15,348 research outputs found
Cellular Blood Flow
The fluid dynamics video that is presented here outlines recent advances in
the simulation of multiphase cellular blood flow through the direct numerical
simulations of deformable red blood cells (RBCs) demonstrated through several
numerical experiments. Videos show particle deformation, shear stress on the
particle surface, and the formation of particle clusters in both
Hagen-Poiseuille and shear flow.Comment: 2 pages, one hyperlink to 2 video
Surface and bulk stresses drive morphological changes in fibrous microtissues
Engineered fibrous tissues consisting of cells encapsulated within collagen gels are widely used three-dimensional in vitro models of morphogenesis and wound healing. Although cell-mediated matrix remodeling that occurs within these scaffolds has been extensively studied, less is known about the mesoscale physical principles governing the dynamics of tissue shape. Here, we show both experimentally and by using computer simulations how surface contraction through the development of surface stresses (analogous to surface tension in fluids) coordinates with bulk contraction to drive shape evolution in constrained three-dimensional microtissues. We used microelectromechanical systems technology to generate arrays of fibrous microtissues and robot-assisted microsurgery to perform local incisions and implantation. We introduce a technique based on phototoxic activation of a small molecule to selectively kill cells in a spatially controlled manner. The model simulations, which reproduced the experimentally observed shape changes after surgical and photochemical operations, indicate that fitting of only bulk and surface contractile moduli is sufficient for the prediction of the equilibrium shape of the microtissues. The computational and experimental methods we have developed provide a general framework to study and predict the morphogenic states of contractile fibrous tissues under external loading at multiple length scales.Published versio
Data-driven discovery of coordinates and governing equations
The discovery of governing equations from scientific data has the potential
to transform data-rich fields that lack well-characterized quantitative
descriptions. Advances in sparse regression are currently enabling the
tractable identification of both the structure and parameters of a nonlinear
dynamical system from data. The resulting models have the fewest terms
necessary to describe the dynamics, balancing model complexity with descriptive
ability, and thus promoting interpretability and generalizability. This
provides an algorithmic approach to Occam's razor for model discovery. However,
this approach fundamentally relies on an effective coordinate system in which
the dynamics have a simple representation. In this work, we design a custom
autoencoder to discover a coordinate transformation into a reduced space where
the dynamics may be sparsely represented. Thus, we simultaneously learn the
governing equations and the associated coordinate system. We demonstrate this
approach on several example high-dimensional dynamical systems with
low-dimensional behavior. The resulting modeling framework combines the
strengths of deep neural networks for flexible representation and sparse
identification of nonlinear dynamics (SINDy) for parsimonious models. It is the
first method of its kind to place the discovery of coordinates and models on an
equal footing.Comment: 25 pages, 6 figures; added acknowledgment
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