@article{15036,
  abstract     = {The assembly of a septin filament requires that homologous monomers must distinguish between one another in establishing appropriate interfaces with their neighbors. To understand this phenomenon at the molecular level, we present the first four crystal structures of heterodimeric septin complexes. We describe in detail the two distinct types of G-interface present within the octameric particles, which must polymerize to form filaments. These are formed between SEPT2 and SEPT6 and between SEPT7 and SEPT3, and their description permits an understanding of the structural basis for the selectivity necessary for correct filament assembly. By replacing SEPT6 by SEPT8 or SEPT11, it is possible to rationalize Kinoshita's postulate, which predicts the exchangeability of septins from within a subgroup. Switches I and II, which in classical small GTPases provide a mechanism for nucleotide-dependent conformational change, have been repurposed in septins to play a fundamental role in molecular recognition. Specifically, it is switch I which holds the key to discriminating between the two different G-interfaces. Moreover, residues which are characteristic for a given subgroup play subtle, but pivotal, roles in guaranteeing that the correct interfaces are formed.},
  author       = {Rosa, Higor Vinícius Dias and Leonardo, Diego Antonio and Brognara, Gabriel and Brandão-Neto, José and D'Muniz Pereira, Humberto and Araújo, Ana Paula Ulian and Garratt, Richard Charles},
  issn         = {0022-2836},
  journal      = {Journal of Molecular Biology},
  keywords     = {Molecular Biology, Structural Biology},
  number       = {21},
  pages        = {5784--5801},
  publisher    = {Elsevier},
  title        = {{Molecular recognition at septin interfaces: The switches hold the key}},
  doi          = {10.1016/j.jmb.2020.09.001},
  volume       = {432},
  year         = {2020},
}

@article{15037,
  abstract     = {Protein abundance and localization at the plasma membrane (PM) shapes plant development and mediates adaptation to changing environmental conditions. It is regulated by ubiquitination, a post-translational modification crucial for the proper sorting of endocytosed PM proteins to the vacuole for subsequent degradation. To understand the significance and the variety of roles played by this reversible modification, the function of ubiquitin receptors, which translate the ubiquitin signature into a cellular response, needs to be elucidated. In this study, we show that TOL (TOM1-like) proteins function in plants as multivalent ubiquitin receptors, governing ubiquitinated cargo delivery to the vacuole via the conserved Endosomal Sorting Complex Required for Transport (ESCRT) pathway. TOL2 and TOL6 interact with components of the ESCRT machinery and bind to K63-linked ubiquitin via two tandemly arranged conserved ubiquitin-binding domains. Mutation of these domains results not only in a loss of ubiquitin binding but also altered localization, abolishing TOL6 ubiquitin receptor activity. Function and localization of TOL6 is itself regulated by ubiquitination, whereby TOL6 ubiquitination potentially modulates degradation of PM-localized cargoes, assisting in the fine-tuning of the delicate interplay between protein recycling and downregulation. Taken together, our findings demonstrate the function and regulation of a ubiquitin receptor that mediates vacuolar degradation of PM proteins in higher plants.},
  author       = {Moulinier-Anzola, Jeanette and Schwihla, Maximilian and De-Araújo, Lucinda and Artner, Christina and Jörg, Lisa and Konstantinova, Nataliia and Luschnig, Christian and Korbei, Barbara},
  issn         = {1674-2052},
  journal      = {Molecular Plant},
  keywords     = {Plant Science, Molecular Biology},
  number       = {5},
  pages        = {717--731},
  publisher    = {Elsevier},
  title        = {{TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants}},
  doi          = {10.1016/j.molp.2020.02.012},
  volume       = {13},
  year         = {2020},
}

