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Multiphysics version 5

Manufactured by Comsol
Sourced in Sweden, United States

COMSOL Multiphysics version 5.2 is a simulation software that allows users to model and solve a wide range of scientific and engineering problems. It provides a platform for coupling different physics interfaces and solving multiphysics problems numerically.

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41 protocols using multiphysics version 5

1

Finite-Element Simulation of Skin Hydration

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For the numerical computation of the above-listed models, the finite-element method (FEM)-based simulation software COMSOL Multiphysics® version 5.6 (COMSOL Multiphysics GmbH, Zurich, Switzerland) was used.
As explained in Section 2.2.1, the dielectric parameters for the SC layer are interpolated with Equation (16). In [22 (link)], the epidermis/dermis layer was approximated by blood and the hypodermis by infiltrated fat. The dielectric parameters for these two layers were taken from [7 (link)], as listed in Table 2.
For the evaluation of the water concentration in the SC and the reproduction of the measurements in [21 (link)], the dynamics of water transport in the SC model was used (1)–(6). The SC was initialized as fully hydrated and exposed to a relative humidity of 30% until equilibrium was reached. The 30% of relative humidity was chosen to simulate a realistic dry environment. The reached equilibrium then served as initial SC hydration for the simulation of the hydration boundaries and other hydration levels, as investigated in Section 3.1. Table 3 summarizes the initial conditions and boundary conditions.
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2

Nutrient Supply Analysis in Cultivation Chambers

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Computational fluid dynamics simulations (CFD) were performed to analyze nutrient supply inside the cultivation chamber designs as described before13 (link),27 (link). For the CFD simulations COMSOL Multiphysics Version 5.6 (COMSOL AB, Sweden) was applied. Glucose concentration profiles during MSCC, assuming a steady state with 181 cells inside the chamber with a constant glucose uptake rate of 3800 nmol per 106 cells and day, were simulated under consideration of the respective cultivation chamber geometry. Cellular uptake was assumed to be homogeneously distributed over the whole cultivation chamber. Glucose concentration inside the supply channels was set to 45 mol m−3.
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3

In silico Fluid Flow Modeling of 3D Scaffold

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For the estimation of fluid flow pattern and its mechanical effects, in silico
modelling was undertaken using COMSOL Multiphysics version 5.6 (COMSOL AB,
Sweden). Briefly, the geometry of the culture chamber including the scaffolds
and the rectifiers was reproduced computationally. The mechanical properties of
the culture medium were assumed to be comparable with water. The scaffolds were
assigned as porous domains so that the Darcy’s law was applied to avoid
excessive computational burden. Porous properties were parameterised using data
previously obtained by microCT analysis of the scaffold, including porosity
91.708% and permeability 5.80216e-09 m2.29 (link)
From the inlet to the outlet, a fully developed flow was applied at a
flow rate of either 0.8 ml/min (FL-L) or 1.6 ml/min (FL-H). Non-slip wall
condition was applied to the boundary condition of the fluid paths (i.e. metal
parts, silicon tubes). As a representative for visualisation of shear stress
within the complex 3D structure, the geometry of the scaffold was obtained by
microCT (Skyscan 1172, SkyScan, Belgium) primarily and converted into an
.stl file. A cube with a diameter of 1.2 mm was dissected
from the middle of the geometry to make it possible to proceed with computation.
The dissected part was assumed to be located at the front row of the scaffold
pile.
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4

Chiral Gold Meta-atom Optical Simulation

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All numerical simulations were performed using the wave optics module in COMSOL Multiphysics version 5.6, where we modeled one glass-gold-air-gold unit cell. The corners of small and large nanobricks are rounded with radii of 30 and 15 nm, respectively. Periodic boundary conditions were applied in both the x and y directions, and perfectly matched layers were used in the z direction to truncate the simulation domain. To obtain complex reflection coefficients in both linear and circular polarization bases, x- and y-polarized light sources were incident onto the chiral gold meta-atom from the upper glass at normal incidence. The glass layer was regarded as a lossless dielectric with a constant refractive index of 1.46, and the permittivity of gold was interpolated from experimental values (36 ).
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5

Finite Element Modeling for Imaging Sensitivity

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The simulative analysis by means of FEM is pivotal for the imaging method. It determines the spatial sensitivity distribution. The simulations were performed with COMSOL Multiphysics version 5.6 (Comsol Multiphysics GmbH, Göttingen, Germany). We used the Alternating Current/Direct Current (AC/DC) and the Computer-Aided Design (CAD) Import module for the simulations. All simulations were conducted on a simulation PC (i9 12900K, 96 GB RAM, RTX3080 Ti).
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6

Optical Simulation and Swelling Analysis

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Numerical simulations were performed using the commercially available finite-difference time-domain (FDTD) solver (Lumerical, Ansys). The measured refractive index of PVA was used throughout. All color conversions and calculations were performed using the open-source package ‘Colour’, in Python, using the CIE 1931 2˚ standard observer and the D50 illuminant. Conversion efficiencies of the meta-atoms were calculated using periodic boundary conditions in the x- and y-directions, with perfectly matched layers in the z-direction. The finite element method solver, COMSOL Multiphysics version 5.6 was used for the swelling simulations.
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7

