IST Austria: PubRep (Institute of Science and Technology)
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ISTA Thesis
No full textThe internal structure of biomolecules and their organization in higher-order arrangements are key factors governing the working principles of biological systems. Bioimaging has successfully revealed arrangements across relevant spatial scales. For example, cryo-electron tomography has become widely used for analyzing biomolecular structures in situ due to its comprehensive structural visualization of near-natively preserved samples, and its capability of sub-nm resolution via averaging. However, the identification of molecules within crowded cellular environments is often hindered by low contrast. Fluorescence microscopy, on the other hand, routinely visualizes specifically labeled targets at single-molecule contrast against essentially zero background. Moreover, it provides comparatively high throughput and is amenable to multiplexing. Due to this complementarity, combining datasets from both modalities acquired on the same region via correlative light and electron microscopy can reveal novel types of information.
The spatial scale at which information can be extracted depends on imaging resolution and correlation accuracy. Since diffraction of light limits the resolution of conventional fluorescence microscopy to few hundreds of nanometers, reaching the full potential of correlative imaging requires super-resolution approaches. Performing imaging at cryogenic temperature preserves structures in a near-native state and minimizes distortions between the fluorescence and the electron microscopy datasets. Implementations of this concept have achieved correlation on the scale of cellular organelles or bacterial domains.
We have worked towards pushing correlative imaging to the single-molecule scale by improving cryo-super-resolution microscopy, and devising a refined image correlation workflow. As part of this project, I constructed a microscopy setup and adopted it for super-resolution fluorescence microscopy at room temperature and cryogenic conditions. I explored different cryo-stages and acquisition strategies. Specifically, I developed a new scheme for correcting sample drift, thus increasing mechanical stability during microscopy acquisitions
Maintaining diversity in structured populations
No full textWe examine population structures for their ability to maintain diversity in neutral evolution. We use the general framework of evolutionary graph theory and consider birth–death (bd) and death–birth (db) updating. The population is of size N. Initially all individuals represent different types. The basic question is: what is the time TN until one type takes over the population? This time is known as consensus time in computer science and as total coalescent time in evolutionary biology. For the complete graph, it is known that TN is quadratic in N for db and bd. For the cycle, we prove that TN is cubic in N for db and bd. For the star, we prove that TN is cubic for bd and quasilinear (N log N) for db. For the double star, we show that TN is quartic for bd. We derive upper and lower bounds for all undirected graphs for bd and db. We also show the Pareto front of graphs (of size N = 8) that maintain diversity the longest for bd and db. Further, we show that some graphs that quickly homogenize can maintain high levels of diversity longer than graphs that slowly homogenize. For directed graphs, we give simple contracting star-like structures that have superexponential time scales for maintaining diversity
Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation
No full textDuring embryonic development, cell behaviors need to be tightly regulated in time and space. Yet how the temporal and spatial regulations of cell behaviors are interconnected during embryonic development remains elusive. To address this, we turned to zebrafish gastrulation, the process whereby dynamic cell behaviors generate the three principal germ layers of the early embryo. Here, we show that Hoxb cluster genes are expressed in a temporally collinear manner at the blastoderm margin, where mesodermal and endodermal (mesendoderm) progenitor cells are specified and ingress to form mesendoderm/hypoblast. Functional analysis shows that these Hoxb genes regulate the timing of cell ingression: under- or overexpression of Hoxb genes perturb the timing of mesendoderm cell ingression and, consequently, the positioning of these cells along the forming anterior-posterior body axis after gastrulation. Finally, we found that Hoxb genes control the timing of mesendoderm ingression by regulating cellular bleb formation and cell surface fluctuations in the ingressing cells. Collectively, our findings suggest that Hoxb genes interconnect the temporal and spatial pattern of cell behaviors during zebrafish gastrulation by controlling cell surface fluctuations
Identification and elimination of surface emission in lanthanide (Co)doped zirconia nanocrystals
