@article{14656,
  abstract     = {Although much is known about how single neurons in the hippocampus represent an animal's position, how circuit interactions contribute to spatial coding is less well understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured CA1 cell-cell interactions in male rats during open field exploration. The statistics of these interactions depend on whether the animal is in a familiar or novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the informativeness of their spatial inputs. This structure facilitates linear decodability, making the information easy to read out by downstream circuits. Overall, our findings suggest that the efficient coding hypothesis is not only applicable to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain.},
  author       = {Nardin, Michele and Csicsvari, Jozsef L and Tkačik, Gašper and Savin, Cristina},
  issn         = {1529-2401},
  journal      = {The Journal of Neuroscience},
  number       = {48},
  pages        = {8140--8156},
  publisher    = {Society for Neuroscience},
  title        = {{The structure of hippocampal CA1 interactions optimizes spatial coding across experience}},
  doi          = {10.1523/JNEUROSCI.0194-23.2023},
  volume       = {43},
  year         = {2023},
}

@article{14759,
  abstract     = {Proper operation of electro-optic I/Q modulators relies on precise adjustment and control of the relative phase biases between the modulator’s internal interferometer arms. We present an all-analog phase bias locking scheme where error signals are obtained from the beat between the optical carrier and optical tones generated by an auxiliary 2 MHz 𝑅𝐹 tone to lock the phases of all three involved interferometers for operation up to 10 GHz. With the developed method, we demonstrate an I/Q modulator in carrier-suppressed single-sideband mode, where the suppressed carrier and sideband are locked at optical power levels <−27dB
 relative to the transmitted sideband. We describe a simple analytical model for calculating the error signals and detail the implementation of the electronic circuitry for the implementation of the method.},
  author       = {Wald, Sebastian and Diorico, Fritz R and Hosten, Onur},
  issn         = {2155-3165},
  journal      = {Applied Optics},
  keywords     = {Atomic and Molecular Physics, and Optics, Engineering (miscellaneous), Electrical and Electronic Engineering},
  number       = {1},
  pages        = {1--7},
  publisher    = {Optica Publishing Group},
  title        = {{Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone}},
  doi          = {10.1364/ao.474118},
  volume       = {62},
  year         = {2023},
}

@article{13200,
  abstract     = {Recent quantum technologies have established precise quantum control of various microscopic systems using electromagnetic waves. Interfaces based on cryogenic cavity electro-optic systems are particularly promising, due to the direct interaction between microwave and optical fields in the quantum regime. Quantum optical control of superconducting microwave circuits has been precluded so far due to the weak electro-optical coupling as well as quasi-particles induced by the pump laser. Here we report the coherent control of a superconducting microwave cavity using laser pulses in a multimode electro-optical device at millikelvin temperature with near-unity cooperativity. Both the stationary and instantaneous responses of the microwave and optical modes comply with the coherent electro-optical interaction, and reveal only minuscule amount of excess back-action with an unanticipated time delay. Our demonstration enables wide ranges of applications beyond quantum transductions, from squeezing and quantum non-demolition measurements of microwave fields, to entanglement generation and hybrid quantum networks.},
  author       = {Qiu, Liu and Sahu, Rishabh and Hease, William J and Arnold, Georg M and Fink, Johannes M},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Nature Research},
  title        = {{Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action}},
  doi          = {10.1038/s41467-023-39493-3},
  volume       = {14},
  year         = {2023},
}

@unpublished{18953,
  abstract     = {The rapid development of superconducting quantum hardware is expected to run into significant I/O restrictions due to the need for large-scale error correction in a cryogenic environment. Classical data centers rely on fiber-optic interconnects to remove similar networking bottlenecks and to allow for reconfigurable, software-defined infrastructures. In the same spirit, ultra-cold electro-optic links have been proposed and used to generate qubit control signals, or to replace cryogenic readout electronics. So far, the latter suffered from either low efficiency, low bandwidth and the need for additional microwave drives, or breaking of Cooper pairs and qubit states. In this work we realize electro-optic microwave photonics at millikelvin temperatures to implement a radio-over-fiber qubit readout that does not require any active or passive cryogenic microwave equipment. We demonstrate all-optical single-shot-readout by means of the Jaynes-Cummings nonlinearity in a circulator-free readout scheme. Importantly, we do not observe any direct radiation impact on the qubit state as verified with high-fidelity quantum-non-demolition measurements despite the absence of shielding elements. This compatibility between superconducting circuits and telecom wavelength light is not only a prerequisite to establish modular quantum networks, it is also relevant for multiplexed readout of superconducting photon detectors and classical superconducting logic. Moreover, this experiment showcases the potential of electro-optic radiometry in harsh environments - an electronics-free sensing principle that extends into the THz regime with applications in radio astronomy, planetary missions and earth observation.},
  author       = {Arnold, Georg M and Werner, Thomas and Sahu, Rishabh and Kapoor, Lucky and Qiu, Liu and Fink, Johannes M},
  booktitle    = {arXiv},
  title        = {{All-optical single-shot readout of a superconducting qubit}},
  doi          = {10.48550/ARXIV.2310.16817},
  year         = {2023},
}

