@inproceedings{11826, abstract = {The diameter, radius and eccentricities are natural graph parameters. While these problems have been studied extensively, there are no known dynamic algorithms for them beyond the ones that follow from trivial recomputation after each update or from solving dynamic All-Pairs Shortest Paths (APSP), which is very computationally intensive. This is the situation for dynamic approximation algorithms as well, and even if only edge insertions or edge deletions need to be supported. This paper provides a comprehensive study of the dynamic approximation of Diameter, Radius and Eccentricities, providing both conditional lower bounds, and new algorithms whose bounds are optimal under popular hypotheses in fine-grained complexity. Some of the highlights include: - Under popular hardness hypotheses, there can be no significantly better fully dynamic approximation algorithms than recomputing the answer after each update, or maintaining full APSP. - Nearly optimal partially dynamic (incremental/decremental) algorithms can be achieved via efficient reductions to (incremental/decremental) maintenance of Single-Source Shortest Paths. For instance, a nearly (3/2+epsilon)-approximation to Diameter in directed or undirected n-vertex, m-edge graphs can be maintained decrementally in total time m^{1+o(1)}sqrt{n}/epsilon^2. This nearly matches the static 3/2-approximation algorithm for the problem that is known to be conditionally optimal.}, author = {Ancona, Bertie and Henzinger, Monika H and Roditty, Liam and Williams, Virginia Vassilevska and Wein, Nicole}, booktitle = {46th International Colloquium on Automata, Languages, and Programming}, isbn = {978-3-95977-109-2}, issn = {1868-8969}, location = {Patras, Greece}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Algorithms and hardness for diameter in dynamic graphs}}, doi = {10.4230/LIPICS.ICALP.2019.13}, volume = {132}, year = {2019}, } @inbook{11847, abstract = {This paper serves as a user guide to the Vienna graph clustering framework. We review our general memetic algorithm, VieClus, to tackle the graph clustering problem. A key component of our contribution are natural recombine operators that employ ensemble clusterings as well as multi-level techniques. Lastly, we combine these techniques with a scalable communication protocol, producing a system that is able to compute high-quality solutions in a short amount of time. After giving a description of the algorithms employed, we establish the connection of the graph clustering problem to protein–protein interaction networks and moreover give a description on how the software can be used, what file formats are expected, and how this can be used to find functional groups in protein–protein interaction networks.}, author = {Biedermann, Sonja and Henzinger, Monika H and Schulz, Christian and Schuster, Bernhard}, booktitle = {Protein-Protein Interaction Networks}, editor = {Canzar, Stefan and Rojas Ringeling, Francisca}, isbn = {9781493998722}, issn = {1940-6029}, pages = {215–231}, publisher = {Springer Nature}, title = {{Vienna Graph Clustering}}, doi = {10.1007/978-1-4939-9873-9_16}, volume = {2074}, year = {2019}, } @inproceedings{11850, abstract = {Modern networked systems are increasingly reconfigurable, enabling demand-aware infrastructures whose resources can be adjusted according to the workload they currently serve. Such dynamic adjustments can be exploited to improve network utilization and hence performance, by moving frequently interacting communication partners closer, e.g., collocating them in the same server or datacenter. However, dynamically changing the embedding of workloads is algorithmically challenging: communication patterns are often not known ahead of time, but must be learned. During the learning process, overheads related to unnecessary moves (i.e., re-embeddings) should be minimized. This paper studies a fundamental model which captures the tradeoff between the benefits and costs of dynamically collocating communication partners on l servers, in an online manner. Our main contribution is a distributed online algorithm which is asymptotically almost optimal, i.e., almost matches the lower bound (also derived in this paper) on the competitive ratio of any (distributed or centralized) online algorithm.