@inproceedings{11822, abstract = {The fully dynamic transitive closure problem asks to maintain reachability information in a directed graph between arbitrary pairs of vertices, while the graph undergoes a sequence of edge insertions and deletions. The problem has been thoroughly investigated in theory and many specialized algorithms for solving it have been proposed in the last decades. In two large studies [Frigioni ea, 2001; Krommidas and Zaroliagis, 2008], a number of these algorithms have been evaluated experimentally against simple, static algorithms for graph traversal, showing the competitiveness and even superiority of the simple algorithms in practice, except for very dense random graphs or very high ratios of queries. A major drawback of those studies is that only small and mostly randomly generated graphs are considered. In this paper, we engineer new algorithms to maintain all-pairs reachability information which are simple and space-efficient. Moreover, we perform an extensive experimental evaluation on both generated and real-world instances that are several orders of magnitude larger than those in the previous studies. Our results indicate that our new algorithms outperform all state-of-the-art algorithms on all types of input considerably in practice.}, author = {Hanauer, Kathrin and Henzinger, Monika H and Schulz, Christian}, booktitle = {18th International Symposium on Experimental Algorithms}, isbn = {9783959771481}, issn = {1868-8969}, location = {Pisa, Italy}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Faster fully dynamic transitive closure in practice}}, doi = {10.4230/LIPIcs.SEA.2020.14}, volume = {160}, year = {2020}, } @inproceedings{11824, abstract = {Independent set is a fundamental problem in combinatorial optimization. While in general graphs the problem is essentially inapproximable, for many important graph classes there are approximation algorithms known in the offline setting. These graph classes include interval graphs and geometric intersection graphs, where vertices correspond to intervals/geometric objects and an edge indicates that the two corresponding objects intersect. We present dynamic approximation algorithms for independent set of intervals, hypercubes and hyperrectangles in d dimensions. They work in the fully dynamic model where each update inserts or deletes a geometric object. All our algorithms are deterministic and have worst-case update times that are polylogarithmic for constant d and ε>0, assuming that the coordinates of all input objects are in [0, N]^d and each of their edges has length at least 1. We obtain the following results: - For weighted intervals, we maintain a (1+ε)-approximate solution. - For d-dimensional hypercubes we maintain a (1+ε)2^d-approximate solution in the unweighted case and a O(2^d)-approximate solution in the weighted case. Also, we show that for maintaining an unweighted (1+ε)-approximate solution one needs polynomial update time for d ≥ 2 if the ETH holds. - For weighted d-dimensional hyperrectangles we present a dynamic algorithm with approximation ratio (1+ε)log^{d-1}N.}, author = {Henzinger, Monika H and Neumann, Stefan and Wiese, Andreas}, booktitle = {36th International Symposium on Computational Geometry}, isbn = {9783959771436}, issn = {1868-8969}, location = {Zurich, Switzerland}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Dynamic approximate maximum independent set of intervals, hypercubes and hyperrectangles}}, doi = {10.4230/LIPIcs.SoCG.2020.51}, volume = {164}, year = {2020}, } @inproceedings{11825, abstract = {We give a fully dynamic (Las-Vegas style) algorithm with constant expected amortized time per update that maintains a proper (Δ+1)-vertex coloring of a graph with maximum degree at most Δ. This improves upon the previous O(log Δ)-time algorithm by Bhattacharya et al. (SODA 2018). Our algorithm uses an approach based on assigning random ranks to vertices and does not need to maintain a hierarchical graph decomposition. We show that our result does not only have optimal running time, but is also optimal in the sense that already deciding whether a Δ-coloring exists in a dynamically changing graph with maximum degree at most Δ takes Ω(log n) time per operation.