@phdthesis{19684,
  abstract     = {The overarching goal of this thesis is to break down the complexity of turbulent flows in terms of enumerable, coherent structures and patterns. In a five-paper series, we adopt a variety of perspectives and techniques to relate the properties of systems of increasing complexity to their underlying coherent structures. 

Initially, we take a dynamical systems point of view, seeing turbulent flow as a chaotic trajectory bouncing between exact unstable solutions of the underlying equations of motion. Using persistent homology, the main tool of topological data analysis capturing the persistence across scales of topological features in a point cloud, we introduce a method that quantifies visits of turbulent trajectories to unstable time-periodic solutions, also called periodic orbits. We demonstrate this method first in the Rössler and Kuramoto–Sivashinsky systems. Using this method in 3D Kolmogorov flow, we extract a Markov chain from turbulent data, where each node corresponds to the neighbourhood of a periodic orbit. The invariant distribution of this Markov chain reproduces expectation values on turbulent data when it is used to weight averages on the respective periodic orbits.

In more realistic, wall-bounded settings, such as plane-Couette flow (pcf) driven by the relative motion of the walls, or plane-Poiseuille flow (ppf) driven by a pressure gradient, finding exact solutions is difficult. We use dynamic mode decomposition (DMD), a dimensionality reduction method for sequential data, to identify and approximate low-dimensional dynamics without knowing any exact solutions. Most spatially-extended systems are equivariant under translations, and in such cases spatial drifts dominate DMD, hindering its use in the search for and modelling of low-dimensional dynamics. We augment DMD with a symmetry reduction method trained on turbulent data to stop it from seeing translations as a feature, improving its ability to extract dynamical information in translation-equivariant systems. We find segments of turbulent trajectories that linearize well with their symmetry-reduced DMD spectra, akin to dynamics near exact solutions. Searching for harmonics in the spectra gives leads for periodic orbits with spatial drifts, one of which converges to a new solution.

In larger domains, turbulence can localize and coexist with surrounding laminar flow. Our preceding approaches are global, taking all of a domain into account at once, and cannot readily treat each localized patch individually. Working first in a minimal oblique domain that can host a single 1D-localized turbulent patch, we find that turbulence in ppf is connected to a stable periodic orbit at a flow velocity much lower than when turbulence is first onset. We show that, well in advance of sustained turbulence, chaos sets in explosively, and for long time horizons, time series are consistent with that of a random process.

Finally, in much larger domains, we study and compare 2D-localized turbulence that appears as large-scale inclined structures, called stripes, in ppf and pcf. While appearing similar, we find that stripes in these two settings differ significantly in terms of how they sustain themselves, and in higher velocities, how they proliferate.},
  author       = {Yalniz, Gökhan},
  issn         = {2663-337X},
  pages        = {155},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Transition to turbulence : Data-, solution-, and pattern-driven approaches}},
  doi          = {10.15479/AT-ISTA-19684},
  year         = {2025},
}

@phdthesis{19906,
  abstract     = {Flows of ordinary fluids such as water or air transition from laminar to turbulent
motion as the velocity increases. This simple dependence of the flow state
solely on inertia, does not apply to more complex substances such as polymericand biofluids which commonly have elastic as well as viscous properties. Here
various different instabilities and turbulent states can arise at low and even
vanishing inertia, while high inertia turbulence counterintuitively is suppressed
and its drag strongly reduced. We here show in experiments of a viscoelastic
model fluid that the phenomena observed at low and high inertia have a
common origin and that the same dynamical state, elasto-inertial turbulence,
persists across four orders of magnitude in Reynolds number, ranging from
very low inertia, all the way to high inertia Maximum drag reduction (MDR)
asymptote. We also explore the transitions from Newtonian turbulence to
MDR, and specific cases of flow at high polymer concentrations, exploring the
relationship between flow at these wide range of control parameters.
},
  author       = {Suresh, Sarath S},
  issn         = {2663-337X},
  pages        = {82},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Turbulence in polymeric flows : A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote}},
  doi          = {10.15479/AT-ISTA-19906},
  year         = {2025},
}

