@phdthesis{19271,
  abstract     = {The medial habenula (MHb) is implicated in regulating emotional responses
to aversive events. Studies in zebrafish have identified a remarkable morphological
left-right asymmetry in the dorsal habenula (zebrafish equivalent of mammalian
MHb)-to-interpeduncular nucleus (IPN) pathway and its left-side specific role in
modulating fear responses. However, there is little evidence for structural or
functional lateralization in the mammalian MHb-IPN pathway.
Here, I investigated the synaptic properties of the left and right MHb
afferents to the IPN in mice and addressed whether these synaptic connections
selectively influence the expression of conditioned fear in mice. My findings reveal
that each individual IPN neuron receives inputs from both left and right MHb.
Electrophysiological recordings from the same postsynaptic IPN neurons
demonstrate that the left MHb-originating synapses exhibit lower release
probability and higher 𝛾-aminobutyric acid type B receptor (GABABR)-mediated
potentiation compared to the right MHb-originating synapses. Interestingly,
chemogenetic inhibition of cholinergic neurons in the left but not the right MHb
significantly attenuated cue-dependent fear recall. Furthermore, conditional
deletion of GABABR in the left MHb interfered with the recall of cued fear memory,
whereas that in the right MHb neurons spared fear memory expression.
Collectively, I demonstrate a functional asymmetry of the MHb in mice,
revealing a predominant role for GABABR-mediated signaling in the left MHb-IPN
pathway in the modulation of fear memories. These findings suggest that
lateralized pathways could represent a fundamental principle in the neural
regulation of emotion across species.},
  author       = {Önal, Hüseyin C},
  issn         = {2663-337X},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula}},
  doi          = {10.15479/AT-ISTA-19271},
  year         = {2025},
}

@phdthesis{19478,
  abstract     = {Auxin is one of the most important phytohormones, playing a crucial role in plant growth and 
development. Genetic studies in Arabidopsis have identified core components of auxin 
signalling and established the classical transcriptional regulation mechanism. This classical 
paradigm recognizes TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN 
SIGNALLING F-BOX (AFB) proteins as auxin receptors possessing E3 ubiquitin ligase 
activity. Auxin functions as a "molecular glue" enhancing TIR1/AFB-Aux/IAA 
(AUXIN/INDOLE-3-ACETIC ACID) inhibitor interactions, leading to Aux/IAAs’ 
ubiquitination and degradation. This process releases AUXIN RESPONSE FACTORs (ARFs) 
from repression, enabling transcriptional activation of auxin-responsive genes. Notably, the 
discovery of adenylate cyclase (AC) activity in TIR1/AFBs, catalysing cAMP production from 
ATP, presents novel transcriptional regulatory possibilities, though cAMP's mechanistic role 
in auxin signalling remains unclear. Beyond transcriptional regulation (slow response) a non
transcriptional pathway (rapid response) mediated by AFB1 also exists, as auxin triggers rapid 
root growth inhibition within 30 seconds. How TIR1 and AFB1, with their distinct subcellular 
localizations, differentially regulate transcriptional and non-transcriptional processes remains 
unclear. To address these two key questions, this study conducted the following investigations.  
TIR1 and AFB1 display distinct subcellular localization patterns, with AFB1 specifically 
mediating auxin-induced rapid root growth inhibition. To examine whether subcellular 
localization differences contribute to functional divergence between TIR1 and AFB1, we 
utilized microfluidic systems combined with genetic complementation assays. Nuclear export 
signal-fused TIR1 failed to rescue the rapid response defects observed in afb1 mutants. In 
contrast, nuclear localization signal-fused AFB1 exhibited dual functional deficiencies: it 
neither restored the rapid response impairment in afb1 mutants nor compensated for 
transcriptional regulation defects in tir1 mutants which limitation stemmed from AFB1's 
intrinsic incapacity to assemble functional SCF complexes. These results collectively establish 
that the functional specialization of TIR1 and AFB1 is governed by both their subcellular 
compartmentalization and inherent biochemical characteristics. 
The mechanism by which cAMP derived from the auxin receptor TIR1/AFB modulates 
transcriptional regulation remains undefined. To address this, we genetically dissociated TIR1 
AC activity from its E3 ubiquitin ligase function to investigate cAMP's signalling role. AC
inactivating mutations preserved TIR1-mediated Aux/IAAs’ degradation but abolished ARF
i 
dependent transcriptional activation. tir1afb2 mutants expressing AC-deficient TIR1 variants 
failed to restore transcriptional responses. Crucially, compartmentalized cAMP accumulation 
within Aux/IAA - ARF complexes vicinity triggered auxin signalling independently of both 
auxin perception and Aux/IAAs’ degradation, confirming its secondary messenger identity. 
Further mechanistic analysis demonstrated cAMP directly interact with ARF. cAMP 
directly promotes ARF dissociation from Aux/IAA repressors and enhances ARF 
homodimerization. Genetic complementation assays revealed that ARF mutants lacking 
conserved cAMP-binding motifs exhibited partial functional recovery, providing direct 
evidence for cAMP-ARF physical interaction during signal propagation. 
These findings collectively challenge the established model of auxin signalling and define 
a novel TIR1-cAMP-ARF regulatory axis, substantially advancing our comprehension of 
auxin-mediated physiological regulation. },
  author       = {Chen, Huihuang},
  issn         = {2663-337X},
  pages        = {118},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{The cAMP second messenger in auxin signalling}},
  doi          = {10.15479/AT-ISTA-19478},
  year         = {2025},
}

