@unpublished{19399,
  abstract     = {Phytohormone auxin and its directional transport mediate much of the remarkably plastic development of higher plants. Positive feedback between auxin signaling and transport is a key prerequisite for (i) self-organizing processes including vascular tissue formation and (ii) directional growth responses such as gravitropism. Here we identify a mechanism, by which auxin signaling directly targets PIN auxin transporters. Via the cell-surface ABP1-TMK1 receptor module, auxin rapidly induces phosphorylation and thus stabilization of PIN2. Following gravistimulation, initial auxin asymmetry activates autophosphorylation of the TMK1 kinase. This induces TMK1 interaction with and phosphorylation of PIN2, stabilizing PIN2 at the lower root side, thus reinforcing asymmetric auxin flow for root bending. Upstream of TMK1 in this regulation, ABP1 acts redundantly with the root-expressed ABP1-LIKE auxin receptor ABL3. Such positive feedback between cell-surface auxin signaling and PIN-mediated polar auxin transport is fundamental for robust root gravitropism and presumably also for other self-organizing developmental phenomena.},
  author       = {Rodriguez Solovey, Lesia and Fiedler, Lukas and Zou, Minxia and Giannini, Caterina and Monzer, Aline and Vladimirtsev, Dmitrii and Randuch, Marek and Yu, Yongfan and Gelová, Zuzana and Verstraeten, Inge and Hajny, Jakub and Chen, Meng and Tan, Shutang and Hörmayer, Lukas and Li, Lanxin and Marques-Bueno, Maria Mar and Quddoos, Zainab and Molnar, Gergely and Xu, Tongda and Kulich, Ivan and Jaillais, Yvon and Friml, Jiří},
  booktitle    = {bioRxiv},
  title        = {{ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism}},
  doi          = {10.1101/2022.11.30.518503},
  year         = {2025},
}

@unpublished{19398,
  abstract     = {Receptor-like kinases (RLKs), particularly the Transmembrane Kinase (TMK) family, play essential roles in signaling and development, with TMKs being key components of auxin perception and downstream phosphorylation events. While TMKs’ involvement in auxin canalization, a process essential for vasculature formation and regeneration, has been established, nonetheless, the additional signaling and regulatory partners remain poorly understood. In this study, we identify and characterize seven leucine-rich repeat RLKs (TINT1–TINT7) as novel interactors of TMK1, revealing their diverse evolutionary, structural, and functional characteristics. Our results show that TINTs interact with TMK1 and highlight their roles in regulating various developmental processes. Majority of TINTs contributes, together with TMK1, to auxin canalization, with TINT5 linking TMK1 to other canalization component CAMEL. Beyond canalization, we also establish the role of TINT-TMK1 interactions in processes such as stomatal movement and the hypocotyl’s gravitropic response. These findings suggest that TINTs, through their interaction with TMK1, are integral components of various signaling networks, contributing to both auxin canalization and broader plant development.},
  author       = {Monzer, Aline and Mazur, Ewa and Rodriguez Solovey, Lesia and Gallei, Michelle C and Zou, Minxia and Smejkal, Michael and Cervenova, Ema and Friml, Jiří},
  booktitle    = {bioRxiv},
  title        = {{TMK interacting network of receptor like kinases for auxin canalization and beyond}},
  doi          = {10.1101/2025.02.28.640727},
  year         = {2025},
}

@inproceedings{21280,
  abstract     = {We give an algorithm that, with high probability, maintains a (1-ε)-approximate s-t maximum flow in undirected, uncapacitated n-vertex graphs undergoing m edge insertions in Õ(m+ n F^*/ε) total update time, where F^{*} is the maximum flow on the final graph. This is the first algorithm to achieve polylogarithmic amortized update time for dense graphs (m = Ω(n²)), and more generally, for graphs where F^* = Õ(m/n). At the heart of our incremental algorithm is the residual graph sparsification technique of Karger and Levine [SICOMP '15], originally designed for computing exact maximum flows in the static setting. Our main contributions are (i) showing how to maintain such sparsifiers for approximate maximum flows in the incremental setting and (ii) generalizing the cut sparsification framework of Fung et al. [SICOMP '19] from undirected graphs to balanced directed graphs.},
  author       = {Goranci, Gramoz and Henzinger, Monika H and Räcke, Harald and Sricharan, A.},
  booktitle    = {52nd International Colloquium on Automata, Languages, and Programming},
  isbn         = {9783959773720},
  location     = {Aarhus, Denmark},
  pages        = {91:1--91:20},
  publisher    = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
  title        = {{Incremental approximate maximum flow via residual graph sparsification}},
  doi          = {10.4230/lipics.icalp.2025.91},
  volume       = {334},
  year         = {2025},
}