}, author = {Henzinger, Monika H and Neumann, Stefan and Schmid, Stefan}, booktitle = {SIGMETRICS'19: International Conference on Measurement and Modeling of Computer Systems}, isbn = {978-1-4503-6678-6}, location = {Phoenix, AZ, United States}, pages = {43–44}, publisher = {Association for Computing Machinery}, title = {{Efficient distributed workload (re-)embedding}}, doi = {10.1145/3309697.3331503}, year = {2019}, } @inproceedings{11851, abstract = {The minimum cut problem for an undirected edge-weighted graph asks us to divide its set of nodes into two blocks while minimizing the weighted sum of the cut edges. In this paper, we engineer the fastest known exact algorithm for the problem. State-of-the-art algorithms like the algorithm of Padberg and Rinaldi or the algorithm of Nagamochi, Ono and Ibaraki identify edges that can be contracted to reduce the graph size such that at least one minimum cut is maintained in the contracted graph. Our algorithm achieves improvements in running time over these algorithms by a multitude of techniques. First, we use a recently developed fast and parallel inexact minimum cut algorithm to obtain a better bound for the problem. Afterwards, we use reductions that depend on this bound to reduce the size of the graph much faster than previously possible. We use improved data structures to further lower the running time of our algorithm. Additionally, we parallelize the contraction routines of Nagamochi et al. . Overall, we arrive at a system that significantly outperforms the fastest state-of-the-art solvers for the exact minimum cut problem.}, author = {Henzinger, Monika H and Noe, Alexander and Schulz, Christian}, booktitle = {33rd International Parallel and Distributed Processing Symposium}, isbn = {978-1-7281-1247-3}, issn = {1530-2075}, location = {Rio de Janeiro, Brazil}, publisher = {Institute of Electrical and Electronics Engineers}, title = {{Shared-memory exact minimum cuts}}, doi = {10.1109/ipdps.2019.00013}, year = {2019}, } @inproceedings{11853, abstract = {We present a deterministic dynamic algorithm for maintaining a (1+ε)f-approximate minimum cost set cover with O(f log(Cn)/ε^2) amortized update time, when the input set system is undergoing element insertions and deletions. Here, n denotes the number of elements, each element appears in at most f sets, and the cost of each set lies in the range [1/C, 1]. Our result, together with that of Gupta~et~al.~[STOC'17], implies that there is a deterministic algorithm for this problem with O(f log(Cn)) amortized update time and O(min(log n, f)) -approximation ratio, which nearly matches the polynomial-time hardness of approximation for minimum set cover in the static setting. Our update time is only O(log (Cn)) away from a trivial lower bound. Prior to our work, the previous best approximation ratio guaranteed by deterministic algorithms was O(f^2), which was due to Bhattacharya~et~al.~[ICALP`15]. In contrast, the only result that guaranteed O(f) -approximation was obtained very recently by Abboud~et~al.~[STOC`19], who designed a dynamic algorithm with (1+ε)f-approximation ratio and O(f^2 log n/ε) amortized update time. Besides the extra O(f) factor in the update time compared to our and Gupta~et~al.'s results, the Abboud~et~al.~algorithm is randomized, and works only when the adversary is oblivious and the sets are unweighted (each set has the same cost). We achieve our result via the primal-dual approach, by maintaining a fractional packing solution as a dual certificate. This approach was pursued previously by Bhattacharya~et~al.~and Gupta~et~al., but not in the recent paper by Abboud~et~al. Unlike previous primal-dual algorithms that try to satisfy some local constraints for individual sets at all time, our algorithm basically waits until the dual solution changes significantly globally, and fixes the solution only where the fix is needed.}, author = {Bhattacharya, Sayan and Henzinger, Monika H and Nanongkai, Danupon}, booktitle = {60th Annual Symposium on Foundations of Computer Science}, isbn = {978-1-7281-4953-0}, issn = {2575-8454}, location = {Baltimore, MD, United States}, pages = {406--423}, publisher = {Institute of Electrical and Electronics Engineers}, title = {{A new deterministic algorithm for dynamic set cover}}, doi = {10.1109/focs.2019.00033}, year = {2019}, } @inproceedings{11865, abstract = {We present the first sublinear-time algorithm that can compute the edge connectivity λ of a network exactly on distributed message-passing networks (the CONGEST model), as long as the network contains no multi-edge. We present the first sublinear-time algorithm for a distributed message-passing network sto compute its edge connectivity λ exactly in the CONGEST model, as long as there are no parallel edges. Our algorithm takes