@phdthesis{20467,
  abstract     = {Prostaglandins play a central role in the inflammatory response. Prostaglandins are synthesized 
in a rate-limiting manner by the enzyme cyclooxygenase (Cox), which exists in two isoforms: 
the Cox-2 and Cox-1 isoforms. Traditionally, Cox-1 is thought to mediate homeostatic 
functions due to its constitutive expression due to its constitutive expression, whereas Cox-2 is 
temporary induced in response to inflammatory stimuli and is associated with the inflammatory 
response. Interestingly, in the central nervous system, Cox-1 is predominantly expressed in 
microglia. As the resident immune cells of the brain, microglia play a key role in inflammation. 
Cox-1 expressing microglia are increased in neurodegenerative diseases, and both global 
knockout of Cox-1 and selective Cox-1 inhibition has been shown to ameliorate inflammatory 
effects in neurodegenerative diseases. However, direct evidence elucidating how microglial 
Cox-1 expression influences their response to insults remains limited and warrants further 
investigation. 
First, I utilize the optic nerve crush (ONC) model to study the microglial response to injury and 
inflammation, confirming a reactive microglial response in both the crushed and uninjured 
contralateral retina using CD68 expression and morphological analysis. While previous studies 
reported retinal ganglion cell (RGC) loss in the contralateral eye, I did not observe this, 
suggesting that unilateral ONC induces microglial activation in the contralateral eye without 
RGC degeneration. To explore the role of Cox-1 in this response, I generated a mouse model 
with microglia-specific deletion of Cox-1. After ONC, these mice exhibited an attenuated 
microglial response in both the ipsilateral and contralateral retinas, as well as in visual 
processing areas of the brain. Notably, Cox-2 does not show any expression after ONC in both 
wild-type and Cox-1 knockout mice Additionally, Cox-1KO mice show a reduction in 
phagocytic cups and a reduction in microglia proliferation after ONC. However, due to 
reproducibility problems of the observed phenotype, even after the generation of two new 
mouse models, I cannot draw any definitive conclusions based on the data. 
Next, due to the ambiguity of the mouse model, I explored an alternative route to investigate 
functional consequences of Cox-1 in microglia. I generated a COX1 knock-out human induced 
pluripotent cell (hIPSC) line using CRISPR/Cas9. These cells are were differentiated in 
microglia-like cells and integrated in dissociated retinal organoids according to protocols 
developed in our lab. In response to LPS and POLY(I:C) stimulation, the release and expression 
of cytokines and chemokines was decreased in COX1 knockout cells. However, the 
prostaglandin PGE2 was not increased in microglia-like cells in both control and COX1 
knockout cells.  
Overall, the results from the COX1 knock-out microglia-like cells suggests that COX1 
expression in microglia play a role in neuroinflammation by affecting the release of 
inflammatory cytokines and chemokines. Hereby further challenging that the dogma of the 
Cox-1 isoform involved in housekeeping functions and the Cox-2 isoform involved in 
inflammation applies for the central nervous system.   },
  author       = {Miteva, Florianne E},
  issn         = {2663-337X},
  pages        = {99},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{The role of cyclooxygenase 1 on microglial response to inflammatory stressors}},
  doi          = {10.15479/AT-ISTA-20467},
  year         = {2025},
}

@article{19566,
  abstract     = {Purpose: Optic nerve crush (ONC) is a model for studying optic nerve trauma. Unilateral ONC induces massive retinal ganglion cell (RGC) degeneration in the affected eye, leading to vision loss within a month. A common assumption has been that the non-injured contralateral eye is unaffected due to the minimal retino-retinal projections of the RGCs at the chiasm. Yet, recently, microglia, the brain-resident macrophages, have shown a responsive phenotype in the contralateral eye after ONC. Whether RGC loss accompanies this phenotype is still controversial.

