@inproceedings{8191,
  abstract     = {There has been a significant amount of research on hardware and software support for efficient concurrent data structures; yet, the question of how to build correct, simple, and scalable data structures has not yet been definitively settled. In this paper, we revisit this question from a minimalist perspective, and ask: what is the smallest amount of synchronization required for correct and efficient concurrent search data structures, and how could this minimal synchronization support be provided in hardware?

To address these questions, we introduce memory tagging, a simple hardware mechanism which enables the programmer to "tag" a dynamic set of memory locations, at cache-line granularity, and later validate whether the memory has been concurrently modified, with the possibility of updating one of the underlying locations atomically if validation succeeds. We provide several examples showing that this mechanism can enable fast and arguably simple concurrent data structure designs, such as lists, binary search trees, balanced search trees, range queries, and Software Transactional Memory (STM) implementations. We provide an implementation of memory tags in the Graphite multi-core simulator, showing that the mechanism can be implemented entirely at the level of L1 cache, and that it can enable non-trivial speedups versus existing implementations of the above data structures.},
  author       = {Alistarh, Dan-Adrian and Brown, Trevor A and Singhal, Nandini},
  booktitle    = {Annual ACM Symposium on Parallelism in Algorithms and Architectures},
  isbn         = {9781450369350},
  location     = {Virtual Event, United States},
  number       = {7},
  pages        = {37--49},
  publisher    = {Association for Computing Machinery},
  title        = {{Memory tagging: Minimalist synchronization for scalable concurrent data structures}},
  doi          = {10.1145/3350755.3400213},
  year         = {2020},
}

@inproceedings{8193,
  abstract     = {Multiple-environment Markov decision processes (MEMDPs) are MDPs equipped with not one, but multiple probabilistic transition functions, which represent the various possible unknown environments. While the previous research on MEMDPs focused on theoretical properties for long-run average payoff, we study them with discounted-sum payoff and focus on their practical advantages and applications. MEMDPs can be viewed as a special case of Partially observable and Mixed observability MDPs: the state of the system is perfectly observable, but not the environment. We show that the specific structure of MEMDPs allows for more efficient algorithmic analysis, in particular for faster belief updates. We demonstrate the applicability of MEMDPs in several domains. In particular, we formalize the sequential decision-making approach to contextual recommendation systems as MEMDPs and substantially improve over the previous MDP approach.},
  author       = {Chatterjee, Krishnendu and Chmelik, Martin and Karkhanis, Deep and Novotný, Petr and Royer, Amélie},
  booktitle    = {Proceedings of the 30th International Conference on Automated Planning and Scheduling},
  issn         = {23340843},
  location     = {Nancy, France},
  pages        = {48--56},
  publisher    = {Association for the Advancement of Artificial Intelligence},
  title        = {{Multiple-environment Markov decision processes: Efficient analysis and applications}},
  volume       = {30},
  year         = {2020},
}

@inproceedings{8194,
  abstract     = {Fixed-point arithmetic is a popular alternative to floating-point arithmetic on embedded systems. Existing work on the verification of fixed-point programs relies on custom formalizations of fixed-point arithmetic, which makes it hard to compare the described techniques or reuse the implementations. In this paper, we address this issue by proposing and formalizing an SMT theory of fixed-point arithmetic. We present an intuitive yet comprehensive syntax of the fixed-point theory, and provide formal semantics for it based on rational arithmetic. We also describe two decision procedures for this theory: one based on the theory of bit-vectors and the other on the theory of reals. We implement the two decision procedures, and evaluate our implementations using existing mature SMT solvers on a benchmark suite we created. Finally, we perform a case study of using the theory we propose to verify properties of quantized neural networks.},
  author       = {Baranowski, Marek and He, Shaobo and Lechner, Mathias and Nguyen, Thanh Son and Rakamarić, Zvonimir},
  booktitle    = {Automated Reasoning},
  isbn         = {9783030510732},
  issn         = {16113349},
  location     = {Paris, France},
  pages        = {13--31},
  publisher    = {Springer Nature},
  title        = {{An SMT theory of fixed-point arithmetic}},
  doi          = {10.1007/978-3-030-51074-9_2},
  volume       = {12166},
  year         = {2020},
}

@inproceedings{8195,
  abstract     = {This paper presents a foundation for refining concurrent programs with structured control flow. The verification problem is decomposed into subproblems that aid interactive program development, proof reuse, and automation. The formalization in this paper is the basis of a new design and implementation of the Civl verifier.},
  author       = {Kragl, Bernhard and Qadeer, Shaz and Henzinger, Thomas A},
  booktitle    = {Computer Aided Verification},
  isbn         = {9783030532871},
  issn         = {1611-3349},
  pages        = {275--298},
  publisher    = {Springer Nature},
  title        = {{Refinement for structured concurrent programs}},
  doi          = {10.1007/978-3-030-53288-8_14},
  volume       = {12224},
  year         = {2020},
}

@article{14891,
  abstract     = {We give the first mathematically rigorous justification of the local density approximation in density functional theory. We provide a quantitative estimate on the difference between the grand-canonical Levy–Lieb energy of a given density (the lowest possible energy of all quantum states having this density) and the integral over the uniform electron gas energy of this density. The error involves gradient terms and justifies the use of the local density approximation in the situation where the density is very flat on sufficiently large regions in space.},
  author       = {Lewin, Mathieu and Lieb, Elliott H. and Seiringer, Robert},
  issn         = {2578-5885},
  journal      = {Pure and Applied Analysis},
  number       = {1},
  pages        = {35--73},
  publisher    = {Mathematical Sciences Publishers},
  title        = {{ The local density approximation in density functional theory}},
  doi          = {10.2140/paa.2020.2.35},
  volume       = {2},
  year         = {2020},
}

@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},
}

@article{177,
  abstract     = {We develop a geometric version of the circle method and use it to compute the compactly supported cohomology of the space of rational curves through a point on a smooth affine hypersurface of sufficiently low degree.},
  author       = {Browning, Timothy D and Sawin, Will},
  journal      = {Annals of Mathematics},
  number       = {3},
  pages        = {893--948},
  publisher    = {Princeton University},
  title        = {{A geometric version of the circle method}},
  doi          = {10.4007/annals.2020.191.3.4},
  volume       = {191},
  year         = {2020},
}

@article{179,
  abstract     = {An asymptotic formula is established for the number of rational points of bounded anticanonical height which lie on a certain Zariski dense subset of the biprojective hypersurface x1y21+⋯+x4y24=0 in ℙ3×ℙ3. This confirms the modified Manin conjecture for this variety, in which the removal of a thin set of rational points is allowed.},
  author       = {Browning, Timothy D and Heath Brown, Roger},
  issn         = {0012-7094},
  journal      = {Duke Mathematical Journal},
  number       = {16},
  pages        = {3099--3165},
  publisher    = {Duke University Press},
  title        = {{Density of rational points on a quadric bundle in ℙ3×ℙ3}},
  doi          = {10.1215/00127094-2020-0031},
  volume       = {169},
  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},
}