@article{19280,
  abstract     = {Recent advancements in superconducting circuits have enabled the experimental study of collective behavior of precisely controlled intermediate-scale ensembles of qubits. In this work, we demonstrate an atomic frequency comb formed by individual artificial atoms strongly coupled to a single resonator mode. We observe periodic microwave pulses that originate from a single coherent excitation dynamically interacting with the multiqubit ensemble. We show that this revival dynamics emerges as a consequence of the constructive and periodic rephasing of the five superconducting qubits forming the vacuum Rabi split comb. In the future, similar devices could be used as a memory with in situ tunable storage time or as an on-chip periodic pulse generator with nonclassical photon statistics.},
  author       = {Redchenko, Elena and Zens, M. and Zemlicka, Martin and Peruzzo, Matilda and Hassani, Farid and Sett, Riya and Zielinski, Przemyslaw D and Dhar, H. S. and Krimer, D. O. and Rotter, S. and Fink, Johannes M},
  issn         = {1079-7114},
  journal      = {Physical Review Letters},
  number       = {6},
  publisher    = {American Physical Society},
  title        = {{Observation of collapse and revival in a superconducting atomic frequency comb}},
  doi          = {10.1103/PhysRevLett.134.063601},
  volume       = {134},
  year         = {2025},
}

@phdthesis{20212,
  abstract     = {Cortical development has been studied for many decades and with each passing year, we learn 
more about the processes that govern the tightly regulated developmental program. Up until 
recently, the field has struggled to gain reliable access to progenitors at the single-cell level, 
limiting the resolution at which we can study cortical development in vivo. Therefore, much of 
the data we have on mammalian cortical development is at the cell population level. The 
subsequent pages of this thesis describe novel elements of cortical development in mice; 
acquired using a candidate gene approach in conjunction with Mosaic Analysis with Double 
Markers (MADM) to achieve single cell resolution. In this thesis, I briefly provide an overview 
of the state of the field, describe the methodology used to quantify morphological 
characteristics of neurons and glia, and delve into the role of Phosphatase and tensin 
homologue on chromosome ten (Pten) in neurogenesis and gliogenesis in the developing mouse 
cortex. By using MADM to generate genetic mosaics, in which only a small fraction of cells 
are mutated, to study population-level changes, we can bypass the early postnatal lethality 
reported in Pten conditional knockouts (cKOs) using Emx1-Cre. We used Emx1-CreERT2 to 
induce clonal deletion of Pten, and quantify RGP neurogenic output at the single progenitor 
level. Pten-mutant neuron populations within the mosaics were significantly expanded. In the 
latter parts of this thesis, we describe how Pten deletion leads to an increase in the abundance 
of astrocytes. We availed ourselves of the flexibility offered by the MADM system to generate 
Pten mosaics within a series of distinct knockout tissues to test for the interactions between 
Pten and a battery of genes involved in distinct pro-gliogenic signaling pathways. Our survey 
of Pten’s interactions with genes in key signaling pathways reveals that ERK1/2 are the critical 
effectors downstream of EGFR signaling essential for gliogenesis. Altogether, our results 
demonstrate that Pten plays critical and distinct roles throughout cortical RGP lineage 
progression. },
  author       = {Miranda, Osvaldo},
  isbn         = {978-3-99078-063-3},
  issn         = {2663-337X},
  keywords     = {Pten, mtor, cortical development, MADM, Mapk},
  pages        = {119},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Unraveling the role of Pten in cortical stem cell lineage progression using MADM}},
  doi          = {10.15479/AT-ISTA-20212},
  year         = {2025},
}

