Multiphysics 5

Manufactured by Comsol

Sourced in United States, Sweden

COMSOL Multiphysics 5.5 is a powerful software package for modeling and simulating physics-based problems. It provides a comprehensive environment for applying numerical methods to a variety of engineering and scientific applications. The software supports multiple physics interfaces, allowing users to couple different physical phenomena within a single simulation.

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Lab products found in correlation

Multiphysics, by Comsol (6 mentions) Matlab, by MathWorks (5 mentions) Ds1102, by Rigol (3 mentions) Multiphysics software, by Comsol (3 mentions) Originpro 2017, by OriginLab (2 mentions) Ac dc module, by Comsol (2 mentions) Meshlab 2016, by Autodesk (2 mentions) Meshmixer 3, by Autodesk (2 mentions) 3dsmax software, by Autodesk (2 mentions) Fusion 360, by Autodesk (2 mentions) Lsm 700, by Zeiss (2 mentions) Abaqus, by Dassault Systèmes (1 mentions) Geforce gtx 2060 gpu, by NVIDIA (1 mentions) Upright microscope, by Nikon (1 mentions) Neuroline 700, by Ambu (1 mentions) Geforce gtx 1050 ti, by NVIDIA (1 mentions) R core tm i7 8700 cpu, by NVIDIA (1 mentions) Multiphysics 4.3a, by Comsol (1 mentions) Multiphysics version 5, by Comsol (1 mentions) Borofloat, by Schott (1 mentions)

434 protocols using multiphysics 5

Thermal Functionalities of Printable Metamaterials

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The thermal functionalities of robustly printable freeform thermal metamaterials are verified by the FEA simulation commercial software COMSOL Multiphysics 5.5. To ensure the model consistency, the interface COMSOL Multiphysics 5.5 with MATLAB R2017a is used to create the simulated model. In COMSOL Multiphysics 5.5, about 3.5 million triangular meshes are used to divide the simulated region freely. Later, the boundary conditions are imposed and the free solver in COMSOL Multiphysics 5.5 is used to solve the steady-state temperature field distribution which can be seen in Fig. 3(m)–(o). For transient cases, the densities and heat capacities of the two materials are set as: H13 (ρ = 7850 kg m⁻³, c_p = 650 J kg⁻¹ K⁻¹); PDMS (ρ = 970 kg m⁻³, c_p = 1460 J kg⁻¹ K⁻¹); ACC AS1802 (ρ = 1060 kg m⁻³, c_p = 1615 J kg⁻¹ K⁻¹). The simulated results of transient cases are shown in Supplementary Fig. 7(a).

Sha W., Xiao M., Zhang J., Ren X., Zhu Z., Zhang Y., Xu G., Li H., Liu X., Chen X., Gao L., Qiu C.W, & Hu R. (2021). Robustly printable freeform thermal metamaterials. Nature Communications, 12, 7228.

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Finite Element Modeling of Cortical NTIRE Ablation

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Finite Element Method calculations were performed with the COMSOL Multiphysics 5.5 software. The physic used was “Electrical Current.” A custom mouse brain mesh model was designed on Blender software and then imported in COMSOL Multiphysics 5.5. The distance and the voltage applied between the electrodes were taken in account to recreate as closely as possible the experimental conditions of the Cortical NTIRE ablation, 245 V between ≃ 1.4 mm. All plots were made and exported with the built-in tool of COMSOL Multiphysics 5.5 (Supplementary Figure 3).

Acerbo E., Safieddine S., Weber P., Botzanowski B., Missey F., Carrère M., Gross R.E., Bartolomei F., Carron R., Jirsa V., Vanzetta I., Trébuchon A, & Williamson A. (2021). Non-thermal Electroporation Ablation of Epileptogenic Zones Stops Seizures in Mice While Providing Reduced Vascular Damage and Accelerated Tissue Recovery. Frontiers in Behavioral Neuroscience, 15, 774999.

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Optimizing Photonic Bandgap Structures

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All numerical band dispersions are obtained by using a finite element method-based software (COMSOL Multiphysics 5.5, eigenfrequency solver). Bulk dispersion is simulated by using a unit cell with Bloch boundary conditions along all boundaries. For surface dispersion, a supercell that consists of 9 unit cells is used with Bloch boundary conditions along the x- and y-axes and perfectly matched layer conditions along the z-axis with air spacing.
The unit cell design is optimized to maximize the relative bandgap, which is defined as a ratio of bandgap width to the bandgap center frequency. More specifically, the relative bandgap is obtained by g = (f_up − f_down)/(f_up + f_down) × 2 for f_up being the minimum frequency of the third band and f_down being the maximum frequency of the second band. In a particle swarm optimization, five parameters, a_z, L, L_z, w, and D, are optimized to yield minimum f = 1/g² by linking COMSOL Multiphysics 5.5 and MATLAB via Livelink for MATLAB. Bulk dispersion of a unit cell along Γ-M-N-Z-Γ-M is simulated iteratively using updated geometrical parameters. The iteration is repeated a hundred times with ten populations per iteration.

