Rise of tissue- and species-specific 3D bioprinting based on decellularized extracellular matrix-derived bioinks and bioresins

Thanks to its natural complexity and functionality, decellularized extracellular matrix (dECM) serves as an excellent foundation for creating highly cell-compatible bioinks and bioresins. This enables the bioprinted cells to thrive in an environment that closely mimics their native ECM composition and offers customizable biomechanical properties. To formulate dECM bioinks and bioresins, one must first pulverize and/or solubilize the dECM into non-crosslinked fragments, which can then be chemically modified as needed. In bioprinting, the solubilized dECM-derived material is typically deposited and/or crosslinked in a layer-by-layer fashion to build 3D hydrogel structures. Since the introduction of the first liver-derived dECM-based bioinks, a wide variety of decellularized tissue have been employed in bioprinting, including kidney, heart, cartilage, and adipose tissue among others. This review aims to summarize the critical steps involved in tissue-derived dECM bioprinting, starting from the decellularization of the ECM to the standardized formulation of bioinks and bioresins, ultimately leading to the reproducible bioprinting of tissue constructs. Notably, this discussion also covers photocrosslinkable dECM bioresins, which are particularly attractive due to their ability to provide precise spatiotemporal control over the gelation in bioprinting. Both in extrusion printing and vat photopolymerization, there is a need for more standardized protocols to fully harness the unique properties of dECM-derived materials. In addition to mammalian tissues, the most recent bioprinting approaches involve the use of microbial extracellular polymeric substances in bioprinting of bacteria. This presents similar challenges as those encountered in mammalian cell printing and represents a fascinating frontier in bioprinting technology

Comparing open-source DEM frameworks for simulations of common bulk processes

Multiple software frameworks based on the Discrete Element Method (DEM) are available for simulating granular materials. All of them employ the same principles of explicit time integration, with each time step consisting of three main steps: contact detection, calculation of interactions, and integration of the equations of motion. However, there exist significant algorithmic differences, such as the choice of contact models, particle and wall shapes, and data analysis methods. Further differences can be observed in the practical implementation, including data structures, architecture, parallelization and domain decomposition techniques, user interaction, and the documentation of resources. This study compares, verifies, and benchmarks nine widely-used software frameworks. Only open-source packages were considered, as these are freely available and their underlying algorithms can be reviewed, edited, and tested. The benchmark consists of three common bulk processes: silo emptying, drum mixing, and particle impact. To keep it simple and comparable, only standard features were used, such as spherical particles and the Hertz-Mindlin model for dry contacts. Scripts for running the benchmarks in each software are provided as a dataset.</p

Comparing open-source DEM frameworks for simulations of common bulk processes

Multiple software frameworks based on the Discrete Element Method (DEM) are available for simulating granular materials. All of them employ the same principles of explicit time integration, with each time step consisting of three main steps: contact detection, calculation of interactions, and integration of the equations of motion. However, there exist significant algorithmic differences, such as the choice of contact models, particle and wall shapes, and data analysis methods. Further differences can be observed in the practical implementation, including data structures, architecture, parallelization and domain decomposition techniques, user interaction, and the documentation of resources.This study compares, verifies, and benchmarks nine widely-used software frameworks. Only open-source packages were considered, as these are freely available and their underlying algorithms can be reviewed, edited, and tested. The benchmark consists of three common bulk processes: silo emptying, drum mixing, and particle impact. To keep it simple and comparable, only standard features were used, such as spherical particles and the Hertz-Mindlin model for dry contacts. Scripts for running the benchmarks in each software are provided as a dataset

Modeling and optimization of algae growth

The wastewater from greenhouses has a high amount of mineral contamination\ud and an environmentally-friendly method of removal is to use algae\ud to clean this runoff water. The algae consume the minerals as part of their\ud growth process. In addition to cleaning the water, the created algal bio-mass\ud has a variety of applications including production of bio-diesel, animal feed,\ud products for pharmaceutical and cosmetic purposes, or it can even be used as\ud a source of heating or electricity .\ud The aim of this paper is to develop a model of algae production and use\ud this model to investigate how best to optimize algae farms to satisfy the dual\ud goals of maximizing growth and removing mineral contaminants.\ud With this aim in mind the paper is split into five main sections. In the\ud first a review of the biological literature is undertaken with the aim of determining\ud what factors effect the growth of algae. The second section contains\ud a review of exciting mathematical models from the literature, and for\ud each model a steady-state analysis is performed. Moreover, for each model\ud the strengths and weaknesses are discussed in detail. In the third section,a new two-stage model for algae production is proposed, careful estimation\ud of parameters is undertaken and numerical solutions are presented. In the\ud next section, a new one-dimensional spatial-temporal model is presented,\ud numerically solved and optimization strategies are discussed. Finally, these\ud elements are brought together and recommendations of how to continue are\ud drawn