Methods: Using the available RGCode algorithm and developing our own RGC-Quant deep-learning-based tool, we quantify RGC's total number and density across the entire retina after ONC.

Results: We confirm a short-term microglia response in the contralateral eye after ONC, but this did not affect the microglia number. Furthermore, we cannot confirm the previously reported RGC loss between naïve and contralateral retinas 5 weeks after ONC induction across the commonly used Cx3cr1creERT2 and C57BL6/J mouse models. Neither sex nor the direct comparison of the RGC markers Brn3a and RBPMS, with Brn3a co-labeling, on average, 89% of the RBPMS+-cells, explained this discrepancy, suggesting that the early microglia-responsive phenotype does not have immediate consequences on the RGC number.

Conclusions: Our results corroborate that unilateral optic nerve injury elicits a microglial response in the uninjured contralateral eye but without RGC loss. Therefore, the contralateral eye should be treated separately and not as an ONC control.},
  author       = {Schoot Uiterkamp, Florianne E and Maes, Margaret E and Alamalhoda, Mohammad and Firoozi, Arsalan and Colombo, Gloria and Siegert, Sandra},
  issn         = {1552-5783},
  journal      = {Investigative Ophthalmology & Visual Science},
  number       = {3},
  publisher    = {Association for Research in Vision and Ophthalmology},
  title        = {{Optic nerve crush does not induce retinal ganglion cell loss in the contralateral eye}},
  doi          = {10.1167/iovs.66.3.49},
  volume       = {66},
  year         = {2025},
}

@article{19421,
  abstract     = {The phytohormone auxin (Aux) is a principal endogenous developmental signal in plants. It mediates transcriptional reprogramming by a well-established canonical signalling mechanism. TIR1/AFB auxin receptors are F-box subunits of an ubiquitin ligase complex; after auxin perception, they associate with Aux/IAA transcriptional repressors and ubiquitinate them for degradation, thus enabling the activation of auxin response factor (ARF) transcription factors1,2,3. Here we revise this paradigm by showing that without TIR1 adenylate cyclase (AC) activity4, auxin-induced degradation of Aux/IAAs is not sufficient to mediate the transcriptional auxin response. Abolishing the TIR1 AC activity does not affect auxin-induced degradation of Aux/IAAs but renders TIR1 non-functional in mediating transcriptional reprogramming and auxin-regulated development, including shoot, root, root hair growth and lateral root formation. Transgenic plants show that local cAMP production in the vicinity of the Aux/IAA–ARF complex by unrelated AC enzymes bypasses the need for auxin perception and is sufficient to induce ARF-mediated transcription. These discoveries revise the canonical model of auxin signalling and establish TIR1/AFB-produced cAMP as a second messenger essential for transcriptional reprograming.},
  author       = {Chen, Huihuang and Qi, Linlin and Zou, Minxia and Lu, Mengting and Kwiatkowski, M and Pei, Yuanrong and Jaworski, K and Friml, Jiří},
  issn         = {1476-4687},
  journal      = {Nature},
  pages        = {1011--1016},
  publisher    = {Springer Nature},
  title        = {{TIR1-produced cAMP as a second messenger in transcriptional auxin signalling}},
  doi          = {10.1038/s41586-025-08669-w},
  volume       = {640},
  year         = {2025},
}

@phdthesis{20415,
  abstract     = {Well-defined powder precursors are important for the rational design of crystalline inorganic 
materials with controlled defects and functional properties. Such powders can be prepared from 
dried nanoparticles synthesized using a surfactant-assisted/colloidal method that provides 
precise control over size, shape, composition, and surface chemistry of nanoparticles. These 
tailored nanoparticles further act as building blocks for three-dimensional assemblies, 
exhibiting collective nanoscale properties and enabling tailored microstructures of crystalline 
inorganic materials. However, the programmable engineering of such materials using 
nanoparticle-based precursors remains limited, due to a lack of fundamental understanding of 
both the synthesis of nanoparticles and their conversion into macroscopic solids. Furthermore, 
the formation of three-dimensional assemblies often requires multi-step post-synthetic 
treatments, which can limit reproducibility and the production of the bulk inorganic materials. 
In this thesis, I demonstrate a key synthetic parameter governing the formation of desired 
nanostructures, especially metal/semiconductor core–shell nanoparticles which are potential 
precursors for engineering composition, crystal structure, and defects of final materials. Then, 
I investigate their transformative pathways to unveil structural and chemical changes that occur 
during heat treatment of the nanoparticle-based precursors. Building on understanding of 
atomic-scale interactions during nanoparticle-based precursor formation, I further demonstrate 
the possibility of synthesizing the nanoparticle assembly directly in the nanoparticle synthesis 
reaction and rationalize the process of in situ self-assembly of nanoparticles. Finally, the impact 
of NP-based precursors on the formation and properties of crystalline inorganic materials is 
evaluated, demonstrating the potential of employing NP-based precursors for the rational 
design of functional inorganic materials. },
  author       = {Lee, Seungho},
  issn         = {2663-337X},
  pages        = {144},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Nanoparticle-based precursors toward advanced crystalline inorganic solids}},
  doi          = {10.15479/AT-ISTA-20415},
  year         = {2025},
}