Õ(n1−1/353D1/353+n1−1/706) time to compute λ and a cut of cardinality λ with high probability, where n and D are the number of nodes and the diameter of the network, respectively, and Õ hides polylogarithmic factors. This running time is sublinear in n (i.e. Õ(n1−є)) whenever D is. Previous sublinear-time distributed algorithms can solve this problem either (i) exactly only when λ=O(n1/8−є) [Thurimella PODC’95; Pritchard, Thurimella, ACM Trans. Algorithms’11; Nanongkai, Su, DISC’14] or (ii) approximately [Ghaffari, Kuhn, DISC’13; Nanongkai, Su, DISC’14]. To achieve this we develop and combine several new techniques. First, we design the first distributed algorithm that can compute a k-edge connectivity certificate for any k=O(n1−є) in time Õ(√nk+D). The previous sublinear-time algorithm can do so only when k=o(√n) [Thurimella PODC’95]. In fact, our algorithm can be turned into the first parallel algorithm with polylogarithmic depth and near-linear work. Previous near-linear work algorithms are essentially sequential and previous polylogarithmic-depth algorithms require Ω(mk) work in the worst case (e.g. [Karger, Motwani, STOC’93]). Second, we show that by combining the recent distributed expander decomposition technique of [Chang, Pettie, Zhang, SODA’19] with techniques from the sequential deterministic edge connectivity algorithm of [Kawarabayashi, Thorup, STOC’15], we can decompose the network into a sublinear number of clusters with small average diameter and without any mincut separating a cluster (except the “trivial” ones). This leads to a simplification of the Kawarabayashi-Thorup framework (except that we are randomized while they are deterministic). This might make this framework more useful in other models of computation. Finally, by extending the tree packing technique from [Karger STOC’96], we can find the minimum cut in time proportional to the number of components. As a byproduct of this technique, we obtain an Õ(n)-time algorithm for computing exact minimum cut for weighted graphs.}, author = {Daga, Mohit and Henzinger, Monika H and Nanongkai, Danupon and Saranurak, Thatchaphol}, booktitle = {Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing}, isbn = {978-1-4503-6705-9}, issn = {0737-8017}, location = {Phoenix, AZ, United States}, pages = {343–354}, publisher = {Association for Computing Machinery}, title = {{Distributed edge connectivity in sublinear time}}, doi = {10.1145/3313276.3316346}, year = {2019}, } @inproceedings{11871, abstract = {Many dynamic graph algorithms have an amortized update time, rather than a stronger worst-case guarantee. But amortized data structures are not suitable for real-time systems, where each individual operation has to be executed quickly. For this reason, there exist many recent randomized results that aim to provide a guarantee stronger than amortized expected. The strongest possible guarantee for a randomized algorithm is that it is always correct (Las Vegas), and has high-probability worst-case update time, which gives a bound on the time for each individual operation that holds with high probability. In this paper we present the first polylogarithmic high-probability worst-case time bounds for the dynamic spanner and the dynamic maximal matching problem. 1. For dynamic spanner, the only known o(n) worst-case bounds were O(n3/4) high-probability worst-case update time for maintaining a 3-spanner, and O(n5/9) for maintaining a 5-spanner. We give a O(1)k log3(n) high-probability worst-case time bound for maintaining a (2k – 1)-spanner, which yields the first worst-case polylog update time for all constant k. (All the results above maintain the optimal tradeoff of stretch 2k – 1 and Õ(n1+1/k) edges.) 2. For dynamic maximal matching, or dynamic 2-approximate maximum matching, no algorithm with o(n) worst-case time bound was known and we present an algorithm with O(log5 (n)) high-probability worst-case time; similar worst-case bounds existed only for maintaining a matching that was (2 + ∊)-approximate, and hence not maximal. Our results are achieved using a new approach for converting amortized guarantees to worst-case ones for randomized data structures by going through a third type of guarantee, which is a middle ground between the two above: an algorithm is said to have worst-case expected update time α if for every update σ, the expected time to process σ is at most α. Although stronger than amortized expected, the worst-case expected guarantee does not resolve the fundamental problem of amortization: a worst-case expected update time of