@phdthesis{21863, abstract = {Atoms and photons, two things so different but yet so alike. The former, the building block of matter, something we learn about in school and imagine it as some tiny marbles encircled by other tinier marbles. The latter, an electromagnetic wave, a light particle or an excitation of the electromagnetic field. Quantum mechanics tells us about the properties of these two entities. And even if it sounds, looks and writes counter-intuitive, it has proven right for over a century now. In this work, I elaborate on how we tested the laws of quantum mechanics and how we used them learn more about the tiny building blocks of nature and the fields they use to talk to each other. The atoms we use, are artificial. Superconducting qubits, small electrical circuits with quantized energy levels behave like electrons that transition between different orbitals in an atom. One of the qubits' advantages, is also a big disadvantage. We design the circuits' energy levels and fabricate them in a cleanroom. This allows for arbitrary spaced energy levels but in contrast to real atoms, prevents two superconducting qubits from being alike. Still, this qubit platform is one of the frontrunners for future quantum computing technology and testing fundamental physics due to their scalability. We interface superconducting qubits, which operate in the GHz regime, with microwave photons. We use 3D aluminum cavities as mediators between qubits and photons. The cavities allow for non-destructive readout of the qubit state, they shield the qubits from noise at the qubit frequency and they give us an easy way to frequency-tune these joint systems. We need to operate superconducting qubits and their cavities at millikelvin temperatures in dilution refrigerators. At higher temperatures, superconductivity suffers and even worse, the environment is filled with thermal noise photons. This poses a fundamental limitation on the scalability of superconducting qubit devices. Also connecting multiple devices in different fridges does not work over room temperature links because the microwave photons used for this purpose will be covered in noise and the quantum information they carry, will be unusable. Infrared photons do not suffer from this noise problem since there are close to zero thermal noise photons at their frequencies at room temperature. We cannot simply interface superconducting devices with optical photons due their frequency mismatch and the destructive effect of optical photons on superconductors. Therefore, we use microwave-to-optics transducers that allow to convert microwave photons into optical ones and vice-versa. The transducers that we use are macroscopic electro-optic transducers using the Pockels effect in a disk-shaped Lithium Niobate whispering gallery mode resonator. By using a strong optical pump, photons from the two frequency domains experience a beam-splitter interaction and get converted from one to the other. We measure the generated optical photons using elaborate optical setups, optical heterodyning and single photon detectors to gain knowledge about the qubit state or the converted microwave photons. Bridging the microwave and the optical world allows us to take advantage of both of their strengths but it also requires deep knowledge about both of their working principles. In this work, we describe two experiments that our group conducted to showcase the opportunities that arise from interfacing superconducting qubits with optical photons but also the pitfalls, one may encounter on the way. In the first experiment, we managed to all-optically read out a superconducting qubit. We show that the assignment fidelity, the probability that a measurement of the qubit state matches the prepared state, is close to equal for all-optical, microwave-to-optics and conventional microwave readout. We show T1 and T2 measurements for all three readout types and give an analysis of the noise caused by the optics. Finally, we show that the infrared light does not affect the qubit performance in a negative way but that the heating it causes does. This is an important insight that we used in the next experiment. The second experiment is the upconversion of itinerant single microwave photons to the optical domain. We show that we can generate single microwave photons from a qubit-cavity system. We upconvert these single photons, measure them with a single photon detector and reconstruct their shape. By conducting a single photon Rabi measurement, we show correlations between the microwave and the optical domain. And by thorough signal-to-noise measurements and noise analysis, we find that we can generate single infrared photons with high signal-to-noise ratio 5.1 and low transducer added noise (<0.012 quanta). We show that this measurement creates a path towards entanglement of a superconducting qubit and an optical photon and what parameters need to be improved to achieve it. Additionally, this experiment is a proof of principle for an on-demand infrared single photon source. More generally, it allows to link microwave quantum technology in general to the optical domain.