6,406 research outputs found
Chiral active fluids: Odd viscosity, active turbulence, and directed flows of hydrodynamic microrotors
While the number of publications on rotating active matter has rapidly increased in recent years, studies on purely hydrodynamically interacting rotors on the microscale are still rare, especially from the perspective of particle based hydrodynamic simulations. The work presented here targets to fill this gap. By means of high-performance computer simulations, performed in a highly parallelised fashion on graphics processing units, the dynamics of ensembles of up to 70,000 rotating colloids immersed in an explicit mesoscopic solvent consisting out of up to 30 million fluid particles, are investigated. Some of the results presented in this thesis have been worked out in collaboration with experimentalists, such that the theoretical considerations developed in this thesis are supported by experiments, and vice versa. The studied system, modelled in order to resemble the essential physics of the experimentally realisable system, consists out of rotating magnetic colloidal particles, i.e., (micro-)rotors, rotating in sync to an externally applied magnetic field, where the rotors solely interact via hydrodynamic and steric interactions. Overall, the agreement between simulations and experiments is very good, proving that hydrodynamic interactions play a key role in this and related systems.
While already an isolated rotating colloid is driven out of equilibrium, only collections of two or more rotors have experimentally shown to be able to convert the rotational energy input into translational dynamics in an orbital rotating fashion. The rotating colloids inject circular flows into the fluid, such that detailed balance is broken, and it is not a priori known whether equilibrium properties of colloids can be extended to isolated rotating colloids. A joint theoretical and experimental analysis of isolated, pairs, and small groups of hydrodynamically interacting rotors is given in chapter 2. While the translational dynamics of isolated rotors effectively resemble the dynamics of non-rotating colloids, the orbital rotation of pairs of rotors can be described with leading order hydrodynamics and a two-dimensional analogy of Faxén’s law is derived.
In chapter 3, a homogeneously distributed ensemble of rotors (bulk) as a realisation of a chiral active fluid is studied and it is explicitly shown computationally and experimentally that it carries odd viscosity. The mutual orbital translation of rotors and an increase of the effective solvent viscosity with rotor density lead to a non-monotonous behaviour of the average translational velocity. Meanwhile, the rotor suspension bears a finite osmotic compressibility resulting from the long-ranged nature of hydrody- namic interactions such that rotational and odd stresses are transmitted through the solvent also at small and intermediate rotor densities. Consequently, density inhomogeneities predicted for chiral active fluids with odd viscosity can be found and allow for an explicit measurement of odd viscosity in simulations and experiments. At intermediate densities, the collective dynamics shows the emergence of multi-scale vortices and chaotic motion which is identified as active turbulence with a self-similar power-law decay in the energy spectrum, showing that the injected energy on the rotor scale is transported to larger scales, similar to the inverse energy cascade of clas- sical two-dimensional turbulence. While either odd viscosity or active turbulence have been reported in chiral active matter previously, the system studied here shows that the emergence of both simultaneously is possible resulting from the osmotic compressibility and hydrodynamic mediation of odd and active stresses. The collective dynamics of colloids rotating out of phase, i.e., where a constant torque instead of a constant angular velocity is applied, is shown to be qualitatively very similar. However, at smaller densities, local density inhomogeneities imply position dependent angular velocities of the rotors resulting from inter-rotor friction.
While the friction of a quasi-2D layer of active colloids with the substrate is often not easily modifiable in experiments, the incorporation of substrate friction into the simulation models typically implies a considerable increase in computational effort. In chapter 4, a very efficient way of incorporating the friction with a substrate into a two-dimensional multiparticle collision dynamics solvent is introduced, allowing for an explicit investigation of the influences of substrate on active dynamics. For the rotor fluid, it is explicitly shown that the influence of the substrate friction results in a cutoff of the hydrodynamic interaction length, such that the maximum size of the formed vortices is controlled by the substrate friction, also resulting in a cutoff in the energy spectrum, because energy is taken out of the system at the respective length. These findings are in agreement with the experiments.