@inproceedings{21262,
  abstract     = {Continuous Group Key Agreement (CGKA) is the primitive underlying secure group messaging. It allows a large group of N users to maintain a shared secret key that is frequently rotated by the
group members in order to achieve forward secrecy and post compromise security. The group messaging scheme Messaging Layer Security (MLS) standardized by the IETF makes use of a CGKA called TreeKEM which arranges the N group members in a binary tree. Here, each node is associated with a public-key, each user is assigned one of the leaves, and a user knows the corresponding secret keys from their leaf to the root. To update the key material known to them, a user must just replace keys at log(N) nodes, which requires them to create and upload log(N) ciphertexts. Such updates must be processed sequentially by all users, which for large groups is impractical. To allow for concurrent updates, TreeKEM uses the “propose and commit” paradigm, where multiple users can concurrently propose to update (by just sampling a fresh leaf key), and a single user can then commit to all proposals at once. Unfortunately, this process destroys the binary tree structure as the tree gets pruned and some nodes must be “blanked” at the cost of increasing the in-degree of others, which makes the commit operation, as well as, future commits more costly. In the worst case, the update cost (in terms of uploaded ciphertexts) per user can grow from log(N) to Ω(N). In this work we provide two main contributions. First, we show that MLS’ communication complexity is bad not only in the worst case but also if the proposers and committers are chosen at random: even if there’s just one update proposal for every commit the expected cost is already over √N, and it approaches N as this ratio changes towards more proposals. Our second contribution is a new variant of propose and commit for
TreeKEM which for moderate amounts of update proposals per commit provably achieves an update cost of Θ(log(N)) assuming the proposers and committers are chosen at random.},
  author       = {Auerbach, Benedikt and Cueto Noval, Miguel and Erol, Boran and Pietrzak, Krzysztof Z},
  booktitle    = {45th Annual International Cryptology Conference},
  isbn         = {9783032019127},
  issn         = {1611-3349},
  location     = {Santa Barbara, CA, United States},
  pages        = {141--172},
  publisher    = {Springer Nature},
  title        = {{Continuous group-key agreement: Concurrent updates without pruning}},
  doi          = {10.1007/978-3-032-01913-4_5},
  volume       = {16007},
  year         = {2025},
}

@article{19278,
  abstract     = {When two insulating, neutral materials are contacted and separated, they exchange electrical charge1. Experiments have long suggested that this ‘contact electrification’ is transitive, with different materials ordering into ‘triboelectric series’ based on the sign of charge acquired2. At the same time, the effect is plagued by unpredictability, preventing consensus on the mechanism and casting doubt on the rhyme and reason that series imply3. Here we expose an unanticipated connection between the unpredictability and order in contact electrification: nominally identical materials initially exchange charge randomly and intransitively, but—over repeated experiments—order into triboelectric series. We find that this evolution is driven by the act of contact itself—samples with more contacts in their history charge negatively to ones with fewer contacts. Capturing this ‘contact bias’ in a minimal model, we recreate both the initial randomness and ultimate order in numerical simulations and use it experimentally to force the appearance of a triboelectric series of our choosing. With a set of surface-sensitive techniques to search for the underlying alterations contact creates, we only find evidence of nanoscale morphological changes, pointing to a mechanism strongly coupled with mechanics. Our results highlight the centrality of contact history in contact electrification and suggest that focusing on the unpredictability that has long plagued the effect may hold the key to understanding it.},
  author       = {Sobarzo Ponce, Juan Carlos A and Pertl, Felix and Balazs, Daniel and Costanzo, Tommaso and Sauer, Markus and Foelske, Annette and Ostermann, Markus and Pichler, Christian M. and Wang, Yongkang and Nagata, Yuki and Bonn, Mischa and Waitukaitis, Scott R},
  issn         = {1476-4687},
  journal      = {Nature},
  number       = {8051},
  publisher    = {Springer Nature},
  title        = {{Spontaneous ordering of identical materials into a triboelectric series}},
  doi          = {10.1038/s41586-024-08530-6},
  volume       = {638},
  year         = {2025},
}