@phdthesis{12726,
  abstract     = {Most motions of many-body systems at any scale in nature with sufficient degrees
of freedom tend to be chaotic; reaching from the orbital motion of planets, the air
currents in our atmosphere, down to the water flowing through our pipelines or
the movement of a population of bacteria. To the observer it is therefore intriguing
when a moving collective exhibits order. Collective motion of flocks of birds, schools
of fish or swarms of self-propelled particles or robots have been studied extensively
over the past decades but the mechanisms involved in the transition from chaos to
order remain unclear. Here, the interactions, that in most systems give rise to chaos,
sustain order. In this thesis we investigate mechanisms that preserve, destabilize
or lead to the ordered state. We show that endothelial cells migrating in circular
confinements transition to a collective rotating state and concomitantly synchronize
the frequencies of nucleating actin waves within individual cells. Consequently,
the frequency dependent cell migration speed uniformizes across the population.
Complementary to the WAVE dependent nucleation of traveling actin waves, we
show that in leukocytes the actin polymerization depending on WASp generates
pushing forces locally at stationary patches. Next, in pipe flows, we study methods
to disrupt the self–sustaining cycle of turbulence and therefore relaminarize the
flow. While we find in pulsating flow conditions that turbulence emerges through a
helical instability during the decelerating phase. Finally, we show quantitatively in
brain slices of mice that wild-type control neurons can compensate the migratory
deficits of a genetically modified neuronal sub–population in the developing cortex.},
  author       = {Riedl, Michael},
  issn         = {2663-337X},
  pages        = {260},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Synchronization in collectively moving active matter}},
  doi          = {10.15479/at:ista:12726},
  year         = {2023},
}

@phdthesis{14530,
  abstract     = {Most motions of many-body systems at any scale in nature with sufficient degrees of freedom tend to be chaotic; reaching from the orbital motion of planets, the air currents in our atmosphere, down to the water flowing through our pipelines or the movement of a population of bacteria. To the observer it is therefore intriguing when a moving collective exhibits order. Collective motion of flocks of birds, schools of fish or swarms of self-propelled particles or robots have been studied extensively over the past decades but the mechanisms involved in the transition from chaos to order remain unclear. Here, the interactions, that in most systems give rise to chaos, sustain order.  In this thesis we investigate mechanisms that preserve, destabilize or lead to the ordered state. We show that endothelial cells migrating in circular confinements transition to a collective rotating state and concomitantly synchronize the frequencies of nucleating actin waves within individual cells. Consequently, the frequency dependent cell migration speed uniformizes across the population. Complementary to the WAVE dependent nucleation of traveling actin waves, we show that in leukocytes the actin polymerization depending on WASp generates pushing forces locally at stationary patches. Next, in pipe flows, we study methods to disrupt the self--sustaining cycle of turbulence and therefore relaminarize the flow. While we find in pulsating flow conditions that turbulence emerges through a helical instability during the decelerating phase. Finally, we show quantitatively in brain slices of mice that wild-type control neurons can compensate the migratory deficits of a genetically modified neuronal sub--population in the developing cortex.  },
  author       = {Riedl, Michael},
  issn         = {2663-337X},
  keywords     = {Synchronization, Collective Movement, Active Matter, Cell Migration, Active Colloids},
  pages        = {260},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Synchronization in collectively moving active matter}},
  doi          = {10.15479/14530},
  year         = {2023},
}

@phdthesis{14641,
  abstract     = {Mutation rates represent the net result of complex interactions among various
cellular processes and can dramatically influence the evolutionary fate of
microbial populations. However, many popular techniques used to study
mutations are subject to the confounding effects of heredity and the subtleties
of adaptation to selection, all of which make it difficult to observe any dynamic
responses of mutation rates to fitness challenges. Furthermore, in spite of the
ubiquity of quorum sensing systems across the bacterial domain and relevance
for many physiological behaviors, the effects of such mechanisms on mutation
rate and adaptation remain poorly understood. In the following work, I
present the development of a microfluidic droplet-based method to measure
single base-pair mutation rates in growing populations of the bacterium
Escherichia coli. I use this method to observe a stress-induced increase in
mutation rate that is mediated by luxS, a highly conserved bacterial quorum
sensing component. I also show that the aforementioned increase in mutation
rate, and its associated control by luxS, corresponds to a higher degree of
adaptability under competitive environments.},
  author       = {Hennessey-Wesen, Mike},
  issn         = {2663-337X},
  keywords     = {microfluidics, miceobiology, mutations, quorum sensing},
  pages        = {104},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Adaptive mutation in E. coli modulated by luxS}},
  doi          = {10.15479/at:ista:14641},
  year         = {2023},
}

@phdthesis{9728,
  abstract     = {Most real-world flows are multiphase, yet we know little about them compared to their single-phase counterparts. Multiphase flows are more difficult to investigate as their dynamics occur in large parameter space and involve complex phenomena such as preferential concentration, turbulence modulation, non-Newtonian rheology, etc. Over the last few decades, experiments in particle-laden flows have taken a back seat in favour of ever-improving computational resources. However, computers are still not powerful enough to simulate a real-world fluid with millions of finite-size particles. Experiments are essential not only because they offer a reliable way to investigate real-world multiphase flows but also because they serve to validate numerical studies and steer the research in a relevant direction. In this work, we have experimentally investigated particle-laden flows in pipes, and in particular, examined the effect of particles on the laminar-turbulent transition and the drag scaling in turbulent flows.