@article{15055,
  abstract     = {<jats:p>Markov decision processes (MDPs) are the defacto framework for sequential decision making in the presence of stochastic uncertainty. A classical optimization criterion for MDPs is to maximize the expected discounted-sum payoff, which ignores low probability catastrophic events with highly negative impact on the system. On the other hand, risk-averse policies require the probability of undesirable events to be below a given threshold, but they do not account for optimization of the expected payoff. We consider MDPs with discounted-sum payoff with failure states which represent catastrophic outcomes. The objective of risk-constrained planning is to maximize the expected discounted-sum payoff among risk-averse policies that ensure the probability to encounter a failure state is below a desired threshold. Our main contribution is an efficient risk-constrained planning algorithm that combines UCT-like search with a predictor learned through interaction with the MDP (in the style of AlphaZero) and with a risk-constrained action selection via linear programming. We demonstrate the effectiveness of our approach with experiments on classical MDPs from the literature, including benchmarks with an order of 106 states.</jats:p>},
  author       = {Brázdil, Tomáš and Chatterjee, Krishnendu and Novotný, Petr and Vahala, Jiří},
  issn         = {2374-3468},
  journal      = {Proceedings of the 34th AAAI Conference on Artificial Intelligence},
  keywords     = {General Medicine},
  location     = {New York, NY, United States},
  number       = {06},
  pages        = {9794--9801},
  publisher    = {Association for the Advancement of Artificial Intelligence},
  title        = {{Reinforcement learning of risk-constrained policies in Markov decision processes}},
  doi          = {10.1609/aaai.v34i06.6531},
  volume       = {34},
  year         = {2020},
}

@article{15057,
  abstract     = {Vaccinia virus–related kinase (VRK) is an evolutionarily conserved nuclear protein kinase. VRK-1, the single Caenorhabditis elegans VRK ortholog, functions in cell division and germline proliferation. However, the role of VRK-1 in postmitotic cells and adult life span remains unknown. Here, we show that VRK-1 increases organismal longevity by activating the cellular energy sensor, AMP-activated protein kinase (AMPK), via direct phosphorylation. We found that overexpression of vrk-1 in the soma of adult C. elegans increased life span and, conversely, inhibition of vrk-1 decreased life span. In addition, vrk-1 was required for longevity conferred by mutations that inhibit C. elegans mitochondrial respiration, which requires AMPK. VRK-1 directly phosphorylated and up-regulated AMPK in both C. elegans and cultured human cells. Thus, our data show that the somatic nuclear kinase, VRK-1, promotes longevity through AMPK activation, and this function appears to be conserved between C. elegans and humans.},
  author       = {Park, Sangsoon and Artan, Murat and Han, Seung Hyun and Park, Hae-Eun H. and Jung, Yoonji and Hwang, Ara B. and Shin, Won Sik and Kim, Kyong-Tai and Lee, Seung-Jae V.},
  issn         = {2375-2548},
  journal      = {Science Advances},
  number       = {27},
  publisher    = {American Association for the Advancement of Science},
  title        = {{VRK-1 extends life span by activation of AMPK via phosphorylation}},
  doi          = {10.1126/sciadv.aaw7824},
  volume       = {6},
  year         = {2020},
}

@inproceedings{15059,
  abstract     = {In this paper we present a room temperature radiometer that can eliminate the need of using cryostats in satellite payload reducing its weight and improving reliability. The proposed radiometer is based on an electro-optic upconverter that boosts up microwave photons energy by upconverting them into an optical domain what makes them immune to thermal noise even if operating at room temperature. The converter uses a high-quality factor whispering gallery
mode (WGM) resonator providing naturally narrow bandwidth and therefore might be useful for applications like microwave hyperspectral sensing. The upconversion process is explained by
providing essential information about photon conversion efficiency and sensitivity. To prove the concept, we describe an experiment which shows state-of-the-art photon conversion efficiency n=10-5 per mW of pump power at the frequency of 80 GHz.},
  author       = {Wasiak, Michal and Botello, Gabriel Santamaria and Abdalmalak, Kerlos Atia and Sedlmeir, Florian and Rueda Sanchez, Alfredo R and Segovia-Vargas, Daniel and Schwefel, Harald G. L. and Munoz, Luis Enrique Garcia},
  booktitle    = {14th European Conference on Antennas and Propagation},
  location     = {Copenhagen, Denmark},
  publisher    = {IEEE},
  title        = {{Compact millimeter and submillimeter-wave photonic radiometer for cubesats}},
  doi          = {10.23919/eucap48036.2020.9135962},
  year         = {2020},
}