@article{20481,
  abstract     = {Kelvin probe force microscopy (KPFM) is widely used in stationary and dynamic studies of contact electrification. An obvious question that connects these two has been overlooked: when are charge dynamics too fast for stationary studies to be meaningful? Using a rapid transfer system to quickly perform KPFM after contact, we find the dynamics are too fast in all but the best insulators. Our data further suggest that dynamics are caused by bulk as opposed to surface conductivity, and that charge-transfer heterogeneity is less prevalent than previously suggested.},
  author       = {Pertl, Felix and Lenton, Isaac C and Cramer, Tobias and Waitukaitis, Scott R},
  issn         = {1079-7114},
  journal      = {Physical Review Letters},
  number       = {14},
  publisher    = {American Physical Society},
  title        = {{No time for surface charge: How bulk conductivity hides charge patterns from Kelvin probe force microscopy in contact-electrified surfaces}},
  doi          = {10.1103/lcsm-xxty},
  volume       = {135},
  year         = {2025},
}

@article{20452,
  abstract     = {Accurate modeling of long-range forces is critical in atomistic simulations, as they play a central role in determining the properties of material and chemical systems. However, standard machine learning interatomic potentials (MLIPs) often rely on short-range approximations, limiting their applicability to systems with significant electrostatics and dispersion forces. We recently introduced the Latent Ewald Summation (LES) method, which captures long-range electrostatics without explicitly learning atomic charges or charge equilibration. We benchmark LES on diverse and challenging systems, including charged molecules, ionic liquids, electrolyte solutions, polar dipeptides, surface adsorption, electrolyte/solid interfaces, and solid-solid interfaces. Here we show that LES can reproduce the exact atomic charges for classical systems with fixed charges and can infer dipole and quadrupole moments, as well as the dipole derivative with respect to atomic positions, for quantum mechanical systems. Moreover, LES can achieve better accuracy in energy and force predictions compared to methods that explicitly learn from charges.},
  author       = {King, Daniel S. and Kim, Dongjin and Zhong, Peichen and Cheng, Bingqing},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{Machine learning of charges and long-range interactions from energies and forces}},
  doi          = {10.1038/s41467-025-63852-x},
  volume       = {16},
  year         = {2025},
}

@misc{22770,
  author       = {Cheng, Bingqing and King, Daniel and Kim, Dongjin and Zhong, Peichen},
  publisher    = {Repository},
  title        = {{BingqingCheng/cace-lr-fit: V0}},
  doi          = {10.5281/zenodo.16415060},
  year         = {2025},
}

