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.
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.
split cylinder is studied numerically solving the Navier--Stokes
equations. The cylinder is completely filled with fluid
and is split at the midplane. Three different types of boundary
conditions were imposed, leading to a variety of instabilities and
complex flow dynamics.
The first configuration has a strong background rotation and a small
differential rotation between the two halves. The axisymmetric flow
was first studied identifying boundary layer instabilities which
produce inertial waves under some conditions. Limit cycle states and
quasiperiodic states were found, including some period doubling
bifurcations. Then, a three-dimensional study was conducted
identifying low and high azimuthal wavenumber rotating waves due to
G’ortler and Tollmien–-Schlichting type instabilities. Over most of
the parameter space considered, quasiperiodic states were found where
both types of instabilities were present.
In the second configuration, both cylinder halves are in exact
counter-rotation, producing an O(2) symmetry in the system. The basic state flow dynamic
is dominated by the shear layer created
in the midplane. By changing the speed rotation and the aspect ratio
of the cylinder, the flow loses symmetries in a variety of ways
creating static waves, rotating waves, direction reversing waves and
slow-fast pulsing waves. The bifurcations, including infinite-period
bifurcations, were characterized and the flow dynamics was elucidated.
Additionally, preliminary experimental results for this case are
presented.
In the third set up, with oscillatory boundary conditions, inertial
wave beams were forced imposing a range of frequencies. These beams
emanate from the corner of the cylinder and from the split at the
midplane, leading to destructive/constructive interactions which
produce peaks in vorticity for some specific frequencies. These
frequencies are shown to be associated with the resonant Kelvin
modes. Furthermore, a study of the influence of imposing a phase
difference between the oscillations of the two halves of the cylinder
led to the interesting result that different Kelvin
modes can be excited depending on the phase difference.
We present a study of three-dimensional Lagrangian coherent structures (LCS) near the Hong Kong International Airport and relate to previous developments of two-dimensional (2D) LCS analyses. The LCS are contrasted among three independent models and against 2D coherent Doppler light detection and ranging (LIDAR) data. Addition of the velocity information perpendicular to the LIDAR scanning cone helps solidify flow structures inferred from previous studies; contrast among models reveals the intramodel variability; and comparison with flight data evaluates the performance among models in terms of Lagrangian analyses. We find that, while the three models and the LIDAR do recover similar features of the windshear experienced by a landing aircraft (along the landing trajectory), their Lagrangian signatures over the entire domain are quite different—a portion of each numerical model captures certain features resembling those LCS extracted from independent 2D LIDAR analyses based on observations.