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Description
There has been important progress in understanding ecological dynamics through the development of the theory of ecological stoichiometry. This fast growing theory provides new constraints and mechanisms that can be formulated into mathematical models. Stoichiometric models incorporate the effects of both food quantity and food quality into a single framework that produce rich dynamics. While the effects of nutrient deficiency on consumer growth are well understood, recent discoveries in ecological stoichiometry suggest that consumer dynamics are not only affected by insufficient food nutrient content (low phosphorus (P): carbon (C) ratio) but also by excess food nutrient content (high P:C). This phenomenon, known as the stoichiometric knife edge, in which animal growth is reduced not only by food with low P content but also by food with high P content, needs to be incorporated into mathematical models. Here we present Lotka-Volterra type models to investigate the growth response of Daphnia to algae of varying P:C ratios. Using a nonsmooth system of two ordinary differential equations (ODEs), we formulate the first model to incorporate the phenomenon of the stoichiometric knife edge. We then extend this stoichiometric model by mechanistically deriving and tracking free P in the environment. This resulting full knife edge model is a nonsmooth system of three ODEs. Bifurcation analysis and numerical simulations of the full model, that explicitly tracks phosphorus, leads to quantitatively different predictions than previous models that neglect to track free nutrients. The full model shows that the grazer population is sensitive to excess nutrient concentrations as a dynamical free nutrient pool induces extreme grazer population density changes. These modeling efforts provide insight on the effects of excess nutrient content on grazer dynamics and deepen our understanding of the effects of stoichiometry on the mechanisms governing population dynamics and the interactions between trophic levels.
ContributorsPeace, Angela (Author) / Kuang, Yang (Thesis advisor) / Elser, James J (Committee member) / Baer, Steven (Committee member) / Tang, Wenbo (Committee member) / Kang, Yun (Committee member) / Arizona State University (Publisher)
Created2014
Description
Presented is a study on the chemotaxis reaction process and its relation with flow topology. The effect of coherent structures in turbulent flows is characterized by studying nutrient uptake and the advantage that is received from motile bacteria over other non-motile bacteria. Variability is found to be dependent on the initial location of scalar impurity and can be tied to Lagrangian coherent structures through recent advances in the identification of finite-time transport barriers. Advantage is relatively small for initial nutrient found within high stretching regions of the flow, and nutrient within elliptic structures provide the greatest advantage for motile species. How the flow field and the relevant flow topology lead to such a relation is analyzed.
ContributorsJones, Kimberly (Author) / Tang, Wenbo (Thesis advisor) / Kang, Yun (Committee member) / Jones, Donald (Committee member) / Arizona State University (Publisher)
Created2015
Description
Earth-system models describe the interacting components of the climate system and
technological systems that affect society, such as communication infrastructures. Data
assimilation addresses the challenge of state specification by incorporating system
observations into the model estimates. In this research, a particular data
assimilation technique called the Local Ensemble Transform Kalman Filter (LETKF) is
applied to the ionosphere, which is a domain of practical interest due to its effects
on infrastructures that depend on satellite communication and remote sensing. This
dissertation consists of three main studies that propose strategies to improve space-
weather specification during ionospheric extreme events, but are generally applicable
to Earth-system models:
Topic I applies the LETKF to estimate ion density with an idealized model of
the ionosphere, given noisy synthetic observations of varying sparsity. Results show
that the LETKF yields accurate estimates of the ion density field and unobserved
components of neutral winds even when the observation density is spatially sparse
(2% of grid points) and there is large levels (40%) of Gaussian observation noise.
Topic II proposes a targeted observing strategy for data assimilation, which uses
the influence matrix diagnostic to target errors in chosen state variables. This
strategy is applied in observing system experiments, in which synthetic electron density
observations are assimilated with the LETKF into the Thermosphere-Ionosphere-
Electrodynamics Global Circulation Model (TIEGCM) during a geomagnetic storm.
Results show that assimilating targeted electron density observations yields on
average about 60%–80% reduction in electron density error within a 600 km radius of
the observed location, compared to 15% reduction obtained with randomly placed
vertical profiles.