@article{14274,
  abstract     = {Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization.},
  author       = {Alanko, Jonna H and Ucar, Mehmet C and Canigova, Nikola and Stopp, Julian A and Schwarz, Jan and Merrin, Jack and Hannezo, Edouard B and Sixt, Michael K},
  issn         = {2470-9468},
  journal      = {Science Immunology},
  keywords     = {General Medicine, Immunology},
  number       = {87},
  publisher    = {American Association for the Advancement of Science},
  title        = {{CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration}},
  doi          = {10.1126/sciimmunol.adc9584},
  volume       = {8},
  year         = {2023},
}

@phdthesis{14226,
  abstract     = {We introduce the notion of a Faustian interchange in a 1-parameter family of smooth
functions to generalize the medial axis to critical points of index larger than 0.
We construct and implement a general purpose algorithm for approximating such
generalized medial axes.},
  author       = {Stephenson, Elizabeth R},
  issn         = {2791-4585},
  pages        = {43},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Generalizing medial axes with homology switches}},
  doi          = {10.15479/at:ista:14226},
  year         = {2023},
}

@phdthesis{14510,
  abstract     = {Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and
development by controlling plasma membrane protein composition and cargo uptake. CME
relies on the precise recruitment control of protein regulators for vesicle maturation and
release. During the early stages of endocytosis, an area of flat membrane is remodelled by
proteins to create a spherical vesicle against intracellular forces. After the Clathrin-coated
vesicle (CCV) is fully formed, scission machinery releases it from the plasma membrane,
and cargo proceeds for recycling or degradation through early endosomes / Trans Golgi
network. Protein machineries that mediate membrane bending and vesicle release in plants
are unknown. However, studies show, that plant endocytosis is actin independent, thus
indicating that plants utilize a unique mechanism to mediate membrane bending against highturgor pressure compared to other model systems. First, by using biochemical and advanced
live microscopy approaches we investigate the TPLATE complex, a plant-specific
endocytosis protein complex. We found that TPLATE is peripherally associated with
clathrin-coated vesicles and localises at the rim of endocytosis events. Next, our study of
plant Dynamin-related protein 1C (DRP1C), which was hypothesised previously to play a
role in vesicle release, shows the recruitment of the protein already at the early stages of
endocytosis. Moreover, DRP1C assembles into organised ring-like structures and is able to
induce membrane deformation and tubulation, suggesting its role also in membrane bending
during early CME. Based on the data from mammalian and yeast systems, plant DynaminRelated Proteins 2 and SH3P2 protein are strong candidates to be part of the plant vesicle
scission machinery; however, their precise role in plant CME has not been yet elucidated.
Here, we characterised DRP2s and SH3P2 roles in CME by combining high-resolution
imaging of endocytic events in vivo and protein characterisation. Although DRP2s and
SH3P2 arrive together during late CME and physically interact, genetic analysis using
∆sh3p1,2,3 mutant and complementation with non-DRP2-interacting SH3P2 variants suggest
that SH3P2 does not directly recruit DRP2s to the site of endocytosis. Summarising our
research, these observations provide new important insights into the mechanism of plant
CME and show that, despite plants posses many homologues of mammalian and yeast CME
components, they do not necessarily act in the same manner. },
  author       = {Gnyliukh, Nataliia},
  isbn         = {978-3-99078-037-4},
  issn         = {2663-337X},
  keywords     = {Clathrin-Mediated Endocytosis, vesicle scission, Dynamin-Related Protein 2, SH3P2, TPLATE complex, Total internal reflection fluorescence microscopy, Arabidopsis thaliana},
  pages        = {180},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Mechanism of clathrin-coated vesicle  formation during endocytosis in plants}},
  doi          = {10.15479/at:ista:14510},
  year         = {2023},
}