O(1) still allows for the possibility that every 1/f(n) updates requires Θ(f(n)) time to process, for arbitrarily high f(n). In this paper we present a black-box reduction that converts any data structure with worst-case expected update time into one with a high-probability worst-case update time: the query time remains the same, while the update time increases by a factor of O(log2(n)). Thus we achieve our results in two steps: (1) First we show how to convert existing dynamic graph algorithms with amortized expected polylogarithmic running times into algorithms with worst-case expected polylogarithmic running times. (2) Then we use our black-box reduction to achieve the polylogarithmic high-probability worst-case time bound. All our algorithms are Las-Vegas-type algorithms.}, author = {Bernstein, Aaron and Forster, Sebastian and Henzinger, Monika H}, booktitle = {30th Annual ACM-SIAM Symposium on Discrete Algorithms}, location = {San Diego, CA, United States}, pages = {1899--1918}, publisher = {Society for Industrial and Applied Mathematics}, title = {{A deamortization approach for dynamic spanner and dynamic maximal matching}}, doi = {10.1137/1.9781611975482.115}, year = {2019}, } @article{11898, abstract = {We build upon the recent papers by Weinstein and Yu (FOCS'16), Larsen (FOCS'12), and Clifford et al. (FOCS'15) to present a general framework that gives amortized lower bounds on the update and query times of dynamic data structures. Using our framework, we present two concrete results. (1) For the dynamic polynomial evaluation problem, where the polynomial is defined over a finite field of size n1+Ω(1) and has degree n, any dynamic data structure must either have an amortized update time of Ω((lgn/lglgn)2) or an amortized query time of Ω((lgn/lglgn)2). (2) For the dynamic online matrix vector multiplication problem, where we get an n×n matrix whose entires are drawn from a finite field of size nΘ(1), any dynamic data structure must either have an amortized update time of Ω((lgn/lglgn)2) or an amortized query time of Ω(n⋅(lgn/lglgn)2). For these two problems, the previous works by Larsen (FOCS'12) and Clifford et al. (FOCS'15) gave the same lower bounds, but only for worst case update and query times. Our bounds match the highest unconditional lower bounds known till date for any dynamic problem in the cell-probe model.}, author = {Bhattacharya, Sayan and Henzinger, Monika H and Neumann, Stefan}, issn = {0304-3975}, journal = {Theoretical Computer Science}, pages = {72--87}, publisher = {Elsevier}, title = {{New amortized cell-probe lower bounds for dynamic problems}}, doi = {10.1016/j.tcs.2019.01.043}, volume = {779}, year = {2019}, } @article{11957, abstract = {Cross-coupling reactions mediated by dual nickel/photocatalysis are synthetically attractive but rely mainly on expensive, non-recyclable noble-metal complexes as photocatalysts. Heterogeneous semiconductors, which are commonly used for artificial photosynthesis and wastewater treatment, are a sustainable alternative. Graphitic carbon nitrides, a class of metal-free polymers that can be easily prepared from bulk chemicals, are heterogeneous semiconductors with high potential for photocatalytic organic transformations. Here, we demonstrate that graphitic carbon nitrides in combination with nickel catalysis can induce selective C−O cross-couplings of carboxylic acids with aryl halides, yielding the respective aryl esters in excellent yield and selectivity. The heterogeneous organic photocatalyst exhibits a broad substrate scope, is able to harvest green light, and can be recycled multiple times. In situ FTIR was used to track the reaction progress to study this transformation at different irradiation wavelengths and reaction scales.}, author = {Pieber, Bartholomäus and Malik, Jamal A. and Cavedon, Cristian and Gisbertz, Sebastian and Savateev, Aleksandr and Cruz, Daniel and Heil, Tobias and Zhang, Guigang and Seeberger, Peter H.}, issn = {1521-3773}, journal = {Angewandte Chemie International Edition}, number = {28}, pages = {9575--9580}, publisher = {Wiley}, title = {{Semi‐heterogeneous dual nickel/photocatalysis using carbon nitrides: Esterification of carboxylic acids with aryl halides}}, doi = {10.1002/anie.201902785}, volume = {58}, year = {2019}, } @article{11982, abstract = {A carbon nitride material can be combined with homogeneous nickel catalysts for light-mediated cross-couplings of aryl bromides with alcohols under mild conditions. The metal-free heterogeneous semiconductor is fully recyclable and couples a broad range of electron-poor aryl bromides with primary and secondary alcohols as well as water. The application for intramolecular reactions and the synthesis of active pharmaceutical ingredients was demonstrated. The catalytic protocol is applicable for the coupling of aryl iodides with thiols as well.