@article{18706,
  abstract     = {We prove discrete-to-continuum convergence for dynamical optimal transport on  Zd
 -periodic graphs with cost functional having linear growth at infinity. This result provides an answer to a problem left open by Gladbach, Kopfer, Maas, and Portinale (Calc Var Partial Differential Equations 62(5), 2023), where the convergence behaviour of discrete boundary-value dynamical transport problems is proved under the stronger assumption of superlinear growth. Our result extends the known literature to some important classes of examples, such as scaling limits of  1 -Wasserstein transport problems. Similarly to what happens in the quadratic case, the geometry of the graph plays a crucial role in the structure of the limit cost function, as we discuss in the final part of this work, which includes some visual representations.},
  author       = {Portinale, Lorenzo and Quattrocchi, Filippo},
  issn         = {1469-4425},
  journal      = {European Journal of Applied Mathematics},
  pages        = {1--29},
  publisher    = {Cambridge University Press},
  title        = {{Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs}},
  doi          = {10.1017/s0956792524000810},
  year         = {2024},
}

@unpublished{20571,
  abstract     = {We prove the convergence of a modified Jordan--Kinderlehrer--Otto scheme to a solution to the Fokker--Planck equation in $\Omega \Subset \mathbb{R}^d$ with general, positive and temporally constant, Dirichlet boundary conditions. We work under mild assumptions on the domain, the drift, and the initial datum.   In the special case where $\Omega$ is an interval in $\mathbb{R}^1$, we prove that such a solution is a gradient flow -- curve of maximal slope -- within a suitable space of measures, endowed with a modified Wasserstein distance.
Our discrete scheme and modified distance draw inspiration from contributions by A. Figalli and N. Gigli [J. Math. Pures Appl. 94, (2010), pp. 107--130], and J. Morales [J. Math. Pures Appl. 112, (2018), pp. 41--88] on an optimal-transport approach to evolution equations with Dirichlet boundary conditions. Similarly to these works, we allow the mass to flow from/to the boundary $\partial \Omega$ throughout the evolution. However, our leading idea is to also keep track of the mass at the boundary by working with measures defined on the whole closure $\overline \Omega$. The driving functional is a modification of the classical relative entropy that also makes use of the information at the boundary. As an intermediate result, when $\Omega$ is an interval in $\mathbb{R}^1$, we find a formula for the descending slope of this geodesically nonconvex functional. },
  author       = {Quattrocchi, Filippo},
  booktitle    = {arXiv},
  keywords     = {gradient flows, Jordan–Kinderlehrer–Otto scheme, curves of maximal slope, optimal transport, Dirichlet boundary conditions, Fokker–Planck equation},
  title        = {{Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions}},
  doi          = {10.48550/arXiv.2403.07803},
  year         = {2024},
}

@unpublished{20570,
  abstract     = {We investigate the minimal error in approximating a general probability
measure $\mu$ on $\mathbb{R}^d$ by the uniform measure on a finite set with
prescribed cardinality $n$. The error is measured in the $p$-Wasserstein
distance. In particular, when $1\le p<d$, we establish asymptotic upper and
lower bounds as $n \to \infty$ on the rescaled minimal error that have the
same, explicit dependency on $\mu$.
  In some instances, we prove that the rescaled minimal error has a limit.
These include general measures in dimension $d = 2$ with $1 \le p < 2$, and
uniform measures in arbitrary dimension with $1 \le p < d$. For some uniform
measures, we prove the limit existence for $p \ge d$ as well.
  For a class of compactly supported measures with H\"older densities, we
determine the convergence speed of the minimal error for every $p \ge 1$.
  Furthermore, we establish a new Pierce-type (i.e., nonasymptotic) upper
estimate of the minimal error when $1 \le p < d$.
  In the initial sections, we survey the state of the art and draw connections
with similar problems, such as classical and random quantization.},
  author       = {Quattrocchi, Filippo},
  booktitle    = {arXiv},
  keywords     = {optimal empirical quantization, vector quantization, Wasserstein distance, semidiscrete optimal transport, Zador’s Theorem, Pierce’s Lemma},
  title        = {{Asymptotics for optimal empirical quantization of measures}},
  doi          = {10.48550/arXiv.2408.12924},
  year         = {2024},
}

