This repository is about a numerical calculation code package to study hydrodynamic and thermodynamic properties during respiration in various animal noses.
The easiest and simplest way to download all codes for modelling an animal nose is by 'nose-calculations' and run in Matlab.
- git clone https://github.com/hyejeonc/nose-calculations.git
- open 'Nose_t.m' file in Matlab.
- modify 'Nose_t.m' file, i.e., changing the ambient air temperature, you should modify
k = Parameters_animals(.. , .. , .. , .. , ... )
k = Parameters_animals(tempCond, noseGeom, Ns, Ns_art, N_cycle, r_shunt, d_mucus, factorRam, factorRij, factorFric, heatTranCoef, factor_rit, factor_rtot, rTide, rFreq, velLim)
% Important parameters are tempCond, noseGeom.
tempCond = the ambient air temperature [degree Celsius], for example, -30.
noseGeom = selection of nose geometry regarding each animal. Selected nose geometry should be added in 'Parameters_animals.m'.-
Depending on the parameters for each animal, modify 'Parameters_animals.m' file.
To add an additional ambient temperature condition, add elseif paragraph here:
k.xa = water mass fraction
which refers from the saturate water vapour in the air from https://www.engineeringtoolbox.com/moist-air-properties-d_1256.html
You can modify relative humidity by changing the multiplying factor, 0.9 (RH = 90 %).
elseif tempCond == -30
% Case 1
k.Ta = 273.15-30; % [K]
k.xa = 34.2/k.pa; % 38 * 0.9
Ma = k.xa.*ktp1.Mw(1)+0.79*(1-k.xa).*ktp1.Mw(2)+0.21*(1-k.xa).*ktp1.Mw(3);
k.wa = k.xa*ktp1.Mw(1)/Ma;To add geometrical information, you should add a length, cross-sectional area and perimeter information here: add another elseif paragraph to avoid a confusion.
elseif noseGeom == 2 % 2: arctic
k.L = 1e-3*(max(seal.xArcPosi) - min(seal.xArcPosi)); [m]
k.Area_a = 1e-6*flip(seal.xArcAreaWoshunt); [m^2]
k.Per_a = 1e-3*flip(seal.xArcPeri); [m]- Check the filename to save 'saveName.mat' file in 'Nose_t.m' file.
k.fileName = ['saveName','.mat'];- Run 'Nose_t.m' in Matlab.
- The output file 'saveName.mat' file is saved automatically after one iteration in the same directory of 'Nose_t.m'.
k = Parameters_animals(tempCond, noseGeom, Ns, Ns_art, N_cycle, r_shunt, d_mucus, factorRam, factorRij, factorFric, heatTranCoef, factor_rit, factor_rtot, rTide, rFreq, velLim)
Important parameters are tempCond, noseGeom.
tempCond = the ambient air temperature [degree Celsius], for example, -30.
noseGeom = selection of nose geometry regarding each animal. Selected nose geometry should be added in 'Parameters_animals.m'.The output file 'saveName.mat' consists of a struct named 'Nose' and this has the following information.
All is saved as [number of iteration * 2 * Nt, Ns] array.
For example, the solution (in the last iteration) of the temperature of the air subsystem during inhalation is: Nose.Ta(end-2*Nt:end-Nt,:)
For exhalation: Nose.Ta(end-Nt:,:)
Nose.Ta = temperature of air subsystem.
Nose.Tw = temperature of mucus subsystem.
Nose.Tit = temperature of interstitial tissue subsystem.
Nose.Tven = temperature of vein subsystem.
Nose.wa = water mass fraction in air subsystem.
Nose.x_a = water mol fraction in air subsystem.
Nose.Tart = temperature of artery subsystem.
Nose.M_tot = total mass of air
Nose.rho = density of air
Nose.rho_vap = density of water vapour in the air
Nose.rho_dry = density of dry air (density after excluding water vapour)
Nose.va = flow velocity of air
Nose.F_vap = mass flow rate of dry air
Nose.Fa = mass flow rate of air
Nose.R_aw = interface resistivity air-mucus (heat, Rqq)
Nose.R_wm = interface resistivity mucus-interstitial tissue (heat)
Nose.R_art = interface resistivity interstitial tissue-artery (heat)
Nose.R_ven = interface resistivity interstitial tissue-vein (heat)
Nose.R_mu = interface resistivity of water mass air-mucus (mass)
Nose.R_qmu = coupling coefficient (heat-mass)
Nose.h_a = enthalpy of air
Nose.h_wa = enthalpy of water vapour
Nose.h_w = enthalpy of liquid water
Nose.X_T = driving force of heat transport (difference between reciprocal of temperature)
Nose.X_mu = driving force of mass transport (chemical potential difference)
Nose.Jw = water mass flux air-mucus subsystem
Nose.Jq_a = heat flux of air-mucus subsystem
Nose.Jq_w = heat flux of mucus-interstitial tissue subsystem
Nose.Jq_art = heat flux of interstitial tissue - artery subsystem
Nose.Jq_ven = heat flux of interstitial tissue - vein subsystemMost of simulation settings can be changed from k = Parameters_animals(.. , .. , .. , .. , ... ) and 'Parameters_animals.m'.
k = Parameters_animals(tempCond, noseGeom, Ns, Ns_art, N_cycle, r_shunt, d_mucus, factorRam, factorRij, factorFric, heatTranCoef, factor_rit, factor_rtot, rTide, rFreq, velLim)
Ns = discretization number in space
Ns_art = discretization number in space for artery only
N_cycle = maximum number of cycle
r_shunt = a fraction to segmentize nose length. default = 0.5. This means you segmentize the nose length where the volume ratio between maxilloturbinate and total air pathway in a nose (maxilloturbinate+olfactory path) is 0.5.
d_mucus = thickness of mucus lining [m]
factorRam = multiplying factor for resistivity between air-mucus
factorRij = multiplying factor for resistivity between two subsystems which does not relate to mass transport (i.e., interstitial tissue-artery, interstitial tissue-vein, mucus-interstitial tissue)
factorFric = multiplying factor for the friction of the air in a turbinate
heatTranCoef = constant heat transfer coefficient regardless of nose geometry
factor_rit = multiplying factor for volume ratio of interstitial tissue; factor_rit * interstitial tissue/(interstitial tissue + artery + vein)
factor_rtot = multiplying factor total volume of (interstitial tissue + artery + vein)
rTide = multiplying factor for tidal volume
rFreq = multiplying factor for respiration frequency
velLim = the minima of air velocity, which avoids Reynolds number diverging to infinity- The solution does not converge.
- Increase Ns and/or Ns_art in k = Parameters_animals()
- Check residuals of several variables in Nose struct, and increase N_cycle in
k = Parameters_animals()
- Message from Matlab 'To run this file, you can either change the MATLAB current folder or add its folder to the MATLAB path'.
- Be sure that the directory for 'Nose_t.m' is with 'AIR_IG' and 'Water_EoS' folders.
Add the following citations when you use this repo for scientific purposes.
[1] Magnanelli, Elisa, et al. "The nasal geometry of the reindeer gives energy-efficient respiration." Journal of Non-Equilibrium Thermodynamics 42.1 (2017): 59-78.
[2] Solberg, Simon Birger Byremo, et al. "Energy efficiency of respiration in mature and newborn reindeer." Journal of Comparative Physiology B 190.4 (2020): 509-520.
[3] Cheon, Hyejeong Lee, et al. "Structure-function relationships in the nasal cavity of Arctic and subtropical seals." Biophysical Journal (2023): XXX-XXX.
If you have any questions or suggestions, please send email to: hyejeong.l.cheon@gmail.com!