}, author = {Cavedon, Cristian and Madani, Amiera and Seeberger, Peter H. and Pieber, Bartholomäus}, issn = {1523-7052}, journal = {Organic Letters}, number = {13}, pages = {5331--5334}, publisher = {American Chemical Society}, title = {{Semiheterogeneous dual nickel/photocatalytic (thio)etherification using carbon nitrides}}, doi = {10.1021/acs.orglett.9b01957}, volume = {21}, year = {2019}, } @article{11984, abstract = {Differentially protected galactosamine building blocks are key components for the synthesis of human and bacterial oligosaccharides. The azidophenylselenylation of 3,4,6-tri-O-acetyl-d-galactal provides straightforward access to the corresponding 2-nitrogenated glycoside. Poor reproducibility and the use of azides that lead to the formation of potentially explosive and toxic species limit the scalability of this reaction and render it a bottleneck for carbohydrate synthesis. Here, we present a method for the safe, efficient, and reliable azidophenylselenylation of 3,4,6-tri-O-acetyl-d-galactal at room temperature, using continuous flow chemistry. Careful analysis of the transformation resulted in reaction conditions that produce minimal side products while the reaction time was reduced drastically when compared to batch reactions. The flow setup is readily scalable to process 5 mmol of galactal in 3 h, producing 1.2 mmol/h of product.}, author = {Guberman, Mónica and Pieber, Bartholomäus and Seeberger, Peter H.}, issn = {1520-586X}, journal = {Organic Process Research and Development}, number = {12}, pages = {2764--2770}, publisher = {American Chemical Society}, title = {{Safe and scalable continuous flow azidophenylselenylation of galactal to prepare galactosamine building blocks}}, doi = {10.1021/acs.oprd.9b00456}, volume = {23}, year = {2019}, } @article{12190, abstract = {Meiotic crossover frequency varies within genomes, which influences genetic diversity and adaptation. In turn, genetic variation within populations can act to modify crossover frequency in cis and trans. To identify genetic variation that controls meiotic crossover frequency, we screened Arabidopsis accessions using fluorescent recombination reporters. We mapped a genetic modifier of crossover frequency in Col × Bur populations of Arabidopsis to a premature stop codon within TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase II general transcription factor TFIID. The Arabidopsis taf4b mutation is a rare variant found in the British Isles, originating in South-West Ireland. Using genetics, genomics, and immunocytology, we demonstrate a genome-wide decrease in taf4b crossovers, with strongest reduction in the sub-telomeric regions. Using RNA sequencing (RNA-seq) from purified meiocytes, we show that TAF4b expression is meiocyte enriched, whereas its paralog TAF4 is broadly expressed. Consistent with the role of TFIID in promoting gene expression, RNA-seq of wild-type and taf4b meiocytes identified widespread transcriptional changes, including in genes that regulate the meiotic cell cycle and recombination. Therefore, TAF4b duplication is associated with acquisition of meiocyte-specific expression and promotion of germline transcription, which act directly or indirectly to elevate crossovers. This identifies a novel mode of meiotic recombination control via a general transcription factor.}, author = {Lawrence, Emma J. and Gao, Hongbo and Tock, Andrew J. and Lambing, Christophe and Blackwell, Alexander R. and Feng, Xiaoqi and Henderson, Ian R.}, issn = {0960-9822}, journal = {Current Biology}, keywords = {General Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology}, number = {16}, pages = {2676--2686.e3}, publisher = {Elsevier}, title = {{Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis}}, doi = {10.1016/j.cub.2019.06.084}, volume = {29}, year = {2019}, } @article{12192, abstract = {Transposable elements (TEs), the movement of which can damage the genome, are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion cell – vegetative cell (VC) – of the flowering plant Arabidopsis thaliana. However, the extent and mechanism of this activation are unknown. Here we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 is required for heterochromatin condensation in plant cells and show that H1 overexpression creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation, heterochromatin relaxation, and TE activation.