}, author = {Werner, Thomas}, issn = {2663-337X}, keywords = {Superconducting qubits, Quantum optics, Single photons and quantum effects, Nonlinear optics}, pages = {97}, publisher = {Institute of Science and Technology Austria}, title = {{Interfacing superconducting qubits with optical photons}}, doi = {10.15479/AT-ISTA-21863}, year = {2026}, } @unpublished{21870, abstract = {Superconducting qubits are a leading candidate for utility-scale quantum computing due to their fast gate speeds and steadily decreasing error rates. The requirement for millikelvin operating temperatures, however, creates a significant scaling bottleneck. Modular architectures using optical fiber links could bridge separate cryogenic nodes, but superconducting circuits do not have coherent optical transitions and microwave-to-optical conversion has not been shown for any non-classical photon state. In this work, we demonstrate the on-demand generation and tomographic reconstruction of itinerant single microwave photons at 8.9 GHz from a superconducting qubit. We upconvert this non-Gaussian state with a transducer added noise below 0.012 quanta and count the converted telecom photons at 193.4 THz with a signal-to-noise ratio of up to 5.1$\pm$1.1. We characterize the trade-offs between throughput and noise, and establish a viable path toward heralded entanglement distribution and gate teleportation. Looking ahead, these results empower existing superconducting devices to take a key role in distributed quantum technologies and heterogeneous quantum systems.}, author = {Werner, Thomas and Riyazi, Erfan and Hawaldar, Samarth and Sahu, Rishabh and Arnold, Georg M and Paul Falthansl-Scheinecker, Paul Falthansl-Scheinecker and Naranjo, Jennifer A. Sánchez and Loi, Dante and Kapoor, Lucky N. and Zemlicka, Martin and Qiu, Liu and Militaru, Andrei and Fink, Johannes M}, booktitle = {arXiv}, title = {{Electro-optic conversion of itinerant Fock states}}, doi = {10.48550/arXiv.2602.00928}, year = {2026}, } @article{20977, abstract = {Hippocampal sharp-wave ripples (SPW-Rs) are high-frequency oscillations critical for memory consolidation. Despite extensive characterization in rodents, their detection in humans is limited by coarse spatial sampling, interictal epileptiform discharges (IEDs), and a lack of consensus on human ripple localization and morphology. Here, we demonstrate that mouse and human hippocampal ripples share spatial, spectral and temporal features, which are clearly distinct from IEDs. In recordings from male APP/PS1 mice, SPW-Rs were distinguishable from IEDs by multiple criteria. Hippocampal ripples recorded during NREM sleep in female and male surgical epilepsy patients exhibited similar narrowband frequency peaks and multiple ripple cycles in the CA1 and subiculum regions. Conversely, IEDs showed a broad spatial extent and wide-band frequency power. We developed a semi-automated, ripple curation toolbox (ripmap) to separate event waveforms by low-dimensional embedding to reduce false-positive rate in selected ripple channels. Our approach improves ripple detection and provides a firm foundation for future human memory research.}, author = {Maslarova, Anna and Shin, Jiyun N. and Navas Olivé, Andrea C and Vöröslakos, Mihály and Hamer, Hajo and Doerfler, Arnd and Henin, Simon and Buzsáki, György and Liu, Anli}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Spatiotemporal patterns differentiate hippocampal sharp-wave ripples from interictal epileptiform discharges in mice and humans}}, doi = {10.1038/s41467-025-66562-6}, volume = {16}, year = {2025}, } @article{18879, abstract = {Our brain has remarkable computational power, generating sophisticated behaviors, storing memories over an individual’s lifetime, and producing higher cognitive functions. However, little of our neuroscience knowledge covers the human brain. Is this organ truly unique, or is it a scaled version of the extensively studied rodent brain? Combining multicellular patch-clamp recording with expansion-based superresolution microscopy and full-scale modeling, we determined the cellular and microcircuit properties of the human hippocampal CA3 region, a fundamental circuit for memory storage. In contrast to neocortical networks, human hippocampal CA3 displayed sparse connectivity, providing a circuit architecture that maximizes associational power. Human synapses showed unique reliability, high precision, and long integration times, exhibiting both species- and circuit-specific properties. Together with expanded neuronal numbers, these circuit characteristics greatly enhanced the memory storage capacity of CA3. Our results reveal distinct microcircuit properties of the human hippocampus and begin to unravel the inner workings of our most complex organ. }, author = {Watson, Jake and Vargas Barroso, Victor M and Morse, Rebecca and Navas Olivé, Andrea C and Tavakoli, Mojtaba and Danzl, Johann G and Tomschik, Matthias and Rössler, Karl and Jonas, Peter M}, issn = {1097-4172}, journal = {Cell}, number = {2}, pages = {501--514.e18}, publisher = {Elsevier}, title = {{Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory}}, doi = {10.1016/j.cell.2024.11.022}, volume = {188}, year = {2025}, } @article{20318, abstract = {Lipid membranes and membrane deformations are a long-standing area of research in soft matter and biophysics. Computer simulations have complemented analytical and experimental approaches as one of the pillars in the field. However, setting up and using membrane simulations can come with barriers due to the multidisciplinary effort involved and the vast choice of existing simulations models. In this review, we introduce the non-expert reader to coarse-grained membrane simulations at the mesoscale. Firstly, we give a concise overview of the modelling approaches to study fluid membranes, together with guidance to more specialized references. Secondly, we provide a conceptual guide on how to develop mesoscale membrane simulations. Lastly, we construct a hands-on tutorial on how to apply mesoscale membrane simulations, by providing a pedagogical examination of membrane tether pulling, shape and mechanics of membrane tubes, and membrane fluctuations with three different membrane models, and discussing them in terms of their scope and how resource-intensive they are. To ease the reader's venture into the field, we provide a repository with ready-to-run tutorials.