@unpublished{14591,
  abstract     = {Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scissin machinery in plants, but the precise roles of these proteins in this process is not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. One Sentence Summary In contrast to predictions based on mammalian systems, plant Dynamin-related proteins 2 are recruited to the site of Clathrin-mediated endocytosis independently of BAR-SH3 proteins.},
  author       = {Gnyliukh, Nataliia and Johnson, Alexander J and Nagel, Marie-Kristin and Monzer, Aline and Hlavata, Annamaria and Isono, Erika and Loose, Martin and Friml, Jiří},
  booktitle    = {bioRxiv},
  title        = {{Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants}},
  doi          = {10.1101/2023.10.09.561523},
  year         = {2023},
}

@phdthesis{12470,
  abstract     = {The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of 
connections that orchestrate our cognition and behavior. To decode its complex connectivity, it is 
pivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of 
nm-small synapses.
To achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across 
Scales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (superresolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular
space, that is compatible with chemical fixation, with information on molecular markers, superresolved data acquisition and machine-learning based data analysis for segmentation and synapse 
identification.
I used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue 
architecture, neuronal in- and output-fields, down to synapse morphology.
Focusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy 
fiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 
pyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal 
connectivity with light microscopy.},
  author       = {Michalska, Julia M},
  isbn         = {978-3-99078-026-8},
  issn         = {2663-337X},
  pages        = {201},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy}},
  doi          = {10.15479/at:ista:12470},
  year         = {2023},
}

@phdthesis{14622,
  abstract     = {This Ph.D. thesis presents a detailed investigation into Variational Quantum Algorithms
(VQAs), a promising class of quantum algorithms that are well suited for near-term quantum
computation due to their moderate hardware requirements and resilience to noise. Our
primary focus lies on two particular types of VQAs: the Quantum Approximate Optimization
Algorithm (QAOA), used for solving binary optimization problems, and the Variational Quantum
Eigensolver (VQE), utilized for finding ground states of quantum many-body systems.
In the first part of the thesis, we examine the issue of effective parameter initialization for
the QAOA. The work demonstrates that random initialization of the QAOA often leads to
convergence in local minima with sub-optimal performance. To mitigate this issue, we propose
an initialization of QAOA parameters based on the Trotterized Quantum Annealing (TQA).
We show that TQA initialization leads to the same performance as the best of an exponentially
scaling number of random initializations.
The second study introduces Transition States (TS), stationary points with a single direction
of descent, as a tool for systematically exploring the QAOA optimization landscape. This
leads us to propose a novel greedy parameter initialization strategy that guarantees for the
energy to decrease with increasing number of circuit layers.
In the third section, we extend the QAOA to qudit systems, which are higher-dimensional
generalizations of qubits. This chapter provides theoretical insights and practical strategies for
leveraging the increased computational power of qudits in the context of quantum optimization
algorithms and suggests a quantum circuit for implementing the algorithm on an ion trap
quantum computer.
Finally, we propose an algorithm to avoid “barren plateaus”, regions in parameter space with
vanishing gradients that obstruct efficient parameter optimization. This novel approach relies
on defining a notion of weak barren plateaus based on the entropies of local reduced density
matrices and showcases how these can be efficiently quantified using shadow tomography.
To illustrate the approach we employ the strategy in the VQE and show that it allows to
successfully avoid barren plateaus in the initialization and throughout the optimization.
Taken together, this thesis greatly enhances our understanding of parameter initialization and
optimization in VQAs, expands the scope of QAOA to higher-dimensional quantum systems,
and presents a method to address the challenge of barren plateaus using the VQE. These
insights are instrumental in advancing the field of near-term quantum computation.},
  author       = {Sack, Stefan},
  issn         = {2663-337X},
  pages        = {142},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems}},
  doi          = {10.15479/at:ista:14622},
  year         = {2023},
}