Kim M., Wang Z., Yang Y., Teo H.T., Rho J, & Zhang B. (2022). Three-dimensional photonic topological insulator without spin–orbit coupling. Nature Communications, 13, 3499.

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Finite Element Modeling of Temperature in Embryo Samples

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A Finite Element Method (FEM) is used to simulate the temperature throughout the models, solving Equations ( 4)-( 13). Employing COMSOL Multiphysics 5.5, adaptive meshes are constructed for each given geometry to balance accuracy and computational cost. The computational model discretises the domain into individual elements, the temperature of which can be defined and calculated at each time point of interest. A mixture of triangle and tetrahedral elements are used, as determined by the solver. A 'fine' element discretisation is employed, which uses a minimum of 2182 tetrahedral elements and 1320 triangular elements. The temperature is calculated over 2 seconds at 0.02 second intervals, and the simulation run time is only a few seconds.
The average temperature within the samples is calculated as a volume average in COMSOL Multiphysics 5.5, by integrating the temperature within the samples, and dividing by the sample volume [11] . Such volume integrals can be expressed in terms of the domain volume V as [9] u(t) = u(x, y, z, t)dV dV .
The code used in this work is available on Github, https://github.com/OstlerT/MultipleEmbryoModels.

Ostler T., Woolley T.E., Swann K., Thomson A., Priddle H., Palmer G, & Kaouri K. (2021). Vitrifying multiple embryos in different arrangements does not alter the cooling rate. Cryobiology, 103.

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Coupled Fluid-Solid Piezoelectric Pump

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The boundary conditions are summarized as:

First, the voltage is applied to the piezoelectric material, and the displacement and velocity are calculated.

The velocity of the piezoelectric material, which is calculated in the previous step, is used as the inlet boundary condition at the interface of the fluid and solid.

At the inlet and outlet of the pump, the outlet boundary condition is considered, which results in free movement of water to inside and outside of the channel.

The valves are elastic materials, which are assumed to be fixed at the walls.

The drag force due to the velocity and pressure field are considered as external forces in the governing equations related to solid mechanics. The drag force is calculated using the software COMSOL Multiphysics 5.5, and the equations are solved using the fully coupled algorithm in COMSOL Multiphysics 5.5.

The valves and other boundaries of the channel are considered as wall boundary condition. Moreover, it is worthwhile to state that ALE (Arbitrary Lagrangian and Eulerian) moving mesh is applied to the fluid domain to track the displacement of the valves.

Moreover, the properties of the water are obtained from the COMSOL Library.

Aboubakri A., Ahmadi V.E, & Koşar A. (2020). Modeling of a Passive-Valve Piezoelectric Micro-Pump: A Parametric Study. Micromachines, 11(8), 752.

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Modeling Microfluidic Oxygen Dynamics

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Finite element software COMSOL Multiphysics 5.2 was used to mathematically study the hydrodynamic properties and oxygen concentration in the microfluidic devices. Two physics modules, Laminar Flow (spf) and transport of diluted species (tds) in COMSOL Multiphysics 5.2 were adopted and three dependent variables—velocity u, pressure p, and molar concentration of oxygen c ‐ were considered. A time‐dependent simulation during a period of 24 hr at 10 min intervals was built, and the Navier‐Stokes and the continuity equations were coupled with transport theory including diffusion and convection to solve the problem. The following boundary conditions were implemented: (a) specific inlet flow rate and no pressure at the outlet; (b) nonslip condition at the chamber/channel wall; (c) incompressible fluid; (d) specific oxygen concentration on the surfaces exposed to the atmosphere (external surface of the device, inlet). The diffusion coefficients and initial oxygen concentration are listed in Table 1 (values referred to a temperature of 25°C; Evenou, Fujii, & Sakai, 2010).

Totaro D., Rothbauer M., Steiger M.G., Mayr T., Wang H., Lin Y., Sauer M., Altvater M., Ertl P, & Mattanovich D. (2020). Downscaling screening cultures in a multifunctional bioreactor array‐on‐a‐chip for speeding up optimization of yeast‐based lactic acid bioproduction. Biotechnology and Bioengineering, 117(7), 2046-2057.

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Computational Modeling of Droplet Reactions

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COMSOL Multiphysics 5.5 and 5.6 were used to compare computational transients to experimental data. When fitting experimental data to simulation to find the k_c,app, the experimental data were adjusted such that the foot of the wave overlaid the simulation before adjusting the k_c parameter. Importantly, in these simulations, k_c and the droplet geometry (observed in optical microscopy) are the only adjustable parameters. A detailed discussion on the performed simulation is provided in the Supporting Information, including information on the important computational parameters of the model and Figure S5. The finite element model accounts for changes in the geometry that may give rise to changes in the mass transfer coefficient. All reaction rates reported were evaluated using a finite element model that accounts for each droplet’s geometry. In these simulations, the only adjustable parameter is the reaction rate.
COMSOL Multiphysics 5.6 was also used to simulate the effect of reactant adsorption to the droplet boundary. This model introduces adjustable parameters to the simulation, all of which are discussed in detail in the Supporting Information (Figures S6 and S7).