@phdthesis{17206,
  abstract     = {Males and females exhibit numerous differences, from the initial stages of sex determination to the
development of secondary sexual characteristics. In Drosophila, these differences have been
thoroughly studied. Extensive research has been performed to understand the role and molecular
mode of action of central sex in determining switch genes, such as transformer (tra) and Sex-lethal
(Sxl). Furthermore, studies have highlighted differential gene expression as an essential mechanism to
create sexual dimorphism. An alternative path to sexual dimorphism that has been less explored is
alternative splicing, the mechanism through which genes can produce multiple transcripts with
distinct properties and functions. The primary switch sex-determining gene Sxl is a good example of
the role of alternative splicing for sex-specific functions: the inclusion of a specific exon determines
the male or female form of the protein, which in turn switches on either the male or female
developmental pathway. The genes that act upstream of Sxl and determine which form is expressed -
the counter genes - have received less attention. This thesis addresses two critical questions about
the molecular encoding of sexes in the Drosophila melanogaster genome: First, the use of splice forms
in male and female tissues in D. melanogaster is examined, inferring the molecular and evolutionary
parameters shaping the diversity of the splicing landscape. Second, the behaviour of counter genes in
Drosophila-related species is investigated, shedding light on potential changes leading to their
incorporation into the sex-determination pathway.
For the alternative splicing analyses, long-read RNA sequencing of testes, ovaries, female and male
midguts, heads, and whole bodies was performed. A novel pipeline was developed to assign unique
transcript identifiers for each sequence of exons and introns in the read, enabling detailed
comparisons of splicing variants in each tissue/sex. Alternative splicing was found to be more
pervasive in females than males (22,201 exclusive splice forms in females versus 12,631 in males),
especially when comparing ovaries to other tissues. The ovaries alone displayed 15,299 exclusive
splice forms, suggesting most female exclusive splice forms originate there. Genome location and gene
age were also correlated with the number of splice forms per gene. In particular, the X and 4th
chromosomes (Muller elements A and F) showed more splice forms per gene than other
chromosomes. Additionally, genes older than 63 million years exhibited more splice forms per gene
than younger genes. Our results suggest that alternative splicing is more prevalent than previously
believed, with numerous female-exclusive forms, age, and location playing significant roles in shaping
its prevalence.
For the counter genes analyses, we combined published gene expression, genomic, and gene
interaction data from various clades (Bactrocera jarvisi, B. oleae, Ceratitis capitata, Mus musculus,
Caenorhabditis elegans, Homo sapiens, and D. melanogaster). The counter genes scute (sc), extra
macrochaetae (emc), groucho (gro), deadpan (dpn), daughterless (da), runt (run), Sxl, hermaphrodite
(her), and tra maintain conserved Muller element locations between C. capitata and D. melanogaster,
which are most of the counter genes identified in the C. capitata genome. Their expression patterns
during early embryogenesis in B. jarvisi and D. melanogaster are also similar for counter genes dpn,
gro, da, and emc. However, Sxl and sc are also found to have more extreme expression ratios between
the species. Lastly, gene interactions within the counter genes are conserved, with da-sc and gro-dpn
interactions occurring in Drosophila, worms, humans, and mice. Interactions such as dpn-sc, dpn-da,
da-emc, and gro-run are present in Drosophila, mice, and humans, suggesting these genes were
recruited by ancestral characteristics, primarily during embryogenesis. The conserved expression,
location, and interactions of counter genes suggest serendipitous recruitment of such genes instead
of a change in those characteristics as they were recruited for this function. },
  author       = {Raices, Julia},
  issn         = {2663-337X},
  pages        = {82},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination}},
  doi          = {10.15479/at:ista:17206},
  year         = {2024},
}

