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How to escape local optima in black box optimisation when non elitism outperforms elitism
Get PDFEscaping local optima is one of the major obstacles to function optimisation. Using the metaphor of a fitness landscape, local optima correspond to hills separated by fitness valleys that have to be overcome. We define a class of fitness valleys of tunable difficulty by considering their length, representing the Hamming path between the two optima and their depth, the drop in fitness. For this function class we present a runtime comparison between stochastic search algorithms using different search strategies. The (1+1) EA is a simple and well-studied evolutionary algorithm that has to jump across the valley to a point of higher fitness because it does not accept worsening moves (elitism). In contrast, the Metropolis algorithm and the Strong Selection Weak Mutation (SSWM) algorithm, a famous process in population genetics, are both able to cross the fitness valley by accepting worsening moves. We show that the runtime of the (1+1) EA depends critically on the length of the valley while the runtimes of the non-elitist algorithms depend crucially on the depth of the valley. Moreover, we show that both SSWM and Metropolis can also efficiently optimise a rugged function consisting of consecutive valleys
Charge sensing and spin relaxation times of holes in Ge hut wires
Get PDFA qubit, a unit of quantum information, is essentially any quantum mechanical two-level system which can be coherently controlled. Still, to be used for computation, it has to fulfill criteria. Qubits, regardless of the system in which they are realized, suffer from decoherence. This leads to loss of the information stored in the qubit. The upper bound of the time scale on which decoherence happens is set by the spin relaxation time.
In this thesis I studied a two-level system consisting of a Zeeman-split hole spin confined in a quantum dot formed in a Ge hut wire. Such Ge hut wires have emerged as a promising material system for the realization of spin qubits, due to the combination of two significant properties: long spin coherence time as expected for group IV semiconductors due to the low hyperfine interaction and a strong valence band spin-orbit coupling. Here, I present how to fabricate quantum dot devices suitable for electrical transport measurements. Coupled quantum dot devices allowed the realization of a charge sensor, which is electrostatically and tunnel coupled to a quantum dot. By integrating the charge sensor into a radio-frequency reflectometry setup, I performed for the first time single-shot readout measurements of hole spins and extracted the hole spin relaxation times in Ge hut wires
Disease defence in garden ants
No full textContagious diseases must transmit from infectious to susceptible hosts in order to reproduce. Whilst vectored pathogens can rely on intermediaries to find new hosts for them, many infectious pathogens require close contact or direct interaction between hosts for transmission. Hence, this means that conspecifics are often the main source of infection for most animals and so, in theory, animals should avoid conspecifics to reduce their risk of infection. Of course, in reality animals must interact with one another, as a bare minimum, to mate. However, being social provides many additional benefits and group living has become a taxonomically diverse and widespread trait. How then do social animals overcome the issue of increased disease?
Over the last few decades, the social insects (ants, termites and some bees and wasps) have become a model system for studying disease in social animals. On paper, a social insect colony should be particularly susceptible to disease, given that they often contain thousands of potential hosts that are closely related and frequently interact, as well as exhibiting stable environmental conditions that encourage microbial growth. Yet, disease outbreaks appear to be rare and attempts to eradicate pest species using pathogens have failed time and again. Evolutionary biologists investigating this observation have discovered that the reduced disease susceptibility in social insects is, in part, due to collectively performed disease defences of the workers. These defences act like a “social immune system” for the colony, resulting in a per capita decrease in disease, termed social immunity. Our understanding of social immunity, and its importance in relation to the immunological defences of each insect, continues to grow, but there remain many open questions.
In this thesis I have studied disease defence in garden ants. In the first data chapter, I use the invasive garden ant, Lasius neglectus, to investigate how colonies mitigate lethal infections and prevent them from spreading systemically. I find that ants have evolved ‘destructive disinfection’ – a behaviour that uses endogenously produced acidic poison to kill diseased brood and to prevent the pathogen from replicating. In the second experimental chapter, I continue to study the use of poison in invasive garden ant colonies, finding that it is sprayed prophylactically within the nest. However, this spraying has negative effects on developing pupae when they have had their cocoons artificially removed. Hence, I suggest that acidic nest sanitation may be maintaining larval cocoon spinning in this species. In the next experimental chapter, I investigated how colony founding black garden ant queens (Lasius niger) prevent disease when a co-foundress dies. I show that ant queens prophylactically perform undertaking behaviours, similar to those performed by the workers in mature nests. When a co-foundress was infected, these undertaking behaviours improved the survival of the healthy queen. In the final data chapter, I explored how immunocompetence (measured as antifungal activity) changes as incipient black garden ant colonies grow and mature, from the solitary queen phase to colonies with several hundred workers. Queen and worker antifungal activity varied throughout this time period, but despite social immunity, did not decrease as colonies matured.