Vannoy K.J, & Dick J.E. (2022). Oxidation of Cysteine by Electrogenerated Hexacyanoferrate(III) in Microliter Droplets. Langmuir : the ACS journal of surfaces and colloids, 38(39), 11892-11898.

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Optimizing Steak Marination through Simulation

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The edges of the steak were identified by image binarization, the code for the cutting action on the meat in the Gaidao process was written in COMSOL Multiphysics 5.6 with MATLAB and the depression on the surface of the steak constructed by the cutting action was set as the new inflow surface for the marinade. The simulated marination time of the steak was 36 h. After calculation, the distribution of marinade concentration in the internal section of the simulated marinated beef model and the point concentration data of some 3-dimensional intercept points were derived as a reference, and the effect of this Gaidao model was evaluated by achieving 70% marinade concentration and above as a passing standard. Subsequently, code was written in MATLAB to continuously vary the depth, length and number of cutting surfaces, using the incremental and uniformity of the marinade as the evaluation criteria. The model that achieves the required marinade concentration and has the smallest cutting surface area is finally selected as the most optimal model.

Li W., Shi Y., Huang X., Li Z., Zhang X., Zou X., Hu X, & Shi J. (2024). Study on the Diffusion and Optimization of Sucrose in Gaido Seak Based on Finite Element Analysis and Hyperspectral Imaging Technology. Foods, 13(2), 249.

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Modeling Oxygen Dynamics in Intestinal Organoid-Embedded Microfluidic Chips

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A finite element method based on COMSOL Multiphysics 5.6 (COMSOL Inc.) was used to predict the oxygen concentration of intestinal organoid-embedded Matrigel in the chip. To compute the process, transport of diluted species with the time-dependent study was used according to Fick's second law, as seen in Eqn (2):

Equation 2.

where

J_{i} = - D_{i} \nabla c_{i}

; c, concentration (mol/m³); t, time (s); J, flux (mol/m²s);

u

, flow velocity (m/s); R, volumetric rate of reaction (mol/m³s); and D, diffusion coefficient (m²/s). The flow channel of culture medium, artificial vessel, and Matrigel-embedded chamber were drawn based on the actual dimensions. The constants used in the COMSOL simulation were listed in Tables S1 and S2, in which the oxygen diffusion coefficients in the culture medium, artificial vessel, and Matrigel were 2.7 × 10⁻⁹ m²/s, 1.8 × 10⁻⁹ m²/s, and 1.7 × 10⁻⁹ m²/s, respectively [42 ,43 (link)]. To confirm the simulation results, the oxygen concentration in the chip was measured with an oxygen meter (Leici, China).

Huang J., Xu Z., Jiao J., Li Z., Li S., Liu Y., Li Z., Qu G., Wu J., Zhao Y., Chen K., Li J., Pan Y., Wu X, & Ren J. (2023). Microfluidic intestinal organoid-on-a-chip uncovers therapeutic targets by recapitulating oxygen dynamics of intestinal IR injury. Bioactive Materials, 30, 1-14.

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Modeling Zinc Electrodeposition Dynamics

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Three-dimensional (3D) models were established with COMSOL (COMSOL Multiphysics 5.6) electrochemistry module to understand the dynamics of Zn electrodeposition processes. Concretely, the electrochemistry was simulated using the Tertiary Current Distribution module (Nernst-Planck Equations interface), where the Deformed Geometry node kept track of the deformation of localized geometry structure during Zn deposition. Nernst-Planck equation was used to describe the diffusion and migration of ions in the electric field:

J_{Zn} = - D_{Zn} \nabla c_{Zn} - z_{Zn} u_{Zn} F c_{Zn} \nabla ϕ_{l}

where

J_{Zn}

denotes the Zn²⁺ flux,

D_{Zn}

the diffusion coefficient,

c_{Zn}

the electrolyte concentration,

z_{Zn}

the charge number,

u_{Zn}

the electric mobility, and

ϕ_{l}

the electrolyte potential. The boundary condition for Zn deposition was given by Butler-Volmer equation, and the local current density was calculated as follows:

i_{Zn} = i_{0} [\exp (\frac{α_{a} F η}{R T}) - \exp (- \frac{α_{c} F η}{R T})]

where

i_{0}

represents the exchange current density, α the charge transfer coefficient, η the overpotential, and F/RT the Nernst parameter. The related physical parameters were defined and listed in Supplementary Table 4.

Zhao Y., Guo S., Chen M., Lu B., Zhang X., Liang S, & Zhou J. (2023). Tailoring grain boundary stability of zinc-titanium alloy for long-lasting aqueous zinc batteries. Nature Communications, 14, 7080.

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