Since active particles in confinement are known to organise in states of collective dynamics, ensembles of rotationally actuated colloids are studied in circular confinement and in the presence of periodic obstacle lattices in chapters 5 and 6, respectively. The results show that the chaotic active turbulent transport of rotors in suspension can be enhanced and guided resulting from edge flows generated at the boundaries, as has recently been reported for a related chiral active system. The consequent collective rotor dynamics can be regarded as a superposition of active turbulent and imposed flows, leading to on average stationary flows. In contrast to the bulk dynamics, the imposed flows inject additional energy into the system on the long length scales, and the same scaling behaviour of the energy spectrum as in bulk is only obtained if the energy injection scales, due to the mutual generation of rotor translational dynamics throughout the system and the edge flows, are well separated. The combination of edge flow and entropic layering at the boundaries leads to oscillating hydrodynamic stresses and consequently to an oscillating vorticity profile. In the presence of odd viscosity, this consequently leads to non-trivial steady-state density modulations at the boundary, resulting from a balance of osmotic pressure and odd stresses.
Relevant for the efficient dispersion and mixing of inert particles on the mesoscale by means of active turbulent mixing powered by rotors, a study of the dynamics of a binary mixture consisting out of rotors and passive particles is presented in chapter 7. Because the rotors are not self-propelled, but the translational dynamics is induced by the surrounding rotors, the passive particles, which do not inject further energy into the system, are transported according to the same mechanism as the rotors. The collective dynamics thus resembles the pure rotor bulk dynamics at the respective density of only rotors. However, since no odd stresses act between the passive particles, only mutual rotor interactions lead to odd stresses leading to the accumulation of rotors in the regions of positive vorticity. This density increase is associated with a pressure increase, which balances the odd stresses acting on the rotors. However, the passive particles are only subject to the accumulation induced pressure increase such that these particles are transported into the areas of low rotor concentration, i.e., the regions of negative vorticity. Under conditions of sustained vortex flow, this results in segregation of both particle types.
Since local symmetry breaking can convert injected rotational into translational energy, microswimmers can be constructed out of rotor materials when a suitable breaking of symmetry is kept in the vicinity of a rotor. One hypothetical realisation, i.e., a coupled rotor pair consisting out of two rotors of opposite angular velocity and of fixed distance, termed a birotor, are studied in chapter 8. The birotor pumps the fluid into one direction and consequently translates into the opposite direction, and creates a flow field reminiscent of a source doublet, or sliplet flow field. Fixed in space the birotor might be an interesting realisation of a microfluidic pump. The trans- lational dynamics of a birotor can be mapped onto the active Brownian particle model for single swimmers. However, due to the hydrodynamic interactions among the rotors, the birotor ensemble dynamics do not show the emergence of stable motility induced clustering. The reason for this is the flow created by birotor in small aggregates which effectively pushes further arriving birotors away from small aggregates, which eventually are all dispersed by thermal fluctuations
Development of in-vitro in-silico technologies for modelling and analysis of haematological malignancies
Worldwide, haematological malignancies are responsible for roughly 6% of all the cancer-related deaths. Leukaemias are one of the most severe types of cancer, as only about 40% of the patients have an overall survival of 10 years or more. Myelodysplastic Syndrome (MDS), a pre-leukaemic condition, is a blood disorder characterized by the presence of dysplastic, irregular, immature cells, or blasts, in the peripheral blood (PB) and in the bone marrow (BM), as well as multi-lineage cytopenias.
We have created a detailed, lineage-specific, high-fidelity in-silico erythroid model that incorporates known biological stimuli (cytokines and hormones) and a competing diseased haematopoietic population, correctly capturing crucial biological checkpoints (EPO-dependent CFU-E differentiation) and replicating the in-vivo erythroid differentiation dynamics. In parallel, we have also proposed a long-term, cytokine-free 3D cell culture system for primary MDS cells, which was firstly optimized using easily-accessible healthy controls. This system enabled long-term (24-day) maintenance in culture with high (>75%) cell viability, promoting spontaneous expansion of erythroid phenotypes (CD71+/CD235a+) without the addition of any exogenous cytokines. Lastly, we have proposed a novel in-vitro in-silico framework using GC-MS metabolomics for the metabolic profiling of BM and PB plasma, aiming not only to discretize between haematological conditions but also to sub-classify MDS patients, potentially based on candidate biomarkers. Unsupervised multivariate statistical analysis showed clear intra- and inter-disease separation of samples of 5 distinct haematological malignancies, demonstrating the potential of this approach for disease characterization.