In addition to the above data chapters, this thesis includes two co-authored reviews. In the first, we examine the state of the art in the field of social immunity and how it might develop in the future. In the second, we identify several challenges and open questions in the study of disease defence in animals. We highlight how social insects offer a unique model to tackle some of these problems, as disease defence can be studied from the cell to the society
Dyson equation and eigenvalue statistics of random matrices
Get PDFThe eigenvalue density of many large random matrices is well approximated by a deterministic measure, the \emph{self-consistent density of states}.
In the present work, we show this behaviour for several classes of random matrices.
In fact, we establish that, in each of these classes, the self-consistent density of states approximates
the eigenvalue density of the random matrix on all scales slightly above the typical eigenvalue spacing.
For large classes of random matrices, the self-consistent density of states exhibits several universal features.
We prove that, under suitable assumptions,
random Gram matrices and Hermitian random matrices with decaying correlations have a -Hölder continuous
self-consistent density of states on , which is analytic,
where it is positive, and has either a square root edge or a cubic root cusp, where it vanishes.
We, thus, extend the validity of the corresponding result for Wigner-type matrices from~\cite{AjankiCPAM,AjankiQVE,Ajankirandommatrix}.
We show that is determined as the inverse Stieltjes transform of the normalized trace of the unique solution to the \emph{Dyson equation}
on \C^{N\times N} with the constraint .
Here, lies in the complex upper half-plane, is a self-adjoint element of \C^{N\times N}
and is a positivity-preserving operator on \C^{N\times N} encoding the first two moments of the random matrix.
In order to analyze a possible limit of for and address some applications in free probability theory,
we also consider the Dyson equation on infinite dimensional von Neumann algebras.
We present two applications to random matrices. We first establish that, under certain assumptions, large random matrices with independent entries have a rotationally symmetric
self-consistent density of states which is supported on a centered disk in \C.
Moreover, it is infinitely often differentiable apart from a jump on the boundary of this disk.
Second, we show edge universality at all regular (not necessarily extreme) spectral edges
for Hermitian random matrices with decaying correlations
Point Interactions in Systems of Fermions
Get PDFIn this thesis we will discuss systems of point interacting fermions, their stability and other
spectral properties. Whereas for bosons a point interacting system is always unstable this ques-
tion is more subtle for a gas of two species of fermions. In particular the answer depends on
the mass ratio between these two species.
Most of this work will be focused on the N + M model which consists of two species
of fermions with N, M particles respectively which interact via point interactions. We will
introduce this model using a formal limit and discuss the N + 1 system in more detail. In
particular, we will show that for mass ratios above a critical one, which does not depend on the
particle number, the N + 1 system is stable. In the context of this model we will prove rigorous
versions of Tan relations which relate various quantities of the point-interacting model.\ud
By restricting the N + 1 system to a box we define a finite density model with point in-
teractions. In the context of this system we will discuss the energy change when introducing
a point-interacting impurity into a system of non-interacting fermions. We will see that this
change in energy is bounded independently of the particle number and in particular the bound
only depends on the density and the scattering length.
As another special case of the N + M model we will show stability of the 2 + 2 model for
mass ratios in an interval around one.