}, author = {Henzinger, Monika H and Peng, Pan}, booktitle = {37th International Symposium on Theoretical Aspects of Computer Science}, isbn = {9783959771405}, issn = {1868-8969}, location = {Montpellier, France}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Constant-time dynamic (Δ+1)-coloring}}, doi = {10.4230/LIPIcs.STACS.2020.53}, volume = {154}, year = {2020}, } @inproceedings{11852, abstract = {We present a general framework of designing efficient dynamic approximate algorithms for optimization problems on undirected graphs. In particular, we develop a technique that, given any problem that admits a certain notion of vertex sparsifiers, gives data structures that maintain approximate solutions in sub-linear update and query time. We illustrate the applicability of our paradigm to the following problems. (1)A fully-dynamic algorithm that approximates all-pair maximum-flows/minimum-cuts up to a nearly logarithmic factor in O~(n2/3) 11The O~(⋅) notation is used in this paper to hide poly-logarithmic factors. amortized time against an oblivious adversary, and O~(m3/4) time against an adaptive adversary. (2)An incremental data structure that maintains O(1) - approximate shortest path in no(1) time per operation, as well as fully dynamic approximate all-pair shortest path and transshipment in O~(n2/3+o(1)) amortized time per operation. (3)A fully-dynamic algorithm that approximates all-pair effective resistance up to an (1+ϵ) factor in O~(n2/3+o(1)ϵ−O(1)) amortized update time per operation. The key tool behind result (1) is the dynamic maintenance of an algorithmic construction due to Madry [FOCS' 10], which partitions a graph into a collection of simpler graph structures (known as j-trees) and approximately captures the cut-flow and metric structure of the graph. The O(1)-approximation guarantee of (2) is by adapting the distance oracles by [Thorup-Zwick JACM '05]. Result (3) is obtained by invoking the random-walk based spectral vertex sparsifier by [Durfee et al. STOC '19] in a hierarchical manner, while carefully keeping track of the recourse among levels in the hierarchy. See https://arxiv.org/pdf/2005.02368.pdf for the full version of this paper.}, author = {Chen, Li and Goranci, Gramoz and Henzinger, Monika H and Peng, Richard and Saranurak, Thatchaphol}, booktitle = {61st Annual Symposium on Foundations of Computer Science}, isbn = {978-1-7281-9622-0}, issn = {2575-8454}, location = {Durham, NC, United States}, pages = {1135--1146}, publisher = {Institute of Electrical and Electronics Engineers}, title = {{Fast dynamic cuts, distances and effective resistances via vertex sparsifiers}}, doi = {10.1109/focs46700.2020.00109}, year = {2020}, } @inproceedings{11880, abstract = {Given a directed graph and a source vertex, the fully dynamic single-source reachability problem is to maintain the set of vertices that are reachable from the given vertex, subject to edge deletions and insertions. It is one of the most fundamental problems on graphs and appears directly or indirectly in many and varied applications. While there has been theoretical work on this problem, showing both linear conditional lower bounds for the fully dynamic problem and insertions-only and deletions-only upper bounds beating these conditional lower bounds, there has been no experimental study that compares the performance of fully dynamic reachability algorithms in practice. Previous experimental studies in this area concentrated only on the more general all-pairs reachability or transitive closure problem and did not use real-world dynamic graphs. In this paper, we bridge this gap by empirically studying an extensive set of algorithms for the single-source reachability problem in the fully dynamic setting. In particular, we design several fully dynamic variants of well-known approaches to obtain and maintain reachability information with respect to a distinguished source. Moreover, we extend the existing insertions-only or deletions-only upper bounds into fully dynamic algorithms. Even though the worst-case time per operation of all the fully dynamic algorithms we evaluate is at least linear in the number of edges in the graph (as is to be expected given the conditional lower bounds) we show in our extensive experimental evaluation that their performance differs greatly, both on generated as well as on real-world instances.