective motion. Using a Self-Propelled Voronoi (SPV) model that links cell mechanics to cell shape and cell motility, we formulate a generalized mechanical inference method to obtain the spatio-temporal distribution of cellular stresses from measured traction forces in motile tissues and show that such traction-based stresses match those calculated from instantaneous cell shapes. We additionally use stress information to characterize the rheological properties of the tissue. We identify a motility-induced swim stress that adds to the interaction stress to determine the global contractility or extensibility of epithelia. We further show that the temporal correlation of the interaction shear stress determines an effective viscosity of the tissue that diverges at the liquid-solid transition, suggesting the possibility of extracting rheological information directly from traction data.Comment: 12 pages, 9 figure

Community composition of zooplankton exported from a shallow polymictic reservoir linked to wind conditions

Zooplankton exported from lentic systems provision lotic systems with easily captured, consumed, and assimilated prey items. Previous studies have demonstrated that the community composition of zooplankton exports (CCZE) vary over time, which introduces temporal differences in lotic resource availability (zooplankton prey) in downstream habitats. In the study presented here, we monitored variation in CCZE from a polymictic reservoir outfall in response to physical–chemical and atmospheric conditions bi-hourly over three different 24-h periods. Community composition of zooplankton export varied over the course of the day, and exports were most closely associated with wind directionality. Future studies of temporal variation in CCZE should incorporate wind conditions, especially in shallow systems where holomixis occurs frequently. Polymictic reservoirs are becoming increasingly common as the global pace of small dam construction quickens, making both the identification of factors influencing CCZE and the impact of zooplankton exports on local biodiversity and ecosystem function increasingly important to understand

Orisometry formalism reveals duality and exotic nonuniform response in origami sheets

Origami metamaterial design enables drastic qualitative changes in the response properties of a thin sheet via the addition of a repeating pattern of folds based around a rigid folding motion. Known also as a mechanism, this folding motion will have a very small energy cost when applied uniformly; and yet uniform activation of such remains highly difficult to observe, these sheets instead generically displaying nonuniform response patterns which are not yet well understood. Here, we present a purely geometric continuum theory which captures the nonuniform, nonlinear response to generic loading as composed locally of the planar mechanism, as well as previously identified ``twist'' and ``bend'' modes which enable the patterned sheet to curve out of the plane across long distances. Our numerical analysis confirms that these three modes govern the observed nonuniform response, varying smoothly across the sheet according to three PDEs which guarantee compatibility. In analogy with the recently solved case of planar mechanism metamaterials, these ``Orisometries'' (origami + isometries, so named by us) are subextensive but infinite in number, with each mode displaying, in the linear limit, ``sheared analytic'' spatial patterns which are controlled by the Poisson's ratio of the uniform folding mechanism. Furthermore, the ``planar'' mechanism-based deformation patterns superimpose with a mathematically dual space of ``non-planar'' twist/bend deformations to span the available soft linear response. Together, our findings furnish the first quantification of the number of soft response modes available, as well as the first intuitive quantification of their spatial distribution.Comment: 7 pages + 17 pages appendices, 5 figure

Chronotopos monasticus : the medieval clock and the rhythm of monastic life at the Mogiła Abbey near Krakow = Średniowieczny zegar i rytm monastycznego życia w klasztorze w Mogile koło Krakowa

Praca recenzowana / Peer-reviewed paperW ramach projektu badawczego „Architektura zakonów mniszych i mendykanckich w wieku XIII i XIV”, nr WAiSP/DS/3/201

A framework for analyzing both linkage and association: An analysis of Genetic Analysis Workshop 16 simulated data

We examine a Bayesian Markov-chain Monte Carlo framework for simultaneous segregation and linkage analysis in the simulated single-nucleotide polymorphism data provided for Genetic Analysis Workshop 16. We conducted linkage only, linkage and association, and association only tests under this framework. We also compared these results with variance-component linkage analysis and regression analyses. The results indicate that the method shows some promise, but finding genes that have very small (<0.1%) contributions to trait variance may require additional sources of information. All methods examined fared poorly for the smallest in the simulated "polygene" range (h(2 )of 0.0015 to 0.0002)