@article{15061,
  abstract     = {The actin cytoskeleton, a dynamic network of actin filaments and associated F-actin–binding proteins, is fundamentally important in eukaryotes. α-Actinins are major F-actin bundlers that are inhibited by Ca2+ in nonmuscle cells. Here we report the mechanism of Ca2+-mediated regulation of Entamoeba histolytica α-actinin-2 (EhActn2) with features expected for the common ancestor of Entamoeba and higher eukaryotic α-actinins. Crystal structures of Ca2+-free and Ca2+-bound EhActn2 reveal a calmodulin-like domain (CaMD) uniquely inserted within the rod domain. Integrative studies reveal an exceptionally high affinity of the EhActn2 CaMD for Ca2+, binding of which can only be regulated in the presence of physiological concentrations of Mg2+. Ca2+ binding triggers an increase in protein multidomain rigidity, reducing conformational flexibility of F-actin–binding domains via interdomain cross-talk and consequently inhibiting F-actin bundling. In vivo studies uncover that EhActn2 plays an important role in phagocytic cup formation and might constitute a new drug target for amoebic dysentery.},
  author       = {Pinotsis, Nikos and Zielinska, Karolina and Babuta, Mrigya and Arolas, Joan L. and Kostan, Julius and Khan, Muhammad Bashir and Schreiner, Claudia and Testa Salmazo, Anita P and Ciccarelli, Luciano and Puchinger, Martin and Gkougkoulia, Eirini A. and Ribeiro, Euripedes de Almeida and Marlovits, Thomas C. and Bhattacharya, Alok and Djinovic-Carugo, Kristina},
  issn         = {1091-6490},
  journal      = {Proceedings of the National Academy of Sciences},
  number       = {36},
  pages        = {22101--22112},
  publisher    = {Proceedings of the National Academy of Sciences},
  title        = {{Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin}},
  doi          = {10.1073/pnas.1917269117},
  volume       = {117},
  year         = {2020},
}

@article{15063,
  abstract     = {We consider the least singular value of a large random matrix with real or complex i.i.d. Gaussian entries shifted by a constant z∈C. We prove an optimal lower tail estimate on this singular value in the critical regime where z is around the spectral edge, thus improving the classical bound of Sankar, Spielman and Teng (SIAM J. Matrix Anal. Appl. 28:2 (2006), 446–476) for the particular shift-perturbation in the edge regime. Lacking Brézin–Hikami formulas in the real case, we rely on the superbosonization formula (Comm. Math. Phys. 283:2 (2008), 343–395).},
  author       = {Cipolloni, Giorgio and Erdös, László and Schröder, Dominik J},
  issn         = {2690-1005},
  journal      = {Probability and Mathematical Physics},
  keywords     = {General Medicine},
  number       = {1},
  pages        = {101--146},
  publisher    = {Mathematical Sciences Publishers},
  title        = {{Optimal lower bound on the least singular value of the shifted Ginibre ensemble}},
  doi          = {10.2140/pmp.2020.1.101},
  volume       = {1},
  year         = {2020},
}

@article{15064,
  abstract     = {We call a continuous self-map that reveals itself through a discrete set of point-value pairs a sampled dynamical system. Capturing the available information with chain maps on Delaunay complexes, we use persistent homology to quantify the evidence of recurrent behavior. We establish a sampling theorem to recover the eigenspaces of the endomorphism on homology induced by the self-map. Using a combinatorial gradient flow arising from the discrete Morse theory for Čech and Delaunay complexes, we construct a chain map to transform the problem from the natural but expensive Čech complexes to the computationally efficient Delaunay triangulations. The fast chain map algorithm has applications beyond dynamical systems.},
  author       = {Bauer, U. and Edelsbrunner, Herbert and Jablonski, Grzegorz and Mrozek, M.},
  issn         = {2367-1734},
  journal      = {Journal of Applied and Computational Topology},
  number       = {4},
  pages        = {455--480},
  publisher    = {Springer Nature},
  title        = {{Čech-Delaunay gradient flow and homology inference for self-maps}},
  doi          = {10.1007/s41468-020-00058-8},
  volume       = {4},
  year         = {2020},
}

@inproceedings{15074,
  abstract     = {We introduce a new graph problem, the token dropping game, and we show how to solve it efficiently in a distributed setting. We use the token dropping game as a tool to design an efficient distributed algorithm for the stable orientation problem, which is a special case of the more general locally optimal semi-matching problem. The prior work by Czygrinow et al. (DISC 2012) finds a locally optimal semi-matching in O(Δ⁵) rounds in graphs of maximum degree Δ, which directly implies an algorithm with the same runtime for stable orientations. We improve the runtime to O(Δ⁴) for stable orientations and prove a lower bound of Ω(Δ) rounds.},
  author       = {Brandt, Sebastian and Keller, Barbara and Rybicki, Joel and Suomela, Jukka and Uitto, Jara},
  booktitle    = {34th International Symposium on Distributed Computing},
  location     = {Virtual},
  publisher    = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
  title        = {{Brief announcement: Efficient load-balancing through distributed token dropping}},
  doi          = {10.4230/LIPIcs.DISC.2020.40},
  volume       = {179},
  year         = {2020},
}

