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895 protocols using multiphysics

1

Numerical Simulation of Absorber Layers

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In numerical simulations, the CST Studio Suite was adopted for fast and efficient computation of the individual layer of the absorber, thanks to the finite-difference time-domain method. The optimization toolbox and parametric-scanning function of CST Studio Suite can be used to find the best parameters. Another commercial software we used is COMSOL Multiphysics (Radio Frequency Module) based on the finite element method. The COMSOL Multiphysics was responsible for the calculation of reflection and diffraction for the hierarchical structure. Both software support the lumped elements used to model the loaded resistors. For the absorption frequency band without diffraction (in the subwavelength region a1<λ ), there was no difference whether we used PEC and PMC side boundaries or the Floquet periodic boundary conditions to guide the plane wave with normal incident angle. However, for the case involving diffraction orders and oblique incidence, only the Floquet periodic boundary condition was appropriate, and the diffraction was calculated by using only COMSOL Multiphysics. The mesh size was set to be smaller than 1/6 wavelength in order to ensure accurate outcomes.
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2

Numerical Solution of Model Equations

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Figure 1 shows the steps taken during the numerical solution of the model equations presented in previous sections. All equations were implemented using the COMSOL Multiphysics TM v4.3b interface, except for the equations used to calculate the relative hydraulic conductivity in the presence of biofilm (k r ) and the volumetric water content (θ) (Eqs. 10 and 11), that were implemented in MATLAB R . The exchange of data between COM-SOL Multiphysics TM and MATLAB R is made at each numerical iteration using the Livelink for MATLAB R COMSOL Multiphysics TM module.
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3

Glucose Diffusion in Hydrogels

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Glucose diffusion coefficients in alginate and fibrin hydrogels were experimentally measured. Hydrogels were formed by pouring alginate and fibrin in a CaCl2 and thrombin bath, respectively. Then, hydrogel beads were soaked in 4 mL of deionized water containing glucose at the initial concentration of 200 mg/mL and 1 mL of solution was sampled every hour for 8 h. Glucose absorbance was red at 193 nm by using a spectrophotometer and the glucose diffusivity within the two hydrogels was calculated through the best fitting of the data obtained from the experimental release studies. Briefly, a simulation of the mass transport process occurring between the medium and the hydrogels was performed by employing the Transport of the diluted species (TDS) module of Comsol Multiphysics (COMSOL AB, Stockholm, Sweden) in order to fit the raw data (not shown) and thus to get the optimal glucose diffusion coefficient by comparing the two resulting curves. The implemented model in Comsol Multiphysics was based on the second Fick law assuming that only the diffusion process in the bath could occur: δcδt+·(J)=0 
where c is the component concentration and J is the mass diffusive flux vector, defined by the Fick law as: J=D c 
where D is the diffusion coefficient of the metabolite.
Experiments were performed in triplicates and the results were expressed as mean and standard deviation.
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4

Optical Simulations and Quantum Cascade Device Characterization

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The optical simulations were carried out with the commercial simulation tool COMSOL Multiphysics ( www.comsol.com). For gold and SiNx, we used a refractive index at λ=6.5 μm of n=3.3–46.7i and n=1.85–0.003i extrapolated from literature21 (link)32 , respectively. The optical properties of the semiconductor materials were calculated using the Drude model. The evanescent decay length was extracted from the numerical simulations via fitting to an exponentially decaying function. The propagation length in Fig. 2d was extracted from the imaginary part of the modal index, as shown in Fig. 2b,c. The absorption coefficient α and the extraction efficiency pe of the QCD were calculated using a single-particle Monte–Carlo transport simulator for quantum cascade devices33 , resulting α=200 cm−1 and pe=43% at room temperature, respectively. With COMSOL Multiphysics, we then obtained an absorption efficiency η for the 200-μm long ridge detector of ~\nη=77% (absorbed power, which passed the detector facet).
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5

Eigenvalue Equation for Elastic Wave Propagation

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We have numerically solved the eigenvalue equation derived from linear Cauchy elasticity23 for the displacement vector field uk,i(r) with band index i at wave vector k and for the angular frequency ωi(k) E21+ν12νuk,i(r)+E21+ν2uk,i(r)=ρωi2(k)uk,i(r) by using the commercial software Comsol Multiphysics, its MUMPS solver, Floquet-Bloch periodic boundary conditions corresponding to the three-dimensional geometry shown in Fig. 3 for all three spatial directions, and traction-free boundary conditions for all interfaces to voids (air or vacuum). E is the Young’s modulus, ν the Poisson’s ratio, and ρ the mass density of the constituent material. The geometry shown in Fig. 3 has been meshed by about 100 thousand tetrahedra to achieve convergence of the results. The energy flux vector averaged over one temporal oscillation period has been evaluated by the formula Ii(k)=12ReEν1+ν12νuk,irduk,i*rdtE21+νuk,irduk,i*rdt+uk,irduk,i*rdt, where * denotes the complex conjugate. In Fig. 4b, the z -component of this vector, Iz , is plotted. This component has been obtained directly from the Solid Mechanics Module of Comsol Multiphysics.
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6