}, author = {Hanauer, Kathrin and Henzinger, Monika H and Schulz, Christian}, booktitle = {2020 Symposium on Algorithm Engineering and Experiments}, location = {Salt Lake City, UT, United States}, pages = {106--119}, publisher = {Society for Industrial and Applied Mathematics}, title = {{Fully dynamic single-source reachability in practice: An experimental study}}, doi = {10.1137/1.9781611976007.9}, year = {2020}, } @inproceedings{11881, abstract = {We introduce the fastest known exact algorithm for the multiterminal cut problem with k terminals. In particular, we engineer existing as well as new data reduction rules. We use the rules within a branch-and-reduce framework and to boost the performance of an ILP formulation. Our algorithms achieve improvements in running time of up to multiple orders of magnitudes over the ILP formulation without data reductions, which has been the de facto standard used by practitioners. This allows us to solve instances to optimality that are significantly larger than was previously possible.}, author = {Henzinger, Monika H and Noe, Alexander and Schulz, Christian}, booktitle = {2020 Symposium on Algorithm Engineering and Experiments}, location = {Salt Lake City, UT, United States}, pages = {42--55}, publisher = {Society for Industrial and Applied Mathematics}, title = {{Shared-memory branch-and-reduce for multiterminal cuts}}, doi = {10.1137/1.9781611976007.4}, year = {2020}, } @article{11889, abstract = {We study the problem of computing a minimum cut in a simple, undirected graph and give a deterministic 𝑂(𝑚log2𝑛loglog2𝑛) time algorithm. This improves on both the best previously known deterministic running time of 𝑂(𝑚log12𝑛) (Kawarabayashi and Thorup [J. ACM, 66 (2018), 4]) and the best previously known randomized running time of 𝑂(𝑚log3𝑛) (Karger [J. ACM, 47 (2000), pp. 46--76]) for this problem, though Karger's algorithm can be further applied to weighted graphs. Moreover, our result extends to balanced directed graphs, where the balance of a directed graph captures how close the graph is to being Eulerian. Our approach is using the Kawarabayashi and Thorup graph compression technique, which repeatedly finds low conductance cuts. To find these cuts they use a diffusion-based local algorithm. We use instead a flow-based local algorithm and suitably adjust their framework to work with our flow-based subroutine. Both flow- and diffusion-based methods have a long history of being applied to finding low conductance cuts. Diffusion algorithms have several variants that are naturally local, while it is more complicated to make flow methods local. Some prior work has proven nice properties for local flow-based algorithms with respect to improving or cleaning up low conductance cuts. Our flow subroutine, however, is the first that both is local and produces low conductance cuts. Thus, it may be of independent interest.}, author = {Henzinger, Monika H and Rao, Satish and Wang, Di}, issn = {1095-7111}, journal = {SIAM Journal on Computing}, number = {1}, pages = {1--36}, publisher = {Society for Industrial & Applied Mathematics}, title = {{Local flow partitioning for faster edge connectivity}}, doi = {10.1137/18m1180335}, volume = {49}, year = {2020}, } @article{11894, abstract = {Graph sparsification aims at compressing large graphs into smaller ones while preserving important characteristics of the input graph. In this work we study vertex sparsifiers, i.e., sparsifiers whose goal is to reduce the number of vertices. We focus on the following notions: (1) Given a digraph 𝐺=(𝑉,𝐸) and terminal vertices 𝐾⊂𝑉 with |𝐾|=𝑘, a (vertex) reachability sparsifier of 𝐺 is a digraph 𝐻=(𝑉𝐻,𝐸𝐻), 𝐾⊂𝑉𝐻 that preserves all reachability information among terminal pairs. Let |𝑉𝐻| denote the size of 𝐻. In this work we introduce the notion of reachability-preserving minors (RPMs), i.e., we require 𝐻 to be a minor of 𝐺. We show any directed graph 𝐺 admits