@inproceedings{15077,
  abstract     = {We consider the following dynamic load-balancing process: given an underlying graph G with n nodes, in each step t≥ 0, one unit of load is created, and placed at a randomly chosen graph node. In the same step, the chosen node picks a random neighbor, and the two nodes balance their loads by averaging them. We are interested in the expected gap between the minimum and maximum loads at nodes as the process progresses, and its dependence on n and on the graph structure. Variants of the above graphical balanced allocation process have been studied previously by Peres, Talwar, and Wieder [Peres et al., 2015], and by Sauerwald and Sun [Sauerwald and Sun, 2015]. These authors left as open the question of characterizing the gap in the case of cycle graphs in the dynamic case, where weights are created during the algorithm’s execution. For this case, the only known upper bound is of 𝒪(n log n), following from a majorization argument due to [Peres et al., 2015], which analyzes a related graphical allocation process. In this paper, we provide an upper bound of 𝒪 (√n log n) on the expected gap of the above process for cycles of length n. We introduce a new potential analysis technique, which enables us to bound the difference in load between k-hop neighbors on the cycle, for any k ≤ n/2. We complement this with a "gap covering" argument, which bounds the maximum value of the gap by bounding its value across all possible subsets of a certain structure, and recursively bounding the gaps within each subset. We provide analytical and experimental evidence that our upper bound on the gap is tight up to a logarithmic factor.},
  author       = {Alistarh, Dan-Adrian and Nadiradze, Giorgi and Sabour, Amirmojtaba},
  booktitle    = {47th International Colloquium on Automata, Languages, and Programming},
  location     = {Saarbrücken, Germany, Virtual},
  publisher    = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
  title        = {{Dynamic averaging load balancing on cycles}},
  doi          = {10.4230/LIPIcs.ICALP.2020.7},
  volume       = {168},
  year         = {2020},
}

@inproceedings{15082,
  abstract     = {Two plane drawings of geometric graphs on the same set of points are called disjoint compatible if their union is plane and they do not have an edge in common. For a given set S of 2n points two plane drawings of perfect matchings M1 and M2 (which do not need to be disjoint nor compatible) are disjoint tree-compatible if there exists a plane drawing of a spanning tree T on S which is disjoint compatible to both M1 and M2.
We show that the graph of all disjoint tree-compatible perfect geometric matchings on 2n points in convex position is connected if and only if 2n ≥ 10. Moreover, in that case the diameter
of this graph is either 4 or 5, independent of n.},
  author       = {Aichholzer, Oswin and Obmann, Julia and Patak, Pavel and Perz, Daniel and Tkadlec, Josef},
  booktitle    = {36th European Workshop on Computational Geometry},
  location     = {Würzburg, Germany, Virtual},
  title        = {{Disjoint tree-compatible plane perfect matchings}},
  year         = {2020},
}

@misc{13056,
  abstract     = {This datasets comprises all data shown in plots of the submitted article "Converting microwave and telecom photons with a silicon photonic nanomechanical interface". Additional raw data are available from the corresponding author on reasonable request.},
  author       = {Arnold, Georg M and Wulf, Matthias and Barzanjeh, Shabir and Redchenko, Elena and Rueda Sanchez, Alfredo R and Hease, William J and Hassani, Farid and Fink, Johannes M},
  publisher    = {Zenodo},
  title        = {{Converting microwave and telecom photons with a silicon photonic nanomechanical interface}},
  doi          = {10.5281/ZENODO.3961561},
  year         = {2020},
}

@misc{13060,
  abstract     = {Coinfections with multiple pathogens can result in complex within-host dynamics affecting virulence and transmission. Whilst multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defenses of ants – their social immunity ­– influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different-species coinfections. Here, it decreased overall pathogen sporulation success, whilst simultaneously increasing co-sporulation on individual cadavers and maintaining a higher pathogen diversity at the community-level. Mathematical modeling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast-germinating, thus less grooming-sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host- and population-level.},
  author       = {Milutinovic, Barbara and Stock, Miriam and Grasse, Anna V and Naderlinger, Elisabeth and Hilbe, Christian and Cremer, Sylvia},
  publisher    = {Dryad},
  title        = {{Social immunity modulates competition between coinfecting pathogens}},
  doi          = {10.5061/DRYAD.CRJDFN318},
  year         = {2020},
}