No full textZirconia nanocrystals (ZrO2 NCs) are a stable host material for lanthanides, but their performance lags behind that of the leading NaYF4 nanomaterials. Here, we leverage surface chemistry and core/shell architectures to uncover the contribution of dopants at the nanocrystal surface and of dopants in the nanocrystal bulk. We first assess the doping efficiency by ICP and find that, while Eu is almost quantitatively incorporated, the other lanthanides (La, Ce, Tb, Tm, Er, Yb) have about 50% incorporation efficiency over the studied doping range of 1–10%. We then determine the nanocrystal surface chemistry using NMR spectroscopy, despite the additional spectral line broadening caused by the paramagnetic lanthanide dopants. By varying the surface ligands and measuring the photoluminescence, we resolve the spectroscopic signals that are sensitive to a change in surface chemistry. Time-resolved emission spectra further reinforce the notion of a bulk component with a long luminescent lifetime and a surface component with a fast lifetime. Upon shelling Eu- or Tb-doped zirconia NCs with pure zirconia, the surface component disappears, and the photoluminescence quantum yield increases. We further functionalized the surface of the core/shell particles with oleylphosphonic acid ligands to obtain excellent dispersibility. These results show that lanthanide-doped zirconia NCs can be engineered to eliminate deactivation pathways
No [C II] or dust detection in two Little Red Dots at zspec > 7
No full textLittle Red Dots (LRDs) are compact, point-like sources characterized by their red color and broad Balmer lines; it is a matter of debate whether they are dominated by active galactic nuclei (AGNs) or dusty star-forming galaxies (DSFGs). Here we report two LRDs (ID9094 and ID2756) at zspec > 7 recently discovered in the JWST FRESCO GOODS-North field. Both satisfy the “v-shaped” color and compactness criteria for LRDs and are identified as Type-I AGN candidates based on their broad Hβ emission lines (full width at half maximum: 2280 ± 490 km s−1 for ID9094 and 1070 ± 240 km s−1 for ID2756) and narrow [O III] lines (≃300 − 400 km s−1). To investigate their nature, we conducted deep NOEMA follow-up observations targeting the [C II] 158 μm emission line and the 1.3 mm dust continuum. We do not detect [C II] or 1.3 mm continuum emission for either source. If the two LRDs were DSFGs, we would expect significant detections: > 16σ for [C II] and > 3σ for the 1.3 mm continuum of ID9094, and > 5σ for the [C II] of ID2756. Using the 3σ upper limits of [C II] and 1.3 mm, we performed two analyses: (1) UV-to-far-infrared spectral energy distribution fitting with and without AGN components, and (2) comparison of their properties with the L[C II]–SFRtot empirical relation. Both analyses are consistent with a scenario in which AGN activity contributes to the observed properties, though a dusty star-forming origin cannot be fully ruled out. Our results highlight the importance of far-infrared observations for studying LRDs, a regime that remains largely unexplored
Safety and liveness of quantitative properties and automata
No full textSafety and liveness stand as fundamental concepts in formal languages, playing a key role in verification. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In the quantitative setting, properties are arbitrary functions from infinite words to partially-ordered domains. Extending this paradigm to the quantitative domain, where properties are arbitrary functions mapping infinite words to partially-ordered domains, we introduce and study the notions of quantitative safety and liveness. First, we formally define quantitative safety and liveness, and prove that our definitions induce conservative quantitative generalizations of both the safety-progress hierarchy and the safety-liveness decomposition of boolean properties. Consequently, like their boolean counterparts, quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. We further establish a connection between quantitative safety and topological continuity and provide alternative characterizations of quantitative safety and liveness in terms of their boolean analogs. Second, we instantiate our framework with the specific classes of quantitative properties expressed by automata. These quantitative automata contain finitely many states and rational-valued transition weights, and their common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum map infinite words into the totally-ordered domain of real numbers. For all common value functions, we provide a procedure for deciding whether a given automaton is safe or live, we show how to construct its safety closure, and we present a min-decomposition into safe and live automata
How a space-time singularity helps remove the ultraviolet divergence problem
No full textParticle creation terms in quantum Hamiltonians are usually ultraviolet
divergent and thus mathematically ill defined. A rather novel way of solving
this problem is based on imposing so-called interior-boundary conditions on the
wave function. Previous papers showed that this approach works in the
non-relativistic regime, but particle creation is mostly relevant in the
relativistic case after all. In flat relativistic space-time (that is,
neglecting gravity), the approach was previously found to work only for certain
somewhat artificial cases. Here, as a way of taking gravity into account, we
consider curved space-time, specifically the super-critical
Reissner-Nordstr\"om space-time, which features a naked timelike singularity.