an RPM 𝐻 of size 𝑂(𝑘3), and if 𝐺 is planar, then the size of 𝐻 improves to 𝑂(𝑘2log𝑘). We complement our upper bound by showing that there exists an infinite family of grids such that any RPM must have Ω(𝑘2) vertices. (2) Given a weighted undirected graph 𝐺=(𝑉,𝐸) and terminal vertices 𝐾 with |𝐾|=𝑘, an exact (vertex) cut sparsifier of 𝐺 is a graph 𝐻 with 𝐾⊂𝑉𝐻 that preserves the value of minimum cuts separating any bipartition of 𝐾. We show that planar graphs with all the 𝑘 terminals lying on the same face admit exact cut sparsifiers of size 𝑂(𝑘2) that are also planar. Our result extends to flow and distance sparsifiers. It improves the previous best-known bound of 𝑂(𝑘222𝑘) for cut and flow sparsifiers by an exponential factor and matches an Ω(𝑘2) lower-bound for this class of graphs.}, author = {Goranci, Gramoz and Henzinger, Monika H and Peng, Pan}, issn = {1095-7146}, journal = {SIAM Journal on Discrete Mathematics}, number = {1}, pages = {130--162}, publisher = {Society for Industrial & Applied Mathematics}, title = {{Improved guarantees for vertex sparsification in planar graphs}}, doi = {10.1137/17m1163153}, volume = {34}, year = {2020}, } @article{11954, abstract = {The combination of nickel and photocatalysis has unlocked a variety of cross-couplings. These protocols rely on a few photocatalysts that can only convert a small portion of visible light (<500 nm) into chemical energy. The high-energy photons that excite the photocatalyst can result in unwanted side reactions. Dyes that absorb a much broader spectrum of light are not applicable because of their short-lived singlet excited states. Here, we describe a self-assembling catalyst system that overcomes this limitation. Immobilization of a nickel catalyst on dye-sensitized titanium dioxide results in a material that catalyzes carbon–heteroatom and carbon–carbon bond formations. The modular approach of dye-sensitized metallaphotocatalysts accesses the entire visible light spectrum and allows tackling selectivity issues resulting from low wavelengths strategically. The concept overcomes current limitations of metallaphotocatalysis by unlocking the potential of dyes that were previously unsuitable.}, author = {Reischauer, Susanne and Strauss, Volker and Pieber, Bartholomäus}, issn = {2155-5435}, journal = {ACS Catalysis}, number = {22}, pages = {13269–13274}, publisher = {American Chemical Society}, title = {{Modular, self-assembling metallaphotocatalyst for cross-couplings using the full visible-light spectrum}}, doi = {10.1021/acscatal.0c03950}, volume = {10}, year = {2020}, } @article{11966, abstract = {The front cover artwork is provided by the group of Dr. Bartholomäus Pieber at the Max Planck Institute of Colloids and Interfaces (Germany). The image symbolizes the activation of a heterogeneous photocatalyst by visible light and its application for organic synthesis. Read the full text of the Review at 10.1002/cptc.202000014.}, author = {Gisbertz, Sebastian and Pieber, Bartholomäus}, issn = {2367-0932}, journal = {ChemPhotoChem}, number = {7}, pages = {454--454}, publisher = {Wiley}, title = {{Heterogeneous photocatalysis in organic synthesis}}, doi = {10.1002/cptc.202000137}, volume = {4}, year = {2020}, } @article{11969, abstract = {Photochemistry enables new synthetic means to form carbon–heteroatom bonds. Photocatalysts can catalyze carbon–heteroatom cross-couplings by electron or energy transfer either alone or in combination with a second catalyst. Photocatalyst-free methods are possible using photolabile substrates or by generating photoactive electron donor-acceptor complexes. This review summarizes and discusses the strategies used in light-mediated carbon–heteroatom bond formations based on the proposed mechanisms.