@phdthesis{18101,
  abstract     = {The Retroviridae family consists of two sub-families, the Orthoretrovirinae and the
Spumaretrovirinae. The Orthoretroviruses contain important human pathogens, such as the
human immunodeficiency virus 1 (HIV-1). They also harbor other retrovirus species which
are regularly used as model systems to study the retroviral life cycle. The main structural
component of the retroviruses, is the Gag protein and its truncation derivatives occurring
during viral maturation. Orthoretroviral Gag assemblies have been extensively studied to
understand the interactions that confer stability and morphology to viral particles.
The Spumaretrovirinae subfamily represent an early diverging branch of the Retroviridae.
Its members, the Foamy viruses (FV), share most of the conventional features found in
retroviruses. However, they also possess multiple characteristics that make them unique. In
particular, FV Gag does not get extensively cleaved as in orthoretroviruses. Hence, the Gag
architecture deviates from the canonical domain arrangement in FV. They also exhibit a
peculiar particle morphology, having no apparent immature state and a seemingly
icosahedral mature particle. Due to this, many fundamental questions on FV structural
assembly mechanisms remain open. To answer these questions, was the main focus of this
thesis.
Mainly, it is not known how FV assemble their core in a virus particle and what are the
important assembly interaction sites within said core. What is the minimum assembly
competent domain of FV Gag? Is there a morphological change in the assembly type of FVGag lattices? If so, what is defining these morphological shifts? Finally, it would be
interesting to know what is the evolutionary relationship between FV and the rest of the
retrotranscribing elements, from a structural point of view?
To answer these questions, membrane-enveloped mammalian cell-derived FV virus-like
particles (VLPs) were produced. Cryo-electron tomography (cryo-ET) analysis suggested
these FV VLPs do not form a canonical retroviral Gag lattice structure, which is in line with
earlier observations. To further evaluate FV Gag assembly competence and morphology,
the first bacterial cell-derived in vitro VLP assembly system was designed and optimized.
Using this system with different truncation variants, the minimum assembly competent
domain of FV Gag was found to be the putative CA300-477 domain. Varying VLP
morphologies were also observed and strongly suggested residues upstream of CA300-477
play a role in morphology determination. Finally, a combined cryo-electron microscopy (cryoEM) and cryo-ET approach was taken to analyze tubular assemblies from the minimal
assembly competent domain. This revealed an unexpectedly unique non-canonical
assembly architecture. Three novel lattice stabilizing interfaces were described which
proved to be as unique as the lattice arrangement. Comparison to a newly published FV CA
core structure revealed the CA-CA interactions in the atypical assembly do not recapitulate
what is described for the FV core lattice. However, the new in vitro VLP assembly system
obtained in this thesis also provides an exciting opportunity to study still unresolved FV
assembly features in a potentially facilitated approach compared to conventional methods.
In summary, this work provided a deeper understanding of the basic FV Gag assembly unit,
as well as presenting the first FV Gag-derived in vitro VLP assembly system. This system
reveals a novel and unique assembly architecture among retroviral in vitro assemblies.},
  author       = {Porley, Dario J},
  isbn         = {978-3-99078-041-1},
  issn         = {2663-337X},
  pages        = {131},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Structural characterization of spumavirus capsid assemblies}},
  doi          = {10.15479/at:ista:18101},
  year         = {2024},
}