}, author = {He, Shengbo and Vickers, Martin and Zhang, Jingyi and Feng, Xiaoqi}, issn = {2050-084X}, journal = {eLife}, keywords = {General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, General Medicine, General Neuroscience}, publisher = {eLife Sciences Publications}, title = {{Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation}}, doi = {10.7554/elife.42530}, volume = {8}, year = {2019}, } @article{27, abstract = {The cerebral cortex is composed of a large variety of distinct cell-types including projection neurons, interneurons and glial cells which emerge from distinct neural stem cell (NSC) lineages. The vast majority of cortical projection neurons and certain classes of glial cells are generated by radial glial progenitor cells (RGPs) in a highly orchestrated manner. Recent studies employing single cell analysis and clonal lineage tracing suggest that NSC and RGP lineage progression are regulated in a profound deterministic manner. In this review we focus on recent advances based mainly on correlative phenotypic data emerging from functional genetic studies in mice. We establish hypotheses to test in future research and outline a conceptual framework how epigenetic cues modulate the generation of cell-type diversity during cortical development. This article is protected by copyright. All rights reserved.}, author = {Amberg, Nicole and Laukoter, Susanne and Hippenmeyer, Simon}, journal = {Journal of Neurochemistry}, number = {1}, pages = {12--26}, publisher = {Wiley}, title = {{Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex}}, doi = {10.1111/jnc.14601}, volume = {149}, year = {2019}, } @article{301, abstract = {A representation formula for solutions of stochastic partial differential equations with Dirichlet boundary conditions is proved. The scope of our setting is wide enough to cover the general situation when the backward characteristics that appear in the usual formulation are not even defined in the Itô sense.}, author = {Gerencser, Mate and Gyöngy, István}, journal = {Stochastic Processes and their Applications}, number = {3}, pages = {995--1012}, publisher = {Elsevier}, title = {{A Feynman–Kac formula for stochastic Dirichlet problems}}, doi = {10.1016/j.spa.2018.04.003}, volume = {129}, year = {2019}, } @article{13366, abstract = {The ability to reversibly assemble nanoparticles using light is both fundamentally interesting and important for applications ranging from reversible data storage to controlled drug delivery. Here, the diverse approaches that have so far been developed to control the self-assembly of nanoparticles using light are reviewed and compared. These approaches include functionalizing nanoparticles with monolayers of photoresponsive molecules, placing them in photoresponsive media capable of reversibly protonating the particles under light, and decorating plasmonic nanoparticles with thermoresponsive polymers, to name just a few. The applicability of these methods to larger, micrometer-sized particles is also discussed. Finally, several perspectives on further developments in the field are offered.}, author = {Bian, Tong and Chu, Zonglin and Klajn, Rafal}, issn = {1521-4095}, journal = {Advanced Materials}, keywords = {Mechanical Engineering, Mechanics of Materials, General Materials Science}, number = {20}, publisher = {Wiley}, title = {{The many ways to assemble nanoparticles using light}}, doi = {10.1002/adma.201905866}, volume = {32}, year = {2019}, } @article{13369, abstract = {Arylazopyrazoles represent a new family of molecular photoswitches characterized by a near-quantitative conversion between two states and long thermal half-lives of the metastable state. Here, we investigated the behavior of a model arylazopyrazole in the presence of a self-assembled cage based on Pd–imidazole coordination. Owing to its high water solubility, the cage can solubilize the E isomer of arylazopyrazole, which, by itself, is not soluble in water. NMR spectroscopy and X-ray crystallography have independently demonstrated that each cage can encapsulate two molecules of E-arylazopyrazole. UV-induced switching to the Z isomer was accompanied by the release of one of the two guests from the cage and the formation of a 1:1 cage/Z-arylazopyrazole inclusion complex. DFT calculations suggest that this process involves a dramatic change in the conformation of the cage. Back-isomerization was induced with green light and resulted in the initial 1:2 cage/E-arylazopyrazole complex. This back-isomerization reaction also proceeded in the dark, with a rate significantly higher than in the absence of the cage.