Topic III proposes a methodology to account for systematic model bias arising
ifrom errors in parametrized solar and magnetospheric inputs. This strategy is ap-
plied with the TIEGCM during a geomagnetic storm, and is used to estimate the
spatiotemporal variations of bias in electron density predictions during the
transitionary phases of the geomagnetic storm. Results show that this strategy reduces
error in 1-hour predictions of electron density by about 35% and 30% in polar regions
during the main and relaxation phases of the geomagnetic storm, respectively.
technological systems that affect society, such as communication infrastructures. Data
assimilation addresses the challenge of state specification by incorporating system
observations into the model estimates. In this research, a particular data
assimilation technique called the Local Ensemble Transform Kalman Filter (LETKF) is
applied to the ionosphere, which is a domain of practical interest due to its effects
on infrastructures that depend on satellite communication and remote sensing. This
dissertation consists of three main studies that propose strategies to improve space-
weather specification during ionospheric extreme events, but are generally applicable
to Earth-system models:
Topic I applies the LETKF to estimate ion density with an idealized model of
the ionosphere, given noisy synthetic observations of varying sparsity. Results show
that the LETKF yields accurate estimates of the ion density field and unobserved
components of neutral winds even when the observation density is spatially sparse
(2% of grid points) and there is large levels (40%) of Gaussian observation noise.
Topic II proposes a targeted observing strategy for data assimilation, which uses
the influence matrix diagnostic to target errors in chosen state variables. This
strategy is applied in observing system experiments, in which synthetic electron density
observations are assimilated with the LETKF into the Thermosphere-Ionosphere-
Electrodynamics Global Circulation Model (TIEGCM) during a geomagnetic storm.
Results show that assimilating targeted electron density observations yields on
average about 60%–80% reduction in electron density error within a 600 km radius of
the observed location, compared to 15% reduction obtained with randomly placed
vertical profiles.
Topic III proposes a methodology to account for systematic model bias arising
ifrom errors in parametrized solar and magnetospheric inputs. This strategy is ap-
plied with the TIEGCM during a geomagnetic storm, and is used to estimate the
spatiotemporal variations of bias in electron density predictions during the
transitionary phases of the geomagnetic storm. Results show that this strategy reduces
error in 1-hour predictions of electron density by about 35% and 30% in polar regions
during the main and relaxation phases of the geomagnetic storm, respectively.
ContributorsDurazo, Juan, Ph.D (Author) / Kostelich, Eric J. (Thesis advisor) / Mahalov, Alex (Thesis advisor) / Tang, Wenbo (Committee member) / Moustaoui, Mohamed (Committee member) / Platte, Rodrigo (Committee member) / Arizona State University (Publisher)
Created2018
Description
The dynamics of a fluid flow inside 2D square and 3D cubic cavities
under various configurations were simulated and analyzed using a
spectral code I developed.
This code was validated against known studies in the 3D lid-driven
cavity. It was then used to explore the various dynamical behaviors
close to the onset of instability of the steady-state flow, and explain
in the process the mechanism underlying an intermittent bursting
previously observed. A fairly complete bifurcation picture emerged,
using a combination of computational tools such as selective
frequency damping, edge-state tracking and subspace restriction.
The code was then used to investigate the flow in a 2D square cavity
under stable temperature stratification, an idealized version of a lake
with warmer water at the surface compared to the bottom. The governing
equations are the Navier-Stokes equations under the Boussinesq approximation.
Simulations were done over a wide range of parameters of the problem quantifying
the driving velocity at the top (e.g. wind) and the strength of the stratification.
Particular attention was paid to the mechanisms associated with the onset of
instability of the base steady state, and the complex nontrivial dynamics
occurring beyond onset, where the presence of multiple states leads to a
rich spectrum of states, including homoclinic and heteroclinic chaos.