@phdthesis{17319,
  abstract     = {This thesis comprises two distinct projects, each offering unique insights into fundamental
cellular processes. While distinct in their focus, these different perspectives have a common
theme: chemiosmotic theory and utilisation of the proton gradient for driving the essential
processes like auxin efflux and ATP synthesis, effectively bridging the membrane protein
structure and function from the realms of plant biology and cellular bioenergetics.
The first project of this thesis centres on the characterisation of PIN proteins, a class of
transmembrane transporters pivotal in the regulation of auxin transport and distribution in
plants. PINs form a conserved and phylogenetically abundant group of transporters present in
land plants and certain algae. Despite their great importance, they were one of the few elusive
proteins essential for plant development not to be structurally and mechanistically
characterised since their discovery almost 30 years ago. This work aimed to uncover the
structural and functional dynamics of the PIN protein-mediated auxin transport using an array
of experimental techniques, including protein purification, biochemical assays and structural
analysis. Through an exhaustive screening process that took several years and included testing
different PIN homologues, expression systems, constructs, and purification conditions, we
developed a robust protocol for isolating the pure, stable, and monodisperse PIN8 protein.
Moreover, utilising biophysical methods and buffer screening, we demonstrated that PIN8
exhibits detergent and pH-dependent stability, with mild detergents and lower pH (5.0 and 6.0)
being optimal for the stability of the protein. Using SEC-MALS and crosslinking, we
determined that PIN8 forms dimers, which was confirmed by our structural studies. We
obtained a cryo-EM map of PIN8 at pH 6.0, and, compared to recently published structures,
our map implies major pH-dependent conformational changes and possibly utilisation of the
proton gradient in the transport mechanism.
The subject of the second project was F1Fo-ATP synthase, an enzyme complex fundamental
to cellular energy metabolism. Through an approach integrating biochemical assays and
structural analysis, this research aimed to unveil the molecular mechanism of inhibition of ATP
synthase by yaku´amide, a bioactive compound with potential therapeutic implications. Using
submitochondrial particles and purified F1Fo-ATP synthase, we demonstrated that, contrary to
published data, yaku´amide inhibits both ATP hydrolysis and ATP synthesis reactions.
Moreover, we found that yaku´amide inhibitory activity is proton motive force (pmf)
dependent, with lower inhibition in a more coupled system. Utilising cryo-EM, we obtained
maps and models for the three main rotational states of murine ATP synthase (State 1 at 3.0 Å,
8
State 2 at 3.1 Å, and State 3 at 3.2 Å, overall). We observed several new features in our maps;
however, we cannot definitively determine the exact mechanism of yaku amide’s inhibition on
the protein due to either resolution limits or suboptimal binding of the inhibitor.},
  author       = {Lukic, Kristina},
  issn         = {2663-337X},
  pages        = {224},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku'amide B}},
  doi          = {10.15479/at:ista:17319},
  year         = {2024},
}

@phdthesis{17346,
  abstract     = {Acquiring, retaining, and retrieving information over a wide range of timescales are crucial
functions of the brain. The successful processing of memories affects many aspects of our
lives and enables us and many other organisms to operate in a complex environment and
to interact with it. In this context, the hippocampus and functionally connected brain
areas, such as the prefrontal cortex, are central and have been subject to intensive research
in the past decades. Storage of memories is believed to rely on distributed neural activity
within these neural circuits. Additionally, neural memory traces of recent experience are
reinstated during periods of rest or sleep. These reactivations are thought to play an
outstanding role in the consolidation of memories and potentially facilitate the transfer of
information from the hippocampus to cortical areas for long-term storage and integration
into existing knowledge.
However, there is growing evidence that memory-related neural representations in the
hippocampus are not as stable as initially thought and that they change even in the
absence of learning. It has been suggested that these changes reflect the accumulation of
experience, but the influence of interspersed consolidation periods has not been considered.
Previous studies have analyzed consolidation periods by detecting activity that strongly
resembled neural activity during the acquisition of memory. Besides being often limited
to only non-rapid eye movement (NREM) sleep, the used approaches were not capable of
tracking changes in neural representations over extended temporal periods. More fluid
representations do not only challenge our understanding of how information is stored, but
they also affect the transfer of information between brain areas during the consolidation
process.
For this thesis, I investigated the evolution of memory-related activity during sleep
periods expected to be involved in consolidation in the hippocampus and between the
hippocampus and prefrontal cortex. I found that reactivated activity in the hippocampus
gradually transformed during prolonged periods of sleep and inactivity. In the beginning,
neural activity strongly resembled acquisition activity, whereas, with the progression of
time, it became more similar to the subsequent recall activity. NREM periods drove
this process, while rapid-eye movement (REM) periods showed a resetting effect. This
reactivation drift was due to firing rate changes of a subset of cells and mirrored the
representational changes from the acquisition to the recall. A stable subset of cells
withstood the drift and maintained their activity. Therefore, my results indicate that
memory-related representations undergo spontaneous modifications during consolidation
periods and that these changes are predictive of representational drift.
Furthermore, I found that the amount of change in the neural activity during subsequent
sleep periods was biased by prior behavioral performance. Observed changes in the
hippocampus and the prefrontal cortex were synchronized and increased after poor
performance, highlighting a potential role in the exchange of information. Low-variance
vii
periods with distinct, more stable activity from a subset of cells significantly contributed
to the heightened synchrony between both areas. Hence, interleaved phases of more stable
neural activity could facilitate the information transfer between brain areas.
In conclusion, my investigations underline the fluidity of memory-related representations
and assign a prominent role to sleep reactivation periods in their evolution. In addition, I
identified a potential mechanism of stable activity phases that might facilitate the synchronization across hippocampal-prefrontal activity despite ongoing changes. Reconciling
and integrating findings from both spontaneous and behaviorally-related representational
changes in functionally related brain areas will help to broaden our understanding of how
knowledge is stored, maintained, updated, and transferred between brain areas.},
  author       = {Bollmann, Lars},
  issn         = {2663-337X},
  keywords     = {Memory, Hippocampus, Consolidation},
  pages        = {103},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Stability and change in the memory system during rest}},
  doi          = {10.15479/at:ista:17346},
  year         = {2024},
}