@article{13125,
  abstract     = {The quantum approximate optimization algorithm (QAOA) is a variational quantum algorithm, where a quantum computer implements a variational ansatz consisting of p layers of alternating unitary operators and a classical computer is used to optimize the variational parameters. For a random initialization, the optimization typically leads to local minima with poor performance, motivating the search for initialization strategies of QAOA variational parameters. Although numerous heuristic initializations exist, an analytical understanding and performance guarantees for large p remain evasive.We introduce a greedy initialization of QAOA which guarantees improving performance with an increasing number of layers. Our main result is an analytic construction of 2p + 1 transition states—saddle points with a unique negative curvature direction—for QAOA with p + 1 layers that use the local minimum of QAOA with p layers. Transition states connect to new local minima, which are guaranteed to lower the energy compared to the minimum found for p layers. We use the GREEDY procedure to navigate the exponentially increasing with p number of local minima resulting from the recursive application of our analytic construction. The performance of the GREEDY procedure matches available initialization strategies while providing a guarantee for the minimal energy to decrease with an increasing number of layers p. },
  author       = {Sack, Stefan and Medina Ramos, Raimel A and Kueng, Richard and Serbyn, Maksym},
  issn         = {2469-9934},
  journal      = {Physical Review A},
  number       = {6},
  publisher    = {American Physical Society},
  title        = {{Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement}},
  doi          = {10.1103/physreva.107.062404},
  volume       = {107},
  year         = {2023},
}

@article{14613,
  abstract     = {Many insects carry an ancient X chromosome - the Drosophila Muller element F - that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 MY. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the two homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.},
  author       = {Lasne, Clementine and Elkrewi, Marwan N and Toups, Melissa A and Layana Franco, Lorena Alexandra and Macon, Ariana and Vicoso, Beatriz},
  issn         = {1537-1719},
  journal      = {Molecular Biology and Evolution},
  keywords     = {Genetics, Molecular Biology, Ecology, Evolution, Behavior and Systematics},
  number       = {12},
  publisher    = {Oxford University Press},
  title        = {{The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome}},
  doi          = {10.1093/molbev/msad245},
  volume       = {40},
  year         = {2023},
}

@article{14032,
  abstract     = {Arrays of Josephson junctions are governed by a competition between superconductivity and repulsive Coulomb interactions, and are expected to exhibit diverging low-temperature resistance when interactions exceed a critical level. Here we report a study of the transport and microwave response of Josephson arrays with interactions exceeding this level. Contrary to expectations, we observe that the array resistance drops dramatically as the temperature is decreased—reminiscent of superconducting behaviour—and then saturates at low temperature. Applying a magnetic field, we eventually observe a transition to a highly resistive regime. These observations can be understood within a theoretical picture that accounts for the effect of thermal fluctuations on the insulating phase. On the basis of the agreement between experiment and theory, we suggest that apparent superconductivity in our Josephson arrays arises from melting the zero-temperature insulator.},
  author       = {Mukhopadhyay, Soham and Senior, Jorden L and Saez Mollejo, Jaime and Puglia, Denise and Zemlicka, Martin and Fink, Johannes M and Higginbotham, Andrew P},
  issn         = {1745-2481},
  journal      = {Nature Physics},
  keywords     = {General Physics and Astronomy},
  pages        = {1630--1635},
  publisher    = {Springer Nature},
  title        = {{Superconductivity from a melted insulator in Josephson junction arrays}},
  doi          = {10.1038/s41567-023-02161-w},
  volume       = {19},
  year         = {2023},
}

@article{12521,
  abstract     = {Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated.},
  author       = {Mrnjavac, Andrea and Khudiakova, Kseniia and Barton, Nicholas H and Vicoso, Beatriz},
  issn         = {2056-3744},
  journal      = {Evolution Letters},
  keywords     = {Genetics, Ecology, Evolution, Behavior and Systematics},
  number       = {1},
  publisher    = {Oxford University Press},
  title        = {{Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution}},
  doi          = {10.1093/evlett/qrac004},
  volume       = {7},
  year         = {2023},
}

