@article{19735,
  abstract     = {The males and females of the brine shrimp Artemia franciscana are highly dimorphic, and this dimorphism is associated with substantial sex-biased gene expression in heads and gonads. How these sex-specific patterns of expression are regulated at the molecular level is unknown. A. franciscana also has differentiated ZW sex chromosomes, with complete dosage compensation, but the molecular mechanism through which compensation is achieved is unknown. Here, we conducted CUT&TAG assays targeting 7 post-translational histone modifications (H3K27me3, H3K9me2, H3K9me3, H3K36me3, H3K27ac, H3K4me3, and H4K16ac) in heads and gonads of A. franciscana, allowing us to divide the genome into 12 chromatin states. We further defined functional chromatin signatures for all genes, which were correlated with transcript level abundances. Differences in the occupancy of the profiled epigenetic marks between sexes were associated with differential gene expression between males and females. Finally, we found a significant enrichment of the permissive H4K16ac histone mark in the Z-specific region in both tissues of females but not males, supporting the role of this histone mark in mediating dosage compensation of the Z chromosome.},
  author       = {Bett, Vincent K and Trejo Arellano, Minerva S and Vicoso, Beatriz},
  issn         = {1537-1719},
  journal      = {Molecular Biology and Evolution},
  number       = {5},
  publisher    = {Oxford University Press},
  title        = {{Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana}},
  doi          = {10.1093/molbev/msaf085},
  volume       = {42},
  year         = {2025},
}

@phdthesis{20357,
  author       = {Ruzickova, Natalia},
  isbn         = {978-3-99078-066-4},
  issn         = {2663-337X},
  keywords     = {gene regulation, networks, omnigenic model, pancreas, collective behaviour},
  pages        = {156},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Effect propagation in biological networks}},
  doi          = {10.15479/AT-ISTA-20357},
  year         = {2025},
}

@phdthesis{20563,
  abstract     = {The theory of optimal transport provides an elegant and powerful description of many evolution
equations as gradient flows. The primary objective of this thesis is to adapt and extend the
theory to deal with important equations that are not covered by the classical framework,
specifically boundary value problems and kinetic equations. Additionally, we establish new
results in periodic homogenization for discrete dynamical optimal transport and in quantization
of measures.
Section 1.1 serves as an invitation to the classical theory of optimal transport, including the
main definitions and a selection of well-established theorems. Sections 1.2-1.5 introduce the
main results of this thesis, outline the motivations, and review the current state of the art.
In Chapter 2, we consider the Fokker–Planck equation on a bounded set with positive Dirichlet
boundary conditions. We construct a time-discrete scheme involving a modification of the
Wasserstein distance and, under weak assumptions, prove its convergence to a solution of this
boundary value problem. In dimension 1, we show that this solution is a gradient flow in a
suitable space of measures.
Chapter 3 presents joint work with Giovanni Brigati and Jan Maas. We introduce a new theory
of optimal transport to describe and study particle systems at the mesoscopic scale. We prove
adapted versions of some fundamental theorems, including the Benamou–Brenier formula and
the identification of absolutely continuous curves of measures.
Chapter 4 presents joint work with Lorenzo Portinale. We prove convergence of dynamical
transportation functionals on periodic graphs in the large-scale limit when the cost functional
is asymptotically linear. Additionally, we show that discrete 1-Wasserstein distances converge
to 1-Wasserstein distances constructed from crystalline norms on R
d
.
Chapter 5 concerns optimal empirical quantization: the problem of approximating a measure
by the sum of n equally weighted Dirac deltas, so as to minimize the error in the p-Wasserstein
distance. Our main result is an analog of Zador’s theorem, providing asymptotic bounds for
the minimal error as n tends to infinity.
},
  author       = {Quattrocchi, Filippo},
  issn         = {2663-337X},
  keywords     = {optimal transport, kinetic equations, boundary value problems, quantization, gradient flows, homogenization},
  pages        = {240},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures}},
  doi          = {10.15479/AT-ISTA-20563},
  year         = {2025},
}