@article{22026,
  abstract     = {We address two pressing questions in the theory of the Korteweg–de Vries (KdV) equation. First, we show the uniqueness of solutions to KdV that are merely bounded, without any further decay, regularity, periodicity, or almost periodicity assumptions. The second question, emphasized by Deift, regards whether almost periodic initial data leads to almost periodic solutions to KdV. Building on the new observation that this is false for the Airy equation, we construct an example of almost periodic initial data whose KdV evolution remains bounded, but fails to be almost periodic at a later time. Our uniqueness result ensures that the solution constructed is the unique development of this initial data.},
  author       = {Chapouto, Andreia and Killip, Rowan and Visan, Monica},
  issn         = {0012-7094},
  journal      = {Duke Mathematical Journal},
  keywords     = {Almost-periodic solutions, Korteweg–de Vries, unconditional uniqueness},
  number       = {7},
  pages        = {1227--1267},
  publisher    = {Duke University Press},
  title        = {{Bounded solutions of KdV: Uniqueness and the loss of almost periodicity}},
  doi          = {10.1215/00127094-2023-0035},
  volume       = {173},
  year         = {2024},
}

@article{20838,
  abstract     = {For any 1 ≤ r ≤ ∞, we show that every diffeomorphism of a manifold of the form
R/Z × M is a total renormalization of a Cr-close to identity map. In other words, for
every diffeomorphism f of R/Z×M, there exists a map g arbitrarily close to identity
such that the first return map of g to a domain is conjugate to f and moreover the
orbit of this domain is equal to R/Z×M. This enables us to localize near the identity
the existence of many properties in dynamical systems, such as being Bernoulli for a
smooth volume form.},
  author       = {Berger, Pierre and Gourmelon, Nicolaz and Helfter, Mathieu},
  issn         = {1432-1297},
  journal      = {Inventiones mathematicae},
  number       = {2},
  pages        = {431--468},
  publisher    = {Springer Nature},
  title        = {{Every diffeomorphism is a total renormalization of a close to identity map}},
  doi          = {10.1007/s00222-024-01305-w},
  volume       = {239},
  year         = {2024},
}

@article{20961,
  abstract     = {Self-replicating molecules and well-defined folded macromolecules are of great significance in the emergence and evolution of life. How they may interconnect and affect each other remains largely elusive. Here, we demonstrate an abiotic system where a single building block can oligomerize to yield either a self-replicating molecule or a foldamer. Specifically, agitation of a disulfide-based dynamic combinatorial library at moderately elevated pH channels it selectively into a self-replicating hexamer assembled into fibers, after passing through a period where a 15-subunit macrocyclic foldamer existed transiently. Without mechanoagitation or at lower pH, the formation of hexamer fiber is suppressed, resulting in the accumulation of the 15mer foldamer. Foldamer and self-replicator can be interconverted in response to external stimuli, including agitation and a change in pH. Furthermore, upon the addition of a photoacid, the pH of the medium can be controlled by irradiation, driving the switching between replicator and foldamer and allowing a dissipative out-of-equilibrium state to be accessed, using light as a source of energy.},
  author       = {Jin, Yulong and Mandal, Pradeep K and Wu, Juntian and Kiani, Armin and Zhao, Rui and Huc, Ivan and Otto, Sijbren},
  issn         = {1520-5126},
  journal      = {Journal of the American Chemical Society},
  number       = {49},
  pages        = {33395--33402},
  publisher    = {American Chemical Society},
  title        = {{Light-mediated interconversion between a foldamer and a self-replicator}},
  doi          = {10.1021/jacs.4c09114},
  volume       = {146},
  year         = {2024},
}

