From 4b10f6d2b00db307beaf2afa087a8767d98da991 Mon Sep 17 00:00:00 2001 From: Gaia Buccino Date: Mon, 28 Apr 2025 12:47:34 +0200 Subject: [PATCH 1/3] Fecal pellets egestion kernel added and documentation of physicskernels updated --- docs/physicskernels.md | 11 +++++ plasticparcels/kernels.py | 91 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 102 insertions(+) diff --git a/docs/physicskernels.md b/docs/physicskernels.md index 4d212e0..52bc771 100644 --- a/docs/physicskernels.md +++ b/docs/physicskernels.md @@ -77,6 +77,17 @@ where {math}`\text{d}W(t)` is a Wiener noise increment with zero mean and a vari A version of this kernel has been used in [@Onink2022](http://dx.doi.org/10.5194/gmd-15-1995-2022). +### Fecal Pellets Egestion +Small organisms belonging to the cathegory of zooplankton can ingest and consequently egest plastic particles. Once egested, plastic particles are packed into fecal pellets, particles with a different density both from virgin plastic and from pure organic matter. The presence of organic matter around the plastic particle can result in a density change, affecting the buoyancy of the particle. An initially buoyant particle may become negatively buoyant, and sink or settle, depending on the surrounding seawater density. + +The modelling of the dynamics of egested fecal pellets (+ plastic particle) has been developed following the approach of [@Omand2020](https://doi.org/10.1038/s41598-020-60424-5), where the settling velocity of a particle (intended as fecal pellet contaminated with a plastic parcel) is computed from the difference between the density of the particle itself and the surrounding seawater. We assume that the organic matter surrounding the plastic particle is remineralized following the equation describing the variation of its equivalent radius {math}`a`: + +```{math} +\frac{\text{d}a}{\text{d}t} := - \text{C} \text{r} \{text}a^{\text{n}-2} . + +Where \text{C}, \text{r} and \text{n} are the remineralization constant, the remineralization rate and a constant related to the type of remineralization. +The decreasing of the volume of the organic matter is responsible for the changing in density of the particle and the consequent changing in the settling velocity of the particle, until the entire amount of organic matter is disgregated and the plastic particle packed inside return to its intial status. + ### Sea-ice capture A sea-ice capture kernel is currently under development and will be released soon. diff --git a/plasticparcels/kernels.py b/plasticparcels/kernels.py index 7961f5e..cdb2cc4 100644 --- a/plasticparcels/kernels.py +++ b/plasticparcels/kernels.py @@ -197,6 +197,97 @@ def SettlingVelocity(particle, fieldset, time): # Update particle depth particle_ddepth += particle.settling_velocity * particle.dt # noqa +def FecalPellets_Egestion(particle, fieldset, time): + """ + Faecal pellets egestion kernel. + + Description + ---------- + Using the approach in [1] the settling velocity of the particle (intended as organic matter + plastic particle) + is determined through Eq. (1), where the density of the particle is updated at each iteration based on the quantity + of organic matter consumed in time described by Eq. (2) in [1] + + + Parameter Requirements + ---------- + fieldset : + - `fieldset.zooplankton` TBD + + Calculation steps: + 1. Compute the seawater dynamic viscosity from Eq. (27) in [2] + 2. Compute the kinematic viscosity from Eq. (25) in [2] + 3. Compute the volume of organic matter present in the particle + 4. Compute the particle density + 5. Compute the settling velocity of the particle from Eq. (1) in [1] + 6. Compute the new radius of the particle due to the organic matter consumption from Eq. (2) in [1] + + Parameter Requirements + ---------- + particle : + - particle diameter + - plastic diameter + - plastic density + - organic matter density + - remineralization type (that determines remineralization constant as described in [1]) + - seawater_density + fieldset : + - `fieldset.G` - Gravity constant. Units [m s-2]. + - `fieldset.conservative_temperature` - The conservative temperature field. Units [C]. + - `fieldset.absolute_salinity` - The absolute salinity field. Units [g/kg]. + - `fieldset.zooplankton_concentration` ??? TBD + + Order of Operations: + This kernel must run after the PolyTEOS10_bsq kernel, which sets the particle.seawater_density variable, relied on by this. + + References + ---------- + [1] Omand (2020) - https://doi.org/10.1038/s41598-020-60424-5 + """ + # seawater_density = particle.seawater_density # [kg m-3] + temperature = fieldset.conservative_temperature[time, particle.depth, particle.lat, particle.lon] + seawater_salinity = fieldset.absolute_salinity[time, particle.depth, particle.lat, particle.lon]# / 1000. #CHECK THIS + plastic_radius = 0.5 * particle.plastic_diameter + + # Compute the seawater dynamic viscosity + water_dynamic_viscosity = 4.2844E-5 + (1. / ((0.156 * (temperature + 64.993) ** 2) - 91.296)) # Eq. (26) from [2] + A = 1.541 + 1.998E-2 * temperature - 9.52E-5 * temperature ** 2 # Eq. (28) from [2] + B = 7.974 - 7.561E-2 * temperature + 4.724E-4 * temperature ** 2 # Eq. (29) from [2] + seawater_dynamic_viscosity = water_dynamic_viscosity * (1. + A * seawater_salinity + B * seawater_salinity ** 2) # Eq. (27) from [2] + + # Compute the zooplankton component TBD + + # Compute the radius, surface area, volume and thickness of the particle including potential organic matter + plastic_volume = (4. / 3.) * math.pi * plastic_radius ** 3. # volume of plastic [m3] + #plastic_surface_area = 4. * math.pi * plastic_radius ** 2. # surface area of plastic particle [m2] + particle_radius = particle.particle_diameter / 2. + particle_volume = (4. / 3.) * math.pi * particle_radius ** 3. # volume of total (biofilm + plastic) [m3] + organic_volume = particle_volume - plastic_volume # volume of organic matter [m3] + # FP_surface_area = 4. * math.pi * particle_radius ** 2. + + # Compute particle density + particle_density = ((particle.plastic_density * plastic_volume) + (particle.organic_density * organic_volume)) / particle_volume + + # Compute the settling velocity of the particle using Eq. (1) from [1] + settling_velocity = - (2. * particle_radius ** 2. * fieldset.G * (particle_density - particle.seawater_density)) / (9. * seawater_dynamic_viscosity) # m s-1 + + # Update the settling velocity + particle.settling_velocity = settling_velocity + + # Update particle depth + particle_ddepth += particle.settling_velocity * particle.dt # noqa + + # Compute the final particle radius using Eq. (2) from [1] + if particle_radius >= plastic_radius: + new_particle_radius = particle_radius - (particle.remineralization_C * fieldset.remineralization_R * (particle_radius ** (particle.remineralization_type - 2.))) * particle.dt + + if new_particle_radius < plastic_radius: + new_particle_radius = plastic_radius + + particle.particle_diameter = 2.* new_particle_radius + + + + def Biofouling(particle, fieldset, time): r"""Settling velocity due to biofouling kernel. From 9b4f90cf11f96f49b3a354cc33f6ac2ca3be6803 Mon Sep 17 00:00:00 2001 From: Gaia Buccino Date: Mon, 28 Apr 2025 15:32:54 +0200 Subject: [PATCH 2/3] Improved documentation --- docs/physicskernels.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/docs/physicskernels.md b/docs/physicskernels.md index 52bc771..bd8a99a 100644 --- a/docs/physicskernels.md +++ b/docs/physicskernels.md @@ -78,15 +78,16 @@ where {math}`\text{d}W(t)` is a Wiener noise increment with zero mean and a vari A version of this kernel has been used in [@Onink2022](http://dx.doi.org/10.5194/gmd-15-1995-2022). ### Fecal Pellets Egestion -Small organisms belonging to the cathegory of zooplankton can ingest and consequently egest plastic particles. Once egested, plastic particles are packed into fecal pellets, particles with a different density both from virgin plastic and from pure organic matter. The presence of organic matter around the plastic particle can result in a density