The work herein presented paves the way for the development of in-vitro in-silico technologies to better, characterize, diagnose, model and target haematological malignancies such as MDS and AML.Open Acces
Search for third generation vector-like leptons with the ATLAS detector
The Standard Model of particle physics provides a concise description of the building blocks of our universe in terms of fundamental particles and their interactions. It is an extremely successful theory, providing a plethora of predictions that precisely match experimental observation. In 2012, the Higgs boson was observed at CERN and was the last particle predicted by the Standard Model that had yet-to-be discovered. While this added further credibility to the theory, the Standard Model appears incomplete. Notably, it only accounts for 5% of the energy density of the universe (the rest being ``dark matter'' and ``dark energy''), it cannot resolve the gravitational force with quantum theory, it does not explain the origin of neutrino masses and cannot account for matter/anti-matter asymmetry. The most plausible explanation is that the theory is an approximation and new physics remains.
Vector-like leptons are well-motivated by a number of theories that seek to provide closure on the Standard Model. They are a simple addition to the Standard Model and can help to resolve a number of discrepancies without disturbing precisely measured observables. This thesis presents a search for vector-like leptons that preferentially couple to tau leptons. The search was performed using proton-proton collision data from the Large Hadron Collider collected by the ATLAS experiment from 2015 to 2018 at center-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 139 inverse femtobarns. Final states of various lepton multiplicities were considered to isolate the vector-like lepton signal against Standard Model and instrumental background. The major backgrounds mimicking the signal are from WZ, ZZ, tt+Z production and from mis-identified leptons. A number of boosted decision trees were used to improve rejection power against background where the signal was measured using a binned-likelihood estimator. No excess relative to the Standard Model was observed. Exclusion limits were placed on vector-like leptons in the mass range of 130 to 898 GeV
Structure and adsorption properties of gas-ionic liquid interfaces
Supported ionic liquids are a diverse class of materials that have been considered
as a promising approach to design new surface properties within solids for gas
adsorption and separation applications. In these materials, the surface morphology and
composition of a porous solid are modified by depositing ionic liquid. The resulting
materials exhibit a unique combination of structural and gas adsorption properties
arising from both components, the support, and the liquid. Naturally, theoretical and
experimental studies devoted to understanding the underlying principles of exhibited
interfacial properties have been an intense area of research. However, a complete
understanding of the interplay between interfacial gas-liquid and liquid-solid
interactions as well as molecular details of these processes remains elusive.
The proposed problem is challenging and in this thesis, it is approached from
two different perspectives applying computational and experimental techniques. In
particular, molecular dynamics simulations are used to model gas adsorption in films
of ionic liquids on a molecular level. A detailed description of the modeled systems is
possible if the interfacial and bulk properties of ionic liquid films are separated. In this
study, we use a unique method that recognizes the interfacial and bulk structures of
ionic liquids and distinguishes gas adsorption from gas solubility. By combining
classical nitrogen sorption experiments with a mean-field theory, we study how liquid-solid interactions influence the adsorption of ionic liquids on the surface of the porous
support.
The developed approach was applied to a range of ionic liquids that feature
different interaction behavior with gas and porous support. Using molecular
simulations with interfacial analysis, it was discovered that gas adsorption capacity
can be directly related to gas solubility data, allowing the development of a predictive
model for the gas adsorption performance of ionic liquid films. Furthermore, it was
found that this CO2 adsorption on the surface of ionic liquid films is determined by the
specific arrangement of cations and anions on the surface. A particularly important
result is that, for the first time, a quantitative relation between these structural and
adsorption properties of different ionic liquid films has been established. This link
between two types of properties determines design principles for supported ionic
liquids.
However, the proposed predictive model and design principles rely on the
assumption that the ionic liquid is uniformly distributed on the surface of the porous
support. To test how ionic liquids behave under confinement, nitrogen physisorption
experiments were conducted for micro‐ and mesopore analysis of supported ionic
liquid materials. In conjunction with mean-field density functional theory applied to
the lattice gas and pore models, we revealed different scenarios for the pore-filling
mechanism depending on the strength of the liquid-solid interactions.
