Fluid flow in scWesterm microwells was modeled in COMSOL Multiphysics 4.2a (Supplementary Note 1, Supplementary Fig. 3 ). Bulk flow above microwells was simulated as steady-state laminar flow of water in a square channel of crossection 100 × 100 µm. The top and side walls of the channel were set to a slip boundary condition. The bottom wall of the channel and the microwell walls were set to no-slip. Inlet velocity was set to 0.0087 m/s to achieve a maximum bulk flow velocity of 0.013 m/s. Outlet pressure was set to 0. Microwell recirculation flow was visualized by the particle tracing module in COMSOL.
Multiphysics 4.2a
Manufactured by Comsol
Sourced in United States
Multiphysics 4.2a is a comprehensive software package for modeling and simulating multi-physics problems. It provides a platform for integrating different physical phenomena, enabling users to analyze complex systems that involve interactions between various physical processes.
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Lab products found in correlation
11 protocols using multiphysics 4.2a
1
Microfluidic Flow Simulation in COMSOL
2
FEM Simulation of Cell Culture Chamber
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FEM was performed through commercially available software (COMSOL Multiphysics 4.2a, Stockholm, Sweden). The geometry characterizing the cell culture chamber [Fig. 2(a) ] was divided into three domains: (i) the fluid domain, representing the culture medium, (ii) the electrodes, and (iii) the insulator comprising the PDMS frame and posts. For the medium, electrodes, and PDMS domain, the electrical conductivity of 1.5 S/m, 1.32 × 106 S/m, and 10−22 S/m and the relative permittivity of 80.1, 1.005, and 2.63 were defined.43 (link) Numerical simulations were performed exploiting the electric current interface, assuming DC and steady state conditions to solve Maxwell's equations.38,49 (link) Insulation boundary conditions were applied to PDMS surfaces; stainless steel electrodes were set to ground and 0.8 V to simulate the application of a 5 V/cm electric field. The electric field and the current density distribution were visualized by plotting colorimetric maps, while the accurate evaluation of the intensity of the generated electric field and current density was investigated by plotting the 1D graph at different quotes, corresponding to the different height of the microtissues.
3
Microfluidic Flow Simulation in COMSOL
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Fluid flow in scWesterm microwells was modeled in COMSOL Multiphysics 4.2a (Supplementary Note 1, Supplementary Fig. 3 ). Bulk flow above microwells was simulated as steady-state laminar flow of water in a square channel of crossection 100 × 100 µm. The top and side walls of the channel were set to a slip boundary condition. The bottom wall of the channel and the microwell walls were set to no-slip. Inlet velocity was set to 0.0087 m/s to achieve a maximum bulk flow velocity of 0.013 m/s. Outlet pressure was set to 0. Microwell recirculation flow was visualized by the particle tracing module in COMSOL.
4
Computational Modeling of Dialyzer Behavior
5
Calcite Crystal Surface Stress Modeling
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The calculations were performed with COMSOL Multiphysics 4.2a. Each element of the elasticity tensor of calcite was rotated to the crystallographic orientation of a crystal with a (012) nucleation plane. Surface stress was modelled by applying a 1-nm thick membrane, which was then uniformly contracted on each crystal facet (Supplementary Fig. 3 ).
6
Finite Element Analysis of Phononic Structures
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COMSOL Multiphysics 4.2a was used to conduct the finite element analysis for simulating the dispersion relationship of phononic configurations, elastic waves propagating in soft matrix, and the structure deformation of DHEMs under strain. Low strain and low linear deformation were also ensured in most simulation cases. The type of the mesh element is free triangular and the maximum size is 0.3 mm (∼ /10) in the simulation of elastic waves concentration. A Neo-Hookean hyperelastic model is utilized to simulate large structure deformation of the DHEM. Related parameters are shown in the supplementary data.
7
Finite Element Analysis of Elastic Wave Propagation
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COMSOL Multiphysics 4.2a was used to conduct the finite element analysis for simulating the elastic waves propagating in SBMC. The type of the mesh element is free triangular and the maximum size is 0.3 mm (about λ/10) in the simulation. The linear elastic model (the isotropic damping is set to be 0.01) is utilized to simulate elastic waves propagating under different conditions. The simulation model and boundary condition settings are shown in Figure S6 (Supporting Information). For material parameters, many material configurations were examined in order to balance the enhancement, working frequency band, flexibility of the device, and sample size. Finally, a urethane rubber (PMC 780, smooth‐on) was chosen as the matrix. The mechanical property of PMC 780 by uniaxial tensile tests was obtained. First, two flat specimens with shoulders (used with serrated grips) were prepared (Figure S4a , Supporting Information). As shown in Figure S4b (Supporting Information), the data within the “small deform region” were picked out and used to establish a fitting profile. The slopes of fitting curves show Young's modulus of standard samples.
8
Microfluidic Flow Simulation in COMSOL
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Fluid flow in scWesterm microwells was modeled in COMSOL Multiphysics 4.2a (Supplementary Note 1, Supplementary Fig. 3). Bulk flow above microwells was simulated as steady-state laminar flow of water in a square channel of crossection 100 × 100 µm. The top and side walls of the channel were set to a slip boundary condition. The bottom wall of the channel and the microwell walls were set to no-slip. Inlet velocity was set to 0.0087 m/s to achieve a maximum bulk flow velocity of 0.013 m/s. Outlet pressure was set to 0. Microwell recirculation flow was visualized by the particle tracing module in COMSOL.
9
Fluorescence Imaging and Electrical Simulations
10
3D Surface Reconstruction of Branched Epithelium
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The surface of the branched epithelium at a snapshot in time (24 hrs after branch induction) was reconstructed from 3D confocal stacks of LifeAct-GFP-transduced cells. Image segmentation was performed manually in ImageJ to define the cellular portion of the 3D stack. A 3D surface was subsequently generated using Amira® (Visage Imaging) and converted to a parasolid object using Mesh2Solid (Sycode). The solid was imported into Comsol Multiphysics 4.2a (Comsol Inc.) and enclosed within a second computational domain of cylindrical geometry (2 mm in height and diameter) representing the collagen gel. A quadratic tetrahedral finite element mesh of the epithelial surface and the surrounding gel was generated.
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