}, author = {Cavedon, Cristian and Seeberger, Peter H. and Pieber, Bartholomäus}, issn = {1099-0690}, journal = {European Journal of Organic Chemistry}, number = {10}, pages = {1379--1392}, publisher = {Wiley}, title = {{Photochemical strategies for carbon–heteroatom bond formation}}, doi = {10.1002/ejoc.201901173}, volume = {2020}, year = {2020}, } @article{11978, abstract = {Dual photocatalysis and nickel catalysis can effect cross-coupling under mild conditions, but little is known about the in situ kinetics of this class of reactions. We report a comprehensive kinetic examination of a model carboxylate O-arylation, comparing a state-of-the-art homogeneous photocatalyst (Ir(ppy)3) with a competitive heterogeneous photocatalyst (graphitic carbon nitride). Experimental conditions were adjusted such that the nickel catalytic cycle is saturated with excited photocatalyst. This approach was designed to remove the role of the photocatalyst, by which only the intrinsic behaviors of the nickel catalytic cycles are observed. The two reactions did not display identical kinetics. Ir(ppy)3 deactivates the nickel catalytic cycle and creates more dehalogenated side product. Kinetic data for the reaction using Ir(ppy)3 supports a turnover-limiting reductive elimination. Graphitic carbon nitride gave higher selectivity, even at high photocatalyst-to-nickel ratios. The heterogeneous reaction also showed a rate dependence on aryl halide, indicating that oxidative addition plays a role in rate determination. The results argue against the current mechanistic hypothesis, which states that the photocatalyst is only involved to trigger reductive elimination.}, author = {Malik, Jamal A. and Madani, Amiera and Pieber, Bartholomäus and Seeberger, Peter H.}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, number = {25}, pages = {11042--11049}, publisher = {American Chemical Society}, title = {{Evidence for photocatalyst involvement in oxidative additions of nickel-catalyzed carboxylate O-arylations}}, doi = {10.1021/jacs.0c02848}, volume = {142}, year = {2020}, } @article{11979, abstract = {Dual photoredox/nickel-catalysed C–N cross-couplings suffer from low yields for electron-rich aryl halides. The formation of catalytically inactive nickel-black is responsible for this limitation and causes severe reproducibility issues. Here, we demonstrate that catalyst deactivation can be avoided by using a carbon nitride photocatalyst. The broad absorption of the heterogeneous photocatalyst enables wavelength-dependent control of the rate of reductive elimination to prevent nickel-black formation during the coupling of cyclic, secondary amines and aryl halides. A second approach, which is applicable to a broader set of electron-rich aryl halides, is to run the reactions at high concentrations to increase the rate of oxidative addition. Less nucleophilic, primary amines can be coupled with electron-rich aryl halides by stabilizing low-valent nickel intermediates with a suitable additive. The developed protocols enable reproducible, selective C–N cross-couplings of electron-rich aryl bromides and can also be applied for electron-poor aryl chlorides.}, author = {Gisbertz, Sebastian and Reischauer, Susanne and Pieber, Bartholomäus}, issn = {2520-1158}, journal = {Nature Catalysis}, number = {8}, pages = {611--620}, publisher = {Springer Nature}, title = {{Overcoming limitations in dual photoredox/nickel-catalysed C–N cross-couplings due to catalyst deactivation}}, doi = {10.1038/s41929-020-0473-6}, volume = {3}, year = {2020}, } @article{11980, abstract = {Small organic radicals are ubiquitous intermediates in photocatalysis and are used in organic synthesis to install functional groups and to tune electronic properties and pharmacokinetic parameters of the final molecule. Development of new methods to generate small organic radicals with added functionality can further extend the utility of photocatalysis for synthetic needs. Herein, we present a method to generate dichloromethyl radicals from chloroform using a heterogeneous potassium poly(heptazine imide) (K-PHI) photocatalyst under visible light irradiation for C1-extension of the enone backbone. The method is applied on 15 enones, with γ,γ-dichloroketones yields of 18–89%. Due to negative zeta-potential (−40 mV) and small particle size (100 nm) K-PHI suspension is used in quasi-homogeneous flow-photoreactor increasing the productivity by 19 times compared to the batch approach. The resulting γ,γ-dichloroketones, are used as bifunctional building blocks to access value-added organic compounds such as substituted furans and pyrroles.