Large Scale Tissue Morphogenesis Simulation on Heterogenous Systems Based on a Flexible Biomechanical Cell Model

2015 ◽  
Vol 12 (5) ◽  
pp. 1021-1033 ◽  
Author(s):  
Anne Jeannin-Girardon ◽  
Pascal Ballet ◽  
Vincent Rodin
2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Deborah O. Dele-Oni ◽  
Karen E. Christianson ◽  
Shawn B. Egri ◽  
Alvaro Sebastian Vaca Jacome ◽  
Katherine C. DeRuff ◽  
...  

AbstractWhile gene expression profiling has traditionally been the method of choice for large-scale perturbational profiling studies, proteomics has emerged as an effective tool in this context for directly monitoring cellular responses to perturbations. We previously reported a pilot library containing 3400 profiles of multiple perturbations across diverse cellular backgrounds in the reduced-representation phosphoproteome (P100) and chromatin space (Global Chromatin Profiling, GCP). Here, we expand our original dataset to include profiles from a new set of cardiotoxic compounds and from astrocytes, an additional neural cell model, totaling 5300 proteomic signatures. We describe filtering criteria and quality control metrics used to assess and validate the technical quality and reproducibility of our data. To demonstrate the power of the library, we present two case studies where data is queried using the concept of “connectivity” to obtain biological insight. All data presented in this study have been deposited to the ProteomeXchange Consortium with identifiers PXD017458 (P100) and PXD017459 (GCP) and can be queried at https://clue.io/proteomics.


Author(s):  
Claudio Ruggieri ◽  
Fernando F. Santos ◽  
Mitsuru Ohata ◽  
Masao Toyoda

This study explores the capabilities of a computational cell framework into a 3-D setting to model ductile fracture behavior in tensile specimens and damaged pipelines. The cell methodology provides a convenient approach for ductile crack extension suitable for large scale numerical analyses which includes a damage criterion and a microstructural length scale over which damage occurs. Laboratory testing of a high strength structural steel provides the experimental stress-strain data for round bar and circumferentially notched tensile specimens to calibrate the cell model parameters for the material. The present work applies the cell methodology using two damage criterion to describe ductile fracture in tensile specimens: (1) the Gurson-Tvergaard (GT) constitutive model for the softening of material and (2) the stress-modified, critical strain (SMCS) criterion for void coalescence. These damage criteria are then applied to predict ductile cracking for a pipe specimen tested under cycling bend loading. While the methodology still appears to have limited applicability to predict ductile cracking behavior in pipe specimens, the cell model predictions of the ductile response for the tensile specimens show good agreemeent with experimental measurements.


Science ◽  
2020 ◽  
Vol 367 (6476) ◽  
pp. 453-458 ◽  
Author(s):  
Mehdi Saadaoui ◽  
Didier Rocancourt ◽  
Julian Roussel ◽  
Francis Corson ◽  
Jerome Gros

Tissue morphogenesis is driven by local cellular deformations that are powered by contractile actomyosin networks. How localized forces are transmitted across tissues to shape them at a mesoscopic scale is still unclear. Analyzing gastrulation in entire avian embryos, we show that it is driven by the graded contraction of a large-scale supracellular actomyosin ring at the margin between the embryonic and extraembryonic territories. The propagation of these forces is enabled by a fluid-like response of the epithelial embryonic disk, which depends on cell division. A simple model of fluid motion entrained by a tensile ring quantitatively captures the vortex-like “polonaise” movements that accompany the formation of the primitive streak. The geometry of the early embryo thus arises from the transmission of active forces generated along its boundary.


2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Yong Xia ◽  
Kuanquan Wang ◽  
Henggui Zhang

Large-scale 3D virtual heart model simulations are highly demanding in computational resources. This imposes a big challenge to the traditional computation resources based on CPU environment, which already cannot meet the requirement of the whole computation demands or are not easily available due to expensive costs. GPU as a parallel computing environment therefore provides an alternative to solve the large-scale computational problems of whole heart modeling. In this study, using a 3D sheep atrial model as a test bed, we developed a GPU-based simulation algorithm to simulate the conduction of electrical excitation waves in the 3D atria. In the GPU algorithm, a multicellular tissue model was split into two components: one is the single cell model (ordinary differential equation) and the other is the diffusion term of the monodomain model (partial differential equation). Such a decoupling enabled realization of the GPU parallel algorithm. Furthermore, several optimization strategies were proposed based on the features of the virtual heart model, which enabled a 200-fold speedup as compared to a CPU implementation. In conclusion, an optimized GPU algorithm has been developed that provides an economic and powerful platform for 3D whole heart simulations.


2020 ◽  
Author(s):  
Joshua Gallaway

This talk will discuss electrochemical impedance spectroscopy (EIS) tracking of aqueous alkaline Zn-MnO2 cells cycled at 20% depth of discharge (DOD) based on cathode capacity. Shallow cycled alkaline batteries have previously been reported as cost effective and safe options for large-scale electrical storage. Periodically collected EIS data was used to fit a full battery model based on Voigt elements, and fitted parameters were tracked over time. These were used as a real-time diagnostic to assess performance and predict future performance in advance of any degradation of the cell voltage.The cell model was based on individual electrode models developed previously by Donne and co-workers for γ-MnO2 and Hampson and McNeil for Zn. Two prismatic cell builds were compared using electrodes fabricated by two different commercial sources with identical compositions. Both cell performance and EIS response were distinctly different between the electrode sources. The model provided an acceptable fit of the experimental data in both cases, as shown in Figure 1. The parameters of the model corresponded to physical phenomena, allowing an analysis of the performance difference despite the fact that all electrode fabrication variables could not be known unless provided by the commercial sources.The combined anode and cathode interfacial models were incorporated into a transmission line porous electrode, shown in Figure 2. Each anode + cathode fit involved a combined 15 parameters, which was the minimum number of parameters that would fit data for all cells in all states of charge. Performance analysis was accomplished by comparing a) the individual parameters, b) lumped parameters such as the RC time constants and RLC Q factors, and c) features of the cycling potential such as the discharge end voltage (DEV). Use of a reference electrode with EIS has been shown to be highly dependent on electrode placement. Battery EIS also faces a challenge in that electrodes may have similar capacity, while ideally the counter electrode should be non-limiting. We will address these factors and discuss steps taken to obtain repeatable data free of inductive loops caused by capacitive coupling with current collectors and electrode tabs.


2019 ◽  
Vol 15 (3) ◽  
pp. 173-188 ◽  
Author(s):  
Eduard Bentea ◽  
Erica A. K. Depasquale ◽  
Sinead M. O’Donovan ◽  
Courtney R. Sullivan ◽  
Micah Simmons ◽  
...  

iPSCs from a schizophrenia patient harboring a mutation in the DISC1 gene show large scale abnormalities in serine/threonine kinase activity.


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