@article{20962,
  abstract     = {Systems chemistry has emerged as a useful paradigm to access structures and phenomena typically exhibited by living systems, including complex molecular systems such as self-replicators and foldamers. As we progress further toward the noncovalent synthesis of life-like systems, and eventually life itself, it is necessary to gain control over assembly pathways. Dissipative chemical fueling has enabled access to stable populations of (self-assembled) structures that would normally form only transiently. Here, we report a synthetic dynamic combinatorial library, made from a single structurally simple building block, from which a self-replicator and a foldamer can emerge along two distinct and competing pathways through an inter- or intramolecular assembly process, respectively. A fueled chemical reaction cycle is then set up to generate the foldamer transiently, in the presence of the self-replicator. The partitioning of the building block between the folding and self-replication pathways and the duration of the fueled reaction cycles are controlled by adjusting the amount of the chemical fuel. An out-of-equilibrium steady state involving the two assemblies could also be achieved by using a continuous stirred tank reactor with inflow and outflow of material. This work connects the domains of folding and self-replication in synthetic systems through dissipative out-of-equilibrium chemistry. It demonstrates that foldamers and self-replicators, formed from the same building block, can stably coexist if the system is continuously supplied with energy, while at equilibrium, the Gibbs phase rule prohibits such coexistence.},
  author       = {Sood, Ankush and Mandal, Pradeep K and Ottelé, Jim and Wu, Juntian and Eleveld, Marcel and Hatai, Joydev and Pappas, Charalampos G. and Huc, Ivan and Otto, Sijbren},
  issn         = {1520-5126},
  journal      = {Journal of the American Chemical Society},
  keywords     = {Fibers, Foldamers, Macrocycles, Monomers, Peptides, Proteins},
  number       = {49},
  pages        = {33386--33394},
  publisher    = {American Chemical Society},
  title        = {{Simultaneous formation of a foldamer and a self-replicator by out-of-equilibrium dynamic covalent chemistry}},
  doi          = {10.1021/jacs.4c09111},
  volume       = {146},
  year         = {2024},
}

@article{20967,
  abstract     = {A biotinylated helical aromatic oligoamide foldamer equivalent in size to a 24mer peptide was designed without any prejudice other than to display various polar and hydrophobic side chains at its surface. It was synthesized on solid phase, its P- and M-helical conformers were separated by HPLC on a chiral stationary phase, and the solid state structure of a non-biotinylated analogue was elucidated by X-ray crystallography. Pull-down experiments from a yeast cell lysate using the foldamer as a bait followed by proteomic analysis revealed potential protein binding partners. Three of these proteins were recombinantly expressed. Biolayer interferometry showed submicromolar binding demonstrating the potential of a given foldamer to have affinity for certain proteins in the absence of design considerations. Yet, binding selectivity was low in all three cases since both P- and M-conformers bound to the proteins with similar affinities.},
  author       = {Kwon, Sunbum and Morozov, Vasily and Wang, Lingfei and Mandal, Pradeep K and Chaignepain, Stéphane and Douat, Céline and Huc, Ivan},
  issn         = {1477-0539},
  journal      = {Organic & Biomolecular Chemistry},
  number       = {48},
  pages        = {9342--9347},
  publisher    = {Royal Society of Chemistry},
  title        = {{Interrogating the potential of helical aromatic foldamers for protein recognition}},
  doi          = {10.1039/d4ob01436g},
  volume       = {22},
  year         = {2024},
}