@phdthesis{17368,
  abstract     = {Recent advancements in molecular diagnostic techniques have enabled the collection of
multiple types of omics data from patients, including genomics, epigenomics, proteomics,
and transcriptomics. However, we lack effective methods for integrating all these different
data types and combining them with clinical outcomes to study the molecular mechanisms
that govern pathological phenotypes. We present multi-omics BayesW, a penalized Bayesian
regression method that can handle general omics data for survival analysis of time-to-event
phenotypes. Our method can: (1) accommodate incomplete data by allowing censored
individuals, (2) use continuous time-to-event data to test associations of markers with a
phenotype and (3) estimate effects jointly while allowing for independent groups of biological
markers. Extensive simulations using planted signals on real data demonstrate that our model
accurately retrieves the true parameters of the model while controlling for false discoveries
and maintaining the expected prediction accuracy. We address data correlations by estimating
the effects jointly, even between omic groups, while also estimating the individual variance
explained by each group. We apply our model to two datasets. Using 18,000 individuals from
the Generation Scotland study we model the association of time at onset of Type 2 Diabetes,
Stroke, Ischemic Disease, and Osteoarthritis from baseline study entry, with 831,724 CpG
methylation probes. We find that large proportions of variation in disease onset times can
be attributed to methylation as measured in whole blood at baseline in individuals without
disease symptoms. We then apply our model to The Cancer Genome Atlas (TCGA) pan-cancer
dataset, in which we use 5 types of omics: copy number variation, epigenetics, somatic
mutations, miRNA, and gene expression. For cancer survival age-at-onset we find that, when
fitting the 5 groups together, almost all variation attributable to "omics" data is explained by
DNA methylation. When considering progression times, both methylation and gene expression
explain a large part of the variance. We found 2 genes that are significantly associated (95%
posterior inclusion probability) with cancer survival time, conditional on all other genome-wide
omics data variation. Owing to the vast variability of mechanisms characterizing different
cancers, there are likely few specific genes with a strong signal in a pan-cancer setting. Taken
together, we showed the applicability of our multi-omics BayesW model to a wide-range of
biological questions in multi-omics data.
},
  author       = {Villanueva Marijuan, Ariadna},
  issn         = {2791-4585},
  keywords     = {Epigenetics, Multi-omics, Bayesian regression},
  pages        = {60},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Bayesian linear regression for analyzing general omics data with time-to-event phenotypes}},
  doi          = {10.15479/at:ista:17368},
  year         = {2024},
}