@unpublished{20569,
  abstract     = {This is the first part of a general description in terms of mass transport for time-evolving interacting particles systems, at a mesoscopic level. Beyond kinetic theory, our framework naturally applies in biology, computer vision, and engineering. The central object of our study is a new discrepancy d between two probability distributions in position and velocity states, which is reminiscent of the 2-Wasserstein distance, but of second-order nature. We construct d in two steps. First, we optimise over transport plans. The cost function is given by the minimal acceleration between two coupled states on a fixed time horizon T. Second, we further optimise over the time horizon T > 0. We prove the existence of optimal transport plans and maps, and study two time-continuous characterisations of d. One is given in terms of dynamical transport plans. The other one -- in the spirit of the Benamou--Brenier formula -- is formulated as the minimisation of an action of the acceleration field, constrained by Vlasov's equations. Equivalence of static and dynamical formulations of d holds true. While part of this result can be derived from recent, parallel developments in optimal control between measures, we give an original proof relying on two new ingredients: Galilean regularisation of Vlasov's equations and a kinetic Monge--Mather shortening principle. Finally, we establish a first-order differential calculus in the geometry induced by d, and identify solutions to Vlasov's equations with curves of measures satisfying a certain d-absolute continuity condition. One consequence is an explicit formula for the d-derivative of such curves.},
  author       = {Brigati, Giovanni and Maas, Jan and Quattrocchi, Filippo},
  booktitle    = {arXiv},
  keywords     = {optimal transport, kinetic theory, second-order discrepancy, Vlasov equation, Wasserstein splines.},
  title        = {{Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures}},
  doi          = {10.48550/arXiv.2502.15665},
  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{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{12178,
  abstract     = {In this paper we consider the stochastic primitive equation for geophysical flows subject to transport noise and turbulent pressure. Admitting very rough noise terms, the global existence and uniqueness of solutions to this stochastic partial differential equation are proven using stochastic maximal L² regularity, the theory of critical spaces for stochastic evolution equations, and global a priori bounds. Compared to other results in this direction, we do not need any smallness assumption on the transport noise which acts directly on the velocity field and we also allow rougher noise terms. The adaptation to Stratonovich type noise and, more generally, to variable viscosity and/or conductivity are discussed as well.},
  author       = {Agresti, Antonio and Hieber, Matthias and Hussein, Amru and Saal, Martin},
  issn         = {2194-041X},
  journal      = {Stochastics and Partial Differential Equations: Analysis and Computations},
  keywords     = {Applied Mathematics, Modeling and Simulation, Statistics and Probability},
  pages        = {53--133},
  publisher    = {Springer Nature},
  title        = {{The stochastic primitive equations with transport noise and turbulent pressure}},
  doi          = {10.1007/s40072-022-00277-3},
  volume       = {12},
  year         = {2024},
}

@article{12485,
  abstract     = {In this paper we introduce the critical variational setting for parabolic stochastic evolution equations of quasi- or semi-linear type. Our results improve many of the abstract results in the classical variational setting. In particular, we are able to replace the usual weak or local monotonicity condition by a more flexible local Lipschitz condition. Moreover, the usual growth conditions on the multiplicative noise are weakened considerably. Our new setting provides general conditions under which local and global existence and uniqueness hold. Moreover, we prove continuous dependence on the initial data. We show that many classical SPDEs, which could not be covered by the classical variational setting, do fit in the critical variational setting. In particular, this is the case for the Cahn-Hilliard equations, tamed Navier-Stokes equations, and Allen-Cahn equation.},
  author       = {Agresti, Antonio and Veraar, Mark},
  issn         = {1432-2064},
  journal      = {Probability Theory and Related Fields},
  pages        = {957--1015},
  publisher    = {Springer Nature},
  title        = {{The critical variational setting for stochastic evolution equations}},
  doi          = {10.1007/s00440-023-01249-x},
  volume       = {188},
  year         = {2024},
}

@article{12486,
  abstract     = {This paper is concerned with the problem of regularization by noise of systems of reaction–diffusion equations with mass control. It is known that strong solutions to such systems of PDEs may blow-up in finite time. Moreover, for many systems of practical interest, establishing whether the blow-up occurs or not is an open question. Here we prove that a suitable multiplicative noise of transport type has a regularizing effect. More precisely, for both a sufficiently noise intensity and a high spectrum, the blow-up of strong solutions is delayed up to an arbitrary large time. Global existence is shown for the case of exponentially decreasing mass. The proofs combine and extend recent developments in regularization by noise and in the Lp(Lq)-approach to stochastic PDEs, highlighting new connections between the two areas.},
  author       = {Agresti, Antonio},
  issn         = {2194-041X},
  journal      = {Stochastics and Partial Differential Equations: Analysis and Computations},
  pages        = {1907--1981},
  publisher    = {Springer Nature},
  title        = {{Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations}},
  doi          = {10.1007/s40072-023-00319-4},
  volume       = {12},
  year         = {2024},
}