}, author = {Muñoz Basagoiti, Maitane and Frey, Felix F and Meadowcroft, Billie and Santana de Freitas Amaral, Miguel and Prada, Adam and Šarić, Anđela}, issn = {1744-6848}, journal = {Soft Matter}, number = {40}, pages = {7736--7756}, publisher = {Royal Society of Chemistry}, title = {{A tutorial for mesoscale computer simulations of lipid membranes: Tether pulling, tubulation and fluctuations}}, doi = {10.1039/d5sm00148j}, volume = {21}, year = {2025}, } @article{20531, abstract = {Genetic drift is potentially an important component of selection for sex, as it is a source of statistical associations between alleles at selected loci. By increasing local drift, population structure may thus amplify the evolutionary advantage of sex. However, most previous models have focused either on haploid populations or on diploid populations without spatial structure. In this article, we use two- and three-locus analytical models and multilocus simulations to explore selection for sex in a diploid population structured according to the island model, in the presence of recurrent deleterious mutations. Our results show that selection generally favors an intermediate rate of sex that decreases as the direct cost of sex increases and increases moderately as the degree of population structure increases. Selection for sex is generated by multiple effects involving genetic associations within and between loci. When selection occurs at many loci, it is generally dominated by interference effects involving deleterious alleles at different loci, captured by our three-locus model. In our multilocus simulations, we observed an irreversible spread of asexual mutants under strong costs of sex, and when deleterious mutations are partially recessive. However, population structure may prevent this spread of asexual mutants when dispersal rates are sufficiently small.}, author = {Fouqueau, Louise and Roze, Denis}, issn = {1558-5646}, journal = {Evolution}, number = {10}, pages = {2167--2180}, publisher = {Oxford University Press}, title = {{Deleterious mutations and selection for sex in spatially structured, diploid populations}}, doi = {10.1093/evolut/qpaf143}, volume = {79}, year = {2025}, } @phdthesis{17133, abstract = {An ideal quantum computer relies on qubits capable of performing fast gate operations and maintaining strong interconnections while preserving their quantum coherence. Since the inception of experimental eforts toward building a quantum computer, the community has faced challenges in engineering such a system. Among the various methods of implementing a quantum computer, superconducting qubits have shown fast gates close to tens of nanoseconds, with the state-of-the-art reaching a coherence of a few milliseconds. However, achieving simultaneously long lifetimes with fast qubit operations poses an inherent paradox. Qubits with high coherence require isolation from the environment, while fast operation necessitates strong coupling of the qubit. This thesis approaches this issue by proposing the idea of engineering superconducting qubits capable of transitioning between operating in a protected regime, where the qubit is completely isolated from the environment, and coupling to the communication channels as needed. In this direction, we use the geometric superinductor to scan the parameter space of rf-SQUID devices, searching for a regime where we can take the qubit protection to its extreme. This leads us to the inductively shunted transmon (IST) regime, characterized by EJ /EC ≫ 1 and EJ /EL ≫ 1, where the circuit potential exhibits a double well with a large barrier separating the local ground states of each quantum well. In this regime, although it is anticipated that the two quantum wells would be isolated from each other, we observe single fuxon tunneling between them. The interplay of the cavity photons and the fuxon transition forms a rich physical system, containing resonance conditions that allow the preparation of the fuxon ground or excited states. This enables us to study the relaxation rate of such transition and show that it can be as large as 3.6 hours. Dynamically controlling the barrier height between the two quantum wells allows for controllable coupling, which scales exponentially, for a qubit encoded in two fuxon states. The 0-π qubit is one of the very few known superconducting circuit types that ofers exponential protection from both relaxation and dephasing simultaneously. However, this qubit is not exempt from the fact that such protection comes at the expense of complex readout and control. In this thesis, we propose a way to controllably break the circuit symmetry, the key reason for the protection, to momentarily restore the ability to control and manipulate the qubit. An asymmetry in capacitances and inductances in the 0-π circuit is detrimental since they lead to coupling of the protected state to the thermally occupied parasitic mode of the circuit. However, here we try to exploit a controlled asymmetry in Josephson energies and show that this can be used as a tunable coupler between the protected states. In the future, this should allow to perform gate operations by dynamically controlling the asymmetry instead of driving the protected transition with microwave pulses. Therefore, we believe that the proposed method can make the use of protected qubits more practical in experimental realizations of quantum computing.