}, author = {Hanopolskyi, Anton I and De, Soumen and Białek, Michał J and Diskin-Posner, Yael and Avram, Liat and Feller, Moran and Klajn, Rafal}, issn = {1860-5397}, journal = {Beilstein Journal of Organic Chemistry}, keywords = {Organic Chemistry}, pages = {2398--2407}, publisher = {Beilstein Institut}, title = {{Reversible switching of arylazopyrazole within a metal–organic cage}}, doi = {10.3762/bjoc.15.232}, volume = {15}, year = {2019}, } @article{13370, abstract = {Efficient isomerization of photochromic molecules often requires conformational freedom and is typically not available under solvent-free conditions. Here, we report a general methodology allowing for reversible switching of such molecules on the surfaces of solid materials. Our method is based on dispersing photochromic compounds within polysilsesquioxane nanowire networks (PNNs), which can be fabricated as transparent, highly porous, micrometer-thick layers on various substrates. We found that azobenzene switching within the PNNs proceeded unusually fast compared with the same molecules in liquid solvents. Efficient isomerization of another photochromic system, spiropyran, from a colorless to a colored form was used to create reversible images in PNN-coated glass. The coloration reaction could be induced with sunlight and is of interest for developing “smart” windows.}, author = {Chu, Zonglin and Klajn, Rafal}, issn = {1530-6992}, journal = {Nano Letters}, keywords = {Mechanical Engineering, Condensed Matter Physics, General Materials Science, General Chemistry, Bioengineering}, number = {10}, pages = {7106--7111}, publisher = {American Chemical Society}, title = {{Polysilsesquioxane nanowire networks as an “Artificial Solvent” for reversible operation of photochromic molecules}}, doi = {10.1021/acs.nanolett.9b02642}, volume = {19}, year = {2019}, } @article{13371, abstract = {Diamondoid nanoporous crystals represent a synthetically challenging class of materials that typically have been obtained from tetrahedral building blocks. In this issue of Chem, Stoddart and coworkers demonstrate that it is possible to generate diamondoid frameworks from a hexacationic building block lacking a tetrahedral symmetry. These results highlight the great potential of self-assembly for rapidly transforming small molecules into structurally complex functional materials.}, author = {Białek, Michał J. and Klajn, Rafal}, issn = {2451-9294}, journal = {Chem}, keywords = {Materials Chemistry, Biochemistry (medical), General Chemical Engineering, Environmental Chemistry, Biochemistry, General Chemistry}, number = {9}, pages = {2283--2285}, publisher = {Elsevier}, title = {{Diamond grows up}}, doi = {10.1016/j.chempr.2019.08.012}, volume = {5}, year = {2019}, } @article{13372, abstract = {The capacity to respond or adapt to environmental changes is an intrinsic property of living systems that comprise highly-connected subcomponents communicating through chemical networks. The development of responsive synthetic systems is a relatively new research area that covers different disciplines, among which nanochemistry brings conceptually new demonstrations. Especially attractive are ligand-protected gold nanoparticles, which have been extensively used over the last decade as building blocks in constructing superlattices or dynamic aggregates, under the effect of an applied stimulus. To reflect the importance of surface chemistry and nanoparticle core composition in the dynamic self-assembly of nanoparticles, we provide here an overview of various available stimuli, as tools for synthetic chemists to exploit. Along with this task, the review starts with the use of chemical stimuli such as solvent, pH, gases, metal ions or biomolecules. It then focuses on physical stimuli: temperature, magnetic and electric fields, as well as light. To reflect on the increasing complexity of current architectures, we discuss systems that are responsive to more than one stimulus, to finally encourage further research by proposing future challenges.}, author = {Grzelczak, Marek and Liz-Marzán, Luis M. and Klajn, Rafal}, issn = {1460-4744}, journal = {Chemical Society Reviews}, keywords = {General Chemistry}, number = {5}, pages = {1342--1361}, publisher = {Royal Society of Chemistry}, title = {{Stimuli-responsive self-assembly of nanoparticles}}, doi = {10.1039/c8cs00787j}, volume = {48}, year = {2019}, }