@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},
}

@article{19795,
  abstract     = {Super-resolution microscopy often entails long acquisition times of minutes to hours. Since drifts during the acquisition adversely affect data quality, active sample stabilization is commonly used for some of these techniques to reach their full potential. Although drifts in the lateral plane can often be corrected after acquisition, this is not always possible or may come with drawbacks. Therefore, it is appealing to stabilize sample position in three dimensions (3D) during acquisition. Various schemes for active sample stabilization have been demonstrated previously, with some reaching sub-nanometer stability in 3D. Here, we present a scheme for active drift correction that delivers the nanometer-scale 3D stability demanded by state-of-the-art super-resolution techniques and is straightforward to implement compared to previous schemes capable of reaching this level of stabilization precision. Using a refined algorithm that can handle various types of reference structure, without sparse signal peaks being mandatory, we stabilized sample position to ∼1 nm in 3D using objective lenses both with high and low numerical aperture. Our implementation requires only the addition of a simple widefield imaging path and we provide an open-source control software with graphical user interface to facilitate easy adoption of the module. Finally, we demonstrate how this has the potential to enhance data collection for diffraction-limited and super-resolution imaging techniques using single-molecule localization microscopy and cryo-confocal imaging as showcases.},
  author       = {Vorlaufer, Jakob and Semenov, Nikolai and Kreuzinger, Caroline and Javoor, Manjunath and Zens, Bettina and Agudelo Duenas, Nathalie and Tavakoli, Mojtaba and Suplata, Marek and Jahr, Wiebke and Lyudchik, Julia and Wartak, Andreas and Schur, Florian Km and Danzl, Johann G},
  issn         = {2667-0747},
  journal      = {Biophysical Reports},
  number       = {2},
  publisher    = {Elsevier},
  title        = {{Image-based 3D active sample stabilization on the nanometer scale for optical microscopy}},
  doi          = {10.1016/j.bpr.2025.100211},
  volume       = {5},
  year         = {2025},
}

@article{15016,
  abstract     = {Amphibians, by virtue of their phylogenetic position, provide invaluable insights on nervous system evolution, development, and remodeling. The genetic toolkit for amphibians, however, remains limited. Recombinant adeno-associated viral vectors (AAVs) are a powerful alternative to transgenesis for labeling and manipulating neurons. Although successful in mammals, AAVs have never been shown to transduce amphibian cells efficiently. We screened AAVs in three amphibian species—the frogs Xenopus laevis and Pelophylax bedriagae and the salamander Pleurodeles waltl—and identified at least two AAV serotypes per species that transduce neurons. In developing amphibians, AAVs labeled groups of neurons generated at the same time during development. In the mature brain, AAVrg retrogradely traced long-range projections. Our study introduces AAVs as a tool for amphibian research, establishes a generalizable workflow for AAV screening in new species, and expands opportunities for cross-species comparisons of nervous system development, function, and evolution.},
  author       = {Jaeger, Eliza C.B. and Vijatovic, David and Deryckere, Astrid and Zorin, Nikol and Nguyen, Akemi L. and Ivanian, Georgiy and Woych, Jamie and Arnold, Rebecca C and Ortega Gurrola, Alonso and Shvartsman, Arik and Barbieri, Francesca and Toma, Florina-Alexandra and Gorbsky, Gary J. and Horb, Marko E. and Cline, Hollis T. and Shay, Timothy F. and Kelley, Darcy B. and Yamaguchi, Ayako and Shein-Idelson, Mark and Tosches, Maria Antonietta and Sweeney, Lora Beatrice Jaeger},
  issn         = {1878-1551},
  journal      = {Developmental Cell},
  number       = {5},
  pages        = {794--812.e6},
  publisher    = {Elsevier},
  title        = {{Adeno-associated viral tools to trace neural development and connectivity across amphibians}},
  doi          = {10.1016/j.devcel.2024.10.025},
  volume       = {60},
  year         = {2025},
}

@inproceedings{20292,
  abstract     = {In automated decision-making, it is desirable that outputs of decision-makers be robust to slight perturbations in their inputs, a property that may be called input-output robustness. Input-output robustness appears in various different forms in the literature, such as robustness of AI models to adversarial or semantic perturbations and individual fairness of AI models that make decisions about humans. We propose runtime monitoring of input-output robustness of deployed, black-box AI models, where the goal is to design monitors that would observe one long execution sequence of the model, and would raise an alarm whenever it is detected that two similar inputs from the past led to dissimilar outputs. This way, monitoring will complement existing offline ''robustification'' approaches to increase the trustworthiness of AI decision-makers. We show that the monitoring problem can be cast as the fixed-radius nearest neighbor (FRNN) search problem, which, despite being well-studied, lacks suitable online solutions. We present our tool Clemont, which offers a number of lightweight monitors, some of which use upgraded online variants of existing FRNN algorithms, and one uses a novel algorithm based on binary decision diagrams--a data-structure commonly used in software and hardware verification. We have also developed an efficient parallelization technique that can substantially cut down the computation time of monitors for which the distance between input-output pairs is measured using the L∞norm. Using standard benchmarks from the literature of adversarial and semantic robustness and individual fairness, we perform a comparative study of different monitors in Clemont, and demonstrate their effectiveness in correctly detecting robustness violations at runtime.},
  author       = {Gupta, Ashutosh and Henzinger, Thomas A and Kueffner, Konstantin and Mallik, Kaushik and Pape, David},
  booktitle    = {Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining},
  isbn         = {9798400714542},
  issn         = {2154-817X},
  location     = {Toronto, Canada},
  pages        = {790--801},
  publisher    = {Association for Computing Machinery},
  title        = {{Monitoring robustness and individual fairness}},
  doi          = {10.1145/3711896.3737054},
  volume       = {2},
  year         = {2025},
}