A third configuration investigates the flow dynamics of a fluid in a rapidly
rotating cube subjected to small amplitude modulations. The responses were
quantified by the global helicity and energy measures, and various peak
responses associated to resonances with intrinsic eigenmodes of the cavity
and/or internal retracing beams were clearly identified for the first time.
A novel approach to compute the eigenmodes is also described, making accessible
a whole catalog of these with various properties and dynamics. When the small
amplitude modulation does not align with the rotation axis (precession) we show
that a new set of eigenmodes are primarily excited as the angular velocity
increases, while triadic resonances may occur once the nonlinear regime kicks in.
under various configurations were simulated and analyzed using a
spectral code I developed.
This code was validated against known studies in the 3D lid-driven
cavity. It was then used to explore the various dynamical behaviors
close to the onset of instability of the steady-state flow, and explain
in the process the mechanism underlying an intermittent bursting
previously observed. A fairly complete bifurcation picture emerged,
using a combination of computational tools such as selective
frequency damping, edge-state tracking and subspace restriction.
The code was then used to investigate the flow in a 2D square cavity
under stable temperature stratification, an idealized version of a lake
with warmer water at the surface compared to the bottom. The governing
equations are the Navier-Stokes equations under the Boussinesq approximation.
Simulations were done over a wide range of parameters of the problem quantifying
the driving velocity at the top (e.g. wind) and the strength of the stratification.
Particular attention was paid to the mechanisms associated with the onset of
instability of the base steady state, and the complex nontrivial dynamics
occurring beyond onset, where the presence of multiple states leads to a
rich spectrum of states, including homoclinic and heteroclinic chaos.
A third configuration investigates the flow dynamics of a fluid in a rapidly
rotating cube subjected to small amplitude modulations. The responses were
quantified by the global helicity and energy measures, and various peak
responses associated to resonances with intrinsic eigenmodes of the cavity
and/or internal retracing beams were clearly identified for the first time.
A novel approach to compute the eigenmodes is also described, making accessible
a whole catalog of these with various properties and dynamics. When the small
amplitude modulation does not align with the rotation axis (precession) we show
that a new set of eigenmodes are primarily excited as the angular velocity
increases, while triadic resonances may occur once the nonlinear regime kicks in.
ContributorsWu, Ke (Author) / Lopez, Juan (Thesis advisor) / Welfert, Bruno (Thesis advisor) / Tang, Wenbo (Committee member) / Platte, Rodrigo (Committee member) / Herrmann, Marcus (Committee member) / Arizona State University (Publisher)
Created2019
Description
Coherent vortices are ubiquitous structures in natural flows that affect mixing and transport of substances and momentum/energy. Being able to detect these coherent structures is important for pollutant mitigation, ecological conservation and many other aspects. In recent years, mathematical criteria and algorithms have been developed to extract these coherent structures in turbulent flows. In this study, we will apply these tools to extract important coherent structures and analyze their statistical properties as well as their implications on kinematics and dynamics of the flow. Such information will aide representation of small-scale nonlinear processes that large-scale models of natural processes may not be able to resolve.
ContributorsCass, Brentlee Jerry (Author) / Tang, Wenbo (Thesis director) / Kostelich, Eric (Committee member) / Department of Information Systems (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Using a simple $SI$ infection model, I uncover the
overall dynamics of the system and how they depend on the incidence
function. I consider both an epidemic and endemic perspective of the
model, but in both cases, three classes of incidence
functions are identified.
In the epidemic form,
power incidences, where the infective portion $I^p$ has $p\in(0,1)$,
cause unconditional host extinction,
homogeneous incidences have host extinction for certain parameter constellations and
host survival for others, and upper density-dependent incidences
never cause host extinction. The case of non-extinction in upper
density-dependent
incidences extends to the case where a latent period is included.
Using data from experiments with rhanavirus and salamanders,
maximum likelihood estimates are applied to the data.
With these estimates,
I generate the corrected Akaike information criteria, which
reward a low likelihood and punish the use of more parameters.
This generates the Akaike weight, which is used to fit
parameters to the data, and determine which incidence functions
fit the data the best.