Optoelectrokinetic Phenomena in REP Chip

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COMSOL Multiphysics (Version 5.3, Burlington, MA, USA) simulations based on the AC/DC, Microfluidics, and Heat Transfer modules were performed to investigate the optoelectrokinetic phenomena (i.e., temperature gradient, electroosmosis, dielectrophoresis, and electrothermal vortex) induced by the REP effect and to explore their effects on the motion and velocity of the particles. The simulations considered the entire geometry of the REP chip and hence a 3D model was used. The colloidal fluid was assumed to be Newtonian and the Brownian motion of the particles was ignored in order to simplify the simulation process. The physical and electrical properties of the conductive fluid (DI water) and particles (polystyrene beads) were listed as Table 1 [21 (link),36 (link),37 (link)]. Note that all the internal boundaries were modelled with a no-slip condition. All the external boundaries except the top and the bottom ITO glass plates were modelled with a constant temperature (28 °C) condition. Furthermore, the laser power intensity was set as 75 W/cm2 and the amplitude and driving frequency of the AC electric field were set as 35 VPP and 25 kHz, respectively.
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8

Finite Element Modeling of Drying Process

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The mathematical model was solved using the finite element method using a commercial computational code (COMSOL Multiphysics ® version 5.3). The Equations 1 (liquid water) and 2 (vapor water) were solved using Chemical Reaction Engineering Module with the interface Transport of Dilute Species, and the Heat Transfer Module with the interface Heat Transfer in Solids was used to solve the Equation 5 (thermal energy).
Triangular elements whit second order interpolation function were used for discretization. As showed in Figure 3, mesh elements of 0.36 mm (inside the domain), 0.18 mm (at surface domain) and 'boundary layers mesh' were used, resulting in a mesh with 8,316 elements and 31,751 degrees of freedom. Direct resolution solver PARDISO solved the linear systems, and the transient problem was solved with the Backward Differentiation Formula (BDF) with a maximum time step restriction of 0.5 s. T he numerical resolution was carried out in a workstation Intel Xeon E3-1240 3.5 GHz with 16 GB of RAM memory (ThinkStation P310 Signature Edition, Lenovo), taking an average time of 10 hours to simulate a drying process of 20 minutes.
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9

Optical Properties of Plasmonic Nanogap Cavities

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The optical properties of the NPoM system were simulated by using the FEM to solve Maxwell’s equations (COMSOL Multiphysics, Version 5.4). The Au NP was modeled as an 80-nm-diameter sphere with a flat lower facet 20 nm in diameter. The permittivity of Au was modeled by a 2-pole Lorentz–Drude permittivity ε(r;ω)=ε0ε(1i=12ωp,i2/(ω2ω0,i2+iωγi)) , where ε =  6, ωp,1 = 5.37 × 1015 rad/s, ω0,1 = 0 rad/s, γ1 = 6.216 × 1013 rad/s, ωp,2 = 2.2636 × 1015 rad/s, ω0,2 = 4.572 × 1015 rad/s, and γ2 = 1.332 × 1015 rad/s. The gap spacer was modeled as a 1-nm-thick dielectric layer with refractive index 1.45, while the background material had a refractive index of 1.
In Fig. 1, a point electric dipole emitter was placed in a NPoM gap at different radial coordinates, and the simulations were carried at a wavelength of 660 nm. The plasmonic nanogap cavity modes (Fig. 2) were modeled as quasinormal modes (QNMs) described with complex eigenfrequencies. The QNMs were calculated by using QNMEig (36 ), an open-source program based on COMSOL. The far-field emission patterns of the emitter and of each QNM were obtained by using RETOP (52 ), an open-source code for near-to-far-field transformations of generalized guided waves. Finally, the out-coupling efficiency of each QNM was computed as the ratio of the far-field radiation power to the total dissipated power.
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10

Multi-scale Modeling of Transdermal Fentanyl

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COMSOL Multiphysics version 5.4 was used in this study to solve the diffusion process of fentanyl from the patch through the skin in the mechanistic model, the distribution of fentanyl in the human body in the pharmacokinetics model, and the drug’s effect in the pharmacodynamics model. The MUMPS (MUltifrontal Massively Parallel sparse direct Solver) was chosen as the solver scheme in this set of simulations. The partial differential equation (PDE) interface was implemented to solve the diffusion process of fentanyl in the mechanistic model. To take to account the distribution, elimination, and metabolization of fentanyl, the boundary ordinary differential equation (ODE) was used. In the pharmacodynamics model, the concentration of fentanyl in the effect compartment was calculated by the PDE interface, and the boundary probe calculated the drug’s effect. To apply the change of the patch and skin location during the therapy, the event interface was used. The population generation was done in RStudio by using the “mixAK” package. Analyzing the sample data, calculating the posterior distribution, generating the virtual patients’ characteristics, calculating the model parameters, and analyzing the result of digital twins are done in RStudio.
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