@inproceedings{21090,
  abstract     = {Fairness in AI is traditionally studied as a static property evaluated once, over a fixed dataset. However, real-world AI systems operate sequentially, with outcomes and environments evolving over time. This paper proposes a framework for analysing fairness as a runtime property. Using a minimal yet expressive model based on sequences of coin tosses with possibly evolving biases, we study the problems of monitoring and enforcing fairness expressed in either toss outcomes or coin biases. Since there is no one-size-fits-all solution for either problem, we provide a summary of monitoring and enforcement strategies, parametrised by environment dynamics, prediction horizon, and confidence thresholds. For both problems, we present general results under simple or minimal assumptions. We survey existing solutions for the monitoring problem for Markovian and additive dynamics, and existing solutions for the enforcement problem in static settings with known dynamics.},
  author       = {Cano Cordoba, Filip and Henzinger, Thomas A and Kueffner, Konstantin},
  booktitle    = {25th International Conference on Runtime Verification},
  issn         = {1611-3349},
  location     = {Graz, Austria},
  pages        = {1--21},
  publisher    = {Springer Nature},
  title        = {{Algorithmic fairness: A runtime perspective}},
  doi          = {10.1007/978-3-032-05435-7_1},
  volume       = {16087},
  year         = {2025},
}

@phdthesis{20117,
  author       = {Wang, Yiqun},
  issn         = {2663-337X},
  pages        = {108},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{The role of dynamin related protein 2A in cytokinin regulated plant growth and development}},
  doi          = {10.15479/AT-ISTA-20117},
  year         = {2025},
}

@phdthesis{20212,
  author       = {Miranda, Osvaldo},
  isbn         = {978-3-99078-063-3},
  issn         = {2663-337X},
  keywords     = {Pten, mtor, cortical development, MADM, Mapk},
  pages        = {119},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Unraveling the role of Pten in cortical stem cell lineage progression using MADM}},
  doi          = {10.15479/AT-ISTA-20212},
  year         = {2025},
}

@phdthesis{19386,
  abstract     = {Crustaceans are a large group of arthropods with a great diversity of species and
different types of sex determination systems and reproductive modes (Subramoniam, 2017).
This makes them a great model for exploring the evolution of sex chromosomes and sexual
dimorphism and investigating the evolutionary mechanisms driving and maintaining the
diversity of reproductive systems. Within this taxon, Brine shrimp of the genus Artemia, a
branchiopod crustacean, are well suited for such explorations, as they have both highly
dimorphic traits and closely related sexual and asexual species. Although brine shrimp are
known to have ZW sex chromosomes (Bowen, 1963; Parraguez et al., 2009), the sex
chromosomes are still not well characterized at the genomic level, the sex-determination gene
is unknown, and it is still unclear whether the same sex chromosomes as shared by the
different species.
The first part of this thesis was to characterize the Z and W chromosomes in Artemia
using an array of methods, from generating multiple chromosome and contig level genome
assemblies to identifying W-linked scaffolds and transcripts in multiple species using k-mer
based approaches.
The second part tackles the conservation of the cell type specific regulatory pathways
in the female reproductive system between Artemia and Drosophila, and the expression of the
Z-specific region throughout meiosis using single-nucleus RNA-seq data. Our results show
that germline cells lack dosage compensation, with a subset of cells showing evidence of
extreme repression of the Z chromosome.
With multiple sexual species and several asexual lineages of parthenogenetic females
that produce rare males at low frequencies, Brine shrimp present the perfect opportunity to
explore the transition to asexuality and shed light on the prerequisites and repercussions of
the form of modified meiosis maintaining the asexual lineages. The last chapter is an
investigation of the molecular pathways involved in asexual reproduction in Artemia using
newly generated single nucleus RNAseq and WGS data and previously published data. },
  author       = {Elkrewi, Marwan N},
  isbn         = {9783990780534},
  issn         = {2663-337X},
  pages        = {170},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp}},
  doi          = {10.15479/AT-ISTA-19386},
  year         = {2025},
}