@article{21064,
  abstract     = {The James Webb Space Telescope (JWST) is revolutionizing our knowledge of z > 5 galaxies and their actively accreting black holes. Using the JWST Cycle 1 Treasury program Ultradeep NIRSpec and NIRCam Observations before the Epoch of Reionization (UNCOVER) in the lensing field A2744, we report the identification of a sample of little red dots at 3 < zphot < 7 that likely contain highly reddened accreting supermassive black holes. Using a NIRCam-only selection to F444W < 27.7 mag, we find 26 sources over the ∼45 arcmin^2 field that are blue in F115W − F200W ∼ 0 (or βUV ∼ –2.0 for fλ ∝ λ^β), red in F200W − F444W = 1−4 (βopt ∼ +2.0), and are dominated by a point-source-like central component. Of the 20 sources with deep Atacama Large Millimeter/submillimeter Array (ALMA) 1.2 mm coverage, none are detected individually or in a stack. For the majority of the sample, spectral energy distribution fits to the JWST+ALMA observations prefer models with hot dust rather than obscured star formation to reproduce the red NIRCam colors and ALMA 1.2 mm nondetections. While compact dusty star formation cannot be ruled out, the combination of extremely small sizes (〈re〉 ≈ 50 pc after correction for magnification), red rest-frame optical slopes, and hot dust can be explained by reddened broad-line active galactic nuclei (AGNs). Our targets have faint M1450 ≈ −14 to −18 mag but inferred bolometric luminosities of Lbol = 10^43–10^46 erg s^−1, reflecting their obscured nature. If the candidates are confirmed as AGNs with upcoming UNCOVER spectroscopy, then we have found an abundant population of reddened luminous AGNs that are at least ten times more numerous than UV-luminous AGNs at the same intrinsic bolometric luminosity.},
  author       = {Labbe, Ivo and Greene, Jenny E. and Bezanson, Rachel and Fujimoto, Seiji and Furtak, Lukas J. and Goulding, Andy D. and Matthee, Jorryt J and Naidu, Rohan P. and Oesch, Pascal A. and Atek, Hakim and Brammer, Gabriel and Chemerynska, Iryna and Coe, Dan and Cutler, Sam E. and Dayal, Pratika and Feldmann, Robert and Franx, Marijn and Glazebrook, Karl and Leja, Joel and Maseda, Michael and Marchesini, Danilo and Nanayakkara, Themiya and Nelson, Erica J. and Pan, Richard and Papovich, Casey and Price, Sedona H. and Suess, Katherine A. and Wang, Bingjie 冰洁 and Weaver, John R. and Whitaker, Katherine E. and Williams, Christina C. and Zitrin, Adi},
  issn         = {1538-4357},
  journal      = {The Astrophysical Journal},
  publisher    = {IOP Publishing},
  title        = {{UNCOVER: Candidate red active galactic nuclei at 3 < z < 7 with JWST and ALMA}},
  doi          = {10.3847/1538-4357/ad3551},
  volume       = {978},
  year         = {2024},
}

@misc{21304,
  abstract     = {No description provided.},
  author       = {Santana de Freitas Amaral, Miguel},
  publisher    = {Zenodo},
  title        = {{archaeal_membranes : code and examples}},
  doi          = {10.5281/ZENODO.13934991},
  year         = {2024},
}

@article{21528,
  abstract     = {We present a framework for the end-to-end optimization of metasurface imaging systems that reconstruct targets using compressed sensing, a technique for solving underdetermined imaging problems when the target object exhibits sparsity (e.g., the object can be described by a small number of nonzero values, but the positions of these values are unknown). We nest an iterative, unapproximated compressed sensing reconstruction algorithm into our end-to-end optimization pipeline, resulting in an interpretable, data-efficient method for maximally leveraging metaoptics to exploit object sparsity. We apply our framework to super-resolution imaging and high-resolution depth imaging with a phase-change material. In both situations, our end-to-end framework effectively optimizes metasurface structures for compressed sensing recovery, automatically balancing a number of complicated design considerations to select an imaging measurement matrix from a complex, physically constrained manifold with millions of dimensions. The optimized metasurface imaging systems are robust to noise, significantly improving over random scattering surfaces and approaching the ideal compressed sensing performance of a Gaussian matrix, showing how a physical metasurface system can demonstrably approach the mathematical limits of compressed sensing.},
  author       = {Arya, Gaurav and Li, William F. and Roques-Carmes, Charles and Soljačić, Marin and Johnson, Steven G. and Lin, Zin},
  issn         = {2330-4022},
  journal      = {ACS Photonics},
  keywords     = {end-to-end, optimization, metasurface, imaging, compressed sensing},
  number       = {5},
  pages        = {2077--2087},
  publisher    = {American Chemical Society},
  title        = {{End-to-end optimization of metasurfaces for imaging with compressed sensing}},
  doi          = {10.1021/acsphotonics.4c00259},
  volume       = {11},
  year         = {2024},
}

@article{21529,
  abstract     = {A central challenge in the emerging field of free-electron quantum optics is to achieve strong quantum interaction and single-photon nonlinearity between a flying free electron and a photonic mode. Existing schemes are intrinsically limited by electron diffraction, which puts an upper bound on the interaction length and, therefore, on the strength of quantum coupling and nonlinearity. Here, we propose “free-electron fibers”: effectively one-dimensional photonic systems where free electrons copropagate with two guided modes. The first mode applies a ponderomotive trap to the free electron, removing the limitations due to electron diffraction. The second mode strongly couples to the guided free electron with an enhanced coupling that is orders of magnitude larger than previous designs. The extended interaction lengths enabled by our scheme allow for strong single-photon nonlinearities mediated by free electrons. We predict novel quantum effects in our system such as deterministic single-photon emission and nonlinear multimode dynamics. Our proposal paves the way toward the realization of heralded macroscopic nonclassical light generation, deterministic single-photon sources, and quantum gates controlled by free-electron–photon interactions.},
  author       = {Karnieli, Aviv and Roques-Carmes, Charles and Rivera, Nicholas and Fan, Shanhui},
  issn         = {2330-4022},
  journal      = {ACS Photonics},
  keywords     = {quantum optics, free electrons, single photon nonlinearity, electron-photon interaction},
  number       = {8},
  pages        = {3401--3411},
  publisher    = {American Chemical Society},
  title        = {{Strong coupling and single-photon nonlinearity in free-electron quantum optics}},
  doi          = {10.1021/acsphotonics.4c00908},
  volume       = {11},
  year         = {2024},
}