From an endemic perspective, I observe
that power incidences cause initial condition dependent host extinction for
some parameter constellations and global stability for others,
homogeneous incidences have host extinction for certain parameter constellations and
host survival for others, and upper density-dependent incidences
never cause host extinction.
The dynamics when the incidence function is homogeneous are deeply explored.
I expand the endemic considerations in the homogeneous case
by adding a predator into the model.
Using persistence theory, I show the conditions for the persistence of each of the
predator, prey, and parasite species. Potential dynamics of the system include parasite mediated
persistence of the predator, survival of the ecosystem at high initial predator levels and
ecosystem collapse at low initial predator levels, persistence of all three species, and much more.
overall dynamics of the system and how they depend on the incidence
function. I consider both an epidemic and endemic perspective of the
model, but in both cases, three classes of incidence
functions are identified.
In the epidemic form,
power incidences, where the infective portion $I^p$ has $p\in(0,1)$,
cause unconditional host extinction,
homogeneous incidences have host extinction for certain parameter constellations and
host survival for others, and upper density-dependent incidences
never cause host extinction. The case of non-extinction in upper
density-dependent
incidences extends to the case where a latent period is included.
Using data from experiments with rhanavirus and salamanders,
maximum likelihood estimates are applied to the data.
With these estimates,
I generate the corrected Akaike information criteria, which
reward a low likelihood and punish the use of more parameters.
This generates the Akaike weight, which is used to fit
parameters to the data, and determine which incidence functions
fit the data the best.
From an endemic perspective, I observe
that power incidences cause initial condition dependent host extinction for
some parameter constellations and global stability for others,
homogeneous incidences have host extinction for certain parameter constellations and
host survival for others, and upper density-dependent incidences
never cause host extinction.
The dynamics when the incidence function is homogeneous are deeply explored.
I expand the endemic considerations in the homogeneous case
by adding a predator into the model.
Using persistence theory, I show the conditions for the persistence of each of the
predator, prey, and parasite species. Potential dynamics of the system include parasite mediated
persistence of the predator, survival of the ecosystem at high initial predator levels and
ecosystem collapse at low initial predator levels, persistence of all three species, and much more.
ContributorsFarrell, Alexander E. (Author) / Thieme, Horst R (Thesis advisor) / Smith, Hal (Committee member) / Kuang, Yang (Committee member) / Tang, Wenbo (Committee member) / Collins, James (Committee member) / Arizona State University (Publisher)
Created2017
Description
This honors thesis explores and models the flow of air around a cylindrical arrow that is rotating as it moves through the air. This model represents the airflow around an archery arrow after it is released from the bow and rotates while it flies through the air. This situation is important in archery because an understanding of the airflow allows archers to predict the flight of the arrow. As a result, archers can improve their accuracy and ability to hit targets. However, not many computational fluid dynamic simulations modeling the airflow around a rotating archery arrow exist. This thesis attempts to further the understanding of the airflow around a rotating archery arrow by creating a mathematical model to numerically simulate the airflow around the arrow in the presence of this rotation. This thesis uses a linearized approximation of the Navier Stokes equations to model the airflow around the arrow and explains the reasoning for using this simplification of the fully nonlinear Navier Stokes equations. This thesis continues to describe the discretization of these linearized equations using the finite difference method and the boundary conditions used for these equations. A MATLAB code solves the resulting system of equations in order to obtain a numerical simulation of this airflow around the rotating arrow. The results of the simulation for each velocity component and the pressure distribution are displayed. This thesis then discusses the results of the simulation, and the MATLAB code is analyzed to verify the convergence of the solution. Appendix A includes the full MATLAB code used for the flow simulation. Finally, this thesis explains potential future research topics, ideas, and improvements to the code that can help further the understanding and create more realistic simulations of the airflow around a flying archery arrow.
ContributorsCholinski, Christopher John (Author) / Tang, Wenbo (Thesis director) / Herrmann, Marcus (Committee member) / Mechanical and Aerospace Engineering Program (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05