Coarse-grained local and objective continuum description of three-dimensional granular flows down an inclined surface

Dry, frictional, steady-state granular flows down an inclined, rough surface are studied with discrete particle simulations. From this exemplary flow situation, macroscopic fields, consistent with the conservation laws of continuum theory, are obtained from microscopic data by time-averaging and spatial smoothing (coarse-graining). Two distinct coarse-graining length scale ranges are identified, where the fields are almost independent of the smoothing length w. The smaller, sub-particle length scale, w ≪ d, resolves layers in the flow near the base boundary that cause oscillations in the macroscopic fields. The larger, particle length scale, w ≈ d, leads to smooth stress and density fields, but the kinetic stress becomes scale-dependent; however, this scale-dependence can be quantified and removed. The macroscopic fields involve density, velocity, granular temperature, as well as strain-rate, stress, and fabric (structure) tensors. Due to the plane strain flow, each tensor can be expressed in an inherently anisotropic form with only four objective, coordinate frame invariant variables. For example, the stress is decomposed as: (i) the isotropic pressure, (ii) the “anisotropy” of the deviatoric stress, i.e., the ratio of deviatoric stress (norm) and pressure, (iii) the anisotropic stress distribution between the principal directions, and (iv) the orientation of its eigensystem. The strain rate tensor sets the reference system, and each objective stress (and fabric) variable can then be related, via discrete particle simulations, to the inertial number, I. This represents the plane strain special case of a general, local, and objective constitutive model. The resulting model is compared to existing theories and clearly displays small, but significant deviations from more simplified theories in all variables – on both the different length scales

Mercury DPM: fast, flexible particle simulations in complex geometries part II: applications

MercuryDPM is a particle-simulation software developed open-source by a global network of researchers. It was designed ​ab initio to simulate realistic geometries and materials, thus it contains several unique features not found in any other particle simulation software. These features have been discussed in a companion paper published in the DEM7 conference proceedings; here we present several challenging setups implemented in MercuryDPM ​ . Via these setups, we demonstrate the unique capability of the code to simulate and analyse highly complex geotechnical and industrial applications.These tups implemented include complex geometries such as (i) a screw conveyor, (ii) steady-state inflow conditions for chute flows, (iii) a confined conveyor belt to simulate a steady-state breaking wave, and(iii)aquasi-2D cylindrical slice to efficiently study shear flows.​MercuryDPM is also parallel, which we showcase via a multi-million particle simulations of a rotating drum. We further demonstrate how to simulate complex particle interactions, including: (i)deformable, charged clay particles; and (ii) liquid bridges and liquid migration in wet particulates, (iii) non-spherical particles implemented via superquadrics. Finally, we show how to analyse and complex systems using the unique micro-macro mapping (coarse-graining) tool MercuryCG

Testing the Wyart-Cates model for non-Brownian shear thickening using bidisperse suspensions

There is a growing consensus that shear thickening of concentrated dispersions is driven by the formation of stress-induced frictional contacts. The Wyart-Cates (WC) model of this phenomenon, in which the microphysics of the contacts enters solely via the fraction $f$ of contacts that are frictional, can successfully fit flow curves for suspensions of weakly polydisperse spheres. However, its validity for "real-life", polydisperse suspensions has yet to be seriously tested. By performing systematic simulations on bidisperse mixtures of spheres, we show that the WC model applies only in the monodisperse limit and fails when substantial bidispersity is introduced. We trace the failure of the model to its inability to distinguish large-large, large-small and small-small frictional contacts. By fitting our data using a polydisperse analogue of $f$ that depends separately on the fraction of each of these contact types, we show that the WC picture of shear thickening is incomplete. Systematic experiments on model shear-thickening suspensions corroborate our findings, but highlight important challenges in rigorously testing the WC model with real systems. Our results prompt new questions about the microphysics of thickening for both monodisperse and polydisperse systems.Comment: 9 pages, 8 figures, ancillary informatio