In this thesis, a combination of computational and experimental studies provides
a framework for the characterization of complex interfacial gas-liquid and liquid-solid
processes. It is shown that interfacial analysis is a powerful tool for studying
molecular-level interactions between different phases. Finally, nitrogen sorption
experiments were effectively used to obtain information on the structure of supported
ionic liquids
Fast Similarity Graph Construction via Data Sketching Techniques
Graphs are mathematical structures used to model objects and their pairwise relationships. Due to their simple but expressive abstract representation, they are commonly used to model various types of relations and processes in technological, social or biological systems and have found numerous applications. A special type of graph is the similarity graph in which nodes represent entities and there is an edge connecting two nodes if the two entities are similar based on some similarity measure. In a typical scenario, raw data of entities are provided in the form of a relational dataset, matrix or a tensor and a similarity graph is built to facilitate graph-based analysis like node importance, node classification, link prediction, community detection, outlier detection, and more.
The ability to construct similarity graphs fast is important and with a potential for high impact, thus several approximation techniques have been proposed. In this work, we propose data sketching based methods for fast approximate similarity graph construction. Data sketching techniques are applied on the raw data and are designed to achieve desired error guarantees. They can drastically reduce the size of raw data on which we operate, allowing for faster construction and analysis of similarity graphs, but with approximate results. This is a desirable tradeoff for many applications in diverse domains.
Through a thorough experimental evaluation, we demonstrate that our sketching methods outperform sensible baselines and competitor methods proposed for the problem. First, they are much faster than exact methods while maintaining high accuracy in constructing the similarity graph. Furthermore, our methods demonstrate significantly higher accuracy than competitive methods on generic graph analysis tasks. We demonstrate the effectiveness of our methods on different real-world graph applications
Seeing the wood and the trees? Lessons from applying ecosystem services in forest planning
In the UK and globally, forestry is experiencing an upsurge in interest as forests are
anticipated to play a major role in addressing the twin crises of biodiversity loss and climate
change that our society currently face. In the UK, forest management has traditionally
focused on timber production yet forests provide many more ecosystem services (ES),
including climate mitigation, slope stabilisation, and numerous wider ecological and social
benefits. Forestry requires long-term planning, and so understanding the impacts of
forest management is a critical part of predicting the future supply of these benefits, that
can then inform decision-making. This thesis has taken a transdisciplinary approach
to operationalise evidence of management impacts on ES to support planning and
management decision-making for a public forest case study in Scotland.
The research questions address three key areas: the link between management and the
supply of ES; demand for ES from the public as a key stakeholder of the public forest
estate; and the use of quantified ES information for supporting forest planning. There is
a growing body of published research on forest ES; this was reviewed to synthesise the
evidence of impacts of management on supply, and the trade-offs and synergies resulting
from different management approaches. The review showed that maintaining the supply of
ES at the forest scale will require a range of management approaches that build resilience
in forests in the face of socio-economic and climate change uncertainty.
A collaborative, case study approach was identified at the outset as critical to meet the
thesis aims. The project was co-developed with a Forest Planning Manager (FM), and the
activities undertaken formed five phases:
Phase 1. Problem scoping and definition, to identify knowledge gaps and research
questions, and select the case study forest. The chosen forest in northwest Scotland is
a predominantly spruce plantation that is important for timber production, recreation and
habitat for a protected species.
Phase 2. Data collection for baseline ES supply, and current and future ES demand: to
address one of the main knowledge gaps identified during Phase 1. Forest users and local
communities were surveyed and the results showed general support for environmental,
health and wellbeing outcomes, while timber production, climate mitigation and economic
growth have lower priority.
Phase 3. Baseline ES mapping: to test the usefulness of these data for operational
decision-making. ES supply hotspots of timber, carbon storage, recreation and
biodiversity benefits were mapped, which highlighted areas where there may be conflicts
in achieving multiple benefits. Hotspot mapping methods were compared with the FM,
who found that individual ES maps were most informative for operational decision-making.
Phase 4. Scenario development and modelling: to explore how ES supply may change
in future in response to management, including the impact of climate change. Forest
development was simulated for 150 years to understand future ES supply under business
as usual management using a dynamically coupled modelling approach. These results
were then compared with alternative management scenarios developed with the FM.