Pressure Drop Analysis of 3D-CC

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The pressure drop profile along the channel of the 3D-CC for multiplexed analysis of Newtonian fluids was analyzed using COMSOL Multiphysics (COMSOL, Burlington, MA, USA) to verify the design criterion for the pressure-drop ratio between the capillary and fluidic chamber. The wall shear rate and pressure drop along the length of each capillary of the 3D-CC for analysis of a non-Newtonian fluid were also analyzed using COMSOL Multiphysics to determine capillary lengths to achieve desired shear-rate conditions. Three-dimensional finite element models were created in the same dimensions as the 3D-CCs and solved using the incompressible Naiver-Stokes equation. The inlet boundary condition was set to a constant pressure, while the outlet boundary condition was set to atmospheric pressure. All other boundary conditions were set with no-slip boundary conditions.
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7

3D Heat and Flow Simulation in Mini-Channels

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In the current work, the Comsol Multiphysics the program was used to simulate and solve three-dimensional heat and flow problems in mini channel.
A CFD module in Comsol Multiphysics built upon a finite element method with a Galerkin aapproach to solve the partial differential equations governing the problem domain (continuity, momentum and energy for solid and fluid domains).
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8

Modeling Membrane Invagination Dynamics

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The coupled system of the reaction-transport equations [Eqs (S1), (S1*), and (S1**)], force-balance equation [Eq (S2)], and Eq (1) was solved using a moving-mesh solver of COMSOL Multiphysics, a software package for solving spatial multiphysics problems on finite element meshes (COMSOL Multiphysics, 2015 ). Because the invaginations were modeled as axially symmetric, computations were simplified by reducing the original three-dimensional (3D) problem to an equivalent 2D model formulated in (r, z) coordinates. Mathematical details of the model and its numerical solution are discussed in the Supplemental Material [Eqs (S1)–(S4)]. More details about the model and its numerical solution can be found in the supplemental material of (Nickaeen et al., 2019 (link)).
The supplemental COMSOL simulation file, Figure2.mph, includes all details of the model implementation with parameters yielding the results of Figure 2. Using this file, one can reproduce other results reported in this study by running it in the COMSOL Multiphysics environment with accordingly modified parameters.
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9

Thermal and Electrical Simulations of CNT-PP Composites

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Heat conduction simulations based on the finite element method (FEM) were performed using COMSOL Multiphysics software. The model structure for the FEM simulation was a multilayer consisting of a CNT film with a thickness of 20 µm and a PP film with a thickness of 200 µm. The thermal conductivity of the CNT film and PP film were 1.2 and 0.2 W/mK, respectively. The laser was converted to heat in the CNT film and the heat was applied to the CNT and PP film. In this simulation, instead of a laser, Gaussian heat flux was applied to the CNT film. The standard deviation of the Gaussian distribution was one-third of the spot diameter (1340 μm).
A Joule heat simulation based on FEM was also performed using COMSOL Multiphysics. Fig. S2 shows the simulated device structure consisting of the PP films (height 16 mm, width 65 mm) and MWNT wirings. MWNT wiring with resistances of 1 and 20 kΩ/cm in a single wire was fabricated by adjusting the width of the wiring.
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10

Computational Simulation and SERS Spectroscopy

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Computational simulation was conducted using COMSOL Multiphysics. A model that can calculate the three-dimensional electromagnetic field was established. The physical field interface is electromagnetic wave (frequency domain). This work takes steady-state as its object of study and simulates the electric field distribution. At last, the model specific parameters are built using COMSOL Multiphysics (Supplementary Information Table S1). All SERS spectra were recorded using a Raman spectrometer (Horiba IHR550, Horiba Trading Co., Ltd., Shanghai, China.) Microscope (Olympus IX73, Olympus Corporation, Tokyo, Japan). All experimental data were excited with laser of 632.8 nm (MELLES GRIOT 25-LHP-991-230, CVI Melles Griot, Albuquerque, NM, USA), and the integration time was 20 s. SEM images were recorded with field-emission SEM (Mira3 LMH, Tscan).
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