arXiv subjects

Ben Fabry

Publications and source records attributed to Ben Fabry.

8 recordsLinked to original sources

arXiv2022

Predicting cell stress and strain during extrusion bioprinting

Bioprinting of living cells can cause major shape deformations, which may severely affect cell survival and functionality. While the shear stresses occurring during cell flow through the printer nozzle have been quantified to some extent, the extensional stresses occurring as cells leave the nozzle into the free printing strand have been mostly ignored. Here we use Lattice-Boltzmann simulations together with a finite-element based cell model to study cell deformation at the nozzle exit. Our simulation results are in good qualitative agreement with experimental microscopy images. We show that for cells flowing in the center of the nozzle extensional stresses can be significant, while for cells flowing off-center their deformation is dominated by the shear flow inside the nozzle. From the results of these simulations, we develop two simple methods that only require the printing parameters (nozzle diameter, flow rate, bioink rheology) to (i) accurately predict the maximum cell stress occurring during the 3D bioprinting process and (ii) approximately predict the cell strains caused by the elongational flow at the nozzle exit.

physics.bio-ph↗

arXiv2020

Detecting long-range interactions between migrating cells

Chemotaxis enables cells to systematically approach distant targets that emit a diffusible guiding substance. However, the visual observation of an encounter between a cell and a target does not necessarily indicate the presence of a chemotactic approach mechanism, as even a blindly migrating cell can come across a target by chance. To distinguish between the chemotactic approach and blind migration, we present an objective method that is based on the analysis of time-lapse recorded cell migration trajectories. First, we validate our method with simulated data, demonstrating that it reliably detects the presence or absence of remote cell-cell interactions. In a second step, we apply the method to data from three-dimensional collagen gels, interspersed with highly migratory natural killer (NK) cells that were derived from two different human donors. We find for one of the donors an attractive interaction between the NK cells, pointing to a cooperative behavior of these immune cells. When adding nearly stationary K562 tumor cells to the system, we find a repulsive interaction between K562 and NK cells for one of the donors. By contrast, we find attractive interactions between NK cells and an IL-15-secreting variant of K562 tumor cells. We therefore speculate that NK cells find wild-type tumor cells only by chance, but are programmed to leave a target quickly after a close encounter. We provide a freely available Python implementation of our p-value method that can serve as a general tool for detecting long-range interactions in collective systems of self-driven agents.

q-bio.QM↗

arXiv2017

CameraTransform: a Scientific Python Package for Perspective Camera Corrections

Scientific applications often require an exact reconstruction of object positions and distances from digital images. Therefore, the images need to be corrected for perspective distortions. We present \textit{CameraTransform}, a python package that performs a perspective image correction whereby the height, tilt/roll angle and heading of the camera can be automatically obtained from the images if additional information such as GPS coordinates or object sizes are provided. We present examples of images of penguin colonies that are recorded with stationary cameras and from a helicopter.

cs.MS↗

arXiv2015

Stress controls the mechanics of collagen networks

Collagen is the main structural and load-bearing element of various connective tissues, where it forms the extracellular matrix that supports cells. It has long been known that collagenous tissues exhibit a highly nonlinear stress-strain relationship (Fung YC, Am J Physiol 213(6),1967; Humphrey JD, Proc R Soc Lond A: Math Phys Eng Sci 459(2029),2003), although the origins of this nonlinearity remain unknown (McMahon TA, Lec Math Life Sci 13,1980). Here, we show that the nonlinear stiffening of reconstituted type I collagen networks is controlled by the applied stress, and that the network stiffness becomes surprisingly insensitive to network concentration. We demonstrate how a simple model for networks of elastic fibers can quantitatively account for the mechanics of reconstituted collagen networks. Our model points to the important role of normal stresses in determining the nonlinear shear elastic response, which can explain the approximate exponential relationship between stress and strain reported for collagenous tissues (Fung YC, Am J Physiol 213(6),1967). This further suggests new principles for the design of synthetic fiber networks with collagen-like properties, as well as a mechanism for the control of the mechanics of such networks.

cond-mat.soft↗

arXiv2014

Bayesian inference of time varying parameters in autoregressive processes

In the autoregressive process of first order AR(1), a homogeneous correlated time series $u_t$ is recursively constructed as $u_t = q\; u_{t-1} + σ\;ε_t$, using random Gaussian deviates $ε_t$ and fixed values for the correlation coefficient $q$ and for the noise amplitude $σ$. To model temporally heterogeneous time series, the coefficients $q_t$ and $σ_t$ can be regarded as time-dependend variables by themselves, leading to the time-varying autoregressive processes TVAR(1). We assume here that the time series $u_t$ is known and attempt to infer the temporal evolution of the 'superstatistical' parameters $q_t$ and $σ_t$. We present a sequential Bayesian method of inference, which is conceptually related to the Hidden Markov model, but takes into account the direct statistical dependence of successively measured variables $u_t$. The method requires almost no prior knowledge about the temporal dynamics of $q_t$ and $σ_t$ and can handle gradual and abrupt changes of these superparameters simultaneously. We compare our method with a Maximum Likelihood estimate based on a sliding window and show that it is superior for a wide range of window sizes.

q-bio.QM↗

arXiv2011

Reconstructing fiber networks from confocal image stacks

We present a numerically efficient method to reconstruct a disordered network of thin biopolymers, such as collagen gels, from three-dimensional (3D) image stacks recorded with a confocal microscope. Our method is based on a template matching algorithm that simultaneously performs a binarization and skeletonization of the network. The size and intensity pattern of the template is automatically adapted to the input data so that the method is scale invariant and generic. Furthermore, the template matching threshold is iteratively optimized to ensure that the final skeletonized network obeys a universal property of voxelized random line networks, namely, solid-phase voxels have most likely three solid-phase neighbors in a $3\times3$ neighborhood. This optimization criterion makes our method free of user-defined parameters and the output exceptionally robust against imaging noise.

q-bio.QM↗

arXiv2011

Poresizes in random line networks

Many natural fibrous networks with fiber diameters much smaller than the average poresize can be described as three-dimensional (3D) random line networks. We consider here a `Mikado' model for such systems, consisting of straight line segments of equal length, distributed homogeneously and isotropically in space. First, we derive analytically the probability density distribution $p(r_{no})$ for the `nearest obstacle distance' $r_{no}$ between a randomly chosen test point within the network pores and its closest neighboring point on a line segment. Second, we show that in the limit where the line segments are much longer than the typical pore size, $p(r_{no})$ becomes a Rayleigh distribution. The single parameter $σ$ of this Rayleigh distribution represents the most probable nearest obstacle distance and can be expressed in terms of the total line length per unit volume. Finally, we show by numerical simulations that $σ$ differs only by a constant factor from the intuitive notion of average `pore size', defined by finding the maximum sphere that fits into each pore and then averaging over the radii of these spheres.

q-bio.QM↗

arXiv2010

Contractile prestress controls stiffening and fluidization of living cells in response to large external forces

We report the simultaneous characterization of time- and force-dependent mechanical properties of adherent cells in the physiologically relevant regime of large forces. We used magnetic tweezers to apply forces to magnetic beads bound to the cytoskeleton, and recorded the resulting deformation (creep response). The creep response followed a weak power law at all force levels. Stress stiffening and fluidization occurred simultaneously and were quantified by the force-dependence of the creep compliance and the power law exponent. The amount of stiffening and fluidization in response to force was controlled solely by the contractile prestress of the cell and followed a simple relationship. This behavior may be of fundamental importance in biological processes that involve a mechanical interaction between cells and their environment.

physics.bio-ph↗