@article{21535,
  abstract     = {Optical phenomena always display some degree of partial coherence between their respective degrees of freedom. Partial coherence is of particular interest in multimodal systems, where classical and quantum correlations between spatial, polarization, and spectral degrees of freedom can lead to fascinating phenomena (e.g., entanglement) and be leveraged for advanced imaging and sensing modalities (e.g., in hyperspectral, polarization, and ghost imaging). Here, we present a universal method to analyze, process, and generate spatially partially coherent light in multimode systems by using self-configuring optical networks. Our method relies on cascaded self-configuring layers whose average power outputs are sequentially optimized. Once optimized, the network separates the input light into its mutually incoherent components, which is formally equivalent to a diagonalization of the input density matrix. We illustrate our method with numerical simulations of Mach-Zehnder interferometer arrays and show how this method can be used to perform partially coherent environmental light sensing, generation of multimode partially coherent light with arbitrary coherency matrices, and unscrambling of quantum optical mixtures. We provide guidelines for the experimental realization of this method, including the influence of losses, paving the way for self-configuring photonic devices that can automatically learn optimal modal representations of partially coherent light fields.},
  author       = {Roques-Carmes, Charles and Fan, Shanhui and Miller, David A. B.},
  issn         = {2047-7538},
  journal      = {Light: Science & Applications},
  publisher    = {Springer Nature},
  title        = {{Measuring, processing, and generating partially coherent light with self-configuring optics}},
  doi          = {10.1038/s41377-024-01622-y},
  volume       = {13},
  year         = {2024},
}

@article{21540,
  abstract     = {Probabilistic machine learning utilizes controllable sources of randomness to encode uncertainty and enable statistical modeling. Harnessing the pure randomness of quantum vacuum noise, which stems from fluctuating electromagnetic fields, has shown promise for high speed and energy-efficient stochastic photonic elements. Nevertheless, photonic computing hardware which can control these stochastic elements to program probabilistic machine learning algorithms has been limited. Here, we implement a photonic probabilistic computer consisting of a controllable stochastic photonic element – a photonic probabilistic neuron (PPN). Our PPN is implemented in a bistable optical parametric oscillator (OPO) with vacuum-level injected bias fields. We then program a measurement-and-feedback loop for time-multiplexed PPNs with electronic processors (FPGA or GPU) to solve certain probabilistic machine learning tasks. We showcase probabilistic inference and image generation of MNIST-handwritten digits, which are representative examples of discriminative and generative models. In both implementations, quantum vacuum noise is used as a random seed to encode classification uncertainty or probabilistic generation of samples. In addition, we propose a path towards an all-optical probabilistic computing platform, with an estimated sampling rate of  ~1 Gbps and energy consumption of  ~5 fJ/MAC. Our work paves the way for scalable, ultrafast, and energy-efficient probabilistic machine learning hardware.},
  author       = {Choi, Seou and Salamin, Yannick and Roques-Carmes, Charles and Dangovski, Rumen and Luo, Di and Chen, Zhuo and Horodynski, Michael and Sloan, Jamison and Uddin, Shiekh Zia and Soljačić, Marin},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{Photonic probabilistic machine learning using quantum vacuum noise}},
  doi          = {10.1038/s41467-024-51509-0},
  volume       = {15},
  year         = {2024},
}