Further we will investigate a different model of point interactions which was discussed
before in the literature and which is, contrary to the N + M model, not given by a limiting
procedure but is based on a Dirichlet form. We will show that this system behaves trivially
in the thermodynamic limit, i.e. the free energy per particle is the same as the one of the
non-interacting system
The influence of sequence context on the evolution of bacterial gene expression
No full textExpression of genes is a fundamental molecular phenotype that is subject to evolution by different types of mutations. Both the rate and the effect of mutations may depend on the DNA sequence context of a particular gene or a particular promoter sequence. In this thesis I investigate the nature of this dependence using simple genetic systems in Escherichia coli. With these systems I explore the evolution of constitutive gene expression from random starting sequences at different loci on the chromosome and at different locations in sequence space. First, I dissect chromosomal neighborhood effects that underlie locus-dependent differences in the potential of a gene under selection to become more highly expressed. Next, I find that the effects of point mutations in promoter sequences are dependent on sequence context, and that an existing energy matrix model performs poorly in predicting relative expression of unrelated sequences. Finally, I show that a substantial fraction of random sequences contain functional promoters and I present an extended thermodynamic model that predicts promoter strength in full sequence space. Taken together, these results provide new insights and guides on how to integrate information on sequence context to improve our qualitative and quantitative understanding of bacterial gene expression, with implications for rapid evolution of drug resistance, de novo evolution of genes, and horizontal gene transfer
Mixing layer instability and vorticity amplification in a creeping viscoelastic flow
Get PDFWe report quantitative evidence of mixing-layer elastic instability in a viscoelastic
fluid flow between two widely spaced obstacles hindering a channel flow at Re<<1 and
Wi>>1. Two mixing layers with nonuniform shear velocity profiles are formed in the
region between the obstacles. The mixing-layer instability arises in the vicinity of an
inflection point on the shear velocity profile with a steep variation in the elastic stress.
The instability results in an intermittent appearance of small vortices in the mixing layers
and an amplification of spatiotemporal averaged vorticity in the elastic turbulence regime.
The latter is characterized through scaling of friction factor with Wi and both pressure and
velocity spectra. Furthermore, the observations reported provide improved understanding
of the stability of the mixing layer in a viscoelastic fluid at large elasticity, i.e., Wi>>1
and Re<<1 and oppose the current view of suppression of vorticity solely by polymer
additives
FlexMaps: Computational Design of Flat Flexible Shells for Shaping 3D Objects
No full textWe propose FlexMaps, a novel framework for fabricating smooth shapes out of flat, flexible panels with tailored mechanical properties. We start by mapping the 3D surface onto a 2D domain as in traditional UV mapping to design a set of deformable flat panels called FlexMaps. For these panels, we design and obtain specific mechanical properties such that, once they are assembled, the static equilibrium configuration matches the desired 3D shape. FlexMaps can be fabricated from an almost rigid material, such as wood or
plastic, and are made flexible in a controlled way by using computationally designed spiraling microstructures
Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow
No full textAssortative mating is an important driver of speciation in populations with gene flow and is predicted to evolve under certain conditions in few-locus models. However, the evolution of assortment is less understood for mating based on quantitative traits, which are often characterized by high genetic variability and extensive linkage disequilibrium between trait loci. We explore this scenario for a two-deme model with migration, by considering a single polygenic trait subject to divergent viability selection across demes, as well as assortative mating and sexual selection within demes, and investigate how trait divergence is shaped by various evolutionary forces. Our analysis reveals the existence of sharp thresholds of assortment strength, at which divergence increases dramatically. We also study the evolution of assortment via invasion of modifiers of mate discrimination and show that the ES assortment strength has an intermediate value under a range of migration-selection parameters, even in diverged populations, due to subtle effects which depend sensitively on the extent of phenotypic variation within these populations. The evolutionary dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal models. We further investigate the sensitivity of our results to the assumptions of the hypergeometric model, using individual-based simulations
PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana
No full textCoordinated cell polarization in developing tissues is a recurrent theme in multicellular organisms. In plants, a directional distribution of the plant hormone auxin is at the core of many developmental programs. A feedback regulation of auxin on the polarized localization of PIN auxin transporters in individual cells has been proposed as a self-organizing mechanism for coordinated tissue polarization, but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport remain unknown. We performed a microarray-based approach to find regulators of the auxin-induced PIN relocation in the Arabidopsis thaliana root. We identified a subset of a family of phosphatidylinositol transfer proteins (PITP), the PATELLINs (PATL). Here, we show that PATLs are expressed in partially overlapping cells types in different tissues going through mitosis or initiating differentiation programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis embryos, primary roots, lateral root primordia, and developing stomata. Higher order patl mutants display reduced PIN1 repolarization in response to auxin, shorter root apical meristem, and drastic defects in embryo and seedling development. This suggests PATLs redundantly play a crucial role in polarity and patterning in Arabidopsis