We find that the interior-boundary approach works fully in this setting; in
particular, we prove rigorously the existence of well-defined, self-adjoint
Hamiltonians with particle creation at the singularity, based on
interior-boundary conditions. We also non-rigorously analyze the asymptotic
behavior of the Bohmian trajectories and construct the corresponding Bohm-Bell
process of particle creation, motion, and annihilation. The upshot is that in
quantum physics, a naked space-time singularity need not lead to a breakdown of
physical laws, but on the contrary allows for boundary conditions governing
what comes out of the singularity and thereby removing the ultraviolet
divergence
On-demand single-microwave-photon source in a superconducting circuit with wideband frequency tunability
No full textIn this article, we propose a method for generating single microwave photons in superconducting circuits. We theoretically show that pure single microwave photons can be generated on demand and tuned over a large frequency band by making use of Landau-Zener transitions under a rapid sweep of a control parameter. We devise a protocol that enables fast control of the frequency of the emitted photon over two octaves, without requiring extensive calibration. Additionally, we make theoretical estimates of the generation efficiency, tunability, purity, and linewidth of the photons emitted using this method for both charge- and flux-qubit-based architectures. We also provide estimates of the optimal device parameters required for these architectures to realize the device
ResiDual transformer alignment with spectral decomposition
No full textWhen examined through the lens of their residual streams, a puzzling property emerges in transformer networks: residual contributions (e.g., attention heads) sometimes specialize in specific tasks or input attributes. In this paper, we analyze this phenomenon in vision transformers, focusing on the spectral geometry of residuals, and explore its implications for modality alignment in vision-language models. First, we link it to the intrinsically low-dimensional structure of visual head representations, zooming into their principal components and showing that they encode specialized roles across a wide variety of input data distributions. Then, we analyze the effect of head specialization in multimodal models, focusing on how improved alignment between text and specialized heads impacts zero-shot classification performance. This specialization-performance link consistently holds across diverse pre-training data, network sizes, and objectives, demonstrating a powerful new mechanism for boosting zero-shot classification through targeted alignment. Ultimately, we translate these insights into actionable terms by introducing ResiDual, a technique for spectral alignment of the residual stream. Much like panning for gold, it lets the noise from irrelevant unit principal components (i.e., attributes) wash away to amplify task-relevant ones. Remarkably, this dual perspective on modality alignment yields fine-tuning level performance on different data distributions while modelling an extremely interpretable and parameter-efficient transformation, as we extensively show on 70 pre-trained network-dataset combinations (7 models, 10 datasets)
Glucose electrooxidation with simultaneous H2 production on nickel-zinc electrocatalysts derived from an ethylenediamine-functionalized zeolitic imidazole framework
No full textThe oxidation of biomass-derived compounds such as glucose within electrochemical cells enables both the energy-efficient production of hydrogen and the generation of additional added-value chemicals from biomass. However, for this biomass valorization approach to become commercially viable, selective, cost-effective, and highly active electrooxidation catalysts need to be developed. In this work, we detail the synthesis of a nickel (Ni) and zinc (Zn)-based electrocatalyst for the glucose oxidation reaction (GOR) to formic acid (FoA) via calcination of a Zn-based zeolitic imidazole framework (ZIF) functionalized with ethylenediamine and doped with Ni. The structure, morphology, and electrochemical performance of the catalysts towards the anodic GOR to FoA coupled with the cathodic hydrogen evolution reaction (HER) are subsequently studied. Chronopotentiometry tests with 0.1 M of glucose show a conversion of 94 % at 250 mA in only 70 min, with a Faradaic efficiency (FE) of 91 % toward the production of FoA. Meanwhile, at the cathode, the HER FE is close to 98 %