}, author = {Hassani, Farid}, isbn = {978-3-99078-040-4}, issn = {2663-337X}, keywords = {Quantum information, Qubits, Superconducting devices}, pages = {161}, publisher = {Institute of Science and Technology Austria}, title = {{Superconducting qubits capable of dynamic switching between protected and high-speed control regimes}}, doi = {10.15479/at:ista:17133}, year = {2024}, } @article{17207, author = {Fouqueau, Louise and Polechova, Jitka}, issn = {1420-9101}, journal = {Journal of evolutionary biology}, number = {6}, pages = {579--587}, publisher = {Oxford University Press}, title = {{Eco-evolutionary dynamics in changing environments: Integrating theory with data}}, doi = {10.1093/jeb/voae067}, volume = {37}, year = {2024}, } @article{12702, abstract = {Hydrocarbon mixtures are extremely abundant in the Universe, and diamond formation from them can play a crucial role in shaping the interior structure and evolution of planets. With first-principles accuracy, we first estimate the melting line of diamond, and then reveal the nature of chemical bonding in hydrocarbons at extreme conditions. We finally establish the pressure-temperature phase boundary where it is thermodynamically possible for diamond to form from hydrocarbon mixtures with different atomic fractions of carbon. Notably, here we show a depletion zone at pressures above 200 GPa and temperatures below 3000 K-3500 K where diamond formation is thermodynamically favorable regardless of the carbon atomic fraction, due to a phase separation mechanism. The cooler condition of the interior of Neptune compared to Uranus means that the former is much more likely to contain the depletion zone. Our findings can help explain the dichotomy of the two ice giants manifested by the low luminosity of Uranus, and lead to a better understanding of (exo-)planetary formation and evolution.}, author = {Cheng, Bingqing and Hamel, Sebastien and Bethkenhagen, Mandy}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Thermodynamics of diamond formation from hydrocarbon mixtures in planets}}, doi = {10.1038/s41467-023-36841-1}, volume = {14}, year = {2023}, } @article{11143, abstract = {Dravet syndrome is a neurodevelopmental disorder characterized by epilepsy, intellectual disability, and sudden death due to pathogenic variants in SCN1A with loss of function of the sodium channel subunit Nav1.1. Nav1.1-expressing parvalbumin GABAergic interneurons (PV-INs) from young Scn1a+/− mice show impaired action potential generation. An approach assessing PV-IN function in the same mice at two time points shows impaired spike generation in all Scn1a+/− mice at postnatal days (P) 16–21, whether deceased prior or surviving to P35, with normalization by P35 in surviving mice. However, PV-IN synaptic transmission is dysfunctional in young Scn1a+/− mice that did not survive and in Scn1a+/− mice ≥ P35. Modeling confirms that PV-IN axonal propagation is more sensitive to decreased sodium conductance than spike generation. These results demonstrate dynamic dysfunction in Dravet syndrome: combined abnormalities of PV-IN spike generation and propagation drives early disease severity, while ongoing dysfunction of synaptic transmission contributes to chronic pathology.}, author = {Kaneko, Keisuke and Currin, Christopher and Goff, Kevin M. and Wengert, Eric R. and Somarowthu, Ala and Vogels, Tim P and Goldberg, Ethan M.}, issn = {2211-1247}, journal = {Cell Reports}, number = {13}, publisher = {Elsevier}, title = {{Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome}}, doi = {10.1016/j.celrep.2022.110580}, volume = {38}, year = {2022}, } @article{10530, abstract = {Cell dispersion from a confined area is fundamental in a number of biological processes, including cancer metastasis. To date, a quantitative understanding of the interplay of single cell motility, cell proliferation, and intercellular contacts remains elusive. In particular, the role of E- and N-Cadherin junctions, central components of intercellular contacts, is still controversial. Combining theoretical modeling with in vitro observations, we investigate the collective spreading behavior of colonies of human cancer cells (T24). The spreading of these colonies is driven by stochastic single-cell migration with frequent transient cell-cell contacts. We find that inhibition of E- and N-Cadherin junctions decreases colony spreading and average spreading velocities, without affecting the strength of correlations in spreading velocities of neighboring cells. Based on a biophysical simulation model for cell migration, we show that the behavioral changes upon disruption of these junctions can be explained by reduced repulsive excluded volume interactions between cells. This suggests that in cancer cell migration, cadherin-based intercellular contacts sharpen cell boundaries leading to repulsive rather than cohesive interactions between cells, thereby promoting efficient cell spreading during collective migration. }, author = {Zisis, Themistoklis and Brückner, David and Brandstätter, Tom and Siow, Wei Xiong and d’Alessandro, Joseph and Vollmar, Angelika M. and Broedersz, Chase P. and Zahler, Stefan}, issn = {0006-3495}, journal = {Biophysical Journal}, keywords = {Biophysics}, number = {1}, pages = {P44--60}, publisher = {Elsevier}, title = {{Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration}}, doi = {10.1016/j.bpj.2021.12.006}, volume = {121}, year = {2022}, }