}, author = {Mazzanti, Stefano and Kurpil, Bogdan and Pieber, Bartholomäus and Antonietti, Markus and Savateev, Aleksandr}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Dichloromethylation of enones by carbon nitride photocatalysis}}, doi = {10.1038/s41467-020-15131-0}, volume = {11}, year = {2020}, } @article{11986, abstract = {Carbon nitride materials have emerged as an efficient and sustainable class of heterogeneous photocatalysts, particularly when paired with nickel in dual catalytic cross-coupling reactions. Performing these transformations on larger scales using a continuous process is difficult due to the problems associated with handling solids in flow. By combining an oscillatory pump with a microstructured plug flow photoreactor, a stable suspension of the photocatalyst can be maintained, circumventing clogging of the reactor channels. Through careful tuning of the oscillator properties, the residence time distribution (RTD) was optimized, whilst maintaining a stable catalyst suspension. Short residence times (20 min) were achieved using optimized conditions and the recyclability of the photocatalyst was demonstrated over 10 cycles with no loss of activity. During a stable 4.5 hour scale-out demonstration, the model substrate could be isolated on 12 g scale (90% yield, 2.67 g h−1). Moreover, the method was applied for the gram scale synthesis of an intermediate of the active pharmaceutical ingredient tetracaine.}, author = {Rosso, Cristian and Gisbertz, Sebastian and Williams, Jason D. and Gemoets, Hannes P. L. and Debrouwer, Wouter and Pieber, Bartholomäus and Kappe, C. Oliver}, issn = {2058-9883}, journal = {Reaction Chemistry and Engineering}, number = {3}, pages = {597--604}, publisher = {Royal Society of Chemistry}, title = {{An oscillatory plug flow photoreactor facilitates semi-heterogeneous dual nickel/carbon nitride photocatalytic C–N couplings}}, doi = {10.1039/d0re00036a}, volume = {5}, year = {2020}, } @article{12188, abstract = {Molecular mechanisms enabling the switching and maintenance of epigenetic states are not fully understood. Distinct histone modifications are often associated with ON/OFF epigenetic states, but how these states are stably maintained through DNA replication, yet in certain situations switch from one to another remains unclear. Here, we address this problem through identification of Arabidopsis INCURVATA11 (ICU11) as a Polycomb Repressive Complex 2 accessory protein. ICU11 robustly immunoprecipitated in vivo with PRC2 core components and the accessory proteins, EMBRYONIC FLOWER 1 (EMF1), LIKE HETEROCHROMATIN PROTEIN1 (LHP1), and TELOMERE_REPEAT_BINDING FACTORS (TRBs). ICU11 encodes a 2-oxoglutarate-dependent dioxygenase, an activity associated with histone demethylation in other organisms, and mutant plants show defects in multiple aspects of the Arabidopsis epigenome. To investigate its primary molecular function we identified the Arabidopsis FLOWERING LOCUS C (FLC) as a direct target and found icu11 disrupted the cold-induced, Polycomb-mediated silencing underlying vernalization. icu11 prevented reduction in H3K36me3 levels normally seen during the early cold phase, supporting a role for ICU11 in H3K36me3 demethylation. This was coincident with an attenuation of H3K27me3 at the internal nucleation site in FLC, and reduction in H3K27me3 levels across the body of the gene after plants were returned to the warm. Thus, ICU11 is required for the cold-induced epigenetic switching between the mutually exclusive chromatin states at FLC, from the active H3K36me3 state to the silenced H3K27me3 state. These data support the importance of physical coupling of histone modification activities to promote epigenetic switching between opposing chromatin states.