@phdthesis{20117,
  abstract     = {Auxin is essential for many aspects of plant growth and development, from 
embryogenesis to organ senescence. Polar auxin transport leads to local auxin maxima and 
gradients, which are important for regulating various plant development process, including 
embryogenesis, organogenesis and vascular tissue formation. The polar auxin transport is 
mediated by auxin influx carrier AUX1/LAX proteins and efflux carrier PIN proteins. The 
regulation of PIN proteins is a key convergence of crosstalk between auxin and other 
hormones, such as cytokinin. Cytokinin promotes the degradation of PIN1 in Arabidopsis 
roots, preferentially the dephosphorylated PIN1, and the process is independent of 
transcription and translation (Marhavý et al., 2011; Marhavý et al., 2014). The internalization 
of PIN proteins from plasma membrane is controlled by clathrin-mediated endocytosis 
(Dhonukshe et al., 2007; Kitakura et al., 2011). However, whether cytokinin affects the PIN1 
degradation through regulating the phosphorylation of PIN1 or trafficking components is 
unknown. Here, we demonstrate that dynamin related protein DRP2s are required for the 
cytokinin regulated trafficking of PIN1 and PIN2 in Arabidopsis root epidermal cells. Despite 
the reported redundancy of DRP2A and DRP2B in gametophyte development, we found that 
CK-mediated PIN1 degradation and –induced PIN2 membrane localization is affected in drp2a 
or drp2b single mutants. Interestingly, we found that cytokinin regulates the recruitment of 
DRP2A—but not DRP2B—to clathrin-coated pits, and affects the stability and plasma 
membrane localization of DRP2A. Furthermore, we studied the involvement of cytokinin 
receptors in the regulation of cytokinin on DRP2A. Additionally, the assembly and disassembly 
cycle of dynamin is mediated by its dephosphorylation and phosphotylation cycle; thus, we 
investigated the role of DRP2A phosphorylation in its cytokinin-regulated assembly and in 
cytokinin-regulated PIN trafficking. Altogether, we found that cytokinin regulated PIN 
trafficking in Arabidopsis root epidermal cells involves modulation of the phosphorylation of 
endocytosis accessory protein DRP2A. },
  author       = {Wang, Yiqun},
  issn         = {2663-337X},
  pages        = {108},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{The role of dynamin related protein 2A in cytokinin regulated plant growth and development}},
  doi          = {10.15479/AT-ISTA-20117},
  year         = {2025},
}

@article{20187,
  abstract     = {Very long-chain fatty acids (VLCFAs), being constituents of different types of lipids, are critical factors in plant development, presumably due to their impact on the endomembrane system. The VLCFAs are synthesized in the endoplasmic reticulum by a heterotetrameric enzymatic complex including β-ketoacyl CoA reductase 1 (KCR1), whose mutant is lethal. Here, we describe the ectopic shoot meristems (esm) mutant, a viable kcr1 allele presumably affecting surface properties of the KCR1 protein. This kcr1-2 mutant shows reduced fatty acyl elongation that impacts VLCFAs. The kcr1-2 plants show severe defects during different stages of development, which all correlate with defects in polar localization and subcellular trafficking of PIN auxin transporters and resulting asymmetric auxin distribution. Detailed analysis of KCR1 expression and patterning defects in kcr1-2 suggests that KCR1 plays a role in delineating boundaries around meristematic and specialized differentiating tissues, including root and shoot meristems, initiating lateral roots, lateral root primordia, and trichomes. In these contexts, KCR1-produced VLCFAs may act in a non-cell-autonomous manner. Viable kcr1-2 represents a useful tool to study VLCFA roles in plant development and highlights VLCFAs as critical developmental factors at the interface of cell polarity and tissue development.},
  author       = {Babic, David and Abualia, Rashed and Fiedler, Lukas and Qi, Linlin and Tellier, Frédérique and Smoljan, Adrijana and Rakusova, Hana and Valošek, Petr and Han, Huibin and Benková, Eva and Faure, Jean Denis and Friml, Jiří},
  issn         = {1365-313X},
  journal      = {Plant Journal},
  number       = {3},
  publisher    = {Wiley},
  title        = {{Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development}},
  doi          = {10.1111/tpj.70396},
  volume       = {123},
  year         = {2025},
}

