Matching Items (3)
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- All Subjects: Chemotaxis
- Creators: Tang, Wenbo
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
A numerical study of chemotaxis in 3D turbulence is presented here. Direct Numerical
Simulation were used to calculate the nutrient uptake for both motile and non-motile bacterial
species and by applying the dynamical systems theory the effect of flow topology on the
variability of chemotaxis is analyzed. It is done by injecting a highly localized patch of nutrient
in the turbulent flow, and analyzing the evolution of reaction associated with the observed
high and low stretching regions. The Gaussian nutrient patch is released at different locations
and the corresponding nutrient uptake is obtained. The variable stretching characteristics of
the flow is depicted by Lagrangian Coherent Structures and the roles they play in affecting the
uptake are analyzed. The Lagrangian Coherent Structures are quantified by the Finite Time
Lyapunov Exponents which is a measure of the average stretching experienced by the flow in
finite time. It is found that in high stretching regions, the motile bacteria are attracted to the
nutrient patch very quickly, but also dispersed quickly; whereas in low stretching regions the
bacteria respond slower towards the nutrient patch. However the total uptake is intricately
determined by stretching history. These reaction characteristics are reflected in the several
realizations of simulations. This helps in understanding turbulence intensity and how it affects
the uptake of the nutrient.
Simulation were used to calculate the nutrient uptake for both motile and non-motile bacterial
species and by applying the dynamical systems theory the effect of flow topology on the
variability of chemotaxis is analyzed. It is done by injecting a highly localized patch of nutrient
in the turbulent flow, and analyzing the evolution of reaction associated with the observed
high and low stretching regions. The Gaussian nutrient patch is released at different locations
and the corresponding nutrient uptake is obtained. The variable stretching characteristics of
the flow is depicted by Lagrangian Coherent Structures and the roles they play in affecting the
uptake are analyzed. The Lagrangian Coherent Structures are quantified by the Finite Time
Lyapunov Exponents which is a measure of the average stretching experienced by the flow in
finite time. It is found that in high stretching regions, the motile bacteria are attracted to the
nutrient patch very quickly, but also dispersed quickly; whereas in low stretching regions the
bacteria respond slower towards the nutrient patch. However the total uptake is intricately
determined by stretching history. These reaction characteristics are reflected in the several
realizations of simulations. This helps in understanding turbulence intensity and how it affects
the uptake of the nutrient.
ContributorsGeorge, Jino (Author) / Tang, Wenbo (Thesis advisor) / Peet, Yulia (Thesis advisor) / Calhoun, Ronald (Committee member) / Arizona State University (Publisher)
Created2017
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