@phdthesis{17465,
  abstract     = {In the modern age of machine learning, artificial neural networks have become an integral part
of many practical systems. One of the key ingredients of the success of the deep learning
approach is recent computational advances which allowed the training of models with billions
of parameters on large-scale data. Such over-parameterized and data-hungry regimes pose a
challenge for the theoretical analysis of modern models since “classical” statistical wisdom
is no longer applicable. In this view, it is paramount to extend or develop new machinery
that will allow tackling the neural network analysis under new challenging asymptotic regimes,
which is the focus of this thesis.
Large neural network systems are usually optimized via “local” search algorithms, such
as stochastic gradient descent (SGD). However, given the high-dimensional nature of the
parameter space, it is a priori not clear why such a crude “local” approach works so remarkably
well in practice. We take a step towards demystifying this phenomenon by showing that
the landscape of the SGD training dynamics exhibits a few beneficial properties for the
optimization. First, we show that along the SGD trajectory an over-parameterized network
is dropout stable. The emergence of dropout stability allows to conclude that the minima
found by SGD are connected via a continuous path of small loss. This in turn means that
the high-dimensional landscape of the neural network optimization problem is provably not so
unfavourable to gradient-based training, due to mode connectivity. Next, we show that SGD
for an over-parameterized network tends to find solutions that are functionally more “simple”.
This in turn means that the SGD minima are more robust, since a less complicated solution
will less likely overfit the data. More formally, for a prototypical example of a wide two-layer
ReLU network on a 1d regression task we show that the SGD algorithm is implicitly selective in
its choice of an interpolating solution. Namely, at convergence the neural network implements
a piece-wise linear function with the number of linear regions depending only on the amount
of training data. This is in contrast to a “smooth”-like behaviour which one would expect
given such a severe over-parameterization of the model.
Diverging from the generic supervised setting of classification and regression problems, we
analyze an auto-encoder model that is commonly used for representation learning and data
compression. Despite the wide applicability of the auto-encoding paradigm, the theoretical
understanding of their behaviour is limited even in the simplistic shallow case. The related
work is restricted to extreme asymptotic regimes in which the auto-encoder is either severely
over-parameterized or under-parameterized. In contrast, we provide a tight characterization
for the 1-bit compression of Gaussian signals in the challenging proportional regime, i.e., the
input dimension and the size of the compressed representation obey the same asymptotics.
We also show that gradient-based methods are able to find a globally optimal solution and
that the predictions made for Gaussian data extrapolate beyond - to the case of compression
of natural images. Next, we relax the Gaussian assumption and study more structured input
sources. We show that the shallow model is sometimes agnostic to the structure of the data
vii
which results in a Gaussian-like behaviour. We prove that making the decoding component
slightly less shallow is already enough to escape the “curse” of Gaussian performance.
},
  author       = {Shevchenko, Aleksandr},
  issn         = {2663-337X},
  pages        = {232},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{High-dimensional limits in artificial neural networks}},
  doi          = {10.15479/at:ista:17465},
  year         = {2024},
}

@phdthesis{17881,
  abstract     = {This work can be broadly classified into the study of critical phenomena in a one dimensional
array of Josephson junctions. While we study quantum criticality when the array is in thermal
equilibrium at zero bias, the non-equilibrium study involves understanding the bistability of the
array at a critical non-zero bias. This work furthers our knowledge in understanding quantum
critical behaviour at finite temperatures in a one dimensional Josephson array, while also
establishing relaxation behaviour dual to that observed in a single Josephson junction.
Chapter 1 briefly introduces the model to understand superconductor-insulator phase transition
in a one dimensional Josephson array and points out the state of the field from where we
started our zero-bias experiments. In this context it discusses the phase-charge duality observed
in a Josephson array and its dual hysteretic behaviour to that of a single junction, setting the
ground for our non-equilibrium study of the array.
Chapter 2 shows the experimental setup and the chip layout of the device we measured.
In chapter 3 we show that, unlike the typical quantum-critical broadening scenario, in one dimensional Josephson arrays temperature dramatically shifts the critical region. This shift leads
to a regime of superconductivity at high temperature, arising from the melted zero-temperature
insulator. Our results quantitatively explain the low-temperature onset of superconductivity in
nominally insulating regimes, and the transition to the strongly insulating phase. We further
present, to our knowledge, the first understanding of the onset of anomalous-metallic resistance
saturation [30]. This work demonstrates a non-trivial interplay between thermal effects and
quantum criticality. A practical consequence is that, counterintuitively, the coherence of
high-impedance quantum circuits is expected to be stabilized by thermal fluctuations.
In chapter 4, we show relaxation oscillations in a current-biased one dimensional array of
Josephson junctions. These oscillations are well described by a circuit model, dual to the
ordinary Josephson relaxation oscillations [72]. Injection locking these oscillations results in
current plateaux. The relaxation step is found to obey a characteristic self-consistent relation,
suggesting that it is governed by overheating effects.
Chapter 5 describes the various checks and analysis we performed to support our conclusions
made in chapters 3 and 4.
Finally, chapter 6 describes the nanofabrication steps and the finite element electromagnetic
simulations we performed to fabricate our devices.},
  author       = {Mukhopadhyay, Soham},
  isbn         = {978-3-99078-043-5},
  issn         = {2663-337X},
  pages        = {82},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Thermal effects in one dimensional Josephson chains}},
  doi          = {10.15479/at:ista:17881},
  year         = {2024},
}