@misc{13065,
  abstract     = {Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale, and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene-flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available.},
  author       = {Arnoux, Stephanie and Fraisse, Christelle and Sauvage, Christopher},
  publisher    = {Dryad},
  title        = {{VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species}},
  doi          = {10.5061/DRYAD.Q2BVQ83HD},
  year         = {2020},
}

@misc{13070,
  abstract     = {This dataset comprises all data shown in the figures of the submitted article "Surpassing the resistance quantum with a geometric superinductor". Additional raw data are available from the corresponding author on reasonable request.},
  author       = {Peruzzo, Matilda and Trioni, Andrea and Hassani, Farid and Zemlicka, Martin and Fink, Johannes M},
  publisher    = {Zenodo},
  title        = {{Surpassing the resistance quantum with a geometric superinductor}},
  doi          = {10.5281/ZENODO.4052882},
  year         = {2020},
}

@misc{13071,
  abstract     = {This dataset comprises all data shown in the plots of the main part of the submitted article "Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State". Additional raw data are available from the corresponding author on reasonable request.},
  author       = {Hease, William J and Rueda Sanchez, Alfredo R and Sahu, Rishabh and Wulf, Matthias and Arnold, Georg M and Schwefel, Harald and Fink, Johannes M},
  publisher    = {Zenodo},
  title        = {{Bidirectional electro-optic wavelength conversion in the quantum ground state}},
  doi          = {10.5281/ZENODO.4266025},
  year         = {2020},
}

@misc{13073,
  abstract     = {The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study "replicated" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.},
  author       = {Simon, Alexis and Fraisse, Christelle and El Ayari, Tahani and Liautard-Haag, Cathy and Strelkov, Petr and Welch, John and Bierne, Nicolas},
  publisher    = {Dryad},
  title        = {{How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels}},
  doi          = {10.5061/DRYAD.R4XGXD29N},
  year         = {2020},
}

@article{13341,
  abstract     = {Scanning nanoscale superconducting quantum interference devices (nanoSQUIDs)
are of growing interest for highly sensitive quantitative imaging of magnetic,
spintronic, and transport properties of low-dimensional systems. Utilizing
specifically designed grooved quartz capillaries pulled into a sharp pipette,
we have fabricated the smallest SQUID-on-tip (SOT) devices with effective
diameters down to 39 nm. Integration of a resistive shunt in close proximity to
the pipette apex combined with self-aligned deposition of In and Sn, have
resulted in SOT with a flux noise of 42 n$\Phi_0$Hz$^{-1/2}$, yielding a record
low spin noise of 0.29 $\mu_B$Hz$^{-1/2}$. In addition, the new SOTs function
at sub-Kelvin temperatures and in high magnetic fields of over 2.5 T.
Integrating the SOTs into a scanning probe microscope allowed us to image the
stray field of a single Fe$_3$O$_4$ nanocube at 300 mK. Our results show that
the easy magnetization axis direction undergoes a transition from the (111)
direction at room temperature to an in-plane orientation, which could be
attributed to the Verwey phase transition in Fe$_3$O$_4$.},
  author       = {Anahory, Y. and Naren, H. R. and Lachman, E. O. and Sinai, S. Buhbut and Uri, A. and Embon, L. and Yaakobi, E. and Myasoedov, Y. and Huber, M. E. and Klajn, Rafal and Zeldov, E.},
  issn         = {2040-3372},
  journal      = {Nanoscale},
  number       = {5},
  pages        = {3174--3182},
  publisher    = {Royal Society of Chemistry},
  title        = {{SQUID-on-tip with single-electron spin sensitivity for high-field and ultra-low temperature nanomagnetic imaging}},
  doi          = {10.1039/C9NR08578E},
  volume       = {12},
  year         = {2020},
}

@article{13361,
  abstract     = {In nature, light is harvested by photoactive proteins to drive a range of biological processes, including photosynthesis, phototaxis, vision, and ultimately life. Bacteriorhodopsin, for example, is a protein embedded within archaeal cell membranes that binds the chromophore retinal within its hydrophobic pocket. Exposure to light triggers regioselective photoisomerization of the confined retinal, which in turn initiates a cascade of conformational changes within the protein, triggering proton flux against the concentration gradient, providing the microorganisms with the energy to live. We are inspired by these functions in nature to harness light energy using synthetic photoswitches under confinement. Like retinal, synthetic photoswitches require some degree of conformational flexibility to isomerize. In nature, the conformational change associated with retinal isomerization is accommodated by the structural flexibility of the opsin host, yet it results in steric communication between the chromophore and the protein. Similarly, we strive to design systems wherein isomerization of confined photoswitches results in steric communication between a photoswitch and its confining environment. To achieve this aim, a balance must be struck between molecular crowding and conformational freedom under confinement: too much crowding prevents switching, whereas too much freedom resembles switching of isolated molecules in solution, preventing communication.