@phdthesis{20362,
  abstract     = {Arabidopsis embryo has long served as a model system for understanding how plant body 
patterning and axis establishment arise. Previous work established that auxin flows, directed 
by polar transport and reinforced by local biosynthesis, underpin axes formation, while recent 
studies suggest that maternal tissue, membrane composition and surface receptor signaling add 
further regulatory layers. In this thesis, we dissect the layers of auxin-mediated processes which 
guide plant embryonic and post-embryonic development. We review methodological advances 
that allow the embryo to be imaged and studied. These tools offer exciting venues for future 
addressing of outstanding research questions. Furthermore, we dissect the contribution of 
maternal auxin for early embryo patterning. Targeted auxin scavenging in the integuments 
lowers the hormone reaching the proembryo, destabilizes PIN7 in the suspensor and weakens 
the initial apical maximum. The resulting deficit dampens downstream embryonic auxin 
biosynthesis, as well as auxin flow towards the root pole, indicating that maternally provided 
auxin controls auxin flows in the embryos on a larger scale than previously understood. 
Intriguingly, we uncover a prolonged maternal effect mediated by the receptor-like kinases 
TMK1 and TMK4. Reciprocal crosses and transgene analyses hint that these genes could be 
preferentially maternally-derived in both embryos and seedlings. Loss of maternal TMK 
activity arrests embryos, affects seedling development and persists into adult growth, 
suggesting that maternal effect could shape development beyond fertilization and early 
embryogenesis. Finally, we describe the role of very-long-chain fatty acids and membrane 
composition on PIN proteins and their auxin-induced relocalization. Disruption in this lipid 
metabolism triggers widespread patterning errors. 
Together, these results reposition early plant patterning as a hierarchical cascade that begins 
with maternal auxin, gets amplified by auxin transport and biosynthesis, potentially modulated 
by maternal receptor signaling and could ultimately be gated by the biophysical properties of 
the membrane. By integrating auxin supply, genetic imprinting and lipid-dependent trafficking 
into a single narrative, this thesis helps shifting the approach of viewing the embryo as an 
autonomous unit to regarding it as a dynamic system, continuously sculpted by its maternal 
context.},
  author       = {Babic, David},
  issn         = {2663-337X},
  pages        = {116},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana}},
  doi          = {10.15479/AT-ISTA-20362},
  year         = {2025},
}

@unpublished{21427,
  abstract     = {While tumor malignancy has been extensively studied under the prism of genetic and epigenetic heterogeneity, tumor cell states also critically depend on reciprocal interactions with the microenvironment. This raises the hitherto untested possibility that heterogeneity of the untransformed tumor stroma can actively fuel malignant progression. As biological heterogeneity is inherently difficult to control, we adopted a reductionist approach and let tumor cells invade micro-engineered environments harboring obstacles with precision-controlled geometry. We find that not only the presence of obstacles, but more surprisingly their spatial disorder, causes a drastic shift from a collective to a single-cell mode of invasion – comparable in strength to cadherin loss. Combining live-imaging and perturbation experiments with minimal biophysical modeling, we demonstrate that cell detachments result both from local geometrical constraints and a global integration of spatial disorder over time. We show that different types of microenvironments map onto different universality classes of invasion dynamics - homogeneous substrates follow Kardar–Parisi–Zhang (KPZ) scaling, while disordered ones exhibit exponents consistent with KPZ with quenched disorder (KPZq). Our findings highlight generic physical principles for how the mode of cancer cell invasion depends on environmental heterogeneity, with potential implications to understand tumor evolution in vivo.},
  author       = {Dunajova, Zuzana and Tasciyan, Saren and Majek, Juraj and Merrin, Jack and Sahai, Erik and Sixt, Michael K and Hannezo, Edouard B},
  booktitle    = {bioRxiv},
  title        = {{Substrate heterogeneity promotes cancer cell dissemination through interface roughening}},
  doi          = {10.1101/2025.05.20.655037},
  year         = {2025},
}

@phdthesis{20393,
  abstract     = {During vertebrate development, the morphogen Sonic Hedgehog (Shh) plays a key role in 
patterning the tissues of the extending body. This requires precise coordination between the 
size of the source of Shh production and the embryo body. Shh is produced by the notochord, 
as well as floorplate of the neural tube. In this thesis, we investigated how the sizes of the 
notochord and floorplate are regulated and how they impact the developing mouse embryo.  
To measure the size and shape of the developing mouse notochord and the cell behaviours 
within this organ, we performed high-resolution measurements in cleared embryos between 
E8.5 and E10.5 of development. Strikingly, our data revealed that the notochord maintains a 
constant cross-sectional area throughout the trunk over time as it lengthens by cell 
proliferation. We show that this is achieved by a feedback between the notochord cell 
proliferation rate and both the cross-sectional area of the trunk notochord and elongation of 
the embryo. Using live imaging, we further show that notochord cells undergo posteriorly
directed active cell migration and that this cell migration contributes to maintaining the 
structural integrity of the notochord. Our results show a complex coordination of cell 
behaviours that allow for robust notochord morphogenesis during mouse development and 
the maintenance of a defined Shh source size.  
Shh produced by the notochord induces a secondary Shh-producing domain, the floor plate. 
How the notochord and floor plate contribute to the formation of the Shh gradient in the 
neural tube and to the regulation of the floor plate size is poorly understood. Our theoretical 
and experimental analysis indicates that only the initial levels of notochord-derived Shh 
influence the size of the floor plate, and the floor plate is insensitive to its own production of 
Shh. After its initial establishment, the floor plate expands by tissue growth, leading to scaling 
of the Shh gradient amplitude with tissue size.   
Altogether, we show that the mechanisms regulating the sizes of the notochord and 
floorplate in mouse development help to achieve size robustness of these tissues. Our data 
demonstrate that the initial establishment of the Shh gradient in the neural tube is strongly 
dependent on the notochord and suggest that the robustness of notochord morphogenesis 
is essential for pattern formation. Later in development, the floor plate size and the Shh 
gradient are coupled to neural tube growth. Our findings provide new insights on how pattern 
formation, tissue growth and morphogenesis interact to ensure reproducible developmental 
outcomes. },
  author       = {Kishi, Kasumi},
  issn         = {2663-337X},
  pages        = {102},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Regulation of notochord and floor plate size during mouse development}},
  doi          = {10.15479/AT-ISTA-20393},
  year         = {2025},
}