change, affecting the buoyancy of the particle. An initially buoyant particle may become negatively buoyant, and sink or settle, depending on the surrounding seawater density. +Plastic particles are susceptible to be ingested and excreted by small organisms belonging to the zooplankton category. +After the egestion, they are incorporated into fecal pellets that differ in density from both virgin plastic and pure organic material. The presence of organic matter surrounding the plastic particle leads to a change in its overall density, thereby affecting its buoyancy. A particle that was initially buoyant may become negatively buoyant and sink or settle, depending on the density of the surrounding seawater. The reduction in the volume of organic matter leads to changes in the particle's density and, consequently, in its settling velocity, until the organic matter is completely degraded and the plastic particle returns to its initial state. The modeling of the dynamics of egested fecal pellets (+ plastic particles) has been developed following approach of [@Omand2020](https://doi.org/10.1038/s41598-020-60424-5). -The modelling of the dynamics of egested fecal pellets (+ plastic particle) has been developed following the approach of [@Omand2020](https://doi.org/10.1038/s41598-020-60424-5), where the settling velocity of a particle (intended as fecal pellet contaminated with a plastic parcel) is computed from the difference between the density of the particle itself and the surrounding seawater. We assume that the organic matter surrounding the plastic particle is remineralized following the equation describing the variation of its equivalent radius {math}`a`: +In this framework, the settling velocity of a particle is computed based on the difference between the particle's density and that of the surrounding seawater. We assume that the organic matter enveloping the plastic particle is remineralized, as time passes by, according to the equation describing the variation of its equivalent radius: {math}`a`: ```{math} -\frac{\text{d}a}{\text{d}t} := - \text{C} \text{r} \{text}a^{\text{n}-2} . +\frac{\text{d}a}{\text{d}t} := - \text{C} \text{r} \, a^{\text{n}-2}. +``` Where \text{C}, \text{r} and \text{n} are the remineralization constant, the remineralization rate and a constant related to the type of remineralization. -The decreasing of the volume of the organic matter is responsible for the changing in density of the particle and the consequent changing in the settling velocity of the particle, until the entire amount of organic matter is disgregated and the plastic particle packed inside return to its intial status. ### Sea-ice capture From 8b2ea2b86b507bf4d8e4f471eba020ce2fb36ddd Mon Sep 17 00:00:00 2001 From: Gaia Buccino Date: Mon, 28 Apr 2025 15:40:46 +0200 Subject: [PATCH 3/3] Fixing doc typos --- docs/physicskernels.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/physicskernels.md b/docs/physicskernels.md index bd8a99a..76f1a11 100644 --- a/docs/physicskernels.md +++ b/docs/physicskernels.md @@ -83,11 +83,11 @@ After the egestion, they are incorporated into fecal pellets that differ in dens In this framework, the settling velocity of a particle is computed based on the difference between the particle's density and that of the surrounding seawater. We assume that the organic matter enveloping the plastic particle is remineralized, as time passes by, according to the equation describing the variation of its equivalent radius: {math}`a`: -```{math} -\frac{\text{d}a}{\text{d}t} := - \text{C} \text{r} \, a^{\text{n}-2}. -``` +$$ +\frac{\text{d}a}{\text{d}t} := - \text{C} \ \text{r} \ a^{\text{n}-2}. +$$ -Where \text{C}, \text{r} and \text{n} are the remineralization constant, the remineralization rate and a constant related to the type of remineralization. +Where $\text{C}$, $\text{r}$ and $\text{n}$ are the remineralization constant, the remineralization rate and a constant related to the type of remineralization. ### Sea-ice capture