@article{21560,
  abstract     = {Scintillation describes the conversion of high-energy particles into light in transparent media and finds diverse applications such as high-energy particle detection and industrial and medical imaging. This process operates on multiple timescales, with the final radiative step consisting of spontaneous emission, which can be modeled within the framework of quasiequilibrium fluctuational electrodynamics. Scintillation can therefore be controlled and enhanced via nanophotonic effects, which has been proposed and experimentally demonstrated. Such designs have thus far obeyed Lorentz reciprocity, meaning there is a direct equivalence between scintillation emission and absorption by the scintillator. However, scintillators that do not obey Lorentz reciprocity have not been explored, even though they represent an alternative platform for probing emission, which is both nonequilibrium and nonreciprocal in nature. In this work, we propose to harness nonreciprocity to achieve directional control of scintillation emission, granting an additional degree of control over scintillation. Such directionality of light output is useful in improving collection efficiencies along the directions where detectors are located. We present the design of a nonreciprocal scintillator using a one-dimensional magnetophotonic crystal in the Voigt configuration. Our work demonstrates the potential of controlling nonequilibrium such as scintillation by breaking reciprocity and expands the space of nanophotonic design for achieving such control.},
  author       = {Long, Olivia Y. and Pajovic, Simo and Roques-Carmes, Charles and Tsurimaki, Yoichiro and Rivera, Nicholas and Soljačić, Marin and Boriskina, Svetlana V. and Fan, Shanhui},
  issn         = {2331-7019},
  journal      = {Physical Review Applied},
  number       = {5},
  publisher    = {American Physical Society},
  title        = {{Nonreciprocal scintillation using one-dimensional magneto-optical photonic crystals}},
  doi          = {10.1103/physrevapplied.22.054062},
  volume       = {22},
  year         = {2024},
}

@article{21564,
  abstract     = {Multimode quantum light is enticing for several applications, spanning imaging, spectroscopy, communication, and more. Parametric nonlinear processes have been vital in realizing squeezed and other quantum states of light. However, most work exploiting these processes has focused on generating multimode squeezed vacua and squeezing in mode superpositions (supermodes). Bright squeezing in multiple discrete frequency modes, if realized, could unlock novel applications in quantum-enhanced spectroscopy and optical quantum computing. Here, we show how dissipation engineering of a multimode nonlinear cavity with cascaded three-wave-mixing processes allows us to shape above-threshold frequency combs that feature strong single-mode output amplitude noise squeezing over 10 dB below the shot-noise limit, tunable across the comb. In addition, we demonstrate squeezing for multiple discrete frequency modes above threshold. This bright squeezing arises from enhancement of the (noiseless) nonlinear rate relative to decay rates in the system due to the cascaded generation of photons in a single idler “bath” mode. A natural consequence of the strong nonlinear coupling in our system is the creation of an effective cavity in the synthetic frequency dimension that sustains Bloch oscillations in the modal energy distribution. Bloch mode engineering could provide an opportunity to better control nonlinear energy flow in the synthetic frequency dimension, with exciting applications in quantum random walks and topological photonics. Lastly, we show evidence of long-range correlations in amplitude noise between discrete frequency modes, enabling long-range entanglement in a synthetic frequency dimension and providing a new resource for quantum communication.},
  author       = {Pontula, Sahil and Salamin, Yannick and Roques-Carmes, Charles and Soljačić, Marin},
  issn         = {2691-3399},
  journal      = {PRX Quantum},
  number       = {4},
  publisher    = {American Physical Society},
  title        = {{Shaping quantum noise through cascaded nonlinear processes in a dissipation-engineered multimode cavity}},
  doi          = {10.1103/prxquantum.5.040345},
  volume       = {5},
  year         = {2024},
}

@article{21582,
  abstract     = {Scintillation materials convert high-energy radiation to optical light through a complex multistage process. The last stage of the process is spontaneous light emission, which usually governs and limits the scintillator emission rate and light yield. For decades, scintillator research focused on developing faster-emitting materials or external photonic coatings for improving light yields. Here, we experimentally demonstrate a fundamentally different approach: enhancing the scintillation rate and yield via the Purcell effect, utilizing optical environment engineering to boost spontaneous emission. This enhancement is universally applicable to any scintillating material and dopant when the material’s nanoscale geometry is engineered. We design a thin multilayer nanophotonic scintillator, demonstrating Purcell-enhanced scintillation with 50% enhancement in emission rate and 80% enhancement in light yield. The emission is robust to fabrication disorder, further highlighting its potential for x-ray applications. Our results show prospects for bridging nanophotonics and scintillator science toward reduced radiation dosage and increased resolution for high-energy particle detection.},
  author       = {Kurman, Yaniv and Lahav, Neta and Schuetz, Roman and Shultzman, Avner and Roques-Carmes, Charles and Lifshits, Alon and Zaken, Segev and Lenkiewicz, Tom and Strassberg, Rotem and Be’er, Orr and Bekenstein, Yehonadav and Kaminer, Ido},
  issn         = {2375-2548},
  journal      = {Science Advances},
  number       = {44},
  publisher    = {American Association for the Advancement of Science},
  title        = {{Purcell-enhanced x-ray scintillation}},
  doi          = {10.1126/sciadv.adq6325},
  volume       = {10},
  year         = {2024},
}