@phdthesis{20798,
  abstract     = {Atom interferometers measure the relative phase shifts between coherent matter-wave paths
that arise from interactions with external fields or inertial forces. Due to their exceptional
phase sensitivity, atom interferometers became an essential tool for precision measurements
and fundamental physics experiments, finding applications in geodesy, gravimetry, and inertial
navigation. However, their measurement precision is limited by quantum projection noise,
which arises from the Heisenberg uncertainty principle, preventing the measurement of atomic
states with absolute precision. The generation of entanglement between the atoms offers a
path to surpass this so-called standard quantum limit, thereby enhancing the interferometer’s
phase sensitivity beyond classical measurement bounds.
This thesis reports on the development of an atom interferometer experiment designed to
realize cavity-mediated, squeezed Mach-Zehnder-type interferometry with ultra-cold 87Rb atoms.
The experiment combines cavity-aided spin-squeezing with cavity-mediated Mach-Zehnder
interferometry to demonstrate entanglement-enhanced phase sensitivity. The experiment is
centered on a triangular optical cavity that mediates all relevant atom-light interactions. The
cavity provides optical trapping, spin-squeezing, and Raman beam-splitter operations, enabling
to perform interferometry on a continuously trapped atomic ensemble.
The thesis elaborates on the fundamental theoretical framework, the cavity design, and the full
optical setup, including the detailed configuration of the developed laser stabilization methods.
Experimentally, continuous loading methods were explored, resulting in an accumulation of
up to 4 × 106
atoms in the dipole trap within a cycle time of 500 ms. The AC Stark shift
compensation method developed for continuous loading was further applied for in-trap cooling
to 10 µK, and optical pumping for efficient atomic state preparation. Coherent state control
was verified via observation of microwave-driven Rabi oscillations, and used to characterize
atom-cavity coupling.
These presented results establish the experimental groundwork for the future development of
cavity-mediated, entanglement-enhanced Mach-Zehnder-type atom interferometry.},
  author       = {Wald, Sebastian},
  isbn         = {978-3-99078-075-6},
  issn         = {2663-337X},
  keywords     = {entanglement-enhanced atom interferometry, cavity QED, spin-squeezing, dipole trap, quantum optics},
  pages        = {152},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry}},
  doi          = {10.15479/AT-ISTA-20798},
  year         = {2025},
}

@article{19498,
  abstract     = {A dynamic interplay between fast synaptic signals and slower neuromodulatory signals controls the excitatory/inhibitory (E/I) balance within neuronal circuits. The mechanisms by which neuropeptide signaling is regulated to maintain E/I balance remain uncertain. We designed a genetic screen to isolate genes involved in the peptidergic maintenance of the E/I balance in the C. elegans motor circuit. This screen identified the C. elegans orthologs of the presynaptic phosphoprotein synapsin (snn-1) and the protein phosphatase 1 (PP1) regulatory subunit PHACTR1 (phac-1). We demonstrate that both phac-1 and snn-1 alter the motor behavior of C. elegans, and genetic interactions suggest that SNN-1 contributes to PP1-PHAC-1 holoenzyme signaling. De novo variants of human PHACTR1, associated with early-onset epilepsies [developmental and epileptic encephalopathy 70 (DEE70)], when expressed in C. elegans resulted in constitutive PP1-PHAC-1 holoenzyme activity. Unregulated PP1-PHAC-1 signaling alters the synapsin and actin cytoskeleton and increases neuropeptide release by cholinergic motor neurons, which secondarily affects the presynaptic vesicle cycle. Together, these results clarify the dominant mechanisms of action of the DEE70 alleles and suggest that altered neuropeptide release may alter E/I balance in DEE70.},
  author       = {Stratigi, Aikaterini and Soler-García, Miguel and Krout, Mia and Shukla, Shikha and De Bono, Mario and Richmond, Janet E. and Laurent, Patrick},
  issn         = {1529-2401},
  journal      = {Journal of Neuroscience},
  number       = {13},
  publisher    = {Society for Neuroscience},
  title        = {{Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans}},
  doi          = {10.1523/JNEUROSCI.1767-23.2024},
  volume       = {45},
  year         = {2025},
}