In this Account, we discuss five classes of synthetic light-switchable compounds—diarylethenes, anthracenes, azobenzenes, spiropyrans, and donor–acceptor Stenhouse adducts—comparing their behaviors under confinement and in solution. The environments employed to confine these photoswitches are diverse, ranging from planar surfaces to nanosized cavities within coordination cages, nanoporous frameworks, and nanoparticle aggregates. The trends that emerge are primarily dependent on the nature of the photoswitch and not on the material used for confinement. In general, we find that photoswitches requiring less conformational freedom for switching are, as expected, more straightforward to isomerize reversibly under confinement. Because these compounds undergo only small structural changes upon isomerization, however, switching does not propagate into communication with their environment. Conversely, photoswitches that require more conformational freedom are more challenging to switch under confinement but also can influence system-wide behavior.

Although we are primarily interested in the effects of geometric constraints on photoswitching under confinement, additional effects inevitably emerge when a compound is removed from solution and placed within a new, more crowded environment. For instance, we have found that compounds that convert to zwitterionic isomers upon light irradiation often experience stabilization of these forms under confinement. This effect results from the mutual stabilization of zwitterions that are brought into close proximity on surfaces or within cavities. Furthermore, photoswitches can experience preorganization under confinement, influencing the selectivity and efficiency of their photoreactions. Because intermolecular interactions arising from confinement cannot be considered independently from the effects of geometric constraints, we describe all confinement effects concurrently throughout this Account.},
  author       = {Grommet, Angela B. and Lee, Lucia M. and Klajn, Rafal},
  issn         = {1520-4898},
  journal      = {Accounts of Chemical Research},
  keywords     = {General Medicine, General Chemistry},
  number       = {11},
  pages        = {2600--2610},
  publisher    = {American Chemical Society},
  title        = {{Molecular photoswitching in confined spaces}},
  doi          = {10.1021/acs.accounts.0c00434},
  volume       = {53},
  year         = {2020},
}

@article{13362,
  abstract     = {Aggregation of organic molecules can drastically affect their physicochemical properties. For instance, the optical properties of BODIPY dyes are inherently related to the degree of aggregation and the mutual orientation of BODIPY units within these aggregates. Whereas the noncovalent aggregation of various BODIPY dyes has been studied in diverse media, the ill-defined nature of these aggregates has made it difficult to elucidate the structure–property relationships. Here, we studied the encapsulation of three structurally simple BODIPY derivatives within the hydrophobic cavity of a water-soluble, flexible PdII6L4 coordination cage. The cavity size allowed for the selective encapsulation of two dye molecules, irrespective of the substitution pattern on the BODIPY core. Working with a model, a pentamethyl-substituted derivative, we found that the mutual orientation of two BODIPY units in the cage’s cavity was remarkably similar to that in the crystalline state of the free dye, allowing us to isolate and characterize the smallest possible noncovalent H-type BODIPY aggregate, namely, an H-dimer. Interestingly, a CF3-substituted BODIPY, known for forming J-type aggregates, was also encapsulated as an H-dimer. Taking advantage of the dynamic nature of encapsulation, we developed a system in which reversible switching between H- and J-aggregates can be induced for multiple cycles simply by addition and subsequent destruction of the cage. We expect that the ability to rapidly and reversibly manipulate the optical properties of supramolecular inclusion complexes in aqueous media will open up avenues for developing detection systems that operate within biological environments.},
  author       = {Gemen, Julius and Ahrens, Johannes and Shimon, Linda J. W. and Klajn, Rafal},
  issn         = {1520-5126},
  journal      = {Journal of the American Chemical Society},
  keywords     = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis},
  number       = {41},
  pages        = {17721--17729},
  publisher    = {American Chemical Society},
  title        = {{Modulating the optical properties of BODIPY dyes by noncovalent dimerization within a flexible coordination cage}},
  doi          = {10.1021/jacs.0c08589},
  volume       = {142},
  year         = {2020},
}