@phdthesis{20364,
  abstract     = {Auxin is a central regulator of plant growth and development, orchestrating processes from 
embryogenesis to senescence through a complex network of biosynthesis, transport, and 
signaling pathways.  
In Arabidopsis thaliana, canonical nuclear auxin signaling is mediated by the TIR1/AFB 
receptors, which promote degradation of AUX/IAA repressors to enable ARF transcription 
factors-driven transcriptional reprogramming. Parallel to this well-established nuclear 
mechanism, auxin also triggers rapid, non-transcriptional responses. In particular, at the cell 
surface, most notably through ABP1 and TMKs. Despite decades of research, the integration 
of these pathways and their links to fundamental cellular processes remains not fully 
understood.  
In this study, we uncover a new role for TIR1/AFB signaling in rapidly activating 
macroautophagy during developmental reprogramming. Auxin induces autophagy via 
TIR1/AFB adenylate cyclase activity, linking auxin perception to cAMP production and 
transcriptional activation of autophagy machinery. Autophagy-deficient mutants exhibit 
delayed meristem differentiation, impaired lateral root progression, and reduced shoot 
organogenesis, demonstrating its necessity for timely developmental transitions. 
We also revisit the ABP1-TMK1 cell-surface auxin perception complex, providing 
biochemical and mass photometry evidence for auxin-dependent complex formation. We show 
that ABP1-TMK1 triggers an ultrafast global phosphorylation response targeting ~1000 
proteins, including the auxin transporter PIN2, and Rho-of-plants (ROP) GTPases regulators. 
This pathway directly regulates PIN2 phosphorylation, for gravitropism and auxin dependent 
ROP activation. 
These findings establish an integrated framework in which nuclear TIR1/AFB signaling and 
cell-surface ABP1-TMK signaling act in parallel to synchronize gene expression, cytoplasmic 
remodelling, and transporter regulation, thereby ensuring robust developmental plasticity in 
Arabidopsis thaliana. },
  author       = {Giannini, Caterina},
  issn         = {2663-337X},
  keywords     = {Auxin Signaling, Plant Development},
  pages        = {151},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Nuclear and cell surface auxin signaling in A. thaliana developmental transitions}},
  doi          = {10.15479/AT-ISTA-20364},
  year         = {2025},
}

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

@phdthesis{20415,
  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{12875,
  abstract     = {The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. However, the developmental principles directing the generation of SC cell-type diversity are not understood. Here, we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic mosaic analysis with double markers (MADM)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at the single-RGP/-cell level of the mammalian SC ontogeny.},
  author       = {Cheung, Giselle T and Pauler, Florian and Koppensteiner, Peter and Krausgruber, Thomas and Streicher, Carmen and Schrammel, Martin and Özgen, Natalie Y and Ivec, Alexis and Bock, Christoph and Shigemoto, Ryuichi and Hippenmeyer, Simon},
  issn         = {0896-6273},
  journal      = {Neuron},
  number       = {2},
  pages        = {230--246.e11},
  publisher    = {Elsevier},
  title        = {{Multipotent progenitors instruct ontogeny of the superior colliculus}},
  doi          = {10.1016/j.neuron.2023.11.009},
  volume       = {112},
  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},
}