@phdthesis{18871,
  abstract     = {"Can we do this with a new type of computer - a quantum computer?". This famous
quotation of the brilliant Richard Feynman within a conference talk on "Simulating physics
with computers.” is often reverently praised as the origin of the field of quantum computing.
The idea was to use quantum mechanical systems itself to simulate "Nature", which is
inherently quantum mechanical. Now, 43 years later, the theoretical framework of how such
a computer can operate has been developed. Two main important concepts for a potential
quantum supremacy, superposition and entanglement, have been exploited to design quantum
algorithms to significantly speed up certain tasks. Yet, the specific hardware implementation
is still far from being certain, in fact the race between the most promising platforms such as
superconducting qubits, bosonic codes, cold atoms, trapped ions, optical computing as well
as spin qubits has recently intensified. If one also includes the most mature applications of
quantum communication technologies, secure quantum key distribution and quantum random
number generators, as part of a quantum information technology ecosystem, we are confronted
with a plethora of different materials, concepts, and also operation frequencies. While
superconducting qubits, bosonic codes and spin qubits work in the regime of approximately 5
GHz and are controlled by electrical fields, trapped ions, cold atoms, and optical quantum
computing operate with light in the infrared or visible range.
Consequently, a quantum frequency converter or microwave-optic transducer is required
to interface the different frequency domains or establish a long-range network connection
with suitable telecom fibers. In fact, the combination of different frequency regimes is also
an essential part in our classical modern communication network, where computations are
performed in electrical circuits and the information exchange over longer distances happens
via optical fibers. However, the specific challenges specific to building a quantum computer,
also apply to the development of such a quantum frequency transducer: 1) As we deal with
single excitations as the carrier of information, i.e. the smallest possible quantity, the signal
can easily be corrupted by other noise sources which needs to be avoided by all means. This
is also the reason why microwave quantum computers operate at temperature environments
close to zero temperature (< 0.1 Kelvin) to avoid corruption by thermal noise. 2) The
frequency interface generally needs to preserve the phase of the signal as an essential part
of the quantum state. And 3) Quantum signals cannot be copied which would be a typical
strategy to account for errors in classical computers. And finally, there is a challenge specific to
microwave-optic transducers: While quantum computers are operating in one specific frequency
domain, microwave-optic transducers combine microwave and optical fields in one device.
This results in the particular challenge that high-energy optical radiation, which is usually
well-shielded from superconducting microwave quantum processors, are now an essential part
of the device. The concomitant optical radiation in the operating transducer will inevitably
have a detrimental effect on the superconducting microwave components. Together with the
requirement of minimal background noise for quantum-limited operation as described above,
v
heating from the absorption of optical photons within the same device where single microwave
excitations are processed forms a formidable challenge.
This thesis aims to address this challenge by developing microwave-optic transducers where
the impact of optical absorption on superconducting circuits in general and superconducting
qubits specifically can be mitigated. In our first approach, we developed a compact device
with optimized interaction strengths between the different frequency domains. This minimizes
the optical powers used for transducer operation and thus the optical absorption heating. This
work was - to the best of our knowledge - the first comprehensive noise study, in an integrated
microwave-optic transducer. Unfortunately, we saw that the optical absorption heating added
noise way above a single excitation. Consequently, a potential quantum signal would have
been buried in the noise, added by the transduction.
Building on this insight, we utilized a three-dimensional microwave-optic transducer instead
of an integrated device. The larger heat capacity of the macroscopic device with a size
of a few millimeters can absorb a larger fraction of the optical heating before it increases
the temperature of the device. This allowed us to interface the transducer directly with a
superconducting qubit to readout the qubit state in a novel all-optical manner. We showed
that the microwave-optic transducer can be operated in a regime in which optical fields don’t
harm the sensitive qubit. This is an important prerequisite for the operation of microwave-optic
transducers in conjunction with microwave quantum processors and brings the integration and
seamless orchestration of different frequency components in a quantum network a step closer.
},
  author       = {Arnold, Georg M},
  issn         = {2663-337X},
  pages        = {135},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Microwave-optic interconnects for superconducting circuits}},
  doi          = {10.15479/at:ista:18871},
  year         = {2025},
}