For particle-laden pipe flows, an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic) transition that occurs via localised turbulent structures called puffs is affected by the addition of particles. In this study, in addition to this known transition, we found a super-critical transition to a globally fluctuating state with increasing particle concentration. At the same time, the Newtonian-type transition via puffs is delayed to larger Reynolds numbers. At an even higher concentration, only the globally fluctuating state is found. The dynamics of particle-laden flows are hence determined by two competing instabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle-induced globally fluctuating state at high, and a coexistence state at intermediate concentrations.

The effect of particles on turbulent drag is ambiguous, with studies reporting drag reduction, no net change, and even drag increase. The ambiguity arises because, in addition to particle concentration, particle shape, size, and density also affect the net drag. Even similar particles might affect the flow dissimilarly in different Reynolds number and concentration ranges. In the present study, we explored a wide range of both Reynolds number and concentration, using spherical as well as cylindrical particles. We found that the spherical particles do not reduce drag while the cylindrical particles are drag-reducing within a specific Reynolds number interval. The interval strongly depends on the particle concentration and the relative size of the pipe and particles. Within this interval, the magnitude of drag reduction reaches a maximum. These drag reduction maxima appear to fall onto a distinct power-law curve irrespective of the pipe diameter and particle concentration, and this curve can be considered as the maximum drag reduction asymptote for a given fibre shape. Such an asymptote is well known for polymeric flows but had not been identified for particle-laden flows prior to this work.},
  author       = {Agrawal, Nishchal},
  issn         = {2663-337X},
  keywords     = {Drag Reduction, Transition to Turbulence, Multiphase Flows, particle Laden Flows, Complex Flows, Experiments, Fluid Dynamics},
  pages        = {118},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Transition to turbulence and drag reduction in particle-laden pipe flows}},
  doi          = {10.15479/at:ista:9728},
  year         = {2021},
}

@phdthesis{8350,
  abstract     = {Cytoplasm is a gel-like crowded environment composed of tens of thousands of macromolecules, organelles, cytoskeletal networks and cytosol. The structure of the cytoplasm is thought to be highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules is very restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the jammed nature of the cytoplasm at the microscopic scale, large-scale reorganization of cytoplasm is essential for important cellular functions, such as nuclear positioning and cell division. How such mesoscale reorganization of the cytoplasm is achieved, especially for very large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, has only begun to be understood.
In this thesis, I focus on the recent advances in elucidating the molecular, cellular and biophysical principles underlying cytoplasmic organization across different scales, structures and species. First, I outline which of these principles have been identified by reductionist approaches, such as in vitro reconstitution assays, where boundary conditions and components can be modulated at ease. I then describe how the theoretical and experimental framework established in these reduced systems have been applied to their more complex in vivo counterparts, in particular oocytes and embryonic syncytial structures, and discuss how such complex biological systems can initiate symmetry breaking and establish patterning.
Specifically, I examine an example of large-scale reorganizations taking place in zebrafish embryos, where extensive cytoplasmic streaming leads to the segregation of cytoplasm from yolk granules along the animal-vegetal axis of the embryo. Using biophysical experimentation and theory, I investigate the forces underlying this process, to show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the embryo. This wave functions in segregation by both pulling cytoplasm animally and pushing yolk granules vegetally. Cytoplasm pulling is mediated by bulk actin network flows exerting friction forces on the cytoplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. This study defines a novel role of bulk actin polymerization waves in embryo polarization via cytoplasmic segregation. Lastly, I describe the cytoplasmic reorganizations taking place during zebrafish oocyte maturation, where the initial segregation of the cytoplasm and yolk granules occurs. Here, I demonstrate a previously uncharacterized wave of microtubule aster formation, traveling the oocyte along the animal-vegetal axis. Further research is required to determine the role of such microtubule structures in cytoplasmic reorganizations therein.
Collectively, these studies provide further evidence for the coupling between cell cytoskeleton and cell cycle machinery, which can underlie a core self-organizing mechanism for orchestrating large-scale reorganizations in a cell-cycle-tunable manner, where the modulations of the force-generating machinery and cytoplasmic mechanics can be harbored to fulfill cellular functions.},
  author       = {Shamipour, Shayan},
  issn         = {2663-337X},
  pages        = {107},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Bulk actin dynamics drive phase segregation in zebrafish oocytes }},
  doi          = {10.15479/AT:ISTA:8350},
  year         = {2020},
}