}, author = {Bloomer, Rebecca H. and Hutchison, Claire E. and Bäurle, Isabel and Walker, James and Fang, Xiaofeng and Perera, Pumi and Velanis, Christos N. and Gümüs, Serin and Spanos, Christos and Rappsilber, Juri and Feng, Xiaoqi and Goodrich, Justin and Dean, Caroline}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, keywords = {Multidisciplinary}, number = {28}, pages = {16660--16666}, publisher = {Proceedings of the National Academy of Sciences}, title = {{The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2}}, doi = {10.1073/pnas.1920621117}, volume = {117}, year = {2020}, } @article{12189, abstract = {Meiotic crossovers (COs) are important for reshuffling genetic information between homologous chromosomes and they are essential for their correct segregation. COs are unevenly distributed along chromosomes and the underlying mechanisms controlling CO localization are not well understood. We previously showed that meiotic COs are mis-localized in the absence of AXR1, an enzyme involved in the neddylation/rubylation protein modification pathway in Arabidopsis thaliana. Here, we report that in axr1-/-, male meiocytes show a strong defect in chromosome pairing whereas the formation of the telomere bouquet is not affected. COs are also redistributed towards subtelomeric chromosomal ends where they frequently form clusters, in contrast to large central regions depleted in recombination. The CO suppressed regions correlate with DNA hypermethylation of transposable elements (TEs) in the CHH context in axr1-/- meiocytes. Through examining somatic methylomes, we found axr1-/- affects DNA methylation in a plant, causing hypermethylation in all sequence contexts (CG, CHG and CHH) in TEs. Impairment of the main pathways involved in DNA methylation is epistatic over axr1-/- for DNA methylation in somatic cells but does not restore regular chromosome segregation during meiosis. Collectively, our findings reveal that the neddylation pathway not only regulates hormonal perception and CO distribution but is also, directly or indirectly, a major limiting pathway of TE DNA methylation in somatic cells.}, author = {Christophorou, Nicolas and She, Wenjing and Long, Jincheng and Hurel, Aurélie and Beaubiat, Sébastien and Idir, Yassir and Tagliaro-Jahns, Marina and Chambon, Aurélie and Solier, Victor and Vezon, Daniel and Grelon, Mathilde and Feng, Xiaoqi and Bouché, Nicolas and Mézard, Christine}, issn = {1553-7404}, journal = {PLOS Genetics}, keywords = {Cancer Research, Genetics (clinical), Genetics, Molecular Biology, Ecology, Evolution, Behavior and Systematics}, number = {6}, publisher = {Public Library of Science (PLoS)}, title = {{AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization}}, doi = {10.1371/journal.pgen.1008894}, volume = {16}, 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}, } @article{13363, abstract = {Temporal activation of biological processes by visible light and subsequent return to an inactive state in the absence of light is an essential characteristic of photoreceptor cells. Inspired by these phenomena, light-responsive materials are very attractive due to the high spatiotemporal control of light irradiation, with light being able to precisely orchestrate processes repeatedly over many cycles. Herein, it is reported that light-driven proton transfer triggered by a merocyanine-based photoacid can be used to modulate the permeability of pH-responsive polymersomes through cyclic, temporally controlled protonation and deprotonation of the polymersome membrane. The membranes can undergo repeated light-driven swelling–contraction cycles without losing functional effectiveness. When applied to enzyme loaded-nanoreactors, this membrane responsiveness is used for the reversible control of enzymatic reactions. This combination of the merocyanine-based photoacid and pH-switchable nanoreactors results in rapidly responding and versatile supramolecular systems successfully used to switch enzymatic reactions ON and OFF on demand.}, author = {Moreno, Silvia and Sharan, Priyanka and Engelke, Johanna and Gumz, Hannes and Boye, Susanne and Oertel, Ulrich and Wang, Peng and Banerjee, Susanta and Klajn, Rafal and Voit, Brigitte and Lederer, Albena and Appelhans, Dietmar}, issn = {1613-6829}, journal = {Small}, keywords = {Biomaterials, Biotechnology, General Materials Science, General Chemistry}, number = {37}, publisher = {Wiley}, title = {{Light‐driven proton transfer for cyclic and temporal switching of enzymatic nanoreactors}}, doi = {10.1002/smll.202002135}, volume = {16}, year = {2020}, }