@inproceedings{17469,
  abstract     = {Autoencoders are a prominent model in many empirical branches of machine learning and lossy data compression. However, basic theoretical questions remain unanswered even in a shallow two-layer setting. In particular, to what degree does a shallow autoencoder capture the structure of the underlying data distribution? For the prototypical case of the 1-bit compression of sparse Gaussian data, we prove that gradient descent converges to a solution that completely disregards the sparse structure of the input. Namely, the performance of the algorithm is the same as if it was compressing a Gaussian source - with no sparsity. For general data distributions, we give evidence of a phase transition phenomenon in the shape of the gradient descent minimizer, as a function of the data sparsity: below the critical sparsity level, the minimizer is a rotation taken uniformly at random (just like in the compression of non-sparse data); above the critical sparsity, the minimizer is the identity (up to a permutation). Finally, by exploiting a connection with approximate message passing algorithms, we show how to improve upon Gaussian performance for the compression of sparse data: adding a denoising function to a shallow architecture already reduces the loss provably, and a suitable multi-layer decoder leads to a further improvement. We validate our findings on image datasets, such as CIFAR-10 and MNIST.},
  author       = {Kögler, Kevin and Shevchenko, Aleksandr and Hassani, Hamed and Mondelli, Marco},
  booktitle    = {Proceedings of the 41st International Conference on Machine Learning},
  location     = {Vienna, Austria},
  pages        = {24964--25015},
  publisher    = {ML Research Press},
  title        = {{Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth}},
  volume       = {235},
  year         = {2024},
}

@unpublished{18057,
  abstract     = {We report relaxation oscillations in a one-dimensional array of Josephson
junctions. The oscillations are circuit-dual to those ordinarily observed in
single junctions. The dual circuit quantitatively accounts for temporal
dynamics of the array, including the dependence on biasing conditions.
Injection locking the oscillations results in well-developed current plateaux.
A thermal model explains the relaxation step of the oscillations.},
  author       = {Mukhopadhyay, Soham and Lancheros Naranjo, Diego A and Senior, Jorden L and Higginbotham, Andrew P},
  booktitle    = {arXiv},
  title        = {{Dual relaxation oscillations in a Josephson junction array}},
  doi          = {10.48550/arXiv.2408.07829},
  year         = {2024},
}

@phdthesis{18129,
  abstract     = {State-of-the-art quantum computers, with roughly a thousand qubits, face a crucial technological challenge of scaling up. Spins confined in quantum dots (QDs) are a promising candidate
for qubits due to their long coherence, tunability, control, and readout. However, their natural
coupling is the short-ranged (∼ 100 nm) exchange interaction, limited to nearest neighbours.
Long-ranged (∼ 1 mm) qubit interactions mediated by a photon could be engineered through a
coherent spin-photon coupling. Achieving a strong coupling to a photon is inherently challenging in QDs due to the small dipole moment of the confined charge. However, the potential of
high-impedance resonators to compensate for this has gained significant attention in the past
decade. Nevertheless, previous QD circuit quantum electrodynamics implementations have not
exceeded the impedance of ∼ 3.8 kΩ, leaving opportunities for significant improvement. The
large kinetic inductance of granular aluminium (grAl) could provide an order-of-magnitude
enhancement. However, fully exploiting the potential of disordered or granular superconductors
is challenging as their impedances close to the superconductor-to-insulator transition are
difficult to control reproducibly. We report on the realization of a wireless ohmmeter which
allows in situ resistance measurements during film deposition and, therefore, indirect control
of the kinetic inductance of grAl films. This allows us to reproducibly fabricate resonators
with characteristic impedance exceeding the resistance quantum, even reaching 22.3 kW, due
to the large sheet kinetic inductance of up to 3 nH □−1
. By integrating an 8 kW resonator
with a germanium double QD, we demonstrate a strong charge-photon coupling with the
highest rate reported, 566 MHz. The demonstrated method and grAl properties make these
resonators suitable for boosting the spin-photon coupling strength, a crucial requirement for
fast, high-fidelity, long-distance two-qubit gates.
},
  author       = {Janik, Marian},
  issn         = {2663-337X},
  pages        = {164},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors}},
  doi          = {10.15479/at:ista:18129},
  year         = {2024},
}