@article{12738,
  abstract     = {We study turn-based stochastic zero-sum games with lexicographic preferences over objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as controllable and adversarial non-determinism. Lexicographic order allows one to consider multiple objectives with a strict preference order. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. For a mixture of reachability and safety objectives, we show that deterministic lexicographically optimal strategies exist and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in NP∩coNP, matching the current known bound for single objectives; and in general the decision problem is PSPACE-hard and can be solved in NEXPTIME∩coNEXPTIME. We present an algorithm that computes the lexicographically optimal strategies via a reduction to the computation of optimal strategies in a sequence of single-objectives games. For omega-regular objectives, we restrict our analysis to one-player games, also known as Markov decision processes. We show that lexicographically optimal strategies exist and need either randomization or finite memory. We present an algorithm that solves the relevant decision problem in polynomial time. We have implemented our algorithms and report experimental results on various case studies.},
  author       = {Chatterjee, Krishnendu and Katoen, Joost P and Mohr, Stefanie and Weininger, Maximilian and Winkler, Tobias},
  issn         = {1572-8102},
  journal      = {Formal Methods in System Design},
  pages        = {40--80},
  publisher    = {Springer Nature},
  title        = {{Stochastic games with lexicographic objectives}},
  doi          = {10.1007/s10703-023-00411-4},
  volume       = {63},
  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{13093,
  abstract     = {The direct, solid state, and reversible conversion between heat and electricity using thermoelectric devices finds numerous potential uses, especially around room temperature. However, the relatively high material processing cost limits their real applications. Silver selenide (Ag2Se) is one of the very few n-type thermoelectric (TE) materials for room-temperature applications. Herein, we report a room temperature, fast, and aqueous-phase synthesis approach to produce Ag2Se, which can be extended to other metal chalcogenides. These materials reach TE figures of merit (zT) of up to 0.76 at 380 K. To improve these values, bismuth sulfide (Bi2S3) particles also prepared in an aqueous solution are incorporated into the Ag2Se matrix. In this way, a series of Ag2Se/Bi2S3 composites with Bi2S3 wt % of 0.5, 1.0, and 1.5 are prepared by solution blending and hot-press sintering. The presence of Bi2S3 significantly improves the Seebeck coefficient and power factor while at the same time decreasing the thermal conductivity with no apparent drop in electrical conductivity. Thus, a maximum zT value of 0.96 is achieved in the composites with 1.0 wt % Bi2S3 at 370 K. Furthermore, a high average zT value (zTave) of 0.93 in the 300–390 K range is demonstrated.},
  author       = {Nan, Bingfei and Li, Mengyao and Zhang, Yu and Xiao, Ke and Lim, Khak Ho and Chang, Cheng and Han, Xu and Zuo, Yong and Li, Junshan and Arbiol, Jordi and Llorca, Jordi and Ibáñez, Maria and Cabot, Andreu},
  issn         = {2637-6113},
  journal      = {ACS Applied Electronic Materials},
  number       = {5},
  pages        = {2807--215},
  publisher    = {American Chemical Society},
  title        = {{Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature}},
  doi          = {10.1021/acsaelm.3c00055},
  volume       = {6},
  year         = {2024},
}

@article{13129,
  abstract     = {We study the representative volume element (RVE) method, which is a method to approximately infer the effective behavior ahom of a stationary random medium. The latter is described by a coefficient field a(x) generated from a given ensemble ⟨⋅⟩ and the corresponding linear elliptic operator −∇⋅a∇. In line with the theory of homogenization, the method proceeds by computing d=3 correctors (d denoting the space dimension). To be numerically tractable, this computation has to be done on a finite domain: the so-called representative volume element, i.e., a large box with, say, periodic boundary conditions. The main message of this article is: Periodize the ensemble instead of its realizations. By this, we mean that it is better to sample from a suitably periodized ensemble than to periodically extend the restriction of a realization a(x) from the whole-space ensemble ⟨⋅⟩. We make this point by investigating the bias (or systematic error), i.e., the difference between ahom and the expected value of the RVE method, in terms of its scaling w.r.t. the lateral size L of the box. In case of periodizing a(x), we heuristically argue that this error is generically O(L−1). In case of a suitable periodization of ⟨⋅⟩
, we rigorously show that it is O(L−d). In fact, we give a characterization of the leading-order error term for both strategies and argue that even in the isotropic case it is generically non-degenerate. We carry out the rigorous analysis in the convenient setting of ensembles ⟨⋅⟩
 of Gaussian type, which allow for a straightforward periodization, passing via the (integrable) covariance function. This setting has also the advantage of making the Price theorem and the Malliavin calculus available for optimal stochastic estimates of correctors. We actually need control of second-order correctors to capture the leading-order error term. This is due to inversion symmetry when applying the two-scale expansion to the Green function. As a bonus, we present a stream-lined strategy to estimate the error in a higher-order two-scale expansion of the Green function.},
  author       = {Clozeau, Nicolas and Josien, Marc and Otto, Felix and Xu, Qiang},
  issn         = {1615-3383},
  journal      = {Foundations of Computational Mathematics},
  pages        = {1305--1387},
  publisher    = {Springer Nature},
  title        = {{Bias in the representative volume element method: Periodize the ensemble instead of its realizations}},
  doi          = {10.1007/s10208-023-09613-y},
  volume       = {24},
  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},
}