@phdthesis{7258,
  abstract     = {Many flows encountered in nature and applications are characterized by a chaotic motion known as turbulence. Turbulent flows generate intense friction with pipe walls and are responsible for considerable amounts of energy losses at world scale. The nature of turbulent friction and techniques aimed at reducing it have been subject of extensive research over the last century, but no definite answer has been found yet. In this thesis we show that in pipes at moderate turbulent Reynolds numbers friction is better described by the power law first introduced by Blasius and not by the Prandtl–von Kármán formula. At higher Reynolds numbers, large scale motions gradually become more important in the flow and can be related to the change in scaling of friction. Next, we present a series of new techniques that can relaminarize turbulence by suppressing a key mechanism that regenerates it at walls, the lift–up effect. In addition, we investigate the process of turbulence decay in several experiments and discuss the drag reduction potential. Finally, we examine the behavior of friction under pulsating conditions inspired by the human heart cycle and we show that under such circumstances turbulent friction can be reduced to produce energy savings.},
  author       = {Scarselli, Davide},
  issn         = {2663-337X},
  pages        = {174},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{New approaches to reduce friction in turbulent pipe flow}},
  doi          = {10.15479/AT:ISTA:7258},
  year         = {2020},
}

@phdthesis{6957,
  abstract     = {In many shear flows like pipe flow, plane Couette flow, plane Poiseuille flow,  etc. turbulence emerges subcritically. Here, when subjected to strong enough perturbations, the flow becomes turbulent in spite of the laminar base flow being linearly stable.  The nature of this instability has puzzled the scientific community for decades. At onset, turbulence appears in localized patches and flows are spatio-temporally intermittent.  In pipe flow the localized turbulent structures are referred to as puffs and in planar flows like plane Couette and channel flow, patches arise in the form of localized oblique bands. In this thesis, we study the onset of turbulence in channel flow in direct numerical simulations from a dynamical system theory perspective, as well as by performing experiments in a large aspect ratio channel.

The aim of the experimental work is to determine the critical Reynolds number where turbulence first becomes sustained. Recently, the onset of turbulence has been described in analogy to absorbing state phase transition (i.e. directed percolation). In particular, it has been shown that the critical point can be estimated from the competition between spreading and decay processes. Here, by performing experiments, we identify the mechanisms underlying turbulence proliferation in channel flow and find the critical Reynolds number, above which turbulence becomes sustained. Above the critical point, the continuous growth at the tip of the stripes outweighs the stochastic shedding of turbulent patches at the tail and the stripes expand. For growing stripes, the probability to decay decreases while the probability of stripe splitting increases. Consequently, and unlike for the puffs in pipe flow, neither of these two processes is time-independent i.e. memoryless. Coupling between stripe expansion and creation of new stripes via splitting leads to a significantly lower critical point ($Re_c=670+/-10$) than most earlier studies suggest.  

While the above approach sheds light on how turbulence first becomes sustained, it provides no insight into the origin of the stripes themselves. In the numerical part of the thesis we investigate how turbulent stripes form from invariant solutions of the Navier-Stokes equations. The origin of these turbulent stripes can be identified by applying concepts from the dynamical system theory. In doing so, we identify the exact coherent structures underlying stripes and their bifurcations and how they give rise to the turbulent attractor in phase space. We first report a family of localized nonlinear traveling wave solutions of the Navier-Stokes equations in channel flow. These solutions show structural similarities with turbulent stripes in experiments like obliqueness, quasi-streamwise streaks and vortices, etc. A parametric study of these traveling wave solution is performed, with parameters like Reynolds number, stripe tilt angle and domain size, including the stability of the solutions. These solutions emerge through saddle-node bifurcations and form a phase space skeleton for the turbulent stripes observed in the experiments. The lower branches of these TW solutions at different tilt angles undergo Hopf bifurcation and new solutions branches of relative periodic orbits emerge. These RPO solutions do not belong to the same family and therefore the routes to chaos for different angles are different.  

In shear flows, turbulence at onset is transient in nature.  Consequently,turbulence can not be tracked to lower Reynolds numbers, where the dynamics may simplify. Before this happens, turbulence becomes short-lived and laminarizes. In the last part of the thesis, we show that using numerical simulations we can continue turbulent stripes in channel flow past the 'relaminarization barrier' all the way to their origin. Here, turbulent stripe dynamics simplifies and the fluctuations are no longer stochastic and the stripe settles down to a relative periodic orbit. This relative periodic orbit originates from the aforementioned traveling wave solutions. Starting from the relative periodic orbit, a small increase in speed i.e. Reynolds number gives rise to chaos and the attractor dimension sharply increases in contrast to the classical transition scenario where the instabilities affect the flow globally and give rise to much more gradual route to turbulence.},
  author       = {Paranjape, Chaitanya S},
  issn         = {2663-337X},
  keywords     = {Instabilities, Turbulence, Nonlinear dynamics},
  pages        = {138},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Onset of turbulence in plane Poiseuille flow}},
  doi          = {10.15479/AT:ISTA:6957},
  year         = {2019},
}