@phdthesis{18104,
  abstract     = {We introduce a new all-electric platform, that strong couples light to mechanical motion
by ensuring that the external environmental coupling dominates over internal mechanical
dissipation. The system only has three everyday components: AC, DC, and a fip-chip, in which
a metallized silicon nitride membrane is fipped on top of the device under test. This everyday
electromechanical device can be operated at low or room temperature and has 10000× lower
insertion loss than a comparable commercial quartz crystal, achieves a position imprecision
matching state-of-the-art optical interferometer, and enables remote cooling of mechanical
motion. The spatial properties of higher order mechanical modes are a promising feature for
reconstructing unknown charge distributions.
},
  author       = {Puglia, Denise},
  issn         = {2663-337X},
  pages        = {63},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Everyday electromechanics: Capacitive strong coupling to mechanical motion}},
  doi          = {10.15479/at:ista:18104},
  year         = {2024},
}

@unpublished{18144,
  abstract     = {High kinetic inductance superconductors are gaining increasing interest for
the realisation of qubits, amplifiers and detectors. Moreover, thanks to their
high impedance, quantum buses made of such materials enable large zero-point
fluctuations of the voltage, boosting the coupling rates to spin and charge
qubits. However, fully exploiting the potential of disordered or granular
superconductors is challenging, as their inductance and, therefore, impedance
at high values are difficult to control. Here we have integrated a granular
aluminium resonator, having a characteristic impedance exceeding the resistance
quantum, with a germanium double quantum dot and demonstrate strong
charge-photon coupling with a rate of $g_\text{c}/2\pi= (566 \pm 2)$ MHz. This
was achieved due to the realisation of a wireless ohmmeter, which allows
\emph{in situ} measurements during film deposition and, therefore, control of
the kinetic inductance of granular aluminium films. Reproducible fabrication of
circuits with impedances (inductances) exceeding 13 k$\Omega$ (1 nH per square)
is now possible. This broadly applicable method opens the path for novel qubits
and high-fidelity, long-distance two-qubit gates.},
  author       = {Janik, Marian and Roux, Kevin Etienne Robert and Borja Espinosa, Carla N and Sagi, Oliver and Baghdadi, Abdulhamid and Adletzberger, Thomas and Calcaterra, Stefano and Botifoll, Marc and Manjón, Alba Garzón and Arbiol, Jordi and Chrastina, Daniel and Isella, Giovanni and Pop, Ioan M. and Katsaros, Georgios},
  booktitle    = {arXiv},
  title        = {{Strong charge-photon coupling in planar germanium enabled by granular  aluminium superinductors}},
  doi          = {10.48550/arXiv.2407.03079},
  year         = {2024},
}

@unpublished{18143,
  abstract     = {Strong optomechanical coupling -- a regime where mechanical motion is damped
by environmental radiation -- has traditionally required demanding experimental
ingredients such as superconducting resonators, high-quality optical cavities,
or large magnetic fields. Here we demonstrate a room temperature, cavity-free,
all-electric device reaching this regime at radio frequencies, enabled by a
mechanically compliant parallel-plate capacitor with a nanoscale plate
separation and an aspect ratio exceeding 1,000. The device has four orders of
magnitude lower insertion loss than a comparable commercial quartz crystal, and
achieves a position imprecision rivaling an optical interferometer. With the
help of a back-action isolation scheme, we observe radiative cooling of
mechanical motion by a remote cryogenic load. This work provides a
technologically accessible route to high-precision sensing, transduction, and
signal processing.},
  author       = {Puglia, Denise and Odessey, Rachel H and Burns, Peter S. and Luhmann, Niklas and Schmid, Silvan and Higginbotham, Andrew P},
  booktitle    = {arXiv},
  title        = {{Room temperature, cavity-free capacitive strong coupling to mechanical  motion}},
  doi          = {10.48550/arXiv.2407.15314},
  year         = {2024},
}