@inproceedings{14459,
  abstract     = {Autoencoders are a popular model in many branches of machine learning and lossy data compression. However, their fundamental limits, the performance of gradient methods and the features learnt during optimization remain poorly understood, even in the two-layer setting. In fact, earlier work has considered either linear autoencoders or specific training regimes (leading to vanishing or diverging compression rates). Our paper addresses this gap by focusing on non-linear two-layer autoencoders trained in the challenging proportional regime in which the input dimension scales linearly with the size of the representation. Our results characterize the minimizers of the population risk, and show that such minimizers are achieved by gradient methods; their structure is also unveiled, thus leading to a concise description of the features obtained via training. For the special case of a sign activation function, our analysis establishes the fundamental limits for the lossy compression of Gaussian sources via (shallow) autoencoders. Finally, while the results are proved for Gaussian data, numerical simulations on standard datasets display the universality of the theoretical predictions.},
  author       = {Shevchenko, Aleksandr and Kögler, Kevin and Hassani, Hamed and Mondelli, Marco},
  booktitle    = {Proceedings of the 40th International Conference on Machine Learning},
  issn         = {2640-3498},
  location     = {Honolulu, Hawaii, HI, United States},
  pages        = {31151--31209},
  publisher    = {ML Research Press},
  title        = {{Fundamental limits of two-layer autoencoders, and achieving them with gradient methods}},
  volume       = {202},
  year         = {2023},
}

@article{13117,
  abstract     = {The ability to control the direction of scattered light is crucial to provide flexibility and scalability for a wide range of on-chip applications, such as integrated photonics, quantum information processing, and nonlinear optics. Tunable directionality can be achieved by applying external magnetic fields that modify optical selection rules, by using nonlinear effects, or interactions with vibrations. However, these approaches are less suitable to control microwave photon propagation inside integrated superconducting quantum devices. Here, we demonstrate on-demand tunable directional scattering based on two periodically modulated transmon qubits coupled to a transmission line at a fixed distance. By changing the relative phase between the modulation tones, we realize unidirectional forward or backward photon scattering. Such an in-situ switchable mirror represents a versatile tool for intra- and inter-chip microwave photonic processors. In the future, a lattice of qubits can be used to realize topological circuits that exhibit strong nonreciprocity or chirality.},
  author       = {Redchenko, Elena and Poshakinskiy, Alexander V. and Sett, Riya and Zemlicka, Martin and Poddubny, Alexander N. and Fink, Johannes M},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{Tunable directional photon scattering from a pair of superconducting qubits}},
  doi          = {10.1038/s41467-023-38761-6},
  volume       = {14},
  year         = {2023},
}

@article{12349,
  abstract     = {Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types.},
  author       = {Gupta, Divyansh and Mlynarski, Wiktor F and Sumser, Anton L and Symonova, Olga and Svaton, Jan and Jösch, Maximilian A},
  issn         = {1546-1726},
  journal      = {Nature Neuroscience},
  pages        = {606--614},
  publisher    = {Springer Nature},
  title        = {{Panoramic visual statistics shape retina-wide organization of receptive fields}},
  doi          = {10.1038/s41593-023-01280-0},
  volume       = {26},
  year         = {2023},
}

@misc{12370,
  abstract     = {Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types. },
  author       = {Gupta, Divyansh and Sumser, Anton L and Jösch, Maximilian A},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields}},
  doi          = {10.15479/AT:ISTA:12370},
  year         = {2023},
}

@misc{13116,
  abstract     = {The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ -- a prokaryotic homologue of the eukaryotic protein tubulin -- polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here, we connect single filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram captures these features quantitatively, demonstrating how the flexibility, density and chirality of active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division. },
  author       = {Dunajova, Zuzana and Prats Mateu, Batirtze and Radler, Philipp and Lim, Keesiang and Brandis, Dörte and Velicky, Philipp and Danzl, Johann G and Wong, Richard W. and Elgeti, Jens and Hannezo, Edouard B and Loose, Martin},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Chiral and nematic phases of flexible active filaments}},
  doi          = {10.15479/AT:ISTA:13116},
  year         = {2023},
}

@article{13314,
  abstract     = {The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ—a prokaryotic homologue of the eukaryotic protein tubulin—polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here we connect single-filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that the density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram quantitatively captures these features, demonstrating how the flexibility, density and chirality of the active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division.},
  author       = {Dunajova, Zuzana and Prats Mateu, Batirtze and Radler, Philipp and Lim, Keesiang and Brandis, Dörte and Velicky, Philipp and Danzl, Johann G and Wong, Richard W. and Elgeti, Jens and Hannezo, Edouard B and Loose, Martin},
  issn         = {1745-2481},
  journal      = {Nature Physics},
  pages        = {1916--1926},
  publisher    = {Springer Nature},
  title        = {{Chiral and nematic phases of flexible active filaments}},
  doi          = {10.1038/s41567-023-02218-w},
  volume       = {19},
  year         = {2023},
}