@phdthesis{19745,
  abstract     = {Cell migration is a crucial process in animal development and maintenance. It is incredibly
heterogeneous, with different cell types utilizing fundamentally distinct migration strategies.
The strategies also depend on the cellular microenvironment, where cells can switch between
migration modes as they encounter new environmental cues. In this thesis, we investigated
how dendritic cells adapt their migration strategy when encountering geometrically,
mechanically and chemically distinct environments.
When dendritic cells are embedded in a homogeneous fibrous network, they migrate in a fast
and directional amoeboid manner. In this migration strategy, extracellular proteolysis and
integrin-mediated adhesions are dispensable. Instead, the cells use topography of the
environment to propel their cell body forward. To migrate efficiently in the maze of different
pore sizes, they position the nucleus ahead of the microtubule organizing center (MTOC) and
use it to gauge the pores to identify the path of least resistance. Our aim was to identify
whether dendritic cells adapt their migration strategy when encountering asymmetrical
transitions into much denser environments with limited choice of large pores. In such invasive
transitions it is unclear if the cells can cross tight pores without the use of adhesions and
extracellular proteolysis and whether they maintain the nucleus in the cell front.
Using various cell migration assays such as fibrous 3D collagen gels, geometrically defined
microchannels with constrictions and simplistic under agarose migration assay, we provide
a comprehensive characterization of invasive migration of dendritic cells. We show that
during invasion the cells stall and stretch, reflecting the difficulty to translocate the bulky cell
body into the dense environment. In collagen gels, we show that dendritic cells can invade
without proteolysis and adhesions. Instead, they utilize contractility, which can lead to largescale collagen compressions. During invasion, the nucleus stalls at tight constrictions, leading
to a transient organelle reorientation. To resolve the stalling, upregulated rear contractility is
required. This contractile force is simultaneously necessary for reverting the nucleus back to
the cell front after invasion and maintaining this positioning during permissive migration.
A functional role of the reorientation was uncovered in the first collaboration project.
A prominent central actin pool was identified around the MTOC, especially pronounced in
dense and compressive environments. The actin pool was shown to generate pushing forces
to dilate the space for cell translocation. These forces are only necessary in non-permissive
environments, where the nucleus reorients to the cell rear, allowing the actin pool to
generate space. In permissive environments where space generation is dispensable, the
MTOC is located behind the nucleus and the actin cloud has reduced intensity, allowing more
actin to be incorporated into the lamellipodium, speeding up migration.
In the second collaboration project, we investigated the effects of distinct chemical
environments on dendritic cell migration. The strikingly persistent migration of these cells
was explained by their ability to modulate and even self-generate chemokine gradients. This
allows the cells to migrate faster and more persistent in uniform chemokine fields compared
to imposed chemokine gradients. The chemokine receptor CCR7 was identified as a crucial
player in this process, both sensing the signal and internalizing the chemokine to create a sink.},
  author       = {Canigova, Nikola},
  isbn         = {978-3-99078-058-9},
  issn         = {2663-337X},
  pages        = {133},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Adaptive strategies of dendritic cell migration in response to environmental cues}},
  doi          = {10.15479/AT-ISTA-19745},
  year         = {2025},
}