Phase 5. Data visualisation, feedback and reflection: to provide the modelling results in an
interactive form that can support the forest planning process, and reflect on the research
process to learn lessons for the future. A data visualisation dashboard was developed that
the FM found useful for exploring the results, although there were unresolved challenges
related to interpretation, particularly benchmarking and scaling issues.
Overall, the main findings of the thesis showed that forest structure is more important
than species for ES supply in this type of forest. In addition, forest management intensity
decisions have more impact than climate in this region on future ES supply. The study
showed that there are more trade-offs among ES under higher intensity management,
and more synergies under lower intensity management. The simulation showed that time
lags must be anticipated and accepted for delivering a wider suite of ES than timber. The
ES framework provides a suitable method for delivering evidence that demonstrates how
management influences the supply of benefits beyond the wood it supplies that can inform
forest planning. It showed that there are time lags in ES responses to management, and
that the scale at which ES are reported can have important consequences for measuring
change. This is a challenge for using ES in planning. Co-developing the approach ensured
the results were salient, as they resulted in direct instrumental changes to the new forest
management plan that are intended to deliver wider environmental and social benefits in
the future. There were also wider benefits from this project, such as improved awareness
of the link between management and ES supply that the FM can apply in future planning
decision-making
Optimización del rendimiento y la eficiencia energética en sistemas masivamente paralelos
RESUMEN Los sistemas heterogéneos son cada vez más relevantes, debido a sus capacidades de rendimiento y eficiencia energética, estando presentes en todo tipo de plataformas de cómputo, desde dispositivos embebidos y servidores, hasta nodos HPC de grandes centros de datos. Su complejidad hace que sean habitualmente usados bajo el paradigma de tareas y el modelo de programación host-device. Esto penaliza fuertemente el aprovechamiento de los aceleradores y el consumo energético del sistema, además de dificultar la adaptación de las aplicaciones.
La co-ejecución permite que todos los dispositivos cooperen para computar el mismo problema, consumiendo menos tiempo y energía. No obstante, los programadores deben encargarse de toda la gestión de los dispositivos, la distribución de la carga y la portabilidad del código entre sistemas, complicando notablemente su programación.
Esta tesis ofrece contribuciones para mejorar el rendimiento y la eficiencia energética en estos sistemas masivamente paralelos. Se realizan propuestas que abordan objetivos generalmente contrapuestos: se mejora la usabilidad y la programabilidad, a la vez que se garantiza una mayor abstracción y extensibilidad del sistema, y al mismo tiempo se aumenta el rendimiento, la escalabilidad y la eficiencia energética. Para ello, se proponen dos motores de ejecución con enfoques completamente distintos.
EngineCL, centrado en OpenCL y con una API de alto nivel, favorece la máxima compatibilidad entre todo tipo de dispositivos y proporciona un sistema modular extensible. Su versatilidad permite adaptarlo a entornos para los que no fue concebido, como aplicaciones con ejecuciones restringidas por tiempo o simuladores HPC de dinámica molecular, como el utilizado en un centro de investigación internacional.
Considerando las tendencias industriales y enfatizando la aplicabilidad profesional, CoexecutorRuntime proporciona un sistema flexible centrado en C++/SYCL que dota de soporte a la co-ejecución a la tecnología oneAPI. Este runtime acerca a los programadores al dominio del problema, posibilitando la explotación de estrategias dinámicas adaptativas que mejoran la eficiencia en todo tipo de aplicaciones.ABSTRACT Heterogeneous systems are becoming increasingly relevant, due to their performance and energy efficiency capabilities, being present in all types of computing platforms, from embedded devices and servers to HPC nodes in large data centers. Their complexity implies that they are usually used under the task paradigm and the host-device programming model. This strongly penalizes accelerator utilization and system energy consumption, as well as making it difficult to adapt applications.
Co-execution allows all devices to simultaneously compute the same problem, cooperating to consume less time and energy. However, programmers must handle all device management, workload distribution and code portability between systems, significantly complicating their programming.
This thesis offers contributions to improve performance and energy efficiency in these massively parallel systems. The proposals address the following generally conflicting objectives: usability and programmability are improved, while ensuring enhanced system abstraction and extensibility, and at the same time performance, scalability and energy efficiency are increased. To achieve this, two runtime systems with completely different approaches are proposed.
EngineCL, focused on OpenCL and with a high-level API, provides an extensible modular system and favors maximum compatibility between all types of devices. Its versatility allows it to be adapted to environments for which it was not originally designed, including applications with time-constrained executions or molecular dynamics HPC simulators, such as the one used in an international research center.
Considering industrial trends and emphasizing professional applicability, CoexecutorRuntime provides a flexible C++/SYCL-based system that provides co-execution support for oneAPI technology. This runtime brings programmers closer to the problem domain, enabling the exploitation of dynamic adaptive strategies that improve efficiency in all types of applications.Funding: This PhD has been supported by the Spanish Ministry of Education (FPU16/03299 grant),
the Spanish Science and Technology Commission under contracts TIN2016-76635-C2-2-R
and PID2019-105660RB-C22.
This work has also been partially supported by the Mont-Blanc 3: European Scalable and
Power Efficient HPC Platform based on Low-Power Embedded Technology project (G.A. No.
671697) from the European Union’s Horizon 2020 Research and Innovation Programme
(H2020 Programme). Some activities have also been funded by the Spanish Science and Technology
Commission under contract TIN2016-81840-REDT (CAPAP-H6 network).
The Integration II: Hybrid programming models of Chapter 4 has been partially performed
under the Project HPC-EUROPA3 (INFRAIA-2016-1-730897), with the support of the EC
Research Innovation Action under the H2020 Programme. In particular, the author gratefully
acknowledges the support of the SPMT Department of the High Performance Computing
Center Stuttgart (HLRS)
Development of a light-sheet fluorescence microscope employing an ALPAO deformable mirror to achieve video-rate remote refocusing and volumetric imaging.
There are numerous situations in microscopy where it is desirable to remotely refocus a microscope employing a high numerical aperture (NA) objective lens. This thesis describes the characterisation,
development and implementation of an Alpao membrane deformable mirror-based system to achieve this goal for a light-sheet fluorescence microscope (LSFM).
The Alpao deformable mirror (DM) DM97-15 used is this work has 97 actuators and was sufficiently
fast to perform refocus sweeps at 25 Hz and faster. However, a known issue with using Alpao
deformable mirrors in open-loop mode is that they exhibit viscoelastic creep and temperature-
dependent variations in the mirror response. The effect of visco-elastic creep was reduced by
ensuring that the mirror profile was on average constant on timescales shorter than the characteristic time of the visco-elastic creep. The thermal effect was managed by ensuring that the electrical power delivered to the actuators was constant prior to optimisation and use. This was achieved by ensuring that the frequency and amplitude of oscillation of the mirror was constant prior to optimisation, so that it reached a thermal steady state, was approximately constant during optimisation and constant during use.
The image-based optimisation procedure employed used an estimate of the Strehl ratio of the optical system calculated from an image of an array of 1 μm diameter holes. The optimisation procedure
included optimising the amount of high-NA defocus and the Zernike modes from Noll indices 4 to 24. The system was tested at 26.3 refocus sweeps per second over a refocus range of -50 to 50 μm with a 40x/0.85 air objective and a 40x/0.80 water immersion objective. The air objective enabled a mean Strehl metric of more than 0.6 over a lateral field of view of 200x200 microns and for a refocus range of 45 microns. The water objective achieved a mean Strehl metric of more than 0.6 over a lateral field of view of 200x200 microns over a larger refocus range of 77 microns.
The DM-based refocusing system was then incorporated into a LSFM setup. The spatial resolution of the system was characterised using fluorescent beads imaged volumetrically at 26.3 volumes per second. The performance of the system was also demonstrated for imaging fluorescence pollen grain samples.Open Acces
Adaptive task selection using threshold-based techniques in dynamic sensor networks
Sensor nodes, like many social insect species, exist in harsh environments in large groups, yet possess very limited amount of resources. Lasting for as long as possible, and fulfilling the network purposes are the ultimate goals of sensor networks. However, these goals are inherently contradictory. Nature can be a great source of inspiration for mankind to find methods to achieve both extended survival, and effective operation. This work aims at applying the threshold-based action selection mechanisms inspired from insect societies to perform action selection within sensor nodes. The effect of this micro-model on the macro-behaviour of the network is studied in terms of durability and task performance quality. Generally, this is an example of using bio-inspiration to achieve adaptivity in sensor networks
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